Miracle-dz/UniFAR-FTUs huggingface dataset:
Associated bacteria of Botryococcus braunii (Chlorophyta)

Botryococcus braunii (Chlorophyta) is a green microalga known for producing hydrocarbons and exopolysaccharides (EPS). Improving the biomass productivity of B. braunii and hence, the productivity of the hydrocarbons and of the EPS, will make B. braunii more attractive for industries. Microalgae usually cohabit with bacteria which leads to the formation of species-specific communities with environmental and biological advantages. Bacteria have been found and identified with a few B. braunii strains, but little is known about the bacterial community across the different strains. A better knowledge of the bacterial community of B. braunii will help to optimize the biomass productivity, hydrocarbons, and EPS accumulation. To better understand the bacterial community diversity of B. braunii, we screened 12 strains from culture collections. Using 16S rRNA gene analysis by MiSeq we described the bacterial diversity across 12 B. braunii strains and identified possible shared communities. We found three bacterial families common to all strains: Rhizobiaceae, Bradyrhizobiaceae, and Comamonadaceae. Additionally, the results also suggest that each strain has its own specific bacteria that may be the result of long-term isolated culture.
Individual and contextual determinants of dental pain in adolescents: Evidence from a national survey.

OBJECTIVE To investigate the prevalence of dental pain among adolescent students and its association with individual, school and city variables, using a multilevel approach. SUBJECTS AND METHODS Individual and school data were obtained from the National Adolescent School-Based Health Survey (PeNSE) conducted in Brazil in 2015 in a sample of 34,776 students from 1,339 schools in the 27 Brazilian capital cities. Secondary data on socioeconomic, structural and health indicators of the cities were obtained from public databases. The outcome was the prevalence of dental pain in the last six months (yes/no). Independent variables, consisting of potential social and behavioural determinants of dental pain, were structured in three levels: individual, school and city. Multilevel logistic regression was performed. RESULTS Prevalence of dental pain was 21.8% (95% CI = 21.0-22.7). Unadjusted analysis showed significant associations between the outcome and most of the factors in the individual and in the contextual levels. In the final adjusted model, adolescents who reported unfavourable health-related behaviours, adverse socioeconomic or psychosocial characteristics, as well as those attending public schools and living in cities with high caries prevalence (DMFT) at age 12, were more likely to report dental pain. CONCLUSIONS Prevalence of dental pain was high and associated with adverse individual and contextual factors in the school and city levels.
Intracerebral hemorrhage in a neonate with an intragenic COL4A2 duplication

Intracerebral hemorrhage is rare in term born neonates. Besides several non‐genetic risk factors, pathogenic variants in COL4A1 and COL4A2 have been described to play a role in the pathophysiology of neonatal intracerebral hemorrhage. To the best of our knowledge, no intragenic COL4A2 duplications have been reported in humans to date. We report a neonate with intracerebral hemorrhage and a de novo intragenic COL4A2 duplication. Although it is not clear yet whether this genetic factor fully explains the clinical phenotype, it may have contributed at least as a risk factor for cerebral hemorrhage. Screening for intragenic COL4A1 and COL4A2 duplications as part of collagen IV diagnostics should be considered as part of the fetal and neonatal work‐up for unexplained cerebral hemorrhages and to collect more evidence of the pathogenicity of this genetic mechanism.
The role of FHL2 in wound healing and inflammation

