Miracle-dz/UniFAR-FTUs huggingface dataset:
The Welfare Implications of Using Exotic Tortoises as Ecological Replacements

Background Ecological replacement involves the introduction of non-native species to habitats beyond their historical range, a factor identified as increasing the risk of failure for translocations. Yet the effectiveness and success of ecological replacement rely in part on the ability of translocatees to adapt, survive and potentially reproduce in a novel environment. We discuss the welfare aspects of translocating captive-reared non-native tortoises, Aldabrachelys gigantea and Astrochelys radiata, to two offshore Mauritian islands, and the costs and success of the projects to date. Methodology/Principal Findings Because tortoises are long-lived, late-maturing reptiles, we assessed the progress of the translocation by monitoring the survival, health, growth, and breeding by the founders. Between 2000 and 2011, a total of 26 A. gigantea were introduced to Ile aux Aigrettes, and in 2007 twelve sexually immature A. gigantea and twelve male A. radiata were introduced to Round Island, Mauritius. Annual mortality rates were low, with most animals either maintaining or gaining weight. A minimum of 529 hatchlings were produced on Ile aux Aigrettes in 11 years; there was no potential for breeding on Round Island. Project costs were low. We attribute the success of these introductions to the tortoises’ generalist diet, habitat requirements, and innate behaviour. Conclusions/Significance Feasibility analyses for ecological replacement and assisted colonisation projects should consider the candidate species’ welfare during translocation and in its recipient environment. Our study provides a useful model for how this should be done. In addition to serving as ecological replacements for extinct Mauritian tortoises, we found that releasing small numbers of captive-reared A. gigantea and A. radiata is cost-effective and successful in the short term. The ability to release small numbers of animals is a particularly important attribute for ecological replacement projects since it reduces the potential risk and controversy associated with introducing non-native species.
Antifungal therapeutics for dimorphic fungal pathogens

ABSTRACT Dimorphic fungi cause several endemic mycoses which range from subclinical respiratory infections to life-threatening systemic disease. Pathogenic-phase cells of Histoplasma, Blastomyces, Paracoccidioides and Coccidioides escape elimination by the innate immune response with control ultimately requiring activation of cell-mediated immunity. Clinical management of disease relies primarily on antifungal compounds; however, dimorphic fungal pathogens create a number of challenges for antifungal drug therapy. In addition to the drug toxicity issues known for current antifungals, barriers to efficient drug treatment of dimorphic fungal infections include natural resistance to the echinocandins, residence of fungal cells within immune cells, the requirement for systemic delivery of drugs, prolonged treatment times, potential for latent infections, and lack of optimized standardized methodology for in vitro testing of drug susceptibilities. This review will highlight recent advances, current therapeutic options, and new compounds on the horizon for treating infections by dimorphic fungal pathogens.
Effect of polyglycolic acid sheet plus esophageal stent placement in preventing esophageal stricture after endoscopic submucosal dissection in patients with early-stage esophageal cancer: A randomized, controlled trial

AIM To assess the effect of polyglycolic acid (PGA) plus stent placement compared with stent placement alone in the prevention of post-endoscopic submucosal dissection (ESD) esophageal stricture in early-stage esophageal cancer (EC) patients. METHODS Seventy EC patients undergoing ESD were enrolled in this randomized, controlled study. Patients were allocated randomly at a 1:1 ratio into two groups as follows: (1) PGA plus stent group (PGA sheet-coated stent placement was performed); and (2) Stent group (only stent placement was performed). This study was registered on http://www.chictr. org.cn (No. chictr-inr-16008709). RESULTS The occurrence rate of esophageal stricture in the PGA plus stent group was 20.5% (n = 7), which was lower than that in the stent group (46.9%, n = 15) (P = 0.024). The mean value of esophageal stricture time was 59.6 ± 16.1 d and 70.7 ± 28.6 d in the PGA plus stent group and stent group (P = 0.174), respectively. Times of balloon dilatation in the PGA plus stent group were less than those in the stent group [4 (2-5) vs 6 (1-14), P = 0.007]. The length (P = 0.080) and diameter (P = 0.061) of esophageal strictures were numerically decreased in the PGA plus stent group, whereas no difference in location (P = 0.232) between the two groups was found. Multivariate logistic analysis suggested that PGA plus stent placement (P = 0.026) was an independent predictive factor for a lower risk of esophageal stricture, while location in the middle third (P = 0.034) and circumferential range = 1/1 (P = 0.028) could independently predict a higher risk of esophageal stricture in EC patients after ESD. CONCLUSION PGA plus stent placement is more effective in preventing post-ESD esophageal stricture compared with stent placement alone in EC patients with early-stage disease.
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

