bluuebunny/crossref_metadata_2025_split huggingface dataset:
Massively parallel disruption of enhancers active during human corticogenesis
Authors: Geller Evan , Gockley Jake , Emera Deena , Uebbing Severin , Cotney Justin , Noonan James P. 
Published: January 2021

AbstractChanges in gene regulation have been linked to the expansion of the human cerebral cortex and to neurodevelopmental disorders. However, the biological effects of genetic variation within developmental regulatory elements on human corticogenesis are not well understood. We used sgRNA-Cas9 genetic screens in human neural stem cells (hNSCs) to disrupt 10,674 expressed genes and 2,227 enhancers active in the developing human cortex and determine the resulting effects on cellular proliferation. Gene disruptions affecting proliferation were enriched for genes associated with risk for human neurodevelopmental phenotypes including primary microcephaly and autism spectrum disorder. Although disruptions in enhancers had overall weaker effects on proliferation than gene disruptions, we identified enhancer disruptions that severely perturbed hNSC self-renewal. Disruptions in Human Accelerated Regions and Human Gain Enhancers, regulatory elements implicated in the evolution of the human brain, also perturbed hNSC proliferation, establishing a role for these elements in human neurodevelopment. Integrating proliferation phenotypes with chromatin interaction maps revealed regulatory relationships between enhancers and target genes that contribute to neurogenesis and potentially to human cortical evolution.
A predictive model for improving placement of wind turbines to minimise collision risk potential for a large soaring raptor
Authors: Murgatroyd Megan , Bouten Willem , Amar Arjun 
Published: January 2021

Abstract

With the rapid growth of wind energy developments world‐wide, it is critical that the negative impacts on wildlife are considered and mitigated. This includes minimising the number of large soaring raptors, which are killed when they collide with wind turbines.

To reduce the likelihood of raptor collisions, turbines should be placed at locations which are least used by sensitive species. For resident or breeding species, this is often delineated crudely through the use of circular buffers centred on nest sites, which assume uniform habitat use around a nest site.

Using GPS tracking data together with a digital elevation model we build and cross‐validate a simple generalisable model, to classify the spatial likelihood of wind turbine collisions for resident adult Verreaux's eagles in any landscape where there are known nests. We apply our methods to operational developments in South Africa to validate the model and demonstrate its ability in predicting actual collision mortalities.

Our collision risk potential (CRP) model included the variables distance to nest, distance to conspecific nest, slope, distance to slope and elevation. Using our model, rather than a circular buffer, resulted in c. 4%–5% improvement in eagle protection while excluding development from the same amount (but not shape) of area. For an equal level of eagle protection, our model can make c. 20%–21% more area available for wind energy development compared to a circular buffer.

Exploring collisions at operational wind farms in South Africa we show that our CRP model correctly predicted 79% of known collisions, while circular buffers (5.2 km radius) only captured 50% of collisions.

Synthesis and applications. We show that by using predictive models to account for habitat use instead of simple buffers around a nest, a greater area of land can be made available for wind energy development without increased mortality risk to raptors. Our predictive model can be used to provide robust guidance on wind turbine placement in South Africa in a way which minimises the conflict between a vulnerable raptor species and the development of renewable energy.
Enrichment and description of novel bacteria performing syntrophic propionate oxidation at high ammonia level
Authors: Singh Abhijeet , Schnürer Anna , Westerholm Maria 
Published: January 2021

