Miracle-dz/UniFAR-FTUs huggingface dataset:
Shotgun Proteomics Analysis of Hibernating Arctic Ground Squirrels*

Mammalian hibernation involves complex mechanisms of metabolic reprogramming and tissue protection. Previous gene expression studies of hibernation have mainly focused on changes at the mRNA level. Large scale proteomics studies on hibernation have lagged behind largely because of the lack of an adequate protein database specific for hibernating species. We constructed a ground squirrel protein database for protein identification and used a label-free shotgun proteomics approach to analyze protein expression throughout the torpor-arousal cycle during hibernation in arctic ground squirrels (Urocitellus parryii). We identified more than 3,000 unique proteins from livers of arctic ground squirrels. Among them, 517 proteins showed significant differential expression comparing animals sampled after at least 8 days of continuous torpor (late torpid), within 5 h of a spontaneous arousal episode (early aroused), and 1–2 months after hibernation had ended (non-hibernating). Consistent with changes at the mRNA level shown in a previous study on the same tissue samples, proteins involved in glycolysis and fatty acid synthesis were significantly underexpressed at the protein level in both late torpid and early aroused animals compared with non-hibernating animals, whereas proteins involved in fatty acid catabolism were significantly overexpressed. On the other hand, when we compared late torpid and early aroused animals, there were discrepancies between mRNA and protein levels for a large number of genes. Proteins involved in protein translation and degradation, mRNA processing, and oxidative phosphorylation were significantly overexpressed in early aroused animals compared with late torpid animals, whereas no significant changes at the mRNA levels between these stages had been observed. Our results suggest that there is substantial post-transcriptional regulation of proteins during torpor-arousal cycles of hibernation.
Detection of Multiple Autoantibodies in Patients with Ankylosing Spondylitis Using Nucleic Acid Programmable Protein Arrays*

Ankylosing spondylitis (AS) is a common, inflammatory rheumatic disease that primarily affects the axial skeleton and is associated with sacroiliitis, uveitis, and enthesitis. Unlike other autoimmune rheumatic diseases, such as rheumatoid arthritis or systemic lupus erythematosus, autoantibodies have not yet been reported to be a feature of AS. We therefore wished to determine whether plasma from patients with AS contained autoantibodies and, if so, characterize and quantify this response in comparison to patients with rheumatoid arthritis (RA) and healthy controls. Two high density nucleic acid programmable protein arrays expressing a total of 3498 proteins were screened with plasma from 25 patients with AS, 17 with RA, and 25 healthy controls. Autoantigens identified were subjected to Ingenuity Pathway Analysis to determine the patterns of signaling cascades or tissue origin. 44% of patients with ankylosing spondylitis demonstrated a broad autoantibody response, as compared with 33% of patients with RA and only 8% of healthy controls. Individuals with AS demonstrated autoantibody responses to shared autoantigens, and 60% of autoantigens identified in the AS cohort were restricted to that group. The autoantibody responses in the AS patients were targeted toward connective, skeletal, and muscular tissue, unlike those of RA patients or healthy controls. Thus, patients with AS show evidence of systemic humoral autoimmunity and multispecific autoantibody production. Nucleic acid programmable protein arrays constitute a powerful tool to study autoimmune diseases.
Effects of Periodic Physical Exercise on Pulse Wave Velocity in Female College Students

Objective The purpose of this study was to examine effects of periodic physical exercise on pulse wave velocity (PWV) with 32 healthy female college students.Methods PWV was measured using VaSera VS-1000 (Fukuda denshi, Co., Ltd, Tokyo, Japan) . PWV was measured at rest in supine position with sensory cuffs wrapped to their both brachials and ankles (brachial-ankle method, baPWV) . baPWV was calculated by dividing the distances (D) from the aorta to the cuff on the left (right) brachial and to that on the left (right) ankle by each pulse transit time (t) . That is, baPWV was calculated as: baPWV=D/t.Result and Discussion All subjects were studied for analysis of the relations of exercise frequency with left-baPWV (L-PWV), right-baPWV (R-PWV) and the each was found significantly correlated. Then, we compared PWV between subjects doing periodic physical exercise (active group, n=14) and those doing no periodic physical exercise (inactive group, n=18) . Both L-PWV and R-PWV values were lower in the active group than in the inactive group showing their lower arterial stiffness.Conclusion These results suggested that young people are also able to reduce arterial stiffness and to prevent the lifestyle related diseases by doing periodic physical exercise.
Rapid Identification of Monospecific Monoclonal Antibodies Using a Human Proteome Microarray*

