International gestational age-specific centiles for umbilical artery Doppler indices: a longitudinal prospective cohort study of the INTERGROWTH-21st Project.
Reference values for umbilical artery Doppler indices are used clinically to assess fetal well-being. However, many studies that have produced reference charts have important methodologic limitations, and these result in significant heterogeneity of reported reference ranges. To produce international gestational age-specific centiles for umbilical artery Doppler indices based on longitudinal data and the same rigorous methodology used in the original Fetal Growth Longitudinal Study of the INTERGROWTH-21st Project. In Phase II of the INTERGROWTH-21st Project (the INTERBIO-21st Study), we prospectively continued enrolling pregnant women according to the same protocol from 3 of the original populations in Pelotas (Brazil), Nairobi (Kenya), and Oxford (United Kingdom) that had participated in the Fetal Growth Longitudinal Study. Women with a singleton pregnancy were recruited at <14 weeks' gestation, confirmed by ultrasound measurement of crown-rump length, and then underwent standardized ultrasound every 5±1 weeks until delivery. From 22 weeks of gestation umbilical artery indices (pulsatility index, resistance index, and systolic/diastolic ratio) were measured in a blinded fashion, using identical equipment and a rigorously standardized protocol. Newborn size at birth was assessed using the international INTERGROWTH-21st Standards, and infants had detailed assessment of growth, nutrition, morbidity, and motor development at 1 and 2 years of age. The appropriateness of pooling data from the 3 study sites was assessed using variance component analysis and standardized site differences. Umbilical artery indices were modeled as functions of the gestational age using an exponential, normal distribution with second-degree fractional polynomial smoothing; goodness of fit for the overall models was assessed. Of the women enrolled at the 3 sites, 1629 were eligible for this study; 431 (27%) met the entry criteria for the construction of normative centiles, similar to the proportion seen in the original fetal growth longitudinal study. They contributed a total of 1243 Doppler measures to the analysis; 74% had 3 measures or more. The healthy low-risk status of the population was confirmed by the low rates of preterm birth (4.9%) and preeclampsia (0.7%). There were no neonatal deaths and satisfactory growth, health, and motor development of the infants at 1 and 2 years of age were documented. Only a very small proportion (2.8%-6.5%) of the variance of Doppler indices was due to between-site differences; in addition, standardized site difference estimates were marginally outside this threshold in only 1 of 27 comparisons, and this supported the decision to pool data from the 3 study sites. All 3 Doppler indices decreased with advancing gestational age. The 3rd, 5th 10th, 50th, 90th, 95th, and 97th centiles according to gestational age for each of the 3 indices are provided, as well as equations to allow calculation of any value as a centile and z scores. The mean pulsatility index according to gestational age = 1.02944 + 77.7456*(gestational age)-2 - 0.000004455*gestational age3. We present here international gestational age-specific normative centiles for umbilical artery Doppler indices produced by studying healthy, low-risk pregnant women living in environments with minimal constraints on fetal growth. The centiles complement the existing INTERGROWTH-21st Standards for assessment of fetal well-being.


The significance of 1793G>A polymorphism in MTHFR gene in women with first trimester recurrent miscarriages.
Recurrent miscarriages (RM) are significant social and clinical problem. One of suggested reason of RM is hyperhomocysteinemia. Polymorphic genes involved in homocysteine and folate metabolism, including 5,10-methylenetetrahydrofolate reductase (MTHFR) gene, are considered as an important risk factors for homocysteine accumulation and modulator of RM susceptibility. Therefore the aim of this study was to evaluate the frequency of MTHFR polymorphisms (677C>T, 1298A>C, and 1793G>A) in women with recurrent miscarriages. We have analyzed 104 Polish women with a history of 3 or more unexplained recurrent miscarriages in the first pregnancy trimester (6-13 gestation week). The control group consisted of 169 women without obstetrical complication, any history of miscarriage and with at least one live birth in anamnesis. The investigated polymorphisms were determined by PCR/RFLP methods. For MTHFR 1793G>A polymorphism we have observed significant overrepresentation of heterozygotic GA genotypes in RM group (15.38% vs. 4.14% in the controls, OR=4.21, p=0.003). For 677C>T and 1298A>C we have shown lack of significant association with RM. Nevertheless, such significant association was observed if more than one mutated MTHFR variant was present in one patient. Our research indicate the possible role of MTHFR 1793G>A polymorphism in pathogenesis of RM. The noticed tendency to more frequent occurrence of haplotypes of MTHFR gene including two or three mutated alleles showed the possibility of summarized amplification of these variants effect influencing RM susceptibility.


Surveillance for hepatocellular carcinoma in patients with primary biliary cirrhosis.
Hepatocellular carcinoma (HCC) occurs with increased frequency in patients with primary biliary cirrhosis (PBC). Effectiveness of surveillance recommendations for HCC is controversial, and data are lacking in patients with PBC. In this study, we attempt to (1) establish the importance of surveillance for HCC in patients with PBC; (2) identify a target population of patients with PBC for HCC surveillance; and (3) propose surveillance recommendations for patients with PBC. We retrospectively identified 36 patients seen at the Mayo Clinic between 1976 and 2007 with a diagnosis of both PBC and HCC. Five patients (14%) were diagnosed incidentally, 17 patients comprised our surveillant population, and 14 patients were diagnosed outside a surveillance program. Patients in the surveillant population were more likely to undergo therapy (88% versus 43%; P = 0.01) and had improved survival (P = 0.002) compared with the nonsurveillant population. All cases of HCC except one were predicted to be at significant risk for HCC based on age, sex, evidence of portal hypertension, and history of blood transfusion using a previous predictive model. We established the importance of surveillance for HCC in patients with PBC. We demonstrated adequate performance of a predictive model and propose it should be refined and used to identify patients with PBC who should be screened for development of HCC. Further studies are needed so that optimal HCC surveillance recommendations in this population can be determined and included in the practice guidelines for PBC.


Multicenter validation of a machine-learning algorithm for 48-h all-cause mortality prediction.
In order to evaluate mortality predictions based on boosted trees, this retrospective study uses electronic medical record data from three academic health centers for inpatients 18 years or older with at least one observation of each vital sign. Predictions were made 12, 24, and 48 hours before death. Models fit to training data from each institution were evaluated using hold-out test data from the same institution, and from the other institutions. Gradient-boosted trees (GBT) were compared to regularized logistic regression (LR) predictions, support vector machine (SVM) predictions, quick Sepsis-Related Organ Failure Assessment (qSOFA), and Modified Early Warning Score (MEWS) using area under the receiver operating characteristic curve (AUROC). For training and testing GBT on data from the same institution, the average AUROCs were 0.96, 0.95, and 0.94 across institutional test sets for 12-, 24-, and 48-hour predictions, respectively. When trained and tested on data from different hospitals, GBT AUROCs achieved up to 0.98, 0.96, and 0.96, for 12-, 24-, and 48-hour predictions, respectively. Average AUROC for 48-hour predictions for LR, SVM, MEWS, and qSOFA were 0.85, 0.79, 0.86 and 0.82, respectively. GBT predictions may help identify patients who would benefit from increased clinical care.


Computational design of molecules for an all-quinone redox flow battery.
Inspired by the electron transfer properties of quinones in biological systems, we recently showed that quinones are also very promising electroactive materials for stationary energy storage applications. Due to the practically infinite chemical space of organic molecules, the discovery of additional quinones or other redox-active organic molecules for energy storage applications is an open field of inquiry. Here, we introduce a high-throughput computational screening approach that we applied to an accelerated study of a total of 1710 quinone (Q) and hydroquinone (QH2) (i.e., two-electron two-proton) redox couples. We identified the promising candidates for both the negative and positive sides of organic-based aqueous flow batteries, thus enabling an all-quinone battery. To further aid the development of additional interesting electroactive small molecules we also provide emerging quantitative structure-property relationships.


Characteristics and risk factors of Plasmodium falciparum malaria in Eastern and Central Nepal.
Very limited information is available on epidemiology of falciparum malaria in Nepal. Such information is very important for malaria control programmes. It is believed that malaria in Eastern region is imported from border districts of India and local transmission follows whereas it is indigenous in Central region. Therefore, the characteristics and risk factors of malaria are believed to be different in Eastern and Central Nepal. The objective of the study is to describe and compare the characteristics and risk factors of falciparum malaria in Eastern and Central Nepal. This cross-sectional study was conducted in falciparum malaria endemic districts of Eastern and Central Nepal, during the period 2007 to 2008. We identified and collected information from 106 patients (62 from Eastern and 44 from Central region). Patient examination, clinical and laboratory assessment were done and patients were interviewed using structured questionnaire for malaria related characteristics, risk factors and behaviours. There were significant differences in risk factors and characteristics of falciparum malaria in the Central than the Eastern region. In the Central region, male, illiteracy and thatched roof hut were significant risk factors of falciparum malaria patients as compared to the Eastern region. Visits outside within three months, previous malaria within three months, taking antimalarial before confirmatory diagnosis were significantly higher in patients of the Eastern region as compared to the Central region. Falciparum malaria in Nepal should not be seen as similar entity, and different strategies for prevention and control is needed for its diverse characteristics and endemicity.


