Miracle-dz/UniFAR-FTUs huggingface dataset:
Walker A Lysine Mutations of TAP1 and TAP2 Interfere with Peptide Translocation but Not Peptide Binding*

We generated mutants of the transporter associated with antigen-processing subunits TAP1 and TAP2 that were altered at the conserved lysine residue in the Walker A motifs of the nucleotide binding domains (NBD). In other ATP binding cassette transporters, mutations of the lysine have been shown to reduce or abrogate the ATP hydrolysis activity and in some cases impair nucleotide binding. Mutants TAP1(K544M) and TAP2(K509M) were expressed in insect cells, and the effects of the mutations on nucleotide binding, peptide binding, and peptide translocation were assessed. The mutant TAP1 subunit is significantly impaired for nucleotide binding relative to wild type TAP1. The identical mutation in TAP2 does not significantly impair nucleotide binding relative to wild type TAP2. Using fluorescence quenching assays to measure the binding of fluorescent peptides, we show that both mutants, in combination with their wild type partners, can bind peptides. Since the mutant TAP1 is significantly impaired for nucleotide binding, these results indicate that nucleotide binding to TAP1 is not a requirement for peptide binding to TAP complexes. Peptide translocation is undetectable for TAP1·TAP2(K509M) complexes, but low levels of translocation are detectable with TAP1(K544M)·TAP2 complexes. These results suggest an impairment in nucleotide hydrolysis by TAP complexes containing either mutant TAP subunit and indicate that the presence of one intact TAP NBD is insufficient for efficient catalysis of peptide translocation. Taken together, these results also suggest the possibility of distinct functions for TAP1 and TAP2 NBD during a single translocation cycle.
Bi-Transferring Deep Neural Networks for Domain Adaptation

Sentiment classification aims to automatically predict sentiment polarity (e.g., positive or negative) of user generated sentiment data (e.g., reviews, blogs). Due to the mismatch among different domains, a sentiment classifier trained in one domain may not work well when directly applied to other domains. Thus, domain adaptation for sentiment classification algorithms are highly desirable to reduce the domain discrepancy and manual labeling costs. To address the above challenge, we propose a novel domain adaptation method, called Bi-Transferring Deep Neural Networks (BTDNNs). The proposed BTDNNs attempts to transfer the source domain examples to the target domain, and also transfer the target domain examples to the source domain. The linear transformation of BTDNNs ensures the feasibility of transferring between domains, and the distribution consistency between the transferred domain and the desirable domain is constrained with a linear data reconstruction manner. As a result, the transferred source domain is supervised and follows similar distribution as the target domain. Therefore, any supervised method can be used on the transferred source domain to train a classifier for sentiment classification in a target domain. We conduct experiments on a benchmark composed of reviews of 4 types of Amazon products. Experimental results show that our proposed approach significantly outperforms the several baseline methods, and achieves an accuracy which is competitive with the state-of-the-art method for domain adaptation.
The Black Box of Organizational Demography

With this first issue, Organization Science inaugurates a new editorial format called "Perspective. " It is intended as an occasional forum for featuring theoretical or critical essays that challenge accepted thinking or established empirical approaches in organization studies. Perspective articles will be selected from among those already accepted for publication in Organization Science. The nomination will be made by the Senior Editor who accepted the paper for publication in Organization Science. The determination for publishing in Perspective will be made on the basis of demonstrated significant potential to redirect contemporary thought and methods relating to important topics and issues in the field. Perspective articles will appear in the earliest possible issue. The paper, "The Black Box of Organizational Demography," by Barbara Lawrence, undertakes the challenging task of questioning and clarifying the logical and methodological underpinning of organizational demography which so far has not been subject to sustained critical reflections. This thoughtful and balanced paper, which questions assumptions and identifies major problems affecting this well-established stream of research, offers new directions that could enrich and redirect organizational demography research.
Approach-Related Complications of Anterior Lumbar Interbody Fusion: Results of a Combined Spine and Vascular Surgical Team

