Miracle-dz/UniFAR-FTUs huggingface dataset:
Ligand-Binding Properties and Conformational Dynamics of Autolysin Repeat Domains in Staphylococcal Cell Wall Recognition

ABSTRACT The bifunctional major autolysin Atl plays a key role in staphylococcal cell separation. Processing of Atl yields catalytically active amidase (AM) and glucosaminidase (GL) domains that are each fused to repeating units. The two repeats of AM (R1 and R2) target the enzyme to the septum, where it cleaves murein between dividing cells. We have determined the crystal structure of R2, which reveals that each repeat folds into two half-open β-barrel subunits. We further demonstrate that lipoteichoic acid serves as a receptor for the repeats and that this interaction depends on conserved surfaces in each subunit. Small-angle X-ray scattering of the mature amidase reveals the presence of flexible linkers separating the AM, R1, and R2 units. Different levels of flexibility for each linker provide mechanistic insights into the conformational dynamics of the full-length protein and the roles of its components in cell wall association and catalysis. Our analysis supports a model in which the repeats direct the catalytic AM domain to the septum, where it can optimally perform the final step of cell division.
Formation of an Intramolecular Periplasmic Disulfide Bond in TcpP Protects TcpP and TcpH from Degradation in Vibrio cholerae

ABSTRACT TcpP and ToxR coordinately regulate transcription of toxT, the master regulator of numerous virulence factors in Vibrio cholerae. TcpP and ToxR are membrane-localized transcription factors, each with a periplasmic domain containing two cysteines. In ToxR, these cysteines form an intramolecular disulfide bond and a cysteine-to-serine substitution affects activity. We determined that the two periplasmic cysteines of TcpP also form an intramolecular disulfide bond. Disruption of this intramolecular disulfide bond by mutation of either cysteine resulted in formation of intermolecular disulfide bonds. Furthermore, disruption of the intramolecular disulfide bond in TcpP decreased the stability of TcpP. While the decreased stability of TcpP-C207S resulted in a nearly complete loss of toxT activation and cholera toxin (CT) production, the second cysteine mutant, TcpP-C218S, was partially resistant to proteolytic degradation and maintained ∼50% toxT activation capacity. TcpP-C218S was also TcpH independent, since deletion of tcpH did not affect the stability of TcpP-C218S, whereas wild-type TcpP was degraded in the absence of TcpH. Finally, TcpH was also unstable when intramolecular disulfides could not be formed in TcpP, suggesting that the single periplasmic cysteine in TcpH may assist with disulfide bond formation in TcpP by interacting with the periplasmic cysteines of TcpP. Consistent with this finding, a TcpH-C114S mutant was unable to stabilize TcpP and was itself unstable. Our findings demonstrate a periplasmic disulfide bond in TcpP is critical for TcpP stability and virulence gene expression. IMPORTANCE The Vibrio cholerae transcription factor TcpP, in conjunction with ToxR, regulates transcription of toxT, the master regulator of numerous virulence factors in Vibrio cholerae. TcpP is a membrane-localized transcription factor with a periplasmic domain containing two cysteines. We determined that the two periplasmic cysteines of TcpP form an intramolecular disulfide bond and disruption of the intramolecular disulfide bond in TcpP decreased the stability of TcpP and reduced virulence gene expression. Normally TcpH, another membrane-localized periplasmic protein, protects TcpP from degradation. However, we found that TcpH was also unstable when intramolecular disulfides could not be formed in TcpP, indicating that the periplasmic cysteines of TcpP are required for functional interaction with TcpH and that this interaction is required for both TcpP and TcpH stability.
Ligation of the Intersphincteric Fistula Tract (LIFT): A Minimally Invasive Procedure for Complex Anal Fistula

