Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of bacterial surface attachment by a network of sensory transduction proteins

Bacteria are often attached to surfaces in natural ecosystems. A surface-associated lifestyle can have advantages, but shifts in the physiochemical state of the environment may result in conditions in which attachment has a negative fitness impact. Therefore, bacterial cells employ numerous mechanisms to control the transition from an unattached to a sessile state. The Caulobacter crescentus protein HfiA is a potent developmental inhibitor of the secreted polysaccharide adhesin known as the holdfast, which enables permanent attachment to surfaces. Multiple environmental cues influence expression of hfiA, but mechanisms of hfiA regulation remain largely undefined. Through a forward genetic selection, we have discovered a multi-gene network encoding a suite of two-component system (TCS) proteins and transcription factors that coordinately control hfiA transcription and surface adhesion. The hybrid HWE-family histidine kinase, SkaH, is central among these regulators and forms heteromeric complexes with the kinases, LovK and SpdS. The response regulator SpdR indirectly inhibits hfiA expression by activating two XRE-family transcription factors that directly bind the hfiA promoter to repress its transcription. This study provides evidence for a model in which a consortium of environmental sensors and transcriptional regulators integrate environmental cues at the hfiA promoter to control the attachment decision. Author summary Living on a surface within a community of cells confers a number of advantages to a bacterium. However, the transition from a free-living state to a surface-attached lifestyle should be tightly regulated to ensure that cells avoid adhering to toxic or resource-limited niches. Many bacteria build adhesive structures at their surfaces that enable attachment. We sought to discover genes that control development of the Caulobacter crescentus surface adhesin known as the holdfast. Our studies uncovered a network of signal transduction proteins that coordinately control the biosynthesis of the holdfast by regulating transcription of the holdfast inhibitor, hfiA. We conclude that C. crescentus uses a multi-component regulatory system to sense and integrate environmental information to determine whether to attach to a surface, or to remain in an unattached state.
Randomised controlled trial of laparoscopic versus open mesh repair for inguinal hernia: outcome and cost

Abstract Objective: To compare tension-free open mesh hernioplasty under local anaesthetic with transabdominal preperitoneal laparoscopic hernia repair under general anaesthetic. Design: A randomised controlled trial of 403 patients with inguinal hernias. Setting: Two acute general hospitals in London between May 1995 and December 1996. Subjects: 400 patients with a diagnosis of groin hernia, 200 in each group. Main outcome measures: Time until discharge, postoperative pain, and complications; patients' perceived health (SF-36), duration of convalescence, and patients' satisfaction with surgery; and health service costs. Results: More patients in the open group (96%) than in the laparoscopic group (89%) were discharged on the same day as the operation (χ2=6.7; 1 df; P=0.01). Although pain scores were lower in the open group while the effect of the local anaesthetic persisted (proportional odds ratio at 2 hours 3.5 (2.3 to 5.1)), scores after open repair were significantly higher for each day of the first week (0.5 (0.3 to 0.7) on day 7) and during the second week (0.7 (0.5 to 0.9)). At 1 month there was a greater improvement (or less deterioration) in mean SF-36 scores over baseline in the laparoscopic group compared with the open group on seven of eight dimensions, reaching significance on five. For every activity considered the median time until return to normal was significantly shorter for the laparoscopic group. Patients randomised to laparoscopic repair were more satisfied with surgery at 1 month and 3 months after surgery. The mean cost per patient of laparoscopic repair was £335 (95% confidence interval £228 to £441) more than the cost of open repair. Conclusion: This study confirms that laparoscopic hernia repair has considerable short term clinical advantages after discharge compared with open mesh hernioplasty, although it was more expensive. Key messages In the 4 hours after surgery laparoscopic hernia repair with general anaesthesia causes more pain than open repair with local anaesthesia (mainly because of the anaesthesia used) and necessitates longer stay in hospital. Laparoscopic hernia repair, however, causes less pain than open hernia repair during the first 2 weeks after discharge Laparoscopic hernia repair results in fewer episodes of wound infection, persistent local pain, genital swelling, numbness, and constipation than open repair. Urinary disturbances are more common after laparoscopic than after open repair Patients' perception of health 1 month after the operation (assessed with the SF-36) and satisfaction with treatment is superior for laparoscopic patients who also have a shorter period of convalescence after surgery The health service cost of day case laparoscopic repair is £335 more than the cost of open mesh hernioplasty performed on a day case basis
HPSLPred: An Ensemble Multi‐Label Classifier for Human Protein Subcellular Location Prediction with Imbalanced Source

