Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of alkB genes within n‐alkane‐degrading bacteria

Fifty‐four bacterial strains belonging to 37 species were tested for their ability to assimilate short chain and/or medium chain liquid n‐alkanes. A gene probe derived from the alkB gene of Pseudomonas oleovorans ATCC 29347 was utilized in hybridization experiments. Results of Southern hybridization of PCR‐amplificates were compared with those of colony hybridization and dot blot hybridization. Strongest signals were received only from Gram‐negative bacteria growing solely with short n‐alkanes (C10). Hybridization results with soil isolates growing with n‐alkanes of different chain lengths suggested as well that alkB genes seem to be widespread only in solely short‐chain n‐alkane‐degrading pseudomonads. PCR products of Rhodococcus sp. , Nocardioides sp. , Gordona sp. and Sphingomonas sp. growing additionally or solely with medium‐chain n‐alkane as hexadecane had only few sequence identity with alkB though hybridizing with the gene probe. The derived amino acid sequence of the alkB‐amplificate of Pseudomonas aureofaciens showed high homology (95%) with AlkB from Ps. oleovorans. alkB gene disruptants were not able to grow with decane.
Optimum diversity receiver structures for combining with estimation errors

Optimum diversity receivers that operate in the presence of estimation errors are proposed. Previous work has mainly examined the performance of maximal ratio combining (MRC) with estimation errors. It is shown that MRC is not optimal when estimation errors occur. Moreover, it is shown that the optimum diversity receiver in the presence of estimation errors can be derived by using knowledge of the channel estimate statistics. Numerical results show that the optimum diversity receiver can perform as much as 2.0 dB in signal-to-noise ratio better than the conventional MRC receiver in some cases.
Perceptual Encoding of Fingerspelled and Printed Alphabet by Deaf Signers: An fMRI Study

We measured brain activation during the perception of fingerspelled letters, printed letters, and abstract shapes (control condition) in six congenitally, profoundly deaf signers and six normal hearing subjects. Normal hearing subjects showed essentially extrastriate activation in the fingerspelled letters and printed letters conditions whereas deaf subjects showed activation of a broader network in printed letters and fingerspelled conditions, comprising supplementary frontal and posterior areas, and the supramarginal gyrus (Brodmann Area 6). These results suggest that, on one hand, different cerebral areas in deaf and hearing subjects mediate processing of printed letters and, on the other hand, common cerebral areas are activated in deaf signers when they are engaged in processing fingerspelled or printed letters.
Decreased TSP-1 following percutaneous coronary intervention is associated with major adverse cardiac events in ST-elevation myocardial infarction.

BACKGROUND TSP-1 is a vasoconstrictive protein, which is released from both endothelium and cardiomyocytes during ischemia and promotes platelet aggregation and adhesion to subendothelial layers in atherosclerotic lesions. During myocardial ischemia and reperfusion, TSP-1 disturbs local microcirculation by disrupting both NO-signaling as well as VEGF-pathways by activation of CD47 and CD36. Furthermore, activation of TGF-ß might induce excessive fibrosis after infarction. It was assumed that TSP-1 is washed out after successful coronary reperfusion. In this study, we examined circulating TSP-1 post emergency PCI as a risk factor for major adverse cardiac events after STEMI with and without ventricular fibrillation. METHODS TSP-1 levels in platelet poor plasma were measured in 54 patients after ST-elevation myocardial infarction. Major adverse cardiac events were monitored for 426 days. RESULTS Patients with decreased TSP levels after coronary stenting showed a significantly higher risk for MACE than patient with higher TSP levels (TSP-1[d0]: n = 46, no MACE = 16.38 ± 1.98 ug/mL vs. MACE 7.11 ± 1.54 ug/mL; p = 0.003). Kaplan-Meyer-analysis for MACE showed a better outcome above 10 ug/mL (p = 0.02). For MACE later than 3 months post-STEMI, the corresponding Kaplan-Meier-analysis yielded a p-value of 0.01. The number needed to diagnose for late MACE was 2.158. CONCLUSION Low plasma levels of TSP1 after PCI are associated with MACE. Due to its procoagulant effects and dysregulation of microvascular tone, adequately powered prospective studies are warranted to test the impact of TSP-1 on cardiac microcirculation, endothelial function and remodeling. TSP-1 might serve as a new diagnostic and therapeutic approach in cardiovascular disease.
Ethical leadership outcomes in nursing: A qualitative study

