Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying target sites for cooperatively binding factors

MOTIVATION Transcriptional activation in eukaryotic organisms normally requires combinatorial interactions of multiple transcription factors. Though several methods exist for identification of individual protein binding site patterns in DNA sequences, there are few methods for discovery of binding site patterns for cooperatively acting factors. Here we present an algorithm, Co-Bind (for COperative BINDing), for discovering DNA target sites for cooperatively acting transcription factors. The method utilizes a Gibbs sampling strategy to model the cooperativity between two transcription factors and defines position weight matrices for the binding sites. Sequences from both the training set and the entire genome are taken into account, in order to discriminate against commonly occurring patterns in the genome, and produce patterns which are significant only in the training set. RESULTS We have tested Co-Bind on semi-synthetic and real data sets to show it can efficiently identify DNA target site patterns for cooperatively binding transcription factors. In cases where binding site patterns are weak and cannot be identified by other available methods, Co-Bind, by virtue of modeling the cooperativity between factors, can identify those sites efficiently. Though developed to model protein-DNA interactions, the scope of Co-Bind may be extended to combinatorial, sequence specific, interactions in other macromolecules. AVAILABILITY The program is available upon request from the authors or may be downloaded from http://ural.wustl. edu.
Fault Diagnosis Graph of time Petri nets

This paper proposes an online approach for the fault diagnosis for time discrete event systems, which are modeled by time Petri net. The observation is given by a subset of transitions whose occurrence is always observable. Faults correspond to a subset of the transitions whose firing are not observable. According to the most of the literature on discrete event systems, we define three fault states, namely N, F and U, corresponding to normal, fault and uncertain states, respectively. The proposed approach use a Fault Diagnosis Graph (FDG). It is adapted from state class graph by keeping only the necessary information for computation of the fault states and removing the unnecessary states. Some algorithms to compute after each observation only part of the FDG required to update the diagnosis states are given.
Endogenous Liquidity and the Business Cycle

I study an economy where asymmetric information about the quality of capital endogenously determines liquidity. Liquid funds are key to relaxing financial constraints on investment and employment. These funds are obtained by selling capital or using it as collateral. Liquidity is determined by balancing the costs of obtaining liquidity under asymmetric information against the benefits of relaxing financial constraints. Aggregate fluctuations follow increases in the dispersion of capital quality, which raise the cost of obtaining liquidity. An estimated version of the model can generate patterns for quantities and credit conditions similar to the Great Recession.
Intrinsic Amygdala–Cortical Functional Connectivity Predicts Social Network Size in Humans

Using resting-state functional magnetic resonance imaging data from two independent samples of healthy adults, we parsed the amygdala's intrinsic connectivity into three partially distinct large-scale networks that strongly resemble the known anatomical organization of amygdala connectivity in rodents and monkeys. Moreover, in a third independent sample, we discovered that people who fostered and maintained larger and more complex social networks not only had larger amygdala volumes, but also amygdalae with stronger intrinsic connectivity within two of these networks: one putatively subserving perceptual abilities and one subserving affiliative behaviors. Our findings were anatomically specific to amygdalar circuitry in that individual differences in social network size and complexity could not be explained by the strength of intrinsic connectivity between nodes within two networks that do not typically involve the amygdala (i.e., the mentalizing and mirror networks), and were behaviorally specific in that amygdala connectivity did not correlate with other self-report measures of sociality.
Effect of Interleaved Non-Woven Carbon Tissue on Interlaminar Fracture Toughness of Laminated Composites: Part I – Mode II

