Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity and Characterization of Symbiotic Bacteria Isolated from Endemic Phaseolus Cultivars Located in Contrasting Agroecosystems in Venezuela

Phaseolus vulgaris is a grain cultivated in vast areas of different countries. It is an excellent alternative to the other legumes in the Venezuelan diet and is of great agronomic interest due to its resistance to soil acidity, drought, and high temperatures. Phaseolus establishes symbiosis primarily with Rhizobium and Ensifer species in most countries, and this rhizobia-legume interaction has been studied in Asia, Africa, and the Americas. However, there is currently no evidence to show that rhizobia nodulate the endemic cultivars of P. vulgaris in Venezuela. Therefore, we herein investigated the phylogenetic diversity of plant growth-promoting and N2-fixing nodulating bacteria isolated from the root nodules of P. vulgaris cultivars in a different agroecosystem in Venezuela. In comparisons with other countries, higher diversity was found in isolates from P. vulgaris nodules, ranging from α- and β-proteobacteria. Some isolates belonging to several new phylogenetic lineages within Bradyrhizobium, Ensifer, and Mesorhizobium species were also specifically isolated at some topographical regions. Additionally, some isolates exhibited tolerance to high temperature, acidity, alkaline pH, salinity stress, and high Al levels; some of these characteristics may be related to the origin of the isolates. Some isolates showed high tolerance to Al toxicity as well as strong plant growth-promoting and antifungal activities, thereby providing a promising agricultural resource for inoculating crops.
Insulin immunotherapy for pretype 1 diabetes

Purpose of review Loss of tolerance to insulin likely contributes to the immunopathogenesis of type 1 diabetes (T1D). Several large clinical trials and smaller mechanistic studies have failed to demonstrate the efficacy of insulin antigen therapy. The growing awareness of the heterogeneity of T1D likely affects the response to various immune therapies including insulin. Identification of biomarkers of clinical response will provide further insight into mechanisms leading to the disease and classify responders in the quest for personalized therapy. Recent findings Several biomarkers have identified subpopulations in posthoc analyses that showed benefit from oral insulin even though the placebo-controlled study was as a whole unsuccessful. High insulin autoantibody titer, low first phase insulin response, and high Diabetes Prevention Trial-Type 1 Risk Score identify at-risk relatives more likely to benefit from oral insulin. Future incorporation of human leukocyte antigen and the variable number of tandem repeats polymorphism located in the insulin gene promoter (INS VNTR) is of interest for both primary and secondary prevention studies. Summary Although primary and secondary prevention trials using oral insulin are ongoing, those completed have been largely unsuccessful. However, we believe that oral insulin should be considered in future trials as part of combination therapies as prerandomization biomarker testing is refined.
Understanding Clinical Significance in Rehabilitation

Supplemental digital content is available in the text. Abstract The objective of this review was to summarize the concept of clinical significance and associated methods focusing on the area of rehabilitation to provide a resource to rehabilitation researchers and clinicians. Studies were searched on electronic databases from inception until July 28, 2020, with no date or language limits. Manual searches as well as Scopus forward citation for relevant references were performed. Narrative synthesis of study results was performed. Definitions of the concepts related to clinical significance, ways of calculating, and interpreting each method were provided using rehabilitation examples. An explanation of methods to evaluate clinical significance (distribution, anchor, and opinion-based methods) and their advantages and disadvantages were also provided. Considering the limitations of statistical significance in assuring meaningfulness of results, clinical interpretation of research outcomes and the report of clinical significance in intervention trials should be a priority in rehabilitation research. When possible, the use of multiple methods (distribution, anchor, and opinion based) is recommended. Thus, clinical researchers are encouraged to present results in a manner that allow the rehabilitation professionals to easily interpret and implement those results in their clinical practice.
Cautionary Notes on the Use of Arabinose- and Rhamnose-Inducible Expression Vectors in Pseudomonas aeruginosa

