Miracle-dz/UniFAR-FTUs huggingface dataset:
An Efficient High Order Method for Dislocation Climb in Two Dimensions

We present an efficient high order method for dislocation dynamics simulation of vacancy-assisted dislocation climb in two dimensions. The method is based on a second kind integral equation (SKIE) formulation that represents the vacancy concentration via the sum of double layer potentials and point sources located at each dislocation, where the climb velocity of each dislocation (or the strength of each point source) is proportional to the integral of the unknown density on the boundary of each dislocation. The method discretizes the interfaces only. Unlike previously used formulations, the proposed method avoids the need for introducing additional unknowns or integrating kernels with logarithmic singularity, and the boundary integrals in the formulation are easily discretized via the trapezoidal rule with spectral accuracy. Thus, the number of unknowns in the linear system to achieve certain accuracy is optimal for typical settings in dislocation dynamics. We compare three different methods for solving r.
DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function

Summary DincRNA aims to provide a comprehensive web-based bioinformatics toolkit to elucidate the entangled relationships among diseases and non-coding RNAs (ncRNAs) from the perspective of disease similarity. The quantitative way to illustrate relationships of pair-wise diseases always depends on their molecular mechanisms, and structures of the directed acyclic graph of Disease Ontology (DO). Corresponding methods for calculating similarity of pair-wise diseases involve Resnik's, Lin's, Wang's, PSB and SemFunSim methods. Recently, disease similarity was validated suitable for calculating functional similarities of ncRNAs and prioritizing ncRNA-disease pairs, and it has been widely applied for predicting the ncRNA function due to the limited biological knowledge from wet lab experiments of these RNAs. For this purpose, a large number of algorithms and priori knowledge need to be integrated. e.g. 'pair-wise best, pairs-average' (PBPA) and 'pair-wise all, pairs-maximum' (PAPM) methods for calculating functional similarities of ncRNAs, and random walk with restart (RWR) method for prioritizing ncRNA-disease pairs. To facilitate the exploration of disease associations and ncRNA function, DincRNA implemented all of the above eight algorithms based on DO and disease-related genes. Currently, it provides the function to query disease similarity scores, miRNA and lncRNA functional similarity scores, and the prioritization scores of lncRNA-disease and miRNA-disease pairs. Availability and implementation http://bio-annotation.cn:18080/DincRNAClient/. Contact biofomeng@hotmail.com or qhjiang@hit.edu. cn. Supplementary information Supplementary data are available at Bioinformatics online.
Comparison of tenoscopic and ultrasonographic methods of examination of the digital flexor tendon sheath in horses

Summary The purpose of this study was to compare sonographic and tenoscopic findings with the purpose of establishing the accuracy and limitations of ultrasonography as a non-invasive diagnostic modality in evaluating the DFTS and its enclosed tendons. The medical records from 22 horses which underwent tenoscopic desmotomy of the palmar/plantar annular ligament were evaluated in a retrospective study. The qualitative assessment of sonographic and tenoscopic findings were documented for the digital flexor tendon sheath (DFTS), the palmar/plantar annular ligament (PAL), the superficial digital flexor tendon (SDFT) and the deep digital flexor tendon (DDFT). The abnormalities diagnosed sonographically within the DFTS were verifiable tenoscopically with a sensitivity of 90.9% and a specificity of 53.8%. The positive predictive value of sonographic examination at the DFTS was 62.5%. The sensitivity of the sonographic examination at the PAL was 68.8%, the specificity was 50% and the positive predictive value 73.3%. Sonographic examination of the SDF tendons revealed abnormal findings in 12 tendons. The tenoscopic examination confirmed these findings on six tendons when they had a pronounced fibrillated or rough tendon surface or tear on the border. Six superficial flexor tendons and seven deep digital flexor tendons had abnormalities seen tenoscopically which were not visible on sonographic examination. Sonographic examination located lesions of the DDFT in four limbs. On tenoscopic examination the lesions could be detected in seven other DDF tendons, including signs of inflammation at the tendon surface that were not seen ultrasonographically (sensitivity 36.4%). Recognition of the limitations of sonographic results should be kept in mind so as not to misinterpret findings, especially if echogenic materials are observed.
Compact lumped element model for TSV in 3D-ICs

