Miracle-dz/UniFAR-FTUs huggingface dataset:
A Probabilistic Model for Information Retrieval Based on Maximum Value Distribution

The main goal of a retrieval model is to measure the degree of relevance of a document with respect to the given query. Probabilistic models are widely used to measure the likelihood of relevance of a document by combining within document term frequency and term specificity in a formal way. Recent research shows that tf normalization that factors in multiple aspects of term salience is an effective scheme. However, existing models do not fully utilize these tf normalization components in a principled way. Moreover, most state of the art models ignore the distribution of a term in the part of the collection that contains the term. In this article, we introduce a new probabilistic model of ranking that addresses the above issues. We argue that, since the relevance of a document increases with the frequency of the query term, this assumption can be used to measure the likelihood that the normalized frequency of a term in a particular document will be maximum with respect to its distribution in the elite set. Thus, the weight of a term in a document is proportional to the probability that the normalized frequency of that term is maximum under the hypothesis that the frequencies are generated randomly. To that end, we introduce a ranking function based on maximum value distribution that uses two aspects of tf normalization. The merit of the proposed model is demonstrated on a number of recent large web collections. Results show that the proposed model outperforms the state of the art models by significantly large margin.
Androgenetic/Biparental Mosaicism in an Infant with Hepatic Mesenchymal Hamartoma and Placental Mesenchymal Dysplasia

Androgenetic/biparental mosaicism, in which a subset of cells has complete paternal uniparental disomy, is associated with placental mesenchymal dysplasia (PMD), which is compatible with fetal development, indicating that fetal organs could also have androgenetic/biparental mosaicism, but few cases of somatic mosaicism have been described. A hepatic mesenchymal hamartoma (HMH) was resected from an otherwise healthy, nondysmorphic, 11-month-old girl, whose prenatal development was complicated by PMD. Placenta, HMH, histologically normal liver, and other tissues were examined for androgenetic/biparental mosaicism by analysis of (1) polymorphic DNA microsatellite markers, (2) the methylation status of an imprinted gene, SNRPN, and (3) immunohistochemically detectable protein products of the imprinted genes p57KIP2 and PHLDA2. The patient's liver, HMH, and 1 placental sample demonstrated an increased ratio of paternal to maternal alleles, indicating androgenetic/biparental mosaicism. The androgenetic component comprised 26% to 60% of the cells. Other tissues, including a 2nd placental sample, white blood cells, umbilical cord, and abdominal fascia, had no detectable androgenetic component. Methylation analysis confirmed a relative excess of the paternally imprinted SNRPN homolog in the normal liver, HMH, and placenta. Placental p57KIP2 immunoreactivity was consistent with androgenetic/biparental mosaicism, but neither p57KIP2 nor PHLDA2 immunohistochemistry were informative for HMH, because neither antigen was detected in control liver samples. We report androgenetic/biparental mosaicism in nonplacental tissues of an infant with PMD and provide the 1st description of genome-wide paternal uniparental disomy in HMH. Androgenetic/biparental mosaicism appears to play a role in the pathogenesis of HMH and other somatic lesions, particularly those associated with PMD.
Writing Errors and Anosognosia in Amyotrophic Lateral Sclerosis with Dementia

Amyotrophic lateral sclerosis (ALS) with dementia (ALS-D) is known to exhibit characteristics of frontotemporal dementia. However, in clinical situations, it is often difficult to evaluate their cognitive functions because of impaired voluntary speech and physical disabilities. In order to identify characteristic and diagnostic cognitive symptoms of relatively advanced ALS-D patients, we retrospectively reviewed the clinical features of seven cases of clinically definitive ALS who had dementia, impaired voluntary speech, and physical disability. Their medical records showed that six out of seven patients made writing errors, and all of the patients demonstrated anosognosia. The writing errors consisted of paragraphia such as substitution, omission, or syntactic errors with individual differences in error types. Dissociation between kana and kanji were also observed. Anosognosia was evaluated by a self-rating scale with which the patients and the medical staff evaluated the patient's physical ability; the results indicated a large discrepancy between the evaluation by the patients and the medical staff. We emphasize that aphasic writing errors have been underestimated, particularly in ALS-D patients with impaired voluntary speech. We also reported that anosognosia was the most important and quantifiable symptom in ALS-D. The relationship between writing errors and anosognosia should be investigated further.
ANALYSIS OF VARIABILITY IN REFLECTIVITY-RAINFALL RELATIONSHIPS ON RUNOFF PREDICTION

