bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of single-nucleotide polymorphism in the promoter region of bovinealpha-lactalbumin(LALBA) gene onLALBAexpression in milk cells and milk traits of cows
Authors: Ostrowska Malgorzata , Zwierzchowski Lech , Brzozowska Paulina , Kawecka-Grochocka Ewelina , Żelazowska Beata , Bagnicka Emilia 
Published: May 2021

AbstractPolymorphisms of milk protein genes have been proposed as candidate markers for dairy production traits in cattle. In the present study, a polymorphism was detected in the 5′-flanking (promoter) region of the bovine alpha-lactalbumin (LALBA) gene, a T/C transition located at nucleotide −1,001 relative to the transcription start site g.-1001T &gt; C (NC_037332.1:g.31183170T &gt; C), which is recognizable with PstI restriction endonuclease. In silico analyses showed that this mutation created novel retinoid X receptor alpha and vitamin D receptor transcription factor binding sites. Real-time PCR found that cows with different genetic variants of the promoter demonstrated different levels of expression of LALBA mRNA in milk somatic cells (MSCs). The TT genotype cows demonstrated low expression, whereas those with CT demonstrated much higher expression (P &lt; 0.05). ELISA analysis found milk LALBA protein levels also differed between the TT and CT cows (P &lt; 0.05) and that these levels were not correlated with the mRNA abundance in MSC. Association analysis found that the g.-1001T &gt; C polymorphism in the promoter region of the LALBA gene influenced milk production traits in Polish Holstein-Friesian cows. High daily milk yield and dry matter yield, and high lactose yield and concentration were associated with the TT genotype. The TT genotype cows also had a lower number of somatic cells in the milk, considered as an indicator of udder health status. Therefore, the TT genotype could be more desirable from the breeder’s perspective.
Birth, Life, and Afterlife of An Indonesian Graveyard: Environmental Rule and Its Discontents
Authors: Zakaria Faizah 
Published: May 2021

Abstract
The social history of graveyards in Asian cities is understudied but provides a uniquely apt ground from which to view socio-environmental concerns in an urban setting. Legally established in 1926, the Mandailing burial ground in the Indonesian city of Medan was produced through a set of legal and racial discourses introduced during the period of high colonialism. As this article demonstrates, these discourses were activated by large-scale land conversions that brought upland migrants down to coastal port cities and provoked them to question their identity. Placing the Mandailing graveyard within the context of “middle landscapes” that balance nature and culture illuminates how landscapes for the dead continue to manifest environmental change, including upland deforestation, flooding, and a rising tide of waste, in and beyond the city among the living. This article posits that such environmental anxieties were accompanied by social renovation from below, with the graveyard lending itself to a quest to enact a better future. The concentration of multiple issues within a single site makes the graveyard a singularly rich entry point for discussing how environmental rule and its discontents promote social change.
Logics for reasoning about degrees of confirmation
Authors: DautoviĆ Šejla , Doder Dragan , OgnjanoviĆ Zoran 
Published: May 2021

Abstract
In this paper, we present a first-order and a propositional logic for reasoning about degrees of confirmation. We define the appropriate formal languages and describe the corresponding classes of models. We provide infinitary axiomatizations for both logics and we prove that the axiomatizations are sound and strongly complete. We also show that our propositional logic is decidable. For some restrictions of the logics, we provide finitary axiomatic systems.
On the vertical shear instability in magnetized protoplanetary discs
Authors: Cui Can , Lin Min-Kai 
Published: May 2021

