bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of carbon fixation on the mitigation of greenhouse gas emissions from livestock activities in Italy and the achievement of carbon neutrality
Authors: De Vivo Roberto , Zicarelli Luigi 
Published: March 2021

Abstract
Among the greenhouse gas emissions due to livestock activities there is, in addition to rumen methane, that which derives from the fermentation and management of manure from farmed animals. To feed the farmed animals, plants are used that fix carbon and therefore subtract carbon dioxide from the atmosphere. The emissions related to rumen fermentations, those related to manure, management, and spreading of animals of species reared in Italy, as well as manure released by grazing animals were quantified and summed. The emissions due to the respiration of animals were calculated and the carbon dioxide fixed by the main crops of zootechnical interest was calculated and then subtracted from the atmosphere. In addition, the emissions from the cultivation of plant species, attributable to the working of the soil, the production of fertilizers and pesticides, electricity, fuels, and the operation of machines, were also taken into account. The results of this elaboration show that in Italy the CO2 fixed in the vegetation cultivated to feed animals is about 10% higher than the sum of that emitted by the animals reared and by the entire process that is part of it. It could therefore be argued that the influence of carbon fixation should probably be taken into account to calculate the environmental impact in terms of carbon footprint of agricultural and animal products. In this way, carbon neutrality would be demonstrated, which characterizes the production processes of agricultural products and animal productions unlike other production cycles.
The balanced life: evolution of ventral shell weighting in gastropods
Authors: Vermeij Geerat J 
Published: March 2021

AbstractExaggerated morphologies present challenges for understanding the factors that enable, prevent or compel lineages to evolve unusual functional traits. Here, I examine the case of gastropods whose adult shells are bottom heavy by virtue of a thick, often broad, convex ventral callus deposit on the inner lip and adapical to the aperture. Data on the spatial, temporal and phylogenetic distribution of callus-bearing gastropods were gleaned from the literature and from personal observations on fossil and living gastropods in collections. An exaggerated ventral callus has evolved in ≥ 72 lineages of gastropods, all in warm, shallow waters, beginning in the Late Ordovician but mostly during and after the Late Cretaceous. The phylogenetic distribution of these gastropods is highly clumped, with multiple acquisitions in some clades (e.g. Stromboidea and Buccinoidea) and none in others (e.g. Conoidea). Functional considerations and comparisons indicate that the enhanced gravitational stability provided by a ventral callus evolved only in conditions of low-cost calcification and when predators capable of dislodging or overturning gastropods or causing them to flee were important agents of selection.
Chromosome-Scale Genome Sequence ofAlternaria alternataCausing Alternaria Brown Spot of Citrus
Authors: Gai Yunpeng , Ma Haijie , Chen Yanan , Li Lei , Cao Yingzi , Wang Mingshuang , Sun Xuepeng , Jiao Chen , Riely Brendan K. , Li Hongye 
Published: March 2021

Alternaria brown spot (ABS), caused by Alternaria alternata, is an economically important fungal disease of citrus worldwide. The ABS pathogen A. alternata tangerine pathotype can produce a host-specific ACT toxin, which is regulated by ACT toxin gene cluster located in the conditionally dispensable chromosome (CDC). Previously, we have assembled a draft genome of A. alternata tangerine pathotype strain Z7, which comprises 165 contigs. In this study, we report a chromosome-level genome assembly of A. alternata Z7 through the combination of Oxford Nanopore sequencing and Illumina sequencing technologies. The assembly of A. alternata Z7 had a total size of 34.28 Mb, with a GC content of 51.01% and contig N50of 3.08 Mb. The genome is encompassed 12,067 protein-coding genes, 34 ribosomal RNAs, and 107 transfer RNAs. Interestingly, A. alternata Z7 is composed of 10 essential chromosomes and 2 CDCs, which is consistent with the experimental evidences of pulsed-field gel electrophoresis. To our best knowledge, this is the first chromosome-level genome assembly of A. alternata. In addition, a database for citrus-related Alternaria genomes has been established to provide public resources for the sequences, annotation and comparative genomics data of Alternaria spp. The improved genome sequence and annotation at the chromosome level is a significant step toward a better understanding of the pathogenicity of A. alternata. The database will be updated regularly whenever the genomes of newly isolated Alternaria spp. are available. The citrus-related Alternaria genomes database is open accessible through the Citrus Fungal Disease Database.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Integration of a Lean Daily Management System into an Antimicrobial Stewardship Program
Authors: Wirtz Ann L. , Monsees Elizabeth A. , Gibbs Kate A. , Myers Angela L. , Burns Alaina N. , Lee Brian R. , El Feghaly Rana E. , Weddle Gina M. , Day James C. , Purandare Amol V. , Goldman Jennifer L. 
Published: March 2021

