Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions between Soil Bacterial Diversity and Plant-Parasitic Nematodes in Soybean Plants

Root-knot and root-lesion nematodes cause losses of billions of dollars every year to agriculture worldwide. Traditionally, they are controlled by using chemical nematicides, which in general have a negative impact on the environment and human health. ABSTRACT Plant-parasitic nematodes are an important group of pests causing economic losses in agriculture worldwide. Among the plant-parasitic nematodes, the root-knot (Meloidogyne spp.) and root-lesion nematodes (Pratylenchus spp.) are considered the two most important ones affecting soybeans. In general, they damage soybean roots, causing a reduction of about one-third in productivity. The soil microbial community can exert a suppressive effect on the parasitism of plant-parasitic nematodes. Here, we investigated the effects of soil bacterial diversity on Meloidogyne javanica (Meloidogyne-assay) and Pratylenchus brachyurus (Pratylenchus-assay) suppression by manipulating microbial diversity using the dilution-to-extinction approach in two independent experiments under controlled conditions. Furthermore, we recorded the changes in the soil microbial community induced by plant-parasitic nematode infection. In Meloidogyne-assay, microbial diversity reduced the population density of M. javanica and improved plant performance. In Pratylenchus-assay, microbial diversity sustained the performance of soybean plants even at high levels of P. brachyurus parasitism. Each nematode population affected the relative abundance of different bacterial genera and altered the core microbiome of key groups within the bacterial community. Our findings provide fundamental insights into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants. IMPORTANCE Root-knot and root-lesion nematodes cause losses of billions of dollars every year to agriculture worldwide. Traditionally, they are controlled by using chemical nematicides, which in general have a negative impact on the environment and human health. Fortunately, the soil microbial community may suppress these pests, acting as an environmentally friendly alternative to control nematodes. However, the effects of soil microbial diversity on the parasitism of plant-parasitic nematodes still poorly understood. In this study, we provide fundamental insight into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants, which may be useful for the development of new strategies to control these phytopathogens.
Linker histone H1FOO is required for bovine preimplantation development by regulating lineage specification and chromatin structure

Abstract Linker histone H1 binds to the nucleosome and is implicated in the regulation of the chromatin structure and function. The H1 variant H1FOO is heavily expressed in oocytes and early embryos. However, given the poor homology of H1FOO among mammals, the functional role of H1FOO during preimplantation embryonic development remains largely unknown, especially in domestic animals. Here, we find that H1FOO is not only expressed in oocytes and preimplantation embryos but granulosa cells and spermatids in cattle. We then demonstrate that the interference of H1FOO results in preimplantation embryonic developmental arrest in cattle using either RNA editing or Trim-Away approach. H1FOO depletion leads to a compromised expression of critical lineage-specific genes at the morula stage and affects the establishment of cell polarity. Interestingly, H1FOO depletion causes a significant increase in the expression of genes encoding other linker H1 and core histones. Concurrently, there is an increase of H3K9me3 and H3K27me3, two markers of repressive chromatin and a decrease of H4K16ac, a marker of open chromatin. Importantly, overexpression of bovine H1FOO results in severe embryonic developmental defects. In sum, we propose that H1FOO controls the proper chromatin structure that is crucial for the fidelity of cell polarization and lineage specification during bovine preimplantation development.
Successful treatment with MEK‐inhibitor in a patient with NRAS ‐related cutaneous skeletal hypophosphatemia syndrome

