Miracle-dz/UniFAR-FTUs huggingface dataset:
bModelTest : Bayesian site model selection for nucleotide data

bModelTest allows for a Bayesian approach to inferring a site model for phylogenetic analysis. It is based on trans dimensional MCMC proposals that allow switching between substitution models, whether gamma rate heterogeneity is used and whether a proportion of the sites is invariant. The model can be used with the set of reversible models on nucleotides, but we also introduce other sets of substitution models, and show how to use these sets of models. With the method, the site model can be inferred during the MCMC analysis and does not need to be pre-determined, as is now often the case in practice, by likelihood based methods.
Crystal Structure of Cryptosporidium parvum Pyruvate Kinase

Pyruvate kinase plays a critical role in cellular metabolism of glucose by serving as a major regulator of glycolysis. This tetrameric enzyme is allosterically regulated by different effector molecules, mainly phosphosugars. In response to binding of effector molecules and substrates, significant structural changes have been identified in various pyruvate kinase structures. Pyruvate kinase of Cryptosporidium parvum is exceptional among known enzymes of protozoan origin in that it exhibits no allosteric property in the presence of commonly known effector molecules. The crystal structure of pyruvate kinase from C. parvum has been solved by molecular replacement techniques and refined to 2.5 Å resolution. In the active site a glycerol molecule is located near the γ-phosphate site of ATP, and the protein structure displays a partially closed active site. However, unlike other structures where the active site is closed, the α6' helix in C. parvum pyruvate kinase unwinds and assumes an extended conformation. In the crystal structure a sulfate ion is found at a site that is occupied by a phosphate of the effector molecule in many pyruvate kinase structures. A new feature of the C. parvum pyruvate kinase structure is the presence of a disulfide bond cross-linking the two monomers in the asymmetric unit. The disulfide bond is formed between cysteine residue 26 in the short N-helix of one monomer with cysteine residue 312 in a long helix (residues 303–320) of the second monomer at the interface of these monomers. Both cysteine residues are unique to C. parvum, and the disulfide bond remained intact in a reduced environment. However, the significance of this bond, if any, remains unknown at this time.
Iron Deficiency Anemia Due to the Long-term Use of a Proton Pump Inhibitor

A 52-year-old man who had been taking omeprazole, a proton pump inhibitor (PPI), for 25 years developed iron deficiency anemia. An evaluation of the entire gastrointestinal tract did not reveal any possible causes of gastrointestinal blood loss. The cause of the iron deficiency was considered to be a reduction in gastrointestinal iron absorption in association with the reduced secretion of gastric acid due to PPI use. This case demonstrates that long-term PPI use for as long as 25 years may cause iron deficiency anemia and should be considered in the differential diagnosis of iron deficiency anemia in long-term PPI users.
Hip Abductor Tendinopathy: Work-Up and Open Versus Arthroscopic Repair of Hip Abductor

Hip abductor tendinopathy encompasses a constellation of etiologies all of which present with the chief complaint of lateral hip pain. It is four times more common in women and is usually seen between the fourth and sixth decades of life [5,6]. Patients with osteoarthritis, iliotibial band tenderness, low back pain, and obesity are at an increased risk [7,8]. Hip abductor tendinopathy falls under a broader classification of greater trochanteric pain syndrome (GTPS). Etiologies of GTPS include gluteus medius and minimus tendinopathy, external coxa saltans (hip snapping), and greater trochanteric bursitis [9,10]. Domb et al. & Williams et al. [7,11] relate the incidence of GTPS is approximately 1.8 per 1,000 people and classically presents as pain on the lateral aspect of the hip that can radiate to the thigh and posteriorly. Chronic, progressive pain is more common than acute-onset pain from an identifiable traumatic event [12,13].
Microarray expression profile of lncRNAs and mRNAs in the placenta of non-diabetic macrosomia