Effect of antidepressant medication treatment on suicidal ideation and behavior in a randomized trial: an exploratory report from the Combining Medications to Enhance Depression Outcomes Study.
To explore relationships between baseline sociodemographic and clinical features and baseline suicidal ideation, and treatment effects on suicidal ideation and behavior, in depressed outpatients. From March 2008 to September 2009, the Combining Medications to Enhance Depression Outcomes study, a single-blind, 7-month randomized trial, enrolled outpatients with nonpsychotic chronic and/or recurrent major depressive disorder (DSM-IV-TR criteria) in primary and psychiatric care (N = 665). Participants received escitalopram plus placebo, bupropion sustained release (SR) plus escitalopram, or venlafaxine extended release (XR) plus mirtazapine. The primary outcome measure for this report is presence of suicidal ideation assessed by the Concise Health Risk Tracking Self-Report, which measures suicidal ideation and behaviors over the last 24 hours. Sociodemographic and clinical features were compared in those with versus without baseline ideation. At 4, 12, and 28 weeks, treatment effects on suicidality were assessed, and unadjusted and adjusted outcomes were compared among those with and without baseline ideation using linear, logistic, ordinal logistic, and negative binomial regression models. Baseline suicidal ideation was associated with greater depressive severity, childhood neglect, childhood abuse, early major depressive disorder onset, greater psychiatric comorbidity, and worse functioning and quality of life. After adjustment for treatment, gender, age at first depressive episode, obsessive-compulsive symptoms, and depressive severity, depressive symptom outcomes did not differ between ideation groups at 12 or 28 weeks or between treatments. Overall, 79% of participants with baseline suicidal ideation had none at week 4, 83% had none at week 12, and 86% had none at week 28. All treatments reduced ideation, with bupropion-SR plus escitalopram the most effective at week 12 (P < .01). In participants without baseline ideation, emergent ideation did not differ between treatments: 2.5% had ideation at 4 weeks, 1.3% had ideation at 12 weeks, and only 1.7% had ideation at 28 weeks. Four patients (all receiving venlafaxine-XR plus mirtazapine) attempted suicide (P = .0162). Baseline ideation did not affect depressive symptom outcome. Bupropion-SR plus escitalopram most effectively reduced ideation. Ideation emergence was uncommon. Venlafaxine-XR plus mirtazapine may pose a higher risk of suicide attempts. clinicaltrials.gov Identifier: NCT00590863.


Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex.
Nuclear receptors modulate the transcription of genes in direct response to small lipophilic ligands. Binding to ligands induces conformational changes in the nuclear receptors that enable the receptors to interact with several types of cofactor that are critical for transcription activation (transactivation). We previously described a distinct set of ligand-dependent proteins called DRIPs, which interact with the vitamin D receptor (VDR); together, these proteins constitute a new cofactor complex. DRIPs bind to several nuclear receptors and mediate ligand-dependent enhancement of transcription by VDR and the thyroid-hormone receptor in cell-free transcription assays. Here we report the identities of thirteen DRIPs that constitute this complex, and show that the complex has a central function in hormone-dependent transactivation by VDR on chromatin templates. The DRIPs are almost indistinguishable from components of another new cofactor complex called ARC, which is recruited by other types of transcription activators to mediate transactivation on chromatin-assembled templates. Several DRIP/ARC subunits are also components of other potentially related cofactors, such as CRSP, NAT, SMCC and the mouse Mediator, indicating that unique classes of activators may share common sets or subsets of cofactors. The role of nuclear-receptor ligands may, in part, be to recruit such a cofactor complex to the receptor and, in doing so, to enhance transcription of target genes.


Corneal epithelial toxicity of antiglaucoma formulations: in vitro study of repeated applications.
By using a biologically relevant and sensitive three-dimensional model of human corneal epithelium and multiple endpoint analysis, assessment of the potential for eye irritation and long-term compatibility of four registered ophthalmological preparations, ie, Timolabak(®), Timoptol(®), Nyogel(®), and Timogel(®), was performed. This approach enables classification of the potential for irritation, discriminating between mildly irritant and non-irritant ocular substances. The exposure protocol included two time periods, ie, 24 hours (acute application) and 72 hours (repeated applications twice daily). This approach allows assessment of not only the acute reaction but also possible recovery, as well as mimicking the potential cumulative effects associated with long-term application. Using benzalkonium chloride (BAK) 0.01% as a positive control, the following parameters were quantified: cellular viability by MTT test, histological analysis by hematoxylin and eosin staining, passive release of interleukin-1α by enzyme-linked immunosorbent assay, and OCLN gene expression by quantitative real-time polymerase chain reaction. Cell viability was reduced to under the 50% cutoff value after acute exposure (24 hours) to BAK 0.01%, and after repeated application (72 hours) of Timoptol and Nyogel. Histological analysis after acute exposure showed signs of superficial damage with all formulations, and severe changes after repeated applications of Timoptol, BAK 0.01%, and Nyogel. Timolabak and Timogel did not significantly alter the morphology of the human corneal epithelial cells after the different exposure times. Interleukin-1α release was greater than that for the negative control (>20 pg/mL) and the positive control (BAK 0.01%), Nyogel, and Timoptol treatments and not different after treatment with Timolabak and Timogel. Expression of OCLN, a sign of epithelial barrier impairment, was only significantly upregulated at 24 hours by BAK 0.01%, suggesting a toxic reaction at the ocular surface. OCLN was also overexpressed after repeated application of Nyogel and Timogel. OVERALL, THE MULTIPLE ENDPOINT ANALYSIS APPROACH ALLOWS CLASSIFICATION OF THESE PRODUCTS ACCORDING TO DECREASING ORDER OF IRRITATION POTENTIAL AS FOLLOWS: BAK 0.01%, Timoptol, Nyogel, Timogel, and Timolabak.


Recent Advances in Pd-Based Membranes for Membrane Reactors.
Palladium-based membranes for hydrogen separation have been studied by several research groups during the last 40 years. Much effort has been dedicated to improving the hydrogen flux of these membranes employing different alloys, supports, deposition/production techniques, etc. High flux and cheap membranes, yet stable at different operating conditions are required for their exploitation at industrial scale. The integration of membranes in multifunctional reactors (membrane reactors) poses additional demands on the membranes as interactions at different levels between the catalyst and the membrane surface can occur. Particularly, when employing the membranes in fluidized bed reactors, the selective layer should be resistant to or protected against erosion. In this review we will also describe a novel kind of membranes, the pore-filled type membranes prepared by Pacheco Tanaka and coworkers that represent a possible solution to integrate thin selective membranes into membrane reactors while protecting the selective layer. This work is focused on recent advances on metallic supports, materials used as an intermetallic diffusion layer when metallic supports are used and the most recent advances on Pd-based composite membranes. Particular attention is paid to improvements on sulfur resistance of Pd based membranes, resistance to hydrogen embrittlement and stability at high temperature.


HIV prevalence and incidence in a cohort of South African men and transgender women who have sex with men: the Sibanye Methods for Prevention Packages Programme (MP3) project.
Men who have sex with men (MSM) and transgender women (TGW) are at increased risk for acquiring HIV, but there are limited HIV incidence data for these key populations in Africa. Understanding HIV prevalence and incidence provides important context for designing HIV prevention strategies, including pre-exposure prophylaxis (PrEP) programmes. We describe HIV prevalence, awareness of HIV infection, HIV incidence and associated factors for a cohort of MSM and TGW in Cape Town and Port Elizabeth, South Africa. From 2015 to 2016, MSM and TGW in Cape Town and Port Elizabeth were enrolled and prospectively followed for 12 months, receiving a comprehensive package of HIV prevention services. HIV testing was conducted at baseline and at follow-up visits (targeted for three, six and twelve months). All HIV-negative PrEP-eligible participants were offered PrEP enrolment during the first four months of study participation. We determined HIV prevalence among participants at baseline, and incidence by repeat screening of initially HIV-negative participants with HIV tests at three, six and twelve months. Among 292 participants enrolled, HIV prevalence was high (43%; 95% CI: 38 to 49) and awareness of HIV status was low (50%). The 167 HIV-negative participants who were followed prospectively for 144.7 person-years; nine incident HIV infections were documented. Overall annual incidence was 6.2% (CI: 2.8 to 11.8) and did not differ by city. Annual HIV incidence was significantly higher for younger (18 to 19 years) MSM and TGW (MSM: 21.8% (CI: 1.2 to 100); TGW: 31.0 (CI: 3.7, 111.2)). About half of participants started PrEP during the study; the annual incidence of HIV among 82 (49%) PrEP starters was 3.6% (CI: 0.4, 13.1) and among those who did not start PrEP was 7.8% (CI: 3.1, 16.1). HIV incidence was high among MSM and TGW in the context of receiving a comprehensive package of prevention interventions and offering of PrEP. PrEP uptake was high; the observed incidence of HIV in those who started PrEP was about half the incidence of HIV in those who did not. Future implementation-oriented studies should focus on decisions to start and continue PrEP for those at highest risk, including young MSM.


Genomic sequencing of DPC4 in the analysis of familial pancreatic carcinoma.
A first-degree relative with pancreatic cancer is found in 5% to 10% of patients with pancreatic carcinomas, suggesting an inherited predisposition for this neoplasm. The recently identified DPC4 tumor suppressor gene is a strong candidate for the gene responsible for the familial form of pancreatic carcinoma. DPC4 was identified in a consensus area of homozygous deletion in pancreatic carcinomas, and it is biallelically inactivated in approximately 50% of sporadic pancreatic carcinomas. The coding sequence of this gene is 1660 nucleotides in length, covering 11 exons. We describe optimized primers and conditions used in polymerase chain reaction and cycle sequencing of the entire DPC4 coding sequence of 25 individuals (eight with pancreatic carcinoma) from 11 kindreds with a familial aggregation of pancreatic carcinoma. No mutations in the coding sequences of the DPC4 gene were found; hence, it appears that germline mutations in DPC4 cannot account for many of the familial aggregations of pancreatic carcinoma.


Genistein synergizes centchroman action in human breast cancer cells.
Despite the progress in the diagnosis and treatment of breast cancer, it remains a major health problem in women. Natural flavones along with chemotherapeutic agents enhance therapeutic response and minimize toxicity of chemical agents. Centchroman (CC) colloquially called as ormeloxifene, is a nonsteroidal oral contraceptive categorized as selective estrogen receptor modulator with anti-breast cancer activity. Genistein (GN), an isoflavone found mainly in soy products possesses anti-cancerous potential against a number of cancers including breast. The present study aims at investigating the combination of CC and GN in human breast cancer cell lines (HBCCs). Cytotoxic effect of CC and GN separately and in combination were assessed by sulforhodamine B (SRB) assay in MDA MB-231, MDA MB-468, MCF-7, T-47D HBCCs, and nontumorigenic human mammary epithelial cell (HMEC) MCF-10A. The drug interaction was analyzed using CompuSyn software through which combination index and dose reduction index were generated. Combination of CC plus GN exerts significantly higher cytotoxicity compared to each drug per se in HBCCs, whereas HMEC-MCF-10A remains unaffected. On an overall basis, the drugs in combination enhanced cell killing in malignant cells. Therefore, the combination of CC with GN may offer a novel approach for the breast cancer.


