Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity and relationships among Turkish okra germplasm by SRAP and phenotypic marker polymorphism

Germplasm characterization is essential and molecular markers provide valuable information for breeding programs. Sequence-related amplified polymorphism (SRAP) and phenotypic markers were studied to determine diversity and relationships among 23 okra (Abelmoschus esculentus (L) Moench) genotypes. The 39 combinations of forward and reverse SRAP primers were used to evaluate the 21 Turkish and two randomly selected USA genotypes as outgroups, and produced 97 scorable markers, of which 50% was polymorphic for all 23 genotypes. Seventeen out of the 23 genotypes (74%) were distinguished from each other with mean similarity of 0.93. As to phenotypic markers, 33 heritable traits were evaluated in field with ten replications, 28 of them (85%) were found to be polymorphic. The UPGMA (unweighted-pair group method arithmetic average) dendrogram based on the 33 phenotypic markers distinguished all genotypes, but failed to detect any geographic association of okra genotypes, being consistent with previous study. It can be concluded that SRAP markers are useful for studying diversity and relationships among okra germplasm, and have potential in marker-aided selection, linkage mapping, and evolutionary studies.
EVALUATION OF CLINICAL PERIODONTAL CONDITIONS IN SMOKERS AND NON-SMOKERS

Given that tobacco smoking habit is a risk factor for periodontal diseases, the aim of this study was to compare clinical periodontal aspects between smokers and non-smokers. The clinical status were assessed in 55 patients, 29 smokers and 26 non-smokers, aged 30 to 50 years, with mean age of 40. The clinical parameters used were: probing depth (PD), plaque index (PI), gingival index (GI), clinical attachment level (CAL), gingival recession (GR) and gingival bleeding index (GBI) for arches (upper and lower) and teeth (anterior and posterior). Tooth loss was also evaluated in both groups. Multiple regression analysis showed: tendency of greater probing depth and clinical attachment level means for smokers; greater amount of plaque in smokers in all regions; greater gingival index means for non-smokers with clinical significance (p<0.05) in all regions. Although, without statistical significance, the analysis showed greater gingival bleeding index means almost always for non-smokers; similar gingival recession means in both groups and tendency of upper tooth loss in smokers and lower tooth loss in non-smokers. The findings of this study showed that clinical periodontal parameters may be different in smokers when compared to non-smokers and that masking of some periodontal signs can be a result of nicotine's vasoconstrictor effect.
Influence of Annealing Temperature on Microstructure and Properties of Warm-Rolled AZ31 Magnesium Alloy Sheets

Warm-rolled AZ31 alloy sheets were annealed at different temperatures ranging from 150 to 450°C. Effects of annealing temperature on microstructure and properties of warm-rolled AZ31 alloy sheets, especially the formability, were investigated. The results revealed that the Lankford value (r-value) and strain-hardening exponent (n-value) first increased and then became relatively steady with the increase of annealing temperature. The Erichsen value (IE) first increased and then decreased with the increase of annealing temperature and the AZ31 alloy sheets exhibited the highest IE of 3.02 mm when annealing at 250°C, which can be mainly attributed to a larger elongation, a lower r-value and a higher n-value.
Effects of rest intervals and training loads on metabolic stress and muscle hypertrophy

We investigated the effects of volume‐matched resistance training (RT) with different training loads and rest intervals on acute responses and long‐term muscle and strength gains. Ten subjects trained with short rest (30 s) combined with low load (20 RM) (SL) and ten subjects performed the same protocol with long rest (3 min) and high load (8 RM) (LH). Cross‐sectional area (CSA) of the upper arm was measured by magnetic resonance imaging before and after 8 weeks of training. Acute stress markers such as growth hormone (GH) and muscle thickness (MT) changes have been assessed pre and post a single RT session. Only the SL group demonstrated significant increases in GH (7704·20 ± 11833·49%, P<0·05) and MT (35·2 ± 16·9%, P<0·05) immediately after training. After 8 weeks, the arm CSA s in both groups significantly increased [SL: 9·93 ± 4·86% (P<0·001), LH: 4·73 ± 3·01% (P<0·05)]. No significant correlation between acute GH elevations and CSA increases could be observed. We conclude that short rest combined with low‐load training might induce a high amount of metabolic stress ultimately leading to improved muscle hypertrophy while long rest with high‐load training might lead to superior strength increases. Acute GH increases seem not to be directly correlated with muscle hypertrophy.
Stress and multiple sclerosis: A systematic review considering potential moderating and mediating factors and methods of assessing stress

