Miracle-dz/UniFAR-FTUs huggingface dataset:
Shape and evolution of thermostable protein structure

Organisms evolved at high temperatures must maintain their proteins' structures in the face of increased thermal disorder. This challenge results in differences in residue utilization and overall structure. Focusing on thermostable/mesostable pairs of homologous structures, we have examined these differences using novel geometric measures: specifically burial depth (distance from the molecular surface to each atom) and travel depth (distance from the convex hull to the molecular surface that avoids the protein interior). These along with common metrics like packing and Wadell Sphericity are used to gain insight into the constraints experienced by thermophiles. Mean travel depth of hyperthermostable proteins is significantly less than that of their mesostable counterparts, indicating smaller, less numerous and less deep pockets. The mean burial depth of hyperthermostable proteins is significantly higher than that of mesostable proteins indicating that they bury more atoms further from the surface. The burial depth can also be tracked on the individual residue level, adding a finer level of detail to the standard exposed surface area analysis. Hyperthermostable proteins for the first time are shown to be more spherical than their mesostable homologues, regardless of when and how they adapted to extreme temperature. Additionally, residue specific burial depth examinations reveal that charged residues stay unburied, most other residues are slightly more buried and Alanine is more significantly buried in hyperthermostable proteins. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Transcription Factor FnrP from Paracoccus denitrificans Contains an Iron-Sulfur Cluster and Is Activated by Anoxia: Identification of Essential Cysteine Residues

ABSTRACT The Paracoccus denitrificans transcription factor FnrP has been characterized using artificial FNR-dependent promoter-lacZ fusion plasmids in Escherichia coli. FnrP can activate both class I and class II FNR-dependent promoters in response to anoxia but shows a marked preference for the class II promoter, where the FNR binding site is centered at −41.5 with respect to the transcription start site. FnrP was found to be inactive in an iscS mutant in vivo, demonstrating a requirement for cysteine desulfurase activity to assemble an iron-sulfur cluster in FnrP. Accordingly, an iron-sulfur cluster could be reconstituted into the purified protein in vitro using cysteine desulfurase, ferrous ions, and cysteine. Thus, FnrP is a true orthologue of FNR from E. coli and switches on target genes in response to anoxia. Inactivation of FnrP by oxygen very likely involves the oxidative disassembly of an iron-sulfur cluster. Possible ligands for the iron-sulfur cluster were identified by substituting each of the seven cysteine residues with serine and characterizing the altered proteins in vivo. Four substituted proteins showed activities less than 5% of the wild type, and so identify the four cysteines (Cys-14, Cys-17, Cys-25, and Cys-113) that are most likely to be involved in cluster ligation. The effects of N-oxides, NO-releasing compounds and a nitrosating agent on FNR and FnrP activity were investigated in vivo using the reporter system. Both proteins are very sensitive to the inclusion of sodium nitroprusside (a source of NO+) in defined growth media but are only moderately sensitive to those sources of NO that were tested.
Glucagon and insulin responses after ingestion of different amounts of intact and hydrolysed proteins

Ingestion of dietary protein is known to induce both insulin and glucagon secretion. These responses may be affected by the dose and the form (intact or hydrolysed) in which protein is ingested. The aim of the study was to investigate the effect of different amounts of intact protein and protein hydrolysate of a vegetable (soya) and animal (whey) protein on insulin and glucagon responses and to study the effect of increasing protein loads for both intact protein and protein hydrolysate in man. The study employed a repeated-measures design with Latin-square randomisation and single-blind trials. Twelve healthy non-obese males ingested three doses (0·3, 0·4 and 0·6 g/kg body weight) of intact soya protein (SPI) and soya protein hydrolysate (SPH). Another group of twelve healthy male subjects ingested three doses (0·3, 0·4 and 0·6 g/kg body weight) of intact whey protein (WPI) and whey protein hydrolysate (WPH). Blood was sampled before (t = 0) and 15, 30, 60, 90 and 120 min after protein ingestion for insulin, glucagon and glucose determination. SPI induced a higher total area under the curve for insulin and glucagon than SPH while no difference between WPI and WPH was found. Insulin and glucagon responses increased with increasing protein load for SPI, SPH, WPI and WPH, but the effect was more pronounced for glucagon. A higher dose of protein or its hydrolysate will result in a lower insulin:glucagon ratio, an important parameter for the control of postprandial substrate metabolism. In conclusion, insulin and glucagon responses were protein and hydrolysate specific.
Noradrenergic and serotonergic receptor system function in panic disorder and depression

