Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved Part-of-Speech Tagging for Online Conversational Text with Word Clusters

We consider the problem of part-of-speech tagging for informal, online conversational text. We systematically evaluate the use of large-scale unsupervised word clustering and new lexical features to improve tagging accuracy. With these features, our system achieves state-of-the-art tagging results on both Twitter and IRC POS tagging tasks; Twitter tagging is improved from 90% to 93% accuracy (more than 3% absolute). Qualitative analysis of these word clusters yields insights about NLP and linguistic phenomena in this genre. Additionally, we contribute the first POS annotation guidelines for such text and release a new dataset of English language tweets annotated using these guidelines. Tagging software, annotation guidelines, and large-scale word clusters are available at: http://www.ark. cs.cmu. edu/TweetNLP This paper describes release 0.3 of the “CMU Twitter Part-of-Speech Tagger” and annotated data. [This paper is forthcoming in Proceedings of NAACL 2013; Atlanta, GA, USA. ]
Stage-Dependent Expression and Up-Regulation of Trypanothione Synthetase in Amphotericin B Resistant Leishmania donovani

Kinetoplastids differ from other organisms in their ability to conjugate glutathione and spermidine to form trypanothione which is involved in maintaining redox homeostasis and removal of toxic metabolites. It is also involved in drug resistance, antioxidant mechanism, and defense against cellular oxidants. Trypanothione synthetase (TryS) of thiol metabolic pathway is the sole enzyme responsible for the biosynthesis of trypanothione in Leishmania donovani. In this study, TryS gene of L. donovani (LdTryS) was cloned, expressed, and fusion protein purified with affinity column chromatography. The purified protein showed optimum enzymatic activity at pH 8.0–8.5. The TryS amino acids sequences alignment showed that all amino acids involved in catalytic and ligands binding of L. major are conserved in L. donovani. Subcellular localization using digitonin fractionation and immunoblot analysis showed that LdTryS is localized in the cytoplasm. Furthermore, RT-PCR coupled with immunoblot analysis showed that LdTryS is overexpressed in Amp B resistant and stationary phase promastigotes (∼2.0-folds) than in sensitive strain and logarithmic phase, respectively, which suggests its involvement in Amp B resistance. Also, H2O2 treatment upto 150 µM for 8 hrs leads to 2-fold increased expression of LdTryS probably to cope up with oxidative stress generated by H2O2. Therefore, this study demonstrates stage- and Amp B sensitivity-dependent expression of LdTryS in L. donovani and involvement of TryS during oxidative stress to help the parasites survival.
Characteristics of Streptococcus pneumoniae Strains Colonizing Upper Respiratory Tract of Healthy Preschool Children in Poland

Antibiotic resistant and invasive pneumococci may spread temporally and locally in day care centers (DCCs). We examined 267 children attending four DCCs located in the same city and 70 children staying at home in three seasons (autumn, winter, and spring) to determine prevalence, serotype distribution, antibiotic resistance patterns, and transmission of pneumococcal strains colonizing upper respiratory tract of healthy children without antipneumococcal vaccination. By pheno- and genotyping, we determined clonality of pneumococci, including drug-resistant strains. The average carriage of pneumococci in three seasons was 38.2%. 73.4% and 80.4% of the isolates belonged to serotypes present in 10- and 13-valent conjugate vaccine, respectively. Among the pneumococcal strains, 33.3% were susceptible to all antimicrobial tested and 39.2% had decreased susceptibility to penicillin. Multidrug resistance was common (35.7%); 97.5% of drug-resistant isolates represented serotypes included to 10- and 13-valent conjugate vaccine. According to BOX-PCR, clonality definitely was observed only in case of serotype 14. Multivariate analysis determined DCC attendance as strongly related to pneumococcal colonization in all three seasons, but important seasonal differences were demonstrated. In children attending DCCs, we observed dynamic turnover of pneumococcal strains, especially penicillin nonsusceptible and multidrug resistant, which were mostly distributed among serotypes included to available pneumococcal conjugate vaccines.
Considering the Impacts of Health Disparities , Inequalities , and Inequities on Early Diagnosis of Pulmonary Arterial Hypertension

