bluuebunny/crossref_metadata_2025_split huggingface dataset:
Empirical Evidence That Complexity Limits Horizontal Gene Transfer
Authors: Burch Christina L , Romanchuk Artur , Kelly Michael , Wu Yingfang , Jones Corbin D 
Published: May 2023

Abstract
Horizontal gene transfer (HGT) is a major contributor to bacterial genome evolution, generating phenotypic diversity, driving the expansion of protein families, and facilitating the evolution of new phenotypes, new metabolic pathways, and new species. Comparative studies of gene gain in bacteria suggest that the frequency with which individual genes successfully undergo HGT varies considerably and may be associated with the number of protein–protein interactions in which the gene participates, that is, its connectivity. Two nonexclusive hypotheses have emerged to explain why transferability should decrease with connectivity: the complexity hypothesis (Jain R, Rivera MC, Lake JA. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A. 96:3801–3806.) and the balance hypothesis (Papp B, Pál C, Hurst LD. 2003. Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194–197.). These hypotheses predict that the functional costs of HGT arise from a failure of divergent homologs to make normal protein–protein interactions or from gene misexpression, respectively. Here we describe genome-wide assessments of these hypotheses in which we used 74 existing prokaryotic whole genome shotgun libraries to estimate rates of horizontal transfer of genes from taxonomically diverse prokaryotic donors into Escherichia coli. We show that 1) transferability declines as connectivity increases, 2) transferability declines as the divergence between donor and recipient orthologs increases, and that 3) the magnitude of this negative effect of divergence on transferability increases with connectivity. These effects are particularly robust among the translational proteins, which span the widest range of connectivities. Whereas the complexity hypothesis explains all three of these observations, the balance hypothesis explains only the first one.
Vision and Hearing Difficulties and Life Expectancy Without ADL/IADL Limitations: Evidence From the English Longitudinal Study of Ageing and the Health and Retirement Study
Authors: Zaninotto Paola , Maharani Asri , Di Gessa Giorgio 
Published: May 2023

AbstractBackgroundHearing and vision difficulties are some of the most common deficits experienced by older adults. Having either visual or hearing difficulties increases the risk of comorbidity, disability, and poor quality of life. So far, however, few studies have examined the association between vision and hearing difficulties on life expectancy without activities of daily living (ADL) or instrumental ADL (IADL) limitations (LEWL).MethodsData came from the English Longitudinal Study of Ageing and the Health and Retirement Study in the United States from 2002 to 2013. The outcome was defined as reporting 2+ limitations with ADL/IADL. Life expectancy was estimated by discrete-time multistate life table models for hearing and vision difficulties separately as well as for combined vision and hearing difficulties by sex and age.ResultsThirteen percent of men in England and the United States had ADL/IADL limitations, whereas, for women, it was 16% and 19% in England and the United States. At all ages, either vision or hearing difficulty was associated with shorter LEWL compared to no difficulties. Dual sensory difficulty (vision and hearing) reduced LEWL by up to 12 years in both countries. At the ages of 50 and 60 in England, hearing difficulty was associated with fewer years lived without ADL/IADL limitations than vision difficulty. In contrast, in the United States, vision difficulty led to fewer years lived without ADL/IADL limitations than hearing difficulty.ConclusionsThe implementation of strategies to reduce the prevalence and incidence of vision and hearing difficulties has the potential to increase the number of years spent without ADL/IADL limitations.
Regional infrasonic observations from surface explosions – influence of atmospheric variations and realistic terrain
Authors: Blom Philip 
Published: May 2023

SUMMARY
A pair of 1-ton, conventional surface explosions were conducted at the Nevada National Security Site in the fall of 2020 producing seismoacoustic signatures observable hundreds of kilometres from the source location. Regional infrasonic observations include tropospheric ducting at large distances to the south, a wide stratospheric waveguide with signals observed more than 700 km to the east, and anomalous arrivals in the stratospheric shadow zone. Notable differences in propagation between the events are identified despite the explosions being conducted just two days apart due to a sharp temporal shift in the tropospheric winds as well as structural changes in the stratospheric winds. Propagation simulations of the two events have been completed using a combination of ray tracing and parabolic equation (PE) methods. Simulations have been conducted to quantify the impact of the temporal variations in the atmosphere as well as the influence of terrain on propagation. Temporal variations in reflection locations are found to produce notable changes in downrange propagation due to spatially varying terrain features. Finite frequency effects modelled by the PE are found to predict ensonification not included in corresponding 2D ray tracing simulations. Notable variations in predicted signal amplitude are found due to focusing by along-path and cross-path terrain gradients; though, the later of these is only modelled using fully 3D ray tracing analysis.
Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids
Authors: Simner Patricia J , Bergman Yehudit , Fan Yunfan , Jacobs Emily B , Ramakrishnan Srividya , Lu Jennifer , Lewis Shawna , Hanlon Ann , Tamma Pranita D , Schatz Michael C , Timp Winston , Carroll Karen C 
Published: May 2023

