bluuebunny/crossref_metadata_2025 huggingface dataset:
PhaseME: Automatic rapid assessment of phasing quality and phasing improvement
Authors: Majidian Sina , Sedlazeck Fritz J
Published: July 2020

Background

The detection of which mutations are occurring on the same DNA molecule is essential to predict their consequences. This can be achieved by phasing the genomic variations. Nevertheless, state-of-the-art haplotype phasing is currently a black box in which the accuracy and quality of the reconstructed haplotypes are hard to assess.

Findings

Here we present PhaseME, a versatile method to provide insights into and improvement of sample phasing results based on linkage data. We showcase the performance and the importance of PhaseME by comparing phasing information obtained from Pacific Biosciences including both continuous long reads and high-quality consensus reads, Oxford Nanopore Technologies, 10x Genomics, and Illumina sequencing technologies. We found that 10x Genomics and Oxford Nanopore phasing can be significantly improved while retaining a high N50 and completeness of phase blocks. PhaseME generates reports and summary plots to provide insights into phasing performance and correctness. We observed unique phasing issues for each of the sequencing technologies, highlighting the necessity of quality assessments. PhaseME is able to decrease the Hamming error rate significantly by 22.4% on average across all 5 technologies. Additionally, a significant improvement is obtained in the reduction of long switch errors. Especially for high-quality consensus reads, the improvement is 54.6% in return for only a 5% decrease in phase block N50 length.

Conclusions

PhaseME is a universal method to assess the phasing quality and accuracy and improves the quality of phasing using linkage information. The package is freely available at https://github.com/smajidian/phaseme.
An Overview of Competition Law Enforcement in Hong Kong
Authors: Snyder Brent
Published: July 2020

The Hong Kong Competition Commission is a young enforcement agency, enforcing a competition law that has been in effect less than five years. Despite its relative youth, the Competition Commission is quickly gaining experience as the pace and breadth of its enforcement is increasing in the aftermath of its first trial wins, its policy advisory work with the Hong Kong Government is gaining traction, and its advocacy is succeeding in educating a wide variety of Hong Kong stakeholders about the benefits of competition and the requirements of the law.
Reduced Hospital Costs for Ultrasound-guided Vacuum-assisted Excision Compared with Open Surgery in Patients with Benign Breast Masses and High-risk Lesions
Authors: Whitworth Pat , Hogan Andrew , Ferko Nicole , Son Daniel , Wang Faye , Xiong Yan , Suri Himanshu , Barclay Ben
Published: July 2020

Objective

Benign breast masses represent a substantial proportion of breast cancer screening results and may require multiple follow-up visits and biopsy. Even with a preceding benign core biopsy, benign masses have been excised via open surgery for a variety of reasons. This study compared the procedural costs of US-guided vacuum-assisted excision (US-VAE) versus open surgical excisions for benign breast masses and high-risk lesions (HRL).

Methods

In this retrospective cohort study, female outpatients receiving US-VAE or open excision of benign breast masses between 2015 and 2018 were identified within the Premier Healthcare Database. A secondary analysis was conducted for patients with HRLs. Propensity score matching and multivariate regression adjusted for patient demographics, encounter level covariates, and hospital characteristics. The total procedural costs were reported from a hospital perspective.

Results

A total of 33 724 patients underwent excisions for benign breast masses (8481 US-VAE and 25 242 open surgery). Procedural costs were significantly lower in unmatched patients who received US-VAE ($1350) versus open surgery ($3045) (P < 0.0001). After matching, a total of 5499 discharges were included in each group, with similar findings for US-VAE ($1348) versus open surgery ($3101) (P < 0.0001). A secondary analysis of matched HRL patients (41 discharges in each group) also showed significantly lower procedural costs with US-VAE ($1620) versus open surgery ($3870) (P < 0.0001).

Conclusion

Among patients with benign breast masses or HRLs, US-VAE was associated with significantly lower procedural costs versus open surgery. If excision is performed and expected clinical outcomes are equal, US-VAE is preferable to reduce costs without compromising the quality of care.
Population-Based Evidence From a Western Canadian Province of the Decreasing Incidence Rates and Trends of Inflammatory Bowel Disease Among Adults
Authors: Osei Jessica Amankwah , Peña-Sánchez Juan Nicolás , Fowler Sharyle A , Muhajarine Nazeem , Kaplan Gilaad G , Lix Lisa M
Published: July 2020

Background and Aims

Canada has one of the highest inflammatory bowel disease (IBD) incidence rates worldwide. Higher IBD incidence rates have been identified among urban regions compared to rural regions. The study objectives were to (i) estimate IBD incidence rates in Saskatchewan from 1999 to 2016 and (ii) test for differences in IBD incidence rates for rural and urban regions of Saskatchewan.