Cutaneous skeletal hypophosphatemia syndrome (CSHS) is caused by somatic mosaic NRAS variants and characterized by melanocytic/sebaceous naevi, eye, and brain malformations, and FGF23‐mediated hypophosphatemic rickets. The MEK inhibitor Trametinib, acting on the RAS/MAPK pathway, is a candidate for CSHS therapy. A 4‐year‐old boy with seborrheic nevus, eye choristoma, multiple hamartomas, brain malformation, pleural lymphangioma and chylothorax developed severe hypophosphatemic rickets unresponsive to phosphate supplementation. The c.182A > G;p.(Gln61Arg) somatic NRAS variant found in DNA from nevus biopsy allowed diagnosing CSHS. We administered Trametinib for 15 months investigating the transcriptional effects at different time points by whole blood RNA‐seq. Treatment resulted in prompt normalization of phosphatemia and phosphaturia, catch‐up growth, chylothorax regression, improvement of bone mineral density, reduction of epidermal nevus and hamartomas. Global RNA sequencing on peripheral blood mononucleate cells showed transcriptional changes under MEK inhibition consisting in a strong sustained downregulation of signatures related to RAS/MAPK, PI3 kinase, WNT and YAP/TAZ pathways, reverting previously defined transcriptomic signatures. CSHS was effectively treated with a MEK inhibitor with almost complete recovery of rickets and partial regression of the phenotype. We identified “core” genes modulated by MEK inhibition potentially serving as surrogate markers of Trametinib action.
Environmental dimensions during and after the Nagorno‐Karabakh conflict of 2020

The 44‐day war between Azerbaijan and Armenia in Nagorno‐Karabakh in 2020 resulted in significant environmental damage. This brief communication presents two aspects of harm to the region's biodiverse‐rich primary forests—(1) hundreds of conflict‐linked landscape fires during and (2) widespread development postconflict, without a due environmental assessment. The use of novel mixed methods research, including satellite remote sensing, has allowed an independent and open response to some of the environmental narratives, which were weaponized by both conflict parties. Integr Environ Assess Manag 2023;19:360–365. © 2022 SETAC
Approaches to improving symptom appraisal: a systematic literature review

Objectives Poor symptom appraisal (detection, interpretation and response to symptoms) plays a major role in prolonged prediagnosis interval in various health conditions. Theories and models have been proposed to study the symptom appraisal process but how they could be employed to improve symptom appraisal remains unclear. We therefore aimed to review approaches to improving symptom appraisal in the literature and to develop a theoretical framework that could guide the development of approaches to improving symptom appraisal among individuals in the general population. Design Systematic review. Data sources Medline, Web of Science, PsycINFO, Embase, CINAHL and Scopus were searched from inception to 30 March 2021. Eligibility criteria We included original articles in English in which approaches to improve the detection, interpretation or response to symptoms for symptomatic individuals were described. We excluded articles in which approaches were developed to improve symptom appraisal among healthcare professionals. Data extraction and synthesis A predefined data extraction form was used to extract the development, characteristics and evaluation of approaches to improving symptom appraisal. This formed the basis for the narrative synthesis. Results Of 19 046 publications identified from the literature search, 112 were selected for full-text review and 29 approaches comprising provision of knowledge of symptoms/signs and additional components (eg, symptom self-examination and comparison) for symptom appraisal were included in the synthesis. Less than half (41.4%) of these approaches were developed based on theories/models. Interestingly, despite the variety of theories/models adopted in developing these approaches, the components of these approaches were similar. Conclusion Symptom appraisal is an essential process in a patient’s journey that can be targeted to facilitate early diagnosis but is largely unstudied. Building on the literature, we proposed a theoretical framework and approaches to improving symptom appraisal. This could facilitate early identification of a variety of health conditions in the general population. Trial registration number CRD42021279500.
Identification of early-induced broadly neutralizing activities against transmitted founder HIV strains

Objectives: Broadly neutralizing antibodies have been proposed as key actors for HIV vaccine development. However, they display features of highly matured antibodies, hampering their induction by vaccination. As protective broadly neutralizing antibodies should be induced rapidly after vaccination and should neutralize the early-transmitted founder (T/F) viruses, we searched whether such antibodies may be induced following HIV infection. Design: Sera were collected during acute infection (Day 0) and at viral set point (Month 6/12) and the neutralizing activity against T/F strains was investigated. Neutralizing activity in sera collected from chronic progressor was analyzed in parallel. Methods: We compared neutralizing activity against T/F strains with neutralizing activity against non-T/F strains using the conventional TZM-bL neutralizing assay. Results: We found neutralizing antibodies (nAbs) preferentially directed against T/F viruses in sera collected shortly after infection. This humoral response evolved by shifting to nAbs directed against non-T/F strains. Conclusion: Although features associated with nAbs directed against T/F viruses need further investigations, these early-induced nAbs may display lesser maturation characteristics; therefore, this might increase their interest for future vaccine designs.
Evaluation of Cerebrovascular Reactivity and Vessel-Wall Imaging in Patients With Prior COVID-19: A Prospective Case-Control MRI Study.