Predicting the subcellular localization of proteins is an important and challenging problem. Traditional experimental approaches are often expensive and time‐consuming. Consequently, a growing number of research efforts employ a series of machine learning approaches to predict the subcellular location of proteins. There are two main challenges among the state‐of‐the‐art prediction methods. First, most of the existing techniques are designed to deal with multi‐class rather than multi‐label classification, which ignores connections between multiple labels. In reality, multiple locations of particular proteins imply that there are vital and unique biological significances that deserve special focus and cannot be ignored. Second, techniques for handling imbalanced data in multi‐label classification problems are necessary, but never employed. For solving these two issues, we have developed an ensemble multi‐label classifier called HPSLPred, which can be applied for multi‐label classification with an imbalanced protein source. For convenience, a user‐friendly webserver has been established at http://server.malab. cn/HPSLPred.
Basement membrane structure in situ: evidence for lateral associations in the type IV collagen network

To determine molecular architecture of the type IV collagen network in situ, the human amniotic basement membrane has been studied en face in stereo relief by high resolution unidirectional metal shadow casting aided by antibody decoration and morphometry. The appearance of the intact basement membrane is that of a thin sheet in which there are regions of branching strands. Salt extraction further exposes these strands to reveal an extensive irregular polygonal network that can be specifically decorated with gold-conjugated anti-type IV collagen antibody. At high magnification one sees that the network, which contains integral (9-11 nm net diameter) globular domains, is formed in great part by lateral association of monomolecular filaments to form branching strands of variable but narrow diameters. Branch points are variably spaced apart by an average of 45 nm with 4.4 globular domains per micron of strand length. Monomolecular filaments (1.7-nm net diameter) often appear to twist around each other along the strand axis; we propose that super helix formation is an inherent characteristic of lateral assembly. A previous study (Yurchenco, P. D., and H. Furthmayr. 1984. Biochemistry. 23:1839) presented evidence that purified murine type IV collagen dimers polymerize to form polygonal arrays of laterally as well as end-domain-associated molecules. The architecture of this polymer is similar to the network seen in the amnion, with lateral binding a major contributor to each. Thus, to a first approximation, isolated type IV collagen can reconstitute in vitro the polymeric molecular architecture it assumes in vivo.
A Natural Infrastructure-Less Human–Robot Interaction System

This letter introduces a novel methodology for letting a user interact with a robotic system in a natural manner. The main idea is that of defining an interaction system that does not require any specific infrastructure or device but relies on commonly utilized objects while leaving the user's hands free. Specifically, we propose to utilize a smartwatch (or any commercial sensorized wristband) for recognizing the motion of the user's forearm. This is achieved by measuring accelerations and angular velocities, which are then elaborated for recognizing gestures and for defining velocity commands for the robot. The proposed interaction system is evaluated experimentally with different users controlling a semiautonomous quadrotor. Results show that the usability and effectiveness of the proposed natural interaction system provide significant improvement in the human–robot interaction experience.
Learning a Policy for Coordinated Sampling in Body Sensor Networks