Study Design Retrospective analysis of prospectively collected cohort data. Objective Anterior lumbar interbody fusion (ALIF) is a commonly performed procedure for the treatment of degenerative diseases of the lumbar spine. Detailed and comprehensive descriptions of intra- and postoperative complications of ALIF are surprisingly limited in the literature. In this report, we describe our experience with a team model for ALIF and report all complications occurring in our patient series. Methods Patients were prospectively enrolled between January 2009 and January 2013 by a combined spine surgeon and vascular surgeon team. All patients underwent an open ALIF using an anterior approach to the lumbosacral spine. Results From the 227 ALIF cases, mean operative blood loss was 103 mL, ranging from 30 to 900 mL. Mean operative time was 78 minutes. The average length of stay was 5.2 days. Intraoperative vascular injury requiring primary repair with suturing occurred in 15 patients (6.6%). There were 2 cases of postoperative retroperitoneal hematoma. Three patients (1.3%) had incisional hernia requiring revision surgery; 7 (3.1%) patients had prolonged ileus (>7 days) managed conservatively. Four patients described retrograde ejaculation. Sympathetic dysfunction occurred in 15 (6.6%) patients. There were 5 (2.2%) cases of superficial wound infection treated with oral antibiotics, with no deep wound infections requiring reoperation or intravenous therapy. There were no mortalities in this series. Conclusions ALIF is a safe procedure when performed by a combined vascular surgeon and spine surgeon team with acceptably low complication rates. Our series confirms that the team approach results in short operative times and length of stay, with rapid control of intraoperative vessel injury and low overall blood loss.
Efficient Cooperative Discovery of Service Compositions in Unstructured P2P Networks

In this paper, we propose an efficient technique for improving the performance of automatic and cooperative compositions in P2P unstructured networks during service discovery. Since the adoption of flooding to exchange queries and partial solutions among the peers of unstructured networks generates a huge amount of messages, the technique exploits a probabilistic forwarding algorithm that uses different sources of knowledge, such as network density and service grouping, to reduce the amount of messages exchanged. The technique, analyzed in several network configurations by using a simulator to observe resolution time, recall and message overhead, has shown good performances especially in dense and large-scale service networks.
Bioinformatics analysis of the molecular mechanism of diffuse intrinsic pontine glioma

The present study aimed to elucidate key molecular mechanisms in the progression of diffuse intrinsic pontine glioma (DIPG). The gene expression profile GSE50021, which consisted of 35 pediatric DIPG samples and 10 normal brain samples, was downloaded from the Gene Expression Omnibus database. The differentially-expressed genes (DEGs) in the pediatric DIPG samples were identified. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathways of DEGs were enriched and analyzed. The protein-protein interaction (PPI) network of the DEGs was constructed and functional modules of the PPI network were disclosed using ClusterONE. A total of 679 DEGs (454 up- and 225 downregulated) were identified in the pediatric DIPG samples. DEGs were significantly enriched in various GO terms, and KEGG and Reactome pathways. The PPI network of upregulated (153 nodes and 298 connections) and downregulated (71 nodes and 124 connections) DEGs, and two crucial modules, were obtained. Downregulated genes in module 2, such as cholecystokinin (CCK), gastrin (GAST), adenylate cyclase 2 (brain) (ADCY2) and 5-hydroxytryptamine (serotonin) receptor 7 (HTR7), were significantly enriched in the calcium signaling pathway, the neuroactive ligand-receptor interaction pathway and in GO terms, such as the G-protein coupled receptor (GPCR) signaling pathway, while upregulated genes in module 1 were not enriched in any pathways or GO terms. CCK and GAST associated with the GPCR signaling pathway, HTR7 enriched in the neuroactive ligand-receptor interaction, and ADCY2 and HTR7 involved in the calcium signaling pathway may be key mechanisms playing crucial roles in the development and progression of DIPG.
Closing Ranks: Closure, Status Competition, and School Segregation1

