The role of self-blaming moral emotions in major depression and their impact on social-economical decision making.
People with major depressive disorder (MDD) are more prone to experiencing moral emotions related to self-blame, such as guilt and shame. DSM-IV-TR recognizes excessive or inappropriate guilt as one of the core symptoms of current MDD, whereas excessive shame is not part of the criteria for MDD. However, previous studies specifically assessing shame suggested its involvement in MDD. In the first part of this review, we will consider literature discussing the role of self-blaming moral emotions in MDD. These self-blaming moral emotions have been purported to influence people when they make social and financial decisions in cognitive studies, particularly those using neuroeconomical paradigms. Such paradigms aim to predict social behavior in activities of daily living, by using important resource tangibles (especially money) in laboratory conditions. Previous literature suggests that guilt promotes altruistic behavior via acting out reparative tendencies, whereas shame reduces altruism by means of increasing social and interpersonal distance. In the second part of this review, we will discuss the potential influence of self-blaming moral emotions on overt behavior in MDD, reviewing clinical and experimental studies in social and financial decision-making, in which guilt, and shame were manipulated. This is not a well-established area in the depression literature, however in this opinion paper we will argue that studies of moral emotions and their impact on behavioral decision-making are of potential importance in the clinical field, by linking specific symptoms of a disorder to a behavioral outcome which may lead to stratification of clinical diagnoses in the future.


Role of Rab5 in the recruitment of hVps34/p150 to the early endosome.
PI 3-kinases are important regulators of endocytic trafficking. We have previously proposed a model in which the Rab5 GTPase recruits EEA1 to the early endosome both directly, by binding to EEA1, and indirectly, through the recruitment of the p150/hVps34 PI 3-kinase and the production of PI[3]P in the endosomal membrane. In this study we have examined this model in vivo. We find that both endogenous hVps34 and p150 are targeted to enlarged endosomal structures in cells expressing constitutively activated Rab5, where they are significantly colocalized with EEA1. Recombinant fragments of p150 disrupt the endosomal localization of EEA1, showing that p150 is required for EEA1 targeting. We further analyzed the mechanism of GTP-dependent Rab5-p150 binding, and showed the p150 HEAT and WD40 domains are required for binding, whereas deletion of the protein kinase domain increases binding to Rab5. Overexpression of constitutively active Rab5 caused a redistribution of epitope-tagged hVps34 and p150 to Rab5-positive endosomes. However, subcellular fractionation showed that this was not due to a significant recruitment of hVps34 or p150 from the cytosolic to the particulate fraction. These data suggest that the binding of Rab5 to the HEAT/WD40 domains of p150 is important in regulating the localization of hVps34/p150. However, Rab5 does not appear to act by directly recruiting p150/hVps34 complexes from the cytosol to the endosomal membrane.


Confocal microscopy demonstrates association of LTBP-2 in fibrillin-1 microfibrils and colocalisation with perlecan in the disc cell pericellular matrix.
Comparative immunolocalisations of latent transforming growth factor-beta-1 binding protein (LTBP)-2, fibrillin-1, versican and perlecan were undertaken in foetal human and wild type C57BL/6 mouse and Hspg2 exon 3 null HS deficient mouse intervertebral discs (IVDs). LTBP-2 was a prominent pericellular component of annular fibrochondrocytes in the posterior annulus fibrosus (AF), interstitial matrix adjacent to nucleus pulposus (NP) cells and to fibrillar and cell associated material in the anterior AF of the human foetal IVD and also displayed a pericellular localisation pattern in murine IVDs. Perlecan and LTBP-2 displayed strong pericellular colocalisation patterns in the posterior AF and to fibrillar material in the outer anterior AF in the foetal human IVD. Versican was a prominent fibril-associated component in the posterior and anterior AF, localised in close proximity to fibrillin-1 in fibrillar arrangements in the cartilaginous vertebral rudiments around paraspinal blood vessels, to major collagen fibre bundles in the anterior and posterior AF and shorter fibres in the NP. Fibrillin-1 was prominent in the outer anterior AF of the human foetal IVD and in fibres extending from the AF into the cartilaginous vertebral rudiments. LTBP-2 was prominently associated with annular fibrils containing fibrillin-1, versican was localised in close proximity to these but not specifically with LTBP-2. The similar deposition levels of LTBP-2 observed in the AF of the Hspg2 exon 3 null and wild type murine IVDs indicated that perlecan HS was not essential for LTBP-2 deposition but colocalisation of LTBP-2 with perlecan in the foetal human IVD was consistent with HS mediated interactions which have already been demonstrated in-vitro.


Essential role of the unordered VP2 n-terminal domain of the parvovirus MVM capsid in nuclear assembly and endosomal enlargement of the virion fivefold channel for cell entry.
The unordered N-termini of parvovirus capsid proteins (Nt) are translocated through a channel at the icosahedral five-fold axis to serve for virus traffick. Heterologous peptides were genetically inserted at the Nt of MVM to study their functional tolerance to manipulations. Insertion of a 5T4-single-chain antibody at VP2-Nt (2Nt) yielded chimeric capsid subunits failing to enter the nucleus. The VEGFR2-binding peptide (V1) inserted at both 2Nt and VP1-Nt efficiently assembled in virions, but V1 disrupted VP1 and VP2 entry functions. The VP2 defect correlated with restricted externalization of V1-2Nt out of the coat. The specific infectivity of MVM and wtVP-pseudotyped mosaic MVM-V1 virions, upon heating and/or partial 2Nt cleavage, demonstrated that some 2Nt domains become intracellularly translocated out of the virus shell and cleaved to initiate entry. The V1 insertion defines a VP2-driven endosomal enlargement of the channel as an essential structural rearrangement performed by the MVM virion to infect.


Reduction in mammary tumorigenesis in the rat by cabbage and cabbage residue.
Mammary cancer was induced in female Sprague-Dawley rats by a single injection of N-methyl-N-nitrosourea (MNU) and rats were randomized to control fat (5%) and high fat (24.6%) diets. In addition, dried cabbage (5 and 10%) and collards (5%) were included in the diets of some animals. No statistically significant differences were observed in food consumption, body wt gain and caloric intake between the MNU-treated and control groups in the rats fed the low-fat diet. However, the groups fed the high-fat diet consumed more than the rats maintained on the control diet. The rats on the control fat diet containing cabbage exhibited a significantly lower incidence of mammary cancer than rats that were fed the control-fat diet without cabbage. This effect was not observed in comparable rats on the high-fat diet. The inhibitory effect on mammary tumorigenesis was demonstrated using a residue obtained from cabbage by exhaustive extraction with methanol, methylene chloride and petroleum ether. These studies reinforce the efficacy of cabbage as a 'suppressor' of cancer in experimental model systems under control-fat dietary conditions.


Neural Network Analysis of Electron Microscopy Video Data Reveals the Temperature-Driven Microphase Dynamics in the Ions/Water System.
Real-time field-emission scanning electron microscopy (FE-SEM) measurements and neural network analysis were successfully merged to observe the temperature-induced behavior of soft liquid microdomains in mixtures of different ionic liquids with water. The combination of liquid FE-SEM and in situ heating techniques revealed temperature-driven solution restructuring for ions/water systems with different water states and their critical point behavior expressed in a rapid switch between thermal expansion and shrinkage of liquid microphases at temperatures of ≈100-130 °C, which was directly recorded on electron microscopy videos. Automation of FE-SEM video analysis by a neural network approach allowed quantification of the morphological changes in ions/water systems during heating on the basis of thousands of images processed with a speed almost equal to the frame rate of original electron microscopy videos. Tracking and evolution of the micro-heterogeneous domains, hypothesized in the Ioliomics concept, was mapped and quantified for the first time. The present study describes the concept for quick acquisition of big data in electron microscopy, develops rapid neural network analysis and shows how to link microscopic data to fundamental molecular properties.


Development of a cell culture system loading cyclic mechanical strain to chondrogenic cells.
Mechanical stimulation is considered to be one of the major epigenetic factors regulating the metabolism, proliferation, survival and differentiation of cells in the skeletal tissues. It is generally accepted that the cytoskeleton can undergo remodeling in response to mechanical stimuli such as tensile strain or fluid flow. Mechanically induced cell deformation is one of the possible mechanotransduction pathways by which chondrocytes sense and respond to changes in their mechanical environment. Mechanical strain has a variety of effects on the structure and function of their cells in the skeletal tissues, such as chondrocytes, osteoblasts and fibroblasts. However, little is known about the effect of the quality and quantity of mechanical strain and the timing of mechanical loading on the differentiation of these cells. The present study was designed to investigate the effect of the deformation of chondrogenic cells, and cyclic compression using a newly developed culture device, by analyzing mechanobiological response to the differentiating chondrocytes. Cyclic compression between 0 and 22% strains, at 23 microHz was loaded on chondrogenic cell line ATDC5 by seeding in a mass mode on PDMS membrane, assuming direct transfer of cyclic deformation from the membrane to the cells at the same frequency. The compressive strain, induced within the membrane, was characterized based on the analysis of the finite element modeling (FEM). The results showed that the tensile strain inhibits the chondrogenic differentiation of ATDC5 cells, whereas the compressive strain enhances the chondrogenic differentiation, suggesting that the differentiation of the chondrogenic cells could be controlled by the amount and the mode of strain. In conclusion, we have developed a unique strain loading culture system to analyze the effect of various types of mechanical stimulation on various cellular activities.


A rapid, reliable, and inexpensive method for detection of di- and trinucleotide repeat markers and disease loci from dried blood spots.
We used a rapid and inexpensive method for studying the FMR1 CGG-repeat from dried blood spots, prepared from heel pricks, finger pricks, or an aliquot of blood from a venipuncture. The procedure includes a single tube for preparation of template DNA for PCR and minimal handling, avoiding opportunities for mislabelling specimens and loss of template. We extended the protocol to numerous di- and trinucleotide repeat markers and disease loci, including FRAXE, FRAXF, DXS548, DRPLA, and ZFY. The use of a highly reliable and very inexpensive method which employs blood spots as a source for target DNA means that newborn Guthrie cards can be used to establish allele frequencies for linkage disequilibrium studies, that large populations can be screened for genetic disorders, and that mapping studies can proceed rapidly even when only small amounts of blood are available from key family members.


