Miracle-dz/UniFAR-FTUs huggingface dataset:
Impaired CD4 T-cell count response to combined antiretroviral therapy in antiretroviral-naive HIV-infected patients presenting with tuberculosis as AIDS-defining condition.

BACKGROUND The impact of human immunodeficiency virus (HIV)-associated tuberculosis on CD4 T-cell count response to combined antiretroviral therapy (cART) is poorly investigated. METHODS A collaborative analysis including HIV-infected patients prospectively enrolled in 4 Italian clinical cohorts was conducted. Patients were grouped according to Centers for Disease Control and Prevention stage at the start of cART as having tuberculosis, having AIDS but not tuberculosis (nontuberculosis AIDS), and not having AIDS (AIDS free). Time to CD4 T-cell count of at least 100, 200, and 300 cells/μL above pre-cART levels and to CD4 T-cell count of >500 cells/μL were major end points. Survival analysis with time-fixed and time-dependent covariates was used. RESULTS A total of 6528 patients were eligible; 125 patients (2%) had tuberculosis, 1062 (16%) had nontuberculosis AIDS, and 5341 (82%) were AIDS free. Patients with tuberculosis had a significantly reduced chance of CD4 T-cell count increase compared with AIDS-free patients as well as those with nontuberculosis AIDS, regardless of the primary outcome considered for a given value of confounders measured at baseline (eg, for >200 cells/μL above baseline; relative hazard, 0.71; P = .02), although it was no longer significant after further adjustment for current level of viral load suppression (relative hazard, 0.80; P = .11). There was a trend for reduced virological response in patients treated concomitantly for tuberculosis and HIV infection compared with those who were treated separately in time (P = .09). CONCLUSIONS HIV-infected patients starting cART with a tuberculosis diagnosis showed an impaired immune recovery to cART compared with AIDS-free patients and those with nontuberculosis AIDS. It seems to be driven mainly by a delay in achieving viral suppression. Whether this may be due to interactions between antituberculosis drugs and antiretrovirals needs to be investigated.
Discovery of six Lyα emitters near a radio galaxy at z ∼ 5.2

We present the results of narrow-band and broad-band imaging with the Very Large Telescope* of the field surrounding the radio galaxy TN J0924-2201 at z = 5.2. Fourteen candidate Lya emitters with a rest-frame equivalent width of >20 A were detected. Spectroscopy of 8 of these objects showed that 6 have redshifts similar to that of the radio galaxy. The density of emitters at the redshift of the radio galaxy is estimated to be a factor 1.5-6.2 higher than in the field, and comparable to the density of Lya emitters in radio galaxy protoclusters at z = 4.1, 3.1 and 2.2. The Lya emitters near TN J0924-2201 could therefore be part of a structure that will evolve into a massive cluster. These observations confirm that substantial clustering of Lyα emitters occurs at z > 5 and support the idea that radio galaxies pinpoint high density regions in the early Universe.
Sampling large conformational transitions: adenylate kinase as a testing ground

A fundamental problem in computational biophysics is to deduce the function of a protein from the structure. Many biological macromolecules such as enzymes, molecular motors or membrane transport proteins perform their function by cycling between multiple conformational states. Understanding such conformational transitions, which typically occur on the millisecond to second time scale, is central to understanding protein function. Molecular dynamics (MD) computer simulations have become an important tool to connect molecular structure to function, but equilibrium MD simulations are rarely able to sample on time scales longer than a few microseconds – orders of magnitudes shorter than the time scales of interest. A range of different simulation methods have been proposed to overcome this time-scale limitation. These include calculations of the free energy landscape and path sampling methods to directly sample transitions between known conformations. All these methods solve the problem to sample infrequently occupied but important regions of configuration space. Many path-sampling algorithms have been applied to the closed open transition of the enzyme adenylate kinase (AdK), which undergoes a large, clamshell-like conformational transition between an open and a closed state. Here we review approaches to sample macromolecular transitions through the lens of AdK. We focus our main discussion on the current state of knowledge – both from simulations and experiments – about the transition pathways of ligand-free AdK, its energy landscape, transition rates and interactions with substrates. We conclude with a comparison of the discussed approaches with a view towards quantitative evaluation of path-sampling methods.
Conceptualising fairness in classroom assessment: exploring the value of organisational justice theory

