Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Genome Sequence of the Metabolically Versatile Halophilic Archaeon Haloferax mediterranei, a Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Producer

ABSTRACT Haloferax mediterranei, an extremely halophilic archaeon, has shown promise for production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) from unrelated cheap carbon sources. Here we report the complete genome (3,904,707 bp) of H. mediterranei CGMCC 1.2087, consisting of one chromosome and three megaplasmids.
A Stenotrophomonas maltophilia Multilocus Sequence Typing Scheme for Inferring Population Structure

ABSTRACT Stenotrophomonas maltophilia is an opportunistic, highly resistant, and ubiquitous pathogen. Strains have been assigned to genogroups using amplified fragment length polymorphism. Hence, isolates of environmental and clinical origin predominate in different groups. A multilocus sequence typing (MLST) scheme was developed using a highly diverse selection of 70 strains of various ecological origins from seven countries on all continents including strains of the 10 previously defined genogroups. Sequence data were assigned to 54 sequence types (ST) based on seven loci. Indices of association for all isolates and clinical isolates of 2.498 and 2.562 indicated a significant linkage disequilibrium, as well as high congruence of tree topologies from different loci. Potential recombination events were detected in one-sixth of all ST. Calculation of the mean divergence between and within predicted clusters confirmed previously defined groups and revealed five additional groups. Consideration of the different ecological origins showed that 18 out of 31 respiratory tract isolates, including 12 out of 19 isolates from cystic fibrosis (CF) patients, belonged to genogroup 6. In contrast, 16 invasive strains isolated from blood cultures were distributed among nine different genogroups. Three genogroups contained isolates of strictly environmental origin that also featured high sequence distances to other genogroups, including the S. maltophilia type strain. On the basis of this MLST scheme, isolates can be assigned to the genogroups of this species in order to further scrutinize the population structure of this species and to unravel the uneven distribution of environmental and clinical isolates obtained from infected, colonized, or CF patients.
NetVLAD: CNN Architecture for Weakly Supervised Place Recognition

We tackle the problem of large scale visual place recognition, where the task is to quickly and accurately recognize the location of a given query photograph. We present the following four principal contributions. First, we develop a convolutional neural network (CNN) architecture that is trainable in an end-to-end manner directly for the place recognition task. The main component of this architecture, NetVLAD, is a new generalized VLAD layer, inspired by the “Vector of Locally Aggregated Descriptors” image representation commonly used in image retrieval. The layer is readily pluggable into any CNN architecture and amenable to training via backpropagation. Second, we create a new weakly supervised ranking loss, which enables end-to-end learning of the architecture's parameters from images depicting the same places over time downloaded from Google Street View Time Machine. Third, we develop an efficient training procedure which can be applied on very large-scale weakly labelled tasks. Finally, we show that the proposed architecture and training procedure significantly outperform non-learnt image representations and off-the-shelf CNN descriptors on challenging place recognition and image retrieval benchmarks.
Sociodemographic and lifestyle factors as the risk of diabetic foot ulcer in the University of Malaya Medical Centre

A case-control study was conducted between November 2005 and May 2007 in the University of Malaya Medical Centre (UMMC), University of Malaya, Kuala Lumpur, Malaysia. The objective of this study was to identify specific socio-demographic and lifestyle factors which were associated with foot ulcer in Type 1 and Type 2 diabetes patients. There were 125 cases and 250 controls by using universal sampling. Diabetic foot ulcer was defined as “the full thickness skin break at least to Grade 1 Wagner Stage, occurring distal to malleoli”. The case was defined as the diabetic patient who was newly diagnosed or who has a known case of diabetic foot ulcer and the control was defined as the diabetic patient without active foot ulcer. Data was collected via face-to-face interview using a structured questionnaire. Results showed that diabetic patients at younger age group, 44 years old and less (OR 5.90 95% CI 2.31, 15.10), Indian (OR 3.24 95% CI 1.66, 6.30), and smoker (OR 3.85 95% CI 1.77, 8.35) were the independent risk factor for diabetic foot ulcer.
Long-Term Temporal Convolutions for Action Recognition

