Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Mouse Model for Stable Engraftment of a Human Immune System and Human Hepatocytes

Hepatic infections by hepatitis B virus (HBV), hepatitis C virus (HCV) and Plasmodium parasites leading to acute or chronic diseases constitute a global health challenge. The species tropism of these hepatotropic pathogens is restricted to chimpanzees and humans, thus model systems to study their pathological mechanisms are severely limited. Although these pathogens infect hepatocytes, disease pathology is intimately related to the degree and quality of the immune response. As a first step to decipher the immune response to infected hepatocytes, we developed an animal model harboring both a human immune system (HIS) and human hepatocytes (HUHEP) in BALB/c Rag2-/- IL-2Rγc-/- NOD.sirpa uPAtg/tg mice. The extent and kinetics of human hepatocyte engraftment were similar between HUHEP and HIS-HUHEP mice. Transplanted human hepatocytes were polarized and mature in vivo, resulting in 20–50% liver chimerism in these models. Human myeloid and lymphoid cell lineages developed at similar frequencies in HIS and HIS-HUHEP mice, and splenic and hepatic compartments were humanized with mature B cells, NK cells and naïve T cells, as well as monocytes and dendritic cells. Taken together, these results demonstrate that HIS-HUHEP mice can be stably (> 5 months) and robustly engrafted with a humanized immune system and chimeric human liver. This novel HIS-HUHEP model provides a platform to investigate human immune responses against hepatotropic pathogens and to test novel drug strategies or vaccine candidates.
FOCAS: An Enginering Environment for Service-Based Applications

Service composition is an important topic, but so far addressed from a technical and low level perspective. The issue is not (too much) the orchestration formalism, but rather the engineering issues related to the many concerns that must be combined, to the technical complexity, to the heterogeneity and incompatibilities between available services, and the low level formalism and tools. The paper presents FOCAS, a full fledge environment that targets the different categories of stakeholders involved in the design, development, and maintenance of a service-based application. FOCAS first separates the different concerns, both functional and non functional, that made up a service-based application; second, it separates different levels of abstraction, and third it establishes links and mediations between these concerns and levels of abstraction. The paper presents FOCAS its principles, implementation and its evaluation.
Clinical Accuracy of a Continuous Glucose Monitoring System With an Advanced Algorithm

Background: We assessed the performance of a modified Dexcom G4 Platinum system with an advanced algorithm, in comparison with frequent venous samples measured on a laboratory reference (YSI) during a clinic session and in comparison to self-monitored blood glucose (SMBG) during home use. Methods: Fifty-one subjects with diabetes were enrolled in a prospective multicenter study. Subjects wore 1 sensor for 7-day use and participated in one 12-hour in-clinic session on day 1, 4, or 7 to collect YSI reference venous glucose every 15 minutes and capillary SMBG test every 30 minutes. Carbohydrate consumption and insulin dosing and timing were manipulated to obtain data in low and high glucose ranges. Results: In comparison with the laboratory reference method (n = 2,263) the system provided a mean and median absolute relative differences (ARD) of 9.0% and 7.0%, respectively. The mean absolute difference for CGM was 6.4 mg/dL when the YSIs were within hypoglycemia ranges (≤ 70 mg/dL). The percentage in the clinically accurate Clarke error grid A zone was 92.4% and in the benign error B zone was 7.1%. Majority of the sensors (73%) had an aggregated MARD in reference to YSI ≤ 10%. The MARD of CGM-SMBG for home use was 11.3%. Conclusions: The study showed that the point and rate accuracy, clinical accuracy, reliability, and consistency over the duration of wear and across glycemic ranges were superior to current commercial real-time CGM systems. The performance of this CGM is reaching that of a self-monitoring blood glucose meter in real use environment.
Balance Optimization Subset Selection (BOSS): An Alternative Approach for Causal Inference with Observational Data

