Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids

Significance Understanding molecular events during virus assembly and genome packaging is important for understanding viral life cycles, and the functioning of other protein–nucleic acid machines. The model system developed for the thermophilic bacteriophage P23-45 offers advantages over other systems. Cryo-EM reconstructions reveal modifications to a canonical capsid protein fold, resulting in capsids that are abnormally large for this virus class. Structural information on the portal protein, through which the genome is packaged, demonstrates that the capsid influences the portal’s conformation. This has implications for understanding how processes inside and outside the capsid can be coordinated. Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermostable bacteriophage, P23-45 of Thermus thermophilus. Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-Å and 4.4-Å resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-Å resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.
Qualitative and quantitative analysis of catechin and quercetin in flavonoids extracted from Rosa roxburghii Tratt

Purpose To perform a qualitative and quantitative analysis of catechin and quercetin in flavonoids extracted from Rosa roxburghii Tratt. Methods Total flavonoids were determined using ultraviolet spectrophotometry (UV) at 500 nm. The optimal gradient program started with 15 % methanol and was kept within a period of 0 – 20 min, while 25 % methanol was kept within 20 – 33 min. Subsequently, the concentration of methanol was reduced to 15 % and was held for 10 min until the next injection. Mass spectrometry spray voltage was 4,000 V, ionization temperature 350 °C, atomizer pressure 35 psi, nitrogen flow rate 8 L/min, and mass scan range 200 – 800 m/z. The detection wavelength used for catechin and quercetin was 270 and 368 nm, respectively. Results Based on the UV results, Rosa roxburghii Tratt content was 73.85 %, which is in agreement with the national standard. Liquid chromatography-mass spectrometry (LC-MS) results indicate that Rosa roxburghii Tratt flavonoids contained quercetin, 34.26 %, with relative standard deviation (RSD) of 2.88 % and catechin content of 2.97 % with RSD of 1.49 %. Conclusion The proposed measurement method for determining the content of flavonoids in Rosa roxburghii Tratt has the advantage of simplicity, feasibility, good repeatability, and rapid and accurate analysis.
Impact of rotavirus vaccination on rotavirus genotype distribution and diversity in England, September 2006 to August 2016

Introduction Rotavirus vaccination with the live-attenuated monovalent (a G1P[8] human rotavirus strain) two-dose Rotarix vaccine was introduced in England in July 2013. Since then, there have been significant reductions in rotavirus gastroenteritis incidence. Aim We assessed the vaccine’s impact on rotavirus genotype distribution and diversity 3 years post-vaccine introduction. Methods Epidemiological and microbiological data on genotyped rotavirus-positive samples between September 2006 and August 2016 were supplied by EuroRotaNet and Public Health England. Multinomial multivariable logistic regression adjusting for year, season and age was used to quantify changes in genotype prevalence in the vaccine period. Genotype diversity was measured using the Shannon’s index (H′) and Simpson’s index of diversity (D). Results We analysed genotypes from 8,044 faecal samples. In the pre-vaccine era, G1P[8] was most prevalent, ranging from 39% (411/1,057) to 74% (527/709) per year. In the vaccine era, G1P[8] prevalence declined each season (35%, 231/654; 12%, 154/1,257; 5%, 34/726) and genotype diversity increased significantly in 6–59 months old children (H’ p < 0.001: D p < 0.001). In multinomial analysis, G2P[4] (adjusted multinomial odds ratio (aMOR): 9.51; 95% confidence interval (CI): 7.02–12.90), G3P[8] (aMOR: 2.83; 95% CI: 2.17–3.81), G12P[8] (aMOR: 2.46; 95% CI: 1.62–3.73) and G4P[8] (aMOR: 1.42; 95% CI: 1.02–1.96) significantly increased relative to G1P[8]. Conclusions In the context of reduced rotavirus disease incidence, genotype diversity has increased, with a relative change in the dominant genotype from G1P[8] to G2P[4] after vaccine introduction. These changes will need continued surveillance as the number and age of vaccinated birth cohorts increase in the future.
Acute Psychotic Syndrome in a Male Adolescent with Succinic Semialdehyde Dehydrogenase Deficiency