ABSTRACT Fairness has recently moved into the spotlight as a core foundation of classroom assessment (CA). However, despite its significance for high-quality CA, fairness definitions and theories have been limited in the literature. Driven by the critiques directed at the ‘inadequacy’ and ‘fuzziness’ around CA fairness and recommendations to conceptualise fairness particularly for CA contexts, this paper aims to provide an explicit definition of CA fairness. Specifically, this paper brings together current scholarship in organisational justice theory and recent findings from the CA fairness literature to offer a more thorough conceptualisation. This conceptualisation not only presents a distinction between justice and fairness, but also provides a novel discussion of the relationship between justice and fairness with consideration for potential effects on students’ learning. The paper concludes with an agenda for further research on CA fairness.
Explicit Analytic Solution for Inverse Kinematics of Bioloid Humanoid Robot

The aim of this paper is to explain basic kinematic concepts applied to humanoid robots. The structure of a Bioloid with three degrees of freedom (DoFs) for the arms and six DoFs for the legs is considered. The solution of direct and inverse kinematics (IK) is presented for both arms and legs. Our main contribution is to solve in a detailed manner the legs IK because this is the basis for planning walking motions.
Composition, morphology and mechanics of hagfish slime

SUMMARY Hagfish slime consists of mucins and protein threads that are released from slime glands and mix with seawater to produce an ephemeral material with intriguing physical properties. We recently characterized the mechanics of the slime's fibrous component, and here we report the first mechanical properties of the mucin component and the slime as a whole. Our results suggest that hagfishes can produce remarkable quantities of the slime because it is almost three orders of magnitude more dilute than typical mucus secretions. Mechanical experiments using whole slime produced in vitro demonstrate that the slime threads dominate the slime's material properties and impart elasticity. Mucins impart viscosity at the strain rates tested and are important for rapid deployment of the slime. We also found that slime threads are tapered at both ends, which suggested to us that hagfish slime might best be modeled as a discontinuous fibre-reinforced composite. Our measurements demonstrate that the mucins are not capable of providing shear linkage between threads, but this is not necessary because the threads are long enough to span an entire slime mass. Our findings suggest that hagfish slime consists mainly of bulk seawater entrained between mucin-coated threads, and in this way functions more like a fine sieve than coherent mucus. These results are consistent with the hypothesis that the slime has evolved as a defense against gill-breathing predators.
Confronting ideologies: A discourse analysis of in-service teachers’ translanguaging stance through an ecological lens

ABSTRACT This study considers the potential for translanguaging to disrupt monolingual ideologies through development of in-service teachers’ (ISTs) translanguaging stance. Using discourse analysis, we examined learning outcomes among five ISTs to consider what ideological constraints limited their adoption of a translanguaging stance and how, if at all, they moved beyond these constraints. Findings highlight micro-, meso-, and macrolevel influences that constrained ISTs’ adoption of translanguaging and the productive ways they imagined addressing these limitations. Included are implications for how teacher education might support teachers in adopting a translanguaging stance.
Myxovirus resistance, osteopontin and suppressor of cytokine signaling 3 polymorphisms predict hepatitis C virus therapy response in an admixed patient population: comparison with IL28B