SummaryInefficient syntrophic propionate degradation causes severe operating disturbances and reduces biogas productivity in many high‐ammonia anaerobic digesters, but propionate‐degrading microorganisms in these systems remain unknown. Here, we identified candidate ammonia‐tolerant syntrophic propionate‐oxidising bacteria using propionate enrichment at high ammonia levels (0.7–0.8 g NH3L−1) in continuously‐fed reactors. We reconstructed 30 high‐quality metagenome‐assembled genomes (MAGs) from the propionate‐fed reactors, which revealed two novel species from the families Peptococcaceae and Desulfobulbaceae as syntrophic propionate‐oxidising candidates. Both MAGs possess genomic potential for the propionate oxidation and electron transfer required for syntrophic energy conservation and, similar to ammonia‐tolerant acetate degrading syntrophs, both MAGs contain genes predicted to link to ammonia and pH tolerance. Based on relative abundance, a Peptococcaceae sp. appeared to be the main propionate degrader and has been given the provisional name “CandidatusSyntrophopropionicum ammoniitolerans”. This bacterium was also found in high‐ammonia biogas digesters, using quantitative PCR. Acetate was degraded by syntrophic acetate‐oxidising bacteria and the hydrogenotrophic methanogenic community consisted ofMethanoculleus bourgensisand a yet to be characterisedMethanoculleussp. This work provides knowledge of cooperating syntrophic species in high‐ammonia systems and reveals that ammonia‐tolerant syntrophic propionate‐degrading populations share common features, but diverge genomically and taxonomically from known species.
Immune response during the onset of coliform mastitis in dairy cows vaccinated with STARTVAC®
Authors: Kawai Kazuhiro , Kondo Yasuha , Shinozuka Yasunori , Kawata Ryusaku , Kaneko Sohei , Iwano Hidetomo , Enokidani Masafumi , Watanabe Aiko , Yuliza‐Purba Fika , Isobe Naoki , Kurumisawa Tomomi 
Published: January 2021

AbstractThe immune response during the onset of coliform mastitis in vaccinated cows was investigated by measuring lactoferrin (LF), interleukin‐8(IL‐8), and interleukin‐1β (IL‐1β) concentrations and somatic cell counts in 28 milk samples at the onset of acute coliform mastitis (ACM) and 73 milk samples at the onset of peracute coliform mastitis (PCM). Vaccinated ACM, unvaccinated ACM, and vaccinated PCM showed significantly higher values for LF and IL‐1β levels than unvaccinated PCM (p < .01). The IL‐8 concentration was lower in vaccinated PCM than in unvaccinated PCM (p < .05). There was no significant difference in somatic cell counts for each parameter. There were no significant differences in the parameters between vaccinated and unvaccinated ACM cows, or vaccinated ACM and PCM cows. From the above results, it is suggested that mastitis vaccination improved the early immune response, particularly at the onset of PCM, and played a large role in host defense against the initial infection.
Idiopathic pulmonary fibrosis–A challenging disease with new horizons and changing therapeutic landscape
Authors: Fahim Ahmed 
Published: January 2021

AbstractObjectivesTo discuss the pathophysiological hypotheses of IPF with a view to summarise the data on pharmacological aspects of treatment of this fibrotic Interstitial Lung Disease. Furthermore, the adverse effects are briefly discussed for the currently available and licenced anti‐fibrotic agents.Data sourceThe data were obtained from the Randomised Controlled Trials and scientific studies published in English literature. The manuscript is kept brief to provide an overview of pathophysiological and pharmacological interplay involved in IPF and it was aimed not to be exhaustive so an update is provided on the aspect of pharmacotherapeutics for physicians involved in managing patients with IPF.ResultsTwo pharmacological agents Pirfenidone and Nintedanib are discussed with the evidence backing up for the rationale of these drugs to slow the disease progression and potentially improve mortality in this disease with a dismal prognosis. The drugs are associated with adverse events and a careful consideration to balance the efficacy with quality of life of individual patient should be considered before commencing these medications. We are seeing real‐world data on the value of these anti‐fibrotic agents and there is further evidence of them to be efficacious in severe disease and even in the cohort with significant progression over 6–12 months period.ConclusionThe landscape of IPF management has seen a paradigm shift in the last decade form anti‐inflammatory to anti‐fibrotic approach and with evidence of slowing disease progression. We are likely to improve IPF management in the near future with multi‐modality and personalised therapy.
Tertiary lymphoid structures with overlapping histopathologic features of cutaneous marginal zone lymphoma during neoadjuvant cemiplimab therapy are associated with antitumor response
Authors: Sweeney Keith J. , Tetzlaff Michael T. , Vega Francisco , Gillenwater Ann , Zuo Zhuang , Gross Neil , Nagarajan Priyadharsini , Wargo Jennifer , Nelson Kelly , Prieto Victor G. , Torres‐Cabala Carlos A. , Curry Jonathan L. 
Published: January 2021