Methods

A population-based study was conducted using provincial administrative health databases. Individuals aged 18+ years with newly diagnosed Crohn’s disease or ulcerative colitis were identified using a validated case definition. Generalized linear models with a negative binomial distribution were used to estimate incidence rates and incidence rate ratios (IRRs) adjusted for age group, sex and rurality with 95% confidence intervals (CIs).

Results

The average annual incidence rate of IBD among adults in Saskatchewan decreased from 75/100,000 (95% CI 67 to 84) in 1999 to 15/100,000 (95% CI 12 to 18) population in 2016. The average annual incidence of IBD declined significantly by 6.9% (95% CI −7.6 to −6.2) per year. Urban residents had a greater overall risk of IBD (IRR = 1.19, 95% CI 1.11 to 1.27) than rural residents. This risk difference was statistically significant for Crohn’s disease (IRR = 1.25, 95% CI 1.14 to 1.36), but not for ulcerative colitis (IRR = 1.08, 95% CI 0.97 to 1.19).

Conclusions

The incidence of IBD in Saskatchewan dropped significantly from 1999 to 2016 with urban dwellers having a 19% higher risk of IBD onset compared to their rural counterparts. Health care providers and decision-makers should plan IBD-specific health care programs considering these specific IBD rates.
Planetary systems in a star cluster II: intermediate-mass black holes and planetary systems
Authors: Flammini Dotti Francesco , Kouwenhoven M B N , Shu Qi , Hao Wei , Spurzem Rainer
Published: July 2020

Most stars form in dense stellar environments. It is speculated that some dense star clusters may host intermediate-mass black holes (IMBHs), which may have formed from runaway collisions between high-mass stars, or from the mergers of less massive black holes. Here, we numerically explore the evolution of populations of planets in star clusters with an IMBH. We study the dynamical evolution of single-planet systems and free-floating planets, over a period of 100 Myr, in star clusters without an IMBH, and in clusters with a central IMBH of mass $100\, \mathrm{M}_\odot$ or $200\, \mathrm{M}_\odot$. In the central region ($r\lesssim 0.2$ pc), the IMBH’s tidal influence on planetary systems is typically 10 times stronger than the average neighbour star. For a star cluster with a $200\, \mathrm{M}_\odot$ IMBH, the region in which the IMBH’s influence is stronger within the virial radius (∼1 pc). The IMBH quenches mass segregation, and the stars in the core tend to move towards intermediate regions. The ejection rate of both stars and planets is higher when an IMBH is present. The rate at which planets are expelled from their host star rate is higher for clusters with higher IMBH masses, for t < 0.5trh, while remains mostly constant while the star cluster fills its Roche lobe, similar to a star cluster without an IMBH. The disruption rate of planetary systems is higher in initially denser clusters, and for wider planetary orbits, but this rate is substantially enhanced by the presence of a central IMBH.
Is there large convective-core overshooting in Kepler targets KIC 2837475 and 11081729?
Authors: Zhang Jianwei
Published: July 2020

The ratio of small-to-large separations r010 has been widely used in helioseismology and asteroseismology to investigate the internal structure of a star, as it is approximately independent of the structure of the outer layers. Several studies have used this tool to constrain the convective-core overshooting of main-sequence stars (i.e. 0.0 ≤ δov ≤ 0.2). This is consistent with the generally accepted values. However, Yang et al. have proposed that there is large convective-core overshooting in the Kepler targets KIC 2837475 and 11081729: 1.2 ≤ δov ≤ 1.6 and 1.7 ≤ δov ≤ 1.8, respectively. These are much larger than the normal values. Thus, the aim of this study is to re-investigate the ratios of the two stars using a model-independent method with the latest p-mode observations. Our results indicate that there is no robustness for including such a large convective-core overshooting while modelling these two stars. In fact, this leads to over-fitting, and the observational constraints of r010 prefer models with a normal convective-core overshooting (i.e. 0.0 ≤ δov ≤ 0.2) as the candidates for the best-fitting model of KIC 2837475 and 11081729.
A commercial grain-free diet does not decrease plasma amino acids and taurine status but increases bile acid excretion when fed to Labrador Retrievers
Authors: Donadelli Renan A , Pezzali Julia G , Oba Patricia M , Swanson Kelly S , Coon Craig , Varney Jessica , Pendlebury Christine , Shoveller Anna K
Published: July 2020

