Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA Primer Handoff in Bacteriophage T4 DNA Replication

In T4 phage, coordinated leading and lagging strand DNA synthesis is carried out by an eight-protein complex termed the replisome. The control of lagging strand DNA synthesis depends on a highly dynamic replisome with several proteins entering and leaving during DNA replication. Here we examine the role of single-stranded binding protein (gp32) in the repetitive cycles of lagging strand synthesis. Removal of the protein-interacting domain of gp32 results in a reduction in the number of primers synthesized and in the efficiency of primer transfer to the polymerase. We find that the primase protein is moderately processive, and this processivity depends on the presence of full-length gp32 at the replication fork. Surprisingly, we find that an increase in the efficiency of primer transfer to the clamp protein correlates with a decrease in the dissociation rate of the primase from the replisome. These findings result in a revised model of lagging strand DNA synthesis where the primase remains as part of the replisome after each successful cycle of Okazaki fragment synthesis. A delay in primer transfer results in an increased probability of the primase dissociating from the replication fork. The interplay between gp32, primase, clamp, and clamp loader dictates the rate and efficiency of primer synthesis, polymerase recycling, and primer transfer to the polymerase.
RESISTANCE TO FREEZING AND THAWING OF FIBER-REINFORCED POLYMER-CONCRETE BOND

This paper presents results from an experimental and theoretical study into the effects of freeze-thaw cycling on the fiber reinforced polymer (FRP)-concrete bond. The results of flexural tests on 39 small-scale flexural beams, reinforced in tension with externally bonded FRP sheets, are presented and discussed. The beams were subjected to from 0-300 freeze-thaw cycles and were plated with 4 different FRP materials. Results indicate that little, if any, damage to the FRP-concrete bond results from freeze-thaw cycling. A simple analytical model to predict bond behavior and the potential for bond damage due to thermal cycling is discussed.
A ultra-pressure liquid chromatography/triple quadrupole tandem mass spectrometry method for the analysis of 13 eicosanoids in human urine and quantitative 24 hour values in healthy volunteers in a controlled constant diet.

RATIONALE Isoprostanes (IsoPs) are a series of prostaglandin (PG)-like compounds formed non-enzymatically through free-radical-induced peroxidation of arachidonic acid. They are considered as 'gold-standard' biomarkers for oxidative stress, in general, and lipid peroxidation, in particular. METHODS A new qualitative and quantitative analytical method for the determination of 13 eicosanoids in human urine using solid-phase extraction (SPE) and ultra-pressure liquid chromatography coupled to tandem mass spectrometry (UPLC/MS/MS) has been developed. The SPE was optimized by comparison of the extraction efficiency and recoveries of three distinct cartridges: Strata X-AW, C18 Sep-Pak, and Oasis HLB. The UPLC/MS/MS approach in the multiple reaction monitoring (MRM) mode was developed using negative electrospray ionization (ESI). RESULTS The validated method provides a high-throughput assay with an adequate linearity from 0.16 to 330 ng mL(-1). The limit of detection (LOD) and limit of quantification (LOQ) for each analyte showed low intervals (0.021-0.64 ng mL(-1) and 0.042-1.28 ng mL(-1), respectively). Urinary IsoPs were determined in 24 healthy volunteers and ranged from 685 to 3480 ng 24 h(-1) and from 864 to 7511 ng 24 h(-1) in urine from women and men, respectively. CONCLUSIONS This analytical method could constitute a useful tool for the determination of oxidative stress biomarkers in clinical studies in which IsoPs may evidence early pathological conditions, as suggested by the determination of the baseline IsoPs content in human urine, since it improves upon the detection capacity of previously described methods. The quantity of IsoPs excreted in urine was higher than that found in previous reports due to the total hydrolysis of the conjugated forms.
Cross-sectional study of factors that influence the 25-hydroxyvitamin D status in pregnant women and in cord blood in Germany

