Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach

MOTIVATION Multiple structural alignments (MSTAs) provide position-specific information on the sequence variability allowed by protein folds. This information can be exploited to better understand the evolution of proteins and the physical chemistry of polypeptide folding. Most MSTA methods rely on a pre-computed library of pairwise alignments. This library will in general contain conflicting residue equivalences not all of which can be realized in the final MSTA. Hence to build a consistent MSTA, these methods have to select a conflict-free subset of equivalences. RESULTS Using a dataset with 327 families from SCOP 1.63 we compare the ability of two different methods to select an optimal conflict-free subset of equivalences. One is an implementation of Reinert et al.'s integer linear programming formulation (ILP) of the maximum weight trace problem (Reinert et al., 1997, Proc. 1st Ann. Int. Conf. Comput. Mol. Biol. (RECOMB-97), ACM Press, New York). This ILP formulation is a rigorous approach but its complexity is difficult to predict. The other method is T-Coffee (Notredame et al., 2000) which uses a heuristic enhancement of the equivalence weights which allow it to use the speed and simplicity of the progressive alignment approach while still incorporating information of all alignments in each step of building the MSTA. We find that although the ILP formulation consistently selects a more optimal set of conflict-free equivalences, the differences are small and the quality of the resulting MSTAs are essentially the same for both methods. Given its speed and predictable complexity, our results show that T-Coffee is an attractive alternative for producing high-quality MSTAs.
Douglas-rachford splitting: Complexity estimates and accelerated variants

We propose a new approach for analyzing convergence of the Douglas-Rachford splitting method for solving convex composite optimization problems. The approach is based on a continuously differentiable function, the Douglas-Rachford Envelope (DRE), whose stationary points correspond to the solutions of the original (possibly nonsmooth) problem. By proving the equivalence between the Douglas-Rachford splitting method and a scaled gradient method applied to the DRE, results from smooth unconstrained optimization are employed to analyze convergence properties of DRS, to tune the method and to derive an accelerated version of it.
Fetal Head Biometry Assessed by Fetal Magnetic Resonance Imaging following in utero Myelomeningocele Repair

Objective: To examine the impact of fetal myelomeningocele (MMC) repair on fetal head biometry and cerebrospinal fluid (CSF) spaces assessed by magnetic resonance imaging (MR) studies. Study Design: Axial measurements of intracranial structures were taken at defined anatomical landmarks. Pre- and postnatal head biometry data and CSF spaces obtained from in utero repaired MMC fetuses (n = 22) were compared to the pre- and postnatal measurements of MMC patients that underwent standard neurosurgical MMC repair after birth (n = 16) and a cohort of age-matched control patients (prenatal, n = 52; postnatal, n = 9). Results: In fetuses with MMC, initial MR scans showed an almost complete absence of supratentorial and posterior fossa CSF spaces. No differences in postnatal CSF spaces were found between controls and prenatally repaired MMC newborns. In fetuses with postnatal MMC repair, CSF spaces remained significantly reduced (p < 0.0001). The mean ventricular diameter (VD) increase in the postnatal repaired MMC group was significantly higher compared to the mean percentage of VD increase in the fetal repaired MMC group (6.4 vs. 4.2 mm; p = 0.02). Pre- and postnatal brain thickness measurements were significantly reduced in both MMC populations compared to age-matched normal values (p < 0.0001). In contrast to postnatally repaired patients, in utero repair fetuses showed significant reversal of hindbrain herniation and normalization of the posterior fossa CSF spaces. Conclusion: Mid-gestational repair of MMC promotes normalization of extra-axial CSF spaces. Due to progressive ventriculomegaly, brain thickness remains decreased in both prenatal repaired and age-matched non-repaired MMC patients when compared to age-matched normal values. Restoration of CSF volume in the posterior fossa after in utero repair is indicative of reversal of hindbrain herniation.
Visual perception and visual dysfunction in autism spectrum disorder: a literature review

