Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple human papillomavirus infections and type‐competition in women from a clinic attendee population in China

To investigate the multi‐infection patterns and type competition for human papillomavirus (HPV) in Chinese clinic attending women and evaluate the association between the infection status and cancer risk. Three hundred and thirty‐two HPV‐DNA‐positive samples were genotyped for 21 HPVs and tested for 13 types of HPV neutralizing antibody using pseudoviron‐based assay. Odds ratios (ORs) were calculated to evaluate the coinfection patterns for both DNA and neutralizing antibody (NAb), and the associations of HSIL+ with HPV DNA and NAb. Of the 332 HPV‐DNA‐positive subjects, 279 (84.0%) were detected as NAb positive. Multi‐positive results were identified in 23.2% (77/332) HPV DNA tests and 60.2% (168/279) HPV NAb assays. The NAb titers for the multiple‐positive samples (geometric mean 214) were significantly higher than the single‐positive samples (geometric mean 114) (P < 0.01). HPV16‐HPV52 was identified as a type‐competition pair for both HPV DNA (OR = 0.09; 95%CI = 0.02–0.42) and NAb (OR = 0.27; 95%CI = 0.11–0.69) data. Compared to other types, HPV16 DNA was associated significantly with high risk of HSIL+ (OR = 2.57; 95%CI = 1.23–5.38). HPV16‐HPV52 was identified as a potential type‐competition pair, which might result in the type modulation with the implementation of the approved bi‐ or quadri‐valent vaccines. J. Med. Virol. 88:1989–1998, 2016. © 2016 Wiley Periodicals, Inc.
Canine atopic dermatitis: a retrospective study of 169 cases examined at the University of California, Davis, 1992-1998. Part II. Response to hyposensitization.

One hundred and sixty-nine dogs were diagnosed with atopic dermatitis, and treated with hyposensitization for at least 1 year based on the results of either intradermal skin tests (IDST) or enzyme-linked immunosorbant serum assays (ELISA). Excellent (i.e. hyposensitization alone controlled clinical signs), good (> 50% improvement), moderate (< 50% improvement) and no (clinical signs were unchanged) responses were seen in 19.5, 32.5, 20.1 and 27.8%, respectively. Age of onset, age when treatment was initiated or the duration of clinical signs had no influence on response to hyposensitization. Dogs having concurrent flea allergy dermatitis were statistically more likely to respond better than dogs with concurrent food allergies. Although not statistically significant, there were trends for Golden Retriever and male dogs to respond better than other breeds and female dogs, respectively. Dogs having more than 21 positive reactions in allergy tests and treated with more than 21 allergens had lower response scores, and a longer time course before achieving beneficial response. Lower response scores were seen in dogs having positive reactions to cultivated plants, grasses, trees or insects. There was no difference in response to hyposensitization whether based on IDST or ELISA results.
The cell adhesion molecule BEN defines a prosensory patch in the developing avian otocyst

The distribution of the cell adhesion molecule BEN in the developing chick inner ear is described. BEN is first detected in the otic placode at stage 11. As the placode begins to invaginate, BEN becomes concentrated in a ventromedial region extending from the anterior to the posterior end of the otic pit. BEN expression levels increase in this region as the pit closes to form the otocyst, and distinct boundaries become defined along the dorsal and ventral edges of the ventromedial band of BEN expression. BEN expression also becomes concentrated dorsally within the otic epithelium as the pit closes and is observed in the condensing otic ganglion. By stage 22, the ventromedial band of BEN expression splits into two distinct regions, a small caudal patch within which the posterior crista will develop, and a larger anterior patch. By stage 26, this larger anterior patch of cells expressing BEN becomes subdivided into five separate areas corresponding to the regions within which the anterior crista, the lateral crista, the utricle, the saccule, and both the basilar papilla and lagenar macula form. Hair cells only develop within these regions defined by BEN distribution. The data suggest that the ventromedial patch of BEN expression observed from stage 11 onwards defines a single sensory competent zone from which all sensory organs of the inner ear develop. BEN immunoreactivity in the inner ear declines after stage 38. In response to noise exposure, upregulation of BEN expression is mainly detected in regions of the posthatch papilla where the damage is severe and regenerating hair cells are not observed. The regenerating hair and supporting cells do not express BEN, highlighting a molecular difference between the processes of development and regeneration. J. Comp. Neurol. 434:275–288, 2001. © 2001 Wiley‐Liss, Inc.
Measurement of thickness of layer and sound velocity in multi-layered structure by the use of angular ultrasonic transducers

