Miracle-dz/UniFAR-FTUs huggingface dataset:
Suicidal events in the Treatment for Adolescents With Depression Study (TADS).

OBJECTIVE The Treatment for Adolescents with Depression Study (TADS) database was analyzed to determine whether suicidal events (attempts and ideation) occurred early in treatment, could be predicted by severity of depression or other clinical characteristics, and were preceded by clinical deterioration or symptoms of increased irritability, akathisia, sleep disruption, or mania. METHOD TADS was a 36-week randomized, controlled clinical trial of pharmacologic and psychotherapeutic treatments involving 439 youths with major depressive disorder (DSM-IV criteria). Suicidal events were defined according to the Columbia Classification Algorithm of Suicidal Assessment. Patients were randomly assigned into the study between spring 2000 and summer 2003. RESULTS Forty-four patients (10.0%) had at least 1 suicidal event (no suicide occurred). Events occurred 0.4 to 31.1 weeks (mean +/- SD = 11.9 +/- 8.2) after starting TADS treatment, with no difference in event timing for patients receiving medication versus those not receiving medication. Severity of self-rated pretreatment suicidal ideation (Suicidal Ideation Questionnaire adapted for adolescents score > or = 31) and depressive symptoms (Reynolds Adolescent Depression Scale score > or = 91) predicted occurrence of suicidal events during treatment (P < .05). Patients with suicidal events were on average still moderately ill prior to the event (mean +/- SD Clinical Global Impressions-Severity of Illness scale score = 4.0 +/- 1.3) and only minimally improved (mean +/- SD Clinical Global Impressions-Improvement scale score = 3.2 +/- 1.1). Events were not preceded by increased irritability, akathisia, sleep disturbance, or manic signs. Specific interpersonal stressors were identified in 73% of cases (N = 44). Of the events, 55% (N = 24) resulted in overnight hospitalization. CONCLUSIONS Most suicidal events occurred in the context of persistent depression and insufficient improvement without evidence of medication-induced behavioral activation as a precursor. Severity of self-rated suicidal ideation and depressive symptoms predicted emergence of suicidality during treatment. Risk for suicidal events did not decrease after the first month of treatment, suggesting the need for careful clinical monitoring for several months after starting treatment.
Genetic variants in fas signaling pathway genes and risk of gastric cancer

Populations in north central China are at high risk for gastric cancers (GC), and altered FAS‐mediated cell signaling and/or apoptosis may contribute to this risk. We examined the association of 554 single nucleotide polymorphisms (SNPs) in 53 Fas signaling‐related genes using a pathway‐based approach in 1758 GC cases (1126 gastric cardia adenocarcinomas (GCA) and 632 gastric noncardia adenocarcinomas (GNCA)), and 2111 controls from a genome‐wide association study (GWAS) of GC in ethnic Chinese. SNP associations with risk of overall GC, GCA and GNCA were evaluated using unconditional logistic regressions controlling for age, sex and study. Gene‐ and pathway‐based associations were tested using the adaptive rank‐truncated product (ARTP) method. Statistical significance was evaluated empirically by permutation. Significant pathway‐based associations were observed for Fas signaling with risk of overall GC (p = 5.5E‐04) and GCA (p = 6.3E‐03), but not GNCA (p= 8.1E‐02). Among examined genes in the Fas signaling pathway, MAP2K4, FAF1, MAPK8, CASP10, CASP8, CFLAR, MAP2K1, CAP8AP2, PAK2 and IKBKB were associated with risk of GC (nominal p < 0.05), and FAF1 and MAPK8 were significantly associated with risk of both GCA and GNCA (nominal p< 0.05). Our examination of genetic variation in the Fas signaling pathway is consistent with an association of altered Fas signaling and/or apoptosis with risk of GC. As one of the first attempts to investigate a pathway‐level association, our results suggest that these genes and the Fas signaling pathway warrant further evaluation in relation to GC risk in other populations.
The Effect of Umbilical Cord-derived Mesenchymal Stem Cell Transplantation in a Patient with Cerebral Palsy: A Case Report

