Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and Biotechnological Studies for Important Traits in Maize

Molecular techniques are now a valuable tool for achieving advances in genome research and generating considerable interest in predicting hybrid performance. Molecular markers are of great value in genetic research and partially in breeding programs since they reflect the genetic variation among individuals. Various PCR-based marker techniques have recently been successfully introduced in the fingerprinting of plant genomes and in genetic diversity studies. Among them random amplified polymorphic DNA (RAPD) analysis which is relatively simple, rapid and cost effective. It is hoped that the present study may help maize breeders to produce new hybrid varieties having higher yielding potential.
The diagnostic performance of CA125 for the detection of ovarian and non-ovarian cancer in primary care: A population-based cohort study

Background The serum biomarker cancer antigen 125 (CA125) is widely used as an investigation for possible ovarian cancer in symptomatic women presenting to primary care. However, its diagnostic performance in this setting is unknown. We evaluated the performance of CA125 in primary care for the detection of ovarian and non-ovarian cancers. Methods and findings We studied women in the United Kingdom Clinical Practice Research Datalink with a CA125 test performed between 1 May 2011–31 December 2014. Ovarian and non-ovarian cancers diagnosed in the year following CA125 testing were identified from the cancer registry. Women were categorized by age: <50 years and ≥50 years. Conventional measures of test diagnostic accuracy, including sensitivity, specificity, and positive predictive value, were calculated for the standard CA125 cut-off (≥35 U/ml). The probability of a woman having cancer at each CA125 level between 1–1,000 U/ml was estimated using logistic regression. Cancer probability was also estimated on the basis of CA125 level and age in years using logistic regression. We identified CA125 levels equating to a 3% estimated cancer probability: the “risk threshold” at which the UK National Institute for Health and Care Excellence advocates urgent specialist cancer investigation. A total of 50,780 women underwent CA125 testing; 456 (0.9%) were diagnosed with ovarian cancer and 1,321 (2.6%) with non-ovarian cancer. Of women with a CA125 level ≥35 U/ml, 3.4% aged <50 years and 15.2% aged ≥50 years had ovarian cancer. Of women with a CA125 level ≥35 U/ml who were aged ≥50 years and who did not have ovarian cancer, 20.4% were diagnosed with a non-ovarian cancer. A CA125 value of 53 U/ml equated to a 3% probability of ovarian cancer overall. This varied by age, with a value of 104 U/ml in 40-year-old women and 32 U/ml in 70-year-old women equating to a 3% probability. The main limitations of our study were that we were unable to determine why CA125 tests were performed and that our findings are based solely on UK primary care data, so caution is need in extrapolating them to other healthcare settings. Conclusions CA125 is a useful test for ovarian cancer detection in primary care, particularly in women ≥50 years old. Clinicians should also consider non-ovarian cancers in women with high CA125 levels, especially if ovarian cancer has been excluded, in order to prevent diagnostic delay. Our results enable clinicians and patients to determine the estimated probability of ovarian cancer and all cancers at any CA125 level and age, which can be used to guide individual decisions on the need for further investigation or referral.
Bidirectional Programming for Parsing and Retentive Printing

Language designers usually need to implement parsers and printers for doing the conversion between program text and abstract syntax trees (ASTs), which are commonly found and constantly used in application scenarios such as resugaring, code refactoring, and observing the results of compiler optimisation. It is desirable that when producing a new piece of program text from a slightly modi ed (e.g. optimised) AST which corresponds to some original piece of program text, the printer can preserve the layouts, comments, and syntactic sugar contained in the original program text as much as possible. In order to do so, the common practice is to enrich ASTs with whatever information that is needed (such as comments), so that the printer can use the enriched information to produce better-printed results. However, the approach violates the design philosophy of ASTs, for ASTs should be abstract and compact and contain only essential information. This thesis reconciles the compactness of ASTs and printing quality by proposing retentive printing, which takes not only an AST but also a piece of original program text, so that there is no need to enrich ASTs with unnecessary information (already in the original program text). We rst propose a domain-speci c language BiYacc, whose program denotes a consistent (i.e. well-behaved) pair of parser and retentive printer for an unambiguous context-free grammar. BiYacc is based on the theory of bidirectional transformations (BX) and in particular (state-based asymmetric) lenses, which helps to guarantee by construction that the generated parser and retentive printer pairs are always well-behaved. We show that BiYacc facilitates many tasks such as resugaring, language evolution, and simple refactoring. However, using only unambiguous grammars can be rather inconvenient in practice, as ambiguous grammars (with disambiguation directives) are often considered more natural and humanfriendly than their unambiguous versions. Therefore, we make the rst move to support ambiguous grammars and tackle grammatical ambiguity in the bidirectional setting by proposing an approach based on generalised parsing and disambiguation lters, which produce all parse results and (try to) select the only desired one in the parsing direction; the lters are carefully bidirectionalised so
Longer Ubiquinone Side Chains Contribute to Enhanced Farnesol Resistance in Yeasts