Introduction. The surgical management of anal fistulas is still a matter of discussion and no clear recommendations exist. The present study analyses the results of the ligation of the intersphincteric fistula tract (LIFT) technique in treating complex anal fistulas, in particular healing, fecal continence, and recurrence. Methods. Between October 2010 and February 2012, a total of 26 consecutive patients underwent LIFT. All patients had a primary complex anal fistula and preoperatively all underwent clinical examination, proctoscopy, transanal ultrasonography/magnetic resonance imaging, and were treated with the LIFT procedure. For the purpose of this study, fistulas were classified as complex if any of the following conditions were present: tract crossing more than 30% of the external sphincter, anterior fistula in a woman, recurrent fistula, or preexisting incontinence. Patient’s postoperative complications, healing time, recurrence rate, and postoperative continence were recorded during follow-up. Results. The minimum follow-up was 16 months. Five patients required delayed LIFT after previous seton. There were no surgical complications. Primary healing was achieved in 19 patients (73%). Seven patients (27%) had recurrence presenting between 4 and 8 weeks postoperatively and required further surgical treatment. Two of them (29%) had previous insertion of a seton. No patients reported any incontinence postoperatively and we did not observe postoperative continence worsening. Conclusion. In our experience, LIFT appears easy to perform, is safe with no surgical complication, has no risk of incontinence, and has a low recurrence rate. These results suggest that LIFT as a minimally invasive technique should be routinely considered for patients affected by complex anal fistula.
The Components of the Unique Zur Regulon of Cupriavidus metallidurans Mediate Cytoplasmic Zinc Handling

ABSTRACT Zinc is an essential trace element, yet it is toxic at high concentrations. In the betaproteobacterium Cupriavidus metallidurans, the highly efficient removal of surplus zinc from the periplasm is responsible for the outstanding metal resistance of the organism. Rather than having a typical Zur-dependent, high-affinity ATP-binding cassette transporter of the ABC protein superfamily for zinc uptake at low concentrations, C. metallidurans has the secondary zinc importer ZupT of the zinc-regulated transporter, iron-regulated transporter (ZRT/IRT)-like protein (ZIP) family. It is important to understand, therefore, how this zinc-resistant bacterium copes with exposure to low zinc concentrations. Members of the Zur regulon in C. metallidurans were identified by comparing the transcriptomes of a Δzur mutant and its parent strain. The consensus sequence of the Zur-binding box was derived for the zupTp promoter-regulatory region by use of a truncation assay. The motif was used to predict possible Zur boxes upstream of Zur regulon members. The binding of Zur to these boxes was confirmed. Two Zur boxes upstream of the cobW1 gene, encoding a putative zinc chaperone, proved to be required for complete repression of cobW1 and its downstream genes in cells cultivated in mineral salts medium. A Zur box upstream of each of zur-cobW2, cobW3, and zupT permitted both low expression levels of these genes and their upregulation under conditions of zinc starvation. This demonstrates a compartmentalization of zinc homeostasis in C. metallidurans, where the periplasm is responsible for the removal of surplus zinc, cytoplasmic components are responsible for the management of zinc as an essential cofactor, and the two compartments are connected by ZupT. IMPORTANCE Elucidating zinc homeostasis is necessary for understanding both host-pathogen interactions and the performance of free-living bacteria in their natural environments. Escherichia coli acquires zinc under conditions of low zinc concentrations via the Zur-controlled ZnuABC importer of the ABC superfamily, and this was also the paradigm for other bacteria. In contrast, the heavy-metal-resistant bacterium C. metallidurans achieves high tolerance to zinc through sophisticated zinc handling and efflux systems operating on periplasmic zinc ions, so that removal of surplus zinc is a periplasmic feature in this bacterium. It is shown here that this process is augmented by the management of zinc by cytoplasmic zinc chaperones, whose synthesis is controlled by the Zur regulator. This demonstrates a new mechanism, involving compartmentalization, for organizing zinc homeostasis.
MonoSLAM: Real-Time Single Camera SLAM

We present a real-time algorithm which can recover the 3D trajectory of a monocular camera, moving rapidly through a previously unknown scene. Our system, which we dub MonoSLAM, is the first successful application of the SLAM methodology from mobile robotics to the "pure vision" domain of a single uncontrolled camera, achieving real time but drift-free performance inaccessible to structure from motion approaches. The core of the approach is the online creation of a sparse but persistent map of natural landmarks within a probabilistic framework. Our key novel contributions include an active approach to mapping and measurement, the use of a general motion model for smooth camera movement, and solutions for monocular feature initialization and feature orientation estimation. Together, these add up to an extremely efficient and robust algorithm which runs at 30 Hz with standard PC and camera hardware. This work extends the range of robotic systems in which SLAM can be usefully applied, but also opens up new areas. We present applications of MonoSLAM to real-time 3D localization and mapping for a high-performance full-size humanoid robot and live augmented reality with a hand-held camera
Functional Characterization of Flagellin Glycosylation in Campylobacter jejuni 81-176