A study on the Mode II interlaminar fracture characteristics of non-woven carbon tissue (NWCT) interleaved composites was carried out using the endnotched-flexure (ENF) test. The NWCT interleaved composites were made by interleaving NWCT-prepreg between CFRP layers. CFRP specimen [024] as well as NWCT interleaved specimen [012/T/012] were prepared to compare the characteristics. The symbol ‘‘/T/’’ means that the NWCT layeris located at the 0/0 mid-plane of the interleaved specimen. Three kinds of interlaminar cracks, which have different positions in the NWCT layer, were introduced to the interleaved specimen. The ENF testing results were analyzed using the normal distribution. The mean G IIC of the interleaved specimen with an upper crack is about 26% higher than that of the CFRP specimen due to a blunt shape of crack tip by Teflon film in the NWCT layer. The mean G IIC of the interleaved specimens with a center crack and a lower crack is about 260 and 205% higherthan that of the CFRP specimen due to the short fiber bridging from in-plain random short carbon fibers in the NWCT layer, respectively. The fracture surfaces of the specimens and the fracture process on the specimen side-sections were observed with an optical microscope and a scanning electron microscope, and then they were analyzed for the failure mechanism. The size and spacing of hackles on the fracture surface are affected by both the length and fiber volume of short carbon fibers in the NWCT layer.
A common NOS1AP genetic polymorphism is associated with increased cardiovascular mortality in users of dihydropyridine calcium channel blockers.

AIM Recently, a polymorphism in the NOS1AP gene (rs10494366), a regulator of neuronal nitric oxide synthase (nNOS), was associated with QTc prolongation. Both nNOS and calcium channel blockers (CCBs) regulate intracellular calcium levels and have an important role in cardiovascular homeostasis. The aim was to investigate whether this polymorphism is associated with cardiovascular mortality in users of CCBs. METHODS The data from the Rotterdam study, a population-based closed cohort study of Caucasian individuals of > or =55 years of age, were used. We identified 1113 participants in the Rotterdam Study who were prescribed CCBs for the first time between 1991 and 2005. All-cause and cardiovascular mortality was assessed in participants who were prescribed CCBs with different NOS1AP rs10494366 genotypes using Cox proportional hazard models. RESULTS In participants starting on dihydropyridine CCBs (amlodipine, nifedipine and others) all-cause mortality (n = 79) risks were higher in participants with the TG [hazard ratio (HR) 2.57, 95% confidence interval (CI) 1.24, 5.34] or the GG genotype (HR 3.18, 95% CI 1.18, 8.58) than in participants with the referent TT genotype. Cardiovascular mortality (n = 54) risks were 3.51 (95% CI 1.41, 8.78) for the TG genotype and 6.00 (95% CI 1.80, 20.0) for the GG genotype. No differences in all-cause mortality or cardiovascular mortality were seen in participants starting with the nondihydropyridine CCBs verapamil or diltiazem. CONCLUSION The minor G allele of rs10494366 in the NOS1AP gene is associated with increased all-cause and cardiovascular mortality in Caucasian users of dihydropyridine CCBs. The mechanism underlying the observed association is unknown.
Effect of submucosal midazolam on behavior and physiologic response when combined with oral chloral hydrate and nitrous oxide sedation.

PURPOSE This study was designed to examine the efficacy and safety of submucosal (SM) midazolam and oral chloral hydrate (CH) when used for pediatric conscious sedation in a clinical dental environment. METHODS Twenty children ages 32 to 63 months participated in this institutionally approved study. Selection criteria included good health (ASA I), 2 to 5 years of age, uncooperative behavior, and the need for multiple restorative visits. In a double-blind crossover design, patients were randomly assigned to receive either oral CH (50 mg/kg) and SM midazolam (0.2 mg/kg), or oral CH (50 mg/kg) and SM saline placebo on their first sedation visit. On the second sedation visit, the patient received the opposite drug regimen than the first visit. Nitrous oxide (50%) was used during each sedation visit. Behavior response was rated as quiet (Q), crying (C), movement (M), or struggling (S) every 2.5 minutes through 40 minutes of operative procedures. Sedations were monitored using a capnograph, pulse oximeter, an automated blood pressure cuff, and precordial stethoscope. Respiratory rate (RR), heart rate (HR), and blood pressure (BP) were evaluated for each procedure. Data was analyzed using ANOVA and multinomial repeated-measures logistic regression. RESULTS Analysis showed a significant difference in behavior during sedation across drug regimen (chi-square = 55.6, df = 3, P < .0001). Patients given SM midazolam in addition to oral CH showed increased Q rating and decreased C, M, and S ratings. RR, BP, and HR for both groups remained within the normal values for 2- to 5-year-olds. CONCLUSIONS SM midazolam improved the quality of sedation without compromising safety. Quiet behavior was increased and struggling behavior was decreased. In addition, mean HR, RR, and BP analysis did not deviate from the norm for this age group.
Characterization of a Spontaneous Nonmagnetic Mutant of Magnetospirillum gryphiswaldense Reveals a Large Deletion Comprising a Putative Magnetosome Island