Refinement of the crystal structure of Li4P2S6 using NMR crystallography.
The structure of Li4P2S6 was solved, based on a combination of X-ray powder diffraction data, quantum chemical calculations and solid state nuclear magnetic resonance (NMR). Two-dimensional 31P single quantum/double quantum correlation spectra yielded important constraints regarding the space group symmetry allowing the crystal structure to be solved by the Rietveld method. Li4P2S6 crystallizes in a trigonal space group with a = 10.51452(6) Å; c = 6.59149(8) Å. The structure contains two distinct P2S64- ions in a 2 : 1 ratio: in the first one the two P atoms of the hexahypothiophosphate unit are crystallographically distinct, whereas in the second one they are crystallographically identical.


HOX genes: potential candidates for the progression of laryngeal squamous cell carcinoma.
Laryngeal squamous cell carcinoma (LSCC) is a very aggressive cancer, considered to be a subtype of the head and neck squamous cell carcinoma (HNSCC). Despite significant advances in the understanding and treatment of cancer, prognosis of patients with LSCC has not improved recently. In the present study, we sought to understand better the genetic mechanisms underlying LSCC development. Thirty-two tumor samples were collected from patients undergoing surgical resection of LSCC. The samples were submitted to whole-genome cDNA microarray analysis aiming to identify genetic targets in LSCC. We also employed bioinformatic approaches to expand our findings using the TCGA database and further performed functional assays, using human HNSCC cell lines, to evaluate viability, cell proliferation, and cell migration after silencing of selected genes. Eight members of the homeobox gene family (HOX) were identified to be overexpressed in LSCC samples when compared to normal larynx tissue. Quantitative RT-PCR analysis validated the overexpression of HOX gene family members in LSCC. Receiver operating characteristic (ROC) statistical method curve showed that the expression level of seven members of HOX gene family can distinguish tumor from nontumor tissue. Correlation analysis of clinical and gene expression data revealed that HOXC8 and HOXD11 genes were associated with the differentiation degree of tumors and regional lymph node metastases, respectively. Additionally, siRNA assays confirmed that HOXC8, HOXD10, and HOXD11 genes might be critical for cell colony proliferation and cell migration. According to our findings, several members of the HOX genes were overexpressed in LSCC samples and seem to be required in biological processes involved in tumor development. This suggests that HOX genes might play a critical role in the physiopathology of LSCC tumors.


Retest reliability of self-reported function, self-care, and disease history.
Exposures and outcomes frequently are measured by self-reports in epidemiologic studies. However, compared with objective data based on physiologic or laboratory tests, self-reports may suffer from lower accuracy and reliability. In addition, few reports examine reliability in population subgroups, such as black adults. The authors examined the retest reliability of common self-reports concerning self-care, function, and chronic conditions in a random subsample of 92 middle-aged black subjects from a larger cohort of 998 subjects in St. Louis, Missouri. Subjects completed in-home interviews between September 2000 and July 2001. Function and self-care measures included 7 basic activities of daily living, 8 instrumental activities of daily living, and 9 items based on the Nagi physical performance scale. Chronic conditions included a list of 11 common diseases and conditions and the 7 items of the Rose Angina protocol. Item level agreement was measured by kappa and scale level agreement was measured by intraclass correlation coefficients. Function and self-care items demonstrated highly variable agreement with 7 items failing to reach even moderate (kappa = 0.40) levels of agreement. Scale reliability was better, and intraclass correlation coefficients ranged from 0.75 to 0.95. Self-reported chronic conditions all achieved at least moderate agreement, except for angina based on the Rose protocol. This study provides evidence that summary measures of function and a number of chronic conditions and diseases are reliable based on self-reports from urban black adults.


Interventional Strategies for Parkinson Disease: Can Neural Precursor Cells Forge a Path Ahead?
Neural precursor cells (NPCs), derived from pluripotent stem cells (PSCs), with their unique ability to generate multiple neuronal and glial cell types are extremely useful for understanding biological mechanisms in normal and diseased states. However, generation of specific neuronal subtypes (mature) from NPCs in large numbers adequate for cell therapy is challenging due to lack of a thorough understanding of the cues that govern their differentiation. Interestingly, neural stem cells (NSCs) themselves are in consideration for therapy given their potency to form different neural cell types, release of trophic factors, and immunomodulatory effects that confer neuroprotection. With the recent COVID-19 outbreak and its accompanying neurological indications, the immunomodulatory role of NSCs may gain additional significance in the prevention of disease progression in vulnerable populations. In this regard, small-molecule mediated NPC generation from PSCs via NSC formation has become an important strategy that ensures consistency and robustness of the process. The development of the mammalian brain occurs along the rostro-caudal axis, and the establishment of anterior identity is an early event. Wnt signaling, along with fibroblast growth factor and retinoic acid, acts as a caudalization signal. Further, the increasing amount of epigenetic data available from human fetal brain development has enhanced both our understanding of and ability to experimentally manipulate these developmental regulatory programs in vitro. However, the impact on homing and engraftment after transplantation and subsequently on therapeutic efficacy of NPCs based on their derivation strategy is not yet clear. Another formidable challenge in cell replacement therapy for neurodegenerative disorders is the mode of delivery. In this Perspective, we discuss these core ideas with insights from our preliminary studies exploring the role of PSC-derived NPCs in rat models of MPTP-induced Parkinson's disease following intranasal injections.


Mathematical reconstruction of human femoral condyles.
There is a direct correlation between ligament function and the articulating surface of the normal knee, and changes to any of these structures can affect the other. This is also true for knee replacements, where the articulating surface is greatly changed compared to the natural knee. This study investigated the morphometry of healthy knees and proposes a method to predict original normal knee profiles. A variety of mathematical techniques are compared in terms of the accuracy with which they can represent the original knee joint geometry. Additionally, a method of predicting the irregular femoral condyle geometry for an individual knee is described by making use of the mathematical techniques presented, and the accuracy of this method is also investigated. The mathematical approach using B-splines provides flexibility and can accurately describe the complex geometry of the femoral condyles in both the sagittal and transverse planes. It was further found that the condyles are highly asymmetrical; therefore simpler methods cannot portray the condyles sufficiently and are especially inaccurate in representing the lateral condyle. The study proposes a method for predicting the geometry of the femoral condyles with good accuracy. The B-spline model showed best results.


Short panicle1 encodes a putative PTR family transporter and determines rice panicle size.
The architecture of the rice inflorescence, which is determined mainly by the number and length of primary and secondary inflorescence branches, is of importance in both agronomy and developmental biology. The position and number of primary branches are established during the phase transition from vegetative to reproductive growth, and several of the genes identified as participating in this process do so by regulating the meristemic activities of inflorescence. However, little is known about the molecular mechanism that controls inflorescence branch elongation. Here, we report on a novel rice mutant, short panicle1 (sp1), which is defective in rice panicle elongation, and thus leads to the short-panicle phenotype. Gene cloning and characterization indicate that SP1 encodes a putative transporter that belongs to the peptide transporter (PTR) family. This conclusion is based on the findings that SP1 contains a conserved PTR2 domain consisting of 12 transmembrane domains, and that the SP1-GFP fusion protein is localized in the plasma membrane. The SP1 gene is highly expressed in the phloem of the branches of young panicles, which is consistent with the predicted function of SP1 and the sp1 phenotype. Phylogenetic analysis implies that SP1 might be a nitrate transporter. However, neither nitrate transporter activity nor any other compounds transported by known PTR proteins could be detected in either a Xenopus oocyte or yeast system, in our study, suggesting that SP1 may need other component(s) to be able to function as a transporter, or that it transports unknown substrates in the monocotyledonous rice plant.


Chronic neurogenic facial pain: lack of response to intravenous phentolamine.
Chronic neurogenic facial pain is commonly resistant to treatment and is often the source of significant patient morbidity. Adrenergic mechanisms are postulated to play a role in producing this type of pain, and adrenergic blocking agents are frequently used in clinical practice for pain control therapy. The analgesic effectiveness of an adrenergic blocking agent, intravenous phentolamine, was compared to saline and intravenous lidocaine in the present study using a single-blind protocol in patients with chronic neurogenic facial pain. Thirty patients were studied whose common clinical features included pain for more than 6 months, unilateral trigeminal distribution, constant dysesthesia, and no evidence of pathology or known etiology. Phentolamine (30 mg), lidocaine (100 mg), and saline were each infused over periods of 5 to 10 minutes. Pain ratings were assessed every 4 minutes throughout each study period using a 10-point pain intensity scale. No patient reported subjective improvement of pain during or immediately following phentolamine or saline infusions alone. Sixteen of the 30 patients reported decreased pain following lidocaine infusion. In the majority of the patients, the duration of lidocaine analgesia was less than 30 minutes; however, some patients reported decreased pain for a longer time. The results do not support an adrenergic mechanism for chronic neurogenic facial pain. The response to lidocaine, a nonadrenergic, membrane-stabilizing agent, suggests that it may have clinical effectiveness in certain neurogenic facial pain patients.


