Miracle-dz/UniFAR-FTUs huggingface dataset:
Substrate Specificity of the Escherichia coli Outer Membrane Protease OmpT

ABSTRACT OmpT is a surface protease of gram-negative bacteria that has been shown to cleave antimicrobial peptides, activate human plasminogen, and degrade some recombinant heterologous proteins. We have analyzed the substrate specificity of OmpT by two complementary substrate filamentous phage display methods: (i) in situ cleavage of phage that display protease-susceptible peptides by Escherichia coli expressing OmpT and (ii) in vitro cleavage of phage-displayed peptides using purified enzyme. Consistent with previous reports, OmpT was found to exhibit a virtual requirement for Arg in the P1 position and a slightly less stringent preference for this residue in the P1′ position (P1 and P1′ are the residues immediately prior to and following the scissile bond). Lys, Gly, and Val were also found in the P1′ position. The most common residues in the P2′ position were Val or Ala, and the P3 and P4 positions exhibited a preference for Trp or Arg. Synthetic peptides based upon sequences selected by bacteriophage display were cleaved very efficiently, with kcat/Km values up to 7.3 × 106 M−1 s−1. In contrast, a peptide corresponding to the cleavage site of human plasminogen was hydrolyzed with a kcat/Km almost 106-fold lower. Overall, the results presented in this work indicate that in addition to the P1 and P1′ positions, additional amino acids within a six-residue window (between P4 and P2′) contribute to the binding of substrate polypeptides to the OmpT binding site.
Outcomes of Out‐of‐Hospital Cardiac Arrest by Public Location in the Public‐Access Defibrillation Era

Background The strategy to place public‐access automated external defibrillators (AEDs) has not yet been established in real settings. Methods and Results This, prospective, population‐based observational study in Osaka, Japan, included consecutive out‐of‐hospital cardiac arrest (OHCA) patients with resuscitation attempts during 7 years, from January 2005 through December 2011. The trends in the proportion of public‐access AED use and 1‐month survival with neurologically favorable outcome were evaluated by location. Factors associated with neurologically favorable outcome (defined as cerebral performance category 1 or 2) after ventricular fibrillation were also assessed using multiple logistic regression analysis. A total of 9453 bystander‐witnessed OHCAs of cardiac origin were documented and 894 (9.5%) of them occurred at public places. The proportion of public‐access AED use significantly increased from 0.0% (0/20) in 2005 to 41.2% (7/17) in 2011 at railway stations and from 0.0% (0/7) to 56.5% (13/23) at sports facilities. Mean time from collapse to shock was 5.0 minutes among those who received shocks with public‐access AEDs. The proportion of neurologically favorable outcome was 28.0% (33/118) at railway stations, 51.6% (48/93) at sports facilities, 23.3% (20/86) in public buildings, and 41.9% (13/31) in schools. In multivariate analysis, early defibrillation, irrespective of bystander or emergency medical service (EMS) personnel, was significantly associated with neurologically favorable outcome (adjusted odds ratio for 1‐minute increment, 0.89; 95% confidence interval, 0.87 to 0.92). Conclusions This large, population‐based OHCA registry demonstrated that earlier shock, irrespective the shock provider (bystander or EMS personnel), contributed to improving outcome, and a public‐access defibrillation program was successfully implemented so that shocks with public‐access AEDs were delivered to over 40% of bystander‐witnessed OHCAs and time to shock was shortened in some kinds of public places.
An Update on Zika Virus in Asia

Zika virus (ZIKV) was first isolated in Asia from mosquitoes from Malaysia in 1966. However, the incidence of Zika and Zika-related neurological complications in Asia is not well known. The few studies of Zika in Asia have been inconsistent in pointing to likely transmission levels, with some studies suggesting substantial transmission and others not. Interpretation of existing epidemiological and public health data from Asia is constrained by the non-specific symptomatology of Zika, the high proportion of subclinical ZIKV infections, relatively low viremia, and the lack of accurate serological assays. Here, we update the status of Zika cases from countries in Asia, and highlight some key knowledge gaps. In particular, accurate determinations of the incidence of Zika-related congenital Zika syndrome should be a priority for Zika research in Asia. Additional information will be critical to make informed strategies for the prevention and control of this global public health threat.
The development of lateral motor column cells in the lumbo‐sacral cord in Rana pipiens I. normal development and development following unilateral limb ablation