Background Cerebral Palsy (CP) is the most common motor disability reason of childhood that occurs secondarily to non-progressive damage in the brain whose development is still ongoing. Methods 6-year-old dystonic-spastic male CP patient received allogenic mesenchymal stem cells treatment four times as 1×106/kg in intrathecal and intravenous administration of Umbilical Cord-derived mesenchymal stem cells (UC-MSCs) ways. Before and after the treatment, the patient was followed-up with FIM (Functional Independent Measurement), GMFCS (Gross Motor Function Classification System 88), Tardieu Scale, TCMS (Trunk Control Measurement Scale), MACS (Manual Ability Classification Scale), CFSS (Communication Function Classification System) for 18 months and received intensive rehabilitation. Results Improvements were observed especially in functional scales except for the Tardieu Scale, and no adverse effects were detected aside from a slight pain in the back. Conclusion Wider future case studies on UC-MSCs will enable us to assess the efficacy of UC-MSCs which have positive impacts especially on functional scales.
Killing in the Name of Islam: Al‐Qaeda's Justification for September 11

In the wake of the September 11 attacks, President Bush moved quickly to dismiss al-Qaeda operatives as part of the lunatic fringe, religious usurpers bent on misrepresenting and “hijacking” Islam to serve terrorism.1 This characterization was echoed in the Muslim world, where an assortment of government officials, religious scholars and opposition figures fervidly denounced the killing of civilians as un-Islamic.2 Abdulaziz bin Abdullah al-Ashaykh, the mufti of Saudi Arabia, argued that “hijacking planes, terrorizing innocent people and shedding blood constitute a form of injustice that cannot be tolerated by Islam, which views them as gross crimes and sinful acts. ”3 Muhammed Sayyid alTantawi, the rector of al-Azhar University in Cairo, issued a similar condemnation: “Attacking innocent people is not courageous, it is stupid and will be punished on the day of judgment. It’s not courageous to attack innocent children, women and civilians. It is courageous to protect freedom, it is courageous to defend oneself and not to attack. ”4 Shaikh Yussuf alQaradawi, a prominent Islamic scholar and television personality from Qatar, emphasized that “Islam, the religion of tolerance, holds the human soul in high esteem, and considers the attack against innocent human beings a grave sin. ”5 Even Islamic fundamentalist groups issued sharp denunciations. Forty-six leaders representing an assortment of Islamist movements and groups signed a letter opposed to the attacks:
Fetal bovine serum‐free culture of endothelial progenitor cells—progress and challenges

Two decades after the first report on endothelial progenitor cells (EPC), their key role in postnatal vasculogenesis and vascular repair is well established. The therapeutic potential of EPC and their growing use in clinical trials calls for the development of more robust, reproducible, and safer methods for the in vitro expansion and maintenance of these cells. Despite many limitations associated with its usage, fetal bovine serum (FBS) is still widely applied as a cell culture supplement. Although different approaches aiming at establishing FBS‐free culture have been developed for many cell types, adequate solutions for endothelial cells, and for EPC in particular, are still scarce, possibly due to the multiple challenges that have to be faced when culturing these cells. In this review, we provide a brief overview on the therapeutic relevance of EPC and critically analyse the available literature on FBS‐free endothelial cell culture methods, including xeno‐free, serum‐free, and chemically defined systems.
Peroxisomal Membrane Proteins Insert into the Endoplasmic Reticulum

We demonstrate that the entry of peroxisomal membrane proteins (PMPs) into the ER is mediated by the general ER import machinery. Within the ER, PMPs attain their correct topology and subsequently travel to peroxisomes. Our results show that the ER forms an obligate requirement to maintain peroxisomes in multiplying cells.
Structure–function analysis reveals that the Pseudomonas aeruginosa Tps4 two-partner secretion system is involved in CupB5 translocation

Pseudomonas aeruginosa is a Gram‐negative opportunistic bacterium, synonymous with cystic fibrosis patients, which can cause chronic infection of the lungs. This pathogen is a model organism to study biofilms: a bacterial population embedded in an extracellular matrix that provide protection from environmental pressures and lead to persistence. A number of Chaperone‐Usher Pathways, namely CupA‐CupE, play key roles in these processes by assembling adhesive pili on the bacterial surface. One of these, encoded by the cupB operon, is unique as it contains a nonchaperone‐usher gene product, CupB5. Two‐partner secretion (TPS) systems are comprised of a C‐terminal integral membrane β‐barrel pore with tandem N‐terminal POTRA (POlypeptide TRansport Associated) domains located in the periplasm (TpsB) and a secreted substrate (TpsA). Using NMR we show that TpsB4 (LepB) interacts with CupB5 and its predicted cognate partner TpsA4 (LepA), an extracellular protease. Moreover, using cellular studies we confirm that TpsB4 can translocate CupB5 across the P. aeruginosa outer membrane, which contrasts a previous observation that suggested the CupB3 P‐usher secretes CupB5. In support of our findings we also demonstrate that tps4/cupB operons are coregulated by the RocS1 sensor suggesting P. aeruginosa has developed synergy between these systems. Furthermore, we have determined the solution‐structure of the TpsB4‐POTRA1 domain and together with restraints from NMR chemical shift mapping and in vivo mutational analysis we have calculated models for the entire TpsB4 periplasmic region in complex with both TpsA4 and CupB5 secretion motifs. The data highlight specific residues for TpsA4/CupB5 recognition by TpsB4 in the periplasm and suggest distinct roles for each POTRA domain.
Sparse Sparse Bundle Adjustment