Multiple-trait genomic selection methods increase genetic value prediction accuracy.
Genetic correlations between quantitative traits measured in many breeding programs are pervasive. These correlations indicate that measurements of one trait carry information on other traits. Current single-trait (univariate) genomic selection does not take advantage of this information. Multivariate genomic selection on multiple traits could accomplish this but has been little explored and tested in practical breeding programs. In this study, three multivariate linear models (i.e., GBLUP, BayesA, and BayesCπ) were presented and compared to univariate models using simulated and real quantitative traits controlled by different genetic architectures. We also extended BayesA with fixed hyperparameters to a full hierarchical model that estimated hyperparameters and BayesCπ to impute missing phenotypes. We found that optimal marker-effect variance priors depended on the genetic architecture of the trait so that estimating them was beneficial. We showed that the prediction accuracy for a low-heritability trait could be significantly increased by multivariate genomic selection when a correlated high-heritability trait was available. Further, multiple-trait genomic selection had higher prediction accuracy than single-trait genomic selection when phenotypes are not available on all individuals and traits. Additional factors affecting the performance of multiple-trait genomic selection were explored.


A systematic review of workplace ergonomic interventions with economic analyses.
This article reports on a systematic review of workplace ergonomic interventions with economic evaluations. The review sought to answer the question: "what is the credible evidence that incremental investment in ergonomic interventions is worth undertaking?" Past efforts to synthesize evidence from this literature have focused on effectiveness, whereas this study synthesizes evidence on the cost-effectiveness/financial merits of such interventions. Through a structured journal database search, 35 intervention studies were identified in nine industrial sectors. A qualitative synthesis approach, known as best evidence synthesis, was used rather than a quantitative approach because of the diversity of study designs and statistical analyses found across studies. Evidence on the financial merits of interventions was synthesized by industrial sector. In the manufacturing and warehousing sector strong evidence was found in support of the financial merits of ergonomic interventions from a firm perspective. In the administrative support and health care sectors moderate evidence was found, in the transportation sector limited evidence, and in remaining sectors insufficient evidence. Most intervention studies focus on effectiveness. Few consider their financial merits. Amongst the few that do, several had exemplary economic analyses, although more than half of the studies had low quality economic analyses. This may be due to the low priority given to economic analysis in this literature. Often only a small part of the overall evaluation of many studies focused on evaluating their cost-effectiveness.


Social influences on neuroplasticity: stress and interventions to promote well-being.
Experiential factors shape the neural circuits underlying social and emotional behavior from the prenatal period to the end of life. These factors include both incidental influences, such as early adversity, and intentional influences that can be produced in humans through specific interventions designed to promote prosocial behavior and well-being. Here we review important extant evidence in animal models and humans. Although the precise mechanisms of plasticity are still not fully understood, moderate to severe stress appears to increase the growth of several sectors of the amygdala, whereas the effects in the hippocampus and prefrontal cortex tend to be opposite. Structural and functional changes in the brain have been observed with cognitive therapy and certain forms of meditation and lead to the suggestion that well-being and other prosocial characteristics might be enhanced through training.


Causes of persistent dizziness in elderly patients in primary care.
Although dizzy patients are predominantly seen in primary care, most diagnostic studies on dizziness have been performed among patients in secondary or tertiary care. Our objective was to describe subtypes of dizziness in elderly patients in primary care and to assess contributory causes of dizziness. We performed a cross-sectional diagnostic study among elderly patients in the Netherlands consulting their family physician for persistent dizziness. All patients underwent a comprehensive evaluation according to a set of diagnostic tests that were developed during an international Delphi procedure. Data for each patient were independently reviewed by a panel consisting of a family physician, a geriatrician, and a nursing home physician, which resulted in major and minor contributory causes of dizziness. From June 2006 to January 2008, we included 417 patients aged 65 to 95 years. Presyncope was the most common dizziness subtype (69%). Forty-four percent of the patients were assigned more than 1 dizziness subtype. Cardiovascular disease was considered to be the most common major contributory cause of dizziness (57%), followed by peripheral vestibular disease (14%), and psychiatric illness (10%). An adverse drug effect was considered to be the most common minor contributory cause of dizziness (23%). Sixty-two percent of the patients were assigned more than 1 contributory cause of dizziness. Contrary to most previous studies, cardiovascular disease was found to be the most common major cause of dizziness in elderly patients in primary care. In one-quarter of all patients an adverse drug effect was considered to be a contributory cause of dizziness, which is much higher than reported in previous studies.


Maximising response to postal questionnaires--a systematic review of randomised trials in health research.
Postal self-completion questionnaires offer one of the least expensive modes of collecting patient based outcomes in health care research. The purpose of this review is to assess the efficacy of methods of increasing response to postal questionnaires in health care studies on patient populations. The following databases were searched: Medline, Embase, CENTRAL, CDSR, PsycINFO, NRR and ZETOC. Reference lists of relevant reviews and relevant journals were hand searched. Inclusion criteria were randomised trials of strategies to improve questionnaire response in health care research on patient populations. Response rate was defined as the percentage of questionnaires returned after all follow-up efforts. Study quality was assessed by two independent reviewers. The Mantel-Haenszel method was used to calculate the pooled odds ratios. Thirteen studies reporting fifteen trials were included. Implementation of reminder letters and telephone contact had the most significant effect on response rates (odds ratio 3.7, 95% confidence interval 2.30 to 5.97 p = or <0.00001). Shorter questionnaires also improved response rates to a lesser degree (odds ratio 1.4, 95% confidence interval 1.19 to 1.54). No evidence was found that incentives, re-ordering of questions or including an information brochure with the questionnaire confer any additional advantage. Implementing repeat mailing strategies and/or telephone reminders may improve response to postal questionnaires in health care research. Making the questionnaire shorter may also improve response rates. There is a lack of evidence to suggest that incentives are useful. In the context of health care research all strategies to improve response to postal questionnaires require further evaluation.


Diffusion model drift rates can be influenced by decision processes: an analysis of the strength-based mirror effect.
Improving memory for studied items (targets) often helps participants reject nonstudied items (lures), a pattern referred to as the strength-based mirror effect (SBME). Criss (2010) demonstrated the SBME in diffusion model drift rates; that is, the target drift rate was higher and the lure drift rate was lower for lists of words studied 5 times versus lists of words studied once. She interpreted the drift rate effect for lures as evidence for the differentiation process, whereby strong memory traces produce a poorer match to lure items than do weak memory traces. However, she noted that strength may have also affected a model parameter called the drift criterion-a participant-controlled decision parameter that defines the zero point in drift rate. We directly contrasted the differentiation and drift-criterion accounts by manipulating list strength either at both encoding and retrieval (which produces a differentiation difference in the studied traces) or at retrieval only (which equates differentiation from the study list but provides the opportunity to change decision processes based on strength). Across 3 experiments, results showed that drift rates for lures were lower on strong tests than on weak tests, and this effect was observed even when strength was varied at retrieval alone. Therefore, results provided evidence that the SBME is produced by changes in decision processes, not by differentiation of memory traces.


Effectiveness of simultaneous independent realizations at low carrier-to-noise ratio to improve heterodyne Doppler lidar performance. I. Theory and numerical simulations.
It is shown that the performance of heterodyne Doppler lidar (HDL) can be improved by (i) at least one good realization for every single shot or (ii) several simultaneous good realizations for accumulation. Until now, several simultaneous independent realizations at high carrier-to-noise ratio (CNR) have been considered. At low CNR, noise may have a detrimental effect on the accumulation techniques. We determine the chances of getting "heavy" speckles in HDL signals from many receiver-detector units on a single-shot basis and several good realizations on a single-shot basis, which is required for an effective accumulation. The use of multiple receiver-detector units at low CNR is worthwhile in contexts such as space lidar, where optimized treatment is at a premium. We conclude on the effectiveness of many receiver-detector units in parallel in order to achieve simultaneous independent realizations at low CNR to improve the performance of HDL on a statistical basis.


Distinctive Steady-State Heart Rate and Blood Pressure Responses to Passive Robotic Leg Exercise during Head-Up Tilt: A Pilot Study in Neurological Patients.
Introduction: Robot-assisted tilt table therapy was proposed for early rehabilitation and mobilization of patients after diseases such as stroke. A robot-assisted tilt table with integrated passive robotic leg exercise (PE) mechanism has the potential to prevent orthostatic hypotension usually provoked by verticalization. In a previous study with rather young healthy subjects [average age: 25.1 ± 2.6 years (standard deviation)], we found that PE effect on the cardiovascular system depends on the verticalization angle of the robot-assisted tilt table. In the current study, we investigated in an older population of neurological patients (a) whether they show the same PE effects as younger healthy population on the cardiovascular system at different tilt angles, (b) whether changing the PE frequency (i.e., stepping speed) influences the PE effect on the cardiovascular system, (c) whether PE could prevent orthostatic hypotension, and finally, (d) whether PE effect is consistent from day to day. Methods: Heart rate (HR), and systolic and diastolic blood pressures (sBP, dBP) in response to PE at two different tilt angles (α = 20°, 60°) with three different PE frequencies (i.e., 0, 24, and 48 steps per minute) of 10 neurological patients [average age: 68.4 ± 13.5 years (standard deviation)] were measured on 2 consecutive days. Linear mixed models were used to develop statistical models and analyze the repeated measurements. Results: The models show that: PE significantly increased sBP and dBP but had no significant effect on HR. (a) Similar to healthy subjects the effect of PE on sBP was dependent on the tilt angle with higher tilt angles resulting in a higher increase. Head-up tilting alone significantly increased HR and dBP but resulted in a non-significant drop in sBP. PE, in general, had a more additive effect on increasing BP. (b) The effect of PE was not influenced by its speed. (c) Neither during head-up tilt alone nor in combination with PE did participants experience orthostatic hypotension. (d) The measurement day was not a statistically significant factor regarding the effects of verticalization and PE on the cardiovascular response. Conclusion: We provide evidence that PE can increase steady-state values of sBP and dBP in neurological patients during head-up tilt. Similar to healthy subjects the effect on sBP depends on the verticalization angle of the robot-assisted tilt table. PE might have the potential to prevent orthostatic hypotension, but as the amount of drop in BP in response to head-up tilting was not leading to orthostatic hypotension in our patients, we could neither conclude nor reject such a preventive compensatory effect. Furthermore, we found that changing the PE speed does not influence the steady-state cardiovascular response.


