LLukas22/scidocs huggingface dataset:
Common mental disorders in asylum seekers and refugees: umbrella review of prevalence and intervention studies

BACKGROUND
In recent years there has been a progressive rise in the number of asylum seekers and refugees displaced from their country of origin, with significant social, economic, humanitarian and public health implications. In this population, up-to-date information on the rate and characteristics of mental health conditions, and on interventions that can be implemented once mental disorders have been identified, are needed. This umbrella review aims at systematically reviewing existing evidence on the prevalence of common mental disorders and on the efficacy of psychosocial and pharmacological interventions in adult and children asylum seekers and refugees resettled in low, middle and high income countries.


METHODS
We conducted an umbrella review of systematic reviews summarizing data on the prevalence of common mental disorders and on the efficacy of psychosocial and pharmacological interventions in asylum seekers and/or refugees. Methodological quality of the included studies was assessed with the AMSTAR checklist.


RESULTS
Thirteen reviews reported data on the prevalence of common mental disorders while fourteen reviews reported data on the efficacy of psychological or pharmacological interventions. Although there was substantial variability in prevalence rates, we found that depression and anxiety were at least as frequent as post-traumatic stress disorder, accounting for up to 40% of asylum seekers and refugees. In terms of psychosocial interventions, cognitive behavioral interventions, in particular narrative exposure therapy, were the most studied interventions with positive outcomes against inactive but not active comparators.


CONCLUSIONS
Current epidemiological data needs to be expanded with more rigorous studies focusing not only on post-traumatic stress disorder but also on depression, anxiety and other mental health conditions. In addition, new studies are urgently needed to assess the efficacy of psychosocial interventions when compared not only with no treatment but also each other. Despite current limitations, existing epidemiological and experimental data should be used to develop specific evidence-based guidelines, possibly by international independent organizations, such as the World Health Organization or the United Nations High Commission for Refugees. Guidelines should be applicable to different organizations of mental health care, including low and middle income countries as well as high income countries.
On Node Virtualization for Scalable Network Emulation

During the development of network protocols and distributed applications, their performance has to be analyzed in appropriate environments. Network emulation testbeds provide a synthetic, configurable network environment for comparative performance measurements of real implementations. Realistic scenarios have to consider hundreds of communicating nodes. Common network emulation approaches limit the number of nodes in a scenario to the number of computers in an emulation testbed. To overcome this limitation, we introduce a virtual node concept for network emulation. The key problem for node virtualization is a transparent, yet efficient separation of node resources. In this paper, we provide a brief survey of candidate node virtualization approaches to facilitate scalable network emulation. Based on the gathered insights, we propose a lightweight virtualization solution to achieve maximum scalability and discuss the main points regarding its implementation. We present extensive evaluations that show the scalability and transparency of our approach in both a traditional wired infrastructure-based, and in a wireless ad hoc network emulation scenario. The measurements indicate that our solution can push the upper limit of emulation scenario sizes by a factor of 20 to 30. Given our emulation testbed consisting of 64 computers, this translates to possible scenario sizes of up to 1920 nodes.
Inventory Model for Items with Weibull Deterioration, Ramp Type Demand and Shortages

The present paper presents an economic order quantity model for the inventory of a deteriorating item with demand rate as a ramp type function of time, in which the inventory is permitted to start with shortages and end without shortages. A two-parameter Weibull distribution is used to represent the distribution of the time to deterioration. A theory is developed to find the optimal solution of the problem. Several numerical examples are then taken to illustrate the solution procedure. Finally, sensitivity of the optimal solution to changes in the values of different system parameters is also studied.
Super deduper, fast PCR duplicate detection in fastq files