ABSTRACT
The vertical shear instability (VSI) is a robust phenomenon in irradiated protoplanetary discs (PPDs). While there is extensive literature on the VSI in the hydrodynamic limit, PPDs are expected to be magnetized and their extremely low ionization fractions imply that non-ideal magnetohydrodynamic effects should be properly considered. To this end, we present linear analyses of the VSI in magnetized discs with Ohmic resistivity. We primarily consider toroidal magnetic fields, which are likely to dominate the field geometry in PPDs. We perform vertically global and radially local analyses to capture characteristic VSI modes with extended vertical structures. To focus on the effect of magnetism, a locally isothermal equation of state is employed. We find that magnetism provides a stabilizing effect to dampen the VSI, with surface modes, rather than body modes, being the first to vanish with increasing magnetization. Subdued VSI modes can be revived by Ohmic resistivity, where sufficient magnetic diffusion overcomes magnetic stabilization, and hydrodynamic results are recovered. We also briefly consider poloidal magnetic fields to account for the magnetorotational instability (MRI), which may develop towards surface layers in the outer regions of PPDs. The MRI grows efficiently at small radial wavenumbers, in contrast to the VSI. When resistivity is considered, the VSI dominates over the MRI for Ohmic Elsässer numbers ≲0.09 at plasma beta parameter βZ ∼ 104.
Tight multimessenger constraints on the neutron star equation of state from GW170817 and a forward model for kilonova light-curve synthesis
Authors: Nicholl Matt , Margalit Ben , Schmidt Patricia , Smith Graham P , Ridley Evan J , Nuttall James 
Published: May 2021

ABSTRACT
We present a rapid analytic framework for predicting kilonova light curves following neutron star (NS) mergers, where the main input parameters are binary-based properties measurable by gravitational wave detectors (chirp mass and mass ratio, orbital inclination) and properties dependent on the nuclear equation of state (tidal deformability, maximum NS mass). This enables synthesis of a kilonova sample for any NS source population, or determination of the observing depth needed to detect a live kilonova given gravitational wave source parameters in low latency. We validate this code, implemented in the public mosfit package, by fitting it to GW170817. A Bayes factor analysis overwhelmingly (B &gt; 1010) favours the inclusion of an additional luminosity source in addition to lanthanide-poor dynamical ejecta during the first day. This is well fit by a shock-heated cocoon model, though differences in the ejecta structure, opacity or nuclear heating rate cannot be ruled out as alternatives. The emission thereafter is dominated by a lanthanide-rich viscous wind. We find the mass ratio of the binary is q = 0.92 ± 0.07 (90 per cent credible interval). We place tight constraints on the maximum stable NS mass, MTOV $=2.17^{+0.08}_{-0.11}$ M⊙. For a uniform prior in tidal deformability, the radius of a 1.4-M⊙ NS is R1.4 ∼ 10.7 km. Re-weighting with a prior based on equations of state that support our credible range in MTOV, we derive a final measurement R1.4 $=11.06^{+1.01}_{-0.98}$ km. Applying our code to the second gravitationally detected NS merger, GW190425, we estimate that an associated kilonova would have been fainter (by ∼0.7 mag at 1 d post-merger) and declined faster than GW170817, underlining the importance of tuning follow-up strategies individually for each GW-detected NS merger.
HELP: the Herschel Extragalactic Legacy Project
Authors: Shirley R , Duncan K , Campos Varillas M C , Hurley P D , Małek K , Roehlly Y , Smith M W L , Aussel H , Bakx T , Buat V , Burgarella D , Christopher N , Duivenvoorden S , Eales S , Efstathiou A , González Solares E A , Griffin M , Jarvis M , Faro B Lo , Marchetti L , McCheyne I , Papadopoulos A , Penner K , Pons E , Prescott M , Rigby E , Rottgering H , Saxena A , Scudder J , Vaccari M , Wang L , Oliver S J 
Published: May 2021

