Miracle-dz/UniFAR-FTUs huggingface dataset:
CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere

Building stable centromeres Each of our chromosomes has a single centromere, seen as a constriction during cell division, which is required for accurate chromosome segregation to daughter cells. Falk et al. show that the special histone protein known as CENP-A, which forms part of the nucleosomes at centromeres, makes the chromatin at these constrictions very stable and long-lived. This stability is conferred by a protein-binding partner, CENP-C, recruited to the centromere by the CENP-A histone. Binding of CENP-C to CENP-A–containing nucleosomes alters the behavior of the macromolecular centromere complex to help it maintain its identity Science, this issue p. 699 The stability of centromeres is driven by interactions between a special histone protein and its binding partner. Inheritance of each chromosome depends upon its centromere. A histone H3 variant, centromere protein A (CENP-A), is essential for epigenetically marking centromere location. We find that CENP-A is quantitatively retained at the centromere upon which it is initially assembled. CENP-C binds to CENP-A nucleosomes and is a prime candidate to stabilize centromeric chromatin. Using purified components, we find that CENP-C reshapes the octameric histone core of CENP-A nucleosomes, rigidifies both surface and internal nucleosome structure, and modulates terminal DNA to match the loose wrap that is found on native CENP-A nucleosomes at functional human centromeres. Thus, CENP-C affects nucleosome shape and dynamics in a manner analogous to allosteric regulation of enzymes. CENP-C depletion leads to rapid removal of CENP-A from centromeres, indicating their collaboration in maintaining centromere identity.
Characteristics of false-negative ThinPrep cervical smears in women with high-grade squamous intraepithelial lesions.

OBJECTIVE To examine the cellular characteristics and other possible factors affecting the correct prediction of ThinPrep cervical smears from patients with high-grade squamous intraepithelial lesions. DESIGN Retrospective study. SETTING Private anatomical pathology service, Hong Kong. PATIENTS Patients (n=98) with biopsy-confirmed high-grade squamous intraepithelial lesion of the uterine cervix encountered between 2004 and 2006. MAIN OUTCOME MEASURES Correct prediction of the cervical ThinPrep Papanicolaou tests. RESULTS There were no significant differences in age, hormonal status, degree of inflammation, and the presence or absence of endocervical/metaplastic cells between the true-positive and false-negative groups. There was a significant difference in the number of abnormal cells present and the screening time between the two groups. Approximately 79% (34/43) false-negative smears had 100 or less abnormal cells, while only 11% (5/45) true-positive smears had 100 or less abnormal cells (P<0.001). The true-positive smears were also more likely to contain koilocytic cells and abnormal cells with hyperchromatic nuclei. CONCLUSIONS The number of abnormal cells present, the presence or absence of koilocytic cells, and the presence or absence of abnormal cells with nuclear hyperchromasia appeared to be independent factors affecting the correct prediction of smears from patients with high-grade squamous intraepithelial lesions.
Treatment of pulmonary hypertension with the continuous infusion of a prostacyclin analogue, iloprost

Objective To compare prostacyclin with an analogue, iloprost, in treatment of severe pulmonary hypertension. Patients Eight patients with severe pulmonary hypertension: primary in five, thromboembolic pulmonary hypertension in three. Methods All patients underwent right heart catheterisation. Mean (SEM) right atrial pressure was 9.9 (2.2) mm Hg, mean pulmonary artery pressure 67.4 (3.0) mm Hg, cardiac index 1.75 (0.13) l/min/m2 and mixed venous oxygen saturation 59.1(3.1)%. Continuous intravenous epoprostenol (prostacyclin, PGI2) or iloprost was given for phase I (three to six weeks); the patients were then crossed over to receive the alternate drug in an equivalent phase II. Main outcome measures Exercise tolerance was measured at baseline and at the end of phase I and II with a 12 minute walk; distance covered, rest period, percentage drop in arterial oxygen saturation (ΔSao 2%) and percentage rise in heart rate (ΔHR%). Results Walking distance covered rose from (mean (SEM)) 407.5 (73) to 591 (46) m with PGI2(p = 0.004) and to 602.5 (60) m while on iloprost (p = 0.008). Rest period decreased from 192 (73) seconds at baseline to 16 (16) seconds with PGI2 (p = 0.01) and to 58 (34) seconds with iloprost (p = 0.008). ΔHR% was 37.5(6)% at baseline, 35(3)% on PGI2, and 24(6)% on iloprost (p = 0.04). Conclusions Both intravenous PGI2 and iloprost caused significant improvement in exercise tolerance. Iloprost offers an alternative to PGI2 treatment of severe pulmonary hypertension.
A New, Conditional Variable-Importance Measure for Random Forests Available in the party Package

