Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Genome Sequence of Citrobacter braakii GW-Imi-1b1, Isolated from Hospital Wastewater in Greifswald, Germany

The imipenem-resistant Citrobacter braakii strain GW-Imi-1b1 was isolated from a hospital wastewater sample in Greifswald, Germany. The genome comprises one chromosome (5.09 Mb), one prophage (41.9 kb), and 13 plasmids (2 to 140.9 kb). The genome harbors 5,322 coding sequences, shows a high potential for genomic mobility, and includes genes encoding proteins for multiple drug resistances. ABSTRACT The imipenem-resistant Citrobacter braakii strain GW-Imi-1b1 was isolated from a hospital wastewater sample in Greifswald, Germany. The genome comprises one chromosome (5.09 Mb), one prophage (41.9 kb), and 13 plasmids (2 to 140.9 kb). The genome harbors 5,322 coding sequences, shows a high potential for genomic mobility, and includes genes encoding proteins for multiple drug resistances.
Trastuzumab Charge Variants: a Study on Physicochemical and Pharmacokinetic Properties

Background: Post-translational modifications in bioprocessing and storage of recombinant mAbs are the main sources of charge variants. While the profile of these kinds of variants is considered an important quality attribute of therapeutic mAbs, there is controversy about their direct role on safety and efficacy. In this study, the physicochemical and PK properties of separated charge variants belonging to a trastuzumab potential biosimilar were examined. Methods: The APs, BPs, and main variants of trastuzumab were separated and enriched by semi-preparative WCX. A panel of analytical techniques was utilized to characterize the physicochemical properties of these variants. The binding affinity to HER2 and FcγRs and the PK parameters were evaluated for each variant. Results: Based on the results, the charge variants of the proposed biosimilar had no significant influence on the examined efficacy and PK parameters. Conclusion: During the development and production of biosimilar mAbs, studying the effects of their charge variants on efficacy and PK parameters is needed.
Racial, gender, and psychosocial disparities in viral suppression trends among people receiving coordinated HIV care in Los Angeles County

Objective: To longitudinally evaluate differences in HIV viral suppression (<200 copies/ml) by intersections of race/ethnicity, gender, and psychosocial issues in people with HIV in the Los Angeles County Medical Care Coordination Program. Design: We analyzed 74 649 viral load measurements over 10 184 people with HIV enrolled in the Medical Care Coordination Program between January 1, 2013 and March 1, 2020. Methods: We fit Bayesian logistic hierarchical random effects models to test interactions between gender, race/ethnicity, and a psychosocial acuity score on viral suppression over time from 1 year prior to program enrollment to 24 months after enrollment. Results: The probability of viral suppression declined prior to enrollment, then increased and stabilized by 6 months after enrollment. Black/African American patients with low and moderate psychosocial acuity scores did not achieve the same increase in percentage of viral suppression as those in other racial/ethnic groups. Transgender women with high psychosocial acuity scores took longer (about 1 year) to achieve the same percentage of viral suppression as clients of other gender identities. Conclusions: Some racial/ethnic and gender disparities in viral suppression persisted after enrollment in the Los Angeles County Medical Care Coordination Program while accounting for psychosocial acuity score, which may be explained by factors not assessed in the program.
Brain-targeted lycopene-loaded microemulsion modulates neuroinflammation, oxidative stress, apoptosis and synaptic plasticity in β-amyloid-induced Alzheimer’s disease mice

