Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken

Long noncoding RNAs (lncRNAs) regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in intramuscular preadipocyte differentiation in chicken. Here, we identified lncRNAs in chicken intramuscular preadipocytes at different differentiation stages using RNA sequencing. A total of 1,311,382,604 clean reads and 25,435 lncRNAs were obtained from 12 samples. In total, 7,433 differentially expressed genes (4,698 lncRNAs and 2,735 mRNAs) were identified by pairwise comparison. These 7,433 differentially expressed genes were grouped into 11 clusters based on their expression patterns by K-means clustering. Using Weighted Gene Coexpression Network Analysis, we identified four stage-specific modules positively related to I0, I2, I4, and I6 stages and two stage-specific modules negatively related to I0 and I2 stages, respectively. Many well-known and novel pathways associated with intramuscular preadipocyte differentiation were identified. We also identified hub genes in each stage-specific module and visualized them in Cytoscape. Our analysis revealed many highly-connected genes, including XLOC_058593, BMP3, MYOD1, and LAMP3. This study provides a valuable resource for chicken lncRNA study and improves our understanding of the biology of preadipocyte differentiation in chicken.
Population ecological parameters and biomass of anchovy kilka Clupeonella engrauliformis in the Caspian Sea

Through most of the last century, three endemic kilka species supported major commercial species in the Caspian Sea. It is clear that catches and abundance of all species have changed, but catch and sampling data are limited and stock assessments are inadequate. Recent changes in the Caspian Sea ecosystem have occurred as a consequence of climatic environmental change (sea level change) and ecologic change caused by the invasive ctenophore Mnemiopsis leidyi. This paper examines the effects of these changes on the population biology and biomass of anchovy kilka Clupeonella engrauliformis in Iranian waters of the Caspian of catch, length-weight relationship, von Bertalanffy growth parameters, condition factors, sex ratios, maturity stages determined from ovarian analysis, natural and fishing mortality, age at first capture, and spawning biomass. The instantaneous coefficient of natural mortality was estimated as 0.473/year and the instantaneous coefficient of fishing mortality varied during the 10-year period between 0.541 and 2.690/year. Biomass of anchovy kilka declined from about 186000 t in 1996 to less than 12000 t in 2004. Recent high fishing rates were not sustainable after the introduction of Mnemiopsis, so overfishing is part of the explanation for the collapse of anchovy kilka in the Caspian Sea.
Pediatric red blood cell transfusions increase resource use.

OBJECTIVE To test the hypothesis that red blood cell transfusions are associated with increased resource utilization and mortality in critically ill children. METHODS Five pediatric intensive care units (PICUs) participated in a retrospective, cohort analysis (1996-1999). Children with a hemoglobin value <or=9 g/dL during their PICU stay were enrolled. Data consisted of descriptive information, hemoglobin values, use of blood products, PICU resource use, and hospital mortality rate. RESULTS Among 240 children, 131 were transfused and 109 were not transfused. After controlling for the effects of other variables, transfusion was associated with an increase in days of oxygen use (4.48 +/- 1.37 days), days of mechanical ventilation (4.05 +/- 1.10 days), days of vasoactive agent infusions (1.27 +/- 0.44 days), and an increase of PICU and hospital lengths of stay (4.44 +/- 1.32, and 7.75 +/- 2.36 days, respectively). CONCLUSION Red blood cell transfusions are associated with an increase in resource utilization in critically ill children. The decision to transfuse patients should incorporate this potential morbidity.
Benign partial epilepsy of childhood: a longitudinal neuropsychological and EEG study of cognitive function