Long term hormone therapy for perimenopausal and postmenopausal women.
Hormone therapy (HT) is widely used for controlling menopausal symptoms and has also been used for the management and prevention of cardiovascular disease, osteoporosis and dementia in older women. This is an updated version of a Cochrane review first published in 2005. To assess the effects of long term HT on mortality, cardiovascular outcomes, cancer, gallbladder disease, fractures, cognition and quality of life in perimenopausal and postmenopausal women, both during HT use and after cessation of HT use. We searched the following databases to February 2012: Cochrane Menstrual Disorders and Subfertility Group Trials Register, Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, PsycINFO. We included randomised double-blind studies of HT versus placebo, taken for at least one year by perimenopausal or postmenopausal women. HT included oestrogens, with or without progestogens, via oral, transdermal, subcutaneous or intranasal routes. Two authors independently assessed study quality and extracted data. We calculated risk ratios (RRS) for dichotomous data and mean differences (MDs) for continuous data, with 95% confidence intervals (CIs). Where findings were statistically significant, we calculated the absolute risk (AR) in the intervention group (the overall risk of an event in women taking HT). Twenty-three studies involving 42,830 women were included. Seventy per cent of the data were derived from two studies (WHI 1998 and HERS 1998). Most participants were postmenopausal American women with at least some degree of co-morbidity, and the mean participant age in most studies was over 60 years. None of the studies focused on perimenopausal women. In relatively healthy postmenopausal women (that is generally fit, without overt disease) combined continuous HT significantly increased the risk of a coronary event (after one year's use: AR 4 per 1000, 95% CI 3 to 7), venous thrombo-embolism (after one year's use: AR 7 per 1000, 95% CI 4 to 11), stroke (after three years' use: AR 18 per 1000, 95% CI 14 to 23), breast cancer (after 5.6 years' use: AR 23 per 1000, 95% CI 19 to 29), gallbladder disease (after 5.6 years' use: AR 27 per 1000, 95% CI 21 to 34) and death from lung cancer (after 5.6 years' use plus 2.4 years' additional follow-up: AR 9 per 1000, 95% CI 6 to 13). Oestrogen-only HT significantly increased the risk of venous thrombo-embolism (after one to two years' use: AR 5 per 1000, 95% CI 2 to 10; after 7 years' use: AR 21 per 1000, 95% CI 16 to 28), stroke (after 7 years' use: AR 32 per 1000, 95% CI 25 to 40) and gallbladder disease (after seven years' use: AR 45 per 1000, 95% CI 36 to 57) but did not significantly increase the risk of breast cancer. Among women aged over 65 years who were relatively healthy and taking continuous combined HT, there was a statistically significant increase in the incidence of dementia (after 4 years' use: AR 18 per 1000, 95% CI 11 to 30). Among women with cardiovascular disease, long term use of combined continuous HT significantly increased the risk of venous thrombo-embolism (at one year: AR 9 per 1000, 95% CI 3 to 29). Women taking HT had a significantly decreased incidence of fractures with long term use (after 5.6 years of combined HT: AR 86 per 1000, 95% CI 79 to 84; after 7.1 years' use of oestrogen-only HT: AR 102 per 1000, 95% CI 91 to 112). Risk of fracture was the only outcome for which there was strong evidence of clinical benefit from HT. There was no strong evidence that HT has a clinically meaningful impact on the incidence of colorectal cancer.One trial analysed subgroups of 2839 relatively healthy 50 to 59 year old women taking combined continuous HT and 1637 taking oestrogen-only HT versus similar-sized placebo groups. The only significantly increased risk reported was for venous thrombo-embolism in women taking combined continuous HT: their absolute risk remained low, at less than 1/500. However, other differences in risk cannot be excluded as this study was not designed to have the power to detect differences between groups of women within 10 years of the menopause. HT is not indicated for primary or secondary prevention of cardiovascular disease or dementia, nor for preventing deterioration of cognitive function in postmenopausal women. Although HT is considered effective for the prevention of postmenopausal osteoporosis, it is generally recommended as an option only for women at significant risk, for whom non-oestrogen therapies are unsuitable. There are insufficient data to assess the risk of long term HT use in perimenopausal women or postmenopausal women younger than 50 years of age.


Respiratory gating of anatomical optical coherence tomography images of the human airway.
Anatomical optical coherence tomography (aOCT) is a long-range endoscopic imaging modality capable of quantifying size and shape of the human airway. A challenge to its in vivo application is motion artifact due to respiratory-related movement of the airway walls. This paper represents the first demonstration of respiratory gating of aOCT airway data, and introduces a novel error measure to guide appropriate parameter selection. Results indicate that at least four gates per respiratory cycle should be used, with only minor improvements as the number of gates is further increased. It is shown that respiratory gating can substantially improve the quality of aOCT images and reveal events and features that are otherwise obscured by blurring.


DNA structural properties of AF9 are similar to MLL and could act as recombination hot spots resulting in MLL/AF9 translocations and leukemogenesis.
The human AF9 gene at 9p22 is one of the most common fusion partner genes with the MLL gene at 11q23, resulting in the t(9;11)(p22;q23). The MLL-AF9 fusion gene is associated with de novo acute myelo-genous leukemia (AML), rarely with acute lymphocytic leukemia (ALL) and with therapy related leukemia (t-AML). The AF9 gene is >100 kb and two patient breakpoint cluster regions (BCRs) have been identified; BCR1 is within intron 4, previously called site A, whereas BCR2 or site B spans introns 7 and 8. Patient breakpoint locations were determined previously by RT-PCR and by genomic DNA cloning. In this study, we defined the exon-intron boundaries and identified several different structural elements in AF9 including a co-localizing in vivo DNA topo II cleavage site and an in vitro DNase I hypersensitive (DNase 1 HS) site in intron 7 in BCR2. Reversibility experiments demonstrated a religation of the topo II cleavage sites. The location of the in vivo topo II cleavage site was confirmed in vitro using a topo II cleavage assay. In addition, two scaffold associated regions (SARs) are located centromeric to the topo II and DNase I HS cleavage sites and border both patient breakpoint regions: SAR1 is located in intron 4, whereas SAR2 encompasses parts of exons 5-7. This study demonstrates that the patient breakpoint regions of AF9 share the same structural elements as the MLL BCR. We describe a DNA breakage and repair model for non-homologous recombination between MLL and its partner genes, particularly AF9.


Optimism and education buffer the effects of syndemic conditions on HIV status among African American men who have sex with men.
The present study sought to replicate effects of the number of syndemic psychosocial health conditions on sexual risk behavior and HIV infection among a sample of high-risk African American men who have sex with men (MSM) and to identify resilience factors that may buffer these effects. We used baseline data from an HIV risk-reduction trial to examine whether a higher number of syndemic conditions was associated with higher rates of self-reported sexual risk behavior and HIV infection. Using logistic regression models, we tested for interactions between number of syndemic conditions and several potential resilience factors to identify buffering effects. Replicating previous studies, we found significant associations between numbers of syndemic conditions and higher rates of sexual risk behavior and HIV infection. Surprisingly, we also replicated a previous finding (Stall et al., Am J Public Health, 93(6):939-942, 2003) that the effects of syndemic burden on HIV status fell off at the highest levels of syndemic conditions. Among a variety of potential resilience factors, two-optimism and education-buffered the syndemic effect on HIV prevalence. This is, to our knowledge, the first paper to identify resilience factors buffering against syndemic effects among MSM. It also constitutes a significant contribution to the literature regarding prevention among black MSM. These results point to the need to identify HIV-positive black MSM and provide effective treatment for them and to develop interventions addressing both syndemic and resilience factors.


Path integration in desert ants, Cataglyphis: how to make a homing ant run away from home.
Path integration is an ant's lifeline on any of its foraging journeys. It results in a homebound global vector that continually informs the animal about its position relative to its starting point. Here, we use a particular (repeated training and displacement) paradigm, in which homebound ants are made to follow a familiar landmark route repeatedly from the feeder to the nest, even after they have arrived at the nest. The results show that during the repeated landmark-guided home runs the ant's path integrator runs continually, so that the current state of the homebound vector increasingly exceeds the reference state. The dramatic result is that the homing ants run away from home. This finding implies that the ants do not rely on cartographic information about the locations of nest and feeder (e.g. that the nest is always south of the feeder), but just behave according to what the state of their egocentric path integrator tells them.


Virtual alignment of pathology image series for multi-gigapixel whole slide images.
Interest in spatial omics is on the rise, but generation of highly multiplexed images remains challenging, due to cost, expertise, methodical constraints, and access to technology. An alternative approach is to register collections of whole slide images (WSI), generating spatially aligned datasets. WSI registration is a two-part problem, the first being the alignment itself and the second the application of transformations to huge multi-gigapixel images. To address both challenges, we developed Virtual Alignment of pathoLogy Image Series (VALIS), software which enables generation of highly multiplexed images by aligning any number of brightfield and/or immunofluorescent WSI, the results of which can be saved in the ome.tiff format. Benchmarking using publicly available datasets indicates VALIS provides state-of-the-art accuracy in WSI registration and 3D reconstruction. Leveraging existing open-source software tools, VALIS is written in Python, providing a free, fast, scalable, robust, and easy-to-use pipeline for registering multi-gigapixel WSI, facilitating downstream spatial analyses.


The Haitian Health Cluster Experience: A comparative evaluation of the professional communication response to the 2010 earthquake and the subsequent cholera outbreak.
The 2010 Haitian earthquake and consequent Cholera epidemic taxed the already fragile health system. A large number of humanitarian organizations participated in the disaster response and the health communication response was analysed. Health Cluster updates from both periods were analysed for contents with a World Health Organization draft check list for monitoring and evaluating the quality of epidemiological data contained in WHO and Health Cluster emergency reports. The Pan-American Health Organization Emergency Operations Centre reports from the Earthquake had the lowest score with an average score of 2.54/17 and the Health Cluster - Cholera reports had the highest average score of 11/17. There is a wide variety and quality of information published in terms of epidemiological information in emergency reports with a distinct difference found between the earthquake reporting and the cholera event. A comprehensive and modifiable template for emergency reporting could alleviate these differences and allow for improved reporting. Dhillon P, Annunziata G. The Haitian Health Cluster Experience: A comparative evaluation of the professional communication response to the 2010 earthquake and the subsequent cholera outbreak. PLOS Currents Disasters. 2012 Sep 5. doi: 10.1371/5014b1b407653.


A facilitated tracking and transcription mechanism of long-range enhancer function.
In the human epsilon-globin gene locus, the HS2 enhancer in the Locus Control Region regulates transcription of the embryonic epsilon-globin gene located over 10 kb away. The mechanism of long-range HS2 enhancer function was not fully established. Here we show that the HS2 enhancer complex containing the enhancer DNA together with RNA polymerase II (pol II) and TBP tracks along the intervening DNA, synthesizing short, polyadenylated, intergenic RNAs to ultimately loop with the epsilon-globin promoter. Guided by this facilitated tracking and transcription mechanism, the HS2 enhancer delivers pol II and TBP to the cis-linked globin promoter to activate mRNA synthesis from the target gene. An insulator inserted in the intervening DNA between the enhancer and the promoter traps the enhancer DNA and the associated pol II and TBP at the insulator site, blocking mid-stream the facilitated tracking and transcription mechanism of the enhancer complex, thereby blocking long-range enhancer function.


