Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution patterns of Acidobacteriota in different fynbos soils

The Acidobacteriota is ubiquitous and is considered as one of the major bacterial phyla in soils. The current taxonomic classifications of this phylum are divided into 15 class-level subdivisions (SDs), with only 5 of these SDs containing cultured and fully described species. Within the fynbos biome, the Acidobacteriota has been reported as one of the dominant bacterial phyla, with relative abundances ranging between 4–26%. However, none of these studies reported on the specific distribution and diversity of the Acidobacteriota within these soils. Therefore, in this study we aimed to first determine the relative abundance and diversity of the Acidobacteriota in three pristine fynbos nature reserve soils, and secondly, whether differences in the acidobacterial composition can be attributed to environmental factors, such as soil abiotic properties. A total of 27 soil samples were collected at three nature reserves, namely Jonkershoek, Hottentots Holland, and Kogelberg. The variable V4-V5 region of the 16S rRNA gene was sequenced using the Ion Torrent S5 platform. The mean relative abundance of the Acidobacteriota were 9.02% for Jonkershoek, 14.91% for Kogelberg, and most significantly (p<0.05), 18.42% for Hottentots Holland. A total of 33 acidobacterial operational taxonomic units (OTUs) were identified. The dominant subdivisions identified in all samples included SDs 1, 2, and 3. Significant differences were observed in the distribution and composition of these OTUs between nature reserves. The SD1 were negatively correlated to soil pH, hydrogen (H+), potassium (K+) and carbon (C). In contrast, SD2, was positively correlated to soil pH, phosphorus (P), and K+, and unclassified members of SD3 was positively correlated to H+, K, and C. This study is the first to report on the specific acidobacterial distribution in pristine fynbos soils in South Africa.
Probing the interaction of a globular protein with a small fluorescent probe in the presence of silver nanoparticles: spectroscopic characterization of its domain specific association and dissociation

Photoinduced intramolecular charge transfer produces a polar excited state in the small fluorescent probe 1-anilino-8-naphthalene-sulfonate (ANS) rendering the resulting emission sensitive to the medium polarity. The binding of ANS to proteins has been well characterized in the literature. The probe binds to the less polar hydrophobic, restricted proteinous environment of bovine serum albumin (BSA) resulting in a blue shift of the emission maximum with an increase in emission intensity. However, upon addition of silver nanoparticles to the probe–BSA system, there was found to be an interaction between the nanoparticle and protein resulting in a weakening of the probe–BSA binding and an associated conformational change of the protein in order to accommodate the silver nanoparticle. This has been hitherto undeciphered. Studies using site markers of flufenamic acid and phenylbutazone coupled with other spectroscopic techniques, REES, time resolved studies, FTIR, and SEM imaging studies have shed light on the interaction of silver nanoparticles with the probe bound protein. ANS was observed to move from its binding site in the protein to accommodate the silver nanoparticle surface which involved conformational changes of the protein near the probe binding site. The association of the probe to the protein and its dissociation from the sites on introduction of silver nanoparticles has thus been investigated using spectroscopic studies.
Factors associated with RVU generation in common sports medicine procedures

