bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of the Experience of Immigrant Nurses in a Diverse Cultural Setting
Authors: AL-NUSAIR Hussam , ALNJADAT Rafi
Published: April 2022

Background

Work-related stress (WRS) is one of the most common stressors in healthcare workplace settings.

Purpose

This research study was designed to examine and discuss perceived WRS, job performance, social support, and the desire of immigrant nurses to work in a multicultural workplace.

Methods

A case research mixed-methodology approach, a quantitative survey, and semistructured qualitative interviews were used in this research study. Three hundred twenty-one respondents were invited, of which 246 (76.6%) returned valid questionnaires. A purposeful sampling technique was used in the qualitative portion of the study. A semistructured interviewing system was used on 20 nurses.

Results

“Workload” was the most common traumatic occurrence, whereas “treatment” and “death and dying” were the least common traumatic occurrences. Similarly, the mean of the social support scale, as defined using the McCain and Marklin Social Integration Scale, was moderate to high, suggesting that most of the participants received strong social support from their colleagues. The qualitative research found that the participants faced high pressures related to work and have struggled to acquire cultural skills, while having difficulties meeting their patients' cultural and spiritual needs and sustaining high-quality nursing care.

Conclusions

The findings of this study support that immigrant nurses working in the Kingdom of Saudi Arabia are stressed. A significant difference between the qualitative and quantitative results was found. The findings further contribute to our understanding of WRS, social support, job performance, and intention to stay among immigrant nurses in the Kingdom of Saudi Arabia.
Comparative study on treatment of acute cerebral infarction between mechanical thrombectomy by micro catheter and thrombectomy by Solitaire AB stent
Authors: Dong Xiaoli , Xu Guodong , Song Yaxue , Ma Liang , Huo Tiantian , Yin Nan , Meng Nan
Published: April 2022

Background:

Acute cerebral artery occlusion is a common disease with high morbidity and mortality. At present, the commonly used mechanical thrombectomy schemes are mechanical thrombectomy and stent thrombectomy. However, the clinical differences between the two methods is not fully understood. The present study aimed to evaluate the clinical effectiveness of Solitaire AB stent thrombectomy for acute cerebral infarction (ACI).

Methods:

A retrospective study was carried out in 96 ACI patients admitted to our department from January 2017 to January 2020. According to the treatment they received, they were divided into group A (conventional microcatheter mechanical thrombectomy, n = 48) and group B (Solitaire AB stent thrombectomy, n = 48). All patients were followed up for 3 months. Their pre- and post-operative nerve function indices were compared between the 2 groups. The therapeutic effects were evaluated by thrombolysis in cerebral infarction scale system, Glasgow coma scale (GCS), National Institutes of Health Stroke Scale (NIHSS), and modified Rankin scale statistics.

Results:

Two groups of patients with NIHSS scores postoperative 3 and 30 days decreased significantly compared with preoperation. NIHSS score of group A 3 and 30 days postoperation was significantly higher than group B (P < .05). Two groups of patients with GCS scores postoperative 3 and 30 days increased significantly compared with preoperation. GCS score of group A 3 and 30 days postoperation was significantly lower than group B (P < .05). Group B with vascular recanalization ratio postoperative 30 days was higher than group A, however with no significant differences (P > .05). Moreover, group B with outcomes (modified Rankin scale score ≤2 points) postoperative 3 months was better than group A, however with no significant differences (P > .05).

Conclusion:

Solitaire AB stent embolectomy shows similar efficacy as mechanical thrombectomy in the treatment of ACI patients.
The performance of HEAR score for identification of low-risk chest pain: a systematic review and meta-analysis
Authors: Khaleghi Rad Mahsan , Pirmoradi Mohammad Mahdi , Doosti-Irani Amin , Thiruganasambandamoorthy Venkatesh , Mirfazaelian Hadi
Published: April 2022

Chest pain is one of the most common presentations to the emergency department (ED) and HEART score (history, ECG, age, risk factors, and cardiac troponin) is recommended for risk stratification. It has been proposed that the sum of four items with no troponin (HEAR score) below 2 can be used safely to lower testing and reduce length of stay. To assess the performance of the HEAR score in hospital and prehospital settings, we performed a systematic review and meta-analysis. English studies on the performance of the HEAR score in patients with acute chest pain were included. They were excluded if data are inaccessible. MEDLINE, Embase, Evidence-Based Medicine Reviews, Scopus, and web of science were searched from 1946 to July 2021. The quality of studies was assessed using Quality Assessment of Diagnostic Accuracy Studies version 2. Acute coronary syndrome or major adverse cardiac events prediction were outcomes of interest. The performance indices with 95% confidence intervals (CIs) were extracted. Inverse variance and the random-effects model were used to report the results. Of the 692 articles on the HEAR score, 10 studies were included in the analysis with 33 843 patients. Studies were at low to moderate risk of bias. Three studies were in prehospital and three were retrospective. The pooling of data on the HEAR score showed that the sensitivity at the HEAR<2, <3, and <4 cutoffs in the ED were 99.03% (95% CI, 98.29–99.77), 97.54% (95% CI, 94.50–100), and 91.80% (95% CI, 84.62–98.98), respectively. The negative predictive values (NPVs) for the above cutoffs were 99.84% (95% CI, 99.72–99.95), 99.75% (95% CI, 99.65–99.85), and 99.57% (95% CI, 99.11–100), respectively. Of note, for the HEAR<2, negative likelihood ratio was 0.07 (95% CI, 0.02–0.12). In the prehospital, at the HEAR<4 cutoff, the pooled sensitivity and NPV were 85.01% (95% CI, 80.56–89.47) and 91.48% (95% CI, 87.10–95.87), respectively. This study showed that in the ED, the HEAR score<2 can be used for an early discharge strategy. Currently, this score cannot be recommended in prehospital setting. Prospero (CRD42021273710).
Development and External Validation of a Machine Learning Model for Prediction of Potential Transfer to the PICU
Authors: Mayampurath Anoop , Sanchez-Pinto L. Nelson , Hegermiller Emma , Erondu Amarachi , Carey Kyle , Jani Priti , Gibbons Robert , Edelson Dana , Churpek Matthew M.
Published: April 2022