Ubiquinones (UQ) are intrinsic lipid components of many membranes. Besides their role in electron-transfer reactions there is evidence for them acting as free radical scavengers, yet their other roles in biological systems have received little study. The dimorphic fungal pathogen Candida albicans secretes farnesol as both a virulence factor and a quorum-sensing molecule. Thus, we were intrigued by the presence of UQ9 isoprenologue in farnesol-producing Candida species while other members of this genera harbor UQ7 as their major electron carrier. We examined the effect of UQ side chain length in Saccharomyces cerevisiae and C. albicans with a view towards identifying the mechanisms by which C. albicans protects itself from the high levels of farnesol it secretes, levels that are toxic to many other fungi including S. cerevisiae. In this study, we identify UQ9 as the major UQ isoprenoid in C. albicans, regardless of growth conditions or cell morphology. A S. cerevisiae model yeast engineered to make UQ9 instead of UQ6 was 4–5 times more resistant to exogenous farnesol than the parent yeast and this resistance was accompanied by greatly reduced reactive oxygen species (ROS) production. The resistance provided by UQ9 is specific for farnesol in that it does not increase resistance to high salt (1M NaCl) or other oxidants (5 mM H2O2 or 1 mM menadione). Additionally, the protection provided by UQ9 appears to be structural rather than transcriptional; UQ9 does not alter key transcriptional responses to farnesol stress. Here, we propose a model in which the longer UQ side chains are more firmly embedded in the mitochondrial membrane making them harder to pry out, so that in the presence of farnesol they remain functional without producing excess ROS. C. albicans and Candida dubliniensis evolved to use UQ9 rather than UQ7 as in other Candida species or UQ6 as in S. cerevisiae. This adaptive mechanism highlights the significance of UQ side chains in farnesol production and resistance quite apart from being an electron carrier in the respiratory chain.
Hypoxia-Preconditioned Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells Mitigate Hypoglycemic Testicular Injury Induced by Insulin in Rats

Hypoglycemia is a neglected metabolic disorder. Thus, we evaluated the protective effect of hypoxia-preconditioned human umbilical cord blood-derived mesenchymal stem cells (hUCB-MSCs) on hypoglycemic testicular injury. We examined 56 testes from 28 animals: 7 rats with insulin-induced hypoglycemia (HG group), 7 hypoglycemic rats which received an intratesticular injection of hUCB-MSCs (HG-MSC group), and 14 untreated control rats. Testosterone level, testicular catalase (CAT) activity, and malondialdehyde (MDA) level were analyzed. Immunostaining for specific testicular germ and somatic cell markers was performed. Proliferating and apoptotic cells were detected by anti-PCNA and anti-caspase-3, respectively. Morphometrical data were statistically analyzed. The hypoglycemic rats showed a significant decrease in testosterone level and CAT activity and a significant increase in MDA production. Examination of histological structure and protein expression of diverse germ cell markers revealed collapsed tubules that were lined by degenerated germ cells, decreased lactate dehydrogenase type C immune expression, as well as decreased proliferating and increased apoptotic cells number in hypoglycemic testes. Injection of MSCs improved testicular biochemical parameters, preserved germ cells and somatic cells, and decreased apoptosis. In conclusion, hypoxia-preconditioned hUCB-MSCs attenuate rat testicular injury caused by insulin-induced hypoglycemia. Avoidance and rapid management of hypoglycemia are necessary to avoid significant testicular injury.
Chain-Selective Isotopic Labeling of the Heterodimeric Type III Secretion Chaperone, Scc4:Scc1, Reveals the Total Structural Rearrangement of the Chlamydia trachomatis Bi-Functional Protein, Scc4