Laparoscopic treatment of simultaneous tumors in the liver and kidney.
To report our experience with laparoscopic treatment of liver tumors during right-sided transperitoneal laparoscopic nephrectomy. Two patients undergoing transperitoneal laparoscopic radical nephrectomy on the right side each had a concomitant tumor in the right lobe of the liver. The first patient was incidentally found to have a lesion suspicious for metastatic disease. The second had a known asymptomatic giant hemangioma of the liver. Total operative time was 130 and 101 min. Estimated blood loss was 400 and 300 ml. There were no complications. The first patient had bilateral papillary renal cell carcinoma and concomitant fibroadipose tissue within the liver. The second patient presented with clear cell carcinoma of the right kidney and a cavernous hemangioma of the liver. When indicated, simultaneous right-sided kidney and liver tumors may be treated by a combined laparoscopic transperitoneal approach. Laparoscopic expertise is advised.


Arabidopsis thaliana DNA methylation mutants.
Three DNA hypomethylation mutants of the flowering plant Arabidopsis thaliana were isolated by screening mutagenized populations for plants containing centromeric repetitive DNA arrays susceptible to digestion by a restriction endonuclease that was sensitive to methylated cytosines. The mutations are recessive, and at least two are alleles of a single locus, designated DDM1 (for decrease in DNA methylation). Amounts of 5-methylcytosine were reduced over 70 percent in ddm1 mutants. Despite this reduction in DNA methylation levels, ddm1 mutants developed normally and exhibited no striking morphological phenotypes. However, the ddm1 mutations are associated with a segregation distortion phenotype. The ddm1 mutations were used to demonstrate that de novo DNA methylation in vivo is slow.


Radiolabeled antibodies to Bacillus anthracis toxins are bactericidal and partially therapeutic in experimental murine anthrax.
Bacillus anthracis is a powerful agent for use in biological warfare, and infection with the organism is associated with a high rate of mortality, underscoring the need for additional effective therapies for anthrax. Radioimmunotherapy (RIT) takes advantage of the specificity and affinity of the antigen-antibody interaction to deliver a microbicidal radioactive nuclide to a site of infection. RIT has proven therapeutic in experimental models of viral, bacterial, and fungal infections; but it is not known whether this approach can successfully employ toxin binding monoclonal antibodies (MAbs) for diseases caused by toxigenic bacteria. Indirect immunofluorescence studies with MAbs to protective antigen (MAbs 7.5G gamma2b and 10F4 gamma1) and lethal factor (MAb 14FA gamma2b) revealed the surface expression of toxins on bacterial cells. Scatchard analysis of MAbs revealed high binding constants and numerous binding sites on the bacterial surface. To investigate the microbicidal properties of these MAbs, our group radiolabeled MAbs with either (188)Re or (213)Bi. In vitro, (213)Bi was more efficient than (188)Re in mediating microbicidal activity against B. anthracis. The administration of MAbs [(213)Bi]10F4 gamma1 and [(213)Bi]14FA gamma2b prolonged the survival of A/JCr mice infected with B. anthracis Sterne bacterial cells but not B. anthracis Sterne spores. These results indicate that RIT with MAbs that target B. anthracis toxin components can be used to treat experimental anthrax infection and suggest that toxigenic bacteria may be targeted with radiolabeled MAbs.


Clinical Evaluation of the Cepheid Xpert TV Assay for Detection of Trichomonas vaginalis with Prospectively Collected Specimens from Men and Women.
Trichomoniasis is the most prevalent curable sexually transmitted disease (STD). It has been associated with preterm birth and the acquisition and transmission of HIV. Recently, nucleic acid amplification tests (NAAT) have been FDA cleared in the United States for detection of Trichomonas vaginalis in specimens from both women and men. This study reports the results of a multicenter study recently conducted using the Xpert TV (T. vaginalis) assay to test specimens from both men and women. On-demand results were available in as little as 40 min for positive specimens. A total of 1,867 women and 4,791 men were eligible for inclusion in the analysis. In women, the performance of the Xpert TV assay was compared to the patient infected status (PIS) derived from the results of InPouch TV broth culture and Aptima NAAT for T. vaginalis The diagnostic sensitivities and specificities of the Xpert TV assay for the combined female specimens (urine samples, self-collected vaginal swabs, and endocervical swabs) ranged from 99.5 to 100% and 99.4 to 99.9%, respectively. For male urine samples, the diagnostic sensitivity and specificity were 97.2% and 99.9%, respectively, compared to PIS results derived from the results of broth culture for T. vaginalis and bidirectional gene sequencing of amplicons. Excellent performance characteristics were seen using both female and male specimens. The ease of using the Xpert TV assay should result in opportunities for enhanced screening for T. vaginalis in both men and women and, hopefully, improved control of this infection.


A phase 2 trial of dasatinib in patients with advanced HER2-positive and/or hormone receptor-positive breast cancer.
SRC-family kinases (SFK) are involved in numerous oncogenic signaling pathways. A phase 2 trial of dasatinib, a potent oral tyrosine kinase inhibitor of SFKs, was carried out in patients with human epidermal growth factor receptor 2-positive (HER2+) and/or hormone receptor-positive (HR+) advanced breast cancer. Patients with measurable tumors and progression after chemotherapy and HER2 and/or HR-targeted agents in adjuvant or metastatic settings (maximum of two prior metastatic setting regimens) received twice daily dasatinib. Primary endpoint was Response Evaluation Criteria in Solid Tumors-defined response rate. Secondary endpoints included toxicity and limited pharmacokinetics. Seventy patients (55 years median age) were treated, 83% of HER2+ patients had received prior HER2-directed therapy, and 61% of HR+ patients had received prior endocrine therapy in the advanced setting. Dasatinib starting dose was reduced from 100 to 70 mg twice daily to limit toxicity. Median therapy duration was 1.8 months in both dose groups and most discontinuations were due to progression. Of 69 evaluable patients, three had confirmed partial responses and six had stable disease for 16 weeks or more (disease control rate = 13.0%); all nine of these tumors were HR+ (two were also HER2+). The most common drug-related toxicities were gastrointestinal complaints, headache, asthenia, and pleural effusion. Grade 3-4 toxicity occurred in 37% of patients and was comparable between doses; drug-related serious adverse events were less frequent with 70 mg twice daily than 100 mg twice daily. Limited single-agent activity was observed with dasatinib in patients with advanced HR+ breast cancer.


Renal dopamine-1 receptors in hypertensive inbred rat strains with and without hyperactivity.
Renal dopamine-1 (DA-1) receptors are involved in the regulation of sodium transport in several nephron segments, including the proximal convoluted tubule (PCT). DA-1 receptors in the PCT and cortical collecting duct of normotensive rats are linked to the stimulation of adenylyl cyclase (AC). We have reported a defect in the DA-1 receptor/AC coupling in the PCT of the spontaneously hypertensive rat (SHR) of the Okamoto-Aoki strain. Hyperactivity and hypertension are both expressed in the SHR. To determine if the DA-1 receptor coupling defect is associated with hyperactivity or hypertension, we studied the DA-1 receptor in the PCT of two new inbred rat strains derived from the SHR: the hyperactive WKHA and the hypertensive WKHT rat. Tail-cuff blood pressures taken at 4 weeks indicated that WKHT rats were not hypertensive (86 +/- 3 mm Hg, n = 6), whereas at 12 weeks systolic pressures in both SHR and WKHT rats exceeded 150 mm Hg. Hyperactivity, however, was noted in WKHA rats even at this early age. Basal AC activity was similar in WKHA and WKHT PCT in either age group. In the older rats, the DA-1 agonist fenoldopam (10(-7) mol/L) stimulated AC activity in WKHA (70.6 +/- 16.1 fmol per 3 mm PCT per 20 minutes, n = 3) but not in WKHT PCT (43.3 +/- 5.3 fmol per 3 mm PCT per 20 minutes, n = 4). Gpp(NH)p (10(-5) mol/L), a nonhydrolyzable GTP analogue, stimulated AC activity to a similar extent in WKHA and WKHT PCT.(ABSTRACT TRUNCATED AT 250 WORDS)


Transcriptome profiling of citrus fruit response to huanglongbing disease.
Huanglongbing (HLB) or "citrus greening" is the most destructive citrus disease worldwide. In this work, we studied host responses of citrus to infection with Candidatus Liberibacter asiaticus (CaLas) using next-generation sequencing technologies. A deep mRNA profile was obtained from peel of healthy and HLB-affected fruit. It was followed by pathway and protein-protein network analysis and quantitative real time PCR analysis of highly regulated genes. We identified differentially regulated pathways and constructed networks that provide a deep insight into the metabolism of affected fruit. Data mining revealed that HLB enhanced transcription of genes involved in the light reactions of photosynthesis and in ATP synthesis. Activation of protein degradation and misfolding processes were observed at the transcriptomic level. Transcripts for heat shock proteins were down-regulated at all disease stages, resulting in further protein misfolding. HLB strongly affected pathways involved in source-sink communication, including sucrose and starch metabolism and hormone synthesis and signaling. Transcription of several genes involved in the synthesis and signal transduction of cytokinins and gibberellins was repressed while that of genes involved in ethylene pathways was induced. CaLas infection triggered a response via both the salicylic acid and jasmonic acid pathways and increased the transcript abundance of several members of the WRKY family of transcription factors. Findings focused on the fruit provide valuable insight to understanding the mechanisms of the HLB-induced fruit disorder and eventually developing methods based on small molecule applications to mitigate its devastating effects on fruit production.


