Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Use of HIV Integrase Inhibitors: A Systematic Review and Meta-Analysis

Background Optimal regimen choice of antiretroviral therapy is essential to achieve long-term clinical success. Integrase inhibitors have swiftly been adopted as part of current antiretroviral regimens. The purpose of this study was to review the evidence for integrase inhibitor use in clinical settings. Methods MEDLINE and Web-of-Science were screened from April 2006 until November 2012, as were hand-searched scientific meeting proceedings. Multiple reviewers independently screened 1323 citations in duplicate to identify randomized controlled trials, nonrandomized controlled trials and cohort studies on integrase inhibitor use in clinical practice. Independent, duplicate data extraction and quality assessment were conducted. Results 48 unique studies were included on the use of integrase inhibitors in antiretroviral therapy-naive patients and treatment-experienced patients with either virological failure or switching to integrase inhibitors while virologically suppressed. On the selected studies with comparable outcome measures and indication (n = 16), a meta-analysis was performed based on modified intention-to-treat (mITT), on-treatment (OT) and as-treated (AT) virological outcome data. In therapy-naive patients, favorable odds ratios (OR) for integrase inhibitor-based regimens were observed, (mITT OR 0.71, 95% CI 0.59–0.86). However, integrase inhibitors combined with protease inhibitors only did not result in a significant better virological outcome. Evidence further supported integrase inhibitor use following virological failure (mITT OR 0.27; 95% CI 0.11–0.66), but switching to integrase inhibitors from a high genetic barrier drug during successful treatment was not supported (mITT OR 1.43; 95% CI 0.89–2.31). Integrase inhibitor-based regimens result in similar immunological responses compared to other regimens. A low genetic barrier to drug-resistance development was observed for raltegravir and elvitegravir, but not for dolutegravir. Conclusion In first-line therapy, integrase inhibitors are superior to other regimens. Integrase inhibitor use after virological failure is supported as well by the meta-analysis. Careful use is however warranted when replacing a high genetic barrier drug in treatment-experienced patients switching successful treatment.
Meninges harbor cells expressing neural precursor markers during development and adulthood

Brain and skull developments are tightly synchronized, allowing the cranial bones to dynamically adapt to the brain shape. At the brain-skull interface, meninges produce the trophic signals necessary for normal corticogenesis and bone development. Meninges harbor different cell populations, including cells forming the endosteum of the cranial vault. Recently, we and other groups have described the presence in meninges of a cell population endowed with neural differentiation potential in vitro and, after transplantation, in vivo. However, whether meninges may be a niche for neural progenitor cells during embryonic development and in adulthood remains to be determined. In this work we provide the first description of the distribution of neural precursor markers in rat meninges during development up to adulthood. We conclude that meninges share common properties with the classical neural stem cell niche, as they: (i) are a highly proliferating tissue; (ii) host cells expressing neural precursor markers such as nestin, vimentin, Sox2 and doublecortin; and (iii) are enriched in extracellular matrix components (e.g., fractones) known to bind and concentrate growth factors. This study underlines the importance of meninges as a potential niche for endogenous precursor cells during development and in adulthood.
Cathepsin Gene Family Reveals Transcriptome Patterns Related to the Infective Stages of the Salmon Louse Caligus rogercresseyi

