Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Usefulness of a Prognostic Score in Histological Analysis of Renal Biopsy in Patients with Lupus Nephritis

Objective. To evaluate active and chronic lesions in association with renal outcome according to the International Society of Nephrology/Renal Pathology Society classification in patients with lupus nephritis. Methods. A retrospective analysis of 99 biopsy-proven subjects with lupus nephritis from 1990 to 2006 was performed in our center using the new classification. Each histological lesion was evaluated by multivariate survival analysis as predictive factor for renal insufficiency in patients with lupus nephritis, and independent predictors were graded to develop the prognostic score based on the regression coefficient. A receiver operating-characteristic curve based on the prognostic score was plotted to determine the most appropriate cutoff point. Results. In class IV, the IV-G group tended to exhibit a worse renal outcome compared with the IV-S group, but the difference was not significant (log-rank test, p = 0.4330). Independent histological predictors of poor renal outcome were extracapillary proliferation, glomerular sclerosis, and fibrous crescents analyzed by Cox proportional hazards model, while predictors of favorable renal outcome were hyaline thrombi and fibrous adhesions. By the prognostic score, renal outcome was significantly worse in the group with the higher score (≥ 0.25) than in the group with the lower score (< 0.25) in class IV patients (log-rank test, p < 0.001). Conclusion. These results demonstrate the advantage of our prognostic score compared to subclasses in predicting the renal outcome of class IV patients [University Hospital Medical Information Network (UMIN) clinical trials registry, number UMIN 000001943].
Asphyxia, Neurologic Morbidity, and Perinatal Mortality in Early-Term and Postterm Birth

BACKGROUND AND OBJECTIVES: Neonatal outcomes vary by gestational age. We evaluated the association of early-term, full-term, and postterm birth with asphyxia, neurologic morbidity, and perinatal mortality. METHODS: Our register-based study used retrospective data on 214 465 early-term (37+0–38+6 gestational weeks), 859 827 full-term (39+0–41+6), and 55 189 postterm (≥42+0) live-born singletons during 1989–2008 in Finland. Asphyxia parameters were umbilical cord pH and Apgar score at 1 and 5 minutes. Neurologic morbidity outcome measures were cerebral palsy (CP), epilepsy, intellectual disability, and sensorineural defects diagnosed by the age of 4 years. Newborns with major congenital anomalies were excluded from perinatal deaths. RESULTS: Multivariate analysis showed that, compared with full-term pregnancies, early-term birth increased the risk for low Apgar score (<4) at 1 and 5 minutes (odds ratio 1.03, 95% confidence interval 1.03–1.04 and 1.24, 1.04–1.49, respectively), CP (1.40, 1.27–1.55), epilepsy (1.14, 1.06–1.23), intellectual disability (1.39, 1.27–1.53), sensorineural defects (1.24, 1.17–1.31), and perinatal mortality (2.40, 2.14–2.69), but risk for low umbilical artery pH ≤7.10 was decreased (0.83, 0.79–0.87). Postterm birth increased the risk for low Apgar score (<4) at 1 minute (1.26, 1.26–1.26) and 5 minutes (1.80, 1.43–2.34), low umbilical artery pH ≤7.10 (1.26, 1.19–1.34), and intellectual disability (1.19, 1.00–1.43), whereas risks for CP (1.03, 0.84–1.26), epilepsy (1.00, 0.87–1.15), sensorineural defects (0.96, 0.86–1.07), and perinatal mortality (0.91, 0.69–1.22) were not increased. CONCLUSIONS: Early-term birth was associated with low Apgar score, increased neurologic morbidity, and perinatal mortality. Asphyxia and intellectual disability were more common among postterm births, but general neurologic morbidity and perinatal mortality were not increased.
Cascaded Bidirectional Recurrent Neural Networks for Protein Secondary Structure Prediction