To broaden the range of tools available for proteomic research, we generated a library of 16,368 unique full-length human ORFs that are expressible as N-terminal GST-His6 fusion proteins. Following expression in yeast, these proteins were then individually purified and used to construct a human proteome microarray. To demonstrate the usefulness of this reagent, we developed a streamlined strategy for the production of monospecific monoclonal antibodies that used immunization with live human cells and microarray-based analysis of antibody specificity as its central components. We showed that microarray-based analysis of antibody specificity can be performed efficiently using a two-dimensional pooling strategy. We also demonstrated that our immunization and selection strategies result in a large fraction of monospecific monoclonal antibodies that are both immunoblot and immunoprecipitation grade. Our data indicate that the pipeline provides a robust platform for the generation of monoclonal antibodies of exceptional specificity.
Tandem Mass Spectral Libraries of Peptides in Digests of Individual Proteins: Human Serum Albumin (HSA) *

This work presents a method for creating a mass spectral library containing tandem spectra of identifiable peptide ions in the tryptic digestion of a single protein. Human serum albumin (HSA1) was selected for this purpose owing to its ubiquity, high level of characterization and availability of digest data. The underlying experimental data consisted of ∼3000 one-dimensional LC-ESI-MS/MS runs with ion-trap fragmentation. In order to generate a wide range of peptides, studies covered a broad set of instrument and digestion conditions using multiple sources of HSA and trypsin. Computer methods were developed to enable the reliable identification and reference spectrum extraction of all peptide ions identifiable by current sequence search methods. This process made use of both MS2 (tandem) spectra and MS1 (electrospray) data. Identified spectra were generated for 2918 different peptide ions, using a variety of manually-validated filters to ensure spectrum quality and identification reliability. The resulting library was composed of 10% conventional tryptic and 29% semitryptic peptide ions, along with 42% tryptic peptide ions with known or unknown modifications, which included both analytical artifacts and post-translational modifications (PTMs) present in the original HSA. The remaining 19% contained unexpected missed-cleavages or were under/over alkylated. The methods described can be extended to create equivalent spectral libraries for any target protein. Such libraries have a number of applications in addition to their known advantages of speed and sensitivity, including the ready re-identification of known PTMs, rejection of artifact spectra and a means of assessing sample and digestion quality.
Profiling Subcellular Protein Phosphatase Responses to Coxsackievirus B3 Infection of Cardiomyocytes*

Cellular responses to stimuli involve dynamic and localized changes in protein kinases and phosphatases. Here, we report a generalized functional assay for high-throughput profiling of multiple protein phosphatases with subcellular resolution and apply it to analyze coxsackievirus B3 (CVB3) infection counteracted by interferon signaling. Using on-plate cell fractionation optimized for adherent cells, we isolate protein extracts containing active endogenous phosphatases from cell membranes, the cytoplasm, and the nucleus. The extracts contain all major classes of protein phosphatases and catalyze dephosphorylation of plate-bound phosphosubstrates in a microtiter format, with cellular activity quantified at the end point by phosphospecific ELISA. The platform is optimized for six phosphosubstrates (ERK2, JNK1, p38α, MK2, CREB, and STAT1) and measures specific activities from extracts of fewer than 50,000 cells. The assay was exploited to examine viral and antiviral signaling in AC16 cardiomyocytes, which we show can be engineered to serve as susceptible and permissive hosts for CVB3. Phosphatase responses were profiled in these cells by completing a full-factorial experiment for CVB3 infection and type I/II interferon signaling. Over 850 functional measurements revealed several independent, subcellular changes in specific phosphatase activities. During CVB3 infection, we found that type I interferon signaling increases subcellular JNK1 phosphatase activity, inhibiting nuclear JNK1 activity that otherwise promotes viral protein synthesis in the infected host cell. Our assay provides a high-throughput way to capture perturbations in important negative regulators of intracellular signal-transduction networks.
A randomized, single‐blind, increasing dose safety trial of an oxygen‐carrying plasma expander (Hemospan®) administered to orthopaedic surgery patients with spinal anaesthesia