The influence of the peripheral fields upon the development of both motor and sensory centers in the spinal cord was observed by Shorey ( ,09). Later workers have demonstrated that hyperor hypoplastic development in the motor and sensory centers may be obtained by respectively increasing or decreasing the mass of the periphery to be innervated (for a review of the literature see Piatt, '48). May ('30) produced sensory and motor hypoplasia by interposing spinal cord pieces between the developing limb and the host cord of Discoglossus pictus, preventing, in some cases, innervation of the limb by the host cord. Conversely, he was able to demonstrate hyperplastic development in the presence of supernumerary limbs (May, '32, '33a, '33b, '34). His ablation experiments revealed a failure of the lumbosacral plexus to form, reduction in spinal cord size on the affected side, sensory hypoplasia, and lack of the motor horn at this level. Even in cases of partial regeneration of the limb complete absence of the motor horn was reported.
Reduced Resting Metabolic Rate in Adults with Hemiparetic Chronic Stroke

Objective Resting metabolic rate (RMR) is the component of energy expenditure that explains the largest proportion of total daily energy requirements. Since RMR is determined largely by fat-free mass and a low RMR predicts weight gain in healthy adults, identifying the role of muscle atrophy following stroke on RMR may help identify ways to mitigate the development of obesity post-stroke. Methods Thirty-nine stroke survivors with chronic hemiparesis (mean ± SEM: age: 61 ± 1 years, latency from stroke: 107 ± 40 months, BMI: 31 ± 3 kg/m2) underwent DXA scans for measurement of body composition, including total, paretic, and non-paretic leg lean mass and fasted, 30-min indirect calorimetry for measurement of RMR. Result Predicted RMR was calculated by the Mifflin-St Jeor equation, which considers weight, height, and age for both men and women. RMR was 14% lower than predicted (1438 ± 45 vs. 1669 ± 38 kcals/24 hrs; P<0.01). Total (r=0.73, P<0.01), paretic (r=0.72, P<0.01) and non-paretic (r=0.67, P<0.01) leg lean mass predicted RMR. Conclusion These data indicate that muscle atrophy post stroke may lead to a reduced RMR. This substantiates the need to attenuate the loss of lean mass after a stroke to prevent declines in RMR and possible weight gain common post-stroke.
Midterm outcomes of single port thoracoscopic surgery for major pulmonary resection

Introduction Single-port thoracoscopic surgery has widened the current minimally invasive surgical techniques toward more less invasive procedures in terms of reducing the number of incisions. However, the current status of oncologic outcome with this technique is not well known for lung cancer surgery. The purpose of this study is to evaluate the oncologic outcomes in early stage lung cancer for impact of the survival outcomes with our experience of conversion to a single-port approach from the conventional three-port approach. Materials and methods Retrospective data of patients who underwent thoracoscopic major lung resection for non-small cell lung cancer between January 2006 and June 2015 were analyzed. Patients’ characteristics, perioperative outcomes, pathologic result, and postoperative follow-up data of thoracoscopic surgery were reviewed and surgical outcomes were compared between conventional three-port (n = 168), two-port (n = 68), and single-port thoracoscopic surgery (n = 203). Results Of the 203 single-port thoracoscopic surgeries, we performed 167 single-port thoracoscopic lobectomy and mediastinal lymph node dissections. During the learning period of each thoracoscopic approach, the mean operation time for single-port thoracoscopic surgery (189±62 min) was not significantly different from those of two-port (175±46 min) and three-port (195±75 min) thoracoscopic lobectomy (p = 0.165). Perioperative outcomes including drain indwelling time (p <0.001), complication (p = 0.185) and conversion event (p = 0.911) were not worsened during learning period with two-port. Midterm survival (p = 0.753) and recurrence free survival (p = 0.656) of single port thoracoscopic lobectomy showed acceptable results compared with two- and three-port approach. Conclusions Single-port thoracoscopic surgery is safe and a feasible option for major lung resection in lung malignancy and this approach following experiences of two-port approach may yield similar oncologic results to those of conventional multi-port approach during thoracoscopic lobectomy.
CLN1 and Its Repression by Xbp1 Are Important for Efficient Sporulation in Budding Yeast

