Miracle-dz/UniFAR-FTUs huggingface dataset:
A supersecondary structure library and search algorithm for modeling loops in protein structures

We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105 950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed ϕ/ψ main chain dihedral angle propensities. Confidence Z-score cut-offs were determined for each loop length that identify those predicted fragments that outperform a competitive ab initio method. A web server implements the method, regularly updates the fragment library and performs prediction. Predicted segments are returned, or optionally, these can be completed with side chain reconstruction and subsequently annealed in the environment of the query protein by conjugate gradient minimization. The prediction method was tested on artificially prepared search datasets where all trivial sequence similarities on the SCOP superfamily level were removed. Under these conditions it is possible to predict loops of length 4, 8 and 12 with coverage of 98, 78 and 28% with at least of 0.22, 1.38 and 2.47 Å of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a ∼5:1 ratio an earlier developed database search method.
Are Children with Siblings Really More Vulnerable than Only Children in Health, Cognition and Non‐Cognitive Outcomes? Evidence from a Multi‐Province Dataset in China

The general goal of the present study is to analyze whether children with siblings lag behind their only-child counterparts in terms of health and nutrition, cognition and educational performance, and non-cognitive outcomes. We draw on a dataset containing 25 871 observations constructed from three school-level surveys spanning four provinces in China. The analysis compares children with siblings and only children aged 9 to 14 years old in terms of eight different health, cognitive and non-cognitive indicators. We find that with the exception of the anemia rate, health outcomes of children with siblings are statistically indistinguishable from those of only children. In terms of cognition, children with siblings performed better than only children. Moreover, outcomes of children with siblings are statistically indistinguishable from those of only children in terms of the non-cognitive outcomes provided by measures of anxiety. According to our results, the same general findings are true regardless of whether the difference between children with and without siblings is disaggregated by gender.
Directly Modulated Semiconductor Lasers

This paper presents a review and discussion of the directly modulated semiconductor lasers and their applications to optical communications and microwave photonics. A detailed and comprehensive demonstration of directly modulated semiconductor lasers from development history to specific techniques on measurement, analysis, and packaging is provided for the first time to the best of our knowledge. A few typical applications based on directly modulated lasers are also illustrated, such as optical fiber communications, free-space optical communications and microwave photonics. Future directions of research are also highlighted.
An Extended Path Following Algorithm for Graph-Matching Problem

The path following algorithm was proposed recently to approximately solve the matching problems on undirected graph models and exhibited a state-of-the-art performance on matching accuracy. In this paper, we extend the path following algorithm to the matching problems on directed graph models by proposing a concave relaxation for the problem. Based on the concave and convex relaxations, a series of objective functions are constructed, and the Frank-Wolfe algorithm is then utilized to minimize them. Several experiments on synthetic and real data witness the validity of the extended path following algorithm.
Breaking the Silence: The Moderating Effects of Self‐Monitoring in Predicting Speaking Up in the Workplace

Whereas both management scholars and practitioners emphasize the importance of employee input for improving workplace practices, research suggests that many employees are hesitant to express their opinions or voice their views because doing so might lead to retaliation. Consequently, they remain silent rather than speak up about workplace happenings, actions or ideas of others, needed changes, and other job-related issues. Drawing on various literatures, we developed and tested a conceptual scheme for examining the influence of self-monitoring on the relationships between two individual (locus of control and self-esteem) and two contextual (top-management openness and trust in supervisor) factors and speaking up. Data from 118 telecommunications employees and their coworkers provided supporting evidence. As predicted, low self-monitors, in comparison to high self-monitors, spoke up more often as internal locus of control, self-esteem, top-management openness, and trust in supervisor increased. The theoretical and practical implications of our results are discussed. Copyright Blackwell Publishing Ltd 2003.
From Here to Eternity: How the Bereaved Maintain Connections to Lost Loved Ones and Why It Matters

Christine Valentine is a researcher and teacher at the Centre for Death and Society at the University of Bath. She wrote ‘‘Academic Constructions of Bereavement,’’ which appeared in Mortality, 2006, 11, 57–79. Phyllis G. Kosminsky is a clinician in private practice in New York and for the past 15 years at the Center for Hope in Darien, Connecticut. She is the author of Getting Back to Life When Grief Won’t Heal (McGrawHill, 2007) and lectures frequently on complicated bereavement, grief counseling and grief related trauma.
Affective Labeling in a Content-Based Recommender System for Images