The study combined prospective neuropsychological and EEG results of 22 children presenting with typical benign partial epilepsy with rolandic spikes (n=19) and occipital spikes (n=3). The aims were to assess the types of cognitive problems which may be encountered in this population, to evaluate the course of cognitive and learning capacities during the active phase of epilepsy, and to see if there was a correlation with paroxysmal activity on the EEG. Average age at entry in the study was 8.4 years and each child was seen two to four times over a period of 1 to 3 years. EEGs showed persistent spike foci in most cases that worsened in three cases, but there were no continuous spike‐waves during sleep. No child had persistent stagnation, marked fluctuations, or a regression in cognitive abilities. Of 22 children, 21 had average IQ (>80). Eight children had school difficulties requiring special adjustment. No single cognitive profile was identified. Four children had delayed language development and eight children had transient weak scores in one isolated domain (verbal, visuospatial, memory) which improved or normalized during the course of the study with concomitant EEG improvement or normalization. In two of the three children with aggravation of the paroxysmal EEG activity, clinical changes were documented. A proportion of children with typical benign partial epilepsy with rolandic spikes showed mild, varied, and transient cognitive difficulties during the course of their epilepsy, and in most cases this probably had a direct relation with the paroxysmal EEG activity.
Perception and Motivation in Face Recognition

Although humans possess well-developed face processing expertise, face processing is nevertheless subject to a variety of biases. Perhaps the best known of these biases is the Cross-Race Effect—the tendency to have more accurate recognition for same-race than cross-race faces. The current work reviews the evidence for and provides a critical review of theories of the Cross-Race Effect, including perceptual expertise and social cognitive accounts of the bias. The authors conclude that recent hybrid models of the Cross-Race Effect, which combine elements of both perceptual expertise and social cognitive frameworks, provide an opportunity for theoretical synthesis and advancement not afforded by independent expertise or social cognitive models. Finally, the authors suggest future research directions intended to further develop a comprehensive and integrative understanding of biases in face recognition.
Multicenter Standardized 18F-FDG PET Diagnosis of Mild Cognitive Impairment, Alzheimer's Disease, and Other Dementias

This multicenter study examined 18F-FDG PET measures in the differential diagnosis of Alzheimer's disease (AD), frontotemporal dementia (FTD), and dementia with Lewy bodies (DLB) from normal aging and from each other and the relation of disease-specific patterns to mild cognitive impairment (MCI). Methods: We examined the 18F-FDG PET scans of 548 subjects, including 110 healthy elderly individuals (“normals” or NLs), 114 MCI, 199 AD, 98 FTD, and 27 DLB patients, collected at 7 participating centers. Individual PET scans were Z scored using automated voxel-based comparison with generation of disease-specific patterns of cortical and hippocampal 18F-FDG uptake that were then applied to characterize MCI. Results: Standardized disease-specific PET patterns were developed that correctly classified 95% AD, 92% DLB, 94% FTD, and 94% NL. MCI patients showed primarily posterior cingulate cortex and hippocampal hypometabolism (81%), whereas neocortical abnormalities varied according to neuropsychological profiles. An AD PET pattern was observed in 79% MCI with deficits in multiple cognitive domains and 31% amnesic MCI. 18F-FDG PET heterogeneity in MCI with nonmemory deficits ranged from absent hypometabolism to FTD and DLB PET patterns. Conclusion: Standardized automated analysis of 18F-FDG PET scans may provide an objective and sensitive support to the clinical diagnosis in early dementia.
Monitoring and debugging parallel software with BCS-MPI on large-scale clusters

Buffered coscheduled (BCS) MPI is a novel implementation of MPI based on global synchronization of all system activities. BCS-MPI imposes a model where all processes and their communication are tightly scheduled at a very fine granularity. Thus, BCS-MPI provides a system that is much more controllable and deterministic. BCS-MPI leverages this regular behavior to provide a simple yet powerful monitoring and debugging subsystem that streamlines the analysis of parallel software. This subsystem, called monitoring and debugging system (MDS), provides exhaustive process and communication scheduling statistics. This paper covers in detail the design and implementation of the MDS subsystem, and demonstrates how the MDS can be used to monitor and debug not only parallel MPI applications but also the BCS-MPI runtime system itself. Additionally, we show that this functionality need not come at a significant performance loss.
Histopathologic features in esophagomyotomy specimens from patients with achalasia.