Heterologous gene expression and complementation constitute a valuable and widely utilized tool in bacterial genetics. The arabinose-inducible ParaBAD (PBAD) and rhamnose-inducible PrhaBAD (PRha) promoter systems are commonly used in P. aeruginosa genetics and prized for the tight control and dynamic expression ranges that can be achieved. ABSTRACT The Pseudomonas aeruginosa virulence factor regulator (Vfr) is a cyclic AMP (cAMP)-responsive transcription factor homologous to the Escherichia coli cAMP receptor protein (CRP). Unlike CRP, which plays a central role in E. coli energy metabolism and catabolite repression, Vfr is primarily involved in the control of P. aeruginosa virulence factor expression. Expression of the Vfr regulon is controlled at the level of vfr transcription, Vfr translation, cAMP synthesis, and cAMP degradation. While investigating mechanisms that regulate Vfr translation, we placed vfr transcription under the control of the rhaBp rhamnose-inducible promoter system (designated PRha) and found that PRha promoter activity was highly dependent upon vfr. Vfr dependence was also observed for the araBp arabinose-inducible promoter (designated PBAD). The observation of Vfr dependence was not entirely unexpected. Both promoters are derived from E. coli, where maximal promoter activity is dependent upon CRP. Like CRP, we found that Vfr directly binds to promoter probes derived from the PRha and PBAD promoters in vitro. Because Vfr-cAMP activity is highly integrated into numerous global regulatory systems, including c-di-GMP signaling, the Gac/Rsm system, MucA/AlgU/AlgZR signaling, and Hfq/sRNAs, the potential exists for significant variability in PRha and PBAD promoter activity in a variety of genetic backgrounds, and use of these promoter systems in P. aeruginosa should be employed with caution. IMPORTANCE Heterologous gene expression and complementation constitute a valuable and widely utilized tool in bacterial genetics. The arabinose-inducible ParaBAD (PBAD) and rhamnose-inducible PrhaBAD (PRha) promoter systems are commonly used in P. aeruginosa genetics and prized for the tight control and dynamic expression ranges that can be achieved. In this study, we demonstrate that the activity of both promoters is dependent upon the cAMP-dependent transcription factor Vfr. While this poses an obvious problem for use in a vfr mutant background, the issue is more pervasive, considering that vfr transcription/synthesis and cAMP homeostasis are highly integrated into the cellular physiology of the organism and influenced by numerous global regulatory systems. Fortunately, the synthetic PTac promoter is not subject to Vfr regulatory control.
The SWEDEHEART secondary prevention and cardiac rehabilitation registry (SWEDEHEART CR registry).

AIMS The quality registry SWEDEHEART covers data across the patient pathway after an acute myocardial infarction (MI), from hospital care to secondary prevention. Although cardiac rehabilitation (CR) is strongly recommended after an MI, there is still heterogeneity regarding standards, uptake, and adherence rates. The aim of the SWEDEHEART-CR registry is to provide continuous information on secondary prevention and CR performance to support the audit and development of evidence-based practice. To facilitate quality improvement and research initiatives, a description of the characteristics and development of the SWEDEHEART-CR registry is needed. METHODS AND RESULTS The SWEDEHEART-CR registry starts with data obtained during hospital care and then collects data at out-patient visits 2 months and 1-year after discharge, and at start and end of an exercise-based CR programme. The registry data covers comorbidities, biochemistry, blood pressure, anthropometric variables, medication, psychosocial- and lifestyle variables, readmissions, patient-reported outcome measures, attendance in CR-related programmes, and physical fitness variables. Over 100 000 patients with MI have been included in the SWEDEHEART-CR registry since its start in 2005. From initially covering 35 centres (47%) and 2200 patients annually (27%), SWEDEHEART-CR has developed to a nation-wide registry with 75 centres (100%) and 8800 patients annually (80%) in 2020. CONCLUSION The SWEDEHEART-CR registry includes a high proportion of the national MI population entering a CR programme and is a powerful tool for quality audit, improvement, and research. The registry provides insights into the characteristics, treatment, and outcomes of evidence-based secondary preventive practice, ultimately leading to better cardiovascular health.
GraS Sensory Activity in Staphylococcus epidermidis Is Modulated by the “Guard Loop” of VraG and the ATPase Activity of VraF