Radar-rainfall information presents a significant potential for improving our ability to provide accurate and timely flood predictions. Similar to other measuring devices, radar data also has many uncertainties. One of the main sources of uncertainties is due to natural and sampling variations in the estimation of rainfall rates from radar reflectivity factors. The National Weather Service (NWS) WSR-88D estimates rainfall rates by employing a relationship between Reflectivity factor Z (mm m) and rainfall rate R (mm h) of the form Z=AR (Ulbrich and Miller, 2001). Both Z and R are defined as different moments of the drop size distribution (DSD) in a sampled volume. Typical default values used by the NWS are A=300 and b=1.4 (for system with deep convection) and A=250 and b=1.2 (for tropical events). Earlier work by Atlas et al. (1999) showed that there can be dramatic changes in Z-R parameters between storms as well as within individual storms. The variability in Z-R relationship is attributed to changes in drop size distributions (DSD) of rainfall events. Lee. (2005) discussed the classification of DSDs according to the dominant physical processes observed by vertical profile of radar and its scale dependence. The Variability of Z-R relationships from storm to storm are due to differences in DSDs caused by governing types of storms (convective, tropical). Variability of Z-R relationships within a storm is due to different microphysical processes involved in the storm. Lee. (2005) showed that optimal Z-R relationships are obtained when the physical process is identified with a unique DSD. The scatter around the Z-R relationship for physical process converges showing a unique relationship.
A School-University Research Partnership to Identify Disengaged Students: A Descriptive Case Analysis of School Climate

Background/Context Much of the literature on school—university research partnerships has focused on collaborations that address curriculum, instruction, and leadership. Less scholarly attention has been paid to how practitioners and academics work together to improve school climate. Purpose We seek to deepen understanding of how educators and researchers collaborate to address aspects of the campus environment that matter to students’ learning. We discuss findings from the first year of a long-term research alliance—between a university research center, a high school, and one of its feeder K–8 school districts—focused on improving school climate. First, we report results from our analysis of students’ responses to a schoolwide survey. Then, we examine the affordances and challenges at every stage of the investigative process, highlighting factors critical to school-university research alliances. Research Design We analyzed students’ school climate survey responses in one low-income predominantly Latino high school (n = 1,606). We linked students’ survey data to their administrative records and employed logistic regression modeling to determine the extent to which students’ school climate perceptions were associated to their educational outcomes. We also analyzed the cohort of students who matriculated to the high school from the nearby elementary school feeder district to see whether the middle-to-high-school transition shifted their views on the school environment. Findings Males, students in Grade 11, and those with at least one suspension reported fewer positive experiences on campus relative to their peers. Also, the middle-to-high-school transition had a positive influence on students who reported low average perceptions of care in their middle school. Reflecting on the partnership process, we found that responding promptly to the concerns of stakeholders helped establish credibility and trust. Open and frequent communication was also essential to maintain focus, sustain commitment, and ensure the longevity of the alliance. Further, allowing partners to contribute and make decisions throughout the analysis helped ensure that all perspectives were considered, thus increasing the validity of research findings. Conclusions/Recommendations School—university collaborations can be challenging to maintain. This study suggests that reforming school climate is a long-term participatory process that demands significant resources and ongoing engagement from both researchers and practitioners. By providing a thorough examination of the give and take, ups and downs, and stops and starts of a school—university research alliance, we aim to identify elements that can help partnerships succeed and provide rich evidence that can serve as a foundation for further inquiry.
Biodoop: Bioinformatics on Hadoop

