bluuebunny/crossref_metadata_2025 huggingface dataset:
The relational road to voice: how members of a low-status occupational group can develop voice behavior that transcends hierarchical levels
Authors: Kee Karin , van Wieringen Marieke , Beersma Bianca
Published: July 2021

Members of frontline low-status occupational groups often have access to a vast pool of knowledge, expertise, and experience that may be valuable for organizations. However, previous research has shown that members of these occupational groups are often reluctant to exhibit voice behavior due to their low position in the organizational hierarchy and perceived status differences. Drawing on in-depth interviews with auxiliary nurses (ANs) who participated in a development trajectory, as well as with their colleagues and supervisors, we demonstrate how members of this low-status occupational group develop voice behavior. Our findings show how acquiring three different types of knowledge and acting on this knowledge can lead to forming new and different types of relationships with members of higher status occupational groups in the organization. Subsequently, these relational changes enhanced voice behavior, as the ANs under study became more skillful in navigating the organization and felt better equipped to share their ideas, concerns, and perspective. We contribute to the literature on voice behavior by members of low-status occupational groups by moving beyond the findings of previous studies that have shown that low-status employees are unlikely to exhibit voice behavior. We detail how the development of knowledge, as well as relationships between different occupational groups, is crucial for the enhancement of voice behavior that transcends hierarchical levels. Moreover, we add to the literature on upward influence of subordinates by showing how such voice allows subordinates to exert upward influence in their organizations and initiate change that benefits their own occupational group.
Sugar water feeding practices are associated with bird species composition in urban backyards
Authors: Erastova Daria A , Galbraith Josie A , Cain Kristal E , van Heezik Yolanda , Filion Antoine , Stanley Margaret C
Published: July 2021

Feeding backyard birds with sugar water is increasingly popular in urban areas, but it has poorly understood effects on bird assemblages. In New Zealand, ca. 20% of households engaged in feeding wild birds use sugar water, often in an attempt to attract native, nectarivorous birds. Developing best practices for sugar water feeding could be a powerful tool for attracting these species in urban areas. However, it is currently unclear whether these feeders actually support native species, and, if so, which feeding practices are most effective in increasing visitation. We surveyed New Zealanders who provide sugar water to birds about their feeding practices via an online questionnaire. The aim of our research was to understand existing practices and their effect on attracting native species, as well as the motivations and social factors behind urban sugar water bird feeding. Our results show that this practice is popular throughout the country with the majority of households successful in attracting native nectarivorous species to their gardens. Sugar water feeder type had the largest effect on reported species richness at feeders in comparison to other factors (e.g. sugar concentration). Feeders specifically designed for nectarivorous birds, namely the Tui Nectar Feeder™, are more successful at attracting natives in comparison to other commonly used feeder types. Thus, individual householder decisions around feeder use can have important consequences for bird species composition in urban gardens. Future research is needed to understand the consequences of sugar water feeding for bird communities and individual bird health.
Development of a base editor for protein evolution via in situ mutation in vivo
Authors: Hao Wenliang , Cui Wenjing , Cheng Zhongyi , Han Laichuang , Suo Feiya , Liu Zhongmei , Zhou Li , Zhou Zhemin
Published: July 2021

Protein evolution has significantly enhanced the development of life science. However, it is difficult to achieve in vitro evolution of some special proteins because of difficulties with heterologous expression, purification, and function detection. To achieve protein evolution via in situ mutation in vivo, we developed a base editor by fusing nCas with a cytidine deaminase in Bacillus subtilis through genome integration. The base editor introduced a cytidine-to-thymidine mutation of approximately 100% across a 5 nt editable window, which was much higher than those of other base editors. The editable window was expanded to 8 nt by extending the length of sgRNA, and conversion efficiency could be regulated by changing culture conditions, which was suitable for constructing a mutant protein library efficiently in vivo. As proof-of-concept, the Sec-translocase complex and bacitracin-resistance-related protein BceB were successfully evolved in vivo using the base editor. A Sec mutant with 3.6-fold translocation efficiency and the BceB mutants with different sensitivity to bacitracin were obtained. As the construction of the base editor does not rely on any additional or host-dependent factors, such base editors (BEs) may be readily constructed and applicable to a wide range of bacteria for protein evolution via in situ mutation.
SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin
Authors: Blanco Enrique , Di Croce Luciano , Aranda Sergi
Published: July 2021

