Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical map of the Treponema denticola circular chromosome

A physical map of the Treponema denticola ATCC 33520 genome was constructed by pulsed-field gel electrophoresis and DNA hybridization. The organism possesses a single, circular chromosome of approximately 3.0 Mbp and a 2.6-kbp circular plasmid, pTD1. The physical map of the A+T-rich genome was constructed with the rare-cutting restriction enzymes AscI, NotI, and SrfI, which have 8-bp G+C-rich recognition sites. The genes flgE, tdpA, and prtB encoding the flagellar hook protein, a 53-kDa immunogenic protein, and chymotrypsinlike protease, respectively, were located on the map. This treponeme was found to have two copies of each of the rRNA genes, as has been found to be the case for both Treponema phagedenis and Treponema pallidum.
Electrical storm: definitions, clinical importance, and treatment

Purpose of review With increasing use of implantable cardioverter defibrillators, physicians are increasingly called upon to manage recurrent ventricular tachycardia, sometimes in the form of frequent recurrences known as electrical storm (or ventricular tachycardia storm). Recent findings Standard antiarrhythmic drug therapy may suppress storms, but, when refractory, interventions such as catheter ablation or in some cases surgical cardiac denervation may be helpful. Earlier interventional management may confer better outcomes than persisting with antiarrhythmic pharmacologic therapy. Summary The clinical syndrome of electrical storm has been defined empirically. An outcome-derived definition may better guide clinicians on when and how to treat this emergent problem. When available, an early interventional approach is preferred.
Study of prognostic value of serum and RBC acetyle cholinesterase level in organophosphorus poisoning and its correlation with the outcome

Introduction: Organophosphorus compound (OPC) poisoning has assumed alarming proportions and it is primarily a problem of the developing countries. Serum cholinesterase levels are easier to estimate and usually depressed after OP poisoning. Peradeniya OP poisoning scale has not been studied much in Indian scenario. So, we decided to have first hand information and hence conducted this study. Aim and objectives: To find out severity of patients with OP poisoning by calculating Peradeniya OP Poisoning score, level of plasma and RBC cholinesterase level of patients of OP poisoning on admission before any treatment, and correlate the level with severity and outcome of patients and requirement of ventilator support with OP poisoning. Material and methods: All patients who presented to emergency department with history of poisoning with known compound were taken as study subjects. A detailed history, clinical examination and relevant biochemical investigations were performed. Peradeniya OP poisoning scale Patel P, Patel VP, Patel H, Rathod GB. Study of prognostic value of serum and RBC acetyle cholinesterase level in organophosphorus poisoning and its correlation with the outcome. IAIM, 2016; 3(3): 147-157. Page 148 was applied to all study subjects and the severity of OP poisoning was graded as mild, moderate, severe. In all study subjects, 3 ml of plain blood was collected on admission before administration of atropine and plasma cholinesterase and RBC cholinesterase was estimated. Results: Most of the patients consumed poison with a suicidal intent. Majority had consumed poison orally. Most patients had consumed 50 – 100 ml of poison. Quantity of poison consumed did not correlate with severity of poisoning. In this study, requirement of ventilatory support was seen in 16% of patients. Mortality in our study was 9%. Pseudo cholinesterase levels were significantly depressed in patients who required ventilatory support and correlated with mortality. Miosis, Bradycardia, increased respiratory rate, impaired level of consciousness, all correlated well with need for ventilatory support and increased mortality. Peradeniya OP poisoning score of more than 8 correlated in predicting the need for ventilatory support and mortality. RBC and Plasma cholinesterase levels estimation in conjunction with Peradeniya OP poisoning score is a useful parameter for grading severity of OP poisoning and in predicting the need for ventilatory support and mortality. Conclusion: The POP scale and RBC Che and plasma cholinesterase levels both showed a significant association in predicting the need for ventilatory support and outcome. Lower grade of poisoning had a better outcome whereas higher severity of poisoning had a poorer outcome.
Early domesticated cowpea (Vigna unguiculata) from Central Ghana

