Miracle-dz/UniFAR-FTUs huggingface dataset:
Liquid crystalline bacterial outer membranes are critical for antibiotic susceptibility

Significance Gram-negative bacteria possess an outer membrane (OM) which reduces antibiotic effectiveness. The OM has a dense outer layer of lipopolysaccharide (LPS), a glycolipid which is directly targeted by the last-resort antibiotic polymyxin B (PmB). However, we lack accurate molecular data on the PmB–OM interaction to inform future drug development. Here we study the PmB–OM interaction in vitro and show that in vivo results are reproduced only when the LPS is in a liquid crystalline phase, which occurs at body temperature. These findings not only explain the temperature dependence of PmB function but also support the notion that bacteria actively control the viscosity of their outer membranes as growth temperatures vary. The outer membrane (OM) of Gram-negative bacteria is a robust, impermeable, asymmetric bilayer of outer lipopolysaccharides (LPSs) and inner phospholipids containing selective pore proteins which confer on it the properties of a molecular sieve. This structure severely limits the variety of antibiotic molecules effective against Gram-negative pathogens and, as antibiotic resistance has increased, so has the need to solve the OM permeability problem. Polymyxin B (PmB) represents those rare antibiotics which act directly on the OM and which offer a distinct starting point for new antibiotic development. Here we investigate PmB’s interactions with in vitro OM models and show how the physical state of the lipid matrix of the OM is a critical factor in regulating the interaction with the antimicrobial peptide. Using neutron reflectometry and infrared spectroscopy, we reveal the structural and chemical changes induced by PmB on OM models of increasing complexity. In particular, only a tightly packed model reproduced the temperature-controlled disruption of the asymmetric lipid bilayer by PmB observed in vivo. By measuring the order of outer-leaflet LPS and inner-leaflet phospholipids, we show that PmB insertion is dependent on the phase transition of LPS from the gel to the liquid crystalline state. The demonstration of a lipid phase transition in the physiological temperature range also supports the hypothesis that bacteria grown at different temperatures adapt their LPS structures to maintain a homeoviscous OM.
Sleep Disorders and Symptoms in Blacks with Metabolic Syndrome: The Metabolic Syndrome Outcome Study (MetSO).

Introduction Sleep disturbance is a major public health issue and is comorbid with the cluster of conditions associated with metabolic syndrome (MetS). Our study explored the presence of sleep disturbance, including daytime sleepiness, the risk for obstructive sleep apnea (OSA), and insomnia symptoms, in a cohort of adult Black men and women with MetS. Methods Patients (n=1,013) from the Metabolic Syndrome Outcome Study (MetSO), 2009-2012, met criteria for MetS based on guidelines from the National Cholesterol Education Program's Adult Treatment Panel and provided sociodemographic data and the Apnea Risk Evaluation System (ARES) questionnaire to assess OSA risk, sleep characteristics, and physician-reported diagnosis of a sleep disorder. Results Prevalence of the components of MetS included: diabetes (60%); obesity (67%); hypertension (94%); and dyslipidemia (74%). Based on the ARES, 49% were at risk for OSA. Of all study patients, slightly more than half (53%) reported feeling sleepy during the day, and 10% reported an insomnia diagnosis. The most common sleep disturbance reported by 46% of the patients was early morning awakenings (EMA). This was closely followed by 42% who reported difficulty staying asleep (DSA) and 38% reporting difficulty falling asleep (DFA). Seventy percent reported short sleep (≤ 6 hours), whereas a minority (19%) reported long sleep (≥ 9 hours). Only 12% used sleep aids. Women, compared with men, reported greater daytime sleepiness, greater DFA, and greater DSA (57% vs 45%; 41% vs 32.4%; 45% vs 37%), respectively. Conclusion Blacks with MetS reported insomnia symptoms and insomnia disorder, use of sleep aids, feeling sleepy during the day, and inadequate sleep durations. The presence of these sleep characteristics suggests that patients with MetS should be referred for further sleep assessment.
Measuring Preweaning Sensorial and Motor Development in the Mouse