Regulation of Gγ-globin gene by ATF2 and its associated proteins through the cAMP-response element.
The upstream Gγ-globin cAMP-response element (G-CRE) plays an important role in regulating Gγ-globin expression through binding of ATF2 and its DNA-binding partners defined in this study. ATF2 knockdown resulted in a significant reduction of γ-globin expression accompanied by decreased ATF2 binding to the G-CRE. By contrast, stable ATF2 expression in K562 cells increased γ-globin transcription which was reduced by ATF2 knockdown. Moreover, a similar effect of ATF2 on γ-globin expression was observed in primary erythroid progenitors. To understand the role of ATF2 in γ-globin expression, chromatographically purified G-CRE/ATF2-interacting proteins were subjected to mass spectrometry analysis; major binding partners included CREB1, cJun, Brg1, and histone deacetylases among others. Immunoprecipitation assays demonstrated interaction of these proteins with ATF2 and in vivo GCRE binding in CD34(+) cells undergoing erythroid differentiation which was correlated with γ-globin expression during development. These results suggest synergism between developmental stage-specific recruitments of the ATF2 protein complex and expression of γ-globin during erythropoiesis. Microarray studies in K562 cells support ATF2 plays diverse roles in hematopoiesis and chromatin remodeling.


Higher dose rate Gamma Knife radiosurgery may provide earlier and longer-lasting pain relief for patients with trigeminal neuralgia.
Gamma Knife radiosurgery (GKRS) utilizes cobalt-60 as its radiation source, and thus dose rate varies as the fixed source decays over its half-life of approximately 5.26 years. This natural decay results in increasing treatment times when delivering the same cumulative dose. It is also possible, however, that the biological effective dose may change based on this dose rate even if the total dose is kept constant. Because patients are generally treated in a uniform manner, radiosurgery for trigeminal neuralgia (TN) represents a clinical model whereby biological efficacy can be tested. The authors hypothesized that higher dose rates would result in earlier and more complete pain relief but only if measured with a sensitive pain assessment tool. One hundred thirty-three patients were treated with the Gamma Knife Model 4C unit at a single center by a single neurosurgeon during a single cobalt life cycle from January 2006 to May 2012. All patients were treated with 80 Gy with a single 4-mm isocenter without blocking. Using an output factor of 0.87, dose rates ranged from 1.28 to 2.95 Gy/min. The Brief Pain Inventory (BPI)-Facial was administered before the procedure and at the first follow-up office visit 1 month from the procedure (mean 1.3 months). Phone calls were made to evaluate patients after their procedures as part of a retrospective study. Univariate and multivariate linear regression was performed on several independent variables, including sex, age in deciles, diagnosis, follow-up duration, prior surgery, and dose rate. In the short-term analysis (mean 1.3 months), patients' self-reported pain intensity at its worst was significantly correlated with dose rate on multivariate analysis (p = 0.028). Similarly, patients' self-reported interference with activities of daily living was closely correlated with dose rate on multivariate analysis (p = 0.067). A 1 Gy/min decrease in dose rate resulted in a 17% decrease in pain intensity at its worst and a 22% decrease in pain interference with activities of daily living. In longer-term follow-up (mean 1.9 years), GKRS with higher dose rates (> 2.0 Gy/min; p = 0.007) and older age in deciles (p = 0.012) were associated with a lower likelihood of recurrence of pain. Prior studies investigating the role of dose rate in Gamma Knife radiosurgical ablation for TN have not used validated outcome tools to measure pain preoperatively. Consequently, differences in pain outcomes have been difficult to measure. By administering pain scales both preoperatively as well as postoperatively, the authors have identified statistically significant differences in pain intensity and pain interference with activities of daily living when comparing higher versus lower dose rates. Radiosurgery with a higher dose rate results in more pain relief at the early follow-up evaluation, and it may result in a lower recurrence rate at later follow-up.


A randomized controlled trial evaluating antioxidant-essential oil gel as a treatment for gingivitis in orthodontic patients.
To evaluate the treatment effect of an antioxidant-essential oil gel on orthodontic patients with generalized gingivitis. The gel contains the essential oils menthol and thymol and the antioxidants ferulic acid and phloretin. Thirty patients from the university's orthodontic clinic were screened for gingivitis and randomly allocated into treatment and placebo-control groups. Each patient was evaluated at three orthodontic treatment visits (T1, T2, and T3). A periodontal examination, including probing depth (PD), bleeding on probing (BOP), gingival index (GI), and plaque index (PI) was performed at each visit. Between T1 and T2, patients were instructed to apply a topical gel (active or placebo) to their gingiva twice daily after brushing. From T2 to T3, patients were instructed to discontinue use of the gel. The treatment group showed statistically significant (P < .05) reductions of BOP (-13.6 percentage points) and GI (-0.14) between T1 and T2, and significant increases in BOP (13.3 percentage points) and GI (0.14) between T2 and T3. Except for an increase in the GI between T2 and T3, the control group showed no significant changes in BOP or GI over time. The only other significant changes that occurred pertained to the treatment group, which showed significant increases in PD (0.08 mm) and PI (0.18) between T2 and T3. Application of a topical antioxidant-essential oil gel is an effective means of reducing inflammation in orthodontic patients with gingivitis.


Mechanism of calcium gating in small-conductance calcium-activated potassium channels.
The slow afterhyperpolarization that follows an action potential is generated by the activation of small-conductance calcium-activated potassium channels (SK channels). The slow afterhyperpolarization limits the firing frequency of repetitive action potentials (spike-frequency adaptation) and is essential for normal neurotransmission. SK channels are voltage-independent and activated by submicromolar concentrations of intracellular calcium. They are high-affinity calcium sensors that transduce fluctuations in intracellular calcium concentrations into changes in membrane potential. Here we study the mechanism of calcium gating and find that SK channels are not gated by calcium binding directly to the channel alpha-subunits. Instead, the functional SK channels are heteromeric complexes with calmodulin, which is constitutively associated with the alpha-subunits in a calcium-independent manner. Our data support a model in which calcium gating of SK channels is mediated by binding of calcium to calmodulin and subsequent conformational alterations in the channel protein.


Muscle metaboreceptor modulation of cutaneous active vasodilation.
Isometric handgrip exercise in hyperthermia has been shown to reduce cutaneous vascular conductance (CVC) by inhibiting the cutaneous active vasodilator system. To identify whether this response was initiated by muscle metaboreceptors, in seven subjects two 3-min bouts of isometric handgrip exercise in hyperthermia were performed, followed by 2 min of postexercise ischemia (PEI). An index of forearm skin blood flow (laser-Doppler flowmetry) was measured on the contralateral arm at an unblocked site and at a site at which adrenergic vasoconstrictor function was blocked via bretylium iontophoresis to reveal active cutaneous vasodilator function unambiguously. Sweat rate was measured via capacitance hygrometry, CVC was indexed from the ratio of skin blood flow to mean arterial pressure and was expressed as a percentage of maximal CVC at that site. In normothermia, neither isometric exercise nor PEI affected CVC (P > 0.05). The first bout of isometric handgrip exercise in hyperthermia reduced CVC at control sites and this reduction persisted through PEI (pre-exercise: 59.8 +/- 5.4, exercise: 49.8 +/- 4.9, PEI: 49.7 +/- 5.3% of maximum; both P < 0.05), whereas there were no significant changes in CVC at the bretylium treated sites. The succeeding bout of isometric exercise in hyperthermia significantly reduced CVC at both untreated (pre-exercise: 59.0 +/- 4.8, exercise: 47.3 +/- 4.0, PEI: 50.1 +/- 4.1% of maximum; both P < 0.05) and bretylium treated sites (pre-exercise: 61.4 +/- 7.3, exercise: 50.6 +/- 5.1, PEI: 53.9 +/- 6.0% of maximum, both P < 0.05). At both sites, CVC during PEI was lower than during the pre-exercise period (P < 0.05). Sweat rate rose significantly during both bouts of isometric exercise and remained elevated during PEI. These data suggest that the reduction in CVC during isometric exercise in hyperthermia, including the inhibition of the active vasodilator system, is primarily mediated by muscle metaboreceptors, whereas central command or muscle mechanoreceptors have less influence.


A simple model for complex dynamical transitions in epidemics.
Dramatic changes in patterns of epidemics have been observed throughout this century. For childhood infectious diseases such as measles, the major transitions are between regular cycles and irregular, possibly chaotic epidemics, and from regionally synchronized oscillations to complex, spatially incoherent epidemics. A simple model can explain both kinds of transitions as the consequences of changes in birth and vaccination rates. Measles is a natural ecological system that exhibits different dynamical transitions at different times and places, yet all of these transitions can be predicted as bifurcations of a single nonlinear model.


Opioid-Induced Nausea Involves a Vestibular Problem Preventable by Head-Rest.
Opioids are indispensable for pain treatment but may cause serious nausea and vomiting. The mechanism leading to these complications is not clear. We investigated whether an opioid effect on the vestibular system resulting in corrupt head motion sensation is causative and, consequently, whether head-rest prevents nausea. Thirty-six healthy men (26.6 ± 4.3 years) received an opioid remifentanil infusion (45 min, 0.15 μg/kg/min). Outcome measures were the vestibulo-ocular reflex (VOR) gain determined by video-head-impulse-testing, and nausea. The first experiment (n = 10) assessed outcome measures at rest and after a series of five 1-Hz forward and backward head-trunk movements during one-time remifentanil administration. The second experiment (n = 10) determined outcome measures on two days in a controlled crossover design: (1) without movement and (2) with a series of five 1-Hz forward and backward head-trunk bends 30 min after remifentanil start. Nausea was psychophysically quantified (scale from 0 to 10). The third controlled crossover experiment (n = 16) assessed nausea (1) without movement and (2) with head movement; isolated head movements consisting of the three axes of rotation (pitch, roll, yaw) were imposed 20 times at a frequency of 1 Hz in a random, unpredictable order of each of the three axes. All movements were applied manually, passively with amplitudes of about ± 45 degrees. The VOR gain decreased during remifentanil administration (p<0.001), averaging 0.92 ± 0.05 (mean ± standard deviation) before, 0.60 ± 0.12 with, and 0.91 ± 0.05 after infusion. The average half-life of VOR recovery was 5.3 ± 2.4 min. 32/36 subjects had no nausea at rest (nausea scale 0.00/0.00 median/interquartile range). Head-trunk and isolated head movement triggered nausea in 64% (p<0.01) with no difference between head-trunk and isolated head movements (nausea scale 4.00/7.25 and 1.00/4.5, respectively). Remifentanil reversibly decreases VOR gain at a half-life reflecting the drug's pharmacokinetics. We suggest that the decrease in VOR gain leads to a perceptual mismatch of multisensory input with the applied head movement, which results in nausea, and that, consequently, vigorous head movements should be avoided to prevent opioid-induced nausea.