Macrosomia, not only is closely associated with short-term, birth-related problems, but also has long-term consequences for the offspring. We investigated the expression of long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in the placenta of macrosomia births using a microarray profile. The data showed that 2929 lncRNAs and 4574 mRNAs were upregulated in the placenta of macrosomia births compared with the normal birth weight group (fold change ⩾2.0, P<0.05), and 2127 lncRNAs and 2511 mRNAs were downregulated (fold change ⩾2.0, P<0.05). To detect the function of the differentially expressed lncRNAs and their possible relationship with the differentially expressed mRNAs, we also performed gene ontology analysis and pathway analysis. The results demonstrated that the PI3K-AKT signalling pathway, the mitogen-activated protein kinase (MAPK) signalling pathway, the focal adhesion pathway, the B cell receptor signalling pathway, and the protein processing in endoplasmic reticulum and lysosome pathway were significantly differentially expressed in the macrosomia placenta. Four lncRNAs were randomly chosen from the differentially expressed lncRNAs to validate the microarray data by quantitative polymerase chain reaction (qPCR). The qPCR results were consistent with the microarray data. In conclusion, lncRNAs were significantly differentially expressed in the placenta of macrosomia patients, and may contribute to the pathogenesis of macrosomia.
Normal perfusion of isolated rat hearts and its influence on interfibrillar and sub-sarcolemmal mitochondria activities

Obvious lack of interfibrillar mitochondria (IFM) sub population in isolated mitochondria attributed to limitations in isolation procedure. In this manuscript, we compared the functional activities of mitochondrial sub-populations namely, IFM and sub-sarcolemmal (SSM) mitochondria obtained from isolated rat heart subjected to different perfusion time namely (minutes) 0.5,5,10,25,60 and 120. Prolonged perfusion of isolated rat heart reduced oxidative phosphorylation capacity in both IFM and SSM, but was distinct among the sub-populations. However, mRNA expression level of ND4, CYT B and ATP 6 and resazurin activity were similar in both IFM and SSM. Even though overall function of myocardium is unchanged, mitochondrial sub- populations were distinct in electron transport chain activities, emphasizes the requirement to assess mitochondrial function as distinct subpopulation rather than whole entity.
Compromised Function of Regulatory T Cells in Rheumatoid Arthritis and Reversal by Anti-TNFα Therapy

Regulatory T cells have been clearly implicated in the control of disease in murine models of autoimmunity. The paucity of data regarding the role of these lymphocytes in human autoimmune disease has prompted us to examine their function in patients with rheumatoid arthritis (RA). Regulatory (CD4+CD25+) T cells isolated from patients with active RA displayed an anergic phenotype upon stimulation with anti-CD3 and anti-CD28 antibodies, and suppressed the proliferation of effector T cells in vitro. However, they were unable to suppress proinflammatory cytokine secretion from activated T cells and monocytes, or to convey a suppressive phenotype to effector CD4+CD25− T cells. Treatment with antitumor necrosis factor α (TNFα; Infliximab) restored the capacity of regulatory T cells to inhibit cytokine production and to convey a suppressive phenotype to “conventional” T cells. Furthermore, anti-TNFα treatment led to a significant rise in the number of peripheral blood regulatory T cells in RA patients responding to this treatment, which correlated with a reduction in C reactive protein. These data are the first to demonstrate that regulatory T cells are functionally compromised in RA, and indicate that modulation of regulatory T cells by anti-TNFα therapy may be a further mechanism by which this disease is ameliorated.
Physiologic correlates of culture-bound dissociation: A comparative study of Brazilian spiritist mediums and controls