Scc4 is an unusual bi-functional protein from Chlamydia trachomatis (CT) that functions as a type III secretion system (T3SS) chaperone and an RNA polymerase (RNAP)-binding protein. Both functions require interactions with protein partners during specific stages of the CT developmental cycle. As a T3SS chaperone, Scc4 binds Scc1 during the late stage of development to form a heterodimer complex, which chaperones the essential virulence effector, CopN. During the early-middle stage of development, Scc4 regulates T3SS gene expression by binding the σ66-containing RNAP holoenzyme. In order to study the structure and association mechanism of the Scc4:Scc1 T3SS chaperone complex using nuclear magnetic resonance (NMR) spectroscopy, we developed an approach to selectively label each chain of the Scc4:Scc1 complex with the 15N-isotope. The approach allowed one protein to be visible in the NMR spectrum at a time, which greatly reduced resonance overlap and permitted comparison of the backbone structures of free and bound Scc4. 1H,15N-heteronuclear single quantum coherence spectra of the 15N-Scc4:Scc1 and Scc4:15N-Scc1 complexes showed a total structural rearrangement of Scc4 upon binding Scc1 and a dynamic region isolated to Scc1, respectively. Development of the chain-selective labeling approach revealed that the association of Scc4 and Scc1 requires partial denaturation of Scc1 to form the high affinity complex, while low affinity interactions occurred between the isolated proteins under non-denaturing conditions. These results provide new models for Scc4′s functional switching mechanism and Scc4:Scc1 association in CT.
Prognostic Factors for 30-Day Mortality in Critically Ill Patients With Coronavirus Disease 2019: An Observational Cohort Study

Supplemental Digital Content is available in the text. OBJECTIVES: To identify characteristics that predict 30-day mortality among patients critically ill with coronavirus disease 2019 in England, Wales, and Northern Ireland. DESIGN: Observational cohort study. SETTING: A total of 258 adult critical care units. PATIENTS: A total of 10,362 patients with confirmed coronavirus disease 2019 with a start of critical care between March 1, 2020, and June 22, 2020, of whom 9,990 were eligible (excluding patients with a duration of critical care less than 24 hr or missing core variables). MEASUREMENTS AND MAIN RESULTS: The main outcome measure was time to death within 30 days of the start of critical care. Of 9,990 eligible patients (median age 60 yr, 70% male), 3,933 died within 30 days of the start of critical care. As of July 22, 2020, 189 patients were still receiving critical care and a further 446 were still in acute hospital. Data were missing for between 0.1% and 7.2% of patients across prognostic factors. We imputed missing data ten-fold, using fully conditional specification and continuous variables were modeled using restricted cubic splines. Associations between the candidate prognostic factors and time to death within 30 days of the start of critical care were determined after adjustment for multiple variables with Cox proportional hazards modeling. Significant associations were identified for age, ethnicity, deprivation, body mass index, prior dependency, immunocompromise, lowest systolic blood pressure, highest heart rate, highest respiratory rate, Pao2/Fio2 ratio (and interaction with mechanical ventilation), highest blood lactate concentration, highest serum urea, and lowest platelet count over the first 24 hours of critical care. Nonsignificant associations were found for sex, sedation, highest temperature, and lowest hemoglobin concentration. CONCLUSIONS: We identified patient characteristics that predict an increased likelihood of death within 30 days of the start of critical care for patients with coronavirus disease 2019. These findings may support development of a prediction model for benchmarking critical care providers.
Transcriptomic Analysis of Age-Associated Periventricular Lesions Reveals Dysregulation of the Immune Response

