Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of insertion sequences associated with Tn1546 and clonal diversity of vancomycin-resistant enterococci isolated from patients in Tehran, Iran

Background and objectives Infection with vancomycin-resistant enterococci (VRE) has caused a therapeutic problem. VanA and VanB resistant types are the predominant phenotypes among vancomycin resistant enetrococci. Transposon 1546 (Tn1546) harboring the vanA gene cluster, plays an important role in the horizontal transfer of vanA gene. In this study, we examined the phenotypic and genotypic diversity of a number of clinical VRE. Materials and Methods Twenty-four clinical VRE isolated from two university hospitals in Tehran were examined based on their antimicrobial susceptibility, Tn1546 related element organization and pulsed-field gel electrophoresis (PFGE) patterns. Integration of well-studied insertion sequence elements IS1216V, IS1542 and IS1251 was examined by PCR mapping and sequencing. Results From 24 isolates, 15 isolates with VanA phenotype and 9 isolates with VanB phenotype were identified which both groups interestingly possessed the vanA gene. According to PCR mapping, our isolates were assigned to 6 main groups. In 14 (58.3%) isolates, IS1216V was inserted in vanX-vanY region and/or in truncated left-hand of Tn1546-like elements. In 11 (45.8%) isolates, both IS1216V and IS1542 were inserted in vanX-vanY and orf2-vanR regions, respectively and none of them harbored IS1251. Interestingly, PFGE of the isolates showed a high degree of diversity. Conclusion PCR mapping revealed that VanA elements in our isolates were highly heterogeneous. Overall, we found no correlation between transposon type and PFGE pattern. Genetic diversity of VRE provides practical information for epidemiological studies and our data showed horizontal transfer of VRE in this region.
Changes in circulating transcobalamin II after injection of cyanocobalamin.

Since transcobalamin II is the plasma binder of vitamin B12(cobalamin) that mediates delivery of cobalamin to tissues, we measured circulating levels of transcobalamin II after intravenous injection unlabeled cyanocobalamin in 12 control subjects and, because the liver is a major source of transcobalamin II, in eight patients with decompensated cirrhosis. Thirty minutes after injection of cyanocobalamin (200 ng per kilogram of body weight), total transcobalamin II (unsaturated plus cobalamin bound) declined in all 20 subjects to levels that averaged (+/- S.E.) 53.5 +/- 4.6 per cent of initial values. Subsequently, unsaturated transcobalamin II rapidly increased so that by eight hours, total transcobalamin II approached preinjection levels. Rates of regeneration of transcobalamin II were similar in control subjects and patients with liver disease. Unlike total transcobalamin II, total transcobalamin I was unaltered by injection of cyanocobalamin. Moreover, addition of cyanocobalamin to plasma in vitro did not alter measurements of total transcobalamin II. The rapid response of circulating transcobalamin II to cyanocobalamin injection strongly supports a dynamic role for this polypeptide during transport of a relatively large load of cobalamin.
Adjuvant chemotherapy after reduced craniospinal irradiation dose in children with average-risk medulloblastoma: a 5-year follow-up study.

PURPOSE This study was undertaken to determine the effect of adjuvant chemotherapy combined with reduced-dose craniospinal irradiation (CSI) on survival and neurocognitive sequelae of radiotherapy (RT) in patients with average- risk medulloblastoma above the age of 3 years. METHODS Thirty-three children between 3 and 10 years of age with average-risk medulloblastoma were treated with postoperative reduced-dose CSI (24.0 Gy) and 30.6 Gy of local RT (total of 54.6 Gy) and then with adjuvant chemotherapy consisting of cisplatin, vincristine, and cyclophosphamide every 4 weeks for 8 cycles. RESULTS At 5 years, event-free survival (EFS) was 79%, while overall survival (OS) was 85%. Sites of relapse were local in 3%, neuraxis in 9% and both local and neuraxis in 9% of the patients. Chemotherapy was well tolerated. Hematopoietic toxicity was the most predominant side effect followed by vomiting and ototoxicity. No grade III or IV nephrotoxicity or neurotoxicity and no treatment-related deaths were encountered. Insignificant decline of intelligence quotient (IQ) was reported in 28.6% of the patients. CONCLUSION The preliminary results of adjuvant chemotherapy after reduced-dose CSI in average-risk medulloblastoma patients are encouraging and effective, and can be applied safely with acceptable toxicity.
Racial differences in adherence and response to combined treatment for full and subthreshold post-traumatic stress disorder and alcohol use disorders: A secondary analysis

