bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peri-operative oxygen consumption revisited
Authors: Jakobsson Julia , Norén Carl , Hagel Eva , Kalman Sigridur , Bartha Erzsébet 
Published: August 2020

BACKGROUND
Monitoring oxygen consumption (VO2) is neither recommended nor included in peri-operative haemodynamic algorithms aiming at optimising oxygen delivery (DO2) in major abdominal surgery. Estimates of peri-operative VO2 changes are uncertain in earlier publications and have limited generalisability in the current high-risk surgical population. In a prospective non-interventional observational study in elderly patients undergoing major abdominal procedures, we investigated the change of VO2 after induction of anaesthesia and secondarily, the further changes during and after surgery in relation to DO2 and estimated oxygen extraction ratio (O2ER) by routine monitoring.

METHODS
VO2 was determined by indirect calorimetry (QuarkRMR) in 20 patients more than 65 years (ASA II to IV), scheduled for elective open upper abdominal surgery with combined epidural and general anaesthesia. Data were collected during 20-minute periods pre-operatively and after anaesthesia induction, with subsequent measurements during surgery and postoperatively. Simultaneously, DO2 was monitored using LiDCOplus. The O2ER was estimated from arterial–central venous oxygen content calculation. Mixed models were used to analyse the peri-operative changes.

RESULTS
VO2 decreased after induction of anaesthesia by a mean of 34% (95% CI, 28 to 39). After 2 h of surgery, VO2 was reduced by 24% (95% CI, 20 to 27) compared with the awake baseline measurements. Pre-operative mean DO2 was 440 (95% CI, 396 to 483) ml min−1 m−2 and decreased by a mean of 37% (95% CI, 30 to 43) during anaesthesia. The estimated O2ER did not change intra-operatively 0.24 (95% CI, 0.21 to 0.26) but increased postoperatively to 0.31 (95% CI, 0.27 to 0.36). The changes of VO2 were parallel with changes of DO2 and O2ER in the intra-operative period.

CONCLUSION
General anaesthesia reduced VO2 by approximately a third in elderly patients undergoing major abdominal surgery. Parallel changes of intra-operative VO2 and delivery were demonstrated while oxygen extraction was low. The relevance of these changes needs further assessment in relation to outcomes and haemodynamic interventions.

TRIAL REGISTRATION
Clinicaltrials.gov NCT 03355118.
A systematic review of the methodology of sonographic assessment of upper limb activities–associated carpal tunnel syndrome
Authors: Fong Sze Wah , Liu Bosco Wang Fung , Sin Chun Lok , Lee King Sang , Wong Tsun Ming , Choi Ka Sin , Yang Yi-Ping , Lin Yi-Ying , Chien Yueh , Tarng Yih-Wen , Chen Cheng-Fong , Lin Liang-Ting 
Published: August 2020

Background:
Various upper limb activities were speculated to be associated with the development of carpal tunnel syndrome (CTS). Nonetheless, there are currently no standardization on the uses of parameters in CTS assessments, nor are there any conclusive findings regarding the usefulness of various sonographic measurements in studies of different upper limb activities. In this review, we intend to evaluate the methodology of assessing CTS induced by upper limb activities with ultrasonographic technique and provide corresponding suggestions.

Methods:
Clinical studies on the association between upper limb activities and prevalence of CTS using ultrasonography were recruited in a database research on the basis of a procedural selection criteria and reviewed. The following qualitative items were extracted: characteristics of studies, scanning methods, selection of sonographic parameters, and related article findings.

Results:
Eleven studies were qualified for this review. Three studies were computer keyboard typing related, five studies were electronic device related, and three studies were wheelchair-related. All sampled articles included cross-sectional area (CSA) at the pisiform level. The swelling ratio (SR) and flattening ratio (FR) at the hamate level are also used in most studies in addition to the CSA at the pisiform level. The effectiveness of such parameters is subjected to various confounding factors such as age, weight, body mass index, and wrist anthropometrics, suggesting CSA and SR with sufficient levels had significant values as sonographic parameters. Values of parameters were found affecting symptomatic signs and hand dominance.

