Miracle-dz/UniFAR-FTUs huggingface dataset:
Site-Directed Disulfide Cross-Linking Shows that Cleft Flexibility in the Periplasmic Domain Is Needed for the Multidrug Efflux Pump AcrB of Escherichia coli

ABSTRACT Escherichia coli AcrB is a multidrug efflux transporter that recognizes multiple toxic chemicals having diverse structures. Recent crystallographic studies of the asymmetric trimer of AcrB suggest that each protomer in the trimeric assembly goes through a cycle of conformational changes during drug export. However, biochemical evidence for these conformational changes has not been provided previously. In this study, we took advantage of the observation that the external large cleft in the periplasmic domain of AcrB appears to become closed in the crystal structure of one of the three protomers, and we carried out in vivo cross-linking between cysteine residues introduced by site-directed mutagenesis on both sides of the cleft, as well as at the interface between the periplasmic domains of the AcrB trimer. Double-cysteine mutants with mutations in the cleft or the interface were inactive. The possibility that this was due to the formation of disulfide bonds was suggested by the restoration of transport activity of the cleft mutants in a dsbA strain, which had diminished activity to form disulfide bonds in the periplasm. Furthermore, rapidly reacting, sulfhydryl-specific chemical cross-linkers, methanethiosulfonates, inactivated the AcrB transporter with double-cysteine residues in the cleft expressed in dsbA cells, and this inactivation could be observed within a few seconds after the addition of a cross-linker in real time by increased ethidium influx into the cells. These observations indicate that conformational changes, including the closure of the external cleft in the periplasmic domain, are required for drug transport by AcrB.
Efferents and Centrifugal Afferents of the Main and Accessory Olfactory Bulbs in the Snake Thamnophis sirtalis

This study reinvestigates the efferent projections of the main and accessory olfactory bulbs and describes for the first time the centrifugal projections to the main and accessory olfactory bulbs in the snake Thamnophis sirtalis, using the intraaxonal transport of the anterograde and retrograde tracer biotinylated dextran amine and the retrograde tracer horseradish peroxidase. The olfactory projection consists of three tracts: the lateral olfactory tract, which projects bilaterally to the lateral cortex and the rostral amygdala, crossing the midline through the stria medullaris-habenular commissure system; the intermediate olfactory tract, which projects ipsilaterally to the olfactory tubercle and contributes to the contralateral projection; and the medial olfactory tract, which projects ipsilaterally to the dorsomedial retrobulbar formation. The vomeronasal projection is formed by a single tract, the accessory olfactory tract, that projects ipsilaterally to the nucleus of the accessory olfactory tract, the medial amygdala and the nucleus sphericus. The centrifugal projections to the main and accessory olfactory bulb are composed of two components: one that arises in areas that receive the olfactory or vomeronasal input (neurons in the olfactory tubercle, retrobulbar formation and lateral cortex project to the main olfactory bulb; and neurons in the nucleus of the accessory olfactory tract, the medial amygdala and the nucleus sphericus project to the accessory olfactory bulb), and another that arises in areas not directly implicated in processing the chemosensory information (the nucleus of the diagonal band of Broca and the dorsal cortex). These data allow the recognition of the general pattern of organization of the reptilian olfactory and vomeronasal systems.
A Method to Segment Maps from Different Modalities Using Free Space Layout MAORIS: Map of Ripples Segmentation

How to divide floor plans or navigation maps into semantic representations, such as rooms and corridors, is an important research question in fields such as human-robot interaction, place categorization, or semantic mapping. While most works focus on segmenting robot built maps, those are not the only types of map a robot, or its user, can use. We present a method for segmenting maps from different modalities, focusing on robot built maps and hand-drawn sketch maps, and show better results than state of the art for both types. Our method segments the map by doing a convolution between the distance image of the map and a circular kernel, and grouping pixels of the same value. Segmentation is done by detecting ripple-like patterns where pixel values vary quickly, and merging neighboring regions with similar values. We identify a flaw in the segmentation evaluation metric used in recent works and propose a metric based on Matthews correlation coefficient (MCC). We compare our results to ground-truth segmentations of maps from a publicly available dataset, on which we obtain a better MCC than the state of the art with 0.98 compared to 0.65 for a recent Voronoi-based segmentation method and 0.70 for the DuDe segmentation method. We also provide a dataset of sketches of an indoor environment, with two possible sets of ground truth segmentations, on which our method obtains an MCC of 0.56 against 0.28 for the Voronoi-based segmentation method and 0.30 for DuDe.
Expression of the p20 Gene from Bacillus thuringiensis H-14 Increases Cry11A Toxin Production and Enhances Mosquito-Larvicidal Activity in Recombinant Gram-Negative Bacteria