White matter lesions (WML) are a common feature of the ageing brain associated with cognitive impairment. The gene expression profiles of periventricular lesions (PVL, n = 7) and radiologically-normal-appearing (control) periventricular white matter cases (n = 11) obtained from the Cognitive Function and Ageing Study (CFAS) neuropathology cohort were interrogated using microarray analysis and NanoString to identify novel mechanisms potentially underlying their formation. Histological characterisation of control white matter cases identified a subgroup (n = 4) which contained high levels of MHC-II immunoreactive microglia, and were classified as “pre-lesional. ” Microarray analysis identified 2256 significantly differentially-expressed genes (p ≤ 0.05, FC ≥ 1.2) in PVL compared to non-lesional control white matter (1378 upregulated and 878 downregulated); 2649 significantly differentially-expressed genes in “pre-lesional” cases compared to PVL (1390 upregulated and 1259 downregulated); and 2398 significantly differentially-expressed genes in “pre-lesional” versus non-lesional control cases (1527 upregulated and 871 downregulated). Whilst histological evaluation of a single marker (MHC-II) implicates immune-activated microglia in lesion pathology, transcriptomic analysis indicates significant downregulation of a number of activated microglial markers and suggests established PVL are part of a continuous spectrum of white matter injury. The gene expression profile of “pre-lesional” periventricular white matter suggests upregulation of several signalling pathways may be a neuroprotective response to prevent the pathogenesis of PVL.
“Dude I’ve Never Felt This Way Towards a Celebrity Death”: Parasocial Grieving and the Collective Mourning of Kobe Bryant on Reddit

Although research acknowledges the existence of parasocial relationships, if these relationships are possible then, inevitably, these relationships will dissolve. The emotions associated with parasocial breakups, especially that of grieving, are vital to understanding the totality of relationships between spectators and sports figures. After the devastating death of NBA legend Kobe Bryant, a content analysis was used to explore the emotional and mental responses of grief posted on Reddit. The results suggest that sadness and shock were the most common responses of grief across Reddit threads, while the use of reminiscing and memorializing was also prevalent across both. Additionally, this study provides evidence to support the notion that like real relationships, emotional responses of grief like sadness dissipate over time, while other emotional responses like love increase. Thus, any study examining parasocial grieving must do so longitudinally as parasocial grief, like real grief, is a process not momentary.
Transcriptome and proteome mapping in the sheep atria reveal molecular featurets of atrial fibrillation progression

Abstract Aims Atrial fibrillation (AF) is a progressive cardiac arrhythmia that increases the risk of hospitalization and adverse cardiovascular events. There is a clear demand for more inclusive and large-scale approaches to understand the molecular drivers responsible for AF, as well as the fundamental mechanisms governing the transition from paroxysmal to persistent and permanent forms. In this study, we aimed to create a molecular map of AF and find the distinct molecular programmes underlying cell type-specific atrial remodelling and AF progression. Methods and results We used a sheep model of long-standing, tachypacing-induced AF, sampled right and left atrial tissue, and isolated cardiomyocytes (CMs) from control, intermediate (transition), and late time points during AF progression, and performed transcriptomic and proteome profiling. We have merged all these layers of information into a meaningful three-component space in which we explored the genes and proteins detected and their common patterns of expression. Our data-driven analysis points at extracellular matrix remodelling, inflammation, ion channel, myofibril structure, mitochondrial complexes, chromatin remodelling, and genes related to neural function, as well as critical regulators of cell proliferation as hallmarks of AF progression. Most important, we prove that these changes occur at early transitional stages of the disease, but not at later stages, and that the left atrium undergoes significantly more profound changes than the right atrium in its expression programme. The pattern of dynamic changes in gene and protein expression replicate the electrical and structural remodelling demonstrated previously in the sheep and in humans, and uncover novel mechanisms potentially relevant for disease treatment. Conclusions Transcriptomic and proteomic analysis of AF progression in a large animal model shows that significant changes occur at early stages, and that among others involve previously undescribed increase in mitochondria, changes to the chromatin of atrial CMs, and genes related to neural function and cell proliferation.
Risk factors for surgical site infections using a data-driven approach