ABSTRACT Introduction Relative value units (RVUs) are integral to the U.S. physician compensation system used by the Centers for Medicare & Medicaid Services. The use of ‘work RVUs’ (herein, wRVUs) is intended to reimburse physicians according to the amount of expertise and effort needed to safely and effectively perform a procedure. Our purpose was to determine: 1) the number of wRVUs/hour generated by common sports medicine surgical procedures; and 2) how patient characteristics, surgical approach, and practice setting are associated with the number of wRVUs/hour. This analysis was performed to infer whether wRVUs are assigned appropriately according to the factors on which they are purported to be based. Methods We queried the American College of Surgeons’ National Surgical Quality Improvement Program (NSQIP) database for common sports medicine surgical procedures performed in 2018. Data from 19,877 patients (8,258 women) with a mean age of 48 years (range, 18–90) who underwent a surgical sports medicine procedure were analyzed. Work RVUs and operative time were used to calculate work RVUs/hour for each surgical procedure. Univariate and multivariate analyses were used to assess correlations between patient characteristics and wRVUs/hour. Results Knee chondroplasty generated the most mean (± standard deviation) wRVUs/hour at 22 ± 0.5, whereas ‘open tenodesis of biceps tendon, long head’ generated the least at 9.6 ± 0.25 wRVUs/hour. Factors associated with a greater mean number of wRVUs/hour were younger patient age, female sex, arthroscopic approach, and outpatient setting. Arthroscopic procedures also generated more wRVUs/hour than the same procedures performed through an open approach. wRVUs were not correlated with case complexity or surgical time. Conclusion wRVUs/hour in surgical sports medicine procedures vary widely depending on the procedure type, patient characteristics, surgical approach, and practice setting.
Epoxidation of Lower Olefins with Hydrogen Peroxide and Titanium Silicalite

Abstract The epoxidation of lower olefins, catalysed by titanium silicalite (TS-1) under mild conditions, is reported. The reaction may be performed at near room temperature, in dilute alcoholic or aqueous solutions of hydrogen peroxide. In methanol C 4 -C 8 linear olefins, allyl chloride, and allyl alcohol show fast reaction rates and high selectivities (72-97% on H 2 O 2 ). The solvolysis of the oxirane ring and the oxidation of the solvent are the main side reactions. Yields and kinetics are decreased by increasing the chain length or the cross-section of the olefin ( n -C n > n -C n +1 , 1-hexene ⪢ cyclohexene), by electron-withdrawing substituents (1-butene > allyl chloride > allyl alcohol), and by solvents in the order methanol > ethanol > t -butanol. The rate of reaction also depends on the position and steric configuration of the double bond and on the branching, as a result of inductive and shape selectivity effects: trans 2-butene cis 2-butene, 2-methyl-1-butene
Influence of cross‐sectional velocity profile on flow characteristics of arterial wall modeled as elastic and viscoelastic material

In the present work, blood flow behavior in a single artery and in arterial network is studied using time domain based one‐dimensional wave propagation model retaining the nonlinear convective force. 1‐D Navier–Stokes equation is used to model the flow behavior of the blood, using three unknown parameters: flow rate (q), cross‐sectional area of artery (A) and pressure (p) based formulation. Three different approximate velocity profile functions across the cross‐section namely modified flat, parabolic and the one proposed by Bessems are used to calculate the nonlinear convective force and the frictional force. Two different constitutive models, linear elastic model and standard linear solid model (Zener model) are used to model the arterial wall mechanical behavior. The system of partial differential equations is discretized using finite element and Crank Nicolson methods in space and time domains, respectively. Based on the formulation, an in house finite element code is developed to simulate flow behavior in both a single artery as well as in arterial network consisting of 20 small and large size arteries. Simulations are performed by enforcing a flow rate at the inlet and Windkessel model at the outlet. The results for elastic arterial wall model are found to be in good agreement with the results available in the literature. The flow rate/pressure predictions using different velocity profile functions are found to be nearly the same, however the Bessems velocity profile predicts more closer to 3D results compared to modified flat and parabolic profiles. Whereas, significant difference is found in the results predicted using elastic and viscoelastic artery wall models.
Applications of marine collagens in bone tissue engineering

For decades, collagen has been among the most widely used biomaterials with several biomedical applications. Recently, researchers have shown a keen interest in collagen obtained from marine sources because of its biocompatibility, biodegradability, ease of extractability, safety, low immunogenicity, and low production costs. A wide variety of marine collagen-based scaffolds have been developed for bone tissue engineering, and these scaffolds display excellent biological effects. This review aims to provide an overview of the biological effects of marine collagen in bone engineering, such as promoting osteogenesis and collagen synthesis, inhibiting inflammation, inducing the differentiation of cartilage, and improving bone mineral density. Marine collagen holds great promise as a biomaterial in bone tissue engineering.
Deconstructing the contribution of sensory cues in social approach