ABSTRACT Experimental analyses with recombinant Escherichia coliand Pseudomonas putida transformed with plasmids bearing genes coding for the Cry11A toxin and P20 protein from Bacillus thuringiensis H-14 showed that cells producing both proteins were more toxic when fed to third-instar Aedes aegypti larvae than were cells expressing cry11A alone; the 50% lethal concentrations were in the range of 104 to 105cells/ml. Western blots revealed a higher production of Cry11A when thep20 gene was coexpressed. Cry11A was detected primarily in insoluble form in recombinant cells. Cry11A was not detected inP. putida when P20 was not coproduced, and these recombinants were not toxic to larvae, whereas P. putidarecombinants producing both proteins were toxic at concentrations similar to those for E. coli. A coelution experiment was conducted, in which a p20 gene construct producing the P20 protein with an extension of six histidines on the C terminus was mixed with the Cry11A protein. The results showed that Cry11A bound to the P20(His6) on a nickel chelating column, whereas Cry11A produced without the P20(His6) protein was washed through the column, thus indicating that Cry11A and P20 physically interact. Thus, P20 protein either stabilizes Cry11A or helps it attain the folding important for its toxic activity.
Antimicrobial Stewardship and Automated Pharmacy Technology Improve Antibiotic Appropriateness for Community-Acquired Pneumonia

Background. The Centers for Medicare and Medicaid Services' (CMS's) Hospital Inpatient Quality Reporting program includes the initial selection of antibiotics for adult community-acquired pneumonia (CAP) patients as a performance measure. A multidisciplinary team denned opportunities for improving performance in appropriate antibiotic use among CAP patients. The team consisted of personnel from the emergency department (ED), the antimicrobial stewardship program (infectious disease, pharmacy), and performance improvement. Design. Quasi-experimental before-after study. Setting. A large, urban, multicampus academic medical center. Interventions. Interventions included an algorithm for ED providers identifying appropriate antibiotic selections, development of a CAP kit consisting of appropriate antibiotics and dosing regimens bundled with the treatment algorithm, and preloading an automated ED medication dispensing and management system. A quality improvement methodology (“plan, do, check, act”) was used to pilot stewardship interventions at one ED campus and later at a second ED campus. Results. In the pilot ED, appropriate antibiotic selection for CAP improved from 54.9% before the intervention in 2008 to 93.4% after the intervention in 2011 (P< .001). Subsequently, in the second ED appropriate antibiotic regimens for CAP improved from 64.6% before the intervention in 2008 to 91.3% after the intervention in 2011 (P = .004). The rates of another CMS measure, antibiotic administration within 6 hours, were not statistically different before and after the interventions. In an interrupted time series logistic regression analysis, the intervention was found to be significantly associated with the improved prescribing (P< .001). Discussion. The combination of interdisciplinary teamwork, antibiotic stewardship, education, and information technology is associated with replicable and sustained prescribing improvements.
Assessing physical activity in Muslim women of South Asian origin.