summary The objective of this study was to further explore the safety of Hemospan® (Sangart Inc., San Diego, CA, USA), an oxygen‐carrying plasma expander. The aim of this study was to determine if Hemospan is well tolerated in orthopaedic surgery patients with spinal anaesthesia in doses up to 1 L. Hemospan was previously found to be well tolerated in normal volunteers and orthopaedic surgery patients with spinal anaesthesia in doses up to 500 mL. Five cohorts of six orthopaedic surgery patients, American Society of Anesthesiologists (ASA) I and II, were studied. In each cohort, four patients received Hemospan in doses ranging from 200 to 1000 mL, and two received Ringer’s lactate immediately prior to induction of spinal anaesthesia. There were no serious adverse events (SAEs). Iohexol clearance measured before and 24 h after dosing was unaffected. There were 14 adverse events (AEs) in the 10 control patients (1·4 per patient) and 30 in the 20 patients receiving Hemospan (1·5 per patient). One patient in the group receiving 200 mL Hemospan had elevated mean arterial pressure after dosing, but there were no elevations in any of the other patients. The peak plasma Hemospan concentration in the 1000 mL group was 1·3 g dL−1, with a dose‐dependent clearance (T1/2) ranging from 14·1 to 23·0 h. Plasma methaemoglobin levels were independent of dose, reaching a maximum at 40 h after dosing and never exceeded 0·125 g dL−1. Troponin T was transiently elevated in two patients receiving Hemospan without symptoms or electrocardiographic abnormalities or elevation of myocardial creatinine kinase isoenzyme. Hemospan was well tolerated in this group of patients at doses up to 1000 mL.
Diagnosis of pulmonary tuberculosis using Ziehl-Neelsen stain or cold staining techniques?

BACKGROUND Acid-fast bacilli microscopy is the first step in the diagnosis and screening of pulmonary tuberculosis (PTB) in developing countries. It remains a rapid and inexpensive diagnostic tool for diagnosing a large number of PTB cases with limited resources. OBJECTIVE To evaluate three different staining techniques used in the detection of acid-fast bacilli. The conventional Ziehl-Neelsen (ZN) stain and two cold stains, Gabbett's cold stain and modified cold stain (MCS), were compared with sputum culture. MATERIALS AND METHODS A total of 300 sputum samples from 100 clinically suspected PTB patients referred to Maamorah Chest Hospital in Alexandria, Egypt, were tested. For staining and culture, three sputum samples from each patient were collected (one 'on spot' and two early morning samples) and pooled together. Smears were prepared using three different staining methods (ZN, Gabbett's cold stain, and MCS) and were inoculated in the Lowenstein-Jensen media. RESULTS Comparison of sputum staining results using three different staining techniques versus culture proved that the highest sensitivity and specificity were seen for Gabbett's stain (76.6 and 98.5%, respectively). ZN stain had a sensitivity and specificity of 70 and 97.1%, whereas MCS had a sensitivity and specificity of 60 and 95.7%, respectively. CONCLUSION Gabbett's stain was more accurate in the diagnosis of PTB compared with both ZN and MCS, even though the results were not statistically significant. It can replace ZN for initial diagnosis and follow up of cases. It is also easier, faster, and does not require a heating step.
A Case Report of Fever of Unknown Origin (FUO)