SSADH deficiency (Semialdehyde Dehydrogenase Deficiency) is inherited in an autosomal recessive fashion, caused by an error in a single DNA gene. Being a recessive disorder, the disease can only occur when a person has two copies of the gene and thus it can only be inherited if both parents are carriers of the gene. It is believed that the genetic basis for SSADH deficiency resides in the human ALDH5A1 gene which maps to chromosome 6p22.1 The symptoms of SSADH deficiency fall into three primary categories: neurological, psychiatric, and ocular. The most constant features are developmental delay, hypotonia and intellectual disability. Nearly half of the patients manifest ataxia, behavior problems, seizures, and hyporeflexia.2 This is a case of a young male adolescent who was diagnosed with a mild intellectual disability and psychomotor developmental delay; he walked at 3 years of age, spoke at the age of 4 years, and joined kindergarten as a 6-year-old and the primary school as an 8-year-old. At the age of two years the diagnosis of SSADH deficiency was established after a sample of lymphocytes was sent to the University Hospital VU Department of Pediatrics in Amsterdam where specific examinations were carried out. He followed a program of speech therapy and physiotherapy. In the school he socialized well and he finished the 9-year obligatory education, having the benefit of special support. At the age of 16 he showed psychomotor agitation and insomnia and suddenly ran away. He wandered around for two days and finally the police found him in a park. He was quite violent, kicking and swearing. Print ISSN 1738-3684 / On-line ISSN 1976-3026 OPEN ACCESS
Esophagogastric junction outflow obstruction successfully treated with laparoscopic Heller myotomy and Dor fundoplication: First case report in the literature

BACKGROUND Esophagogastric junction outflow obstruction (EGJOO) is a rare syndrome, characterized by an elevation of the integrated relaxation pressure of the lower esophageal sphincter, not accompanied by alterations in esophageal motility that may lead to the criteria for achalasia. We were unable to find any prior report of the combination of Heller myotomy with anterior partial fundoplication (Dor) as the treatment for EGJOO. We herein report a case of EGJOO treated with laparoscopic Heller myotomy combined with Dor fundoplication. CASE SUMMARY A 26-year-old man presented with a 3-year history of solid dysphagia and a 30-kg weight loss. He was treated with oral nifedipine, isosorbide, and omeprazole, without resolution of symptoms. An upper gastrointestinal series (barium swallow) revealed a “bird’s beak” sign. Esophagogastroduodenoscopy was positive for Los Angeles grade A peptic esophagitis. High-resolution esophageal manometry was compatible with EGJOO. Esophageal pH monitoring showed pathological acid reflux both in orthostatic and decubitus position. An 8-cm laparoscopic Heller myotomy combined with an anterior 220° Dor fundoplication was performed. Solid diet was introduced on postoperative day 2, and the patient was discharged home the same day. At 17-mo follow-up, he reported no symptoms. Barium swallow was compatible with complete radiologic resolution. Both esophageal manometry and upper endoscopy showed normal findings 9 mo after the operation. CONCLUSION Surgical treatment with Heller myotomy and Dor fundoplication is a potential treatment option for EGJOO refractory to medical treatment.
A population-based study on prevalence and risk factors of gastroesophageal reflux disease in the Tibet Autonomous Region, China

