bluuebunny/crossref_metadata_2025_split huggingface dataset:
First mitochondrial genome-wide association study with metabolomics
Authors: Aboulmaouahib Brahim , Kastenmüller Gabi , Suhre Karsten , Zöllner Sebastian , Weissensteiner Hansi , Prehn Cornelia , Adamski Jerzy , Gieger Christian , Wang-Sattler Rui , Lichtner Peter , Strauch Konstantin , Flaquer Antònia 
Published: October 2021

AbstractIn the era of personalized medicine with more and more patient-specific targeted therapies being used, we need reliable, dynamic, faster and sensitive biomarkers both to track the causes of disease and to develop and evolve therapies during the course of treatment. Metabolomics recently has shown substantial evidence to support its emerging role in disease diagnosis and prognosis. Aside from biomarkers and development of therapies, it is also an important goal to understand the involvement of mitochondrial DNA (mtDNA) in metabolic regulation, aging and disease development. Somatic mutations of the mitochondrial genome are also heavily implicated in age-related disease and aging. The general hypothesis is that an alteration in the concentration of metabolite profiles (possibly conveyed by lifestyle and environmental factors) influences the increase of mutation rate in the mtDNA and thereby contributes to a range of pathophysiological alterations observed in complex diseases. We performed an inverted mitochondrial genome-wide association analysis between mitochondrial nucleotide variants (mtSNVs) and concentration of metabolites. We used 151 metabolites and the whole sequenced mitochondrial genome from 2718 individuals to identify the genetic variants associated with metabolite profiles. Because of the high coverage, next-generation sequencing-based analysis of the mitochondrial genome allows for an accurate detection of mitochondrial heteroplasmy and for the identification of variants associated with the metabolome. The strongest association was found for mt715G &gt; A located in the MT-12SrRNA with the metabolite ratio of C2/C10:1 (P-value = 6.82*10−09, β = 0.909). The second most significant mtSNV was found for mt3714A &gt; G located in the MT-ND1 with the metabolite ratio of phosphatidylcholine (PC) ae C42:5/PC ae C44:5 (P-value = 1.02*10−08, β = 3.631). A large number of significant metabolite ratios were observed involving PC aa C36:6 and the variant mt10689G &gt; A, located in the MT-ND4L gene. These results show an important interconnection between mitochondria and metabolite concentrations. Considering that some of the significant metabolites found in this study have been previously related to complex diseases, such as neurological disorders and metabolic conditions, these associations found here might play a crucial role for further investigations of such complex diseases. Understanding the mechanisms that control human health and disease, in particular, the role of genetic predispositions and their interaction with environmental factors is a prerequisite for the development of safe and efficient therapies for complex disorders.
Plankton monitoring in the Northwest Atlantic: a comparison of zooplankton abundance estimates from vertical net tows and Continuous Plankton Recorder sampling on the Scotian and Newfoundland shelves, 1999–2015
Authors: Head Erica J H , Johnson Catherine L , Pepin Pierre 
Published: October 2021

Abstract
Assessment of zooplankton abundance, distribution, community composition, and temporal variability is critical to understanding the effects of climate variability and change on lower trophic level production and availability for consumption by larger consumers. Zooplankton sampling is performed across the Canadian continental shelf system by Fisheries and Oceans Canada's Atlantic Zone Monitoring Programme (AZMP). Sampling includes semi-monthly to monthly collection of zooplankton using vertical net tows (VNTs) deployed from near-bottom to surface at stations on the central Scotian Shelf (Stn 2, 150 m depth) and Newfoundland Shelf (Stn 27, 175 m depth), and by Continuous Plankton Recorders (CPRs) in the near-surface layers along routes over the Scotian and Newfoundland shelves (0–10 m depth). Here, we compare abundance metrics for 11 copepod taxa collected using both gear types in both regions between 1999 and 2015. Seasonal cycles of VNT and CPR abundance were similar for near-surface residents. VNT: CPR abundance ratios varied year-round for vertical migrants, as ontogenetic migrants shifted their vertical distribution, and as diel migrants changed their migratory behaviour. For some taxa, differences in annual average VNT: CPR abundance ratios between regions suggest differences in vertical distribution, while for others differences in inter-annual variability for VNT and CPR abundances suggest differences in the dynamics of the near- and sub-surface components of the populations.
Auxiliary diagnostic analyses used to detect model misspecification and highlight potential solutions in stock assessments: application to yellowfin tuna in the eastern Pacific Ocean
Authors: Minte-Vera Carolina V , Maunder Mark N , Aires-da-Silva Alexandre M 
Published: October 2021