ABSTRACT The major flagellin of Campylobacter jejuni strain 81-176, FlaA, has been shown to be glycosylated at 19 serine or threonine sites, and this glycosylation is required for flagellar filament formation. Some enzymatic components of the glycosylation machinery of C. jejuni 81-176 are localized to the poles of the cell in an FlhF-independent manner. Flagellin glycosylation could be detected in flagellar mutants at multiple levels of the regulatory hierarchy, indicating that glycosylation occurs independently of the flagellar regulon. Mutants were constructed in which each of the 19 serine or threonines that are glycosylated in FlaA was converted to an alanine. Eleven of the 19 mutants displayed no observable phenotype, but the remaining 8 mutants had two distinct phenotypes. Five mutants (mutations S417A, S436A, S440A, S457A, and T481A) were fully motile but defective in autoagglutination (AAG). Three other mutants (mutations S425A, S454A, and S460A) were reduced in motility and synthesized truncated flagellar filaments. The data implicate certain glycans in mediating filament-filament interactions resulting in AAG and other glycans appear to be critical for structural subunit-subunit interactions within the filament.
Catabolite Repression of the TodS/TodT Two-Component System and Effector-Dependent Transphosphorylation of TodT as the Basis for Toluene Dioxygenase Catabolic Pathway Control

ABSTRACT The TodS/TodT two-component system of Pseudomonas putida regulates the expression of the toluene dioxygenase (tod) operon for the metabolism of toluene, benzene, and ethylbenzene. The sensor kinase TodS has a complex domain arrangement containing two functional modules, each harboring a sensor and an autokinase domain separated by a receiver domain. The TodT protein is the cognate response regulator that activates transcription of the toluene dioxygenase (TOD) pathway genes at the P todX promoter. We report in this study that the todST operon is transcribed from a main promoter and that the +1 initiation point is located 31 nucleotides upstream from the A of the first ATG codon and is preceded by a −10/−35 canonical promoter. Expression from P todS is under catabolite control, and in cells growing with glucose, the level of expression from this promoter is reduced, which in turn translates to low levels of the TodS/TodT regulators and results in a decrease of transcription from the P todX promoter. Thus, the main underlying regulatory mechanisms of the tod structural genes are at the levels of catabolite repression control from P todS and transcription activation, mediated by the TodT response regulator through a regulatory cascade in which the effector enhances autophosphorylation of TodS by ATP, with subsequent transphosphorylation of TodT.
Endoscopy-Assisted Total Mastectomy Followed by Immediate Pedicled Transverse Rectus Abdominis Musculocutaneous (TRAM) Flap Reconstruction

Background. Endoscopy-assisted breast surgery performed through minimal axillary and/or periareolar incisions is a viable option for patients with breast cancer. In this study, we report the preliminary results of patients with breast cancer who underwent endoscopy-assisted total mastectomy (EATM) followed immediately by pedicled transverse abdominis musculocutaneous (TRAM) flap reconstruction. Methods. Patients in this study comprised women with breast cancer who received EATM and pedicled TRAM flap reconstruction. Clinicopathologic characteristics, type of surgery, complications, and rate of recurrence were recorded. The cosmetic outcomes were evaluated objectively by the surgeons and subjectively by the patients at 3-month postoperative follow-up. Results. A total of 48 patients underwent 49 EATM procedures followed by pedicled TRAM flap reconstruction. Of them, 79.6% underwent endoscopic-assisted nipple-sparing mastectomy and 20.4% received endoscopic-assisted skin-sparing mastectomy. The types of cancer among these patients included ductal carcinoma in situ in 34.7%, stage I cancer in 36.7%, stage II cancer in 24.5%, and stage IIIa cancer in 4.1% patients. Mean tumor size was 2.1 ± 1.4 cm. There were no cases of flap failure. Partial nipple areolar complex ischemia/necrosis occurred in 4 (10.3%) patients; however, all cases resolved after conservative treatment. In the aesthetic outcome evaluation, EATM + TRAM were associated with 89.8% good, 8.2% fair, and 2% unsatisfactory result. No local recurrence was observed during the follow-up period. Conclusion. EATM followed immediately by pedicled TRAM flap reconstruction is a safe procedure and results in good cosmetic outcome in women with early-stage breast cancer.
Infrapatellar Plica as a Cause of Anterior Knee Pain