BACKGROUND & AIMS A previous study evaluating the morphological features of esophagi resected for endstage achalasia showed marked depletion of myenteric ganglion cells, widespread destruction of nerves, and variable chronic inflammation. The aim of this study was to evaluate the histological features in esophagomyotomy specimens from 11 patients with early achalasia, defined as minimal to moderate esophageal dilation without sigmoid deformity. METHODS The histological features of esophagomyotomy specimens from 11 patients with achalasia were analyzed and compared with the findings of control specimens obtained from 8 patients who underwent esophagectomy for intramucosal adenocarcinoma. RESULTS Control specimens had normal numbers of ganglion cells (0.70-0.91 ganglion cells per high-power field) and minimal inflammation. Three patients with vigorous achalasia had normal ganglion cell numbers (0.79-0.91 ganglion cells per high-power field) and at least mild myenteric inflammation without neural fibrosis. The remaining 8 patients had few or no ganglion cells (0-0.30 ganglion cells per high-power field) and at least mild myenteric inflammation and neural fibrosis. Ganglionitis was found in 2 cases. Ganglion cell number was inversely correlated with degree of myenteric neural fibrosis (P < 0.001). CONCLUSIONS Vigorous achalasia has pathological features that are distinct from classic achalasia. The earliest pathological changes consist of myenteric inflammation with injury to and subsequent loss of ganglion cells and injury to and fibrosis of myenteric nerves.
A randomised, open‐label, crossover study of the dopamine agonist, pramipexole, in patients with sleep bruxism

Sleep bruxism bears several similarities to restless legs syndrome, and a link to changes in central dopamine activity has been considered in both conditions. The dopamine agonist pramipexole is currently indicated for the symptomatic treatment of restless legs. The effect of pramipexole on sleep bruxism was investigated in subjects with ‘probable bruxism’ recruited at the Orofacial Pain Clinic. Thirteen patients underwent polysomnographic recordings, including bilateral masseter electromyographic activity. Following habituation to the recording equipment, a baseline registration was used to confirm bruxism [total episodes per hour, mean 11.3 (6.3)]. Following randomisation, subjects received no treatment or pramipexole titrated from 0.09 to 0.54 mg, o.d. , for 3 weeks according to a crossover procedure. A polysomnographic‐electromyographic registration was performed at the end of each period. Pramipexole was associated with more frequent awakenings and a reduction in rapid eye movement sleep (both P ≤ 0.02). Sleep apnea decreased marginally after pramipexole (apnea–hypopnea index 17.1 compared with control 21.5, P ≤ 0.05). The number of bruxism episodes, phasic, tonic and mixed per hour, remained unchanged after pramipexole [total episodes per hour 12.7 (8.5) and 9.8 (5.2) during pramipexole and control conditions, respectively]. It is concluded, from this pilot study, that sleep bruxism is not affected by the dopaminergic agent, pramipexole.
Skeletal variation as a possible reflection of relatedness within three medieval British populations

Nonmetric traits (NMTs) are often used by osteoarchaeologists in the study of human variation. Some NMTs are affected by environmental factors whereas others are genetic in origin. Such genetic variants have long been used to support the hypotheses on the history and divergence of human populations suggesting that some population groups can be genetically distinguished. However, when genetic NMTs occur in higher than expected frequency these can be interpreted as possible indicators of relatedness. This method is applied to a sample of 977 individuals from the Medieval Poulton Chapel, St. Owen’s Church and Norton Priory Collections, U.K. One hundred and twenty-six cranial and postcranial NMTs were examined to determine: 1) the prevalence, 2) whether there are significant differences between the sexes and/or by age category, 3) if there is variation in mechanical and genetic NMT frequency between the three samples and, 4) to explore possible familial relationships through hierarchal cluster analysis and burial spatial distribution. It is thought that family members are often buried near one another, suggesting that individuals sharing similar genetic NMTs would be buried within close proximity to each other. This thesis has revealed the frequency of 126 NMTs for each sample. No significant differences were reported between the sexes at Poulton Chapel whereas significant differences were noted at St. Owen’s Church and Norton Priory, especially for NMTs considered genetic in origin. For all samples, significant differences were found among the age categories. Intra-populational differences were explored between the three samples. The results of these comparisons highlight that 60 NMTs are shared between the Poulton Chapel and Norton Priory Collection, while St. Owen’s Church only shares few traits with both sites. This suggests a probable geographical north-south divide between the three sites. Finally, the hierarchal cluster analysis identified probable familial relationships for the Norton Priory sample. This is supported by the burial spatial distribution and historical documentary evidence. Unfortunately, this analysis was unsuccessful for St. Owen’s Church with limited results for the Poulton Chapel sample. Future research is required to incorporate aDNA analysis to confirm the likelihood of familial links within these sites, supporting the use of certain NMTs is the use of establishing familial relationships.
Adverse drug reaction reporting by doctors in a developing country: a case study from Ghana.