The possibilities of measurement of thickness of layer and the velocity propagation of ultrasound signals in layered structures by the use of the angular electroacoustical transducers with known parameters are analyzed. It is shown that, when the velocity propagation of ultrasound signals in the separate layer of structure is unknown, the thickness and the velocity propagation of signals in them may be measured by the use of the single measuring channel with angular ultrasonic transducers. The algorithms for determination of thickness of separate layers and ultrasound velocity in them are developed, when the layered structure is iradiated at a known angle to the surface of structure. The modeling of measuring channel with the angular ultrasonic transducers is performed. When modeling the propagation and reflection of ultrasound signals in duralumin – plexiglass layered structure and the spatial and temporal distributions of them on the surface of layered structure are revealed. The variation of temporal and spatial distributions of received signals is investigated when the angle of incidence to the layered structure is changed. It is shown that temporal and spatial distributions of shear and longitudinal waves do not coincide to each other and alter differently, when the angle of incidence is changed. The results of experimental investigation are presented.
Modeling and probabilistic reasoning of population evacuation during large-scale disaster

The Great East Japan Earthquake and the Fukushima nuclear accident cause large human population movements and evacuations. Understanding and predicting these movements is critical for planning effective humanitarian relief, disaster management, and long-term societal reconstruction. In this paper, we construct a large human mobility database that stores and manages GPS records from mobile devices used by approximately 1.6 million people throughout Japan from 1 August 2010 to 31 July 2011. By mining this enormous set of Auto-GPS mobile sensor data, the short-term and long-term evacuation behaviors for individuals throughout Japan during this disaster are able to be automatically discovered. To better understand and simulate human mobility during the disasters, we develop a probabilistic model that is able to be effectively trained by the discovered evacuations via machine learning technique. Based on our training model, population mobility in various cities impacted by the disasters throughout the country is able to be automatically simulated or predicted. On the basis of the whole database, developed model, and experimental results, it is easy for us to find some new features or population mobility patterns after the recent severe earthquake, tsunami and release of radioactivity in Japan, which are likely to play a vital role in future disaster relief and management worldwide.
Preliminary Version Self-Enhancing Transmission Bias and Active Investing

Individual investors often invest actively and lose thereby. Social interaction seems to exacerbate the bias toward active trading. In the model here, conversational biases in the social transmission of performance information favor active over passive investment strategies. Senders’ propensity to communicate their returns is increasing in returns. Receivers’ propensity to attend to and be converted by senders is increasing and convex in sender return. Active strategies (high variance, skewness, and personal involvement) dominate the population unless the mean return penalty to active investing is too large. Thus, the model can explain overvaluation of assets with these characteristics even if investors have no inherent preference over them.
COMPUTATIONAL MODELS CONSTRAINED BY VOLTAGE-CLAMP DATA FOR INVESTIGATING DENDRITIC CURRENTS

We have investigated dendritic currents using a combination of experimental and modeling approaches. Voltage-clamp recordings were obtained in neurons with and without dendrites (intact vs. dissociated cells), and the recordings were compared to simulations that incorporated the corresponding dendritic morphology. This approach was applied to thalamic reticular cells to examine dendritic location of the low-threshold calcium current (ITs). The simulations matched the recordings only if ITs was located in distal dendrites with high density. Moreover, dendritic ITs was also necessary to reproduce the typical responses of these cells seen in intracellular recordings in vivo. This approach can be used to investigate other types of neurons with active dendritic currents. Introduction Thalamic reticular (RE) cells typically re burst discharges, which play a central role in the genesis of various types of synchronized sleep oscillations and epileptic behavior (Steriade et al., 1993). A low-threshold Ca current, ITs, underlies the production of these bursts (Bal and McCormick,1993; Huguenard and Prince 1992). As
Effect of Cup Feeding and Bottle Feeding on Breastfeeding in Late Preterm Infants

Background: Cup feeding has been used as an alternative feeding method for preterm infants. Objective: The purpose of this study was to determine the effect of bottle and cup feeding on exclusive breastfeeding rates at hospital discharge and 3 and 6 months post-discharge in late preterm infants. Methods: Included in the study were preterm infants of 32 to 35 weeks’ gestation fed only by intermittent gastric tube at the time of recruitment; 522 infants were randomly assigned to 2 groups: the cup-fed group (n = 254) and bottle-fed group (n = 268). Main outcomes were prevalence of exclusive breastfeeding at discharge and 3 and 6 months after discharge, and length of hospital stay. Results: Infants randomized to cup versus bottle feeding were more likely to be exclusively breastfed at discharge home (relative risk [RR], 1.58; 95% confidence interval [CI], 1.36-1.83), 3 months after discharge (RR, 1.64; 95% CI, 1.42-1.89), and 6 months after discharge (RR, 1.36; 95% CI, 1.14-1.63). There was no significant difference between groups for length of hospital stay. The mean hospital stay was 25.96 ± 2.20 days in the bottle-fed group and 25.68 ± 2.22 days in the cup-fed group. There was no significant difference between groups for time spent feeding, feeding problems, or weight gain in hospital. Conclusion: Cup feeding significantly increased the likelihood of late preterm infants being exclusively breastfed at discharge and 3 and 6 months after discharge, and cup feeding did not increase the length of hospital stay. Overall, we recommend cup feeding as a transitional method prior to breastfeeding for late preterm infants during hospitalization.
Practical prefetching techniques for parallel file systems