Research about the effects of stress on multiple sclerosis has yielded contradictory results. This study aims to systematically review the evidence focusing on two possible causes: the role of stress assessment and potential moderating and mediating factors. The Web of Knowledge (MEDLINE and Web of Science), Scopus, and PsycINFO databases were searched for relevant articles published from 1900 through December 2014 using the terms “stress*” AND “multiple sclerosis. ” Twenty-three articles were included. Studies focused on the effect of stress on multiple sclerosis onset (n = 9) were mostly retrospective, and semi-structured interviews and scales yielded the most consistent associations. Studies focused on multiple sclerosis progression (n = 14) were mostly prospective, and self-reported diaries yielded the most consistent results. The most important modifying factors were stressor duration, severity, and frequency; cardiovascular reactivity and heart rate; and social support and escitalopram intake. Future studies should consider the use of prospective design with self-reported evaluations and the study of moderators and mediators related to amount of stress and autonomic nervous system reactivity to determine the effects of stress on multiple sclerosis.
A mutation in mouse Disc1 that models a schizophrenia risk allele leads to specific alterations in neuronal architecture and cognition

DISC1 is a strong candidate susceptibility gene for schizophrenia, bipolar disorder, and depression. Using a mouse strain carrying an endogenous Disc1 orthologue engineered to model the putative effects of the disease-associated chromosomal translocation we demonstrate that impaired Disc1 function results in region-specific morphological alterations, including alterations in the organization of newly born and mature neurons of the dentate gyrus. Field recordings at CA3/CA1 synapses revealed a deficit in short-term plasticity. Using a battery of cognitive tests we found a selective impairment in working memory (WM), which may relate to deficits in WM and executive function observed in individuals with schizophrenia. Our results implicate malfunction of neural circuits within the hippocampus and medial prefrontal cortex and selective deficits in WM as contributing to the genetic risk conferred by this gene.
Experimental assessment of out‐of‐field dose components in high energy electron beams used in external beam radiotherapy

The purpose of this work was to experimentally investigate the out‐of‐field dose in a water phantom, with several high energy electron beams used in external beam radiotherapy (RT). The study was carried out for 6, 9, 12, and 18 MeV electron beams, on three different linear accelerators, each equipped with a specific applicator. Measurements were performed in a water phantom, at different depths, for different applicator sizes, and off‐axis distances up to 70 cm from beam central axis (CAX). Thermoluminescent powder dosimeters (TLD‐700) were used. For given cases, TLD measurements were compared to EBT3 films and parallel‐plane ionization chamber measurements. Also, out‐of‐field doses at 10 cm depth, with and without applicator, were evaluated. With the Siemens applicators, a peak dose appears at about 12–15 cm out of the field edge, at 1 cm depth, for all field sizes and energies. For the Siemens Primus, with a 10×10cm2 applicator, this peak reaches 2.3%, 1%, 0.9% and 1.3% of the maximum central axis dose (Dmax) for 6, 9, 12 and 18 MeV electron beams, respectively. For the Siemens Oncor, with a 10×10cm2 applicator, this peak dose reaches 0.8%, 1%, 1.4%, and 1.6% of Dmax for 6, 9, 12, and 14 MeV, respectively, and these values increase with applicator size. For the Varian 2300C/D, the doses at 12.5 cm out of the field edge are 0.3%, 0.6%, 0.5%, and 1.1% of Dmax for 6, 9, 12, and 18 MeV, respectively, and increase with applicator size. No peak dose is evidenced for the Varian applicator for these energies. In summary, the out‐of‐field dose from electron beams increases with the beam energy and the applicator size, and decreases with the distance from the beam central axis and the depth in water. It also considerably depends on the applicator types. Our results can be of interest for the dose estimations delivered in healthy tissues outside the treatment field for the RT patient, as well as in studies exploring RT long‐term effects. PACS number(s): 87.53. Bn, 87.56. bd, 87.56. J‐
Effects of purified SeqA protein on oriC‐dependent DNA replication in vitro