BACKGROUND We assessed the quality of data on physical activity obtained by recall from Muslim women of South Asian origin, and the feasibility of using accelerometer-based physical activity monitors to provide more objective measures of physical activity in this group. METHODS In this largely qualitative study, 22 British Pakistani women were asked to wear accelerometers (the GT1M Actigraph and/or the Sensewear Armband) for 4 days, provided 2 24-hour recalls of activities, and were interviewed about their experiences with the monitors. RESULTS Women reported spending most of their time in housework and childcare, activities which generated the majority of recorded bouts of moderate to vigorous physical activity. However, women had difficulty in recalling the timing, and assessing the intensity, of these usually unstructured activities. A significant minority of accelerometer datasets were incomplete and some women reported either forgetting to wear the accelerometer or finding it intrusive. CONCLUSIONS Questionnaires are unlikely to provide an accurate assessment of physical activity in this group of women. This suggests that accelerometer data will be preferable. However, collecting sufficient data for large-scale studies using activity monitors in this population will be challenging.
Tracking control design for autonomous underwater vehicle using robust filter approach

Autonomous Underwater Vehicle (AUV) play an important role in underwater inspection mission. However, there are external disturbances and parameter uncertainties which degrade the performance of an AUV. A robust control is needed to minimize the effects of external influences on AUV's system behaviour, subjects to the constraint of not having a complete representation of the AUV system. This paper proposed a time invariant tracking control method for AUV using robust filter approach. The proposed controller is able to achieve robustness against parameter uncertainties, model nonlinearities, and unexpected external disturbances with only rigid-body system inertia matrix information of AUV. Simulation results are presented to illustrate the performance of designed robust tracking control.
Cadmium accumulation and binding characteristics in intact Sertoli/germ cell units, and associated effects on stage‐specific functions in vitro: insights from a shark testis model

The increased human use of cadmium (Cd) and its increased occurrence in the environment is of concern. The testis is sensitive to Cd because of the steroid‐mediated regulation of spermatogenesis, high levels of DNA synthesis and gene transcription, all of which varies in a stage‐related manner. Validated techniques (acridine orange vital staining to detect apoptosis and dextran‐rhodamine exclusion to assess blood–testis barrier function) were recently developed and the shark testis was proposed as an alternative model for assessing stage‐specific functions in living testicular tissue and to study toxicant actions on spermatogenesis. The present paper shows that 109Cd accumulation and binding in vitro was stage‐dependent (premeiotic, PrM > meiotic, M > postmeiotic, PoM), rapid and persisted in spermatocysts (intact germ cell/Sertoli cell units) 49 h after washout. In competitive binding analyses of all three spermatocyst stages, Hg, but not Zn, could replace bound 109Cd, suggesting that Cd binding was specific. These findings were associated with a biphasic apoptotic response in the PrM spermatocysts, which was maximal at 10 µm CdCl2 and 1 µm CdCl2 after 2 and 4 days in culture, respectively. Although Cd uptake in PoM cysts was more than 2‐fold less than uptake in PrM cysts, the percentage dextran‐rhodamine permeant PoM cysts was ∼8‐fold greater than in controls in the presence of both 10 µm CdCl2 and 30 µm CdCl2 after 4 days culture, indicating that blood–testis barrier function in PoM spermatocysts was compromised. These findings demonstrate that this model has utility for use in screening assays of environmental toxicants. Copyright © 2007 John Wiley & Sons, Ltd.
Effects of downsizing strategies on survivors’ organizational commitment: the case of Ethio Telecom

The study sought to analyze the effects of downsizing strategies on survivors’ organizational commitment (affective, continuous, and normative) at Ethio Telecom. This study used descriptive and causal effect type of study. It focused on both qualitative and quantitative approaches for collection and analysis of data. This research made use of both primary and secondary sources of data. The researcher employed simple random sampling technique to select 362respondents from each zone and headquarter offices. In this study, Structural Equation Modeling (SEM) was employed. As the findings depict that positive and significant effect of exogenous variables (organizational justice: procedural and distributive justice) with the standardized estimate for procedural justice on affective, continuous, and normative commitment effects were all significant but they are not that much strong (s =0.22, 0.18, 0.17) while distributive justice had high effect on affective, continuous, and normative commitment0.97, 0.99, 0.98 and respectively. Based on the above findings the researcher inferred that there was organizational procedural injustice in the time of downsizing at Ethio Telecom. Consequently, these perceptions affected adversely survivors’ organizational commitment. As a result, survivors are neither emotionally attached nor have feeling of continuous commitment to the company. Hence, the researcher recommends that the strategists should do the following in order to make it effective: plan the process properly, study the overall scenario prior to the attempt, do human resource planning industriously, set clear selection criteria, make the process transparent, communicate timely, conduct behavioral trainings, align each unit activity with company’s strategic objectives, and prepare victims for other jobs.
High-resolution magnetic resonance histology of the embryonic and neonatal mouse: A 4D atlas and morphologic database