Individual responsiveness to induction of micronuclei in human lymphocytes after exposure in vitro to 1800-MHz microwave radiation.
The widespread application of microwaves is of great concern in view of possible consequences for human health. Many in vitro studies have been carried out to detect possible effects on DNA and chromatin structure following exposure to microwave radiation. The aim of this study is to assess the capability of microwaves, at different power densities and exposure times, to induce genotoxic effects as evaluated by the in vitro micronucleus (MN) assay on peripheral blood lymphocytes from nine different healthy donors, and to investigate also the possible inter-individual response variability. Whole blood samples were exposed for 60, 120 and 180 min to continuous microwave radiation with a frequency of 1800 MHz and power densities of 5, 10 and 20 mW/cm(2). Reproducibility was tested by repeating the experiment 3 months later. Multivariate analysis showed that lymphocyte proliferation indices were significantly different among donors (p<0.004) and between experiments (p<0.01), whereas the applied power density and the exposure time did not have any effect on them. Both spontaneous and induced MN frequencies varied in a highly significant way among donors (p<0.009) and between experiments (p<0.002), and a statistically significant increase of MN, although rather low, was observed dependent on exposure time (p=0.0004) and applied power density (p=0.0166). A considerable decrease in spontaneous and induced MN frequencies was measured in the second experiment. The results show that microwaves are able to induce MN in short-time exposures to medium power density fields. Our data analysis highlights a wide inter-individual variability in the response, which was confirmed to be a characteristic reproducible trait by means of the second experiment.


Parameterization of a coarse-grained model with short-ranged interactions for modeling fuel cell membranes with controlled water uptake.
The design of polymer electrolyte membranes with controlled water uptake is of high importance for high-performance fuel cells, because the water content of the membranes modulates their conductivity, chemical stability and mechanical strength. The water activity aw controls the equilibrium water uptake of a system. Predicting aw of materials is currently a daunting challenge for molecular simulations, because calculations of water activity require grand canonical simulations that are extremely expensive even with classical non-polarizable force fields. Moreover, force fields do not generally reproduce aw of solutions. Here, we first present a general strategy to parameterize force fields that reproduce the experimental aw of solutions, and then implement that strategy to re-parameterize the interactions in FFcomp, a coarse-grained model for hydrated polyphenylene oxide/trimethylamine chloride (PPO/TMACl) membranes in which the TMA cation is attached to the PPO backbone and the Cl anion is in the mobile water nanophase. Coarse-grained models based on short-ranged potentials successfully model fuel cell membranes and other concentrated aqueous electrolyte solutions because electrostatic interactions are highly screened in these systems. The new force field, FFpvap, differs from the original FFcomp only in the parameters of the ion-ion interactions, yet it reproduces aw in TMACl solutions with accuracy within 0.5 and 3% of the experimental value in all the concentration range relevant to the operation of fuel cell membranes. We find that the heat needed to vaporize water in solutions with as little as five water molecules per ion pair is essentially the same as in pure water, despite the strong water-ion interactions and their impact on the water activity. We review the literature to demonstrate that this is independent of the model and a general feature of water solutions. FFpvap reproduces the radial distribution functions and captures well the relative diffusivities of water and ions in the ionic solution as predicted by the reference atomistic GAFF-TIP4P/2005 model, while providing a hundred-fold gain in computing efficiency with respect to the atomistic model. With the backbone fragments inherited from FFcomp, the new FFpvap force field can be used to model hydrated polymer electrolyte membranes and advance the design of fuel cell membranes with controlled water uptake and conductivity.


[Interaction of dNTP-binding sites of human DNA polymerase alpha and The Klenow fragment of Escherichia coli DNA polymerase I with nucleotides, pyrophosphate and their analogs].
AMP and NaF each taken separately were shown to activate DNA polymerization catalyzed by Klenow fragment of DNA polymerase I by means of interaction of AMP or NaF with 3'----5'-exonuclease center of the enzyme. In the presence of NaF which is a selective inhibitor of 3'----5'-exonuclease center, AMP is an inhibitor of polymerization competitive with respect to dATP. Ki values and the pattern of inhibition with respect to dATP were determined for AMP, ADP, ATP, carboxymethylphosphonyl-5'-AMP, Pi, PPi, PPPi, methylenediphosphonic acid and its ethylated esters, phosphonoformic acid, phosphonoacetic acid and its ethylated esters as well as for some bicarbonic acids in the reactions of DNA polymerization catalyzed by Klenow fragment of DNA polymerase I (in the presence of NaF) and DNA polymerase alpha from human placenta in the presence of poly(dT) template and r(pA)10 primer. All nucleotides and their analogs were found to be capable of competing with dATP for the active center of the enzyme. Most of the analogs of PPi and phosphonoacetic acid are inhibitors of Klenow fragment competitive with respect to dATP. Nowever these analogs display a mixed-type inhibition in the case of human DNA polymerase alpha. We postulated a similar mechanism of interaction for dNTP with both DNA-polymerases. It is suggested that each phosphate group of PPi makes equal contribution to the interaction with DNA polymerases and that the distance between the phosphate groups is important for this interaction. beta-phosphate of NTP or dNTP is suggested to make negligible contribution to the efficiency of the formation of enzyme complexes with dNTP. beta-phosphate is likely to be an essential point of PPi interaction with the active center of proteins during the cleavage of the alpha-beta-phosphodiester bond of dNTP in the reaction of DNA polymerization.


3D Cell Culture Models Demonstrate a Role for FGF and WNT Signaling in Regulation of Lung Epithelial Cell Fate and Morphogenesis.
FGF signaling plays an essential role in lung development, homeostasis, and regeneration. We employed mouse 3D cell culture models and imaging to study ex vivo the role of FGF ligands and the interplay of FGF signaling with epithelial growth factor (EGF) and WNT signaling pathways in lung epithelial morphogenesis and differentiation. In non-adherent conditions, FGF signaling promoted formation of lungospheres from lung epithelial stem/progenitor cells (LSPCs). Ultrastructural and immunohistochemical analyses showed that LSPCs produced more differentiated lung cell progeny. In a 3D extracellular matrix, FGF2, FGF7, FGF9, and FGF10 promoted lung organoid formation. FGF9 showed reduced capacity to promote lung organoid formation, suggesting that FGF9 has a reduced ability to sustain LSPC survival and/or initial divisions. FGF7 and FGF10 produced bigger organoids and induced organoid branching with higher frequency than FGF2 or FGF9. Higher FGF concentration and/or the use of FGF2 with increased stability and affinity to FGF receptors both increased lung organoid and lungosphere formation efficiency, respectively, suggesting that the level of FGF signaling is a crucial driver of LSPC survival and differentiation, and also lung epithelial morphogenesis. EGF signaling played a supportive but non-essential role in FGF-induced lung organoid formation. Analysis of tissue architecture and cell type composition confirmed that the lung organoids contained alveolar-like regions with cells expressing alveolar type I and type II cell markers, as well as airway-like structures with club cells and ciliated cells. FGF ligands showed differences in promoting distinct lung epithelial cell types. FGF9 was a potent inducer of more proximal cell types, including ciliated and basal cells. FGF7 and FGF10 directed the differentiation toward distal lung lineages. WNT signaling enhanced the efficiency of lung organoid formation, but in the absence of FGF10 signaling, the organoids displayed limited branching and less differentiated phenotype. In summary, we present lung 3D cell culture models as useful tools to study the role and interplay of signaling pathways in postnatal lung development and homeostasis, and we reveal distinct roles for FGF ligands in regulation of mouse lung morphogenesis and differentiation ex vivo.


Analysis of Fas and Fas ligand expression and function in lung cancer cell lines.
The aim of this study was to investigate the expression of Fas and Fas ligand (FasL) and to determine the significance of these molecules in lung cancer cell lines. Immunoblotting, RT-PCR and flow cytometric analyses were carried out to measure the expression of Fas and FasL and to examine their interactions and effects on cell growth and apoptosis. Fas and FasL were co-expressed in most of the cell lines but to varying degrees. Apoptosis induced by the agonistic anti-Fas antibody was significantly correlated with Fas expression (P=0.0075), whereas cisplatin-induced apoptosis was not. Upregulation of Fas and FasL expression by the administration of cisplatin was found in 7 of 11 (64%) and 9 of 11 (82%) cell lines, respectively. However, cisplatin-induced apoptosis was not suppressed by antagonistic anti-FasL antibody. Thus, our data indicated that Fas and FasL were co-expressed in lung cancer cell lines, and that Fas ligation induced by agonistic anti-Fas antibody is functional and induced apoptosis that was dependent on the levels of Fas expression. In contrast, Fas-FasL interactions appeared to be non-functional. Furthermore, our results suggest that cisplatin-induced apoptosis in lung cancer cells was independent of the Fas-FasL interaction.


Pupillometry reveals perceptual differences that are tightly linked to autistic traits in typical adults.
The pupil is primarily regulated by prevailing light levels but is also modulated by perceptual and attentional factors. We measured pupil-size in typical adult humans viewing a bistable-rotating cylinder, constructed so the luminance of the front surface changes with perceived direction of rotation. In some participants, pupil diameter oscillated in phase with the ambiguous perception, more dilated when the black surface was in front. Importantly, the magnitude of oscillation predicts autistic traits of participants, assessed by the Autism-Spectrum Quotient AQ. Further experiments suggest that these results are driven by differences in perceptual styles: high AQ participants focus on the front surface of the rotating cylinder, while those with low AQ distribute attention to both surfaces in a more global, holistic style. This is the first evidence that pupillometry reliably tracks inter-individual differences in perceptual styles; it does so quickly and objectively, without interfering with spontaneous perceptual strategies.


