bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Adenosine Pathway and Human Immunodeficiency Virus-Associated Inflammation
Authors: Hixson Emily A , Borker Priya V , Jackson Edwin K , Macatangay Bernard J 
Published: July 2021

AbstractHuman immunodeficiency virus (HIV) is associated with an increased risk of age-associated comorbidities and mortality compared to people without HIV. This has been attributed to HIV-associated chronic inflammation and immune activation despite viral suppression. The adenosine pathway is an established mechanism by which the body regulates persistent inflammation to limit tissue damage associated with inflammatory conditions. However, HIV infection is associated with derangements in the adenosine pathway that limits its ability to control HIV-associated inflammation. This article reviews the function of purinergic signaling and the role of the adenosine signaling pathway in HIV-associated chronic inflammation. This review also discusses the beneficial and potential detrimental effects of pharmacotherapeutic strategies targeting this pathway among people with HIV.
Comparison between Annona squamosa, Annona cherimolia and Annona atemoya ethanolic extracts extenuative impact against oxidative stress, inflammation and apoptosis in rat kidney induced by Ifosfamid
Authors: Abd-Elrazek Areeg , Shapana Hadeer , Shukry Wafaa , Galilah Doaa 
Published: July 2021

Abstract
Up-regulation of NF-kB and depletion of glutathione are acceptable mechanisms of Ifosfamide (IFO) renal toxicity. This investigation elucidates the role of free radicals, inflammatory and apoptotic markers in ifosfamide-induced rentoxicity and the protection of Annona species planted in Egypt (squamosa, cherimolia), and the hybrid between them (atemoya). Annona seeds extracts were prepared and phytochemical analyses were assessed. Rats were injected with saline or with IFO alone or in combination with Annona squamosa or Annona cherimolia or Annona atemoya orally. Biochemical, gene expression, histological and immune-histological examinations were performed. The results demonstrated that IFO elevated creatinine, sodium, magnesium and urea, along with depleted serum potassium and albumin levels. IFO caused a significant reduction in renal GSH, significant increases in renal MDA, and NOx, and up-regulated iNOS. In addition, IFO treatment showed increase mRNA and protein expression of NF-kB, while down-regulated mRNA and protein expression of Bcl-2, and strong immunohistological expression of caspase-3 as well as BAX in kidney tissues. Different Annona seed extracts significantly enhanced the sharpness of renal injury and improved oxidant responses induced by IFO. Annona extracts down-regulated iNOS, NF-kB expressions, as well as, down-regulated caspase-3 and BAX immunohistological expressions, and up-regulated Bcl-2 expression. A. squamosa showed a more pronounced protective effect. Histopathological examination was in accordance with biochemical results. Recent results suggest that Annona species ameliorated the renal toxicity of ifosfamide by down-regulation of NOx, iNOS, NF-kB, BAX, caspase-3 and MDA in addition to up-regulation of GSH and Bcl-2.
Hypercapnia versus normocapnia for emergence from desflurane anaesthesia
Authors: Shinohara Ayako , Nozaki-Taguchi Natsuko , Yoshimura Akiko , Hasegawa Makoto , Saito Kei , Okazaki Junko , Kitamura Yuji , Sato Yasunori , Isono Shiroh 
Published: July 2021

BACKGROUND
Rapid emergence from general anaesthesia is desirable only if safety is not sacrificed. Mechanical hyperventilation during hypercapnia produced by carbon dioxide infusion into the inspired gas mixture or by rebreathing was reported to shorten emergence time from inhalation anaesthesia.

OBJECTIVES
To test the hypothesis that hypercapnia produced by hypoventilation before desflurane cessation shortens emergence time from general anaesthesia (primary hypothesis) and reduces undesirable cardiorespiratory events.

DESIGN
A single-blinded randomised controlled study.

SETTING
A single university hospital.

PATIENTS
Fifty adult patients undergoing elective abdominal surgery under general anaesthesia using desflurane inhalation and intra-operative epidural anaesthesia.

INTERVENTION
The patients were randomly assigned to either the normocapnia or hypercapnia group.

MAIN OUTCOME MEASURES
Emergence time from desflurane anaesthesia and comparison of the incidence of 11 predefined undesirable cardiorespiratory events during and after emergence from anaesthesia between the groups.