From examining the remains of charred cowpeas from rock shelters in Central Ghana, the authors throw light on the subsistence strategies of the Kintampo people of the second millennium BCE. Perhaps driven southwards from the Sahel by aridification, the Kintampo operated as both foragers and farmers, cultivating selected plants of the West African tropics, notably cowpea, pearl millet and oil palm.
Static Analysis Alert Audits: Lexicon & Rules

There is no widely-accepted lexicon or standard set of rules for auditing static analysis alerts in the software engineering community. Auditing rules and a lexicon should guide different auditors to make the same determination for an alert. Standard terms and processes are necessary so that initial determinations are correctly interpreted, which helps organizations reduce code flaws. They are also needed to improve the quality of audit data to benefit research on alert prioritization. This paper provides a suggested set of auditing rules and a lexicon, detailing rationales based on modern software engineering practices for each rule and each lexicon term. Some code examples are provided with the auditing rules. The authors' hope is that this suggested framework will motivate community discussion leading to agreed-upon standards.
An evaluation of built-in vs. off-chip strategies for online transient current testing

We evaluate the possibilities of transient current testing practical implementation by comparing the transient supply current signature at the external circuit supply pins to its internal behavior. To do this we develop and analyze a hierarchical power-grid equivalent circuit to evaluate the supply current frequency components and their distribution over the power/ground grid hierarchy. This is a key step to determine the feasibility of on-chip vs. off-chip idd(t) strategies and their successive application to online testing.
Herpes Simplex Virus 1-Encoded Protein Kinase UL 13 Phosphorylates Viral Us 3 Protein Kinase and Regulates Nuclear Localization of Viral Envelopment Factors UL 34 and UL 31

Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Department of Virology, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8550, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, and Department of Pathology, National Institute of Infectious Disease, Shinjuku-ku, Tokyo 162-8640, Japan
Gentamicin Pharmacokinetic Changes Related to Mechanical Ventilation

trations; therefore, we calculated hemodialysis plasma clearance. Our method of calculating Clhd tends to underestimate Clh• of drugs that are contained within red blood cells (RBCs) and whose concentrations rapidly equilibrate between RBCs and plasma. ' However, our calculation of Clh• is probably a fair estimate since McNicol et al. reported that, although ACA concentrations within RBCs follow changes in ACA plasma concentrations, this is a slow, gradual process. ' This feature would tend to minimize the risk of underestimating Clh• with the equation we used. Even if a rapid transfer of ACA from RBCs to plasma occurred, the actual Clh• would be increased over our calculated value which already suggests that hemodialysis would have a significant effect on ACA removal. Based on the results of Fish et al. _and our patient, ACA total body clearance is markedly decreased from normal in patients with renal failure. It would appear that ACA doses 15-25 percent of normal are necessary to avoid excessive plasma concentrations. Literature suggests! s ACA plasma concentrations >130 rng/L but <300 mg/L are desirable. Unfortunately, ACA plasma concentrations are not readily available for monitoring purposes. In addition, ACA plasma concentrations decrease considerably and ACA total body clearance is markedly increased during hemodialysis. This would suggest that patients should continue to receive intravenous ACA during hemodialysis and possibly even an increase in dosage to prevent decreases in ACA plasma concentrations. Given the limited data and the variability that exists among hemodialysis procedures, no specific recommendations regarding dosing alterations during hemodialysis can be made at this time.
Effect of hospital ownership status and payment structure on the adoption and use of drug-eluting stents for percutaneous coronary interventions