The regions bound by sequence-specific transcription factors can be highly variable across different cell types despite the static nature of the underlying genome sequence. This has been partly attributed to changes in chromatin accessibility, but a systematic picture has been hindered by the lack of large-scale data sets. Here, we use 456 binding experiments for 119 regulators and 84 chromatin maps generated by the ENCODE in six human cell types, and relate those to a global map of regulatory motif instances for these factors. We find specific and robust chromatin state preferences for each regulator beyond the previously reported open-chromatin association, suggesting a much richer chromatin landscape beyond simple accessibility. The preferentially bound chromatin states of regulators were enriched for sequence motifs of regulators relative to all states, suggesting that these preferences are at least partly encoded by the genomic sequence. Relative to all regions bound by a regulator, however, regulatory motifs were surprisingly depleted in the regulator's preferentially bound states, suggesting additional non-sequence-specific binding beyond the level predicted by the regulatory motifs. Such permissive binding was largely restricted to open-chromatin regions showing histone modification marks characteristic of active enhancer and promoter regions, whereas open-chromatin regions lacking such marks did not show permissive binding. Lastly, the vast majority of cobinding of regulator pairs is predicted by the chromatin state preferences of individual regulators. Overall, our results suggest a joint role of sequence motifs and specific chromatin states beyond mere accessibility in mediating regulator binding dynamics across different cell types.
Effect of Protein Intake on Lean Body Mass in Functionally Limited Older Men: A Randomized Clinical Trial

Importance The Institute of Medicine set the recommended dietary allowance (RDA) for protein at 0.8 g/kg/d for the entire adult population. It remains controversial whether protein intake greater than the RDA is needed to maintain protein anabolism in older adults. Objective To investigate whether increasing protein intake to 1.3 g/kg/d in older adults with physical function limitations and usual protein intake within the RDA improves lean body mass (LBM), muscle performance, physical function, fatigue, and well-being and augments LBM response to a muscle anabolic drug. Design, Setting, and Participants This randomized clinical trial with a 2 × 2 factorial design was conducted in a research center. A modified intent-to-treat analytic strategy was used. Participants were 92 functionally limited men 65 years or older with usual protein intake less thanor equal to 0.83 g/kg/d within the RDA. The first participant was randomized on September 21, 2011, and the last participant completed the study on January 19, 2017. Interventions Participants were randomized for 6 months to controlled diets with 0.8 g/kg/d of protein plus placebo, 1.3 g/kg/d of protein plus placebo, 0.8 g/kg/d of protein plus testosterone enanthate (100 mg weekly), or 1.3 g/kg/d of protein plus testosterone. Prespecified energy and protein contents were provided through custom-prepared meals and supplements. Main Outcomes and Measures The primary outcome was change in LBM. Secondary outcomes were muscle strength, power, physical function, health-related quality of life, fatigue, affect balance, and well-being. Results Among 92 men (mean [SD] age, 73.0 [5.8] years), the 4 study groups did not differ in baseline characteristics. Changes from baseline in LBM (0.31 kg; 95% CI, −0.46 to 1.08 kg; P = .43) and appendicular (0.04 kg; 95% CI, −0.48 to 0.55 kg; P = .89) and trunk (0.24 kg; 95% CI, −0.17 to 0.66 kg; P = .24) lean mass, as well as muscle strength and power, walking speed and stair-climbing power, health-related quality of life, fatigue, and well-being, did not differ between men assigned to 0.8 vs 1.3 g/kg/d of protein regardless of whether they received testosterone or placebo. Fat mass decreased in participants given higher protein but did not change in those given the RDA: between-group differences were significant (difference, −1.12 kg; 95% CI, −2.04 to −0.21; P = .02). Conclusions and Relevance Protein intake exceeding the RDA did not increase LBM, muscle performance, physical function, or well-being measures or augment anabolic response to testosterone in older men with physical function limitations whose usual protein intakes were within the RDA. The RDA for protein is sufficient to maintain LBM, and protein intake exceeding the RDA does not promote LBM accretion or augment anabolic response to testosterone. Trial Registration clinicaltrials.gov Identifier: NCT01275365
Structural Evidence of  T Cell Xeno-reactivity in the Absence of Molecular Mimicry

