Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-Genome Sequencing of 11 High-Risk Clone ST111 Pseudomonas aeruginosa Isolates from French Hospitals

This study reports high-quality genomes of 11 sequence type 111 (ST111) isolates of Pseudomonas aeruginosa. This ST is known for its worldwide dissemination and high capacity to acquire antibiotic resistance mechanisms. This study used long- and short-read sequencing to provide high-quality closed genomes for most of the isolates. ABSTRACT This study reports high-quality genomes of 11 sequence type 111 (ST111) isolates of Pseudomonas aeruginosa. This ST is known for its worldwide dissemination and high capacity to acquire antibiotic resistance mechanisms. This study used long- and short-read sequencing to provide high-quality closed genomes for most of the isolates.
Fermi arc electronic structure and Chern numbers in the type-II Weyl semimetal candidate Mo x W 1 − x Te 2

It has recently been proposed that electronic band structures in crystals give rise to a previously overlooked type of Weyl fermion, which violates Lorentz invariance and, consequently, is forbidden in particle physics. It was further predicted that Mo$_x$W$_{1-x}$Te$_2$ may realize such a Type II Weyl fermion. One crucial challenge is that the Weyl points in Mo$_x$W$_{1-x}$Te$_2$ are predicted to lie above the Fermi level. Here, by studying a simple model for a Type II Weyl cone, we clarify the importance of accessing the unoccupied band structure to demonstrate that Mo$_x$W$_{1-x}$Te$_2$ is a Weyl semimetal. Then, we use pump-probe angle-resolved photoemission spectroscopy (pump-probe ARPES) to directly observe the unoccupied band structure of Mo$_x$W$_{1-x}$Te$_2$. For the first time, we directly access states $> 0.2$ eV above the Fermi level. By comparing our results with $\textit{ab initio}$ calculations, we conclude that we directly observe the surface state containing the topological Fermi arc. Our work opens the way to studying the unoccupied band structure as well as the time-domain relaxation dynamics of Mo$_x$W$_{1-x}$Te$_2$ and related transition metal dichalcogenides.
Assessing violence risk in first-episode psychosis: external validation, updating and net benefit of a prediction tool (OxMIV)

Background Violence perpetration is a key outcome to prevent for an important subgroup of individuals presenting to mental health services, including early intervention in psychosis (EIP) services. Needs and risks are typically assessed without structured methods, which could facilitate consistency and accuracy. Prediction tools, such as OxMIV (Oxford Mental Illness and Violence tool), could provide a structured risk stratification approach, but require external validation in clinical settings. Objectives We aimed to validate and update OxMIV in first-episode psychosis and consider its benefit as a complement to clinical assessment. Methods A retrospective cohort of individuals assessed in two UK EIP services was included. Electronic health records were used to extract predictors and risk judgements made by assessing clinicians. Outcome data involved police and healthcare records for violence perpetration in the 12 months post-assessment. Findings Of 1145 individuals presenting to EIP services, 131 (11%) perpetrated violence during the 12 month follow-up. OxMIV showed good discrimination (area under the curve 0.75, 95% CI 0.71 to 0.80). Calibration-in-the-large was also good after updating the model constant. Using a 10% cut-off, sensitivity was 71% (95% CI 63% to 80%), specificity 66% (63% to 69%), positive predictive value 22% (19% to 24%) and negative predictive value 95% (93% to 96%). In contrast, clinical judgement sensitivity was 40% and specificity 89%. Decision curve analysis showed net benefit of OxMIV over comparison approaches. Conclusions OxMIV performed well in this real-world validation, with improved sensitivity compared with unstructured assessments. Clinical implications Structured tools to assess violence risk, such as OxMIV, have potential in first-episode psychosis to support a stratified approach to allocating non-harmful interventions to individuals who may benefit from the largest absolute risk reduction.
Ranking patterns, an application to refrigerants