Background: Leadership style adopted by nursing managers is a key element in progress and development of nursing and quality of healthcare services received by the patients. In this regard, the role of ethical leadership is of utmost importance. Objectives: The objective of the study was to elaborate on the ethical leadership and its role in professional progress and growth of nurses in the light of work condition in health providing institutes. Methods: The study was carried out as a qualitative study following conventional content analysis method. In total, 14 nursing faculty members and nursing managers at different levels were selected through purposive sampling method. Semi-structured interviews were used for data gathering. The data were analyzed using latent content analysis and constant comparison analysis. Ethical considerations: This study was conducted in accordance with ethical issues in research with human participants and national rules and regulations related to informed consent and confidentiality. The study was approved by the Committee of Ethics in Research at the Shahid Beheshti University of Medical Sciences in Tehran, Iran, under the code: sbmu.rec. 1393.695 on 15 February 2015. Findings: Five subcategories were obtained based on the analysis, which constituted two main categories including “all-inclusive satisfaction” and “productivity. ” Nursing leaders highlighted the point that their ethical behavior creates “inner satisfaction of the leader,” “employees’ job satisfaction,” and “patients’ satisfaction. ” Improvement of productivity was another outcome of ethical behavior of the leaders. This kind of behavior resulted in “providing better services” and “inspiring ethical behavior in the employees. ” It has great influence on progress and growth of the nursing profession. Conclusion: By creating an ethical climate, ethical leadership leads to positive and effective outcomes—for the patients as well as for the nurses and the leaders—and professional progress and development of the nursing profession. Therefore, an ethical work environment that supports nurses’ progress and development can be developed by paying more attention to moralities in recruitment, teaching ethical values to the leaders, and using a systematic and objective approach to assess morality in the environment.
Joint trajectory generator for powered orthosis based on gait modelling using PCA and FFT

SUMMARY In this work, we propose a method able to find user-oriented gait trajectories that can be used in powered lower limb orthosis applications. Most research related to active orthotic devices focuses on solving hardware issues. However, the problem of generating a set of joint trajectories that are user-oriented still persists. The proposed method uses principal component analysis to extract shared features from a gait dataset, taking into consideration gait-related variables such as joint angle information and the user's anthropometric features, used directly in an orthosis application. The trajectories of joint angles used by the model are represented by a given number of harmonics according to their respective Fourier series analyses. This representation allows better performance of the model, whose capability to generate gait information is validated through experiments using a real active orthotic device, analysing both joint motor energy consumption and user metabolic effort.
Denaturants can accelerate folding rates in a class of globular proteins

We present a lattice Monte Carlo study to examine the effect of denaturants on the folding rates of simplified models of proteins. The two‐dimensional model is made from a three‐letter code mimicking the presence of hydrophobic, hydrophilic, and cysteine residues. We show that the rate of folding is maximum when the effective hydrophobic interaction ϵH is approximately equal to the free energy gain ϵS upon forming disulfide bonds. In the range 1 ≤ ϵH/ϵS ≤ 3, multiple paths that connect several intermediates to the native state lead to fast folding. It is shown that at a fixed temperature and ϵS the folding rate increases as ϵH decreases. An approximate model is used to show that ϵH should decrease as a function of the concentration of denaturants such as urea or guanidine hydrochloride. Our simulation results, in conjunction with this model, are used to show that increasing the concentration of denaturants can lead to an increase in folding rates. This occurs because denaturants can destabilize the intermediates without significantly altering the energy of the native conformation. Our findings are compared with experiments on the effects of denaturants on the refolding of bovine pancreatic trypsin inhibitor and ribonuclease T1. We also argue that the phenomenon of denaturant‐enhanced folding of proteins should be general.
The embedding kernel on the IBM victor multiprocessor for program mapping and network reconfiguration

The design of a functional embedding kernel (E-kernel) to support automatic mapping of parallel programs having higher dimensional mesh or torus task graphs onto the 2D mesh network of Victor is described. E-kernel supports two levels of embeddings: in the first level, the mapping of a parallel program onto the system network; and in the second level, the mapping of a network topology onto the 2D mesh. The first level of embeddings corresponds to the support of automatic program mapping, and the second level the support of network reconfiguration. <<ETX>>
Truncated variants of gp120 bind CD4 with high affinity and suggest a minimum CD4 binding region.