ABSTRACT Objectives β-Amyloid protein (Aβ) plays pivotal roles in pathogenesis of Alzheimer’s disease (AD) and triggers various pathophysiological events. Lycopene is a promising neuroprotector with multiple bioactivities, while its bioavailability is limited. Lycopene-loaded microemulsion (LME) possessing superior bioavailability and brain-targeting efficiency was developed in our previous study. In this investigation, we aimed to comprehensively evaluate its neuroprotective effects and underlying mechanisms using intracerebroventricular (ICV) Aβ1–42 injection mice. Methods Mice were assigned to the Sham, Aβ, Aβ + LME and Aβ + lycopene dissolved in olive oil (LOO) groups. ICV Aβ1–42 administration was performed, followed by oral gavage of brain-targeted LME or conventional LOO formulation for 3 weeks. Brain samples were harvested for immunohistochemistry, biochemical assays and western blotting analyses. Results Our findings verified Aβ-induced neurotoxicity on neuroinflammation, oxidative stress, apoptosis, Aβ metabolisms and synaptic plasticity. LME supplementation dramatically attenuated astrocytosis and microgliosis, decreased malondialdehyde production and rescued antioxidant capacities, normalized apoptotic parameters and alleviated neuronal loss, inhibited amyloidogenic processing and activated non-amyloidogenic pathway, together with upregulating synaptic protein expressions and restoring synaptic plasticity. Nevertheless, most of these phenomena were not observed for mice treated with LOO, implying that LME showed significantly higher therapeutic efficacy against Aβ injury. Discussion In summary, brain-targeted LME could exert neuroprotective function via suppressing a series of cascades triggered by Aβ aggregates, thus ameliorating Aβ neurotoxicity and associated abnormalities. Given this, LME may serve as an attractive candidate for AD prevention and treatment, and superiority of brain-targeting delivery is highlighted.
Trocar number and placement for laparoscopic sleeve gastrectomy and comparison of single-incision and conventional laparoscopic sleeve gastrectomy: a systematic review and meta-analysis

Background: Conventional laparoscopic sleeve gastrectomy (CLSG) has been conducted in multiple centers for treating morbid obesity, however, there are no standard criteria for (1) placing the trocar; and (2) how many trocars should be used. Single-incision laparoscopic sleeve gastrectomy (SLSG), a newly emerged technique in 2008, has been proposed as an alternative to CLSG in recent years, however, there is no definite evidence for this. Materials and methods: A systematic literature search was performed using the PubMed, Embase, Web of Science, and Cochrane Library databases for laparoscopic sleeve gastrectomy cases from January 2006 to October 2022. We then summarized the trocar numbers and placement patterns among these studies. A meta-analysis was conducted to compare the difference between SLSG and CLSG in the perioperative and postoperative indices. Results: A total of 61 studies involving 20 180 patients who underwent laparoscopic sleeve gastrectomy for treating morbid obesity were included in the systematic review, including 11 on SLSG, 35 on CLSG, and 15 studies comparing SLSG and CLSG. A systematic review showed that the trocar number varied in different CLSG studies, mainly using four or five trocars. The trocars were mainly placed in position, presenting an inverted trapezoid pattern and a left-predominant pattern. Meta-analysis showed that the operative time in the SLSG was significantly higher than that in the CLSG, and the pain Visual Analog Scale rating on postoperative day 1 in the CLSG was significantly higher than in the SLSG. There were no statistical significances in the other complications or surgical efficiency. Conclusions: In the CLSG, the majority of the trocars were arranged in an inverted trapezoid pattern and were of the left-predominant type. Although SLSG is a feasible technique in selected patients, there is insufficient evidence to recommend its widespread use compared with CLSG. High-quality randomized controlled trials with large study populations and long follow-up periods will be required in the future.
Donor Liver Blood Tests and Liver Transplant Outcomes: UK Registry Cohort Study

Background. Safely increasing organ utilization is a global priority. Donor serum transaminase levels are often used to decline livers, despite minimal evidence to support such decisions. This study aimed to investigate the impact of donor “liver blood tests” on transplant outcomes. Methods. This retrospective cohort study used the National Health Service registry on adult liver transplantation (2016–2019); adjusted regressions models were used to assess the effect of donor “liver blood tests” on outcomes. Results. A total of 3299 adult liver transplant recipients were included (2530 following brain stem death, 769 following circulatory death). Peak alanine transaminase (ALT) ranged from 6 to 5927 U/L (median = 45). Donor cause of death significantly predicted donor ALT; 4.2-fold increase in peak ALT with hypoxic brain injury versus intracranial hemorrhage (adjusted P < 0.001). On multivariable analysis, adjusting for a wide range of factors, transaminase level (ALT or aspartate aminotransferase) failed to predict graft survival, primary nonfunction, 90-d graft loss, or mortality. This held true in all examined subgroups, that is, steatotic grafts, donation following circulatory death, hypoxic brain injury donors, and donors, in which ALT was still rising at the time of retrieval. Even grafts from donors with extremely deranged ALT (>1000 U/L) displayed excellent posttransplant outcomes. In contrast, donor peak alkaline phosphatase was a significant predictor of graft loss (adjusted hazard ratio = 1.808; 1.016-3.216; P = 0.044). Conclusions. Donor transaminases do not predict posttransplant outcomes. When other factors are favorable, livers from donors with raised transaminases can be accepted and transplanted with confidence. Such knowledge should improve organ utilization decision-making and prevent future unnecessary organ discard. This provides a safe, simple, and immediate option to expand the donor pool.
Using electric fields to induce patterning in leaky dielectric fluids in a rod-annular geometry

