Visualization of Mycobacterial Biomarkers and Tuberculosis Drugs in Infected Tissue by MALDI-MS Imaging.
MALDI mass-spectrometry imaging (MALDI-MSI) is a technique capable of the label-free identification and visualization of analytes in tissue sections. We have previously applied MALDI-MSI to the study of the spatial distribution of tuberculosis (TB) drugs in necrotic lung granulomas characteristic of pulmonary TB disease, revealing heterogeneous and often suboptimal drug distributions. To investigate the impact of differential drug distributions at sites of infection, we sought to image mycobacterial biomarkers to coregister drugs and bacteria in lesion sections. The traditional method of visualizing Mycobacterium tuberculosis inside lesions is acid-fast staining and microscopy. Directly analyzing and visualizing mycobacteria-specific lipid markers by MALDI-MSI provides detailed molecular information on bacterial distributions within granulomas, complementary to high-spatial-resolution staining and microscopy approaches. Moreover, spatial monitoring of molecular changes occurring in bacteria during granuloma development can potentially contribute to a greater understanding of pulmonary-TB pathogenesis. In this study, we developed a MALDI-MSI method to detect and visualize specific glycolipids of mycobacteria within TB lesions. The biomarker signal correlated well with the bacteria visualized by IHC and acid-fast staining. This observation was seen in samples collected from multiple animal models. Although individual bacteria could not be visualized because of the limit of spatial resolution (50 μm), bacterial clusters were clearly detected and heterogeneously distributed throughout lesions. The ability to visualize drugs, metabolites, and bacterial biomarkers by MALDI-MSI enabled direct colocalization of drugs with specific bacterial target populations (identifiable by distinct metabolic markers). Future applications include assessing drug activity in lesions by visualizing drug-mediated lipid changes and other drug-induced mycobacterial metabolic responses.


Evolutionary analysis and lateral gene transfer of two-component regulatory systems associated with heavy-metal tolerance in bacteria.
Microorganisms have adapted intricate signal transduction mechanisms to coordinate tolerance to toxic levels of metals, including two-component regulatory systems (TCRS). In particular, both cop and czc operons are regulated by TCRS; the cop operon plays a key role in bacterial tolerance to copper, whereas the czc operon is involved in the efflux of cadmium, zinc, and cobalt from the cell. Although the molecular physiology of heavy metal tolerance genes has been extensively studied, their evolutionary relationships are not well-understood. Phylogenetic relationships among heavy-metal efflux proteins and their corresponding two-component regulatory proteins revealed orthologous and paralogous relationships from species divergences and ancient gene duplications. The presence of heavy metal tolerance genes on bacterial plasmids suggests these genes may be prone to spread through horizontal gene transfer. Phylogenetic inferences revealed nine potential examples of lateral gene transfer associated with metal efflux proteins and two examples for regulatory proteins. Notably, four of the examples suggest lateral transfer across major evolutionary domains. In most cases, differences in GC content in metal tolerance genes and their corresponding host genomes confirmed lateral gene transfer events. Three-dimensional protein structures predicted for the response regulators encoded by cop and czc operons showed a high degree of structural similarity with other known proteins involved in TCRS signal transduction, which suggests common evolutionary origins of functional phenotypes and similar mechanisms of action for these response regulators.


Induction of cell-mediated immunity against Mycobacterium tuberculosis using DNA vaccines encoding cytotoxic and helper T-cell epitopes of the 38-kilodalton protein.
Cell-mediated immune responses are crucial in the protection against tuberculosis. In this study, we constructed DNA vaccines encoding cytotoxic T lymphocytes (CTL) and T helper cell (Th) epitopes of the 38-kDa lipoglycoprotein of Mycobacterium tuberculosis and analyzed and compared their immunogenicities with that of pXJ38, a DNA vaccine encoding the entire 38-kDa protein (X. Zhu, N. Venkataprasad, H. S. Thangaraj, M. Hill, M. Singh, J. Ivanyi, and H. M. Vordermeier, J. Immunol. 158:5921-5926, 1997). Plasmid DNAs encoding a CTL epitope, P3 (pP3), a Th epitope (vTh), or both the Th and the P3 epitopes (pThP3) were prepared and tested in C57BL6/J (H-2(b)) mice. Our results confirmed that DNA immunization with pXJ38 induces strong CD8(+) CTL and Th1 responses (high gamma interferon [IFN-gamma], low interleukin-4 [IL-4]). Coadministration of plasmid DNAs encoding a Th epitope with those encoding a CTL epitope (vTh+pP3) elicited both antigen-specific CD8(+) CTL and Th1 responses. High levels of IFN-gamma were secreted by spleen cells from all plasmid DNA-vaccinated mice after in vitro stimulation with the recombinant 38-kDa protein. Small or undetectable amounts of IL-4 were observed, which indicates the induction of a Th1-like response. Multiple-epitope vaccination by vTh+pP3 or pThP3 resulted in a broader Th1 response to peptide or epitopes than the single-epitope plasmid DNAs. Antigen-specific immunoglobulin G2a was only detected in sera from mice immunized with the plasmid pXJ38, and not in mice immunized with the epitope-based DNA vaccines. Thus, the absence of an antibody response after immunization with epitope plasmid DNAs and their ability to trigger only a specific cellular immune response may prove to be important advantages for a vaccine against tuberculosis.


Phase transition behaviors of the supported DPPC bilayer investigated by sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM).
The phase transition behaviors of a supported bilayer of dipalmitoylphosphatidyl-choline (DPPC) have been systematically evaluated by in situ sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM). By using an asymmetric bilayer composed of per-deuterated and per-protonated monolayers, i.e., DPPC-d75/DPPC and a symmetric bilayer of DPPC/DPPC, we were able to probe the molecular structural changes during the phase transition process of the lipid bilayer by SFG spectroscopy. It was found that the DPPC bilayer is sequentially melted from the top (adjacent to the solution) to bottom leaflet (adjacent to the substrate) over a wide temperature range. The conformational ordering of the supported bilayer does not decrease (even slightly increases) during the phase transition process. The conformational defects in the bilayer can be removed after the complete melting process. The phase transition enthalpy for the bottom leaflet was found to be approximately three times greater than that for the top leaflet, indicating a strong interaction of the lipids with the substrate. The present SFG and AFM observations revealed similar temperature dependent profiles. Based on these results, the temperature-induced structural changes in the supported lipid bilayer during its phase transition process are discussed in comparison with previous studies.


This script gives a pragmatic advice for general dentists on accurate use of amoxicillin with clavulanic acid considering current literature at acute inflammatory disease. In absence of contraindications a twice daily formulation of 1g amoxicillin with clavulanic acid is the first choice for concomitant therapy after treating the cause of inflammation or prophylaxis. Compared to clindamycin the concentration of amoxicillin in teeth and bone (Hallig 2014) is higher and has less gastrointestinal side-effects (Bax 2007). Furthermore it is prescribable during pregnancy and lactation. With these advantages amoxicillin with clavulanic acid is the first choice of antibiotics in general dental medicine.


Magnetic resonance imaging flowmetry demonstrates portal vein dilatation subsequent to oxaliplatin therapy in patients with colorectal liver metastasis.
Sinusoidal injury (SI) after oxaliplatin-based therapies for colorectal liver metastasis (CRLM) can increase postoperative morbidity. Preoperative methods to estimate SI are lacking. The aim of this study was to identify SI by evaluating portal vein haemodynamics. Magnetic resonance imaging flowmetry (MRIF) was used to estimate portal vein haemodynamics in 29 patients with CRLM before liver surgery. Sinusoidal injury was evaluated from resected non-tumorous liver parenchyma according to the combined vascular injury (CVI) score of ≥3. All patients with SI (six of 29) received oxaliplatin; however, a significant association could not be proven (P= 0.148). Oxaliplatin-treated patients showed portal vein dilatation in both the SI and non-SI groups compared with patients who had not received oxaliplatin (Bonferroni corrected P= 0.003 and P= 0.039, respectively). Mean portal velocity tended to be lower in patients with SI compared with oxaliplatin-treated patients without SI (Bonferroni corrected P= 0.087). A mean portal velocity of ≤14.35 cm/s together with a cross-section area of ≥1.55 cm(2) was found to predict SI with sensitivity of 100% and specificity of 78%. Oxaliplatin treatment was associated with portal vein dilatation. Patients with SI showed a tendency towards decreased mean portal flow velocity. This may indicate that SI is associated with an increased resistance to blood flow in the liver parenchyma. Portal vein haemodynamic variables estimated by MRIF can identify patients without SI non-invasively.


Rescue of dystrophic muscle through U7 snRNA-mediated exon skipping.
Most mutations in the dystrophin gene create a frameshift or a stop in the mRNA and are associated with severe Duchenne muscular dystrophy. Exon skipping that naturally occurs at low frequency sometimes eliminates the mutation and leads to the production of a rescued protein. We have achieved persistent exon skipping that removes the mutated exon on the dystrophin messenger mRNA of the mdx mouse, by a single administration of an AAV vector expressing antisense sequences linked to a modified U7 small nuclear RNA. We report the sustained production of functional dystrophin at physiological levels in entire groups of muscles and the correction of the muscular dystrophy.


G1/ELE Functions in the Development of Rice Lemmas in Addition to Determining Identities of Empty Glumes.
Rice empty glumes, also named sterile lemmas or rudimentary lemmas according to different interpretations, are distinct from lemmas in morphology and cellular pattern. Consistently, the molecular mechanism to control the development of lemmas is different from that of empty glumes. Rice LEAFY HULL STERILE1(OsLHS1) and DROOPING LEAF(DL) regulate the cellular pattern and the number of vascular bundles of lemmas respectively, while LONG STERILE LEMMA1 (G1)/ELONGATED EMPTY GLUME (ELE) and PANICLE PHYTOMER2 (PAP2)/OsMADS34 determine identities of empty glumes. Though some progress has been made, identities of empty glumes remain unclear, and genetic interactions between lemma genes and glume genes have been rarely elucidated. In this research, a new G1/ELE mutant g1-6 was identified and the phenotype was analyzed. Similar to previously reported mutant lines of G1/ELE, empty glumes of g1-6 plants transform into lemma-like organs. Furthermore, Phenotypes of single and double mutant plants suggest that, in addition to their previously described gene-specific functions, G1/ELE and OsLHS1 play redundant roles in controlling vascular bundle number, cell volume, and cell layer number of empty glumes and lemmas. Meanwhile, expression patterns of G1/ELE in osmads1-z flowers and OsLHS1 in g1-6 flowers indicate they do not regulate each other at the level of transcription. Finally, down-regulation of the empty glume gene OsMADS34/PAP2 and ectopic expression of the lemma gene DL, in the g1-6 plants provide further evidence that empty glumes are sterile lemmas. Generally, our findings provided valuable information for better understanding functions of G1 and OsLHS1 in flower development and identities of empty glumes.