Scientists in all disciplines attempt to identify and document causal relationships. Those not fortunate enough to be able to design and implement randomized control trials must resort to observational studies. To make causal inferences outside the experimental realm, researchers attempt to control for bias sources by postprocessing observational data. Finding the subset of data most conducive to unbiased or least biased treatment effect estimation is a challenging, complex problem. However, the rise in computational power and algorithmic sophistication leads to an operations research solution that circumvents many of the challenges presented by methods employed over the past 30 years.
Building large ROLAP data cubes in parallel

The pre-computation of data cubes is critical to improving the response time of on-line analytical processing (OLAP) systems and can be instrumental in accelerating data mining tasks in large data warehouses. However, as the size of data warehouses grows, the time it takes to perform this pre-computation becomes a significant performance bottleneck. This work presents a fast parallel method for generating ROLAP data cubes on a shared-nothing multiprocessor based on a novel optimized data partitioning technique. Since no shared disk is required, this method can be applied on highly scalable processor clusters consisting of standard PCs with local disks, connected via a data switch. The approach taken, which uses a ROLAP representation of the data cube, is well suited to large data warehouses on high dimensional data, and supports the generation of both fully materialized and partially materialized cubes. In comparison with previous approaches, our new method does significantly improve the scalability with respect to both, the number of processors and the I/O bandwidth (number of parallel disks). We have implemented our new parallel shared-nothing data cube generation method and evaluated it on a PC cluster, exploring relative speedup, scaleup, sizeup, output sizes and data skew. For a fact table with 16 million rows and 8 attributes, our parallel data cube generation method achieves close to optimal speedup for as many as 32 processors, generating a full data cube in under 7 minutes. For a fact table with 256 million rows and 8 attributes, our parallel method achieves optimal speedup for 32 processors, generating a full data cube consisting of /spl ap/7 billion rows (200 Gigabytes) in under 88 minutes.
Cortical Hierarchies Perform Bayesian Causal Inference in Multisensory Perception

To form a veridical percept of the environment, the brain needs to integrate sensory signals from a common source but segregate those from independent sources. Thus, perception inherently relies on solving the “causal inference problem. ” Behaviorally, humans solve this problem optimally as predicted by Bayesian Causal Inference; yet, the underlying neural mechanisms are unexplored. Combining psychophysics, Bayesian modeling, functional magnetic resonance imaging (fMRI), and multivariate decoding in an audiovisual spatial localization task, we demonstrate that Bayesian Causal Inference is performed by a hierarchy of multisensory processes in the human brain. At the bottom of the hierarchy, in auditory and visual areas, location is represented on the basis that the two signals are generated by independent sources (= segregation). At the next stage, in posterior intraparietal sulcus, location is estimated under the assumption that the two signals are from a common source (= forced fusion). Only at the top of the hierarchy, in anterior intraparietal sulcus, the uncertainty about the causal structure of the world is taken into account and sensory signals are combined as predicted by Bayesian Causal Inference. Characterizing the computational operations of signal interactions reveals the hierarchical nature of multisensory perception in human neocortex. It unravels how the brain accomplishes Bayesian Causal Inference, a statistical computation fundamental for perception and cognition. Our results demonstrate how the brain combines information in the face of uncertainty about the underlying causal structure of the world.
Structural study of the microtubule-associated protein tau locus of Alzheimer′s disease in Taiwan

Background: Haplotype structure of the microtubule-associated protein tau (MAPT) gene is associated with various tauopathies in the Caucasian population. With the knowledge that the association between MAPT structure and disease may be distinct in different ethnics, we intend to investigate the haplotype structure of MAPT in Taiwanese and test it for association with Alzheimer′s disease (AD). Methods: One hundred and eight AD patients and 108 sex- and-age matched healthy controls were recruited from the dementia outpatient clinic of Chang Gung Medical center. We genotyped the del-In9 marker that defines the extended H1 and H2 clades. We selected 21 single-nucleotide polymorphisms (SNPs) in the extended MAPT region from Japanese SNPs database and dbSNP database. Using the software TagIt, we analyzed the linkage disequilibrium structure of MAPT and compared the allele and genotype distribution between patient group and control group. Results: All the Taiwanese participants were H1 haplotypes. Linkage disequilibrium analysis showed the haplotype blocks in Taiwanese population had a smaller size in comparison to that of the Caucasian population. Single locus association showed significant p value in one of the tagging variants (rs242557) in our Taiwanese AD case-control cohorts. Conclusion: MAPT gene has four haplotype blocks in the Taiwanese population, each of around 40 kbp. In both European study and our study, the SNP rs242557 showed association with AD. Given the position of this SNP, the most possible explanation is that genetic variability in tau expression contributes to the risk of developing AD.
Exploiting Nontrivial Connectivity for Automatic Speech Recognition