Conclusion:
Ultrasound scan is a suitable tool to assess the relationship between upper limb activity and CTS. CSA at the pisiform level and SR and the FR at the hamate levels are generally suitable in upper limb–associated CTS investigations. Specific study designs are required to eliminate different confounding factors accordingly.
Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades
Authors: Teng Xufei , Li Qianpeng , Li Zhao , Zhang Yuansheng , Niu Guangyi , Xiao Jingfa , Yu Jun , Zhang Zhang , Song Shuhui 
Published: August 2020

AbstractCOVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months and a global fight against both is still going on. Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code, to molecular mechanisms based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on replicase-transcriptase complex. Our analysis starts with primary sequence information and identity-based phylogeny based on 22,051 SARS-CoV-2 genome sequences and evaluation of sequence variation patterns as mutation spectrum and its 12 permutations among organized clades tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings include: (1) The most dominant mutation is C-to-U permutation whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity albeit assumed most slightly deleterious. (2) The second abundance group includes: three negative-strand mutations U-to-C, A-to-G, G-to-A and a positive-strand mutation G-to-U generated through an identical mechanism as C-to-U. (3) A clade-associated and biased mutation trend is found attributable to elevated level of the negative-sense strand synthesis. (4) Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes. These findings demand a bioinformatics platform where emerging mutations are mapped on to mostly subtle but fast-adjusting viral proteomes and transcriptomes to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications. Such thoughts and actions are in desperate need, especially in the middle of theWar against COVID-19.
Climate change and chill accumulation: implications for tree fruit production in cold-winter regions
Authors: Noorazar Hossein , Kalcsits Lee , Jones Vincent P. , Jones Matthew S. , Rajagopalan Kirti 
Published: August 2020

AbstractWinter chill accumulation is critical for the productivity and profitability of perennial tree fruit systems. Several studies have quantified the impacts of global warming on chill accumulation in the warmer production regions of the world, where insufficient chill events occur and their frequency is increasing. In contrast, we focus on a region with relatively cold winters–the Pacific Northwest United States (PNW)–where insufficient chill events are currently absent, and quantify the potential for introduction of these risks under climate change. Results identified spatial variation within the PNW, with chill accumulation projected to increase in some areas but decrease in others. There was also spatiotemporal variation in the driving factors of changes to chill accumulation. Even with decreases in chill accumulations, there are likely minimal issues with insufficient chill accumulation. However, delayed chill accumulation in combination with advances in the onset of heat accumulation can potentially shift the region from one where spring phenology is primarily forcing-driven to one where the dynamic interplay between chilling and forcing processes become important. These interactions might create production risks for varieties with high chill requirements, post mid-21st-century under high emissions scenarios. Future work should focus on understanding, modeling, and projecting responses across these overlapping chilling and forcing processes. Additionally, given significant spatial differences across a relatively small geographic range, it is also critical to understand and model these dynamics at a local landscape resolution for regions such as the PNW.
Rapidin vitroprototyping of O-methyltransferases for pathway applications inEscherichia coli
Authors: Haslinger Kristina , Hackl Thomas , Prather Kristala L.J. 
Published: August 2020

AbstractO-methyltransferases are ubiquitous enzymes involved in biosynthetic pathways for secondary metabolites such as bacterial antibiotics, human catecholamine neurotransmitters, and plant phenylpropanoids. While thousands of putative O-methyltransferases are found in sequence databases, few examples are functionally characterized. From a pathway engineering perspective, however, it is crucial to know the substrate and product ranges of the respective enzymes to fully exploit their catalytic power.In this study, we developed anin vitroprototyping workflow that allowed us to screen ~30 enzymes against five substrates in three days with high reproducibility. We combinedin vitrotranscription/translation of the genes of interest with a microliter-scale enzymatic assay in 96-well plates. The substrate conversion was indirectly measured by quantifying the consumption of the S-adenosyl-L-methionine co-factor by time-resolved fluorescence resonance energy transfer rather than time-consuming product analysis by chromatography. This workflow allowed us to rapidly prototype thus-far uncharacterized O-methyltransferases for future use as biocatalysts.
Nonclassical nucleation of protein mesocrystals via oriented attachment
Authors: Van Driessche Alexander E.S. , Van Gerven Nani , Joosten Rick R.M. , Ling Wai Li , Bacia Maria , Schoehn Guy , Sommerdijk Nico A.J.M. , Sleutel Mike 
Published: August 2020