Dietary dried plum increases bone mass, suppresses proinflammatory cytokines and promotes attainment of peak bone mass in male mice.
Nutrition is an important determinant of bone health and attainment of peak bone mass. Diets containing dried plum (DP) have been shown to increase bone volume and strength. These effects may be linked to the immune system and DP-specific polyphenols. To better understand these relationships, we studied DP in skeletally mature (6-month-old) and growing (1- and 2-month-old) C57Bl/6 male mice. In adult mice, DP rapidly (<2 weeks) increased bone volume (+32%) and trabecular thickness (+24%). These changes were associated with decreased osteoclast surface (Oc.S/BS) and decreased serum CTX, a marker of bone resorption. The reduction in Oc.S/BS was associated with a reduction in the osteoclast precursor pool. Osteoblast surface (Ob.S/BS) and bone formation rate were also decreased suggesting that the gain in bone in adult mice is a consequence of diminished bone resorption and formation, but resorption is reduced more than formation. The effects of DP on bone were accompanied by a decline in interleukins, TNF and MCP-1, suggesting that DP is acting in part through the immune system to suppress inflammatory activity and reduce the size of the osteoclast precursor pool. Feeding DP was accompanied by an increase in plasma phenolics, some of which have been shown to stimulate bone accrual. In growing and young adult mice DP at levels as low as 5% of diet (w/w) increased bone volume. At higher levels (DP 25%), bone volume was increased by as much as 94%. These data demonstrate that DP feeding dramatically increases peak bone mass during growth.


Bcl-2 accelerates retinoic acid-induced growth arrest and recovery in human gastric cancer cells.
The role of Bcl-2 as an anti-apoptotic protein has been well documented. In the present work, we present evidence that Bcl-2 may also be involved in cell growth regulation. SC-M1 is an unique cell line which responds to retinoic acid (RA) treatment with reversible growth arrest [Shyu, Jiang, Huang, Chang, Wu, Roffler and Yeh (1995) Eur. J. Cancer 31, 237-243]. In this study, when treated with RA, SC-M1/Bcl2 cells, which were generated by transfecting SC-M1 cells with bcl-2 DNA, were growth-arrested two days earlier than SC-M1/neo cells, which were generated by transfecting SC-M1 cells with vector DNA. This indicates that Bcl-2 accelerates RA-induced growth arrest. In addition to the accelerated growth arrest, RA-treated SC-M1/Bcl2 cells also recovered from growth arrest two days faster than SC-M1/neo cells after the removal of RA. Previously, we had identified the cyclin-dependent kinase inhibitor p21((WAF1/CIP1)) (p21) as a mediator of RA-induced growth arrest [Tsao, Li, Kuo, Liu and Chen (1996) Biochem. J. 317, 707-711]. In a search for the mechanism by which Bcl-2 affects growth regulation, we found that p21 gene expression was more prominent in SC-M1/Bcl2 cells than in SC-M1/neo cells in the presence of RA, but when RA was removed, p21 gene expression levels in SC-M1/Bcl2 cells were also reduced earlier than in SC-M1/neo cells. The present report is the first to show that Bcl-2 accelerates not only growth arrest but also recovery from growth arrest. Moreover, the close correlation between the effect of Bcl-2 on both RA-induced growth arrest and RA-induced p21 gene expression suggests the possibility that Bcl-2 affects cell growth through the mechanism of p21.


Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events.
Lung cancer is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole-genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and three lung tumor/normal pairs. Overall, our data show that cell line models exhibit similar mutation spectra to human tumor samples. Smoker and never-smoker cancer samples exhibit distinguishable patterns of mutations. A number of epigenetic regulators, including KDM6A, ASH1L, SMARCA4, and ATAD2, are frequently altered by mutations or copy number changes. A systematic survey of splice-site mutations identified 106 splice site mutations associated with cancer specific aberrant splicing, including mutations in several known cancer-related genes. RAC1b, an isoform of the RAC1 GTPase that includes one additional exon, was found to be preferentially up-regulated in lung cancer. We further show that its expression is significantly associated with sensitivity to a MAP2K (MEK) inhibitor PD-0325901. Taken together, these data present a comprehensive genomic landscape of a large number of lung cancer samples and further demonstrate that cancer-specific alternative splicing is a widespread phenomenon that has potential utility as therapeutic biomarkers. The detailed characterizations of the lung cancer cell lines also provide genomic context to the vast amount of experimental data gathered for these lines over the decades, and represent highly valuable resources for cancer biology.


Lunar impact basins revealed by Gravity Recovery and Interior Laboratory measurements.
Observations from the Gravity Recovery and Interior Laboratory (GRAIL) mission indicate a marked change in the gravitational signature of lunar impact structures at the morphological transition, with increasing diameter, from complex craters to peak-ring basins. At crater diameters larger than ~200 km, a central positive Bouguer anomaly is seen within the innermost peak ring, and an annular negative Bouguer anomaly extends outward from this ring to the outer topographic rim crest. These observations demonstrate that basin-forming impacts remove crustal materials from within the peak ring and thicken the crust between the peak ring and the outer rim crest. A correlation between the diameter of the central Bouguer gravity high and the outer topographic ring diameter for well-preserved basins enables the identification and characterization of basins for which topographic signatures have been obscured by superposed cratering and volcanism. The GRAIL inventory of lunar basins improves upon earlier lists that differed in their totals by more than a factor of 2. The size-frequency distributions of basins on the nearside and farside hemispheres of the Moon differ substantially; the nearside hosts more basins larger than 350 km in diameter, whereas the farside has more smaller basins. Hemispherical differences in target properties, including temperature and porosity, are likely to have contributed to these different distributions. Better understanding of the factors that control basin size will help to constrain models of the original impactor population.


Services oriented architectures and rapid deployment of ad-hoc health surveillance systems: lessons from Katrina relief efforts.
During the Hurricane Katrina relief efforts, a new city was born overnight within the City of Houston to provide accommodation and health services for thousands of evacuees deprived of food, rest, medical attention, and sanitation. The hurricane victims had been exposed to flood water, toxic materials, physical injury, and mental stress. This scenario was an invitation for a variety of public health hazards, primarily infectious disease outbreaks. Early detection and monitoring of morbidity and mortality among evacuees due to unattended health conditions was an urgent priority and called for deployment of real-time surveillance to collect and analyze data at the scene, and to enable and guide appropriate response and planning activities. The University of Texas Health Science Center at Houston (UTHSC) and the Houston Department of Health and Human Services (HDHHS) deployed an ad hoc surveillance system overnight by leveraging Internet-based technologies and Services Oriented Architecture (SOA). The system was post-coordinated through the orchestration of Web Services such as information integration, natural language processing, syndromic case finding, and online analytical processing (OLAP). Here we will report the use of Internet-based and distributed architectures in providing timely, novel, and customizable solutions on demand for unprecedented events such as natural disasters.


Breastfeeding during COVID-19: A Narrative Review of the Psychological Impact on Mothers.
The COVID-19 pandemic has altered the normal course of life, with measures to reduce the virus spread impacting motherhood expectations and, in particular, breastfeeding practices. This study aimed to review evidence regarding the impact of COVID-19 on breastfeeding plans and how these relate to women's psychological outcomes. Searches were conducted on PubMed and Web of Science for studies in English, Spanish, and Portuguese between January 2020 and January 2021. All study designs and pre-prints were considered. Twelve studies were included. Reports suggest that COVID-19 impacts differently on breastfeeding plans, which in turn leads to distinctive mental health outcomes. Positive breastfeeding experiences have been observed when mothers perceive that they have more time for motherhood, which may be associated with better mental health outcomes. Negative breastfeeding experiences have been observed when mothers are separated from their newborns, when mothers struggle with breastfeeding, or when mothers perceive decreased family and professional support, which seems to be associated with worse mental health outcomes. These preliminary results highlight the need for further research into the association between COVID-19, breastfeeding expectations, and maternal mental health. Filling this gap will foster the development of guidelines and interventions to better support mothers experiencing the obstacles of COVID-19 pandemic.


The Brain in Kidney Disease (BRINK) Cohort Study: Design and Baseline Cognitive Function.
The Brain in Kidney Disease (BRINK) Study aims to identify mechanisms that contribute to increased risk for cognitive impairment in patients with chronic kidney disease (CKD). We describe the rationale, design, and methods of the study and report baseline recruitment and cognitive function results. Longitudinal observational cohort study of the epidemiology of cognitive impairment in CKD. The primary aim is to characterize the association between (1) baseline and incident stroke, white matter disease, estimated glomerular filtration rate (eGFR), inflammation, microalbuminuria, and dialysis initiation and (2) cognitive decline over 3 years in a CKD cohort with a mean eGFR<45 mL/min/1.73 m(2). Community-dwelling participants 45 years or older recruited from 4 health systems into 2 groups: reduced eGFR, defined as eGFR<60 mL/min/1.73 m(2) (non-dialysis dependent), and control, defined as eGFR≥60 mL/min/1.73 m(2). eGFR group. Performance on cognitive function tests and structural brain magnetic resonance imaging. Sequential cognitive and physical function testing, serum and urine biomarker measurement, and brain magnetic resonance images over 3 years. Of 554 participants, mean age was 69.3 years; 333, 88, and 133 had eGFRs<45 (non-dialysis dependent, nontransplantation), 45 to <60, and ≥60 (controls) mL/min/1.73 m(2), respectively. Mean eGFR in reduced-eGFR participants was 34.3 mL/min/1.73 m(2). Baseline cognitive performance was significantly associated with eGFR in all domains except language. Participants with eGFRs<30 mL/min/1.73 m(2) performed significantly worse than those with eGFRs≥30 mL/min/1.73 m(2) on tests of memory, processing speed, and executive function. Participants with reduced eGFRs overall scored worst on the Immediate Brief Visual-Spatial Memory Test-Revised. Healthy cohort bias, competing risk for death versus cognitive decline. Cognitive function was significantly worse in participants with eGFRs<30 mL/min/1.73 m(2). Future BRINK analyses will measure risk factors for cognitive decline using the longitudinal data.


