Miracle-dz/UniFAR-FTUs huggingface dataset:
Achieving Optimal Covariate Balance Under General Treatment Regimes ∗

Balancing covariates across treatment levels provides an effective and increasingly popular strategy for conducting causal inference in observational studies. Matching procedures, as a means of achieving balance, pre-process the data through identifying a subset of control observations with similar background characteristics to the treated observations. Inference in a matched sample is unbiased and robust to model specification. The proposed method adapts the support vector machine (SVM) classifier to the matching problem. The SVM separates easy to classify observations from hard to classify observations, and only uses the hard to classify cases in estimating a decision boundary between two classes. The treatment levels for these hard to classify observations are estimated with some uncertainty, the hallmark of random assignment. A series of lemmas prove that these hard to classify observations are balanced, for both binary and continuous treatment regimes. Unlike existing methods, the proposed method maximizes balance across all covariates simultaneously, rather than along a summary measure of balance. The method accommodates both binary and continuous treatment regimes. The proposed method is applied to four prominent social science datasets: the effect of a job training program on income, the effect of UN interventions on conflict duration, the effect of changes in foreign aid on domestic insurgent conflict, and the effect of education on political participation. The method is shown to recover an experimental benchmark, retain more observations than its competitors, and avoid dichotomization of a continuous treatment. ∗I thank Kosuke Imai for continued support throughout this project. I also thank participants at Yale’s ISPS Experiments Lunch seminar for useful comments and feedback.
c-Jun-N-terminal phosphorylation regulates DNMT1 expression and genome wide methylation in gliomas

High-grade gliomas (HGG) are the most common brain tumors, with an average survival time of 14 months. A glioma-CpG island methylator phenotype (G-CIMP), associated with better clinical outcome, has been described in low and high-grade gliomas. Mutation of IDH1 is known to drive the G-CIMP status. In some cases, however, the hypermethylation phenotype is independent of IDH1 mutation, suggesting the involvement of other mechanisms. Here, we demonstrate that DNMT1 expression is higher in low-grade gliomas compared to glioblastomas and correlates with phosphorylated c-Jun. We show that phospho-c-Jun binds to the DNMT1 promoter and causes DNA hypermethylation. Phospho-c-Jun activation by Anisomycin treatment in primary glioblastoma-derived cells attenuates the aggressive features of mesenchymal glioblastomas and leads to promoter methylation and downregulation of key mesenchymal genes (CD44, MMP9 and CHI3L1). Our findings suggest that phospho-c-Jun activates an important regulatory mechanism to control DNMT1 expression and regulate global DNA methylation in Glioblastoma.
Recombinant Haemonchus contortus 24 kDa excretory/secretory protein (rHcES-24) modulate the immune functions of goat PBMCs in vitro

A 24 kDa protein is one of the important components in Haemonchus contortus (barber pole worm) excretory/secretory products (HcESPs), which was shown to have important antigenic function. However, little is known about the immunomodulatory effects of this proteinon host cell. In the present study gene encoding 24kDa excretory/secretory protein (HcES-24) was cloned. The recombinant protein of HcES-24 (rHcES-24) was expressed in a histidine-tagged fusion protein soluble form in Escherichia coli. Binding activity of rHcES-24 to goat PBMCs was confirmed by immunofluorescence assay (IFA) and its immunomudulatory effect on cytokine secretion, cell proliferation, cell migration and nitric oxide production were observed by co-incubation of rHcES-24. IFA results revealed that rHcES-24 could bind to the PBMCs. The interaction of rHcES-24 increased the production of IL4, IL10, IL17 and cell migration in dose dependent manner. However, rHcES-24 treatment significantly suppressed the production of IFNγ, proliferation of the PBMC and Nitric oxide (NO) production. Our findings showed that the rHcES-24 played important regulatory effects on the goat PBMCs.
Guidelines on the management of drug‐induced immune and secondary autoimmune, haemolytic anaemia