Mediumship and spirit possession are cultural phenomena found in many societies worldwide. In Brazil, Spiritism (a tradition in which mediumship is emphasized) is the third largest religious denomination. The present study aimed to investigate physiologic correlates of nonpathological dissociative experiences by comparing 20 female spiritist mediums with several years of socially sanctioned practice to 20 female nonmedium control subjects from the same religious context. We measured plasma levels of hormones and neuroactive substances, as well as vital signs and heart rate variability (HRV) parameters, before and immediately after spirit communication. Although no between-group differences were noted in basal physiological parameters, in response to the possession experiences the groups differed in heart rate and in plasma concentrations of noradrenaline, thyroid-stimulating hormone (TSH), prolactin, and creatine phosphokinase (CPK). The changes in parameters indicated an arousal response in mediums and a relaxation response in control participants, and the same pattern of changes was observed in HRV parameters from each group during the possession experiences. However, the changes in physiologic parameters for mediums were mild and of short duration: 1 hour after the possession experiences, no difference in cardiac autonomic regulation was noted. No significant group effect was noted for melatonin. Cognitive control processes may explain the arousal associated with the dissociative state. Findings from this study suggest that pathological and nonpathological dissociation may have different physiological correlates.
Autonomous Mapping of Underwater 3-D Structures: From View Planning To Execution

Three-dimensional mapping of submerged industrial facilities or underwater sites with complex geometries is still a challenge for nowadays autonomous underwater vehicles (AUVs), which are restricted to more simple survey missions. This letter presents a complete framework to plan and execute autonomous missions to map a region of interest, coping with the particularities of the underwater domain. The proposed solution consists of the following steps: First, if a previous model is not available, a preliminary bathymetry of the area to be covered is gathered and an octree representation is created. Next, using this a priori model, an offline view-planner computes a minimum set of sensor configurations to cover the volume of interest by taking into account the mapping sensor and the vehicle safety constraints. It also computes the free path to be followed by the AUV to traverse all these sensor configurations. Finally, the planned mission is executed while an online simultaneous localization and mapping algorithm prevents the AUV from drifting, ensuring that the planned path is correctly followed. Preliminary results regarding the view planner have been obtained in a shipwreck site with the Girona 500 AUV, while results involving the whole framework have been achieved using the Gazebo simulator and a realistic AUV model equipped with a multibeam sonar mounted on a pan & tilt unit.
A Survey on Optical Handwriting Recognition System using Machine Learning Algorithms

The recent advancement and development in technical fields and logistics has tackled the challenges of science and have delivered a good impact ratio by avoiding issues faced by fully or partially challenged and impaired people. The purpose of this paper is to provide easy facilities and improved services to a wide range of customers from school going children to teachers, professors, home tutors, visually impaired, and literary scholars. The title says it all, the concepts and theoretical background in the paper explains how the handwriting scripted in the image can be converted into textual information using several machine learning algorithms which follow the principles of supervised and unsupervised learning respectively. With the help of microcontrollers, feature extraction material, trainers and image processing concepts the proposed idea can be implemented feasibly. Machine learning algorithms such as Support Vector Machine, Random forest and neural nets algorithms have been compared and evaluated on basis of precision, recall, accuracy and other performance parameters. On comparing the mentioning algorithms it has been observed that ‘SVM’ algorithm outclasses the comparison test and gives out the best result in terms of accuracy, latency and robustness. On observing the overall effects of algorithms and conversions between handwritten text into textual information (maybe pdf’s). It has been concluded that the work can be further implemented on platforms such as e-learning, in which the application can be deployed on internet for android and IoS users with the help of mobile computing principles. Students in the classroom can just click a picture of what’s written on the board by the professor and the application will convert the text written on the image into a PDF and save it in the internal memory of your gadget.
Investigating the Relationships Between Subjective Well-Being and Psychological Well-Being Over Two Decades

Although much research has been conducted on the predictors and outcomes of both subjective well-being (SWB) and psychological well-being (PWB), the magnitude and direction of the causal relationship between these constructs remain unclear. The studies reported in this article were designed to assess the temporal relationship between SWB and PWB during a period of 20 years. The studies used 3 waves of survey data, with intervals of 10 years, from the Midlife in the United States project, a representative longitudinal panel study of American adults (N = 2,731). Cross-lagged panel analyses were conducted to examine directionality of the relationships. Results showed that the autoregressive effects were large, suggesting a high degree of stability in SWB and PWB over time. Yet the levels of stability were generally higher for PWB than SWB. Whereas PWB unequivocally predicted increases in SWB over time, the prospective effects of SWB on PWB were inconsistent (i.e., positive, negative, or nonsignificant) across various points in time. The study findings suggest that PWB represents a more robust and consistent antecedent of future well-being than SWB.
Magnesium sulfate in combination with nimodipine for the treatment of subarachnoid hemorrhage: a randomized controlled clinical study

