Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel

Significance The M2 channel in the influenza A virus is one of three commonly targeted proteins in the viral membrane. Proton permeation across the M2 channel acidifies the virion, releasing the viral RNA and core proteins. This work constitutes, to our knowledge, the first complete characterization of this process by multiscale computer simulation, and the results are in quantitative agreement with prior experimental measurements. The simulations confirm that the mechanism involves a “shuttling” of protons through the His37 tetrad and that the rate-limiting step is histidine deprotonation. The results also reveal several important features, including a large barrier for protons to reach the His37 tetrad and increased conductance for lower pH values due to channel broadening and increased solvent dynamics despite larger charge repulsion. The influenza A virus M2 channel (AM2) is crucial in the viral life cycle. Despite many previous experimental and computational studies, the mechanism of the activating process in which proton permeation acidifies the virion to release the viral RNA and core proteins is not well understood. Herein the AM2 proton permeation process has been systematically characterized using multiscale computer simulations, including quantum, classical, and reactive molecular dynamics methods. We report, to our knowledge, the first complete free-energy profiles for proton transport through the entire AM2 transmembrane domain at various pH values, including explicit treatment of excess proton charge delocalization and shuttling through the His37 tetrad. The free-energy profiles reveal that the excess proton must overcome a large free-energy barrier to diffuse to the His37 tetrad, where it is stabilized in a deep minimum reflecting the delocalization of the excess charge among the histidines and the cost of shuttling the proton past them. At lower pH values the His37 tetrad has a larger total charge that increases the channel width, hydration, and solvent dynamics, in agreement with recent 2D-IR spectroscopic studies. The proton transport barrier becomes smaller, despite the increased charge repulsion, due to backbone expansion and the more dynamic pore water molecules. The calculated conductances are in quantitative agreement with recent experimental measurements. In addition, the free-energy profiles and conductances for proton transport in several mutants provide insights for explaining our findings and those of previous experimental mutagenesis studies.
Abell 2218: X-Ray Lensing, Merger, or Both?

Comparison of the high-resolution X-ray image of A2218 obtained with the ROSAT HRI with the optical HST image shows several interesting correlations. The X-ray emission within a 1' radius core is resolved into several components; the central dominant galaxy does not coincide with either of them or with the emission centroid. The major X-ray peak is an elongated feature that lies between the two mass concentrations known from the optical lensing analysis, and coincides with optical arcs at r ≃ 20'' from the cD galaxy. We speculate that this may be lensed X-ray emission, for example (but not necessarily) of the same object lensed in the optical. Alternatively, this feature may be a merger shock or a gas trail of an infalling subgroup. Two other X-ray enhancements are close to the two major mass concentrations. Both lensing and a merger are likely. Previous X-ray derivations of the A2218 mass used a β-model fit to the data with angular resolution that blurred the features mentioned above into a broad constant core. As the HRI data show, such a core does not exist. Because of this, under certain assumptions and using only the improved imaging data, the hydrostatic estimate of the projected mass within the lensing radius can in principle be increased by a factor of ~1.4 (and the mass within a sphere of the same radius by a factor of 2.6) compared to previous analyses. However, for a merging cluster, the hydrostatic analysis is generally inapplicable. Most other lensing clusters are more distant than A2218, and obtaining adequate X-ray images and temperature maps of them is even more difficult. Together with the likely overestimation of mass by the lensing analysis (as in the simulations), oversimplification of the gas density and temperature models resulting from inadequate resolution may account for the lensing/X-ray mass discrepancy as suggested for A2218.
Crowd-sourcing Literal Review

Our user feedback framework requires some robust techniques in order to tackle the scalability issue of schema matching network. One approach is employing crowdsourcing/human computation models. Crowdsourcing is one of cutting-edge research areas which involves human computers to perform pre-defined tasks. In this literal review, we try to explore some certain concepts such as task, work-flow, feedback aggregation, quality control and reward system. We show that there are a lot of aspects which can be integrated into our user feedback framework.
Recognizing Keystrokes Using WiFi Devices

Keystroke privacy is critical for ensuring the security of computer systems and the privacy of human users as what is being typed could be passwords or privacy sensitive information. In this paper, we show for the first time that WiFi signals can also be exploited to recognize keystrokes. The intuition is that while typing a certain key, the hands and fingers of a user move in a unique formation and direction and thus generate a unique pattern in the time-series of channel state information (CSI) values, which we call CSI-waveform for that key. In this paper, we propose a WiFi signal-based keystroke recognition system called WiKey. WiKey consists of two commercial off-the-shelf WiFi devices, a sender (such as a router) and a receiver (such as a laptop). The sender continuously emits signals and the receiver continuously receives signals. When a human subject types on a keyboard, WiKey recognizes the typed keys based on how the CSI values at the WiFi signal receiver end. We implemented the WiKey system using a TP-Link TL-WR1043ND WiFi router and a Lenovo X200 laptop. WiKey achieves over 97.5% detection rate for detecting the keystroke and 96.4% recognition accuracy for classifying single keys. In real-world experiments, WiKey can recognize keystrokes in a continuously typed sentence with an accuracy of 93.5%. WiKey can also recognize complete words inside a sentence with over 85% accuracy.
Brain activation during emotion regulation in women with premenstrual dysphoric disorder