The 4‐and‐a‐half LIM domain protein 2 (FHL2) is a multifunctional adaptor protein that can interact with cell surface receptors, cytosolic adaptor and structural proteins, kinases, and nuclear transcription factors. It is involved in numerous functional activities, including the epithelial‐mesenchymal transition, cell proliferation, apoptosis, adhesion, migration, structural stability, and gene expression. Despite this, FHL2‐knockout (KO) mice are viable and fertile with no obvious abnormalities, rather suggesting a high capacity for fine‐tuning adjustment and functional redundancy of FHL2. Indeed, challenging FHL2‐KO cells or mice provided numerous evidences for the great functional significance of FHL2. In recent years, several reviews have been published describing the high capacity of FHL2 to bind diverse proteins as well as the versatile functions of FHL2, emphasizing in particular its role in cardiovascular diseases and carcinogenesis. Here, we view the function of FHL2 from a different perspective. We summarize the published data demonstrating the impact of FHL2 on wound healing and inflammation. FHL2 seems to be involved in numerous steps of these extremely complex and multidirectional but tightly regulated tissue remodeling processes, supporting tissue repair and coordinating inflammation. Deficiency of FHL2 not only slows down ongoing wound healing but also often turns it into a chronic condition. —Wixler, V. The role of FHL2 in wound healing and inflammation. FASEB J. 33, 7799–7809 (2019). www.fasebj. org
Tranexamic Acid Use in Open Reduction and Internal Fixation of Fractures of the Pelvis, Acetabulum, and Proximal Femur: A Randomized Controlled Trial.

OBJECTIVES Assess the safety and efficacy of tranexamic acid(TXA) use in fractures of the pelvic ring, acetabulum, and proximal femur DESIGN:: Prospective, randomized controlled trial SETTING:: Single Level 1 trauma center PATIENTS:: Fourty-seven patients were randomized to the study group and 46 patients comprised the control group INTERVENTION:: The study group received 15mg/kg IV TXA prior to incision and a second identical dose 3 hours after the initial dose. MAIN OUTCOME MEASUREMENTS transfusion rates, total blood loss (via hemoglobin dilutional method, rates of venous thromboembolic events) RESULTS:: Total blood loss was significantly higher in the control group (TXA=952mL, No TXA=1325mL, p=0.028). The total transfusion rates between the TXA and control groups were not significantly different (TXA 1.51, No TXA= 1.17, P=0.41). There were no significant differences between the TXA and control groups in inpatient VTE events (p=0.57) CONCLUSION:: The use of TXA in high-energy fractures of the pelvis, acetabulum and femur significantly decreased calculated total blood loss but did not decrease overall transfusion rates. TXA did not increase the rate of VTE. Further study is warranted prior to making broad recommendations for use of TXA in these fractures.
Description of the Follicular Fluid Cytokine and Hormone Profiles in Human Physiological Natural Cycles

Abstract Purpose Exogenous gonadotrophins administration during in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) cycles could significantly alter the endogenous follicular regulation system and could influence oocyte quality. The analysis of the follicular fluid (FF) cytokine and hormone profiles in physiological natural cycles is crucial to appreciate the role of FF milieu on follicle development. So far, the FF cytokine profile has been analyzed only in controlled ovarian stimulation cycles and in modified natural cycles. Our study defines, in physiological natural cycles, the cytokine and hormone profiles of individual FF aspirated from antral follicles. Methods A total of 203 FFs obtained from 83 women with regular menstrual cycles undergoing ovarian tissue cryopreservation were analyzed: 115 FFs from Group 1 (10 to 29 years of age) and 88 FFs from Group 2 (30 to 40 years of age). In individual FF, 27 cytokines were measured with xMAP technology, and progesterone, estrone, estradiol, testosterone, androstenedione concentrations were determined by liquid chromatography–tandem mass spectrometry. Results FF hormone profiles were not different in follicular and luteal phase, suggesting that FF hormones are regulated independently of the endogenous gonadotrophins—possibly because 74% of the punctured follicles, which were ≤6 mm, did not require cyclic pituitary function. The follicle size was influenced not only by the FF cytokine profile but also by the FF hormone profile, both of which are dependent on age. Main Conclusions In physiological natural cycles, FF hormones seems to be regulated independently of the endogenous gonadotropins. Age influences FF hormone and cytokine profiles and the compelling relationship between FF hormones and FF cytokines could influence the follicle development.
Effect of Renin-angiotensin System Inhibitors on Acute Kidney Injury among Patients undergoing Cardiac Surgery: A Review and Meta-analysis.