Random forests are one of the most popular statistical learning algorithms, and a variety of methods for fitting random forests and related recursive partitioning approaches is available in R. This paper points out two impor- tant features of the random forest implementa- tion cforest available in the party package: The resulting forests are unbiased and thus prefer- able to the randomForest implementation avail- able in randomForest if predictor variables are of different types. Moreover, a conditional per- mutation importance measure has recently been added to the party package, which can help eval- uate the importance of correlated predictor vari- ables. The rationale of this new measure is illus- trated and hands-on advice is given for the usage of recursive partitioning tools in R.
Tag simplification: Achieving power efficiency through reducing the complexity of the wakeup logic

Contemporary microprocessor cores employ out-of-order execution in order to boost performance. One of the artifacts of the out-of-order execution is the Content Addressable Memory (CAM) cells that allow comparison of the incoming data with the stored value. Many components use these cells inside the processor such as the Issue Queue (IQ), which holds the instructions until their source operands are ready. These processor components receive lookup data each cycle and dissipate significant energy for the comparison operation. In this paper we propose a methodology to remove the capacitive load from the lookup buses and reduce the complexity of the comparison circuitry inside the CAM logic. For demonstration purposes we show the design of a new implementation of the IQ that allows the designers to transfer the complexity to the frontend stages of the processor. Our design reduces the dynamic energy dissipation of the CAM array inside the issue queue 15% with virtually no impact on performance.
The Performance of Multinational Affiliates versus Domestic Firms

While some authors argue that multinational companies (MNCs) have several firm and location specific advantages over domestic firms, others point to the liability of foreignness as a handicap to MNCs. We argue that while the impact on the ultimate performance of MNC in foreign countries is unclear, the impact on firms affiliated to these MNC should be positive. We also hypothesize that the age of the affiliate is an important moderator for the benefit of affiliation with an MNC. We find that MNC affiliates outperform domestic firms and that the benefit of affiliation decreases with the age of the affiliate.
A pilot genome wide association and gene expression array study of suicide with and without major depression

Abstract Objectives. Suicide is partly heritable but the responsible genes have not been identified. We conducted a gene-centric, low coverage single nucleotide polymorphism (SNP) pilot genome-wide association study (GWAS) seeking new candidate regions in suicides with and without depression, combined with gene expression assay of brain tissue. Methods. Ninety-nine Caucasian subjects, including 68 who completed suicide and 31 who died suddenly from other causes, were genotyped postmortem using GeneChip® Mapping 50K Xba. Clinical data were obtained from relatives. SNPs with Hardy–Weinberg equilibrium P values below 0.001 were excluded from analysis. Illumina chip expression arrays assayed the transcriptome in prefrontal cortex in a drug-free subgroup. Results. GWAS analysis (cutoff P < 0.001) yielded 58 SNPs, 22 of them in or near 19 known genes, with risk allele-associated odds ratios between 2.7 and 6.9. Diagnosis of mood disorder did not explain the associations. Some of the SNPs matched into four functional groups in gene ontology. Gene expression in the prefrontal and the anterior cingulate cortex for these 19 genes was measured on a separate, though overlapping, sample of suicides and seven of 19 genes showed altered expression in suicides as compared with controls, especially in immune system related genes. Conclusions. Matching GWAS findings with expression data assesses functional effect of new candidate genes in suicide, and is an alternative form of confirmation or replication study. Results highlight a role for neuroimmunological effects in suicidal behaviour.
The L_2-L_{\infinity} Control for Leader-following Coordination with Switching Topology