Social interaction is a complex and highly conserved behavior that safeguards survival and reproductive success. Although considerable progress has been made regarding our understanding of same‐sex conspecific and non‐aggressive interactions, questions regarding the precise contribution of sensory cues in social approach and their specific neurobiological correlates remain open. Here, by designing a series of experiments with diverse social and object stimuli manipulations in custom‐made enclosures, we first sought to deconstruct key elements of social preference as assessed by the three‐chamber task. Our results highlight the importance of social olfactory cues in approach behavior. Subsequently, we interrogated whether a social odor would activate dopaminergic neurons of the Ventral Tegmental Area in the same way as a juvenile conspecific would. Employing in vivo recordings in freely behaving mice, we observed an increase of the firing only during the transition toward the juvenile mouse and not during the transition toward the object impregnated with social odor, suggesting that these two experiences are distinct and can be differentiated at the neuronal level. Moreover, using a four‐choice task, we further showed that mice prefer to explore complex social stimuli compared to isolated sensory cues. Our findings offer insights toward understanding how different sensory modalities contribute to the neurobiological basis of social behavior which can be essential when studying social deficits observed in autism‐, depression‐, anxiety‐, or schizophrenia‐related mouse models.
Comparison of Public Responses to Containment Measures During the Initial Outbreak and Resurgence of COVID-19 in China: Infodemiology Study

Background COVID-19 cases resurged worldwide in the second half of 2020. Not much is known about the changes in public responses to containment measures from the initial outbreak to resurgence. Monitoring public responses is crucial to inform policy measures to prepare for COVID-19 resurgence. Objective This study aimed to assess and compare public responses to containment measures during the initial outbreak and resurgence of COVID-19 in China. Methods We curated all COVID-19–related posts from Sina Weibo (China’s version of Twitter) during the initial outbreak and resurgence of COVID-19 in Beijing, China. With a Python script, we constructed subsets of Weibo posts focusing on 3 containment measures: lockdown, the test-trace-isolate strategy, and suspension of gatherings. The Baidu open-source sentiment analysis model and latent Dirichlet allocation topic modeling, a widely used machine learning algorithm, were used to assess public engagement, sentiments, and frequently discussed topics on each containment measure. Results A total of 8,985,221 Weibo posts were curated. In China, the containment measures evolved from a complete lockdown for the general population during the initial outbreak to a more targeted response strategy for high-risk populations during COVID-19 resurgence. Between the initial outbreak and resurgence, the average daily proportion of Weibo posts with negative sentiments decreased from 57% to 47% for the lockdown, 56% to 51% for the test-trace-isolate strategy, and 55% to 48% for the suspension of gatherings. Among the top 3 frequently discussed topics on lockdown measures, discussions on containment measures accounted for approximately 32% in both periods, but those on the second-most frequently discussed topic shifted from the expression of negative emotions (11%) to its impacts on daily life or work (26%). The public expressed a high level of panic (21%) during the initial outbreak but almost no panic (1%) during resurgence. The more targeted test-trace-isolate measure received the most support (60%) among all 3 containment measures in the initial outbreak, and its support rate approached 90% during resurgence. Conclusions Compared to the initial outbreak, the public expressed less engagement and less negative sentiments on containment measures and were more supportive toward containment measures during resurgence. Targeted test-trace-isolate strategies were more acceptable to the public. Our results indicate that when COVID-19 resurges, more targeted test-trace-isolate strategies for high-risk populations should be promoted to balance pandemic control and its impact on daily life and the economy.
Investigation of Burkholderia cepacia Complex Methylomes via Single-Molecule, Real-Time Sequencing and Mutant Analysis