Bioinformatics applications currently require both processing of huge amounts of data and heavy computation. Fulfilling these requirements calls for simple ways to implement parallel computing. MapReduce is a general-purpose parallelization model that seems particularly well-suited to this task and for which an open source implementation (Hadoop) is available. Here we report on its application to three relevant algorithms: BLAST, GSEA and GRAMMAR. The first is characterized by relatively low-weight computation on large data sets, while the second requires heavy processing of relatively small data sets. The third one can be considered as containing a mixture of these two computational flavors. Our results are encouraging and indicate that the framework could have a wide range of bioinformatics applications while maintaining good computational efficiency, scalability and ease of maintenance.
Functional Non‐Nucleoside Adenylyl Cyclase Inhibitors

In this study, we describe the synthesis of novel functional non‐nucleoside adenylyl cyclase inhibitors, which can be easily modified with thiol containing biomolecules such as tumour targeting structures. The linkage between inhibitor and biomolecule contains cleavable bonds to enable efficient intracellular delivery in the reductive milieu of the cytosol as well as in the acidic environment within endosomes and lysosomes. The suitability of this synthetic approach was shown by the successful bioconjugation of a poor cell‐permeable inhibitor with a cell‐penetrating peptide. Additionally, we have demonstrated the excellent inhibitory effect of the compounds presented here in a live‐cell Förster resonance energy transfer‐based assay in human embryonic kidney cells.
cAMP Stimulates Transepithelial Short-Circuit Current and Fluid Transport Across Porcine Ciliary Epithelium.

Purpose To investigate the effects of cAMP on transepithelial electrical parameters and fluid transport across porcine ciliary epithelium. Methods Transepithelial electrical parameters were determined by mounting freshly isolated porcine ciliary epithelium in a modified Ussing chamber. Similarly, fluid movement across intact ciliary body was measured with a custom-made fluid flow chamber. Results Addition of 1, 10, and 100 μM 8-Br-cAMP (cAMP) to the aqueous side (nonpigmented ciliary epithelium, NPE) induced a sustained increase in short-circuit current (Isc). Addition of niflumic acid (NFA) to the aqueous surface effectively blocked the cAMP-induced Isc stimulation. The administration of cAMP to the stromal side (pigmented ciliary epithelium, PE) triggered a significant stimulation of Isc only at 100 μM. No additive effect was observed with bilateral application of cAMP. Likewise, forskolin caused a significant stimulation of Isc when applied to the aqueous side. Concomitantly, cAMP and forskolin increased fluid transport across porcine ciliary epithelium, and this stimulation was effectively inhibited by aqueous NFA. Depleting Cl- in the bathing solution abolished the baseline Isc and inhibited the subsequent stimulation by cAMP. Pretreatment with protein kinase A (PKA) blockers (H89/KT5720) significantly inhibited the cAMP- and forskolin-induced Isc responses. Conclusions Our results suggest that cAMP triggers a sustained stimulation of Cl- and fluid transport across porcine ciliary epithelium; Cl- channels in the NPE cells are potentially a cellular site for this PKA-sensitive cAMP-mediated response.
Arterial and Mixed Venous Blood Acid‐Base Balance During Hypoperfusion With Incremental Positive End‐Expiratory Pressure in the Pig