Background: The impact of the use of drug-eluting stents in percutaneous coronary intervention (PCI) on cardiac care is still uncertain. We examined the influence of systemic factors, such as hospital ownership status, organizational characteristics and payment structure, on the use of drug-eluting stents in PCI and the effect on cardiac surgery volume. Methods: We conducted a cross-sectional analysis of drug-eluting stent use in 12 993 patients undergoing PCI with stenting (drug-eluting or bare-metal) and time-series regression analyses of the monthly number of cardiac surgery and PCI procedures performed using data collected from 1998 to 2004 at 13 public and private hospitals in the Emilia-Romagna region of Italy. Results: Public hospitals used drug-eluting stents more selectively than private hospitals, targeting the new device to patients at high risk of adverse events. The time-series regression analyses showed that the number of PCI procedures performed per year increased during this period, both in public (slope coefficient 36.4, 95% confidence interval [CI] 30.2 to 43.1) and private centres (slope coefficient 6.4, 95% CI 3.1 to 9.2 ). Concurrently, there was a reduction in the number of isolated coronary artery bypass graft (CABG) surgeries, although the degree of change was higher in public than in private hospitals (coefficient –16.1 v. –6.2 respectively ). The number of CABG procedures associated with valve surgery decreased in public hospitals (coefficient –5.0, 95% CI –6.1 to –3.8) but increased in private hospitals (coefficient 4.1, 95% CI 2.0 to 6.1). Interpretation: Public and private hospitals behaved differently in adopting drug-eluting stents and in using PCI with drug-eluting stents as a substitute for surgical revascularization.
Delivery and expression of a heterologous antigen on the surface of streptococci

We have developed a system in which a foreign antigen replaces nearly all of the surface-exposed region of the fibrillar M protein from Streptococcus pyogenes and is fused to the C-terminal attachment motif of the M molecule. The fusion protein is thus expressed on the surface of Streptococcus gordonii, a commensal organism of the oral cavity. The antigen chosen to be expressed within the context of the M6 molecule was the E7 protein (98 amino acids) of human papillomavirus type 16. Stable recombinant streptococci were obtained by integrating genetic constructs into the chromosome, exploiting in vivo homologous recombination. The M6-E7 fusion protein expressed on the S. gordonii surface was shown to be immunogenic in mice. This is the first step in the construction of recombinant live vaccines in which nonpathogenic streptococci as well as other gram-positive bacteria may be used as vectors to deliver heterologous antigens to the immune system.
Aggravation de l’anémie et polymorphisme de l’haptoglobine au cours de la drépanocytose au Sénégal

La drepanocytose homozygote s’accompagne d’une augmentation de l’hemoglobine (Hb) plasmatique, susceptible d’exposer les hematies a un stress oxydant. L’haptoglobine presente trois phenotypes majeurs (Hp 1-1, Hp 2-1 et Hp 2-2) susceptibles de fixer l’hemoglobine extracellulaire avec une efficacite differente. L’objectif de ce travail est de voir si la connaissance du phenotype d’Hp pouvait constituer un element predictif de l’anemie severe. Pour cela, il a ete recrute 68 drepanocytaires homozygotes, âges de 5 a 31 ans. Pour chaque patient, un temoin de meme sexe et de meme âge ± 2 ans a ete recrute. Le phenotypage de l’Hp a ete realise par electrophorese sur gel de polyacrylamide. Les resultats du dosage de l’Hb font ressortir que les taux d’Hb sont significativement differentes chez les patients comparees a celles des temoins (p = 0,001). Lorsque la repartition a ete faite en fonction du phenotype d’Hp, une difference statistiquement significative a ete retrouvee entre le phenotype Hp1-1 et le phenotype Hp2-2 (p < 0,001) chez les patients et non chez les temoins. Les resultats de cette etude preliminaire suggereraient que la connaissance du phenotype d’Hp serait un facteur predictif de l’anemie severe au cours de la drepanocytose. Mots cles : Drepanocytose, anemie, phenotypes d’haptoglobine.
The American paradox: the role of energy-dense fat-reduced food in the increasing prevalence of obesity.

Although surveys have reported that the fat content of the diet has decreased over past decades, the prevalence of obesity has continued to rise in Europe and North America. This phenomenon, 'the American paradox', has been attributed partly to an inability of the reduction in dietary fat to reduce excess body fat, and partly to the over-consumption of low-fat products, which, despite their reduced fat content, have in some cases been accused of maintaining a high energy density due to low fibre and water contents, and a high content of refined carbohydrates. In Denmark, the prevalence of obesity has increased in a period in which national dietary surveys have reported a reduction of more than 10% in dietary fat content. Analysing the Danish situation, it seems unlikely that the occurrence of the American paradox in Denmark is caused by the increased consumption of energy-dense, low-fat foods. Other explanations, e.g. the under-reporting of dietary fat in surveys and the clustering of obesity-promoting lifestyles in subgroups of the population, should be sought.
Non-Asymptotic Bounds on the Performance of Dual Methods for Resource Allocation Problems