Aim: To describe autistic spectrum disorder (ASD), and to review the evidence for associated visual dysfunction in the disorder. Method: An initial literature search was performed using Web of Science with the key words: autism and sensory; autism and vision; autism and visual; and autism and oculomotor. Papers which reported investigation of basic vision in autism were obtained, and any additional references listed in these articles that referred to other relevant data but didn’t emerge from the original search were followed up. Results: There is evidence that basic visual function may be affected in individuals with ASD, however the mixed nature and limited number of empirical studies conducted make it difficult to draw clear conclusions as to specific deficits and areas of spared visual function in ASD. Conclusion: It is likely that patients with ASD may present to the orthoptic department. Specific vision screening of this population may be indicated, and further study based on large well defined samples would be of significant value.
Collective Risk-Taking with Threshold Effects

It is commonly found that the presence of uncertainty helps discipline economic agents in strategic contexts where incentives would otherwise induce inecient behavior (Eso and White (2004), Bramoulle and Treich (2009)). We consider a variant of the celebrated Nash Demand Game (Nash, 1953) where two values of the resource (low and high) are possible. We show that the presence of uncertainty here may actually have an opposite eect: strategic interactions may lead groups of risk-averse agents to take ineciently risky decisions. We then develop an experimental setting to assess the severity of the coordination problem in the lab. Our findings confirm our theoretical predictions that the (Pareto-dominant) cautious equilibria are predominantly played at the individual level. In the aggregate, however, coordination failures abound but are decreasing in the likelihood of the high value of the resource. It is only when this likelihood becomes low enough that cautious behavior translates in high rates of cautious equilibria.
Endoplasmic Reticulum Stress Regulates Adipocyte Resistin Expression

OBJECTIVE Resistin is a secreted polypeptide that impairs glucose metabolism and, in rodents, is derived exclusively from adipocytes. In murine obesity, resistin circulates at elevated levels but its gene expression in adipose tissue is paradoxically reduced. The mechanism behind the downregulation of resistin mRNA is poorly understood. We investigated whether endoplasmic reticulum (ER) stress, which is characteristic of obese adipose tissue, regulates resistin expression in cultured mouse adipocytes. RESEARCH DESIGN AND METHODS The effects of endoplasmic stress inducers on resistin mRNA and secreted protein levels were examined in differentiated 3T3-L1 adipocytes, focusing on the expression and genomic binding of transcriptional regulators of resistin. The association between downregulated resistin mRNA and induction of ER stress was also investigated in the adipose tissue of mice fed a high-fat diet. RESULTS ER stress reduced resistin mRNA in 3T3-L1 adipocytes in a time- and dose-dependent manner. The effects of ER stress were transcriptional because of downregulation of CAAT/enhancer binding protein-α and peroxisome proliferator–activated receptor-γ transcriptional activators and upregulation of the transcriptional repressor CAAT/enhancer binding protein homologous protein-10 (CHOP10). Resistin protein was also substantially downregulated, showing a close correspondence with mRNA levels in 3T3-L1 adipocytes as well as in the fat pads of obese mice. CONCLUSIONS ER stress is a potent regulator of resistin, suggesting that ER stress may underlie the local downregulation of resistin mRNA and protein in fat in murine obesity. The paradoxical increase in plasma may be because of various systemic abnormalities associated with obesity and insulin resistance.
Is Religiosity a Protective Factor Against Attempted Suicide: A Cross-Cultural Case-Control Study

This cross-cultural study investigates whether religiosity assessed in three dimensions has a protective effect against attempted suicide. Community controls (n = 5484) were more likely than suicide attempters (n = 2819) to report religious denomination in Estonia (OR = 0.5) and subjective religiosity in four countries: Brazil (OR = 0.2), Estonia (OR = 0.5), Islamic Republic of Iran (OR = 0.6), and Sri Lanka (OR = 0.4). In South Africa, the effect was exceptional both for religious denomination (OR = 5.9) and subjective religiosity (OR = 2.7). No effects were found in India and Vietnam. Organizational religiosity gave controversial results. In particular, subjective religiosity (considering him/herself as religious person) may serve as a protective factor against non-fatal suicidal behavior in some cultures.
Inovação e desempenho organizacional: um estudo com empresas brasileiras inovadoras