OBJECTIVES: Suppressor of cytokine signaling 3, myxovirus resistance protein and osteopontin gene polymorphisms may influence the therapeutic response in patients with chronic hepatitis C, and an association with IL28 might increase the power to predict sustained virologic response. Our aims were to evaluate the association between myxovirus resistance protein, osteopontin and suppressor of cytokine signaling 3 gene polymorphisms in combination with IL28B and to assess the therapy response in hepatitis C patients treated with pegylated-interferon plus ribavirin. METHOD: Myxovirus resistance protein, osteopontin, suppressor of cytokine signaling 3 and IL28B polymorphisms were analyzed by PCR-restriction fragment length polymorphism, direct sequencing and real-time PCR. Ancestry was determined using genetic markers. RESULTS: We analyzed 181 individuals, including 52 who were sustained virologic responders. The protective genotype frequencies among the sustained virologic response group were as follows: the G/G suppressor of cytokine signaling 3 (rs4969170) (62.2%); T/T osteopontin (rs2853744) (60%); T/T osteopontin (rs11730582) (64.3%); and the G/T myxovirus resistance protein (rs2071430) genotype (54%). The patients who had ≥3 of the protective genotypes from the myxovirus resistance protein, the suppressor of cytokine signaling 3 and osteopontin had a greater than 90% probability of achieving a sustained response (p<0.0001). The C/C IL28B genotype was present in 58.8% of the subjects in this group. The sustained virological response rates increased to 85.7% and 91.7% by analyzing C/C IL28B with the T/T osteopontin genotype at rs11730582 and the G/G suppressor of cytokine signaling 3 genotype, respectively. Genetic ancestry analysis revealed an admixed population. CONCLUSION: Hepatitis C genotype 1 patients who were responders to interferon-based therapy had a high frequency of multiple protective polymorphisms in the myxovirus resistance protein, osteopontin and suppressor of cytokine signaling 3 genes. The combined analysis of the suppressor of cytokine signaling 3 and IL28B genotypes more effectively predicted sustained virologic response than IL28B analysis alone.
Mergers of Neutron Star-Black Hole Binaries with Small Mass Ratios: Nucleosynthesis, Gamma-Ray Bursts, and Electromagnetic Transients

We discuss simulations of the coalescence of black hole-neutron star binary systems with black hole masses between 14 and 20 M☉. The calculations use a three-dimensional smoothed particle hydrodynamics code, a temperature-dependent, nuclear equation of state, and a multiflavor neutrino scheme. General relativistic effects are mimicked using the Paczyński-Wiita pseudo-potential and gravitational radiation reaction forces. Unlike previous, purely Newtonian calculations, in none of the explored cases does episodic mass transfer occur. The neutron star is always completely disrupted after most of its mass has been transferred directly into the hole. For black hole masses between 14 and 16 M☉ an accretion disk forms; large parts of it, however, are inside the last stable orbit and therefore falling with large radial velocities into the hole. These disks are (opposite to the neutron star merger case) thin and—except for a spiral shock—essentially cold. For higher mass black holes (MBH ≥ 18 M☉) almost the entire neutron star disappears in the hole without forming an accretion disk. In these cases the surviving material is spun up by tidal torques and ejected as a half-ring of neutron-rich matter. None of the investigated systems is a promising gamma-ray burst (GRB) central engine. We find between 0.01 and 0.2 M☉ of the neutron star to be dynamically ejected. Like in a Type Ia supernova, the radioactive decay of this material powers a light curve with a peak luminosity of a few times 1044 ergs s-1. The maximum is reached about 3 days after the coalescence and is mainly visible in the optical/near-infrared band. The coalescence itself may produce a precursor pulse with a thermal spectrum of ~10 ms duration.
Characterization of lignocellulolytic activities from fungi isolated from the deep-sea sponge Stelletta normani