A wide-band lumped element model for a through silicon via (TSV) is proposed based on electromagnetic simulations. Closed form expressions for the TSV parasitics based on the dimensional analysis method are introduced. The proposed model enables direct extraction of the TSV resistance, self-inductance, oxide capacitance, and parasitic elements due to the finite substrate resistivity. The model's compactness and compatibility with SPICE simulations allows the fast investigation of a TSV impact on a 3-D circuit performance. The parameters' values of the proposed TSV model are fitted to the simulated S-parameters up to 10 GHz with an error less than 5%. It is shown that a TSV capacitance is highly dependent on the positions of ground contacts and has a value of tens of femto farads in a typical current technology. This value is much higher than a minimum device capacitance and requires special design methodologies such as cascaded buffers. Coupling between TSVs will be handled in another paper.
Sex ratio rather than population size affects genetic diversity in Antennaria dioica.

Habitat fragmentation and small population size can lead to genetic erosion in threatened plant populations. Classical theory implies that dioecy can counteract genetic erosion as it decreases the magnitude of inbreeding and genetic drift due to obligate outcrossing. However, in small populations, sex ratios may be strongly male- or female-biased, leading to substantial reductions in effective population size. This may theoretically result in a unimodal relationship between sex ratios and genetic diversity; yet, empirical studies on this relationship are scarce. Using AFLP markers, we studied genetic diversity, structure and differentiation in 14 highly fragmented Antennaria dioica populations from the Central European lowlands. Our analyses focused on the relationship between sex ratio, population size and genetic diversity. Although most populations were small (mean: 35.5 patches), genetic diversity was moderately high. We found evidence for isolation-by-distance, but overall differentiation of the populations was rather weak. Females dominated 11 populations, which overall resulted in a slightly female-biased sex ratio (61.5%). There was no significant relationship between population size and genetic diversity. The proportion of females was not unimodally but positively linearly related to genetic diversity. The high genetic diversity and low genetic differentiation suggest that A. dioica has been widely distributed in the Central European lowlands in the past, while fragmentation occurred only in the last decades. Sex ratio has more immediate consequences on genetic diversity than population size. An increasing proportion of females can increase genetic diversity in dioecious plants, probably due to a higher amount of sexual reproduction.
Informal Care and Sleep Disturbance Among Caregivers in Paid Work: Longitudinal Analyses From a Large Community-Based Swedish Cohort Study

Abstract Study Objectives To examine cross-sectionally and prospectively whether informal caregiving is related to sleep disturbance among caregivers in paid work. Methods Participants (N = 21604) in paid work from the Swedish Longitudinal Occupational Survey of Health. Sleeping problems were measured with a validated scale of sleep disturbance (Karolinska Sleep Questionnaire). Random-effects modeling was used to examine the cross-sectional association between informal caregiving (self-reports: none, up to 5 hours per week, over 5 hours per week) and sleep disturbance. Potential sociodemographic and health confounders were controlled for and interactions between caregiving and gender included. Longitudinal random-effects modeling of the effects of changes in reported informal caregiving upon sleep disturbance and change in sleep disturbance was performed. Results In multivariate analyses controlling for sociodemographics, health factors, and work hours, informal caregiving was associated cross-sectionally with sleep disturbance in a dose–response relationship (compared with no caregiving, up to 5 hours of caregiving: β = 0.03; 95% CI: 0.01, 0.06, and over 5 hours: β = 0.08; 95% CI: 0.02, 0.13), results which varied by gender. Cessation of caregiving was associated with reductions in sleep disturbance (β = −0.08; 95% CI: −0.13, −0.04). Conclusions This study provides evidence for a causal association of provision of informal care upon self-reported sleep disturbance. Even low-intensity care provision was related to sleep disturbance among this sample of carers in paid work. The results highlight the importance of addressing sleep disturbance in caregivers.
UNION: A unified inter/intra-chip optical network for chip multiprocessors