Ranking methods are of great importance for assessing the relative importance or potential impact of different objects, e.g. chemicals, screening methods, etc. When a ranking procedure is applied it is desired to obtain a total order of the ranked objects. With most methods, this is achieved through the mathematical combination of descriptors characterising the objects, often under the inclusion of descriptor priorities. However, such priority settings affect the final ranking and the contribution of each descriptor to the final result becomes obscure. In this paper, METEOR (Method of evaluation by order theory) is described, a ranking procedure which allows to explore the complete space of possible descriptor priorities in such a way that total orders are obtained. METEOR permits 1) to study the total order resulting from any descriptors’ prioritisation, 2) to determine the priorities necessary to obtain a particular total order, 3) to calculate the probability of having a particular total order, and 4) to
Trajectories of life satisfaction in Hispanic individuals over the 10 years after traumatic brain injury: A model systems study

ABSTRACT Purpose To identify life satisfaction trajectories at 1–10 years post-traumatic brain injury (TBI) and examine which demographic and injury characteristics at the time of injury are associated with those trajectories. Methods Participants included 1,051 Hispanic individuals from the multi-site, longitudinal TBI Model Systems (TBIMS) database. Individuals were enrolled after sustaining a TBI and while undergoing inpatient rehabilitation at a TBIMS site; they were included if they completed the Satisfaction with Life Scale during one or more follow-up data collections at 1, 2, 5, or 10 years after TBI. Results A linear (straight-line) movement of life satisfaction trajectories was the best fit to the data. Across the overall sample, life satisfaction increased over time, with higher trajectories for Hispanic individuals who had been partnered at baseline, born outside the US and experienced a nonviolent injury cause. There were no significant interactions between time and any of these main effect predictors, suggesting no differential change over time in life satisfaction trajectories as a function of these characteristics. Conclusions Results revealed increases in life satisfaction over time among Hispanic individuals with TBI and shed light on critical risks and protective factors that may inform targeted rehabilitation services with this underserved group.
The Impact of Hill-Type Actuator Components on the Performance of Reinforcement Learning Controllers to Reverse Upper-Limb Paralysis

Functional electrical stimulation (FES) may allow people who are paralyzed due to spinal cord injuries (SCIs) to regain the ability to move. Deep neural networks (DNNs) trained with reinforcement learning (RL) have been recently explored as a promising methodology to control FES systems to restore upper-limb movements. However, previous studies suggested that large asymmetries in antagonistic upper-limb muscle strengths could impair RL controller performance. In this work, we investigated the underlying causes of asymmetry-associated decreases in controller performance by comparing different Hill-type models of muscle atrophy, and by characterizing RL controller sensitivity to passive mechanical properties of the arm. Simulations indicated that RL controller performance is relatively insensitive to moderate (up to 50%) changes in tendon stiffness and in flexor muscle stiffness. However, the viable workspace for RL control was substantially affected by flexor muscle weakness and by extensor muscle stiffness. Furthermore, we uncovered that RL controller performance issues previously attributed to asymmetrical antagonistic muscle strength resulted from flexor muscle active forces that were insufficient to counteract extensor muscle passive resistance. The simulations supported the adoption of rehabilitation protocols for reaching tasks that prioritize decreasing muscle passive resistance, and counteracting passive resistance with increased antagonistic muscle strength.
Primary postpartum haemorrhage and longer-term physical, psychological, and psychosocial health outcomes for women and their partners in high income countries: A mixed-methods systematic review