Abstract
Integrated models (IMs) for stock assessment are simultaneously fit to diverse data sets to estimate parameters related to biological and fishery processes. Model misspecification may appear as contradictory signals in the data about these processes and may bias the estimate of quantities of interest. Auxiliary diagnostic analyses may be used to detect model misspecification and highlight potential solutions, but no set of good practices on what to use exist yet. In this study, we illustrate how to use auxiliary diagnostic analyses not only to identify model misspecification, but also to understand what data components provided information about abundance. The diagnostic tools included likelihood component profiles on the scaling parameter, age-structured production models, catch-curve analyses, and two novel analyses: empirical selectivity and monthly depletion models. While the likelihood profile indicated model misspecification, subsequent analyses were required to indicate the causes as unmodelled changes in selectivity and spatial structure of the population. The consistency between the catch-curve models, the monthly depletion models and the IM information on abundance comes from a strong signal shared by several purse-seine fisheries data sets: the length composition data informs absolute abundance while the indices of abundance constrain the trend in relative abundance.
El mandato transformador del Sistema Interamericano como respuesta a la pandemia a la luz del test democráticoThe Inter-American System’s transformative mandate as a response to the pandemic in light of the democratic test
Authors: Morales Antoniazzi Mariela 
Published: October 2021

Abstract
This article analyzes how Latin American democracies should react to the COVID-19 pandemic. From the perspective of a ius constitutionale commune in Latin America, it argues that the greatest challenge lies in passing the inter-American democratic test, which at the intersection of human rights, democracy and the rule of law can guarantee compliance with inter-American standards. A new rationale derives from the mechanisms adopted by the Inter-American Court of Human Rights and the Inter-American Commission on Human Rights, in the exercise of the transformative mandate in times of pandemic. It concludes by identifying a “double” democratic test in Latin America that relies on the notion of collective guarantee of human rights standards.
Direct transaortic transcather valve-in-valve implantation into a mechanical aortic valve prosthesis during left ventricular assist device implantation: description of a surgical technique
Authors: Kiefer Philipp , Hoyer Alexandro , Borger Michael Andrew , Garbade Jens 
Published: October 2021

Abstract
The presence of a mechanical aortic valve prosthesis is considered a relative contraindication for left ventricular assist device implantation (LVAD) due to the occurrence of thromboembolic events. Five patients were operated on for LVAD implantation with status post mechanical aortic valve implantation (n = 3 with status post Bentall procedure). After removal of the leaflets, a transcatheter balloon-expandable valve was placed within the mechanical ring in all patients. Three patients were discharged from hospital with a maximum follow-up of 3.3 years. Transaortic transcatheter valve implantation into a mechanical aortic valve during LVAD implantation is a feasible option. It reduces operative times and might also prevent thromboembolic events.
Effect of preoperative radiotherapy on overall survival in N2 non-small-cell lung cancer: a propensity score-matched analysis of Surveillance, Epidemiology, and End Results database
Authors: Wang Yunan , Cao Yunliang , Wu Mengjia , Lu Yanyi , He Bo , Zhou Lei , Hu Wei 
Published: October 2021

Abstract

OBJECTIVES
The aim of this study was to investigate the effect of preoperative radiotherapy (PrORT) on the overall survival (OS) of patients with stage ipsilateral mediastinal lymph node metastasis (N2) non-small-cell lung cancer.

METHODS
A total of 1390 patients with stage N2 non-small-cell lung cancer between 2010 and 2015 were identified from the Surveillance, Epidemiology, and End Results database. The efficacy of PrORT combined with surgery was compared with that of surgery alone on OS. Propensity score matching (PSM) was performed to balance the baseline characteristics of patients who received (n = 239) and did not receive (n = 1151) PrORT. We compared the OS of the 2 groups using the Kaplan–Meier method and log-rank were used to compare the OS between the 2 groups test before and after PSM and to analyse subgroups of patients with squamous cell carcinoma (SCC) and adenocarcinoma.