RESULTS
Forty-six patients were included in the analysis. End-tidal carbon dioxide concentrations at cessation of desflurane were 35 ± 6 mmHg (mean ± SD) and 52 ± 6 mmHg in normocapnia (n = 23) and hypercapnia groups (n = 23), respectively. Emergence time was significantly faster in the hypercapnia group than the normocapnia group: 9.4 ± 2.4 min, hypercapnia: 5.5 ± 2.6 min, (P < 0.001) with a difference of 3.8 min on average (95% CI: 2.4 to 5.3). Spontaneous breathing established before recovery of consciousness was more evident in hypercapnia patients (normocapnia: 13%, hypercapnia: 96%, P < 0.001). Hypercapnia patients had more episodes of bradypnoea and apnoea before emergence of consciousness. In contrast, after tracheal extubation, incidences of bradypnoea and hypopnoea were more common in the normocapnia group. Undesirable cardiovascular events were not common, and no group differences were observed during emergence and postextubation periods.

CONCLUSION
Hypoventilation-induced hypercapnia before desflurane cessation shortens the emergence time without causing additional clinically significant undesirable events.

TRIAL REGISTRATION
UMIN Clinical Trials Registry (UMIN000020143) https://upload.umin.ac.jp/cgi-open-bin/ctr/ctr.cgi?function=brows&recptno=R000023266&language=E
Walter Jakob Gehring. 20 March 1939—29 May 2014
Authors: ForMemRS Ginés Morata , Affolter Markus 
Published: July 2021

Walter Jakob Gehring was one of the most influential developmental biologists of the last 50 years. First as a student with Professor Ernst Hadorn in Zurich, later as a postdoc in Yale and finally as group leader in Basel, he was involved in a number of major discoveries that had a profound impact in the understanding of the genetic and molecular mechanisms of animal development, not only for the fruit fly
Drosophila
but for the whole animal kingdom.

Throughout his career Gehring demonstrated an outstanding ability to recognize key problems and then to push experimental work on these problems with great energy. Gehring pioneered the application of molecular techniques to developmental problems, an approach that was at the root of many of his contributions. His laboratory was involved in a number of key findings: the first cloning of a Hox gene, the discovery of the homeobox, the enhancer trap method, and the remarkable conservation of features of the visual system in metazoans.
He was an excellent speaker, with special ability to emphasize the relevant aspects of his work and to draw conclusions of general interest. This attracted a number of gifted students and postdocs who were key for the success of his research group.
Passionately interested in science, he was also very excited about other scientific disciplines; he was an accomplished bird watcher and was also fascinated by marine life. But he also had non-scientific interests, too; he claimed to be an excellent football player and frequently commented that he had had to decide whether to be a scientist or a professional footballer. He decided on the former, but one wonders if he might have been a Swiss version of Messi or Ronaldo.
Severity of SARS-CoV-2 reinfections in second wave determines likelihood of mild endemicity
Authors: Lavine Jennie S , Bjornstad Ottar N , Coombs Daniel , Antia Rustom 
Published: July 2021

AbstractImmunity to SARS-CoV-2 is building up globally, but will this be sufficient to prevent future COVID-19 epidemics in the face of variants and waning immunity? Manaus, Brazil offers a concerning glimpse of what may come: six months after the majority of the city’s population experienced primary infection, a second wave with a new strain resulted in more deaths than the first wave. Current hypotheses for this surge rely on prior immunity waning due to time and antigenic distance. Here we show this hypothesis predicts a severe endemic state. We propose an alternative hypothesis in which individuals infected in the first wave lose protection against transmission but retain immunity against severe disease and show this hypothesis is equally compatible with existing data. In this scenario, the increased number of deaths is due to an increased infection fatality ratio (IFR) for primary infections with the new variant. This alternative predicts a mild endemic state will be reached within decades. Collecting data on the severity of reinfections and infections post-vaccination as a function of time and antigenic distance from the original exposure is crucial for optimizing control strategies.
Ethnic disparities in incident SARS-CoV-2 infections became wider during the second wave of SARS-CoV-2 in Amsterdam, the Netherlands: a population-based longitudinal study
Authors: Coyer Liza , Boyd Anders , Schinkel Janke , Agyemang Charles , Galenkamp Henrike , Koopman Anitra D M , Leenstra Tjalling , van Duijnhoven Yvonne T H P , van Charante Eric P Moll , van den Born Bert-Jan H , Lok Anja , Verhoeff Arnoud , Zwinderman Aeilko H , Jurriaans Suzanne , Stronks Karien , Prins Maria 
Published: July 2021

