Miracle-dz/UniFAR-FTUs huggingface dataset:
Survival Outcomes of Patients With Breast Cancer in a Mexican Population

PURPOSE The Instituto Mexicano del Seguro Social is a tripartite contribution providing care to more than 74 million beneficiaries, representing more than 50% of the country's general population. This study aims to describe the survival outcomes and clinicopathologic characteristics of patients with breast cancer at our Center. METHODS A retrospective cohort of patients with breast cancer treated between January 2012 and December 2020 was conducted. Survival outcomes were assessed using the Kaplan-Meier method. Univariate and multivariate analyses were performed using a Cox proportional hazards model. RESULTS There were 5,264 patients included with a median follow-up of 54.9 months. Forty-three percent (n = 2,274) were diagnosed in stage I-IIA, 43.1% (n = 2,269) in stage IIB-III, and 7% (n = 383) in stage IV. At 5 years, disease-free survival was 74.9% (95% CI, 73.5 to 76.3) and overall survival (OS) 90.4% (95% CI, 89.4 to 91.3). For stage IV, it was 22.7% (95% CI, 17.3 to 28.5). High histologic grade (hazard ratio, 1.51 [95% CI, 1.34 to 1.7]; P < .001) and lymphovascular invasion (LVI; hazard ratio, 1.85 [95% CI, 1.62 to 2.1]; P < .001) were associated with a higher risk of recurrence. CONCLUSION Histologic grade and LVI should be considered in the decision to treat with adjuvant chemotherapy in sites where genomic signatures are not available. Our OS data are comparable with other Mexican series; however, it is lower in stage IV. Much remains to be done at the national level, mainly regarding access to additional therapies for each breast cancer subtype. This work contributes to the evaluation of areas for improvement in outcomes in our population.
Inference for elliptical copula multivariate response regression models

The estimation of the coefficient matrix in a multivariate response linear regression model is considered in situations where we can observe only strictly increasing transformations of the continuous responses and covariates. It is further assumed that the joint dependence between all the observed variables is characterized by an elliptical copula. Penalized estimators of the coefficient matrix are obtained in a high-dimensional setting by assuming that the coefficient matrix is either element-wise sparse or row-sparse, and by incorporating the precision matrix of the error, which is also assumed to be sparse. Estimation of the copula parameters is achieved by inversion of Kendall’s tau. It is shown that when the true coefficient matrix is row-sparse, the estimator obtained via a group penalty outperforms the one obtained via a simple element-wise penalty. Simulation studies are used to illustrate this fact and the advantage of incorporating the precision matrix of the error when the correlation among the components of the error vector is strong. Moreover, the use of the normal-score rank correlation estimator is revisited in the context of high-dimensional Gaussian copula models. It is shown that this estimator remains as the optimal estimator of the copula correlation matrix in this setting. MSC 2010 subject classifications: Primary 62F12, 62J02; secondary 62H20, 62H99.
Galactomannan inhibits Trichinella spiralis invasion of intestinal epithelium cells and enhances antibody-dependent cellular cytotoxicity related killing of larvae by driving macrophage polarization

Previous studies have shown that recombinant Trichinella spiralis galectin (rTsgal) is characterized by a carbohydrate recognition domain sequence motif binding to beta-galactoside, and that rTsgal promotes larval invasion of intestinal epithelial cells. Galactomannan is an immunostimulatory polysaccharide composed of a mannan backbone with galactose residues. The aim of this study was to investigate whether galactomannan inhibits larval intrusion of intestinal epithelial cells and enhances antibody-dependent cellular cytotoxicity (ADCC), killing newborn larvae by polarizing macrophages to the M1 phenotype. The results showed that galactomannan specially binds to rTsgal, and abrogated rTsgal facilitation of larval invasion of intestinal epithelial cells. The results of qPCR, Western blotting, and flow cytometry showed that galactomannan and rTsgal activated macrophage M1 polarization, as demonstrated by high expression of iNOS (M1 marker) and M1 related genes (IL-1β, IL-6, and TNF-α), and increased CD86+ macrophages. Galactomannan and rTsgal also increased NO production. The killing ability of macrophage-mediated ADCC on larvae was also significantly enhanced in galactomannan- and rTsgal-treated macrophages. The results demonstrated that Tsgal may be considered a potential vaccine target molecule against T. spiralis invasion, and galactomannan may be a novel adjuvant therapeutic agent and potential vaccine adjuvant against T. spiralis infection.
Encephalitis in HIV-negative immunodeficient patients: a prospective multicentre study, France, 2016 to 2019