O estudo teve como objetivo analisar a relacao entre empresas consideradas inovadoras e seu desempenho. A introducao de novidade ou aperfeicoamento no ambiente produtivo ou social que resulte em novos produtos, processos ou servicos representa a essencia da inovacao que alem de ser uma questao de vantagem competitiva para as organizacoes e crescimento economico nas nacoes, envolve tambem uma forma de captar recursos e de receber incentivos fiscais. A amostra da pesquisa foi constituida por empresas que receberam subsidios da Financiadora de Estudos e Projetos (FINEP): Brakem, Natura e Embraer. A pesquisa apresentou carater quantitativo, foram utilizados dados publicados em relatorios gerenciais e realizou-se a analise de correlacao entre variaveis do processo de inovacao e de resultados. Foi possivel apontar que ha efeitos entre investimento em inovacao e crescimento das vendas em todas as empresas deste estudo. Porem, nenhuma empresa apresentou correlacao entre investimento em inovacao e evolucao da margem liquida.
Processing Load Induced by Informational Masking Is Related to Linguistic Abilities

It is often assumed that the benefit of hearing aids is not primarily reflected in better speech performance, but that it is reflected in less effortful listening in the aided than in the unaided condition. Before being able to assess such a hearing aid benefit the present study examined how processing load while listening to masked speech relates to inter-individual differences in cognitive abilities relevant for language processing. Pupil dilation was measured in thirty-two normal hearing participants while listening to sentences masked by fluctuating noise or interfering speech at either 50% and 84% intelligibility. Additionally, working memory capacity, inhibition of irrelevant information, and written text reception was tested. Pupil responses were larger during interfering speech as compared to fluctuating noise. This effect was independent of intelligibility level. Regression analysis revealed that high working memory capacity, better inhibition, and better text reception were related to better speech reception thresholds. Apart from a positive relation to speech recognition, better inhibition and better text reception are also positively related to larger pupil dilation in the single-talker masker conditions. We conclude that better cognitive abilities not only relate to better speech perception, but also partly explain higher processing load in complex listening conditions.
Efficient multiclass object detection: Detecting pedestrians and bicyclists in a truck's blind spot camera

In this paper we propose an efficient detection and tracking framework targeting vulnerable road users in the blind spot camera images of a truck. Existing non-vision based safety solutions are not able to handle this problem completely. Therefore we aim to develop an active safety system, based solely on the vision input of the blind spot camera. This is far from trivial: vulnerable road users are a diverse class and consist of a wide variety of poses and appearances. Evidently we need to achieve excellent accuracy results and furthermore we need to cope with the large lens distortion and extreme viewpoints induced by the blind spot camera. In this work we present a multiclass detection methodology which enables the efficient detection of both pedestrians and bicyclists in these challenging images. To achieve this we propose the integration of a warping window approach with multiple object detectors which we intelligently combine in a probabilistic manner. To validate our framework we recorded several simulated dangerous blind spot scenarios with a genuine blind spot camera mounted on a real truck. We show that our approach achieves excellent accuracy on these challenging datasets.
Effects of Resolution of Satellite-Based Rainfall Estimates on Hydrologic Modeling Skill at Different Scales