Background: SARS-CoV2 infection is associated with acute stroke, possibly caused by viral tropism to the vascular endothelium. Whether cerebrovascular endothelial dysfunction and inflammation persist after acute infection is poorly understood. Objective: To assess the association of prior SARS-CoV2 infection with cerebrovascular reactivity (CVR) and vessel-wall imaging (VWI) abnormalities, as well as to explore the association of CVR impairment with post-COVID neurologic conditions. Methods: This prospective study enrolled fifteen participants with prior SARS-CoV2 infection (11 female, 4 male; mean age, 43 years; mean, 238 days after infection; 3 with prior critical illness, 12 with prior mild illness; seven with post-COVID neurologic conditions) and ten never-infected controls participants (8 female, 2 male; mean age, 44 years) from July 1st 2021 to February 9th, 2022. Participants underwent research MRI that included arterial spin labeling perfusion imaging with acetazolamide stimulus to measure cerebral blood flow (CBF) and calculate CVR. Examinations also included VWI, performed using a contrast-enhanced black-blood 3D T1-weighted sequence. An age- and sex-adjusted linear model was used to assess associations between CVR and prior infection. A t test was used to assess associations between CVR and post-COVID neurologic conditions in previously infected participants. A difference of proportions test was used to assess associations between VWI abnormalities and infection status. Results: Mean whole-cortex CBF following acetazolamide administration was greater in never-infected than in previously infected participants (73.8±13.2 vs 60.5±15.8 mL/100 gm/min; p=.04). Whole-brain CVR was lower in previously infected than in never-infected participants (difference of -8.9 ml/100g/min; p<.001); significantly lower CVR was also observed in previously infected participants after excluding those with prior critical illness. Among previously infected participants, CVR was smaller in those with than without post-COVID neurologic conditions, although this difference was not significant (16.9 vs 21.0 ml/100g/min; p=.22). Six of fifteen (40%) previously infected participants versus one of ten (10%) never-infected participants had at least one VWI abnormality (p=.18). All VWI abnormalities were consistent with atherosclerosis. Conclusion: SARS-CoV2 infection is associated with chronic CVR impairment. The mechanistic basis is unknown from this study. Clinical Impact: Future studies are needed to determine the clinical implications arising from SARS-CoV2-associated CVR impairment.
The Effects of Training Load During Dietary Intervention Upon Fat Loss: A Randomized Crossover Trial

ABSTRACT Purpose: To date no studies have compared resistance training loading strategies combined with dietary intervention for fat loss. Methods: Thus, we performed a randomised crossover design comparing four weeks of heavier- (HL; ~80% 1RM) and lighter-load (LL; ~60% 1RM) resistance training, combined with calorie restriction and dietary guidance, including resistance trained participants (n=130; males=49, females=81). Both conditions performed low-volume, (single set of 9 exercises, 2x/week) effort matched (to momentary failure), but non-work-matched protocols. Testing was completed pre- and post-each intervention. Fat mass (kg) was the primary outcome, and a smallest effect size of interest (SESOI) was established at 3.3% loss of baseline bodyweight. Body fat percentage, lean mass, and strength (7-10RM) for chest press, leg press, and pull-down exercises were also measured. An 8-week washout period of traditional training with normal calorie interspersed each intervention. Results: Both interventions showed small statistically equivalent (within the SESOI) reductions in fat mass (HL: -0.67 kg [95%CI -0.91 to 0.42]; LL: -0.55 kg [95%CI -0.80 to -0.31]) which were also equivalent between conditions (HL – LL: -0.113 kg [95%CI -0.437 kg to 0.212 kg]). Changes in body fat percentage and lean mass were also minimal. Strength increases were small, similar between conditions, and within a previously determined SESOI for the population included (10.1%). Conclusions: Fat loss reductions are not impacted by resistance training load; both HL and LL produce similar, yet small, changes to body composition over a 4-week intervention. However, the maintenance of both lean mass and strength highlights the value of resistance training during dietary intervention.
An overview of suicides related to motor vehicles