ABSTRACT Frequent spontaneous loss of the magnetic phenotype was observed in stationary-phase cultures of the magnetotactic bacterium Magnetospirillum gryphiswaldense MSR-1. A nonmagnetic mutant, designated strain MSR-1B, was isolated and characterized. The mutant lacked any structures resembling magnetosome crystals as well as internal membrane vesicles. The growth of strain MSR-1B was impaired under all growth conditions tested, and the uptake and accumulation of iron were drastically reduced under iron-replete conditions. A large chromosomal deletion of approximately 80 kb was identified in strain MSR-1B, which comprised both the entire mamAB and mamDC clusters as well as further putative operons encoding a number of magnetosome-associated proteins. A bacterial artificial chromosome clone partially covering the deleted region was isolated from the genomic library of wild-type M. gryphiswaldense. Sequence analysis of this fragment revealed that all previously identified mam genes were closely linked with genes encoding other magnetosome-associated proteins within less than 35 kb. In addition, this region was remarkably rich in insertion elements and harbored a considerable number of unknown gene families which appeared to be specific for magnetotactic bacteria. Overall, these findings suggest the existence of a putative large magnetosome island in M. gryphiswaldense and other magnetotactic bacteria.
The Rose (Rosa hybrida) NAC Transcription Factor 3 Gene, RhNAC3, Involved in ABA Signaling Pathway Both in Rose and Arabidopsis

Plant transcription factors involved in stress responses are generally classified by their involvement in either the abscisic acid (ABA)-dependent or the ABA-independent regulatory pathways. A stress-associated NAC gene from rose (Rosa hybrida), RhNAC3, was previously found to increase dehydration tolerance in both rose and Arabidopsis. However, the regulatory mechanism involved in RhNAC3 action is still not fully understood. In this study, we isolated and analyzed the upstream regulatory sequence of RhNAC3 and found many stress-related cis-elements to be present in the promoter, with five ABA-responsive element (ABRE) motifs being of particular interest. Characterization of Arabidopsis thaliana plants transformed with the putative RhNAC3 promoter sequence fused to the β-glucuronidase (GUS) reporter gene revealed that RhNAC3 is expressed at high basal levels in leaf guard cells and in vascular tissues. Moreover, the ABRE motifs in the RhNAC3 promoter were observed to have a cumulative effect on the transcriptional activity of this gene both in the presence and absence of exogenous ABA. Overexpression of RhNAC3 in A. thaliana resulted in ABA hypersensitivity during seed germination and promoted leaf closure after ABA or drought treatments. Additionally, the expression of 11 ABA-responsive genes was induced to a greater degree by dehydration in the transgenic plants overexpressing RhNAC3 than control lines transformed with the vector alone. Further analysis revealed that all these genes contain NAC binding cis-elements in their promoter regions, and RhNAC3 was found to partially bind to these putative NAC recognition sites. We further found that of 219 A. thaliana genes previously shown by microarray analysis to be regulated by heterologous overexpression RhNAC3, 85 are responsive to ABA. In rose, the expression of genes downstream of the ABA-signaling pathways was also repressed in RhNAC3-silenced petals. Taken together, we propose that the rose RhNAC3 protein could mediate ABA signaling both in rose and in A. thaliana.
The normal vaginal flora, H2O2-producing lactobacilli, and bacterial vaginosis in pregnant women.