AbstractBackgroundSurveillance data in high-income countries have reported more frequent SARS-CoV-2 diagnoses in ethnic minority groups. We examined the cumulative incidence of SARS-CoV-2 and its determinants in six ethnic groups in Amsterdam, the Netherlands.MethodsWe analyzed participants enrolled in the population-based HELIUS cohort, who were tested for SARS-CoV-2-specific antibodies and answered COVID-19-related questions between June 24-October 9, 2020 (after the first wave) and November 23, 2020-March 31, 2021 (during the second wave). We modeled SARS-CoV-2 incidence from January 1, 2020-March 31, 2021 using Markov models adjusted for age and sex. We compared incidence between ethnic groups over time and identified determinants of incident infection within ethnic groups.Findings2,497 participants were tested after the first wave; 2,083 (83·4%) were tested during the second wave. Median age at first visit was 54 years (interquartile range=44-61); 56·6% were female. Compared to Dutch-origin participants (15·9%), cumulative SARS-CoV-2 incidence was higher in participants of South-Asian Surinamese (25·0%; adjusted hazard ratio [aHR]=1·66;95%CI=1·16-2·40), African Surinamese (28·9%;aHR=1·97;95%CI=1·37-2·83), Turkish (37·0%;aHR=2·67;95%CI=1·89-3·78), Moroccan (41·9%;aHR=3·13;95%CI=2·22-4·42), and Ghanaian (64·6%;aHR=6·00;95%CI=4·33-8·30) origin. Compared to those of Dutch origin, differences in incidence became wider during the second versus first wave for all ethnic minority groups (all p for interaction<0.05), except Ghanaians. Having household members with suspected SARS-CoV-2 infection, larger household size, and low health literacy were common determinants of SARS-CoV-2 incidence across groups.InterpretationSARS-CoV-2 incidence was higher in the largest ethnic minority groups of Amsterdam, particularly during the second wave. Prevention measures, including vaccination, should be encouraged in these groups.FundingZonMw, Public Health Service of Amsterdam, Dutch Heart Foundation, European Union, European Fund for the Integration of non-EU immigrants.
hafeZ: Active prophage identification through read mapping
Authors: Turkington Christopher J. R. , Abadi Neda Nezam , Edwards Robert A. , Grasis Juris A. 
Published: July 2021

AbstractSummaryBacteriophages that have integrated their genomes into bacterial chromosomes, termed prophages, are widespread across bacteria. Prophages are key components of bacterial genomes, with their integration often contributing novel, beneficial, characteristics to the infected host. Likewise, their induction—through the production and release of progeny virions into the surrounding environment—can have considerable ramifications on bacterial communities. Yet, not all prophages can excise following integration, due to genetic degradation by their host bacterium. Here, we present hafeZ, a tool able to identify ‘active’ prophages (i.e. those undergoing induction) within bacterial genomes through genomic read mapping. We demonstrate its use by applying hafeZ to publicly available sequencing data from bacterial genomes known to contain active prophages and show that hafeZ can accurately identify their presence and location in the host chromosomes.Availability and ImplementationhafeZ is implemented in Python 3.7 and freely available under an open-source GPL-3.0 license from https://github.com/Chrisjrt/hafeZ. Bugs and issues may be reported by submitting them via the hafeZ github issues page.Contactcturkington@ucmerced.edu or chrisjrt1@gmail.com
Forest tree species composition and abiotic site conditions drive soil fungal communities and functional groups
Authors: Likulunga Likulunga Emmanuel , Rivera Pérez Carmen Alicia , Schneider Dominik , Daniel Rolf , Polle Andrea 
Published: July 2021