The T cell receptor (TCR), from a xeno-reactive murine cytotoxic T lymphocyte clone AHIII12.2, recognizes murine H-2Db complexed with peptide p1027 (FAPGVFPYM), as well as human HLA-A2.1 complexed with peptide p1049 (ALWGFFPVL). A commonly proposed model (the molecular mimicry model) used to explain TCR cross-reactivity suggests that the molecular surfaces of the recognized complexes are similar in shape, charge, or both, in spite of the primary sequence differences. To examine the mechanism of xeno-reactivity of AHIII12.2, we have determined the crystal structures of A2/p1049 and Db/p1027 to 2.5 Å and 2.8 Å resolution, respectively. The crystal structures show that the TCR footprint regions of the two class I complexes are significantly different in shape and charge. We propose that rather than simple molecular mimicry, unpredictable arrays of common and differential contacts on the two class I complexes are used for their recognition by the same TCR.
Shadow fading cross-correlation of multi-frequencies in curved subway tunnels

Radio propagation characteristics in curved tunnels are important for designing reliable communications in subway systems. In this paper, shadow fading is characterized, and cross-correlation property of shadow fading for different frequency bands is investigated based on empirical measurements. The measurements were conducted in two types of curved subway tunnels with 300 m and 500 m radii of curvatures at 980 MHz, 2400 MHz, and 5705 MHz, respectively. The impact of antenna polarization and propagation environment on shadow fading correlation at the receiver is evaluated. It is found that shadow fading with horizontal polarized antenna exhibits less correlation than with vertical polarized antenna. Strong independence of shadowing correlation and tunnel type is observed. Furthermore, a heuristic explanation of the particular shadowing correlation property in subway tunnel is presented.
Introducing Memory and Association Mechanism Into a Biologically Inspired Visual Model

A famous biologically inspired hierarchical model (HMAX model), which was proposed recently and corresponds to V1 to V4 of the ventral pathway in primate visual cortex, has been successfully applied to multiple visual recognition tasks. The model is able to achieve a set of position- and scale-tolerant recognition, which is a central problem in pattern recognition. In this paper, based on some other biological experimental evidence, we introduce the memory and association mechanism into the HMAX model. The main contributions of the work are: 1) mimicking the active memory and association mechanism and adding the top down adjustment to the HMAX model, which is the first try to add the active adjustment to this famous model and 2) from the perspective of information, algorithms based on the new model can reduce the computation storage and have a good recognition performance. The new model is also applied to object recognition processes. The primary experimental results show that our method is efficient with a much lower memory requirement.
Semiparametric Estimation of a Binary Choice Model with Sample Selection

In this paper we provide semiparametric estimation strategies for a sample selection model with a binary dependent variable. To the best of our knowledge, this has not been done before. We propose a control function approach based on two di erent identifying assumptions. This gives rise to semiparametric estimators which are extensions of the Klein and Spady (1993), maximum score (Manski, 1975) and smoothed maximum score (Horowitz, 1992) estimators. We provide Monte Carlo evidence and an empirical example to study the nite sample properties of our estimators. Finally, we outline an extension of these estimators to the case of endogenous covariates.
Thermally Stable Ohmic Contact to p-Type 4H-SiC Based on Ti3SiC2 Phase