ABSTRACT Xbp1, a transcriptional repressor of Saccharomyces cerevisiae with homology to Swi4 and Mbp1, is induced by stress and starvation during the mitotic cycle. It is also induced late in the meiotic cycle. Using RNA differential display, we find that genes encoding three cyclins (CLN1, CLN3, andCLB2), CYS3, and SMF2 are downregulated when Xbp1 is overexpressed and that Xbp1 can bind to sequences in their promoters. During meiosis, XBP1 is highly induced and its mRNA appears at the same time asDIT1 mRNA, but its expression remains high for up to 24 h. As such, it represents a new class of meiosis-specific genes. Xbp1-deficient cells are capable of forming viable gametes, although ascus formation is delayed by several hours. Furthermore, Xbp1 target genes are normally repressed late in meiosis, and loss ofXBP1 results in their derepression. Interestingly, we find that a deletion of CLN1 also reduces the efficiency of sporulation and delays the meiotic program but that sporulation in a Δcln1 Δxbp1 strain is not further delayed. Thus, CLN1 may be Xbp1's primary target in meiotic cells. We hypothesize that CLN1 plays a role early in the meiotic program but must be repressed, by Xbp1, at later stages to promote efficient sporulation.
Efficacy of an elective regional lymph node dissection of 1 to 4 mm thick melanomas for patients 60 years of age and younger.

OBJECTIVE A prospective multi-institutional randomized surgical trial involving 740 stage I and II melanoma patients was conducted by the Intergroup Melanoma Surgical Program to determine whether elective (immediate) lymph node dissection (ELND) for intermediate-thickness melanoma (1-4 mm) improves survival rates compared with clinical observation of the lymph nodes. A second objective was to define subgroups of melanoma patients who would have a higher survival with ELND. METHODS The eligible patients were stratified according to tumor thickness, anatomic site, and ulceration, and then were prerandomized to either ELND or nodal observation. Femoral, axillary, or modified neck dissections were performed using standardized surgical guidelines. RESULTS The median follow-up was 7.4 years. A multifactorial (Cox regression) analysis showed that the following factors independently influenced survival: tumor ulceration, trunk site, tumor thickness, and patient age. Surgical treatment results were first compared based on randomized intent. Overall 5-year survival was not significantly different for patients who received ELND or nodal observation. However, the 552 patients 60 years of age or younger (75% of total group) with ELND has a significantly better 5-year survival. Among these patients, 5-year survival was better with ELND versus nodal observation for the 335 patients with tumors 1 to 2 mm thick, the 403 patients without tumor ulceration, and the 284 patients with tumors 1 to 2 mm thick and no ulceration. In contrast, patients older than 60 years of age who had ELND actually had a lower survival trend than those who had nodal observation. When survival rates were compared based on treatment actually received (i.e., including crossover patients), the patients with significantly improved 5-year survival rates after ELND included those with tumors 1 to 2 mm thick, those without tumor ulceration, and those 60 years of age or younger with tumors 1 to 2 mm thick or without ulceration. CONCLUSION This is the first randomized study to prove the value of surgical treatment for clinically occult regional metastases. Patients 60 years or age or younger with intermediate-thickness melanomas, especially with nonulcerative melanoma and those with tumors 1 to 2 mm thick, may benefit from ELND. However, because some patients still are developing distant disease, these results should be considered an interim analysis.
Smoking Prevalence and Its Effect on Dental Health Attitudes and Behavior among Dental Students