Recent studies which have utilized the administration of neurotransmitter agonists and antagonists to study presynaptic and postsynaptic receptor system function in panic disorder and major depression are reviewed. In panic disorder, patients have been found to be overly sensitive to the alpha‐2 adrenergic agonist clonidine, and the alpha‐2 adrenergic antagonist yohimbine, but they have relatively normal responses to tryptophan, the precursor of serotonin, and MCPP, a directly acting serotonin agonist. In depression, patients appear to have relatively normal responses to clonidine and yohimbine except for some supersensitivity to yohimbine effects on blood pressure and subjective symptoms. In contrast to the panic disorder patients, depressed patients demonstrate a neuroendocrine subsensitivity to tryptophan. Taken together, these studies suggest a relative abnormality in the alpha‐2 adrenergic regulation of the noradrenergic system in panic disorder and a subsensitivity of the serotonergic system in depression. The pharmacologic treatment response in panic disorder and depression is similar in that both conditions respond to tricyclic antidepressants and monoamine oxidase inhibitors, but different in that panic disorder does not respond to atypical antidepressants such as trazodone and bupropion, but does respond to benzodiazepines, in contrast to depression. The possible mechanisms involved in producing these findings and the methods to more fully study possible receptor system abnormalities in these illnesses are discussed.
Effects of bovine somatotropin on dry matter intake, milk yield and body temperature in Holstein and Jersey cows during heat stress.

Thirty-one lactating Holstein and Jersey cows were used to determine the effect of daily injections of 0 or 20 mg of recombinant bST in hot, humid weather. The comparison period lasted 80 d, from mid-June through August. The maximum and minimum ambient temperature and relative humidity averaged 34.6 and 22.2 degrees C and 100 and 59.8%, respectively. Body temperatures of somatotropin-treated Holsteins were elevated over controls by . 2 and . 3 degrees C at the a.m. and p.m. milkings, respectively, whereas corresponding treatment effects for Jerseys were . 5 and . 6 degrees C, thus demonstrating a breed by treatment interaction. The response of milk and FCM yields and apparent efficiency of production to somatotropin administration depended on the level of production prior to treatment. Cows at low pretreatment production increased milk and FCM yields to a greater degree than did cows at higher production. A breed by treatment interaction showed that Holsteins increased milk and FCM yields more than Jerseys upon administration of somatotropin. Intake of DM was not affected by treatment. Cows administered bST lost BW and condition score. Greater heat stress was associated with the higher milk production of cows administered bST.
Coping With Violence

Interpersonal violence is present at all levels of influence in the social ecology and can have comprehensive and devastating effects on child and adolescent development through multiple simultaneous channels of exposure. Children’s experiences with violence have been linked with a range of behavioral and mental health difficulties including posttraumatic stress disorder and aggressive behavior. In this article, we offer a conceptual framework delineating the ways in which children and adolescents might encounter violence, and a theoretical integration describing how violence might impact mental and behavioral health outcomes through short- and long-term processes. We propose that coping reactions are fundamental to the enduring effects of violence exposure on their psychosocial development and functioning. Finally, we discuss the manner in which coping efforts can support resilience among children exposed to violence and suggest new directions for research and preventive intervention aimed at optimizing outcomes for children at risk of exposure.
Origins of R2∗ orientation dependence in gray and white matter