Background Data on infectious encephalitis in immunodeficient (ID) individuals are scarce. This population may present with atypical clinical symptoms, be infected by uncommon pathogens and develop poor outcomes. Aim We aimed to describe the epidemiology of infectious encephalitis among HIV-negative ID patients. Methods Patients from the ENCEIF (Etude Nationale de Cohorte des Encéphalites Infectieuses en France) prospective cohort meeting criteria for infectious encephalitis between January 2016 and December 2019 were included. We compared clinical presentation, magnetic resonance imaging (MRI) results, biological results, infection causes and outcome of ID patients with immunocompetent (IC) patients using Pearson’s chi-squared test and Student’s t-test. We carried out logistic regression to assess the role of immunodeficiency as risk factor for poor outcome. Results ID patients (n = 58) were older (mean 72 vs 59 years), had higher prevalence of diabetes (26% vs 12%), pre-existing neurological disorders (12% vs 5%) and higher case-fatality rate (23.6% vs 5.6%) compared to IC patients (n = 436). Varicella zoster virus was the primary cause of encephalitis in ID patients (this aetiology was more frequent in ID (25.9%) than in IC patients (11.5%)), with herpes simplex virus second (22.4% in ID patients vs 27.3% in IC patients). Immunodeficiency was an independent risk factor for death or major sequelae (odds ratio: 3.41, 95%CI: 1.70–6.85). Conclusions Varicella zoster virus is the most frequent cause of infectious encephalitis in ID patients. Immunodeficiency is a major risk factor for poor outcome. ID encephalitis patients should benefit from stringent investigation of cause and early empiric treatment.
Insight into planktonic protistan and fungal communities across the nutrient-depleted environment of the South Pacific Subtropical Gyre

ABSTRACT Ocean microorganisms constitute ~70% of the marine biomass, contribute to ~50% of the Earth’s primary production, and play a vital role in global biogeochemical cycles. The marine heterotrophic and mixotrophic protistan and fungal communities have often been overlooked mainly due to limitations in morphological species identification. Despite the accumulation of studies on biogeographic patterns observed in microbial communities, our understanding of the abundance and distribution patterns within the microbial community of the largest subtropical gyre, the South Pacific Gyre (SPG), remains incomplete. Here, we investigated the diversity and vertical composition of protistan and fungal communities in the water column of the ultra-oligotrophic SPG. Our results showed apparent differences in protistan community diversity in the photic and aphotic regions. The entire protistan community diversity was significantly affected by temperature, salinity, oxygen, and nutrient concentrations, while the parasitic community diversity was also affected by chlorophyll a concentration. The parasitic protists were assigned to the class Syndiniales accounting for over 98% of the total parasitic protists, exhibiting higher relative sequence abundance along the water depth and displaying consistent patterns among different sampling stations. In contrast to the protistan community, the fungal community along the SPG primarily clustered based on the sampling station and pelagic zones. In particular, our study reveals a significant presence of parasitic protists and functionally diverse fungi in SPG and their potential impact on carbon cycling in the gyre. IMPORTANCE Our findings carry important implications for understanding the distribution patterns of the previously unrecognized occurrence of parasitic protists and functionally diverse fungi in the nutrient-limited South Pacific Gyre. In particular, our study reveals a significant presence of parasitic Syndiniales, predominantly abundant in the upper 300 m of the aphotic zone in the gyre, and a distinct presence of fungal communities in the aphotic zone at the central part of the gyre. These findings strongly suggest that these communities play a substantial role in yet insufficiently described microbial food web. Moreover, our research enhances our understanding of their contribution to the dynamics of the food webs in oligotrophic gyres and is valuable for projecting the ecological consequences of future climate warming.
What is the best fixation method in medial patellofemoral ligament reconstruction? A biomechanical comparison of common methods for femoral graft attachment