The stability and axisymmetric deformation of two immiscible, viscous, perfect or leaky dielectric fluids confined in the annulus between two concentric cylinders are studied in the presence of radial electric fields. The fields are set up by imposing a constant voltage potential difference between the inner and outer cylinders. We derive a set of equations for the interface in the long-wavelength approximation which retains the essential physics of the system and allows for interfacial deformations to be as large as the annular gap hence accounting for possible touchdown at the inner or outer electrode. The effects of the electric parameters are evaluated initially by performing a linear stability analysis which shows excellent agreement with the linear theory of the full axisymmetric problem in the appropriate long wavelength regime. The nonlinear interfacial dynamics are investigated by carrying out direct numerical simulations of the derived long wave models, both in the absence and presence of electric fields. For non-electrified thin layer flows (i.e. one of the layers thin relative to the other) the long-time dynamics agree with the lubrication approximation results found in literature. When the liquid layers have comparable thickness our results demonstrate the existence of both finite time and infinite time singularities (asymptotic touching solutions) in the system. It is shown that a two-side touching solution is possible for both the non-electrified and perfect dielectric cases, while only one-side touching is found in the case of leaky dielectric liquids, where the flattened interface shape resembles the pattern solutions found in literature. Meanwhile the finite-time singular solution agrees qualitatively with the experiments of~\cite{Reynolds1965}.
Comprehensive Model Simulation of Thermal Tides in the Martian Atmosphere

Abstract This paper discusses the thermotidal oscillations in simulations performed with a newly developed comprehensive general circulation model of the Martian atmosphere. With reasonable assumptions about the effective thermal inertia of the planetary surface and about the distribution of radiatively active atmospheric aerosol, the model produces both realistic zonal-mean temperature distributions and a diurnal surface pressure oscillation of at least roughly realistic amplitude. With any reasonable aerosol distribution, the simulated diurnal pressure oscillation has a very strong zonal variation, in particular a very pronounced zonal wavenumber-2 modulation. This results from a combination of the prominent wave-2 component in the important boundary forcings (topography and surface thermal inertia) and from the fact that the eastward-propagating zonal wave-1 Kelvin normal mode has a period near 1 sol (a Martian mean solar day of 88 775 s). The importance of global resonance is explicitly demonstrated w.
Comparison of platelet quality and function across apheresis collection platforms

Platelet concentrates (PLT) can be manufactured using a combination of apheresis collection devices and suspension media (plasma or platelet additive solution (PAS)). It is unclear how platelet quality and hemostatic function differ across the current in‐use manufacturing methods in the United States. The objective of this study was therefore to compare baseline function of PLT collected using different apheresis collection platforms and storage media.
Obstacle detection algorithm based on stereoscopic images A navigation aid system for the visually impaired

This article presents an algorithm for stereoscopic image processing taken by the same camera in a real environment and considering two shifted captures. The aim of this treatment is to extract two important informational data about the environment: the distance separating the obstacles from the camera and their sizes. The depth calculation of an obstacle is performed by exploiting the disparity map between two considered stereoscopic images. This disparity is estimated by using the Block Matching program implemented in Matlab. In order to obtain an accurate and fast result, improvements are added to this estimation by combining "sub-pixel accuracy", "dynamic programming" and "the pyramid image technique". Finally, the determined disparity, associated with the camera calibration data, allowed us to obtain a precise estimation of the depth. The obstacle size is obtained by using the established calibration curve, giving the proportionality between the surface in pixels² of the image of object, and its real surface in m², according to the depth of the object. The tests performed in a real environment based on the elaborated algorithm give the results about the obstacle depth and its size. Tests results are completely similar to the experimental data.
Reconstructing the landscape of gut microbial species across 29,000 diverse individuals