AbstractThe development of immune checkpoint inhibitor (ICI) therapy with anti‐CTLA‐4 and anti‐PD‐1/L1 monoclonal antibodies has led to a paradigm shift in cancer therapy. ICI neoadjuvant therapy followed by surgery has become the standard of care for several advanced‐stage cancers. The pathology associated with ICI therapy is vast and includes neoadjuvant‐associated tissue reactions and activation of tertiary lymphoid structures (TLSs) at the site of the tumor bed and off‐target immune‐related adverse events. TLSs are thought to recapitulate lymph node function and may act as localized immune machinery to mount an antitumor response. B‐cell activation in TLSs during neoadjuvant ICI therapy has been correlated with antitumor response. We report a patient with a history of sarcomatoid squamous cell carcinoma treated with neoadjuvant ICI cemiplimab who developed clonal expansion of B‐cells in the TLSs of the tumor bed. The TLSs morphologically mimicked a cutaneous marginal zone lymphoma with plasmacytic differentiation. Awareness of clonal expansion of B‐cells in TLSs during neoadjuvant ICI therapy is critical to recognize a response to ICI therapy and to avoiding an incorrect diagnosis of low‐grade B‐cell lymphoma.
New microsatellite markers for the population studies ofRacodium therryanum, a causal agent of snow blight in Japan
Authors: Iwakiri Ayuka , Sakaue Daisuke , Matsushita Norihisa , Fukuda Kenji 
Published: January 2021

AbstractSnow mold fungi cause serious damage to the seedlings of some coniferous species in the boreal region where deep snow covers the seedlings in winter.Racodium therryanumis one of the fungi causing such damage in Japan. Neither sexual nor asexual spores ofR. therryanumhave been found in the field, and thus, the taxonomy and life cycle of this fungus is unclear. In this study, we developed seven microsatellite markers for population studies such as population structure, recombination and genetic diversity ofR. therryanumthrough de novo genome assembly. Seven microsatellite markers were developed and applied for 133R. therryanumisolates fromPicea glehnii,P. jezoensisandAbies sachalinensisin a nursery and two planted sites in forests (forest sites) situating 10–20 km apart. Little genetic differentiation between the two forest sites suggests that gene flow had occurred between the forest sites. The nursery population was characterized by low genetic diversity compared to the two forest sites. Discriminant analysis of principal components (DAPC) indicated three genetically differentiated clusters ofR. therryanumwhich occurred sympatrically in each site. No dominant clusters were observed in the three host species, and no genetic differentiation was observed among the host species. The observed not significant linkage disequilibrium suggested the genetic recombination ofR. therryanum. Microsatellite markers developed in this study can be useful for the further population studies ofR. therryanum.
Autopsy‐reported cause of death in a population‐based cohort of sudden unexpected death in epilepsy
Authors: Keller Anne E. , Ho Jordan , Whitney Robyn , Li Shelly‐Anne , Williams Andrew S. , Pollanen Michael S. , Donner Elizabeth J. 
Published: January 2021

AbstractObjectiveSudden unexpected death in epilepsy (SUDEP) is a diagnosis of exclusion; the definition includes individuals with epilepsy who die suddenly without an identifiable toxicological or anatomical cause of death. Limited data suggest underidentification of SUDEP as the cause of death on death certificates. Here, we evaluate the autopsy‐reported cause of death in a population‐based cohort of SUDEP cases.MethodsCase summaries of forensic autopsies conducted in Ontario, Canada between January 2014 and June 2016 were retrospectively screened using a language processing script for decedents with a history of epilepsy or seizures. After manual review for potential SUDEP cases, two neurologists independently examined the autopsy reports and classified deaths by Nashef criteria. Demographic characteristics and consideration by the forensic pathologist of the role of epilepsy, seizure, and SUDEP in death were summarized.ResultsOne hundred and eight Definite, 34 Definite Plus, and 22 Possible SUDEP cases were identified. Seventy‐five percent of Definite/Definite Plus SUDEP cases identified by the neurologists were attributed to SUDEP, epilepsy, or seizure disorder in the autopsy report. There was a significant association between the proportion of cases listed in the autopsy report as SUDEP, epilepsy, or seizure disorder and neurologists' SUDEP classification (86% of Definite, 38% of Definite Plus, 0% of Possible). Age was significantly associated with SUDEP classification; Definite cases were younger than Definite Plus, which were younger than Possible SUDEP cases.SignificanceMost SUDEP cases identified by neurologists were classified concordantly by forensic pathologists in Ontario, Canada; however, concordance decreased with increased case complexity. Although the role of epilepsy/seizures was considered in most Definite/Definite Plus cases, this study highlights the need for autopsy report review of potential SUDEP cases in research studies and assessments of the public health burden of SUDEP. The relationship between age and SUDEP classification has important public health implications; SUDEP incidence may be underappreciated in older adults.
Feasibility of a single‐species quota system for management of the Malaysian multispecies purse‐seine fishery
Authors: Harlyan Ledhyane Ika , Matsuishi Takashi Fritz , Md Saleh Mohammad Faisal 
Published: January 2021