Cathepsins are proteases involved in the ability of parasites to overcome and/or modulate host defenses so as to complete their own lifecycle. However, the mechanisms underlying this ability of cathepsins are still poorly understood. One excellent model for identifying and exploring the molecular functions of cathepsins is the marine ectoparasitic copepod Caligus rogercresseyi that currently affects the Chilean salmon industry. Using high-throughput transcriptome sequencing, 56 cathepsin-like sequences were found distributed in five cysteine protease groups (B, F, L, Z, and S) as well as in an aspartic protease group (D). Ontogenic transcriptome analysis evidenced that L cathepsins were the most abundant during the lifecycle, while cathepsins B and K were mostly expressed in the larval stages and adult females, thus suggesting participation in the molting processes and embryonic development, respectively. Interestingly, a variety of cathepsins from groups Z, L, D, B, K, and S were upregulated in the infective stage of copepodid, corroborating the complexity of the processes involved in the parasitic success of this copepod. Putative functional roles of cathepsins were conjectured based on the differential expressions found and on roles previously described in other phylogenetically related species. Moreover, 140 single nucleotide polymorphisms (SNP) were identified in transcripts annotated for cysteine and aspartic proteases located into untranslated regions, or the coding region. This study reports for the first time the presence of cathepsin-like genes and differential expressions throughout a copepod lifecycle. The identification of cathepsins together with functional validations represents a valuable strategy for pinpointing target molecules that could be used in the development of new delousing drugs or vaccines against C. rogercresseyi.
DNN acoustic modeling with modular multi-lingual feature extraction networks

In this work, we propose several deep neural network architectures that are able to leverage data from multiple languages. Modularity is achieved by training networks for extracting high-level features and for estimating phoneme state posteriors separately, and then combining them for decoding in a hybrid DNN/HMM setup. This approach has been shown to achieve superior performance for single-language systems, and here we demonstrate that feature extractors benefit significantly from being trained as multi-lingual networks with shared hidden representations. We also show that existing mono-lingual networks can be re-used in a modular fashion to achieve a similar level of performance without having to train new networks on multi-lingual data. Furthermore, we investigate in extending these architectures to make use of language-specific acoustic features. Evaluations are performed on a low-resource conversational telephone speech transcription task in Vietnamese, while additional data for acoustic model training is provided in Pashto, Tagalog, Turkish, and Cantonese. Improvements of up to 17.4% and 13.8% over mono-lingual GMMs and DNNs, respectively, are obtained.
A probabilistic model of information retrieval: development and comparative experiments - Part 1

The paper combines a comprehensive account of a probabilistic model of retrieval with new systematic experiments on TREC Programme material. It presents the model from its foundations through its logical development to cover more aspects of retrieval data and a wider range of system functions. Each step in the argument is matched by comparative retrieval tests, to provide a single coherent account of a major line of research. The experiments demonstrate, for a large test collection, that the probabilistic model is e(cid:128)ective and robust, and that it responds appropriately, with major improvements in performance, to key features of retrieval situations. Part 1 covers the foundations and the model development for document collection and relevance data, along with the test apparatus. Part 2 covers the further development and elaboration of the model, with extensive testing, and brieﬂy considers other environment conditions and tasks, model training, concluding with comparisons with other approaches and an overall assessment. Data and results tables for both parts are given in Part 1. Key results are summarised in Part 2 . 7 2000 Elsevier Science Ltd. All rights reserved.
Binge Drinkers Are Fast, Able to Stop – but They Fail to Adjust

Abstract Binge drinking leads to brain damage. However, at present few studies have taken into account the continuity in the binge drinking phenomenon, and treated binge drinking as a clearly separable category from other types of drinking patterns. The aim of the present study was to investigate whether severity of binge drinking can predict specific neurocognitive changes in healthy young adults. A total of 121 students aged 18 to 25 were assessed by means of the three last questions of the Alcohol Use Questionnaire combined into binge score. The binge score was entered as a predictor of cognitive performance of the CANTAB Stop Signal Task including reaction time, inhibition processing time, and response adjustment. Anxiety and depression symptoms were also measured. Binge score significantly predicted less adjustment following failures, and faster reaction times. Binge score did not predict inhibition performance. Symptoms of depression and anxiety were not significantly related to binge score. Binge drinking in healthy young adults predicts impairment in response adjustment and fast reaction time, but is unrelated to inhibition. The study supports the view that binge drinking is a continuous phenomenon, rather than discrete category, and the findings are possibly shedding light on why binge drinkers continue their drinking pattern despite negative consequences. (JINS, 2016, 22, 38–46)
Text analysis of MEDLINE for discovering functional relationships among genes: evaluation of keyword extraction weighting schemes