Uncertainty due to resolution of current satellite-based rainfall products is believed to be an important source of error in applications of hydrologic modeling and forecasting systems. A method to account for the input’s resolution and to accurately evaluate the hydrologic utility of satellite rainfall estimates is devised and analyzed herein. A radar-based Multisensor Precipitation Estimator (MPE) rainfall product (4km, 1h) was utilized to assess the impact of resolution of precipitation products on the estimation of rainfall and subsequent simulation of streamflow on a cascade of basins ranging from approximately 500 to 5000km 2 . MPE data were resampled to match the Tropical Rainfall Measuring Mission’s (TRMM) 3B42RT satellite rainfall product resolution (25km, 3h) and compared with its native resolution data to estimate errors in rainfall fields. It was found that resolution degradation considerably modifies the spatial structure of rainfall fields. Additionally, a sensitivity analysis was designed to effectively isolate the error on hydrologic simulations due to rainfall resolution using a distributed hydrologic model. These analyses revealed that resolution degradation introduces a significant amount of error in rainfall fields, which propagated to the streamflow simulations as magnified bias and dampened aggregated error (RMSEs). Furthermore, the scale dependency of errors due to resolution degradation was found to intensify with increasing streamflow magnitudes. The hydrologic model was calibrated with satellite- and original-resolution MPE using a multiscale approach. The resulting simulations had virtually the same skill, suggesting that the effects of rainfall resolution can be accounted for during calibration of hydrologic models, which was further demonstrated with 3B42RT.
Black Hole or MECO? Decided by a Thin Luminous Ring Structure Deep Within Quasar Q0957

Optical, Infrared, X-ray, and radio wavelength studies of quasars are beginning to define the luminous quasar structure from techniques of reverberation and microlensing. An important result is that the inner quasar structure of the first identified gravitational lens, Q0957+561 A,B seems not to show the kind of structure expected for a supermassive black hole, but instead show a clean-swept interior region as due to the action of a magnetic propeller, just as expected for a MECO (Magnetic Eternally Collapsing Object) structure. Given the present state of the observations, the strongest model discriminant seems to be the existence of a thin luminous band around the inner edge of the accretion disc, at a distant radius ~ 70 R_g from the ~ 4 x 10^9 Mo central object. Since the existence of a clean magnetic propeller swept inner region ~70 R_g surrounded by a sharp ~ 1 R_g disc edge are the low-hard state spectral properties associated with a highly redshifted central MECO object, we are led to the conclusion that these observations imply that the Q0957 quasar contains a central supermassive MECO instead of a black hole. In this report we review the details of the observations which have compelled us to reach this conclusion.
Clopidogrel – a Platelet Inhibitor which Inhibits Thrombogenesis in Non-Anticoagulated Human Blood Independently of the Blood Flow Conditions

Summary The goal of the present study was to investigate the effect of 7 and 14 days of daily oral administration of 75 mg clopidogrel on collagen-induced thrombogenesis in flowing non-anticoagulated human blood. Blood was drawn directly from an antecubital vein over immobilised collagen type III fibrils positioned in a parallel-plate perfusion chamber. The wall shear rates at the collagen surface were those characteristic for veins (100 s−1), and for medium sized (650 s−1) and moderately stenosed (2600 s−1) arteries. Clopidogrel ingestion reduced the thrombus volume significantly (p <0.05) at 100 and 2600 s−1 (39 and 51% respectively). The β-thromboglobulin plasma levels were reduced concomitantly. However, it was not possible to measure accurately the thrombus volume at 650 s−1, due to loose packing of the platelet thrombi. Transmission electron micros-copy substantiated this observation and showed that clopidogrel profoundly reduced the platelet degranulation process (p <0.005). The inhibitory effect of clopidogrel on platelet consumption by the growing thrombi resulted apparently in higher platelet concentration at the collagen surface, which enhanced the platelet-collagen adhesion at all three shear rates (p <0.05). Despite the low deposition of fibrin on collagen, clopidogrel reduced significantly the fibrinopeptide A plasma levels and the fibrin deposition at shear rates below 650 s−1. This was apparently a consequence of the reduced platelet recruitment and the lower activation of platelets, since activated platelets in thrombi promote deposition of fibrin. Thus, it appears that clopidogrel inhibits thrombus formation in human blood primarily by interfering with platelet-platelet binding and the inhibition is effective independently of the wall shear rate.
Korean American Mothers' Perception: Investigating the Role of Cultural Capital Theory and Parent Involvement