Abstract

Objectives
Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat. A better understanding of the molecular epidemiology and transmission dynamics of CRE is necessary to limit their dissemination within healthcare settings. We sought to investigate the mechanisms of resistance and spread of CRE within multiple hospitals in Maryland.

Methods
From 2016 to 2018, all CRE were collected from any specimen source from The Johns Hopkins Medical Institutions. The isolates were further characterized using both phenotypic and genotypic approaches, including short- and/or long-read WGS.

Results
From 2016 to 2018, 302 of 40 908 (0.7%) unique Enterobacterales isolates were identified as CRE. Of CRE, 142 (47%) were carbapenemase-producing CRE with KPC (80.3%) predominating among various genera. Significant genetic diversity was identified among all CRE with high-risk clones serving as major drivers of clonal clusters. Further, we found the predominance of pUVA-like plasmids, with a subset harbouring resistance genes to environmental cleaning agents, involved in intergenus dissemination of blaKPC genes.

Conclusions
Our findings provide valuable data to understand the transmission dynamics of all CRE within the greater Maryland region. These data can help guide targeted interventions to limit CRE transmission in healthcare facilities.
Heritability and genetic trend of body weight in dogs of different breeds in Sweden
Authors: Strandberg Erling , Andersson Linda , Emanuelson Ulf , Bjørnvad Charlotte Reinhard , Ringmark Sara , Hedhammar Åke , Höglund Katja 
Published: May 2023

Abstract
High body weight (BW) in dogs has been associated with developmental as well as degenerative diseases, but the heritability of BW in dog breeds is largely unknown. The aim of the current study was to estimate heritability and genetic change (genetic trend) for BW in a range of dog breeds in Sweden. Body weight registrations from 19 dog breeds (with n ranging from 412 to 4,710) of varying body size, type and usage were collected from 2007 to 2016. The average BW of the breeds was 8 to 56 kg. The BW registrations were performed when the dogs were 12 to 24 mo of age (18 to 30 mo for one large-sized breed) in connection with an official radiographic screening program for hip dysplasia. Collected weight records were used to estimate heritability and genetic trends for BW. Several statistical models were used. The preliminary model included the fixed effects of breed (P &lt; 0.001), sex (P &lt; 0.001), year of screening (P &lt; 0.001), litter size (P = 0.06), parity of the dam (P = 0.03) and linear regression on age at screening (P &lt; 0.001), the latter five effects all nested within breed, and the random effects of litter and dam. Season of birth and the quadratic effect of age were also tested, but were not significant (P &gt; 0.10). For the genetic analysis, various mixed linear models were tested within breed with different combinations of random effects; the most complex model included random effects of litter, direct additive, and maternal genetic effects, and maternal permanent environmental effects. The average heritability for BW over all 19 breeds was 51%, with a range of 35% to 70%, and the additive genetic coefficient of variance was around 9%. Maternal heritability was 5% to 9% and litter variance was below 10% with one exception (15% in Shetland Sheepdogs). For nine breeds, there was a genetic trend of increasing BW, whereas seven breeds had a genetic trend of decreasing BW. The largest absolute genetic change over a 10-yr period was around 0.6 kg or about 2% of the mean. In conclusion, given the small genetic changes in spite of the high heritability, it seems that there is generally a very weak selection, if any, for BW in the included dog breeds.
Leucine (and lysine) increased plasma levels of the satiety hormone cholecystokinin (CCK), and phenylalanine of the incretin glucagon-like peptide 1 (GLP-1) after oral gavages in pigs
Authors: Müller Maximiliano , Xu Chenjing , Navarro Marta , Masiques Nuria Elias , Tilbrook Alan , van Barneveld Robert , Roura Eugeni 
Published: May 2023

