bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical assessment of persistence and adaptation in weeds with complex life cycles
Authors: Lauenroth Dana , Gokhale Chaitanya S.
Published: August 2022

Abstract

Herbicide-resistant weeds pose a significant threat to global food security. Perennial weed species are particularly troublesome. Such perennials asSorghum halepensespread quickly and are difficult to manage due to their ability to reproduce sexually via seeds and asexually through rhizomes. Our theoretical study ofSorghum halepenseincorporates this complex life cycle with control measures of herbicide application and tillage. Rooted in the biology and experimental data ofSorghum halepense, our population-based model predicts population dynamics and target-site resistance evolution in this perennial weed. We found that the resistance cost determines the standing genetic variation for herbicide resistance. The sexual phase of the life cycle, including self-pollination and seed bank dynamics, contributes substantially to the persistence and rapid adaptation ofSorghum halepense. While self-pollination accelerates target-site resistance evolution, seed banks significantly increase the probability of escape from control strategies and maintain genetic variation. Combining tillage and herbicide application effectively reduces weed densities and the risk of control failure without delaying resistance adaptation. We also show how mixtures of different herbicide classes are superior to rotations and monotreatment in controlling perennial weeds and resistance evolution. Thus, by integrating experimental data and agronomic views, our theoretical study synergistically contributes to understanding and tackling the global threat to food security from resistant weeds.
Automated cell type annotation and exploration of single cell signalling dynamics using mass cytometry
Authors: Kleftogiannnis Dimitrios , Gavasso Sonia , Tislevoll Benedicte Sjo , van der Meer Nisha , Motzfeldt Inga K. F. , Hellesøy Monica , Gullaksen Stein-Erik , Griessinger Emmanuel , Fagerholt Oda , Lenartova Andrea , Fløisand Yngvar , Gjertsen Bjørn Tore , Jonassen Inge
Published: August 2022

Mass cytometry by time-of-flight (CyTOF) is an emerging technology allowing for in-depth characterisation of cellular heterogeneity in cancer and other diseases. However, computational identification of cell populations from CyTOF, and utilisation of single cell data for biomarker discoveries faces several technical limitations, and although some computational approaches are available, high-dimensional analyses of single cell data remains quite demanding. Here, we deploy a bioinformatics framework that tackles two fundamental problems in CyTOF analyses namely: a) automated annotation of cell populations guided by a reference dataset, and b) systematic utilisation of single cell data for more effective patient stratification. By applying this framework on several publicly available datasets, we demonstrate that the Scaffold approach achieves good tradeoff between sensitivity and specificity for automated cell type annotation. Additionally, a case study focusing on a cohort of 43 leukemia patients, reported salient interactions between signalling proteins that are sufficient to predict short-term survival at time of diagnosis using the XGBoost algorithm. Our work introduces an automated and versatile analysis framework for CyTOF data with many applications in future precision medicine projects. Datasets and codes are publicly available at:https://github.com/dkleftogi/singleCellClassification
Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish
Authors: Rivera-Colón Angel G. , Rayamajhi Niraj , Minhas Bushra Fazal , Madrigal Giovanni , Bilyk Kevin T. , Yoon Veronica , Hüne Mathias , Gregory Susan , Cheng C.-H. Christina , Catchen Julian M.
Published: August 2022

Abstract

White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefishChampsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of bothC. esoxand its Antarctic sister species,Champsocephalus gunnari. TheC. esoxgenome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation inC. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonicalAFGPlocus organization is conserved inC. esoxandC. gunnari, but both show a translocation of twoAFGPcopies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.
3rd-ChimeraMiner: A pipeline for integrated analysis of whole genome amplification generated chimeric sequences using long-read sequencing
Authors: Lu Na , Qiao Yi , An Pengfei , Luo Jiajian , Bi Changwei , Li Musheng , Lu Zuhong , Tu Jing
Published: August 2022

Multiple displacement amplification (MDA) has become one of the most commonly used method of whole genome amplification (WGA) due to the high processivity, strand displacement capacity and high fidelity of the phi29 DNA polymerase, MDA generate vast amount of DNA with higher molecules weight (up to 100kb) and greater genome coverage. Along with the development of the sequencing platform, it is possible to sequence the MDA-amplified DNA molecules with over 20kb by long-read sequencing. However, one of the challenges is the formation of chimeras, which exist in all MDA products, and seriously interfere with the downstream analysis of the long-read sequencing data of MDA-amplified DNA. In this study, we constructed 3rd-ChimeraMiner, a chimera detection pipeline for analyzing the long-read sequencing of MDA products, recognizing chimeras, and integrating chimeras into the downstream analysis. Five sequencing data of MDA with different magnification fold were analyzed in here, the proportions of chimeras are much higher than that of next-generation sequencing reads and increase with the increase of magnification folds, ranging from 42% to over 76%. After comparing, 99.92% of recognized chimeras have been demonstrated not to exist in original genomes. After detecting chimeras by 3rd-ChimeraMiner, the full-length mapping ratio increased, means more PacBio data could be used in downstream analysis, and mean 97.77% inversions were removed after transferred chimeras into normal reads. 3rd-ChimeraMiner revealed efficiency and accuracy in discovering chimeras from long-read sequencing data of MDA, and is promising to be widely used in single-cell sequencing.
Long term maintenance of heterologous symbiont association in Acropora palmata on natural reefs
Authors: Elder Holland , Million Wyatt C. , Bartels Erich , Krediet Cory , Muller Erinn , Kenkel Carly D.
Published: August 2022