The immaturity at birth and the slowness of ontogenic processes in mice provide the opportunity to measure rates of development. We describe here 18 measures covering the sensorial and motor onset from birth to weaning. The measures are non‐invasive, making a follow‐up strategy possible. The first basic protocol indicates how to produce mice with known conceptional or chronological age, as the control of the age is a prerequisite to compare rates of development in groups of mice. The second basic protocol describes a set of methods for identifying the pups during a follow‐up study. A third basic protocol describes testing newborn mice for the appearance of sensorial and motor abilities in a follow‐up design. Taken together, the three protocols make possible the validation of potential murine models of interest for understanding human developmental disorders. © 2018 by John Wiley & Sons, Inc.
Resistance to Radiotherapy and PD-L1 Blockade Is Mediated by TIM-3 Upregulation and Regulatory T-Cell Infiltration

Purpose: Radiotherapy (RT) can transform the immune landscape and render poorly immunogenic tumors sensitive to PD-L1 inhibition. Here, we established that the response to combined RT and PD-L1 inhibition is transient and investigated mechanisms of resistance. Experimental Design: Mechanisms of resistance to RT and PD-L1 blockade were investigated in orthotopic murine head and neck squamous cell carcinoma (HNSCC) tumors using mass cytometry and whole-genome sequencing. Mice were treated with anti–PD-L1 or anti–TIM-3 alone and in combination with and without RT. Tumor growth and survival were assessed. Flow cytometry was used to assess phenotypic and functional changes in intratumoral T-cell populations. Depletion of regulatory T cells (Treg) was performed using anti-CD25 antibody. Results: We show that the immune checkpoint receptor, TIM-3, is upregulated on CD8 T cells and Tregs in tumors treated with RT and PD-L1 blockade. Treatment with anti–TIM-3 concurrently with anti–PD-L1 and RT led to significant tumor growth delay, enhanced T-cell cytotoxicity, decreased Tregs, and improved survival in orthotopic models of HNSCC. Despite this treatment combination, the response was not durable, and analysis of relapsed tumors revealed resurgence of Tregs. Targeted Treg depletion, however, restored antitumor immunity in mice treated with RT and dual immune checkpoint blockade and resulted in tumor rejection and induction of immunologic memory. Conclusions: These data reveal multiple layers of immune regulation that can promote tumorigenesis and the therapeutic potential of sequential targeting to overcome tumor resistance mechanisms. We propose that targeted Treg inhibitors may be critical for achieving durable tumor response with combined radiotherapy and immunotherapy. Clin Cancer Res; 24(21); 5368–80. ©2018 AACR.
Activation of the reninangiotensin system in mice aggravates mechanical loadinginduced knee osteoarthritis

Epidemiological studies have shown an association between hypertension and knee osteoarthritis (OA). The purpose of this study was to investigate whether activation of the renin–angiotensin system (RAS) can aggravate mechanical loading-induced knee OA in mice. Eight-week-old male Tsukuba hypertensive mice (THM) and C57BL/6 mice were divided into four groups: i) running THM group, ii) running C57BL/6 mice group, iii) non-running THM group, and iv) non-running C57BL/6 mice group. Mice in the running group were forced to run (25 m/min, 30 min/day, 5 days/week) on a treadmill. All mice in the four groups (n=10 in each group) were euthanized after 0, 2, 4, 6, or 8 weeks of running or natural breeding. Cartilage degeneration in the left knees was histologically evaluated using the modified Mankin score. Expression of Col X, MMP-13, angiotensin type 1 receptor (AT1R), and AT2R was examined immunohistochemically. To study the effects of stimulation of the AT1R in chondrocytes by mechanical loading and/or Angiotensin II (AngII) on transduction of intracellular signals, phosphorylation levels of JNK and Src were measured in bovine articular chondrocytes cultured in three-dimensional agarose scaffolds. After 4 weeks, the mean Mankin score for the lateral femoral condylar cartilage was significantly higher in the THM running group than in the C57BL/6 running group and non-running groups. AT1R and AT2R expression was not detected at 0 weeks in any group but was noted after 4 weeks in the THM running group. AT1R expression was also noted at 8 weeks in the C57BL/6 running group. The expression levels of AT1R, COL X, and MMP-13 in chondrocytes were significantly higher in the THM running group than in the control groups. Positive significant correlations were noted between the Mankin score and the rate of AT1R-immunopositive cells, between the rates of AT1R- and Col X-positive cells, and between the rates of AT1Rand AT2R-positive cells. The phosphorylation level of JNK was increased by cyclic compression loading or addition of AngII to the cultured chondrocytes and was reversed by pretreatment with an AT1R blocker. A synergistic effect on JNK phosphorylation was observed between compression loading and AngII addition. Transgene activation of renin and angiotensinogen aggravated mechanical load-induced knee OA in mice. These findings suggest that AT1R expression in chondrocytes is associated with early knee OA and plays a role in the progression of cartilage degeneration. The RAS may be a common molecular mechanism involved in the pathogenesis of hypertension and knee OA.
A mechanism for exocytotic arrest by the Complexin C-terminus