Early recognition, diagnosis, and treatment of pulmonary arterial hypertension (PAH) is a worthwhile endeavor in that it remains underdiagnosed in an era where 9 FDA-approved treatments are available, which have shown to provide clinical improvements and prolonged survival. Furthermore, despite the significant advances in understanding the etiology of PAH, the time from onset of symptoms to recognition of the disease has not improved over the past 2 decades, the delay of which results in progression of pathologic changes that are life threatening and irreversible when left untreated. This is particularly concerning in that the potential for optimal clinical outcomes and survival is diminished even after a 2-year delay in diagnosis. The aim of this article is to evaluate the current public health framework to highlight social determinants that influence and may result in barriers in achieving optimal health outcomes, with a focus on factors that may contribute to delayed diagnosis of PAH.
In Vivo Analysis of Insertional Torque During Pedicle Screwing Using Cortical Bone Trajectory Technique

Study Design. The insertional torque of pedicle screws using the cortical bone trajectory (CBT) was measured in vivo. Objective. To investigate the effectiveness of the CBT technique by measurement of the insertional torque. Summary of Background Data. The CBT follows a mediolateral and caudocephalad directed path, engaging with cortical bone maximally from the pedicle to the vertebral body. Some biomechanical studies have demonstrated favorable characteristics of the CBT technique in cadaveric lumbar spine. However, no in vivo study has been reported on the mechanical behavior of this new trajectory. Methods. The insertional torque of pedicle screws using CBT and traditional techniques were measured intraoperatively in 48 consecutive patients. A total of 162 screws using the CBT technique and 36 screws using the traditional technique were compared. In 8 of 48 patients, the side-by-side comparison of 2 different insertional techniques for each vertebra were performed, which formed the H group. In addition, the insertional torque was correlated with bone mineral density. Results. The mean maximum insertional torque of CBT screws and traditional screws were 2.49 ± 0.99 Nm and 1.24 ± 0.54 Nm, respectively. The CBT screws showed 2.01 times higher torque and the difference was significant between the 2 techniques (P < 0.01). In the H group, the insertional torque were 2.71 ± 1.36 Nm in the CBT screws and 1.58 ± 0.44 Nm in the traditional screws. The CBT screws demonstrated 1.71 times higher torque and statistical significance was achieved (P < 0.01). Positive linear correlations between maximum insertional torque and bone mineral density were found in both technique, the correlation coefficient of traditional screws (r = 0.63, P < 0.01) was higher than that of the CBT screws (r = 0.59, P < 0.01). Conclusion. The insertional torque using the CBT technique is about 1.7 times higher than the traditional technique. Level of Evidence: 2
Ecology and Biogeography of Free-Living Nematodes Associated with Chemosynthetic Environments in the Deep Sea: A Review

Background Here, insight is provided into the present knowledge on free-living nematodes associated with chemosynthetic environments in the deep sea. It was investigated if the same trends of high standing stock, low diversity, and the dominance of a specialized fauna, as observed for macro-invertebrates, are also present in the nematodes in both vents and seeps. Methodology This review is based on existing literature, in combination with integrated analysis of datasets, obtained through the Census of Marine Life program on Biogeography of Deep-Water Chemosynthetic Ecosystems (ChEss). Findings Nematodes are often thriving in the sulphidic sediments of deep cold seeps, with standing stock values ocassionaly exceeding largely the numbers at background sites. Vents seem not characterized by elevated densities. Both chemosynthetic driven ecosystems are showing low nematode diversity, and high dominance of single species. Genera richness seems inversely correlated to vent and seep fluid emissions, associated with distinct habitat types. Deep-sea cold seeps and hydrothermal vents are, however, highly dissimilar in terms of community composition and dominant taxa. There is no unique affinity of particular nematode taxa with seeps or vents. Conclusions It seems that shallow water relatives, rather than typical deep-sea taxa, have successfully colonized the reduced sediments of seeps at large water depth. For vents, the taxonomic similarity with adjacent regular sediments is much higher, supporting rather the importance of local adaptation, than that of long distance distribution. Likely the ephemeral nature of vents, its long distance offshore and the absence of pelagic transport mechanisms, have prevented so far the establishment of a successful and typical vent nematode fauna. Some future perspectives in meiofauna research are provided in order to get a more integrated picture of vent and seep biological processes, including all components of the marine ecosystem.
Case–control study of subjective and objective differences in sleep patterns in older adults with insomnia symptoms