While the genome sequence determines an organism’s proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, MTs modify specific nucleotide motifs to allow discrimination of “self” from “nonself” DNA, e.g., from bacteriophages. ABSTRACT Bacterial genomes can be methylated at particular motifs by methyltransferases (MTs). This DNA modification allows restriction endonucleases (REs) to discriminate between self and foreign DNA. While the accepted primary function of such restriction modification (RM) systems is to degrade incoming foreign DNA, other roles of RM systems and lone RE or MT components have been found in genome protection, stability, and the regulation of various phenotypes. The Burkholderia cepacia complex (Bcc) is a group of closely related opportunistic pathogens with biotechnological potential. Here, we constructed and analyzed mutants lacking various RM components in the clinical Bcc isolate Burkholderia cenocepacia H111 and used single-molecule, real-time (SMRT) sequencing of single mutants to assign the B. cenocepacia H111 MTs to their cognate motifs. DNA methylation is shown to affect biofilm formation, cell shape, motility, siderophore production, and membrane vesicle production. Moreover, DNA methylation had a large effect on the maintenance of the Bcc virulence megaplasmid pC3. Our data also suggest that the gp51 MT-encoding gene, which is essential in H111 and is located within a prophage, is required for maintaining the bacteriophage in a lysogenic state, thereby ensuring a constant, low level of phage production within the bacterial population. IMPORTANCE While the genome sequence determines an organism’s proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, MTs modify specific nucleotide motifs to allow discrimination of “self” from “nonself” DNA, e.g., from bacteriophages. Restriction enzymes detect “nonself” methylation patterns and cut foreign DNA. Furthermore, methylation of promoter regions can influence gene expression and hence affect various phenotypes. In this study, we determined the methylated motifs of four strains from the Burkholderia cepacia complex of opportunistic pathogens. We deleted all genes encoding the restriction and modification components in one of these strains, Burkholderia cenocepacia H111. It is shown that DNA methylation affects various phenotypic traits, the most noteworthy being lysogenicity of a bacteriophage and maintenance of a virulence megaplasmid.
The evolutionary trade-offs in phage-resistant Klebsiella pneumoniae entail cross-phage sensitization and loss of multidrug resistance.

Bacteriophage therapy is currently being evaluated as a critical complement to traditional antibiotic treatment. However, the emergence of phage resistance is perceived as a major hurdle to the sustainable implementation of this antimicrobial strategy. By combining comprehensive genomics and microbiological assessment, we show that the receptor-modification resistance to capsule-targeting phages involves either escape mutation(s) in the capsule biosynthesis cluster or qualitative changes in exopolysaccharides, converting clones to mucoid variants. These variants introduce cross-resistance to phages specific to the same receptor yet sensitize to phages utilizing alternative ones. The loss/modification of capsule, the main Klebsiella pneumoniae virulence factor, did not dramatically impact population fitness, nor the ability to protect bacteria against the innate immune response. Nevertheless, the introduction of phage drives bacteria to expel multidrug resistance clusters, as observed by the large deletion in K. pneumoniae 77 plasmid containing blaCTX-M , ant(3″), sul2, folA, mph(E)/mph(G) genes. The emerging bacterial resistance to viral infection steers evolution towards desired population attributes and highlights the synergistic potential for combined antibiotic-phage therapy against K. pneumoniae. This article is protected by copyright. All rights reserved.
Factors Affecting Pathologic Complete Response Following Neoadjuvant Chemotherapy in Breast Cancer: Development and Validation of a Predictive Nomogram.