Improvements in the processing speed of multiprocessors are outpacing improvements in the speed of disk hardware. Parallel disk I/O subsystems have been proposed as one way to close the gap between processor and disk speeds. In a previous paper the authors showed that prefetching and caching have the potential to deliver the performance benefits of parallel file systems to parallel applications. They describe experiments with practical prefetching policies, and show that prefetching can be implemented efficiently even for the more complex parallel file access patterns. They also test the ability of these policies across a range of architectural parameters. (see IEEE Trans. on Parallel and Distributed Systems, vol.1, no.2, p.218-30, 1990). <<ETX>>
Human T Cell Leukemia Virus Reactivation with Progression of Adult T-Cell Leukemia-Lymphoma

Background Human T-cell leukemia virus-associated adult T-cell leukemia-lymphoma (ATLL) has a very poor prognosis, despite trials of a variety of different treatment regimens. Virus expression has been reported to be limited or absent when ATLL is diagnosed, and this has suggested that secondary genetic or epigenetic changes are important in disease pathogenesis. Methods and Findings We prospectively investigated combination chemotherapy followed by antiretroviral therapy for this disorder. Nineteen patients were prospectively enrolled between 2002 and 2006 at five medical centers in a phase II clinical trial of infusional chemotherapy with etoposide, doxorubicin, and vincristine, daily prednisone, and bolus cyclophosphamide (EPOCH) given for two to six cycles until maximal clinical response, and followed by antiviral therapy with daily zidovudine, lamivudine, and alpha interferon-2a for up to one year. Seven patients were on study for less than one month due to progressive disease or chemotherapy toxicity. Eleven patients achieved an objective response with median duration of response of thirteen months, and two complete remissions. During chemotherapy induction, viral RNA expression increased (median 190-fold), and virus replication occurred, coincident with development of disease progression. Conclusions EPOCH chemotherapy followed by antiretroviral therapy is an active therapeutic regimen for adult T-cell leukemia-lymphoma, but viral reactivation during induction chemotherapy may contribute to treatment failure. Alternative therapies are sorely needed in this disease that simultaneously prevent virus expression, and are cytocidal for malignant cells. Trial Registration ClinicalTrials.gov NCT00041327
An HRP study of the relation between cell size and motor unit type in cat ankle extensor motoneurons

The dimensions of the somata and stem dendrites of 57 α‐ and three γ‐ motoneurons, identified as to motor unit type and labeled by intracelluar injection of horseradish peroxidase, were measured in the triceps surae and plantaris motor pools. The somata of type S motoneurons tended to be smaller (mean diameter 47.9 μm) than those of FF and FR units (52.5 and 53.1 μm, respectively) but these mean values were not significantly different and the data distributions showed considerable overlap between the unit types. The mean numbers and diameters of stem dendrites of stem dendrites exhibited somewhat larger differences related to motor unit type and some of these were statistically significant. The total membrane area (AN) of each cell was estimated from measurements of the soma and stem dendrites, by using recent data of Ulfhake and Kellerth ('81) to calculate the membrane area of a dendritic tree from stem dendrite diameter. Mean AN varied with motor unit type in the sequence FF > FR > S (average values: 369 × 1003 μm2, 323 × 1003 μm2, and 250 × 1003 μm2, respectively). There was covariation between AN and the conduction velocity of the motor axon, as well as with the force output from the muscle unit. Comparison of AN and motoneuron input resistance (RN) in 19 α‐motoneurons suggested that the specific resistivity of the cell membrane in type S motoneurons was systematically higher than that characteristic of type FF or FR motoneurons.
Proteomic analysis of human osteoprogenitor response to disordered nanotopography

Previous studies have shown that microgroove-initiated contact guidance can induce bone formation in osteoprogenitor cells (OPGs) and produce changes in the cell proteome. For proteomic analysis, differential in-gel electrophoresis (DIGE) can be used as a powerful diagnostic method to provide comparable data between the proteomic profiles of cells cultured in different conditions. This study focuses on the response of OPGs to a novel nanoscale pit topography with osteoinductive properties compared with planar controls. Disordered near-square nanopits with 120 nm diameter and 100 nm depth with an average 300 nm centre-to-centre spacing (300 nm spaced pits in square pattern, but with ±50 nm disorder) were fabricated on 1×1 cm2 polycaprolactone sheets. Human OPGs were seeded onto the test materials. DIGE analysis revealed changes in the expression of a number of distinct proteins, including upregulation of actin isoforms, beta-galectin1, vimentin and procollagen-proline, 2-oxoglutarate 4-dioxygenase and prolyl 4-hydroxylase. Downregulation of enolase, caldesmon, zyxin, GRASP55, Hsp70 (BiP/GRP78), RNH1, cathepsin D and Hsp27 was also observed. The differences in cell morphology and mineralization are also reported using histochemical techniques.
Gene body H2B monoubiquitylation regulates gene-selective RNA Polymerase II pause release and is not rate limiting for transcription elongation