Staphylococcus epidermidis has become an important opportunistic pathogen that is responsible for nosocomial and device-related infections that account for considerable morbidity worldwide. A thorough understanding of the mechanisms that enable S. epidermidis to colonize human skin successfully is essential for the development of alternative treatment strategies and prophylaxis. ABSTRACT Antimicrobial peptides (AMPs) are one of the key immune responses that can eliminate pathogenic bacteria through membrane perturbation. As a successful skin commensal, Staphylococcus epidermidis can sense and respond to AMPs through the GraXRS two-component system and an efflux system comprising the VraG permease and VraF ATPase. GraS is a membrane sensor known to function in AMP resistance through a negatively charged, 9-residue extracellular loop, which is predicted to be linear without any secondary structure. An important question is how GraS can impart effective sensing of AMPs through such a small unstructured sequence. In this study, we verified the role of graS and vraG in AMP sensing in S. epidermidis, as demonstrated by the failure of the ΔgraS or ΔvraG mutants to sense. Deletion of the extracellular loop of VraG did not affect sensing but reduced survival with polymyxin B. Importantly, a specific region within the extracellular loop, termed the guard loop (GL), has inhibitory activity since sensing of polymyxin B was enhanced in the ΔGL mutant, indicating that the GL may act as a gatekeeper for sensing. Bacterial two-hybrid analysis demonstrated that the extracellular regions of GraS and VraG interact, but interaction appears dispensable to sensing activity. Mutation of the extracellular loop of VraG, the GL, and the active site of VraF suggested that an active detoxification function of VraG is necessary for AMP resistance. Altogether, we provide evidence for a unique sensory scheme that relies on the function of a permease to impart effective information processing. IMPORTANCE Staphylococcus epidermidis has become an important opportunistic pathogen that is responsible for nosocomial and device-related infections that account for considerable morbidity worldwide. A thorough understanding of the mechanisms that enable S. epidermidis to colonize human skin successfully is essential for the development of alternative treatment strategies and prophylaxis. Here, we demonstrate the importance of an AMP response system in a clinically relevant S. epidermidis strain. Furthermore, we provide evidence for a unique sensory scheme that would rely on the detoxification function of a permease to effect information processing.
Order processing of number symbols is influenced by direction, but not format

This study probed the cognitive mechanisms that underlie order processing for number symbols, specifically the extent to which the direction and format in which number symbols are presented influence the processing of numerical order, as well as the extent to which the relationship between numerical order processing and mathematical achievement is specific to Arabic numerals or generalisable to other notational formats. Seventy adults who were bilingual in English and Chinese completed a Numerical Ordinality Task, using number sequences of various directional conditions (i.e., ascending, descending, mixed) and notational formats (i.e., Arabic numerals, English number words, and Chinese number words). Order processing was found to occur for ascending and descending number sequences (i.e., ordered but not non-ordered trials), with the overall pattern of data supporting the theoretical perspective that the strength and closeness of associations between items in the number sequence could underlie numerical order processing. However, order processing was found to be independent of the notational format in which the numerical stimuli were presented, suggesting that the psychological representations and processes associated with numerical order are abstract across different formats of number symbols. In addition, a relationship between the processing speed for numerical order judgements and mathematical achievement was observed for Arabic numerals and Chinese number words, and to a weaker extent, English number words. Together, our findings have started to uncover the cognitive mechanisms that could underlie order processing for different formats of number symbols, and raise new questions about the generalisability of these findings to other notational formats.
Comparison of extra-articular radiographic parameters of distal radius fractures on plain radiographs and CT scans