The sensitivity of reef-building coral to elevated temperature is a function of their symbiosis with dinoflagellate algae in the family Symbiodiniaceae. Changes in the composition of the endosymbiont community in response to thermal stress can increase coral thermal tolerance. Consequently, this mechanism is being investigated as a human-assisted intervention for rapid acclimation of coral in the face of climate change. Successful establishment of novel symbioses that increase coral thermal tolerance have been demonstrated in laboratory conditions; however, it is unclear how long these heterologous relationships persist in nature. Here, we show that Acropora palmata can form a novel symbiosis with Durusdinium spp. when reared in land-based aquaria. We tested the stability of this heterologous relationship by outplanting clonal replicates (ramets) of five A. palmata host genotypes to natural reefs in the lower Florida Keys. Amplicon sequencing analysis of ITS2-type profiles revealed that the majority of surviving ramets remained dominated by Durusdinium spp. two years after transplantation. However, 15% of ramets, including representatives of all genotypes, did exhibit some degree of symbiont shuffling or switching at six of eight sites, including complete takeover by site-specific strains of the native symbiont, Symbiodinium fitti. The predominant long-term stability of the novel symbiosis supports the potential effectiveness of symbiont modification as a management tool. However, the finding that 6–7 year-old coral can alter symbiont community composition in the absence of bleaching indicates that Symbiodiniaceae communities are indeed capable of greater flexibility under ambient conditions.
Temporal structure of two call types produced by competing male cicadas
Authors: Ishimaru Takahiro , Aihara Ikkyu
Published: August 2022

Male cicadas vocalize sounds to attract conspecific females. The acoustic traits of calls vary significantly among species and show unique temporal and spectral patterns that dynamically change, even in the same bout. While the calling behavior of a single cicada has been quantified for many species, the acoustic interaction between multiple cicadas and the usage of different call types have not been well studied. In this study, we examined the interaction between male cicadas (Meimuna opalifera) that utilize two types of calls. First, we caught two cicadas in their natural habitat and recorded their calls in the laboratory. Second, we detected the calls of each cicada and classified them into two types: Type I calls with a short duration and high repetition rate and Type II calls with a longer duration and low repetition rate. The analysis of the chorus structure demonstrated that the cicadas vocalized a Type II call immediately after another cicada vocalized a Type I call. Furthermore, we tested the hypothesis that such a timing strategy allowed the cicadas to effectively mask the calls of their competitors. Specifically, we conducted a numerical simulation randomizing the onsets of calls and compared the masking performance with empirical data, which did not support our hypothesis. This study highlights the well-organized structure of cicada calls, even in the choruses with multiple call types, and indicates these calls have a function other than male-male acoustic interaction that requires further investigation.

Summary statement

Male cicadas (Meimuna opalifera) produce two types of calls by synchronizing their temporal structure and switching call types when positioned close together.
Genetic Association of LDHA Variant g.2582481G>A with Racing Performance of Pakistani Pigeons
Authors: Saif Rashid , Zafar Muhammad Osama , Raza Muhammad Hassan
Published: August 2022

Pigeons are being used as a means of communication back in history due to their efficient flight stamina, navigational (homing) ability and endurance to harsh weather conditions. Due to these distinctive characteristics, pigeon racing and rearing has become a popular sport and hobby throughout the world, predominantly in Pakistan. The genetic tendency of LDHA gene in pigeons should be considered for understanding racing ability. The present study aimed to examine the genetic association of LDHA variant g.2582481G>A with racing performance in Pakistani pigeons. Our results demonstrated that 55% of the pigeon’s population was homozygous wild-type (G/G), 37.5% was heterozygous (G/A) and the remaining 7.5% was homozygous-mutant (A/A) at this locus. Furthermore, alternative allele frequencies within the best and low-performing cohorts of pigeons were 0.45 and 0.075 respectively. Furthermore, the Chi-Square association test was applied using PLINK data analysis toolset which showed a significant p-value of 1.381×10-4 with odds ratio (OR) of 10.09. Consequently, Pakistani pigeon population suggests a significant association of g.2582481G>A with racing performance similar to the other pigeon population of the world.
The Translation Initiation Factor Homolog,eif4e1c, Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration
Authors: Rao Anupama , Lyu Baken , Jahan Ishrat , Lubertozzi Anna , Zhou Gao , Tedeschi Frank , Jankowsky Eckhard , Kang Junsu , Carstens Bryan , Poss Ken , Baskin Kedryn , Goldman Joseph Aaron
Published: August 2022