Our goal was to explore the accuracy and utility of identifying and removing PCR duplicates from HTS data using Super Deduper. Super Deduper is a pre-alignment, sequence read based technique developed at the University of Idaho, which examines and uses only a small portion of each read's sequence in order to identify and remove PCR and/or optical duplicates. Through comparisons with well-known pre- and post-alignment techniques, Super Deduper's parameters were optimized and its performance assessed. The results conclude that Super Deduper is a viable pre-alignment alternative to post-alignment techniques. Super Deduper is both independent of a reference genome and choice in alignment application, allowing for its use in a greater variety of HTS applications. Super Deduper is an open source application and can be found at https://github.com/dstreett/Super-Deduper.
Schwinger Model in the Light-Cone Representation

I present a solution to the Schwinger model in the light-cone representation which corrects an error in a previous work. I emphasize the details of the mechanism by which the physical vacuum is different than the perturbative vacuum. I suggest that the method of analyzing vacuum structure presented here may be of use in more complicated theories such as QCD.
Measuring protein-protein and protein-nucleic Acid interactions by biolayer interferometry.

Biolayer interferometry (BLI) is a simple, optical dip-and-read system useful for measuring interactions between proteins, peptides, nucleic acids, small molecules, and/or lipids in real time. In BLI, a biomolecular bait is immobilized on a matrix at the tip of a fiber-optic sensor. The binding between the immobilized ligand and another molecule in an analyte solution produces a change in optical thickness at the tip and results in a wavelength shift proportional to binding. BLI provides direct binding affinities and rates of association and dissociation. This unit describes an efficient approach using streptavidin-based BLI to analyze DNA-protein and protein-protein interactions. A quantitative set of equilibrium binding affinities (K(d)) and rates of association and dissociation (k(a)/k(d)) can be measured in minutes using nanomole quantities of sample.
Antiviral activity of boceprevir monotherapy in treatment-naive subjects with chronic hepatitis C genotype 2/3.

BACKGROUND & AIMS
To examine the antiviral activity of boceprevir, a hepatitis C virus (HCV) protease inhibitor, in HCV genotype (G) 2/3-infected patients.


METHODS
We assessed boceprevir and telaprevir activity against an HCV G2 and G3 isolates enzyme panel, in replicon, and in phenotypic cell-based assays. Additionally, a phase I study evaluated the antiviral activity of boceprevir monotherapy (200mg BID, 400mg BID, or 400mg TID) vs. placebo for 14 days in HCV G2/3 treatment-naive patients.


RESULTS
Boceprevir and telaprevir similarly inhibited G1 and G2 NS3/4A enzymes and replication in G1 and G2 replicon and cell-based assays. However, telaprevir demonstrated lower potency than boceprevir against HCV G3a enzyme (Ki=75 nM vs. 17 nM), in the G3a replicon assay (EC₅₀=953 nM vs. 159 nM), and against HCV G3a NS3 isolates (IC₅₀=3312 nM vs. 803 nM) in the cell-based assay. In HCV G2/3-infected patients, boceprevir (400 mg TID) resulted in a maximum mean decrease in HCV RNA of -1.60 log vs. -0.21 log with placebo.


CONCLUSIONS
In vitro, boceprevir is more active than telaprevir against the HCV G3 NS3/4A enzyme in cell-based and biochemical assays and against G3 isolates in replicon assays. In HCV G2/3-infected treatment-naive patients, decreases in HCV RNA levels with boceprevir (400 mg TID) were comparable to those observed with the same dose in HCV treatment-experienced G1-infected patients.
Serverless Computation with OpenLambda

We present OpenLambda, a new, open-source platform for building next-generation web services and applications in the burgeoning model of serverless computation. We describe the key aspects of serverless computation, and present numerous research challenges that must be addressed in the design and implementation of such systems. We also include a brief study of current web applications, so as to better motivate some aspects of serverless application construction.
Tofacitinib or Adalimumab versus Placebo for Psoriatic Arthritis.

BACKGROUND
Tofacitinib is an oral Janus kinase inhibitor that is under investigation for the treatment of psoriatic arthritis. We evaluated tofacitinib in patients with active psoriatic arthritis who previously had an inadequate response to conventional synthetic disease-modifying antirheumatic drugs (DMARDs).