Introduction: A variety of techniques have been described for femoral fixation in medial patellofemoral ligament reconstruction (MPFLr). The aim of this study was to compare the biomechanical performance of the most used methods for graft fixation in the femur using human cadaveric tissue. We wondered what is the best fixation method for femoral fixation in MPFL reconstruction? Hypothesis: A suspensory fixation device provides the best femoral fixation. Material and method: Twenty cadaveric knees were tested. Four femoral fixation methods were compared (5 knees per group): interference fixation with a Biosure© RG 5 mm and a 7 mm, suture anchor (Healicoil Regenesorb 4.75 mm ©) and suspensory fixation with the Ultrabutton©. The testing was divided in preconditioning, cyclic loading and load to failure. Load to failure, elongation, stiffness and mode of failure were recorded and compared. Results: The Ultrabutton© had the highest mean ultimate load (427 ± 215 N (p = 0.5)), followed by Healicoil anchor © (308 ± 44 N (p > 0.05)) and the interference screw of 7 mm (255 ± 170 N (p > 0.05)). Mean stiffness was similar in the Ultrabutton© and 4.75 mm. Healicoil anchor © groups (111 ± 21 N/mm and 119 ± 20 N/mm respectively), and lowest in 7 mm Biosure© screw fixation group (90 ± 5 N/mm). The Biosure© 5 mm RG screw presented 100% of premature rupture because of tendon slippage. The Ultrabutton© presented the lowest premature rupture (40%). Discussion: A suspensory fixation for the femur had the lowest number of graft failures and highest load to failure. This study has implications for surgeons’ choice of graft fixation in MPFLr. It is the first study to test the most commonly femoral used fixation methods, allowing direct comparisons between each method.
Exposure to moral stressors and associated outcomes in healthcare workers: prevalence, correlates, and impact on job attrition

ABSTRACT Introduction: Healthcare workers (HCWs) often experience morally challenging situations in their workplaces that may contribute to job turnover and compromised well-being. This study aimed to characterize the nature and frequency of moral stressors experienced by HCWs during the COVID-19 pandemic, examine their influence on psychosocial-spiritual factors, and capture the impact of such factors and related moral stressors on HCWs’ self-reported job attrition intentions. Methods: A sample of 1204 Canadian HCWs were included in the analysis through a web-based survey platform whereby work-related factors (e.g. years spent working as HCW, providing care to COVID-19 patients), moral distress (captured by MMD-HP), moral injury (captured by MIOS), mental health symptomatology, and job turnover due to moral distress were assessed. Results: Moral stressors with the highest reported frequency and distress ratings included patient care requirements that exceeded the capacity HCWs felt safe/comfortable managing, reported lack of resource availability, and belief that administration was not addressing issues that compromised patient care. Participants who considered leaving their jobs (44%; N = 517) demonstrated greater moral distress and injury scores. Logistic regression highlighted burnout (AOR = 1.59; p < .001), moral distress (AOR = 1.83; p < .001), and moral injury due to trust violation (AOR = 1.30; p = .022) as significant predictors of the intention to leave one’s job. Conclusion: While it is impossible to fully eliminate moral stressors from healthcare, especially during exceptional and critical scenarios like a global pandemic, it is crucial to recognize the detrimental impacts on HCWs. This underscores the urgent need for additional research to identify protective factors that can mitigate the impact of these stressors.
Race effects on impression formation in social interaction: An instrumental learning account.

How does race influence the impressions we form through direct interaction? In two preregistered experiments (N = 239/179), White American participants played a money-sharing game with Black and White players, based on a probabilistic reward reinforcement learning task, in which they chose to interact with players and received feedback on whether a player shared. We found that participants formed stronger reward preferences for White relative to Black players despite equivalent reward feedback between groups-a pattern that was stronger among participants with low internal motivation to respond without prejudice and high explicit prejudice. This race effect in reward learning was evident in participants' behavioral choice preferences, but not in their self-reported perceptions of group members' reward rates. Computational modeling suggested two mechanisms through which race affected instrumental learning: race (a) influenced White participants' initial expectancies (i.e., priors) about Black compared with White players' behavior and (b) led participants to update reward representations of Black and White players according to separate learning rates. These findings demonstrate that race can influence the formation of impressions through direct social interaction and introduce an instrumental learning framework to understand the effects of bias in intergroup interactions. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
Adsorptive Removal of Amido Black 10B from Aqueous Solution using Stem Carbon of Ricinus communis as Adsorbent

In the present work the efficiency of activated carbon made from stems of Ricinus communis (CRC) has been studied for removal of anionic dye- Amido black 10B from aqueous solution. The adsorbent has been characterized with scanning electron microscopy (SEM) and Fourier transformer infrared (FT-IR). The effects of various experimental parameters such as contact time, adsorbent dose, initial dye concentrations, pH, concentration of salt and temperature have been studied. Langmuir, Freundlich and Tempkin isotherm models have been used for describing the adsorption process. Of these, Langmuir isotherm model has best fitted the experimental data with a maximum adsorption capacity of 7.12 mg/g. Kinetics studies indicate that the adsorption of Amido black 10B has favoured toward pseudo-second-order model with high correlation coefficients. Thermodynamics parameters confirmed that the adsorption has been found to be spontaneous and endothermic in nature. These results suggested that CRC has a potential low-cost adsorbent for the removal of toxic dye Amido black 10B.
Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes)