As modern computing systems become increasingly complex, communication efficiency among and inside chips has become as important as the computation speeds of individual processor cores. Traditionally, inter-chip and intra-chip communication architectures are separately designed to maximize design flexibility under different constraints. However, jointly designing communication architectures for both inter-chip and intra-chip communication could potentially yield better solutions. In this paper, we present a unified inter/intra-chip optical network, called UNION, for chip multiprocessors (CMP). UNION is based on recent progress in nano-photonic technologies. It connects not only processors on a single CMP but also multiple CMPs in a system. UNION employs a hierarchical optical network to separate inter-chip communication traffic from intra-chip communication traffic. It fully utilizes a single optical network to transmit both payload packets and control packets. The network controller on each CMP not only manages intra-chip communications but also collaborate with each other to facilitate inter-chip communications. We compared CMPs using UNION with those using a matched electronic counterpart in 45 nm process. Based on eight applications, simulation results show that on average UNION improves CMP performance by 3.1X while reducing 92% of network energy consumption and 52% of communication delay.
Treatment Outcomes of Mycobacterium avium Complex Lung Disease: A Systematic Review and Meta-analysis

Background The advent of macrolides has led to therapeutic advances in the treatment of Mycobacterium avium complex lung disease (MAC-LD). The aim of this study was to elucidate the treatment outcomes of macrolide-containing regimens. Methods We performed a systematic review and meta-analysis of published studies reporting treatment outcomes of macrolide-containing regimens for MAC-LD using the Medline, Embase, and Cochrane Library databases through 31 July 2016. The rates of treatment success, default from treatment, and adverse events of macrolide-containing regimens were assessed. Treatment success was defined as either 12 months of sustained culture negativity while on therapy or achievement of culture conversion and completion of the planned treatment without relapse. Results In total, 16 studies involving 1462 patients were included. The rate of treatment success was 60.0% (95% confidence interval [CI], 55.1%-64.8%). The proportion of patients who defaulted from the treatment was 16.0% (95% CI, 12.3%-19.7%). When a thrice-weekly dosing schedule was available, the default rate was 12.0% (95% CI, 8.9%-15.0%). Adverse events necessitating treatment discontinuation or dosage modification of macrolides were observed in 6.4% of patients (95% CI, 3.2%-9.5%), and decreased auditory acuity was the most common adverse event. Conclusions Treatment outcomes of macrolide-containing regimens are relatively poor in terms of both the treatment success and default rates. The default rate could be reduced if a thrice-weekly dosing schedule is available. Clinicians should be aware of decreased auditory function as the most common adverse event associated with macrolide-containing regimens.
A Full Pharmacological Analysis of the Three Turkey β-Adrenoceptors and Comparison with the Human β-Adrenoceptors

Background There are three turkey β-adrenoceptors: the original turkey β-adrenoceptor from erythrocytes (tβtrunc, for which the X-ray crystal structure has recently been determined), tβ3C and tβ4C-receptors. This study examined the similarities and differences between these avian receptors and mammalian receptors with regards to binding characteristics and functional high and low affinity agonist conformations. Methodology/Principal Findings Stable cell lines were constructed with each of the turkey β-adrenoceptors and 3H-CGP12177 whole cell binding, CRE-SPAP production and 3H-cAMP accumulation assays performed. It was confirmed that the three turkey β-adrenoceptors are distinct from each other in terms of amino acid sequence and binding characteristics. The greatest similarity of any of the turkey β-adrenoceptors to human β-adrenoceptors is between the turkey β3C-receptor and the human β2-adrenoceptor. There are pharmacologically distinct differences between the binding of ligands for the tβtrunc and tβ4C and the human β-adrenoceptors (e.g. with CGP20712A and ICI118551). The tβtrunc and tβ4C-adrenoceptors appear to exist in at least two different agonist conformations in a similar manner to that seen at both the human and rat β1-adrenoceptor and human β3-adrenoceptors. The tβ3C-receptor, similar to the human β2-adrenoceptor, does not, at least so far, appear to exist in more than one agonist conformation. Conclusions/Significance There are several similarities, but also several important differences, between the recently crystallised turkey β-adrenoceptor and the human β-adrenoceptors. These findings are important for those the field of drug discovery using the recently structural information from crystallised receptors to aid drug design. Furthermore, comparison of the amino-acid sequence for the turkey and human adrenoceptors may therefore shed more light on the residues involved in the existence of the secondary β-adrenoceptor conformation.
Sleep and Alertness in Medical Interns and Residents: An Observational Study on the Role of Extended Shifts