8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage.
Ten years on from the finishing of the human reference genome sequence, it remains unclear what fraction of the human genome confers function, where this sequence resides, and how much is shared with other mammalian species. When addressing these questions, functional sequence has often been equated with pan-mammalian conserved sequence. However, functional elements that are short-lived, including those contributing to species-specific biology, will not leave a footprint of long-lasting negative selection. Here, we address these issues by identifying and characterising sequence that has been constrained with respect to insertions and deletions for pairs of eutherian genomes over a range of divergences. Within noncoding sequence, we find increasing amounts of mutually constrained sequence as species pairs become more closely related, indicating that noncoding constrained sequence turns over rapidly. We estimate that half of present-day noncoding constrained sequence has been gained or lost in approximately the last 130 million years (half-life in units of divergence time, d1/2 = 0.25-0.31). While enriched with ENCODE biochemical annotations, much of the short-lived constrained sequences we identify are not detected by models optimized for wider pan-mammalian conservation. Constrained DNase 1 hypersensitivity sites, promoters and untranslated regions have been more evolutionarily stable than long noncoding RNA loci which have turned over especially rapidly. By contrast, protein coding sequence has been highly stable, with an estimated half-life of over a billion years (d1/2 = 2.1-5.0). From extrapolations we estimate that 8.2% (7.1-9.2%) of the human genome is presently subject to negative selection and thus is likely to be functional, while only 2.2% has maintained constraint in both human and mouse since these species diverged. These results reveal that the evolutionary history of the human genome has been highly dynamic, particularly for its noncoding yet biologically functional fraction.


Glutamate-induced depression of EPSP-spike coupling in rat hippocampal CA1 neurons and modulation by adenosine receptors.
The presence of high concentrations of glutamate in the extracellular fluid following brain trauma or ischaemia may contribute substantially to subsequent impairments of neuronal function. In this study, glutamate was applied to hippocampal slices for several minutes, producing over-depolarization, which was reflected in an initial loss of evoked population potential size in the CA1 region. Orthodromic population spikes recovered only partially over the following 60 min, whereas antidromic spikes and excitatory postsynaptic potentials (EPSPs) showed greater recovery, implying a change in EPSP-spike coupling (E-S coupling), which was confirmed by intracellular recording from CA1 pyramidal cells. The recovery of EPSPs was enhanced further by dizocilpine, suggesting that the long-lasting glutamate-induced change in E-S coupling involves NMDA receptors. This was supported by experiments showing that when isolated NMDA-receptor-mediated EPSPs were studied in isolation, there was only partial recovery following glutamate, unlike the composite EPSPs. The recovery of orthodromic population spikes and NMDA-receptor-mediated EPSPs following glutamate was enhanced by the adenosine A1 receptor blocker DPCPX, the A2A receptor antagonist SCH58261 or adenosine deaminase, associated with a loss of restoration to normal of the glutamate-induced E-S depression. The results indicate that the long-lasting depression of neuronal excitability following recovery from glutamate is associated with a depression of E-S coupling. This effect is partly dependent on activation of NMDA receptors, which modify adenosine release or the sensitivity of adenosine receptors. The results may have implications for the use of A1 and A2A receptor ligands as cognitive enhancers or neuroprotectants.


Unmet need for chronic disease and end-of-life care at urban family health centers in the Bronx, NY.
With population demographic shifts and as people live longer with progressive incurable illnesses, there will be a growing need for community-based chronic disease and end-of-life care services. Family practice sites could be strategic community-based settings in which to offer chronic disease and end-of-life care. This study determined whether two urban family health centers were meeting the chronic disease and end-of-life care needs of health center users, their families, and the local community. Using a brief structured interview instrument, we interviewed a convenience sample of 218 patients at two hospital-affiliated family health centers in the Bronx, NY, about their recent experiences with serious illness and death of immediate family members. In addition, we developed geographically defined medical service areas for each health center and compared the age distribution of residents of the geographic areas with that of actual health center users. Of 218 health center users, 18% (n=39) had experienced the death of an immediate family member in the past year, of whom only 8% (n=3) stated that their family member had received end-of-life/chronic disease care at the health center, and only 23% (n=9) knew that their family member could have received such care. Of 26% (n=56) of study subjects who reported having an immediate family member who was currently seriously ill, 18% (n=10) stated that their family members were receiving care at the health center, and 23% (n=13) knew that their family members could have received such care. Eighty percent (n=174) of study subjects stated that they themselves would be interested in receiving end-of life/ chronic disease care at the health center in the event that they needed such care. The age distribution of health center users significantly differed from that of the residents of the geographically defined medical service areas, with an underrepresentation of people over the age of 75 among the health center users. We identified a potential unmet need for chronic disease and end-of-life care among families of health center users and the larger community served by two family health centers in the Bronx, NY. Despite the frequent occurrence of serious illness and recent death among close family members, relatively small proportions of these family members had received care at the health centers, and few actual users were aware that such services could be provided there. Moreover, there was a significant demographic mismatch in age distribution between health center users and the surrounding community. These findings signal an important opportunity for the discipline of family medicine and its training programs to define and respond to the chronic disease and end-of-life care needs of patients and their families in community-based settings.


Pre-selection of most significant SNPS for the estimation of genomic breeding values.
The availability of a large amount of SNP markers throughout the genome of different livestock species offers the opportunity to estimate genomic breeding values (GEBVs). However, the estimation of many effects in a data set of limited size represent a severe statistical problem. A pre-selection of SNPS based on single regression may provide a reasonable compromise between accuracy of results, number of independent variables to be considered and computing requirements.A total of 595 and 618 SNPS were pre-selected using a simple linear regression for each SNP, based on phenotypes or polygenic EBVs, respectively, with an average distance of 9-10 cM between them. Chromosome four had the largest frequency of selected SNPS. Average correlations between GEBVs and TBVs were about 0.82 and 0.73 for the TRAINING generations when phenotypes or polygenic EBVs were considered as dependent variable, whereas they tend to decrease to 0.66 and 0.54 for the PREDICTION generations. The pre-selection of SNPs using the phenotypes as dependent variable together with a BLUP estimation of marker genotype effects using a variance contribution of each marker equal to sigma2a/nsnps resulted in a remarkable accuracy of GEBV estimation (0.77) in the PREDICTION generations.


Efficacy and safety of clindamycin-tretinoin gel versus clindamycin or tretinoin alone in acne vulgaris: a randomized, double-blind, vehicle-controlled study.
Topical combination therapy containing a retinoid and an antimicrobial is an effective treatment for acne vulgaris. To evaluate the efficacy and safety of a new topical formulation containing clindamycin phosphate 1.2% and tretinoin 0.025% solubilized in an aqueous-based gel (CT gel). 1,649 participants were randomized 2:2:2:1 to 12 weeks of double-blind treatment with CT gel, clindamycin, tretinoin, or vehicle gel administered once daily. Significantly more participants achieved 2-grade or greater improvement on the Investigator's Static Global Assessment score with CT gel versus clindamycin, tretinoin, or vehicle gel. CT gel produced a significantly greater reduction in absolute number of total lesions versus all other treatment groups, in total and noninflammatory lesions versus clindamycin, and in total and inflammatory lesions versus tretinoin. Local tolerability was similar to that of tretinoin alone; signs and symptoms of irritation were most notable at week 2. There were no more adverse events with CT gel than with tretinoin gel. CT gel is more effective than clindamycin or tretinoin monotherapy, with a safety and tolerability profile similar to that of tretinoin.


Apparent diffusion coefficient and sodium concentration measurements in human prostate tissue via hydrogen-1 and sodium-23 magnetic resonance imaging in a clinical setting at 3T.
Multiparametric magnetic resonance imaging (MRI) of the prostate involves morphologic and functional imaging techniques, which could potentially enable to distinguish between common benign prostate diseases, especially prostatitis and prostate cancer. The aim of this study was to determine the apparent diffusion coefficient (ADC) and the tissue sodium concentration (TSC) in 2 different regions of the human prostate, that is, the central gland (CG) and the peripheral gland (PG), by means of standard hydrogen-1 (H) MRI and quantitative sodium-23 (Na) MRI at 3 T to increase the spectrum of diagnostic parameters for prostate examinations. All measurements were performed on a 3-T clinical whole-body magnetic resonance (MR) scanner. Na MR images were acquired with density-adapted 3-dimensional radial sequence and isotropic voxel resolution of 5 × 5 × 5 mm. After approval by the institutional review board and informed consent were obtained, 8 healthy volunteers were included in this study. Diffusion-weighted imaging and T2-weighted images were also recorded and hence enabled the correlation of measured TSC values with current state-of-the-art H MRI techniques. The ADC in both subregions was measured to be at normal levels (CG, 1.19 [0.09] ×10 mm/s; PG, 1.54 [0.14] × 10 mm/s) in all 8 volunteers. Good spatial resolution of the Na images allowed for an easy identification of the same subregions from the Na MR images. In healthy adult volunteers (age, 29 [2] years), the TSC was measured lower in central (55 [15] mmol/L) and higher in peripheral (69 [16] mmol/L) prostate tissue. A correlation between the TSC and the ADC in the 2 subregions was found in the same volunteer group (Pearson correlation coefficient = 0.87). For the first time, TSC was spatially resolved in human prostate tissue by means of Na MRI. Interestingly, the herein found TSC values of ∼60 mmol/L were half as high as in a previously reported Na MRI study where prostate TSC was measured in 5-month-old mice. Future studies are required to determine the prostate TSC in cancer patients as well as in older volunteers. In conclusion, TSC can be measured in humans with sufficiently high spatial and temporal resolution at 3 T and could hence provide an additional noninvasive marker for the diagnosis of various prostate pathologies.