Examining the relationship between alcohol-energy drink risk profiles and high-risk drinking behaviors.
The mixing of alcohol and energy drinks (AMEDs) is a trend among college students associated with higher rates of heavy episodic drinking and negative alcohol-related consequences. The goals of this study were to take a person-centered approach to identify distinct risk profiles of college students based on AMED-specific constructs (expectancies, attitudes, and norms) and examine longitudinal associations between AMED use, drinking, and consequences. A random sample of incoming freshmen (n = 387, 59% female) completed measures of AMED use, AMED-specific expectancies, attitudes, and normative beliefs, and drinking quantity and alcohol-related consequences. Data were collected at 2 occasions: spring semester of freshmen year and fall semester of sophomore year. Latent profile analysis identified 4 subgroups of individuals: occasional AMED, anti-AMED, pro-AMED, and strong peer influence. Individuals in the pro-AMED group reported the most AMED use, drinking, and consequences. There was a unique association between profile membership and AMED use, even after controlling for drinking. Findings highlighted the importance of AMED-specific expectancies, attitudes, and norms. The unique association between AMED risk profiles and AMED use suggests AMED use is a distinct behavior that could be targeted by AMED-specific messages included in existing brief interventions for alcohol use.


Tetrodotoxin: a brief history.
Tetrodotoxin (TTX), contained in puffer, has become an extremely popular chemical tool in the physiological and pharmacological laboratories since our discovery of its channel blocking action in the early 1960s. This brief review describes the history of discovery of TTX action on sodium channels, and represents a story primarily of my own work. TTX inhibits voltage-gated sodium channels in a highly potent and selective manner without effects on any other receptor and ion channel systems. TTX blocks the sodium channel only from outside of the nerve membrane, and is due to binding to the selectivity filter resulting in prevention of sodium ion flow. It does not impairs the channel gating mechanism. More recently, the TTX-resistant sodium channels have been discovered in the nervous system and received much attention because of their role in pain sensation. TTX is now known to be produced not by puffer but by bacteria, and reaches various species of animals via food chain.(Communicated by Masanori OTSUKA, M.J.A.).


Desaturation of bile and cholesterol gallstone dissolution with chenodeoxycholic acid.
The feeding of one of the major biliary bile acids, chenodeoxycholic acid, at a dose of 10 to 15 mg/kg per day causes the circulating bile acid pool to become greatly enriched in this bile acid. When chenodeoxycholic acid composes more than 70% of the biliary bile acids, the amount of cholesterol secreted in bile falls, and bile becomes unsaturated in cholesterol. If cholesterol gallstones are present and are exposed to this unsaturated bile, they will dissolve in 4 to 24 months in the majority of patients. Extensive clinical experience indicates that such medical therapy is safe, despite unequivocal toxicity of chenodeoxycholic acid in several nonhuman primates. When therapy is stopped, bile resaturates, and stones may recur. Since cholecystecomy is a rapid, safe, effective, and usually permanent treatment for all gallstones, the value of medical therapy remains uncertain at present, except for patients in whom surgery is inadvisable. Nonetheless, the demonstration that chenodeoxycholic acid ingestion will desaturate bile and induce gallstone dissolution would appear to be an important pharmacological advance.


Bacterial and fungal infection in acute liver failure.
Patients with acute liver failure (ALF) have increased susceptibility to infections, principally as a result of impaired phagocytic function, reduced complement levels, and the need for invasive procedures. Bacteriologically proven infection is recorded in up to 80% of these patients and fungal infection (predominantly candidiasis) in 32%. Clinical signs such as high temperature and high WBC are absent in 30% of the cases. Pneumonia accounts for 50% of infective episodes, and bacteremia and urinary tract infection a further 20 to 25% each, at a median 5, 3, and 2 days, respectively, after the onset of ALF. Selective parenteral and enteral antisepsis regimens (SPEAR) were evaluated in prospective controlled studies, but early systemic antibiotics alone are as effective as SPEAR. With early antibiotics, the incidence of infective episodes is reduced to 20% and the overall mortality to 44%, with a reduction in progression to encephalopathy and an increased opportunity for transplantation.


Shape analysis of the peripapillary RPE layer in papilledema and ischemic optic neuropathy.
Geometric morphometrics (GM) was used to analyze the shape of the peripapillary retinal pigment epithelium-Bruch's membrane (RPE/BM) layer imaged on the SD-OCT 5-line raster in normal subjects and in patients with papilledema and ischemic optic neuropathy. Three groups of subjects were compared: 30 normals, 20 with anterior ischemic optic neuropathy (AION), and 25 with papilledema and intracranial hypertension. Twenty equidistant semilandmarks were digitized on OCT images of the RPE/BM layer spanning 2500 μm on each side of the neural canal opening (NCO). The data were analyzed using standard GM techniques, including a generalized least-squares Procrustes superimposition, principal component analysis, thin-plate spline (to visualize deformations), and permutation statistical analysis to evaluate differences in shape variables. The RPE/BM layer in normals and AION have a characteristic V shape pointing away from the vitreous; the RPE/BM layer in papilledema has an inverted U shape, skewed nasally inward toward the vitreous. The differences were statistically significant. There was no significant difference in shapes between normals and AION. Pre- and posttreatment OCTs, in select cases of papilledema, showed that the inverted U-shaped RPE/BM moved posteriorly into a normal V shape as the papilledema resolved with weight loss or shunting. The shape difference in papilledema, absent in AION, cannot be explained by disc edema alone. The difference is a consequence of both the translaminar pressure gradient and the material properties of the peripapillary sclera. GM offers a novel way of statistically assessing shape differences of the peripapillary optic nerve head.


Teamwork and error in the operating room: analysis of skills and roles.
To analyze the effects of surgical, anesthetic, and nursing teamwork skills on technical outcomes. The value of team skills in reducing adverse events in the operating room is presently receiving considerable attention. Current work has not yet identified in detail how the teamwork and communication skills of surgeons, anesthetists, and nurses affect the course of an operation. Twenty-six laparoscopic cholecystectomies and 22 carotid endarterectomies were studied using direct observation methods. For each operation, teams' skills were scored for the whole team, and for nursing, surgical, and anesthetic subteams on 4 dimensions (leadership and management [LM]; teamwork and cooperation; problem solving and decision making; and situation awareness). Operating time, errors in surgical technique, and other procedural problems and errors were measured as outcome parameters for each operation. The relationships between teamwork scores and these outcome parameters within each operation were examined using analysis of variance and linear regression. Surgical (F(2,42) = 3.32, P = 0.046) and anesthetic (F(2,42) = 3.26, P = 0.048) LM had significant but opposite relationships with operating time in each operation: operating time increased significantly with higher anesthetic but decreased with higher surgical LM scores. Errors in surgical technique had a strong association with surgical situation awareness (F(2,42) = 7.93, P < 0.001) in each operation. Other procedural problems and errors were related to the intraoperative LM skills of the nurses (F(5,1) = 3.96, P = 0.027). Detailed analysis of team interactions and dimensions is feasible and valuable, yielding important insights into relationships between nontechnical skills, technical performance, and operative duration. These results support the concept that interventions designed to improve teamwork and communication may have beneficial effects on technical performance and patient outcome.


State-of-the-lagoon reports as vehicles of cross-disciplinary integration.
An integrative approach across disciplines is needed for sustainable lagoon and estuary management as identified by integrated coastal zone management. The ARCH research project (Architecture and roadmap to manage multiple pressures on lagoons) has taken initial steps to overcome the boundaries between disciplines and focus on cross-disciplinary integration by addressing the driving forces, challenges, and problems at various case study sites. A model was developed as a boundary-spanning activity to produce joint knowledge and understanding. The backbone of the model is formed by the interaction between the natural and human systems, including economy and governance-based subsystems. The model was used to create state-of-the-lagoon reports for 10 case study sites (lagoons and estuarine coastal areas), with a geographical distribution covering all major seas surrounding Europe. The reports functioned as boundary objects to build joint knowledge. The experiences related to the framing of the model and its subsequent implementation at the case study sites have resulted in key recommendations on how to address the challenges of cross-disciplinary work required for the proper management of complex social-ecological systems such as lagoons, estuarine areas, and other land-sea regions. Cross-disciplinary integration is initially resource intensive and time consuming; one should set aside the required resources and invest efforts at the forefront. It is crucial to create engagement among the group of researchers by focusing on a joint, appealing overall concept that will stimulate cross-sectoral thinking and focusing on the identified problems as a link between collected evidence and future management needs. Different methods for collecting evidence should be applied including both quantitative (jointly agreed indicators) and qualitative (narratives) information. Cross-disciplinary integration is facilitated by functional boundary objects. Integration offers important rewards in terms of developing a better understanding and subsequently improved management of complex social-ecological systems. Integr Environ Assess Manag 2016;12:690-700. © 2016 SETAC.


Viewing RNA-seq data on the entire human genome.
RNA-Seq Viewer is a web application that enables users to visualize genome-wide expression data from NCBI's Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. The application prototype was created by a small team during a three-day hackathon facilitated by NCBI at Brandeis University. The backend data pipeline was developed and deployed on a shared AWS EC2 instance. Source code is available at https://github.com/NCBI-Hackathons/rnaseqview.


Demography of aging and the epidemiology of gastrointestinal disorders in the elderly.
Population aging is a global phenomenon. It is estimated that there were 600 million people in the world aged 60 and over in 2000 and that there will be 1.2 billion by 2025. People aged 65 and over comprise 16% of the population of Europe. About half of the world's elderly population live in the developing world. Many of the gastrointestinal disorders seen in specialist practise show age-specific incidence and prevalence rates that increase substantially with increasing age. In this review, hospitalization rates for gastroenterological disorders in England are presented by age to demonstrate gradients with age. Some of the disorders, such as colorectal cancer, appendicitis, diverticular disease and inflammatory bowel disease, became common in developed countries in association with economic development and changes in lifestyle. As the developing world becomes more urbanised and westernised, disorders that are now rare in the developing world will probably become much more common.