Grain-free diets tend to have greater inclusions of pulses in contrast to grain-based diets. In 2018, the Food and Drug Administration (FDA) released a statement that grain-free diets may be related to the development of canine dilated cardiomyopathy (DCM). However, all dog foods met regulatory minimums for nutrient inclusion recommended by the Association of American Feed Controls Official. In some FDA case reports, but not all, dogs diagnosed with DCM also had low concentrations of plasma or whole blood taurine; thus, we hypothesized that feeding these diets will result in reduced taurine status from baseline measures. The objective of this study was to determine the effects of feeding a grain-free diet to large-breed dogs on taurine status and overall health. Eight Labrador Retrievers (four males and four females; Four Rivers Kennel, MO) were individually housed and fed a commercial complete and balanced grain-free diet (Acana Pork and Squash formula; APS) for 26 wk. Fasted blood samples were collected prior to the start of the trial (baseline; week 0) and at weeks 13 and 26 for analyses of blood chemistry, hematology, plasma amino acids, and whole blood taurine. Urine was collected by free catch at weeks 0 and 26 for taurine and creatinine analyses. Fresh fecal samples were collected at weeks 0 and 26 for bile acid analyses. Data were analyzed using the GLIMMIX procedure with repeated measures in SAS (v. 9.4). Plasma His, Met, Trp, and taurine and whole blood taurine concentrations increased over the course of the study (P < 0.05). Urinary taurine to creatinine ratio was not affected by diet (P > 0.05). Fecal bile acid excretion increased after 26 wk of feeding APS to dogs. Despite the higher fecal excretion of bile acids, plasma and whole blood taurine increased over the 26-wk feeding study. These data suggest that feeding APS, a grain-free diet, over a 26-wk period improved taurine status in Labrador Retrievers and is not the basis for the incidence of DCM for dogs fed APS. Other factors that may contribute to the etiology of DCM should be explored.
LncRNA NR_030777 Alleviates Paraquat-Induced Neurotoxicity by Regulating Zfp326 and Cpne5
Authors: Yang Hongyu , Lin Qingxia , Chen Nengzhou , Luo Zhousong , Zheng Chunyan , Li Jing , Zheng Fuli , Guo Zhenkun , Cai Ping , Wu Siying , Wang Yuan-Liang , Li Huangyuan
Published: July 2020

Paraquat (PQ) is herbicide widely used in agricultural production. It is identified as an environmental toxicant that could lead to neurodegeneration damage. Parkinson’s disease (PD) is a central nervous system degenerative disease that occurs in the elderly. Main risk factors for PD include genetic and environmental variables, but its specific mechanism is still not well understood. Emerging evidence suggests that long noncoding RNAs (lncRNAs) play an important role in PD. LncRNA NR_030777 has a full length of 2208 bp and is highly conserved among species. RNA profiling showed a significant alteration in lncRNA NR_030777 expression upon PQ-induced neurotoxicity. However, little is known on the functional relevance of lncRNA NR_030777 in the development of PQ. In this study, we discovered a vital protective role of lncRNA NR_030777 in PQ-induced neurotoxicity. The expression of NR_030777 correlates with elevated level of reactive oxygen species induced by PQ. In addition, activated expression of NR_030777 alleviates neurotoxicity by regulating the expression of Zfp326 and Copine 5. We report that lncRNA NR_030777 has a vital protective role in neurotoxicity induced by environmental toxicants such as PQ. This study could serve as an exemplary case for lncRNAs to be considered as a potential target for the prevention and treatment of PQ-induced neurodegenerative disorders such as PD.
Interplay of Cucurbit Yellow Stunting Disorder Virus With Cucurbit Chlorotic Yellows Virus and Transmission Dynamics by Bemisia tabaci MED
Authors: Orfanidou Chrysoula , Katsiani Asimina , Papayiannis Lambros , Katis Nikolaos I. , Maliogka Varvara I.
Published: July 2020

Cucurbit chlorotic yellows virus (CCYV) and cucurbit yellow stunting disorder virus (CYSDV) are two closely related criniviruses that often coinfect cucurbits and are associated with cucurbit yellows disease. Both viruses are distributed worldwide and are transmitted in a semipersistent manner by the whitefly vectors Bemisia tabaci MED or MEAM1. The major goal of this study was to provide insight into the interaction of CCYV and CYSDV in cucumber and to study the effect on transmission by B. tabaci MED. The titers of both viruses were estimated in single- and dually infected cucumber plants via reverse transcription PCR assays. In mixed infections, the accumulation of both viruses was significantly decreased. When B. tabaci MED adults were placed on cucumber infected with both viruses, their simultaneous transmission efficiency was significantly higher, whereas transmission efficiency of each individual virus was low. Moreover, nonviruliferous whiteflies preferentially settled on crinivirus-infected cucumber plants, whereas viruliferous whiteflies were attracted by healthy cucumber plants. Finally, the titer of both viruses was calculated in five commercial cucumber hybrids, followed by subsequent transmission experiments. Our results show that although the titers of CYSDV and CCYV were significantly lower in mixed infections in cucumbers, their simultaneous transmission increased.
Parental-to-Embryo Switch of Chromosome Organization in Early Embryogenesis
Authors: Collombet Samuel , Ranisavljevic Noémie , Nagano Takashi , Varnai Csilla , Shisode Tarak , Leung Wing , Piolot Tristan , Galupa Rafael , Borensztein Maud , Servant Nicolas , Fraser Peter , Ancelin Katia , Heard Edith
Published: July 2020