Sparse Bundle Adjustment (SBA) is a method for simultaneously optimizing a set of camera poses and visible points. It exploits the sparse primary structure of the problem, where connections exist just between points and cameras. In this paper, we implement an efficient version of SBA for systems where the secondary structure (relations among cameras) is also sparse. The method, which we call Sparse SBA (sSBA), integrates an efficient method for setting up the linear subproblem with recent advances in direct sparse Cholesky solvers. sSBA outperforms the current SBA standard implementation on datasets with sparse secondary structure by at least an order of magnitude, while also being more efficient on dense datasets.
Sufficient Statistics Feature Mapping over Deep Boltzmann Machine for Detection

As an important and fundamental methodology in the fields of pattern recognition and image processing, learning middle level feature has attracted increasing interest during the recent years, where generative feature mapping has shown highly completive performance in diverse applications. In this paper, a middle level feature representation is proposed based on Deep Boltzmann Machine (DBM) and sufficient statistics (SS) feature mapping for detection. In the approach, DBM is employed to model data distribution and the hidden information inferred by DBM together with other informative variables are then exploited by SS to form the middle level features. The features, learnt from data, can be fed to standard classifiers for classification. In order to evaluate the performance of our method, we apply our feature mapping method to two challenging tasks: (1) contour detection through distinguishing border and non-border pixels, (2) sales pipeline prediction, which predicts the winning propensity of the ongoing sales opportunity in the pipeline. In comparison with other leading methods in the literature on the Berkeley Segmentation Dataset and Sales Pipeline Database (SPDB), our proposed algorithm performs favorably against state-of-the-art methods in terms of effectiveness and efficiency.
WORTAKZENT IM SPRACHKONTAKT DEUTSCH-ITALIENISCH

This study explores the extent to which German word accent distribution is influenced by language contact with Italian. To this end, speakers from three populations with differing degrees of language contact were asked to pronounce artificial polysyllabic words: (a) monolingual German speakers, (b) German-dominant bilinguals from the South Tyrol, and (c) Italian-dominant bilinguals from the same language region. In that the choice of artificial words largely precludes speakers resorting to the idiosyncratic lexical information which can steer stress distribution in real words, the results reported here enable conclusions about the influence of the contact language on speakers' implicit word accent rules. The study demonstrates that the contact language exerts a systematic influence. Compared to the German monolinguals, bilingual participants produced distinctly fewer words with penultimate and distinctly more with antepenultimate stress, with the degree of shift in accenting behaviour dependent upon the individual degree of language contact. Taking word accent distribution in the relevant languages into account, the altered accenting behaviour intimates the effects of (gradual rather than categorical) hypercorrection.
Prevalence estimation subject to misclassification: the mis‐substitution bias and some remedies

We consider the problem of estimating the prevalence of a disease under a group testing framework. Because assays are usually imperfect, misclassification of disease status is a major challenge in prevalence estimation. To account for possible misclassification, it is usually assumed that the sensitivity and specificity of the assay are known and independent of the group size. This assumption is often questionable, and substitution of incorrect values of an assay's sensitivity and specificity can result in a large bias in the prevalence estimate, which we refer to as the mis‐substitution bias. In this article, we propose simple designs and methods for prevalence estimation that do not require known values of assay sensitivity and specificity. If a gold standard test is available, it can be applied to a validation subsample to yield information on the imperfect assay's sensitivity and specificity. When a gold standard is unavailable, it is possible to estimate assay sensitivity and specificity, either as unknown constants or as specified functions of the group size, from group testing data with varying group size. We develop methods for estimating parameters and for finding or approximating optimal designs, and perform extensive simulation experiments to evaluate and compare the different designs. An example concerning human immunodeficiency virus infection is used to illustrate the validation subsample design. Copyright © 2014 John Wiley & Sons, Ltd.
USH1H, a novel locus for type I Usher syndrome, maps to chromosome 15q22‐23