OBJECTIVES:

Unrecognized clinical deterioration during illness requiring hospitalization is associated with high risk of mortality and long-term morbidity among children. Our objective was to develop and externally validate machine learning algorithms using electronic health records for identifying ICU transfer within 12 hours indicative of a child’s condition.

DESIGN:

Observational cohort study.

SETTING:

Two urban, tertiary-care, academic hospitals (sites 1 and 2).

PATIENTS:

Pediatric inpatients (age <18 yr).

INTERVENTIONS:

None.

MEASUREMENT AND MAIN RESULTS:

Our primary outcome was direct ward to ICU transfer. Using age, vital signs, and laboratory results, we derived logistic regression with regularization, restricted cubic spline regression, random forest, and gradient boosted machine learning models. Among 50,830 admissions at site 1 and 88,970 admissions at site 2, 1,993 (3.92%) and 2,317 (2.60%) experienced the primary outcome, respectively. Site 1 data were split longitudinally into derivation (2009–2017) and validation (2018–2019), whereas site 2 constituted the external test cohort. Across both sites, the gradient boosted machine was the most accurate model and outperformed a modified version of the Bedside Pediatric Early Warning Score that only used physiologic variables in terms of discrimination (C-statistic site 1: 0.84 vs 0.71, p < 0.001; site 2: 0.80 vs 0.74, p < 0.001), sensitivity, specificity, and number needed to alert.

CONCLUSIONS:

We developed and externally validated a novel machine learning model that identifies ICU transfers in hospitalized children more accurately than current tools. Our model enables early detection of children at risk for deterioration, thereby creating opportunities for intervention and improvement in outcomes.
Resuscitative endovascular balloon occlusion of the aorta for life-threatening postpartum hemorrhage: A nationwide observational study in Japan
Authors: Kamijo Kyosuke , Nakajima Mikio , Shigemi Daisuke , Kaszynski Richard H. , Ohbe Hiroyuki , Goto Tadahiro , Sasabuchi Yusuke , Fushimi Kiyohide , Matsui Hiroki , Yasunaga Hideo
Published: April 2022

BACKGROUND

Resuscitative endovascular balloon occlusion of the aorta (REBOA) is used for postpartum hemorrhage (PPH), which is one of the leading causes of maternal mortality worldwide; however, its utility in the obstetrics setting remains unclear. Thus, this study aimed to describe the characteristics, demographics, and mortality of patients with PPH who underwent REBOA.

METHODS

We used the Japanese Diagnosis Procedure Combination inpatient database to identify patients with PPH who underwent REBOA from April 2012 to March 2020. We examined the patients' characteristics, interventions administered, and in-hospital mortality.

RESULTS

We identified 143 patients with PPH who underwent REBOA. The most common cause of PPH was atonic postpartum hemorrhage (52.4%), followed by disseminated intravascular coagulation (29.4%) and amniotic fluid embolism documented (11.2%). Among patients who delivered at hospitals in which REBOA was performed (n = 55), 38.2% of patients experienced preterm births, and 70.9% delivered via cesarean delivery. The proportion of patients who underwent transcatheter arterial embolization and hysterectomy was 53.8% and 16.1%, respectively. In-hospital mortality was 7.0%.

CONCLUSION

The results of the present study could be helpful in clinical decision making and providing patients and families with additional treatment options for PPH.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level IV.
Beyond Graft Survivl: A National Cohort Study Quantifying the Impact of Increasing Kidney Donor Profile Index on Recipient Outcomes 1 Year Post-transplantation
Authors: Tully Emma K. , Hayes Ian P. , Hughes Peter D. , Sypek Matthew P.
Published: April 2022

Background.

The reporting of a locally validated kidney donor profile index (KDPI) began in Australia in 2016. Across diverse populations, KDPI has demonstrated utility in predicting allograft survival and function. A metric that incorporates both elements may provide a more comprehensive picture of suboptimal recipient outcomes.

Methods.