Older adults have high prevalence rates of insomnia symptoms, yet it is unclear if these insomnia symptoms are associated with objective impairments in sleep. We hypothesized that insomnia complaints in older adults would be associated with objective differences in sleep compared with those without insomnia complaints. To test this hypothesis, we conducted a cross‐sectional study in which older adults with insomnia complaints (cases, n = 100) were compared with older adults without insomnia complaints (controls, n = 100) using dual‐night in‐lab nocturnal polysomnography, study questionnaires and 7 days of at‐home actigraphy and sleep diaries. Cases were noted to have reduced objective total sleep time compared with controls (25.8 ± 8.56 min, P = 0.003). This was largely due to increased wakefulness after sleep onset, and not increased sleep latency. When participants with sleep‐related breathing disorder or periodic limb movement disorder were excluded, the polysomnography total sleep time difference became even larger. Cases also had reduced slow‐wave sleep (5.10 ± 1.38 min versus 10.57 ± 2.29 min, effect size −0.29, P = 0.04). When comparing self‐reported sleep latency and sleep efficiency with objective polysomnographic findings, cases demonstrated low, but statistically significant correlations, while no such correlations were observed in controls. Cases tended to underestimate their sleep efficiency by 1.6% (±18.4%), while controls overestimated their sleep efficiency by 12.4% (±14.5%). In conclusion, we noted that older adults with insomnia complaints have significant differences in several objective sleep findings relative to controls, suggesting that insomnia complaints in older adults are associated with objective impairments in sleep.
How Well Can We Estimate the Information Carried in Neuronal Responses from Limited Samples?

It is difficult to extract the information carried by neuronal responses about a set of stimuli because limited data samples result in biased es timates. Recently two improved procedures have been developed to calculate information from experimental results: a binning-and-correcting procedure and a neural network procedure. We have used data produced from a model of the spatiotemporal receptive fields of parvocellular and magnocellular lateral geniculate neurons to study the performance of these methods as a function of the number of trials used. Both procedures yield accurate results for one-dimensional neuronal codes. They can also be used to produce a reasonable estimate of the extra information in a three-dimensional code, in this instance, within 0.05-0.1 bit of the asymptotically calculated valueabout 10 of the total transmitted information. We believe that this performance is much more accurate than previous procedures.
Biorthogonal $p$-wavelet packets related to the Walsh polynomials

This paper deals with the construction of biorthogonal p -wavelet packets on R+ related to the Walsh polynomials and their properties are investigated by means of Walsh-Fourier transform. Three biorthogonal formulas regarding these p -wavelet packets are derived. Moreover, it is shown how to obtain several new Riesz bases of the space L2(R+) by constructing a series of subspaces of these p -wavelet packets. Mathematics subject classification (2010): 42C40, 42C15, 42C10.
MuProp: Unbiased Backpropagation for Stochastic Neural Networks

Deep neural networks are powerful parametric models that can be trained efficiently using the backpropagation algorithm. Stochastic neural networks combine the power of large parametric functions with that of graphical models, which makes it possible to learn very complex distributions. However, as backpropagation is not directly applicable to stochastic networks that include discrete sampling operations within their computational graph, training such networks remains difficult. We present MuProp, an unbiased gradient estimator for stochastic networks, designed to make this task easier. MuProp improves on the likelihood-ratio estimator by reducing its variance using a control variate based on the first-order Taylor expansion of a mean-field network. Crucially, unlike prior attempts at using backpropagation for training stochastic networks, the resulting estimator is unbiased and well behaved. Our experiments on structured output prediction and discrete latent variable modeling demonstrate that MuProp yields consistently good performance across a range of difficult tasks.
LIT1 and H19 methylation defects in isolated hemihyperplasia

