Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitric-oxide Synthase Output State

Mammalian nitric-oxide synthases are large modular enzymes that evolved from independently expressed ancestors. Calmodulin-controlled isoforms are signal generators; calmodulin activates electron transfer from NADPH through three reductase domains to an oxygenase domain. Structures of the reductase unit and its homologs show FMN and FAD in contact but too isolated from the protein surface to permit exit of reducing equivalents. To study states in which FMN/heme electron transfer is feasible, we designed and produced constructs including only oxygenase and FMN binding domains, eliminating strong internal reductase complex interactions. Constructs for all mammalian isoforms were expressed and purified as dimers. All synthesize NO with peroxide as the electron donor at rates comparable with corresponding oxygenase constructs. All bind cofactors nearly stoichiometrically and have native catalytic sites by spectroscopic criteria. Modest differences in electrochemistry versus independently expressed heme and FMN binding domains suggest interdomain interactions. These interactions can be convincingly demonstrated via calmodulin-induced shifts in high spin ferriheme EPR spectra and through mutual broadening of heme and FMNH· radical signals in inducible nitricoxide synthase constructs. Blue neutral FMN semiquinone can be readily observed; potentials of one electron couple (in inducible nitric-oxide synthase oxygenase FMN, FMN oxidized/semiquione couple =+70 mV, FMN semiquinone/hydroquinone couple =–180 mV, and heme =–180 mV) indicate that FMN is capable of serving as a one electron heme reductant. The construct will serve as the basis for future studies of the output state for NADPH derived reducing equivalents.
Soil moisture retrieval from remotely sensed data: Neural network approach versus Bayesian method

Neural network (NN) approaches and statistical methods, based on a Bayesian procedure, are applied and compared in soil moisture (SM) retrieval from remotely sensed data. The principles and the practical implementations of Bayesian procedures and NNs are briefly discussed in terms of the advantages and disadvantages of each. Experimental tests are carried out by using the same set of training and test data for each method. The methodologies have been applied to two sets of data to retrieve SM from bare soils and to verify their accuracy. One data set contains scatterometer and radiometer data acquired on a variety of agricultural fields in different polarizations, frequencies, and incidence angles. The other is made up of five experiments carried out with a C-band scatterometer on rough and smooth soils at different polarizations and incidence angles. There are significant similarities in the performance of each method; they both retrieve the same features and trends in the analyzed data sets. Algorithm performances change according to SM level and data configuration. The main difficulties are found in retrieving low SM values, and in this case, the error on estimates is reduced when the data with two polarizations or two incidence angles are inserted in the inversion procedure. One major difference between the methodologies is that the NN performance improves, with respect to the Bayesian method, when more inputs are presented as two polarizations or two incidence angles in the training phase.
What effect does Distributed Version Control have on OSS project organization?

Many Open Source Software (OSS) projects are moving form Centralized Version Control (CVC) to Distributed Version Control (DVC). The effect of this shift on project organization and developer collaboration is not well understood. In this paper, we use a theoretical argument to evaluate the appropriateness of using DVC in the context of two very common organization forms in OSS: a dictatorship and a peer group. We find that DVC facilitates large hierarchical communities as well as smaller groups of developers, while CVC allows for consensus-building by a peer group. We also find that the flexibility of DVC systems allows for diverse styles of developer collaboration. With CVC, changes flow up and down (and publicly) via a central repository. In contrast, DVC facilitates collaboration in which work output can flow sideways (and privately) between collaborators, with no repository being inherently more important or central. These sideways flows are a relatively new concept. Developers on the Linux project, who tend to be experienced DVC users, cluster around “sandboxes:” repositories where developers can work together on a particular topic, isolating their changes from other developers. In this work, we focus on two large, mature OSS projects to illustrate these findings. However, we suggest that social media sites like GitHub may engender other original styles of collaboration that deserve further study.
Psychosocial Perspectives and the Issue of Prevention in Childhood Obesity