Acute kidney injury (AKI) is a frequent complication of cardiac surgery, which can lead to higher mortality and long-term renal function impairment. The effect of perioperative renin-angiotensin system inhibitors (RASi) therapy on AKI incidence in patients undergoing cardiac surgery remains controversial. We reviewed related studies in PubMed, Scopus, and Cochrane Library from inception to February 2020. Two randomized controlled trials (RCTs) and 21 cohort studies were included in the meta-analysis, involving 76,321 participants. The pooled odds ratio and 95% confidence interval were calculated using the DerSimonian and Laird random-effects model. The results showed no significant association between perioperative RASi therapy and postoperative AKI in patients undergoing cardiac surgery. We highlighted the limitations of existing studies and called for well-designed large-scale RCTs to verify the conclusion.
Oncogenic effects of exosomes in γ‐herpesvirus‐associated neoplasms

Kaposi's sarcoma‐associated herpesvirus (KSHV) and Epstein–Barr virus (EBV) are herpesviruses associated with human malignancies. As exosomes can shuttle many herpesvirus‐associated biomolecules from host cells to recipient cells, the exosomal pathway is utilized by herpesviruses to achieve extensive infections and even oncogenesis. In this review, we discuss the oncogenic biomolecules present in exosomes derived from KSHV‐ and EBV‐infected cells. Moreover, oncogenesis via exosomal biomolecules mainly occurs through three processes, including regulation of downstream signals, promotion of immune dysfunction and transformation of cells. Also, the exosomes may provide diagnostic markers and therapeutic targets specific for KSHV‐ and EBV‐associated malignancies.
Passive stiffness of fibrotic skeletal muscle in mdx mice relates to collagen architecture

The amount of fibrotic material in dystrophic mouse muscles relates to contractile function, but not passive function. Collagen fibres in skeletal muscle are associated with increased passive muscle stiffness in fibrotic muscles. The alignment of collagen is independently associated with passive stiffness in dystrophic skeletal muscles. These outcomes demonstrate that collagen architecture rather than collagen content should be a target of anti‐fibrotic therapies to treat muscle stiffness.
Development of a novel histological and histomorphometric evaluation protocol for a standardized description of the mid‐palatal suture – An ex vivo study

The hard palate and mid‐palatal suture are highly important for orthodontic treatment. In cases of transverse maxillary deficiency, palatal expansion is the treatment of choice. As nowadays a growing number of adult patients receive orthodontic treatment, an understanding of suture development throughout life is important to derive tailored orthodontic treatment techniques for each age group. Histological, histochemical and immunohistochemical stains (haematoxylin & eosin, Azan, Movat pentachrome, Masson–Goldner trichrome, Sirius Red, CD 31, osteopontin and TRAP) and histomorphometric analyses were re‐established to detect the structural conditions of the mid‐palatal suture in human cadavers of three different age groups (20–39, 40–59 and 60–80 years). The mid‐palatal suture of the selected age groups (total of n = 12; n = 4 in every group m = f) exhibited marked differences in sutural morphology and metabolism. A wide, interdigitated and well‐vascularized suture was observed in younger specimens compared with straighter and smaller sutures with fewer vessels and lower bone density in the 60–80 year group. The fibre composition within the sutural gap differed between the three age groups. Delicate fibres were found in the 20–39 year group, and a tightly interwoven 3D fibre‐network was observed in the 40–59 year group. Atrophy primarily characterized the fibres in the 60–80 year group. This evidence demonstrates differences between the evaluated groups. These results suggest that the staining methods used are suitable for the description and evaluation of the morphology and metabolism of mid‐palatal sutures. Further investigation is necessary to provide an in‐depth description of sutural maturation over a lifetime.
Lipidomic and transcriptomic analysis of western diet-induced nonalcoholic steatohepatitis (NASH) in female Ldlr -/- mice