Abstract
Excess dietary amino acids (AA) has been associated with reduced feed intake, increased satiation, and extended satiety in pigs. Recent ex vivo studies suggested that satiety peptide cholecystokinin (CCK) and insulinotropic glucagon-like peptide 1 (GLP-1), mediated the anorexigenic or insulinotropic effects of Lys, Glu, Phe, Ile, and Leu. However, the ex vivo model limitations require validation in vivo. The aim of the present study was to assess the effect of orally administered AA in vivo in pigs. It was hypothesized that oral Lys, Ile, and Leu have an anorexigenic effect via CCK, while Glu and Phe have an insulinotropic effect increasing circulating levels of GLP-1. Eight entire male pigs (Landrace × Large White) of 18.23 ± 1.06 kg of body weight were administered an oral gavage of water (control) or a 3 mmol/kg of Glu, Ile, Leu, Lys, Phe, or glucose (positive control for GLP-1 release) following an overnight fasting during 5 consecutive days using an incomplete latin square design. Blood samples were collected from the jugular vein before (−5 min, baseline value) and after the gavage (5, 15, 30, 60 and 90 min) to assess CCK and GLP-1 plasma levels. Pigs administered the oral gavage of Leu (P &lt; 0.05), or Lys (P &lt; 0.1) had increased levels of plasma CCK from 0 to 90 min post-gavage when compared to the control. A strong association (P &lt; 0.001) was observed between GLP-1 plasma levels with Phe intake. The impact was significant starting 30 min post-gavage and was sustained until the end of the experiment (90 min post-gavage). Glucose administration increased GLP-1 early after the intake at the 5 min mark (P &lt; 0.1). A positive correlation (P &lt; 0.05, r = 0.89) driven by the impact of Phe at the 60 to 90 min post-gavage was identified between CCK and GLP-1 indicating feedback mechanisms between proximal and distal small intestine. In conclusion, oral gavages of Leu and Lys increased anorexigenic hormone CCK plasma levels in pigs. Phe caused a significant long-lasting increase in incretin GLP-1 plasma levels. Blood CCK and GLP-1 concentrations in Phe gavaged pigs were positively correlated indicating a potential feedback mechanism between proximal (CCK) and distal (GLP-1) small intestine. The present results are compatible with the known anorexigenic effects of excess dietary Leu and Lys, and the insulinotropic effect of Phe in pigs. These results demonstrate the relevance of accurate feed formulation practices particularly in post weaning pigs.
The Impact of Covid-19 Pandemic on Acute Burn Admissions at the University College Hospital, Ibadan, Nigeria
Authors: Olawoye Olayinka A , Isamah Chinsunum P , Obadan Izegaegbe O , Ademola Samuel A , Aderibigbe Rotimi O , Michael Afieharo I , Iyun Ayodele O , Oluwatosin Odunayo M 
Published: May 2023

Abstract
The coronavirus disease and the subsequent pandemic that followed drastically changed human civilization with disruptive effects on health and overall wellbeing of mankind. This disruptive effect has been shown to include changes in epidemiology of burn injuries. This study therefore aimed to determine the impact of covid-19 on acute burn presentation at the University College Hospital (UCH), Ibadan. This was a retrospective study carried out between April 1, 2019 and March 31, 2021. The period was divided into two: April 1, 2019 to March 31, 2020 and April 1, 2020 to March 31, 2021. Data obtained from the burn unit registry were analyzed using the Scientific Package For Social Sciences version 25. The only statistically significant finding from this study was the marked reduction in burn ICU admission during the pandemic (P &lt; 0.001). A total of 144 patients presented to the burn intensive care unit at UCH, Ibadan during the period under review with 92 patients in the prepandemic year, and 52 patients in the pandemic year. Patient group from 0- to 9-year-olds representing 42% in prepandemic, and 30.8% in the pandemic period was the most affected age group. Scald was predominantly among the pediatric age group in both groups. Males were more likely to suffer flame burn in both study periods with a near gender equilibration during the pandemic. Burn injury during the pandemic resulted in more total body surface area burned. The lockdown effect of the pandemic resulted in a significant reduction in acute burn admissions at the UCH, Ibadan.
Heightened Human Rights Due Diligence in Practice: Prohibiting or Facilitating Investment in Conflict Affected Areas?
Authors: Aguirre Daniel , Pietropaoli Irene 
Published: May 2023