Abstract The human gut microbiome has been linked to health and disease. Investigation of the human microbiome has largely employed 16S amplicon sequencing, with limited ability to distinguish microbes at the species level. Herein, we describe the development of Reference-based Exact Mapping (RExMap) of microbial amplicon variants that enables mapping of microbial species from standard 16S sequencing data. RExMap analysis of 16S data captures ∼75% of microbial species identified by whole-genome shotgun sequencing, despite hundreds-fold less sequencing depth. RExMap re-analysis of existing 16S data from 29,349 individuals across 16 regions from around the world reveals a detailed landscape of gut microbial species across populations and geography. Moreover, RExMap identifies a core set of fifteen gut microbes shared by humans. Core microbes are established soon after birth and closely associate with BMI across multiple independent studies. RExMap and the human microbiome dataset are presented as resources with which to explore the role of the human microbiome.
Glucocorticoid-driven mitochondrial damage stimulates Tau pathology.

Prolonged exposure to glucocorticoids, the main stress hormones, damages the brain and is a risk factor for depression and Alzheimer's disease. Two major drivers of glucocorticoid-related neurotoxicity are mitochondrial dysfunction and Tau pathology; however, the molecular/cellular mechanisms precipitating these events, and their causal relationship, remain unclear. Using cultured murine hippocampal neurons and 4-5-month-old mice treated with the synthetic glucocorticoid dexamethasone, we investigate the mechanisms underlying glucocorticoid-induced mitochondrial damage and Tau pathology. We find that glucocorticoids stimulate opening of the mitochondrial permeability transition pore via transcriptional upregulation of its activating component, Cyclophilin D. Inhibition of Cyclophilin D is protective against glucocorticoid-induced mitochondrial damage as well as Tau phosphorylation and oligomerization in cultured neurons. We further identify the mitochondrially-targeted compound mito-apocynin as an inhibitor of glucocorticoid-induced permeability transition pore opening, and show that this compound protects against mitochondrial dysfunction, Tau pathology, synaptic loss, and behavioral deficits induced by glucocorticoids in vivo. Finally, we demonstrate that mito-apocynin and the glucocorticoid receptor antagonist mifepristone rescue Tau pathology in cytoplasmic hybrid cells, an ex vivo Alzheimer's disease model wherein endogenous mitochondria are replaced with mitochondria from Alzheimer's subjects. These findings show that mitochondrial permeability transition pore opening is a precipitating factor in glucocorticoid-induced mitochondrial dysfunction, and that this event stimulates Tau pathogenesis. Our data also link glucocorticoids to mitochondrial dysfunction and Tau pathology in the context of Alzheimer's disease, and suggest that mitochondria are promising therapeutic targets for mitigating stress- and Tau-related brain damage.
Evolution of Avian Influenza Virus (H3) with Spillover into Humans, China

The continuous evolution of avian influenza viruses (AIVs) of subtype H3 in China and the emergence of human infection with AIV subtype H3N8 highlight their threat to public health. Through surveillance in poultry-associated environments during 2009–2022, we isolated and sequenced 188 H3 AIVs across China. Performing large-scale sequence analysis with publicly available data, we identified 4 sublineages of H3 AIVs established in domestic ducks in China via multiple introductions from wild birds from Eurasia. Using full-genome analysis, we identified 126 distinct genotypes, of which the H3N2 G23 genotype predominated recently. H3N8 G25 viruses, which spilled over from birds to humans, might have been generated by reassortment between H3N2 G23, wild bird H3N8, and poultry H9N2 before February 2021. Mammal-adapted and drug-resistance substitutions occasionally occurred in H3 AIVs. Ongoing surveillance for H3 AIVs and risk assessment are imperative for potential pandemic preparedness.
Improved wall weight function with polygon boundary in moving particle semi-implicit method

A wall boundary condition represented by polygons was presented by Harada et al. based on the moving particle semi-implicit (MPS) method to reduce the memory cost and calculation time for the wall particles. However, the inaccuracy of the wall weight function near a non-planar wall boundary causes the unphysical motion of the fluid. Therefore, this paper proposes an improved wall weight function for non-planar wall boundaries. Hydrostatic and dam break simulations with and without a wedge in a water tank are conducted to demonstrate the improvement.
A Biomimetic Approach Utilizing Pulsatile Perfusion Generates Contractile Vascular Grafts.