A retrospective cohort study of adult kidney transplant recipients in Australia (January 2009 to December 2014) was conducted. Conventional recipient outcomes and a composite measure of suboptimal outcome (1-y allograft failure or estimated glomerular filtration rate [eGFR] <30 mL/min) were evaluated across KDPI intervals (KDPI quintiles and 5-point increments in the KDPI 81–100 cohort). The impact of increasing KDPI on allograft function (1-y eGFR) and a suboptimal outcome was explored using multivariable regression models, adjusting for potential confounding factors.

Results.

In 2923 donor kidneys eligible for analysis, median KDPI was 54 (interquartile range [IQR], 31–77), and Kidney Donor Risk Index was 1.39 (IQR, 1.03–1.67). The median 1-y eGFR was 52.74 mL/min (IQR, 40.79–66.41 mL/min). Compared with the first quintile reference group, progressive reductions in eGFR were observed with increasing KDPI and were maximal in the fifth quintile (adjusted β-coefficient: −27.43 mL/min; 95% confidence interval, –29.44 to –25.42; P < 0.001). A suboptimal outcome was observed in 359 recipients (12.3%). The adjusted odds for this outcome increased across quintiles from a baseline of odds ratio of 1.00 (first quintile) to odds ratio of 11.68 (95% confidence interval, 6.33-21.54, P < 0.001) in the fifth quintile cohort.

Conclusions.

Increases in donor KDPI were associated with higher probabilities of a suboptimal outcome and poorer baseline allograft function, particularly in the KDPI > 80 cohort. These findings may inform pretransplant discussions with potential recipients of high-KDPI allografts.
Streptomyces sennicomposti sp. nov., an actinomycete isolated from compost of Senna siamea (Lam.)
Authors: Duangupama Thitikorn , Pittayakhajonwut Pattama , Intaraudom Chakapong , Suriyachadkun Chanwit , Sirirote Pramote , He Ya-Wen , Thawai Chitti
Published: April 2022

A member of the genus

Streptomyces

, designated RCPT1-4T, was isolated from compost of Senna siamea (Lam.), collected from an agricultural area in Rayong province, Thailand. The spore morphology and the presence of ll-diaminopimelic acid in the peptidoglycan indicate that RCPT1-4T shows the typical properties of members of the genus

Streptomyces

. On the basis of the results of 16S rRNA gene sequence analysis, the strain should be classified as representing a member of the genus

Streptomyces

and was most closely related to

Streptomyces fumigatiscleroticus

NBRC 12999T with the highest 16S rRNA gene sequence similarity of 99.2 %, followed by

Streptomyces spiralis

NBRC 14215T (99.0 %). In addition, RCPT1-4T shared the highest average nucleotide identity by blast (ANIb) (86.0 %), and digital DNA–DNA hybridization (dDDH) (32.1 %) values with

S. spiralis

NBRC 14215T. Furthermore, several physiological and biochemical differences were observed between RCPT1-4T and the closely related type strains of species with validly published names. These taxonomic data indicated that RCPT1-4T could be considered to represent a novel species of the genus

Streptomyces

and the name Streptomyces sennicomposti sp. nov. is proposed for this strain. The type strain is RCPT1-4T (=TBRC 11260T=NBRC 114303T).
Evolutionary changes between pre- and post-vaccine South African group A G2P[4] rotavirus strains, 2003–2017
Authors: Mwangi Peter N. , Page Nicola A. , Seheri Mapaseka L. , Mphahlele M. Jeffrey , Nadan Sandrama , Esona Mathew D. , Kumwenda Benjamin , Kamng’ona Arox W. , Donato Celeste M. , Steele Duncan A. , Ndze Valantine N. , Dennis Francis E. , Jere Khuzwayo C. , Nyaga Martin M.
Published: April 2022

The transient upsurge of G2P[4] group A rotavirus (RVA) after Rotarix vaccine introduction in several countries has been a matter of concern. To gain insight into the diversity and evolution of G2P[4] strains in South Africa pre- and post-RVA vaccination introduction, whole-genome sequencing was performed for RVA positive faecal specimens collected between 2003 and 2017 and samples previously sequenced were obtained from GenBank (n=103; 56 pre- and 47 post-vaccine). Pre-vaccine G2 sequences predominantly clustered within sub-lineage IVa-1. In contrast, post-vaccine G2 sequences clustered mainly within sub-lineage IVa-3, whereby a radical amino acid (AA) substitution, S15F, was observed between the two sub-lineages. Pre-vaccine P[4] sequences predominantly segregated within sub-lineage IVa while post-vaccine sequences clustered mostly within sub-lineage IVb, with a radical AA substitution R162G. Both S15F and R162G occurred outside recognised antigenic sites. The AA residue at position 15 is found within the signal sequence domain of Viral Protein 7 (VP7) involved in translocation of VP7 into endoplasmic reticulum during infection process. The 162 AA residue lies within the hemagglutination domain of Viral Protein 4 (VP4) engaged in interaction with sialic acid-containing structure during attachment to the target cell. Free energy change analysis on VP7 indicated accumulation of stable point mutations in both antigenic and non-antigenic regions. The segregation of South African G2P[4] strains into pre- and post-vaccination sub-lineages is likely due to erstwhile hypothesized stepwise lineage/sub-lineage evolution of G2P[4] strains rather than RVA vaccine introduction. Our findings reinforce the need for continuous whole-genome RVA surveillance and investigation of contribution of AA substitutions in understanding the dynamic G2P[4] epidemiology.
SARS-CoV-2 evolution and immune escape in immunocompromised patients treated with exogenous antibodies
Authors: Scherer Erin M. , Babiker Ahmed , Adelman Max W. , Allman Brent , Key Autum , Kleinhenz Jennifer M. , Langsjoen Rose M. , Nguyen Phuong-Vi , Onyechi Ivy , Sherman Jacob D. , Simon Trevor W. , Soloff Hannah , Tarabay Jessica , Varkey Jay , Webster Andrew S. , Weiskopf Daniela , Weissman Daniel B. , Xu Yongxian , Waggoner Jesse J. , Koelle Katia , Rouphael Nadine , Pouch Stephanie M. , Piantadosi Anne
Published: April 2022