Abstract Objective Cerebral vasospasm(CVS) after Subarachnoid hemorrhage (SAH) can cause delayed cerebral ischemia,secondary cerebral infarction, and rehemorrhage, which are the leading causes of mutilation and death. Nimodipine has been shown to prevent CVS. Magnesium ion (Mg2+) can competitively inhibit the influx of calcium (Ca2+) and prevent vasospasm. There is evidence that magnesium sulfate can prevent CVS and reduce infarct volume after SAH. In this study, we evaluated the efficacy and safety of intravenous magnesium sulfate combined with oral nimodipine on CVS, delayed cerebral ischemia, secondary cerebral infarction, and rehemorrhage after SAH. Methods This is a prospective randomized, double-blind trial of 120 patients with SAH who were recruited between January 2003 and January 2009. These patients were assigned to two groups and received the same basic treatment and symptomatic treatment. In group A, patients received 14 days of intravenous administration of 1400 mL 0.9% normal saline + 40 mL 25% magnesium sulfate, 1 mL/min, once per day, followed 7 days of intravenous administration of 500 mL 0.9% normal saline + 15 mL 25% magnesium sulfate, 1 mL/min, once per day and oral nimodipine, 20 mg once, four times a day, for 21 days. Patients in group B received identical treatment to that in group A, except that 25% magnesium sulfate was replaced by placebo. On day 22 of treatment, incidences of intracranial CVS, delayed cerebral ischemia, secondary cerebral infarction, rehemorrhage, neurologic deficits, and death were assessed and adverse events were monitored. Results CVS occurred in 4, 12 patients, lasting for 11.09 ± 5.38, 13.73 ± 6.24 hours, mean velocity (Vm) of 143.2 ± 12.7, 149.6 ± 18.9 cm/s in group A, B; Delayed cerebral ischemia occurred in 3, 10 patients, lasting for 13.16 ± 4.82, 15.57 ± 5.35 hours in group A, B; Secondary cerebral infarction occurred in 2 and 8 patients in groups A and B; Neurologic deficits occurred in3 and 11 patients in groups A and B, All P < 0.05; Rehemorrhage occurred in 4 and 5 patients; Death occurred in 5 and 8 patients in groups A and B, respectively, P >0.05. No obvious adverse events were found in both groups. Conclusion Intravenous magnesium sulfate in combination with oral nimodipine for the treatment of SAH can help reduce the incidences of CVS, delayed cerebral ischemia, secondary cerebral infarction, and neurologic deficits with good safety, but it does not reduce the incidences of rehemorrhage and death.
Celecoxib for the Prevention of Colorectal Adenomas: Results of a Suspended Randomized Controlled Trial.