Histone H2B monoubiquitylation (H2Bub1) is localized preferentially to transcribed regions of genes and spreads concomitantly with the progression of RNA polymerase II (Pol II). In mammalian cells, H2Bub1 levels are highly correlated with transcription elongation rates, consistent with the general belief that H2Bub1 facilitates the elongation process. Yet, a causative role of H2Bub1 in regulating elongation rates within live cells remains to be proven. Using our recently developed 4sUDRB-seq method, we examined the impact of H2Bub1 downregulation, through silencing of its cognate E3 ubiquitin ligase RNF20, on genomewide transcription elongation rates. Surprisingly, H2Bub1 downregulation had no measurable effect on global elongation rates. Instead, it led to upregulation of over 1,000 genes by altering their Pol II pause release times; notably, those genes are characterized by the presence of H2Bub1 in relatively close proximity to the paused Pol II. Conversely, another set of genes was downregulated upon partial H2Bub1 depletion, and in those genes H2Bub1 appeared to be required for efficient recruitment of Pol II to the promoter region. Overall, our data shed new light on the molecular mechanisms by which H2Bub1 regulates gene expression and imply that the role of H2Bub1 in transcription elongation should be reconsidered. AUTHOR SUMMARY Transcription elongation is an important component of the gene expression process. Numerous factors and chromatin modifications, including some that are misregulated in various human diseases, have been suggested to regulate transcription elongation. New methods to measure genomewide transcription elongation rates now enable, for the first time, to determine how a specific factor affects transcription elongation and what is the outcome of its misregulation. Using such method, we examined the role of one specific chromatin modification, histone H2B monoubiquitination (H2Bub1), in regulating transcription. Strikingly, although H2Bub1 is widely believed to serve as a regulator of transcription elongation, its downregulation did not affect genomewide elongation rates. Instead, we found that H2Bub1 regulates the expression of distinct subsets of genes by either promoting recruitment of the transcription machinery or, conversely, favoring the pausing of this machinery shortly after initiation of transcription. Our findings demonstrate that the use of genomewide elongation rate measurements can redefine the true roles of putative transcription elongation factors. Furthermore, they provide a new understanding of the functions of H2Bub1 and its impact on gene expression patterns, which is of particular interest because H2Bub1 is often downregulated in human cancer.
Pattern discovery in sequences under a Markov assumption

In this paper we investigate the general problem of discovering recurrent patterns that are embedded in categorical sequences. An important real-world problem of this nature is motif discovery in DNA sequences. We investigate the fundamental aspects of this data mining problem that can make discovery "easy" or "hard. " We present a general framework for characterizing learning in this context by deriving the Bayes error rate for this problem under a Markov assumption. The Bayes error framework demonstrates why certain patterns are much harder to discover than others. It also explains the role of different parameters such as pattern length and pattern frequency in sequential discovery. We demonstrate how the Bayes error can be used to calibrate existing discovery algorithms, providing a lower bound on achievable performance. We discuss a number of fundamental issues that characterize sequential pattern discovery in this context, present a variety of empirical results to complement and verify the theoretical analysis, and apply our methodology to real-world motif-discovery problems in computational biology.
miR379–410 cluster miRNAs regulate neurogenesis and neuronal migration by fine‐tuning N‐cadherin

N‐cadherin‐mediated adhesion is essential for maintaining the tissue architecture and stem cell niche in the developing neocortex. N‐cadherin expression level is precisely and dynamically controlled throughout development; however, the underlying regulatory mechanisms remain largely unknown. MicroRNAs (miRNAs) play an important role in the regulation of protein expression and subcellular localisation. In this study, we show that three miRNAs belonging to the miR379–410 cluster regulate N‐cadherin expression levels in neural stem cells and migrating neurons. The overexpression of these three miRNAs in radial glial cells repressed N‐cadherin expression and increased neural stem cell differentiation and neuronal migration. This phenotype was rescued when N‐cadherin was expressed from a miRNA‐insensitive construct. Transient abrogation of the miRNAs reduced stem cell differentiation and increased cell proliferation. The overexpression of these miRNAs specifically in newborn neurons delayed migration into the cortical plate, whereas the knockdown increased migration. Collectively, our results indicate a novel role for miRNAs of the miR379–410 cluster in the fine‐tuning of N‐cadherin expression level and in the regulation of neurogenesis and neuronal migration in the developing neocortex.