Relationships between versional and vergent quick phases of the involuntary version-vergence nystagmus.
We used ground-plane motion stimuli displayed on a computer monitor positioned below eye level to induce involuntary version-vergence nystagmus (VVN). The VVN was recorded with a search coil system. It was shown that the VVN had both vertical versional and horizontal vergence components. The VVN induced by backward motion (toward subjects) had upward versional and divergence quick phases, whereas those induced by forward motion (away from subjects) had downward and biphasic divergence-convergence quick phases. The versional and vergence components of the VVN quick phases were analyzed. A temporal dissociation of about 20 ms between version velocity peak and convergence velocity peak was revealed, which supported a modified saccade-related vergence burst neuron (SVBN) model. We suggest that the temporal dissociation may be partly because of a lower-level OKN control mechanism. Vergence peak time was dependent on version peak time. Linear relationships between vergence peak velocity and versional saccadic peak velocity were demonstrated, which was in line with the new multiplicative model. Our data support the hypothesis that the vergence system and the saccadic system can act separately but interact with each other whenever their movements occur simultaneously.


The effect of augmenting early nutritional energy delivery on quality of life and employment status one year after ICU admission.
Augmenting energy delivery during the acute phase of critical illness may reduce mortality and improve functional outcomes. The objective of this sub-study was to evaluate the effect of early augmented enteral nutrition (EN) during critical illness, on outcomes one year later. We performed prospective longitudinal evaluation of study participants, initially enrolled in The Augmented versus Routine approach to Giving Energy Trial (TARGET), a feasibility study that randomised critically ill patients to 1.5 kcal/ml (augmented) or 1.0 kcal/ml (routine) EN administered at the same rate for up to ten days, who were alive at one year. One year after randomisation Short Form-36 version 2 (SF-36v2) and EuroQol-5D-5L quality of life surveys, and employment status were assessed via telephone survey. At one year there were 71 survivors (1.5 kcal/ml 38 versus 1.0 kcal/ml 33; P=0.55). Thirty-nine (55%) patients consented to this follow-up study and completed the surveys (n = 23 and 16, respectively). The SF-36v2 physical and mental component summary scores were below normal population means but were similar in 1.5 kcal/ml and 1.0 kcal/ml groups (P=0.90 and P=0.71). EuroQol-5D-5L data were also comparable between groups (P=0.70). However, at one-year follow-up, more patients who received 1.5 kcal/ml were employed (7 versus 2; P=0.022). The delivery of 1.5 kcal/ml for a maximum of ten days did not affect self-rated quality of life one year later.


Decision-making for foot-and-mouth disease control: Objectives matter.
Formal decision-analytic methods can be used to frame disease control problems, the first step of which is to define a clear and specific objective. We demonstrate the imperative of framing clearly-defined management objectives in finding optimal control actions for control of disease outbreaks. We illustrate an analysis that can be applied rapidly at the start of an outbreak when there are multiple stakeholders involved with potentially multiple objectives, and when there are also multiple disease models upon which to compare control actions. The output of our analysis frames subsequent discourse between policy-makers, modellers and other stakeholders, by highlighting areas of discord among different management objectives and also among different models used in the analysis. We illustrate this approach in the context of a hypothetical foot-and-mouth disease (FMD) outbreak in Cumbria, UK using outputs from five rigorously-studied simulation models of FMD spread. We present both relative rankings and relative performance of controls within each model and across a range of objectives. Results illustrate how control actions change across both the base metric used to measure management success and across the statistic used to rank control actions according to said metric. This work represents a first step towards reconciling the extensive modelling work on disease control problems with frameworks for structured decision making.


Caregiver opinions about fragile X population screening.
We sought to determine caregiver perceptions about population screening for fragile X and to examine factors potentially associated with support for screening. We asked 1,099 caregivers of a child with fragile X syndrome or a fragile X carrier to rate whether free, voluntary screening should be offered preconception, prenatally, neonatally, or when problems occur. Caregivers chose a preferred time for screening, reported whether screening would affect parent-child bonding, indicated preferences for carrier detection, and gave reasons for their choices. Caregivers endorsed all forms of screening, but prenatal screening was less strongly endorsed than preconception or postnatal screening. Most (79%) preferred preconception carrier testing, allowing more options when making reproductive decisions. Most thought that screening should also disclose carrier status and believed a positive screen would not negatively affect parent-child bonding. Maternal education, caregiver depression, family impact, and severity of disability were not associated with screening opinions, but parents who only had carrier children were less likely to endorse prenatal screening. Caregivers of children with fragile X widely endorse screening. However, because different parents will make different choices, screening may need to be offered at multiple times with careful consideration of consent and informed decision-making.


A new 'mechanistic-practical" framework for designing and interpreting randomized trials.
Methodologists have traditionally categorized randomized controlled trials (RCTs) as explanatory (representing the ideal setting) and pragmatic (representing the real-world setting). Although this framework has greatly advanced the design and interpretation of RCTs, current interpretations of the explanatory-pragmatic framework suffer from two major limitations. First, they confound purpose with structure. Second, they ignore the varying perspective of those using RCT results to make clinical and policy decisions in the real world. The purpose of a trial should determine researchers' choices regarding the trial's structure and the structure of a trial determines the extent to which a decision maker will find the results useful. In this article, we introduce two terms that refer explicitly to the purpose of a trial: A trial is mechanistic to the extent that it addresses a biological relationship. In contrast, a trial is practical to the extent that it provides comprehensive information that bears directly on specific health care decisions. This revised framework facilitates investigators' choice of optimal trial design, and clinicians' optimal interpretation of RCT results. If our goal is clinical trials most relevant to individual patient decision making, we will eschew the use of trials that enroll patients unlikely to benefit (e.g., those with uncertain diagnosis); those likely to be noncompliant; treated by practitioners whose differing expertise is likely to result in differing outcomes; and permitting cointerventions that are likely to influence treatment effectiveness-i.e., the conventional pragmatic trial. Instead we will design, implement, and apply the results of practical trials to our patients.


Discovery and exploration of novel somatostatin receptor subtype 5 (SSTR5) antagonists for the treatment of cholesterol gallstones.
The shortage of cholesterol gallstones treatment intensifies the need to discover of effective small molecule drugs. Clinical follow-up and studies have found that activation of somatostatin receptor subtype 5 (SSTR5) reduce gallbladder contraction and thus increase the risk of cholesterol gallstones, implying that antagonizing SSTR5 may promote gallbladder emptying and reduce the formation of gallstones. Herein, we discovered novel SSTR5 antagonists and firstly investigated its effects on cholesterol gallstone. From loperamide, a reported seed structure with micromole activity, we identified optimal compound 23 as an SSTR5 antagonist exhibiting single-digit nanomolar potency, low hERG inhibition and oral availability. Further in vivo evaluation revealed that 23 significantly promoted gallbladder emptying. Moreover, in a mouse cholesterol gallstone model, 23 (3 mg/kg) effectively reduced the cholesterol gallstones formation, showing better efficacy than the clinical first-line drug UDCA (60 mg/kg), providing a new insight into the development of anti-gallstone drugs.


Similarity-Based Recommendation of New Concepts to a Terminology.
Terminologies can suffer from poor concept coverage due to delays in addition of new concepts. This study tests a similarity-based approach to recommending concepts from a text corpus to a terminology. Our approach involves extraction of candidate concepts from a given text corpus, which are represented using a set of features. The model learns the important features to characterize a concept and recommends new concepts to a terminology. Further, we propose a cost-effective evaluation methodology to estimate the effectiveness of terminology enrichment methods. To test our methodology, we use the clinical trial eligibility criteria free-text as an example text corpus to recommend concepts for SNOMED CT. We computed precision at various rank intervals to measure the performance of the methods. Results indicate that our automated algorithm is an effective method for concept recommendation.


Androgen receptor signaling in androgen-refractory prostate cancer.
Prostate cancer is the second most prevalent cancer in males in the United States. Standard therapy relies on removing, or blocking the actions of, androgens. In most cases, this therapy results in a regression of the cancer because the prostate and most primary prostate tumors depend on androgens for growth and the avoidance of apoptosis. However, a portion of the cancers eventually relapse, at which point they are termed "androgen refractory" and can no longer be cured by conventional therapy of any type. The precise molecular events that lead from androgen-sensitive prostate cancer to androgen-refractory prostate cancer are, therefore, of great interest. This review seeks to identify specific molecular events that may be linked directly to the progression to androgen-refractory cancer. Some of the mechanisms appear to involve the androgen receptor (AR) directly and include mutations in, or amplification of, the AR gene in a manner that allows the AR to respond to low doses of androgens, other steroids, or antiandrogens. In a less direct manner, coactivators may increase the sensitivity of the AR to androgens and even other nonandrogenic substances through a number of mechanisms. Additional indirect mechanisms that do not result from mutation of the AR may involve activation of the AR by peptide growth factors or cytokines or may involve bypassing the AR entirely via other cellular pathways. Identification of the role of these mechanisms in the progression to androgen-refractory prostate cancer is critical for developing therapies capable of curing this disease.


Improving MHC-I Ligand Identifications from LC-MS/MS Data by Incorporating Allelic Peptide Motifs.
MHC class I (MHC-I)-bound ligands play a pivotal role in CD8 T cell immunity and are hence of major interest in understanding and designing immunotherapies. One of the most commonly utilized approaches for detecting MHC ligands is LC-MS/MS. Unfortunately, the effectiveness of current algorithms to identify MHC ligands from LC-MS/MS data is limited because the search algorithms used were originally developed for proteomics approaches detecting tryptic peptides. Consequently, the analysis often results in inflated false discovery rate (FDR) statistics and an overall decrease in the number of peptides that pass FDR filters. Andreatta et al. describe a new scoring tool (MS-rescue) for peptides from MHC-I immunopeptidome datasets. MS-rescue incorporates the existence of MHC-I peptide motifs to rescore peptides from ligandome data. The tool is demonstrated here using peptides assigned from LC-MS/MS data with PEAKs software but can be deployed on data from any search algorithm. This new approach increased the number of peptides identified by up to 20-30% and promises to aid the discovery of novel MHC-I ligands with immunotherapeutic potential.