Protein secondary structure (PSS) prediction is an important topic in bioinformatics. Our study on a large set of nonhomologous proteins shows that long-range interactions commonly exist and negatively affect PSS prediction. Besides, we also reveal strong correlations between secondary structure (SS) elements. In order to take into account the long-range interactions and SS-SS correlations, we propose a novel prediction system based on a cascaded bidirectional recurrent neural network (BRNN). We compare the cascaded BRNN against two other BRNN architectures, namely, the original BRNN architecture used for speech recognition and Pollastri's BRNN, which was proposed for PSS prediction. Our cascaded BRNN achieves an overall three-state accuracy Q3 of 74.38 percent and reaches a high Segment Overlap (SOV) of 66.0455. It outperforms the original BRNN and Pollastri's BRNN in both Q3 and SOV. Specifically, it improves the SOV score by 4-6 percent.
Mapping a sensory-motor network onto a structural and functional ground plan in the hindbrain

The hindbrain of larval zebrafish contains a relatively simple ground plan in which the neurons throughout it are arranged into stripes that represent broad neuronal classes that differ in transmitter identity, morphology, and transcription factor expression. Within the stripes, neurons are stacked continuously according to age as well as structural and functional properties, such as axonal extent, input resistance, and the speed at which they are recruited during movements. Here we address the question of how particular networks among the many different sensory-motor networks in hindbrain arise from such an orderly plan. We use a combination of transgenic lines and pairwise patch recording to identify excitatory and inhibitory interneurons in the hindbrain network for escape behaviors initiated by the Mauthner cell. We map this network onto the ground plan to show that an individual hindbrain network is built by drawing components in predictable ways from the underlying broad patterning of cell types stacked within stripes according to their age and structural and functional properties. Many different specialized hindbrain networks may arise similarly from a simple early patterning.
Experimental study of the gear effect in ball collisions

The gear effect arises when a ball collides with an object and the object recoils with a component of its acceleration in a direction parallel to the two contacting surfaces. Two experiments are described that show how the surfaces of the ball and the object can engage without slip similar to two gears. The effect is used in golf to correct for off-center impacts and it plays a minor role in baseball.
The Emergency Use Authorization of peramivir for treatment of 2009 H1N1 influenza.

On October 23 the FDA issued an Emergency Use Authorization for peramivir for the treatment of suspected or confirmed cases of 2009 H1N1 influenza. Drs. Debra Birnkrant and Edward Cox discuss the limited data on safety and efficacy and the criteria for emergency use of peramivir.
Glutathione Protects Lactococcus lactis against Oxidative Stress

ABSTRACT Glutathione was found in several dairy Lactococcus lactis strains grown in M17 medium. None of these strains was able to synthesize glutathione. In chemically defined medium, L. lactis subsp. cremoris strain SK11 was able to accumulate up to ∼60 mM glutathione when this compound was added to the medium. Stationary-phase cells of strain SK11 grown in chemically defined medium supplemented with glutathione showed significantly increased resistance (up to fivefold increased resistance) to treatment with H2O2 compared to the resistance of cells without intracellular glutathione. The resistance to H2O2 treatment was found to be dependent on the accumulation of glutathione in 16 strains of L. lactis tested. We propose that by taking up glutathione, L. lactis might activate a glutathione-glutathione peroxidase-glutathione reductase system in stationary-phase cells, which catalyzes the reduction of H2O2. Glutathione reductase, which reduces oxidized glutathione, was detectable in most strains of L. lactis, but the activities of different strains were very variable. In general, the glutathione reductase activities of L. lactis subsp. lactis are higher than those of L. lactis subsp. cremoris, and the activities were much higher when strains were grown aerobically. In addition, glutathione peroxidase is detectable in strain SK11, and the level was fivefold greater when the organism was grown aerobically than when the organism was grown anaerobically. Therefore, the presence of glutathione in L. lactis could result in greater stability under storage conditions and quicker growth upon inoculation, two important attributes of successful starter cultures.
Driven Concrete Pile Foundation Monitoring with Embedded Data Collector System