The envelope glycoprotein, gp120, of human immunodeficiency virus type 1 (HIV‐1) binds the cellular protein CD4 with high affinity. By deletion we show that 62 N‐ and 20 C‐terminal residues along with the V1, V2 and V3 variable regions of gp 120 are unnecessary for CD4 binding. A 287 residue variant (ENV59), missing those 197 amino acids, binds to CD4 with high affinity. A polyclonal antibody failed to efficiently precipitate ENV59 which is consistent with the loss of immunodominant antigenic structures in the regions deleted. This suggests that ENV59 may have potential as an immunogen, able to elicit antibodies against more conserved regions of gp120. Additionally, complementing co‐expressed gp120 fragments as well as a circularly permuted molecule bind CD4, and suggest either that the molecular termini are adjacent in the folded structure, or that an N‐terminal region folds into the structure unconstrained by its method of attachment to the rest of the molecule.
ADAPTING EXISTING MODELS TO EXAMINE EFFECTS OF AGRICULTURAL CONSERVATION PROGRAMS ON STREAM HABITAT QUALITY 1

Annual expenditures by the federal government in the United States for agricultural conservation programs increased about 80 percent with passage of the 2002 Farm Bill. However, environmental benefits of these programs have not been quantified. A national project is under way to estimate the effect of conservation practices on environmental resources. The watershed models intended for use in that project are focused on water quantity and quality and have minimal habitat assessment capability. Major impairments to aquatic ecosystems in many watersheds consist of physical habitat degradation, not water quality, suggesting that current models for this national initiative do not address one of the most significant aspects of aquatic ecosystem degradation. Currently used models contain some components relevant to aquatic habitat, and this paper describes specific components that should be added to allow rudimentary stream habitat quality assessments. At least six types of variables could be examined for ecological impact: land use, streamflow, water temperature, streambed material type, large woody debris, and hydraulic conditions at base flow. All of these variables are influenced by the presence, location, and quality of buffers. Generation of stream corridor ecological or habitat quality indices might contribute to assessments of the success or failure of conservation programs. Additional research is needed to refine procedures for combining specific measures of stream habitat into ecologically meaningful indices.
Selección de contenidos basada en reuso para caches compartidas en exclusión

Publicaciones previas revelan que el flujo de referencias que llega a la cache compartida (SLLC) de un chip multiprocesador muestra poca localidad temporal. Sin embargo, muestra localidad de reuso, es decir, los bloques referenciados varias veces tienen mas probabilidad de ser referenciados en un futuro. Esto provoca que, si se realiza una gestion convencional, el uso de la cache es ineficiente. Existen varias propuestas que abordan este problema para caches inclusivas, pero pocas que se centren en caches exclusivas. En este trabajo se propone un nuevo mecanismo de seleccion de contenidos para caches exclusivas que aprovecha la localidad de reuso que presentan los accesos a la SLLC. Consiste en incluir un Detector de Reuso entre cada cache L2 y la SLLC. Su mision es detectar bloques sin reuso para evitar que sean insertados en la SLLC. Esta propuesta se evalua con un conjunto de cargas multiprogramadas ejecutando en un simulador detallado de un sistema con 8 procesadores en chip y su jerarquia de memoria. Los resultados muestran que el Detector de Reuso permite incrementar el rendimiento por encima de otras propuestas recientes como CHAR o la Reuse Cache. Por ejemplo, para una configuracion del Detector de Reuso balanceada entre coste y prestaciones, se obtiene un 8,5% de reduccion de la tasa de fallos de la SLLC y un incremento del IPC de un 2,5%, frente a un sistema base con reemplazo TC-AGE.
ON THE EARLY-TIME EXCESS EMISSION IN HYDROGEN-POOR SUPERLUMINOUS SUPERNOVAE