Affective labeling of multimedia content has proved to be useful in recommender systems. In this paper we present a methodology for the implicit acquisition of affective labels for images. It is based on an emotion detection technique that takes as input the video sequences of the users' facial expressions. It extracts Gabor low level features from the video frames and employs a k nearest neighbors machine learning technique to generate affective labels in the valence-arousal-dominance space. We performed a comparative study of the performance of a content-based recommender (CBR) system for images that uses three types of metadata to model the users and the items: (i) generic metadata, (ii) explicitly acquired affective labels and (iii) implicitly acquired affective labels with the proposed methodology. The results show that the CBR performs best when explicit labels are used. However, implicitly acquired labels yield a significantly better performance of the CBR than generic metadata while being an unobtrusive feedback tool.
The interrelationship between dengue incidence and diurnal ranges of temperature and humidity in a Sri Lankan city and its potential applications

Background Temperature, humidity, and other weather variables influence dengue transmission. Published studies show how the diurnal fluctuations of temperature around different mean temperatures influence dengue transmission. There are no published studies about the correlation between diurnal range of humidity and dengue transmission. Objective The goals of this study were to determine the correlation between dengue incidence and diurnal fluctuations of temperature and humidity in the Sri Lankan city of Kandy and to explore the possibilities of using that information for better control of dengue. Design We calculated the weekly dengue incidence in Kandy during the period 2003–2012, after collecting data on all of the reported dengue patients and estimated midyear populations. Data on daily maximum and minimum temperatures and night-time and daytime humidity were obtained from two weather stations, averaged, and converted into weekly data. The number of days per week with a diurnal temperature range (DTR) of >10°C and <10°C and the number of days per week with a diurnal humidity range (DHR) of >20 and <15% were calculated. Wavelet time series analysis was performed to determine the correlation between dengue incidence and diurnal ranges of temperature and humidity. Results There were negative correlations between dengue incidence and a DTR >10°C and a DHR >20% with 3.3-week and 4-week lag periods, respectively. Additionally, positive correlations between dengue incidence and a DTR <10°C and a DHR <15% with 3- and 4-week lag periods, respectively, were discovered. Conclusions These findings are consistent with the results of previous entomological studies and theoretical models of DTR and dengue transmission correlation. It is important to conduct similar studies on diurnal fluctuations of humidity in the future. We suggest ways and means to use this information for local dengue control and to mitigate the potential effects of the ongoing global reduction of DTR on dengue incidence.
Identification of novel biomarkers for preeclampsia on the basis of differential expression network analysis

Preeclampsia (PE) is a severe pregnancy complication, which is a leading cause of maternal and fetal mortality. The present study aimed to screen potential biomarkers for the diagnosis and prediction of PE and to investigate the underlying mechanisms of PE development based on the differential expression network (DEN). The microarray datasets E-GEOD-6573 and E-GEOD-48424 were downloaded from the European Bioinformatics Institute database. Differentially expressed genes (DEGs) between the PE and normal groups were screened by Significant Analysis of Microarrays with the cutoff value of a |log2 fold change| of >2, and a false discovery rate of <0.05. The DEN was constructed based on the differential and non-differential interactions observed. In addition, genes with higher connectivity degrees in the DEN were identified on the basis of centrality analysis, while disease genes were also extracted from the DEN. In order to understand the functional roles of genes in DEN, Gene Ontology (GO) and pathway enrichment analyses were performed. The present results indicated that a total of 225 genes were considered as DEGs in the PE group, while 466 nodes and 314 gene interactions were involved in the DEN. Among these 466 nodes, 4 nodes with higher degrees were identified, including ubiquitin C (UBC), small ubiquitin-like modifier 1 (SUMO1), SUMO2 and RAD21 homolog (S. pombe) (RAD21). Notably, UBC was also found to be a disease gene. UBC, RAD21, SUMO2 and SUMO1 were markedly enriched in the regulation of programmed cell death, as well as in the regulation of apoptosis, cell cycle and chromosomal part. In conclusion, based on these results, we suggest that UBC, RAD21, SUMO2 and SUMO1 may be reliable biomarkers for the prediction of the development and progression of PE.
Clinical significance of plasma presepsin levels in patients with systemic lupus erythematosus