Significance Differences in the apparent transverse relaxation rate () between tissues are exploited in numerous magnetic resonance imaging (MRI) techniques from functional MRI to susceptibility weighted imaging. Recent results show a surprising dependence of tissue on orientation. This study demonstrates that the orientation dependence of in both white and cortical gray matter has a sinusoidal dependence on tissue orientation and a linear dependence on the perturber volume fraction (measured by quantitative histology). A biophysical model is used to relate the observed orientation dependence to the local Larmor frequency shift and volume magnetic susceptibility of the tissue. Estimates of the apparent transverse relaxation rate () can be used to quantify important properties of biological tissue. Surprisingly, the mechanism of dependence on tissue orientation is not well understood. The primary goal of this paper was to characterize orientation dependence of in gray and white matter and relate it to independent measurements of two other susceptibility based parameters: the local Larmor frequency shift (fL) and quantitative volume magnetic susceptibility (Δχ). Through this comparative analysis we calculated scaling relations quantifying (reversible contribution to the transverse relaxation rate from local field inhomogeneities) in a voxel given measurements of the local Larmor frequency shift. is a measure of both perturber geometry and density and is related to tissue microstructure. Additionally, two methods (the Generalized Lorentzian model and iterative dipole inversion) for calculating Δχ were compared in gray and white matter. The value of Δχ derived from fitting the Generalized Lorentzian model was then connected to the observed orientation dependence using image-registered optical density measurements from histochemical staining. Our results demonstrate that the and fL of white and cortical gray matter are well described by a sinusoidal dependence on the orientation of the tissue and a linear dependence on the volume fraction of myelin in the tissue. In deep brain gray matter structures, where there is no obvious symmetry axis, and fL have no orientation dependence but retain a linear dependence on tissue iron concentration and hence Δχ.
Out-of-hours palliative care: a qualitative study of cancer patients, carers and professionals.

BACKGROUND New out-of-hours healthcare services in the UK are intended to offer simple, convenient access and effective triage. They may be unsatisfactory for patients with complex needs, where continuity of care is important. AIM To explore the experiences and perceptions of out-of-hours care of patients with advanced cancer, and with their informal and professional carers. DESIGN OF STUDY Qualitative, community-based study using in-depth interviews, focus groups and telephone interviews. SETTING Urban, semi-urban and rural communities in three areas of Scotland. METHOD Interviews with 36 patients with advanced cancer who had recently used out-of-hours services, and/or their carers, with eight focus groups with patients and carers and 50 telephone interviews with the patient's GP and other key professionals. RESULTS Patients and carers had difficulty deciding whether to call out-of-hours services, due to anxiety about the legitimacy of need, reluctance to bother the doctor, and perceptions of triage as blocking access to care and out-of-hours care as impersonal. Positive experiences related to effective planning, particularly transfer of information, and empathic responses from staff. Professionals expressed concern about delivering good palliative care within the constraints of a generic acute service, and problems accessing other health and social care services. CONCLUSIONS Service configuration and access to care is based predominantly on acute illness situations and biomedical criteria. These do not take account of the complex needs associated with palliative and end-of-life care. Specific arrangements are needed to ensure that appropriately resourced and integrated out-of-hours care is made accessible to such patient groups.
Voting and Values: Grassroots Elections in Rural and Urban China

Authoritarian leaders often claim that they promote democratic institutions such as elections and democratic values. In China, the central propaganda often promotes the right and duty of citizens to vote in local elections as well as the importance of citizens’ input into the policy making process. However, there is often a gap between government rhetoric and reality. In this article, we use the China General Social Survey (CGSS) 2013 to evaluate the determinants of voting in local elections and democratic values (attitudes) in rural and urban China. The results show that respondents with higher education tend to have lower levels of democratic values and participate less in local elections, but respondents with only compulsory education are more likely to display democratic orientations and vote. This suggests the relative success as well as the limits of authoritarian democratic propaganda.
Combat Exposure in Early Adulthood Interacts with Recent Stressors to Predict PTSD in Aging Male Veterans.