We performed LIT1 and H19 methylation studies on 27 children with isolated hemihyperplasia (IH). Eight children (29.6%) had a defect in methylation of one or both of these alleles, supporting our hypothesis that these epigenetic changes can result in a phenotype distinct from typical Beckwith–Wiedemann syndrome. © 2005 Wiley‐Liss, Inc.
Footprint Parameters as a Measure of Arch Height

The human foot has frequently been categorized into arch height groups based upon analysis of footprint parameters. This study investigates the relationship between directly measured arch height and many of the footprint parameters that have been assumed to represent arch height. A total of 115 male subjects were measured and footprint parameters were calculated from digitized outlines. Correlation and regression analyses were used to determine the relationship between footprint measures and arch height. It may be concluded from the results that footprint parameters proposed in the literature (arch angle, footprint index, and arch index) and two further parameters suggested in this study (arch length index and truncated arch index) are invalid as a basis for prediction or categorization of arch height. The categorization of the human foot according to the footprint measures evaluated in this paper represent no more than indices and angles of the plantar surface of the foot itself.
The role of spatial and temporal information in biological motion perception

Point-light biological motion stimuli provide spatio-temporal information about the structure of the human body in motion. Manipulation of the spatial structure of point-light stimuli reduces the ability of human observers to perceive biological motion. A recent study has reported that interference with the spatial structure of pointlight walkers also reduces the evoked eventrelated potentials over the occipitotemporal cortex, but that interference with the temporal structure of the stimuli evoked event-related potentials similar to normal biological motion stimuli. We systematically investigated the influence of spatial and temporal manipulation on 2 common discrimination tasks and compared it with predictions of a neurocomputational model previously proposed. This model first analyzes the spatial structure of the stimulus independently of the temporal information to derive body posture and subsequently analyzes the temporal sequence of body postures to derive movement direction. Similar to the model predictions, the psychophysical results show that human observers need only intact spatial configuration of the stimulus to discriminate the facing direction of a point-light walker. In contrast, movement direction discrimination needs a fully intact spatiotemporal pattern of the stimulus. The activation levels in the model predict the observed eventrelated potentials for the spatial and temporal manipulations.
Casein Kinase 1 Delta (CK1δ) Regulates Period Length of the Mouse Suprachiasmatic Circadian Clock In Vitro

Background Casein kinase 1 delta (CK1δ) plays a more prominent role in the regulation of circadian cycle length than its homologue casein kinase 1 epsilon (CK1ε) in peripheral tissues such as liver and embryonic fibroblasts. Mice lacking CK1δ die shortly after birth, so it has not been possible to assess the impact of loss of CK1δ on behavioral rhythms controlled by the master circadian oscillator in the suprachiasmatic nuclei (SCN). Methodology/Principal Findings In the present study, mPER2::LUCIFERASE bioluminescence rhythms were monitored from SCN explants collected from neonatal mice. The data demonstrate that SCN explants from neonatal CK1δ-deficient mice oscillate, but with a longer circadian period than littermate controls. The cycle length of rhythms recorded from neonatal SCN explants of CK1ε-deficient mice did not differ from control explants. Conclusions/Significance The results indicate that CK1δ plays a more prominent role than CK1ε in the maintenance of 24-hour rhythms in the master circadian oscillator.
Self-repairing hardware with astrocyte-neuron networks

A Self-rePAiring spiking Neural NEtwoRk (SPANNER) hardware architecture is presented in this paper. It is based on a software model of an astrocyte-neuron network which previously demonstrated the ability to self-detect faults and self-repair autonomously. Experimental results in this paper show that when faults occur at the synapse, remaining healthy synapses of the same neuron are enhanced by the feedback from the astrocyte, which enables system functionality to be maintained. This is the first time that astrocyte cells merged within spiking neurons demonstrate a self-repairing capability in hardware. This repair capability achieves a much more finegrained repair capability in hardware compared to the conventional fault tolerance techniques.
An intercalation-locked parallel-stranded DNA tetraplex