There is increasing evidence of an association between a low maternal vitamin D status and a high risk of adverse pregnancy outcomes. In a cross-sectional study, we investigated the vitamin D status of pregnant women to determine potentially influencing factors. Between December 2010 and February 2012, 261 maternal blood samples and 328 cord blood samples were collected for the analysis of 25-hydroxyvitamin D (25(OH)D), intact parathyroid hormone, alkaline phosphatase and Ca concentrations. Demographical characteristics and clinical data were recorded by a questionnaire and from medical files. The overall median maternal and cord blood 25(OH)D levels were 25·0 (interquartile range 12·6–45·5) nmol/l and 34·1 (interquartile range 17·7–58·6) nmol/l, respectively. During the winter months, 98 % of the maternal blood samples and 94 % of the cord blood samples had 25(OH)D levels < 50 nmol/l. In the summer months, 49 % of the women and 35 % of the cord blood samples were vitamin D deficient. Using logistic regression models, significant risk factors for maternal vitamin D deficiency were found to be physical inactivity (adjusted OR (aOR) 2·67, 95 % CI 1·06, 6·69, P= 0·032) and a non-European country of origin (aOR 3·21, 95 % CI 1·0, 10·28, P= 0·047) after controlling for season and independent risk factors. These results are the first 25(OH)D data for pregnant women in Germany. They indicate the need for urgent implementation of strategies to prevent vitamin D deficiency by healthcare authorities that are in charge of preventing vitamin D deficiency, especially during these sensitive stages of life.
Antidepressant exposure in pregnancy and risk of autism spectrum disorders

Background Both the use of antidepressant medication during pregnancy and the prevalence of autism spectrum disorder have increased during recent years. A causal link has recently been suggested, but the association may be confounded by the underlying indication for antidepressant use. We investigated the association between maternal use of antidepressant medication in pregnancy and autism, controlling for potential confounding factors. Methods We identified all children born alive in Denmark 1996–2006 (n=668,468) and their parents in the Danish Civil Registration System. We obtained information on the mother’s prescriptions filled during pregnancy from the Danish National Prescription Registry, and on diagnoses of autism spectrum disorders in the children and diagnoses of psychiatric disorders in the parents from the Danish Psychiatric Central Register. In a cohort analysis, we estimated hazard ratios of autism spectrum disorders in children exposed to antidepressant medication during pregnancy compared with children who were not exposed, using Cox proportional hazards regression analysis. Furthermore, we estimated the risk for autism spectrum disorder in a sibling design. Results Children exposed prenatally to antidepressants had an adjusted hazard ratio of 1.5 (95% confidence interval [CI] 1.2–1.9) for autism spectrum disorder compared with unexposed children. Restricting the analysis to children of women with a diagnosis of affective disorder, the adjusted hazard ratio was 1.2 (95% CI 0.7–2.1), and the risk was further reduced when exposed children were compared with their unexposed siblings (adjusted hazard ratio 1.1; 95% CI 0.5–2.3). Conclusion After controlling for important confounding factors, there was no significant association between prenatal exposure to antidepressant medication and autism spectrum disorders in the offspring.
Sexual modulation of sex‐shared neurons and circuits in Caenorhabditis elegans

Studies using the nematode C. elegans have provided unique insights into the development and function of sex differences in the nervous system. Enabled by the relative simplicity of this species, comprehensive studies have solved the complete cellular neuroanatomy of both sexes as well as the complete neural connectomes of the entire adult hermaphrodite and the adult male tail. This work, together with detailed behavioral studies, has revealed three aspects of sex differences in the nervous system: sex‐specific neurons and circuits; circuits with sexually dimorphic synaptic connectivity; and sex differences in the physiology and functions of shared neurons and circuits. At all of these levels, biological sex influences neural development and function through the activity of a well‐defined genetic hierarchy that acts throughout the body to translate chromosomal sex into the state of a master autosomal regulator of sexual differentiation, the transcription factor TRA‐1A. This Review focuses on the role of genetic sex in implementing sex differences in shared neurons and circuits, with an emphasis on linking the sexual modulation of specific neural properties to the specification and optimization of sexually divergent and dimorphic behaviors. An important and unexpected finding from these studies is that chemosensory neurons are a primary focus of sexual modulation, with genetic sex adaptively shaping chemosensory repertoire to guide behavioral choice. Importantly, hormone‐independent functions of genetic sex are the principal drivers of all of these sex differences, making nematodes an excellent model for understanding similar but poorly understood mechanisms that likely act throughout the animal kingdom. © 2016 Wiley Periodicals, Inc.
Arabic handwriting recognition using baseline dependant features and hidden Markov modeling