Abstract
Companies operating or seeking to invest in conflict-affected areas are expected to carry out a heightened human rights due diligence (HRDD) process to identify, address and mitigate their impact on human rights and the conflict. The heightened HRDD process put forward in the UN Guiding Principles on Business and Human Rights and clarified by the UN Working Group constitutes best practice but raises questions regarding implementation. This article explains what heightened HRDD in conflict means in practice. It examines how heightened HRDD expands the business responsibility from identifying and mitigating the impact of its operations on human rights to the impact on the conflict itself. This article draws on lessons from Myanmar, where a military coup in February 2021 caused prominent businesses to leave the country. Would a heightened HRDD process have identified additional risks and discouraged initial investment? Or would it have legitimized investment with a public rights-based, conflict sensitive HRDD process that included a clear exit strategy?
Suppression of the gene encoding PDZ domain-containing protein decreases cold tolerance and overwintering survival of the mosquito, Culex pipiens (Culicidae: Diptera)
Authors: King Bryan , Larsen Mazie , Ikenga Arinze , Sim Cheolho 
Published: May 2023

Abstract
In diapausing mosquitoes, cold tolerance and prolonged lifespan are important features that are crucial for overwintering success. In the mosquito Culex pipiens, we suggest that PDZ domain-containing protein (PDZ) (post synaptic density protein [PSD95], drosophila disc large tumor suppressor [Dlg1], and zonula occludens-1 protein [zo-1]) domain-containing protein is involved with these diapause features for overwintering survival in Culex mosquitoes. The expression level of pdz was significantly higher in diapausing adult females in the early stage in comparison to their nondiapausing counterparts. Suppression of the gene that encodes PDZ by RNA interference significantly decreased actin accumulation in the midgut of early-stage adult diapausing females. Inhibition of pdz also significantly reduced the survivability of diapausing females which indicates that this protein could play a key role in preserving the midgut tissues during early diapause.
The Utility of Performing Anaerobic Blood Cultures in Pediatric Intensive Care Units
Authors: Kato Hiroki , Shoji Kensuke , Jinguji Miyuki , Nishimura Nao , Nakagawa Satoshi , Miyairi Isao 
Published: May 2023

Abstract

Background
Several reports have suggested that routine use of anaerobic blood culture bottles together with aerobic bottles may improve blood culture positivity. However, the information is still limited regarding the utility of anaerobic blood culture bottles in the pediatric intensive care unit (PICU), where bacteremia due to anaerobic bacteria is relatively rare.

Methods
A retrospective observational study was conducted at a PICU in a tertiary children’s hospital in Japan from May 2016 to January 2020. Patients aged ≤15 years old with bacteremia, for which both aerobic and anaerobic blood cultures were submitted, were included in the study. We investigated whether the positive blood culture cases were from aerobic or anaerobic bottles. We also compared the amount of blood inoculated into culture bottles to determine the effect of blood volume on the rate of detection.

Results
During the study period, a total of 276 positive blood cultures from 67 patients were included in this study. Among the paired blood culture bottles, 22.1% were positive only for the anaerobic bottles. Escherichia coli and Enterobacter cloacae were the most common pathogens that were detected in anaerobic bottles only. Obligate anaerobic bacteria were detected in 2 (0.7%) bottles. There was no significant difference in the amount of blood inoculated into aerobic and anaerobic culture bottles.

Conclusions
The use of anaerobic blood culture bottles in the PICU may increase the detection rate of facultative anaerobic bacteria.
OsBAK2/OsSERK2 expression is repressed by OsBZR1 to modulate brassinosteroid response and grain length in rice
Authors: Du Huaying , Yong Rong , Zhang Jiaqi , Cai Guang , Wang Ruqin , Li Jianbo , Wang Yuji , Zhang Hongsheng , Gao Xiuying , Huang Ji 
Published: May 2023