The shift away from school desegregation policies toward market-based reforms necessitates a deeper understanding of the social and institutional forces driving contemporary school segregation. The author conceptualizes school segregation as a mode of monopolistic closure amid status competition, where racial/ethnic groups compete for school-based status and resources. He tests the theory by analyzing primary and secondary school segregation throughout the United States from 1993 to 2010. Findings support the hypotheses that segregation increases with the salience of race/ethnicity and the decentralization of school systems, which fuels differentiation and provides incentives and opportunities to monopolize schools. Parallel findings for black-white, Hispanic-white, and black-Hispanic segregation suggest that a core set of processes drives school segregation as a general phenomenon.
Inequality of Opportunity, Income Inequality and Economic Mobility: Some International Comparisons

Despite a recent surge in the number of studies attempting to measure inequality of opportunity in various countries, methodological differences have so far prevented meaningful international comparisons. This paper presents a comparison of ex-ante measures of inequality of economic opportunity (IEO) across 41 countries, and of the Human Opportunity Index (HOI) for 39 countries. It also examines international correlations between these indices and output per capita, income inequality, and intergenerational mobility. The analysis finds evidence of a "Kuznets curve" for inequality of opportunity, and finds that the IEO index is positively correlated with overall income inequality, and negatively with measures of intergenerational mobility, both in incomes and in years of schooling. The HOI is highly correlated with the Human Development Index, and its internal measure of inequality of opportunity yields very different country rankings from the IEO measure.
Prosthetic vision: devices, patient outcomes and retinal research

Retinal disease and its associated retinal degeneration can lead to the loss of photoreceptors and therefore, profound blindness. While retinal degeneration destroys the photoreceptors, the neural circuits that convey information from the eye to the brain are sufficiently preserved to make it possible to restore sight using prosthetic devices. Typically, these devices consist of a digital camera and an implantable neurostimulator. The image sensor in a digital camera has the same spatiotopic arrangement as the photoreceptors of the retina. Therefore, it is possible to extract meaningful spatial information from an image and deliver it via an array of stimulating electrodes directly to the surviving retinal circuits. Here, we review the structure and function of normal and degenerate retina. The different approaches to prosthetic implant design are described in the context of human and preclinical trials. In the last section, we review studies of electrical properties of the retina and its response to electrical stimulation. These types of investigation are currently assessing a number of key challenges identified in human trials, including stimulation efficacy, spatial localisation, desensitisation to repetitive stimulation and selective activation of retinal cell populations.
A PUBLIC KEY MANAGEMENT SCHEME AND THRESHOLD-MULTISIGNATURE SCHEME FOR MOBILE AD HOC NETWORKS

Mobile ad hoc networks offer communication over a shared wireless channel without any pre-existing infrastructure. Threshold digital signatures are an important cryptographic tool used in most existing key management schemes for mobile ad hoc networks. This paper proposes a threshold-multisignature scheme designed specifically for mobile ad hoc networks. The signature scheme allows a subset of shareholders with threshold t, to sign an arbitrary message on behalf of the group. The group signature is publicly verifiable and allows any outsider to establish the identity of the individual signers. The paper proposes a self-certified public key issuing protocol that allows negotiation between a single entity and a distributed certificate authority for an implicit self-certified public key.
Relationships Among Live Animal Carcass Traits, the Estrous Cycle, and Synchronization of Estrus in Beef Heifers

Studies were conducted to determine whether fluctuations in body composition quality traits occur in relation to stage of the estrous cycle and type of estrous synchronization protocol in beef heifers. In Experiment I, measurements of live animal carcass traits by ultrasound (intramuscular fat [IMF]; rib (back) fat [BF]; rump fat [RF]; longissimus area [LMA] and gluteus medius depth [GMD]) were initiated following synchronization of estrus (prostaglandin F2α; PGF2α) in Angus beef heifers (n = 20) through two consecutive estrous cycles. Results indicated no direct relationship (P>0.10) among stage of the estrous cycle, hormonal status, and body composition traits. In Experiment 2, crossbred (n = 78) beef heifers were assigned to one of two estrous synchronization groups: 1) melengestrol acetate (MGA) feeding or 2) two-injection PGF2α. Body composition traits were measured at weekly intervals from estrous synchrony through breeding. Body fat parameters measured were found to not be affected by synchronization protocol, and percentage IMF at breeding had no effect (P > 0.10) on conception rates. However, noncycling heifers had less (P<0.05) IMF than heifers that expressed estrus and became pregnant. Moreover, heifers that expressed estrus and did not conceive had less BF (P<0.05). Reproductive status had no relationship to LMA, RF, or GMD. These data suggest that body composition in beef heifers is not affected by stage of the estrous cycle or method of estrous synchronization. However, differences in body composition were noted between heifers that became pregnant and non-pregnant (less BF) and non-cyclic (less IMF) heifers.
Psychosocial Correlates of Smoking Trajectories Among Urban African American Adolescents