Extreme habitats have usually been regarded as a source of microorganisms that possess robust proteins that help enable them to survive in such harsh conditions. The deep sea can be considered an extreme habitat due to low temperatures (<5°C) and high pressure, however marine sponges survive in these habitats. While bacteria derived from deep-sea marine sponges have been studied, much less information is available on fungal biodiversity associated with these sponges. Following screening of fourteen fungi isolated from the deep-sea sponge Stelletta normani sampled at a depth of 751 metres, three halotolerant strains (TS2, TS11 and TS12) were identified which displayed high CMCase and xylanase activities. Molecular based taxonomic approaches identified these strains as Cadophora sp. TS2, Emericellopsis sp. TS11 and Pseudogymnoascus sp. TS 12. These three fungi displayed psychrotolerance and halotolerant growth on CMC and xylan as sole carbon sources, with optimal growth rates at 20°C. They produced CMCase and xylanase activities, which displayed optimal temperature and pH values of between 50–70°C and pH 5–8 respectively, together with good thermostability and halotolerance. In solid-state fermentations TS2, TS11 and TS12 produced CMCases, xylanases and peroxidase/phenol oxidases when grown on corn stover and wheat straw. This is the first time that CMCase, xylanase and peroxidase/phenol oxidase activities have been reported in these three fungal genera isolated from a marine sponge. Given the biochemical characteristics of these ligninolytic enzymes it is likely that they may prove useful in future biomass conversion strategies involving lignocellulosic materials.
Using Convolutional Neural Networks to Recognize Rhythm Stimuli from Electroencephalography Recordings

Electroencephalography (EEG) recordings of rhythm perception might contain enough information to distinguish different rhythm types/genres or even identify the rhythms themselves. We apply convolutional neural networks (CNNs) to analyze and classify EEG data recorded within a rhythm perception study in Kigali, Rwanda which comprises 12 East African and 12 Western rhythmic stimuli - each presented in a loop for 32 seconds to 13 participants. We investigate the impact of the data representation and the pre-processing steps for this classification tasks and compare different network structures. Using CNNs, we are able to recognize individual rhythms from the EEG with a mean classification accuracy of 24.4% (chance level 4.17%) over all subjects by looking at less than three seconds from a single channel. Aggregating predictions for multiple channels, a mean accuracy of up to 50% can be achieved for individual subjects.
Functional polymorphisms in cell death pathway genes FAS and FASL contribute to risk of lung cancer

Background: The FAS and FASL system plays a key role in regulating apoptotic cell death and corruption of this signalling pathway has been shown to participate in immune escape and tumorigenesis. There is reduced expression of FAS but elevated expression of FASL in many types of human cancers including lung cancer. We recently reported an association between functional polymorphisms in FAS (−1377G→A) and FASL (−844T→C) and risk of oesophageal cancer. Objective: To examine the contribution of these polymorphisms to risk of developing lung cancer. Methods: Genotypes of 1000 lung cancer patients and 1270 controls were analysed by PCR based restriction fragment length polymorphism. Associations with risk of lung cancer were estimated by logistic regression. Results: Compared with non-carriers, there was a 1.6 fold excess risk of developing lung cancer for carriers of the FAS −1377AA genotype (odds ratio (OR) 1.59, 95% confidence interval (CI) 1.21 to 2.10; p = 0.001), and 1.8 fold excess risk (OR 1.79, 95% CI 1.26 to 2.52; p = 0.001) for carriers of FASL −844CC. Gene–gene interaction of FAS and FASL polymorphisms increased risk of lung cancer in a multiplicative manner (OR for the carriers of both FAS −1377AA and FASL −844CC genotypes 4.18, 95% CI 2.83 to 6.18). Gene–environment interaction of FAS or FASL polymorphism and smoking associated with increased risk of lung cancer was also found. Conclusion: These results are consistent with our initial findings in oesophageal cancer and further support the hypothesis that the FAS and FASL triggered apoptosis pathway plays an important role in human carcinogenesis.
Physicochemical and Phytochemical Analyses of Copra and Oil of Cocos nucifera L. (West Coast Tall Variety)