Abstract
Brassinosteroids (BRs) are a class of polyhydroxylated steroidal phytohormones that are essential for plant growth and development. Rice BRASSINOSTEROID-INSENSITIVE1 (BRI1)-ASSOCIATED RECEPTOR KINASES (OsBAKs) are plasma membrane-localized receptor kinases belonging to the subfamily of leucine-rich repeat receptor kinases. It has been found that in Arabidopsis, BRs induce the formation of a BRI1–BAK1 heterodimer complex and transmit the cascade signal to BRASSINAZOLE RESISTANT1/bri1-EMS-SUPPRESSOR1 (BZR1/BES1) to regulate BR signaling. Here, in rice (Oryza sativa ssp. japonica), we found that OsBZR1 binds directly to the promoter of OsBAK2, but not OsBAK1, and represses the expression of OsBAK2 to form a BR feedback inhibition loop. Additionally, the phosphorylation of OsBZR1 by OsGSK3 reduced its binding to the OsBAK2 promoter. The osbak2 mutant displays a typical BR-deficiency phenotype and negative modulates the accumulation of OsBZR1. Interestingly, the grain length of the osbak2 mutant was increased whereas in the cr-osbak2/cr-osbzr1 double mutant, the reduced grain length of the cr-osbzr1 mutant was restored, implying that the increased grain length of osbak2 may be due to the rice somatic embryogenesis receptor kinase-dependent pathway. Our study reveals a novel mechanism by which OsBAK2 and OsBZR1 engage in a negative feedback loop to maintain rice BR homeostasis, facilitating a deeper understanding of the BR signaling network and grain length regulation in rice.
Role of ionizing background on the statistics of metal absorbers in hydrodynamical simulations
Authors: Mallik Sukanya , Srianand Raghunathan , Maitra Soumak , Gaikwad Prakash , Khandai Nishikanta 
Published: May 2023

ABSTRACT
We study the statistical properties of O vi, C iv, and Ne viii absorbers at low-z (i.e. z &lt; 0.5) using Sherwood simulations with ‘WIND’ only and ‘WIND + AGN’ feedback and massive black-II simulation that incorporates both ‘WIND’ i.e. outflows driven by stellar feedback and active galactic nucleus (AGN) feedbacks. For each simulation, by considering a wide range of metagalactic ionizing ultraviolet background (UVB), we show the statistical properties such as distribution functions of column density (N), b-parameter and velocity spread (ΔV90), the relationship between N and b-parameter, and the fraction of Ly α absorbers showing detectable metal lines as a function of N(H i) are influenced by the UVB used. This is because UVB changes the range in density, temperature, and metallicity of gas contributing to a given absorption line. For simulations considered here, we show the difference in some of the predicted distributions between different simulations is similar to the one obtained by varying the UVB for a given simulation. Most of the observed properties of O vi absorbers are roughly matched by Sherwood simulation with ‘WIND + AGN’ feedback when using the UVB with a lower O vi ionization rate. However, this simulation fails to produce observed distributions of C iv and fraction of H i absorbers with detectable metals. Therefore, in order to constrain different feedback processes and/or UVBs, using observed properties of H i and metal ions, it is important to perform simultaneous analysis of various observable parameters.
Efficient formation of massive galaxies at cosmic dawn by feedback-free starbursts
Authors: Dekel Avishai , Sarkar Kartick C , Birnboim Yuval , Mandelker Nir , Li Zhaozhou 
Published: May 2023

ABSTRACT
JWST observations indicate a surprising excess of luminous galaxies at z ∼ 10 and above, consistent with efficient conversion of the accreted gas into stars, unlike the suppression of star formation by feedback at later times. We show that the high densities and low metallicities at this epoch guarantee  a high star formation efficiency (SFE) in the most massive dark-matter haloes. Feedback-free starbursts (FFBs) occur when the free-fall time is shorter than ∼$1\, {\rm Myr}$, below the time for low-metallicity massive stars to develop winds and supernovae. This corresponds to a characteristic density of ∼$3\!\times \!10^3\, {\rm cm}^{-3}$. A comparable threshold density permits a starburst by allowing cooling to star-forming temperatures in a free-fall time. The galaxies within ∼1011 M⊙ haloes at z ∼ 10 are expected to have FFB densities. The halo masses allow efficient gas supply by cold streams in a halo crossing time ∼$80\, {\rm Myr}$. The FFBs gradually turn all the accreted gas into stars in clusters of ∼104–7 M⊙ within galaxies that are rotating discs or shells. The starbursting clouds are insensitive to radiative feedback and are shielded against feedback from earlier stars. We predict high SFE above thresholds in redshift and halo mass, where the density is $10^{3\!-\!4}\, {\rm cm}^{-3}$. The z ∼ 10 haloes of ∼1010.8 M⊙ are predicted to host galaxies of ∼1010 M⊙ with star formation rate ∼$65\,\mathrm{ M}_\odot \, {\rm yr}^{-1}$, blue colours, and sub-kpc sizes. The metallicity is ≤0.1 Z⊙ with little dust, gas, outflows, and hot circumgalactic gas, allowing a top-heavy initial mass function but not requiring it. The compact galaxies with thousands of young FFB clusters may have implications on reionization, black hole growth, and globular clusters.