Although vehicles may be used in a wide variety of suicides, this has not been a focus in the forensic literature. Thus, an analysis of coronial autopsy reports at Forensic Science SA, Adelaide, South Australia over a 16-year period from January 2005 to December 2020 was undertaken to provide an overview of cases in which it was considered that a vehicle had been integral to the successful completion of a suicide. De-identified details were collected from all cases in which a vehicle had facilitated or been used as a method of suicide. A number of different types of vehicle-related suicide methods were identified, including cases where vehicles had been used as secure places for suicide or where the vehicle had been used to cause significant blunt force trauma or to enter a lethal environment such as water. Specific examples were taken from the following categories: (1) inhalation of gas, (2) drug toxicity, (3) hanging or ligature strangulation, (4) self-immolation, (5) drowning, (6) vehicle collision, (7) driving off a cliff, (8) jumping or lying in front of a vehicle and (9) the use of more than one method (i.e. complex). This report is not intended to provide an epidemiological analysis of car-related suicides. Instead, the details of selected cases have been used to illustrate the spectrum of methods that may be used in vehicle-assisted suicides.
Ecological Note about the Impact on the Marine Ecosystem of an Underwater Pipeline for the Transport of Natural Gas

The structure of the soft-bottom macrozoobenthic community of a Northern Adriatic Sea area had been studied and characterized both quantitatively and qualitatively, as part of a wider environmental monitoring project, elaborated and carried out by the Institute for Environmental Protection and Research (ISPRA). The aim of this project was to identify the possible effects on the marine ecosystem of the construction and presence of a pipeline that connects an offshore Liquefied Natural Gas (LNG) re-gasifying Terminal to the coast. In order to study the possible alterations of the macrozoobenthic community due to anthropogenic activities during the ante operam, construction and post operam phases, univariate and multivariate statistical analyses of the soft-bottom macrozoobenthos community data were carried out. The data acquired during the monitoring activities along the pipeline showed no long-term alterations of the macrozoobenthic community. The studied macrozoobenthic assemblage presented ecological charateristics in line with that typical of a coastal-wide transept of the Northern Adriatic.
Robust adaptive observers for unknown linear exosystems

Given a measured scalar signal generated by an unknown linear exosystem with simple eigenvalues on the imaginary axis whose order is unknown, we address the problem of designing a robust adaptive exosystem of fixed order that is able to reproduce the measured signal within an error. The magnitude of such an error clearly depends on the unmodeled dynamics and vanishes if the order of the adaptive exosystem is greater than or equal to the order of the unknown exosystem. Adaptive exosystems are useful for prediction purposes, to generate successive time derivatives of the measured signal for control purposes (PID, model predictive control and feedback linearization) and in the design of regulators. The posed problem can also be interpreted as an adaptive synchronization problem in the presence of high frequency unmodeled dynamics for linear systems. It can also be viewed as the design of an estimator of m frequencies, amplitudes and phases by processing a signal constituted by the sum of r ≥ m sinusoidal terms. The posed problem will be solved by using the theory of robust adaptive observers and the key concept of persistency of excitation. Copyright © 2012 John Wiley & Sons, Ltd.
Frege and the Logic of Sense and Reference