Usher syndrome (USH) is a hereditary disorder associated with sensorineural hearing impairment, progressive loss of vision attributable to retinitis pigmentosa (RP) and variable vestibular function. Three clinical types have been described with type I (USH1) being the most severe. To date, six USH1 loci have been reported. We ascertained two large Pakistani consanguineous families segregating profound hearing loss, vestibular dysfunction, and RP, the defining features of USH1. In these families, we excluded linkage of USH to the 11 known USH loci and subsequently performed a genome‐wide linkage screen. We found a novel USH1 locus designated USH1H that mapped to chromosome 15q22‐23 in a 4.92‐cM interval. This locus overlaps the non‐syndromic deafness locus DFNB48 raising the possibility that the two disorders may be caused by allelic mutations.
Overview of Admixture Mapping

Admixture mapping is a powerful method of gene mapping for diseases or traits that show differential risk by ancestry. Admixture mapping has been applied most often to African Americans who trace ancestry to Europeans and West Africans. Recent developments in admixture mapping include improvements in methods to take advantage of higher densities of genetic variants, as well as extensions to admixed populations with three or more ancestral populations, such as Latino Americans. In this unit, the author outlines the key concepts of admixture mapping. The author describes several approaches for inferring local ancestry and provides strategies for performing admixture mapping depending on the study design. Finally, the author compares and contrasts linkage analysis, association analysis, and admixture mapping, with an emphasis on integrating admixture mapping and association testing. Curr. Protoc. Hum. Genet. 76:1.23. 1‐1.23. 8. © 2013 by John Wiley & Sons, Inc.
Synthetic Activation of Endogenous PI3K and Rac Identifies an AND-Gate Switch for Cell Polarization and Migration

Phosphatidylinositol 3-OH kinase (PI3K) has been widely studied as a principal regulator of cell polarization, migration, and chemotaxis [1], [2], [3], [4]. Surprisingly, recent studies showed that mammalian neutrophils and Dictyostelium discoideum cells can polarize and migrate in the absence of PI3K activity [5], [6], [7]. Here we directly probe the roles of PI3K and its downstream effector, Rac, in HL-60 neutrophils by using a chemical biology approach whereby the endogenously present enzymes are synthetically activated in less than one minute [8], [9], [10]. We show that uniform activation of endogenous PI3K is sufficient to polarize previously unpolarized neutrophils and trigger effective cell migration. After a delay following symmetrical phosphatidylinositol (3,4,5)-triphosphate (PIP3) production, a polarized distribution of PIP3 was induced by positive feedback requiring actin polymerization. Pharmacological studies argue that this process does not require receptor-coupled trimeric G proteins. Contrary to the current working model, rapid activation of endogenous Rac proteins triggered effective actin polymerization but failed to feed back to PI3K to generate PIP3 or induce cell polarization. Thus, the increase in PIP3 concentration at the leading edge is generated by positive feedback with an AND gate logic with a PI3K-Rac-actin polymerization pathway as a first input and a PI3K initiated non-Rac pathway as a second input. This AND-gate control for cell polarization can explain how Rac can be employed for both PI3K-dependent and -independent signaling pathways coexisting in the same cell.
Estimation and Inference for the Causal Effect of Receiving Treatment on a Multinomial Outcome: An Alternative Approach

Summary Recently, Cheng (2009 , Biometrics 65, 96–103) proposed a model for the causal effect of receiving treatment when there is all‐or‐none compliance in one randomization group, with maximum likelihood estimation based on convex programming. We discuss an alternative approach that involves a model for all‐or‐none compliance in two randomization groups and estimation via a perfect fit or an expectation–maximization algorithm for count data. We believe this approach is easier to implement, which would facilitate the reproduction of calculations.
That Makes Sense: Joint Sense Retrofitting from Contextual and Ontological Information

While recent word embedding models demonstrate their abilities to capture syntactic and semantic information, the demand for sense level embedding is getting higher. In this study, we propose a novel joint sense embedding learning model that retrofits the word representation into sense representation from contextual and ontological information. The experiment shows the effectiveness and robustness of our model that outperforms previous approaches in four public available benchmark datasets.
No Evidence for Spread of Plasmodium falciparum Artemisinin Resistance to Savannakhet Province, Southern Laos