In this study, the electrical properties of Ti3SiC2 based ohmic contacts formed on p-type 4H-SiC(0001) 4°-off substrates were studied. The Ti3SiC2 thin films were grown by thermal annealing (from 900°C to 1200°C) of Ti50Al50 layer deposited by magnetron sputtering. XRD analyzes were performed on the samples to further investigate the compounds formed after annealing. Using TLM structures, the Specific Contact Resistance (SCR) at room temperature of all contacts was measured. The temperature dependence (up to 600°C) of the SCR was studied to understand the current mechanisms at the interface and to determine the barrier height value by fitting the experimental results using the thermionic field emission theory. Aging tests showed that Ti3SiC2 based contacts were stable up to 200h at 600°C under Ar.
Review of computerized cognitive behavioral therapy for depression in adolescents

Rate of depression among adolescents is increasing each year but only few received evidence-based treatment due to limited access. Computerized cognitive behavioral therapy (CBT) is invented to address this problem and is proven efficient to treat depression in adults. However, its effectiveness to treat adolescents still remains a question. Current literature suggests that engagement when using computerized CBT is an issue. The objective of this study is to analyze existing computerized CBT programs to address the engagement issue. Interviews with professionals also have been conducted to get some verifications and views on engagement in computerized CBT with adolescents. From the study, we can conclude that further research needs to be conducted especially on how to engage adolescents better.
EmotionSpot: Monitoring of user preferences and viewing habits

New method for monitoring of user preferences and viewing habits is suggested. It is based on registration of user emotional estimates during content consumption and creation of corresponding user emotional profiles. This method is applicable to any type of content. In contrast to people meters approach it provides “quality” evaluation and analysis of content consumption. Moreover it does not require additional equipment and can be used with existing consumer devices.
Feature Selection via Pareto Multi-objective Genetic Algorithms

ABSTRACT Feature selection, an important combinatorial optimization problem in data mining, aims to find a reduced subset of features of high quality in a dataset. Different categories of importance measures can be used to estimate the quality of a feature subset. Since each measure provides a distinct perspective of data and of which are their important features, in this article we investigate the simultaneous optimization of importance measures from different categories using multi-objective genetic algorithms grounded in the Pareto theory. An extensive experimental evaluation of the proposed method is presented, including an analysis of the performance of predictive models built using the selected subsets of features. The results show the competitiveness of the method in comparison with six feature selection algorithms. As an additional contribution, we conducted a pioneer, rigorous, and replicable systematic review on related work. As a result, a summary of 93 related papers strengthens features of our method.
Robots and Socio-Ethical Implications [Guest Editorial]

The articles in this special section focus on the social implications of robotics and artificial intelligence. From lifelike androids to virtual assistants, industrial machines to drones, today’s robot creations, including those in automation, are used to perform any number of specific tasks. These undertakings are repetitive in nature and suggest that we are still a long way from manufacturing “all-purpose” utility robots. History teaches us much about technological innovation and the perils of over-promising.
The effect of the first-generation HCV-protease inhibitors boceprevir and telaprevir and the relation to baseline NS3 resistance mutations in genotype 1: experience from a small Swedish cohort