Literature review details. Recommendations are based on the systematic review of published English language literature from January 1960 to October 2015 (see Appendix S1 for further details). Although recommendations are unchanged, an expanded version of this guideline is available as Appendix S2. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) nomenclature was used to evaluate levels of evidence and to assess the strength of recommendations. The GRADE criteria are specified in the British Committee for Standards in Haematology (BCSH) guidance pack (http://www.bcshguidances.com/BCSH_PRO CESS/42_EVIDENCE_LEVELS_AND_GRADES_OF_RECOM MENDATION.html) and the GRADE working group website (http://www.gradeworkinggroup. org.
BRM Promoter Polymorphisms and Survival of Advanced Non–Small Cell Lung Cancer Patients in the Princess Margaret Cohort and CCTG BR.24 Trial

Introduction: BRM, a key catalytic subunit of the SWI/SNF chromatin remodeling complex, is a putative tumor susceptibility gene that is silenced in 15% of non–small cell lung cancer (NSCLC). Two novel BRM promoter polymorphisms (BRM-741 and BRM-1321) are associated with reversible epigenetic silencing of BRM protein expression. Experimental Design: Advanced NSCLC patients from the Princess Margaret (PM) cohort study and from the CCTG BR.24 clinical trial were genotyped for BRM promoter polymorphisms. Associations of BRM variants with survival were assessed using log-rank tests, the method of Kaplan and Meier, and Cox proportional hazards models. Promoter swap, luciferase assays, and chromatin immunoprecipitation (ChIP) experiments evaluated polymorphism function. In silico analysis of publicly available gene expression datasets with outcome were performed. Results: Carrying the homozygous variants of both polymorphisms (“double homozygotes”, DH) when compared with those carrying the double wild-type was associated with worse overall survival, with an adjusted hazard ratios (aHR) of 2.74 (95% CI, 1.9–4.0). This was confirmed in the BR.24 trial (aHR, 8.97; 95% CI, 3.3–18.5). Lower BRM gene expression (by RNA-Seq or microarray) was associated with worse outcome (P < 0.04). ChIP and promoter swap experiments confirmed binding of MEF2D and HDAC9 only to homozygotes of each polymorphism, associated with reduced promoter activity in the DH. Conclusions: Epigenetic regulatory molecules bind to two BRM promoter sequence variants but not to their wild-type sequences. These variants are associated with adverse overall and progression-free survival. Decreased BRM gene expression, seen with these variants, is also associated with worse overall survival. Clin Cancer Res; 23(10); 2460–70. ©2016 AACR.
Analytical Technique for Designing an RC Snubber Circuit for Ringing Suppression in a Phase-Leg Configuration

Herein, we propose an analytical technique for use in designing a resistor capacitor (RC) snubber circuit for suppressing ringing in phase-leg configurations that are among the main components in electric power converters. In our study, a double pulse circuit is used to examine the effects of RC snubber circuit ringing suppression because the phase-leg and double pulse configuration ringing mechanisms are the same. First, a high-frequency equivalent circuit of the double pulse circuit is derived. Next, an RC snubber circuit for ringing suppression is analytically designed by scrutinizing the characteristic equations via the root locus method. Prior to using the root locus method, we conducted an investigation to determine if that method could be used to analyze the derived high-frequency equivalent circuit when RC snubber circuit parasitic inductances and inductances between the upper and lower modules connectors are small enough to ignore. Finally, the ringing suppression effect of the RC snubber designed by using the proposed analytical technique in a double pulse circuit with practical parasitic inductance values is confirmed via circuit simulations and experimental demonstrations.
Accelerometer-Measured Patterns of Shared Physical Activity Among Mother-Young Child Dyads.