BACKGROUND Spontaneous adverse drug reaction reporting is the most widely used and cost effective method of monitoring the safety of drugs. This method is heavily afflicted by underreporting by healthcare professionals. The study aims at assessing adverse drug reaction (ADR) reporting rate by doctors, knowledge of the reporting system and attitudes to SADR in the Greater Accra region. METHODS This was a cross sectional survey of 259 doctors randomly selected from 23 hospitals classified as government 199 (76.8%), quasi-governmental 43(16.6%) and private 17 (6.6%) hospitals in the Greater Accra Region of Ghana. Data collection was by self-administered questionnaire from May 5, 2012-July 6, 2012. Descriptive statistics was used to describe the background characteristics of the doctors and the outcome measures like training and reasons for ADR reporting were summarized as frequencies and percentages. RESULTS One-third (27.4%) of doctors surveyed had received previous training on drug safety monitoring and ADR reporting; training and knowledge of the reporting system was found to improve reporting. More than half 154 (59.5%) of the doctors had seen a patient with suspected ADR in the past one year although only 31 (20%) had reported it by completing the SADR reporting form. Doctors working in government hospitals were about 5 times more likely to report than those in private hospitals [OR=4.94, 95%CI (1.55-15.69)]. CONCLUSION Training and knowledge of the ADR reporting system were found to be associated with the likelihood of reporting an ADR. Most of the doctors had not previously received training on ADR reporting.
A Multiscale Particle Filter and Winding Number Constrained for Contour Detection

paper compares the basic contour detection algorithms. A contour detection algorithm which jointly tracks at two scales small pieces of edges called edgelets. This multiscaleedgelet structure naturally embeds semi-local information and is the basic element of the recursive Bayesian modeling. The underlying model is estimated using a sequential Monte Carlo approach, and the soft contour detection map is retrieved from the approximated trajectory distribution. The winding number constrained contour detection (WNCCD) is an energy minimization framework based on winding number constraints. In this framework, both region cues, such as color/texture homogeneity, and contour cues, such as local contrast and continuity, are represented in a joint objective function, which has both region and contour labels. This technique is based on the topological concept of winding number. Using a fast method for winding number computation, a small number of linear constraints are derived to ensure label consistency. Experiments conducted on the Berkeley Segmentation data sets show that the Multi Scale Particle Filter Contour Detector method performs a comparable result with the winding number constrained contour detection method. Keywordsfiltering, sequential Monte Carlo methods, statistical model, multiscale contour detection, BSDS
A prospective, randomized, pivotal trial of a novel extravascular collagen-based closure device compared to manual compression in diagnostic and interventional patients.