METHODS
In this 12-month, double-blind, active-controlled and placebo-controlled, phase 3 trial, we randomly assigned patients in a 2:2:2:1:1 ratio to receive one of the following regimens: tofacitinib at a 5-mg dose taken orally twice daily (107 patients), tofacitinib at a 10-mg dose taken orally twice daily (104), adalimumab at a 40-mg dose administered subcutaneously once every 2 weeks (106), placebo with a blinded switch to the 5-mg tofacitinib dose at 3 months (52), or placebo with a blinded switch to the 10-mg tofacitinib dose at 3 months (53). Placebo groups were pooled for analyses up to month 3. Primary end points were the proportion of patients who had an American College of Rheumatology 20 (ACR20) response (≥20% improvement from baseline in the number of tender and swollen joints and at least three of five other important domains) at month 3 and the change from baseline in the Health Assessment Questionnaire-Disability Index (HAQ-DI) score (scores range from 0 to 3, with higher scores indicating greater disability) at month 3.


RESULTS
ACR20 response rates at month 3 were 50% in the 5-mg tofacitinib group and 61% in the 10-mg tofacitinib group, as compared with 33% in the placebo group (P=0.01 for the comparison of the 5-mg dose with placebo; P<0.001 for the comparison of the 10-mg dose with placebo); the rate was 52% in the adalimumab group. The mean change in the HAQ-DI score was -0.35 in the 5-mg tofacitinib group and -0.40 in the 10-mg tofacitinib group, as compared with -0.18 in the placebo group (P=0.006 for the comparison of the 5-mg dose with placebo; P<0.001 for the comparison of the 10-mg dose with placebo); the score change was -0.38 in the adalimumab group. The rate of adverse events through month 12 was 66% in the 5-mg tofacitinib group, 71% in the 10-mg tofacitinib group, 72% in the adalimumab group, 69% in the placebo group that switched to the 5-mg tofacitinib dose, and 64% in the placebo group that switched to the 10-mg tofacitinib dose. There were four cases of cancer, three serious infections, and four cases of herpes zoster in patients who received tofacitinib during the trial.


CONCLUSIONS
The efficacy of tofacitinib was superior to that of placebo at month 3 in patients with psoriatic arthritis who had previously had an inadequate response to conventional synthetic DMARDs. Adverse events were more frequent with tofacitinib than with placebo. (Funded by Pfizer; OPAL Broaden ClinicalTrials.gov number, NCT01877668 .).
Mechanism for rapid growth of organic–inorganic halide perovskite crystals

Optoelectronic devices based on hybrid halide perovskites have shown remarkable progress to high performance. However, despite their apparent success, there remain many open questions about their intrinsic properties. Single crystals are often seen as the ideal platform for understanding the limits of crystalline materials, and recent reports of rapid, high-temperature crystallization of single crystals should enable a variety of studies. Here we explore the mechanism of this crystallization and find that it is due to reversible changes in the solution where breaking up of colloids, and a change in the solvent strength, leads to supersaturation and subsequent crystallization. We use this knowledge to demonstrate a broader range of processing parameters and show that these can lead to improved crystal quality. Our findings are therefore of central importance to enable the continued advancement of perovskite optoelectronics and to the improved reproducibility through a better understanding of factors influencing and controlling crystallization.
MODELTEST: testing the model of DNA substitution

SUMMARY
The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.