Objective The objective of this study was to identify risk factors for surgical site infection from digestive, thoracic and orthopaedic system surgeries using clinical and data-driven cut-off values. A second objective was to compare the identified risk factors in this study to risk factors identified in literature. Summary background data Retrospective data of 3 250 surgical procedures performed in large tertiary care hospital in The Netherlands during January 2013 to June 2014 were used. Methods Potential risk factors were identified using a literature scan and univariate analysis. A multivariate forward-step logistic regression model was used to identify risk factors. Standard medical cut-off values were compared with cut-offs determined from the data. Results For digestive, orthopaedic and thoracic system surgical procedures, the risk factors identified were preoperative temperature of ≥38°C and antibiotics used at the time of surgery. C-reactive protein and the duration of the surgery were identified as a risk factors for digestive surgical procedures. Being an adult (age ≥18) was identified as a protective effect for thoracic surgical procedures. Data-driven cut-off values were identified for temperature, age and CRP which can explain the SSI outcome up to 19.5% better than generic cut-off values. Conclusions This study identified risk factors for digestive, orthopaedic and thoracic system surgical procedures and illustrated how data-driven cut-offs can add value in the process. Future studies should investigate if data-driven cut-offs can add value to explain the outcome being modelled and not solely rely on standard medical cut-off values to identify risk factors.
Effects of Intestinal Microbiota on Pharmacokinetics of Crocin and Crocetin in Male Sprague-Dawley Rats

In addition to the hepatic metabolism, the role of intestinal microbiota in drug metabolism has been considered important in the biotransformation of xenobiotics. Crocin and its aglycone, crocetin, isolated from many plants, including the dried stigma of Crocus sativus and the fruit of Gardenia jasminoides, have been used in treatment of inflammation, cancer, and metabolic disorders. In this study, the effect of intestinal microbiota on the pharmacokinetics of crocin was studied following single oral treatment with 600 mg/kg crocin to male rats pre-treated with a mixture of antibiotics, such as cefadroxil, oxytetracycline, and erythromycin, for three consecutive days. Following crocin treatment, blood, urine, and feces were collected at various time points for evaluating pharmacokinetic characteristics of crocin and crocetin by using LC-MS. Results showed that intestinal absorption of crocin was relatively marginal when compared with that of crocetin, and that crocin metabolism to crocetin by intestinal microbiota would be a critical step for absorption. The present results clearly suggested that the in vivo pharmacological effects of crocin might be considered as the effects by its aglycone, crocetin, mainly, and that the metabolism of glycosidic natural products by intestinal microbiota should be considered to understand their pharmacodynamic actions.
Pince optique et microscopie de fluorescence pour l'étude de la synthèse des protéines en molécule unique

Ce memoire rapporte deux approches de la synthese des proteines a l'echelle de la molecule unique. Nous utilisons la microscopie de fluorescence en onde evanescente pour sonder l'activite traductionnelle de deux types de ribosomes. Les premiers, issus d'E. Coli (organisme procaryote), sont mutes afin de les marquer d'un nanocristal semiconducteur (QD). La fin de la traduction, qui correspond au decrochage du ribosome de l'ARNm lorsque celui-ci atteint le codon stop, est alors mise en evidence par la disparition du QD de la surface de l'echantillon. Le deuxieme type de ribosome etudie est quant a lui extrait de cellules de lapins (organisme eucaryote) et est dit "sauvage", c'est a dire qu'il n'a pas subi de modification, tandis qu'un oligonucleotide marque d'un fluorophore est hybride a l'ARNm. L'activite helicase du ribosome lui permettant de separer deux brins complementaires, l'oligonucleotide et donc le fluorophore disparaissent en meme temps que le ribosome parcourt l'ARNm, permettant ainsi de sonder l'activite du ribosome. Nous donnons pour ces deux types de ribosomes une vitesse moyenne de la traduction dans des milieux contenant les facteurs de la traduction issus d'extraits cellulaires.La deuxieme approche de la synthese des proteines porte sur les proprietes de l'ARNm, support de l'information genetique codant pour la sequence des proteines. Nous avons developpe un montage de pince optique permettant de manipuler et caracteriser les proprietes mecaniques d'oligonucleotides, ainsi qu'une methode originale de calibration de ce piege optique. La coherence de nos mesures sur l'etirement d'un double brin d'ADN avec la litterature nous permettra de poursuivre notre etude sur la mesure des forces necessaires pour ouvrir une structure secondaire de l'ARNm.