ABSTRACT
We present the Herschel Extragalactic Legacy Project (HELP). This project collates, curates, homogenizes, and creates derived data products for most of the premium multiwavelength extragalactic data sets. The sky boundaries for the first data release cover 1270 deg2 defined by the Herschel SPIRE extragalactic survey fields; notably the Herschel Multi-tiered Extragalactic Survey (HerMES) and the Herschel Atlas survey (H-ATLAS). Here, we describe the motivation and principal elements in the design of the project. Guiding principles are transparent or ‘open’ methodologies with care for reproducibility and identification of provenance. A key element of the design focuses around the homogenization of calibration, meta data, and the provision of information required to define the selection of the data for statistical analysis. We apply probabilistic methods that extract information directly from the images at long wavelengths, exploiting the prior information available at shorter wavelengths and providing full posterior distributions rather than maximum-likelihood estimates and associated uncertainties as in traditional catalogues. With this project definition paper, we provide full access to the first data release of HELP; Data Release 1 (DR1), including a monolithic map of the largest SPIRE extragalactic field at 385 deg2 and 18 million measurements of PACS and SPIRE fluxes. We also provide tools to access and analyse the full HELP data base. This new data set includes far-infrared photometry, photometric redshifts, and derived physical properties estimated from modelling the spectral energy distributions over the full HELP sky. All the software and data presented is publicly available.
Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations
Authors: Huang Xin , Fortier Alyssa Lyn , Coffman Alec J , Struck Travis J , Irby Megan N , James Jennifer E , León-Burguete José E , Ragsdale Aaron P , Gutenkunst Ryan N 
Published: May 2021

AbstractThe effect of a mutation on fitness may differ between populations depending on environmental and genetic context, but little is known about the factors that underlie such differences. To quantify genome-wide correlations in mutation fitness effects, we developed a novel concept called a joint distribution of fitness effects (DFE) between populations. We then proposed a new statistic w to measure the DFE correlation between populations. Using simulation, we showed that inferring the DFE correlation from the joint allele frequency spectrum is statistically precise and robust. Using population genomic data, we inferred DFE correlations of populations in humans, Drosophila melanogaster, and wild tomatoes. In these species, we found that the overall correlation of the joint DFE was inversely related to genetic differentiation. In humans and D. melanogaster, deleterious mutations had a lower DFE correlation than tolerated mutations, indicating a complex joint DFE. Altogether, the DFE correlation can be reliably inferred, and it offers extensive insight into the genetics of population divergence.
Spliceosome-regulated RSRP1-dependent NF-κB activation promotes the glioblastoma mesenchymal phenotype
Authors: Li Yaomin , Wang Xiran , Qi Songtao , Gao Lei , Huang Guanglong , Ren Zhonglu , Li Kaishu , Peng Yuping , Yi Guozhong , Guo Jinglin , Yang Runwei , Wang Hai , Zhang Xian , Liu Yawei 
Published: May 2021

Abstract

Background
The glioblastoma (GBM) mesenchymal (MES) phenotype, induced by NF-κB activation, is characterized by aggressive tumor progression and poor clinical outcomes. Our previous analysis indicated that MES GBM has a unique alternative splicing (AS) pattern; however, the underlying mechanism remains obscure. We aimed to reveal how splicing regulation contributes to MES phenotype promotion in GBM.

Methods
We screened novel candidate splicing factors that participate in NF-κB activation and MES phenotype promotion in GBM. In vitro and in vivo assays were used to explore the function of RSRP1 in MES GBM.

Results
Here, we identified that arginine/serine-rich protein 1 (RSRP1) promotes the MES phenotype by facilitating GBM cell invasion and apoptosis resistance. Proteomic, transcriptomic, and functional analyses confirmed that RSRP1 regulates AS in MES GBM through mediating spliceosome assembly. One RSRP1-regulated AS event resulted in skipping PARP6 exon 18 to form truncated, oncogenic PARP6-s. This isoform was unable to effectively suppress NF-κB. Cotreatment of cultured GBM cells and GBM tumor-bearing mice with spliceosome and NF-κB inhibitors exerted a synergistic effect on MES GBM growth.

Conclusion
We identified a novel mechanism through which RSRP1-dependent splicing promotes the GBM MES phenotype. Targeting AS via RSRP1-related spliceosomal factors might constitute a promising treatment for GBM.
Metformin effects on brain development following cranial irradiation in a mouse model
Authors: Yuen Nili , Szulc-Lerch Kamila U , Li Yu-Qing , Morshead Cindi M , Mabbott Donald J , Wong C Shun , Nieman Brian J 
Published: May 2021