Background

SARS-CoV-2 mutations conferring escape from neutralizing antibodies can arise in immunocompromised patients with prolonged infection, but the conditions that facilitate immune escape are still not fully understood.

Methods

We characterized endogenous immune responses, within-host SARS-CoV-2 evolution, and autologous neutralization of the viral variants that arose in five immunocompromised patients with prolonged infection and B cell deficiencies.

Results

In two patients treated with the monoclonal antibody bamlanivimab, viral resistance to autologous serum arose early and persisted for several months, accompanied by ongoing evolution in the spike protein. These patients exhibited deficiencies in both T and B cell arms, and one patient succumbed to disease. In contrast, we did not observe spike mutations in immunologically important regions in patients who did not receive exogenous antibodies or who received convalescent plasma and had intact T cell responses to SARS-CoV-2.

Conclusions

Our results underscore the potential importance of multiple factors – the absence of an effective endogenous immune response, persistent virus replication, and selective pressure such as single-agent bamlanivimab – in promoting the emergence of SARS-CoV-2 mutations associated with immune evasion. These findings highlight the need for larger clinical studies in immunocompromised populations to better understand the ramifications of different therapies. Our results also confirm that patients with B cell deficiencies can elicit effector T cells and may suggest an important role for T cells in controlling infection, which is relevant to vaccines and therapeutics.
Global reports of takotsubo (stress) cardiomyopathy following COVID-19 vaccination: a systematic review and meta-analysis
Authors: Ahmed Sirwan Khalid , Mohamed Mona Gamal , Essa Rawand Abdulrahman , Ahmed Rashad Dabou Eman Abdelaziz , Abdulqadir Salar Omar , Omar Rukhsar Muhammad
Published: April 2022

Concerns have been raised recently about takotsubo cardiomyopathy (TCM) after receiving COVID-19 vaccines, particularly the messenger RNA (mRNA) vaccines. The goal of this study was to compile case reports to provide a comprehensive overview of takotsubo cardiomyopathy (TCM) associated with COVID-19 vaccines. A systematic literature search was conducted in PubMed, Scopus, Embase, Web of Science, and Google Scholar between 2020 and June 1, 2022. The study included individuals who developed cardiac takotsubo cardiomyopathy from receiving COVID-19 vaccinations. Ten studies, including 10 cases, participated in the current systematic review. The mean age was 61.8 years; 90% were female, while 10% were male. 80% of the patients received the mRNA COVID-19 vaccine, while 20% received other types. In addition, takotsubo cardiomyopathy (TCM) occurred in 50% of patients receiving the first dose and another 40% after the second dose of COVID-19 vaccines. Moreover, the mean number of days to the onset of symptoms was 2.62 days. All cases had an elevated troponin test and abnormal ECG findings. The left ventricular ejection fraction (LVEF) was lower than 50% in 90% of patients. In terms of the average length of hospital stay, 50% stayed for 10.2 days, and all cases recovered from their symptoms. In conclusion, takotsubo (stress) cardiomyopathy (TCM) complications associated with COVID-19 vaccination are rare but can be life-threatening. Chest pain should be considered an alarming symptom, especially in those who have received the first and second doses of the COVID-19 vaccine.
Coding Long COVID: Characterizing a new disease through an ICD-10 lens
Authors: Pfaff Emily R , Madlock-Brown Charisse , Baratta John M. , Bhatia Abhishek , Davis Hannah , Girvin Andrew , Hill Elaine , Kelly Liz , Kostka Kristin , Loomba Johanna , McMurry Julie A. , Wong Rachel , Bennett Tellen D , Moffitt Richard , Chute Christopher G , Haendel Melissa ,   The N3C Consortium,   The RECOVER Consortium
Published: April 2022

Background

Naming a newly discovered disease is a difficult process; in the context of the COVID-19 pandemic and the existence of post-acute sequelae of SARS-CoV-2 infection (PASC), which includes Long COVID, it has proven especially challenging. Disease definitions and assignment of a diagnosis code are often asynchronous and iterative. The clinical definition and our understanding of the underlying mechanisms of Long COVID are still in flux, and the deployment of an ICD-10-CM code for Long COVID in the US took nearly two years after patients had begun to describe their condition. Here we leverage the largest publicly available HIPAA-limited dataset about patients with COVID-19 in the US to examine the heterogeneity of adoption and use of U09.9, the ICD-10-CM code for “Post COVID-19 condition, unspecified.”