Little is known of smoking trajectories or of the correlates of smoking trajectories among African American youth. Ninth-grade African American adolescents (n = 566) were interviewed in Year 1 and then were subsequently interviewed annually for 3 additional years. Five trajectories of cigarette smokers were identified: abstainers, experimenters/consistent light smokers, consistent regular smokers, accelerators, and quitters. Psychological well-being at Year 1 was lower among consistent regular smokers and accelerators as compared to abstainers. Variance in other problem behaviors mirrored the smoker trajectories. At Year 4,the abstainers and experimenters/consistent light smokers reported greater participation in sports activities as compared to the quitters, whereas the abstainers reported greater participation in other school activities as compared to the consistent regular smokers.
Joint Effects of Alcohol Consumption and Polymorphisms in Alcohol and Oxidative Stress Metabolism Genes on Risk of Head and Neck Cancer

Background: Single-nucleotide polymorphisms (SNP) in alcohol metabolism genes are associated with squamous cell carcinoma of the head and neck (SCCHN) and may influence cancer risk in conjunction with alcohol. Genetic variation in the oxidative stress pathway may impact the carcinogenic effect of reactive oxygen species produced by ethanol metabolism. We hypothesized that alcohol interacts with these pathways to affect SCCHN incidence. Methods: Interview and genotyping data for 64 SNPs were obtained from 2,552 European- and African-American subjects (1,227 cases and 1,325 controls) from the Carolina Head and Neck Cancer Epidemiology Study, a population-based case–control study of SCCHN conducted in North Carolina from 2002 to 2006. We estimated ORs and 95% confidence intervals (CI) for SNPs and haplotypes, adjusting for age, sex, race, and duration of cigarette smoking. P values were adjusted for multiple testing using Bonferroni correction. Results: Two SNPs were associated with SCCHN risk: ADH1B rs1229984 A allele (OR = 0.7; 95% CI, 0.6–0.9) and ALDH2 rs2238151 C allele (OR = 1.2; 95% CI, 1.1–1.4). Three were associated with subsite tumors: ADH1B rs17028834 C allele (larynx, OR = 1.5; 95% CI, 1.1–2.0), SOD2 rs4342445 A allele (oral cavity, OR = 1.3; 95% CI, 1.1–1.6), and SOD2 rs5746134 T allele (hypopharynx, OR = 2.1; 95% CI, 1.2–3.7). Four SNPs in alcohol metabolism genes interacted additively with alcohol consumption: ALDH2 rs2238151, ADH1B rs1159918, ADH7 rs1154460, and CYP2E1 rs2249695. No alcohol interactions were found for oxidative stress SNPs. Conclusions and Impact: Previously unreported associations of SNPs in ALDH2, CYP2E1, GPX2, SOD1, and SOD2 with SCCHN and subsite tumors provide evidence that alterations in alcohol and oxidative stress pathways influence SCCHN carcinogenesis and warrant further investigation. Cancer Epidemiol Biomarkers Prev; 20(11); 2438–49. ©2011 AACR.
Cognitive Function in an Elderly Population With Persistent Impaired Glucose Tolerance