Florida Department of Transportation (FDOT) sponsored research performed at the University of Florida resulted in developing a wireless monitoring and real time static capacity estimate technology for driven piles. This new technology, Embedded Data Collector (EDC), uses two levels of instrumentation, embedded in the body of precast prestressed concrete piles near the head and tip. Strain and acceleration measurements obtained at these instrumentation levels during driving are sent wirelessly to a receiver in the field, and analyzed in real time to provide the operator with estimates of static capacity, stresses in the pile, transfer energy, damping factor, stroke height, and other relevant parameters used to evaluate the pile driving process and the driving system. The EDC system is currently undergoing phase one of a two phase field evaluation program planned by the FDOT to determine the level of reliability that can be anticipated by its use. The first phase consists of monitoring piles with EDC instrumentation and concurrently monitoring them with the Pile Driving Analyzer (PDA), given that there is ample data supporting the reliability of PDA. Measurements of strain and particle acceleration converted to force and velocity traces can then be compared between the two systems, along with the corresponding calculated magnitude of downward and upward traveling stress waves as they move along the pile at any point in time. Selected hammer blows recorded by PDA equipment are analyzed by means of signal matching software (CAPWAP) and the estimated static skin, end bearing, and total resistance obtained are compared against EDC static resistance predictions. The second phase of the evaluation will compare EDC estimates of static capacity against instrumented static load test results. The purpose of this paper, is only to present a summary of results obtained thus far in phase one, and compares EDC estimates of static capacity results with those from PDA and CAPWAP.
Platycodon grandiflorus Root Extract Improves Learning and Memory by Enhancing Synaptogenesis in Mice Hippocampus

Platycodon grandiflorus (Jacq.) A.DC. (PG) has long been used as an ingredient of foods and is known to have beneficial effects on cognitive functions as well. The present study examined the effect of each PG extract (PGE) from root, aerial part, and seeds on cognitive functions in mice. Changes in spatial learning and memory using a Y-maze test, and markers of adult hippocampal neurogenesis and synaptogenesis were examined. Moreover, changes in neuritogenesis and activation of the ERK1/2 pathway were investigated. Results indicated that mice administered PGE (root) showed increased spontaneous alternation in the Y-maze test and synaptogenesis in the hippocampus. In addition, PGE (root) and platycodin D, the major bioactive compound from the PG root, significantly stimulated neuritic outgrowth by phosphorylation of the ERK1/2 signaling pathway in vitro. These results indicate that the PGE (root), containing platycodin D, enhances cognitive function through synaptogenesis via activation of the ERK1/2 signaling pathway.
Inhibitor of streptokinase gene expression improves survival after group A streptococcus infection in mice

The widespread occurrence of antibiotic resistance among human pathogens is a major public health problem. Conventional antibiotics typically target bacterial killing or growth inhibition, resulting in strong selection for the development of antibiotic resistance. Alternative therapeutic approaches targeting microbial pathogenicity without inhibiting growth might minimize selection for resistant organisms. Compounds inhibiting gene expression of streptokinase (SK), a critical group A streptococcal (GAS) virulence factor, were identified through a high-throughput, growth-based screen on a library of 55,000 small molecules. The lead compound [Center for Chemical Genomics 2979 (CCG-2979)] and an analog (CCG-102487) were confirmed to also inhibit the production of active SK protein. Microarray analysis of GAS grown in the presence of CCG-102487 showed down-regulation of a number of important virulence factors in addition to SK, suggesting disruption of a general virulence gene regulatory network. CCG-2979 and CCG-102487 both enhanced granulocyte phagocytosis and killing of GAS in an in vitro assay, and CCG-2979 also protected mice from GAS-induced mortality in vivo. These data suggest that the class of compounds represented by CCG-2979 may be of therapeutic value for the treatment of GAS and potentially other Gram-positive infections in humans.
The Client Role in Staff Burn‐Out

The intense involvement with clients required of professional staff in various human service institutions includes a great deal of emotional stress, and failure to cope successfully with such stress can result in the emotional exhaustion syndrome of burn-out, in which staff lose all feeling and concern for their clients and treat them in detached or even dehumanized ways. This paper focuses on the role that clients themselves play in staff burn-out. Important client factors include the type and severity of the clients' problems, the prognosis of change or cure, the degree of personal relevance for the staff member of the clients' problems, the rules governing staff-client interaction, and the clients' reactions to the staff themselves. Changes in the structure of the staff-client interaction and changes in client expectations about staff can alleviate staff burn-out. It should be recognized that clients can dehumanize staff just as staff can dehumanize them, and that steps to humanize the staff-client relationship must focus on both participants in this interaction.
N400 amplitudes reflect change in a probabilistic representation of meaning: Evidence from a connectionist model