HNF4beta, a new gene of the HNF4 family with distinct activation and expression profiles in oogenesis and embryogenesis of Xenopus laevis.
The transcription factor hepatocyte nuclear factor 4 (HNF4) is an orphan member of the nuclear receptor superfamily expressed in mammals in liver, kidney, and the digestive tract. Recently, we isolated the Xenopus homolog of mammalian HNF4 and revealed that it is not only a tissue-specific transcription factor but also a maternal component of the Xenopus egg and distributed within an animal-to-vegetal gradient. We speculate that this gradient cooperates with the vegetally localized embryonic induction factor activin A to activate expression of HNF1alpha, a tissue-specific transcription factor with an expression pattern overlapping that of HNF4. We have now identified a second Xenopus HNF4 gene, which is more distantly related to mammalian HNF4 than the previously isolated gene. This new gene was named HNF4beta to distinguish it from the known HNF4 gene, which is now called HNF4alpha. By reverse transcription-PCR, we detected within the 5' untranslated region of HNF4beta two splice variants (HNF4beta2 and HNF4beta3) with additional exons, which seem to affect RNA stability. HNF4beta is a functional transcription factor acting sequence specifically on HNF4 binding sites known for HNF4alpha, but it seems to have a lower DNA binding activity and is a weaker transactivator than the alpha isoform. Furthermore, the two factors differ with respect to tissue distribution in adult frogs: whereas HNF4alpha is expressed in liver and kidney, HNF4beta is expressed in addition in stomach, intestine, lung, ovary, and testis. Both factors are maternal proteins and present at constant levels throughout embryogenesis. However, using reverse transcription-PCR, we found the RNA levels to change substantially: whereas HNF4alpha is expressed early during oogenesis and is absent in the egg, HNF4beta is first detected in the latest stage of oogenesis, and transcripts are present in the egg and early cleavage stages. Furthermore, zygotic HNF4alpha transcripts appear in early gastrula and accumulate during further embryogenesis, whereas HNF4beta mRNA transiently appears during gastrulation before it accumulates again at the tail bud stage. All of these distinct characteristics of the newly identified HNF4 protein imply that the alpha and beta isoform have different functions in development and in adult tissues.


Phenotypic and genetic integration of personality and growth under competition in the sheepshead swordtail, Xiphophorus birchmanni.
Competition for resources including food, physical space, and potential mates is a fundamental ecological process shaping variation in individual phenotype and fitness. The evolution of competitive ability, in particular social dominance, depends on genetic (co)variation among traits causal (e.g., behavior) or consequent (e.g., growth) to competitive outcomes. If dominance is heritable, it will generate both direct and indirect genetic effects (IGE) on resource-dependent traits. The latter are expected to impose evolutionary constraint because winners necessarily gain resources at the expense of losers. We varied competition in a population of sheepshead swordtails, Xiphophorus birchmanni, to investigate effects on behavior, size, growth, and survival. We then applied quantitative genetic analyses to determine (i) whether competition leads to phenotypic and/or genetic integration of behavior with life history and (ii) the potential for IGE to constrain life history evolution. Size, growth, and survival were reduced at high competition. Male dominance was repeatable and dominant individuals show higher growth and survival. Additive genetic contributions to phenotypic covariance were significant, with the G matrix largely recapitulating phenotypic relationships. Social dominance has a low but significant heritability and is strongly genetically correlated with size and growth. Assuming causal dependence of growth on dominance, hidden IGE will therefore reduce evolutionary potential.


Exposure to atmospheric particulate matter enhances Th17 polarization through the aryl hydrocarbon receptor.
Lung diseases, including asthma, COPD, and other autoimmune lung pathologies are aggravated by exposure to particulate matter (PM) found in air pollution. IL-17 has been shown to exacerbate airway disease in animal models. As PM is known to contain aryl hydrocarbon receptor (AHR) ligands and the AHR has recently been shown to play a role in differentiation of Th17 T cells, the aim of this study was to determine whether exposure to PM could impact Th17 polarization in an AHR-dependent manner. This study used both cell culture techniques and in vivo exposure in mice to examine the response of T cells to PM. Initially experiments were conducted with urban dust particles from a standard reference material, and ultimately repeated with freshly collected samples of diesel exhaust and cigarette smoke. The readout for the assays was increased T cell differentiation as indicated by increased generation of IL-17A in culture, and increased populations of IL-17 producing cells by intracellular flow cytometry. The data illustrate that Th17 polarization was significantly enhanced by addition of urban dust in a dose dependent fashion in cultures of wild-type but not AHR(-/-) mice. The data further suggest that polycyclic aromatic hydrocarbons played a primary role in this enhancement. There was both an increase of Th17 cell differentiation, and also an increase in the amount of IL-17 secreted by the cells. In summary, this paper identifies a novel mechanism whereby PM can directly act on the AHR in T cells, leading to enhanced Th17 differentiation. Further understanding of the molecular mechanisms responsible for pathologic Th17 differentiation and autoimmunity seen after exposure to pollution will allow direct targeting of proteins involved in AHR activation and function for treatment of PM exposures.


A dynamical model for plant cell wall architecture formation.
We discuss a dynamical mathematical model to explain cell wall architecture in plant cells. The highly regular textures observed in cell walls reflect the spatial organisation of the cellulose microfibrils (CMFs), the most important structural component of cell walls. Based on a geometrical theory proposed earlier [A. M. C. Emons, Plant, Cell and Environment 17, 3-14 (1994)], the present model describes the space-time evolution of the density of the so-called rosettes, the CMF synthesizing complexes. The motion of these rosettes in the plasma membrane is assumed to be governed by an optimal packing constraint on the CMFs plus adherent matrix material, that couples the direction of motion, and hence the orientation of the CMF being deposited, to the local density of rosettes. The rosettes are created inside the cell in the endoplasmatic reticulum and reach the cell-membrane via vesicles derived from Golgi-bodies. After being inserted into the plasma membrane they are assumed to be operative for a fixed, finite lifetime. The plasma membrane domains within which rosettes are activated are themselves also supposed to be mobile. We propose a feedback mechanism that precludes the density of rosettes to rise beyond a maximum dictated by the geometry of the cell. The above ingredients lead to a quasi-linear first order PDE for the rosette-density. Using the method of characteristics this equation can be cast into a set of first order ODEs, one of which is retarded. We discuss the analytic solutions of the model that give rise to helicoidal, crossed polylamellate, helical, axial and random textures, since all cell walls are composed of (or combinations of) these textures.


In-Line Sorting of Harumanis Mango Based on External Quality Using Visible Imaging.
The conventional method of grading Harumanis mango is time-consuming, costly and affected by human bias. In this research, an in-line system was developed to classify Harumanis mango using computer vision. The system was able to identify the irregularity of mango shape and its estimated mass. A group of images of mangoes of different size and shape was used as database set. Some important features such as length, height, centroid and parameter were extracted from each image. Fourier descriptor and size-shape parameters were used to describe the mango shape while the disk method was used to estimate the mass of the mango. Four features have been selected by stepwise discriminant analysis which was effective in sorting regular and misshapen mango. The volume from water displacement method was compared with the volume estimated by image processing using paired t-test and Bland-Altman method. The result between both measurements was not significantly different (P > 0.05). The average correct classification for shape classification was 98% for a training set composed of 180 mangoes. The data was validated with another testing set consist of 140 mangoes which have the success rate of 92%. The same set was used for evaluating the performance of mass estimation. The average success rate of the classification for grading based on its mass was 94%. The results indicate that the in-line sorting system using machine vision has a great potential in automatic fruit sorting according to its shape and mass.


Shigella flexneri enters human colonic Caco-2 epithelial cells through the basolateral pole.
The commonly accepted view that enteroinvasive bacteria enter cells of the intestinal epithelial lining through the apical surface can be challenged in the case of shigellosis. This study is based on in vitro experiments that showed that the invasion of human colonic Caco-2 cells by Shigella flexneri occurred through the basolateral pole of these cells. In these experiments, the few bacteria that interacted with the apical surface either bound to microvilli of the cell dome without causing detectable alteration or bound at the level of intercellular junctions at which they demonstrated a limited capacity for paracellular invasion, which permitted subsequent entry through the lateral domain of the cells. Treatment of Caco-2 cell monolayers with ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA), which disrupts intercellular junctions, greatly enhanced the rate of cell infection. These observations suggest a physiopathological paradox that may have important consequences for the understanding of the process of colonic invasion in vivo during shigellosis.


Causes of death in children younger than five years in China in 2015: an updated analysis.
Substantial progress in reducing the child mortality rate has been made globally in the last two decades. However, for China, the number of children dying from preventable diseases is still very large. It is important to have regularly updated information on the distribution of causes of death (COD) in children to inform policy and research. In this study, we aim to estimate the COD spectrum in children younger than five years old from 2009 to 2015 with a focus on the year 2015 and to provide an updated COD prediction model for China. Updated data of under-five mortality rates (U5MRs) and the number of live births at national and provincial levels were obtained from United Nation's Inter-agency Group for Child Mortality Estimation (UN IGME), Institute for Health Metrics and Evaluation (IHME), and United Nations Population Division (UNPD). Then, we conducted a systematic review across four Chinese and English bibliographic databases and identified high-quality community-based longitudinal studies of COD in children younger than five years in China. We developed a number of single-cause models to predict the number of child death for main COD in different age groups at both national and provincial levels. The jackknife procedure was applied to construct the 95% Uncertainty Ranges (URs). From 2009 to 2015, the under-five mortality rates have declined by 37.1%. The leading causes of death in 2015 were preterm birth complications (17.4%), birth asphyxia (15.2%), congenital abnormalities (14.1%), accidents (13.5%) and pneumonia (12.4%) for children under five years old. The COD spectrum varied substantially across Chinese provinces with different development levels. The leading cause in children under five years in the wealthier provinces (with lower U5MRs) was congenital abnormalities (up to 18.9%), while in the poorer provinces (with higher U5MRs), pneumonia was the dominant COD (up to 23.4%). This study updates and validates the accuracy of the findings of our previous COD study and proposes a new modelling method to predict proportions for the most common causes of child death in China. These updated COD estimates suggest that current strategies to reduce child mortality should prioritise action on neonatal deaths and target interventions against the top COD according to the local COD spectrum. Special attention should also be given to reducing differences between Chinese provinces and regions with differing development levels.