(Abstracted from Nature 2020;580:142–146)

Paternal and maternal epigenome analysis has shown atypical patterns of histone modification in oocytes, sperm, and preimplantation embryos that undergo marked changes after fertilization. Previous studies have led to inconclusive evidence on the dynamics of local topological-associated domains (TADs) regarding their absence in the oocyte and appearance in the embryo versus preexistence in the zygote.
Neonatal Abstinence Syndrome Incidence and Health Care Costs in the United States, 2016
Authors: Strahan Andrea E. , Guy Gery P. , Bohm Michele , Frey Meghan , Ko Jean Y.
Published: July 2020

(Abstracted from JAMA Pediatr 2020;174(2):200–202)

One of the immediate effects of the opioid crisis is the rise of neonatal abstinence syndrome (NAS), a withdrawal condition primarily occurring in infants who have been exposed to opioids in utero. In the United States, incidence rates for NAS have increased from 1.5 per 1000 births in 2004 to 8.0 per 1000 births in 2014.
Female Genital Tract Microbiota Affecting the Risk of Preterm Birth: What Do We Know So Far? A Review
Authors: Tsonis O. , Gkrozou F. , Harrison E. , Stefanidis K. , Vrachnis N. , Paschopoulos M.
Published: July 2020

(Abstracted from Eur J Obstet Gynecol Reprod Biol 2020;245:168–173)

Spontaneous preterm birth (sPTB) is a major cause of neonatal morbidity and mortality worldwide. The literature has suggested that vaginal microbiota and its genome, known as the microbiome, may play a role in regulating the maternal immune response that induces early labor.
Long-term Device Outcomes of Mesh Implants in Pelvic Organ Prolapse Repairs
Authors: Chughtai Bilal , Mao Jialin , Asfaw Tirsit S. , Heneghan Carl , Rardin Charles R. , Sedrakyan Art
Published: July 2020

(Abstracted from Obstet Gynecol 2020;135:591–598)

During the past 2 decades, more than 2 million women in the United States have been implanted with transvaginal mesh as surgical treatment for both stress urinary incontinence and pelvic organ prolapse (POP). Several mesh devices were adopted and widely used to address the high failure rates of traditional POP repairs.
Masks and Face Covers
Authors: Joseph Rachel , Highton Mary
Published: July 2020

The emergence of COVID-19 swept through the nations, and measures to prevent transmission of infection became the focus for all health care organizations internationally. With the increase in number of cases, the unanticipated consumption of personal protective equipment exceeded the capacity. With the scarcity of masks, the type, use, and reuse became a topic of debate. This article explores the origin, types, and the challenges nurses face regarding the use of masks.
Use of Cannabinoids in Cancer Patients: A Society of Gynecologic Oncology (SGO) Clinical Practice Statement
Authors: Whitcomb B. , Lutman C. , Pearl M. , Medlin E. , Prendergast E. , Robison K. , Burke W.
Published: July 2020

(Abstracted from Gynecol Oncol 2020;157:307–311)

A comprehensive report published by the National Academies of Science, Engineering and Medicine in 2017 concluded that there exists “conclusive or substantial evidence that cannabis or cannabinoids are effective” in treatment of chronic pain in adults and as an antiemetic agent in patients undergoing chemotherapy. Despite this recommendation, barriers remain to determining the significant short- and long-term health effects of cannabis.
Length of Labour in Mothers and Their Daughters: A Matched Cohort Study
Authors: Ebrahimoff Mindy , Many Ariel , Downe Soo , Tishkovskaya Svetlana , Hall-Moran Victoria
Published: July 2020

(Abstracted from Eur J Obstet Gynecol Reprod Biol 2020;245:77–83)

Determining safe limits for the length of labor has increasingly become a topic for debate. While there are a number of known associations between mother and daughter reproductive outcomes, there are no reports in the literature comparing the length of labor in daughters versus their mothers.
Genetic correlates of phenotypic heterogeneity in autism
Authors: Warrier Varun , Zhang Xinhe , Reed Patrick , Havdahl Alexandra , Moore Tyler M , Cliquet Freddy , Leblond Claire S , Rolland Thomas , Rosengren Anders ,   EU-AIMS-LEAP,   iPSYCH-Autism Working Group,   Spectrum 10K and APEX Consortium, Rowitch David H , Hurles Matthew E , Geschwind Daniel H , Børglum Anders D , Robinson Elise B , Grove Jakob , Martin Hilary C , Bourgeron Thomas , Baron-Cohen Simon
Published: July 2020