ComplexinII (CpxII) inhibits non-synchronized vesicle fusion, but the underlying mechanisms have remained unclear. Here, we provide evidence that the far C-terminal domain (CTD) of CpxII interferes with SNARE assembly, thereby arresting tonic exocytosis. Acute infusion of a CTD-derived peptide into mouse chromaffin cells enhances synchronous release by diminishing premature vesicle fusion like full-length CpxII, indicating a direct, inhibitory function of the CTD that sets the magnitude of the primed vesicle pool. We describe a high degree of structural similarity between the CpxII CTD and the SNAP25-SN1 domain (C-terminal half) and show that the CTD peptide lowers the rate of SDS-resistant SNARE complex formation in vitro. Moreover, corresponding CpxII:SNAP25 chimeras do restore complexin’s function and even ‘superclamp’ tonic secretion. Collectively, these results support a so far unrecognized clamping mechanism wherein the CpxII C-terminus hinders spontaneous SNARE complex assembly, enabling the build-up of a release-ready pool of vesicles for synchronized Ca2+-triggered exocytosis.
Mixed-methods pre-match cooling improves simulated soccer performance in the heat

ABSTRACT This investigation examined the effects of three pre-match and half-time cooling manoeuvres on physical performance and associated physiological and perceptual responses in eight University soccer players during a non-motorised treadmill based individualised soccer-specific simulation [intermittent soccer performance test (iSPT)] at 30°C. Four randomised experimental trials were completed; following 30-min (pre-match) and 15-min (half-time) cooling manoeuvres via (1) ice slurry ingestion (SLURRY); (2) ice-packs placed on the quadriceps and hamstrings (PACKS); (3) mixed-methods (MM; PACKS and SLURRY concurrently); or no-cooling (CON). In iSPT first half, a moderate increase in total (Mean ± Standard Deviation: 108 ± 57 m, qualitative inference: most likely, Cohen’s d: 0.87, 90%CL: ±0.31), high-speed (56 ± 46 m, very likely, 0.68 ± 0.38) and variable run (15 ± 5 m, very likely, 0.81 ± 0.47) distance covered was reported in MM compared with CON. Additionally, pre-match reductions in thermal sensation (–1.0 ± 0.5, most likely, –0.91 ± 0.36), rectal (–0.6 ± 0.1°C, very likely, –0.86 ± 0.35) and skin temperature (–1.1 ± 0.3°C, very likely, –0.88 ± 0.42) continued throughout iSPT first half. Physical performance during iSPT first half was unaltered in SLURRY and PACKS compared to CON. Rectal temperature was moderately increased in SLURRY at 45-min (0.2 ± 0.1°C, very likely, 0.67 ± 0.36). Condition did not influence any measure in iSPT second half compared to CON. Only MM pre-match cooling augmented physical performance during iSPT first half, likely due to peripheral and central thermoregulatory factors favourably influencing first half iSPT performance. Further practical half-time cooling manoeuvres which enhance second half performance are still required.
Robust Dimension Reduction for Clustering With Local Adaptive Learning