Objective To investigate the prevalence and risk factors of gastroesophageal reflux disease (GERD) in the Tibet Autonomous Region, China. Methods In this cross-sectional study, a stratified random sampling method was used for collecting samples in the Tibet Autonomous Region. A total of 10,000 individuals were selected from October 2016 to June 2017. A previously-published, validated questionnaire including six items related to the symptoms of GERD was used for evaluating GERD. In addition, basic demographic data, lifestyle, dietary habits, medical history and family history of GERD were investigated to identify risk factors of GERD. Results A total of 5,680 completed questionnaires were collected and analyzed. The prevalence of GERD in this area was 10.8%. Age (30–40 years vs. under 18 years, odds ratio (OR): 3.025; 40–50 years vs. under 18 years, OR: 4.484), education level (high school vs. primary, OR: 0.698; university vs. primary, OR: 2.804), ethnic group (Han vs. Tibetan, OR: 0.230; others vs. Tibetan, OR: 0.304), altitude of residence (4.0–4.5 km vs. 2.5–3.0 km, OR: 2.469), length of residence (<5 years vs. ≥5 years, OR: 2.218), Tibetan sweet tea (yes vs. no, OR: 2.158), Tibetan barley wine (yes vs. no, OR: 1.271), Tibetan dried meat (yes vs. no, OR: 1.278) and staying up late (yes vs. no, OR: 1.223) were significantly (all P < 0.05) and independently associated with GERD. Conclusions The prevalence of GERD is high in the Tibet Autonomous Region, China. Geographic conditions, ethnic group and lifestyle are risk factors for GERD.
Incidence of acute kidney disease after receiving hematopoietic stem cell transplantation: a single-center retrospective study

Background Previous reports have shown that acute kidney injury (AKI) is common after hematopoietic stem cell transplantation (HSCT), which is a crucial treatment for patients with hematological disorders. AKI could increase mortality and induce adverse effects including the development of chronic kidney disease. The incidence of AKI in association with HSCT reportedly varies significantly because several definitions of AKI have been adopted. Acute kidney disease (AKD) is a new concept that can clinically define both AKI and persistent decreases in glomerular filtration rate (GFR) state. We conducted a retrospective cohort study to determine the incidence of AKD after HSCT. Methods This study included 108 patients aged between 16 and 70 years undergoing HSCT. In this study, AKD included clinical condition of AKI or subacute decreases in GFR. AKI was defined according to the Kidney Disease: Improving Global Outcomes guidelines based on serum creatinine. However, urine output data were not included to define AKI because the database lacked some of these data. Comparisons were made between groups using the Mann–Whitney U test. Results Acute kidney disease occurred in 17 patients (15.7%). There were significant differences between the AKD and non-AKD with respect to ABO-incompatible HSCT (p = 0.001) and incidence of acute graft versus host disease (GVHD) after HSCT (p < 0.001). The 100-day overall survival of patients with AKD and without AKD after HSCT was 70.6% and 79.8%, respectively (p = 0.409). Discussion ABO-incompatible HSCT and acute GVHD after HSCT were risk factors for the incidence of AKD. However, we could not find a significant association between AKD after HSCT and mortality.
Recruitment of cognitive control regions during effortful self-control is associated with altered brain activity in control and reward systems in dieters during subsequent exposure to food commercials

Engaging in effortful self-control can sometimes impair people’s ability to resist subsequent temptations. Existing research has shown that when chronic dieters’ self-regulatory capacity is challenged by prior exertion of effort, they demonstrate disinhibited eating and altered patterns of brain activity when exposed to food cues. However, the relationship between brain activity during self-control exertion and subsequent food cue exposure remains unclear. In the present study, we investigated whether individual differences in recruitment of cognitive control regions during a difficult response inhibition task are associated with a failure to regulate neural responses to rewarding food cues in a subsequent task in a cohort of 27 female dieters. During self-control exertion, participants recruited regions commonly associated with inhibitory control, including dorsolateral prefrontal cortex (DLPFC). Those dieters with higher DLPFC activity during the initial self-control task showed an altered balance of food cue elicited activity in regions associated with reward and self-control, namely: greater reward-related activity and less recruitment of the frontoparietal control network. These findings suggest that some dieters may be more susceptible to the effects of self-control exertion than others and, whether due to limited capacity or changes in motivation, these dieters subsequently fail to engage control regions that may otherwise modulate activity associated with craving and reward.
PD‐1/PD‐L1 Blockade Therapy in Advanced Non‐Small‐Cell Lung Cancer: Current Status and Future Directions