AbstractSoil fungi, especially the functional guilds of saprotrophic and mycorrhizal fungi, play a central role in ecosystem processes by degrading litter, mining for mineral nutrients and linking above- and belowground nutrient fluxes. Fungal community structures are influenced by abiotic habitat filters and management decisions such as tree species selection. Yet, the implications of the enrichment of temperate forests consisting of tree species in their natural range with non-native tree species on soil fungal diversity and their functional groups are unknown. Here, we studied fungal communities in 40 plots located in two regions differing in site conditions (nutrient content and soil moisture) in forests composed of European beech, Norway spruce and Douglas-fir (non-native) and mixtures of beech with either spruce or Douglas-fir. We hypothesized that fungal community structures are driven by soil resources and tree species composition, generally resulting in higher fungal diversity in mixed than in mono-specific forests. We further hypothesized that Douglas-fir has a negative effect on ectomycorrhizal fungal species richness compared to native species, whereas saprotrophic fungal richness is unaffected. We found strong separation of fungal communities between nutrient-rich and nutrient-poor sites and taxonomic divergence between beech and conifer fungal communities and an intermediate pattern in mixed forests. Mycorrhizal species richness did not vary with forest type, but the relative abundance of mycorrhizal species was lower in Douglas-fir and in mixed beech-Douglas-fir forests than in spruce or beech- spruce mixture. Conifer forests contained higher relative abundances of saprotrophic fungi than mono-specific beech forests. Among 16 abundant fungal orders in soil, two containing saprotrophic fungi (Tremellales, Hymenochaetales) were enriched in conifer forests, regardless of site conditions and tree species mixture. The other fungal orders, including those dominated by mycorrhizal fungi (Russulales, Boletales, Atheliales, Cantharellales) showed variable patterns depending on site conditions and tree species. In conclusion, Douglas-fir mono-specific or mixed forests show no loss of fungal species richness, but a shift in functional composition towards saprotrophic fungi.
The mystery of COVID-19 reinfections: A global systematic review and meta-analysis of 577 cases
Authors: Dhillon Rubaid Azhar , Qamar Mohammad Aadil , Irfan Omar , Gilani Jaleed Ahmed , Waqar Usama , Sajid Mir Ibrahim , Mahmood Syed Faisal 
Published: July 2021

AbstractBackgroundAs the COVID-19 pandemic rages on, reports on disparities in vaccine roll out alongside reinfection and reactivation from previously recovered cases have been emerging. With newer waves and variants of COVID-19, we conducted a systematic review to assess the determinants and disease spectrum of COVID-19 reinfection.MethodsA comprehensive search covering relevant databases was conducted for observational studies reporting Polymerase Chain Reaction (PCR) confirmed infection and reinfection cases. Quality assessment tool developed by the National Institute of Health (NIH) for assessment of case series was used. Meta-analyses were performed using RevMan 5.3 for pooled proportions of findings in first infection and reinfection with 95% confidence interval (CI).ResultsEighty-one studies reporting 577 cases were included from 22 countries. The mean age of patients was 46.2±18.9 years with males accounting for 45.8% of the study population while 179 (31.0%) cases of comorbidities were reported. The average time duration between first infection and reinfection was 63.6±48.9 days. During first infection and reinfection, fever was the most common symptom (41.4% and 36.4%, respectively) whilst anti-viral therapy was the most common treatment regimen administered (44.5% and 43.0%, respectively). Overall, comparable odds of symptomatic presentation and management were reported in the two infections. However, a higher Intensive Care Unit (ICU) admission rate was observed in reinfection compared to first infection (10 vs 3). Ten deaths were reported with 565 patients fully recovering. Respiratory failure was the most common cause of death (7/10 deaths). Seventy-two studies were determined to be of good quality whilst nine studies were of fair quality.ConclusionAs the first global-scale systematic review of its kind, our findings support immunization practices given increased ICU admissions and mortality in reinfections. Our cohort serves as a guide for clinicians and authorities for devising an optimal strategy for controlling the pandemic.
Disrupted PGR-B and ESR1 signaling underlies preconceptional defective decidualization linked to severe preeclampsia
Authors: Garrido-Gomez Tamara , Castillo-Marco Nerea , Clemente-Ciscar Mónica , Cordero Teresa , Muñoz-Blat Irene , Amadoz Alicia , Jimenez-Almazan Jorge , Monfort Rogelio , Climent Reyes , Perales Alfredo , Simón Carlos 
Published: July 2021