Objectives Most research about outcomes following postpartum haemorrhage (PPH) has focused on immediate outcomes. There are fewer studies investigating longer-term maternal morbidity following PPH, resulting in a significant knowledge gap. This review aimed to synthesize the evidence about the longer-term physical and psychological consequences of primary PPH for women and their partners from high income settings. Methods The review was registered with PROSPERO and five electronic databases were searched. Studies were independently screened against the eligibility criteria by two reviewers and data were extracted from both quantitative and qualitative studies that reported non-immediate health outcomes of primary PPH. Results Data were included from 24 studies, of which 16 were quantitative, five were qualitative and three used mixed-methods. The included studies were of mixed methodological quality. Of the nine studies reporting outcomes beyond five years after birth, only two quantitative studies and one qualitative study had a follow-up period longer than ten years. Seven studies reported outcomes or experiences for partners. The evidence indicated that women with PPH were more likely to have persistent physical and psychological health problems after birth compared with women who did not have a PPH. These problems, including PTSD symptoms and cardiovascular disease, may be severe and extend for many years after birth and were more pronounced after a severe PPH, as indicated by a blood transfusion or hysterectomy. There was limited evidence about outcomes for partners after PPH, but conflicting evidence of association between PTSD and PPH among partners who witnessed PPH. Conclusion This review explored existing evidence about longer-term physical and psychological health outcomes among women who had a primary PPH in high income countries, and their partners. While the evidence about health outcomes beyond five years after PPH is limited, our findings indicate that women can experience long lasting negative impacts after primary PPH, including PTSD symptoms and cardiovascular disease, extending for many years after birth. PROSPERO registration PROSPERO registration number: CRD42020161144
Removal of Pixel Structures by Optimizing the Parameters of Imaging System in Digital Photolithography

The pixel structure is removed by optimizing the parameters of imaging system rather than other techniques that make the setup of digital photolithography complexity.The simulation results show that the pixel structure can be effectively deduced when numerical aperture(NA) is 0.3 and demagnification factor(DF) is from 10× to 20× with 0.365 μm illumination wavelength.The analysis of aerial images of practical microstructures shows that the parameters above have different effects on binary and gray-tone patterns.Arbitrary binary pattern can be fabricated without any correction if DF is in the range of 10×～15×. However,the imaging quality of gray-tone pattern is greatly worsened for the parameters above,but it can be improved by use of the feature of programmable DMD.Finally,the experimental results demonstrate the parameters are suitable for removing pixel structure.
Dissipative Forces in the Electrowetted Cassie-Wenzel Transition on Hydrophobic Rough Surfaces

Dissipative forces in the electrowetting-induced Cassie-Wenzel transition on hydrophobic rough surfaces are explored. High-speed imaging of droplet shape evolution during the electrically induced spreading process allows for the location of the contact line to be tracked as a function of time. A surface energy analysis quantifies the total energy dissipated via nonconservative forces during the spreading process. Though identified as the dominant dissipative effect in droplet spreading on smooth surfaces, contact line friction is shown to have a relatively weak influence on the spreading on rough surfaces. Supplemental files are available for this article. Go to the publisher's online edition of Nanoscale and Microscale Thermophysical Engineering to view the free supplemental file.
Presence of EBV antigens detected by a sensitive method in pediatric and adult Diffuse Large B‐cell lymphomas

In 2017, the World Health Organization (WHO) confirmed a new entity, Epstein Barr virus (EBV) + Diffuse large B cell lymphoma (DLBCL), not otherwise specified (NOS). Traces of EBV transcripts were described in lymphomas, including DLBCL, that were diagnosed as EBV negative by conventional methods. The aim of this study was to detect viral genome by qPCR, as well as LMP1 and EBNA2 transcripts, with a more sensitive method in DLBCL cases from Argentina. Fourteen cases originally considered as EBV negative expressed LMP1 and/or EBNA2 transcripts. In addition, LMP1 and/or EBNA2 transcripts were also observed in bystander cells. However, EBERs+ cells cases by conventional ISH showed higher numbers of cells with LMP1 transcripts and LMP1 protein. In the cases that were EBERS− in tumor cells but with expression of LMP1 and/or EBNA2 transcripts, the viral load was below the limit of detection. This study provides further evidence that EBV could be detected in tumor cells by more sensitive methods. However, higher expression of the most important oncogenic protein, LMP1, as well as increased viral load, are only observed in cases with EBERs+ cells by conventional ISH, suggesting that traces of EBV might not display a key role in DLBCL pathogenesis.
The effects of air vitiation on the supersonic turbulent channel flow using direct numerical simulation