This article summarizes the latest clinical applications of PD‐1/PD‐L1 blockade therapy in advanced non‐small cell lung cancer (NSCLC) worldwide and in China, reporting the bottlenecks related to the use of this therapy in clinic. An exploration of the underlying mechanism of PD‐1/PD‐L1 blockade therapy and biomarker identification will maximize the application of immune checkpoint inhibitors in advanced NSCLC and facilitate bedside‐to‐bench studies in cancer immunotherapy.
Evaluating forearm vascular adaptations to training interventions: an in vivo and in vitro approach

Exercise training promotes a beneficial endothelial cell (EC) phenotype and results in conduit vessel adaptation. The specific underlying mechanisms have been proposed (shear stress, circumferential stress, hypoxia, metabolic) but are yet to be fully elucidated. This thesis investigated the predominant stimuli responsible for conduit vessel adaptation with training. Further, it developed a method of in situ EC extraction to allow for determination of the cellular and molecular mechanisms underpinning these adaptations. The methodology utilised two-dimensional (2D) Doppler ultrasound, strain gauge plethysmography, immunocytochemistry and RT-qPCR to provide insight in to vascular characteristics, predominantly of the brachial artery and peripheral EC. Long-term repeated isometric forearm muscle contractions as performed by well-trained rock climbers promoted greater resting, peak (in response to 5 min ischaemia) and maximal (in response to ischaemic exercise) brachial artery diameters compared with controls. This structural response is dependent upon confounders associated with exercise additional to shear stress as evidenced by the lack of brachial artery remodelling in response to 8 weeks of ischaemic preconditioning (IPC). A transient increase in flow-mediated dilation (FMD)% was observed following 6 weeks exposure to IPC, which became significant when controlled for baseline artery diameter, despite an absence of augmentation following long-term (≥ 8 weeks) exposure to a shear stimulus. This is in line with the suggested timeline of conduit vessel adaptation to exercise training of a transient increase in function at 2-4 weeks. Underpinning molecular mechanisms responsible were not determined but may be further investigated given that the endovascular biopsy technique was developed and improved in this thesis. The endovascular biopsy successfully yields approximately 2100 ± 1700 EC per sample, providing sufficient material for determination of expression of both mRNA (RT-qPCR) and protein (immunocytochemistry). Specifically, type 2 diabetics (T2DM) with symptomatic cardiac abnormalities exhibited augmented eNOS mRNA and protein in brachial artery EC as compared with non-diabetic controls with symptomatic cardiac abnormalities. In conclusion, this thesis demonstrates that although shear stress promotes a transient trend for enhancement in function of the peripheral conduit arteries, additional factors are required for long-term structural adaptations. Further, the endovascular biopsy technique offers a novel method of extracting and analysing EC for genes and proteins of interest to vascular health. The use of this technique to decipher the underlying cellular and molecular mechanisms involved in vascular adaptations with exercise requires further investigation.
Perceptions and practices regarding menstruation: A comparative study in urban and rural adolescent girls.