Typical human actions last several seconds and exhibit characteristic spatio-temporal structure. Recent methods attempt to capture this structure and learn action representations with convolutional neural networks. Such representations, however, are typically learned at the level of a few video frames failing to model actions at their full temporal extent. In this work we learn video representations using neural networks with long-term temporal convolutions (LTC). We demonstrate that LTC-CNN models with increased temporal extents improve the accuracy of action recognition. We also study the impact of different low-level representations, such as raw values of video pixels and optical flow vector fields and demonstrate the importance of high-quality optical flow estimation for learning accurate action models. We report state-of-the-art results on two challenging benchmarks for human action recognition UCF101 (92.7%) and HMDB51 (67.2%).
Psychological distress in pregnancy and preterm delivery.

OBJECTIVE--To investigate if psychological distress during pregnancy is associated with increased risk of preterm delivery. DESIGN--Prospective, population based, follow up study with repeated measures of psychological distress (general health questionnaire), based on the use of questionnaires. SETTING--Antenatal care clinic and delivery ward, Aarhus University Hospital, Denmark. SUBJECTS--8719 women with singleton pregnancies attending antenatal care for the initial visit between 1 August 1989 and 30 September 1991; 5872 women (67%) completed all questionnaires. MAIN OUTCOME MEASURE--Preterm delivery. Estimation of gestational age at delivery was mainly based on early ultrasound measurements. RESULTS--In 197 cases (3.6%) the woman delivered prematurely (less than 259 days). A dose-response relation between psychological distress in the 30th week of pregnancy and risk of preterm delivery was found, but distress measured in the 16th week was not related to preterm delivery. Control of confounding was secured by the use of multivariate logistic regression models. Relative risk for preterm delivery was 1.22 (95% confidence interval 0.84 to 1.79) for moderate distress and 1.75 (1.20 to 2.54) for high distress in comparison to low distress. CONCLUSIONS--Psychological distress later in pregnancy is associated with an increased risk of preterm delivery. Future interventional studies should focus on ways of lowering psychological distress in late pregnancy.
Differential Interactions between Tat-Specific Redox Enzyme Peptides and Their Chaperones

ABSTRACT The twin-arginine translocase (Tat) system is used by many bacteria to move proteins across the cytoplasmic membrane. Tat substrates are prefolded and contain a conserved SRRxFLK twin-arginine (RR) motif at their N termini. Many Tat substrates in Escherichia coli are cofactor-containing redox enzymes that have specific chaperones called redox enzyme maturation proteins (REMPs). Here we characterized the interactions between 10 REMPs and 15 RR peptides of known and predicted Tat-specific redox enzyme subunits. A combination of in vitro and in vivo experiments demonstrated that some REMPs were specific to a redox enzyme(s) of similar function, whereas others were less specific and bound peptides of unrelated enzymes. Results from Biacore surface plasmon resonance (SPR) and bacterial two-hybrid experiments identified interactions in addition to those found in far-Western experiments, suggesting that conformational freedom and/or other cellular factors may be required. Furthermore, we show that the interaction of the two prevents both from being proteolytically degraded in vivo, and kinetic data from SPR show up to 10-fold-tighter binding to the expected RR substrate when multiple binding partners existed. Investigations using full-length sequences of the RR proteins showed that the mature portion for some redox enzyme subunits is required for detection of the interactions. Sequence alignments among the REMPs and RR peptides indicated that homology between the REMPs and the hydrophobic regions following the RR motifs in the peptides correlates to cross-recognition.
Timing of Debridement and Infection Rates in Open Fractures of the Hand