The eIF4E family of translation initiation factors bind 5’ methylated caps and act as the limiting-step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting Eif4e1c functions in a novel pathway. Deletion ofeif4e1cin zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Althougheif4e1cis broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
Flexible multitask computation in recurrent networks utilizes shared dynamical motifs
Authors: Driscoll Laura , Shenoy Krishna , Sussillo David
Published: August 2022

Flexible computation is a hallmark of intelligent behavior. Yet, little is known about how neural networks contextually reconfigure for different computations. Humans are able to perform a new task without extensive training, presumably through the composition of elementary processes that were previously learned. Cognitive scientists have long hypothesized the possibility of a compositional neural code, where complex neural computations are made up of constituent components; however, the neural substrate underlying this structure remains elusive in biological and artificial neural networks. Here we identified an algorithmic neural substrate for compositional computation through the study of multitasking artificial recurrent neural networks. Dynamical systems analyses of networks revealed learned computational strategies that mirrored the modular subtask structure of the task-set used for training. Dynamical motifs such as attractors, decision boundaries and rotations were reused across different task computations. For example, tasks that required memory of a continuous circular variable repurposed the same ring attractor. We show that dynamical motifs are implemented by clusters of units and are reused across different contexts, allowing for flexibility and generalization of previously learned computation. Lesioning these clusters resulted in modular effects on network performance: a lesion that destroyed one dynamical motif only minimally perturbed the structure of other dynamical motifs. Finally, modular dynamical motifs could be reconfigured for fast transfer learning. After slow initial learning of dynamical motifs, a subsequent faster stage of learning reconfigured motifs to perform novel tasks. This work contributes to a more fundamental understanding of compositional computation underlying flexible general intelligence in neural systems. We present a conceptual framework that establishes dynamical motifs as a fundamental unit of computation, intermediate between the neuron and the network. As more whole brain imaging studies record neural activity from multiple specialized systems simultaneously, the framework of dynamical motifs will guide questions about specialization and generalization across brain regions.
Morphological Subprofile Analysis for Bioactivity Annotation of Small Molecules
Authors: Pahl Axel , Schölermann Beate , Rusch Marion , Dow Mark , Hedberg Christian , Nelson Adam , Sievers Sonja , Waldmann Herbert , Ziegler Slava
Published: August 2022

Fast prediction of mode of action for bioactive compounds would immensely foster bioactivity annotation in compound collections and may early on reveal off-targets in chemical biology research and drug discovery. A variety of target-based assays is available for addressing the modulation of druggable proteins. However, they cannot precisely predict how a compound would influence cellular processes due to polypharmacology. Furthermore, non-protein targets are often not considered. Morphological profiling, e.g., using the Cell Painting assay that monitors hundreds of morphological features upon compound perturbation and staining of cellular components, offers a fast, unbiased assessment of compound activity on various targets and cellular processes in one single experiment. However, due to incomplete bioactivity annotation and unknown activities of reference (landmark) compounds, prediction of bioactivity is not straightforward. Here we introduce the concept of subprofile analysis to map the mode of action for both reference and unexplored compounds. We defined mode-of-action clusters for a group of reference compounds and extracted cluster subprofiles that contain only a subset of morphological features (i.e., subprofiles) to represent a consensus profile. Subprofile analysis allows for assignment of compounds to, currently, ten different targets or modes of action in one single assay and bypasses the need of exploring all biosimilar reference compounds for the generation of target hypothesis. This approach will enable rapid bioactivity annotation of compound collections, particularly of uncharacterized small molecules, and will be extended to further bioactivity clusters in future. The data is public accessible viahttps://github.com/mpimp-comas/2022_pahl_ziegler_subprofilesand the web app toolhttp://cpcse.pythonanywhere.com/.
Outer membrane utilisomes mediate oligosaccharide uptake in gut Bacteroidetes
Authors: White Joshua B. R. , Silale Augustinas , Feasey Matthew , Heunis Tiaan , Zhu Yiling , Zheng Hong , Gajbhiye Akshada , Firbank Susan , Baslé Arnaud , Trost Matthias , Bolam David N. , Ranson Neil A. , van den Berg Bert
Published: August 2022

Bacteroidetes are abundant members of the human microbiota, with species occupying the distal gut capable of utilising a myriad of diet- and host-derived glycans. Transport of glycans across the outer membrane (OM) of these bacteria is mediated by SusCD protein complexes, comprising a membrane-embedded barrel and a lipoprotein lid, that are thought to operate via a ‘pedal-bin’ mechanism in which the lids open and close to facilitate substrate binding. However, additional cell surface-exposed lipoproteins, namely surface glycan binding proteins and glycoside hydrolases, play critical roles in the capture and processing of large glycan chains into transport-competent substrates. Despite constituting a crucial mechanism of nutrient acquisition by our colonic microbiota, the interactions between these components in the OM are poorly understood. Here we show that for the levan and dextran utilisation systems of Bacteroides thetaiotaomicron, the additional OM components assemble on the core SusCD transporter, forming stable glycan utilising machines which we term ‘utilisomes’. Single particle electron cryogenic electron microscopy (cryo-EM) structures in the absence and presence of substrate reveal concerted conformational changes that rationalise the role of each component for efficient nutrient capture, as well as providing a direct demonstration of the pedal bin mechanism of substrate capture in the intact utilisome.
Clonal evolution during metastatic spread in high-risk neuroblastoma
Authors: Gundem Gunes , Levine Max F. , Roberts Stephen S. , Cheung Irene Y , Medina-Martínez Juan S. , Feng Yi , Arango-Ossa Juan E. , Chadoutaud Loic , Rita Mathieu , Asimomitis Georgios , Zhou Joe , You Daoqi , Bouvier Nancy , Spitzer Barbara , Solit David B. , Cruz Dela Filemon , LaQuaglia Michael P. , Kushner Brian H. , Modak Shakeel , Shukla Neerav , Iacobuzio-Donahue Christine A. , Kung Andrew L. , Cheung Nai-Kong V. , Papaemmanuil Elli
Published: August 2022