Abstract Background Difficulties in regulating emotions are linked to the core symptoms of premenstrual dysphoric disorder (PMDD). We therefore investigated the neural substrates of emotion-regulation problems in women with PMDD. Methods On the basis of self-evaluations over 2 months on the Daily Record of Severity of Problems, eligible participants were assigned to two groups: PMDD and control (18 per group). Functional magnetic resonance imaging (fMRI) and a well-validated task were used to assess brain function during emotion regulation. Participants were tested twice, once during the follicular (asymptomatic) and once in the late luteal (symptomatic) phase of the menstrual cycle. Results Women with PMDD gave higher ratings of negative affect in the luteal phase than in the follicular phase, and compared with healthy control participants during the luteal phase. A region-of-interest fMRI analysis indicated that during the late luteal phase, women with PMDD had hypoactivation in right dorsolateral prefrontal cortex (dlPFC) during all conditions of the emotion-regulation task, not only in the contrast that isolated emotion regulation. An exploratory whole-brain, voxel-wise analysis showed that women with PMDD had less activation in the precentral gyrus during the luteal phase than the follicular phase, and less activation in the postcentral gyrus compared with control participants. Conclusions During the luteal phase of the menstrual cycle, women with PMDD experience difficulty regulating emotions. Hypoactivation in the right dlPFC may contribute to this problem, but may be related more generally to other affective symptoms of PMDD. Hypofunction in the right pre- and postcentral gyri warrants additional study.
Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague

Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19th and 20th centuries, during which plague was spread around the world, and the second pandemic of the 14th–17th centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6th–8th centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics.
Relationship between ankle–brachial index and carotid intima-media thickness in HIV-infected patients

Both low and high ankle–brachial index are considered as indicators of systemic atherosclerosis in older HIV-negative adults. Whether those ankle–brachial index values are predictors of atherosclerosis in HIV-positive subjects remains unknown. We measured ankle–brachial index in 139 HIV-infected patients and compared the results obtained with carotid intima-media thickness, a well established marker of subclinic atherosclerosis. Ankle–brachial index was associated with carotid intima-media thickness. Patients with low ankle–brachial index, but not those with high ankle–brachial index, had high carotid intima-media thickness.
The Origins of Spatial Interaction Evidence from Chinese Rice Markets, 1742-1795 ∗

This paper uses spatial empirical methods to detect and analyze trade patterns in a historical data set on Chinese rice prices. Our results suggest that spatial features were important for the expansion of interregional trade. Geography dictates, first, over what distances trade was possible in different regions, because the costs of ship transport were considerably below those for land transport. Spatial features also influence the direction in which a trading network is expanding. Moreover, our analysis captures the impact of new trade routes both within and outside the trading areas.
Kullback-Leibler Distance Optimization for Non-rigid Registration of Echo-Planar to Structural Magnetic Resonance Brain Images

This paper presents the use of Kullback-Leibler Distance (KLD) as part of an optimization framework to incorporate prior knowledge from field maps into non-rigid registration of echo-planar (EPI) to structural magnetic resonance brain images. An analytical expression is derived for the derivatives of KLD with respect to registration transformation parameters, which is shown to be computationally more efficient as compared to the derivatives of mutual information. Quantitative gold standard validation is carried out on simulated digital brain phantom images with synthesized deformations. In addition, in-vivo validation is performed via a cross-comparison of the similarity of high-resolution and low-resolution EPI to T1-and T2-weighted structural images. The results obtained indicate that the developed KLD-based non-rigid registration technique provides an effective way of correcting local distortions in echo-planar imaging.
The abbreviated vigilance task and cerebral hemodynamics

Transcranial Doppler sonography (TCD) and transcranial cerebral oximetry (TCCO) measures of cerebral blood flow velocity and oxygenation levels were collected during an abbreviated 12-min vigilance task. Both the TCD and TCCO measures showed higher levels of cerebral vascular activity in the right than in the left cerebral hemisphere; the cerebral laterality of vigilance occurs in an abbreviated task. Although there was a significant decline in performance over time, there was no significant change in the physiological measures over time during the abbreviated vigil. This latter finding does not match the physiological changes detected in long-duration vigils.
An assessment of the resistance gene analogues of Oryza sativa ssp. japonica: their presence and structure.