Objective: To determine smoking prevalence and its effect on dental health attitudes and behavior among dental students in Jordan. Subjects and Methods: A cross-sectional study of 314 dental students was conducted at Jordan University of Science and Technology. Subjects were surveyed using a modified version of the Hiroshima University Dental Behavior Inventory (HU-DBI) questionnaire. Multivariate logistic regression analyses were performed to study differences between male smokers and nonsmokers only. Results: The response rate was 83.7%, with 48% males and 52% females. The prevalence of smoking was 17.2%. Smoking was more prevalent among male students (31%) than female (4.3%). For male students, the multivariate logistic regression analysis showed 6 items that were different between smokers and nonsmokers. Nonsmokers tended to brush their teeth more often than smokers (OR 8.67, 95% CI 1.66–45.25); claimed that they had never been professionally taught how to brush their teeth (OR 11.15, 95% CI 1.89–65.67); believed that they spend too much time brushing their teeth (OR 12.24, 95% CI 2.0–75.05); were more concerned about having bad breath (OR 41.86, 95% CI 3.44–58.75) and were more concerned about the color of their gums (OR 8.04, 95% CI 1.55–41.84). Conclusions: Smoking prevalence among male dental students in Jordan was high, 7 times greater than for females. Male smokers and nonsmokers had different attitudes and oral health behaviors as indicated by the study survey.
Rainfall-Runoff Modelling – Comparison of Modelling Strategies with a Focus on Ungauged Predictions and Model Integration

This work is an integrative study of methods for rainfall-runoff simulation. The thesis addresses process description considerations, problems associated with ungauged predictions, and tools for sharing data and computational procedures over the Internet. Simple runoff model structures can be preferred as they facilitate systematic uncertainty assessments and can fit streamflow data as well as more complex structures. A more complex model structure can be invoked when assessing hydrological problems involving water quality considerations, which often necessitates explicit representation of runoff generation mechanisms and different flow pathways. Models that have more ambitious objectives than merely to reproduce streamflow should also be validated against other measured data than just flow records. It is demonstrated that two different model parameterisations can yield both good quality fits to observed streamflow data, but generate drastically different evapotranspiration time series. This thesis also presents a case study where a physics-based hydrological model is calibrated and validated using groundwater levels and isotope tracer results. Runoff predictions for a catchment lacking streamflow records can be based on establishing relationships between physical catchment attributes and runoff model parameters using flow data from other catchments belonging to the same region. Results of this thesis suggest that consideration of correlation among runoff model parameters can improve performance of such a regionalisation exercise. Ideally, one would wish to exploit available information on catchment properties in a more physics-based way where observed values of physical catchment properties are incorporated into the model structure and parameters directly. Although physics-based models still face problems which are not readily solvable, results of this study show some promise in predicting streamflow in a physically more consistent way with a minimum amount of parameter calibration. The final part of this thesis explores tools for distribution of environmental data sets and simulation models over the Internet. The idea is to promote openness in environmental simulation studies by providing means for data and model integration from resources published by different parties. %%%%Helsinki University of Technology, Water Resources publications, ISSN 1456-2596; 9
Ortholog Clustering on a Multipartite Graph

We present a method for automatically extracting groups of orthologous genes from a large set of genomes by a new clustering algorithm on a weighted multipartite graph. The method assigns a score to an arbitrary subset of genes from multiple genomes to assess the orthologous relationships between genes in the subset. This score is computed using sequence similarities between the member genes and the phylogenetic relationship between the corresponding genomes. An ortholog cluster is found as the subset with the highest score, so ortholog clustering is formulated as a combinatorial optimization problem. The algorithm for finding an ortholog cluster runs in time O(|E| + |V| log |V|), where V and E are the sets of vertices and edges, respectively, in the graph. However, if we discretize the similarity scores into a constant number of bins, the runtime improves to O(|E| + |V|). The proposed method was applied to seven complete eukaryote genomes on which the manually curated database of eukaryotic ortholog clusters, KOG, is constructed. A comparison of our results with the manually curated ortholog clusters shows that our clusters are well correlated with the existing clusters
Percutaneous treatment of thrombosed hemodialysis arteriovenous fistulas: use of thromboaspiration and balloon angioplasty