Introduction:
Growing demands and limited guidance on efficient use of resources to advance stewardship initiatives challenge antimicrobial stewardship programs (ASP).

Methods:
The primary aim was to incorporate a Lean Readiness and Metrics Board (RMB) into ASP and assess team member accountability and satisfaction with weekly 15-minute huddle participation within 1 year of implementation. ASP team survey data were analyzed for comments regarding Lean integration, team communication, and productivity. The second aim was to develop 5 shared metrics associated with quality, people, delivery, safety, and stewardship and evaluate ASP team productivity by assessing the impact of projects targeted at each specific metric. Pharmacist-physician ASP scheduling conflicts were addressed through identified rounding times under the “People” metric. The “Quality” metric assessed ASP intervention disagreement rate and collaborations that occurred to reduce disagreement. ASP tracked the number of individuals educated by ASP monthly through the “Delivery” metric.

Results:
Since August 2018, ASP replaced hour-long monthly meetings with weekly huddles at the RMB. On average, 14 members (88%) of the ASP participate weekly. Team members report improvement in communication and satisfaction with Lean integration. Metric utilization enhanced productivity. For the metrics under “People,” “Quality,” and “Delivery,” reduced scheduling conflicts occurred, the ASP intervention disagreement rate decreased (37.0%–25.6%; P < 0.001), and the ASP educated an average of 79 learners per month.

Conclusions:
Weekly huddles at the RMB enhanced communication and team accountability while visually displaying program needs, progress, and achievements. The RMB helps to ensure ongoing institutional commitment, and Lean methods show promise for evaluating and improving ASP productivity.
Decreasing Inappropriate Use of Antireflux Medications by Standardizing Gastroesophageal Reflux Disease Management in NICU
Authors: Shakeel Fauzia M. , Crews Jacquelyn , Jensen Preceous , Ritchey Andrea , Allen Megan , Mateus Jazmine , Machry Joana 
Published: March 2021

Introduction:
Gastroesophageal reflux (GER) is a functional self-limiting condition in neonates. When pathologic, it is called GER disease (GERD). There are wide variations in the management of signs, symptoms, and complications associated with GERD in the neonatal intensive care unit (NICU). Evidence does not support an empiric trial of GERD medications as a diagnostic tool or therapy in premature infants.

Methods:
A multidisciplinary team developed evidence-based clinical practice guidelines (CPG) for GERD management. Process improvement included developing a GERD management algorithm, electronic order sets, and education for all providers. Multiple plan-do-study-act cycles done.

Results:
Implementation of standardized GERD management guideline, decreased the overall use of antireflux medications from baseline, 15.1%–6.8% [χ2 (1, N = 1259) = 12.98, P < 0.001]. There was elimination of GERD medication use in preterm from baseline of 19.3% [χ2 (1, N = 220) = 12.18, P < 0.001]. The most frequently used GERD medication was lansoprazole, with an incorrect initial dosing rate of 55.0% that deceased to zero [χ2 (1, N = 33) = 10.73, P = 0.001]. Appropriate testing with PH probe with 24-hour multichannel impedance was observed (17.1%–28.0%) identifying patients with correct GERD diagnosis [χ2 (1, N = 101) = 1.41, P = 0.236]. Length of stay for GERD patient’s improved from a median of 89–53 days.