High-risk neuroblastoma is generally metastatic and often lethal. Using genomic profiling of 470 sequential and spatially separated samples from 283 patients, we characterize subtype-specific genetic evolutionary trajectories from diagnosis, through progression and end-stage metastatic disease. Clonal tracing timed disease initiation to embryogenesis. Continuous acquisition of structural variants at disease defining loci (MYCN, TERT, MDM2-CDK4) followed by convergent evolution of mutations targeting shared pathways emerged as the predominant feature of progression. At diagnosis metastatic clones were already established at distant sites where they could stay dormant, only to cause relapses years later and spread via metastasis-to-metastasis and polyclonal seeding after therapy.
Not all seed transfer zones are created equal: Using fire history to identify seed needs in the Cold Deserts of the Western US
Authors: Barga Sarah C. , Kilkenny Francis F , Jensen Scott , Kulpa Sarah M. , Agneray Alison C. , Leger Elizabeth A.
Published: August 2022

Restoration planning requires a reliable seed supply, yet many projects occur in response to unplanned events. Identifying regions of greater risk could help guide seed procurement. Using fire perimeters (2000–2019), we investigated differences in fire occurrence (frequency, area burned, percent of area burned) among seed transfer zones within Cold Deserts of the US. We considered both provisional seed transfer zones (PSTZs), created using climate and stratified by ecoregion, and empirical seed transfer zones (ESTZs) for two species commonly used in restoration. Finally, we present a case study on fire occurrence within Northern Basin and Range greater sage-grouse Priority Areas for Conservation (PACs). Historic fire was effective for prioritizing seed zones: 23 of 132 PSTZs burned every year, and, within each ecoregion, two PSTZs comprised ≧ 50% of the total area burned across all years. Similarly, fire disproportionately occurred in some ESTZs; in the Northern Basin and Range, one (Artemisia tridentata- 83%) or two zones (Pseudoroegneria spicata- 65%) made up a majority of total area burned. Fire occurrence within PACs largely reflected the PSTZ and ESTZ priorities found for the ecoregion, with small exceptions. Imperiled PSTZs (high proportion burned) in PACs largely reflected the patterns found across the ecoregion, while imperiled ESTZs departed from ecoregional patterns. Considering historic disturbance can focus seed procurement efforts on regions that encounter regular disturbance, experience large disturbances, or have particular conservation value. This information can guide seed production, purchase, and storage, create more certainty for growers and managers, and ultimately increase restoration success.

IMPLICATIONS FOR PRACTICE

Available data on past disturbance patterns may inform strategies for prioritizing seed procurement decisions, especially as geospatial information becomes more widely available

The methods presented here illustrate an approach for using historic disturbance data to identify regions that are of greatest need for seed collection and conservation, using seed transfer zones within US Cold Desert ecoregions as an example

Identifying regions that experience disturbance over large areas or are likely to be imperiled due to disturbance at a high proportion can guide the collection and conservation of plant materials and better align available plant material with future restoration needs
The role of calcium, Akt and ERK signaling in cadmium-induced hair cell death
Authors: Galdieri Jennifer , Adams Chloe , Padilla María , Stawicki Tamara M.
Published: August 2022

Exposure to heavy metals has been shown to cause damage to a variety of different tissues and cell types including hair cells, the sensory cells of our inner ears responsible for hearing and balance. Elevated levels of one such metal, cadmium, have been associated with hearing loss and shown to cause hair cell death in multiple experimental models. While the mechanisms of cadmium-induced cell death have been extensively studied in other cell types they remain relatively unknown in hair cells. We have found that calcium signaling, which is known to play a role in cadmium-induced cell death in other cell types through calmodulin and CaMKII activation as well as IP3 receptor and mitochondrial calcium uniporter mediated calcium flow, does not appear to play a significant role in cadmium-induced hair cell death. While calmodulin inhibition can partially protect hair cells this may be due to impacts on mechanotransduction activity. Removal of extracellular calcium, and inhibiting CaMKII, the IP3 receptor and the mitochondrial calcium uniporter all failed to protect against cadmium-induced hair cell death. We also found cadmium treatment increased pAkt levels in hair cells and pERK levels in supporting cells. This activation may be protective as inhibiting these pathways enhances cadmium-induced hair cell death rather than protecting cells. Thus cadmium-induced hair cell death appears distinct from cadmium-induced cell death in other cell types where calcium, Akt and ERK signaling all promote cell death.
Single-cell analysis of non-alcoholic fatty livers identifies a role for the constitutive androstane receptor
Authors: Coassolo Laetitia , Liu Tianyun , Jung Yunshin , Taylor Nikki P. , Zhao Meng , Charville Gregory W. , Nissen Silas Boye , Yki-Jarvinen Hannele , Altman Russ , Svensson Katrin J.
Published: August 2022