AbstractSelf-assembly of proteins holds great promise for the bottom-up design and production of synthetic biomaterials. In conventional approaches, designer proteins are pre-programmed with specific recognition sites that drive the association process towards a desired organized state. Although proven effective, this approach poses restrictions on the complexity and material properties of the end-state. An alternative, hierarchical approach that has found wide adoption for inorganic systems, relies on the production of crystalline nanoparticles which in turn become the building blocks of a next-level assembly process driven by oriented attachment (OA). As it stands, OA has not been observed for proteins. Here we employ cryoEM in the high nucleation rate limit of protein crystals and map the self-assembly route at molecular resolution. We observe the initial formation of facetted nanocrystals that merge lattices by means of OA alignment well before contact is made, satisfying non-trivial symmetry rules in the process. The OA mechanism yields crystal morphologies that are not attainable through conventional crystallization routes. Based on these insights we revisit a system of protein crystallization that has long been classified as non-classical, but our data is in direct conflict with that conclusion supporting a classical mechanism that implicates OA. These observations raise further questions about past conclusions for other proteins and illustrate the importance of maturation stages after primary nucleation has taken place.
Assessing the Cognitive Status of Drosophila by the Value-Based Feeding Decision
Authors: Yu Chih-Chieh , Chang Ferng-Chang , Hong Yong-Huei , Li Jian-Chiuan , Chen Po-Lin , Chen Chun-Hong , Chiu Tzai-Wen , Lu Tsai-Te , Wang Yun-Ming , Kao Chih-Fei 
Published: August 2020

AbstractDecision making is considered an important aspect of cognitive function. Impaired decision making is a consequence of cognitive decline caused by various physiological conditions, such as aging and neurodegenerative diseases. Here we exploited the value-based feeding decision (VBFD) assay, which is a simple sensory-motor task, to determine the cognitive status of Drosophila. Our results indicated the deterioration of VBFD is notably correlated with aging and neurodegenerative disorders. Restriction of the mushroom body (MB) neuronal activity partly blunted the proper VBFD. Furthermore, using the Drosophila polyQ disease model, we demonstrated the impaired VBFD is ameliorated by the dinitrosyl iron complex (DNIC-1), a novel and steady nitric oxide (NO)-releasing compound. Therefore we propose that the VBFD assay provides a robust assessment of Drosophila cognition and can be used to characterize additional neuroprotective interventions.
Histone demethylome map reveals combinatorial gene regulatory functions in embryonic stem cells
Authors: Kumar Yogesh , Tripathi Pratibha , Dakle Pushkar , Mehravar Majid , Pandey Varun K. , Bullen Michael J. , Zhang Zhongming , Hathiwala Dhaval , Kerenyi Marc , Woo Andrew , Ghamari Alireza , Cantor Alan B. , Wong Lee H. , Kim Jonghwan , Glass Kimberly , Yuan Guo-Cheng , Pinello Luca , Orkin Stuart H. , Das Partha Pratim 
Published: August 2020

SummaryEpigenetic regulators and transcription factors establish distinct regulatory networks for gene regulation to maintain the embryonic stem cell (ESC) state. Although much has been learned regarding individual epigenetic regulators, their combinatorial functions remain elusive. Here, we report previously unknown combinatorial functions of histone demethylases (HDMs) in gene regulation of mouse ESCs. Generation of a histone demethylome (HDMome) map of 20 well-characterized HDMs based on their genome-wide binding revealed co-occupancy of HDMs in different combinations: KDM1A-KDM4B-KDM6A and JARID2-KDM2B-KDM4A-KDM4C-KDM5B largely co-occupy at enhancers and promoters, respectively. Mechanistic studies uncover that KDM1A-KDM6A combinatorially modulates P300/H3K27ac, H3K4me2 deposition and OCT4 recruitment that directs the OCT4/CORE regulatory network for target gene expression; while co-operative actions of JARID2-KDM2B-KDM4A-KDM4C-KDM5B control H2AK119ub1 and bivalent marks of polycomb-repressive complexes that facilitate the PRC regulatory network for target gene repression. Thus, combinatorial functions of HDMs differentially impact gene expression programs in mESCs.
Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney
Authors: Takemon Yuka , Chick Joel M. , Gyuricza Isabela Gerdes , Skelly Daniel A. , Devuyst Olivier , Gygi Steven P. , Churchill Gary A. , Korstanje Ron 
Published: August 2020