ABSTRACT We conducted a secondary data analysis to examine whether there were racial differences in adherence and treatment outcomes for participants with co-occurring full and subthreshold post-traumatic stress disorder (PTSD) and alcohol/substance use disorders (A/SUD) who were treated with Seeking Safety (a cognitive-behavioral therapy) and sertraline or Seeking Safety and placebo as part of a clinical trial. Bivarate analyses examined the association between race and adherence, and generalized estimating equations assessed whether race moderated the effect of combination treatment on PTSD and alcohol use outcomes. Except for education, there were no statistically significant racial differences in baseline demographic and psychiatric characteristics. African Americans and Caucasians were equally adherent in number of psychotherapy and medication sessions attended and medication compliance. After controlling for baseline demographics and psychiatric symptoms, however, a race by treatment condition interaction emerged suggesting that African Americans who received the Seeking Safety and sertraline treatment had significantly lower PTSD symptom severity posttreatment and at six months follow-up compared to their counterparts who received Seeking Safety and placebo. No differential effect of treatment condition was found for Caucasians. Moreover, results indicated that a diagnosis of major depressive disorder negatively impacted PTSD symptom recovery for African American participants but not for Caucasians. In conclusion, no differences emerged between African Americans and Caucasians in adherence to combination treatments for PTSD and A/SUD. Findings also suggest assessment and treatment of MDD among African Americans may improve treatment outcomes. More research is needed to determine whether the differential response to Seeking Safety and sertraline among African Americans compared to Caucasians can be replicated.
Older age and liver transplantation: A review

Patients older than 60 are undergoing transplantation with increasing frequency. Reports from several transplant centers document that overall short‐term patient survival rates in seniors undergoing liver transplantation are comparable to survival rates of younger adults. However, specific subgroups of older patients may not fare as well. Seniors with far‐advanced end‐stage liver disease are high‐risk for liver transplantation and have poor survival rates. In addition, seniors older than 65 have worse outcomes than those who are 60 to 65, and studies have shown increased mortality with increasing age as a continuous variable. On the other hand, the majority of seniors who survive liver transplantation have full or only minimally limited functional status. Preoperative evaluation of older patients for transplantation requires careful screening to exclude cardiopulmonary disease, malignancy, and other diseases of the aged. Paradoxically, seniors may benefit from a senescent immune system, which results in decreased requirements for immunosuppressive drugs, and possibly a lower rate of acute allograft rejection. Despite good overall short‐term survival in the elderly, long‐term survival may be worse because of an increased rate of long‐term complications, such as malignancy and heart disease. In conclusion, although advanced age is a negative risk factor, advanced age alone should not exclude a patient from liver transplantation; however, it mandates thorough pretransplant evaluation and careful long‐term follow‐up with attention to usual health maintenance issues in the elderly. (Liver Transpl 2004;10:957–967.)
Self-Expandable Metallic Stent Placement in Malignant Gastric Outlet Obstruction