Conclusion:
Standardizing clinical management leads to best practices for GERD management with appropriate diagnostic testing, eliminating incorrect medication dosing, and improved patient safety with value-based outcomes.
Evidence-based Standardization of Constipation Management in the Emergency Department: A Quality Improvement Study
Authors: Lipshaw Matthew J. , Zamor Ronine L. , Carson Rebecca , Mallon Daniel , Sobolewski Brad , Vukovic Adam A. , Kurowski Eileen Murtagh 
Published: March 2021

Introduction:
Constipation is a common problem in pediatric patients. Abdominal radiographs (AXRs) are frequently obtained in the pediatric emergency department for diagnosis despite their poor reliability to rule out underlying pathology or prognostic ability to determine the degree of constipation. The goal of this quality improvement (QI) initiative was to standardize the diagnosis and management of constipation in the pediatric emergency department and urgent care in patients ages 6 months to 21 years and decrease AXR use by 20% and sustain this reduction for 12 months.

Methods:
This prospective QI project involved a multidisciplinary team at a large urban pediatric tertiary care center. The study team constructed a key driver diagram and identified interventions, such as creating a standardized evaluation and management algorithm for constipation, using free open-access medical education platforms, incorporating the electronic medical record interface, and expanding educational conferences to include standardized approach and discharge instructions for patients with constipation across all acuity levels. The primary measure of AXR utilization was tracked overtime on a statistical process control chart to evaluate the impact of interventions.

Results:
The percentage of visits for constipation that included an AXR decreased from a baseline of 49.6%–37.1%, a 25% reduction. Length-of-stay, return visits within 7 days, and inpatient admissions remained unchanged by the interventions.

Conclusions:
QI methodology successfully decreased AXR utilization in the evaluation of constipation across a broad spectrum of acuity levels. Further interventions may help to decrease the length of stay and further decrease AXR utilization.
A Fully Automated Pulsating Support System for Pressure Injury Prevention and Treatment in 10 Belgium Nursing Homes
Authors: Raepsaet Charlotte , Zwaenepoel Elien , Manderlier Bénédicte , Van Damme Nele , Verhaeghe Sofie , Van Hecke Ann , Beeckman Dimitri 
Published: March 2021

PURPOSE:
We studied pressure injury (PI) stage II-IV cumulative incidence and the change of PI status in the sacral area of nursing home residents associated with the use of a fully automated pulsating support system air mattress in use for 30 days. We also assessed caregivers', residents', and their family members' experiences and perceptions of mattress comfort and other factors such as pain.

DESIGN:
Multicenter cohort study.

SUBJECT AND SETTING:
A convenience sample of 40 residents residing in 10 Belgian nursing homes was recruited.

METHODS:
Pressure injury classification was confirmed using the European Pressure Ulcer Advisory Panel classification system. The Pressure Ulcer Scale for Healing (PUSH) tool was used to assess and measure PI status change. A comfort assessment was performed at end of the study. Cumulative PI incidence of stages II-IV was calculated, and frequencies and percentages were used to describe the results of the comfort assessments.

RESULTS:
Residents were allocated to the prevention group (n = 22) and to the treatment group (n = 18). The cumulative PI incidence was 4.5% (n = 1/22) in the prevention group. In the treatment group, the mean score on the PUSH tool decreased from 9.36 to 7.70 during the observation period, indicating an overall improvement. Four of the existing PIs healed, 17 PIs remained stable, and 1 PI deteriorated. The comfort questionnaires were completed by 76 nursing home caregivers, 21 family members, and 11 residents in the 10 participating nursing homes; the mattress comfort was perceived as very good, and pain was noted to decrease.