AbstractMalaysian fisheries employ multiple measures to improve management; however, not all are well‐suited to the multispecies fisheries. As part of a pilot project, an individual quota system was introduced for the purse‐seine fishery off the East Coast of Peninsular Malaysia (ECPM), but no assessment of this particular measure nor the feasibly of its implementation has been confirmed. Therefore, this study analysed spatial and temporal patterns of purse‐seine fishing, by collecting catch composition data per landing and its fishing ground within three period fishery surveys between August 2017 and September 2018 at six different landing sites. Similarity and cluster analysis examined species composition and diversity to determine the feasibility of implementing a single‐species quota system in this multispecies fishery. Some overlapped of indices results and minor difference in catch composition were found due to changes in spatial and temporal fishing activities. However, no specific spatial or temporal patterns were discernible as structuring the fishing grounds used by purse‐seiners. The absence of patterns, using the available data, might be attributable to huge species aggregations and widely distributed and homogenously mixed fish stocks. Thus, it is likely impractical to manage species individually in such a multispecies fishery.
An American lineage of Helicobacter pylori prophages found in Colombia
Authors: Muñoz Angela B , Trespalacios‐Rangel Alba A , Vale Filipa F 
Published: January 2021

AbstractBackgroundHelicobacter pylori is a human gastric carcinogen that is highly prevalent in Latin American. The prophages of H. pylori show a structured population and contribute to the diversity of this bacterium. However, H. pylori prophages present in American strains have not been described to date. In this study, we identified, characterized, and present the phylogenetic analysis of the prophages present in Colombian H. pylori strains.MethodsTo characterize Colombian H. pylori strains and their prophages, a Multilocus Sequences Typing (MLST) and a Prophage Sequences Typing (PST), using the integrase and holin genes, were performed. Furthermore, five Colombian H. pylori had their full genome sequenced, and six Colombian H.pylori retrieved from databases, allowing to determine the prophage complete genome and insertion site.ResultsThe integrase gene frequency was 12.6% (27/213), while both integrase and holin genes were present in 4.2% (9/213) of the samples analyzed. The PST analysis showed that Colombian prophages belong to different populations, including hpSWEurope, hpNEurope, hpAfrica1, and a new population, named hpColombia. The MLST analysis classified most of the Colombia strains in the hpEurope population.ConclusionsThe new H. pylori prophage population revealed that Colombian prophages follow a unique evolutionary trajectory, contributing to bacterial diversity. The global H. pylori prophage phylogeny highlighted five phylogenetic groups, one more than previously reported. After the arrival of Europeans, the Colombian H. pylori bacteria and their prophages formed an independent evolutionary line to adapt to the new environment and new human hosts.
Age‐related differences in responses to hydrogen sulfide in the bladder of spontaneously hypertensive rats
Authors: Zou Suo , Shimizu Takahiro , Yamamoto Masaki , Shimizu Shogo , Higashi Youichirou , Karashima Takashi , Saito Motoaki 
Published: January 2021