The authors sought to determine how hypoperfusion influences acid-base balance in arterial and mixed venous blood. In anesthetized, ventilated pigs (n = 12), we determined hemodynamics, O2 uptake, CO, output, dead-space ventilation, arterial and mixed venous blood acid-base balances, and lactate concentrations during graded reductions in cardiac output by incremental positive end-expiratory pressure (PEEP, 0–20 cm H2O). Cardiac output decreased from 3.2 ± 0.2 (mean ± sem) to 1.2 ± 0.1 L/min at 20 cm H2O PEEP. Oxygen delivery declined more than O2 uptake did by 60% ± 2% and 27% ± 2%, respectively. The decrease in CO2 output (by 21% ± 2%) was less than that in O2 uptake. Fractional dead-space ventilation increased. At a slight increase in carbon dioxide tension (Pco2) of 4 ± 1 mm Hg, pH decreased in arterial blood from 7.54 plusmn; 0.01 to 7.47 ± 0.02 mmol/L, and standard bicarbonate decreased from 30.3 ± 0.5 to 27.5 ± 0.6 mmol/L. The decrease in standard bicarbonate exceeded the increase in blood lactate concentrations. At a similar decrease in standard bicarbonate, the decrease in pH was larger (P < 0.005) in mixed venous blood than in arterial blood owing to a larger increase in Pco2 (from 40 ± 2 to 50 ± 2 mm Hg, P < 0.005). The changes were reversed after discontinuing PEEP. The authors conclude that ischemia after incremental PEEP results in tissue metabolic acidosis with superimposed respiratory acidosis. This is not caused by increased tissue production or by impaired pulmonary excretion of CO2 but by a larger decrease in blood flow than in CO2 production in the tissues, so that CO2 stores increase. Decreased pulmonary blood flow and increased dead-space ventilation prevent a decrease in arterial Pco2 by diminished CO2 production. A smaller reduction in CO2 production than in O2 uptake is only partly explained by bicarbonate buffering of lactic acid.
Automating algorithms for the identification of fault-prone files

This research investigates ways of predicting which files would be most likely to contain large numbers of faults in the next release of a large industrial software system. Previous work involved making predictions using several different models ranging from a simple, fully-automatable model (the LOC model) to several different variants of a negative binomial regression model that were customized for the particular software system under study. Not surprisingly, the custom models invariably predicted faults more accurately than the simple model. However, development of customized models requires substantial time and analytic effort, as well as statistical expertise. We now introduce new, more sophisticated models that yield more accurate predictions than the earlier LOC model, but which nonetheless can be fully automated. We also extend our earlier research by presenting another large-scale empirical study of the value of these prediction models, using a new industrial software system over a nine year period.
Detection of Attractive Phrases from Musical Lyrics Focusing on “Uniqueness of Co-occurred Terms” and “Repetition”

This paper proposes a method to detect attractive phrases from musical lyrics. The method considers not only acoustic but also lyrical features which attract human attention. Through the interview on impression for lyrics, we have found that “uniqueness of co-occurred terms” and “repetition” significantly influence human attraction. Therefore, we modeled these linguistic expressions as mathematical features. The proposed method detected attractive phrases using support vector machine with the modeled features. The results of the model evaluation experiments showed the 69% accuracy and 86% precision. Moreover, the results were compared and discussed with the key sentences detected by the existing summarization methods. As the result of comparison, it is confirmed that the proposed method detected attractive phrases more accurate than the existing summarization methods.
Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering

Accurately identifying the protein-ligand binding sites or pockets is of significant importance for both protein function analysis and drug design. Although much progress has been made, challenges remain, especially when the 3D structures of target proteins are not available or no homology templates can be found in the library, where the template-based methods are hard to be applied. In this paper, we report a new ligand-specific template-free predictor called TargetS for targeting protein-ligand binding sites from primary sequences. TargetS first predicts the binding residues along the sequence with ligand-specific strategy and then further identifies the binding sites from the predicted binding residues through a recursive spatial clustering algorithm. Protein evolutionary information, predicted protein secondary structure, and ligand-specific binding propensities of residues are combined to construct discriminative features; an improved AdaBoost classifier ensemble scheme based on random undersampling is proposed to deal with the serious imbalance problem between positive (binding) and negative (nonbinding) samples. Experimental results demonstrate that TargetS achieves high performances and outperforms many existing predictors. TargetS web server and data sets are freely available at: http://www.csbio. sjtu.edu. cn/bioinf/TargetS/ for academic use.
Testing the robustness of the likelihood-ratio test in a variance-component quantitative-trait loci-mapping procedure.