A dramatic increase in childhood overweight/obesity has been recognized globally over the past 50 years. This observed increase may reflect genetic, as well as psychological, environmental, and socio-cultural influences. In the first part of this review, we present an updated summary of the psychosocial factors associated with this change and discuss possible ways in which they operate. Among these factors, lower socio economic status (in both industrialized and non-industrialized countries), being female, belonging to a minority group, and being exposed to adverse life events may all be associated with a greater risk of childhood overweight/obesity. These influences may be mediated via a variety of mechanisms, in particular above-average food intake of low nutritional quality and reduction in physical activity. Other important psychosocial mediators include the influence of the family and peer environment, and exposure to the media. In the second part of the review, we discuss the potential of psychosocial prevention programs to intervene in the processes involved in the rise of childhood overweight/obesity. Two points are emphasized. First, prevention programs should be multidisciplinary, combining the knowledge of experts from different professions, and taking into consideration the important role of the family environment and relevant influential social organizations, particularly school. Second, effective change is unlikely to occur without large-scale programs carried out on a public policy level.
Peer mentorship program on HIV/AIDS knowledge, beliefs, and prevention attitudes among orphaned adolescents: an evidence based practice

Adolescents and young adults in sub-Saharan Africa (SSA) are particularly vulnerable to human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) infection. Adolescents orphaned as a direct result of HIV/AIDS are at an elevated risk of acquiring HIV/AIDS and other sexually transmitted infections. However, limited empirical evidence exists on HIV knowledge and prevention programs, especially those designed to address HIV information gaps among adolescents. This study evaluates the effect of a peer mentorship program provided in addition to other supportive services on HIV/AIDS knowledge, beliefs, and prevention attitudes, among school-going orphaned adolescents in southern Uganda. We utilize data from the Bridges to the Future Study, a 5-year longitudinal randomized experimental study funded by the National Institute of Child Health and Human Development. Out of the 1410 adolescents enrolled in the study (average age = 12.7 at study initiation), 855 of them participated in a nine-session, curriculum based peer mentorship program. We analyzed data collected at baseline and 12-months post intervention initiation. The results from bivariate and regression analysis indicate that, controlling for socioeconomic characteristics, adolescents who participated in a peer mentorship program were more likely than non-participants to report increased scores on HIV/AIDS knowledge; better scores on desired HIV/AIDS-related beliefs ; and better scores on HIV/AIDS prevention attitudes . Overall, the study findings point to the potential role of a peer mentorship program in promoting the much-desired HIV/AIDS knowledge, beliefs, and prevention attitudes among orphaned adolescents. Future programs and policies that support AIDS-orphaned adolescents in sub-Saharan Africa should consider incorporating peer mentoring programs that provide correct, age, and culturally appropriate HIV information to help protect orphaned adolescents and reduce the risk of HIV infections.
Reduced in vivo oxidative stress following 5‐methyltetrahydrofolate supplementation in patients with early‐onset thrombosis and 677TT methylenetetrahydrofolate reductase genotype

The protective role of folate in vascular disease has been related to antioxidant effects. In 45 patients with previous early‐onset (at age <50 years) thrombotic episodes and the 677TT methylenetetrahydrofolate reductase genotype, we evaluated the effects of a 28d‐course (15 mg/d) of 5‐methyltetrahydrofolate (MTHF) on homocysteine metabolism and on in vivo generation of 8‐iso‐prostaglandin F2α (8‐iso‐PGF2α), a reliable marker of oxidative stress. At baseline, patients’ fasting total homocysteine (tHcy) was 11·5 μmol/l (geometric mean) and urinary excretion of 8‐iso‐PGF2α was 304 pg/mg creatinine, with the highest metabolite levels in the lowest quartile of plasma folate distribution (P < 0·05). After 5‐MTHF supplementation, plasma folate levels increased approximately 13‐fold (P < 0·0001 versus baseline); tHcy levels (6·7 μmol/l, P < 0·0001) and urinary 8‐iso‐PGF2α (254 pg/mg creatinine, P < 0·001) were both significantly lowered, their reduction being proportional to baseline values (r = 0·98 and r = 0·77, respectively) and maximal in patients with the lowest pre‐supplementation folate levels (P < 0·05). The effects on folate (P < 0·0001) and tHcy (P = 0·0004) persisted for at least up to 2 months after withdrawing 5‐MTHF. In parallel with long‐lasting tHcy‐lowering effects, a short‐course 5‐MTHF supplementation reduces in vivo formation of 8‐iso‐PGF2α in this population, supporting the antioxidant protective effects of folate in vascular disease.
Early Prediction of Gestational Diabetes Mellitus in Vietnam