Non-alcoholic fatty liver disease is a heterogeneous disease with unclear underlying molecular mechanisms. While several genetic risk factors have been identified, the cellular and molecular heterogeneity associated with the development of hepatic steatosis are still not fully understood. Here, we perform single-cell RNA sequencing of hepatocytes and hepatic nonparenchymal cells to map the lipid signatures in mice with non-alcoholic fatty liver disease (NAFLD). We uncover previously unidentified clusters of hepatocytes characterized by either high or low srebp1 expression with unique molecular signatures of lipid synthesis. We find that NAFLD livers have elevated expression of the constitutive androstane receptor (CAR), a gene previously associated with lipid synthesis. Furthermore, nuclear expression of CAR positively correlates with steatohepatitis in humans. These findings demonstrate significant cellular differences in lipid signatures and identify a gene with a high likelihood of being linked to hepatic steatosis in humans.
Wenzhou shrimp virus 8 (WzSV8) detection by unique inclusions in shrimp hepatopancreatic E-cells and by RT-PCR
Authors: Srisala Jiraporn , Thaiue Dararat , Saguanrut Piyachat , Taengchaiyaphum Suparat , Flegel Timothy W. , Sritunyalucksana Kallaya
Published: August 2022

The genome sequence of Wenzhou shrimp virus 8 (WzSV8) (GenBank recordKX883984.1) was described in 2015 from wide screening for RNA viruses in aquatic animals. A closely related sequence (GenBank recordOK662577.1) from the whiteleg shrimpPenaeus vannameiwas deposited in 2021 under the name Penaeus vannamei picornavirus (PvPV). In 2022 another closely related sequence (GenBank accession:OP265432) was submitted under the name Penaeus vannamei solinvivirus (PvSV). In 2021, prior to the publication of PvPV and PvSV, we used an RT-PCR method devised from the sequence of KX883984.1 (described herein) to screen for WzSV8 in specimens of cultivated shrimp. Samples that gave positive RT-PCR results were subsequently tested byin situhybridization (ISH) analysis to identify virus target tissues. Several tissues gave positive ISH results within morphologically normal nuclei. Thus, these tissues were of no use for diagnosis of WzSV8 by normal histological analysis. However, unique basophilic, cytoplasmic inclusions within vacuoles in the hepatopancreatic E-cells were also found in the same WzSV8-positive shrimp specimens, sometimes accompanied by a smaller eosinophilic inclusion. We call these Lightner double Inclusions (LDI) that can be considered pathognomonic for diagnosis of WzSV8 infection when detected using the light microscope. Although no current proof of WzSV8 is the cause of disease, it is important to investigate new viruses and related tissue anomalies, even from normal cultivated shrimp, to determine whether they may have any relationship to significant negative effects on the production of cultivated shrimp.
Vasodilators for acute heart failure—A protocol for a systematic review of randomized clinical trials with meta‐analysis and Trial Sequential Analysis
Authors: Grand Johannes , Nielsen Olav W. , Møller Jacob Eifer , Hassager Christian , Jakobsen Janus Christian
Published: August 2022

Background

Above one million annual hospitalizations occur with a primary diagnosis of acute heart failure in the US, with comparable numbers in Europe. Within 1 year, over a third of patients have died or been re‐hospitalized. Most patients have acutely elevated systemic and/or intra‐cardiac blood pressures as part of the acute heart failure syndrome. Most clinical trials of acute heart failure have aimed at reducing preload and/or afterload through drug‐induced vasodilation. However, recent European guidelines downgraded the treatment recommendation of vasodilators. We aim to assess the beneficial and harmful effects of vasodilators in the treatment of acute heart failure.

Methods

This protocol for a systematic review was undertaken using the recommendations of The Cochrane Collaboration and the Preferred Reporting Items for Systematic Reviews and Meta‐Analysis Protocols. We plan to include all randomized clinical trials assessing the use of vasodilators in the treatment of AHF. The systematic review will be conducted based on a systematic search of relevant major medical databases without date restrictions, including MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials (CENTRAL) in addition to clinical trial registries. We will begin the searches in August 2022. All included trials will be assessed and classified at low risk of bias or at high risk of bias. Our conclusions will be based on the results from the primary outcomes with concomitant low risk of bias. Extracted data will be analyzed using Trial Sequential Analysis 0.9.5.10, Review Manager 5.3, and SAS. We will assess the certainty of the evidence using the Grading of Recommendations Assessment, Development and Evaluation. We will register this systematic review at Prospero and aim to update it when new trials are published.