Background There is an increasing need to develop a more accurate prediction model for pathologic complete response (pCR) after neoadjuvant chemotherapy (NAC) in breast cancer. Purpose To develop a nomogram based on MRI and clinical-pathologic variables to predict pCR. Materials and Methods In this single-center retrospective study, consecutive women with stage II-III breast cancer who underwent NAC followed by surgery between January 2011 and December 2017 were considered for inclusion. The women were divided into a development cohort between January 2011 and September 2015 and a validation cohort between October 2015 and December 2017. Clinical-pathologic data were collected, and mammograms and MRI scans obtained before and after NAC were analyzed. Logistic regression analyses were performed to identify independent variables associated with pCR in the development cohort from which the nomogram was created. Nomogram performance was assessed with the area under the receiver operating characteristic curve (AUC) and calibration slope. Results A total of 359 women (mean age, 49 years ± 10 [standard deviation]) were in the development cohort and 351 (49 years ± 10) in the validation cohort. Hormone receptor negativity (odds ratio [OR], 3.1; 95% CI: 1.4, 7.1; P = .006), high Ki-67 index (OR, 1.05; 95% CI: 1.03, 1.07; P < .001), and post-NAC MRI variables, including small tumor size (OR, 0.6; 95% CI: 0.4, 0.9; P = .03), low lesion-to-background parenchymal signal enhancement ratio (OR, 0.2; 95% CI: 0.1, 0.6; P = .004), and absence of enhancement in the tumor bed (OR, 3.8; 95% CI: 1.4, 10.5; P = .009) were independently associated with pCR. The nomogram incorporating these variables showed good discrimination (AUC, 0.90; 95% CI: 0.86, 0.94) and calibration abilities (calibration slope, 0.91; 95% CI: 0.69, 1.13) in the independent validation cohort. Conclusion A nomogram incorporating hormone receptor status, Ki-67 index, and MRI variables showed good discrimination and calibration abilities in predicting pathologic complete response. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Imbriaco and Ponsiglione in this issue.
Survival in Immunocompromised Patients Ultimately Requiring Invasive Mechanical Ventilation: A Pooled Individual Patient Data Analysis.

RATIONALE Acute respiratory failure (ARF) is associated with high mortality in immunocompromised patients, particularly when invasive mechanical ventilation is needed. Therefore, noninvasive oxygenation/ventilation strategies have been developed to avoid intubation, with uncertain impact on mortality, especially when intubation is delayed. OBJECTIVES We sought to report trends of survival over time in immunocompromised patients receiving invasive mechanical ventilation. The impact of delayed intubation after failure of noninvasive strategies was also assessed. METHODS Systematic review and meta-analysis using individual data (IPD) of studies which focused on immunocompromised adult patients with ARF requiring invasive mechanical ventilation. Studies published in English were identified through PubMed, Web of science, and Cochrane Central (2008-2018). IPD were requested to corresponding authors for all identified studies. We used mixed-effect models to estimate the effect of delayed intubation on hospital mortality and described mortality rates over time. MEASUREMENTS AND MAIN RESULTS 11087 patients were included (24 studies, 3 controlled trials and 21 cohorts), of whom 7736 (74%) were intubated within 24h of ICU admission (early intubation). Crude mortality rate was 53.2%. Adjusted survivals improved over time (from 1995 to 2017, OR for hospital mortality per year: 0.96[0.95-0.97]). For each elapsed day between ICU admission and intubation, mortality was higher (OR:1.38[1.26-1.52], p<0.001). Early intubation was significantly associated with lower mortality (OR: 0.83[0.72-0.96]), regardless of initial oxygenation strategy. These results persisted after propensity score analysis (matched OR associated with delayed intubation :1.56[1.44-1.70]). CONCLUSION In immunocompromised intubated patients, survival has improved over time. Time between ICU admission and intubation is a strong predictor of mortality, suggesting a detrimental effect of late initial oxygenation failure.
Spectacle non‐tolerance in clinical practice – a systematic review with meta‐analysis

Spectacle non‐tolerance or adverse events to spectacle wear are serious concerns for both patients and practitioners. Non‐tolerance may contribute to a negative impact on the practitioner’s ability and practice. Therefore, a detailed understanding of frequency and causes of spectacle non‐tolerance in clinical ophthalmic practice is essential. This review aimed to determine the prevalence and causes of non‐tolerance to spectacles prescribed and dispensed in clinical practice.