PURPOSE OF THE STUDY Combat is a risk factor for posttraumatic stress disorder (PTSD); however, less is known about how exposure to combat in early adulthood may contribute to the development of PTSD as the individual ages. Prior exposure to trauma may "sensitize" people to respond more intensely to subsequent stressors. Further, aging initiates new challenges that may undermine previous coping strategies. Over the life course combat veterans may be more reactive to new stressors and thus be more vulnerable to PTSD. DESIGN AND METHODS This study draws on the two waves of the National Comorbidity Survey (NCS-1) and NCS-2 (10-year follow-up). Participants were male (noncombat N = 620 and combat N = 107) and 50-65 years of age at Wave-2. At baseline, participants were assessed for exposure to wartime combat, number of Diagnostic and Statistical Manual of Mental Disorders (DSM) diagnoses in the past year, and life-time PTSD. At follow-up, PTSD occurring between waves was determined. A measure of recent life stressors was also obtained. RESULTS Using logistic regression analyses, combat predicted PTSD at follow-up (controlling for baseline demographics, number of DSM diagnoses in the past year, life-time PTSD). Recent life stressors were also associated with PTSD. Importantly, the effect of combat on PTSD was significant at high levels, but not low levels, of recent life stress. IMPLICATIONS Veterans who have experienced combat may be more reactive to new stressors, and in turn be more vulnerable to PTSD. Combat veterans should be regularly assessed for current stressors and PTSD.
Research on spectral clustering algorithms based on building different affinity matrix

As one of the most popular researches in the field of machine learning, spectral clustering algorithms have made great process in many different applications such as image processing. However, there are still some unsolved problems about spectral clustering algorithms, which should be immediately dealt with . These problems include how to build the affinity matrix, and how to deal with the eigenvectors. This paper mainly focuses on building the affinity matrix, which is the most important problem of spectral clustering algorithms. We propose four different methods to build the affinity matrix including the Gaussian kernel function, the Minkowski function, the nearest-correlation function and the local scale function. Then, we develop four new algorithms to contrast the clustering results. Finally, we find that building appropriate local scale function is the most available method to formulate the affinity matrix for spectral clustering algorithm.
Deficits in information transfer between anaesthesiologist and postanaesthesia care unit staff: an analysis of patient handover

Background The immediate postoperative period is important, as the patient recovers from the acute derangements resulting from the surgical insult and anaesthesia. Incomplete or incorrect communication between the anaesthesiologist and the postanaesthesia care unit nurse during the transfer process may lead to dangerous clinical mistakes. The literature examining handovers from operating room to the postanaesthesia care unit is scarce. Objectives The primary objective of this study was to examine the current transfer practice through observation of handovers between the anaesthesiologists and the postanaesthesia care unit staff in order to identify data omissions. The secondary objective was to learn which data items the clinicians and nurses thought were a necessary part of the transfer process and whether this information was communicated at the time of handover. Design A prospective observational study. Setting Academic hospital in Toronto, Canada. Participants and interventions After Research Ethics Board approval, a prospective observational study was conducted at a university-affiliated teaching centre. During a 2-month period, multiple observations of patient handover were performed. The data provided were marked on a checklist. At the end of the study, participating nurses and physicians were surveyed regarding the necessity of communicating different items on the checklist. Results A total of 526 transfers were observed. Of 29 data items examined, only two items (type of surgery and analgesics given) were reported in more than 90% of handovers. Only three items (difficult intubation, ST-wave changes and co-morbidities/healthy) were reported in more than 80% of cases. Many items deemed as needed to be reported by the participants in the study were not communicated. Conclusion This study demonstrates that the handover process is inconsistent and in some cases information defined as important by the physicians and the nurses is not transferred. Further studies need to investigate whether a handover protocol leads to a minimisation of omissions in information transfer.
Different regulatory elements are required for response of hepcidin to interleukin‐6 and bone morphogenetic proteins 4 and 9