In this paper, we describe a 1D HMM offline handwriting recognition system employing an analytical approach. The system is supported by a set of robust language independent features extracted on binary images. Parameters such as lower and upper baselines are used to derive a subset of baseline dependent features. Thus, word variability due to lower and upper parts of words is better taken into account. In addition, the proposed system learns character models without character pre-segmentation. Experiments that have been conducted on the benchmark IFN/ENIT database of Tunisian handwritten country/village names, show the advantage of the proposed approach and of the baseline-dependant features.
What Parents Know About How Well Their Children Are Doing in School

ABSTRACT The authors used data from the Early Childhood Longitudinal Study–Kindergarten cohort to examine whether parents’ knowledge of their children's reading and mathematics skills varies by academic domain and parents’ income group or ethnicity. Of particular interest was how parents’ knowledge is moderated by school- or home-based involvement. Parents’ knowledge was moderately related to their children's reading and mathematics scores. However, there were systematic income- and ethnicity-related differences in the correlations. Poor parents were reportedly less involved at home and school than nonpoor parents. White, non-Hispanic parents were more involved at school than other parents. School-based rather than home-based involvement was related to the strength of the correlations between parents’ knowledge and children's reading and mathematics scores.
Optimal Dialysate Sodium—What is the Evidence?

Oligo‐anuric patients with end‐stage kidney disease are dependent on hemodialysis to achieve and maintain the desired goal of euvolemia. The dialysis prescription, in addition to sodium and fluid restriction, is therefore a critically important factor in the care of hemodialysis patients. Various dialysate sodium concentrations have been favored throughout the history of dialysis, but the “optimal” concentration remains unclear. In this manuscript, we examine the historical context of changes to the dialysate sodium prescription, review the evidence of its associated effects, discuss ‘individualization’ of dialysate sodium, and highlight the need for definitive trials that are powered for important clinical outcomes.
Rapid carrier relaxation in self-assembled InxGa1-xAs/GaAs quantum dots.

Carrier capture and relaxation processes in self-assembled 15-nm ${\mathrm{In}}_{0.5}$${\mathrm{Ga}}_{0.5}$As/GaAs quantum dots are investigated by means of time-resolved photoluminescence spectroscopy. In a systematic study of photoluminescence rise times and barrier decay times (variation of temperature, excitation energy, and excitation density) we aim to identify the physical mechanisms responsible for fast carrier capture and relaxation in quantum dots. Both processes are separated by using appropriate excitation energies. Carrier capture and relaxation are shown to proceed with rates as high as \ensuremath{\sim}2\ifmmode\times\else\texttimes\fi{}${10}^{10}$ ${\mathrm{s}}^{\mathrm{\ensuremath{-}}1}$ at low temperature even if less than one electron-hole pair per dot and excitation pulse is created. We interpret our results in terms of multiphonon processes at low excitation densities and in terms of Auger processes at high excitation densities. \textcopyright{} 1996 The American Physical Society.
Functional Gene-Expression Analysis Shows Involvement of Schizophrenia-Relevant Pathways in Patients with 22q11 Deletion Syndrome