OBJECTIVES The RESPECT trial was aimed at evaluating safety/efficacy of a new extravascular closure system in diagnostic (Dx) and interventional (Ix) procedures performed through 6 or 7 Fr introducer sheaths. BACKGROUND Although vascular closure devices (VCDs) have been available for two decades, manual compression (MC) remains the standard of care in many institutions. VCDs have not been shown to have greater safety than MC. METHODS The RESPECT trial was a multicenter, randomized comparison of the Vascade VCD (Cardiva Medical, Inc) versus MC in Dx and Ix patients undergoing femoral access. Endpoints included time to hemostasis (TTH), time to ambulation (TTA), time to discharge eligibility (TTDe), device and procedure success, major and minor complications. Subjects were randomized 2:1 (Vascade vs MC). RESULTS A total of 420 patients were enrolled (211 Dx, 209 Ix). Mean age was 62 ± 11 years and 29% were female. For Ix Vascade/MC patients, 77%/69% received bivalirudin, 27%/26% received heparin, and 8%/3% received glycoprotein IIb/IIIa inhibitors, respectively. Patients were followed for 30 ± 7 days. A total of 415 subjects (98.8%) completed follow-up. TTH was 3.0 minutes (range, 0.6-31.6 minutes) for Vascade vs 20.0 minutes (range, 0.0-97.0 minutes) for MC; TTA was 3.2 hours (range, 1.0-78.0 hours) for Vascade vs. 5.2 hours (range, 1.7-22.8 hours) for MC; and TTDe was 3.6 hours (range, 1.4-78.4 hours) for Vascade vs. 5.7 hours (range, 2.2-23.2 hours) for MC. Device and procedure success rates were 98% for Vascade and 100% for MC. Minor events were 1.1% for Vascade and 7% for MC. No major access-site related complications were reported in either arm. CONCLUSION Despite high percentage of bivalirudin use, there were no major access-site related complications in either arm. Vascade use reduced rates of minor access-site related complications, and significantly shortened TTH, TTA, and TTDe compared to MC.
The microbiota link to irritable bowel syndrome

Irritable Bowel Syndrome (IBS) is a clinically heterogeneous disorder which is likely to involve a number of causative factors. The contribution of altered intestinal microbiota composition or function to this disorder is controversial, and is the subject of much current research. Until recently, the technical limitations of the methodologies available have not permitted an adequate survey of low-abundance microbial species. Recent technological developments have enabled the analysis of the global population of the microbiome using high through-put, culture independent, 16S rRNA amplicon pyrosequencing. Using these new methodologies, we are able to gain important biological insights into the link between functional bowel disorders and the microbiome. This addendum contextualizes and summarizes the results of these studies, and defines the future challenges and opportunities in the field.
Maximal lactate-steady-state independent of performance.

PURPOSE The maximal lactate steady state (MLSS) corresponds to the highest workload that can be maintained over time without a continual blood lactate accumulation. MLSS and MLSS intensity have been speculated to depend on performance. Experimental proof of this hypothesis is missing. METHODS 33 male subjects (age: 23.7 +/- 5.5 yr, height: 181.2 +/- 5.3 cm, body mass: 73.4 +/- 6.4 kg) performed an exhausting incremental load test to measure peak workload and three to six 30-min constant load tests on a cycle ergometer to determine MLSS. RESULTS MLSS (4.9 +/- 1.4 mmol x L(-1)) was independent of MLSS workload (3.4 +/- 0.6 W x kg(-1)) and peak workload (4.8 +/- 0.6 W x kg(-1)). MLSS intensity (71.1 +/- 6.7%) did not correlate with peak workload or MLSS (P > 0.05). A positive correlation was found between peak workload and MLSS workload (r = 0.82, P < 0.001). CONCLUSIONS MLSS and MLSS intensity are independent of performance but subjects with higher maximum performance have higher MLSS workloads. The combination of various fitness related effects on both, the production and the disappearance of lactate during exercise, may explain that different MLSS workloads coincide with similar levels of MLSS and MLSS intensity.
Ku80 removal from DNA through double strand break–induced ubiquitylation

The Ku70/Ku80 heterodimer, or Ku, is the central component of the nonhomologous end joining (NHEJ) pathway of double strand break (DSB) repair. Because Ku forms a ring through which the DSB threads, it likely becomes topologically attached to DNA during repair. The mechanism for its removal was unknown. Using a method to identify proteins recruited to DSBs in Xenopus laevis egg extract, we show that DSB-containing DNAs accumulate members of the Skp1–Cul1–F-box complex and K48-linked polyubiquitylated proteins in addition to known repair proteins. We demonstrate that Ku80 is degraded in response to DSBs in a ubiquitin-mediated manner. Strikingly, K48-linked polyubiquitylation, but not proteasomal degradation, is required for the efficient removal of Ku80 from DNA. This removal is DNA length dependent, as Ku80 is retained on duplex oligonucleotides. Finally, NHEJ completion and removal of Ku80 from DNA are independent from one another. We propose that DSB-induced ubiquitylation of Ku80 provides a mechanism to efficiently eliminate Ku from DNA for pre- and postrepair processes.