Characterization of a Protein Phosphatase Type-1 and a Kinase Anchoring Protein in Plasmodium falciparum.
With its multiple regulatory partners, the conserved Protein Phosphatase type-1 (PP1) plays a central role in many functions of the biology of eukaryotic cells, including Plasmodium falciparum. Here, we characterized a protein named PfRCC-PIP, as a major partner of PfPP1. We established its direct interaction in vitro and its presence in complex with PfPP1 in the parasite. The use of Xenopus oocyte model revealed that RCC-PIP can interact with the endogenous PP1 and act in synergy with suboptimal doses of progesterone to trigger oocyte maturation, suggesting a regulatory effect on PP1. Reverse genetic studies suggested an essential role for RCC-PIP since no viable knock-out parasites could be obtained. Further, we demonstrated the capacity of protein region containing RCC1 motifs to interact with the parasite kinase CDPK7. These data suggest that this protein is both a kinase and a phosphatase anchoring protein that could provide a platform to regulate phosphorylation/dephosphorylation processes.


Recombinant plasma gelsolin infusion attenuates burn-induced pulmonary microvascular dysfunction.
Reduced plasma concentrations of the extracellular actin-binding proteins gelsolin and Gc-globulin correlate with pulmonary failure and death in humans after injury. The purpose of this study was to investigate the role of plasma gelsolin in the pathophysiology of inflammation-induced lung injury. We postulated that plasma gelsolin levels decrease at an early time point after burn injury and that the intravenous infusion of gelsolin prevents burn-induced pulmonary microvascular dysfunction. Adult Sprague-Dawley rats were randomized to undergo a 40% body surface area thermal injury (Burn) or manipulation without burn (Sham). Plasma gelsolin and Gc-globulin concentrations were determined at various times during the first 6 days of injury by Western blotting. Other animals were randomized to receive either recombinant human gelsolin (0.078, 0.78, or 7.8 mg) or albumin (7.8 mg) before and 8 h after Burn or Sham. Twenty-four hours later, pulmonary microvascular permeability was assessed by measuring the capillary filtration by use of an isolated, perfused lung model. We found that plasma gelsolin levels of burn-injured rats decreased to 10% of normal levels within 12 h and remained below normal levels for up to 6 days postinjury. Gc-globulin values also fall, but to a lesser extent and only transiently. Treatment of burned animals with intravenous infusions of recombinant human gelsolin prevented the increase in pulmonary microvascular permeability that accompanies this injury. Our findings are consistent with the hypothesis that plasma gelsolin depletion contributes to the pathophysiology of pulmonary microvascular dysfunction during inflammation.


Person-centred pain management for the patient with acute abdominal pain: An ethnography informed by the Fundamentals of Care framework.
To explore and describe the impact of the organizational culture on and the patient-practitioner patterns of actions that contributes to or detract from successful pain management for the patient with acute abdominal pain (AAP) across the acute care pathway. Although pain management is a recognized human right, unmanaged pain continues to cause suffering and prolong hospital care. Unanswered questions about how to successfully manage pain relate to both organizational culture and individual practitioners' performance. Focused ethnography, applying the Developmental Research Sequence and the Fundamentals of Care framework. Participant observation and informal interviews (92 hr) were performed at one emergency department (ED) and two surgical wards at a University Hospital during April-November 2015. Data include 261 interactions between patients, aged ≥18 years seeking care for AAP at the ED and admitted to a surgical ward (N = 31; aged 20-90 years; 14 men, 17 women; 9 with communicative disabilities) and healthcare practitioners (N = 198). The observations revealed an organizational culture with considerable impact on how well pain was managed. Well-managed pain presupposed the patient and practitioners to connect in a holistic pain management including a trustful relationship, communication to share knowledge and individualized analgesics. Person-centred pain management requires an organization where patients and practitioners share their knowledge of pain and pain management as true partners. Leaders and practitioners should make small behavioural changes to enable the crucial positive experience of pain management.


Study on the decay mechanisms of surface plasmon coupling features with a light emitter through time-resolved simulations.
The transient behaviors of the dipole coupling with surface plasmon (SP) features in an Ag/dielectric-interface grating structure in order to understand the characteristics of those dipole-coupling features are demonstrated. In particular, the major decay mechanisms of those coupling features can be identified. For comparison, the time-resolved behaviors of the resonant surface plasmon polariton (SPP) coupling feature on a flat interface are also illustrated. Among the three major grating-induced SP-dipole coupling features, two of them are identified to be localized surface plasmons (LSPs). The third one is a grating-assisted SPP, which shows two decay components, corresponding to the first stage of SPP in-plane propagation and the second stage of coupling system decay. In all the dipole coupling features, metal dissipation can dominate the energy relaxation process, depending on the assumption of damping factor. All the dissipation rates are proportional to the assumed damping factor in the Drude model of the metal. The dissipation rates of the LSP and resonant SPP features are about the same as the damping rate, implying their local electron oscillation natures. The dissipation rate of the grating-assisted SSP feature is consistent with theoretical calculation. In the LSP features under study, dielectric-side emission is prominent. The coupled energy in the grating-assisted SPP feature can be efficiently stored in the coupling system due to its low emission efficiency and effective energy confinement through grating diffraction.


Abnormal gastroscopy findings were related to lower meridian energy.
According to the theories of Traditional Chinese Medicine (TCM), energy runs through 12 meridians longitudinally up and down the body. The study objectives were to compare the meridian energy between subjects with and without abnormal gastroscopy findings. We applied a cross-sectional and correlational research design. The study included 1,223 participants who had their health examinations at a university hospital in Taipei from 1st August 2005 through 31st August 2007. Meridian energy was examined using a meridian energy analysis device. The gastroscopy was operated by certified gastroenterologists. Participants with abnormal stomach and esophageal findings using gastroscopy had significantly lower mean meridian energy. There were no significant differences in meridian energy between participants with and without abnormal duodenum findings. When all of the meridians were examined individually, participants with abnormal findings in esophagus and stomach had significantly lower meridian energy in each of the meridians. The results of this study demonstrated that structural abnormality in the gastric area was related to lower meridian energy. Whether enhancing meridian energy could improve gastric and esophageal health merits further studies.


Type I interferons are associated with subclinical markers of cardiovascular disease in a cohort of systemic lupus erythematosus patients.
Systemic lupus erythematosus (SLE) patients have a striking increase in cardiovascular (CV) comorbidity not fully explained by the Framingham risk score. Recent evidence from in vitro studies suggests that type I interferons (IFN) could promote premature CV disease (CVD) in SLE. We assessed the association of type I IFN signatures with functional and anatomical evidence of vascular damage, and with biomarkers of CV risk in a cohort of lupus patients without overt CVD. Serum type I IFN activity (induction of five IFN-inducible genes; IFIGs) from 95 SLE patient and 38 controls was quantified by real-time PCR. Flow mediated dilatation (FMD) of the brachial artery and carotid intima media thickness (CIMT) were quantified by ultrasound, and coronary calcification by computed tomography. Serum vascular biomarkers were measured by ELISA. We evaluated the effect of type I IFNs on FMD, CIMT and coronary calcification by first applying principal components analysis to combine data from five IFIGs into summary components that could be simultaneously modeled. Three components were derived explaining 97.1% of the total IFIG variation. Multivariable linear regression was utilized to investigate the association between the three components and other covariates, with the outcomes of FMD and CIMT; zero-inflated Poisson regression was used for modeling of coronary calcification. After controlling for traditional CV risk factors, enhanced serum IFN activity was significantly associated with decreased endothelial function in SLE patients and controls (p<0.05 for component 3), increased CIMT among SLE patients (p<0.01 for components 1 and 2), and severity of coronary calcification among SLE patients (p<0.001 for component 3). Type I IFNs are independently associated with atherosclerosis development in lupus patients without history of overt CVD and after controlling for Framingham risk factors. This study further supports the hypothesis that type I IFNs promote premature vascular damage in SLE.


Dientamoeba fragilis, the Neglected Trichomonad of the Human Bowel.
Dientamoeba fragilis is a protozoan parasite of the human bowel, commonly reported throughout the world in association with gastrointestinal symptoms. Despite its initial discovery over 100 years ago, arguably, we know less about this peculiar organism than any other pathogenic or potentially pathogenic protozoan that infects humans. The details of its life cycle and mode of transmission are not completely known, and its potential as a human pathogen is debated within the scientific community. Recently, several major advances have been made with respect to this organism's life cycle and molecular biology. While many questions remain unanswered, these and other recent advances have given rise to some intriguing new leads, which will pave the way for future research. This review encompasses a large body of knowledge generated on various aspects of D. fragilis over the last century, together with an update on the most recent developments. This includes an update on the latest diagnostic techniques and treatments, the clinical aspects of dientamoebiasis, the development of an animal model, the description of a D. fragilis cyst stage, and the sequencing of the first D. fragilis transcriptome.


Accuracy of ultrasound-guided and palpation-guided knee injections by an experienced and less-experienced injector using a superolateral approach: a cadaveric study.
To evaluate the accuracy of ultrasound (US)-guided and palpation-guided knee injections by an experienced and a less-experienced clinician with use of a superolateral approach. Single-blinded, prospective study. Academic institution procedural skills laboratory. Twenty cadaveric knee specimens without trauma, surgery, or major deformity. US-guided and palpation-guided knee injections of colored liquid latex were performed in each specimen by an experienced and a less-experienced clinician with use of a superolateral approach. The order of injections was randomized. The specimens were subsequently dissected by a blinded investigator and assessed for accuracy. Accuracy was divided into 3 categories: (1) accurate (all of the injectate was within the joint), (2) partially accurate (some of the injectate was within the joint and some was within the periarticular tissues), and (3) inaccurate (none of the injectate was within the joint). The accuracy rates were calculated for each clinician and guidance method. US-guided knee injections that used a superolateral approach were 100% accurate for both clinicians. Palpation-guided knee injections that used a superolateral approach were significantly influenced by experience, with the less-experienced investigator demonstrating an accuracy rate of 55% (95% confidence interval = 34%-74%) and the more experienced investigator demonstrating an accuracy rate of 100% (95% confidence interval = 81%-100%). US-guided knee injections that use a superolateral approach are very accurate in a cadaveric model, whereas the accuracy of palpation-guided knee injections that use the same approach is variable and appears to be significantly influenced by clinician experience. These findings suggest that US guidance should be considered when one performs knee injections with a superolateral approach that require a high degree of accuracy.