A 10-year-old boy had a long time of fever, and was diagnosed as JRA at first, but the patient’s condition got worse and worse after the treatment, then we did the cervical lymph node biopsy, which showed ALCL (Anaplastic Large Cell Lymphoma). After receiving the correct treatment, the patient’s condition got better.
Maternal IgM anti‐D, borderline foetal Doppler middle cerebral artery velocities and absent neonatal haemolysis

Anti‐D was detected for the first time at 36 weeks gestation in a group A RhD‐negative primigravida without prior sensitizing events or anti‐D administration. Simultaneously, foetal ultrasound showed middle cerebral artery maximum velocity (MCA Vmax) at the 95th centile but no hydrops. Labour was induced at 37 weeks. Although neonatal anaemia was anticipated, the baby, who was group O RhD‐positive, was born with a normal haemoglobin and negative direct antiglobulin test and antibody screen. Retrospectively, the maternal anti‐D proved to be exclusively immunoglobulin M (IgM), which does not cross the placenta. Foetal Doppler MCA Vmax measurements can give false positive results especially late in the third trimester. Thus, antibody class, especially in first pregnancies without prior sensitizing events, and the timing of foetal Doppler MCA velocity measurements should be considered when evaluating the likelihood and severity of haemolytic disease of the foetus and newborn.
A survey of physicians' reasons to transfuse plasma and platelets in the critically ill: a prospective single‐centre cohort study

Data on the rationality of transfusion practice of fresh frozen plasma (FFP) and platelets in the critically ill are sparse and may contribute to efforts to reduce transfusion rates. To provide insight into determinants of the decision of intensive care unit (ICU)‐physicians to transfuse, a survey study was performed. The reasons of ICU‐physicians to transfuse FFP and platelets were determined during a 10‐week period. Transfusion triggers were assessed, as well as correction of prolonged coagulation test results. Of 310 admissions, 44 patients (14%) received a transfusion of FFP and 35 patients (11%) received a platelet transfusion. In 67% patients, FFPs were transfused in bleeding patients and in 33% in non‐bleeding patients. FFP was transfused at a prothrombin time (PT) of 19 s (17–22). After FFP transfusion, PT levels of 15–18, 18–20 and 20–26 s decreased with a median of 0.7, 1.9 and 3.5 s, respectively. On average, 3.2 FFP units were ordered, of which 28% was not transfused. The major reason to transfuse platelets was bleeding. Platelets were transfused at a platelet count of 95 (36–116) × 109 L−1 in bleeding and 13 (10–18) × 109 L−1 in non‐bleeding patients. On average, 1.4 platelet units were ordered, of which 20% was not transfused. The agreement between physicians reporting a major bleeding and a definition of bleeding was poor (κ < 0.10 for FFP and 0.20 for platelets). In conclusion, one‐third of FFP transfusions was given to non‐bleeding patients. FFP transfusion failed to normalize prolonged coagulation test results in the majority of the patients. Transfusion of platelets was restrictive in non‐bleeding patients and liberal in bleeding patients. Education on indications of FFP transfusion and improved identification of bleeding may reduce transfusion rates.
Physical therapy management of Pompe disease

Pompe disease (Glycogen storage disease type II, GSDII, or acid maltase deficiency) is an autosomal recessive disorder characterized by deficiency of acid α-glucosidase resulting in intra-lysosomal accumulation of glycogen and leading to progressive muscle dysfunction. The natural history of infantile-onset Pompe disease is characterized by hypertrophic cardiomyopathy and profound generalized weakness presenting in the first few months of life, with rapid progression and death usually occurring by one year of age. Late-onset Pompe disease is characterized by onset of symptoms after one year of age, less severe or absence of cardiac involvement and slower progression, with symptoms primarily related to progressive dysfunction of skeletal muscles and respiratory muscle involvement. Recent clinical trials of enzyme replacement therapy have begun to allow greater opportunity for potential improvement in motor status, function, and survival than ever before, with hopes of moving toward maximizing physical function for individuals with Pompe disease. Children are living longer with some achieving independent sitting, creeping, and walking–milestones typically never achieved in the untreated natural history of the disorder. With increased survival, clinical management based on an understanding of the pathology and pathokinesiology of motor function gains importance. This article reviews current knowledge regarding the motor system in Pompe disease and provides an overview of physical therapy management of Pompe disease, including management strategies for individuals on enzyme replacement therapy.
Bacterial screening by flow cytometry offers potential for extension of platelet storage: results of 14 months of active surveillance