Objective:This study seeks to show that in the case of a patient not responding to nonoperative measures for the treatment of anterior knee pain, arthroscopic release of a symptomatic infrapatellar plica can successfully resolve the disability. Design:We report a retrospective study of 12 cases of anterior knee pain not responding to nonoperative treatment that underwent isolated infrapatellar plica resection without other noted knee pathology. Setting:Patients were evaluated and treated in an outpatient orthopedic sports medicine clinic. Participants:Any patient who presented with anterior knee pain, underwent subsequent arthroscopy, and was treated by isolated resection of the infrapatellar plica was included in the study. Intervention:The surgical procedure involved arthroscopic division of the infrapatellar plica at its attachment on the superior intercondylar notch of the femur. Main Outcome Measurements:Patients were reviewed at least 12 months following the date of surgery. Two subjective knee scales were used to assess knee function. Results:A subjective scale used in prior studies assessing symptomatic medial plica demonstrated 91% percent (11 of 12) excellent (6) or good (5) outcomes at follow-up greater than 1 year. The Knee Injury and Osteoarthritis Outcome Scores of knee function on the subscales of pain, symptoms, activities of daily living, sports activity, and quality of life were 97, 96, 99, 99, and 87, respectively. Conclusions:These cases demonstrate a potential role for the infrapatellar plica as a cause of anterior knee pain. A prospective study is warranted to measure causality.
Patient-Related Risk Factors for Recurrence After Inguinal Hernia Repair

Background. Several factors influence the risk of recurrence after inguinal hernia surgery; however, a systematic review and meta-analysis of patient-related risk factors for recurrence after inguinal hernia surgery has not been performed earlier. Methods. MEDLINE, Embase, and Cochrane databases were searched in June 2013 for studies evaluating patient-related risk factors for recurrence after inguinal hernia operation. Observational studies evaluating nontechnical patient-related risk factors for recurrence after inguinal hernia surgery were included. Outcome variables were grouped under patient demographics, hernia characteristics, connective tissue composition and degradation, habits and social relations, and conditions related to inguinal hernia recurrence. Results. From a total of 5061 records screened, we included 40 observational studies enrolling 720 651 inguinal hernia procedures in 714 917 patients in the systematic review. Of the 40 studies, 14 studies were included in 8 meta-analyses evaluating sex, hernia type, hernia size, re-recurrence, bilaterality, mode of admission, age, and smoking as risk factors for recurrence after inguinal hernia surgery in a total of 378 824 procedures in 375 620 patients. Conclusions. We found that female sex, direct inguinal hernias at the primary procedure, operation for a recurrent inguinal hernia, and smoking were significant risk factors for recurrence after inguinal hernia surgery. This knowledge of patient-related risk factors for recurrence after inguinal hernia surgery could be implemented in clinical practice.
Faster and Better: A Machine Learning Approach to Corner Detection

The repeatability and efficiency of a corner detector determines how likely it is to be useful in a real-world application. The repeatability is important because the same scene viewed from different positions should yield features which correspond to the same real-world 3D locations. The efficiency is important because this determines whether the detector combined with further processing can operate at frame rate. Three advances are described in this paper. First, we present a new heuristic for feature detection and, using machine learning, we derive a feature detector from this which can fully process live PAL video using less than 5 percent of the available processing time. By comparison, most other detectors cannot even operate at frame rate (Harris detector 115 percent, SIFT 195 percent). Second, we generalize the detector, allowing it to be optimized for repeatability, with little loss of efficiency. Third, we carry out a rigorous comparison of corner detectors based on the above repeatability criterion applied to 3D scenes. We show that, despite being principally constructed for speed, on these stringent tests, our heuristic detector significantly outperforms existing feature detectors. Finally, the comparison demonstrates that using machine learning produces significant improvements in repeatability, yielding a detector that is both very fast and of very high quality.
Lessons Learned From Google Glass