Elaboration and Physicochemical Characterization of Niosome-Based Nioplexes for Gene Delivery Purposes.
Niosome formulations for gene delivery purposes are based on nonionic surfactants, helper lipids, and cationic lipids that interact electrostatically with negatively charged DNA molecules to form the so-called nioplexes. Niosomes are elaborated by different techniques, such as solvent emulsion-evaporation, thin film hydration, hand-shaking, dissolvent injection, and microfluidization method, among many others. In this chapter, we have described some protocols for the elaboration of niosomes and nioplexes and their physicochemical characterization that guarantees the quality criteria of the formulation in terms of size, morphology, ζ-potential, and stability.


Massively parallel cis-regulatory analysis in the mammalian central nervous system.
Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery to target organs in vivo. As a proof of concept, we introduce a capture library of about 46,000 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as nonhuman primates and human stem cell-derived organoids.


The Effects of Neighborhood Built Environment on Walking for Leisure and for Purpose Among Older People.
Characteristics of a neighborhood's built environment affect the walking behavior of older people, yet studies typically rely on small nonrepresentative samples that use either subjective reports or aggregate indicators from administrative sources to represent neighborhood characteristics. Our analyses examine the usefulness of a novel method for observing neighborhoods-virtual observations-and assess the extent to which virtual-based observations predict walking among older adults. Using Google Street View, we observed the neighborhoods of 2,224 older people and examined how characteristics of the neighborhood built environments are associated with the amount of time older people spend walking for leisure and purpose. Multilevel model analyses revealed that sidewalk characteristics had significant associations with both walking for purpose and leisure. Land use, including the presence of multifamily dwellings, commercial businesses, and parking lots were positively associated with walking for purpose and single-family detached homes were negatively associated with walking for purpose, but none of these characteristics were associated with leisure walking. Gardens/flowers were associated with walking for leisure but not purpose. Garbage/litter was not associated with either type of walking behavior. Virtual observations are a useful method that provides meaningful information about neighborhoods. Findings demonstrate how neighborhood characteristics assessed virtually differentially impact walking for leisure and purpose among older adults and are interpreted within a social-ecological model.


Clinical profile of suvorexant for the treatment of insomnia over 3 months in women and men: subgroup analysis of pooled phase-3 data.
Sex-related differences in the clinical profiles of some insomnia medications have been previously reported. To evaluate the clinical profile of suvorexant, a novel orexin receptor antagonist approved for treating insomnia at doses up to 20 mg, by sex subgroups. Efficacy analyses by sex were based on pooled data from two similar phase 3, randomized, double-blind, placebo-controlled, 3-month trials in elderly (≥65 years) and non-elderly (18-64 years) insomnia patients. Two age-adjusted (non-elderly/elderly) dose regimes of 40/30 and 20/15 mg were evaluated, with fewer patients assigned to 20/15 mg. Efficacy was assessed by patient-reported outcomes (N = 1264 women, 707 men) and by polysomnography endpoints in ~75% of patients. Safety analyses by sex (N = 1744 women, 1065 men) included pooled data from the two 3-month trials plus 3-month data from a safety trial of 40/30 mg. The sex subgroup efficacy analyses mirrored the improvements seen for suvorexant 40/30 and 20/15 mg over placebo on patient-reported outcomes and polysomnography sleep maintenance and onset endpoints in the primary analyses; 95% CIs excluded zero in favor of suvorexant for most endpoints in both sexes, and similar efficacy was observed between sexes (95% CIs overlapped). Suvorexant was well-tolerated in women and men, although women in all treatment groups (including placebo) reported more adverse events than men. The most frequent adverse event was somnolence (women: 11.1% for 40/30 mg, 8.5% for 20/15 mg, 2.3% for placebo; men: 10.1% for 40/30 mg, 3.4% for 20/15 mg, 4.2% for placebo). Suvorexant was generally effective and well-tolerated in both women and men with insomnia. ClinicalTrials.gov trial registration numbers: NCT01097616, NCT01097629, NCT01021813.


COVIDiSTRESS Global Survey dataset on psychological and behavioural consequences of the COVID-19 outbreak.
This N = 173,426 social science dataset was collected through the collaborative COVIDiSTRESS Global Survey - an open science effort to improve understanding of the human experiences of the 2020 COVID-19 pandemic between 30th March and 30th May, 2020. The dataset allows a cross-cultural study of psychological and behavioural responses to the Coronavirus pandemic and associated government measures like cancellation of public functions and stay at home orders implemented in many countries. The dataset contains demographic background variables as well as measures of Asian Disease Problem, perceived stress (PSS-10), availability of social provisions (SPS-10), trust in various authorities, trust in governmental measures to contain the virus (OECD trust), personality traits (BFF-15), information behaviours, agreement with the level of government intervention, and compliance with preventive measures, along with a rich pool of exploratory variables and written experiences. A global consortium from 39 countries and regions worked together to build and translate a survey with variables of shared interests, and recruited participants in 47 languages and dialects. Raw plus cleaned data and dynamic visualizations are available.


Pore structure of soot deposits from several combustion sources.
Soot was harvested from five combustion sources: a dodecane flame, marine and bus diesel engines, a wood stove, and an oil furnace. The soots ranged from 20% to 90% carbon by weight and molar C/H ratios from 1 to 7, the latter suggesting a highly condensed aromatic structure. Total surface areas (by nitrogen adsorption using the Brunauer Emmett Teller, BET method) ranged from 1 to 85 m2 g(-1). Comparison of the surface area and meso-pore (pores 2-50 nm) surface area predicted by density functional theory (DFT) suggested that the soot was highly porous. Total meso-pore volume and surface area ranged from 0.004-0.08 cm3 g(-1) and from 0.33-6.9 m2 g(-1) respectively, accounting for up 33% of the BET surface area. The micro-pore volume (pores <2 nm) calculated from CO2 adsorption data (by DFT) ranged from 0.0009 to 0.013 cm3 g(-1) and micro-pore surface area was 3.1-41 m2 g(-1), accounting for 10-20% of the total intra-particle (meso-plus micro-pores) pore volume and 70-90% of the total intra-particle surface area. Higher pore volume and surface area values were computed using the Dubinin Radushkevich plot technique; ranging from 0.004-0.04 cm3 g(-1) to 11-102 m2 g(-1) for micro-pore volume and surface area, respectively. Comparison of the C/H ratio and the micro-pore structure showed a strong correlation, suggesting a relationship between the condensation of the skeletal structure and micro-porosity of the soot. These data contradict literature reports that soot particles are non-porous and are consistent with recent literature reports that soil organic matter has large micro-pore surface areas.


The first reported snakebite by an African snake-eater, Polemon spp. (Atractaspididae, Aparallactinae); Local envenoming by Reinhardt's snake-eater, Polemon acanthias (Reinhardt, 1860).
The first reported snakebite by an African snake-eater, Polemon spp. (Atractaspididae, Aparallactinae); Local envenoming by Reinhardt's snake-eater, Polemon acanthias (Reinhardt, 1860). Toxicon XX, xxx. A 51-yr-old male herpetologist was bitten on the left index finger by a captive male Polemon acanthias while manually removing fragments of incompletely shed skin from the specimen. The snake sustained its bite for approximately 2 mins, advancing its jaws several times. The victim rapidly developed moderate pain, erythema, progressive edema that ultimately extended to the left wrist; a blister later developed in the wound site, as well as joint stiffness in the bitten and adjacent two fingers that limited flexion and extension. These effects regressed during the week following the bite, but recurred thereafter and were similar to the effects that developed immediately post-envenoming. There were no systemic signs or symptoms. The victim sought medical advice and was treated with broad-spectrum antibiotics, antihistamines and wound care; no laboratory investigations were conducted. He improved during the subsequent month with complete resolution in 5 and one-half weeks. This is the first documented bite by a Polemon spp. and the victim's clinical course suggests the development of local effects from venom components. The phylogenetic relationship of Polemon spp. with the burrowing asps (Atractaspis spp.) and the similarity of some of the features of this local envenoming by P. acanthias with mild/moderate envenoming by some Atractaspis spp., suggests that none of these snakes should be handled; they should be considered capable of inflicting potentially serious envenoming.


Data standards for proteomics: mitochondrial two-dimensional polyacrylamide gel electrophoresis data as a model system.
Proteomics has emerged as a major discipline that led to a re-examination of the need for consensus and a nationally sanctioned set of proteomics technology standards. Such standards for databases and data reporting may be applied to two-dimensional polyacrylamide gel electrophoresis (2D PAGE) technology as a pilot project for assessing global and national needs in proteomics, and the role of the National Institute of Standards and Technology (NIST) and other similar standards and measurement organizations. The experience of harmonizing the heterogeneous data included in the Protein Data Bank (PDB) provides a paradigm for technology in an area where significant heterogeneity in technical detail and data storage has evolved. Here we propose an approach toward standardizing mitochondrial 2D PAGE data in support of a globally relevant proteomics consensus.


Relationship of anti-Lewis x and anti-Lewis y antibodies in serum samples from gastric cancer and chronic gastritis patients to Helicobacter pylori-mediated autoimmunity.
Lewis (Le) antigens have been implicated in the pathogenesis of atrophic gastritis and gastric cancer in the setting of Helicobacter pylori infection, and H. pylori-induced anti-Le antibodies have been described that cross-react with the gastric mucosa of both mice and humans. The aim of this study was to examine the presence of anti-Le antibodies in patients with H. pylori infection and gastric cancer and to examine the relationships between anti-Le antibody production, bacterial Le expression, gastric histopathology, and host Le erythrocyte phenotype. Anti-Le antibody production and H. pylori Le expression were determined by enzyme-linked immunosorbent assay, erythrocyte Le phenotype was examined by agglutination assays, and histology was scored blindly. Significant levels of anti-Le(x) antibody (P < 0.0001, T = 76.4, DF = 5) and anti-Le(y) antibody (P < 0.0001, T = 73.05, DF = 5) were found in the sera of patients with gastric cancer and other H. pylori-associated pathology compared with H. pylori-negative controls. Following incubation of patient sera with synthetic Le glycoconjugates, anti-Le(x) and -Le(y) autoantibody binding was abolished. The degree of the anti-Le(x) and -Le(y) antibody response was unrelated to the host Le phenotype but was significantly associated with the bacterial expression of Le(x) (r = 0.863, r(2) = 0.745, P < 0.0001) and Le(y) (r = 0.796, r(2) = 0.634, P < 0.0001), respectively. Collectively, these data suggest that anti-Le antibodies are present in most patients with H. pylori infection, including those with gastric cancer, that variability exists in the strength of the anti-Le response, and that this response is independent of the host Le phenotype but related to the bacterial Le phenotype.