OBJECTIVE To study cognitive function in an elderly population with persistent impaired glucose tolerance (IGT). RESEARCH DESIGN AND METHODS Fasting and postload 2-h plasma glucose and insulin levels were determined at baseline in a population-based sample of 1,300 people and repeated an average of 3.5 years later in 980 subjects. At follow-up, cognitive function was evaluated in subjects with persistent normal glucose tolerance (NGT; n = 506) and IGT (n = 80) with a brief neuropsychological test battery. RESULTS Subjects with persistent IGT scored lower in the Mini-Mental State Examination (MMSE) and in the Buschke Selective Reminding Test long-term memory scores. Multiple linear regression analysis revealed that age, education, and insulin levels (either fasting or 2-h value) were associated with the MMSE score in subjects with persistent IGT. Other potential risk factors for impaired cognitive function were not significantly associated with the MMSE score. CONCLUSIONS Our study showed that persistent IGT in the elderly is associated with mildly impaired cognitive function, and hyperinsulinemia may account for this association.
Working women in France, nineteenth and twentieth centuries. Where, when, and which women were in work at marriage?

We look at women's labour force participation for the whole of France in the nineteenth and twentieth centuries. We study to what extent young women were working at the time of their marriage, in which occupations, and how differences in labour force participation might be explained. Using a sample of 53,451 marriage records from the TRA project, we identify regional and temporal differences in rates of female labour force participation and in types of work in France between 1860 and 1986.We observe rather stable levels of female labour force participation between 1860 and 1950 of about 60 per cent, but higher levels in the second half of the twentieth century. Over time, women started to work across virtually all occupational sectors. Regional differences declined over time but continued to exist in the late twentieth century. We formulate a set of hypotheses to explain which women worked, taking into account their resources, as well as their expectations, in a male-breadwinner-dominated society. The results of our hierarchical logistic analysis indicate that women with fewer parental resources were more likely to work.
Patients' perception of hospital care in the United States.

BACKGROUND Patients' perceptions of their care, especially in the hospital setting, are not well known. Data from the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey provide a portrait of patients' experiences in U.S. hospitals. METHODS We assessed the performance of hospitals across multiple domains of patients' experiences. We examined whether key characteristics of hospitals that are thought to enhance patients' experiences (i.e., a high ratio of nurses to patient-days, for-profit status, and nonacademic status) were associated with a better experience for patients. We also examined whether a hospital's performance on the HCAHPS survey was related to its performance on indicators of the quality of clinical care. RESULTS We found moderately high levels of satisfaction with care (e.g., on average, 67.4% of a hospital's patients said that they would definitely recommend the hospital), with a high degree of correlation among the measures of patients' experiences (Cronbach's alpha, 0.94). As compared with hospitals in the bottom quartile of the ratio of nurses to patient-days, those in the top quartile had a somewhat better performance on the HCAHPS survey (e.g., 63.5% vs. 70.2% of patients responded that they "would definitely recommend" the hospital; P<0.001). Hospitals with a high level of patient satisfaction provided clinical care that was somewhat higher in quality for all conditions examined. For example, those in the top quartile of HCAHPS ratings performed better than those in the bottom quartile with respect to the care that patients received for acute myocardial infarction (actions taken to provide appropriate care as a proportion of all opportunities for providing such actions, 95.8% vs. 93.1% in unadjusted analyses; P<0.001) and for pneumonia (90.5% vs. 88.6% in unadjusted analyses, P<0.001). CONCLUSIONS This portrait of patients' experiences in U.S. hospitals offers insights into areas that need improvement, suggests that the same characteristics of hospitals that lead to high nurse-staffing levels may be associated with better experiences for patients, and offers evidence that hospitals can provide both a high quality of clinical care and a good experience for the patient.
Examining Implementation Fidelity in America’s Choice Schools

The research on professional development (PD) consists mostly of studies utilizing cross-sectional data. We examined effects of change in school-level PD on change in teachers’ practice longitudinally. Using survey reports from 1,722 teachers in 31 schools implementing a popular comprehensive school reform (America’s Choice), we found that although schools were implementing the same reform model, they varied in their implementation of PD. Teachers successfully changed their practice toward reform-aligned instructional goals only in schools demonstrating high growth in providing reform-aligned PD (both in the content and process of their PD). Our findings have implications for understanding interventions in schools and for thinking about the rigor of PD effects on teaching.