Hepcidin is a major regulator of iron homeostasis. Hepcidin expression is upregulated by inflammatory cytokines, particularly interleukin (IL)‐6 and even more potently by the bone morphogenetic proteins 2, 4 and 9 (BMP‐2, BMP‐4 and BMP‐9). This study showed that the regulation of hepcidin expression by IL‐6 and BMPs occurs through distinct regulatory elements. The induction of hepcidin by BMPs requires at least two regions of the Hamp1 promoter, one between 140–260 bp and the other between 1·6–2·0 kb upstream of the start of translation. Reporter constructs including 1·6–2·0 kb of the Hamp1 promoter were induced >16‐fold by BMPs whereas a 260 bp reporter Hamp1 promoter construct was induced only two‐ to threefold. The distal 1·6–2·0 kb region appeared to contain several different BMP‐responsive elements, as incremental lengthening of the promoter construct in this region produced gradual escalation of BMP‐responsiveness. In contrast, the IL‐6 response required only the proximal 260 bp Hamp1 promoter region. Furthermore, there were no regulatory elements located in the non‐coding or coding regions of Hamp1 and activation of the Hamp1 promoter was absent or markedly reduced in cells of non‐hepatic origin.
Senescence as a novel mechanism involved in β-adrenergic receptor mediated cardiac hypertrophy

Pathological cardiac hypertrophy used to be elucidated by biomechanical, stretch-sensitive or neurohumoral mechanisms. However, a series of hints have indicated that hypertrophy process simulates senescence program. However, further evidence need to be pursued. To verify this hypothesis and examine whether cardiac senescence is a novel mechanism of hypertrophy induced by isoproterenol, 2-month-old male Sprague Dawley rats were subjected to isoproterenol infusion (0.25mg/kg/day) for 7 days by subcutaneous injection). Key characteristics of senescence (senescence-associated β-galactosidase activity, lipofuscin, expression of cyclin-dependent kinase inhibitors) were examined in cardiac hypertrophy model. Senescence-like phenotype, such as increased senescence-associated β-galactosidase activity, accumulation of lipofuscin and high levels of cyclin-dependent kinase inhibitors (e.g. p16, p19, p21 and p53) was found along the process of cardiac hypertrophy. Cardiac-specific transcription factor GATA4 increased in isoproterenol-treated cardiomyocytes as well. We further found that myocardial hypertrophy could be inhibited by resveratrol, an anti-aging compound, in a dose-dependent manner. Our results showed for the first time that cardiac senescence is involved in the process of pathological cardiac hypertrophy induced by isoproterenol.
Orexin A in rat rostral ventrolateral medulla is pressor, sympatho‐excitatory, increases barosensitivity and attenuates the somato‐sympathetic reflex

BACKGROUND AND PURPOSE The rostral ventrolateral medulla (RVLM) maintains sympathetic nerve activity (SNA), and integrates adaptive reflexes. Orexin A‐immunoreactive neurones in the lateral hypothalamus project to the RVLM. Microinjection of orexin A into RVLM increases blood pressure and heart rate. However, the expression of orexin receptors, and effects of orexin A in the RVLM on splanchnic SNA (sSNA), respiration and adaptive reflexes are unknown.
Broadband Channel Measurement for the High-Speed Railway Based on WCDMA

The paper describes the measurement campaigns for the broadband channel properties under the high- speed condition, which have been carried out on Zhengzhou to Xi'an (ZX) High-Speed Railway and Beijing to Tianjin (BT) High-Speed Railway. WCDMA with the bandwidth of 3.84MHz is employed as the excitation signal that is transmitted from the base station along the railway and received by the TSMQ by ROHDE & SCHWARZ inside the train. Different scenarios including plain, U-shape cutting, station and hilly terrain are chosen in the measurements and the parameters about the channel multipath properties are extracted, analyzed and briefly reported here. These results are informative for the system designers in the future wireless communication of High-Speed Railway.