The aim of this study was to compare extra-articular radiographic parameters of distal radial fractures measured on plain radiographs and CT scans. Two researchers independently measured four extra-articular radiographic parameters (dorsal tilt, carpal alignment, radial inclination and ulnar variance) on both radiographs and CT scans in 85 patients. Inter-observer reliability for both techniques was assessed, along with the agreement between CT scans and radiographs using the intraclass correlation coefficient and Bland–Altman plots. The results showed that dorsal tilt, carpal alignment, radial inclination and ulnar variance can be measured reliably on both radiographs and CT scans. At a patient level, carpal alignment, radial inclination and ulnar variance CT scan measurements are an acceptable alternative to plain radiograph measurements in the vast majority of patients. In contrast, dorsal tilt CT scan measurements are not comparable with radiographs in 40% of the cases. Therefore, caution should be taken in measuring dorsal tilt on CT scans.
“We All Get Raped”: Sexual Violence Against Latin American Women in Migratory Transit in Mexico

The article addresses some forms of sexual violence suffered by Latin American women during migratory transit through Mexico. In-depth, semi-structured, qualitative–phenomenological interviews were conducted with 10 women in different stages of major transmigration states. The findings demonstrate the ubiquity of sexual violence during the migration. Five themes were identified: (a) The migration dimension of “being a woman”; (b) Recognition of contextual factors associated with the migratory process: “Intermediaries, road, shelters and sisterhood”; (c) The costs of migration: Abuse, discrimination, and persecution: “Criminal groups, physical violence, and “La Bestia”; (d) Triggers and supports: “Escape and future expectations”; and (e) God as a support.
Clinical practice guideline of BRCA1/2 testing for patients with breast cancer: Chinese Society of Breast Surgery (CSBrS) practice guideline 2021

Breast cancer is the most common female cancer around the world. Approximately 5% to 10% of breast cancer is associated with a hereditary predisposition from inherited germline mutations, with about 15% of mutations occurring in the breast cancer susceptibility genes (BRCA1/2). Individuals carrying BRCA1/2 mutations may reduce their risk of breast cancer through screening and preventing managements. It is essential for breast oncologists to improve their ability of identifying individuals with high risk of BRCA1/2 mutations, providing reasonable genetic counselling guidance to high risk individuals. Chinese Society of Breast Surgery (CSBrS) evaluated the relevant evidences using the Grading of Recommendations Assessment, Development, and Evaluation system, and developed the Clinical Practice Guideline of BRCA1/2 Testing for Patients with Breast Cancer (Version 2021), with the aim of providing guidance to the clinical practices of breast surgeons in China.
Patient-centeredness in Physiotherapy – A literature mapping review

ABSTRACT Background and purpose Research on patient-centeredness within physiotherapy points to a need for clarification about what the concept entails in science and practice and how research positions itself within health care. Thus, the aim is to systematically map the characteristics of research on patient-centeredness in physiotherapy and critically discuss the dominant understandings within. Methods A systematic research mapping was carried out, based on searches in leading bibliographic databases. Four categories were selected in order to characterize the research field: focus, design, theoretical approach and inherent logic. Findings Of 5,324 studies, 101 were included in the final mapping, pointing to a limited amount of research. The papers included were published in 47 different journals. Two major research foci emerges: one testing or developing technologies (tools) to promote patient-centeredness and one exploring patients’ or professionals’ experiences related to physiotherapy practice. Most papers reported on empirical research and there seems to be a dearth of conceptual papers. The theoretical approaches applied were mainly psychological, pedagogical and biomedical. The papers included were divided into equal amounts of studies carried out within inherent logics of causality and complexity. Conclusion The mapping suggests an incipient awareness of patient-centeredness within the research field of physiotherapy. Empirical studies dominate the field, whereas conceptual and critical papers seem in need of wider acknowledgment. The research field is divided into two mutually disconnected trends: one concerned with understanding the complexity of clinical practice and patients’ experiences of treatment and illness, and another trend concerned with solving “the problem” of patient involvement.
Money justice