RESULTS
In whole group analysis before PSM, the median OS was superior in the PrORT group than in the surgery alone group (44.0 [34.4–56.6] vs 39.0 [34.5–43.5] months). There was a significant difference in OS [hazard ratio (HR): 0.819; 95% confidence interval (CI): 0.677–0.991; P = 0.029]. Nevertheless, no statistically significant difference was found in OS between the 2 groups after PSM (HR: 0.856; 95% CI: 0.654–1.122; P = 0.260). Among subgroup analysis of the SCC group before PSM revealed that patients who received PrORT had significantly higher median OS than those who did not receive PrORT (52.0 [40.0–NA] vs 27.0 [22.0–32.0] months; HR: 0.591, 95% CI: 0.442–0.792, P = 0.000) and the differences in OS existed after PSM (P = 0.043). However, no significant difference was found in OS before and after matching in the adenocarcinoma group (P = 0.827 and P = 0.801, respectively).

CONCLUSIONS
PrORT demonstrated an OS benefit for patients with stage N2 lung SCC; however, further prospective randomized clinical trials are warranted to confirm this finding.
Urban Particulate Matter Impairment of Airway Surface Liquid–Mediated Coronavirus Inactivation
Authors: Stapleton Emma M , Welch Jennifer L , Ubeda Erika A , Xiang Jinhua , Zabner Joseph , Thornell Ian M , Nonnenmann Matthew W , Stapleton Jack T , Comellas Alejandro P 
Published: October 2021

Abstract
Air pollution particulate matter (PM) is associated with SARS-CoV-2 infection and severity, although mechanistic studies are lacking. We tested whether airway surface liquid (ASL) from primary human airway epithelial cells is antiviral against SARS-CoV-2 and human alphacoronavirus 229E (CoV-229E) (responsible for common colds), and whether PM (urban, indoor air pollution [IAP], volcanic ash) affected ASL antiviral activity. ASL inactivated SARS-CoV-2 and CoV-229E. Independently, urban PM also decreased SARS-CoV-2 and CoV-229E infection, and IAP PM decreased CoV-229E infection. However, in combination, urban PM impaired ASL’s antiviral activity against both viruses, and the same effect occurred for IAP PM and ash against SARS-CoV-2, suggesting that PM may enhance SARS-CoV-2 infection.
Reduced transmission of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP) in patients with haematological malignancies hospitalized in an Italian hospital during the COVID-19 pandemic
Authors: Micozzi Alessandra , Assanto Giovanni Manfredi , Cesini Laura , Minotti Clara , Cartoni Claudio , Capria Saveria , Ciotti Giulia , Alunni Fegatelli Danilo , Donzelli Livia , Martelli Maurizio , Gentile Giuseppe 
Published: October 2021

Abstract

Objectives
During the lockdown that started in Italy on 10 March 2020 to address the COVID-19 pandemic, aggressive procedures were implemented to prevent SARS-CoV-2 transmission in SARS-CoV-2-negative patients with haematological malignancies. These efforts progressively reduced Klebsiella pneumonia carbapenemase-producing K. pneumoniae (KPC-KP) spread among these patients. Here we evaluated the potential effects of measures against COVID-19 that reduced KPC-KP transmission.

Patients and methods
We analysed KPC-KP spread among 123 patients with haematological malignancies, hospitalized between March and August 2020, who were managed using measures against COVID-19. Their outcomes were compared with those of 80 patients hospitalized during the preceding 4 months (November 2019–February 2020).

Results
During March–August 2020, 15.5% of hospitalized patients were KPC-KP positive, compared with 52.5% in November 2019–February 2020 (P &lt; 0.0001); 8% and 27.5% of patients in these two groups were newly KPC-KP positive, respectively (P = 0.0003). There were eight new KPC-KP-positive patients during January 2020 and none during June 2020. The weekly rate of hospitalized KPC-KP-positive patients decreased from 50% during March 2020 to 17% during August 2020. Four KPC-KP bloodstream infections (BSIs) were experienced by 123 patients (3%) in March–August 2020, and seven BSIs (one fatal) by 80 patients (8%) in November 2019–February 2020 (P = 0.02). Consumption and expense of ceftazidime/avibactam administered to KPC-KP-positive patients significantly decreased in March–August 2020.