In order to evaluate cell- and disease-specific changes in the interacting strength of chromatin targets, ChIP-seq signal across multiple conditions must undergo robust normalization. However, this is not possible using the standard ChIP-seq scheme, which lacks a reference for the control of biological and experimental variabilities. While several studies have recently proposed different solutions to circumvent this problem, substantial analytical differences among methodologies could hamper the experimental reproducibility and quantitative accuracy. Here, we propose a computational method to accurately compare ChIP-seq experiments, with exogenous spike-in chromatin, across samples in a genome-wide manner by using a local regression strategy (spikChIP). In contrast to the previous methodologies, spikChIP reduces the influence of sequencing noise of spike-in material during ChIP-seq normalization, while minimizes the overcorrection of non-occupied genomic regions in the experimental ChIP-seq. We demonstrate the utility of spikChIP with both histone and non-histone chromatin protein, allowing us to monitor for experimental reproducibility and the accurate ChIP-seq comparison of distinct experimental schemes. spikChIP software is available on GitHub (https://github.com/eblancoga/spikChIP).
International Fisheries Law
Authors: Schatz Valentin J. , Honniball Arron N.
Published: July 2021

International fisheries law is a broad field of international law within which significant state practice, instruments, and relevant fora are found at the global, regional, subregional, bilateral, and national level. For the purposes of this bibliography, the analysis of international fisheries law is limited to the law governing marine capture fisheries (other fisheries law definitions may include the regulation of aquaculture or inland fisheries). This bibliography also primarily approaches fisheries law as a matter of fisheries conservation and management under the international law of the sea. The two main treaties of global application which reflect its foundational framework are the 1982 United Nations Convention on the Law of the Sea (UNCLOS) and the United Nations Agreement for the Implementation of the Provisions of the United Nations Convention on the Law of the Sea of 10 December 1982 relating to the Conservation and Management of Straddling Fish Stocks and Highly Migratory Fish Stocks (UNFSA). As a starting point, one should consult the maritime zones established under UNCLOS and customary law, whereby the distribution of rights and obligations among the various capacities of states differs per maritime zone. As fish do not respect legal boundaries, special rules of international law that emphasize cooperation and management between states must be adopted and adapted for shared fish stocks such as transboundary fish stocks, straddling fish stocks, and highly migratory fish stocks. In addition, various treaties of global application dealing with specific issues exist, such as the 1993 Agreement to Promote Compliance with International Conservation and Management Measures by Fishing Vessels on the High Seas (Compliance Agreement) and, most recently, the 2009 Agreement on Port State Measures to Prevent, Deter and Eliminate Illegal, Unreported and Unregulated Fishing (PSMA). This global treaty framework is complemented by various global non–legally binding instruments, most of which were adopted under the Food and Agriculture Organization of the United Nations (FAO). On the regional level, countless multilateral and bilateral fisheries treaties have been concluded, and the field remains highly dynamic. Notably, many fisheries are nowadays managed by Regional Fisheries Management Organizations and Arrangements (RFMO/As) or bilateral fisheries commissions. As a thematically defined field of law, international fisheries law is not restricted to the rules governing conservation and management of marine fisheries, but may equally raise, among other issues, questions of general international law of the sea such as jurisdiction and maritime law enforcement operations, international environmental law, international trade law, international human rights law, and international dispute settlement.
Postacute Sequelae of SARS-CoV-2 Infection and Impact on Quality of Life 1–6 Months After Illness and Association With Initial Symptom Severity
Authors: O’Keefe James B , Minton H Caroline , Morrow Mary , Johnson Colin , Moore Miranda A , O’Keefe Ghazala A D , Benameur Karima , Higdon Jason , Fairley Jessica K
Published: July 2021

Background

Individuals with coronavirus disease 2019 (COVID-19) may have persistent symptoms following their acute illness. The prevalence and predictors of these symptoms, termed postacute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; PASC), have not been fully described.