PREFACE, ABBREVIATIONS, 1. THE NEED FOR A LOGICAL CALCULUS FOR THE THEORY OF SINN AND BEDEUTUNG, Introduction, Frege's Project: Logicism and the Notion of Begriffsschrift, The Theory of Sinn and Bedeutung, The Limitations of the Begriffsschrift, Filling the Gap, 2. THE LOGIC OF THE GRUNDGESETZE, Logical Language and the Content of Logic, Functionality and Predication, Quantifiers and Gothic Letters, Roman Letters: An Alternative Notation for Generality, Value-Ranges and Extensions of Concepts, The Syntactic Rules of the Begriffsschrift, The Axiomatization of Frege's System, Responses to the Paradox, 3. SINNE AND GEDANKEN, The Nature of Sinne Generally, The Sinne of Incomplete Expressions and the Composition of Gedanken, Context Principle, Priority Thesis, and Multiple Analyses: Challenges to Compositionality, The Identity Conditions of Sinne and Gedanken, 4. CHURCH'S LOGIC OF SENSE AND DENOTATION, Overview, The Method of Transparent Intensional Logic, Alternatives (0), (1) and (2) and Synonymous Isomorphism, The Formulation of the Systems, Problems in Church's Logic of Sense and Denotation, The UnFregean Elements of Church's Logic of Sense and Denotation, 5. A LOGICAL CALCULUS FOR THE THEORY OF SINN AND BEDEUTUNG, Basic Features, Names and Variables for Sinne, The New Constants of the Expanded Language, Syntactic Rules of the Expanded Language, Axioms and Inference Rules of the Expanded Calculi, Inferences Involving Propositional Attitudes and Quantifying In, Difficulties with the Expanded Calculi, 6. COMPARISON WITH RUSSELL AND OTHER THINKERS, "Solatium miseris, socios habuisse malorum. ", Russell's Ontology of Propositions, Russell and the Principles of Mathematics Appendix B Paradox, Frege and the Principles of Mathematics Appendix B Paradox, Lessons Learned from Russell, Other Systems of Intensional Logic, 7. POSSIBLE REVISIONS TO FREGE'S PHILOSOPHY, Adequate versus Ad Hoc Solutions, A Cantorian Analysis of the Difficulties, Dropping Classes and/or Concepts, Reducing the Number of Sinne and Gedanken, Ramification as a Solution to the Paradoxes, The Justification of Ramification, Conclusion, APPENDIX: SUMMARY OF DEFINITIONS, AXIOMS AND INFERENCE RULES, BIBLIOGRAPHY, INDEX
University of Birmingham Individualised lung function trends in AATD: a need for patience in order to provide patient centred management?

Background: Chronic obstructive pulmonary disease (COPD) is characterized by fixed airflow obstruction and accelerated decline of forced expired volume in 1 second (FEV 1 ). Alpha-1-antitrypsin deficiency is a genetic cause of COPD and associated with more rapid decline in lung function, even in some never smokers (NS) but the potential for individualized assessment to reveal differences when compared to group analyses has rarely been considered. Methods: We analyzed decline in post-bronchodilator FEV 1 and gas transfer (% predicted) over at least 3 years (mean = 6.11, 95% CI 5.80–6.41) in our unique data set of 482 patients with alpha-1-antitrypsin deficiency (PiZ) to determine individual rates of decline, implications for prognosis, and potential clinical management. Findings: There was a marked variation in individual rates of FEV 1 decline from levels consistent with normal aging (observed in 23.5% of patients with established COPD, 57.5% of those without) to those of rapidly declining COPD. Gas transfer did not decline in 12.8% of NS and 20.7% of ex-smokers with established COPD (33.3% and 25.0%, respectively, for those without COPD). There was no correlation between decline in gas transfer and FEV 1 for those with COPD, although a weak relationship existed for those without ( r = 0.218; P , 0.025). Conclusion: These data confirm differing individual rates of lung function decline in alpha-1-antitrypsin deficiency, indicating the importance of comprehensive physiological assessment and a personalized approach to patient management.
Evolving Ensembles

An ensemble forecast method using evolutionary programming, including various forms of genetic ex- change,disease,mutation,andthetrainingof solutionswithinecological niches,ispresented.A2344-member ensemble generated in this way is tested for 60-h minimum temperature forecasts for Chicago, Illinois. The ensemble forecasts are superior in both ensemble average root-mean-square error and Brier skill score to those obtained from a 21-member operational ensemble model output statistics (MOS) forecast. While both ensembles are underdispersive, spread calibration produces greater gains in probabilistic skill for the evolutionary program ensemble than for the MOS ensemble. When a Bayesian model combination cali- bration is used, the skill advantage for the evolutionary program ensemble relative to the MOS ensemble increases for root-mean-square error, but decreases for Brier skill score. Further improvement in root-mean- square error is obtained when the raw evolutionary program and MOS forecasts are pooled, and a new Bayesian model combination ensemble is produced. Future extensions to the method are discussed, including those capable of producing more complex forms, those involving 1000-fold increases in training populations, and adaptive methods.