OBJECTIVE We aimed to compare the discriminative power of prognostic models for early prediction of women at risk for the development of gestational diabetes mellitus (GDM) using four currently recommended diagnostic criteria based on the 75-g oral glucose tolerance test (OGTT). We also described the potential effect of application of the models into clinical practice. RESEARCH DESIGN AND METHODS A prospective cross-sectional study of 2,772 pregnant women was conducted at a referral maternity center in Vietnam. GDM was determined by the American Diabetes Association (ADA), International Association of the Diabetes and Pregnancy Study Groups (IADPSG), Australasian Diabetes in Pregnancy Society (ADIPS), and World Health Organization (WHO) criteria. Prognostic models were developed using the Bayesian model averaging approach, and discriminative power was assessed by area under the curve. Different thresholds of predicted risk of developing GDM were applied to describe the clinical impact of the diagnostic criteria. RESULTS The magnitude of GDM varied substantially by the diagnostic criteria: 5.9% (ADA), 20.4% (IADPSG), 20.8% (ADIPS), and 24.3% (WHO). The ADA prognostic model, consisting of age and BMI at booking, had the best discriminative power (area under the curve of 0.71) and the most favorable cost-effective ratio if implemented in clinical practice. Selective screening of women for GDM using the ADA model with a risk threshold of 3% gave 93% sensitivity for identification of women with GDM with a 27% reduction in the number of OGTTs required. CONCLUSIONS A simple prognostic model using age and BMI at booking could be used for selective screening of GDM in Vietnam and in other low- and middle-income settings.
Comparing Practical Knowledge Storage of Deaf and Hearing Teachers of Students Who Are Deaf or Hard of Hearing

Especially in the education of students who are deaf or hard of hearing, teachers' practical knowledge storage is almost never measured. The Survey of Practical Knowledge was used to compare the practical knowledge storage of deaf and hearing teachers of these students. Surveyed were 48 deaf and 115 hearing individuals at the preservice and in-service experience levels. Practical knowledge storage was defined as images, rules of practice, and practical principles. Results indicate that deaf teachers tend to view students as equals but are more likely to emphasize control over classroom behavior than hearing teachers. Hearing teachers tend to stress efforts to engage students in subject matter by providing variety and relating it to life experiences. Given the trend toward high-stakes testing of teachers, further research is encouraged on role differences between deaf and hearing teachers working with students who are deaf or hard of hearing.
Cohesin regulates VSG monoallelic expression in trypanosomes

Antigenic variation allows Trypanosoma brucei to evade the host immune response by switching the expression of 1 out of ∼15 telomeric variant surface glycoprotein (VSG) expression sites (ESs). VSG ES transcription is mediated by RNA polymerase I in a discrete nuclear site named the ES body (ESB). However, nothing is known about how the monoallelic VSG ES transcriptional state is maintained over generations. In this study, we show that during S and G2 phases and early mitosis, the active VSG ES locus remains associated with the single ESB and exhibits a delay in the separation of sister chromatids relative to control loci. This delay is dependent on the cohesin complex, as partial knockdown of cohesin subunits resulted in premature separation of sister chromatids of the active VSG ES. Cohesin depletion also prompted transcriptional switching from the active to previously inactive VSG ESs. Thus, in addition to maintaining sister chromatid cohesion during mitosis, the cohesin complex plays an essential role in the correct epigenetic inheritance of the active transcriptional VSG ES state.
Distributed fault-tolerant classification in wireless sensor networks

Fault-tolerance and data fusion have been considered as two fundamental functions in wireless sensor networks. In this paper, we propose a novel approach for distributed multiclass classification using a fault-tolerant fusion rule for wireless sensor networks. Binary decisions from local sensors, possibly in the presence of faults, are forwarded to the fusion center that determines the final classification result. Classification fusion in our approach is implemented via error correcting codes to incorporate fault-tolerance capability. This new approach not only provides an improved fault-tolerance capability but also reduces computation time and memory requirements at the fusion center. Code matrix design is essential for the design of such systems. Two efficient code matrix design algorithms are proposed in this paper. The relative merits of both algorithms are also studied. We also develop sufficient conditions for asymptotic detection of the correct hypothesis by the proposed approach. Performance evaluation of the proposed approach in the presence of faults is provided. These results show significant improvement in fault-tolerance capability as compared with conventional parallel fusion networks.
Pathways involved in sasang constitution from genome-wide analysis in a Korean population.