Income-based drug coverage in British Columbia: the impact on private and public expenditures.
In May 2003, the government of British Columbia adopted income-based pharmacare, replacing an age-based program. Stated policy goals included the reduction and reallocation of government spending. It was also hoped that income-based deductibles would increase consumer price sensitivity in decision-making. This analysis measured policy impacts on private and public expenditure and on expenditure drivers. We employed a longitudinal research design using PharmaNet records of every prescription dispensed in the province from January 1996 to December 2004. Expenditure dynamics were analyzed using non-stochastic decompositions of trends. Analyses were stratified by five age categories and five socio-economic quintiles. The effect of the policy on expenditure trends and their sources was assessed using time series analysis. Additional analyses, using equivalent methods, were conducted using market-level data to compare per capita expenditure in British Columbia to the Canadian average over the period 1998-2004. The BC Ministry of Health was successful in reducing the public share of drug expenditure through the introduction of seniors' co-payments in 2002 and then income-based pharmacare in 2003. The policy change did not have major effects on aggregate expenditure trends in the province. While several statistically significant changes in expenditure dynamics occurred during the period of study, only an increase in seasonal "stockpiling" of medicines by seniors can reasonably be attributed to the policy changes. The lack of large and differential policy impacts on drug expenditure and utilization rates across age and income groups suggests that changes in the BC PharmaCare Program were designed in a manner that ensured continued access to medicines for the populations previously served by the drug plan (e.g., senior citizens). It also indicates that the policy did not significantly increase access to medicines by populations that might have been better served under the new policy (e.g., non-seniors). Finally, although it was hoped that income-based pharmacare might increase consumer cost consciousness, changes in the relative cost of certain drugs purchased following the policy change appear to have stemmed from other policies directly targeting the expenditure impact of therapeutic choices.


Characterizing the Aerobic and Anaerobic Energy Costs of Polynesian Dances.
This study characterized both aerobic and anaerobic energy expenditure (EE) for several Polynesian dances in a group of experienced professional Polynesian dancers. Thirteen men and 17 women were tested using indirect calorimetry to assess aerobic EE (and converted to METs), and fingertip blood lactate to estimate anaerobic EE, during both resting and dancing activities. Total EE was then computed as the sum of both aerobic and anaerobic activity energy expenditure (AEE, or EE above resting). One sample t-tests compared mean MET values for each type of dance to the 3-MET and 6-MET thresholds for moderate and vigorous physical activity (MVPA), respectively. Mean MET values for all dances, except the Maori poi balls dance (Mean±SD: 3.7±1.1 METs; P=0.340), were significantly >3.0 METs (5.9±3.1 METS; P=0.005 for Maori haka; 6.5±2.4 METs for Hawaiian hula; 6.6±1.2 METs for Samoan sasa; 9.6±1.5 METs for Samoan slap; 8.3±1.8 METs for Tahitian; 6.0±2.3 METs for Tongan; 7.0±2.6 METs for Fijian; P<0.001). Mean METs for Samoan slap and Tahitian were also significantly >6.0 METs (P=0.002 and P<0.001, respectively). Aerobic and anaerobic AEE contributed an average of 83.4% and 16.6%, respectively, across all Polynesian dances, with Hawaiian hula being the most aerobic (88.7%) and Samoan slap being the least aerobic (74.2%). Thus, the Polynesian dances tested not only met the current MVPA intensity guidelines (i.e., ≥3.0 METs), each dance also had a large anaerobic EE. These data suggest that Polynesian dancing is an appropriate mode of aerobic exercise for health promotion and disease prevention.


Predicting Cognitive Improvement in Normal Pressure Hydrocephalus Patients Using Preoperative Neuropsychological Testing and Cerebrospinal Fluid Biomarkers.
Though it is well known that normal pressure hydrocephalus (NPH) patients can cognitively improve after ventriculoperitoneal shunting (VPS), one of the major dilemmas in NPH is the ability to prospectively predict which patients will improve. To prospectively assess preoperative predictors of postshunt cognitive improvement. This was a prospective observational cohort including 52 consecutive patients with approximately 1-yr follow-up. Patients underwent neuropsychological testing at baseline, postlumbar drainage, and postshunt. Cerebrospinal fluid (CSF) biomarkers and cortical biopsies were also collected to examine their relationship with postshunt cognitive improvement. Rey Auditory Verbal Learning Test-L (RAVLT-L) was the only neuropsychological test to demonstrate statistically significant improvement both postlumbar drain and postshunt. Improvement on the RAVLT-L postlumbar drain predicted improvement on the RAVLT-L postshunt. Patients with biopsies demonstrating Aβ+ Tau+ had lower ventricular CSF Aβ42 and higher lumbar CSF pTau compared to Aβ- Tau- patients. A receiver operating curve analysis using lumbar pTau predicted Aβ+ Tau+ biopsy status but was not related to neuropsychological test outcome. The RAVLT can be a useful preoperative predictor of postoperative cognitive improvement, and thus, we recommend using the RAVLT to evaluate NPH patients. CSF biomarkers could not be related to neuropsychological test outcome. Future research in a larger patient sample will help determine the prospective utility of CSF biomarkers in the evaluation of NPH patients.


Maternal monocytes in pregnancy and preeclampsia in humans and in rats.
Monocytes are short-lived cells, arising from the bone marrow and maturing in the circulation. They play an important role in immune responses and are thought to be important for healthy pregnancy. In humans, 3 subpopulations of monocytes have been identified: classical, intermediate and non-classical monocytes. These subpopulations have different functions and phenotypical characteristics. Healthy pregnancy is characterized by a pro-inflammatory condition, with increased numbers of monocytes and monocyte activation as well as with increased numbers of intermediate monocytes and decreased numbers of classical monocytes. This may suggest monocyte maturation. Preeclampsia is an important pregnancy complication characterized by hypertension and proteinuria developing in the second half of pregnancy. The pathophysiology of preeclampsia is associated with further activation of the inflammatory response, further activation of monocytes and further monocyte maturation. In the present review we focus on the role of monocyte activation and maturation in healthy and preeclamptic pregnancy.


Evaluation of somatic copy number estimation tools for whole-exome sequencing data.
Whole-exome sequencing (WES) has become a standard method for detecting genetic variants in human diseases. Although the primary use of WES data has been the identification of single nucleotide variations and indels, these data also offer a possibility of detecting copy number variations (CNVs) at high resolution. However, WES data have uneven read coverage along the genome owing to the target capture step, and the development of a robust WES-based CNV tool is challenging. Here, we evaluate six WES somatic CNV detection tools: ADTEx, CONTRA, Control-FREEC, EXCAVATOR, ExomeCNV and Varscan2. Using WES data from 50 kidney chromophobe, 50 bladder urothelial carcinoma, and 50 stomach adenocarcinoma patients from The Cancer Genome Atlas, we compared the CNV calls from the six tools with a reference CNV set that was identified by both single nucleotide polymorphism array 6.0 and whole-genome sequencing data. We found that these algorithms gave highly variable results: visual inspection reveals significant differences between the WES-based segmentation profiles and the reference profile, as well as among the WES-based profiles. Using a 50% overlap criterion, 13-77% of WES CNV calls were covered by CNVs from the reference set, up to 21% of the copy gains were called as losses or vice versa, and dramatic differences in CNV sizes and CNV numbers were observed. Overall, ADTEx and EXCAVATOR had the best performance with relatively high precision and sensitivity. We suggest that the current algorithms for somatic CNV detection from WES data are limited in their performance and that more robust algorithms are needed.


An EGFR ligand promotes EGFR-mutant but not KRAS-mutant lung cancer in vivo.
EGFR ligands (e.g., EGF and TGFA) have been shown to be clinically associated with poor survival in lung cancer. Since TGFA itself initiates autochthonous tumors in liver, breast, and pancreas but not in the lung in transgenic mice in vivo, it would appear that an EGFR ligand may not initiate but rather promote lung cancer. However, it has not been proven in vivo whether lung cancer is promoted by an EGFR ligand. Using transgenic mouse models conditionally expressing EGFRL858R or KrasG12D with TGFA (an EGFR ligand) in lung epithelium, we determined that TGFA promoted the growth of EGFRL858R-lung tumors in airway regions but not that of KrasG12D-lung tumors. Analysis of TCGA datasets identified ΔNp63 and AGR2 as potential key tumor-promoting regulators, which were highly induced in the TGFA-induced EGFRL858R-lung tumors. The expression of AGR2 was positively correlated with the expression of TGFA in human EGFR-mutant lung adenocarcinomas. The expression of TGFA in human EGFR-mutant lung adenocarcinomas but not in the EGFR wild-type lung adenocarcinoma was associated with poor survival. These results suggest that targeting EGFR ligands may benefit patients who carry EGFR-mutant lung tumors but will not benefit patients with KRAS-mutant lung tumors.


Alcohol Interaction with Cocaine, Methamphetamine, Opioids, Nicotine, Cannabis, and γ-Hydroxybutyric Acid.
Millions of people around the world drink alcoholic beverages to cope with the stress of modern lifestyle. Although moderate alcohol drinking may have some relaxing and euphoric effects, uncontrolled drinking exacerbates the problems associated with alcohol abuse that are exploding in quantity and intensity in the United States and around the world. Recently, mixing of alcohol with other drugs of abuse (such as opioids, cocaine, methamphetamine, nicotine, cannabis, and γ-hydroxybutyric acid) and medications has become an emerging trend, exacerbating the public health concerns. Mixing of alcohol with other drugs may additively or synergistically augment the seriousness of the adverse effects such as the withdrawal symptoms, cardiovascular disorders, liver damage, reproductive abnormalities, and behavioral abnormalities. Despite the seriousness of the situation, possible mechanisms underlying the interactions is not yet understood. This has been one of the key hindrances in developing effective treatments. Therefore, the aim of this article is to review the consequences of alcohol's interaction with other drugs and decipher the underlying mechanisms.


