bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii
Authors: Hasan Ahmed R , Ness Rob W 
Published: March 2020

AbstractRecombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.
Effect of fluid saturation on the shear modulus of artificial clay-rich tight sandstones
Authors: Li Dongqing , Wei Jianxin , Di Bangrang , Shuai Da , Tian Lihui , Ding Pinbo 
Published: March 2020

SUMMARY
For many geophysical problems it is important to understand the influence of clay on the elastic behaviour of the rocks. However, this is difficult to measure because the complex petrophysical characteristics of tight sandstones make it challenging to control the clay parameters in natural samples. In this study, we synthesized nine tight sandstones with different clay types and content. Ultrasonic measurements and theoretical simulations were then used to analyse the influence of clay on the elastic modulus of brine saturated samples. We found that the shear modulus of smectite-rich samples decreased drastically after saturation, while the decrease observed in kaolinite-rich samples was relatively low. We propose that the reduction in surface energy caused by surface-particle clay hydration is a common mechanism that leads to shear softening in both kaolinite-rich and smectite-rich samples. However, the contact deformation caused by cation hydration of smectite is the primary mechanism leading to greater shear softening of tight sandstones containing smectite. Although the differential Kuster–Toksöz model is based on idealized pore shapes, a dual-porosity scheme can be used to explain and simulate the shear softening of artificial clay-rich tight sandstones.
The role of pre-existing weak zones in the formation of the Himalaya and Tibetan plateau: 3-D thermomechanical modelling
Authors: Chen Lin , Liu Lijun , Capitanio Fabio A , Gerya Taras V , Li Yang 
Published: March 2020

SUMMARY
The Tibetan crust is sliced by several east–west trending suture zones. The role of these suture zones in the evolution of the Himalayan range and Tibetan plateau remains unclear. Here we use 3-D thermomechanical simulations to investigate the role of pre-existing weak zones within the Asian Plate in the formation of orogen and plateau growth during continental collision. Our results show that partitioning of deformation along the convergent margin leads to scraping off of crustal material into an orogenic wedge above the margin and crustal thickening in the retro-continent, eventually forming a large orogenic plateau in front of the indenter. Pre-existing weak zone(s) within the retro-continent is reactivated at the early stage of convergence, and facilitates the northward propagation of strain and widening of the orogenic plateau. The northernmost weak zone sets the northern limit of the Tibetan plateau. Our models also show rheological weakening of the congested buoyant crust within the collisional zone drives wedge-type exhumation of deeply buried crust at the southern flank of the plateau, which may explain the formation of the Greater Himalayan Sequence.
Utilization of traditional medicine in primary health care in low- and middle-income countries: a systematic review
Authors: Kim Jae Kyoun , Kim Kyeong Han , Shin Yong Cheol , Jang Bo-Hyoung , Ko Seong-Gyu 
Published: March 2020

Abstract
This paper reports the findings from the first systematic review of the utilization of traditional medicine (TM) in primary health care (PHC) in low- and middle-income countries (LMICs). PHC is an important component of health care and essential for achieving universal health coverage (UHC). For countries where there is a gap in PHC, TM plays a vital role. It is widely used and has the potential to increase the coverage of PHC and UHC. Hence in situations where TM is recognized in a considerable magnitude, there are scarce evidence and minimal regulation on it and TM practitioners (TMPs). This study aims to identify the current situation in the utilization of TM in PHC or UHC in LMICs. A systematic review and thematic synthesis of qualitative and quantitative studies have been conducted. A total of 56 articles met the criteria and were included in the review. In all, 14 analytic themes have been developed including the current use of TM in PHC, higher accessibility of TM, medical pluralism, national health system, national health policy and national health insurance to include TM, including TMPs in the referral system, utilizing TMPs as community health workers, the needs of scientific research on TM and the need for training both TMPs and conventional medical staffs for better collaboration. The study concluded that it is necessary to further focus on TM in the macro level on strengthening the referral system by including TM to establish a comprehensive service delivery network under UHC and in the micro level to focus on training the TMPs and conventional medicine health workers on both areas to attain more in-depth understanding of each other, which can lead to better collaboration and quality patient care.
Lactic Acid Bacteria Isolated From Korean Kimchi Activate the Vitamin D Receptor–autophagy Signaling Pathways
Authors: Lu Rong , Shang Mei , Zhang Yong-Guo , Jiao Yang , Xia Yinglin , Garrett Shari , Bakke Danika , Bäuerl Christine , Martinez Gaspar Perez , Kim Cheol-Hyun , Kang Sang-Moo , Sun Jun 
Published: March 2020

Abstract

Background
Probiotic lactic acid bacteria (LAB) have been used in the anti-inflammation and anti-infection process of various diseases, including inflammatory bowel disease (IBD). Vitamin D receptor (VDR) plays an essential role in pathogenesis of IBD and infectious diseases. Previous studies have demonstrated that the human VDR gene is a key host factor to shape gut microbiome. Furthermore, intestinal epithelial VDR conditional knockout (VDRΔIEC) leads to dysbiosis. Low expressions of VDR is associated with impaired autophagy, accompanied by a reduction of ATG16L1 and LC3B. The purpose of this study is to investigate probiotic effects and mechanism in modulating the VDR-autophagy pathways.