AbstractThe kidney is an excellent model for studying organ aging. Kidney function shows steady decline with age and is easy to assay using urine or blood samples. However, little is known about the molecular changes that take place in the kidney during the aging process. In order to better understand the molecular changes that occur with age, we measured mRNA and protein levels in 188 genetically diverse mice at ages 6, 12, and 18 months. We observed distinctive change in mRNA and protein levels as a function of age. Changes in both mRNA and protein are associated with increased immune infiltration and decreases in mitochondrial function. Proteins show a greater extent of change and reveal changes in a wide array of biological processes including unique, organ-specific features of aging in kidney. Most importantly, we observed functionally important age-related changes in protein that occur in the absence of corresponding changes in mRNA. Our findings suggest that mRNA profiling alone provides an incomplete picture of molecular aging in the kidney and that examination of changes in proteins is essential to understand aging processes that are not transcriptionally regulated.
The ascorbate-deficient guinea pig model of shigellosis allows the study of the entireShigellalife cycle
Authors: André Antonin C , Mulet Céline , Anderson Mark C , Injarabian Louise , Buch Achim , Prade Verena Marina , Walch Axel Karl , Lykkesfeldt Jens , Sansonetti Philippe , Marteyn Benoit S 
Published: August 2020

AbstractShigellaspp. are the causative agents of bacillary dysentery or shigellosis, mainly in children living in developing countries. The study ofShigellaentire life cyclein vivoand the evaluation of vaccine candidates’ protection efficacy have been hampered by the lack of a suitable animal model of infection (1). None of the ones evaluated so far (mouse, rabbit, guinea pig) allows to recapitulate shigellosis symptoms uponShigellaoral challenge. Historical reports suggest that dysentery and scurvy are both metabolic diseases associated with ascorbate-deficiency. Mammals which are susceptible toShigellainfection (humans, non-human primates and guinea pigs) are the lonely ones which are unable to synthesize ascorbate. We optimized a low-ascorbate diet to induce moderate ascorbate-deficiency but not scurvy in guinea pigs (Ascplasmaconc.=1.6 μM vs 36 μM with optimal ascorbate supply). We demonstrated that moderate ascorbate-deficiency increases shigellosis severity during extended period of time (up to 48h) with all strains tested (Shigella flexneri5a and 2a,Shigella sonnei). At late time-points, a massive influx of neutrophils was observed both within the disrupted colonic mucosa and in the luminal compartment, althoughShigellaremains able to disseminate deep into the organ to reach the sub-mucosal layer and the bloodstream. This new model of shigellosis opens new doors for the study both ofShigellainfection strategy and innate and adaptive immune responses toShigellainfection. It may be also of a great interest to study the virulence of other pathogen for which no suitable animal model of infection is available (Vibrio cholerae, Yersinia pestis, Mycobacterium tuberculosisorCampylobacter jejuni, among others).SignificanceThe study ofShigellavirulence cyclein vivohas been hampered by the lack of a suitable animal model, which would allow the colonic mucosa infection upon oral challenge. Based on historical reports and physiological aspects, it was suggested that ascorbate-deficiency may stand as a new dysentery risk-factor. To test this hypothesis, we set up a new ascorbate-deficient guinea pig model and demonstrated for the first time that theShigellainfectious process occurred for extended period of time (up to 48h) and demonstrated that shigellosis severity was higher in ascorbate-deficient animal. Ascorbate-deficient guinea pig model of infection may be used to assess the virulence of other pathogens for which no suitable animal model of infection is still lacking.
Structural analysis of theLegionella pneumophilaDot/Icm Type IV Secretion System Core Complex
Authors: Durie Clarissa L. , Sheedlo Michael J. , Chung Jeong Min , Byrne Brenda G. , Su Min , Knight Thomas , Swanson Michele S. , Lacy D. Borden , Ohi Melanie D. 
Published: August 2020