Study Objectives Fatigue from sleep loss is a risk to physician and patient safety, but objective data on physician sleep and alertness on different duty hour schedules is scarce. This study objectively quantified differences in sleep duration and alertness between medical interns working extended overnight shifts and residents not or rarely working extended overnight shifts. Methods Sleep-wake activity of 137 interns and 87 PGY-2/3 residents on 2-week Internal Medicine and Oncology rotations was assessed with wrist-actigraphy. Alertness was assessed daily with a brief Psychomotor Vigilance Test (PVT) and the Karolinska Sleepiness Scale. Results Interns averaged 6.93 hours (95% confidence interval [CI] 6.84-7.03 hours) sleep per 24 hours across shifts, significantly less than residents not working overnight shifts (7.18 hours, 95% CI 7.06-7.30 hours, p = .007). Interns obtained on average 2.19 hours (95% CI 2.02-2.36 hours) sleep during on-call nights (17.5% obtained no sleep). Alertness was significantly lower on mornings after on-call nights compared to regular shifts (p < .001). Naps between 9 am and 6 pm on the first day post-call were frequent (90.8%) and averaged 2.84 hours (95% CI 2.69-3.00 hours), but interns still slept 1.66 hours less per 24 hours (95% CI 1.56-1.76 hours) compared to regular shift days (p < .001). Sleep inertia significantly affected alertness in the 60 minutes after waking on-call. Conclusions Extended overnight shifts increase the likelihood of chronic sleep restriction in interns. Reduced levels of alertness after on-call nights need to be mitigated. A systematic comparison of sleep, alertness, and safety outcomes under current and past duty hour rules is encouraged.
Hippocampal corticotropin-releasing hormone neurons support recognition memory and modulate hippocampal excitability

Corticotropin-releasing hormone (CRH) signaling in the hippocampus has been established to be important for mediating the effects of stress on learning and memory. Given our laboratory’s recent characterization of a subset of hippocampal CRH neurons as a novel class of GABAergic interneurons, we hypothesized that these local GABAergic hippocampal CRH neurons may influence hippocampal function. Here we applied an array of molecular tools to selectively label and manipulate hippocampal CRH neurons in mice, in order to assess this interneuron population’s impact on hippocampus-dependent behaviors and hippocampal network excitability. Genetically-targeted ablation of hippocampal CRH neurons in vivo impaired object recognition memory and substantially enhanced the severity of kainic acid-induced seizures. Conversely, selective activation of CRH neurons in vitro suppressed the excitability of the mossy fiber-CA3 pathway. Additional experiments are needed to reconcile the functions of GABA and CRH signaling of hippocampal CRH neurons on hippocampal function. However, our results indicate that this interneuron population plays an important role in maintaining adaptive network excitability, and provide a specific circuit-level mechanism for this role.
Predictors of Treatment Response and Survival Outcomes in Meningioma Recurrence with Atypical or Anaplastic Histology