Rice is the first cereal genome of known draft sequence, and the finished sequence for it is now nearly complete. In this paper, we describe a preliminary analysis of known rice genes aimed to detect resistance gene analogues of known structural classes. Putative resistance genes were identified in a dual approach--by using BLASTP searches to identify candidate sequences and by using Hidden Markov Models to predict domain presence in the candidates. The set of proteins examined was obtained from the publicly available data of TIGR (The Institute for Genomic Research). 1744 distinct RGAs were identified, 597 of which belonged to the NBS-LRR class. Supplementary data (sequences and annotations) is available on the web site http:/gkoczyk.bioinfo. pl/CMBL.
Fine-mapping of translocations in K562 cell line. Hi-C data provides evidence not only for pre- translocation chromosomal proximity, but also for translocations

Fine-mapping of translocations in K562 cell line. Hi-C data provides evidence not only for pre-translocation chromosomal proximity, but also for translocations that have already occurred (Figure 1). We thus attempted to use Hi-C data to fine-map chromosomal breakpoints in K562 cells. Although K562 is a widely used cancer cell, the exact breakpoints and genes implicated in its translocations remain largely unknown. We assembled a set of 13 previously described, coarsely-mapped translocations in K562 cells (Table S1), and explored the raw Hi-C data at these loci to locally refine breakpoint intervals. We observed a local hotspot of inter-chromosomal reads for 6 of these 13 previously described rearrangements; signal was highest at the location of the chromosomal breakpoints, where ligation has occurred, and decayed with distance away from the breakpoints along the fused chromosomal bands. At 3 of the 6 regions, raw Hi-C read counts at 50-kb resolution showed a characteristic pattern for an unbalanced translocation, with peak signal at a corner decaying in a single direction along both chromosomes (Figure S1A-C). At the 6 loci at which Hi-C signal was detected, we counted the number of raw Hi-C reads mapping to 50-kilobase intervals in the broad region of peak interaction signal. At 3 of the 6 regions, a heat map showing read counts at 50-kb resolution showed a pattern of peak signal at a corner, with signal decaying in a single direction along both chromosomes (Figure S1A-C). This is an expected pattern for an unbalanced translocation; signal is highest at the location of the chromosomal breakpoints, where ligation has occurred, and decays with distance away from the breakpoints along the fused chromosomal bands. For the BCR-ABL translocation, for example, we mapped the breakpoint to a 50-kb region Within this region, three reads (the highest local density) mapped to within a kilobase of the described precise breakpoint for the BCR-We next attempted to identify the breakpoint region for the other loci showing Hi-C signal characteristic for a translocation in the K562 cell line. Sequence-based identification of fusion gene transcripts in the K562 cell line has recently identified a second translocation between chr9 and chr22 involving the gene partners NUP214 and XKR3 [2]. The Hi-C data also showed clear evidence for a translocation between these loci; fine-mapping at the 50-kilobase scale revealed a likely breakpoint at Further fine-mapping revealed that 14 reads (nearly all reads mapping to the 50-kilobase region) clustered tightly within …
Distributing excess cash: the role of specially designated dividends

This study explores why firms distribute excess cash as specially designated dividends (SDDs) instead of using regular dividends or repurchasing shares. We survey top managers of NASDAQ, AMEX, and NYSE firms issuing at least one SDD between 1994 and 2001. The results show that firms tend to pay SDDs when they experience strong earnings and cash flows and want to increase at least temporarily the yield to shareholders. Having strong earnings and cash flows also provide an impetus for regular dividend increases, but paying regular dividends is part of a firm’s standard dividend policy. The primary motives for repurchasing shares are to take advantage of perceived market undervaluation of the firm’s shares and to improve performance measures, especially. Overall, the results lend support to the signaling explanation for the disbursement of excess funds, but not the free cash flow or wealth transfer explanations.
Folate Receptor-α (FOLR1) Expression and Function in Triple Negative Tumors