Discussion

This protocol defines the detailed methodology and approach used for a systematic review on whether vasodilation for acute heart failure improves patient outcome. This systematic review will potentially aid clinicians in deciding the optimal treatment of patients admitted with acute heart failure. Furthermore, this review will explore gaps in our knowledge and thus guide future research within acute heart failure.
Can cash incentives modify groundwater pumping behaviors? Evidence from an experiment in Punjab
Authors: Mitra Archisman , Balasubramanya Soumya , Brouwer Roy
Published: August 2022

As groundwater levels steadily decline in India, authorities are concerned about reducing extraction for irrigation purposes without jeopardizing food security. Very low or zero prices for electricity and water in agriculture is partly responsible for overextraction, but charging higher prices is politically not feasible. In this study, we describe the results of a pilot scheme implemented in Punjab, India, where farmers who enrolled were allocated a monthly entitlement of electricity units and compensated for unused electricity. Eight hours of uninterrupted daytime electricity supply were also provided under the scheme instead of the usual mix of daytime and night‐time supply. Analyzing data from a cross‐sectional farm household survey and instrumenting for enrollment, we find that self‐reported hours of irrigation for enrolled farmers were significantly lower than for non‐enrolled ones, with no impact on rice yields. We also find a reduction in monthly electricity consumption at electricity‐feeder level due to the pilot scheme using the synthetic control method. Our results suggest that the combination of daytime electricity provision and cash incentives for unused electricity has the potential to incentivize farmers to reduce electricity consumption and irrigation hours by at least 7.5% and up to 30% without impacting paddy yields.
Insights for Modern Applications of Psilocybin Therapy from a Case Study of Traditional Mazatec Medicine
Authors: González‐Mariscal Jesús M. , Sosa‐Cortés Paulina E.
Published: August 2022

The "people of knowledge" of traditional Mazatec medicine have preserved until today the ritual use of psilocybin mushrooms as part of their health care systems. The renewed interest in the effect of psilocybin on human consciousness for both therapeutic and recreational purposes usually obviates the historical and cultural background of indigenous peoples, as well as the legitimation of their practices and knowledge. In this article, through the case study of a foreign person who attended a Mazatec ritual specialist to participate in a ritual night ceremony known as velada, we show the importance of approaching research on psychoactive plants and mushrooms from a transdisciplinary and intercultural perspective, so that we can appreciate the profound complexity of the healing processes that take place in traditional indigenous contexts, as well as the limits of recreational uses or exclusively neopositivist and clinical approaches.
Laparoscopic versus open surgery for elderly patients with colorectal cancer: a systematic review and meta‐analysis of matched studies
Authors: Luo Weimin , Wu Mengyuan , Chen Yanling
Published: August 2022

Background

To compare clinical and survival outcomes between laparoscopic versus open surgery in elderly colorectal cancer patients.

Methods

PubMed, Embase and Scopus databases were systematically searched. The review included studies that were either randomized controlled trials (RCTs) or observational in design. STATA was used for statistical analysis.

Results

The meta‐analysis was conducted with 24 studies. Compared with elderly subjects with open surgery, those undergoing laparoscopic surgery had a lower risk of mortality (within 3 months postoperatively) (RR 0.70, 95% CI: 0.53, 0.94). The long‐term overall survival (HR 0.96, 95% CI: 0.89, 1.04), disease‐free survival (HR 1.02, 95% CI: 0.93, 1.13), risk of recurrence (RR 1.44, 95% CI: 0.90, 2.30) and readmission (RR 1.11, 95% CI: 0.88, 1.40) rates were statistically similar in both the groups. The operative time (in minutes) was higher (WMD 30.37, 95% CI: 17.75, 43.0) and the blood loss (in ml) was lower (WMD −78.85, 95% CI: −101.96, −55.75) in those undergoing laparoscopic surgery. The length of hospital stay (in days) (WMD −2.53, 95% CI: −3.11, −1.95) and the time of return of bowel movements (in days) (WMD −1.06, 95% CI: −1.20, −0.93) was lower in those with laparoscopic surgery. The pooled risk of complications was lower in those with laparoscopic surgery (RR 0.66, 95% CI: 0.60, 0.74), compared with open surgery.

Conclusions

Findings suggest that in elderly subjects with colorectal cancer, laparoscopic surgery appears to be more beneficial than open surgery and should be prioritized, subject to the availability of required technical skills and facilities.
The Water Budget Myth and Its Recharge Controversy: Linear vs. Nonlinear Models
Authors: Louwyck Andy , Vandenbohede Alexander , Heuvelmans Griet , Van Camp Marc , Walraevens Kristine
Published: August 2022