ObjectivesTo investigate whether a response to hydrogen sulfide donors (GYY4137 and sodium hydrosulfide) and the endogenous hydrogen sulfide system (hydrogen sulfide level and expression of cysteine aminotransferase, cystathionine β‐synthase, cystathionine γ‐lyase, and 3‐mercaptopyruvate sulfurtransferase) in the spontaneously hypertensive rat bladder differ with age, we compared the responses of hydrogen sulfide donors to micturition and bladder relaxation, and the endogenous hydrogen sulfide system in the bladder of 18‐week versus 12‐week‐old spontaneously hypertensive rats.MethodsGYY4137 was intravesically administered and cystometry was performed in anesthetized rats. The responses of sodium hydrosulfide were evaluated in carbachol‐mediated precontracted bladder strips. Bladder hydrogen sulfide levels and expression levels of each enzyme were investigated using the methylene blue method and Western blotting, respectively.ResultsGYY4137 treatment significantly prolonged intercontraction intervals only in 12‐week‐old rats. Sodium hydrosulfide‐induced bladder relaxation was significantly attenuated in the strips of 18‐week‐old rats compared with that in 12‐week‐old rats. In the bladder dome, significant increases in hydrogen sulfide levels and in the expression of cystathionine β‐synthase, 3‐mercaptopyruvate sulfurtransferase, and cysteine aminotransferase were observed in 18‐week‐old rats compared with 12‐week‐old rats. However, cystathionine γ‐lyase bands were not detected in bladder tissues of either group.ConclusionsBladder relaxation induced by hydrogen sulfide may be attenuated in spontaneously hypertensive rats in an age‐dependent manner.
A clustering‐based review on project portfolio optimization methods
Authors: Saiz Miguel , Lostumbo Marisa A. , Juan Angel A. , Lopez‐Lopez David 
Published: January 2021

AbstractProject portfolio management and optimization constitutes a critical activity for organizations in different industrial sectors and business. The scientific literature in this subject is extremely vast, which makes it difficult to understand the connections among the existing approaches and perspectives. This paper provides a clustering map of the existing work on the subject, thus identifying the main trends and approaches from different scientific communities. After analyzing each of the identified clusters, the paper provides insights and emerging trends that can be useful both for researchers and practitioners in the area.
Preventive effect of aspirin on preeclampsia in high‐risk pregnant women with stage 1 hypertension
Authors: Huai Jing , Lin Li , Juan Juan , Chen Jiahui , Li Boya , Zhu Yuchun , Yu Mengting , Yang Huixia 
Published: January 2021

AbstractStudies reported that women in a low‐risk cohort with stage 1 hypertension defined as 130–139 mmHg/80–89 mmHg, according to the American College of Cardiology/American Heart Association, are more likely to develop into preeclampsia than women with normotensive in the early gestation. In this study, the authors investigated whether preeclampsia was more likely to occur in stage 1 hypertensive women compared to the normotensive pregnant women in a high‐risk cohort, which was based on the randomized controlled trial of "Low‐dose Aspirin in the Prevention of Preeclampsia in China." Meanwhile, the authors further evaluated the preventive effect of aspirin for preeclampsia in stage 1 hypertension subset. In women enrolled at or before 16 weeks of gestation, in the control group, the preeclampsia occurrence was significantly higher in stage 1 hypertensive woman than in the normotensive women (20.4% vs. 6.2%, aOR 3.960, 95% CI 1.299–12.074, p = .016), while no difference was observed in the aspirin group (4.5% vs. 4.2%, aOR 0.921, 95% CI 0.140–6.070, p = .932). In stage 1 hypertension, the incidences of preeclampsia and preterm birth were significantly lower in the aspirin group as compared to the control group (4.5% vs. 20.4%, aOR 0.139, 95% CI 0.027–0.716, p = .018; 4.5% vs. 18.4%, aOR 0.141, 95% CI 0.025–0.782, p = .025). Compared with the control group, the aspirin group displayed significantly prolonged gestational age at delivery (38.6 ± 1.2 vs. 37.4 ± 3.4, p = .042). This study indicates that the newly classified stage 1 hypertension might be an additional risk factor for preeclampsia in Chinese high‐risk pregnant women, and aspirin intervention might be useful.