Histopathology Image Analysis in Two Long-Term Animal Experiments with Helical Flow Total Artificial Heart.
Histopathological analysis can provide important information in long-term experiments with total artificial heart (TAH). Recently, a new type of blood pump, the helical flow total artificial heart (HF-TAH) was developed. This study aimed to investigate the changes in selected vital organs in animal experiments with implanted HF-TAH. Samples from lung, liver, and kidneys from two female goats (No. 1301 and No. 1304) with implanted HF-TAH were analyzed. Tissue samples were fixed in 10% formaldehyde and 4 µm thick transverse sections were stained with hematoxylin-eosin (HE). Additional staining was done for detection of connective tissue (Masson-Goldner stain) and for detection of iron (hemosiderin) deposits (Perls stain). Sections were scanned at 100× and 500× magnification with a light microscope. Experiment no. 1301 survived 100 days (cause of termination was heavy damage of the right pump); experimental goat no.1304 survived 68 days and was sacrificed due to severe right hydrodynamic bearing malfunction. Histopathological analysis of liver samples proved signs of chronic venostasis with limited focal necrotic zones. Dilated tubules, proteinaceous material in tubular lumen, and hemosiderin deposits were detected in kidney samples. Contamination of the organs by embolized micro-particles was suspected at the autopsy after discovery of visible damage (scratches) of the pump impeller surface (made from titanium alloy) in both experiments. Sporadic deposits of foreign micro-particles (presumably titanium) were observed in most of the analyzed parenchymal organs. However, the described deposits were not in direct connection with inflammatory reactions in the analyzed tissues. Histopathological analysis showed the presence of minimal contamination of the lung, kidney, and liver tissue samples by foreign material (titanium very likely). The analysis showed only limited pathological changes, especially in liver and kidneys, which might be attributed to the influence of artificial perfusion often observed in chronic TAH experiments.


Respiration during sleep in normal man.
Respiratory volumes and timing have been measured in 19 healthy adults during wakefulness and sleep. Minute ventilation was significantly less (p less than 0.05) in all stages of sleep than when the subject was awake (7.66 +/- 0.34(SEM) 1/min), the level in rapid-eye-movement (REM) sleep (6.46 +/- 0.29 1/min) being significantly lower than in non-REM sleep (7.18 +/- 0.39 1/min). The breathing pattern during all stages of sleep was significantly more rapid and shallow than during wakefulness, tidal volume in REM sleep being reduced to 73% of the level during wakefulness. Mean inspiratory flow rate (VT/Ti), an index of inspiratory drive, was significantly lower in REM sleep than during wakefulness or non-REM sleep. Thus ventilation falls during sleep, the greatest reduction occurring during REM sleep, when there is a parallel reduction in inspiratory drive. Similar changes in ventilation may contribute to the REM-associated hypoxaemia observed in normal subjects and in patients with chronic obstructive pulmonary disease.


Practice recommendations for risk-adapted head and neck cancer radiotherapy during the COVID-19 pandemic: An ASTRO-ESTRO consensus statement.
Because of the unprecedented disruption of health care services caused by the COVID-19 pandemic, the American Society of Radiation Oncology (ASTRO) and the European Society for Radiotherapy and Oncology (ESTRO) identified an urgent need to issue practice recommendations for radiation oncologists treating head and neck cancer (HNC) in a time of limited resources and heightened risk for patients and staff. A panel of international experts from ASTRO, ESTRO, and select Asia-Pacific countries completed a modified rapid Delphi process. Topics and questions were presented to the group, and subsequent questions were developed from iterative feedback. Each survey was open online for 24 hours, and successive rounds started within 24 hours of the previous round. The chosen cutoffs for strong agreement (≥80%) and agreement (≥66%) were extrapolated from the RAND methodology. Two pandemic scenarios, early (risk mitigation) and late (severely reduced radiation therapy resources), were evaluated. The panel developed treatment recommendations for 5 HNC cases. In total, 29 of 31 of those invited (94%) accepted, and after a replacement 30 of 30 completed all 3 surveys (100% response rate). There was agreement or strong agreement across a number of practice areas, including treatment prioritization, whether to delay initiation or interrupt radiation therapy for intercurrent SARS-CoV-2 infection, approaches to treatment (radiation dose-fractionation schedules and use of chemotherapy in each pandemic scenario), management of surgical cases in event of operating room closures, and recommended adjustments to outpatient clinic appointments and supportive care. This urgent practice recommendation was issued in the knowledge of the very difficult circumstances in which our patients find themselves at present, navigating strained health care systems functioning with limited resources and at heightened risk to their health during the COVID-19 pandemic. The aim of this consensus statement is to ensure high-quality HNC treatments continue, to save lives and for symptomatic benefit.


Psychosocial therapeutic interventions for volatile substance use: a systematic review.
Volatile substance use (VSU) is associated with a range of adverse outcomes, including cognitive impairment and death. It occurs disproportionately within young and marginalized populations. A previous international systematic review of VSU treatment identified no relevant studies. This paper reports on a systematic review of a range of study types concerning psychosocial interventions for VSU. Search parameters were developed using the Population, Intervention, Professionals, Outcomes, Health care setting and Contexts (PIPOH) tool with input from an expert committee. Included were randomized controlled trials (RCTs), comparative studies with or without concurrent controls, case series studies and grey literature, published in English during 1980-2010. The initial search identified 2344 references. After two screening phases, 23 studies of VSU therapeutic interventions remained. Of these, 19 concerned psychosocial interventions, which we discuss as: case management; counselling; recreation and engagement programmes; and residential treatment. Studies were conducted in Australia, Canada, the United States, United Kingdom and Brazil. No RCTs were identified and studies were generally of low evidentiary levels. Even when a range of study types are included, clear conclusions for volatile substance use psychological treatment are not supported, but three intervention types merit further examination: family therapy, activity-based programmes and Indigenous-led residential approaches. Future volatile substance use research could be enhanced by developing and validating outcome measurement tools. Robust multi-site studies are also required.


Comparing shower-based oral hygiene with traditional and electric toothbrushing.
Despite the importance of self-care for disease prevention, dentists and hygienists have been largely unsuccessful as oral hygiene motivators. Because of competing values, patients commonly fail to comply with prescribed oral hygiene regimens. In this investigation, attitudes of 84 adult dental patients were evaluated following a 30-day trial in which a shower-based oral hygiene system (SBOHS) was compared with manual and electric toothbrushing regimens performed in traditional settings. While attitudinal differences between manual and electric toothbrushing groups were insignificant, the SBOHS was perceived as substantially more enjoyable, convenient and reinforcing than either conventional or electric toothbrushing performed outside the shower. Significantly more SBOHS users reported spending more time on oral self-care, taking better care of their teeth and gums, feeling better about plaque control, appreciating oral hygiene practices more and perceiving cleaner teeth and a fresher mouth after oral hygiene than either the conventional or electric toothbrush users.


Recommendations on Physical Activity and Exercise for Older Adults Living in Long-Term Care Facilities: A Taskforce Report.
A taskforce, under the auspices of The International Association of Gerontology and Geriatrics-Global Aging Research Network (IAGG-GARN) and the IAGG European Region Clinical Section, composed of experts from the fields of exercise science and geriatrics, met in Toulouse, in December 2015, with the aim of establishing recommendations of physical activity and exercise for older adults living in long-term care facilities (LTCFs). Due to the high heterogeneity in terms of functional ability and cognitive function that characterizes older adults living in LTCFs, taskforce members established 2 sets of recommendations: recommendations for reducing sedentary behaviors for all LTCF residents and recommendations for defining specific, evidence-based guidelines for exercise training for subgroups of LTCF residents. To promote a successful implementation of recommendations, taskforce experts highlighted the importance of promoting residents' motivation and pleasure, the key factors that can be increased when taking into account residents' desires, preferences, beliefs, and attitudes toward physical activity and exercise. The importance of organizational factors related to LTCFs and health care systems were recognized by the experts. In conclusion, this taskforce report proposes standards for the elaboration of strategies to increase physical activity as well as to prescribe exercise programs for older adults living in LTCFs. This report should be used as a guide for professionals working in LTCF settings.


State and trait anxiety and depression in patients with primary brain tumors before and after surgery: 1-year longitudinal study.
The aim in this study was to assess the state and trait types of anxiety as well as current depression before and after surgery in patients affected by brain tumors. The relationships between these affective disorders and the patient's sex, tumor histology, and laterality of the tumor were also evaluated. A total of 72 patients affected by a primary brain tumor were enrolled in the study. Histological grades were assigned according to the World Health Organization classification. State and trait anxiety were assessed using the State and Trait Anxiety Inventory; current depression was assessed using the Zung Self-Rating Depression Scale. Cognitive impairment was assessed using the 10-item Short Portable Mental Status Questionnaire. Psychometric evaluation was assessed before surgery and at 1, 3, 6, and 12 months after surgery. Before brain surgery, 62.5% of patients showed state anxiety, 50% of patients showed trait anxiety, and 9.7% of patients showed current depression. During the follow-up period there was no significant variation in the percentage of patients with state anxiety (p=0.416) and trait anxiety (p=0.7), whereas a significant increase in the percentage of those with current depression was found (p<0.0001), in particular at 1 month (p=0.002) and 3 months (p=0.039) after surgical treatment. The tumor's laterality and histology showed no correlation with psychometric variables, whereas a relationship between the presence of trait anxiety at the enrollment and current depression after surgery (p<0.0001) was found. Patients affected by brain tumors frequently experience affective disorders. After brain surgery, a depressive state can develop. The psychometric assessment could be useful in these patients for quick recognition of psychological disorders.


Isoform-specific 3'-untranslated sequences sort alpha-cardiac and beta-cytoplasmic actin messenger RNAs to different cytoplasmic compartments.
We demonstrate that in differentiating myoblasts, the mRNAs encoding two actin isoforms, beta-cytoplasmic, and alpha-cardiac, can occupy different cytoplasmic compartments within the same cytoplasm. beta-actin mRNA is localized to the leading lamellae and alpha-actin mRNA is associated with a perinuclear compartment. This was revealed by co-hybridizing, in situ, fluorochrome-conjugated oligonucleotide probes specific for each isoform. To address the mechanism of isoform-specific mRNA localization, molecular chimeras were constructed by insertion of actin sequences between the Lac Z coding region and SV-40 3'UTR in a reporter plasmid. These constructs were transiently expressed in a mixed culture of embryonic fibroblasts, myoblasts and myotubes, beta-galactosidase activity within transfectants was revealed by a brief incubation with its substrate (X-gal). Since the blue-insoluble reaction product co-localized with the specific mRNAs expressed from each construct, it was used as a bioassay for mRNA localization. Transfectants were scored as either perinuclear, peripheral or nonlocalized with respect to the distribution of the blue product. The percentage of transfectants within those categories was quantitated as a function of the various constructs. This analysis revealed that for each actin mRNA its 3'UTR is necessary and sufficient to direct reporter transcripts to its appropriate compartment; beta-actin peripheral and alpha-actin perinuclear. In contrast, sequences from the 5'UTR through the coding region of either actin gene did not localize the blue product. Therefore, 3'UTR sequences play a key role in modulating the distribution of actin mRNAs in muscle cells. We propose that the mechanism of mRNA localization facilitates actin isoform sorting in the cytoplasm.