In this study of the vaginal flora of 171 pregnant women in labor at term, the flora was categorized as normal (Lactobacillus predominant), intermediate, or representative of bacterial vaginosis (BV) on the basis of a vaginal smear. BV was diagnosed in 39 women (23%); the vaginal flora was classified as normal in 50% of cases and as intermediate in 27%. H2O2-producing lactobacilli were recovered from 5% of women with BV, 37% of those with an intermediate flora, and 61% of those with a normal flora. H2O2-negative lactobacilli were equally frequent (57%-65%) in all three groups. The microorganisms most frequently recovered from women with BV included Gardnerella vaginalis, Prevotella bivia/disiens, Bacteroides ureolyticus, Prevotella corporis/Bacteroides levii, Fusobacterium nucleatum, Mobiluncus species, Peptostreptococcus prevotii, Peptostreptococcus tetradius, Peptostreptococcus anaerobius, viridans streptococci, Ureaplasma urealyticum, and Mycoplasma hominis (P < .05 for each). The presence of all but three of these organisms was inversely related to vaginal colonization by H2O2-producing lactobacilli; the exceptions were B. ureolyticus, F. nucleatum, and P. prevotii. Other microorganisms were equally frequent among women with and without BV. We conclude that specific groups of anaerobes are associated with BV in this population and that a strong association exists between species associated with BV and those inhibited by H2O2-producing lactobacilli.
Synergy and Other Interactions between Polymethoxyflavones from Citrus Byproducts

The citrus by-products released from citrus processing plants may contain high levels of potentially bioactive compounds such as flavonoids, which are a widely distributed group of polyphenolic compounds with health-related properties based on their antioxidant activity. In the study reported here, the potential bioactivities and antioxidant activities of extracts, fractions and compounds from citrus by-products were evaluated along with the chemical interactions of binary mixtures of compounds and complex mixtures. The bioactivities and interactions were evaluated in wheat coleoptile bioassays and the antioxidant activity was evaluated by the al DPPH (2,2-diphenyl-1-picrylhdrazyl radical) radical scavenging assay. The extracts, fractions and most of the isolated compounds (mainly polymethoxyflavones) showed high activity in the wheat coleoptile bioassay. However, the antioxidant activity was not consistently high, except in the acetone extract fractions. Moreover, a study of the interactions with binary mixtures of polymethoxyflavones showed the occurrence of synergistic effects. The complex mixtures of fractions composed mainly of polymethoxyflavones caused a synergistic effect when it was added to a bioactive compound such as anethole. The results reported here highlight a new application for the wheat coleoptile bioassay as a quick tool to detect potential synergistic effects in compounds or mixtures.
Selective Preservation of Naming from Description and the “Restricted Preverbal Message”

We report the case of a patient, LEW, who presents with modality-specific naming deficits. He is seriously impaired in naming pictures of both objects and actions. His naming to auditory verbal definitions and of actions carried out by the experimenter is, however, relatively well preserved. He has no visual perceptual deficits and his access to the semantics of pictures is as good as that to the semantics of spoken words. While LEW is not an optic aphasic patient, his pattern of performance is relevant to the debate that has taken place of the organization of the semantic system. We discuss his case from this perspective and argue that LEW's selective deficits support the multiple semantics position. We also argue that the "preverbal message" level in the speech production model of Levelt (1989) is the equivalent of "verbal semantics. " We provide additional constraints and principles to the concept of the preverbal message and we term the system so constrained the "restricted preverbal message. "
How do scientists develop and use scientific software?

New knowledge in science and engineering relies increasingly on results produced by scientific software. Therefore, knowing how scientists develop and use software in their research is critical to assessing the necessity for improving current development practices and to making decisions about the future allocation of resources. To that end, this paper presents the results of a survey conducted online in October-December 2008 which received almost 2000 responses. Our main conclusions are that (1) the knowledge required to develop and use scientific software is primarily acquired from peers and through self-study, rather than from formal education and training; (2) the number of scientists using supercomputers is small compared to the number using desktop or intermediate computers; (3) most scientists rely primarily on software with a large user base; (4) while many scientists believe that software testing is important, a smaller number believe they have sufficient understanding about testing concepts; and (5) that there is a tendency for scientists to rank standard software engineering concepts higher if they work in large software development projects and teams, but that there is no uniform trend of association between rank of importance of software engineering concepts and project/team size.
Autonomic dysfunction in chronic liver disease