Methods
Five LAB strains were isolated from Korean kimchi. Conditional medium (CM) from these strains was used to treat a human cell line HCT116 or intestinal organoids to measure the expression of VDR and autophagy. Mouse embryonic fibroblast (MEF) cells with or without VDR were used to investigate the dependence on the VDR signaling. To test the role of LAB in anti-inflammation, VDR+/+ organoids were treated with 121-CM before infection with Salmonella enterica serovar Enteritidis. In vivo, the role of LAB in regulating VDR-autophagy signaling was examined using LAB 121-CM orally administrated to VDRLoxp and VDRΔIEC mice.

Results
The LAB-CM-treated groups showed higher mRNA expression of VDR and its target genes cathelicidin compared with the control group. LAB treatment also enhanced expressions of Beclin-1 and ATG16L1 and changed the ratio of LC3B I and II, indicating the activation of autophagic responses. Furthermore, 121-CM treatment before Salmonella enterica serovar Enteritidis infection dramatically increased VDR and ATG16L1 and inhibited the inflammation. Administration of 121-CM to VDRLoxp and VDRΔIEC mice for 12 and 24 hours resulted in an increase of VDR and LC3B II:I ratio. Furthermore, we identified that probiotic proteins P40 and P75 in the LAB-CM contributed to the anti-inflammatory function by increasing VDR.

Conclusions
Probiotic LAB exert anti-inflammation activity and induces autophagy. These effects depend on the VDR expression. Our data highlight the beneficial effects of these 5 LAB strains isolated from food in anti-infection and anti-inflammation.
Arterioplasty using gastroepiploic artery patch for common femoral artery occlusive disease
Authors: Nakai Shingo , Hamasaki Azumi , Uchida Tetsuro , Sadahiro Mitsuaki 
Published: March 2020

Abstract
We present the first case of arterioplasty of the common femoral artery performed using a gastroepiploic artery (GEA) patch for a 59-year-old man on haemodialysis. He was incidentally diagnosed with coronary artery disease with left main trunk stenosis and double-vessel disease upon screening examination for peripheral artery disease. Preoperative computed tomography revealed a severely narrowed right common femoral artery. We planned a simultaneous off-pump coronary artery bypass grafting (CABG) involving the bilateral internal thoracic arteries and GEA, and endarterectomy of the right common femoral artery. Because the remnant GEA was sufficiently long and its diameter was sufficiently large, we used a GEA patch during arterioplasty to preserve the saphenous vein. This method is limited to simultaneous surgery with CABG using GEA but is a useful alternative for preserving the saphenous vein.
Sound and Vibration as Research Variables in Terrestrial Vertebrate Models
Authors: Reynolds Randall , Garner Angela , Norton John 
Published: March 2020

Abstract
Sound and vibration have been shown to alter animal behavior and induce physiological changes as well as to cause effects at the cellular and molecular level. For these reasons, both environmental factors have a considerable potential to alter research outcomes when the outcome of the study is dependent on the animal existing in a normal or predictable biological state. Determining the specific levels of sound or vibration that will alter research is complex, as species will respond to different frequencies and have varying frequencies where they are most sensitive. In consideration of the potential of these factors to alter research, a thorough review of the literature and the conditions that likely exist in the research facility should occur specific to each research study. This review will summarize the fundamental physical properties of sound and vibration in relation to deriving maximal level standards, consider the sources of exposure, review the effects on animals, and discuss means by which the adverse effects of these factors can be mitigated.
Complex Multiplication in Twistor Spaces
Authors: Huybrechts D 
Published: March 2020

AbstractDespite the transcendental nature of the twistor construction, the algebraic fibres of the twistor space of a K3 surface share certain arithmetic properties. We prove that for a polarised K3 surface with complex multiplication, all algebraic fibres of its twistor space away from the equator have complex multiplication as well.
Hospital Readmissions After Laboratory-Confirmed Influenza Hospitalization
Authors: Dobrzynski David M , Ndi Danielle N , Zhu Yuwei , Markus Tiffanie , Schaffner William , Talbot H Keipp 
Published: March 2020

Abstract

Background
Influenza infection causes substantial morbidity and mortality. However, little is known about hospital readmissions after an influenza hospitalization. The aim of our study was to characterize frequency of hospital readmissions among patients hospitalized with laboratory-confirmed influenza.