Methods

We undertook a number of analyses to characterize the N3C population with a U09.9 diagnosis code (n = 21,072), including assessing person-level demographics and a number of area-level social determinants of health; diagnoses commonly co-occurring with U09.9, clustered using the Louvain algorithm; and quantifying medications and procedures recorded within 60 days of U09.9 diagnosis. We stratified all analyses by age group in order to discern differing patterns of care across the lifespan.

Results

We established the diagnoses most commonly co-occurring with U09.9, and algorithmically clustered them into four major categories: cardiopulmonary, neurological, gastrointestinal, and comorbid conditions. Importantly, we discovered that the population of patients diagnosed with U09.9 is demographically skewed toward female, White, non-Hispanic individuals, as well as individuals living in areas with low poverty, high education, and high access to medical care. Our results also include a characterization of common procedures and medications associated with U09.9-coded patients.

Conclusions

This work offers insight into potential subtypes and current practice patterns around Long COVID, and speaks to the existence of disparities in the diagnosis of patients with Long COVID. This latter finding in particular requires further research and urgent remediation.
Read2Tree: scalable and accurate phylogenetic trees from raw reads
Authors: Dylus David , Altenhoff Adrian , Majidian Sina , Sedlazeck Fritz J , Dessimoz Christophe
Published: April 2022

The inference of phylogenetic trees is foundational to biology. However, state-of-the-art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and annotation quality. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes. In a benchmark encompassing a broad variety of datasets, our assembly-free approach was 10-100x faster than conventional approaches, and in most cases more accurate—the exception being when sequencing coverage was high and reference species very distant. To illustrate the broad applicability of the tool, we reconstructed a yeast tree of life of 435 species spanning 590 million years of evolution. Applied toCoronaviridaesamples, Read2Tree accurately classified highly diverse animal samples and near-identical SARS-CoV-2 sequences on a single tree—thereby exhibiting remarkable breadth and depth. The speed, accuracy, and versatility of Read2Tree enables comparative genomics at scale.
A flexible modeling and inference framework for estimating variant effect sizes from GWAS summary statistics
Authors: Spence Jeffrey P. , Sinnott-Armstrong Nasa , Assimes Themistocles L. , Pritchard Jonathan K.
Published: April 2022

Genome-wide association studies (GWAS) have highlighted that almost any trait is affected by many variants of relatively small effect. On one hand this presents a challenge for inferring the effect of any single variant as the signal-to-noise ratio is high for variants of small effect. This challenge is compounded when combining information across many variants in polygenic scores for predicting trait values. On the other hand, the large number of contributing variants provides an opportunity to learn about the average behavior of variants encoded in the distribution of variant effect sizes. Many approaches have looked at aspects of this problem, but no method has unified the inference of the effects of individual variants with the inference of the distribution of effect sizes while requiring only GWAS summary statistics and properly accounting for linkage disequilibrium between variants. Here we present a flexible, unifying framework that combines information across variants to infer a distribution of effect sizes and uses this distribution to improve the estimation of the effects of individual variants. We also develop a variational inference (VI) scheme to perform efficient inference under this framework. We show this framework is useful by constructing polygenic scores (PGSs) that outperform the state-of-the-art. Our modeling framework easily extends to jointly inferring effect sizes across multiple cohorts, where we show that building PGSs using additional cohorts of differing ancestries improves predictive accuracy and portability. We also investigate the inferred distributions of effect sizes across many traits and find that these distributions have effect sizes ranging over multiple orders of magnitude, in contrast to the assumptions implicit in many commonly-used statistical genetics methods.
A multi-continental analysis of the responses of freshwater food webs to climate and land use change
Authors: Barbosa Gedimar Pereira , Siqueira Tadeu
Published: April 2022

Food web responses to environmental change are not straightforward to understand as they occur through an intricate arrangement of direct and indirect effects. Although previous investigations have advanced knowledge on freshwater food web structure, we must better understand the intricate relationships between the main drivers of environmental change and trophic networks in lentic and lotic ecosystems.

We compiled multicontinental data to investigate how climate and land use change are related to the structure of freshwater food webs, considering the inherent differences in lentic and lotic ecosystems. We analyzed the direct and indirect relationships between land use intensity, and temperature and precipitation temporal trends, and food webs using multi-group structural equation modeling.

The strength and direction of the relationships between climate, land use, and food webs varied considerably among lentic and lotic ecosystems, but most indicated indirect effects through the number of links in the network. While network connectance both increased and decreased with land use and climate change, the number of trophic levels decreased with land use intensity and maximum temperature and increased with increasing precipitation. Omnivory increased with land use intensity in both ecosystems but was negatively related to changes on maximum temperature in lake food webs.

Even though food webs are expected to become more connected in face of disturbances, and our work supported this regarding local warming, the negative relationships between network connectance and land use intensification suggests that food webs become more specialized at disturbed sites. On the other hand, reduction in the number of trophic levels indicates the loss of top consumers in face of warming and increasing land use intensity.