In pattern recognition and data mining, clustering is a classical technique to group matters of interest and has been widely employed to numerous applications. Among various clustering algorithms, K-means (KM) clustering is most popular for its simplicity and efficiency. However, with the rapid development of the social network, high-dimensional data are frequently generated, which poses a considerable challenge to the traditional KM clustering as the curse of dimensionality. In such scenarios, it is difficult to directly cluster such high-dimensional data that always contain redundant features and noises. Although the existing approaches try to solve this problem using joint subspace learning and KM clustering, there are still the following limitations: 1) the discriminative information in low-dimensional subspace is not well captured; 2) the intrinsic geometric information is seldom considered; and 3) the optimizing procedure of a discrete cluster indicator matrix is vulnerable to noises. In this paper, we propose a novel clustering model to cope with the above-mentioned challenges. Within the proposed model, discriminative information is adaptively explored by unifying local adaptive subspace learning and KM clustering. We extend the proposed model using a robust $l_{2,1}$ -norm loss function, where the robust cluster centroid can be calculated in a weighted iterative procedure. We also explore and discuss the relationships between the proposed algorithm and several related studies. Extensive experiments on kinds of benchmark data sets demonstrate the advantage of the proposed model compared with the state-of-the-art clustering approaches.
Evaluation of the Functional Performance in Turned Workpieces: Methodology and Application to UNS A92024-T3

Turning of light alloys as aluminum-based UNS A92024-T3 is broadly implemented in the manufacture of critical aircraft parts, so ensuring a good functional performance of these pieces is essential. Moreover, operational conditions of these pieces include saline environments where corrosion processes are present. In this paper, a methodology for the evaluation of the functional performance in turned pieces is proposed. Specimens affected and not affected by corrosion are compared. In addition, performance in service through tensile stress tests of these parts is considered. The results show that turning improves the functional performance of UNS A92024-T3 alloy and that corrosion can enhance the mechanical properties of this alloy.
The mRNA cap methyltransferase gene TbCMT1 is not essential in vitro but is a virulence factor in vivo for bloodstream form Trypanosoma brucei

Messenger RNA is modified by the addition of a 5′ methylated cap structure, which protects the transcript and recruits protein complexes that mediate RNA processing and/or the initiation of translation. Two genes encoding mRNA cap methyltransferases have been identified in T. brucei: TbCMT1 and TbCGM1. Here we analysed the impact of TbCMT1 gene deletion on bloodstream form T. brucei cells. TbCMT1 was dispensable for parasite proliferation in in vitro culture. However, significantly decreased parasitemia was observed in mice inoculated with TbCMT1 null and conditional null cell lines. Using RNA-Seq, we observed that several cysteine peptidase mRNAs were downregulated in TbCMT1 null cells lines. The cysteine peptidase Cathepsin-L was also shown to be reduced at the protein level in TbCMT1 null cell lines. Our data suggest that TbCMT1 is not essential to bloodstream form T. brucei growth in vitro or in vivo but that it contributes significantly to parasite virulence in vivo.
Deep Generative Adversarial Neural Networks for Compressive Sensing MRI

Undersampled magnetic resonance image (MRI) reconstruction is typically an ill-posed linear inverse task. The time and resource intensive computations require tradeoffs between <italic>accuracy</italic> and <italic>speed</italic>. In addition, state-of-the-art compressed sensing (CS) analytics are not cognizant of the image <italic>diagnostic quality</italic>. To address these challenges, we propose a novel CS framework that uses generative adversarial networks (GAN) to model the (low-dimensional) manifold of high-quality MR images. Leveraging a mixture of least-squares (LS) GANs and pixel-wise <inline-formula> <tex-math notation="LaTeX">$\ell _{1}/\ell _{2}$ </tex-math></inline-formula> cost, a deep residual network with skip connections is trained as the generator that learns to remove the <italic>aliasing</italic> artifacts by projecting onto the image manifold. The LSGAN learns the texture details, while the <inline-formula> <tex-math notation="LaTeX">$\ell _{1}/\ell _{2}$ </tex-math></inline-formula> cost suppresses high-frequency noise. A discriminator network, which is a multilayer convolutional neural network (CNN), plays the role of a perceptual cost that is then jointly trained based on high-quality MR images to score the quality of retrieved images. In the operational phase, an initial aliased estimate (e.g., simply obtained by zero-filling) is propagated into the trained generator to output the desired reconstruction. This demands a very low computational overhead. Extensive evaluations are performed on a large contrast-enhanced MR dataset of pediatric patients. Images rated by expert radiologists corroborate that GANCS retrieves higher quality images with improved fine texture details compared with conventional Wavelet-based and dictionary-learning-based CS schemes as well as with deep-learning-based schemes using pixel-wise training. In addition, it offers reconstruction times of under a few milliseconds, which are two orders of magnitude faster than the current state-of-the-art CS-MRI schemes.
Communication With Physicians as a Mediator in the Relationship Between the Nursing Work Environment and Select Nurse Outcomes in Jordan