Nontrivial connectivity has allowed the training of very deep networks by addressing the problem of vanishing gradients and offering a more efficient method of reusing parameters. In this paper we make a comparison between residual networks, densely-connected networks and highway networks on an image classification task. Next, we show that these methodologies can easily be deployed into automatic speech recognition and provide significant improvements to existing models.
Phosphatase activity of aerobic and facultative anaerobic bacteria.

1115 strains of aerobic and facultatively anaerobic bacteria were tested for phosphatase activity by a conventional plate method and a microtest. The microtest was devised to allow results to be read after 4 h cultivation. Phosphatase activity was found in wide range of species and strains. Besides staphylococci, where the test for phosphatase is successfully used, it may be applied as one of the valuable tests for the differentiation of the following species: Bacillus cereus, B. licheniformis, Aeromonas spp. , Vibrio parahaemolyticus, Actinobacillus spp. , Pasteurella spp. , Xanthomonas spp. , Flavobacterium spp. , Alteromonas putrefaciens, Pseudomonas maltophilia, Ps. cepacia, and some other species of Pseudomonas. The species which gave uniformly negative phosphatase reaction were as follows: Staph. saprophyticus, Acinetobacter calcoaceticus, Alcaligenes faecalis, and Bordetella bronchiseptica.
Phytoplankton essential fatty acid and phosphorus content constraints on Daphnia somatic growth and reproduction

We performed 12 experiments where the herbivorous zooplankter Daphnia pulex was fed three different phytoplankton food types (cyanophytes, chlorophytes, or cryptophytes) at two phosphorus (P) deficiency levels (C : P ~ 400 or 600) and with two different fatty acid (FA) supplements. Phosphatidylcholine liposome amendments were used to manipulate P availability and/or deliver FA in order to simultaneously test the relative importance of phytoplankton P and FA limitation as constraints on Daphnia somatic growth rate and reproduction. We used multiple regression analyses to test the data set for six main effects and three interaction terms. The six main effects tested were phytoplankton taxa, FA supplementation, FA type (EPA or FA‐mix), direct (P‐D) and indirect (P‐ID) phosphorus limitation, and P deficiency level. Food quality was most strongly affected by phytoplankton taxa followed by P‐ID, FA supplementation, the interaction between phytoplankton taxa and P‐ID, and P‐D. Daphnia fed cryptophytes grew 0.18 day‐1 faster and had an additional 2.6 eggs individual‐1 than Daphnia fed cyanophytes. Indirect P limitation reduced Daphnia somatic growth rates by 0.16 day‐1 and egg production by 2.6 eggs individual‐1. Direct P limitation reduced Daphnia growth rates by 0.04 day‐1 and egg production by 1.2 eggs individual‐1. FA supplementation improved growth by 0.09 day‐1 and egg production by 2.2 eggs individual‐1. These results suggest that FA supplementation exerted stronger effects on Daphnia somatic growth rate and reproduction than did direct P limitation. Furthermore, these results suggest that phytoplankton taxa and indirect P limitation had the greatest effects on Daphnia growth and reproduction.
Effects of dialyzer reuse on dialysis adequacy, anemia control, erythropoieting-stimulating agents use and phosphate level

Almost 50 years have passed since the first time the concept of dialyzer reuse in hemodialyzed patients was introduced for primarily economic reasons [1]. Hemodialyzers are labeled by the Food and Drug Administration (FDA) and European Medicines Agency (EMA) as single use only. In recognition of the widespread practice of reuse in the United States, in 1996 the FDA required manufacturers to label dialyzers for multiple use and to back up this claim with data showing that the performance of the dialyzer is sustained over multiple uses [2]. In Poland there is also a tendency to stop the reuse of dialyzers. There are three major concerns with reuse: the risk of infection; biochemical and immunologic effects; and loss of performance with impairment in clearance and/or ultrafiltration [3].
Development of a Genus-Specific Antigen Capture ELISA for Orthopoxviruses – Target Selection and Optimized Screening