In this paper, dual methods based on Lagrangian relaxation for multiuser multicarrier resource allocation problems are analyzed. Their application to non-convex resource allocation problems is based on results guaranteeing asymptotic optimality as the number of subcarriers tends to infinity. This work analyzes the workings and performance of dual methods for resource allocation problems with concave rate functions and a finite number of subcarriers. The core results are the convexity of resource allocation problems with subcarrier sharing and an upper bound on the number of subcarriers being shared. Based on these results, absolute and relative performance bounds are presented for dual methods when applied to the resource allocation problem without subcarrier sharing. The exemplary problems considered in this work are sum rate maximization with global and individual power budgets and sum power minimization with global and individual rate demands.
Perspectives: A proposed general model of the “mechanostat” (suggestions from a new skeletal‐biologic paradigm)

This provisional general model for the skeleton's mechanostat spans the biologic “distance” between the organ and macromolecule. It could apply to bone, cartilage and fibrous tissue, and to bones, joints, ligaments and other organs made wholly or in part from the basic tissues. It suggests where small things such as a cytokine effect on some cell should fit in the overall scheme of skeletal physiology. It proposes that interlocking negative feedback loops provide mechanical‐usage‐dedicated message traffic routes on which nonmechanical agents could act to optimize or impair postnatal skeletal adaptations to varied mechanical and nonmechanical challenges, and treatments of disease too. It suggests that future research must try to understand the mechanostat's cell‐ and molecular‐biologic roots. © 1996 Wiley‐Liss, Inc.
The effect of hypothyroidism on Sertoli cell proliferation and differentiation and hormone levels during testicular development in the rat.

In this study we show that 6-propyl-2-thiouracil (PTU) treatment of Wistar rats from birth up to day 26 p.p. retards the morphological differentiation of Sertoli cells, and prolongs the proliferation of these cells up to day 30. Sertoli cell numbers per testis, determined at day 36, were increased by 84% compared to controls. PTU treatment increased serum thyroid-stimulating hormone (TSH) levels and reduced serum levels of thyroxine (T4) from 5 days onwards, indicative of severe hypothyroidism. Follicle-stimulating hormone (FSH) levels were reduced from day 5 to 9, normal at day 12 and 16, and reduced again from day 20 to 36. Inhibin levels were decreased from day 9 to 20 and increased at 36 days of age. The increase in the number of Sertoli cells per testis in PTU treated rats, as has been reported in the present study, is likely to be responsible for the increased testis size observed by other groups (1) in these animals, when adult.
Fuzzy Neural Networks and Genetic Algorithms for Medical Images Interpretation

In this paper, we propose an approach for detection and specification of anomalies present in medical images. The idea is to combine three metaphors: neural networks, fuzzy logic and genetic algorithms in a hybrid system. The neural networks and fuzzy logic metaphors are coupled in one system called fuzzy neural networks. The genetic algorithm adds to this hybridizing the property of total research like an initialization of the fuzzy neural networks training algorithm witch is based on an adapted version of the back propagation algorithm. After applying the growing region algorithm to extract regions, the fuzzy neural network detect the suspect regions, which are interpreted by the fuzzy neural network of specification. Some of experimental results on brain images show the feasibility of the proposed approach
Objectively measured daily physical activity related to cardiac size in young children