In this paper, we investigate the L_2-L_{\infinity} leader-following coordination problems with undirected switching topologies and external disturbance. The agent dynamics is expressed in the form of a second-order model and the control laws are neighbor-based feedback laws. We first establish a LMI sufficient condition to guarantee that all following agents can track the leader agent and the L_2-L_{\infinity} disturbance attenuation of the system is not greater than a given constant. Furthermore, we get a explicit estimation expression of L_2-L_{\infinity} disturbance attenuation by constructing a parameter-dependent common Lyapunov function. Finally, a numerical example is provided to illustrate the effectiveness of our results.
A tracking converter for resistive sensors based on a feedback active bridge

A so-called active bridge structure has been previously introduced as an alternative to the classical Wheatstone bridge structure combined with a low noise amplifier. It shows an advantage in terms of trade off between SNR and power consumption. The aim of this paper is to show the possibility of using the active bridge in a feedback structure that converts a relative variation of resistance into a digital word. This structure has been applied to a resistive spin-valve sensor with a nominal resistance of 750 Ω. The total power consumption is about 2 mA instead of 4.4 mA that would be consumed only by a Wheatstone bridge. A resolution of 12 bits is expected.
Proactive driving modeling in blind intersections based on expert driver data

This paper presents a model for velocity control in blind corners and intersections based on expert driver data. Accurate expert driver data was collected with a car equipped with a 3D LiDAR and high definition maps. A model based on human expert driver data is used to control the velocity of the ego-vehicle when facing blind intersections. The model regulates ego-vehicle velocity based on the visibility of the road at the blind intersection. As the vehicle approximates the intersection and crossing roads are not visible, the vehicle slows down, then as the roads become visible the vehicle accelerates. Experimental results show the performance of the velocity model compared towards 270 trajectories taken from 7 expert drivers towards 6 different intersections without mandatory stops.
Positive bias temperature stress induced degradation in p-channel poly-Si thin-film transistors

Positive bias temperature stress induced degradation in p-channel poly-Si thin-film transistors (TFTs) was systematically investigated. Two-stage degradation behavior is observed. The first-stage degradation is related to electron trapping via Fowler-Nordheim (F-N) tunnelling and de-trapping through Poole-Frenkel (P-F) emission. While the second-stage degradation is attributed to hydrogen related positive charge creation in the gate oxide.
The mechanism of blood concentrations of the Shenqi pill repairing injured epithelial cells of renal tubular in vitro

In the present study, we investigated the best blood concentration of the mechanism of Shenqi pill repairing the injured epithelial cells of renal tubular in vitro. First, the injured hypoxia/reoxygenation model of rat proximal renal tubular epithelial cell strain (NRK-52E) was established. The animals were divided randomly into control, model, low concentration (5 µg/ml), moderate concentration (10 µg/ml) and high concentration (20 µg/ml) groups. The apoptotic rate was measured with flow cytometry and Jag2/Notch2/hes1 mRNA, and the protein expression was measured for 1, 3 and 7 days. It was found that in comparison to the control group, the growth of each group was prolonged with time, the levels of apoptosis, and the Jag2/Notch2/hes1 mRNA and protein expression decreased. Furthermore, the levels of the apoptotic rate, Jag2/Notch2/hes1 mRNA and protein expression of the moderate concentration and high concentration groups were significantly lower than those of the model and low-dose groups at each time-point (P<0.05). In conclusion, the Shenqi Pill alleviates the damage of renal tubular epithelial cells by inhibiting the Jag2/Notch2/hes1 signaling pathway; suitable concentration such as 10–20 µg/ml can exert protective effect.
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