Adolescence in girls is a turbulent period which includes stressful events like menarche considered as a landmark of female puberty. One might expect that menarche will be positively received by young women; however negative responses such as shame fear anxiety and depression are more common. The manner in which a girl learns about menstruation and its associated changes may have an impact on her response to the event of menarche. Myth mystery and superstition have long enveloped the facts about menstruation. In India even mere mention of the topic has been a taboo in the past and even to this date the cultural and social influences appear to be hurdle for advancement of the knowledge of the subject. The social practices about menstruation make girl child feel subnormal and may hamper her development. Menarche may remain a traumatic event for her unless she is prepared for it. Adolescent girls constitute a vulnerable group particularly in India where female child is neglected one. Most studies on female adolescence focus on the gynecological problems but problems of nutritional and psychological origin cannot be ignored. Hence present study was undertaken to assess the 1) source of information regarding menstruation 2) reaction to first and subsequent menstruation 3) taboos and restrictions as result of menstruation and 4) hygiene practiced during menstruation. (excerpt)
En cabras subtropicales paridas en el otoño, los días largos artificiales incrementan la produccion de leche, la proporción de hembras que ovulan y el peso de las crías al destete

Objetivo general Investigar en las cabras subtropicales paridas en el otono, la influencia que tienen los dias largos artificiales sobre la lactancia, la actividad ovarica postparto y el crecimiento de las crias. Objetivos especificos Experimento 1 El objetivo fue para determinar si los dias largos artificiales incrementan la produccion de leche en las cabras subtropicales paridas en el otono ordenadas una o dos veces al dia. Experimento 2 Determinar si los dias largos artificiales pueden incrementar la produccion de leche en las cabras subtropicales manejadas bajo condiciones de pastoreo extensivo o si es necesaria una complementacion nutricional para observar dicho efecto. Experimento 3 Investigar si la prolongada exposicion a un fotoperiodo de dias largos artificiales en las cabras del subtropico que paren en el otono induce el establecimiento de un estado refractario a los dias largos artificiales y asi, el reinicio de la actividad ovarica postparto. Experimento 4 Determinar si la exposicion a un fotoperiodo de dia largo artificial puede incrementar la ganancia de peso diaria y el peso al destete de los cabritos nacidos en el otono cuando son amamantados o no por sus madres.
Web-Based Research Using Delphi Methodology to Explore the Discrepancy in Qualitative Research

Purpose: The purpose of this study was to identify the key discrepancies in the qualitative research approach and its effect on research outcomes using Delphi web technique. Methods: An electronic questionnaire was used to collect experts’ opinions over two rounds. A panel of 24 experts filled questionnaire in the first round and 17 of them continued in the second round. Answers to open-ended questions were tabulated, summarized and analyzed thematically generating 44 items. Participants then were asked to rate their level of agreement with these item statements in the second round. Results: Scholars used and viewed the same qualitative approaches differently with a percentage of 76.5%. The paradigm for qualitative research is not well defined with a percentage of 70.6%. Every book and every published research article seems to describe qualitative methods differently. Furthermore, schools of qualitative research defined assumptions and their purposes differently. Conclusion: Recently there is an increase in using qualitative research methods in nursing. For novice researchers, a qualitative approach is not always clear. The experts were from different countries with diverse experiences and reached the consensus on some topics. This survey implies that the qualitative textbooks need to be more consistent with more simplification of the ambiguous terms.
Safety, nutrition, and health in early education

Safety, Nutrition, and Health in Early Education, 3E covers the four major subject areas of safety, nutrition, health, and special topics, emphasizes the realities of working with children, and provides valuable information for those who seek to provide optimum environments for children. This new edition aids in building awareness and understanding of cultural competence while working with children and families from diverse backgrounds. New to this edition is expanded coverage of children with special needs; updated information on nutrition, including the new My Pyramid Food Guidance System; and practical information on creating linkages with children, families, staff, community, and community resources. Special features include vignettes; checklists; case studies; Pause for Reflection, which offers students a time to pause and examine how they feel about specific topics; Reality Checks with Checkpoints that allow readers to critically examine the information presented; and new tables, charts, photos, and graphics. In addition, special attention is given to bullying, disaster planning for human-generated disasters, how America eats, the impact of war and terrorism on children, Autism, Fetal Alcohol Syndrome, and being at risk for preventable diseases. This text combines basic information and theory, as well as practical applications, resources, and other early education skills needed for working with children, families, and staff.