Methods

Participants discharged from an outpatient telemedicine program for COVID-19 were emailed a survey (1–6 months after discharge) about ongoing symptoms, acute illness severity, and quality of life. Standardized telemedicine notes from acute illness were used for covariates (comorbidities and provider-assessed symptom severity). Bivariate and multivariable analyses were performed to assess predictors of persistent symptoms.

Results

Two hundred ninety patients completed the survey, of whom 115 (39.7%) reported persistent symptoms including fatigue (n = 59, 20.3%), dyspnea on exertion (n = 41, 14.1%), and mental fog (n = 39, 13.5%), among others. The proportion of persistent symptoms did not differ based on duration since illness (<90 days: n = 32, 37.2%; vs >90 days: n = 80, 40.4%; P = .61). Predictors of persistent symptoms included provider-assessed moderate–severe illness (adjusted odds ratio [aOR], 3.24; 95% CI, 1.75–6.02), female sex (aOR, 1.99; 95% CI, 0.98–4.04; >90 days out: aOR, 2.24; 95% CI, 1.01–4.95), and middle age (aOR, 2.08; 95% CI, 1.07–4.03). Common symptoms associated with reports of worse physical health included weakness, fatigue, myalgias, and mental fog.

Conclusions

Symptoms following acute COVID-19 are common and may be predicted by factors during the acute phase of illness. Fatigue and neuropsychiatric symptoms figured prominently. Select symptoms seem to be particularly associated with perceptions of physical health following COVID-19 and warrant specific attention on future studies of PASC.
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

Human 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

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.
Electronic Health Record Transition
Authors: Monturo Cheryl , Brockway Cindy , Ginev Alex
Published: July 2021

Use of the EHR at the bedside is now commonplace, and some fear this may compromise their relationship with the patient. The purpose of this study was to assess the impact of a transition of an EHR on the patient experience. Three non-equivalent groups consisting of 55 patients responded to instrument questions at three distinct time points: baseline prior to transition and twice after the transition at 6 weeks and 6 months. Questions investigated the point-of-care computer use, user's comfort, and impact on patient relationship with a nurse or provider. Patients perceived more use of the computer by Nurses and a declining use by Others. Nurses remained comfortable using the computer over time, and the perception of Others declined. Nurses were perceived 2.3 times more likely than Others as changing the patient relationship and two times higher with a positive impact. The transition in the EHR did not seem to affect the overall patient experience; however, results should be viewed with caution given the limitations of this study and the dearth of evidence. Evidence-based guidelines for EHR integration may be helpful in the future to address inpatient encounters with all clinicians.
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
Building a Transition Program for Senior Nurse Leaders
Authors: Kauffman Sharon R. , Aucoin Julia W.
Published: July 2021

Professional development educators undertake a primary role in building organizational transition programs for nurses. Transitions of senior nurse leaders are complex and poorly understood. A Hermeneutic phenomenological study was conducted to investigate the lived experiences of nine novice senior nurse leaders. Four principle themes and five subthemes are identified so that professional development educators may customize situation-specific learning for senior nurse leader onboarding.
Innovative Utilization of Wright’s Model for Competency Validation
Authors: Salmela Lynn M. , LaValley Michelle L.
Published: July 2021

Wright’s competency assessment model is well known, yet implementation has been largely challenging. Some organizations have attempted enterprise-wide implementation. This article summarizes how Wright’s model was used from a specific topic perspective. Centralized nursing professional development practitioners created flexible competency validation guidelines and supplemental tools (literature review, exemplar, and peer review) for use by sedation nurses regardless of experience or practice setting. Post-implementation data show 62% adoption of new validation methods after 1 year.
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.
Network pharmacology and molecular docking analysis on mechanisms of Tibetan Hongjingtian (Rhodiola crenulata) in the treatment of COVID-19
Authors: Wang Li , Wang Yuhe , Yang Wei , He Xue , Xu Shilin , Liu Xiaoli , He Yongjun , Hu Qunying , Yuan Dongya , Jin Tianbo
Published: July 2021

Introduction. Coronavirus disease 2019 (COVID-19) is a highly contagious disease and ravages the world.