Orthopoxvirus species like cowpox, vaccinia and monkeypox virus cause zoonotic infections in humans worldwide. Infections often occur in rural areas lacking proper diagnostic infrastructure as exemplified by monkeypox, which is endemic in Western and Central Africa. While PCR detection requires demanding equipment and is restricted to genome detection, the evidence of virus particles can complement or replace PCR. Therefore, an easily distributable and manageable antigen capture enzyme-linked immunosorbent assay (ELISA) for the detection of orthopoxviruses was developed to facilitate particle detection. By comparing the virus particle binding properties of polyclonal antibodies developed against surface-exposed attachment or fusion proteins, the surface protein A27 was found to be a well-bound, highly immunogenic and exposed target for antibodies aiming at virus particle detection. Subsequently, eight monoclonal anti-A27 antibodies were generated and characterized by peptide epitope mapping and surface plasmon resonance measurements. All antibodies were found to bind with high affinity to two epitopes at the heparin binding site of A27, toward either the N- or C-terminal of the crucial KKEP-segment of A27. Two antibodies recognizing different epitopes were implemented in an antigen capture ELISA. Validation showed robust detection of virus particles from 11 different orthopoxvirus isolates pathogenic to humans, with the exception of MVA, which is apathogenic to humans. Most orthopoxviruses could be detected reliably for viral loads above 1 × 103 PFU/mL. To our knowledge, this is the first solely monoclonal and therefore reproducible antibody-based antigen capture ELISA able to detect all human pathogenic orthopoxviruses including monkeypox virus, except variola virus which was not included. Therefore, the newly developed antibody-based assay represents important progress towards feasible particle detection of this important genus of viruses.
Culturally Informed Sport Psychology: Introduction to the Special Issue

Sport psychologists work with athletes from a vast array of cultural backgrounds. Numerous factors comprise the cultural composition of both the client and the practitioner, including, though not necessarily limited to, ethnicity, socioeconomic background and status, race, socialization, sexual orientation, religion, gender, and geographic location. These intersecting and often deeply ingrained personal variables can certainly impact the nature of the therapeutic relationship, intervention strategies, and intervention outcomes with athletic clientele. Yet, while other domains of professional psychology have long embraced the integration of cultural aspects, the field of sport psychology has been slow to join the dialogue or to learn from these relevant sources. Therefore, this special issue of the Journal of Clinical Sport Psychology was conceptualized and constructed with the intention of opening these lines of discussion to help ensure that sport psychologists are gaining a comprehensive understanding o.
Electrical Degradation and Recovery of Low-Temperature Polycrystalline Silicon Thin-Film Transistors in Polycrystalline Silicon Plasma Process

The plasma-process-induced damage (PPID) of low-temperature polycrystalline silicon (poly-Si) thin-film transistors (TFTs) during the etching of the poly-Si film was investigated in this paper. The results reveal the relationship between the device degradation and the PPID during TFT liquid-crystal-display fabrication. This degradation is caused in part by the damage at the edge of the poly-Si film in plasma exposure. The trapped-state densities Ntrap are measured to clarify the relationship between instability and plasma etching damages. The plasma-process condition substantially affects the PPID of the poly-Si etching process. The main mechanism is the generation of charge trapping states at the poly-Si grain boundary in the damaged edge of the TFT channel active region. The electrical recovery from the plasma damage is also studied with various postetching treatments. Hydrogen-base plasma treatment and laser anneal process are revealed to improve the device characteristics due to reduction of charge trapping states.
Recognition of dileucine-based sorting signals from HIV-1 Nef and LIMP-II by the AP-1 γ–σ1 and AP-3 δ–σ3 hemicomplexes