Background Endovascular strategies have been used to manage patients with thrombosed vascular access for hemodialysis. We analyzed primary success rate and patency rates of balloon angioplasty following mechanical thrombectomy for the treatment of thrombosed native arteriovenous fistulas. Methods This was a retrospective study of 24 patients with thrombosed native arteriovenous fistulas who were referred for treatment in the intervention unit of the Radiology Department. All patients had been performed percutaneous thrombo-aspiration and balloon angioplasty. Technical and clinical success rates as well as the 6th and 12th months primary and secondary patency of fistulas were evaluated. Results Technical and clinical success was 83%. In the 6 of 20 patients, early re-thrombosis were detected. Patent AVF with primary and secondary patency rates at 6 and 12 months was 55%-40%. The secondary patency rates at 6 and 12 months were 75% and 70%. Conclusion Mechanical thrombectomy with balloon angioplasty is a minimally invasive and effective procedure for the treatment of thrombosed native arteriovenous fistula. Advantages of this technique are minor complication rates, cost effectiveness, high technical success rate.
An advanced low complexity double error correction of an BCH decoder

Bose, Ray-Chaudhuri, Hocquenghem (BCH) codes are one of the efficient error-correcting codes used to correct errors occurred during the transmission of the data in the unreliable communication mediums. This paper presents a low-complexity and area efficient error-correcting BCH decoder architecture for detecting and correction of two errors. The advanced Peterson error locator computation algorithm, which significantly reduces computational complexity, is proposed for the IBM block in the BCH decoder. In addition, a modified syndrome calculator and chien search are proposed to reduce hardware complexity. The proposed model and design techniques have considerably less hardware complexity and latency than those using conventional algorithms. For a (15,7) BCH decoder over GF(4), the proposed design can lead to a reduction in complexity of at least 30 % compared to conventional architectures. The enhanced chase BCH decoder is designed using hardware description language called Verilog and synthesized in Xilinx ISE 13.2.
Key-value Attention Mechanism for Neural Machine Translation

In this paper, we propose a neural machine translation (NMT) with a key-value attention mechanism on the source-side encoder. The key-value attention mechanism separates the source-side content vector into two types of memory known as the key and the value. The key is used for calculating the attention distribution, and the value is used for encoding the context representation. Experiments on three different tasks indicate that our model outperforms an NMT model with a conventional attention mechanism. Furthermore, we perform experiments with a conventional NMT framework, in which a part of the initial value of a weight matrix is set to zero so that the matrix is as the same initial-state as the key-value attention mechanism. As a result, we obtain comparable results with the key-value attention mechanism without changing the network structure.
Best choice of central venous insertion site for the prevention of catheter-related complications in adult patients who need cancer therapy: a randomized trial.

BACKGROUND Central venous access is extensively used in oncology, though practical information from randomized trials on the most convenient insertion modality and site is unavailable. METHODS Four hundred and three patients eligible for receiving i.v. chemotherapy for solid tumors were randomly assigned to implantation of a single type of port (Bard Port, Bard Inc., Salt Lake City, UT), through a percutaneous landmark access to the internal jugular, a ultrasound (US)-guided access to the subclavian or a surgical cut-down access through the cephalic vein at the deltoid-pectoralis groove. Early and late complications were prospectively recorded until removal of the device, patient's death or ending of the study. RESULTS Four hundred and one patients (99.9%) were assessable: 132 with the internal jugular, 136 with the subclavian and 133 with the cephalic vein access. The median follow-up was 356.5 days (range 0-1087). No differences were found for early complication rate in the three groups {internal jugular: 0% [95% confidence interval (CI) 0.0% to 2.7%], subclavian: 0% (95% CI 0.0% to 2.7%), cephalic: 1.5% (95% CI 0.1% to 5.3%)}. US-guided subclavian insertion site had significantly lower failures (e.g. failed attempts to place the catheter in agreement with the original arm of randomization, P = 0.001). Infections occurred in one, three and one patients (internal jugular, subclavian and cephalic access, respectively, P = 0.464), whereas venous thrombosis was observed in 15, 8 and 11 patients (P = 0.272). CONCLUSIONS Central venous insertion modality and sites had no impact on either early or late complication rates, but US-guided subclavian insertion showed the lowest proportion of failures.