The response of food webs in both lentic and lotic ecosystems to climate and land use change occurred mostly through changes in species interactions. Our results indicate that the intensification of land use makes food webs more specialized, with less trophic levels. Also, inherent aspects of freshwater ecosystems seemed to play a major role in the way food webs respond to disturbance and must be considered to fully understand and predict the effects of global changes on freshwater biodiversity.
Expanding risk predictions of pesticide resistance evolution in arthropod pests with a proxy for selection pressure
Authors: Thia Joshua A. , Maino James , Kelly Alicia , Hoffmann Ary A. , Umina Paul A.
Published: April 2022

Chemical resistance in pest organisms threatens global food security and human health, yet resistance issues are mostly dealt with reactively. Predictive models of resistance risk provide an avenue for field practitioners to implement proactive pest management but require knowledge of factors that drive resistance evolution. Despite the importance of chemical selection pressure on resistance evolution, poor availability of chemical usage data has limited the use of a general multi-species measure of selection pressure in predictive models. We demonstrate the use of pesticide product registrations as a predictor of resistance status and potential proxy of chemical selection pressure. Pesticide product registrations were obtained for 427 USA and 209 Australian agricultural arthropod pests, for 42 and 39 chemical Mode of Action (MoA) groups, respectively. We constructed Bayesian logistic regressions of resistance status as a function of the number of pesticide product registrations and two ecological traits, phagy and voltinism. Our models were well-supported with demonstrated power to discriminate between resistant and susceptible observations in both USA and Australian species sets using cross-validation. Importantly, we observed strong support for a positive association between pesticide products and resistance status. Our work expands the horizon for proactive management by quantitatively linking a proxy for selection pressure on pest species to different chemical MoAs. This proxy for selection pressure can be combined with ecological information to predict the resistance risk in agricultural pests. Because pesticide product registrations can typically be derived from publicly available data, we believe there is broad applicability to other agricultural pests such as weeds and fungi, and to other geographical regions beyond the USA and Australia.
Stress fibers orient traction forces on micropatterns: A hybrid cellular Potts model study
Authors: Schakenraad Koen , Martorana Gaia I. , Bakker Bente H. , Giomi Luca , Merks Roeland M.H.
Published: April 2022

Adhering cells exert traction forces on the underlying substrate. We numerically investigate the intimate relation between traction forces, the structure of the actin cytoskeleton, and the shape of cells adhering to adhesive micropatterned substrates. By combining the Cellular Potts Model with a model of cytoskeletal contractility, we reproduce prominent anisotropic features in previously published experimental data on fibroblasts, endothelial cells, and epithelial cells on adhesive micropatterned substrates. Our work highlights the role of cytoskeletal anisotropy in the generation of cellular traction forces, and provides a computational strategy for investigating stress fiber anisotropy in dynamical and multicellular settings.

Author summary

Cells that make up multicellular life perform a variety of mechanical tasks such as pulling on surrounding tissue to close a wound. The mechanisms by which cells perform these tasks are, however, incompletely understood. In order to better understand how they generate forces on their environment, cells are often studiedin vitroon compliant substrates, which deform under the so called “traction forces” exerted by the cells. Mathematical models complement these experimental approaches because they help to interpret the experimental data, but most models for traction forces on adhesive substrates assume that cells contract isotropically, i.e., they do not contract in a specific direction. However, many cell types contain organized structures of stress fibers - strong contracting cables inside the cell - that enable cells to exert forces on their environment in specific directions only. Here we present a computational model that predicts both the orientations of these stress fibers as well as the forces that cells exert on the substrates. Our model reproduces both the orientations and magnitudes of previously reported experimental traction forces, and could serve as a starting point for exploring mechanical interactions in multicellular settings.
The gut microbiome and early-life growth in a population with high prevalence of stunting
Authors: Robertson Ruairi C. , Edens Thaddeus J. , Carr Lynnea , Mutasa Kuda , Evans Ceri , Gough Ethan K. , Geum Hyun Min , Baharmand Iman , Gill Sandeep K. , Ntozini Robert , Smith Laura E , Chasekwa Bernard , Majo Florence D. , Tavengwa Naume V. , Mutasa Batsirai , Francis Freddy , Tome Joice , Stoltzfus Rebecca J. , Humphrey Jean H. , Prendergast Andrew J. , Manges Amee R. ,   the SHINE Trial Team
Published: April 2022

Stunting affects one-in-five children globally and is associated with greater infectious morbidity, mortality and neurodevelopmental deficits. Recent evidence suggests that the early-life gut microbiome affects child growth through immune, metabolic and endocrine pathways, and microbiome perturbations may contribute to undernutrition. We examined early-life fecal microbiome composition and function in 875 stool samples collected longitudinally in 335 children from 1-18 months of age in rural Zimbabwe, from a cluster-randomized trial of improved water, sanitation, and hygiene (WASH), and improved infant and young child feeding (IYCF). Using whole metagenome shotgun sequencing, we examined the effect of the interventions, in addition to environmental or host factors including maternal HIV infection, on the succession of the early-life gut microbiome, and employed extreme gradient boosting machines (XGBoost) to model microbiome maturation and to predict child growth. WASH and IYCF interventions had little impact on the fecal microbiome, however children who were HIV-exposed but uninfected exhibited over-diversification and over-maturity of the early-life gut microbiome in addition to reduced abundance ofBifidobacteriaspecies. Taxonomic microbiome features were poorly predictive of linear and ponderal growth, however functional metagenomic features, particularly B-vitamin and nucleotide biosynthesis pathways, moderately predicted both attained linear and ponderal growth and growth velocity. We find that the succession of the gut microbiome in a population at risk of stunting is unresponsive to WASH and IYCF interventions, but is strongly associated with maternal HIV infection, which may contribute to deficits in growth. New approaches targeting the gut microbiome in early childhood may complement efforts to combat child undernutrition.