Ocular expression and distribution of products of the POAG-associated chromosome 9p21 gene region.
It has recently been shown that there are highly significant associations for common single nucleotide polymorphisms (SNPs) near the CDKN2B-AS1 gene region at the 9p21 locus with primary open angle glaucoma (POAG), a leading cause of irreversible blindness. This gene region houses the CDKN2B/p15(INK4B) , CDKN2A/p16(INK4A) and p14ARF (rat equivalent, p19(ARF) ) tumour suppressor genes and is adjacent to the S-methyl-5'-thioadenosine phosphorylase (MTAP) gene. In order to understand the ocular function of these genes and, therefore, how they may be involved in the pathogenesis of POAG, we studied the distribution patterns of each of their products within human and rat ocular tissues. MTAP mRNA was detected in the rat retina and optic nerve and its protein product was localised to the corneal epithelium, trabecular meshwork and retinal glial cells in both human and rat eyes. There was a very low level of p16(INK4A) mRNA present within the rat retina and slightly more in the optic nerve, although no protein product could be detected in either rat or human eyes with any of the antibodies tested. P19(ARF) mRNA was likewise only present at very low levels in rat retina and slightly higher levels in the optic nerve. However, no unambiguous evidence was found to indicate expression of specific P19(ARF)/p14(ARF) proteins in either rat or human eyes, respectively. In contrast, p15(INK4B) mRNA was detected in much higher amounts in both retina and optic nerve compared with the other genes under analysis. Moreover, p15(INK4B) protein was clearly localised to the retinal inner nuclear and ganglion cell layers and the corneal epithelium and trabecular meshwork in rat and human eyes. The presented data provide the basis for future studies that can explore the roles that these gene products may play in the pathogenesis of glaucoma and other models of optic nerve damage.


Duplicated dockerin subdomains of Clostridium thermocellum endoglucanase CelD bind to a cohesin domain of the scaffolding protein CipA with distinct thermodynamic parameters and a negative cooperativity.
Mutagenized dockerin domains of endoglucanase CelD (type I) and of the cellulosome-integrating protein CipA (type II) were constructed by swapping residues 10 and 11 of the first or the second duplicated segment between the two polypeptides. These residues have been proposed to determine the specificity of cohesin-dockerin interactions. The dockerin domain of CelD still bound to the seventh cohesin domain of CipA (CohCip7), provided that mutagenesis occurred in one segment only. Binding was no longer detected by nondenaturing gel electrophoresis when both segments were mutagenized. The dockerin domain of CipA bound to the cohesin domain of SdbA as long as the second segment was intact. None of the mutated dockerins displayed detectable binding to the noncognate cohesin domain. Isothermal titration calorimetry showed that binding of the CelD dockerin to CohCip7 occurred with a high affinity [K(a) = (2.6 +/- 0.5) x 10(9) M(-1)] and a 1:1 stoichiometry. The reaction was weakly exothermic (DeltaHdegrees = -2.22 +/- 0.2 kcal x mol(-1)) and largely entropy driven (TDeltaSdegrees = 10.70 +/- 0.5 kcal x mol(-1)). The heat capacity change on complexation was negative (DeltaC(p) = -305 +/- 15 cal x mol(-1) x K(-1)). These values show that cohesin-dockerin binding is mainly hydrophobic. Mutations in the first or the second dockerin segment reduced or enhanced, respectively, the hydrophobic character of the interaction. Due to partial enthalpy-entropy compensation, these mutations induced only small changes in binding affinity. However, the binding affinity was strongly decreased when both segments were mutated, indicating strong negative cooperativity between the two mutated sites.


Phase resetting of the mammalian circadian clock by DNA damage.
To anticipate the momentum of the day, most organisms have developed an internal clock that drives circadian rhythms in metabolism, physiology, and behavior [1]. Recent studies indicate that cell-cycle progression and DNA-damage-response pathways are under circadian control [2-4]. Because circadian output processes can feed back into the clock, we investigated whether DNA damage affects the mammalian circadian clock. By using Rat-1 fibroblasts expressing an mPer2 promoter-driven luciferase reporter, we show that ionizing radiation exclusively phase advances circadian rhythms in a dose- and time-dependent manner. Notably, this in vitro finding translates to the living animal, because ionizing radiation also phase advanced behavioral rhythms in mice. The underlying mechanism involves ATM-mediated damage signaling as radiation-induced phase shifting was suppressed in fibroblasts from cancer-predisposed ataxia telangiectasia and Nijmegen breakage syndrome patients. Ionizing radiation-induced phase shifting depends on neither upregulation or downregulation of clock gene expression nor on de novo protein synthesis and, thus, differs mechanistically from dexamethasone- and forskolin-provoked clock resetting [5]. Interestingly, ultraviolet light and tert-butyl hydroperoxide also elicited a phase-advancing effect. Taken together, our data provide evidence that the mammalian circadian clock, like that of the lower eukaryote Neurospora[6], responds to DNA damage and suggest that clock resetting is a universal property of DNA damage.


Getting around when you're round: quantitative analysis of the locomotion of the blunt-spined brittle star, Ophiocoma echinata.
Brittle stars (Ophiuroidea, Echinodermata) are pentaradially symmetrical echinoderms that use five multi-jointed limbs to locomote along the seafloor. Prior qualitative descriptions have claimed coordinated movements of the limbs in a manner similar to tetrapod vertebrates, but this has not been evaluated quantitatively. It is uncertain whether the ring-shaped nervous system, which lacks an anatomically defined anterior, is capable of generating rhythmic coordinated movements of multiple limbs. This study tested whether brittle stars possess distinct locomotor modes with strong inter-limb coordination as seen in limbed animals in other phyla (e.g. tetrapods and arthropods), or instead move each limb independently according to local sensory feedback. Limb tips and the body disk were digitized for 56 cycles from 13 individuals moving across sand. Despite their pentaradial anatomy, all individuals were functionally bilateral, moving along the axis of a central limb via synchronous motions of contralateral limbs (±~13% phase lag). Two locomotor modes were observed, distinguishable mainly by whether the central limb was directed forwards or backwards. Turning was accomplished without rotation of the body disk by defining a different limb as the center limb and shifting other limb identities correspondingly, and then continuing locomotion in the direction of the newly defined anterior. These observations support the hypothesis that, in spite of their radial body plan, brittle stars employ coordinated, bilaterally symmetrical locomotion.


T-cell receptor transfer for boosting HIV-1-specific T-cell immunity in HIV-1-infected patients.
Strategies to cure HIV-1 infection require the eradication of viral reservoirs. An innovative approach for boosting the cytotoxic T-lymphocyte response is the transfer of T-cell receptors (TCRs). Previously, we have shown that electroporation of TCR-encoding mRNA is able to reprogram CD8 T cells derived from healthy donors. So far, it is unknown whether the transfer of HIV-1-specific TCRs is capable to reprogram CD8 T cells of HIV-1-infected patients. To assess the efficiency of TCR-transfer by mRNA electroporation and the functionality of reprogramed T cells in HIV-1-infected patients, we performed an in-vitro analysis of TCR-transfer into T cells from HIV-1-infected patients in various stages of disease and from healthy controls. Peripheral blood mononuclear cells from 16 HIV-1-infected patients (nine HLA-A02-positive, seven HLA-A02-negative) and from five healthy controls were electroporated with mRNA-constructs encoding TCRs specific for the HLA-A02/HIV-1-gag p17 epitope SLYNTVATL (SL9). Functionality of the TCRs was measured by γIFN-ELISpot assays. SL9/TCR transfection into peripheral blood mononuclear cells from both HLA-A02-positive and HLA-A02-negative HIV-1-infected patients and from healthy blood donors reprogramed T cells for recognition of SL9-presenting HLA-A02-positive cells in γIFN-ELISpot assays. SL9/TCR-transfer into T cells from an immunodeficient AIDS patient could induce recognition of SL9-expressing target cells only after reversion of T-cell dysfunction by antiretroviral therapy. The transfer of HIV-1-p17-specific TCRs into T cells is functional both in HIV-1-infected patients as well as in healthy blood donors. TCR-transfer is a promising method to boost the immune system against HIV-1.


Escherichia coli acid resistance: cAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes.
Acid resistance is an important feature of both pathogenic and non-pathogenic Escherichia coli. It enables survival in the acidic regions of mammalian gastrointestinal tracts and is largely responsible for the small number of bacteria required for infection/colonization. Three systems of acid resistance have been identified, the most efficient of which requires glutamic acid during pH 2 acid challenge. Three proteins associated with glutamate-dependent acid resistance have been identified. They are glutamate decarboxylase (encompassing two isozymes encoded by gadA and gadB) and a putative glutamate:gamma-amino butyric acid antiporter (encoded by gadC). The results confirm that the GadA and GadB proteins increase in response to stationary phase and low environmental pH. The levels of these proteins correspond to concomitant changes in gadA and gadBC mRNA levels. Fusions between lacZ and the gadA and gadBC operons indicate that this control occurs at the transcriptional level. Western blot, Northern blot and fusion analyses reveal that regulation of these genes is complex. Expression in rich media is restricted to stationary phase. However, in minimal media, acid pH alone can trigger induction in exponential or stationary phase cells. Despite this differential control, there is only one transcriptional start site for each gene. Expression in rich media is largely dependent on the alternate sigma factor sigma(S) and is repressed by the cAMP receptor protein (CRP). In contrast, sigma(S) has only a minor role in gad transcription in cells grown in minimal media. Deletions of the regulatory region upstream of gadA provided evidence that a 20 bp conserved region located 50 bp from the transcriptional start of both operons is required for expression.