Methods
We conducted a retrospective study using Tennessee Emerging Infections Program Influenza Surveillance data from 2006 to 2016 and the concurrent Tennessee Hospital Discharge Data System. We analyzed demographic characteristics and outcomes to better understand frequency and factors associated with hospital readmissions.

Results
Of the 2897 patients with a laboratory-confirmed influenza hospitalization, 409 (14%) and 1364 (47%) had at least 1 hospital readmission within 30 days and 1 year of the influenza hospitalization, respectively. Multiple readmissions occurred in 739 patients (54%). The readmission group was older, female predominant, and had more comorbidities than patients not hospitalized. Pneumonia, acute chronic obstructive pulmonary disease/asthma exacerbation, septicemia, acute respiratory failure, and acute renal failure were the most common causes for readmission at 30 days. Underlying cardiovascular disease, lung disease, kidney disease, diabetes, immunosuppression, and liver disease were associated with increased risk of readmission during the subsequent year.

Conclusions
After an admission with laboratory-confirmed influenza, there is a high likelihood of readmission within 30 days and 1 year adding to the morbidity of influenza.
Vicious cycle of chronic disease and poverty: a qualitative study in present day Nepal
Authors: Sapkota Taranath , Houkes Inge , Bosma Hans 
Published: March 2020

Abstract

Background
In countries with out-of-pocket (OOP) payment systems for healthcare, the combination of chronic disease and poverty can have damaging socio-economic and health impacts for affected households. Using a life course perspective, this article aims to explore how Nepalese people struggle with, experience and adapt to chronic disease, poverty and their consequences, and how chronic diseases and poverty reinforce each other.

Methods
In-depth semi-structured interviews were conducted with 21 chronically ill Nepalese people with one or more chronic diseases and/or their caretakers. Data were transcribed and analysed thematically.

Results
The adaptation strategies for the consequences of the huge OOP costs make patients and their households financially disadvantaged. The impoverishment has major social impacts and often persists across generations. The situation forces people to choose between avoiding medical treatment or further impoverishing their families.

Conclusions
This study explored how chronically ill Nepalese people struggle with socio-economic and health consequences of OOP payments for their disease. The article sheds light on circumstances and adaptation strategies that obstruct every attempt to escape from the vicious cycle of the poverty trap. Hence poverty and health adversities accumulate across generations and contribute to greater health expenditures, worse health outcomes and severely compromised social life.
Civil Conflict and Agenda-Setting Speed in the United Nations Security Council
Authors: Binder Martin , Golub Jonathan 
Published: March 2020

AbstractThe United Nations Security Council (UNSC) can respond to a civil conflict only if that conflict first enters the Council's agenda. Some conflicts reach the Council's agenda within days after they start, others after years (or even decades), and some never make it. So far, only a few studies have looked at the crucial UNSC agenda-setting stage, and none have examined agenda-setting speed. To fill this important gap, we develop and test a novel theoretical framework that combines insights from realist and constructivist theory with lessons from institutionalist theory and bargaining theory. Applying survival analysis to an original dataset, we show that the parochial interests of the permanent members (P-5) matter, but they do not determine the Council's agenda-setting speed. Rather, P-5 interests are constrained by normative considerations and concerns for the Council's organizational mission arising from the severity of a conflict (in terms of spillover effects and civilian casualties); by the interests of the widely ignored elected members (E-10); and by the degree of preference heterogeneity among both the P-5 and the E-10. Our findings contribute to a better understanding of how the United Nations (UN) works, and they have implications for the UN's legitimacy.
Accountability to Contain Corruption in Procurement Tenders
Authors: Caillaud Bernard , Lambert-Mogiliansky Ariane 
Published: March 2020

Abstract
This article addresses the issue of favoritism at the design stage of a complex procurement auction. A community of citizens procures a project but lacks the ability to translate its preferences into operational technical specifications. This task is delegated to a public officer who may collude with one of the firms in exchange of a bribe. We investigate a simple accountability mechanism that requires justifying one aspect of the technical decision determined by the alerts of competitors (alert-based accountability [ABA]). We find that relying on competitors enables the community to deter favoritism significantly more easily than random challenges. The penalty needed to fully deter corruption is independent of the complexity of the project. It depends on the degree of differentiation within the industry. In an illustrative example, we study the patterns of favoritism when corruption occurs under ABA and compare them with the patterns in the random challenge mechanism. (JEL D73, D82, H57).
Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 endoplasmic reticulum–plasma membrane contact site complexes in Arabidopsis
Authors: Lee EunKyoung , Santana Brenda Vila Nova , Samuels Elizabeth , Benitez-Fuente Francisco , Corsi Erica , Botella Miguel A , Perez-Sancho Jessica , Vanneste Steffen , Friml Jiří , Macho Alberto , Azevedo Aristea Alves , Rosado Abel 
Published: March 2020