Abstract Malignant gastric outlet obstruction is a late complication of intraabdominal malignancy. Self-expandable metallic stent placement has been a safe palliative treatment to relieve obstructive symptoms. We aimed to assess the efficacy and safety of metallic stents in our patients and analyzed the clinical outcome of different brands. Seventy-one patients with inoperable gastric outlet obstruction receiving WallFlex enteral stents (WallFlex group) or Bonastents (Bonastent group) since April 2010 were analyzed retrospectively. The overall technical and clinical success rates of stent placement were 100% and 93%, respectively. The baseline characteristics and clinical outcomes including procedure-related complications, restenosis, and reintervention rates were comparable between the 2 groups. However, the Bonastent group had a higher rate of stent fracture than the WallFlex group (13.3% vs 0%, P = 0.03). The mean duration of overall stent patency was 132.7 days. The mean duration of survival was 181.9 days. Resumption of regular diet or low residual diet at day 7 after stent insertion predicted stent patency (hazard ratio [HR]: 0.28, P = 0.01). Cancer with gastric origin (HR: 0.25, P = 0.045) and poststent chemotherapy (HR: 0.38, P = 0.006) predicted lower mortality; however, peritoneal carcinomatosis (HR: 3.09, P = 0.04) correlated with higher mortality. Metallic stent placement is a safe and effective method for relieving gastric outlet obstruction. Except higher rate of stent fracture in the Bonastent group, there is no significant difference in clinical outcomes between the Bonastent group and the WallFlex group.
Impeded Industrial Restructuring: The Growth Penalty

This paper documents that a process of industrial restructuring has been transforming the developed economies, where large corporations are accounting for less economic activity and small firms are accounting for a greater share of economic activity. Not all countries, however, are experiencing the same shift in their industrial structures. Very little is known about the cost of resisting this restructuring process. The goal of this paper is to identify whether there is a cost, measured in terms of foregone growth, of an impeded restructuring process. The cost is measured by linking growth rates of European countries to deviations from the optimal industrial structure. The empirical evidence suggests that countries impeding the restructuring process pay a penalty in terms of foregone growth.
An evaluation of bipartitioning techniques

Logic partitioning is an important issue in VLSI CAD, and has been an active area of research for at least the last 25 years. Numerous approaches have been developed and many different techniques have been combined for a wide range of applications. In this paper, we examine many of the existing techniques for logic bipartitioning and present a methodology for determining the best mix of approaches. The result is a novel bipartitioning algorithm that includes both new and pre-existing techniques. Our algorithm produces results that are at least 17% better than the state-of-the-art while also being efficient in run time.
A Tight Bound of Hard Thresholding

This paper is concerned with the hard thresholding operator which sets all but the $k$ largest absolute elements of a vector to zero. We establish a {\em tight} bound to quantitatively characterize the deviation of the thresholded solution from a given signal. Our theoretical result is universal in the sense that it holds for all choices of parameters, and the underlying analysis depends only on fundamental arguments in mathematical optimization. We discuss the implications for two domains: Compressed Sensing. On account of the crucial estimate, we bridge the connection between the restricted isometry property (RIP) and the sparsity parameter for a vast volume of hard thresholding based algorithms, which renders an improvement on the RIP condition especially when the true sparsity is unknown. This suggests that in essence, many more kinds of sensing matrices or fewer measurements are admissible for the data acquisition procedure. Machine Learning. In terms of large-scale machine learning, a significant yet challenging problem is learning accurate sparse models in an efficient manner. In stark contrast to prior work that attempted the $\ell_1$-relaxation for promoting sparsity, we present a novel stochastic algorithm which performs hard thresholding in each iteration, hence ensuring such parsimonious solutions. Equipped with the developed bound, we prove the {\em global linear convergence} for a number of prevalent statistical models under mild assumptions, even though the problem turns out to be non-convex.
Early results of the Sorin® Perceval S sutureless valve: systematic review and meta-analysis.