Hypothesis/Gap Statement. We proposed that R. crenulata might have potential value in the treatment of COVID-19 patients by regulating the immune response and inhibiting cytokine storm.

Aim. We aimed to explore the potential molecular mechanism for Rhodiola crenulata (R. crenulata), against the immune regulation of COVID-19, and to provide a referenced candidate Tibetan herb (R. crenulata) to overcome COVID-19.

Methodology. Components and targets of R. crenulata were retrieved from the TCMSP database. GO analysis and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment were built by R bioconductor package to explore the potential biological effects for targets of R. crenulata. The R. crenulata-compound-target network, target pathway network and protein–protein interaction (PPI) network were constructed using Cytoscape 3.3.0. Autodock 4.2 and Discovery Studio software were applied for molecular docking.

Result. Four bioactive components (quercetin, kaempferol, kaempferol-3-O-α-l-rhamnoside and tamarixetin) and 159 potential targets of R. crenulata were identified from the TCMSP database. The result of GO annotation and KEGG-pathway-enrichment analyses showed that target genes of R. crenulata were associated with inflammatory response and immune-related signalling pathways, especially IL-17 signalling pathway, and TNF signalling pathway. Targets-pathway network and PPI network showed that IL-6, IL-1B and TNF-α were considered to be hub genes. Molecular docking showed that core compound (quercetin) had a certain affinity with IL-1β, IL-6 and TNF-α.

Conclusion.

R. crenulata might play an anti-inflammatory and immunoregulatory role in the cytokine storm of COVID-19.
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

Immunity 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

Background

Surveillance 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.

Methods

We 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.

Findings

2,497 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.

Interpretation

SARS-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.

Funding

ZonMw, 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

Bacteriophages 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 Implementation

hafeZ 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.

Contact

cturkington@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

Soil 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

Background

As 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.

Methods

A 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).

Results

Eighty-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.

Conclusion

As 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

Decidualization 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.
Prolonged Pain Reliably Slows Peak Alpha Frequency by Reducing Fast Alpha Power
Authors: Furman Andrew J. , Prokhorenko Mariya , Keaser Michael L. , Zhang Jing , Chen Shuo , Mazaheri Ali , Seminowicz David A.
Published: July 2021

The relationship between the 8-12 Hz “alpha: rhythm, the predominant oscillatory activity of the brain, and pain remains unclear. In healthy individuals, acute, noxious stimuli suppress alpha power while patients with chronic pain demonstrate both enhanced alpha power and slowing of the peak alpha frequency (PAF). To investigate these apparent differences, EEG was recorded from healthy individuals while they completed two models of prolonged pain, Phasic Heat Pain and Capsaicin Heat Pain, at two testing visits occurring roughly 8 weeks apart. We report that PAF is reliably slowed and that alpha power is reliably decreased in response to prolonged pain. Furthermore, we show that alpha power changes, but not PAF changes, are fully reversed with stimulus removal suggesting that PAF slowing reflects pain associated states such as sensitization rather than the presence of ongoing pain. Finally, we provide evidence that changes to alpha power and PAF are due to power decreases in the “fast” (10-12 Hz) range of the alpha rhythm. This frequency dependent pain response aligns with the hypothesis that the alpha rhythm is composed of multiple, independent oscillators, and suggest that modulation of a putative “fast” oscillator may represent a promising therapeutic target for treating ongoing pain. In sum, we provide strong evidence that PAF is reliably slowed during prolonged pain and additionally identify a mechanism, “fast” alpha Power, which is responsible for these PAF changes.
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

Parkinson’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

Genome-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
The interaction between a parasite and sub-optimal temperatures contributes to honey bee decline
Authors: Frizzera Davide , Andreuzza Laura , Boaro Giulia , D’Agaro Mauro , Del Fabbro Simone , Zanni Virginia , Annoscia Desiderato , Nazzi Francesco
Published: July 2021

Global insect decline and, in particular, honey bee colony losses are related to multiple stress factors, including landscape deterioration, pollution, parasites and climate change. However, the implications of the interaction among different stress factors for insect health are still poorly understood; in particular, little is known on how challenging environmental conditions can influence the impact of parasites. Here we exploited the honey bee as a model system to approach this problem and carried out extensive lab and field work aiming at assessing how suboptimal temperatures and parasitic challenges can alter the homeostatic balance of individual bees and the whole colony, leading to individual death and colony collapse.