AbstractBackgroundCranial radiation therapy (CRT) is a mainstay of treatment for malignant pediatric brain tumors and high-risk leukemia. Although CRT improves survival, it has been shown to disrupt normal brain development and result in cognitive impairments in cancer survivors. Animal studies suggest that there is potential to promote brain recovery after injury using metformin. Our aim was to evaluate whether metformin can restore brain volume outcomes in a mouse model of CRT.MethodsC57BL/6J mice were irradiated with a whole-brain radiation dose of 7 Gy during infancy. Two weeks of metformin treatment started either on the day of or 3 days after irradiation. In vivo magnetic resonance imaging was performed prior to irradiation and at 3 subsequent time points to evaluate the effects of radiation and metformin on brain development.ResultsWidespread volume loss in the irradiated brain appeared within 1 week of irradiation with limited subsequent recovery in volume outcomes. In many structures, metformin administration starting on the day of irradiation exacerbated radiation-induced injury, particularly in male mice. Metformin treatment starting 3 days after irradiation improved brain volume outcomes in subcortical regions, the olfactory bulbs, and structures of the brainstem and cerebellum.ConclusionsOur results show that metformin treatment has the potential to improve neuroanatomical outcomes after CRT. However, both timing of metformin administration and subject sex affect structure outcomes, and metformin may also be deleterious. Our results highlight important considerations in determining the potential benefits of metformin treatment after CRT and emphasize the need for caution in repurposing metformin in clinical studies.
Sociodemographic predictors and transportation patterns of COVID-19 infection and mortality
Authors: Pekmezaris Renee , Zhu Xu , Hentz Roland , Lesser Martin L , Wang Jason J , Jelavic Matthew 
Published: May 2021

AbstractBackgroundThe United States Centers for Disease Control and Prevention (CDC)-sanctioned prevention strategies have included frequent handwashing with soap and water, covering the mouth and nose with a mask when around others, cleaning and disinfecting maintaining a distance of at least 6 feet from others, etc. Although many of these recommendations are based upon observation and past infection control practices, it is important to combine and explore public data sets to identify predictors of infection, morbidity and mortality to develop more finely honed interventions, based on sociodemographic factors.MethodCross-sectional study of both states in the US and counties in NY state.ResultsPopulation density was found to be significantly associated with state-level coronavirus infection and mortality rate (b = 0.49, 95% confidence interval (CI): 0.34, 0.64, P &lt; .0001). States that have lower socioeconomic status, lower mean age and denser populations are associated with higher incidence rates. In regard to NY state, counties with a higher percentage of minority residents had higher COVID-19 mortality rates (b = 2.61, 95% CI: 0.36, 4.87, P = 0.023). Larger population cohorts were associated with lower COVID-19 mortality rates after adjusting for other variables in the model (b = −1.39, 95% CI: −2.07, −0.71, P &lt; 0.001). Population density was not significantly associated with COVID-19 mortality rates after adjustment across counties in the NY state. Public ridership was not indicative of cases or mortality across states in the USA; however, it is a significant factor associated with incidence (but not mortality) in NY counties.ConclusionPopulation density was the only significant predictor of mortality across states in the USA. Lower mean age, lower median household incomes and more densely populated states were at higher risk of COVID-19 infection. Population density was not found to be a significant independent variable compared to minority status and socioeconomic factors in the New York epicenter. Meanwhile, public ridership was found to be a significant factor associated with incidence in New York counties.
Phytophthora Crown Rot of Florida Strawberry: Inoculum Sources and Thermotherapy of Transplants for Disease Management
Authors: Baggio Juliana S. , Marin Marcus V. , Peres Natalia A. 
Published: May 2021