In vivo studies suggest that the Escherichia coli SeqA protein modulates replication initiation in two ways: by delaying initiation and by sequestering newly replicated origins from undergoing re‐replication. As a first approach towards understanding the biochemical bases for these effects, we have examined the effects of purified SeqA protein on replication reactions performed in vitro on an oriC plasmid. Our results demonstrate that SeqA directly affects the biochemical events occurring at oriC. First, SeqA inhibits formation of the pre‐priming complex. Secondly, SeqA can inhibit replication from an established pre‐priming complex, without disrupting the complex. Thirdly, SeqA alters the dependence of the replication system on DnaA protein concentration, stimulating replication at low concentrations of DnaA. Our data suggest that SeqA participates in the assembly of initiation‐competent complexes at oriC and, at a later stage, influences the behaviour of these complexes.
Mutant number distribution in an exponentially growing population

We present an explicit solution to a classic model of cell-population growth introduced by Luria and Delbrück (1943 Genetics 28 491–511) 70 years ago to study the emergence of mutations in bacterial populations. In this model a wild-type population is assumed to grow exponentially in a deterministic fashion. Proportional to the wild-type population size, mutants arrive randomly and initiate new sub-populations of mutants that grow stochastically according to a supercritical birth and death process. We give an exact expression for the generating function of the total number of mutants at a given wild-type population size. We present a simple expression for the probability of finding no mutants, and a recursion formula for the probability of finding a given number of mutants. In the ‘large population-small mutation’ limit we recover recent results of Kessler and Levine (2014 J. Stat. Phys. doi:10.1007/s10955-014-1143-3) for a fully stochastic version of the process.
The phase model of psychotherapy outcome: Domain-specific trajectories of change in outpatient treatment

Abstract Objective: The Phase model of psychotherapy outcome assumes a log-linear trajectory of change and allows predictions about the three outcome domains of Well-being, Symptoms, and Interpersonal functioning. Although the model has been partly validated, little is known about the types of trajectories in the specific domains and about the transferability of the model to treatments of longer duration. This study tested whether the domain-specific change trajectories followed a log-linear curve as postulated by the Phase model. Furthermore, it was examined whether the speed of change differed between the domains. Method: Growth curves were modeled using hierarchical linear modeling on an outpatient sample (N = 351), with treatment duration averaging 52 sessions. Results: A log-linear curve best explained the change trajectories of the domains Well-being and Symptoms as well as the Global score of psychopathology, whereas Interpersonal functioning tends to improve in a linear pattern. Estimated slopes were biggest for Well-being and smallest for Interpersonal functioning. Conclusions: In the present study, the predictions of the Phase model concerning multidimensional phases were validated. The finding that trajectories of change are not uniformly log-linear, but either log-linear or linear in a domain-specific manner, is partly inconsistent with the model. Clinical or methodological significance of this article: This article extends previous research in the field of psychotherapeutic change by providing results from the modeling of change trajectories in psychotherapeutic treatments with larger amounts of sessions (i.e., more than 20 sessions). Our findings of domain-specific different shapes (i.e., log-linear for Well-Being and Symptoms and linear for Interpersonal functioning) and speed (i.e., fastest for Well-Being and slowest for Interpersonal function) of trajectories of psychotherapeutic change may be clinically applied by means of guidelines for therapists to plan and adapt their treatments. In addition to content-related aspects of a continuous adjustment of treatment goals (e.g., merely symptom-oriented or focusing on interpersonal change) and interventions, this adaptive planning is also related to health care considerations (e.g., may justify longer treatments if therapy goals target several domains of change).
Somatosensory and Brainstem Auditory Evoked Potential Studies in Nontraumatic Coma