BACKGROUND Surgical implantation of decellularized cadaveric arteries is routinely used to treat right-sided congenital cardiac lesions. These acellular conduits lack the capacity for somatic growth and are prone to stenosis and calcification necessitating multiple operations throughout childhood. Islet-1+ cardiovascular progenitor cells (CPCs) have demonstrated the capacity for differentiation into all cell types of the heart and outflow tracts. We hypothesize that CPC-seeding of decellularized pulmonary arteries and bioreactor culture under physiologic flow conditions will drive vascular differentiation of CPCs and result in a conduit more suitable for implantation and long-term growth. METHODS We began by decellularizing ovine pulmonary arteries and characterizing the composition of the extracellular matrix (ECM). Hemodynamic testing of decellularized vessels in a custom bioreactor was used to define the scaffold mechanical properties over a range of pressures and flow rates. Next, our expanded ovine CPCs were suspended in growth media and injected intramurally into decellularized pulmonary arteries which were subsequently cultured in either static or pulsatile cultures. A combination of immunohistochemistry, RT-PCR, and tissue bath contraction studies were used to evaluate the bioengineered arteries prior to transplantation. Pulmonary artery patches from the most favorable culture conditions were then implanted into juvenile sheep to provide proof of concept. RESULTS Hematoxylin and eosin staining indicated complete removal of cell nuclei (n=9), while double-stranded DNA isolation from tissue homogenates showed 99.1% DNA removal (P<0.01, n=4). Furthermore, trichrome and elastin staining verified maintenance of collagen and elastin. Immunohistochemistry and PCR analyses (n=4 per group) confirmed contractile smooth muscle presence on only our 3-week pulsatile scaffolds via presence of calponin 1 and myosin heavy chain 11. Tissue bath studies demonstrated that smooth muscle contraction generated by our 3-week pulsatile scaffolds (2.23 ± 0.19grams, n=4) is comparable with native tissue contraction strength (2.78 ± 0.06grams, n=4). Ovine transplantation confirmed that our graft can be safely implanted, retains contractile smooth muscle cells, and recruits native endothelium. CONCLUSIONS Longer duration of physiologic pulsatile culture drives differentiation of CPCs seeded on ECM conduits toward a mature, contractile phenotype that is maintained for several weeks in vivo. Longer term studies to assess somatic growth potential are needed.
Individual Differences in Affect Dynamics and Alcohol-Related Outcomes

Abstract Background: To examine whether individual differences in intensive longitudinal data-derived affective dynamics (i.e. positive and negative affect variability and inertia and positive affect-negative affect bipolarity) – posited to be indicative of emotion dysregulation – are uniquely related to drinking level and affect-regulation drinking motives after controlling for mean levels of affective states. Method: We used a large sample of college student drinkers (N = 1640, 54% women) who reported on their affective states, drinking levels and drinking motives daily for 30 days using a web-based daily diary. We then calculated from the daily data positive and negative affect variability, inertia, affect bipolarity and mean levels of affect and used these as predictors of average drinking level and affect-regulation drinking motives (assessed using both retrospective and daily reporting methods). Results: Findings from dynamic structural equation models indicated that mean levels of affect were uniquely related to drinking motives, but not drinking level. Few dynamic affect predictors were uniquely related to outcomes in the predicted direction after controlling for mean affect levels. Conclusion: Our results add to the inconsistent literature regarding the associations between affective dynamics and alcohol-related outcomes, suggesting that any effects of these indicators, after controlling for mean affect levels, might be more complex than can be detected with simple linear models.