The role of cryptochrome 2 in flowering in Arabidopsis.
We have investigated the genetic interactions between cry2 and the various flowering pathways in relation to the regulation of flowering by photoperiod and vernalization. For this, we combined three alleles of CRY2, the wild-type CRY2-Landsberg erecta (Ler), a cry2 loss-of-function null allele, and the gain-of-function CRY2-Cape Verde Islands (Cvi), with mutants representing the various photoreceptors and flowering pathways. The analysis of CRY2 alleles combined with photoreceptor mutants showed that CRY2-Cvi could compensate the loss of phyA and cry1, also indicating that cry2 does not require functional phyA or cry1. The analysis of mutants of the photoperiod pathway showed epistasis of co and gi to the CRY2 alleles, indicating that cry2 needs the product of CO and GI genes to promote flowering. All double mutants of this pathway showed a photoperiod response very much reduced compared with Ler. In contrast, mutations in the autonomous pathway genes were additive to the CRY2 alleles, partially overcoming the effects of CRY2-Cvi and restoring day length responsiveness. The three CRY2 alleles were day length sensitive when combined with FRI-Sf2 and/or FLC-Sf2 genes, which could be reverted when the delay of flowering caused by FRI-Sf2 and FLC-Sf2 alleles was removed by vernalization. In addition, we looked at the expression of FLC and CRY2 genes and showed that CRY2 is negatively regulated by FLC. These results indicate an interaction between the photoperiod and the FLC-dependent pathways upstream to the common downstream targets of both pathways, SOC1 and FT.


On the synthesis of brain-state-in-a-box neural models with application to associative memory.
In this article we present techniques for designing associative memories to be implemented by a class of synchronous discrete-time neural networks based on a generalization of the brain-state-in-a-box neural model. First, we address the local qualitative properties and global qualitative aspects of the class of neural networks considered. Our approach to the stability analysis of the equilibrium points of the network gives insight into the extent of the domain of attraction for the patterns to be stored as asymptotically stable equilibrium points and is useful in the analysis of the retrieval performance of the network and also for design purposes. By making use of the analysis results as constraints, the design for associative memory is performed by solving a constraint optimization problem whereby each of the stored patterns is guaranteed a substantial domain of attraction. The performance of the designed network is illustrated by means of three specific examples.


Predictors of clinical and social outcomes following involuntary hospital admission: a prospective observational study.
The Study aimed to assess clinical and social outcomes following involuntary admissions over 1 year and identify socio-demographic and clinical patient characteristics associated with more or less favourable outcomes. Seven hundred and seventy-eight involuntary patients admitted to one of 22 hospitals in England were assessed within the first week after admission and at 1 month, 3 month and 12 month follow-ups. Outcome criteria were symptom levels, global functioning, objective social outcomes, and subjective quality of life (SQOL). Baseline characteristics and patients' initial experience were tested as predictors. Symptom levels and global functioning improved moderately. Objective social outcomes showed a small, but statistically significant deterioration, and SQOL a small, but significant improvement at 1 year. In multivariable analyses, admission due to risk to oneself and receiving benefits predicted poorer symptom outcomes. Female gender and higher perceived coercion were associated with better objective social outcomes, whilst higher initial satisfaction with treatment predicted more positive SQOL at follow-ups. Over a 1-year period following involuntary hospital admission, patients on average showed only limited health and social gains. Different types of outcomes are associated with different predictor variables. Patients' initial experience of treatment, in the form of perceived coercion or satisfaction with treatment, has predictive value for up to a year following the admission.


Role of CD4+ T Cells in the Control of Viral Infections: Recent Advances and Open Questions.
CD4+ T cells orchestrate adaptive immune responses through their capacity to recruit and provide help to multiple immune effectors, in addition to exerting direct effector functions. CD4+ T cells are increasingly recognized as playing an essential role in the control of chronic viral infections. In this review, we present recent advances in understanding the nature of CD4+ T cell help provided to antiviral effectors. Drawing from our studies of natural human immunodeficiency virus (HIV) control, we then focus on the role of high-affinity T cell receptor (TCR) clonotypes in mediating antiviral CD4+ T cell responses. Last, we discuss the role of TCR affinity in determining CD4+ T cell differentiation, reviewing the at times divergent studies associating TCR signal strength to the choice of a T helper 1 (Th1) or a T follicular helper (Tfh) cell fate.


The effects of biological lubricating molecules on flexor tendon reconstruction in a canine allograft model in vivo.
Using allograft is an attractive alternative for flexor tendon reconstruction because of the lack of donor-site morbidity, and better matching to the intrasynovial environment. The purpose of this study was to use biological lubricant molecules to modify the graft surface to decrease adhesions and improve digit function. Twenty-eight flexor digitorum profundus tendons from the second and fifth digits of 14 dogs were lacerated and repaired to create a model with repair failure and scar digit for tendon reconstruction. Six weeks after the initial operation, the tendons were reconstructed with flexor digitorum profundus allograft tendons obtained from canine cadavers. One graft tendon in each dog was treated with saline as a control and the other was treated with carbodiimide-derivatized hyaluronic acid and gelatin plus lubricin. Six weeks postoperatively, digit function, graft mechanics, and biology were analyzed. Allograft tendons treated with carbodiimide-derivatized hyaluronic acid-lubricin had decreased adhesions at the proximal tendon/graft repair and within the flexor sheath, improved digit function, and increased graft gliding ability. The treatment also reduced the strength at the distal tendon-to-bone repair, but the distal attachment rupture rate was similar for both graft types. Histologic evaluation showed that viable cells migrated to the allograft, but these were limited to the tendon surface. Carbodiimide-derivatized hyaluronic acid-lubricin treatment of tendon allograft improves digit functional outcomes after flexor tendon reconstruction. However, delayed bone-to-tendon healing should be a caution. Furthermore, the cell infiltration into the allograft tendon substance should be a target for future studies, to shorten the allograft self-regeneration period.


A genealogical approach to quantifying lineage divergence.
We introduce a statistic, the genealogical sorting index (gsi), for quantifying the degree of exclusive ancestry of labeled groups on a rooted genealogy and demonstrate its application. The statistic is simple, intuitive, and easily calculated. It has a normalized range to facilitate comparisons among different groups, trees, or studies and it provides information on individual groups rather than a composite measure for all groups. It naturally handles polytomies and accommodates measures of uncertainty in phylogenetic relationships. We use coalescent simulations to explore the behavior of the gsi across a range of divergence times, with the mean value increasing to 1, the maximum value when exclusivity within a group reached monophyly. Simulations also demonstrate that the power to reject the null hypothesis of mixed genealogical ancestry increased markedly as sample size increased, and that the gsi provides a statistically more powerful measure of divergence than FST. Applications to data from published studies demonstrated that the gsi provides a useful way to detect significant exclusivity even when groups are not monophyletic. Although we describe this statistic in the context of divergence, it is more broadly applicable to quantify and assess the significance of clustering of observations in labeled groups on any tree.


Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture.
With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale bioreactors can experience setbacks due to, for example, bacteriophage blooms. By shaping microbial communities through mortality, horizontal gene transfer, and metabolic reprogramming, bacteriophages are important players in most ecosystems. Here, we analyzed an infected Methylomirabilis sp. bioreactor enrichment culture using (advanced) electron microscopy, viral metagenomics and bioinformatics. Electron micrographs revealed four different viral morphotypes, one of which was observed to infect Methylomirabilis cells. The infected cells contained densely packed ~55 nm icosahedral bacteriophage particles with a putative internal membrane. Various stages of virion assembly were observed. Moreover, during the bacteriophage replication, the host cytoplasmic membrane appeared extremely patchy, which suggests that the bacteriophages may use host bacterial lipids to build their own putative internal membrane. The viral metagenome contained 1.87 million base pairs of assembled viral sequences, from which five putative complete viral genomes were assembled and manually annotated. Using bioinformatics analyses, we could not identify which viral genome belonged to the Methylomirabilis- infecting bacteriophage, in part because the obtained viral genome sequences were novel and unique to this reactor system. Taken together these results show that new bacteriophages can be detected in anaerobic cultivation systems and that the effect of bacteriophages on the microbial community in these systems is a topic for further study.


Monte Carlo Simulations for the Analysis of Non-linear Parameter Confidence Intervals in Optimal Experimental Design.
Especially in biomanufacturing, methods to design optimal experiments are a valuable technique to fully exploit the potential of the emerging technical possibilities that are driving experimental miniaturization and parallelization. The general objective is to reduce the experimental effort while maximizing the information content of an experiment, speeding up knowledge gain in R&D. The approach of model-based design of experiments (known as MBDoE) utilizes the information of an underlying mathematical model describing the system of interest. A common method to predict the accuracy of the parameter estimates uses the Fisher information matrix to approximate the 90% confidence intervals of the estimates. However, for highly non-linear models, this method might lead to wrong conclusions. In such cases, Monte Carlo sampling gives a more accurate insight into the parameter's estimate probability distribution and should be exploited to assess the reliability of the approximations made through the Fisher information matrix. We first introduce the model-based optimal experimental design for parameter estimation including parameter identification and validation by means of a simple non-linear Michaelis-Menten kinetic and show why Monte Carlo simulations give a more accurate depiction of the parameter uncertainty. Secondly, we propose a very robust and simple method to find optimal experimental designs using Monte Carlo simulations. Although computational expensive, the method is easy to implement and parallelize. This article focuses on practical examples of bioprocess engineering but is generally applicable in other fields.