BACKGROUND Many mothers and young children are not meeting physical activity guidelines. Parent-child coparticipation in physical activity (ie, shared physical activity) provides opportunities for social modeling and might be associated with child physical activity. There is very little information about shared physical activity using objective measures. METHODS Participants (N = 17 mother-young child dyads) completed a demographic survey and height/weight measurements, and wore a Bluetooth® accelerometer for 1 week. Accelerometers were initialized using the proximity function to yield both individual and proximity [a minute-by-minute log of whether the 2 accelerometers were in- or out-of-range (∼50 m or less)] data. Shared physical activity was calculated in MATLAB by overlaying individual and proximity accelerometer data. RESULTS Mother-child dyads spent approximately 2 hours per day in shared time that was mostly shared sedentary activities. Less than 1% of shared minutes per day were spent in shared moderate to vigorous physical activity. CONCLUSIONS Mothers and young children spent a small portion of their day in shared activities. Most mother-child shared time was spent in sedentary or light activities rather than moderate to vigorous physical activity. This method for objectively measuring shared physical activity provides novel information about the context in which physical activity occurs and could be used to understand patterns of physical activity among other dyads.
Learning to Represent Programs with Graphs

Learning tasks on source code (i.e., formal languages) have been considered recently, but most work has tried to transfer natural language methods and does not capitalize on the unique opportunities offered by code's known syntax. For example, long-range dependencies induced by using the same variable or function in distant locations are often not considered. We propose to use graphs to represent both the syntactic and semantic structure of code and use graph-based deep learning methods to learn to reason over program structures. In this work, we present how to construct graphs from source code and how to scale Gated Graph Neural Networks training to such large graphs. We evaluate our method on two tasks: VarNaming, in which a network attempts to predict the name of a variable given its usage, and VarMisuse, in which the network learns to reason about selecting the correct variable that should be used at a given program location. Our comparison to methods that use less structured program representations shows the advantages of modeling known structure, and suggests that our models learn to infer meaningful names and to solve the VarMisuse task in many cases. Additionally, our testing showed that VarMisuse identifies a number of bugs in mature open-source projects.
Usefulness of initial plasma dabigatran concentration to predict rebound after reversal

Major bleeding occurs in about 4% of patients treated with direct oral anticoagulants. Following the RE-VERSE AD trial, idarucizumab administered as a single 5g IV dose has been licensed for the management of patients with life-threatening bleeding or in case of urgent surgery/procedures while on treatment with dabigatran etexilate. The 5g dose was calculated to reverse the total body load of dabigatran that was associated with the 99th percentile of the dabigatran levels measured in the phase III study RE-LY. However, since idarucizumab commercialization, several case studies as well as the complete analysis of RE-VERSE AD, highlighted several cases of patients either having required a second dose of idarucizumab, or with a rebound effect of plasma dabigatran levels (in 114 of 497 patients in complete RE-VERSE AD study). Herein, the authors defined reappearance as an increase of the dabigatran plasma concentration above the 20ng/mL threshold of detection after reversal. In REVERSE AD, these reappearances were associated with recurrent or continued bleeding in 10 patients with overt, uncontrollable, or life-threatening bleeding; among which 3 required an additional dose of idarucizumab. In RE-VERSE AD phase III study, the protocol did not include dabigatran measurement before administration of the antidote to guide clinical follow up; plasma samples were collected before and after injection and analyzed post hoc. Initial and post reversal dabigatran measurement would indeed be important for any physician deciding upon the proper use of idarucizumab. Since we think that "no testing" before reversal is questionable, our objective was to identify a patient profile with rebound after reversal. Thus, the aim of our study was to analyze clinical and biological data reported in literature to date. We also present 10 new cases referred to our center (Table 1). To improve patient follow up after reversal and idarucizumab use in our daily practice, we analyzed the impact of initial dabigatran plasma concentrations on the incidence of rebound. The study included 33 cases of patients found in literature between December 1 2015 and February 1 2017, and 10 cases referred to our institution (European Hospital Georges Pompidou, Paris, France), of which 7 received idarucizumab for serious bleeding and 3 for required surgery or other emergent invasive procedure (Table 1 and Online Supplementary Figure S1). We collected clinical and biological data from all patients. In our study, dabigatran plasma concentrations were analyzed when determined using the specific diluted thrombin time (TTd) assay, as reported in RE-VERSE AD. Patients
Prophylactic effects of ellagic acid and rosmarinic acid on doxorubicin‐induced neurotoxicity in rats