One of the key challenges of microarray studies is to derive biological insights from the gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the functional links among genes. However, the quality of the keyword lists significantly affects the clustering results. We compared two keyword weighting schemes: normalised z-score and term frequency-inverse document frequency (TFIDF). Two gene sets were tested to evaluate the effectiveness of the weighting schemes for keyword extraction for gene clustering. Using established measures of cluster quality, the results produced from TFIDF-weighted keywords outperformed those produced from normalised z-score weighted keywords. The optimised algorithms should be useful for partitioning genes from microarray lists into functionally discrete clusters.
General and Analytic Solutions of the Ortega Equation

[Ortega (1985)][1] proposed a simple first-order differential equation to describe plant cell extension and, unlike the Lockhart equation ([Lockhart, 1965][2]), it takes into account elastic deformation of the cell wall. [Cosgrove (1985)][3] and [Ortega (1985)][1] solved the equation for the
Influence of firing conditions and production methods on fracture strength of titanium-based metal ceramic crowns

Abstract Objectives: This study evaluated the effect of argon atmosphere compared with vacuum during porcelain firing on the fracture strength of crowns made of porcelain and electron beam melted (EBM) Ti-6Al-4 V, cast commercially pure titanium or milled commercially pure titanium. Methods: Sixty crown copings of c. p. titanium, Ti-6Al-4 V alloy and porcelain were fabricated using three production techniques. The copings were fired either under vacuum or in an argon gas atmosphere. Specimens were subdivided into groups of cast c. p. titanium, milled c. p. titanium and EBM Ti-6Al-4 V which were further subdivided according to firing modes employing either vacuum or argon gas. The 60 specimens were subjected to cyclic preloading and thermocycling, and were then individually loaded until interface fractured. Differences between the group mean values were calculated using the one-way ANOVA and Tukey’s range test. Two fractured samples from each group were cut with a diamond blade and examined using SEM and EDS for visualization and chemical composition analysis of the fractured interface. Results: The highest mean fracture strength values, though not significant, were recorded for the groups fired in argon atmosphere, and the lowest mean fracture strength values were recorded for the groups fired in vacuum, with one exception. Comparing the two main groups of firing atmosphere, no significant difference could be documented. SEM and EDS analysis indicated clear differences in composition and structure between the groups included in the study. Conclusions: Firing in argon atmosphere does not significantly improve the fracture strength of porcelain bonded to titanium.
Trauma in Pregnancy

Acute traumatic injury during pregnancy is a significant contributor to maternal and fetal morbidity and mortality in the United States. Motor vehicle accidents are the leading cause of injury-related maternal death, followed by violence and assault. Lack of seat belts or other restraints increases the risks of both maternal and fetal morbidity and mortality. The American College of Obstetricians and Gynecologists recommends proper seat belt use by all pregnant women and screening for domestic abuse. Maternal injury and death from physical abuse is prevalent, and in some communities, homicide is a major cause of pregnancy-associated maternal death. Blunt trauma most often occurs as a result of motor vehicle accidents, whereas penetrating trauma results from gunshots or stabbings. Blunt trauma to the abdomen increases the risk for placental abruption, and direct fetal injury is more likely with penetrating trauma. Management strategies in acute maternal trauma must focus on a thorough assessment of the mother. A coordinated team effort that includes the obstetrician is essential to ensure optimal maternal and fetal outcomes. Imaging studies should not be delayed because of concerns of fetal radiation exposure, because the risk is minimal with usual imaging procedures, especially in mid-to-late pregnancy. The obstetrician should serve in a consultative role if nonobstetric surgical care is required and must also be prepared to intervene on behalf of the mother and the fetus if trauma care is compromised by the pregnancy. Perimortem cesarean delivery should be considered early in the resuscitation of a pregnant trauma victim, especially when fetal viability is a concern. Once the mother is stabilized in the emergency setting, she should be transported for appropriate maternal and fetal observation until both mother and fetus are clear of danger. It is essential that the clinician and staff maintain thorough and accurate documentation and recording of the chronology of events, the maternal and fetal assessment, and the management and outcome of the pregnancy.
Immunization with Recombinant Helicobacter pylori Urease in Specific-Pathogen-Free Rhesus Monkeys (Macaca mulatta)