We conducted an open-label, randomized clinical trial to assess parasite clearance times (PCT) and the efficacy of 4 mg/kg (group 1, n = 22) and 2 mg/kg (group 2, n = 22) of oral artesunate for three days followed by artemether-lumefantrine in patients with uncomplicated Plasmodium falciparum malaria at Xepon Interdistrict Hospital, Savannakhet Province in southern Laos. Slides were read in duplicate. The overall mean (95% confidence interval; range) PCT in hours was 23.2 (21.2–25.3; 12–46) and 22.4 (20.3–24.5; 12–46) for the first and second microscopists, respectively (P = 0.57). Ten (23%) patients remained parasitemic on day 1 after treatment (4 [18%] in group 1 and 6 [27%] in group 2; P = 0.47). No patient had patent asexual parasitemia on the second and third days of treatment. The 42-day polymerase chain reaction–corrected cure rates were 100% in both treatment groups. Serious adverse events did not develop during or after treatment in any patients. In conclusion, no evidence of P. falciparum in vivo resistance to artesunate was found in southern Laos.
Development of the Korean Version of The World Health Organization Quality of Life Scale(WHOQOL)

연구목적: 본 연구는 세계보건기구에서 개발한 세계보건기구 삶의 질 척도(WHOQOL:World Health Organization Quality of Life assessment instrument)를 한국어로 번역하고 그 타당도 및 신뢰도를 검증하는 것이다. 방 법: WHO의 지침에 따라 영문판 WHOQOL을 한국어로 번역하고 응답점 설정작업을 한후, 일반인 및 전문가 초점 그룹으로 하여금 검토 수정하였다. 이를 영문으로 다시 재 번역하여 WHO의 검토를 받고 다시 수정하 였다. 이 한국어판을 정상인, 의학적 환자, 그리고 대학생 등 583명을 대상으로 평가하게 하여, 통계분석을 하였다. WHOQOL 검사-재검사 신뢰도를 보기 위하여 3주 간격으로 113명에게 재검사를 시행하였다. 결 과: 검사-재검사 신뢰도 하부척도에 따라 0.639(p<0.0001)에서 0.857(p<0.0001)까지로 시간에 따른 안정 성을 보였다. 내적 일관성에 있어 Cronbach's α는 0. 898이었으며 각 영역(domain)과 하부척도(facet)에 서도 일관성이 높았다. 총점, 영역 및 하부척도의 점수가 전반적인 삶의 질 점수 및 전반적 추정치와 유의한 상관관계가 있어 기준 타당도도 입증되었다. 내용 타당도에 있어 경로분석상 영역간 일정한 연관을 보였다. 성별, 나이, 및 질병의 유무에 따라 유의한 차이가 있는 등 변별 타당도가 입증되었다. 결 론: 한국판 WHOQOL이 삶의 질을 측정하는 도구로써 신뢰롭고 타당한 검사인 것으로 나타났다.
A knock‐in allele of En1 expressing dre recombinase

Engrailed 1 (En1) is a homeobox‐containing transcription factor expressed during development in diverse tissues, including the embryonic midbrain and anterior hindbrain. To facilitate investigation of genetic and developmental heterogeneity among cells with a history of En1 expression, we have generated En1Dre, a knock‐in allele expressing Dre recombinase. En1Dre can be used with existing Cre and Flp recombinase lines for genetic intersectional labeling, fate mapping, and functional manipulation of subpopulations of cells characterized by transient expression of En1. To avoid disrupting En1 function, the Dre cDNA is inserted at the 3′ end of the En1 coding sequence, together with a viral 2A peptide to mediate translation of separate EN1 and Dre proteins. Consequently, viable and fertile En1Dre homozygotes can be used to increase the proportion of useful genotypes produced in complex crosses. The pattern of Dre expression from En1Dre is indistinguishable from wild‐type En1 expression in mid‐gestation mouse embryos, and En1Dre controls Dre‐responsive indicator alleles by efficiently recombining rox sites in vivo. Through the application of genetic tools that allow manipulation of cells based on combinatorial expression of multiple distinct recombinases, En1Dre will significantly extend the ability to target important subpopulations of neurons and other cells within the broader En1 expression domain. genesis 54:447–454, 2016. Published 2016. This article is a US Government work and is in the public domain in the USA.