Doxorubicin (DOX) is a chemotherapeutic agent widely used in human malignancies. Its long‐term use cause neurobiological side effects. The aim of the present study was to investigate the prophylactic effect exerted by daily administration of ellagic acid (EA) and rosmarinic acid (RA) on DOX‐induced neurotoxicity in rats. Our data showed that DOX‐induced significant elevation of brain malondialdehyde, tumor necrosis factor‐alpha (TNF‐α), inducible nitric oxide synthase (iNOS), caspase‐3, and cholinesterase associated with significant reduction in reduced glutathione, monoamines namely serotonin, dopamine, as well as norepinephrine. Concomitant administration of EA (10 mg/kg/day, p.o. for 14 days) and/or RA (75 mg/kg/day, p.o. for 14 days) with DOX significantly mitigated the neural changes induced by DOX. Meanwhile, treatment ameliorated pro‐inflammatory cytokines as TNF‐α, iNOS, and attenuated oxidative stress biomarkers as well as brain monoamines. In conclusion, EA and RA can effectively protect against DOX‐induced neurotoxicity, and the mechanisms underlying the neuroprotective effect are potentially associated with its antioxidant, anti‐inflammatory, and antiapoptotic properties.
Safer Ratios, Riskier Portfolios: Banks’ Response to Government Aid

Using novel data on bank applications to the Troubled Asset Relief Program (TARP), we study the effect of government assistance on bank risk taking. Bailed-out banks initiate riskier loans and shift assets toward riskier securities after receiving government support. However, this shift in risk occurs mostly within the same asset class and, therefore, remains undetected by regulatory capital ratios, which indicate improved capitalization at bailed-out banks. Consequently, these banks appear safer according to regulatory ratios, but show an increase in volatility and default risk. These findings are robust to controlling for credit demand and account for selection of TARP recipients by exploiting banks׳ geography-based political connections as an instrument for bailout approvals.
Inhibition of centrosome protein assembly leads to p53-dependent exit from the cell cycle

Previous evidence has indicated that an intact centrosome is essential for cell cycle progress and that elimination of the centrosome or depletion of individual centrosome proteins prevents the entry into S phase. To investigate the molecular mechanisms of centrosome-dependent cell cycle progress, we performed RNA silencing experiments of two centrosome-associated proteins, pericentriolar material 1 (PCM-1) and pericentrin, in primary human fibroblasts. We found that cells depleted of PCM-1 or pericentrin show lower levels of markers for S phase and cell proliferation, including cyclin A, Ki-67, proliferating cell nuclear antigen, minichromosome maintenance deficient 3, and phosphorylated retinoblastoma protein. Also, the percentage of cells undergoing DNA replication was reduced by >50%. At the same time, levels of p53 and p21 increased in these cells, and cells were predisposed to undergo senescence. Conversely, depletion of centrosome proteins in cells lacking p53 did not cause any cell cycle arrest. Inhibition of p38 mitogen-activated protein kinase rescued cell cycle activity after centrosome protein depletion, indicating that p53 is activated by the p38 stress pathway.
The experiences and needs of individuals with disabilities exposed to chronic political violence