This paper describes a method for learning coordination policies in body sensor networks. The learning of a compact coordination policy is important for implementing the policy in sensor nodes with limited memory. We present a novel algorithm, Reinforcement Learning Average Approximation (RLAA), to learn local coordination policies for each sensor node from globally joint rewards. These local policies are obtained by reinforcement learning and averaging state-action tables under a stochastic process model. We show results on a simulation of an existing body sensor network interfaced with transdermal sensors that demonstrate the performance of this learning scheme. Experimental results show that the performance of the RLAA algorithm is significantly better than a random policy and is close to the optimal policy that can be obtained from solving a global Markov Decision Process while the learning step is fast. The results also show that the RLAA algorithm is scalable to networks represented by large state spaces (in terms of number s of sensors and degree of discretization).
Ascorbic Acid and Ozone: Novel Perspectives to Explain an Elusive Relationship

A huge amount of studies highlighted the importance of high ascorbic acid (AA) content in ozone tolerance, yet the relationship between them appears more complex than a simple direct correlation. Sometimes the connection is clear, for example, two Arabidopsis mutants defective in the main AA biosynthetic pathway (vtc mutants) were identified by means of their ozone sensitivity. However, some low-AA containing mutants are relatively tolerant, suggesting that AA location/availability could be more relevant than total content. A clear distinction should also be made between ozone tolerance obtained when AA content is increased by experimental supplementation (exogenous AA), and the physiological role of plant-synthesized AA (endogenous AA), whose amount is apparently subjected to tight regulation. Recent findings about the role of AA in signal transduction and epigenetic regulation of gene expression open new routes to further research.
STIM Proteins and Glutamate Receptors in Neurons: Role in Neuronal Physiology and Neurodegenerative Diseases

Neuronal calcium (Ca2+) influx has long been ascribed mainly to voltage-gated Ca2+ channels and glutamate receptor channels. Recent research has shown that it is also complemented by stromal interaction molecule (STIM) protein-mediated store-operated Ca2+ entry (SOCE). SOCE is described as Ca2+ flow into cells in response to the depletion of endoplasmic reticulum Ca2+ stores. The present review summarizes recent studies that indicate a relationship between neuronal SOCE that is mediated by STIM1 and STIM2 proteins and glutamate receptors under both physiological and pathological conditions, such as neurodegenerative disorders. We present evidence that the dysregulation of neuronal SOCE and glutamate receptor activity are hallmarks of acute neurodegenerative diseases (e.g., traumatic brain injury and cerebral ischemia) and chronic neurodegenerative diseases (e.g., Alzheimer’s disease and Huntington’s disease). Emerging evidence indicates a role for STIM proteins and glutamate receptors in neuronal physiology and pathology, making them potential therapeutic targets.
DOGMA: a web server for proteome and transcriptome quality assessment

Abstract Even in the era of next generation sequencing, in which bioinformatics tools abound, annotating transcriptomes and proteomes remains a challenge. This can have major implications for the reliability of studies based on these datasets. Therefore, quality assessment represents a crucial step prior to downstream analyses on novel transcriptomes and proteomes. DOGMA allows such a quality assessment to be carried out. The data of interest are evaluated based on a comparison with a core set of conserved protein domains and domain arrangements. Depending on the studied species, DOGMA offers precomputed core sets for different phylogenetic clades. We now developed a web server for the DOGMA software, offering a user-friendly, simple to use interface. Additionally, the server provides a graphical representation of the analysis results and their placement in comparison to publicly available data. The server is freely available under https://domainworld-services.uni-muenster.de/dogma/. Additionally, for large scale analyses the software can be downloaded free of charge from https://domainworld.uni-muenster.de.
Very-High-Frequency Resonant Boost Converters

This paper presents a resonant boost topology suitable for very-high-frequency (VHF, 30-300 MHz) DC-DC power conversion. The proposed design features low device voltage stress, high efficiency over a wide load range, and excellent transient performance. Two experimental prototypes have been built and evaluated. One is a 110-MHz, 23-W converter that uses a high-performance RF lateral DMOSFET. The converter achieves higher than 87% efficiency at nominal input and output voltages, and maintains good efficiency down to 5% of full load. The second implementation, aimed toward integration, is a 50-MHz, 17-W converter that uses a transistor from a 50-V integrated power process. In addition, two resonant gate drive schemes suitable for VHF operation are presented, both of which provide rapid startup and low-loss operation. Both converters regulate the output using high-bandwidth, on-off hysteretic control, which enables fast transient response and efficient light-load operation. The low energy storage requirements of the converters allow the use of aircore inductors in both designs, thereby eliminating magnetic core loss and introducing the possibility of easy integration.
Visual evoked potentials and nitrous oxide-induced neuronal depression: role for benzodiazepine receptors.