A glyphosate-based herbicide induces necrosis and apoptosis in mature rat testicular cells in vitro, and testosterone decrease at lower levels.
The major herbicide used worldwide, Roundup, is a glyphosate-based pesticide with adjuvants. Glyphosate, its active ingredient in plants and its main metabolite (AMPA) are among the first contaminants of surface waters. Roundup is being used increasingly in particular on genetically modified plants grown for food and feed that contain its residues. Here we tested glyphosate and its formulation on mature rat fresh testicular cells from 1 to 10000ppm, thus from the range in some human urine and in environment to agricultural levels. We show that from 1 to 48h of Roundup exposure Leydig cells are damaged. Within 24-48h this formulation is also toxic on the other cells, mainly by necrosis, by contrast to glyphosate alone which is essentially toxic on Sertoli cells. Later, it also induces apoptosis at higher doses in germ cells and in Sertoli/germ cells co-cultures. At lower non toxic concentrations of Roundup and glyphosate (1ppm), the main endocrine disruption is a testosterone decrease by 35%. The pesticide has thus an endocrine impact at very low environmental doses, but only a high contamination appears to provoke an acute rat testicular toxicity. This does not anticipate the chronic toxicity which is insufficiently tested, and only with glyphosate in regulatory tests.


Inhibition of intestinal epithelial DNA synthesis and adaptive hyperplasia after jejunectomy in the rat by suppression of polyamine biosynthesis.
Transient increases in the activity of ornithine decarboxylase (ODC), the first and rate-limiting enzyme in polyamine biosynthesis, may be critical to initiation of cell growth. We previously reported such increases in ODC activity, and the polyamines, putrescine, and spermidine in rat ileal mucosa between days 1 and 4 after intestinal resection. During this time, there is initiation of mucosal cell hyperplasia, as measured morphologically and biochemically. Intestinal weight and mucosal thickness increase, as do mucosal DNA content and DNA synthesis. In the present study, we gave rats the specific irreversible ODC inhibitor, alpha-difluoromethyl ornithine (DFMO), beginning 3 d before jejunectomy. DFMO completely suppressed the increases in ODC activity and polyamine content in the intestinal mucosa. The suppression in ODC activity was associated with an 87% suppression of DNA synthesis, and resulted in a complete abolition of intestinal adaptation, as manifested by the absence of intestinal weight gain, increase in mucosal thickness, or increase in crypt cell production. Our results indicate that the increases in ODC activity and polyamine biosynthesis are critical for adaptive postresectional crypt cell proliferation in vivo, and that the critical step mediated by polyamines in this adaptive process is the onset of new DNA synthesis.


Synthetic fibronectin peptides interrupt inflammatory cell infiltration in transforming growth factor beta 1 knockout mice.
Pronounced mononuclear leukocyte (MNL) infiltration occurs in multiple organs of mice homozygous for a transforming growth factor beta 1 (TGF-beta 1) loss-of-function gene mutation [TGF-beta 1 (-/-)], followed by cachexia and eventually death. Consistent with the increased leukocyte adhesion and tissue infiltration, MNLs isolated from spleen, thymus, and peripheral blood of symptomatic TGF-beta 1 (-/-) mice, as compared to littermate controls, exhibited increased adhesion to extracellular matrix proteins and to endothelial cells in vitro. Incubation of TGF-beta 1 (-/-) MNLs with selected synthetic peptides corresponding to cell- and heparin-binding sequences of fibronectin (FN) significantly attenuated adhesion of these cells not only to FN but also to endothelial cells in vitro. Based on these observations, mice were treated with the FN peptides in an attempt to rescue them from tissue inflammation and cardiopulmonary failure. Daily injections of a combination of four synthetic FN peptides that interact with beta 1-integrins and/or cell surface proteoglycans blocked the massive infiltration of MNLs into the heart and lungs of TGF-beta 1 (-/-) mice. Peptide treatment initiated on day 8, coincident with the first evidence of increased leukocyte-endothelial cell interactions, not only blocked tissue infiltration but also moderated the lethal wasting syndrome.


Impact of Charlson's comorbidity index on overall survival following tumor nephrectomy for renal cell carcinoma.
To study the impact of Charlson's comorbidity index on overall survival following radical and partial nephrectomy performed for renal cell carcinoma (RCC). Patients with primary RCC treated by tumor nephrectomy with at least 1 year of follow-up were included. The outcome parameters assessed were overall survival, impact of surgery on quality of life of patients using Karnofsky's index and correlation of survival with respect to comorbid conditions, using Charlson's index comorbidity score, grade and stage of disease. A total of 214 tumor nephrectomies were performed during study period, of which 157 (73%) fulfilling the criteria were included in the final analysis. The mean age at presentation was 57 + or - 12 years. The mean Charlson's index was 2.89 + or - 2.22. Tumor stages were I-IV in 33, 30, 16 and 21%, respectively. The overall survival was 65% at a mean follow-up of 39 + or - 5 months. The mean pre op Karnofsky's index was 79.5 + or - 7.13 and at follow-up it was 95.41 + or - 10.65 (P < .001). The difference in functional status of patient (Karnofsky's Index) for every stage including Stage-IV was statistically significant (P 0.01). Survival analysis showed a significant differences in overall survival according to stage (P 0.001), grade (P 0.001), size of tumor (P 0.001) and Charlson's index (P = 0.05). There was significant improvement in the quality of life, following tumor nephrectomy, even for Stage-IV cancers. Multivariate analysis indicated besides tumor stage, grade, and size of the tumor, Charlson's index has a significant predictive value on overall survival.


Ascorbic acid and iron nutrition.
Iron deficiency anemia is prevalent throughout the world because of the inefficient absorption of nonheme iron which forms the bulk of the iron in the diet. Absorption of this type of iron is impaired by substances in food which reduce its availability. Ascorbic acid reverses the effect of dietary inhibitors and is one of the most powerful known promoters of nonheme iron absorption. It facilitates iron absorption by forming a chelate with the ferric iron in food at the acid pH of the stomach; the chelated iron remains soluble at the alkaline pH of the duodenum. However, the consumption of ascorbic acid with a vegetarian meal containing primarily nonheme iron could improve the absorption of iron for an individual whose diet contains little or no heme iron. Unfortunately, relatively high cost and instability of ascorbic acid during food storage have proven to be major obstacles to its use in combating nutritional iron deficiency in developing countries.


Validation of a condition-specific measure for women having an abnormal screening mammography.
The aim of this study is to assess the validity of a new condition-specific instrument measuring psychosocial consequences of abnormal screening mammography (PCQ-DK33). The draft version of the PCQ-DK33 was completed on two occasions by 184 women who had received an abnormal screening mammography and on one occasion by 240 women who had received a normal screening result. Item Response Theories and Classical Test Theories were used to analyze data. Construct validity, concurrent validity, known group validity, objectivity and reliability were established by item analysis examining the fit between item responses and Rasch models. Six dimensions covering anxiety, behavioral impact, sense of dejection, impact on sleep, breast examination, and sexuality were identified. One item belonging to the dejection dimension had uniform differential item functioning. Two items not fitting the Rasch models were retained because of high face validity. A sick leave item added useful information when measuring side effects and socioeconomic consequences of breast cancer screening. Five "poor items" were identified and should be deleted from the final instrument. Preliminary evidence for a valid and reliable condition-specific measure for women having an abnormal screening mammography was established. The measure includes 27 "good" items measuring different attributes of the same overall latent structure-the psychosocial consequences of abnormal screening mammography.


Consistency and convergence rate of phylogenetic inference via regularization.
It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough information in the gene sequences alone to accurately reconstruct the correct "gene tree." Although the gene tree may deviate from the "species tree" due to a variety of genetic processes, in the absence of evidence to the contrary it is parsimonious to assume that they agree. A common statistical approach in these situations is to develop a likelihood penalty to incorporate such additional information. Recent studies using simulation and empirical data suggest that a likelihood penalty quantifying concordance with a species tree can significantly improve the accuracy of gene tree reconstruction compared to using sequence data alone. However, the consistency of such an approach has not yet been established, nor have convergence rates been bounded. Because phylogenetics is a non-standard inference problem, the standard theory does not apply. In this paper, we propose a penalized maximum likelihood estimator for gene tree reconstruction, where the penalty is the square of the Billera-Holmes-Vogtmann geodesic distance from the gene tree to the species tree. We prove that this method is consistent, and derive its convergence rate for estimating the discrete gene tree structure and continuous edge lengths (representing the amount of evolution that has occurred on that branch) simultaneously. We find that the regularized estimator is "adaptive fast converging," meaning that it can reconstruct all edges of length greater than any given threshold from gene sequences of polynomial length. Our method does not require the species tree to be known exactly; in fact, our asymptotic theory holds for any such guide tree.


[Historical report: first isolation of Vibrio cholera serogroup O1 biovar El Tor serovar Inaba during the cholerae epidemic in Peru ‑ 1991].
20 years ago, a new diarrheal disease was introduced in Peru and the Enteropathogens Reference Laboratory of the Instituto Nacional de Salud had an outstanding role in the isolation and rapid and timely identification of Vibrio cholerae. Cholera had not been seen before, but during the last week of January 1991 an outbreak of acute diarrhea was detected, presenting intense dehydration and some deaths. The epidemic affected, in the beginning, many locations of the peruvian coast. Some working teams of the General Office of Epidemiology and of the Instituto Nacional de Salud obtained fecal samples from patients with acute diarrhea coming from the cities of Chancay, Chimbote, Piura and some hospitals in Lima. The collected samples were transported on Cary and Blair media and processed in the National Reference Laboratory of Enteropathogens (LANARE) of the Instituto Nacional de Salud. Vibrio cholerae serogroup 01 biovar El Tor serovar Inaba was isolated from all the samples, it was sensible to tetracyclines and other antibiotics. This research confirmed the first outbreak of cholera in Peru.