One sentence summary

The gut microbiome of rural Zimbabwean infants undergoes programmed maturation that is unresponsive to sanitation and nutrition interventions but is comprehensively modified by maternal HIV infection and can moderately predict linear growth.
eIf2α-regulated translation modulates the early adhesion of mesenchymal-like cells
Authors: Caillier Alexia , Morin Nadine , Lavigne Mathilde , Lambert Jean-Philippe , Mazrouï Rachid , Bergeman Jonathan , Huot Marc-Étienne
Published: April 2022

Cellular invasion is a complex process that requires several interdependent biological mechanisms, which are initiated by changes in adhesion that establish a morphology favorable for migration. Hence, the regulation of adhesion potential is a rate-limiting step in metastasis. Our previous work revealed that de novo translation is necessary to regulate the adhesion of mesenchymal-like cells; however, the underlying translational regulatory mechanism and the identity of newly synthesized proteins needed for the adhesion process remain unidentified. Here, we describe a translational regulatory mechanism that modulates mesenchymal cell adhesion. We observed a drastic decrease in translation during the initial phase of adhesion, followed by a reprogramming of the translatome, characterized by an orchestrated wave of mRNA translation that increases the expression of specific proteins involved in adhesion. We observed that phosphorylation of eukaryotic translation initiation factor 2 subunit alpha (eIF2α), which inhibits general translation initiation, was drastically increased at the beginning of cell adhesion. As adhesion progressed, the selective increase in the translation of adhesion-related mRNAs intensified as eIF2α phosphorylation gradually decreased over time in mensenchymal cells, but not in epithelial cells. Taken together, we have identified a translational regulatory mechanism specifically affecting the adhesion process of mesenchymal cells, as well as metastatic cells that have undergone epithelial-to-mesenchymal transition.

One sentence summary

Translation regulates mesenchymal cell adhesion
Mechanism of dopamine traveling waves in the striatum: theory and experiment
Authors: Matityahu Lior , Gilin Naomi , Atamna Yara , Tiroshi Lior , Wickens Jeffery R. , Goldberg Joshua A.
Published: April 2022

Striatal dopamine (DA) encodes reward, with recent work showing that DA release occurs in spatiotemporal waves. However, the mechanism of DA waves is unknown. Here we report that the striatal cholinergic neuropil also exhibits wave-like activity, and that the spatial scale of striatal DA release is extended by nicotinic receptors. Based on these findings we hypothesized that the local reciprocal interaction between cholinergic interneurons (CIN) and DA axons suffices to drive endogenous traveling waves. We show that the morphological and physiological properties of the CIN-DA interaction can be modeled as a reaction-diffusion system that gives rise to traveling waves. Analytically-tractable versions of the model show that the structure and the nature of propagation of CIN and DA traveling waves depend on their coupling, and that traveling waves can give rise to empirically observed correlations between these signals. Our model provides a biophysical mechanism for wave formation and predicts that the observed DA and CIN waves are strongly coupled phenomena.
CPGL: Prediction of compound-protein interaction by integrating graph attention network with long short-term memory neural network
Authors: Zhao Minghua , Yuan Min , Yang Yaning , Xu Steven X
Published: April 2022

Recent advancements of artificial intelligence based on deep learning algorithms have made it possible to computationally predict compound-protein interaction (CPI) without conducting laboratory experiments. In this manuscript, we integrated a graph attention network (GAT) for compounds and a long short-term memory neural network (LSTM) for proteins, used end-to-end representation learning for both compounds and proteins, and proposed a deep learning algorithm, CPGL (CPI with GAT and LSTM) to optimize the feature extraction from compounds and proteins and to improve the model robustness and generalizability. CPGL demonstrated an excellent predictive performance and outperforms recently reported deep learning models. Based on 3 public CPI datasets, C.elegans, Human and BindingDB, CPGL represented 1 - 5% improvement compared to existing deep-learning models. Our method also achieves excellent results on datasets with imbalanced positive and negative proportions constructed based on the above two datasets. More importantly, using 2 label reversal datasets, GPCR and Kinase, CPGL showed superior performance compared to other existing deep learning models. The AUC were substantially improved by 15% to 50% on the Kinase dataset, indicative of the robustness and generalizability of CPGL.
Functional characterization of bacterial isolates from dye decolorizing consortia and a step-up metabolic engineering based on NADH-regeneration
Authors: Rathod Jagat , Archana G.
Published: April 2022