The water budget myth, which is the idea that safe pumping must not exceed the initial recharge, gave rise to a controversy about the role of recharge in assessing the sustainability of groundwater development. To refute the concept of safe yield, a simplified water budget equation is used, which equals the total pumping rate to the sum of capture and storage change. Since initial recharge and discharge are canceled out from this equation, it is concluded that sustainable pumping has nothing to do with recharge. Investigating the assumptions underlying this equation, it is seen that it expresses the superposition principle, which implicitly assumes the groundwater reservoir can be depleted indefinitely and boundary conditions are an infinite source of water. To evaluate sustainability, however, the limits of the aquifer system must be examined accurately. Theoretically, this can only be accomplished applying nonlinear models, in which case setting up the simplified water budget equation is impossible without knowing the initial conditions. Hence, excluding recharge when assessing sustainable pumping may not be done inconsiderately, which is illustrated by two examples. An analytical solution, developed by Ernst in 1971 to simulate flow to a well in a polder area with a nonlinear function for drainage, even shows that it is not necessarily a misconception to assume the cone of depression stops expanding when the pumping rate is balanced by the infiltration rate.
Structural characterization of the near‐surface region of soda–lime–silica glass by X‐ray photoelectron spectroscopy
Authors: Roy Barsheek , Baier Felix , Rosin Andreas , Gerdes Thorsten , Schafföner Stefan
Published: August 2022

The structural chemistry of the near‐surface region of soda–lime–silica (SLS) glass is described in terms of silicate network connectivity using X‐ray photoelectron spectroscopy (XPS). A thorough investigation of O1s and Si2p spectral lines by sequential XPS measurements, accompanied by Ar+ sputtering, revealed the variation of concentration of bridging oxygen, non‐bridging oxygen (NBO), and hydrous species (SiOH/H2O) as a function of depth from the glass surface. The Ototal/Si atomic ratio was calculated to vary in the range of 2.90–3.74 throughout the depth of sputtering for a total duration of 110 min, while considering each of the aforementioned oxygen speciations in the curve‐fitted spectra of O1s orbital. The glass surface up to a depth of 1–3 nm had the highest Ototal/Si ratio of 3.74, which was representative for a mechanically weak structure with Q0 and Q1 species, marked by the respective linkages of four and three NBOs per silica tetrahedral unit. This dictates the vital contribution of the hydrous species associated with silanol groups to the near‐surface structure of SLS glass.
The effect of educational interventions in managing nurses' alarm fatigue: An integrative review
Authors: Nyarko Brenda Abena , Nie Huiyu , Yin Zengzhen , Chai Xiaoya , Yue Liqing
Published: August 2022

Background

Alarm fatigue is becoming more widely acknowledged as a serious safety concern in modern clinical practice. Nurses are not always proficient in the alarms' functions and capabilities, and they do not undertake training regularly. Educating nurses on alarms maintains their knowledge and abilities in complex clinical settings. Some education has been undertaken to improve clinical alarm response, but the evidence for evaluating the effectiveness of nurse education interventions is limited.

Objective

To evaluate the effects of educational interventions for reducing alarm fatigue in nurses, including the reduction of excessive, false and non‐actionable alarms, which are major factors causing alarm fatigue in nurses.

Data sources

PUBMED, EMBASE, CINAHL, SCOPUS and OVID databases were systematically searched from 2016 to 2021.

Design

Integrative Review.

Review methods

An integrative review of literature was performed using the PRISMA checklist. Critical appraisal was done using Joanna Briggs Institute level of evidence.

Results

Thirteen studies met the inclusion criteria. The results of most studies showed that educational intervention was beneficial for reducing the total number of alarms and false alarms. Furthermore, nurses' perceptions and knowledge improved, but the reduction in nurses' alarm fatigue is uncertain. A positive effect in alarm management practices was identified after the educational intervention.

Conclusion

Educational intervention may be the way to manage nurses' alarm fatigue. The use of medical devices in hospitals is increasing exponentially, and for this reason, alarms are inevitable. The introduction of effective and continuous education and training programs for nurses concerning clinical alarm management as well as raising nurses' awareness of the occurrence of alarm fatigue is vital.
Eradicating ageism through social campaigns: An Israeli case study in the shadows of the COVID‐19 pandemic
Authors: Okun Sarit , Ayalon Liat
Published: August 2022

This study examined three social campaigns for the eradication of ageism that were undertaken in Israel during the COVID‐19 pandemic (April, 2020–May, 2021). The documentation and analysis of the campaigns were undertaken via the lens of the Theory of Change and Five Key Principles for social campaigns: planning strategically, communicating effectively, fostering community engagement, implementing key activities, and using research. We conducted desk reviews and qualitative interviews with the campaigns’ organizers. The Theory of Change implemented by the campaigns targeted self‐ageism among independent older people and/or employers of older adults. All campaigns emphasized “active aging” and “successful aging,” to decrease (self)‐ageism. The focus on one dimension of active and positive aging may result in ageism and exclusion of older people who do not fit into the category of independent and active people. The complex timing of the campaigns had influenced the degree of implementation of the five key principles. The joining of forces of different organizations and the employment of more diverse representations of old age, may facilitate the achievement of campaign goals. Finally, an empirical evaluation of social campaigns’ efforts is still necessary to gather evidence about the effectiveness of social campaigns.
Reducing neuropathies between the 2020 and 2021 Covid‐19 surges in a large UK intensive care unit: A quality improvement project
Authors: Jeffrey Jack , Miller Caroline , O'Sullivan Joel , Cahill Emma , Barrios Alejandro , Power Dominic
Published: August 2022

Background

Peripheral nerve injuries (PNIs) can be acquired by patients in intensive care unit (ICU) who are critically unwell with Covid pneumonitis. Prone position ventilation has been linked to this life‐changing complication.