AVAILABILITY
The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
The data grid: Towards an architecture for the distributed management and analysis of large scientific datasets

In an increasing number of scientific disciplines, large data collections are emerging as important community resources. In domains as diverse as global climate change, high energy physics, and computational genomics, the volume of interesting data is already measured in terabytes and will soon total petabytes. The communities of researchers that need to access and analyze this data (often using sophisticated and computationally expensive techniques) are often large and are almost always geographically distributed, as are the computing and storage resources that these communities rely upon to store and analyze their data [17]. This combination of large dataset size, geographic distribution of users and resources, and computationally intensive analysis results in complex and stringent performance demands that are not satisfied by any existing data management infrastructure. A large scientific collaboration may generate many queries, each involving access to—or supercomputer-class computations on—gigabytes or terabytes of data. Efficient and reliable execution of these queries may require careful management of terabyte caches, gigabit/s data transfer over wide area networks, coscheduling of data transfers and supercomputer computation, accurate performance estimations to guide the selection of dataset replicas, and other advanced techniques that collectively maximize use of scarce storage, networking, and computing resources. The literature offers numerous point solutions that address these issues (e.g., see [17, 14, 19, 3]). But no integrating architecture exists that allows us to identify requirements and components common to different systems and hence apply different technologies in a coordinated fashion to a range of dataintensive petabyte-scale application domains. Motivated by these considerations, we have launched a collaborative effort to design and produce such an integrating architecture. We call this architecture the data grid, to emphasize its role as a specialization and extension of the “Grid” that has emerged recently as an integrating infrastructure for distributed computation [10, 20, 15]. Our goal in this effort is to define the requirements that a data grid must satisfy and the components and APIs that will be required in its implementation. We hope that the definition of such an architecture will accelerate progress on petascale data-intensive computing by enabling the integration of currently disjoint approaches, encouraging the deployment of basic enabling technologies, and revealing technology gaps that require further research and development. In addition, we plan to construct a reference implementation for this architecture so as to enable large-scale experimentation.
Lack of effect of a moderate hypocaloric diet on visfatin levels in morbid obese patients: relationship with insulin resistance.

OBJECTIVES
The insulin-mimetic adipocytokine visfatin has been related to obesity. The aim of this study was to examine whether weight loss could change visfatin concentrations in morbidly obese patients and its relationship with insulin resistance.


MATERIAL AND METHODS
This was an interventional study analyzing a population of 41 morbidly obese patients. A biochemical analysis was realized before and after 2 months on a hypocaloric diet.


RESULTS
After weight loss (average 4.41%), BMI, weight, fat mass, fat free mass, waist circumference, systolic blood pressure, serum glucose, total cholesterol, insulin and HOMA decreased. The serum concentrations of visfatin did not decrease (43.5 + 30.8 vs. 47.1 + 38.1 ng/ml). In the multivariate analysis visfatin concentrations as a dependent variable, only C reactive protein remained as an independent predictor in the model before diet, with an increase of 1.82 ng/ml (CI 95%: 0.02 - 3.61) basal visfatin concentrations with each increase of 1 mg/dl of CRP. Only HOMA remained as an independent predictor in the model after diet, with an increase of 11.4 ng/ml (CI 95%: 1.76 - 21.11) posttreatment visfatin concentrations with each increase of 1 unit HOMA.


CONCLUSION
Weight reduction after a 2 months on a hypocaloric diet is not associated with a significant change in circulating visfatin in morbidly obese patients.
Arterial coupling for microvascular free tissue transfer in head and neck reconstruction.

OBJECTIVE
To demonstrate the efficacy of arterial coupling.


DESIGN
We report our experience in head and neck reconstruction with the Unilink Microvascular Anastomotic System (Synovis MCA, Birmingham, Ala). Data were collected in a consecutive series of 49 patients undergoing composite resection of head and neck tumors followed by free tissue transfer.


SETTING
All patient care took place at Yale-New Haven Hospital, New Haven, Conn, a university-based tertiary care facility.


PATIENTS
Forty-nine consecutive patients aged 43 to 85 years underwent a total of 50 microvascular free tissue transfers using the Unilink coupling device. There were 18 women and 31 men, and the following 3 types of flaps were performed: radial forearm (n = 36), fibula (n = 12), and rectus abdominus (n = 2).