We believe that somatosensory and brainstem auditory evoked response studies help in the understanding of the dysfunction of the ascending sensory pathyways at various levels. In some patients where EEGs showed a significant contamination of muscle and background noise, the SEP studies helped to identify the level of dysfunction. The severity of the clinical condition (GCS score) correlated significantly (p = 0.003) with the prolongation of the CCT. Asymmetries in CCTs were more frequent in the stroke group than in the other groups. The presence of asymmetries in CCT in diffuse encephalopathies indicated a variable degree of dysfunction in the ascending sensory pathways, which clinically were not easily identifiable. This fact raised the possibility of either pre-existing lesion(s) or recent insult(s) such as ischemia. The presence or absence of N20 appeared to influence the duration of survival in subgroups. Some degree of difference in duration of survival was noted among the metabolic group with and without N20 potential. The subset of patients with N20 potential survived relatively longer than the group without it. A suggestion of influence was seen in the stroke group, but caution must be exercised because the absence of N20 was compatible with survival. The hypoxic group did not show any difference. A combination of prolonged interpeak EP-N13 and N13-N20 indicated a poor prognosis. A distinct absence of Wave I in BAER limited its usefulness on some occasions. A combination of abnormal interpeak III-V and abnormal CCT seemed to suggest a poor prognosis. Although death generally occurred earlier in the stroke group, age did not seem to influence the mortality in the first 10 days. Similarly, the cause of death also did not seem to influence the course in those 10 days. None of the adult patients survived.
An Energy-aware Scheduling Algorithm in DVFS-enabled Networked Data Centers

In this paper, we propose an adaptive online energy-aware scheduling algorithm by exploiting the reconfiguration capability of a Virtualized Networked Data Centers (VNetDCs) processing large amount of data in parallel. To achieve energy efficiency in such intensive computing scenarios, a joint balanced provisioning and scaling of the networking-plus-computing resources is required. We propose a scheduler that manages both the incoming workload and the VNetDC infrastructure to minimize the communication-plus-computing energy dissipated by processing incoming traffic under hard real-time constraints on the per-job computingplus-communication delays. Specifically, our scheduler can distribute the workload among multiple virtual machines (VMs) and can tune the processor frequencies and the network bandwidth. The energy model used in our scheduler is rather sophisticated and takes into account also the internal/external frequency switching energy costs. Our experiments demonstrate that the proposed scheduler guarantees high quality of service to the users respecting the service level agreements. Furthermore, it attains minimum energy consumptions under two real-world operating conditions: a discrete and finite number of CPU frequencies and not negligible VMs reconfiguration costs. Our results confirm that the overall energy savings of data center can be significantly higher with respect to the existing solutions.
Nitroxyl (HNO): A Reduced Form of Nitric Oxide with Distinct Chemical, Pharmacological, and Therapeutic Properties

Nitroxyl (HNO), the one-electron reduced form of nitric oxide (NO), shows a distinct chemical and biological profile from that of NO. HNO is currently being viewed as a vasodilator and positive inotropic agent that can be used as a potential treatment for heart failure. The ability of HNO to react with thiols and thiol containing proteins is largely used to explain the possible biological actions of HNO. Herein, we summarize different aspects related to HNO including HNO donors, chemistry, biology, and methods used for its detection.
Emotional intelligence and recovering from induced negative emotional state