Background Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide, particularly in obese and type 2 diabetic individuals. NAFLD ranges in severity from benign steatosis to nonalcoholic steatohepatitis (NASH); and NASH can progress to cirrhosis, primary hepatocellular carcinoma (HCC) and liver failure. As such, NAFLD has emerged as a major public health concern. Herein, we used a lipidomic and transcriptomic approach to identify lipid markers associated with western diet (WD) induced NASH in female mice. Methods Female mice (low-density lipoprotein receptor null (Ldlr -/-) were fed a reference or WD diet for 38 and 46 weeks. Transcriptomic and lipidomic approaches, coupled with statistical analyses, were used to identify associations between major NASH markers and transcriptomic & lipidomic markers. Results The WD induced all major hallmarks of NASH in female Ldlr -/- mice, including steatosis (SFA, MUFA, MUFA-containing di- and triacylglycerols), inflammation (TNFα), oxidative stress (Ncf2), and fibrosis (Col1A). The WD also increased transcripts associated with membrane remodeling (LpCat), apoptosis & autophagy (Casp1, CtsS), hedgehog (Taz) & notch signaling (Hey1), epithelial-mesenchymal transition (S1004A) and cancer (Gpc3). WD feeding, however, suppressed the expression of the hedgehog inhibitory protein (Hhip), and enzymes involved in triglyceride catabolism (Tgh/Ces3, Ces1g), as well as the hepatic abundance of C18-22 PUFA-containing phosphoglycerolipids (GpCho, GpEtn, GpSer, GpIns). WD feeding also increased hepatic cyclooxygenase (Cox1 & 2) expression and pro-inflammatory ω6 PUFA-derived oxylipins (PGE2), as well as lipid markers of oxidative stress (8-iso-PGF2α). The WD suppressed the hepatic abundance of reparative oxylipins (19, 20-DiHDPA) as well as the expression of enzymes involved in fatty epoxide metabolism (Cyp2C, Ephx). Conclusion WD-induced NASH in female Ldlr -/- mice was characterized by a massive increase in hepatic neutral and membrane lipids containing SFA and MUFA and a loss of C18-22 PUFA-containing membrane lipids. Moreover, the WD increased hepatic pro-inflammatory oxylipins and suppressed the hepatic abundance of reparative oxylipins. Such global changes in the type and abundance of hepatic lipids likely contributes to tissue remodeling and NASH severity.
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries

Abstract The exponential growth of genomic/genetic data in the era of Big Data demands new solutions for making these data findable, accessible, interoperable and reusable. In this article, we present a web-based platform named Gene Expression Time-Course Research (GETc) Platform that enables the discovery and visualization of time-course gene expression data and analytical results from the NIH/NCBI-sponsored Gene Expression Omnibus (GEO). The analytical results are produced from an analytic pipeline based on the ordinary differential equation model. Furthermore, in order to extract scientific insights from these results and disseminate the scientific findings, close and efficient collaborations between domain-specific experts from biomedical and scientific fields and data scientists is required. Therefore, GETc provides several recommendation functions and tools to facilitate effective collaborations. GETc platform is a very useful tool for researchers from the biomedical genomics community to present and communicate large numbers of analysis results from GEO. It is generalizable and broadly applicable across different biomedical research areas. GETc is a user-friendly and efficient web-based platform freely accessible at http://genestudy.org/
Site U1487

Y. Rosenthal, A.E. Holbourn, D.K. Kulhanek, I.W. Aiello, T.L. Babila, G. Bayon, L. Beaufort, S.C. Bova, J.-H. Chun, H. Dang, A.J. Drury, T. Dunkley Jones, P.P.B. Eichler, A.G.S. Fernando, K. Gibson, R.G. Hatfield, D.L. Johnson, Y. Kumagai, T. Li, B.K. Linsley, N. Meinicke, G.S. Mountain, B.N. Opdyke, P.N. Pearson, C.R. Poole, A.C. Ravelo, T. Sagawa, A. Schmitt, J.B. Wurtzel, J. Xu, M. Yamamoto, and Y.G. Zhang2
System Factors Affecting Intraoperative Risk and Resilience