BACKGROUND Cyclooxygenase (COX)-2 inhibitors such as celecoxib were designed to preserve anti-inflammatory activity without inhibiting COX-1. Downregulation of COX-2 inhibits colorectal carcinogenesis. METHODS The Selenium and Celecoxib Trial was a randomized, placebo-controlled trial of once-daily selenium 200 µg and celecoxib 400 mg, alone or together, for colorectal adenoma prevention. Men and women between age 40 and 80 years were eligible following colonoscopic removal of adenomas. The primary outcome was development of new adenomas. Celecoxib was suspended early because of cardiovascular toxicity in other trials. Accrual to selenium or placebo continued. Before suspension, 824 participants were randomly assigned to celecoxib or placebo, of whom 712 (86.4%) were available for analysis. All statistical tests were two-sided. RESULTS In the placebo and celecoxib arms of 356 participants each, adenoma detection was 47.5% and 49.7% (relative risk [RR] = 1.04, 95% confidence interval [CI] = 0.90 to 1.21, P = .58), respectively, after median periods of 13.6 and 14.2 months on intervention. Among participants colonoscoped within 12 months of discontinuing intervention (n = 244), overall adenoma recurrence (RR = 0.69, 95% CI = 0.48 to 0.98, P = .04) and recurrence with advanced adenomas (RR = 0.23, 95% CI = 0.07 to 0.80, P = .02) were reduced with celecoxib. Reduction of adenoma recurrence was greatest in participants with previous advanced adenomas. Celecoxib increased risk of hypertension in participants with pre-existing cardiovascular risk factors compared with placebo (hazard ratio = 2.19, 95% CI = 1.07 to 4.50, P = .03). CONCLUSIONS Limited-duration celecoxib prevents adenoma recurrence in patients with prior high-risk adenomas, in whom strategies to minimize cardiovascular toxicity might be feasible.
Sense-aid: a framework for enabling network as a service for participatory sensing

The rapid adoption of smartphones with different types of advanced sensors has led to an increasing trend in the usage of mobile crowdsensing applications, e.g., to create hyper-local weather maps. However, the high energy consumption of crowdsensing, chiefly due to expensive network communication, has been found to be detrimental to the wide-spread adoption. We propose a framework, called Sense-Aid, that can provide energy-efficient mobile crowdsensing service, coexisting with the cellular network. There are two key innovations in Sense-Aid beyond prior work (Piggyback Crowdsensing-Sensys13)---the middleware running on the cellular network edge to orchestrate multiple devices present in geographical proximity to suppress redundant data collection and communication. It understands the state of each device (radio state, battery state, etc.) to decide which ones should be selected for crowdsensing activities at any point in time. It also provides a simple programming abstraction to help with the development of crowdsensing applications. We show the benefit of Sense-Aid by conducting a user study consisting of 60 students in our campus, compared to a baseline periodic data collection method and Piggyback Crowdsensing. We find that energy saving is 93.3% for Sense-Aid compared with Piggyback Crowdsensing in a representative case which requires 2 devices to provide barometric values within an area of a circle whose radius is 1 kilometer and requires periodic data collection every 5 minutes for a 90-minute test. The selection algorithm of Sense-Aid also ensures reasonable fairness in the use of the different devices.
Towards harmonization of quality indicators in laboratory medicine

Abstract The identification of reliable quality indicators (QIs) in the total testing process (TTP) represents a crucial step in enabling users to quantify the quality of laboratory services, but the current lack of attention to extra-laboratory factors is in stark contrast with the body of evidence showing the multitude of errors that continue to occur in the pre- and post-analytical phases. Although interesting programs on indicators of the extra-analytical phases have been developed in some countries, there is no consensus on the production of joint recommendations for the adoption of universal QIs and the use of common terminology in the total testing process. In view of the different QIs and terminologies currently used, there an urgent need to harmonize proposed QIs, which should comply with three main principles: they must be patient-centered, consistent with the requirements of the International Standard for medical laboratories accreditation, and address all stages of the TTP. A model of quality indicators (MQI), consensually developed by a group of clinical laboratories according to a project launched by a working group of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC), includes 56 QIs related to key processes (34 pre-, 7 intra- and 15 post-analytical phase) and three to support processes. The scope of harmonization in laboratory medicine, more far-reaching than method harmonization, should cover a wider range of topics, namely all steps of the “brain-to-brain loop”. The identification of valuable QIs is a key step in paving the way towards quality and patient safety in laboratory medicine.
Integrative genome analysis of somatic p53 mutant osteosarcomas identifies Ets2-dependent regulation of small nucleolar RNAs by mutant p53 protein

Pourebrahim et al. developed a traceable somatic osteosarcoma mouse model that is initiated with either a single p53 mutation (p53R172H) or p53 loss in osteoblasts. They identified a cluster of Ets2-dependent small nucleolar RNAs (snoRNAs) that are highly up-regulated in p53 mutant tumors.