Aim

To reduce the occurrence and severity of PNIs for patients with Covid pneumonitis requiring prone positioning whilst sedated and ventilated in ICU.

Study Design

This study is a quality improvement project that evolved over the course of the first two surges of Covid pneumonitis admissions within the ICU at the Queen Elizabeth Hospital Birmingham (Surge 1: March 2020–July 2020, 93 prone ventilation survivors; Surge 2: September 2020–May 2021, 309 prone ventilation survivors). Implementation of updated prone positioning guidelines that aimed to reduce the risk of PNI. This was supplemented by face‐to‐face teaching for ICU professionals. The number of patients who sustained PNI and the severity of such injuries were recorded.

Results

During the first surge 21 patients (22.6%) had at least one high grade PNI. During the second surge there were 12 patients (3.9%) sustaining an intermediate or high grade PNI. For PNI patients, there was an increase in the mean proning episodes (6–13) and duration (17.8–18.6 h). This represents an 82% reduction in PNI cases. High grade injuries reduced from 14/21 (66%) to 4/12 (33%).

Conclusions

Optimizing the position of patients in the prone position in ICU with Covid pneumonitis may be key in reducing the development of PNI. Changes to pharmacological management may have influenced the results seen in this study.

Relevance to Clinical Practice

Clinicians working within ICU with acutely unwell patients with Covid pneumonitis should acknowledge the heightened risk of PNI and take relevant steps to reduce the risk of injury acquisition.
Characterization of the novel HLA‐C*07:1023 allele by sequencing‐based typing
Authors: Blandin Lucie , Visentin Jonathan , Guidicelli Gwendaline , Rouzaire Paul , Lemal Richard
Published: August 2022

HLA‐C*07:1023 differs from HLA‐C*07:01:01:01 by one nucleotide substitution in codon 313 in exon 5.
History of Ultrasound in Medicine from its birth to date (2022), on occasion of the 50 Years Anniversary of EFSUMB. A publication of the European Federation of Societies for Ultrasound In Medicine and Biology (EFSUMB), designed to record the historical development of medical ultrasound
Authors: Dietrich Christoph F. , Bolondi Luigi , Duck Francis , Evans David H , Ewertsen Caroline , Fraser Alan G. , Gilja Odd Helge , Jenssen Christian , Merz Eberhard , Nolsoe Christian , Nürnberg Dieter , Lutz Harald , Piscaglia Fabio , Saftoiu Adrian , Vilmann Peter , Dong Yi , Hill Christopher R (Kit)
Published: August 2022

The history of the European Federation of Societies in Ultrasound in Medicine and Biology (EFSUMB) is closely related to the general history of ultrasound. In the presented paper the physical background and history of technologies including A-mode, Time motion or M-mode, 2D Imaging (B-mode) are summarized. In addition, ultrasound tissue characterization, Doppler ultrasound, 3D and 4D ultrasound, intracavitary and endoscopic ultrasound, interventional ultrasound, ultrasonic therapy, contrast enhanced ultrasound (CEUS) and key developments in echocardiography are discussed.
New Perspectives on Antimicrobial Agents: Isavuconazole
Authors: Lewis James S. , Wiederhold Nathan P. , Hakki Morgan , Thompson George R.
Published: August 2022

Isavuconazole is the newest of the clinically available advanced generation triazole antifungals and is active against a variety of yeasts, molds, and dimorphic fungi. Its current FDA-approved indications include the management of invasive aspergillosis as well as mucormycosis, though the latter indication is supported by limited clinical data.
Expansion of the Plaquing Host Range and Improvement of the Absorption Rate of a T5-like Salmonella Phage by Altering the Long Tail Fibers
Authors: Zhang Jing , Ning Houqi , Lin Hong , She Jiaying , Wang Luokai , Jing Yujie , Wang Jingxue
Published: August 2022

Genetic editing can be used to change or expand the host range of phages and have been successfully applied in T2, T4 and other phages to obtain engineered phages. However, there are hardly any similar reports on T5-like phages due to that the determinant regions related to their host ranges have not been completely clarified and the editing of T5-like phages is more difficult compared to other phages.
An Adjuvant-Based Approach Enables the Use of Dominant
HYG
and
KAN
Selectable Markers in Candida albicans
Authors: Park Sang On , Frazer Corey , Bennett Richard J.
Published: August 2022

Only a single dominant selectable marker has been widely adopted for use in the opportunistic fungal pathogen
Candida albicans
. This is in stark contrast to model fungi where a repertoire of dominant markers is readily available.
Library Screening for Synergistic Combinations of FDA-Approved Drugs and Metabolites with Vancomycin against VanA-Type Vancomycin-Resistant Enterococcus faecium
Authors: Gargvanshi Shivani , Gutheil William G.
Published: August 2022

Resistance to currently used antibiotics poses a serious threat to public health. This study reports a complete screen of 1,000 FDA-approved drugs and their metabolites against vancomycin-resistant
Enterococcus faecium
(VREfm) in both the absence and presence of vancomycin.