Background: Literature on open fracture infections has focused primarily on long bones, with limited guidelines available for open hand fractures. In this study, we systematically review the available hand surgery literature to determine infection rates and the effect of debridement timing and antibiotic administration. Methods: Searches of the MEDLINE, EMBASE, and Cochrane computerized literature databases and manual bibliography searches were performed. Descriptive/quantitative data were extracted, and a meta-analysis of different patient cohorts and treatment modalities was performed to compare infection rates. Results: The initial search yielded 61 references. Twelve articles (4 prospective, 8 retrospective) on open hand fractures were included (1669 open fractures). There were 77 total infections (4.6%): 61 (4.4%) of 1391 patients received preoperative antibiotics and 16 (9.4%) of 171 patients did not receive antibiotics. In 7 studies (1106 open fractures), superficial infections (requiring oral antibiotics only) accounted for 86%, whereas deep infections (requiring operative debridement) accounted for 14%. Debridement within 6 hours of injury (2 studies, 188 fractures) resulted in a 4.2% infection rate, whereas debridement within 12 hours of injury (1 study, 193 fractures) resulted in a 3.6% infection rate. Two studies found no correlation of infection and timing to debridement. Conclusions: Overall, the infection rate after open hand fracture remains relatively low. Correlation does exist between the administration of antibiotics and infection, but the majority of infections can be treated with antibiotics alone. Timing of debridement, has not been shown to alter infection rates.
Prospective Evaluation of Opioid Consumption Following Carpal Tunnel Release Surgery

Background: Postoperative pain management and opioid consumption following carpal tunnel release (CTR) surgery may be influenced by many variables. To understand factors affecting opioid consumption, a prospective study was undertaken with the hypothesis that CTR performed under local anesthesia (wide awake local anesthesia with no tourniquet [WALANT]) would result in increased opioid consumption postoperatively compared with cases performed under sedation. Methods: All patients undergoing open CTR surgery were consecutively enrolled over a 6-month period. Information collected included patient demographics, surgical technique, amount and type of narcotic prescribed, number of pills taken, and type of anesthesia. Results: 277 patients were enrolled (56% women, 44% men). On average, 21 pills were prescribed, and 4.3 pills (median = 2) were consumed. There was no difference in consumption between patients who received WALANT (78 cases) versus (198 cases) sedation (4.9 vs 3.9 pills, respectively) (P = .22). There was no difference in opioid consumption based on insurance type (P = .47) or type of narcotic (P = .85). However, more men consumed no opioids (47%) compared with women (36%) (P < .05) and older patients consumed less than younger patients (P < .05). Conclusions: Opioid consumption following CTR is more influenced by age and gender, and less influenced by anesthesia type, insurance type, or the type of opioid prescribed. Many more opioids were prescribed than needed, on an average of 5:1. Many patients, particularly older patients, do not require any opioid analgesia after CTR.
A Preliminary Assessment of the Utility of Large-Caliber Processed Nerve Allografts for the Repair of Upper Extremity Nerve Injuries

Background: Cabled sensory nerve autografts are the historical gold standard for overcoming gaps in larger diameter nerves as repair utilizing large-diameter autograft risks central graft necrosis. Commercially available processed nerve allograft (PNA) is available in diameters up to 5 mm but represents an acellular 3-dimensional matrix as opposed to viable tissue. The purpose of this study is to specifically evaluate whether similar concerns regarding the use of large-caliber PNA are warranted. Methods: The RANGER Registry is an active database designed to collect injury, repair, safety, and outcomes data for PNAs (Avance® Nerve Graft; AxoGen, Inc, Alachua, Florida) according to an institutional review board–approved protocol. The database was queried for patients presenting with large-caliber nerve allograft repairs in the upper extremity. Identified patients reporting quantitative outcomes with a minimum of 9-month follow-up were included in the data set. Results: The large-caliber PNA subgroup included 13 patients with 15 injuries. The mean ± SD age was 36 ± 22 years. Large-caliber single-stranded repairs included twelve 4- to 5-mm-diameter grafts. Large-caliber cabled repairs included the combined use of 3- to 4-mm and 4- to 5-mm-diameter nerve allografts in 3 repairs. The mean nerve gap was 33 ± 10 mm with a mean follow-up time of 13 months. Available quantitative data reported meaningful recovery of sensory and motor function in 67% and 85% of the repairs, respectively. Conclusion: Although based on a small subset of patients, PNAs of up to 5 mm in diameter appear capable of supporting successful nerve regeneration.
Staff perceptions of e‐learning for teaching delivery in healthcare