Coconut copra from West coast tall variety, cultivated in Kerala, India, was subjected to aqueous and solvent extractions (using n-hexane). Additionally, oil was extracted from the copra in Soxhlet assembly using petroleum ether (b.p. 60–80°C). Physicochemical and phytochemical analyses were conducted for the extracts and the oil, with commercial coconut oil as the experimental control. The physicochemical analyses showed that the aqueous extract of copra was milky-white in color with a sweet odor, while the solvent extract was pale yellow and odorless. The commercial oil had 0.08 ± 0.02% oleic acid and a TOTOX value of 7.73 ± 0.78, lower than the Soxhlet extracted oil. Among all the extracts and oils, best phytochemical properties, antioxidant activity (DPPH activity, IC50 value 0.04 ± 0.01 mg/mL), total phenol (0.96 ± 0.04 mg gallic acid eq./g dry copra), reducing power (40.49 ± 1.84 mg BHT eq./g dry copra), and anti-inflammatory activity (NO activity, IC50 value 0.77 ± 0.06 mg/mL) were obtained in the commercial coconut oil, followed by the Soxhlet extracted oil, aqueous extract, and solvent extract. Fatty acid composition analyses showed mainly medium chain fatty acids in the copra oil with lauric acid as the predominant fatty acid (51.88% and 44.84% in Soxhlet extracted and commercial oils, resp.).
Major changes in the core developmental pathways of nematodes: Romanomermis culicivorax reveals the derived status of the Caenorhabditis elegans model

Background Despite its status as a model organism, the development of Caenorhabditis elegans is not necessarily archetypical for nematodes. The phylum Nematoda is divided into the Chromadorea (indcludes C. elegans) and the Enoplea. Compared to C. elegans, enoplean nematodes have very different patterns of cell division and determination. Embryogenesis of the enoplean Romanomermis culicivorax has been studied in great detail, but the genetic circuitry underpinning development in this species is unknown. Results We created a draft genome of R. culicivorax and compared its developmental gene content with that of two nematodes, C. elegans and Trichinella spiralis (another enoplean), and a representative arthropod Tribolium castaneum. This genome evidence shows that R. culicivorax retains components of the conserved metazoan developmental toolkit lost in C. elegans. T. spiralis has independently lost even more of the toolkit than has C. elegans. However, the C. elegans toolkit is not simply depauperate, as many genes essential for embryogenesis in C. elegans are unique to this lineage, or have only extremely divergent homologues in R. culicivorax and T. spiralis. These data imply fundamental differences in the genetic programmes for early cell specification, inductive interactions, vulva formation and sex determination. Conclusions Thus nematodes, despite their apparent phylum-wide morphological conservatism, have evolved major differences in the molecular logic of their development. R. culicivorax serves as a tractable, contrasting model to C. elegans for understanding how divergent genomic and thus regulatory backgrounds can generate a conserved phenotype. The availability of the draft genome will promote use of R. culicivorax as a research model.
The Benefits of Option Use by Mutual Funds

Based on comprehensive regulatory data on equity mutual fund option use from the SEC's N-SAR filings, we are the first to present consistent evidence that equity funds' option use generates higher risk-adjusted performance. We further show that this is a direct effect of option use and not an indirect effect of other fund characteristics. Option use also directly results in lower systematic risk, as funds show significantly lower market betas during periods of options usage. Finally, mutual funds use options mainly for hedging as they primarily use protective puts and covered calls. These results are independent of known phenomena, such as the low beta anomaly, and robust to tests for endogeneity and a novel 5-factor model including an investable option strategy factor (IOS). Overall, our findings show that mutual fund option use is beneficial to investors and does not pose risk to the financial system as feared by the SEC. Our results are thus important for investors as well as regulators.
Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L.) Genome

Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare) proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns with larger pattern sizes than those in nonorphan genes. The average microsatellite content and the percentage of trinucleotide repeats in orphan genes are also significantly higher than in nonorphan genes. Microsatellites are found less often in PROSITE patterns in orphan genes. Taken together, these orphan gene characteristics suggest that microsatellites play an important role in orphan gene evolution and expression.