Training studies in children have suggested that endurance training can give enlargement of cardiac dimensions. This relationship has not been studied on a population‐based level in young children with objective methods. A cross‐sectional study was made of 248 children (140 boys and 108 girls), aged 8–11 years, from a population‐based cohort. Left ventricular end‐diastolic diameter (LVDD) and left atrial end‐systolic diameter (LA) were measured with echocardiography and indexed for body surface area (BSA). Physical activity was assessed by accelerometry, and the duration of vigorous physical activity per day (VPA) was calculated. Acceptable accelerometer and echocardiography measurements were obtained in 228 children (boys=127, girls=101). Univariate correlations between VPA and LVDD were indexed for BSA in boys (r=0.27, P<0.05) and in girls (r=0.10, NS). Multiple regression analysis showed that independent factors for LVDD, indexed for BSA for boys, were age and VPA. LA indexed for BSA was not related to physical activity variables in either gender. No clear relationship exists between cardiac size and daily physical activity in children aged 8–11 years. This suggests that significant cardiac remodelling due to volume exposure secondary to a high amount of physical activity begins later in life.
Loss of G Protein γ7 Alters Behavior and Reduces Striatal αolf Level and cAMP Production*

The G protein βγ-dimer is required for receptor interaction and effector regulation. However, previous approaches have not identified the physiologic roles of individual subtypes in these processes. We used a gene knockout approach to demonstrate a unique role for the G protein γ7-subunit in mice. Notably, deletion ofGng7 caused behavioral changes that were associated with reductions in the αolf-subunit content and adenylyl cyclase activity of the striatum. These data demonstrate that an individual γ-subunit contributes to the specificity of a given signaling pathway and controls the formation or stability of a particular G protein heterotrimer.
A statistical model for 1-hour- to 24-hour-ahead prediction of hourly ozone concentrations at ground level in Singapore

A spatio-temporal statistical model is proposed for 1- to 24-hour-ahead prediction of hourly ozone concentrations. This is a joint work with the National Environmental Agency Singapore, and is Singapore’s first predictive model for ozone concentrations. Unlike many existing models which focus on either daily maximum or 8h average daylight ozone concentrations, the present work is concerned with the prediction of hourly ozone concentrations which are usually associated with higher variability. A recently proposed framework for spatiotemporal prediction is used to model ozone concentration data. The macroscale spatio-temporal variation of ozone concentrations is modeled by a linear function of five carefully constructed predictors, while the micro-scale variation is captured by a mean-zero spatio-temporally correlated random process. We show that this model also provides useful insights about the effects of some complex environmental processes on ozone concentration; this is indeed an attractive feature for any data-driven air quality model.
Built Environment and Physical Activity Promotion: Place-Based Obesity Prevention Strategies

This paper seeks to encourage continued innovation in translating built environment and transportation-focused physical activity research into practice. Successful strategies, policies, and tools from across the U.S. and globally that demonstrate potential for wider-scale implementation are highlighted. The importance of building practice and translational research partnerships with groups and organizations outside traditional public health spheres, such as those who work in real estate and land-use development, is also discussed.
Kinesin-3 and dynein mediate microtubule-dependent co-transport of mRNPs and endosomes

Long-distance transport of mRNAs is important in determining polarity in eukaryotes. Molecular motors shuttle large ribonucleoprotein complexes (mRNPs) containing RNA-binding proteins and associated factors along microtubules. However, precise mechanisms including the interplay of molecular motors and a potential connection to membrane trafficking remain elusive. Here, we solve the motor composition of transported mRNPs containing the RNA-binding protein Rrm4 of the pathogen Ustilago maydis. The underlying transport process determines the axis of polarity in infectious filaments. Plus-end-directed Kin3, a kinesin-3 type motor, mediates anterograde transport of mRNPs and is also present in transport units moving retrogradely. Split dynein Dyn1–Dyn2 functions in retrograde movement of mRNPs. Plus-end-directed conventional kinesin Kin1 is indirectly involved by transporting minus-end-directed dynein back to plus ends. Importantly, we additionally demonstrate that Rrm4-containing mRNPs colocalise with the t-SNARE Yup1 on shuttling endosomes and that functional endosomes are essential for mRNP movement. Either loss of Kin3 or removal of its lipid-binding pleckstrin-homology domain abolishes Rrm4-dependent movement without preventing colocalisation of Rrm4 and Yup1-positive endosomes. In summary, we uncovered the combination of motors required for mRNP shuttling along microtubules. Furthermore, intimately linked co-transport of endosomes and mRNPs suggests vesicle hitchhiking as mode of mRNP transport.