The substantial phenotypic heterogeneity in autism limits our understanding of its genetic aetiology. To address this gap, we investigated genetic differences between autistic individuals (Nmax= 12,893) based on core (i.e., social communication difficulties, and restricted and repetitive behaviours) and associated features of autism, co-occurring developmental disabilities (e.g. language, motor, and intellectual developmental disabilities and delays), and sex. We conducted a comprehensive factor analysis of core autism features in autistic individuals and identified six factors. Common genetic variants including autism polygenic scores (PGS) were associated with the core factors butde novovariants were not, even though the latent factor structure was similar between carriers and non-carriers ofde novovariants. We identify that increasing autism PGS decrease the likelihood of co- occurring developmental disabilities in autistic individuals, which reflects both a true protective effect and additivity between rare and common variants. Furthermore in autistic individuals without co-occurring intellectual disability (ID), autism PGS are overinherited by autistic females compared to males. Finally, we observe higher SNP heritability for males and autistic individuals without ID, but found no robust differences in SNP heritability by the level of core autism features. Deeper phenotypic characterisation will be critical to determining how the complex underlying genetics shapes cognition, behaviour, and co- occurring conditions in autism.
Prevalence and clinical correlates of COVID-19 outbreak among health care workers in a tertiary level hospital in Delhi
Authors: Khurana Ankit , Kaushal GP , Gupta Rishi , Verma Vansh , Sharma Kabir , Kohli Manmohan
Published: July 2020

In this study, we summarize the epidemiological characteristics of COVID-19 outbreak among Healthcare workers (HCWs) in a tertiary care hospital and compared various parameters and preventive measures taken by positive HCWs to a comparable cohort of COVID negative HCWs. 52.1% of COVID-19 positive HCWs showed symptoms of which only three needed hospitalization possibly due to a younger cohort of HCWs who got infected (35.9 ± 9.3 years). Findings of present study found some protective role of full course prophylactic hydroxychloroquine as compared to a control group (p=0.021) and use of N95 masks over others (p<0.001). Our results did not show any added protection with the use of prophylactic Vitamin C, D, Zinc, or betadine gargles. We also observed outbreak control with increased awareness, near universal testing, PPE provision, sanitization drive, and promoting social distancing among HCWs.
Examining audiology students’ clinical reasoning skills with virtual audiology cases aided with no collaboration, live collaboration, and virtual collaboration
Authors: Shaaban Ramy
Published: July 2020

The purpose of this study was to examine the difference in clinical reasoning skills of students when using virtual audiology cases aided with no collaboration, virtual collaboration, and live collaboration. The theoretical framework discussed five major approaches that could explain this effect; Situated Learning Theory, Social Development Theory, Scaffolding, Collaborative Learning, and Cognitive Load Theory. A quasi-experimental design was conducted at two U.S. universities to examine whether there is a significant difference in clinical reasoning skills between the three treatment groups using IUP Audiosim software. The clinical reasoning data were analyzed using One-Way ANOVA, and Tukey HSD for ANOVA. The results indicated that there was a significant difference in clinical reasoning skills between the three treatment groups. Further analyses are shown in the body of the study.
Synthetic Photoplethysmography (PPG) of the radial artery through parallelized Monte Carlo and its correlation to Body Mass Index (BMI)
Authors: Boonya-ananta Tananant , Rodriguez Andres J. , Ajmal Ajmal , Du Le Vinh Nguyen , Hansen Anders K. , Hutcheson Joshua D. , Ramella-Roman Jessica C.
Published: July 2020

Cardiovascular disease is one of the leading causes of death in the United States and obesity significantly increases the risk of cardiovascular disease. The measurement of blood pressure (BP) is critical in monitoring and managing cardiovascular disease hence new wearable devices are being developed to make the BP metric mode accessible to physicians and patients. Several wearables utilize photoplethysmography from the wrist vasculature to derive BP assessment although many of these devices are still at the experimental stage. With the ultimate goal of supporting instrument development, we have developed a model the photoplethysmographic waveform derived from the radial artery at the volar surface of the wrist. To do so we have utilized the relation between vessel biomechanics through Finite Element Method and Monte Carlo light transport model. The model shows similar features to that seen in PPG waveform captured using an off the shelf device. We observe the influence of body mass index (BMI) on the PPG signal. A degradation the PPG signal of up to 40% in AC to DC signal ratio was thus observed.
The frailty syndrome as an emergent state of parallel dysregulation in multiple physiological systems
Authors: Ghachem Ahmed , Fried Linda P. , Legault Véronique , Bandeen-Roche Karen , Presse Nancy , Cohen Alan A.
Published: July 2020