Background Web-based e-learning methods are increasingly used in higher education to support learning in pre- and post-registration healthcare subjects. Although new technologies are central to teaching and learning strategies, e-learning is not currently accepted universally by academic staff. Aim The aim of the study was to determine the attitudes towards and use of e-learning among academic staff in nursing and midwifery. Methods A questionnaire survey was completed by 102 teaching staff to determine their opinions towards and use of e-learning in teaching. Results Staff opinions were divergent with most acknowledging the benefits of e-learning but many also expressing concerns over barriers such as lack of time, resources or technical support. Staff did not fully utilize the range of technologies available. Conclusion Most staff exhibited positive attitudes towards the pedagogical value of technology in teaching and learning, though some remained hesitant or lacking in confidence to embark on e-learning teaching developments or delivery. Barriers exist that may be partially addressed through better understanding of e-learning tools and their potential application, and additional support and resources. E-learning strategies need to focus on improving staff awareness of e-learning methods to supplement rather than replace traditional teaching methods, while providing ongoing support and mentoring for development and delivery, technological training and incentives for staff involvement.
Pediatric Hereditary Angioedema as a Cause of Acute Compartment Syndrome of the Hand and Forearm: A Case Report

Background: Compartment syndrome of the upper extremity is a surgical emergency that, when left untreated, can have dire consequences. Its causes are numerous, one of which is the uncommon entity hereditary angioedema, an autosomal dominant disease resulting in edema in a variety of potential locations, including the extremities. This is only the second time hereditary angioedema has been mentioned in the literature as a cause of compartment syndrome. Methods: We present a case of hereditary angioedema leading to hand and forearm compartment syndrome in a 13-year-old pediatric patient. Diagnosis of hereditary angioedema was made by our Rheumatology colleagues with physical exam and a thorough history, and confirmed by laboratory studies. Results: Our patient presented with compartment syndrome of the hand and forearm and underwent hand and volar forearm fasciotomies. She was subsequently worked up for hereditary angioedema with laboratory results confirming the diagnosis. She was discharged after a 5-day hospitalization with prophylactic C1-inhibitor therapy. Conclusions: Hereditary angioedema is a rare but known cause of compartment syndrome of the upper extremity, and must be considered when patients present with compartment syndrome of unknown etiology. This disease can be diagnosed by laboratory studies and symptoms can be controlled with medical therapy.
The Major Catalase Gene (katA) of Pseudomonas aeruginosa PA14 Is under both Positive and Negative Control of the Global Transactivator OxyR in Response to Hydrogen Peroxide

ABSTRACT The adaptive response to hydrogen peroxide (H2O2) in Pseudomonas aeruginosa involves the major catalase, KatA, and OxyR. However, neither the molecular basis nor the relationship between the aforementioned proteins has been established. Here, we demonstrate that the transcriptional activation of the katA promoter (katAp) in response to H2O2 was abrogated in the P. aeruginosa PA14 oxyR null mutant. Promoter deletion analyses revealed that H2O2-mediated induction was dependent on a region of DNA −76 to −36 upstream of the H2O2-responsive transcriptional start site. This region harbored the potential operator sites (OxyR-responsive element [ORE]) of the Escherichia coli OxyR binding consensus. Deletion of the entire ORE not only abolished H2O2-mediated induction but also elevated the basal transcription, suggesting the involvement of OxyR and the ORE in both transcriptional activation and repression. OxyR bound to the ORE both in vivo and in vitro, demonstrating that OxyR directly regulates the katAp. Three distinct mobility species of oxidized OxyR were observed in response to 1 mM H2O2, as assessed by free thiol trapping using 4-acetamido-4′-maleimidylstilbene-2,2′-disulfonic acid. These oxidized species were not observed for the double mutants with mutations in the conserved cysteine (Cys) residues (C199 and C208). The uninduced transcription of katAp was elevated in an oxyR mutant with a mutation of Cys to serine at 199 (C199S) and even higher in the oxyR mutant with a mutation of Cys to alanine at 199 (C199A) but not in oxyR mutants with mutations in C208 (C208S and C208A). In both the C199S and the C208S mutant, however, katAp transcription was still induced by H2O2 treatment, unlike in the oxyR null mutant and the C199A mutant. The double mutants with mutations in both Cys residues (C199S C208S and C199A C208S) did not differ from the C199A mutant. Taken together, our results suggest that P. aeruginosa OxyR is a bona fide transcriptional regulator of the katA gene, sensing H2O2 based on the conserved Cys residues, involving more than one oxidation as well as activation state in vivo.
Characterization of a New GlnR Binding Box in the Promoter of amtB in Streptomyces coelicolor Inferred a PhoP/GlnR Competitive Binding Mechanism for Transcriptional Regulation of amtB