Engineered mice play an ever-increasing role in defining connections between genotype and phenotypic expression. The potential of magnetic resonance microscopy (MRM) for morphologic phenotyping in the mouse has previously been demonstrated; however, applications have been limited by long scan times, availability of the technology, and a foundation of normative data. This article describes an integrated environment for high-resolution study of normal, transgenic, and mutant mouse models at embryonic and neonatal stages. Three-dimensional images are shown at an isotropic resolution of 19.5 μm (voxel volumes of 8 pL), acquired in 3 h at embryonic days 10.5–19.5 (10 stages) and postnatal days 0–32 (6 stages). A web-accessible atlas encompassing this data was developed, and for critical stages of embryonic development (prenatal days 14.5–18.5), >200 anatomical structures have been identified and labeled. Also, matching optical histology and analysis tools are provided to compare multiple specimens at multiple developmental stages. The utility of the approach is demonstrated in characterizing cardiac septal defects in conditional mutant embryos lacking the Smoothened receptor gene. Finally, a collaborative paradigm is presented that allows sharing of data across the scientific community. This work makes magnetic resonance microscopy of the mouse embryo and neonate broadly available with carefully annotated normative data and an extensive environment for collaborations.
Cutaneous afferents provide a neuronal population vector that encodes the orientation of human ankle movements

The aim of this study was to analyse the directional coding of two‐dimensional limb movements by cutaneous afferents from skin areas covering a multidirectional joint, the ankle. The activity of 89 cutaneous afferents was recorded in the common peroneal nerve, and the mean discharge frequency of each unit was measured during the outward phase of ramp and hold movements imposed in 16 different directions. Forty‐two afferents responded to the movements in the following decreasing order (SA2, n= 24/27; FA2, n= 13/17; FA1, n= 3/24; SA1, n= 2/21). All the units activated responded to a specific range of directions, defining their ‘preferred sector’, within which their response peaked in a given direction, their ‘preferred direction’. Based on the distribution of the preferred directions, two populations of afferents, and hence two skin areas were defined: the anterior and the external lateral parts of the leg. As the directional tuning of each population was cosine shaped, the neuronal population vector model was applied and found to efficiently describe the movement direction encoded by cutaneous afferents, as it has been previously reported for muscle afferents. The responses of cutaneous afferents were then considered with respect to those of the afferents from the underlying muscles, which were previously investigated, and an almost perfect matching of directional sensitivity was observed. It is suggested that the common movement‐encoding characteristics exhibited by cutaneous and muscle afferents, as early as the peripheral level, may facilitate the central co‐processing of their feedbacks subserving kinaesthesia.
Role of Lipase from Community-Associated Methicillin-Resistant Staphylococcus aureus Strain USA300 in Hydrolyzing Triglycerides into Growth-Inhibitory Free Fatty Acids

ABSTRACT Part of the human host innate immune response involves the secretion of bactericidal lipids on the skin and delivery of triglycerides into abscesses to control invading pathogens. Two Staphylococcus aureus lipases, named SAL1 and SAL2, were identified in the community-associated methicillin-resistant S. aureus strain USA300, which, presumably, are produced and function to degrade triglycerides to release free fatty acids. We show that the SAL2 lipase is one of the most abundant proteins secreted by USA300 and is proteolytically processed from the 72-kDa proSAL2 to the 44-kDa mature SAL2 by the metalloprotease aureolysin. We show that spent culture supernatants had lipase activity on both short- and long-chain fatty acid substrates and that deletion of gehB, encoding SAL2, resulted in the complete loss of these activities. With the use of gas chromatography-mass spectrometry, we show that SAL2 hydrolyzed trilinolein to linoleic acid, a fatty acid with known antistaphylococcal properties. When added to cultures of USA300, trilinolein and, to a lesser extent, triolein inhibited growth in a SAL2-dependent manner. This effect was shown to be due to the enzymatic activity of SAL2 on these triglycerides, since the catalytically inactive SAL2 Ser412Ala mutant was incapable of hydrolyzing the triglycerides or yielding delayed growth in their presence. Overall, these results reveal that SAL2 hydrolyzes triglycerides of both short- and long-chain fatty acids and that the released free fatty acids have the potential to cause significant delays in growth, depending on the chemical nature of the free fatty acid.
Multilayer Image Grid Reconstruction Technology: Four-Dimensional Interactive Image Reconstruction of Microsurgical Neuroanatomic Dissections