ABSTRACT Immunization with urease can protect mice from challenge withHelicobacter pylori, though results vary depending on the particular vaccine, challenge strain, and method of evaluation. Unlike mice, rhesus monkeys are naturally colonized with H. pyloriand so may provide a better estimate of vaccine efficacy in humans. The purpose of this study was to examine the effectiveness of H. pylori urease as a vaccine in specific-pathogen (H. pylori)-free rhesus monkeys. Monkeys raised from birth and documented to be free of H. pylori were vaccinated with orogastric (n = 4) or intramuscular (n = 5) urease. Two control monkeys were sham vaccinated. All monkeys were challenged with a rhesus monkey-derived strain of H. pylori, and the effects of vaccination were evaluated by use of quantitative cultures of gastric tissue, histology, and measurement of serum immunoglobulin G (IgG) and salivary IgA. Despite a humoral immune response, all monkeys were infected afterH. pylori challenge, and there were no differences in the density of colonization. Immunization with urease therefore does not fully protect against challenge with H. pylori. An effective vaccine to prevent H. pylori infection will require different or more likely additional antigens, as well as improvements in the stimulation of the host immune response.
Effects of nucleus prepositus hypoglossi lesions on visual climbing fiber activity in the rabbit flocculus.

The caudal dorsal cap (dc) of the inferior olive is involved in the control of horizontal compensatory eye movements. It provides those climbing fibers to the vestibulocerebellum that modulate optimally to optokinetic stimulation about the vertical axis. This modulation is mediated at least in part via an excitatory input to the caudal dc from the pretectal nucleus of the optic tract and the dorsal terminal nucleus of the accessory optic system. In addition, the caudal dc receives a substantial GABAergic input from the nucleus prepositus hypoglossi (NPH). To investigate the possible contribution of this bilateral inhibitory projection to the visual responsiveness of caudal dc neurons, we recorded the climbing fiber activity (i.e., complex spikes) of vertical axis Purkinje cells in the flocculus of anesthetized rabbits before and after ablative lesions of the NPH. When the NPH ipsilateral to the recorded flocculus was lesioned, the spontaneous complex spike firing frequency did not change significantly; but when both NPHs were lesioned, the spontaneous complex spike firing frequency increased significantly. When only the contralateral NPH was lesioned, the spontaneous complex spike firing frequency decreased significantly. Neither unilateral nor bilateral lesions had a significant influence on the depth of complex spike modulation during constant velocity optokinetic stimulation or on the transient continuation of complex spike modulation that occurred when the constant velocity optokinetic stimulation stopped. The effects of the lesions on the spontaneous complex spike firing frequency could not be explained when only the projections from the NPH to the inferior olive were considered. Therefore we investigated at the electron microscopic level the nature of the commissural connection between the two NPHs. The terminals of this projection were found to be predominantly GABAergic and to terminate in part on GABAergic neurons. When this inhibitory commissural connection is taken into consideration, then the effects of NPH lesions on the spontaneous firing frequency of floccular complex spikes are qualitatively explicable in terms of relative weighting of the commissural and caudal dc projections of the NPH. In summary, we conclude that in the anesthetized rabbit the inhibitory projection of the NPH to the caudal dc influences the spontaneous firing frequency of floccular complex spikes but not their modulation by optokinetic stimulation.
Analysis and simulation of sales receipt data in supermarkets