ABSTRACT The transcription of amtB in Streptomyces coelicolor has been proposed to be counter-regulated by GlnR (a global regulator for nitrogen metabolism) and PhoP (a global regulator for phosphate metabolism). However, the GlnR-protected region, which was deduced to be two 22-bp GlnR binding boxes (gTnAc-n6-GaAAc-n6-GtnAC-n6-GAAAc-n6, abbreviated as a1-b1 and a2-b2), was separated from the PhoP-protected region in the promoter of amtB, leaving the mechanism for this regulation undefined. In this study, another 22-bp GlnR binding box, which consisted of a3-site-n6-b3-site (a3-b3) overlapping with the PhoP-binding sequences, was identified in the promoter region of amtB by a DNase I footprinting assay. An electrophoretic mobility shift assay (EMSA) using purified recombinant GlnR and the synthetic amtB promoter fragments with the three GlnR binding boxes individually mutated demonstrated that every box was involved in GlnR binding in vitro. Further in vivo assays using the egfp reporter gene fused to various kinds of mutated promoter regions of amtB demonstrated that all of the three GlnR binding boxes were required for GlnR-mediated activation of amtB transcription under the nitrogen-limited condition. The results of EMSA using the amtB promoter with mixtures of recombinant His-tagged GlnR and Trx-His-S-tagged PhoP inferred that PhoP might compete against GlnR from binding at the a3-b3 site, attributable to the PhoP/GlnR counter-regulatory function subjected to further experimental proof.
Alkyl Hydroperoxide Reductase Repair by Helicobacter pylori Methionine Sulfoxide Reductase

ABSTRACT Protein exposure to oxidants such as HOCl leads to formation of methionine sulfoxide (MetSO) residues, which can be repaired by methionine sulfoxide reductase (Msr). A Helicobacter pylori msr strain was more sensitive to HOCl-mediated killing than the parent. Because of its abundance in H. pylori and its high methionine content, alkyl hydroperoxide reductase C (AhpC) was hypothesized to be prone to methionine oxidation. AhpC was expressed as a recombinant protein in Escherichia coli. AhpC activity was abolished by HOCl, while all six methionine residues of the enzyme were fully to partially oxidized. Upon incubation with a Msr repair mixture, AhpC activity was restored to nonoxidized levels and the MetSO residues were repaired to methionine, albeit to different degrees. The two most highly oxidized and then Msr-repaired methionine residues in AhpC, Met101 and Met133, were replaced with isoleucine residues by site-directed mutagenesis, either individually or together. E. coli cells expressing variant versions were more sensitive to t-butyl hydroperoxide than cells expressing native protein, and purified AhpC variant proteins had 5% to 39% of the native enzyme activity. Variant proteins were still able to oligomerize like the native version, and circular dichroism (CD) spectra of variant proteins revealed no significant change in AhpC conformation, indicating that the loss of activity in these variants was not related to major structural alterations. Our results suggest that both Met101 and Met133 residues are important for AhpC catalytic activity and that their integrity relies on the presence of a functional Msr.