ABSTRACT The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded program. Fruiting bodies reached the highest complexity levels in the Agaricomycetes; yet, the underlying genetics is currently poorly known. In this work, we functionally characterized a highly conserved gene termed snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologs of snb1 are present in almost all agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. snb1 deletion mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes, and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed differentially regulated genes and gene families that, based on wild-type RNA-Seq data, were upregulated early during development and showed tissue-specific expression, suggesting a potential role in differentiation. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying developmental patterning in the Agaricomycetes. IMPORTANCE Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are complex multicellular structures, with a spatially and temporally integrated developmental program that is, however, currently poorly known. In this study, we present a novel, conserved gene family, Snowball (snb), termed after the unique, differentiation-less fruiting body morphology of snb1 knockout strains in the model mushroom Coprinopsis cinerea. snb is a gene of unknown function that is highly conserved among agaricomycetes and encodes a protein of unknown function. A comparative transcriptomic analysis of the early developmental stages of differentiated wild-type and non-differentiated mutant fruiting bodies revealed conserved differentially expressed genes which may be related to tissue differentiation and developmental patterning fruiting body development.
Visualization of immune pathways that enhance the neutralizing antibody response to vaccines after primary immunization

ABSTRACT We examined the relationship between the association of a vaccine antigen with immune cells in secondary lymphoid organs shortly after immunization and the resulting neutralizing antibody response induced by that antigen using three antigenic forms of anthrax protective antigen (PA) that induce qualitatively different antibody responses. The three PA forms used were wild-type PA, which binds to anthrax toxin receptors and elicits a robust antibody response that includes both neutralizing and non-neutralizing antibodies; a receptor-binding-deficient (RBD) mutant form of PA, which does not bind cellular receptors and elicits only barely detectable antibody responses; and an engineered chimeric form of PA, which binds cholera toxin receptors and elicits a robust total antibody response but a poor neutralizing antibody response. We found that both wild-type PA and the PA chimera associated with immune cells in secondary lymphoid organs after immunization, but the RBD mutant PA exhibited minimal association, revealing a relationship between antigen binding to toxin receptors on immune cells after immunization and subsequent antibody responses. A portion of wild-type PA that bound to immune cells was cell surface-associated and maintained its native conformation. Much lower amounts of conformationally intact PA chimera were associated with immune cells after immunization, correlating with the lower neutralizing antibody response elicited by the PA chimera. Thus, binding of an antigen to receptors on immune cells in secondary lymphoid organs after immunization and maintenance of conformational integrity of the cell-associated antigen help dictate the magnitude of the resulting neutralizing antibody response, but not necessarily the total antibody response. IMPORTANCE Many vaccines protect by the induction of antibodies that neutralize the action of the pathogen. Here, we followed the fate of three antigenic forms of a vaccine antigen in secondary lymphoid organs after immunization to investigate events leading to a robust neutralizing antibody response. We found that the magnitude of the neutralizing antibody response, but not the total antibody response, correlates with the levels of conformationally intact antigen associated with immune cells in secondary lymphoid organs after primary immunization. We believe that these results provide important insights into the genesis of neutralizing antibody responses induced by vaccine antigens and may have implications for vaccine design.
Study of History of Uplift and Denudation in Southeast Sichuan since Yanshan Epoch

T-t thermal history path of apatite fission track from the Jurassic sandstone shows two stages of uplift and denudation in southeast Sichuan since Yanshan epoch. The initial uplift took place during 127 Ma-105 Ma with a rate of uplift and denudation of about 5 m/Ma, resulting in denudation of 106 m thick Lowery Cretaceous. The second uplift took place during 75 Ma-0 Ma. This stage may be divided into four interval with different uplift rates such as 75 Ma-65 Ma, 65 Ma-20 Ma, 20 Ma-10 Ma and 10 Ma-0 Ma. The uplift during 75 Ma-65 Ma was rapid with a rate of uplift and denudation of about 28 m/Ma. The uplift during 65 Ma-20 Ma and 10 Ma-0 Ma was slow with rates of uplift and denudation of 14 m/Ma and 10 m/Ma, respectively. Rapid uplift happened during 20Ma-10Ma with a rate of uplift and denudation of about 147 m/Ma. Strata with a thickness of about 2580 m were denuded in the two stages of uplift since the Yanshan epoch.