BACKGROUND Minimally invasive aortic valve replacement (MAVR) has demonstrated a benefit with respect to increased patient satisfaction due to minimised pain and earlier recovery. Sutureless valves may benefit MAVR and conventional aortic valve replacement (AVR) by reducing operative times and blood transfusion requirements. The Perceval valve (Sorin, Salluggia, Italy) is a self-expanding prosthesis made from bovine pericardium mounted in a nitinol stent, designed to simplify the implantation of an aortic valve. This meta-analysis evaluates the clinical, haemodynamic, and survival outcomes of the Perceval sutureless valve. METHODS An electronic search of 4 databases was performed from January 2000 to December 2016. Primary outcomes included mortality and stroke. Secondary outcomes included minimally invasive access, paravalvular leak, overall long-term survival, postoperative echocardiographic findings, and functional class improvement. RESULTS After the application of inclusion and exclusion criteria, 14 of 66 relevant articles were selected for assessment. Of these 14 studies, a total number of 2,505 patients were included. The current evidence on the Perceval valve for aortic valve disease is limited to observational studies only. Minimally invasive surgery was performed in 976 patients, of which 336 were via the right anterior thoracotomy approach. The Perceval M and L sutureless valves were the most frequently used, 782 and 770 respectively. The incidence of major adverse events included 30-day mortality (0 to 4.9%), cerebrovascular accident (0 to 3%), permanent pacemaker insertion (0 to 17%), moderate to severe paravalvular leak (0 to 8.6%), and re-operation (0 to 4.8%). Post-operative mean aortic valve gradient ranged from 9 to 15.9 mmHg and post-operative New York Heart Association (NYHA) Class I or II ranged from 82% to 96%. The 1-year survival ranged from 86% to 100%; and 5-year survival was 71.3% to 85.5% in two studies. CONCLUSIONS The Perceval valve is associated with excellent post-operative results in MAVR and in conventional AVR. Larger randomised controlled studies are required to evaluate the long-term efficacy of the prosthesis.
Towards a more pleasant social atmosphere: Not with your Smartphone but with each other : An investigation of the relation between own mobile phone Behavior and Acceptance of the use by others in Public Social Settings.

This study aims to investigate the relation between own mobile phone behavior and the degree of acceptance of the same behavior of others. Why are we annoyed by the use of mobile phones in public social settings while we, at other moments, also perform this behavior ourselves? Two perspectives are taken into account, the Offender (person deciding to use a mobile phone in a public social setting) and the Victim (person in the companionship of a mobile phone user). Related individual motivations and external drivers, e.g. descriptive and injunctive norms, for the offender’s own mobile phone use in public social settings are examined. In addition the victim’s degree of (overall and behavioral) acceptance and related feelings towards other people’s mobile phone use are studied. A focus group and online survey provide insights into both perspectives of the research. Results show a significant positive correlation between own behavior and overall acceptance indicating that the more mobile phone use, the higher the overall acceptance. Furthermore, there is a strong negative correlation between both variables and injunctive norms. Consequently, clarifying the injunctive norms related to mobile phone use in public social settings is recommended for influencing people’s mobile phone behavior and at the same time the degree of acceptance of the use by surrounding others.
Bacterially induced bone destruction: mechanisms and misconceptions