Abstract Objectives: Presepsin (PSEP: soluble CD14 subtype) is produced from bacteria-stimulated monocytes or neutrophils, thus recognized as a biomarker of sepsis. Aberrant functions in monocyte or neutrophils are increasingly recognized in systemic lupus erythematosus (SLE). We investigated whether plasma PSEP reflects disease activity in patients with SLE. Methods: This retrospective study comprised 35 patients with SLE and 72 with non-SLE autoimmune diseases who visited our facility during the period from August 2012 to September 2015. Plasma PSEP levels and laboratory data were compared between SLE and non-SLE. Clinical markers of SLE disease activity, including SLE disease activity index 2000 (SLEDAI-2K), serum complement concentrations and serum anti-ds-DNA antibodies were assessed in correlation with plasma PSEP levels. Results: Plasma PSEP levels in SLE were higher than those in non-SLE. This phenomenon holds true when comparing SLE and non-SLE patients in the absence of infection (p = .0008). Plasma PSEP levels in SLE patients negatively correlated with C3 (r = –0.4454, p = .0430), CH50 (r = –0.4502, p = .0406) and positively with SLEDAI-2K (r = 0.4801, p = .0237). Conclusion: Elevated plasma PSEP levels were correlated with disease activity of SLE, suggesting inappropriate monocyte or neutrophil activation in the pathophysiology of SLE exacerbation.
Impact of Socioeconomic Status on Physiological Health in Adolescents: an Experimental Manipulation of Psychosocial Factors

Objective: To examine the effects of a brief psychosocial manipulation on physiological responses to laboratory stress in lower and higher socioeconomic status (SES) adolescents. Methods: A total of 115 adolescents participated in two acute laboratory stress tasks: one with psychosocial intervention and one with no intervention. In the intervention condition, half of the adolescents were given control over the stressor parameters; the other half received social informational resources (hints provided by another person) for dealing with the stressor. Physiological reactivity was monitored. Results: Lower SES adolescents exhibited less physiological reactivity when provided with intervention compared with no intervention. Within the lower SES group, the resource condition reduced physiological reactivity more than the control condition did. Higher SES adolescents did not respond physiologically to intervention. Conclusions: This study provides a preliminary illustration of an experimental laboratory approach to studying SES-health relationships and suggests that providing informational support during a stressor may have beneficial implications for the physiological health of lower SES adolescents. SES = socioeconomic status; HR = heart rate; SBP = systolic blood pressure; DBP = diastolic blood pressure
The University College London Archive of Stuttered Speech (UCLASS).

PURPOSE This research note gives details of 2 releases of audio recordings available from speakers who stutter that can be accessed on the Web. METHOD Most of the recordings are from school-age children. These are available on the University College London Archive of Stuttered Speech (UCLASS) Web site, and information is provided about how to access the site. A description of the recordings and background information about the speakers who contributed recordings to UCLASS Releases One and Two are given. The sample types available in Release One are monologs. Release Two has monologs, readings, and conversations. Three optional software formats that can be used with the archive are described (although processing the archive is not restricted to these formats). Some perceptual assessment of the quality of each recording is given. An assessment of the strengths and limitations of the recording archive is presented. Finally, some past applications and future research possibilities using the recordings are discussed.
Dynamic Mode Decomposition with Control

We develop a new method which extends dynamic mode decomposition (DMD) to incorporate the effect of control to extract low-order models from high-dimensional, complex systems. DMD finds spatial-temporal coherent modes, connects local-linear analysis to nonlinear operator theory, and provides an equation-free architecture which is compatible with compressive sensing. In actuated systems, DMD is incapable of producing an input-output model; moreover, the dynamics and the modes will be corrupted by external forcing. Our new method, dynamic mode decomposition with control (DMDc), capitalizes on all of the advantages of DMD and provides the additional innovation of being able to disambiguate between the underlying dynamics and the effects of actuation, resulting in accurate input-output models. The method is data-driven in that it does not require knowledge of the underlying governing equations---only snapshots in time of observables and actuation data from historical, experimental, or black-box simulations. W.
Requirement for a Noncoding RNA in Drosophila Polar Granules for Germ Cell Establishment

In Drosophila embryos, germ cell formation is induced by specialized cytoplasm at the posterior of the egg, the pole plasm. Pole plasm contains polar granules, organelles in which maternally produced molecules required for germ cell formation are assembled. An untranslatable RNA, called Polar granule component (Pgc), was identified and found to be localized in polar granules. Most pole cells in embryos produced by transgenic females expressing antisense Pgc RNA failed to complete migration and to populate the embryonic gonads, and females that developed from these embryos often had agametic ovaries. These results support an essential role for Pgc RNA in germline development.
The Ethical Maze