AbstractDecidualization of the uterine mucosa drives the maternal adaptation to invasion by the placenta. Appropriate depth of placental invasion is needed to support a healthy pregnancy; shallow invasion is associated with the development of severe preeclampsia (sPE). Maternal contribution to sPE through failed decidualization is an important determinant of placental phenotype. However, the molecular mechanism underlaying the in vivo defect linking decidualization to sPE is unknown. Here, we discover the footprint encoding this decidualization defect comprising of 166 genes using global gene expression profiling in decidua from women who developed sPE in a previous pregnancy. This signature allowed us to effectively segregate samples into sPE and control groups. Estrogen receptor 1 (ESR1) and progesterone receptor B (PGR-B) were found highly interconnected with the dynamic network of defective decidualization fingerprint. ESR1 and PGR-B gene expression and protein abundance were remarkably disrupted in sPE. Thus, the transcriptomic signature of impaired decidualization implicates dysregulated hormonal signaling in the decidual endometria in women who developed sPE. These findings reveal a potential footprint that may be leverage for a preconception or early prenatal screening of sPE risk, thus improving prevention and early treatments.
Proteome Profiling of Cerebrospinal Fluid Reveals Novel Biomarker Candidates for Parkinson’s Disease
Authors: Karayel Ozge , Winter Sebastian Virreira , Padmanabhan Shalini , Kuras Yuliya I. , Vu Duc Tung , Tuncali Idil , Merchant Kalpana , Wills Anne-Marie , Scherzer Clemens R. , Mann Matthias 
Published: July 2021

SUMMARYParkinson’s disease (PD) is a growing burden worldwide, and despite ongoing efforts to find reliable biomarkers for early and differential diagnosis, prognosis and disease monitoring, there is no biofluid biomarker used in clinical routine to date. Cerebrospinal fluid (CSF) is collected often and should closely reflect structural and functional alterations in PD patients’ brains. Here we describe a scalable and sensitive mass spectrometry (MS)-based proteomics workflow for CSF proteome profiling to find specific biomarkers and identify disease-related changes in CSF protein levels in PD. From two independent cohorts consisting of more than 200 individuals, our workflow reproducibly quantified over 1,700 proteins from minimal sample amounts. Combined with machine learning, this identified a group of several proteins, including OMD, CD44, VGF, PRL, and MAN2B1 that were altered in PD patients or significantly correlate with clinical scores, indicative of disease progression. Interestingly, we uncovered signatures of enhanced neuroinflammation in patients with familial PD (LRRK2 G2019S carriers) as indicated by increased levels of CTSS, PLD4, HLA-DRA, HLA-DRB1, and HLA-DPA1. A comparison with urinary proteome changes in PD patients revealed a large overlap in protein composition PD-associated changes in these body fluids, including lysosomal factors like CTSS. Our results validate MS-based proteomics of CSF as a valuable strategy for biomarker discovery and patient stratification in a neurodegenerative disease like PD. Consistent proteomic signatures across two independent CSF cohorts and previously acquired urinary proteome profiles open up new avenues to improve our understanding of PD pathogenesis.
Enzyme-constrained models predict the dynamics of Saccharomyces cerevisiae growth in continuous, batch and fed-batch bioreactors
Authors: Moreno-Paz Sara , Schmitz Joep , Martins dos Santos Vitor A.P. , Suarez-Diez Maria 
Published: July 2021

AbstractGenome-scale, constraint-based models (GEM) and their derivatives are commonly used to model and gain insights into microbial metabolism. Often, however, their accuracy and predictive power are limited and enable only approximate designs. To improve their usefulness for strain and bio-process design, we studied here their capacity to accurately predict metabolic changes in response to operational conditions in a bioreactor, as well as intracellular, active reactions. We used flux balance analysis (FBA) and dynamic FBA (dFBA) to predict growth dynamics of the model organism Saccharomyces cerevisiae under different industrially relevant conditions. We compared simulations with the latest developed GEM for this organism (Yeast8) and its enzyme-constrained version (ecYeast8) herein described with experimental data and found that ecYeast8 outperforms Yeast8 in all the simulations. EcYeast8 was able to predict well-known traits of yeast metabolism including the onset of the Crabtree effect, the order of substrate consumption during mixed carbon cultivation and production of a target metabolite. We showed how the combination of ecGEM and dFBA links reactor operation and genetic modifications to flux predictions, enabling the prediction of yields and productivities of different strains and (dynamic) production processes. Additionally, we present flux sampling as a tool to analyze flux predictions of ecGEM, of major importance for strain design applications. We showed that constraining protein availability substantially improves accuracy of the description of the metabolic state of the cell under dynamic conditions. This therefore enables more realistic and faithful designs of industrially relevant cell-based processes and, thus, the usefulness of such models