Detection of linkage to genes for quantitative traits remains a challenging task. Recently, variance components (VC) techniques have emerged as among the more powerful of available methods. As often implemented, such techniques require assumptions about the phenotypic distribution. Usually, multivariate normality is assumed. However, several factors may lead to markedly nonnormal phenotypic data, including (a) the presence of a major gene (not necessarily linked to the markers under study), (b) some types of gene x environment interaction, (c) use of a dichotomous phenotype (i.e., affected vs. unaffected), (d) nonnormality of the population within-genotype (residual) distribution, and (e) selective (extreme) sampling. Using simulation, we have investigated, for sib-pair studies, the robustness of the likelihood-ratio test for a VC quantitative-trait locus-detection procedure to violations of normality that are due to these factors. Results showed (a) that some types of nonnormality, such as leptokurtosis, produced type I error rates in excess of the nominal, or alpha, levels whereas others did not; and (b) that the degree of type I error-rate inflation appears to be directly related to the residual sibling correlation. Potential solutions to this problem are discussed. Investigators contemplating use of this VC procedure are encouraged to provide evidence that their trait data are normally distributed, to employ a procedure that allows for nonnormal data, or to consider implementation of permutation tests.
Institutional Stock Trading and Loan Renegotiation Information

Objectives: The purpose of this study was to investigate the relationship between institutional stock trading and loan renegotiation information. As lenders, institutional investors routinely receive private information about borrowers. However, most of these investors also trade in public securities. Institutional investor maybe use inside information acquired from the borrowers to trade in public securities. This study examines the stock trading of institutional investors whose portfolios also hold loans, and the effect of internet information.
Successive Nanosecond Discharges in Water

Successive discharges of alternating polarities in distilled water have been studied. Cathode-initiated discharges develop in two possible configurations: slow and weakly luminescent bushlike mode or fast and luminous treelike mode with well-pronounced branching. Under our experimental conditions, the two modes originate with approximately equal probability. Positive discharge demonstrates only one discharge morphology with two hemispherical weakly luminescent structures. Successive negative pulse results in the formation of one of the negative modes, bushlike or treelike.
Metabolic Response to Heat Stress in Late-Pregnant and Early Lactation Dairy Cows: Implications to Liver-Muscle Crosstalk

Climate changes lead to rising temperatures during summer periods and dramatic economic losses in dairy production. Modern high-yielding dairy cows experience severe metabolic stress during the transition period between late gestation and early lactation to meet the high energy and nutrient requirements of the fetus or the mammary gland, and additional thermal stress during this time has adverse implications on metabolism and welfare. The mechanisms enabling metabolic adaptation to heat apart from the decline in feed intake and milk yield are not fully elucidated yet. To distinguish between feed intake and heat stress related effects, German Holstein dairy cows were first kept at thermoneutral conditions at 15°C followed by exposure to heat-stressed (HS) at 28°C or pair-feeding (PF) at 15°C for 6 days; in late-pregnancy and again in early lactation. Liver and muscle biopsies and plasma samples were taken to assess major metabolic pathway regulation using real-time PCR and Western Blot. The results indicate that during heat stress, late pregnant cows activate Cahill but reduce Cori cycling, prevent increase in skeletal muscle fatty acid oxidation, and utilize increased amounts of pyruvate for gluconeogenesis, without altering ureagenesis despite reduced plane of nutrition. These homeorhetic adaptations are employed to reduce endogenous heat production while diverting amino acids to the growing fetus. Metabolic adaptation to heat stress in early lactation involves increased long-chain fatty acid degradation in muscle peroxisomes, allowance for muscle glucose utilization but diminished hepatic use of amino acid-derived pyruvate for gluconeogenesis and reduced peroxisomal fatty acid oxidation and ATP production in liver of HS compared to PF cows in early lactation. Consequently, metabolic adaptation to heat stress and reduced feed intake differ between late pregnancy and early lactation of dairy cows to maintain energy supply for fetus development or milk production simultaneously reducing endogenous heat production.