Abstract Purpose The main objective of this study was to understand, describe and map the experiences, challenges and needs of individuals with lifelong disabilities, who have been exposed to chronic politically violent events (terror, war or continuous missile attacks) in Israel. Method The study was conducted within the qualitative-constructivist paradigm. Three focus groups consisting of 18 individuals with lifelong disabilities were conducted; each focus group included a specific disability type (physical, visual and hearing impairment). Results The participants reported encountering environmental barriers, such as inaccessibly of the physical environment and information as well as dependency on others. These barriers limited the participants' functioning during emergency period and thus increased their level of distress. The participants also emphasized their physical, social and psychological needs. Conclusions The needs of individuals with disabilities in emergency situations can be met if they have a safe place to stay in, are with someone else, and plan every daily action in advance. It is also imperative to provide accessible services and information. Furthermore, it is recommended to develop training sessions for individuals with disabilities and for service providers regarding how to locate, communicate with and assist individuals with disabilities during security threat situations. Implications for Rehabilitation Successful coping of individuals with lifelong disabilities with chronic politically violent events depends on personal and organizational accommodations. Besides an accessible physical environment, the information provided should be available and accessible through mass media and assistive technologies. A comprehensive emergency service for various disabilities is needed. Service providers should be trained on how to locate, communicate with, and assist individuals with disabilities during security threat situations.
INITIAL RESULTS FROM NuSTAR OBSERVATIONS OF THE NORMA ARM

Results are presented for an initial survey of the Norma Arm gathered with the focusing hard X-Ray Telescope NuSTAR. The survey covers 0.2 deg2 of sky area in the 3–79 keV range with a minimum and maximum raw depth of 15 ks and 135 ks, respectively. Besides a bright black-hole X-ray binary in outburst (4U 1630−47) and a new X-ray transient (NuSTAR J163433−473841), NuSTAR locates three sources from the Chandra survey of this region whose spectra are extended above 10 keV for the first time: CXOU J163329.5−473332, CXOU J163350.9−474638, and CXOU J163355.1−473804. Imaging, timing, and spectral data from a broad X-ray range (0.3–79 keV) are analyzed and interpreted with the aim of classifying these objects. CXOU J163329.5−473332 is either a cataclysmic variable or a faint low-mass X-ray binary. CXOU J163350.9−474638 varies in intensity on year-long timescales, and with no multi-wavelength counterpart, it could be a distant X-ray binary or possibly a magnetar. CXOU J163355.1−473804 features a helium-like iron line at 6.7 keV and is classified as a nearby cataclysmic variable. Additional surveys are planned for the Norma Arm and Galactic Center, and those NuSTAR observations will benefit from the lessons learned during this pilot study.
Effects of Organic and Conventional Cropping Systems on Technological Properties and Phenolic Compounds of Freshly Harvested and Stored Rice.

This study compared the physicochemical and technological properties of the IRGA 410 rice cultivar, obtained from organic and conventional cropping systems, and showed its susceptibility to changes during storage at 0, 6, and 12 mo. The rice conventional cropping system exhibited greater protein, lipids, and ash levels, and a head rice yield. However, organic rice presented greater total carbohydrates, soluble protein, amylose content, 33% greater free phenolics, and phenolic acids, but exhibited a greater percentage of stained grains during the storage period. The free phenolic content of cooked rice was lower than the free phenolic content of the raw rice. By Liquid chromatography with mass spectrometer (LC-MS) were identified p-coumaric and ferulic acids in both fractions (free and bound). The content of p-coumaric acid and ferulic acid in bound fraction was higher in organic brown rice than in conventional brown rice. At 6 and 12 mo of storage, the main fungi found were Aspergillus sp. and Penicillium sp. Prior to storage, the Bipolaris sp. fungi was identified only in organic rice. For conventional rice, the infestation level by Aspergillus sp. increased from 3% to 70% at the 6th mo of storage. In addition to the advantage of organic rice being free of agrochemicals, this study revealed that natural plant defense compounds could be produced when the rice was subjected to more biotic and abiotic stresses. However, some disadvantages were observed, such as lower protein content and a greater percentage of soluble protein, which favored the breaking of rice in processing, and a greater percentage of grain stained before and during storage. PRACTICAL APPLICATION The organic and conventional cropping systems affect the physicochemical and technological properties of rice grains, which is one of the main cereals grown and consumed in the world. This study shows the advantages and disadvantages of the cropping system in grain properties that are in the interest of both consumers and processing industries.