For the prediction of product sales, simulations of interactions of different individual customer behaviors in supermarkets are an appropriate approach. In order to parameterize the simulation close to reality, analysis of shopping baskets based on real sales receipt data is one of the key steps. The combination of the data analysis and simulation is in the scope of this paper Analysis of real sales receipt data was done by determining so-called customer prototypes, which are representatives of different customer classes. In order to make the simulation insensitive against short transient changes, longitudinal analysis and clustering was carried out, additionally to the common cross section analysis. Longitudinal analysis was necessary to calculate similarities between shopping basket clusters of different points in time. The resulting stabile customer prototypes then were used to parameterize a supermarket simulation. As result, this paper shows the analysis of consumer data as well as the parameterizing and validation of a supermarket simulation. The combining of data mining with simulation results in a better accuracy of analysis and the ability to evaluate influencing factors that can not be extracted directly through data mining.
A nonlocal theory of sediment transport on hillslopes

[1] Hillslopes are typically shaped by varied processes which have a wide range of event-based downslope transport distances, some of the order of the hillslope length itself. We hypothesize that this can lead to a heavy-tailed distribution of displacement lengths for sediment particles. Here, we propose that such a behavior calls for a nonlocal computation of the sediment flux, where the sediment flux at a point is not strictly a function (linear or nonlinear) of the gradient at that point only but is an integral flux taking into account the upslope topography (convolution Fickian flux). We encapsulate this nonlocal behavior in a simple fractional diffusive model which involves fractional derivatives, with the order of differentiation (1 < α ≤ 2) dictating the degree of nonlocality (α = 2 corresponds to linear diffusion and strictly local dependence on slope). The model predicts an equilibrium hillslope profile which is parabolic close to the ridgetop and transits, at a short downslope distance, to a power law with an exponent equal to the parameter α of the fractional transport model. Hillslope profiles reported in previously studied sites support this prediction. Furthermore, we show that the nonlocal transport model gives rise to a nonlinear dependency on local slope and that variable upslope topography leads to widely varying rates of sediment flux for a given local hillslope gradient. Both of these results are consistent with available field data and suggest that nonlinearity in hillslope flux relationships may arise in part from nonlocal transport effects in which displacement lengths increase with hillslope gradient. The proposed hypothesis of nonlocal transport implies that field studies and models of sediment fluxes should consider the size and displacement lengths of disturbance events that mobilize hillslope colluvium.
Alert Threshold Algorithms and Malaria Epidemic Detection

We describe a method for comparing the ability of different alert threshold algorithms to detect malaria epidemics and use it with a dataset consisting of weekly malaria cases collected from health facilities in 10 districts of Ethiopia from 1990 to 2000. Four types of alert threshold algorithms are compared: weekly percentile, weekly mean with standard deviation (simple, moving average, and log-transformed case numbers), slide positivity proportion, and slope of weekly cases on log scale. To compare dissimilar alert types on a single scale, a curve was plotted for each type of alert, which showed potentially prevented cases versus number of alerts triggered over 10 years. Simple weekly percentile cutoffs appear to be as good as more complex algorithms for detecting malaria epidemics in Ethiopia. The comparative method developed here may be useful for testing other proposed alert thresholds and for application in other populations.
Statistical Learning Across Development: Flexible Yet Constrained

Much research in the past two decades has documented infants’ and adults’ ability to extract statistical regularities from auditory input. Importantly, recent research has extended these findings to the visual domain, demonstrating learners’ sensitivity to statistical patterns within visual arrays and sequences of shapes. In this review we discuss both auditory and visual statistical learning to elucidate both the generality of and constraints on statistical learning. The review first outlines the major findings of the statistical learning literature with infants, followed by discussion of statistical learning across domains, modalities, and development. The second part of this review considers constraints on statistical learning. The discussion focuses on two categories of constraint: constraints on the types of input over which statistical learning operates and constraints based on the state of the learner. The review concludes with a discussion of possible mechanisms underlying statistical learning.