The N400 component of the event-related brain potential is widely used in research on language and semantic memory, but the cognitive functions underlying N400 amplitudes are still unclear and actively debated. Recent simulations with a neural network model of word meaning suggest that N400 amplitudes might reflect implicit semantic prediction error. Here, we extend these simulations to sentence comprehension, using a neural network model of sentence processing to simulate a number of N400 effects obtained in empirical research. In the model, sequentially incoming words update a representation capturing probabilities of elements of sentence meaning, not only reflecting the constituents presented so far, but also the model’s best guess at all features of the sentence meaning based on the statistical regularities in the model’s environment internalized in its connection weights. Simulating influences of semantic congruity, cloze probability, a word’s position in the sentence, reversal anomalies, semantic and associative priming, categorically related incongruities, lexical frequency, repetition, and interactions between repetition and semantic congruity, we found that the update of the predictive representation of sentence meaning consistently patterned with N400 amplitudes. These results are in line with the idea that N400 amplitudes reflect semantic surprise, defined as the change in the probability distribution over semantic features in an integrated representation of meaning occasioned by the arrival of each successive constituent of a sentence.
Transcriptome-based systematic identification of extracellular matrix proteins

Extracellular matrix (ECM), which provides critical scaffolds for all adhesive cells, regulates proliferation, differentiation, and apoptosis. Different cell types employ customized ECMs, which are thought to play important roles in the generation of so-called niches that contribute to cell-specific functions. The molecular entities of these customized ECMs, however, have not been elucidated. Here, we describe a strategy for transcriptome-wide identification of ECM proteins based on computational screening of >60,000 full-length mouse cDNAs for secreted proteins, followed by in vitro functional assays. These assays screened the candidate proteins for ECM-assembling activities, interactions with other ECM molecules, modifications with glycosaminoglycans, and cell-adhesive activities, and were then complemented with immunohistochemical analysis. We identified 16 ECM proteins, of which seven were localized in basement membrane (BM) zones. The identification of these previously unknown BM proteins allowed us to construct a body map of BM proteins, which represents the comprehensive immunohistochemistry-based expression profiles of the tissue-specific customization of BMs.
The effects of pregnancy on the sexual life of Turkish women

Aim: To investigate the effects of pregnancy on the sexual life of Turkish women Materials and Methods: One thousand twenty six pregnant women were included in the study. The Libido Scoring System, which is a questionnaire consisting of four questions about the frequency of intercourse, the partner initiating the intercourse, orgasm and masturbation status of the pregnant women, was completed by all patients. Both prepregnancy and pregnancy sexuality was evaluated independently using this scale. Results: The frequency of sexual intercourse during pregnancy significantly decreased from 3.07/week to 2.40/week (p<0.05). The masturbation rate during pregnancy was significantly lower than the pre-pregnancy period (3.6% vs 4.9 %, p<0.001). The percentage of pregnant women who never had an orgasm was significantly higher compared to the pre-pregnant period (21.7 % vs 10.8 %, p<0.01). The rates of initiation of sexual intercourse in the pre-pregnancy period by men and by women were 94.5% (970/1026) and 5.3% (54/1026) respectively. In pregnancy period the rates of initiation of sexual intercourse by man and woman were 93.4% (904/968) and 6.6% (64/968) respectively (p=0.0001). The mean libido scores during pregnancy were statistically lower than the prepregnancy period (6.38±0.04 vs 7.31±0.04, p<0.001). Conclusion: Pregnancy has a negative effect on the sexual life of women, but more prospective studies are required to clarify the
Optimal distributed beamforming for MISO interference channels