We present the light curves of the hydrogen-poor superluminous supernovae (SLSNe I) PTF 12dam and iPTF 13dcc, discovered by the (intermediate) Palomar Transient Factory. Both show excess emission at early times and a slowly declining light curve at late times. The early bump in PTF 12dam is very similar in duration (∼10 days) and brightness relative to the main peak (2–3 mag fainter) compared to that observed in other SLSNe I. In contrast, the long-duration (>30 days) early excess emission in iPTF 13dcc, whose brightness competes with that of the main peak, appears to be of a different nature. We construct bolometric light curves for both targets, and fit a variety of light-curve models to both the early bump and main peak in an attempt to understand the nature of these explosions. Even though the slope of the late-time decline in the light curves of both SLSNe is suggestively close to that expected from the radioactive decay of 56Ni and 56Co, the amount of nickel required to power the full light curves is too large considering the estimated ejecta mass. The magnetar model including an increasing escape fraction provides a reasonable description of the PTF 12dam observations. However, neither the basic nor the double-peaked magnetar model is capable of reproducing the light curve of iPTF 13dcc. A model combining a shock breakout in an extended envelope with late-time magnetar energy injection provides a reasonable fit to the iPTF 13dcc observations. Finally, we find that the light curves of both PTF 12dam and iPTF 13dcc can be adequately fit with the model involving interaction with the circumstellar medium.
The emerging relevance of heterogeneity of treatment effect in clinical care: a study using stage IV prostate cancer as a model.

AIM Heterogeneity of treatment effect (HTE) occurs when patient factors modify a treatment's effect on health outcomes due to interactions between these factors and the treatment. This article reviews evidence regarding HTE in stage IV prostate cancer (S4PC). METHOD A systematic literature review was conducted in the MEDLINE and PubMed databases. Inclusion criteria required that articles examine the treatment-related impact of HTE factors on survival, adverse events or health-related quality of life in S4PC patients. The quality of evidence was graded good, fair or poor based on Agency for Healthcare Research and Quality guidelines. RESULTS The search identified 2659 articles, of which 92 met the inclusion/exclusion criteria. HTE in S4PC was studied for biologic factors including age, race, clinical signs/symptoms, measures of S4PC disease severity, genetic factors, laboratory data, prior treatment, concurrent medications and comorbidities. Nonbiologic factors that were studied included social, geographic and dietary factors. Age and race seldom showed any correlation with S4PC outcomes. CONCLUSION Diverse biologic and nonbiologic factors contribute to HTE in S4PC. This review in S4PC also provides an approach for examining HTE for other medical conditions. Ultimately, such knowledge can help oncologists prescribe more personalized medicine, help patients make more informed treatment choices, and inform policy-making and treatment coverage decisions.
Vitamin D and its analogues: do they protect against cardiovascular disease in patients with kidney disease?

BACKGROUND Patients with chronic kidney disease (CKD) are at high risk for cardiovascular disease, and despite recent advances in hypertension control, anemia management, and dialysis adequacy, mortality remains high. Improved understanding of nontraditional risk factors, including those present at early phases in CKD, may lead to novel therapeutic strategies. CKD has been demonstrated to be an independent risk factor for cardiovascular disease in the general population, but data are lacking as to the associated potential abnormalities that occur in association with reduced glomerular filtration rate (GFR), which may contribute to this increased risk. Data are accumulating regarding the role of abnormalities of calcium, phosphorus, vitamin D, and parathyroid hormone (PTH) in cardiovascular disease. Vitamin D deficiency is present even in the early stages of CKD. Vitamin D plays a central role in calcium-phosphorus homeostasis, regulation of PTH, and formation and maintenance of bone. However, until recently, vitamin D has not been considered to have a biologic role in CKD beyond mineral regulation, or has been considered as a negative factor contributing to soft tissue and cardiovascular calcification. In light of recent observational studies showing an association of vitamin D therapy and survival benefit in hemodialysis patients, the effects of vitamin D on cardiovascular system have become a heavily debated issue. METHODS A Medline search was performed to identify relevant literature describing the role of vitamin D in the pathogenesis of cardiovascular disease. Both the experimental and clinical literatures in English were reviewed. RESULTS The accumulating published data demonstrate both associative relationships and mechanisms for biologic plausibility. The following three potential mechanisms may be important for the protective effects of vitamin D against cardiovascular disease mortality: vitamin D can inhibit various aspects of inflammation, which have been established as a key pathogenic mechanism in atherosclerosis; vitamin D exerts an antiproliferative effect on myocardial cell hypertrophy and proliferation, which underlies the pathogenesis of congestive heart failure; and vitamin D acts as a negative endocrine regulator for the renin-angiotensin system, which itself plays an important independent role in hypertension and cardiovascular health. CONCLUSION Vitamin D deficiency might be an underestimated nonclassical risk factor for cardiovascular disease in CKD. Based on a review of the evidence, from both basic science and clinical studies, this article supports the possible protective role of vitamin D beyond its effect on mineral metabolism, and suggests the need for ongoing evaluation of the role of vitamin D in cardiovascular health in the CKD population.
Imitation et agentivité