Folate receptor alpha (FOLR1) has been identified as a potential prognostic and therapeutic target in a number of cancers. A correlation has been shown between intense overexpression of FOLR1 in breast tumors and poor prognosis, yet there is limited examination of the distribution of FOLR1 across clinically relevant breast cancer subtypes. To explore this further, we used RNA-seq data from multiple patient cohorts to analyze the distribution of FOLR1 mRNA across breast cancer subtypes comprised of estrogen receptor positive (ER+), human epidermal growth factor receptor positive (HER2+), and triple negative (TNBC) tumors. FOLR1 expression varied within breast tumor subtypes; triple negative/basal tumors were significantly associated with increased expression of FOLR1 mRNA, compared to ER+ and HER2+ tumors. However, subsets of high level FOLR1 expressing tumors were observed in all clinical subtypes. These observations were supported by immunohistochemical analysis of tissue microarrays, with the largest number of 3+ positive tumors and highest H-scores of any subtype represented by triple negatives, and lowest by ER+ tumors. FOLR1 expression did not correlate to common clinicopathological parameters such as tumor stage and nodal status. To delineate the importance of FOLR1 overexpression in triple negative cancers, RNA-interference was used to deplete FOLR1 in overexpressing triple negative cell breast lines. Loss of FOLR1 resulted in growth inhibition, whereas FOLR1 overexpression promoted folate uptake and growth advantage in low folate conditions. Taken together, our data suggests patients with triple negative cancers expressing high FOLR1 expression represent an important population of patients that may benefit from targeted anti-FOLR1 therapy. This may prove particularly helpful for a large number of patients who would typically be classified as triple negative and who to this point have been left without any targeted treatment options.
Healthcare-associated vancomycin resistant Enterococcus faecium infections in the Mansoura University Hospitals intensive care units, Egypt

Vancomycin resistant Enterococcus faecium (VREF) ia an emerging and challenging nosocomial pathogen. This study aimed to determine the prevalence, risk factors and clonal relationships between different VREF isolates in the intensive care units (ICUs) of the university hospitals in our geographic location. This prospective study was conducted from July, 2012 until September, 2013 on 781 patients who were admitted to the ICUs of the Mansoura University Hospitals (MUHs), and fulfilled the healthcare-associated infection (HAI) criteria. Susceptibility testing was determined using the disk diffusion method. The clonal relationships were evaluated with pulsed field gel electrophoresis (PFGE). Out of 52 E. faecium isolates, 12 (23.1%) were vancomycin resistant. The significant risk factors for the VREF infections were: transfer to the ICU from a ward, renal failure, an extended ICU stay and use of third-generation cephalosporins, gentamicin, or ciprofloxacin. PFGE with the 12 isolates showed 9 different patterns; 3 belonged to the same pulsotype and another 2 carried a second pulsotypes. The similar pulsotypes isolates were isolated from ICUs of one hospital (EICUs); however, all of the isolates from the other ICUs had different patterns. Infection control policy, in conjunction with antibiotic stewardship, is important to combat VREF transmission in these high-risk patients.
Proton Magnetic Resonance Spectroscopy (1H-MRS) Reveals Geniculocalcarine and Striate Area Degeneration in Primary Glaucoma

Background Glaucoma is a collection of neurodegenerative diseases that affect both the retina and the central visual pathway. We investigated whether metabolites' concentrations changed in the geniculocalcarine (GCT) and the striate area of occipital lobe by proton magnetic resonance spectroscopy (1H-MRS), suggesting neurodegeneration of the central visual pathway in primary glaucoma. Methodology/Principal Findings 20 patients with glaucoma in both eyes were paired with 20 healthy volunteers in same gender and an age difference less than 3 years. All the participants were examined by MR imaging including T1 Flair, T2 FSE and 1H-MRS. The T1 intensity and T2 intensity of their GCTs and striate areas were measured. The ratio of N-acetylaspartate (NAA)/Creatine (Cr), Choline (Cho)/Cr, glutamine and glutamate (Glx)/Cr were derived by multi-voxels 1H-MRS in the GCT and the striate area of each brain hemisphere. The T1 intensity and T2 intensity had no difference between the groups. Significant decreases in NAA/Cr and Cho/Cr but no difference in Glx/Cr was found between the groups in both the GCT and the striate area. Conclusions/Significance Primary glaucoma affects metabolites' concentrations in the GCT and the striate area suggesting there is ongoing neurodegenerative process.
A PLSA-based language model for conversational telephone speech

This paper describes experiments with a PLSA-based language model for conversational telephone speech. This model uses a long-range history and exploits topic information in the test text to adjust probabilities of test words. The PLSA-based model was found to lower test set perplexity over a traditional word+class-based 4-gram by 13% (optimistic estimate using a reference transcript as history) or by 6% (realistic estimate using recognised transcript as history). Moreover, this paper introduces a use of confidence scores to weight words in the history, a weight of the prior topic distribution and a way of calculating perplexity that accounts for recognition errors in the model context.
On Turbulent Flow Near a Wall

y* h k* a* A* = = = = = = = = = = = = = = = = = = = = = = = = = = = = distance from wall pipe radius pipe diameter mean local velocity parallel to wall velocity fluctuations parallel and normal to flow mass density coefficient of viscosity shear stress velocity correlation coefficient mixing length universal constant in I = Ky modified universal constant eddy viscosity size of roughness friction factor = 8rw/p V 2