It is becoming increasingly clear that quality of life (QOL) is impaired in those with chronic liver disease (CLD). One of the most important contributors to impaired QOL is the symptomatic burden which can range from slight to debilitating. Autonomic dysfunction accounts for a significant proportion of these symptoms, which can be common, non-specific and challenging to treat. Investigating the autonomic nervous system can be straight forward and can assist the clinician to diagnose and treat specific symptoms. Evidence-based treatment options for autonomic symptoms, specifically in CLD, can be lacking and must be extrapolated from other studies and expert opinion. For those with severely impaired quality of life, liver transplantation may offer an improvement; however, more research is needed to confirm this.
Effect of coatings and packaging on external and internal quality with emphasis on "cold injury"

Previous work has shown the advantages of low temperature storage (2oC) for decreasing the risk of mesocarp discoloration in ‘Pinkerton’. However, at such temperatures external chilling injury is manifested in greenskins. An interaction between fruit water loss and skin damage was found, which could be modified by decreasing post-harvest water loss. Further work was, however, needed to evaluate packaging so as to enhance the economic viability of the proposed system. Microperforated polypropylene packaging was used in formats of single fruit packs, 10 fruit packs, and carton liners. These results were compared to those of the untreated controls and commercially waxed fruit. Storage was at 8oC, 5.5oC and 2oC. Fruit quality was checked at 10, 20 and 30 days of storage. The highest mass loss occurred in the control fruit, with the lowest in the sealed packaging. Carton liners resulted in mass loss intermediate between waxing and sealed packaging. No chilling injury occurred at 2oC for sealed packages, but waxing resulted in approximately 8% of fruit surface being damaged. Carton liners reduced this significantly, but did not eliminate it. Regression analysis indicated that chilling injury was considerably increased at a fruit mass loss of 8% and greater. It is suggested that the use of polypropylene packaging, carton liners or up-scaled derivatives such as pallet bags, would allow for the advantages of low temperature shipping to be realised, without external chilling injury.
Prediction of delivery mode with transperineal ultrasound in women with prolonged first stage of labor

A recent review by Gyselaers et al. in this journal1 discussed the role of the abdominal venous system in regulating cardiac output (CO) in pregnancy and speculated that abdominal and pelvic venous congestion may contribute to placental and uterine dysfunction and pre-eclampsia. The authors did not mention, however, the role of compression of the inferior vena cava (IVC) by the gravid uterus in causing uterine venous congestion and uterine ischemia, especially when the patient is in the supine position. Even renal perfusion may be affected by increased intra-abdominal pressure, whether or not the pressure is applied above or below the level of the renal veins2. All of their measurements were taken using the supine position and no comparisons were made of renal venous flow in the lateral and supine positions. We have been intrigued by the possibility that obstruction of the IVC by the gravid uterus and resultant abdominal and pelvic venous congestion might cause poor placental and uterine function and might contribute to pre-eclampsia3,4. The placenta and uterus must function best when they are well perfused and optimal perfusion requires decompressed, low-pressure venous outflow. But how does one know when the uterine veins are decompressed? We have proposed that a new impedance cardiographic technique for measuring CO, known as electrical cardiometry (EC), might be useful for determining when the IVC is unobstructed and, by inference, when uterine venous pressure has been minimized3,4. With this approach, the maximization of CO is used as a marker to identify the maternal position in which the IVC is unobstructed and uterine venous pressure is presumably at its minimum. Figure 1 illustrates how position affects maternal CO (and presumably pelvic venous congestion) at an estimated gestational age of 26 + 3 weeks. This effect of maternal position on CO is well known. What is new is that we may now have an easy-to-apply, non-invasive and continuous means of measuring CO and, by inference, a method of predicting whether or not the pelvic venous system is congested due to an obstructed IVC. In the patients we have studied to date, the full left lateral position usually