Frailty is a clinical syndrome often present in older adults and characterized by a heightened vulnerability to stressors. The biological antecedents and etiology of frailty are unclear despite decades of research: frailty is associated with dysregulation in a wide range of physiological systems, but no specific cause has been identified. Here, we test predictions stemming from the hypothesis that there is no specific cause: that frailty is an emergent property arising from the complex systems dynamics of the broad loss of organismal homeostasis. Specifically, we use dysregulation of six physiological systems using the Mahalanobis distance approach in two cohorts of older adults to test the breadth, diffuseness, and nonlinearity of associations between frailty and system-specific dysregulation. We find clear support for the breadth of associations between frailty and physiological dysregulation: positive associations of all systems with frailty in at least some analyses. We find partial support for diffuseness: the number of systems or total amount of dysregulation is more important than the identity of the systems dysregulated, but results only partially replicate across cohorts. We find partial support for nonlinearity: trends are exponential but not always significantly so, and power is limited for groups with very high levels of dysregulation. Overall, results are consistent with – but not definitive proof of – frailty as an emergent property of complex systems dynamics. Substantial work remains to understand how frailty relates to underlying physiological dynamics across systems.
Pure species discriminate against hybrids in theDrosophila melanogasterspecies subgroup
Authors: Serrato-Capuchina Antonio , Schwochert Timothy D. , Zhang Stephania , Roy Baylee , Peede David , Koppelman Caleigh , Matute Daniel R.
Published: July 2020

Introgression, the exchange of alleles between species, is a common event in nature. This transfer of alleles between species must happen through fertile hybrids. Characterizing the traits that cause defects in hybrids illuminate how and when gene flow is expected to occur. Inviability and sterility are extreme examples of fitness reductions but are not the only type of defects in hybrids. Some traits specific to hybrids are more subtle but are important to determine their fitness. In this report, we study whether F1 hybrids between two species pairs ofDrosophilaare as attractive as the parental species. We find that in both species pairs, the sexual attractiveness of the F1 hybrids is reduced and that pure species discriminate strongly against them. We also find that the cuticular hydrocarbon (CHC) profile of the hybrids is intermediate between the parental species. Perfuming experiments show that modifying the CHC profile of the hybrids to resemble pure species improves their chances of mating. Our results show that behavioral discrimination against hybrids might be an important component of the persistence of species that can hybridize.
A novel PS4 criterion approach based on symptoms of rare diseases and in-house frequency data in a Bayesian framework
Authors: Cho You Kyung , Won Dhong-gun , Keum Changwon , Lee Beom Hee , Seo Go Hun , Lee Byung-Chul
Published: July 2020

The American College of Medical Genetics (ACMG) and Genomics/Association for Molecular Pathology (AMP) previously reported standardized guidance for the assessment of genetic variants. One of the criteria regarding the prevalence in a case-control study, PS4, is important due to its evidence of pathogenicity. Despite recent studies approaching gene- and disease-specific probands, interpretation of a variant to PS4 still has certain limitations for rare variants. Here, we suggest a generalized method, Bayesian odds ratio (BayesianOR), applicable to PS4 via decomposing a disease to its symptoms and applying a Bayesian framework. Using this approach, we demonstrate reproducibility of the calculation of the original odds ratio from well-studied epilepsy data and verify the applicability to in-house frequencies for various rare diseases. In addition, BayesianOR showed a significant difference in tendency with different ClinVar pathogenicity, using in-house data. Thus, the novel method described here should provide an improved interpretation of sequence variants. Furthermore, we anticipate that it will enhance the diagnosis of patients with rare diseases.
Methylation-directed Acetylation of Histone H3 Regulates Developmental Sensitivity to Histone Deacetylase Inhibition
Authors: Huang Li-Yao , Hsu Duen-Wei , Pears Catherine
Published: July 2020

Background

Treatment of cells with hydroxamate-based lysine deacetylase inhibitors (KDACis) such as Trichostatin A (TSA) can induce biological effects such as differentiation or apoptosis of cancer cells, and a number of related compounds have been approved for clinical use. TSA treatment induces rapid initial acetylation of histone 3 (H3) proteins which are already modified by tri-methylation on lysine 4 (H3K4me3) while acetylation of bulk histones, lacking this mark, is delayed. Sgf29, a subunit of the SAGA acetyltransferase complex, interacts with H3K4me3 via a tandem tudor domain (TTD) and has been proposed to target the acetyltransferase activity to H3K4me3. However the importance of acetylation of this pool of H3 in the biological consequences of KDACi treatment is not known.

Results

We investigated the role of H3K4me3-directed acetylation in the mechanism of action of TSA on inhibiting development of the eukaryotic social amoebaDictyostelium discoideum. Loss of H3K4me3 in strains with mutations in the gene encoding Set1 or the histone proteins confers resistance to TSA-induced inhibition of development and delays accumulation of histone acetylation on H3K9 and K14. A candidate orthologue of Sgf29 inDictyosteliumhas been identified which specifically recognizes the H3K4me3 modification via its tandem Tudor domain (TTD). Disruption of the gene encoding Sgf29 delayed accumulation of H3K9Ac, abolished targeted H3K4me3-directed H3Ac and led to developmental resistance to TSA, which is dependent on a functional TTD. TSA resistance also results from overexpression of Sgf29.