Conclusions
Aggressive strategies to prevent SARS-CoV-2 transmission were applied to all hospitalized patients, characterized by high levels of KPC-KP endemicity and nosocomial transmission. Such measures prevented SARS-CoV-2 infection acquisition and KPC-KP horizontal transmission. Reduced KPC-KP spread, fewer associated clinical complications and decreased ceftazidime/avibactam consumption represented unexpected ‘collateral benefits’ of strategies to prevent COVID-19.
The roles of the US National Library of Medicine and Donald A.B. Lindberg in revolutionizing biomedical and health informatics
Authors: Miller Randolph A , Shortliffe Edward H 
Published: October 2021

Abstract
Over a 31-year span as Director of the U.S. National Library of Medicine (NLM), Donald A.B. Lindberg, MD, and his extraordinary NLM colleagues fundamentally changed the field of biomedical and health informatics—with a resulting impact on biomedicine that is much broader than its influence on any single subfield. This article provides substance to bolster that claim. The review is based in part on the informatics section of a new book, “Transforming biomedical informatics and health information access: Don Lindberg and the US National Library of Medicine” (IOS Press, forthcoming 2021). After providing insights into selected aspects of the book’s informatics-related contents, the authors discuss the broader context in which Dr. Lindberg and the NLM accomplished their transformative work.
The impact of genetic merit on ewe performance and efficiency parameters
Authors: Fetherstone Nicola , McHugh Noirin , Boland Tommy M , Creighton Philip , Galvin Norann , McGovern Fiona M 
Published: October 2021

Abstract
The aim of this study was to investigate the impact of ewe genetic merit on ewe performance and efficiency parameters. The study consisted of three genetic merit groups (New Zealand [NZ], High Irish, and Low Irish) and ran from 2016 to 2019, inclusive. Each genetic merit group contained 30 purebred Suffolk and 30 purebred Texel ewes, which were selected based on their maternal genetic indexes in their country of origin, namely Ireland (€uro-star Replacement index) or New Zealand (New Zealand Maternal worth). Ewe body condition score (BCS), ewe body weight (BW), milk yield, milk composition, dry matter intake (DMI), and efficiency parameters were all analyzed using linear mixed models. Ewe BW was similar across all genetic merit groups at each time point (P &gt; 0.05). In comparison to both High and Low Irish ewes, NZ ewes had a higher BCS at mating, mid-pregnancy, lambing, week 10 post-lambing (PL, P &lt; 0.05). Ewe BW change was similar across genetic merit groups, except between mating and mid-pregnancy where ewe BW loss was greater for NZ ewes than Irish ewes (P &lt; 0.05) and between weeks 6 PL and 10 PL, where NZ ewes gained BW and High and Low Irish ewes lost BW (P &lt; 0.01). Ewe milk yield, milk fat, total solids, and gross energy content were superior for milk produced by NZ ewes at week 6 PL in comparison to milk produced by High Irish and Low Irish ewes (P &lt; 0.01). NZ ewes produced a greater quantity of milk solids/kg of BW at week 6 PL compared with High Irish ewes (P &lt; 0.01), whereas Low Irish ewes did not differ from either NZ or High Irish (P &gt; 0.05). Low Irish ewes had a greater daily DMI than High Irish ewes in late lactation (week 10 PL, P &lt; 0.05) and had a greater DMI/kg of ewe BW compared with the High Irish ewes at the same time point (P &lt; 0.05). NZ ewes weaned a litter BW equivalent to 60.4% of their mating BW, which was more than the Low Irish ewes who weaned 57.1% of the ewe’s BW at mating (P &lt; 0.01), whereas the High Irish ewes did not differ from either the NZ or Low Irish ewes at 59.3% of the ewe’s BW at mating (P &gt; 0.05). This study presents a range of parameters across ewes of high and low genetic merit, demonstrating the ability to achieve gains through selection of animals of high genetic merit. Sheep producers should consider genetic indexes as a tool to assist in the decision-making process of selecting replacement ewes and/or breeding rams, once satisfied the animal is correct, and meeting the breeding objectives of the system.
Effect ofTMEM154E35K variant (haplotypes 1 and 3) on the incidence of ovine lentivirus infection and ewe productivity during lifetime exposure
Authors: Murphy Thomas W , Chitko-McKown Carol G , Heaton Mike P , Freking Brad A 
Published: October 2021