CONCLUSIONS:
Low cumulative PI incidence findings were observed with use of the mattress for the prevention of PIs and resulted in improvements in existing PIs, results which are consistent with several existing studies. The majority of the caregivers, residents, and family members evaluated the mattress as comfortable. Future research is needed to corroborate findings in larger randomized clinical trials.
The Microbiome and Metabolome of Malignant Fungating Wounds
Authors: Tilley Charles P. , Fu Mei R. , Qiu Jeanna M. , Comfort Christopher , Crocilla Brooke L. , Li Zujun , Axelrod Deborah 
Published: March 2021

PURPOSE:
Malignant fungating wounds (MFWs) afflict up to 14% of patients with advanced cancer. The bacterial community structures of MFW may influence the development and severity of wound symptoms. The purpose of this systematic review was to evaluate existing evidence regarding the relationship between microbiome and symptoms of MFWs.

METHODS:
A systematic review of the published literature from January 1995 to January 2020 was conducted. An established quality assessment tool was used to assess the quality of the included studies.

SEARCH STRATEGY:
We searched 4 major electronic databases and retrieved 724 articles; 7 met inclusion criteria.

FINDINGS/CONCLUSIONS:
Seven studies were included; the overall quality of the included 7 studies was ranked as adequate. Findings from the studies provided an incomplete characterization of the microbiome and metabolome of MFW; none included modern genomic technologies. Twenty different species of aerobes and 14 species of anaerobes were identified, with inconsistent identification of biofilms and multi-drug-resistant bacteria. Symptom occurrence increased with the number of bacteria species (P = .0003) and the presence of at least 1 anaerobe (P = .0006) in malignant wound beds. Cancer wound-derived odor was associated with dimethyl trisulfide and 4 fatty acid volatiles. Periwound and moisture-associated skin damage were associated with higher putrescine levels in exudates.

IMPLICATIONS:
Understanding the role of microbiota of MFW in developing or amplifying the severity of wound symptoms is the first step toward development of more precise and effective topical interventions.
Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps
Authors: Park Jiwoon , Foox Jonathan , Hether Tyler , Danko David , Warren Sarah , Kim Youngmi , Reeves Jason , Butler Daniel J. , Mozsary Christopher , Rosiene Joel , Shaiber Alon , Afshinnekoo Ebrahim , MacKay Matthew , Bram Yaron , Chandar Vasuretha , Geiger Heather , Craney Arryn , Velu Priya , Melnick Ari M. , Hajirasouliha Iman , Beheshti Afshin , Taylor Deanne , Saravia-Butler Amanda , Singh Urminder , Wurtele Eve Syrkin , Schisler Jonathan , Fennessey Samantha , Corvelo André , Zody Michael C. , Germer Soren , Salvatore Steven , Levy Shawn , Wu Shixiu , Tatonetti Nicholas , Shapira Sagi , Salvatore Mirella , Loda Massimo , Westblade Lars F. , Cushing Melissa , Rennert Hanna , Kriegel Alison J. , Elemento Olivier , Imielinski Marcin , Borczuk Alain C. , Meydan Cem , Schwartz Robert E. , Mason Christopher E. 
Published: March 2021

AbstractThe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression states. In particular, cardiac and lung tissues revealed the largest degree of splicing isoform switching and cell expression state loss. Overall, these findings reveal a systemic disruption of cellular and transcriptional pathways from COVID-19 across all tissues, which can inform subsequent studies to combat the mortality of COVID-19, as well to better understand the molecular dynamics of lethal SARS-CoV-2 infection and other viruses.
A multi-phase multi-objective dynamic genome-scale model shows different redox balancing among yeast species in fermentation
Authors: Henriques David , Minebois Romain , Mendoza Sebastian , Macías Laura G. , Pérez-Torrado Roberto , Barrio Eladio , Teusink Bas , Querol Amparo , Balsa-Canto Eva 
Published: March 2021