We consider the problem of quantifying the Pareto optimal boundary in the achievable rate region over multiple-input single-output (MISO) interference channels, where the problem boils down to solving a sequence of convex feasibility problems after certain transformations. The feasibility problem is solved by two new distributed optimal beamforming algorithms, where the first one is to parallelize the computation based on the method of alternating projections, and the second one is to localize the computation based on the method of cyclic projections. Convergence proofs are established for both algorithms.
Towards a Unified Approach to Modality Annotation in Portuguese

This paper introduces the first efforts towards a common ground for modality annotation for Portuguese. We take into account two existing schemes for European and Brazilian Portuguese, already implemented to written texts, and to spontaneous speech data, respectively. We compare the two schemes, discuss their strengths and weaknesses, and, then, introduce our unifying proposal, pointing out the issues which seem to be already pacified and points that should be considered when the scheme starts to be implemented.
Dynamic Linkages between Hedge Funds and Traditional Financial Assets: Evidence from Emerging Markets

This paper analyses the short- and long-term relationships between hedge funds and traditional financial assets using multivariate cointegration analysis in order to investigate if the fees charged by hedge funds are justified for the kind of exposure they provide to investors. We therefore create an emerging market composite hedge fund index as well as region specific indices based upon a unique and large sample of 404 emerging market hedge funds obtained from the merger of two different databases. As to whether diversification benefits arise from adding emerging markets hedge funds to an emerging markets bond/equity portfolio, our results show that the advantages are significantly less for Eastern Europe than for the other emerging market regions of Asia and Latin America during the period January 1998 through May 2006. In summary, we find evidence that emerging market hedge funds in general are redundant securities for long-term investment horizons.
Building a Statistical Model for Predicting Cancer Genes

More than 400 cancer genes have been identified in the human genome. The list is not yet complete. Statistical models predicting cancer genes may help with identification of novel cancer gene candidates. We used known prostate cancer (PCa) genes (identified through KnowledgeNet) as a training set to build a binary logistic regression model identifying PCa genes. Internal and external validation of the model was conducted using a validation set (also from KnowledgeNet), permutations, and external data on genes with recurrent prostate tumor mutations. We evaluated a set of 33 gene characteristics as predictors. Sixteen of the original 33 predictors were significant in the model. We found that a typical PCa gene is a prostate-specific transcription factor, kinase, or phosphatase with high interindividual variance of the expression level in adjacent normal prostate tissue and differential expression between normal prostate tissue and primary tumor. PCa genes are likely to have an antiapoptotic effect and to play a role in cell proliferation, angiogenesis, and cell adhesion. Their proteins are likely to be ubiquitinated or sumoylated but not acetylated. A number of novel PCa candidates have been proposed. Functional annotations of novel candidates identified antiapoptosis, regulation of cell proliferation, positive regulation of kinase activity, positive regulation of transferase activity, angiogenesis, positive regulation of cell division, and cell adhesion as top functions. We provide the list of the top 200 predicted PCa genes, which can be used as candidates for experimental validation. The model may be modified to predict genes for other cancer sites.
Proteomic analysis of membrane proteins from Streptococcus pneumoniae with multiple separation methods plus high accuracy mass spectrometry.

Abstract Streptococcus pneumoniae is a Gram-positive human pathogen that causes a variety of serious mucosal and invasive diseases in human. Bacterial membrane proteins play crucial roles in host-pathogen interactions and bacterial pathogenesis, and thus are potential drug targets or vaccine candidates. In this study, membranes from Streptococcus pneumoniae D39 were enriched by mechanical grinding and ultracentrifugation, and then the membrane proteins were extracted with trifluroethanol and chloroform. Around 60% of the extracted proteins were identified to be membrane proteins with 2-DE coupled with MALDI-MS/MS and 2D-LC-ESI-MS/MS. These identified membrane proteins can be functionally categorized into various groups involved in nutriment transport, signal transduction, protein folding or secretion, oxidation, carbohydrate metabolism, and other physiological processes. A protein interaction network was constructed for understanding the regulation relationship of the membrane proteins. This study represents the first global characterization of membrane proteome from Gram-positive streptococcus species of bacteria, providing valuable clues for further investigation aiming at identifying drug/vaccine targets for the bacterial infection.