OBJECTIVE Sasang constitution (SC) medicine, a branch of Korean traditional medicine, classifies the individual into one of four constitutional types (Taeum, TE; Soeum, SE; Soyang, SY; and Taeyang, TY) based on physiologic characteristics. The authors of the current article recently reported individual genetic elements associated with SC types via genome-wide association (GWA) analysis. However, to understand the biologic mechanisms underlying constitution, a comprehensive approach that combines individual genetic effects was applied. DESIGN Genotypes of 1222 subjects of defined constitution types were measured for 341,998 genetic loci across the entire genome. The biologic pathways associated with SC types were identified via GWA analysis using three different algorithms--namely, the Z-static method, a restandardized gene set assay, and a gene set enrichment assay. RESULTS Distinct pathways were associated (p<0.05) with each constitution type. The TE type was significantly associated with cytoskeleton-related pathways. The SE type was significantly associated with cardio- and amino-acid metabolism-related pathways. The SY type was associated with enriched melanoma-related pathways. TY subjects were excluded because of the small size of that sample. Among these functionally related pathways, core-node genes regulating multiple pathways were identified. TJP1, PTK2, and SRC were selected as core-nodes for TE; RHOA, and MAOA/MAOB for SE; and GNAO1 for SY (p<0.05), respectively. CONCLUSIONS The current authors systematically identified the biologic pathways and core-node genes associated with SC types from the GWA study; this information should provide insights regarding the molecular mechanisms inherent in constitutional pathophysiology.
Simultaneous Recognition and Homography Extraction of Local Patches with a Simple Linear Classifier

CAMP | Computer Aided Medical Procedures | http://campar.cs. tum.edu | Technische Universitat Munchen | TUM References [1] Hinterstoisser, S. et al.: Online Learning of Patch Perspective Rectification for Efficient Object Detection, CVPR 2008, Anchorage, Alaska, USA. [2] Ozuysal, M. et al.: Fast Keypoint Recognition in Ten Lines of Code, CVPR 2007, Minneapolis, Minnesota, USA. [3] Jurie, F. et al.: Hyperplane approximation for template matching, PAMI, 2002 Problem •Previous approaches (Leopar1 [Same authors,CVPR'08]) showed that we can efficiently estimate the 3D pose of a poorly textured object by learning the patch appearance. Leopar1 is performed in 4 steps: (a) Pre-classify feature points with e.g. Ferns2 (b) Rough orientation estimation of the patch with respect to the feature point identity (c) Rectification refinement by applying a Template Matching algorithm3 (d) Outlier removal by simple correlation measure Leopar1 gives much better results concerning the accuracy and repeatability of the pose than affine region detectors but still suffers from a decreasing robustness towards large viewpoint changes. Reasons for that: • Error-prone pre-classification of initial feature points in (a) (by Ferns2) without taking into account the pose of the patch • Rough estimation of the pose of the patch in (b) is limited to orientations
Improvement of Endurance of DMD Animal Model Using Natural Polyphenols

Duchenne muscular dystrophy (DMD), the most common form of muscular dystrophy, is characterized by muscular wasting caused by dystrophin deficiency that ultimately ends in force reduction and premature death. In addition to primary genetic defect, several mechanisms contribute to DMD pathogenesis. Recently, antioxidant supplementation was shown to be effective in the treatment of multiple diseases including muscular dystrophy. Different mechanisms were hypothesized such as reduced hydroxyl radicals, nuclear factor-κB deactivation, and NO protection from inactivation. Following these promising evidences, we investigated the effect of the administration of a mix of dietary natural polyphenols (ProAbe) on dystrophic mdx mice in terms of muscular architecture and functionality. We observed a reduction of muscle fibrosis deposition and myofiber necrosis together with an amelioration of vascularization. More importantly, the recovery of the morphological features of dystrophic muscle leads to an improvement of the endurance of treated dystrophic mice. Our data confirmed that ProAbe-based diet may represent a strategy to coadjuvate the treatment of DMD.
Psychoeducational Characteristics of Children with Hypohidrotic Ectodermal Dysplasia