Temporally evolving supersonic turbulent channel flows are simulated using direct numerical simulation (DNS) approach at Mach number 2.56, Reynolds number 7000 with water vapor (H2O) mass fraction from 0.00 to 0.161 to study the air vitiation effects. Then, the turbulent statistical characteristics and velocity-temperature correlations have been studied based on the DNS database. It is found that in fully developed turbulent channel flow, many of turbulent statistical characteristics used to express supersonic turbulent channel flow of pure air also hold for the H2O considered. After a nondimensional static temperature parameters introduced, the mean velocity-temperature correlation collapses between current DNS results. The results of strong Reynolds analogy decrease with H2O mass fraction increasing, and modified strong Reynolds analogy show a better agreement than original strong Reynolds analogy. In addition, the correlation Ru’T’isn’t remained the same between the different H2O mass fraction cases. © 2016, American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.
Impact of Extra-Corporeal Membrane Oxygenation and Blood Purification Therapy on Early Mobilization in the Intensive Care Unit: Retrospective Cohort Study

Objective To investigate the effect on early mobilization in patients undergoing extra-corporeal membrane oxygenation (ECMO) and acute blood purification therapy in the intensive care unit (ICU). Methods We conducted this multicenter retrospective cohort study by collecting data from six ICUs in Japan. Consecutive patients who were admitted to the ICU, aged ≥18 years, and received mechanical ventilation for >48 hours were eligible. The analyzed were divided into two groups: ECMO/blood purification or control group. Clinical outcomes; time to first mobilization, number of total ICU rehabilitations, mean and highest ICU mobility scale (IMS); and daily barrier changes were also investigated. Results A total of 204 patients were included in the analysis, 43 in the ECMO/blood purification group and 161 in the control group. In comparison of clinical outcome, the ECMO/blood purification group had a significantly longer time to first mobilization: ECMO/blood purification group 6 vs. control group 4 (p=0.003), higher number of total ICU rehabilitations: 6 vs. 5 (p=0.042), lower mean: 0 vs. 1 (p=0.043) and highest IMS: 2 vs. 3 (p=0.039) during ICU stay. Circulatory factor were most frequently described as barriers to early mobilization on days 1 (51%), 2 (47%), and 3 (26%). On days 4 to 7, the most frequently described barrier was consciousness factors (21%, 16%, 19%, and 21%, respectively) Conclusion The results of this study comparing the ECMO/blood purification group and the untreated group in the ICU showed that the ECMO/blood purification group had significantly longer days to mobilization and significantly lower mean and highest IMS.
Detecting Asymmetry of Upper Limb Activity with Accelerometry in Infants at Risk for Unilateral Spastic Cerebral Palsy

Abstract Aims To examine whether accelerometry can quantitate asymmetry of upper limb activity in infants aged 3–12 months at risk for developing unilateral spastic cerebral palsy (USCP). Method A prospective study was performed in 50 infants with unilateral perinatal brain injury at high risk of developing USCP. Triaxial accelerometers were worn on the ipsilateral and contralesional upper limb during the Hand Assessment for Infants (HAI). Infants were grouped in three age intervals (3–5 months, 5–7.5 months and 7.5 until 12 months). Each age interval group was divided in a group with and without asymmetrical hand function based on HAI cutoff values suggestive of USCP. Results In a total of 82 assessments, the asymmetry index for mean upper limb activity was higher in infants with asymmetrical hand function compared to infants with symmetrical hand function in all three age groups (ranging from 41 to 51% versus − 2–6%, p < 0.01), while the total activity of both upper limbs did not differ. Conclusions Upper limb accelerometry can identify asymmetrical hand function in the upper limbs in infants with unilateral perinatal brain injury from 3 months onwards and is complementary to the Hand Assessment for Infants.
Saikosaponins regulate bile acid excretion in mice liver and ileum by activating farnesoid X receptor and bile acid transporter