Conclusion

Preferential acetylation of H3K4me3 histones, regulated by Sgf29 via its TTD, is important in developmental sensitivity to TSA. Levels of H3K4me3 or Sgf29 will provide useful biomarkers for sensitivity to this class of chemotherapeutic drug.
Exclusion of the fittest predicts microbial community diversity in fluctuating environments
Authors: Shibasaki Shota , Mobilia Mauro , Mitri Sara
Published: July 2020

Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species’ ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.
Activation microswitches in GPCRs function as rheostats in cell membrane
Authors: Ma Ning , Lee Sangbae , Vaidehi Nagarajan
Published: July 2020

Although multiple components of the cell membrane modulate the stability and activation of G protein coupled receptors (GPCRs), the activation mechanism comes from detergent studies, since it is challenging to study activation in multi-component lipid bilayer. Using the multi-scale molecular dynamics simulations(50μs), our comparative study between cell membrane and detergents shows that: the changes in inter-residue distances, known as activation microswitches, show an ensemble of states in the extent of activation in cell membrane. We forward a rheostat model of GPCR activation rather than a binary switch model. Phosphatidylinositol bisphosphate (PIP2) and calcium ions, through a tug of war, maintain a balance between the GPCR stability and activity in cell membrane. Due to the lack of receptor stiffening effects by PIP2, detergents promote more transitions among conformational states than cell membrane. These findings connect the chemistry of cell membrane lipids to receptor activity useful to design detergents mimicking cell membrane.
In VitroEfficacy of Five Biofungicides againstRhizoctonia solaniKuhn in Rice
Authors: Bauzon-Cantila Irish Mae , Silvestre Jaime C. , Evangelista Raquel B. , Catubay Edralyn
Published: July 2020

Rhizoctonia solaniKuhn, the causal pathogen of sheath blight is second most damaging fungal disease in rice. While using chemical fungicides present high detriment to environment, the study investigate the efficacy of treatments composing five biofungicides in three different rates along with a biological agent, chemical check and untreated against the pathogen inin vitrolevel.In vitroefficacy showed thatMelaleuca alternifolia+ terpenes at 3.00 ml/L of H20 (T6),Aloe verapowder (Manopol) +Melaleucaoil at 3.00 ml/L of H20 (T15) and at 2.00 ml/L of H20 (T14) andMelaleuca alternifolia+ terpenes at 2.00 ml/L of H20 (T5) as very effective (0-10 mm diameter zone of growth) treatments comparable to the chemical check (T17). Therefore, attaining high yield rice while having low risk to environment can always be done.
A Systematic Review and Meta-analysis of the Protective Effect of FMDV VP1 on Animals
Authors: Wu Peng , Liu Qingqing , He Jinke , Deng Xiaoyu , Yin Xinyue , Wang Yueli , Zhang Yunfeng , Chen Changfu
Published: July 2020

The FMDV VP1 protein has different structures which could decrease or increase the immune response. We undertook a meta-analysis to evaluate the protective effect of VP1 on the FMDV. A systematic search of the PubMed, Embase, CNKI and Wan fang DATA was conducted up to April 2020. Experimental studies involving the VP1 protection effect on FMDV were included. Extracted data were analyzed using Rev-Man 5.3 software. Chi-square tests were used to analyze the heterogeneity among the documents. The fixed-effect model was used for meta-analysis to find the combined effect value and 95% confidence interval. Sensitivity analysis was performed on the differences in the combined values of model effects, and the inverted funnel chart method was used to assess the publication bias of the included literature. A total of 12 articles were included for meta-analysis. The results of showed that VP1 had a protective effect on FMDV [MH= -0.66, 95%CI= (−0.75, -0.56),P< 0.00001]. Sensitivity analysis showed that the results were robust. The funnel graph method showed that the published literature had a small publication bias and met the requirements of this study. It is necessary to study the epitopes of VP1 to produce new vaccines. VP1 could protect animals from FMDV attacks. It is necessary to study the VP1 protein and its epitopes and use it as a new vaccine and diagnostic product.
The clinical and molecular significance associated with STING signaling in estrogen receptor-positive early breast cancer
Authors: Parkes EE , Humphries MP , Gilmore E , Sidi FA , Bingham V , Phyu SM , Craig SG , Graham C , Miller J , Griffin D , Kennedy RD , Bakhoum SF , McQuaid S , Salto-Tellez M , Buckley NE
Published: July 2020