The sorting of transmembrane proteins to endosomes and lysosomes is mediated by signals present in the cytosolic tails of the proteins. A subset of these signals conform to the [DE]XXXL[LI] consensus motif and mediate sorting via interactions with heterotetrameric adaptor protein (AP) complexes. However, the identity of the AP subunits that recognize these signals remains controversial. We have used a yeast three-hybrid assay to demonstrate that [DE]XXXL[LI]-type signals from the human immunodeficiency virus negative factor protein and the lysosomal integral membrane protein II interact with combinations of the γ and σ1 subunits of AP-1 and the δ and σ3 subunits of AP-3, but not the analogous combinations of AP-2 and AP-4 subunits. The sequence requirements for these interactions are similar to those for binding to the whole AP complexes in vitro and for function of the signals in vivo. These observations reveal a novel mode of recognition of sorting signals involving the γ/δ and σ subunits of AP-1 and AP-3.
Exploration in Feature Space for Reinforcement Learning

The infamous exploration-exploitation dilemma is one of the oldest and most important problems in reinforcement learning (RL). Deliberate and effective exploration is necessary for RL agents to succeed in most environments. However, until very recently even very sophisticated RL algorithms employed simple, undirected exploration strategies in large-scale RL tasks. We introduce a new optimistic count-based exploration algorithm for RL that is feasible in high-dimensional MDPs. The success of RL algorithms in these domains depends crucially on generalization from limited training experience. Function approximation techniques enable RL agents to generalize in order to estimate the value of unvisited states, but at present few methods have achieved generalization about the agent's uncertainty regarding unvisited states. We present a new method for computing a generalized state visit-count, which allows the agent to estimate the uncertainty associated with any state. In contrast to existing exploration techniques, our $\phi$-$\textit{pseudocount}$ achieves generalization by exploiting the feature representation of the state space that is used for value function approximation. States that have less frequently observed features are deemed more uncertain. The resulting $\phi$-$\textit{Exploration-Bonus}$ algorithm rewards the agent for exploring in feature space rather than in the original state space. This method is simpler and less computationally expensive than some previous proposals, and achieves near state-of-the-art results on high-dimensional RL benchmarks. In particular, we report world-class results on several notoriously difficult Atari 2600 video games, including Montezuma's Revenge.
Growth and hormonal response of intact and castrate male cattle to trenbolone acetate and estradiol.

Effects of castration and anabolic implants on weight gain, rib soft tissue composition and serum hormones were studied in cattle using a completely random design with a 2 x 2 factorial arrangement. Half of 16 bulls and 16 steers (Angus or Angus x Brahman) aged 9 mo and weighing 290 kg were treated with an implant (200 mg trenbolone acetate and 24 mg estradiol). Half of each group were not treated with an implant. A growing diet was fed for 95 d and half the animals in each group were slaughtered. Animals in the treated groups were reimplanted with trenbolone acetate and fed a finishing diet for 84 d and slaughtered. Percentage dry matter, fat and protein were determined on soft tissue from the 9-10-11th rib. Two blood samples were collected from each animal every 2 wk. Serum was assayed for five hormones. During the growing phase, untreated and treated bulls and treated steers gained more weight and had leaner rib sections that untreated steers (P less than .05); after the finishing phase, there were no differences among groups. Untreated steers had lower insulin-like growth factor (IGF-I) and higher cortisol concentrations during both phases of growth than untreated bulls did (P less than .05). Treatment with implants increased IGF-I concentrations in steers during both phases and reduced cortisol during the finishing phase. (ABSTRACT TRUNCATED AT 250 WORDS)
Fast and reliable plagiarism detection system

Plagiarism and similarity detection software is well-known in universities for years. Despite the variety of methods and approaches used in plagiarism detection, the typical trade-off between the speed and the reliability of the algorithm still remains. We introduce a new two-step approach to plagiarism detection that combines high algorithmic performance and the quality of pairwise file comparison. Our system uses fast detection method to select suspicious files only, and then invokes precise (and slower) algorithms to get reliable results. We show that the proposed method does not noticeably reduce the quality of the pairwise comparison mechanism while providing better speed characteristics.