Radix Bupleuri exerts effective hepatoprotective and cholagogic effects through its Saikosaponins (SSs) component. Therefore, we attempted to determine the mechanism of saikosaponins used to promote bile excretion by studying their effects on intrahepatic bile flow, focusing on the synthesis, transport, excretion, and metabolism of bile acids. C57BL/6N mice were continuously gavaged with saikosaponin a (SSa), saikosaponin b2 (SSb2), or saikosaponin D (SSd) (200 mg/kg) for 14 days. Liver and serum biochemical indices were determined using Enzyme‐linked immunosorbent assay (ELISA) kits. In addition, an ultra‐performance liquid chromatography‐mass spectrometer (UPLC–MS) was used to measure the levels of the 16 bile acids in the liver, gallbladder, and cecal contents. Furthermore, SSs pharmacokinetics and docking between SSs and farnesoid X receptor (FXR)‐related proteins were analyzed to investigate the underlying molecular mechanisms. Administration of SSs and Radix Bupleuri alcohol extract (ESS) did not cause significant changes in alanine aminotransferase (ALT), aspartate aminotransferase (AST), or alkaline phosphatase (ALP) levels. Saikosaponin‐regulated changes in bile acid (BA) levels in the liver, gallbladder, and cecum were closely related to genes involved in BA synthesis, transport, and excretion in the liver. Pharmacokinetic studies indicated that SSs were characterized by rapid elimination (t1/2 as 0.68–2.47 h), absorption (Tmax as 0.47–0.78 h), and double peaks in the drug–time curves of SSa and SSb2. A molecular docking study revealed that SSa, SSb2, and SSd docked well with the 16 protein FXR molecules and target genes (<−5.2 kcal/mol). Collectively, saikosaponins may maintain BA homeostasis in mice by regulating FXR‐related genes and transporters in the liver and intestine.
Combined REGN-COV2 Antibody Therapy Immediately Prevented a Patient with Refractory Type 1 Autoimmune Pancreatitis from Contracting SARS-CoV-2 during the Sixth Wave in Japan

A 51-year-old man who had been receiving steroid therapy for type 1 autoimmune pancreatitis (AIP) for 3 years contracted coronavirus disease 2019 (COVID-19). As he had a high-grade fever and dry cough, and because his SpO2 level had dropped below 95% in the supine position, he was considered as being at a high risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); therefore, he received combined REGN-COV2 antibody therapy. The patient's fever resolved immediately after this treatment, and he went into remission. A high cumulative steroid dose is associated with an increased susceptibility to infection. Early antibody cocktail therapy may be effective and rewarding for steroid-dependent type 1 AIP patients with a potential risk for SARS-CoV-2.
Resolving the Heat Generated from ZrO2 Atomic Layer Deposition Surface Reactions.

In situ pyroelectric calorimetry and spectroscopic ellipsometry were used to investigate surface reactions in atomic layer deposition (ALD) of zirconium oxide (ZrO2 ). Calibrated and time-resolved in situ ALD calorimetry provides new insights into the thermodynamics and kinetics of saturating surface reactions for tetrakis(dimethylamino)zirconium(IV) (TDMAZr) and water. The net ALD reaction heat ranged from 0.197 mJ cm-2 at 76 °C to 0.155 mJ cm-2 at 158 °C, corresponding to an average of 4.0 eV/Zr at all temperatures. A temperature dependence for reaction kinetics was not resolved over the range investigated. The temperature dependence of net reaction heat and distribution among metalorganic and oxygen source exposure is attributed to factors including growth rate, equilibrium surface hydroxylation, and the extent of the reaction. ZrO2 -forming surface reactions were investigated computationally using DFT methods to better understand the influence of surface hydration on reaction thermodynamics.