Abstract Background: The clinical experience with protease-inhibitor (PI) triple regimen appears disappointing regarding effect, side effects, high work load, and costs. This real-world study evaluates baseline and emerging resistance-associated substitutions (RASs) and their significance for treatment outcome. Method: Thirty-six genotype 1a/b patients treated according to Swedish recommendations during 2011–2013 with triple therapy including pegylated interferon and ribavirin in combination with a protease-inhibitor, either boceprevir (BOC) or telaprevir (TVR), were retrospectively evaluated. Frozen serum samples from the patients were tested for resistance with pan-genotypic population sequencing. Results: Overall, 56% (20/36) of the patients achieved sustained viral response (SVR). The SVR was comparable between BOC (64%; 9/14) and TVR (50%; 11/22) (p = 0.07), and the IL28B type non-CC (48%; 12/25) and CC (46%; 6/13) (p = 0.77). The SVR was higher in patients without cirrhosis (89.5%; 17/19) (p < 0.0005), in treatment-naïve patients (70%; 14/20) (p = 0.02), and those with low viral load (<800,000 IU/mL) (66.7%; 8/12) (p < 0.0002), compared to those with cirrhosis (17.6%; 3/17), treatment-experienced (37.5%; 6/16), and high viral load (>800,000 IU/mL) (50%; 12/24). Conclusion: PI triple regimes were highly effective in treatment-naïve patients without cirrhosis, but in this real-world cohort an inferior effect was evident in cirrhotic and treatment-experienced patients. Although tested on a limited sample, the baseline resistance testing seems to have no impact on prediction of therapy outcome. The reason could be that the baseline RASs T54S and V55A have relatively low resistance towards BOC and TVR. Emerging RASs, mainly R155K, with known high resistance to BOC and TVR were frequently found in non-responders.
An Adaptively Speculative Execution Strategy Based on Real-Time Resource Awareness in a Multi-Job Heterogeneous Environment

MapReduce (MRV1), a popular programming model, proposed by Google, has been well used to process large datasets in Hadoop, an open source cloud platform. Its new version MapReduce 2.0 (MRV2) developed along with the emerging of Yarn has achieved obvious improvement over MRV1. However, MRV2 suffers from long finishing time on certain types of jobs. Speculative Execution (SE) has been presented as an approach to the problem above by backing up those delayed jobs from low-performance machines to higher ones. In this paper, an adaptive SE strategy (ASE) is presented in Hadoop-2.6. 0. Experiment results have depicted that the ASE duplicates tasks according to real-time resources usage among work nodes in a cloud. In addition, the performance of MRV2 is largely improved using the ASE strategy on job execution time and resource consumption, whether in a multi-job environment.
King cobra peptide OH-CATH30 as a potential candidate drug through clinic drug-resistant isolates

Cationic antimicrobial peptides (AMPs) are considered as important candidate therapeutic agents, which exert potent microbicidal properties against bacteria, fungi and some viruses. Based on our previous findings king cobra cathelicidin (OH-CATH) is a 34-amino acid peptide that exerts strong antibacterial and weak hemolytic activity. The aim of this research is to evaluate the efficacy of both OH-CATH30 and its analog D-OH-CATH30 against clinical isolates comparing with routinely utilized antibiotics in vitro. In this study, 584 clinical isolates were tested (spanning 2013–2016) and the efficacy of the candidate peptides and antibiotics were determined by a broth microdilution method according to the CLSI guidelines. Among the 584 clinical isolates, 85% were susceptible to OH-CATH30 and its analogs. Both L- and D-OH-CATH30 showed higher efficacy against (toward) Gram-positive bacteria and stronger antibacterial activity against nearly all Gram-negative bacteria tested compare with antibiotics. The highest bactericidal activity was detected against Acinetobacter spp. , including multi-drug-resistant Acinetobacter baumannii (MRAB) and methicillin-resistant Staphylococcus aureus (MRSA). The overall efficacy of OH-CATH30 and its analogs was higher than that of the 9 routinely used antibiotics. OH-CATH30 is a promising candidate drug for the treatment of a wide variety of bacterial infections which are resistant to many routinely used antimicrobial agents.
A New Method for the Construction of Evolving Embedded Representations of Words

There are several natural language processing tasks such as natural language understanding, information retrieval and social network analysis which require dynamic update of the word embeddings representation so as to keep pace with the words meanings evolving. Thanks to their ability to capture both syntactic and semantic information within language, the continuous bag-of-words, a learning word representation model, has gained a lot of attention from researchers and has been successfully applied to different NLP tasks. However, this model does not adequately capture the change of word semantics over time. This paper provides a new perspective to determine the semantic similarity of words over time by constructing several representations of words that reflect the semantic change of words based on latest embeddings. We examine the performance of our improved CBOW on an evolved data base collected from English Wikipedia pages. Our learned embeddings illustrate the semantic evolution of words better than the original CBOW.