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5′-most A–A base pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.
Moku Virus in Invasive Asian Hornets, Belgium, 2016

We report the detection of Moku virus in invasive Asian hornets (Vespa velutina nigrithorax) in Belgium. This constitutes an unexpected report of this iflavirus outside Hawaii, USA, where it was recently described in social wasps. Although virulence of Moku virus is unknown, its potential spread raises concern for European honeybee populations.
Refining Angiographic Biomarkers of Revascularization: Improving Outcome Prediction After Intra-arterial Therapy

Background and Purpose— Angiographic revascularization grading after intra-arterial stroke therapy is limited by poor standardization, making it unclear which scale is optimal for predicting outcome. Using recently standardized criteria, we sought to compare the prognostic performance of 2 commonly used reperfusion scales. Methods— Inclusion criteria for this multicenter retrospective study were acute ischemic stroke attributable to middle cerebral artery M1 occlusion, intra-arterial therapy, and 90-day modified Rankin scale score. Post–intra-arterial therapy reperfusion was graded using the Thrombolysis in Myocardial Infarction (TIMI) and Modified Thrombolysis in Cerebral Infarction (mTICI) scales. The scales were compared for prediction of clinical outcome using receiver-operating characteristic analysis. Results— Of 308 patients, mean age was 65 years, and median National Institutes of Health Stroke Scale score was 17. The mean time from stroke onset to groin puncture was 305 minutes. There was no difference in the time to treatment between patients grouped by final TIMI (ie, 0 versus 1 versus 2 versus 3) or mTICI grades (ie, 0 versus 1 versus 2a versus 2b versus 3). Good outcome (modified Rankin scale, 0–2) was achieved in 32.5% of patients, and mortality rate was 25.3% at 90 days. There was a 6.3% rate of parenchymal hematoma type 2. In receiver-operating characteristic analysis, mTICI was superior to TIMI for predicting 90-day modified Rankin scale 0 to 2 (c-statistic: 0.74 versus 0.68; P<0.0001). The optimal threshold for identifying a good outcome was mTICI 2b to 3 (sensitivity 78.0%; specificity 66.1%). Conclusions— mTICI is superior to TIMI for predicting clinical outcome after intra-arterial therapy. mTICI 2b to 3 is the optimal biomarker for procedural success.
The 2-oxoglutarate analog 3-oxoglutarate decreases normoxic hypoxia-inducible factor-1α in cancer cells, induces cell death, and reduces tumor xenograft growth

The cellular response to hypoxia is primarily regulated by the hypoxia-inducible factors (HIFs). HIF-1α is also a major mediator of tumor physiology, and its abundance is correlated with therapeutic resistance in a broad range of cancers. Accumulation of HIF-1α under hypoxia is mainly controlled by the oxygen-sensing HIF prolyl 4-hydroxylases (EGLNs, also known as PHDs). Here, we identified a high level of normoxic HIF-1α protein in various cancer cell lines. EGLNs require oxygen and 2-oxoglutarate for enzymatic activity. We tested the ability of several cell-permeable 2-oxoglutarate analogs to regulate the abundance of HIF-1α protein. We identified 3-oxoglutarate as a potent regulator of HIF-1α in normoxic conditions. In contrast to 2-oxoglutarate, 3-oxoglutarate decreased the abundance of HIF-1α protein in several cancer cell lines in normoxia and diminished HIF-1α levels independent of EGLN enzymatic activity. Furthermore, we observed that 3-oxoglutarate was detrimental to cancer cell survival. We show that esterified 3-oxoglutarate, in combination with the cancer chemotherapeutic drug vincristine, induces apoptosis and inhibits tumor growth in vitro and in vivo. Our data imply that a novel treatment strategy targeting HIF-1α in combination with the use of existing cytotoxic agents could serve as potent, future antitumor chemotherapies.