Historic and recent events contribute to the disease dynamics of Beijing-like Mycobacterium tuberculosis isolates in a high incidence region.
A retrospective study in an urban setting with a high tuberculosis incidence. To study the molecular epidemiology and disease dynamics of a prevalent Mycobacterium tuberculosis strain family, F29, a subset of the Beijing strains. Multi-locus DNA fingerprinting and genomic analysis was used to characterise F29 isolates. Demographic and molecular epidemiologic data were correlated with those of other isolates from the setting. The geographic locations of five F29 strain clusters were plotted using a geographic information system (GIS) and an index for geographic distribution was calculated. Their cumulative temporal occurrence was also plotted. The genomic similarity of F29 to the Beijing-strains was confirmed. A high degree of clustering predicted high disease transmission. Spatial distribution was mostly widespread except for one cluster. Smaller foci of transmission were observed. The temporal spread showed ongoing transmission. F29 belongs to the Beijing strain group. The prevalence and high degree of strain clustering, with limited geographic clustering, indicates that F29 strains are endemic in the study community. However, recent epidemiologic events also contributed to the disease spread. The combination of molecular epidemiologic, spatial and temporal data has enhanced our understanding of the disease dynamics of Beijing strains in our study community.


A deficiency in Drak2 results in a T cell hypersensitivity and an unexpected resistance to autoimmunity.
DRAK2 is a member of the death-associated protein (DAP)-like family of serine/threonine kinases. Members of this family induce apoptosis in various cell types. DRAK2, in particular, is specifically expressed in T cells and B cells, and it is differentially regulated during T cell development. To determine whether DRAK2 regulates lymphocyte apoptosis, we produced Drak2(-/-) mice. Contrary to our expectations, Drak2(-/-) T cells did not demonstrate any defects in apoptosis or negative selection; however, T cells from Drak2(-/-) mice exhibited enhanced sensitivity to T cell receptor-mediated stimulation with a reduced requirement for costimulation. These results provide evidence that DRAK2 raises the threshold for T cell activation by negatively regulating signals through the TCR. In contrast to other models of T cell hypersensitivity, Drak2(-/-) mice were remarkably resistant to experimental autoimmune encephalomyelitis (EAE). These results expose a new pathway regulating T cell activation and highlight the intricacies of induced autoimmune disease.


European framework for tuberculosis control and elimination in countries with a low incidence. Recommendations of the World Health Organization (WHO), International Union Against Tuberculosis and Lung Disease (IUATLD) and Royal Netherlands Tuberculosis Association (KNCV) Working Group.
As countries approach the elimination phase of tuberculosis, specific problems and challenges emerge, due to the steadily declining incidence in the native population, the gradually increasing importance of the importation of latent tuberculosis infection and tuberculosis from other countries and the emergence of groups at particularly high risk of tuberculosis. Therefore, a Working Group of the World Health Organization (WHO), the International Union Against Tuberculosis and Lung Disease (IUATLD) and the Royal Netherlands Tuberculosis Association (KNCV) have developed a new framework for low incidence countries based on concepts and definitions consistent with those of previous recommendations from WHO/IUATLD Working Groups. In low-incidence countries, a broader spectrum of interventions is available and feasible, including: 1) a general approach to tuberculosis which ensures rapid detection and treatment of all the cases and prevention of unnecessary deaths; 2) an overall control strategy aimed at reducing the incidence of tuberculosis infection (risk-group management and prevention of transmission of infection in institutional settings) and 3) a tuberculosis elimination strategy aimed at reducing the prevalence of tuberculosis infection (outbreak management and provision of preventive therapy for specified groups and individuals). Government and private sector commitment towards elimination, effective case detection among symptomatic individuals together with active case finding in special groups, standard treatment of disease and infection, access to tuberculosis diagnostic and treatment services, prevention (e.g. through screening and bacille Calmette-Guéria immunization in specified groups), surveillance and treatment outcome monitoring are prerequisites to implementing the policy package recommended in this new framework document.


Lipid-mediated impairment of axonal lysosome transport contributing to autophagic stress.
Efficient degradation of autophagic vacuoles (AVs) generated at axon terminals by mature lysosomes enriched in the cell body represents an exceptional challenge that neurons face in maintaining cellular homeostasis. Here, we discuss our recent findings revealing a lipid-mediated impairment of lysosome transport to distal axons contributing to axonal AV accumulation in the neurodegenerative lysosomal storage disorder Niemann-Pick disease type C (NPC). Using transmission electron microscopy, we observed a striking buildup of endocytic and autophagic organelles in NPC dystrophic axons, indicating defects in the clearance of organelles destined for lysosomal degradation. We further revealed that elevated cholesterol on NPC lysosome membranes abnormally sequesters motor-adaptors of axonal lysosome delivery, resulting in impaired anterograde lysosome transport into distal axons that disrupts maturation of axonal AVs during their retrograde transport route. Together, our study demonstrates a mechanism by which altered membrane lipid composition compromises axonal lysosome trafficking and positioning and shows that lowering lysosomal lipid levels rescues lysosome transport into NPC axons, thus reducing axonal autophagic stress at early stages of NPC disease.


The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated.
Staphylococcus aureus is major human and animal pathogen. Plasmids often carry resistance genes and virulence genes that can disseminate through S. aureus populations by horizontal gene transfer (HGT) mechanisms. Sequences of S. aureus plasmids in the public domain and data from multi-strain microarrays were analysed to investigate (i) the distribution of resistance genes and virulence genes on S. aureus plasmids, and (ii) the distribution of plasmids between S. aureus lineages. A total of 21 plasmid rep gene families, of which 13 were novel to this study, were characterised using a previously proposed classification system. 243 sequenced plasmids were assigned to 39 plasmid groups that each possessed a unique combination of rep genes. We show some resistance genes (including ermC and cat) and virulence genes (including entA, entG, entJ, entP) were associated with specific plasmid groups suggesting there are genetic pressures preventing recombination of these genes into novel plasmid groups. Whole genome microarray analysis revealed that plasmid rep, resistance and virulence genes were associated with S. aureus lineages, suggesting restriction-modification (RM) barriers to HGT of plasmids between strains exist. Conjugation transfer (tra) complex genes were rare. This study argues that genetic pressures are restraining the spread of resistance and virulence genes amongst S. aureus plasmids, and amongst S. aureus populations, delaying the emergence of fully virulent and resistant strains.


p-Benzoquinone, a reactive metabolite of benzene, prevents the processing of pre-interleukins-1 alpha and -1 beta to active cytokines by inhibition of the processing enzymes, calpain, and interleukin-1 beta converting enzyme.
Chronic exposure of humans of benzene affects hematopoietic stem and progenitor cells and leads to aplastic anemia. The stromal macrophage, a target of benzene toxicity, secretes interleukin-1 (IL-1), which induces the stromal fibroblast to synthesize hematopoietic colony-stimulating factors. In a mouse model, benzene causes an acute marrow hypocellularity that can be prevented by the concomitant administration of IL-1 alpha. The ability of benzene to interfere with the production and secretion of IL-1 alpha was tested. Stromal macrophages from benzene-treated mice were capable of the transcription to the IL-1 alpha gene and the translation of the message but showed an inability to process the 34-kDa pre-IL-1 alpha precursor to the 17-kDa biologically active cytokine. Treatment of normal murine stromal macrophages in culture with hydroquinone (HQ) also showed an inhibition in processing of pre-IL-1 alpha. Hydroquinone is oxidized by a peroxidase-mediated reaction in the stromal macrophage to p-benzoquinone, which interacts with the sulfhydryl (SH) groups of proteins and was shown to completely inhibit the activity of calpain, the SH-dependent protease that cleaves pre-IL-1 alpha. In a similar manner, HQ, via peroxidase oxidation to p-benzoquinone, was capable of preventing the IL-1 beta autocrine stimulation of growth of human B1 myeloid tumor cells by preventing the processing of pre-IL-1 beta to mature cytokine. Benzoquinone was also shown to completely inhibit the ability of the SH-dependent IL-1 beta converting enzyme. Thus benzene-induced bone marrow hypocellularity may result from apoptosis of hematopoietic progenitor cells brought about by lack of essential cytokines and deficient IL-1 alpha production subsequent to the inhibition of calpain by p-benzoquinone and the prevention of pre-IL-1 processing.


Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves.
Chalcophaps is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of Chalcophaps. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized Chalcophaps species. Despite this general concordance, we identify discordant mitochondrial and nuclear ancestries in the subspecies C. longirostris timorensis, raising further questions about the evolutionary history of this Timor endemic population. Within each of the three species, we find evidence for isolation by distance or hierarchical population structure, indicating an important role for geography in the diversification of this genus. Despite being distributed broadly across a highly fragmented geographic region known as a hotspot for avian diversification, the Chalcophaps doves show modest levels of phenotypic and genetic diversity, a pattern potentially explained by strong population connectivity owing to high overwater dispersal capability.


Retinal degeneration in mice lacking the gamma subunit of the rod cGMP phosphodiesterase.
The retinal cyclic guanosine 3',5'-monophosphate (cGMP) phosphodiesterase (PDE) is a key regulator of phototransduction in the vertebrate visual system. PDE consists of a catalytic core of alpha and beta subunits associated with two inhibitory gamma subunits. A gene-targeting approach was used to disrupt the mouse PDEgamma gene. This mutation resulted in a rapid retinal degeneration resembling human retinitis pigmentosa. In homozygous mutant mice, reduced rather than increased PDE activity was apparent; the PDEalphabeta dimer was formed but lacked hydrolytic activity. Thus, the inhibitory gamma subunit appears to be necessary for integrity of the photoreceptors and expression of PDE activity in vivo.