BACKGROUND Recurrence rates for atypical and anaplastic meningiomas range between 9% and 50% after gross total resection and between 36% and 83% after subtotal resection. Optimal treatment of recurrent meningiomas exhibiting atypical/anaplastic histology is complicated because they are often refractory to both surgery and radiation. OBJECTIVE To evaluate clinical determinants of recurrence and treatment‐specific outcomes in patients with recurrent meningiomas exhibiting atypical/anaplastic histology at our institution. METHODS A cohort study was conducted using clinical data of all patients treated for meningiomas with atypical/anaplastic histology at first recurrence between January 1985 and July 2014 at a tertiary cancer center. Predictors of second recurrence were analyzed using competing risks regression models. RESULTS Nine hundred eighteen patients with meningioma were screened, of whom 60 (55% female) had recurrent disease with atypical/anaplastic histology at a median age of 58.1 yr at diagnosis. The median follow‐up from the time of first recurrence was 36.7 mo, with 32 (53%) patients alive at last follow‐up. There was no effect of extent of resection at first recurrence on time to a subsequent recurrence. Inclusion of radiation as primary or adjuvant therapy at first recurrence reduced the risk of progression or subsequent recurrence compared to surgery alone (P = .07). CONCLUSION Treatment of recurrent meningiomas with atypical/anaplastic histology remains challenging. Our data, from one of the largest cohorts, suggest better tumor control with the addition of radiation and challenges the importance of extent of resection at first recurrence. A multicenter effort is needed to confirm these findings and propose treatment guidelines.
Section 5: Decision Support, Knowledge Representation and Management: Free and Open Source Enabling Technologies for Patient-Centric, Guideline-Based Clinical Decision Support: A Survey

Summary Objectives Guideline-based clinical decision support is an emerging paradigm to help reduce error, lower cost, and improve quality in evidence-based medicine. The free and open source (FOS) approach is a promising alternative for delivering cost-effective information technology (IT) solutions in health care. In this paper, we survey the current FOS enabling technologies for patient-centric, guideline-based care, and discuss the current trends and future directions of their role in clinical decision support. Methods We searched PubMed, major biomedical informatics websites, and the web in general for papers and links related to FOS health care IT systems. We also relied on our background and knowledge for specific subtopics. We focused on the functionalities of guideline modeling tools, and briefly examined the supporting technologies for terminology, data exchange and electronic health record (EHR) standards. Results To effectively support patient-centric, guideline-based care, the computerized guidelines and protocols need to be integrated with existing clinical information systems or EHRs. Technologies that enable such integration should be accessible, interoperable, and scalable. A plethora of FOS tools and techniques for supporting different knowledge management and quality assurance tasks involved are available. Many challenges, however, remain in their implementation. Conclusions There are active and growing trends of deploying FOS enabling technologies for integrating clinical guidelines, protocols, and pathways into the main care processes. The continuing development and maturation of such technologies are likely to make increasingly significant contributions to patient-centric, guidelinebased clinical decision support.
KEC_DAlab @ EventXtract-IL-FIRE2017: Event Extraction using Support Vector Machines

Nowadays, Social media has become a major part to transfer the message that must be shared with the people ideas and express the information globally in our day-to-day life. Through social media can able to connect the people together, they are vulnerable to crimes like Identity thefts, false information, and identity masking etc. Identifying the event from the social media messages and news headlines are the important area of research in the current era. This paper illustrates work done on Event Extraction for Indian language shared task which is conducted in Forum for Information Retrieval Evaluation (FIRE) 2017. For this Event extraction task, organizers release the dataset with three languages Tamil, Hindi, and Malayalam. Each language dataset consists of two files Original Tweet file and Annotation files. We only participated in the Tamil event extraction task. In this task, we converted the original tweet file into Bio-format to apply the machine learning directly. Then analyzing each chunk of the word is an event is said to [B] beginner and the other events will be given as Intermediate and the others are assigned as O tag. Each word or chunk should be trained whether it is the event or not an event with the help of rich features and SVM classifier. Here we also find out the CrossValidation accuracy using Natural language techniques.
Quaternion based adaptive control for package delivery using variable-pitch quadrotors

Quadrotors have enormous application in the area of automated delivery systems. In such scenarios, payload can vary with time, and cannot be tackled by traditional controllers. This work presents a nonlinear adaptive control design of a variable-pitch quadrotor. Sudden changes in mass and uncertainty in the rotational inertia of the quadrotor emphasizes the necessity for an adaptive control technique. Quadrotors with variable-pitch propellers are chosen as they provide higher rate of change of thrust and inverted flight capabilities. MATLAB environment is utilized to show a drone-delivery simulation along with trajectory tracking and inverted flight.