Significance For the 2m DNA to fit into the tiny cell nucleus, it is wrapped around nucleosomes and folded into loops clustering together in domains. Genome function depends on this 3D-organization, especially on-going dynamic processes like transcription. Techniques studying the network of DNA contacts genome-wide have recently revealed this 3D architecture, but the protein factors behind this are not understood. We study two proteins that are known to help form DNA loops: cohesin and CTCC-binding factor (CTCF). Respective depletion and analysis of DNA contacts genome-wide show that CTCF is required to separate neighboring folding domains and keep cohesin in place, whereas cohesin is important for shaping the domains. Consistently, we observe different changes of gene expression. Recent studies of genome-wide chromatin interactions have revealed that the human genome is partitioned into many self-associating topological domains. The boundary sequences between domains are enriched for binding sites of CTCC-binding factor (CTCF) and the cohesin complex, implicating these two factors in the establishment or maintenance of topological domains. To determine the role of cohesin and CTCF in higher-order chromatin architecture in human cells, we depleted the cohesin complex or CTCF and examined the consequences of loss of these factors on higher-order chromatin organization, as well as the transcriptome. We observed a general loss of local chromatin interactions upon disruption of cohesin, but the topological domains remain intact. However, we found that depletion of CTCF not only reduced intradomain interactions but also increased interdomain interactions. Furthermore, distinct groups of genes become misregulated upon depletion of cohesin and CTCF. Taken together, these observations suggest that CTCF and cohesin contribute differentially to chromatin organization and gene regulation.
Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions

A statistical analysis method can identify short, functionally important linear motifs in disordered regions of proteins. Finding the Hidden Meaning in Disordered Regions Many proteins, including those involved in signal transduction, have large disordered regions, in addition to their clearly defined domains or motifs. Although these disordered regions are functionally important, identifying the important residues in these regions has proved challenging because the regions are not visualized in crystal structures and tend to exhibit high sequence divergence. Nguyen Ba et al. modified the phylogenetic hidden Markov model so that it could be applied to these disordered regions. Application of this method to yeast proteins not only revealed the presence of known short conserved motifs in proteins not known to have these motifs but also predicted previously unknown short conserved motifs. Experimental analysis suggested that both sets of motifs were functionally important. Thus, this approach should provide an effective method for discovering biologically important conserved motifs within the disordered regions of proteins. At least 30% of human proteins are thought to contain intrinsically disordered regions, which lack stable structural conformation. Despite lacking enzymatic functions and having few protein domains, disordered regions are functionally important for protein regulation and contain short linear motifs (short peptide sequences involved in protein-protein interactions), but in most disordered regions, the functional amino acid residues remain unknown. We searched for evolutionarily conserved sequences within disordered regions according to the hypothesis that conservation would indicate functional residues. Using a phylogenetic hidden Markov model (phylo-HMM), we made accurate, specific predictions of functional elements in disordered regions even when these elements are only two or three amino acids long. Among the conserved sequences that we identified were previously known and newly identified short linear motifs, and we experimentally verified key examples, including a motif that may mediate interaction between protein kinase Cbk1 and its substrates. We also observed that hub proteins, which interact with many partners in a protein interaction network, are highly enriched in these conserved sequences. Our analysis enabled the systematic identification of the functional residues in disordered regions and suggested that at least 5% of amino acids in disordered regions are important for function.
Ontology-based Virtual Query System for the SemanticLIFE Digital Memory Project : Concepts , Designs and Implementation

— Ever increasing capacities of contemporary storage devices inspire the vision to accumulate (personal) information without the need to delete old data over a long time-span. Hence the target of the SemanticLIFE project is to create a personal information management system for a human lifetime data. One of the most important characteristics of the system is its dedication to retrieve information and data in a very efficient way by adopting user demands regarding the reduction of ambiguities aiming at a user-friendly and yet powerful enough system with a satisfactory query performance. In this paper, we introduce the concepts and a design of the query system of SemanticLIFE, the Virtual Query System, which uses emerging Semantic Web technologies to fulfill necessary requirements.
Progressive Probabilistic Hough Transform