AbstractIn plant cells, environmental stressors promote changes in connectivity between the cortical endoplasmic reticulum (ER) and the plasma membrane (PM). Although this process is tightly regulated in space and time, the molecular signals and structural components mediating these changes in interorganelle communication are only starting to be characterized. In this report, we confirm the presence of a putative tethering complex containing the synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+- and lipid-binding protein 1 (CLB1/SYT7). This complex is enriched at ER–PM contact sites (EPCSs), has slow responses to changes in extracellular Ca2+, and displays severe cytoskeleton-dependent rearrangements in response to the trivalent lanthanum (La3+) and gadolinium (Gd3+) rare earth elements (REEs). Although REEs are generally used as non-selective cation channel blockers at the PM, here we show that the slow internalization of REEs into the cytosol underlies the activation of the Ca2+/calmodulin intracellular signaling, the accumulation of phosphatidylinositol-4-phosphate (PI4P) at the PM, and the cytoskeleton-dependent rearrangement of the SYT1/SYT5 EPCS complexes. We propose that the observed EPCS rearrangements act as a slow adaptive response to sustained stress conditions, and that this process involves the accumulation of stress-specific phosphoinositide species at the PM.
Giant star-forming clumps?
Authors: Ivison R J , Richard J , Biggs A D , Zwaan M A , Falgarone E , Arumugam V , van der Werf P P , Rujopakarn W 
Published: March 2020

ABSTRACT
With the spatial resolution of the Atacama Large Millimetre Array (ALMA), dusty galaxies in the distant Universe typically appear as single, compact blobs of dust emission, with a median half-light radius, ≈1 kpc. Occasionally, strong gravitational lensing by foreground galaxies or galaxy clusters has probed spatial scales 1–2 orders of magnitude smaller, often revealing late-stage mergers, sometimes with tantalizing hints of sub-structure. One lensed galaxy in particular, the Cosmic Eyelash at z = 2.3, has been cited extensively as an example of where the interstellar medium exhibits obvious, pronounced clumps, on a spatial scale of ≈100 pc. Seven orders of magnitude more luminous than giant molecular clouds in the local Universe, these features are presented as circumstantial evidence that the blue clumps observed in many z ∼ 2–3 galaxies are important sites of ongoing star formation, with significant masses of gas and stars. Here, we present data from ALMA which reveal that the dust continuum of the Cosmic Eyelash is in fact smooth and can be reproduced using two Sérsic profiles with effective radii, 1.2 and 4.4 kpc, with no evidence of significant star-forming clumps down to a spatial scale of ≈80 pc and a star formation rate of &lt;3 M⊙ yr−1.
Diversity and evolution of bacterial bioluminescence genes in the global ocean
Authors: Vannier Thomas , Hingamp Pascal , Turrel Floriane , Tanet Lisa , Lescot Magali , Timsit Youri 
Published: March 2020

AbstractAlthough bioluminescent bacteria are the most abundant and widely distributed of all light-emitting organisms, the biological role and evolutionary history of bacterial luminescence are still shrouded in mystery. Bioluminescence has so far been observed in the genomes of three families of Gammaproteobacteria in the form of canonical lux operons that adopt the CDAB(F)E(G) gene order. LuxA and luxB encode the two subunits of bacterial luciferase responsible for light-emission. Our deep exploration of public marine environmental databases considerably expands this view by providing a catalog of new lux homolog sequences, including 401 previously unknown luciferase-related genes. It also reveals a broader diversity of the lux operon organization, which we observed in previously undescribed configurations such as CEDA, CAED and AxxCE. This expanded operon diversity provides clues for deciphering lux operon evolution and propagation within the bacterial domain. Leveraging quantitative tracking of marine bacterial genes afforded by planetary scale metagenomic sampling, our study also reveals that the novel lux genes and operons described herein are more abundant in the global ocean than the canonical CDAB(F)E(G) operon.
A3-A3 Bypass for Giant Anterior Cerebral Artery Aneurysm: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F 
Published: March 2020

Abstract
Large fusiform anterior cerebral artery aneurysms often require revascularization to allow for the treatment of the aneurysm and preservation of distal perfusion. The A3-A3 side-to-side anastomosis maintains ipsilateral distal perfusion. The inflow to the fusiform segment can then be clip occluded to treat the diseased vessel segment. This procedure is illustrated by the case in this video. The patient had a large right anterior cerebral artery fusiform aneurysm. An anterior interhemispheric craniotomy with the right side down was utilized for the approach. Postprocedural angiography demonstrated occlusion of the aneurysmal segment and patent distal perfusion within the ipsilateral distal segment. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.