Importance. Wearable devices such as Google Glass could potentially be used in the health care setting to expand access and improve quality of care. Objective. This study aims to assess the demographics of Google Glass users in health care and determine the obstacles to using Google Glass by surveying those who are known to use the device. Design. A 48-question survey was designed to assess demographics of users, technological limitations of Google Glass, and obstacles to implementation of the device. Setting. The physicians surveyed worked in various fields of health care, with 50% of the respondents being surgeons. Participants. Potential participants were found using an Internet search for physicians using Google Glass in their practice. Main Outcome Measures. Outcome measures were divided into demographic information of users, technological limitations of the device, and administrative obstacles. Results. A 43.6% response rate was observed. The majority of users were male, assistant professors, in academic hospitals, and in the United States. Numerous technological limitations were observed by the majority, including device ergonomics, display location, video quality, and audio quality. Patient confidentiality and data security were the major concerns among administrative obstacles. Conclusions and Relevance. Despite the potential of Google Glass, numerous obstacles exist that limit its use in health care. While Google Glass has been discontinued, the results of this study may be used to guide future designs of wearable devices.
A Review of Recent Research on Internet Access, Use, and Online Health Information Seeking

The 2013 data from the Pew Research Center’s Internet and American Life project show that 85% of United States adults use the Internet. This includes 86% of non-Hispanic whites, 85% of non-Hispanic blacks, and 76% of Hispanics interviewed. Eighty-six percent of urban and suburban respondents report Internet use. Nevertheless, some groups lag behind. Internet use in rural areas is estimated to be 80%, and seniors (65 years and older), Hispanics, and those with a high school education or less or making less than $30,000 per year all report lower Internet usage rates than other age, racial, educational attainment, or household income groups (1). The 15% of American adults that report no Internet usage, of which 49% of this group of nonusers are Americans 65 years and older, cite a number of reasons, including relevance (34%), usability (32%), price (19%), and availability (7%) (2). The similarities between groups that are low or nonusers of the Internet and those that are historically medically underserved are striking. Further data from the Pew Research Center highlight the increasing importance of the Internet when it comes to patients finding health information. Seventy-two percent of participants reported searching for health information online within the past year, with 55% looking for information about a particular condition and 43% looking for information about a treatment or procedure. Within the participants looking for health information
Draft Genome Sequence of Staphylococcus aureus 118 (ST772), a Major Disease Clone from India

ABSTRACT We report the draft genome sequence of an ST772 Staphylococcus aureus disease isolate carrying staphylococcal cassette chromosome mec (SCCmec) type V from a pyomyositis patient. Our de novo short read assembly is ∼2.8 Mb and encodes a unique Panton-Valentine leukocidin (PVL) phage with structural genes similar to those of φ7247PVL and novel lysogenic genes at the N termini.
Magnetohydrodynamics and Radiation Effects on Unsteady Convection Flow of Micropolar Fluid Past a Vertical Porous Plate with Variable Wall Heat Flux

An analysis is presented for the problem of the unsteady two-dimensional laminar flow of a viscous incompressible micropolar fluid past a vertical porous plate in the presence of a transverse magnetic field and thermal radiation with variable heat flux. The free stream velocity follows an exponentially increasing or decreasing small perturbation law. A uniform magnetic field acts perpendicularly to the porous surface in which it absorbs the micropolar fluid with a suction velocity varying with time. The Rosseland approximation is used to describe radiative heat transfer in the limit of optically thick fluids. The effects of flow parameters and thermophysical properties on the flow temperature fields across the boundary layer are investigated. The method of solution can be applied for small perturbation approximation. Numerical results of velocity profiles of micropolar fluids are compared with the corresponding flow problems for a Newtonian fluid. Also, the results of the skin-friction coefficient and the couple stress coefficient at the wall are prepared with various values of the fluid properties.