In the paper we present the Progressive Probabilistic Hough Transform (PPHT). Unlike the Probabilistic Hough Transform [4] where Standard Hough Transform is performed on a pre-selected fraction of input points, PPHT minimises the amount of computation needed to detect lines by exploiting the difference in the fraction of votes needed to reliably detect lines with different numbers of supporting points . The fraction of points used for voting need not be specified ad hoc or using a priori knowledge, as in the Probabilistic Hough Transform; it is a function of the inherent complexity of data. The algorithm is ideally suited for real-time applications with a fixed amount of available processing time, since voting and line detection is interleaved. The most salient features are likely to be detected first. Experiments show PPHT has, in many circumstances, advantages over the Standard Hough Transform.
Understanding Factors that Shape Gender Attitudes in Early Adolescence Globally: A Mixed-Methods Systematic Review

Background Early adolescence (ages 10–14) is a period of increased expectations for boys and girls to adhere to socially constructed and often stereotypical norms that perpetuate gender inequalities. The endorsement of such gender norms is closely linked to poor adolescent sexual and reproductive and other health-related outcomes yet little is known about the factors that influence young adolescents’ personal gender attitudes. Objectives To explore factors that shape gender attitudes in early adolescence across different cultural settings globally. Methods A mixed-methods systematic review was conducted of the peer-reviewed literature in 12 databases from 1984–2014. Four reviewers screened the titles and abstracts of articles and reviewed full text articles in duplicate. Data extraction and quality assessments were conducted using standardized templates by study design. Thematic analysis was used to synthesize quantitative and qualitative data organized by the social-ecological framework (individual, interpersonal and community/societal-level factors influencing gender attitudes). Results Eighty-two studies (46 quantitative, 31 qualitative, 5 mixed-methods) spanning 29 countries were included. Ninety percent of studies were from North America or Western Europe. The review findings indicate that young adolescents, across cultural settings, commonly express stereotypical or inequitable gender attitudes, and such attitudes appear to vary by individual sociodemographic characteristics (sex, race/ethnicity and immigration, social class, and age). Findings highlight that interpersonal influences (family and peers) are central influences on young adolescents’ construction of gender attitudes, and these gender socialization processes differ for boys and girls. The role of community factors (e.g. media) is less clear though there is some evidence that schools may reinforce stereotypical gender attitudes among young adolescents. Conclusions The findings from this review suggest that young adolescents in different cultural settings commonly endorse norms that perpetuate gender inequalities, and that parents and peers are especially central in shaping such attitudes. Programs to promote equitable gender attitudes thus need to move beyond a focus on individuals to target their interpersonal relationships and wider social environments. Such programs need to start early and be tailored to the unique needs of sub-populations of boys and girls. Longitudinal studies, particularly from low-and middle-income countries, are needed to better understand how gender attitudes unfold in adolescence and to identify the key points for intervention.
Work wellness in the chemical industry

The aim of the study was to investigate the components of well-being. The study was done in the chemical industry, with a sample (Af=490) representing all different job levels in the organisation. A cross-sectional survey design was used. Measuring instruments were the Affectometer 2, the Life Orientation Test-Revised, the Organisational Commitment Questionnaire, the Minnesota Satisfaction Questionnaire, Maslach Burnout Inventory-General Survey, the Satisfaction with Life Scale, and the General Health Questionnaire. A principal factor analysis with a varimax rotation indicated a three-factor model of well-being. The first factor ("general well-being expectations"), consisted of satisfaction with life, positive and negative affect, optimism, pessimism, and professional efficacy. The second factor was labelled "motivation", and included intrinsic and extrinsic job satisfaction, as well as affective commitment. The third factor ("energy") included cynicism, exhaustion, and general health.