PURPOSE To test whether communication mediated relationships among nurses' work environments and nurse outcomes of job satisfaction and intent to stay. DESIGN This study used a cross-sectional, quantitative survey design to query 650 nurses who worked in three hospitals in Jordan. METHODS We used Arabic versions of valid, reliable instruments measuring the nursing work environment, nurse perceptions of communication with physicians, intent to stay, and job satisfaction. Mediation analysis was used to test hypotheses. FINDINGS A total of 582 questionnaires were returned (89.5% response rate). Nurse perceptions of communication with physicians mediated the relationship between the nursing work environment and job satisfaction in medical, surgical, and critical care units. Nurse perceptions of communication with physicians mediated the relationship between the nursing work environment and intent to stay in all but maternity and "other" units. CONCLUSIONS Depending on the nurse outcome, communication was a significant mediator for various unit types. These results may be related to the type of work that is done in each unit and the influence of patient care. Communication is one of many mechanisms that can specify how a positive nursing work environment can contribute to nurses' job satisfaction and intent to stay. CLINICAL RELEVANCE A potential solution to the nursing shortage in Jordan emerges by identifying communication with physicians as a mediator in the relationship between the work environment and selected nurse outcomes.
A novel sideways fall simulator to study hip fractures ex vivo

Falls to the side are the leading cause of hip fractures in the elderly. The load that a person experiences during a fall cannot be measured with volunteers for ethical reasons. To evaluate injurious loads, while considering relevant energy input and body posture for a sideways fall, a subject-specific cadaveric impact experiment was developed. Full cadaveric femur-pelvis constructs (N = 2) were embedded in surrogate soft tissue material and attached to metallic surrogate lower limbs. The specimens were then subjected to an inverted pendulum motion, simulating a fall to the side with an impact to the greater trochanter. The load at the ground and the deformation of the pelvis were evaluated using a 6-axis force transducer and two high-speed cameras. Post-test, a trauma surgeon (PG) evaluated specimen injuries. Peak ground contact forces were 7132 N and 5641 N for the fractured and non-fractured specimen, respectively. We observed a cervical fracture of the femur in one specimen and no injuries in a second specimen, showing that the developed protocol can be used to differentiate between specimens at high and low fracture risk.
Nucleobase and Nucleoside Analogues: Resistance and Re-Sensitisation at the Level of Pharmacokinetics, Pharmacodynamics and Metabolism

Antimetabolites, in particular nucleobase and nucleoside analogues, are cytotoxic drugs that, starting from the small field of paediatric oncology, in combination with other chemotherapeutics, have revolutionised clinical oncology and transformed cancer into a curable disease. However, even though combination chemotherapy, together with radiation, surgery and immunotherapy, can nowadays cure almost all types of cancer, we still fail to achieve this for a substantial proportion of patients. The understanding of differences in metabolism, pharmacokinetics, pharmacodynamics, and tumour biology between patients that can be cured and patients that cannot, builds the scientific basis for rational therapy improvements. Here, we summarise current knowledge of how tumour-specific and patient-specific factors can dictate resistance to nucleobase/nucleoside analogues, and which strategies of re-sensitisation exist. We revisit well-established hurdles to treatment efficacy, like the blood-brain barrier and reduced deoxycytidine kinase activity, but will also discuss the role of novel resistance factors, such as SAMHD1. A comprehensive appreciation of the complex mechanisms that underpin the failure of chemotherapy will hopefully inform future strategies of personalised medicine.