Cost-effectiveness of Ward Closure to Control Outbreaks of Norovirus Infection in United Kingdom National Health Service Hospitals.
Norovirus is the most common cause of outbreaks of acute gastroenteritis in National Health Service hospitals in the United Kingdom. Wards (units) are often closed to new admissions to stop the spread of the virus, but there is limited evidence describing the cost-effectiveness of ward closure. An economic analysis based on the results from a large, prospective, active-surveillance study of gastroenteritis outbreaks in hospitals and from an epidemic simulation study compared alternative ward closure options evaluated at different time points since first infection, assuming different efficacies of ward closure. A total of 232 gastroenteritis outbreaks occurring in 14 hospitals over a 1-year period were analyzed. The risk of a new outbreak in a hospital is significantly associated with the number of admission, general medical, and long-stay wards that are concurrently affected but is less affected by the level of community transmission. Ward closure leads to higher costs but reduces the number of new outbreaks by 6%-56% and the number of clinical cases by 1%-55%, depending on the efficacy of the intervention. The incremental cost per outbreak averted varies from £10 000 ($14 000) to £306 000 ($428 000), and the cost per case averted varies from £500 ($700) to £61 000 ($85 000). The cost-effectiveness of ward closure decreases as the efficacy of the intervention increases, and the cost-effectiveness increases with the timing of the intervention. The efficacy of ward closure is critical from a cost-effectiveness perspective. Ward closure may be cost-effective, particularly if targeted to high-throughput units.


A Novel Selective JAK2 Inhibitor Identified Using Pharmacological Interactions.
The JAK2/STAT signaling pathway mediates cytokine receptor signals that are involved in cell growth, survival and homeostasis. JAK2 is a member of the Janus kinase (JAK) family and aberrant JAK2/STAT is involved with various diseases, making the pathway a therapeutic target. The similarity between the ATP binding site of protein kinases has made development of specific inhibitors difficult. Current JAK2 inhibitors are not selective and produce unwanted side effects. It is thought that increasing selectivity of kinase inhibitors may reduce the side effects seen with current treatment options. Thus, there is a great need for a selective JAK inhibitor. In this study, we identified a JAK2 specific inhibitor. We first identified key pharmacological interactions in the JAK2 binding site by analyzing known JAK2 inhibitors. Then, we performed structure-based virtual screening and filtered compounds based on their pharmacological interactions and identified compound NSC13626 as a potential JAK2 inhibitor. Results of enzymatic assays revealed that against a panel of kinases, compound NSC13626 is a JAK2 inhibitor and has high selectivity toward the JAK2 and JAK3 isozymes. Our cellular assays revealed that compound NSC13626 inhibits colorectal cancer cell (CRC) growth by downregulating phosphorylation of STAT3 and arresting the cell cycle in the S phase. Thus, we believe that compound NSC13626 has potential to be further optimized as a selective JAK2 drug.


Two centuries of biodiversity discovery and loss in Singapore.
There is an urgent need for reliable data on the impacts of deforestation on tropical biodiversity. The city-state of Singapore has one of the most detailed biodiversity records in the tropics, dating back to the turn of the 19th century. In 1819, Singapore was almost entirely covered in primary forest, but this has since been largely cleared. We compiled more than 200 y of records for 10 major taxonomic groups in Singapore (>50,000 individual records; >3,000 species), and we estimated extinction rates using recently developed and novel statistical models that account for "dark extinctions," i.e., extinctions of undiscovered species. The estimated overall extinction rate was 37% (95% CI [31 to 42%]). Extrapolating our Singapore observations to a future business-as-usual deforestation scenario for Southeast Asia suggests that 18% (95% CI [16 to 22%]) of species will be lost regionally by 2100. Our extinction estimates for Singapore and Southeast Asia are a factor of two lower than previous estimates that also attempted to account for dark extinctions. However, we caution that particular groups such as large mammals, forest-dependent birds, orchids, and butterflies are disproportionately vulnerable.


Selective ROCK Inhibitor Enhances Blood Flow Recovery after Hindlimb Ischemia.
The impairment in microvascular network formation could delay the restoration of blood flow after acute limb ischemia. A high-content screen of a GSK-published kinase inhibitor library identified a set of ROCK inhibitor hits enhancing endothelial network formation. Subsequent kinase activity profiling against a panel of 224 protein kinases showed that two indazole-based ROCK inhibitor hits exhibited high selectivity for ROCK1 and ROCK2 isoforms compared to other ROCK inhibitors. One of the chemical entities, GSK429286, was selected for follow-up studies. We found that GSK429286 was ten times more potent in enhancing endothelial tube formation than Fasudil, a classic ROCK inhibitor. ROCK1 inhibition by RNAi phenocopied the angiogenic phenotype of the GSK429286 compound. Using an organotypic angiogenesis co-culture assay, we showed that GSK429286 formed a dense vascular network with thicker endothelial tubes. Next, mice received either vehicle or GSK429286 (10 mg/kg i.p.) for seven days after hindlimb ischemia induction. As assessed by laser speckle contrast imaging, GSK429286 potentiated blood flow recovery after ischemia induction. At the histological level, we found that GSK429286 significantly increased the size of new microvessels in the regenerating areas of ischemic muscles compared with vehicle-treated ones. Our findings reveal that selective ROCK inhibitors have in vitro pro-angiogenic properties and therapeutic potential to restore blood flow in limb ischemia.


Fine mapping of the IBD1 locus did not identify Crohn disease-associated NOD2 variants: implications for complex disease genetics.
Crohn disease (CD) is a chronic relapsing inflammatory condition of the gastrointestinal tract. Recently, polymorphisms in NOD2 (CARD15), a gene mapping to the chromosome 16 IBD1 susceptibility locus, have been associated with susceptibility to CD. One group identified the gene by using classic positional cloning methods. Here, we report linkage and fine mapping analyses using 27 microsatellite markers encompassing the IBD1 susceptibility locus in 131 CD affected sibling pairs, and a simplex family cohort. No evidence for linkage was observed, and microsatellite markers close to NOD2 did not show association. However, significant association was confirmed in 294 CD trios for the NOD2 variants Arg702Trp and Leu1007fsinsC. Our fine mapping study of the IBD1 locus did not enable us to identify NOD2 as a CD gene, despite the presence of association with disease-causing alleles. This study illustrates the difficulties facing microsatellite linkage and linkage disequilibrium mapping methods for identifying disease genes in complex traits.


Survey of construction workers repeatedly exposed to chlorine over a three to six month period in a pulpmill: I. Exposure and symptomatology.
The admission to hospital of three construction workers with acute respiratory distress caused by inhalation of chlorine gas prompted the inspection of a building site located in a kraft pulpmill. The accidental emissions had taken place in the bleach plant and the construction workers assigned there were surveyed to uncover possible large scale health effects. A questionnaire was presented to 281 workers (participation rate = 97%); 257 workers reported an average of 24 exposure episodes to chlorine and derivatives over a three to six month period. The air monitoring data available from the pulpmill's industrial hygienist were not useful in linking specific events reported by the workers to environmental conditions in the bleach plant. Over 60% of the workers described a characteristic flu like syndrome that lasted for an average of 11 days and was exacerbated by new bouts of exposure. Irritation of the throat (78%) and eyes (77%), cough (67%), and headache (63%) were the most often reported symptoms. Shortness of breath was reported by 54% of the participants and was not associated with age, smoking state, or history of asthma or chronic bronchitis. First aid self referral was associated with significantly greater reporting of most symptoms, including dyspnoea and cough. A significantly greater proportion of workers in the dyspnoea group had gone at least once for first aid care after a gassing incident (64% as opposed to 48%, p = 0.008). Throat irritation and cough persisted for mean intervals of eight and 11 days respectively. A flu like syndrome lasted for an average of 20 days. Seventy one subjects were considered to be a moderate to high risk of having persisting respiratory symptoms. Throat and eye irritation as well as cough and flu like symptoms are frequent occurrences after repeated accidental inhalation of chlorine. Subjects who consulted first aid care stations after a gassing incident are more likely to have persisting dyspnoea.


Comparative analysis of argonaute-dependent small RNA pathways in Drosophila.
The specificity of RNAi pathways is determined by several classes of small RNAs, which include siRNAs, piRNAs, endo-siRNAs, and microRNAs (miRNAs). These small RNAs are invariably incorporated into large Argonaute (Ago)-containing effector complexes known as RNA-induced silencing complexes (RISCs), which they guide to silencing targets. Both genetic and biochemical strategies have yielded conserved molecular components of small RNA biogenesis and effector machineries. However, given the complexity of these pathways, there are likely to be additional components and regulators that remain to be uncovered. We have undertaken a comparative and comprehensive RNAi screen to identify genes that impact three major Ago-dependent small RNA pathways that operate in Drosophila S2 cells. We identify subsets of candidates that act positively or negatively in siRNA, endo-siRNA, and miRNA pathways. Our studies indicate that many components are shared among all three Argonaute-dependent silencing pathways, though each is also impacted by discrete sets of genes.


Late complications of high-voltage electrical injury might involve multiple systems and be related to current path.
Delayed complications of electrical burns are mostly unexpected, and the link between the injury and the symptoms often goes unrecognized. A possible relation between source-ground sites and late clinical manifestations was recently emphasized. We report a unique case of combined intestinal-spinal delayed complications following a high-voltage electrical injury, a possible explanation being a greater current flow through the right hemisoma. The potential for late complications is an additional feature that physicians must consider in managing electrical injuries. Manifestations are variable and presentation is confounding, but current flow path can constitute a precious source of information to predict complications in the late phase of management.


JMJD6 is a histone arginine demethylase.
Arginine methylation occurs on a number of proteins involved in a variety of cellular functions. Histone tails are known to be mono- and dimethylated on multiple arginine residues where they influence chromatin remodeling and gene expression. To date, no enzyme has been shown to reverse these regulatory modifications. We demonstrate that the Jumonji domain-containing 6 protein (JMJD6) is a JmjC-containing iron- and 2-oxoglutarate-dependent dioxygenase that demethylates histone H3 at arginine 2 (H3R2) and histone H4 at arginine 3 (H4R3) in both biochemical and cell-based assays. These findings may help explain the many developmental defects observed in the JMJD6(-/-) knockout mice.


Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns.
The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat.


Malaria: Biology and Disease.
Malaria has been a major global health problem of humans through history and is a leading cause of death and disease across many tropical and subtropical countries. Over the last fifteen years renewed efforts at control have reduced the prevalence of malaria by over half, raising the prospect that elimination and perhaps eradication may be a long-term possibility. Achievement of this goal requires the development of new tools including novel antimalarial drugs and more efficacious vaccines as well as an increased understanding of the disease and biology of the parasite. This has catalyzed a major effort resulting in development and regulatory approval of the first vaccine against malaria (RTS,S/AS01) as well as identification of novel drug targets and antimalarial compounds, some of which are in human clinical trials.