Objective. Hypohidrotic ectodermal dysplasia (HED) is an X-linked hereditary disorder characterized by hypohidrosis, hypotrichosis, and anomalous dentition. Estimates of up to 50% of affected children having intellectual disability are controversial. Method. In a cross-sectional study, 45 youth with HED (77% males, mean age 9.75 years) and 59 matched unaffected controls (70% males, mean age 9.79 years) were administered the Kaufman Brief Intelligence Test and the Kaufman Test of Educational Achievement, and their parents completed standardized neurodevelopmental and behavioral measures, educational, and health-related information regarding their child, as well as standardized and nonstandardized data regarding socioeconomic information for their family. Results. There were no statistically significant differences between the two groups in intelligence quotient composite and educational achievement scores, suggesting absence of learning disability in either group. No gender differences within or between groups were found on any performance measures. Among affected youth, parental education level correlated positively with (1) cognitive vocabulary scores and cognitive composite scores; (2) educational achievement for mathematics, reading, and composite scores. Conclusion. Youth affected with HED and unaffected matched peers have similar profiles on standardized measures of cognition, educational achievement, and adaptive functioning although children with HED may be at increased risk for ADHD.
Cutting Edge: Cyclooxygenase-2 Activation Suppresses Th1 Polarization in Response to Helicobacter pylori 1

Helicobacter pylori infection causes a Th1-driven mucosal immune response. Cyclooxygenase (COX)-2 is up-regulated in lamina propria mononuclear cells in H. pylori gastritis. Because COX-2 can modulate Th1/Th2 balance, we determined whether H. pylori activates COX-2 in human PBMCs, and the effect on cytokine and proliferative responses. There was significant up-regulation of COX-2 mRNA and PGE2 release in response to H. pylori preparations. Addition of COX-2 inhibitors or an anti-PGE2 Ab resulted in a marked increase in H. pylori-stimulated IL-12 and IFN-γ production, and a decrease in IL-10 levels. Addition of PGE2 or cAMP, the second messenger activated by PGE2, had the opposite effect. Similarly, stimulated cell proliferation was increased by COX-2 inhibitors or anti-PGE2 Ab, and was decreased by PGE2. Our findings indicate that COX-2 has an immunosuppressive role in H. pylori gastritis, which may protect the mucosa from severe injury, but may also contribute to the persistence of the infection.
Tight regulation of the unfolded protein sensor Ire1 by its intramolecularly antagonizing subdomain

Accumulation of unfolded proteins in the endoplasmic reticulum (ER) accompanies ER stress and causes the type‐I transmembrane protein Ire1 (also known as ERN1) to trigger the unfolded protein response (UPR). When dimerized, the core stress‐sensing region (CSSR) of Ire1 directly captures unfolded proteins and forms a high‐order oligomer, leading to clustering and activation of Ire1. The CSSR is N‐terminally flanked by an intrinsically disordered subdomain, which we previously named Subregion I, in Saccharomyces cerevisiae Ire1. In this study, we describe tight repression of Ire1 activity by Subregion I under conditions of no or weak stress. Weak hyperactivation of an Ire1 mutant lacking Subregion I slightly retarded growth of yeast cells cultured under unstressed conditions. Fungal Ire1 orthologs and the animal Ire1 family protein PERK (also known as EIF2AK3) carry N‐terminal intrinsically disordered subdomains with a similar structure and function to that of Subregion I. Our observations presented here cumulatively indicate that Subregion I is captured by the CSSR as an unfolded protein substrate. This intramolecular subdomain interaction is likely to compromise self‐association of the CSSR, explaining why Subregion I can suppress Ire1 activity when ER‐accumulated unfolded proteins are not abundant.