Phytophthora crown rot, caused mainly by Phytophthora cactorum but also by P. nicotianae, reported in 2018, is an important disease in the Florida strawberry annual production system. Mefenoxam is the most effective and widely used fungicide to manage this disease. However, because of pathogen resistance, alternatives to chemical control are needed. Phytophthora spp. were rarely recovered during the summer from soil of commercial farms where the disease was observed during the season. In a more detailed survey on research plots, neither of the two species was recovered 1 month after the crop was terminated and water was shut off. Therefore, Phytophthora spp. does not seem to survive in the soil over summer in Florida. In a field trial, asymptomatic nursery transplants harboring quiescent infections were confirmed as the major source of inoculum for these pathogens in Florida. Heat treatment of P. cactorum zoospores at 44°C for as little as 5 min was effective in inhibiting germination and colony formation; however, oospore germination was not inhibited by any of the tested temperatures in vitro. In the field, thermotherapy treatment of inoculated plants was shown to have great potential to serve as a nonchemical approach for managing Phytophthora crown rot in production fields and reducing mefenoxam-resistant populations in nursery transplants.
Change of preoperative symptoms of the late-onset hypogonadism syndrome after robot-assisted radical prostatectomy
Authors: Teishima Jun , Inoue Shogo , Hayashi Tetsutaro , Matsubara Akio 
Published: May 2021

Abstract

Background:
As prostate cancer (PCa) is a common cancer among older men, patients with PCa often show aging male symptoms (AMSs). This study aimed to investigate the preoperative AMSs of the late-onset hypogonadism (LOH) syndrome and the effects on them after robot-assisted radical prostatectomy (RARP).

Materials and methods:
One hundred eighty-eight patients who underwent RARP without androgen deprivation therapy were measured for serum free and serum total testosterone, and were preoperatively assessed for symptoms of the LOH syndrome using a questionnaire containing an AMS score. Patients with a preoperative AMS score higher than 37 and a serum free testosterone level lower than 8.5 pg/mL were classified as Group A, with the remaining classified as Group B. AMS scores were measured at 1, 3, 6, 9, and 12 months after surgery.

Results:
Of the 188 patients, 49 and 139 patients were classified as Groups A and B, respectively. Preoperative AMS scores were 44.5 ± 8.2 in Group A and 28.6 ± 5.3 in Group B (p < 0.0001). AMS scores in Group A significantly improved 1 month after RARP (30.6 ± 8.4, p < 0.0001) compared with their preoperative scores and remained at the same level from 3 to 12 months postoperatively, whereas those in Group B became significantly worse (32.0 ± 7.8, p < 0.0001) than their preoperative ones. There were no differences between AMS scores in Groups A and B at every postoperative period (p = 0.3259, 0.2730, 0.2429, 0.4629, 0.1771 at 1, 3, 6, 9, and 12 months after surgery, respectively).

Conclusions:
Our results indicate that AMSs in PCa patients with the LOH syndrome can expect the same level of improvement as patients without it.
A vascular surgery exchange program between Ethiopia and Sweden: a plus for both
Authors: Lundgren Fredrik , Hodza-Beganovic Ruhija , Johansson Mats , Seyoum Nebyou , Tadesse Mahelet , Andersson Peter 
Published: May 2021

Background:
Slightly >200 million people world-wide are estimated to be affected by peripheral arterial disease. About 14 million of these are in sub-Saharan Africa where surgical resources required to meet their needs for vascular care are scarce or missing.

Methods:
The International Medical Program at Linköping University Hospital, Sweden operates exchange programs for health care professionals between Swedish hospitals and partner-hospitals in low- and middle-income countries such as Ethiopia. The aim is to strengthen health care systems and medical proficiency of both partners. An exchange program in vascular surgery between Linköping University Hospital including affiliated county hospitals and Tikur Anbessa Specialized Hospital (TASH) in Addis Abeba, Ethiopia was launched in 2017.

Results:
Swedish vascular surgeons have participated in open surgery of advanced vascular conditions rarely seen in Sweden or other high-income contexts such as surgery for carotid body tumors. Their innovative skills and ability to cope with limited resources have improved. Vascular activities at TASH have developed and the number of patients operated on has increased due to improved opportunities for recruiting fellows and residents after establishing a formal curriculum for training. In total 68 vascular procedures of different complexity have been performed at TASH with the involvement of Swedish visitors. Preoperative multidisciplinary planning of surgery has been introduced at TASH and demanding techniques in vascular surgery have been acquired such as below-knee anastomoses.

Conclusions:
The program fills an educational gap in vascular surgery in Ethiopia but also a gap in Sweden regarding training in open vascular surgery.