AbstractLegionella pneumophilais an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires’ Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver effector proteins into host cells. Compared to prototypical T4SSs, the Dot/Icm assembly is much larger, containing ~27 different components including a core complex reported to be composed of five proteins: DotC, DotD, DotF, DotG, and DotH. Using single particle cryo-electron microscopy (cryo-EM), we report reconstructions of the core complex of the Dot/Icm T4SS that includes a symmetry mismatch between distinct structural features of the outer membrane cap (OMC) and periplasmic ring (PR). We present models of known core complex proteins, DotC, DotD, and DotH, and two structurally similar proteins within the core complex, DotK and Lpg0657. This analysis reveals the stoichiometry and contact interfaces between the key proteins of the Dot/Icm T4SS core complex and provides a framework for understanding a complex molecular machine.
Estimation of greenhouse gas emissions from three livestock production systems in Ethiopia
Authors: Berhe Amanuel , Bariagabre Solomon Abera , Balehegn Mulubrhan 
Published: August 2020

Purpose
Different livestock production systems contribute to globally Greenhouse gas emission (GHG) emission differently. The aim of this paper is to understand variation in emission in different production systems and it is also important for developing mitigation interventions that work for a specific production system.

Design/methodology/approach
In this study, the authors used the Global Livestock Environmental Assessment interactive model (GLEAM-i) to estimate the GHG emission and emission intensity and tested the effectiveness of mitigation strategies from 180 farms under three production systems in northern Ethiopia, namely, pastoral, mixed and urban production systems.

Findings
Production systems varied in terms of herd composition, livestock productivity, livestock reproductive parameters and manure management systems, which resulted in difference in total GHG emission. Methane (82.77%) was the largest contributor followed by carbon dioxide (13.40%) and nitrous oxide (3.83%). While both total carbon dioxide and methane were significantly higher (p < 0.05) in urban production system than the other systems emission intensities of cow’s milk and goat and sheep’s meat were lower in urban systems. Improvement in feed, manure management and herd parameters resulted in reduction of total GHG emission by 30, 29 and 21% in pastoral, mixed and urban production systems, respectively.

Originality/value
This study is a first time comparison of the GHG emission production by various production systems in northern Ethiopia. Moreover, it uses the GLEAM-i program for the first time in the ex ante settings for measuring and comparing emissions as well as for developing mitigation scenarios. By doing so, it provides information on the various livestock production system properties that contribute to the increase or decrease in GHG emission and helps in developing guidelines for low emission livestock production systems.
Does gender equality bridge or buffer the entrepreneurship gender gap? A cross-country investigation
Authors: Vracheva Veselina , Stoyneva Irina 
Published: August 2020

PurposeGender equality levels opportunities for men and women and reduces the initial capital constraints women often face, and yet as entrepreneurship opportunities for women open up in more developed and egalitarian societies, fewer women are choosing entrepreneurship. This paper explores this contradiction as it relates to female economic and political participation in the context of business regulation efficiency.Design/methodology/approachDrawing on panel data from 89 countries from the Global Entrepreneurship Monitor survey and the Global Gender Gap report, we use random effects regression to examine relationships. Analyses included 252 country-years, and all data used during analyses were at the country level.FindingsResults suggest that equality in economic participation narrows and political participation widens the entrepreneurship gender gap, but a country's business regulation efficiency moderates both relationships negatively.Research limitations/implicationsThis study does not distinguish opportunity- and necessity-driven entrepreneurship, and does not consider the survival rates of enterprises and their industries.Practical implicationsFindings are pertinent to policymakers interested in advancing female entrepreneurship. They also apply to female entrepreneurs who must begin to recognize the diversity in work-life preferences among women and men.Originality/valueA theoretical model is informed by two competing theories, suggesting that in the context of female entrepreneurship, removal of economic and political participation barriers, combined with business regulation efficiency, intensifies the entrepreneurship gender gap.