OBJECTIVE: Cadaveric dissection is the gold standard for training physicians in various surgical specialties. However, limitations in acquiring and storing sufficient cadaveric material, recent pressures in training opportunities, and progress in digital image technology have led to advances in virtual or artificial visual means to augment surgical training. For training neurosurgeons, the appearance of reality is still crucial for learning anatomic structures and procedures. We developed a four-dimensional (including time) multilayer digital image reconstruction technology (MIGRT) that allows users to manipulate a "volumetric" set of photographic image data from exquisite cadaveric intracranial dissections and to navigate through stages of neurosurgical procedures as the dissection progresses. METHODS: A robotic microscope with two digital cameras was used to capture dissection images, usually in stereoscopic mode. A grid space was created to define positions at which images are captured. Images were acquired from identical angles at the same grid coordinates but at different stages of various dissections. RESULTS: Image data are reconstructed according to the sequence of acquisition into a multilayer image grid system by the MIGRT software. The single interactive, four-dimensional montage is viewable a on common computer platform. CONCLUSION: MIGRT uniquely focuses on capturing anatomic content that preserves natural appearances, including procedure, texture, and color, which is far superior and preferable to images and a reconstructed image environment based on artificial or animated concepts. MIGRT shows time-dependent changes in procedures, provides depth perception by stereoscopy or unique sequential motion, and allows simultaneous interactivity at each step of the procedure.
Efficacy of low load resistive muscle training in patients with rheumatoid arthritis functional class II and III.

OBJECTIVE To determine the effect of a low load resistance exercise training program on muscle strength, functional outcome, and cardiovascular endurance. METHODS Forty-nine patients, 37 women and 12 men between the ages of 35-76 yrs (mean 60.5 yrs), with definite rheumatoid arthritis (RA) functional class II and III (mean disease duration of 10.5 yrs) were randomly assigned to exercise and control groups for a 12 wk resistive muscle training program. A circuit weight bearing form of training was incorporated using light loads with high repetitions. A video tape demonstrating the exercises was given to all exercising participants to enable them to continue the program at home at least 3 times per wk with a biweekly self-report evaluation. Baseline and post-intervention evaluations included joint activity, muscle strength, endurance, functional outcome, and self-report. Cardiovascular fitness measured by treadmill time, anaerobic threshold and peak oxygen consumption (VO2) in this group were assessed at baseline and 12 wks. RESULTS A significant improvement at 12 wks was noted in the exercise group for self-reported joint count (p = 0.02), number of painful joints (p = 0.004), HAQ (p = 0.012), sit-to-stand time (p = 0.02), grip strength (p = 0.05) knee extension 60 degrees (p = 0.03), Arthritis Impact Measurement Scales dexterity (p = 0.02), and time to anaerobic threshold (p = 0.03). Significant improvement in the exercise group compared to the control group was noted for self-reported joint count (p = 0.02), night time pain (p = 0.05), and sit-to-stand time (p = 0.02). Increase in treadmill time was not statistically significant nor was a change in peak oxygen consumption (VO2) noted. Abnormalities on initial treadmill screening were detected in 2 of 49 asymptomatic patients. They were excluded from the study and subsequent workup revealed significant coronary artery disease. CONCLUSION Low load resistive muscle training increased functional capacity as reported by patients and is a clinically safe form of exercise in functional class II and III RA. Screening this population for dormant coronary artery disease is recommended.