Normal bone remodelling requires the coordinated regulation of the genesis and activity of osteoblast and osteoclast lineages. Any interference with these integrated cellular systems can result in dysregulation of remodelling with the consequent loss of bone matrix. Bacteria are important causes of bone pathology in common conditions such as periodontitis, dental cysts, bacterial arthritis, and osteomyelitis. It is now established that many of the bacteria implicated in bone diseases contain or produce molecules with potent effects on bone cells. Some of these molecules, such as components of the gram-positive cell walls (lipoteichoic acids), are weak stimulators of bone resorption in vitro, while others (PMT, cpn60) are as active as the most active mammalian osteolytic factors such as cytokines like IL-1 and TNF. The complexity of the integration of bone cell lineage development means that there are still question marks over the mechanism of action of many well-known bone-modulatory molecules such as parathyroid hormone. The key questions which must be asked of the now-recognized bacterial bone-modulatory molecules are as follows: (i) what cell population do they bind to, (ii) what is the nature of the receptor and postreceptor events, and (iii) is their action direct or dependent on the induction of secondary extracellular bone-modulating factors such as cytokines, eicosanoids, etc. In the case of LPS, this ubiquitous gram-negative polymer probably binds to osteoblasts or other cells in bone through the CD14 receptor and stimulates them to release cytokines and eicosanoids which then induce the recruitment and activation of osteoclasts. This explains the inhibitor effects of nonsteroidal and anticytokine agents on LPS-induced bone resorption. However, other bacterial factors such as the potent toxin PMT may act by blocking the normal maturation pathway of the osteoblast lineage, thus inducing dysregulation in the tightly regulated process of resorption and replacement of bone matrix. At the present time, it is not possible to define a general mechanism by which bacteria promote loss of bone matrix. Many bacteria are capable of stimulating bone matrix loss, and the information available would suggest that each organism possesses different factors which interact with bone in different ways. With the rapid increase in antibiotic resistance, particularly with Staphylococcus aureus and M. tuberculosis, organisms responsible for much bone pathology in developed countries only two generations ago, we would urge that much greater attention should be focused on the problem of bacterially induced bone remodelling in order to define pathogenetic mechanisms which could be therapeutic targets for the development of new treatment modalities.
A Linear Chain Markov Model for Detection and Localization of Cells in Early Stage Embryo Development

We address the problem of detecting and localizing cells in time lapse microscopy images during early stage embryo development. Our approach is based on a linear chain Markov model that estimates the number and location of cells at each time step. The state space for each time step is derived from a randomized ellipse fitting algorithm that attempts to find individual cell candidates within the embryo. These cell candidates are combined into embryo hypotheses, and our algorithm finds the most likely sequence of hypotheses over all time steps. We restrict our attention to detect and localize up to four cells, which is sufficient for many important applications such as predicting blast cyst and can be used for assessing embryos in vitro fertilization procedures. We evaluate our method on twelve sequences of developing embryos and find that we can reliably detect and localize cells up to the four cell stage.
Relative Roles of Soil Moisture, Nutrient Supply, Depth, and Mechanical Impedance in Determining Composition and Structure of Wisconsin Prairies

Ecologists have long classified Midwestern prairies based on compositional variation assumed to reflect local gradients in moisture availability. The best known classification is based on Curtis’ continuum index (CI), calculated using the presence of indicator species thought centered on different portions of an underlying moisture gradient. Direct evidence of the extent to which CI reflects differences in moisture availability has been lacking, however. Many factors that increase moisture availability (e.g., soil depth, silt content) also increase nutrient supply and decrease soil mechanical impedance; the ecological effects of the last have rarely been considered in any ecosystem. Decreased soil mechanical impedance should increase the availability of soil moisture and nutrients by reducing the root costs of retrieving both. Here we assess the relative importance of soil moisture, nutrient supply, and mechanical impedance in determining prairie composition and structure. We used leaf δ13C of C3 plants as a measure of growing-season moisture availability, cation exchange capacity (CEC) x soil depth as a measure of mineral nutrient availability, and penetrometer data as a measure of soil mechanical impedance. Community composition and structure were assessed in 17 remnant prairies in Wisconsin which vary little in annual precipitation. Ordination and regression analyses showed that δ13C increased with CI toward “drier” sites, and decreased with soil depth and % silt content. Variation in δ13C among remnants was 2.0‰, comparable to that along continental gradients from ca. 500–1500 mm annual rainfall. As predicted, LAI and average leaf height increased significantly toward “wetter” sites. CI accounted for 54% of compositional variance but δ13C accounted for only 6.2%, despite the strong relationships of δ13C to CI and CI to composition. Compositional variation reflects soil fertility and mechanical impedance more than moisture availability. This study is the first to quantify the effects of soil mechanical impedance on community ecology.