The aim of the present study was to examine the relationship between emotional intelligence (EI) and recovering from negative emotions induction, using a performance test to measure EI. Sixty seven undergraduates participated in the procedure, which lasted 75 min and was divided into three stages. At Time 1, subjects answered the State-Trait Anxiety Inventory (STAI)-S, Profile of Mood States (POMS)-A, and EI was assessed by Mayer–Salovey–Caruso Emotional Intelligence Test (MSCEIT). At Time 2, negative emotions were induced by nine pictures taken from the International Affective Picture System and participants were asked to complete a second STAI-S and POMS-B questionnaires. At Time 3 participants were allowed to rest doing a distracting task and participants were asked to complete a third STAI-S and POMS-A questionnaires. Results showed that the branches of the MSCEIT emotional facilitation and emotional understanding are related to previous mood states and mood recovery, but not to mood reactivity. This finding contrasts nicely with studies on which emotional recovery was assessed in relation to EI self-reported measures, highlighting the perception and emotional regulation.
Residues of the Human Metapneumovirus Fusion (F) Protein Critical for Its Strain-Related Fusion Phenotype: Implications for the Virus Replication Cycle

ABSTRACT The paramyxovirus F protein promotes fusion of the viral and cell membranes for virus entry, as well as cell-cell fusion for syncytium formation. Most paramyxovirus F proteins are triggered at neutral pH to initiate membrane fusion. Previous studies, however, demonstrated that human metapneumovirus (hMPV) F proteins are triggered at neutral or acidic pH in transfected cells, depending on the strain origin of the F sequences (S. Herfst et al., J. Virol. 82:8891–8895, 2008). We now report an extensive mutational analysis which identifies four variable residues (294, 296, 396, and 404) as the main determinants of the different syncytial phenotypes found among hMPV F proteins. These residues lie near two conserved histidines (H368 and H435) in a three-dimensional (3D) model of the pretriggered hMPV F trimer. Mutagenesis of H368 and H435 indicates that protonation of these histidines (particularly His435) is a key event to destabilize the hMPV F proteins that require low pH for cell-cell fusion. The syncytial phenotypes were reproduced in cells infected with the corresponding hMPV strains. However, the low-pH dependency for syncytium formation could not be related with a virus entry pathway dependent on an acidic environment. It is postulated that low pH may be acting for some hMPV strains as certain destabilizing mutations found in unusual strains of other paramyxoviruses. In any case, the results presented here and those reported by Schowalter et al. (J. Virol. 83:1511–1522, 2009) highlight the relevance of certain residues in the linker region and domain II of the pretriggered hMPV F protein for the process of membrane fusion.
Tailoring sparse multivariable regression techniques for prognostic single‐nucleotide polymorphism signatures

When seeking prognostic information for patients, modern technologies provide a huge amount of genomic measurements as a starting point. For single‐nucleotide polymorphisms (SNPs), there may be more than one million covariates that need to be simultaneously considered with respect to a clinical endpoint. Although the underlying biological problem cannot be solved on the basis of clinical cohorts of only modest size, some important SNPs might still be identified. Sparse multivariable regression techniques have recently become available for automatically identifying prognostic molecular signatures that comprise relatively few covariates and provide reasonable prediction performance. For illustrating how such approaches can be adapted to the specific features of SNP data, we propose different variants of a componentwise likelihood‐based boosting approach. The latter links SNP measurements to a time‐to‐event endpoint by a regression model that is built up in a large number of steps. The variants allow for strategic choices in dealing with SNPs that differ in variance because of their variation in minor allele frequencies. In addition, we propose a heuristic that allows computationally efficient handling of millions of covariates, thus opening the door for incorporating SNP × treatment interactions. We illustrate this using data from patients with acute myeloid leukemia. We judge the resulting models according to prediction error curves and using resampling data sets. We obtain increased stability by moving interpretation from the SNP to the gene level. By considering these different aspects, we outline a more general strategy for linking SNP measurements to a time‐to‐event endpoint by means of sparse multivariable regression models. Copyright © 2012 John Wiley & Sons, Ltd.