Money justice—defined as money offered and paid to victims in the aftermath of wrongs—permeates society and everyday life. Current mechanisms of money justice are civil justice awards or out-of-court settlements for personal or cultural injury; redress programs or schemes for mass atrocities, political repression, historical injustice, and institutional abuse; and payments for war-related wrongs, terrorism, violent common crime, and contaminated blood products, among many others. In this article, we elucidate the concept of money justice, sketch the relationship of revenge and recompense in human history, distil relevant research, and put forward the money justice matrix, which provides a systematic way to analyse money payments (or lack of payments) in varied contexts of victimisation and with different justice mechanisms. Money justice is a new concept that analyses diverse wrongs studied in criminology, socio-legal studies, other social sciences, transitional justice, and historical injustice. Its contribution to new knowledge is two-fold. First, it will map and compare payments to survivors for diverse wrongs, investigate why payments differ, and assess inequalities in payments. Second, it will critically examine the money justice paradox. If, as victims say, money cannot recompense a wrong, why is money sought by victims and offered as justice? More generally, what does money achieve (or not achieve) as justice and for victims?
A landscape of synergistic drug combinations in non-small-cell lung cancer

Targeted therapeutics have advanced cancer treatment, but single agent activity remains limited by de novo and acquired resistance. Combining targeted drugs is broadly seen as a way to improve treatment outcome, motivating the ongoing search for efficacious combinations. To identify synergistic targeted therapy combinations and study the impact of tumor heterogeneity on combination outcome, we systematically tested over 5,000 two drug combinations at multiple doses across a collection of 81 non-small cancer cell lines. Both known and novel synergistic combinations were identified. Strikingly, very few combinations yield synergy across the majority of cell line models. Importantly, synergism mainly arises due to sensitization of single agent resistant models, rather than further sensitize already sensitive cell lines, frequently via dual targeting of a single or two highly interconnected pathways. This drug combinations resource, the largest of its kind should help delineate new synergistic regimens by facilitating the understanding of drug synergism in cancer.
The effect of non‐storm time substorms on the ring current dynamics

During geomagnetically active times such as geomagnetic storms, large amounts of energy can be released into the Earth’s magnetosphere and change the ring current intensity. Previous studies showed that significant enhancement of the ring current was related to geomagnetic storms, while few studies have examined substorm effects on ring current dynamics. In this study, we examine the ring current variation during non‐storm time (SYM‐H > −50 nT) substorms, especially during super‐substorms ( AE > 1000 nT). We perform a statistical analysis of ring current plasma pressure and number flux of various ion species under different substorm conditions, based on Van Allen Probe observations. The plasma pressure and ion fluxes of the ring current increased dramatically during super‐substorms, while little change was observed for substorms with AE < 1000 nT. The results shown in this study indicate that a non‐storm time super‐substorm may also have a significant contribution to the ring current.
Modeling freight mode choice using machine learning classifiers: a comparative study using Commodity Flow Survey (CFS) data

ABSTRACT This study explores the usefulness of machine learning classifiers for modeling freight mode choice. We investigate eight commonly used machine learning classifiers, namely Naïve Bayes, Support Vector Machine, Artificial Neural Network, K-Nearest Neighbors, Classification and Regression Tree, Random Forest, Boosting and Bagging, along with the classical Multinomial Logit model. US 2012 Commodity Flow Survey data are used as the primary data source; we augment it with spatial attributes from secondary data sources. The performance of the classifiers is compared based on prediction accuracy results. The current research also examines the role of sample size and training-testing data split ratios on the predictive ability of the various approaches. In addition, the importance of variables is estimated to determine how the variables influence freight mode choice. The results show that the tree-based ensemble classifiers perform the best. Specifically, Random Forest produces the most accurate predictions, closely followed by Boosting and Bagging. With regard to variable importance, shipment characteristics, such as shipment distance, industry classification of the shipper and shipment size, are the most significant factors for freight mode choice decisions.