22q11 Deletion Syndrome (22q11DS) is associated with dysmorphology and a high prevalence of schizophrenia-like symptoms. Several genes located on chromosome 22q11 have been linked to schizophrenia. The deletion is thought to disrupt the expression of multiple genes involved in maturation and development of neurons and neuronal circuits, and neurotransmission. We investigated whole-genome gene expression of Peripheral Blood Mononuclear Cells (PBMC's) of 8 22q11DS patients and 8 age- and gender-matched controls, to (1) investigate the expression levels of 22q11 genes and (2) to investigate whether 22q11 genes participate in functional genetic networks relevant to schizophrenia. Functional relationships between genes differentially expressed in patients (as identified by Locally Adaptive Statistical procedure (LAP) or satisfying p<0.05 and fold-change >1.5) were investigated with the Ingenuity Pathways Analysis (IPA). 14 samples (7 patients, 7 controls) passed quality controls. LAP identified 29 deregulated genes. Pathway analysis showed 262 transcripts differentially expressed between patients and controls. Functional pathways most disturbed were cell death, cell morphology, cellular assembly and organization, and cell-to-cell signaling. In addition, 10 canonical pathways were identified, among which the signal pathways for Natural Killer-cells, neurotrophin/Trk, neuregulin, axonal guidance, and Huntington's disease. Our findings support the use of 22q11DS as a research model for schizophrenia. We identified decreased expression of several genes (among which COMT, Ufd1L, PCQAP, and GNB1L) previously linked to schizophrenia as well as involvement of signaling pathways relevant to schizophrenia, of which Neurotrophin/Trk and neuregulin signaling seems to be especially notable.
Initial psychometric evaluation of the Moral Injury Questionnaire--Military version.

UNLABELLED Moral injury is an emerging construct related to negative consequences associated with war-zone stressors that transgress military veterans' deeply held values/beliefs. Given the newness of the construct, there is a need for instrumentation that might assess morally injurious experiences (MIEs) in this population. Drawing on a community sample of 131 Iraq and/or Afghanistan Veterans and clinical sample of 82 returning Veterans, we conducted an initial psychometric evaluation of the newly developed Moral Injury Questionnaire-Military version (MIQ-M)-a 20-item self-report measure for assessing MIEs. Possibly due to low rates of reporting, an item assessing sexual trauma did not yield favourable psychometric properties and was excluded from analyses. Veterans in the clinical sample endorsed significantly higher scores across MIQ-M items. Factor analytic results for the final 19 items supported a unidimensional structure, and convergent validity analyses revealed that higher scores (indicative of more MIEs) were correlated with greater general combat exposure, impairments in work/social functioning, posttraumatic stress and depression in the community sample. In addition, when controlling for demographics, deployment-related factors and exposure to life threat stressors associated with combat, tests of incremental validity indicated that MIQ-M scores were also uniquely linked with suicide risk and other mental health outcomes. These findings provide preliminary evidence for the validity of the MIQ-M and support the applicability of this measure for further research and clinical work with Veterans. KEY PRACTITIONER MESSAGE Military service can confront service members with experiences that undermine their core sense of humanity and violate global values and beliefs. These types of experiences increase the risk for posttraumatic maladjustment in this population, even when accounting for rates of exposure to life threat traumas. Moral injury is an emerging construct to more fully capture the many possible psychological, ethical, and spiritual/existential challenges among persons who served in modern wars and other trauma-exposed professional groups. There is currently a need for psychometrically sound instrumentation for assessing morally injurious experiences (MIEs). The Moral Injury Questionnaire - Military Version (MIQ-M) was developed to provide a tool for assessing possible MIEs among military populations. This study provides preliminary evidence of the validity - including factorial, concurrent, and incremental - and clinical utility of the MIQ-M for further applications in clinical and research contexts.
Lipid-based nutrient supplements do not affect the risk of malaria or respiratory morbidity in 6- to 18-month-old Malawian children in a randomized controlled trial.