Azo dye decolorizing acclimatized decolorizing consortia are enriched microbial sources of potential azoreductase-efficient bioremediation strains. Here, we characterized eight selected consortial members for their azo decolorization and azoreductase profiling. These efficient dye decolorizing bacterial isolates were affiliated to two major phyla viz. Firmicute (genus-Enterococcus) and Proteobacteria (γ-group). Redox-mediators such as AQDS and AQS were found to significantly increase decolorization except for menadione, and IR functional group signatures highlighted the azo bond reduction and degraded metabolites profiles of each strain. Among isolates, Enterococcus sp. L2 was found to be the most effective strain as it could reduce >90mg/L Reactive violet 5R (RV5R) dye in 3h of incubation. Furthermore, strain L2 possesses profound high NADH and NADPH-dependent azoreductase activity which also corroborated with its superior azo decolorization. As per physicochemical parameters, strain L2 showed an optimum decolorization at pH 8, 40 °C and up to 2% w/v salinity. To channelize reducing equivalence (NADH) to further enhance the dye decolorization in NADH-azoreductase efficient Enterococcus sp. L2, we augmented an NADH co-factor regeneration system. Using pMGS100, a Gram-positive expression vector a constitutive heterologous expression of Mycobacterium vaccae encoded NAD+-dependent formate dehydrogenase enhanced NADH pool which led to a significant 3.2 fold increased dye decolorization in Enterococcus sp. L2 harboring pMGS100 fdh along with a positive effect on growth. Ultimately, an augmentation of formate utilization step could further accelerate azo dye decolorization by fulfilling the co-factor (NADH) requirement of azoreductase along with a growth advantage in the non-model azoreductase-efficient environmentally important strain L2.
3D printed SAXS chamber for controlled in-situ dialysis and optical characterization
Authors: Ehm Tamara , Philipp Julian , Barkey Martin , Ober Martina , Brinkop Achim Theo , Simml David , Westphalen Miriam von , Nickel Bert , Beck Roy , Rädler Joachim O.
Published: April 2022

3D printing changes the scope of how samples can be mounted for small angle X-ray scattering (SAXS). In this paper we present a 3D printed X-ray chamber, which allows for in-situ exchange of buffer and in-situ optical transmission spectroscopy. The chamber is made of cyclic olefin copolymers (COC), including COC X-ray windows providing ultra low SAXS background. The design integrates a membrane insert for in-situ dialysis of the 100 µl sample volume against a reservoir, which enables measurements of the same sample under multiple conditions using an in-house X-ray setup equipped with a 17.4 keV molybdenum source. We demonstrate the design’s capabilities by measuring reversible structural changes in lipid and polymer systems as a function of salt concentration and pH. In the same chambers optical light transmission spectroscopy was carried out measuring optical turbidity of the mesophases and local pH values using pH-responsive dyes. Microfluidic exchange and optical spectroscopy combined with in-situ X-ray scattering enables vast applications for the study of responsive materials.
Why resource dynamics matter in the optimization of microbial communities
Authors: Letten Andrew D. , Ludington William B.
Published: April 2022

The impact of resource supply on microbial community dynamics is rarely treated explicitly in research into the control and optimization of natural and synthetic microbial communities. Using simulations, we show that compositional overlap between microbial communities decays rapidly with a change in the frequency of resource pulsing, particularly in the presence of a metabolic trade-off in resource affinity and maximum growth rate. We conclude that resource supply dynamics should be considered both a constraint and a tuning mechanism in microbial community optimization.
Do Neotropical adult dobsonflies (Megaloptera, Corydalidae) feed on solid material in the nature? Information from a gut content study
Authors: Álvarez Hugo Alejandro , de Figueroa José Manuel Tierno , Cebada-Ruiz Jorge Alejandro
Published: April 2022

Females of two species of corydalids (Megaloptera),Corydalus magnusContreras-Ramos, 1998 andPlatyneuromus soror(Hagen, 1861), are studied with the aim to determine if solid food is present in their guts, which would indicate the existence of feeding on solid food during the imaginal life in nature. Gut anatomical architecture is also studied and described for females of both species, showing no peculiarities regarding the existing information in other close related species and confirming that digestive morphology is conserved in Megaloptera, as previously reported in literature. No significant solid food was detected in any of the species, so in the nature, they may rely more on liquid sources and/or fat reserves produced in the larval stage for the energetic requirements of adult life.
Estimation of microtubule-generated forces using a DNA origami nanospring
Authors: Maleki Ali Nick , Huis in’t Veld Pim J. , Akhmanova Anna , Dogterom Marileen , Volkov Vladimir A.
Published: April 2022

Microtubules are dynamic cytoskeletal filaments that can generate forces when polymerizing and depolymerizing. Proteins that follow growing or shortening microtubule ends and couple forces to cargo movement are important for a wide range of cellular processes. Quantifying these forces and the composition of protein complexes at dynamic microtubule ends is challenging and requires sophisticated instrumentation. Here we present an experimental approach to estimate microtubule-generated forces through the extension of a fluorescent spring-shaped DNA origami molecule. Optical readout of the spring extension enables recording of force production simultaneously with single-molecule fluorescence of proteins getting recruited to the site of force generation. DNA nanosprings enable multiplexing of force measurements and only require a fluorescence microscope and basic laboratory equipment. We validate the performance of DNA nanosprings against results obtained using optical trapping. Finally, we demonstrate the use of the nanospring to study proteins that couple microtubule growth and shortening to force generation.