We have examined the role of benzodiazepine receptors in nitrous oxide-induced neuronal depression in rats. The changes in neuronal excitability induced by nitrous oxide and the benzodiazepine inverse agonist, Ro15-4513, were monitored by measurement of visual evoked potentials (VEP). Administration of Ro15-4513 10 mg kg-1 i.p., in rats breathing air, did not affect the amplitude or latency of VEP. However, the same concentrations of Ro15-4513 antagonized nitrous oxide-induced depression of VEP amplitudes. We conclude that antagonism of nitrous oxide-induced depression by Ro15-4513 indicates that at least part of the decreased neuronal excitability caused by nitrous oxide could be ascribed to interactions with the GABAA receptor complex.
Enhanced Humidity Sensing Response of SnO2/Silicon Nanopillar Array by UV Irradiation

In this work, a silicon nanopillar array was created with nanosphere lithography. SnO2 film was deposited on this nanostructure by magnetron sputtering to form an SnO2/silicon nanopillar array sensor. The humidity sensitivity, response time, and recovery time were all measured at room temperature (25 °C) with UV or without UV irradiation. As a result, the humidity sensitivity properties were improved by enlarging the specific surface area with ordered nanopillars and irradiating with UV light. These results indicate that nanostructure sensors have potential applications in the field of sensors.
A comprehensive review of the clinical utility of and a combined analysis of the clozapine/norclozapine ratio in therapeutic drug monitoring for adult patients

ABSTRACT Introduction: This article comprehensively reviews the clinical utility of the serum clozapine/norclozapine (CLO/NCLO) ratio. Areas covered: Fifty-four published studies used this ratio (21 from a PubMed search from onset to 10/21/18 and 33 identified by the authors). To estimate a combined mean of the CLO/NCLO ratio in published studies, a PubMed search on 10/21/18 identified 422 articles leading to 19 included. The systematic review focused on 1) the combined analysis, 2) CYP1A2 activity, 3) clinical response, 4) cognition, and 5) renal function. Expert opinion: Our combined analysis provided a weighted mean CLO/NCLO ratio of 1.73 in 2,317 adult patients from 19 studies, but the range in the studies varied widely from 1.19 to 3.37. No study provided data on variability of the CLO/NCLO ratios within individual patients. The CLO/NCLO ratio is not a measure of CYP1A2 activity and is not associated with clinical response. The association of the CLO/NCLO ratio with cognitive measures is unclear (4 cross-sectional studies were positive and post-hoc analysis of a randomized clinical trial was negative). Future studies must replicate the finding of a case report that gemfibrozil may invert the CLO/NCLO ratio (making it <1), indicating that gemfibrozil inhibits the renal transporter that excretes NCLO.
he intersection of amyloid beta and tau in glutamatergic synaptic ysfunction and collapse in Alzheimer ’ s disease

The synaptic connections that form between neurons during development remain plastic and able to adapt throughout the lifespan, enabling learning and memory. However, during aging and in particular in neurodegenerative diseases, synapses become dysfunctional and degenerate, contributing to dementia. In the case of Alzheimer’s disease (AD), synapse loss is the strongest pathological correlate of cognitive decline, indicating that synaptic degeneration plays a central role in dementia. Over the past decade, strong evidence has emerged that oligomeric forms of amyloid beta, the protein that accumulates in senile plaques in the AD brain, contribute to degeneration of synaptic structure and function. More recent
Vinculin is a component of an extensive network of myofibril-sarcolemma attachment regions in cardiac muscle fibers