BACKGROUND There is evidence to support the use of lipid-based nutrient supplements (LNSs) to promote child growth and development in low-income countries, but there is also a concern regarding the safety of using iron-fortified products in malaria-endemic areas. OBJECTIVE The objective of this study was to test the hypothesis that 6- to 18-mo-old rural Malawian children receiving iron-containing (6 mg/d) LNSs would not have excess morbidity compared with infants receiving no supplementation. METHODS A randomized controlled trial allocated 840 children to receive daily supplementation with 54 g/d LNS with milk protein base (milk-LNS), 54 g/d LNS with soy protein base (soy-LNS), 71 g/d corn-soy blend (CSB), or no supplementation from 6 to 18 mo of age. Morbidity was compared using a non-inferiority margin set at 20% excess morbidity in supplemented groups compared with the nonsupplemented group. RESULTS Baseline characteristics were similar across groups. The proportion of days with febrile illness between 6 and 18 mo was 4.9%, and there were no differences between the groups: 4.9% (95% CI: 4.3, 5.5%), 4.5% (95% CI: 3.9, 5.1%), 4.7% (95% CI: 4.1, 5.3%), and 5.5% (95% CI: 4.7-6.3%) in the milk-LNS, soy-LNS, CSB, and control groups, respectively. The proportion of days with respiratory problems and diarrhea between 6 and 18 mo also did not differ between groups. Compared with controls, the incident rate ratio (95% CI) for clinical malaria was 0.80 (0.59, 1.09), 0.77 (0.56, 1.06), and 0.79 (0.58, 1.08) in milk-LNS, soy-LNS, and CSB, respectively, with 95% CIs confirming non-inferiority. The incidence of febrile episodes, diarrhea, respiratory problems or admission to hospital, prevalence of malaria parasitemia throughout the follow-up, and mean change in hemoglobin concentration from baseline were also similar between the groups. CONCLUSIONS Daily supplementation with 54 g of milk-based or soy protein-based LNS or 71 g of CSB did not result in increases in malaria or respiratory morbidity in children in a malaria-endemic setting. However, we could not conclude whether LNSs did or did not increase diarrheal morbidity. This trial was registered at clinicaltrials.gov as NCT00524446.
Stimulus specific responses from beyond the classical receptive field: neurophysiological mechanisms for local-global comparisons in visual neurons.

We perceive the visual world as a unitary whole, yet one of the guiding principles of nearly a half century of neurophysiological research since the early recordings by Hartline (1938) has been that the visual system consists of neurons that are driven by stimulation within small discrete portions of the total visual field. These classical receptive fields (CRFs) have been mapped with the excitatory responses evoked by a flashed or moving stimulus, usually a spot or bar of light. Most of the visual neurons, in turn, are organized in a series of maps of the visual field, at least 10 of which exist in the visual cortex in primates as well as additional topographic representations in the lateral geniculate body, pulvinar and optic tectum (Allman 1977, Newsome & Allman 1980, Allman & Kaas 1984). It has been widely assumed that perceptual functions that require the integration of inputs over large portions of the visual field must be either collective properties of arrays of neurons representing the visual field, or features of those neurons at the highest processing levels in the visual system, such as the cells in inferotemporal or posterior parietal cortex that typically possess very large receptive fields and do not appear to be organized in visuotopic maps. These assumptions have been based on the results of the many studies in which receptive fields were mapped with conventional stimuli, presented one at a time, against a featureless background. However, unlike the neurophysiologist's tangent screen, the natural visual scene is rich in features, and there is a growing body of evidence that in many visual neurons stimuli presented outside the CRF strongly and selectively influence neural responses to stimuli presented within the CRF. These results suggest obvious mechanisms for local-global comparisons within visuotopically organized structures. Such broad and specific surround mechanisms could participate in many functions that require the integration of inputs over wide regions of the visual space such as the perceptual constancies, the segregation of figure from ground, and depth perception through motion parallax. In the first section of this paper, we trace the historical development of the evidence of response selectivity for visual stimuli presented beyond the CRF; in the second, examine the anatomical pathways that sub serve these far-reaching surround mechanisms; and in the third, explore the possible relationships between these mechanisms and perception.