INTERVENTIONS
The Unilink coupling device was used in this case series. Each arterial and venous anastomosis was performed with the coupling device. Free tissue transfers were monitored clinically and outcomes were recorded.


MAIN OUTCOME MEASURES
Flap survival and thrombosis of the arterial anastomoses were determined, as was median length of stay.


RESULTS
There were no flap failures in the series. Of the 50 coupled arterial anastomoses, the predominant coupler size used was 2.5 mm in diameter. Reconstructions included 36 radial forearm, 12 fibular osteocutaneous, and 2 rectus abdominus myocutaneous free flaps. One intraoperative arterial thrombosis occurred, requiring hand-sewn anastomosis, and another pulled away from the intact coupler in a steroid-dependent patient. There were no complications related to technical performance of the coupling device. The median length of stay was 14 days.


CONCLUSION
While hand-sewn anastomoses in free tissue transfer remain the preferred technique for many microsurgeons, use of the coupler is a viable alternative to sutured anastomoses.
Intensive Versus Distributed Aphasia Therapy: A Nonrandomized, Parallel-Group, Dosage-Controlled Study.

BACKGROUND AND PURPOSE
Most studies comparing different levels of aphasia treatment intensity have not controlled the dosage of therapy provided. Consequently, the true effect of treatment intensity in aphasia rehabilitation remains unknown. Aphasia Language Impairment and Functioning Therapy is an intensive, comprehensive aphasia program. We investigated the efficacy of a dosage-controlled trial of Aphasia Language Impairment and Functioning Therapy, when delivered in an intensive versus distributed therapy schedule, on communication outcomes in participants with chronic aphasia.


METHODS
Thirty-four adults with chronic, poststroke aphasia were recruited to participate in an intensive (n=16; 16 hours per week; 3 weeks) versus distributed (n=18; 6 hours per week; 8 weeks) therapy program. Treatment included 48 hours of impairment, functional, computer, and group-based aphasia therapy.


RESULTS
Distributed therapy resulted in significantly greater improvements on the Boston Naming Test when compared with intensive therapy immediately post therapy (P=0.04) and at 1-month follow-up (P=0.002). We found comparable gains on measures of participants' communicative effectiveness, communication confidence, and communication-related quality of life for the intensive and distributed treatment conditions at post-therapy and 1-month follow-up.


CONCLUSIONS
Aphasia Language Impairment and Functioning Therapy resulted in superior clinical outcomes on measures of language impairment when delivered in a distributed versus intensive schedule. The therapy progam had a positive effect on participants' functional communication and communication-related quality of life, regardless of treatment intensity. These findings contribute to our understanding of the effect of treatment intensity in aphasia rehabilitation and have important clinical implications for service delivery models.
Multilevel analysis of HIV related risk behaviors among heroin users in a low prevalence community

BACKGROUND
Injecting drug users (IDU) are at increased risk of human immunodeficiency virus (HIV) infection. Their HIV prevalence however varies from place to place and may not be directly linked with the level of individual risk. This study explores the relative importance of individual and community level characteristics in the practice of HIV-related risk behaviors in IDU in Hong Kong where the HIV prevalence has remained low at below 1%.


METHODS
Methadone clinics were used as the channel for accessing drug users in Hong Kong. HIV-related risk factors in drug users attending these clinics were retrieved from a questionnaire routinely administered to newly admitted and readmitted clients, and assessed using logistic regression and multilevel analyses.


RESULTS
Between 1999 and 2005, a total of 41,196 person-admissions were recorded by 20 methadone clinics. Male gender, older age and new admissions in bigger clinics located in districts with older median age were more likely to have engaged in HIV related risk behaviors including heroin injection, needle sharing, unprotected sex and having multiple sex partners (p < 0.05).


CONCLUSION
Multilevel analysis is a useful adjunct for determining the association between risk behaviors and both individual and community factors in IDUs, which can be demonstrated even in low HIV prevalence settings.