Background: Bacterial contamination is currently the major infectious hazard of platelet transfusion in developed countries. It has been demonstrated that a significant transfusion risk remains, in particular with older platelet concentrates (PCs). In 2009, the shelf life of PCs was therefore reduced in Germany to 4 days after the day of production according to Vote 38. The aim of the present study was the application and implementation of a recently developed flow cytometry‐based rapid screening method (BactiFlow) for bacterial contamination at the end of PC shelf life as a routine in‐process control.
Clinical evidence from ONTARGET: the value of an angiotensin II receptor blocker and an angiotensin-converting enzyme inhibitor

The Heart Outcomes Prevention Evaluation study established the angiotensin-converting enzyme inhibitor ramipril, versus placebo, for prevention of cardiovascular events in high-risk patients. The ONgoing Telmisartan Alone and in combination with Ramipril Global Endpoint Trial (ONTARGET) was later conducted in similar high-risk patients using multifactorial treatment to control hypertension, platelet aggregation, and dyslipidemia, while comparing ramipril, telmisartan, or their combination, without placebo. In ONTARGET, the first angiotensin II receptor blocker-based study to be performed in a broader population of patients without congestive heart failure and/or left ventricular hypertrophy/dysfunction, telmisartan provided cardiovascular protection that was noninferior to ramipril. However, greater blockade of the renin–angiotensin system, using their combination, was not superior to ramipril alone. Telmisartan was better tolerated than ramipril in this high-risk population: notably, the incidence of cough and angioedema was significantly lower with telmisartan alone. Thus, telmisartan provides comparable efficacy to ramipril with less adverse events, which may encourage patient compliance.
Endothelial dysfunction in spontaneously hypertensive rats: focus on methodological aspects

Despite the apparent consensus on the existence of endothelial dysfunction in conduit and resistance arteries of spontaneously hypertensive rats (SHR), a commonly employed experimental model of hypertension, there are a number of reports showing that endothelium-dependent vasodilatory responses are similar, or even increased, in SHR compared with their normotensive counterparts. The present paper aims to discuss the rationale for these apparent discrepancies, including the effect of age, type of artery and methodological aspects. Data from the literature indicate that the age of the animal is a contributing factor and that endothelial dysfunction is likely to be a consequence of hypertension. In addition, the use of antioxidant additives, such as ascorbic acid or ethylene diaminetetraacetic acid, and differences in the level of initial arterial stretch, might also be of importance because they may modify the oxidative status of the artery and the levels of vasoactive factors released by the endothelium.
Women's perceptions relating to the introduction of mandatory iodine fortification in Australia

Aim: In Australia, the mandatory fortification of salt used in bread with iodine has recently been approved by the regulatory authorities (Food Standards Australia New Zealand). Apart from thiamine fortification of bread that has been in place since 1991, no other mandatory fortification programs exist in the country. The aim of the present study was to explore women's understanding of mandatory fortification as a public health strategy and their opinions regarding its appropriateness for addressing the re-emergence of iodine deficiency. Methods: Four focus group discussions with 20 women of child-bearing age, recruited from Wollongong in New South Wales. Results: Women had little knowledge about the role of iodine in the diet and were unaware that iodine deficiency was a public health issue in Australia. Mandatory fortification was viewed with concern, especially regarding the possible risk of toxicity. Clear labelling of fortified foods, in conjunction with education initiatives to accompany the pending iodine fortification program, were considered by the research participants to be essential in order to address these concerns. Conclusion: Women in the present study expect an authority, either a government body or health professionals, to take responsibility in making proactive decisions for the health of the population. When accompanied by transparent processes that include widespread consultation with consumers and clear explanations for the process, mandatory fortification is considered acceptable as an appropriate and effective strategy for ameliorating iodine deficiency.