Title of Dissertation: KOREAN AMERICAN MOTHERS’ PERCEPTION: INVESTIGATING THE ROLE OF CULTURAL CAPITAL THEORY AND PARENT INVOLVEMENT Yong-Mi Kim, Doctor of Education, 2014 Dissertation directed by: Professor Carol S. Parham Department of Counseling, Higher Education, and Special Education The strongest and most consistent predictors of parent involvement at school and at home are the specific school programs and teacher practices that encourage parent involvement at school and guide parents in how to help their children at home (Dauber & Epstein, 1995). Joyce Epstein (2004) developed a framework for defining six different types of parent involvement. This framework assists educators in developing school and family partnership programs. "Schools have a vested interest in becoming true learning communities. They are now accountable for all students' learning,” she writes. "To learn at high levels, all students need the guidance and support of their teachers, families, and others in the community. " School improvement no longer rests solely on the shoulders of the principal, but rather takes the collaborative effort of the entire school community to increase achievement levels of all students. A major stakeholder of that community is the parents who want what is in the best interest of their children. This mixed-methods study examined the perceptions of Korean American mothers regarding their own parent involvement practices and investigated the role of Bourdieu’s Cultural Capital Theory using the conceptual framework of Epstein’s Parent Involvement Framework. Data for this study were collected by way of survey responses and interview probes with focus groups of six Korean American mothers. In the quantitative phase of the study, 81 mothers from a single school district in the midAtlantic United States were identified. The results from the quantitative phase of the study found that English proficiency had a significant impact on whether Korean American mothers engaged in parent involvement activities. Examination of the focus group responses revealed that the Korean American mothers identified English and time as major factors in determining in what types of parent involvement activities they engaged. Parent involvement is essential for promoting successful school improvement. It plays a pivotal part in school reform. Further research is recommended with larger samples of participants in rural and urban settings. In addition, future research should examine the role of fathers in parent involvement. KOREAN AMERICAN MOTHERS’ PERCEPTION: INVESTIGATING THE ROLE OF CULTURAL CAPITAL THEORY AND
Nonlinear Equalization of Digital Satellite Channels

Conventional techniques attempting to compensate for the influence of linear and nonlinear distortion in digital satellite channels include optimization of channel filtering. With conventional linear filtering it has been experienced that there is still room for considerable improvement, so that it appears reasonable to investigate some forms of nonlinear filtering in an attempt to cope with those distortions. In this paper a nonlinear equalizer structure is proposed, and its performance is analyzed. It is shown, by some examples Of application to a 4-phase PSK satellite channel, that it can prove quite effective in terms of a tradeoff between performance improvement and hardware complexity.
Restless and confused

Purpose – The purpose of this study is to examine the nature of the emotions experienced by targets of bullying in the workplace.Design/methodology/approach – A sample of 180 employees in Canada took part in a cross‐sectional self‐report survey study.Findings – The study found that, for men, in the presence of belittlement and work being undermined, verbal abuse was negatively associated with confusion, suggesting an active coping strategy. In contrast, for women, in the presence of belittlement and work being undermined, verbal abuse was positively associated with confusion, suggesting a passive coping strategy.Research limitations/implications – Although this study's cross‐sectional methodology provided a static snapshot of the emotions of bullying, it may be informative to capture emotions as they arise in response to specific episodes and forms of bullying as well as in response to repeated acts of bullying.Practical implications – Workers should be offered resources for understanding and coping const.
Breaking the species barrier: use of SCID mouse–human chimeras for the study of human infectious diseases

Mouse–human chimeras have become a novel way to model the interactions between microbial pathogens and human cells, tissues or organs. Diseases studied with human xenografts in severe combined immunodeficient (SCID) mice include Pseudomonas aeruginosa infection in cystic fibrosis, group A streptococci and impetigo, bacillary and amoebic dysentery, and AIDS. In many cases, disease in the human xenograft appears to accurately reproduce the disease in humans, providing a powerful model for identifying virulence factors, host responses to infection and the effects of specific interventions on disease. In this review, we summarize recent studies that have used mouse–human chimeras to understand the pathophysiology of specific bacterial and protozoan infections.