We found that mite infestation further than increasing the mortality of bees, induces an anorexia that in turn reduces the capacity of bees to thermoregulate, thus exposing them to the detrimental effect of lower temperatures. This, in turn, has important implications for the colony as a whole. The results highlight the role that abiotic factors can have in shaping the effect of parasitic challenges on honey bees. Furthermore, the multilevel and holistic approach adopted here can represent a useful template for similar studies on other insect species, which are particularly urgent in view of climate change and the continuous pressure of natural and exotic parasites on insect populations.
Context dependency of nucleotide probabilities and variants in human DNA
Authors: Liang Yuhu , Grønbæk Christian , Fariselli Piero , Krogh Anders
Published: July 2021

Background

Genomic DNA has been shaped by mutational processes through evolution. The cellular machinery for error correction and repair has left its marks in the nucleotide composition along with structural and functional constraints. Therefore, the probability of observing a base in a certain position in the human genome is highly context-dependent.

Results

Here we develop context-dependent nucleotide models. We first investigate models of nucleotides conditioned on sequence context. We develop a bidirectional Markov model that use an average of the probability from a Markov model applied to both strands of the sequence and thus depends on up to 14 bases to each side of the nucleotide. We show how the genome predictability varies across different types of genomic regions. Surprisingly, this model can predict a base from its context with an average of more than 50% accuracy. For somatic variants we show a tendency towards higher probability for the variant base than for the reference base. Inspired by DNA substitution models, we develop a model of mutability that estimates a mutation matrix (called the alpha matrix) on top of the nucleotide distribution. The alpha matrix can be estimated from a much smaller context than the nucleotide model, but the final model will still depend on the full context of the nucleotide model. With the bidirectional Markov model of order 14 and an alpha matrix dependent on just one base to each side, we obtain a model that compares well with a model of mutability that estimates mutation probabilities directly conditioned on three nucleotides to each side. For somatic variants in particular, our model fits better than the simpler model. Interestingly, the model is not very sensitive to the size of the context for the alpha matrix.

Conclusions

Our study found strong context dependencies of nucleotides in the human genome. The best model uses a context of 14 nucleotides to each side. Based on these models, a substitution model was constructed that separates into the context model and a matrix dependent on a small context. The model fit somatic variants particularly well.
Groping in the fog: soaring migrants exhibit wider scatter in flight directions and respond differently to wind under low visibility conditions
Authors: Becciu Paolo , Panuccio Michele , Dell’Omo Giacomo , Sapir Nir
Published: July 2021

Atmospheric conditions are known to affect flight propensity, behaviour during flight, and migration route in birds. Yet, the effects of fog have only rarely been studied although they could disrupt orientation and hamper flight. Fog could limit the visibility of migrating birds such that they might not be able to detect landmarks that guide them during their journey. Soaring migrants modulate their flight speed and direction in relation to the wind vector to optimize the cost of transport. Consequently, landmark-based orientation, as well as adjustments of flight speed and direction in relation to wind conditions, could be jeopardized when flying in fog. Using a radar system operated in a migration bottleneck (Strait of Messina, Italy), we studied the behaviour of soaring birds under variable wind and fog conditions over two consecutive springs (2016 and 2017), discovering that migrating birds exhibited a wider scatter of flight directions and responded differently to wind under fog conditions. Birds flying through fog deviated more from the mean migration direction and increased their speed with increasing crosswinds. In addition, airspeed and groundspeed increased in the direction of the crosswind, causing the individuals to drift laterally. Our findings represent the first quantitative empirical evidence of flight behaviour changes when birds migrate through fog and explain why low visibility conditions could risk their migration journey.