Immunofluorescent staining of bovine and avian cardiac tissue with affinity-purified antibody to chicken gizzard vinculin reveals two new sites of vinculin reactivity. First, vinculin is organized at the sarcolemma in a striking array of rib-like bands, or costameres. The costameres encircle the cardiac muscle cell perpendicular to the long axis of the fiber and overlie the I bands of the immediately subjacent sarcomeres. The second new site of vinculin reactivity is found in bovine cardiocytes at tubular invaginations of the plasma membrane. The frequency and location of these invaginations correspond to the known frequency and distribution of the transverse tubular system in bovine atrial, ventricular, and Purkinje fibers. We do not detect tubular invaginations that stain with antivinculin in avian cardiocytes and, in fact, a transverse tubular system has not been found in avian cardiac fibers. Apparent lateral Z-line attachments to the sarcolemma and its invaginations have been observed in cardiac muscle by electron microscopy in the same regions where we find vinculin. On the basis of these previous ultrastructural findings and our published evidence for a physical connection between costameres and the underlying myofibrils in skeletal muscle, we interpret the immunofluorescence data of this study to mean that, in cardiac muscle, vinculin is a component of an extensive system of lateral attachment of myofibrils to the plasma membrane and its invaginations.
A Study of the Agile Software Development Methods, Applicability and Implications in Industry

There has been a tremendous importance in the field of agile software development approaches in the recent past. This is because of the fastness that agile approaches bring in the life cycle of software development. This interest in the field shows that there are benefits to reap through successful implementation of agile methods. The field is relatively nascent and research is in its initial stages. The paper has been carried with the distinct objectives of examine and gain insights into the current agile methods and practices, understanding the strengths and weaknesses of agile methods and various issues of their applicability. To meet the set goals and objectives, we used both qualitative and quantitative research methodologies. Apart from a systematized literature survey and review, we performed a case study of four software companies in India. The data collection methods included questionnaires, interviews and analysis of the companies’ web-sites.
The opacity of spiral galaxy disks VII. The accuracy of galaxy counts as an extinction probe

The "Synthetic Field Method" (SFM) was introduced by Gonzalez et al. (1998, ApJ, 506, 152) to calibrate numbers of distant galaxies as a probe of extinction in a foreground spiral disk. Gonzalez et al. (2003, AJ, 125, 1182) studied the effect of the foreground disk on these numbers using simulations of current and future instruments for fields in the LMC, M31 and NGC 4536, a galaxy in Virgo. They concluded that: (1) the brighter centers of disks were unsuitable; (2) the granularity of the disk at a fixed surface brightness is the limiting factor in the detection of distant galaxies; and (3) the optimum distance for measurements would be that of the Virgo cluster for the current instruments on board HST. At this distance the foreground disk is smoothed with distance, improving detection of distant background galaxies. Holwerda et al. (2005a, AJ, 129, 1381) automated the SFM and Holwerda et al. (2005b, AJ, 129, 1396) applied it to a large set of WFPC2 fields. In this paper, the quality of the extinction measurement in these fields is compared to their distance, granularity, surface brightness and structure. The average surface brightness of the of a field is shown to directly influence the accuracy of the SFM. This restricts meaningful measurements to the disks of spiral galaxies. Large structures such as spiral arms have a similar effect. The granularity or small scale structure in a field influences the detection of distant galaxies, limiting the SFM measurements in nearby disks. From the trends in the accuracy and maximum practical field-of-view considerations, the minimum and maximum distance for SFM application, approximately 5 and 35 Mpc respectively. Using the same instrument and detection method, the relations with SFM parameters and field characteristics can be used to forgo the synthetic fields altogether. For the wealth of ACS fields becoming available in the archive, these relations can be used to select those fields based on expected SFM accuracy.