ABSTRACTYeasts constitute over 1500 species with great potential for biotechnology. Still, the yeastSaccharomyces cerevisiaedominates industrial applications and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts’ metabolic specificity in batch cultures. Here we propose a multi-phase multi-objective dynamic genome-scale model of yeast batch cultures that describes the uptake of carbon and nitrogen sources and the production of primary and secondary metabolites. The model integrates a specific metabolic reconstruction, based on the consensus Yeast8, and a kinetic model describing the time-varying culture environment. Besides, we proposed a multi-phase multi-objective flux balance analysis to compute the dynamics of intracellular fluxes. We then compared the metabolism ofS. cerevisiaeandS. uvarumstrains in a rich medium fermentation. The model successfully explained the experimental data and brought novel insights into how cryotolerant strains achieve redox balance. The proposed model (along with the corresponding code) provides a comprehensive picture of the main steps occurring inside the cell during batch cultures and offers a systematic approach to prospect or metabolically engineering novel yeast cell factories.IMPORTANCENon-conventional yeast species hold the promise to provide novel metabolic routes to produce industrially relevant compounds and tolerate specific stressors, such as cold temperatures. This work presented and validated the first multi-phase multi-objective genome-scale dynamic model to describe carbon and nitrogen metabolism throughout batch fermentation. To test and illustrate its performance, we considered the comparative metabolism of three yeast strains of the Saccharomyces genus in rich medium fermentation. The study revealed that cryotolerant Saccharomyces species might use the GABA shunt and the production of reducing equivalents as alternative routes to achieve redox balance, a novel biological insight worth being explored further. The proposed model (along with the provided code) can be applied to a wide range of batch processes started with different yeast species and media, offering a systematic and rational approach to prospect non-conventional yeast species metabolism and engineering novel cell factories.
A High Rate of COVID-19 Vaccine Hesitancy Among Arabs: Results of a Large-scale Survey
Authors: Qunaibi Eyad A. , Helmy Mohamed , Basheti Iman , Sultan Iyad 
Published: March 2021

AbstractIn this study, we present the results of the first large-scale multinational study (36,220 participants) that measures vaccine hesitancy among Arab-speaking subjects. Our analysis shows a significant rate of vaccine hesitancy among Arabs in and outside the Arab region (83% and 81%, respectively). The most cited reasons for hesitancy are concerns about side effects and distrust in healthcare policies, vaccine expedited production, published studies and vaccine producing companies. We also found that female participants, participants 30-59 year-old, those with no chronic diseases, those with lower-level of academic education, and those who do not know the type of vaccine authorized in their countries are more hesitant to receive COVID-19 vaccination. On the other hand, participants who regularly receive the influenza vaccine, health care workers, and those from countries with higher rates of COVID-19 infections showed more vaccination willingness. Interactive representation of our results is posted on our project website at https://mainapp.shinyapps.io/CVHAA.
c-Myc plays a key role in IFN-γ induced persistence ofChlamydia trachomatis
Authors: Vollmuth Nadine , Janaki-Raman Sudha , Schlicker Lisa , Kurmasheva Naziia , Schmitz Werner , Schulze Almut , Rudel Thomas , Rajeeve Karthika 
Published: March 2021

SummaryChlamydia trachomatis (Ctr)can persist over long periods of time within their host cell and thereby establish chronic infections. One of the major inducers of chlamydial persistence is interferon-gamma (IFN-γ) released by immune cells as a mechanism of immune defence. IFN-γ activates the catabolic depletion of L-tryptophan (Trp) via indoleamine 2,3-dioxygenase (IDO), resulting in persistentChlamydia. Here we show that IFN-γ depletes c-Myc, the key regulator of host cell metabolism, in a STAT1-dependent manner. Expression of c-Myc rescuedChlamydiafrom IFN-γ-induced persistence in cultured cell lines, but also in human fallopian tube organoids. L-tryptophan concentrations control c-Myc levels via the PI3K-GSK3ß axis. Unbiased metabolic analysis revealed thatChlamydiainfection reprograms the host cell tricarboxylic acid (TCA) cycle to support pyrimidine biosynthesis. Addition of TCA cycle intermediates or pyrimidine/purine nucleosides to infected cells rescuedChlamydiafrom IFN-γ-induced persistence. Thus, our results challenge the longstanding hypothesis of L-tryptophan depletion through IDO as the major mechanism of IFN-γ-induced metabolic immune defence and significantly extends the understanding of the role IFN-γ as a broad modulator of host cell metabolism.