AbstractOvine progressive pneumonia virus (OPPV) is a small ruminant lentivirus that is widespread throughout U.S. sheep flocks. Infections with OPPV are lifelong and effects are multi-systemic with significant implications for animal well-being and productivity. A protein isoform with lysine at position 35 (K35, haplotype “1”) encoded by the ovine transmembrane protein 154 (TMEM154) gene has been associated with reduced susceptibility to infection when two copies are present (i.e., diplotype “1,1”). Conversely, the ancestral protein isoform with glutamate at position 35 (E35, haplotype “3”) is associated with high susceptibility to infection when at least one copy is present. The beneficial effect of TMEM154 K35 alleles on ewe productivity has not been previously measured in controlled challenge experiments and was a major objective of this study. Ewes with TMEM154 diplotypes “1,1”; “1,3”; and “3,3” (n = 31, 47, and 30, respectively) were born and reared by OPPV-infected dams and managed under continual natural exposure to OPPV. Ewes were tested for serological status at 4-mo intervals for up to 5.5 yr. The incidence of infection in ewes with diplotype “1,1” was 6.5% to 9.7% and significantly lower (P &lt; 0.001) than ewes with diplotype “1,3” (60.5 to 97.3%) or “3,3” (64.0 to 91.4%). Furthermore, the incidence among ewes with diplotype “1,1” did not increase from 10 to 67 mo of age (P &gt; 0.99), whereas the incidence among diplotype “1,3” and “3,3” ewes increased steadily until reaching an asymptote at approximately 52 mo of age. Total number and weight of lamb weaned per ewe exposed through 5.5 yr from ewes with diplotype “1,1” far exceeded (P ≤ 0.05) those with diplotypes “1,3” and “3,3” by, on average, 2.1 lambs and 40 kg, respectively. The present study confirmed that TMEM154 diplotype “1,1” animals have reduced incidence of OPPV infection and, correspondingly, improved productivity. In flocks with a high frequency of TMEM154 haplotype “3,” selection for haplotype “1” appears to be a cost-effective approach to mitigate the impact of this economically important disease.
The Effect of Horn Fly (Diptera: Muscidae) Infestation on Behavior, Water, and Feed Intake, and Digestion Characteristics of Beef Cattle
Authors: Sanchez-Sandoval U A , Figueroa-Zamudio J J , Ramirez J , Löest C A , Soto-Navarro S A , Smythe B G 
Published: October 2021

Abstract
Seven mature Angus × Hereford crossbreed cows (544 ± 23.2 kg of body weight) fitted with duodenal and ruminal cannulas were used in a crossover design to evaluate the effects of horn fly (Haematobia irritans) (L.) infestation on horn fly-induced defensive behaviors, feed and water intake, as well as digestion characteristics of beef cows. Cows were randomly assigned to one of two treatment groups: 1) a horn fly infested (1,000 flies per cow) or 2) a noninfested control group. All cows were housed in individual screened pens. Fly counts and infestations were performed daily to maintain consistent populations throughout the study. Sudan hay (11.4 % crude protein, dry matter basis) was selected to mimic forage quality that range cattle frequently graze in the southwest region. Horn fly-induced host defensive behaviors were greater (P ≤ 0.0002) for horn fly infested cattle. Intake of water, dry matter, organic matter, crude protein, and neutral detergent fiber were similar (P ≥ 0.4765) among infested and noninfested cows. However, total volatile fatty acid concentration tended to increase (P = 0.0967) when horn flies were present. Dry matter fecal excretion and total tract digestion were not affected (P ≥ 0.2602) by horn fly infestation. These data indicate that horn fly infestations do not affect forage intake or digestion characteristics of beef cattle (Bos taurus) in confinement settings.