Ce chapitre propose une analyse conceptuelle de l'imitation comme action de second ordre. Une action de second ordre suppose 1) que l'agent se represente l'action de premier ordre, 2) que l'action de premier ordre ait veritablement eu lieu (condition de factivite). La notion de plan de reference de l'imitation permet de mettre en evidence le role de la representation du contexte dans la production et dans l'interpretation de l'imitation. L'agent peut imiter pour atteindre le meme objectif que le modele, pour marquer son intention de partager les objets dans un projet commun, mais aussi pour rendre saillante telle ou telle propriete du modele, ou pour marquer la difference entre l'action effectuee et l'action attendue. Cette variete des plans de reference explique que la reussite de la communication par imitation exige de l'emetteur et du destinataire qu'ils possedent des capacites de mentalisation, c'est-a-dire qu'ils puissent simuler l'action sur des plans de reference distincts.
Value of FDG PET Imaging in the Management of Patients With Thyroid, Neuroendocrine, and Neural Crest Tumors

Objectives: The purpose of this study was to evaluate the value and impact on management of FDG PET imaging in patients with biopsy-proved neuroendocrine and neural crest tumors, as well as thyroid carcinoma of various types. Materials and Methods: This is a retrospective review of imaging and clinical data of 60 consecutive patients presenting for evaluation of suspected recurrence who underwent FDG PET imaging between August 1993 and February 2002. All patients were referred for PET because of equivocal findings on conventional evaluation (most often increasing tumor markers and negative conventional workup) or for restaging. The final diagnosis was established with pathology (n = 19) or at least 6 months of follow-up (n = 41). The FDG images were acquired 1 hour after the intravenous administration of 10 mCi FDG with 1 of 2 dedicated PET tomographs (Siemens ECAT 933, CTI, Knoxville, TN; and GE Advance, General Electric Medical Systems, Milwaukee, WI). Results: Thirty-four patients had recurrent disease and 26 had no evidence of recurrence. FDG PET imaging revealed at least as many focal abnormalities as concurrent CT, magnetic resonance, or other nuclear imaging modalities in 46 of 60 patients (77%). There were 17 patients (28%) in whom FDG PET found abnormalities not seen with other modalities. In the small group (n = 18) of cases of carcinoid, pheochromocytoma, Merkel cell tumor, and neuroblastoma, all cases were true positive (T+) or true negative (T–). In the group of 42 cases of thyroid carcinoma, the sensitivity was 67%. There were 16 T+, 18 T–, and 8 false-negative (F–) cases. Six F– cases presented with increasing thyroglobulin levels and negative whole-body I-131 scans. Four of these 6 F– cases were proved by surgery, 1 by a positive post I-131 therapy scan, and 1 by normalization of thyroglobulin levels after I-131 therapy. Two of the 8 F– PET cases had a positive I-131 scan. FDG PET imaging had an impact on the management of 13 of 60 of these patients (22%) by demonstrating extensive metastases and canceling surgery (n = 2), and by detecting recurrence and guiding surgery (n = 5) or radiation therapy (n = 6). Conclusions: FDG PET is helpful in the evaluation of thyroid, neuroendocrine, and neural crest tumors. Although the sensitivity was only 76%, there were no false-positive findings, and FDG PET findings changed the management of 22% of the patients.