Objective: To identify and categorize system factors in complex laparoscopic surgery that have the potential to either threaten patient safety or support system resilience. Background: The operating room is a uniquely complex sociotechnical work system wherein surgical successes prevail despite pervasive safety threats. Holistically characterizing intraoperative factors that thus support system resilience in addition to those that threaten patient safety using contextual methodologies is critical for optimizing surgical safety overall. Method: In this prospective descriptive interdisciplinary study, 19 audio/video recordings of complex laparoscopic general surgical procedures were directly observed and transcribed. Using a qualitative systems-based approach, intraoperative human factors with the potential to impact patient safety, either as a safety threat or as a support for resilience, were identified. Adverse events were further assessed for shared threats and supports. Data collection was guided by the Systems Engineering Initiative for Patient Safety 2.0 work system model. Results: A total of 1083 relevant observations were made over 39.8 hours of operative time, enabling the identification of 79 distinct safety threats and 67 resilience supports within the surgical system. Safety threats associated with the physical environment, tasks, organization, and equipment were prevalent and observed in equal measure, whereas supports for resilience were predominantly attributed to clinician behaviors, including proactive team management and skills coaching. Two subclinical adverse events were identified; shared safety threats included suboptimal technology design, whereas shared resilience supports included calm clinician behavior and redundant intraoperative resourcing. Conclusions: Safety threats and resilience supports were found to be systematic in the surgical setting. Identified safety threats should be prioritized for remediation, and clinician behaviors that contribute to fostering resilience should be valued and protected.
Racial disparities in school-based disciplinary actions are associated with county-level rates of racial bias

Significance Black students in the United States are subject to disciplinary action at rates much higher than their white counterparts. These disciplinary actions put students at higher risk for negative life outcomes, including involvement in the criminal justice system. Using federal data covering over 32 million students at nearly 96,000 schools, our research demonstrates that the disciplinary gap between black and white students across five types of disciplinary actions is associated with county-level rates of racial bias. Our work emphasizes the need for policy targeting racial disparities in education and psychological bias. There are substantial gaps in educational outcomes between black and white students in the United States. Recently, increased attention has focused on differences in the rates at which black and white students are disciplined, finding that black students are more likely to be seen as problematic and more likely to be punished than white students are for the same offense. Although these disparities suggest that racial biases are a contributor, no previous research has shown associations with psychological measurements of bias and disciplinary outcomes. We show that county-level estimates of racial bias, as measured using data from approximately 1.6 million visitors to the Project Implicit website, are associated with racial disciplinary disparities across approximately 96,000 schools in the United States, covering around 32 million white and black students. These associations do not extend to sexuality biases, showing the specificity of the effect. These findings suggest that acknowledging that racial biases and racial disparities in education go hand-in-hand may be an important step in resolving both of these social ills.
Academization of Nursing and Its Possible Consequences for Hospital Management in Germany

The history of nursing academization worldwide spans over a century. In Germany, this process started in the early 1990’s and, relative to many other countries, has remained slow. However, some of the latest developments in the country are promising a constant increase in the number of nurses with academic education. Consequently, this process arouses new challenges and opportunities for hospital management. Through a literature review, this paper aimed to give an overview over the progress toward nursing academization in Germany, in comparison with the United States and the European Union. The other objective was to identify examples of the consequences of the process for German hospital management and to design proposals to facilitate adaptation to possible challenges.
Tolerating Slowdowns in Replicated State Machines using Copilots

Replicated state machines are linearizable, fault-tolerant groups of replicas that are coordinated using a consensus algorithm. Copilot replication is the first 1-slowdown-tolerant consensus protocol: it delivers normal latency despite the slowdown of any 1 replica. Copilot uses two distinguished replicas—the pilot and copilot—to proactively add redundancy to all stages of processing a client’s command. Copilot uses dependencies and deduplication to resolve potentially differing orderings proposed by the pilots. To avoid dependencies leading to either pilot being able to slow down the group, Copilot uses fast takeovers that allow a fast pilot to complete the ongoing work of a slow pilot. Copilot includes two optimizations—ping-pong batching and null dependency elimination—that improve its performance when there are 0 and 1 slow pilots respectively. Our evaluation of Copilot shows its performance is lower but competitive with MultiPaxos and EPaxos when no replicas are slow. When a replica is slow, Copilot is the only protocol that avoids high latencies.