In the UK, the ethics of engaging in sociological research directly involving children have primarily been shaped by definitions of ‘competence’. While this has been a crucial guideline for researchers in shaping the concept of informed consent, it has also acted, perhaps inadvertently, as a way of excluding particular children from the research agenda. This article discusses the problems of informed consent that were encountered in research with children with learning impairments. It proposes that the process of seeking ‘assent’, when used within an ethical framework, is a more comprehensive method of gaining the agreement of children in research, which transcends language, ability, cultural, social and international borders
The Cultural Turn and the Civilizational Approach

The revival of civilizational analysis is closely linked to a broader cultural turn in the human sciences. Comparative civilizational approaches accept the primacy of culture, but at the same time, they strive to avoid the cultural determinism familiar from twentieth-century sociology, especially from the Parsonian version of functionalism. To situate this twofold strategy within contemporary cultural sociology, it seems useful to link up with the distinction between a strong and a weak program for the sociological analysis of culture, proposed by Jeffrey Alexander and Philip Smith. The strong program, also described as cultural sociology, stresses the constitutive role of culture in all domains and across the field of social life; the weak program, more precisely the sociology of culture, treats culture as a variable factor among others, and in some important respects subordinate to others. From this point of view, civilizational analysis is, first and foremost, a particularly ambitious version of the strong program: its emphasis on different cultural articulations of the world, as well as on the large-scale and long-term social-historical formations crystallizing around such articulations, adds new dimensions to the autonomy of culture. It also reinforces the hermeneutical stance of cultural sociology and cautions against the acceptance of mainstream explanatory models. On the other hand, the civilizational perspective highlights the variety of interconnections between culture and other components of the social world, and thus takes into account some of the themes favoured by the weak program.
DOES NITRIC OXIDE MODULATE TRANSMITTER RELEASE AT THE MAMMALIAN NEUROMUSCULAR JUNCTION?

1 Application of the nitric oxide (NO) donor, sodium nitrite and the NO synthase substrate l‐arginine had no effect on nerve‐evoked transmitter release in the rat isolated phrenic nerve/hemidiaphragm preparation; however, when adenosine A1 receptors were blocked with the adenosine A1 receptor antagonist 1,3‐dipropyl‐8‐cyclopentylxanthine (DPCPX) prior to application of sodium nitrate or l‐arginine, a significant increase in transmitter release was observed. In addition, the NO donor s‐nitroso‐N‐acetylpenicillamine (SNAP) significantly increased transmitter release in the presence of DPCPX. In the present study, we have made the assumption that these NO donors elevate the level of NO in the tissue. Future studies should test other NO‐donating compounds and also monitor the NO concentrations in the tissue to ensure that these effects are, in fact, NO induced. 2 Elevation of cGMP in this preparation with the guanylyl cyclase activator 3‐(5′‐hydroxymethyl‐2′‐furyl)‐1‐benzyl indazole (YC‐1) significantly enhanced transmitter release. In the presence of DPCPX and the selective guanylyl cyclase inhibitor 1H‐[1,2,4]oxadiazolo[4,3‐a]quinoxalin‐1‐one (ODQ), which blocks the production of cGMP, the excitatory effects of sodium nitrite and l‐arginine were abolished. 3 These results suggest that NO serves to enhance transmitter release at the rat neuromuscular junction (NMJ) via a cGMP pathway and this facilitation of transmitter release can be blocked with adenosine. Previously, we demonstrated that adenosine inhibits N‐type calcium channels. Because NO only affects transmitter release when adenosine A1 receptors are blocked, we suggest that NO enhances transmitter release by enhancing calcium influx via N‐type calcium channels. Further studies are needed to confirm that NO alters transmitter release via cGMP and that this action involves the N‐type calcium channel. 4 The results of the present study are consistent with a model of NO neuromodulation that has been proposed for the mammalian vagal–atrial junction. This model suggests that NO acts on NO‐sensitive guanylyl cyclase to increase the intracellular levels of cGMP. In turn, cGMP inhibits phosphodiesterase‐3, increasing levels of cAMP, which then acts on the N‐type calcium channels to enhance calcium influx, leading to an increase in transmitter release. Our only modification to this model for the NMJ is that adenosine serves to block the modulation of transmitter release by NO.