STING signaling in cancer is a crucial component of response to immunotherapy and other anti-cancer treatments. Conversely, STING signaling can promote tumor invasion and metastasis. Currently, there is no robust method of measuring STING activation in cancer. Here, we describe an immunohistochemistry-based assay with digital pathology assessment of STING in tumor cells. Using this novel approach, we identify perinuclear-localized expression of STING (pnSTING) in estrogen receptor-positive (ER+) breast cancer as an independent predictor of good prognosis, associated with immune cell infiltration and upregulation of immune checkpoints. Tumors with low pnSTING are immunosuppressed with increased infiltration of “M2” -polarised macrophages. In ER-disease, pnSTING does not have a significant prognostic role, and STING appears to be uncoupled from interferon responses. Importantly, a gene signature defining low pnSTING expression in ER+ disease is predictive of poor prognosis in independent datasets. Low pnSTING is associated with chromosomal instability,MYCamplification and mTOR signaling, suggesting novel therapeutic approaches for this subgroup.
UPLC-MS analysis of characterization of bioactive compounds produced by endophytic Bacillus tequilensis ALR-2 from Aloe vera plant
Authors: Akinsanya Mushafau Adewale , Goh Joo Kheng , Ting Adeline Su Yien
Published: July 2020

Endophytic Bacillus tequilensis ALR-2 isolated from Aloe vera plant, was found to have antimicrobial activities attributed to a series of lipopeptide antibiotics and biosurfactants produced. Partial-purification of ethylacetate extracts by column chromatography revealed that fraction SF5 (5mg mL−1) effectively inhibited Bacillus cereus and Staphylococcus aureus (28.6±0.5 and 30.3±0.5 mm zone of inhibition, respectively), and was significantly more effective than the standard antibiotics Ciprofloxacin (5μg) (23.6 ±0.5 and 18.6 ±0.5 mm, respectively) and Kanamycin (30μg) (20.3 ±0.5 and 13.6 ±0.5 mm, respectively). UPLC-MS analysis of SF5 showed three series of ion peaks. The quadrupole-orthogonal ionization time-of-flight mass spectrometer revealed [M+H]+ of 678.4601; 679.4690 and 680.5076 which corresponded to the oligopeptide antibiotic monamycin (mol. wt. 677.84). The [M+H]+ of 1119.8870; 1120.8992 and 1121.9119 corresponded to antibiotic complex 61-26 (mol. wt. 1120.348), a lipopeptide. The third peak of [M+H]+ of 1356.0151 and 1358.0664 could not be classified to existing known compounds in the literatures.
Inter-annual stability and age-dependent changes in plasma testosterone levels in a longitudinally monitored free-living passerine bird
Authors: Tešický Martin , Krajzingrová Tereza , Eliáš Jiří , Velová Hana , Svobodová Jana , Bauerová Petra , Albrecht Tomáš , Vinkler Michal
Published: July 2020

While seasonal trends in the testosterone-driven hormonal regulation of resource allocation are known from cohort population samples, data on the inter-annual individual stability of blood plasma testosterone levels in wild birds are lacking, and our understanding of age-dependent changes is limited. We assessed plasma testosterone levels in 105 samples originating from 49 repeatedly captured free-living great tits (Parus major) to investigate their relative long-term stability and lifetime changes. Furthermore, we examined the inter-annual stability of selected condition-related traits (carotenoid- and melanin-based plumage ornamentation, ptilochronological feather growth rate, body mass, and haematological heterophil/lymphocyte ratio) and their relationships to testosterone levels. We show that testosterone levels in both sexes are inter-annually repeatable, both in their absolute values and individual ranks (indicating the maintenance of relative status in a population), yet with higher stability in females. Despite this stability, in males we found a quadratic dependence of testosterone levels on age, with a peak in midlife. In contrast, female testosterone levels showed no lifetime trend. The inter-annual stability of condition-related traits was mostly moderate and unrelated to plasma testosterone concentrations. However, males with elevated testosterone had significantly higher carotenoid-pigmented yellow plumage brightness, presumably serving as a sexually selected trait. Showing inter-annual stability in testosterone levels, this research opens the way to further understanding of the causes of variation in fitness-related traits. Based on a unique longitudinal dataset, this study demonstrates that male plasma testosterone undergoes age-related changes that may regulate resource allocation. Our results thus demonstrate that male birds undergo hormonal senescence similar to mammals.
Synthesis, crystal structure and docking studies of tetracyclic 10-iodo-1,2-dihydroisoquinolino[2,1-b][1,2,4]benzothiadiazine 12,12-dioxide and its precursors
Authors: Kolade Sherif O. , Izunobi Josephat U. , Hosten Eric C. , Olasupo Idris A. , Ogunlaja Adeniyi S. , Familoni Oluwole B.
Published: July 2020

The title compound, 10-iodo-1,2-dihydroisoquinolino[2,1-b][1,2,4]benzothiadiazine 12,12-dioxide, C15H11IN2O2S (8), was synthesized via the metal-free intramolecular N-iodosuccinimide (NIS)-mediated radical oxidative sp
3-C—H aminative cyclization of 2-(2′-aminobenzenesulfonyl)-1,3,4-trihydroisoquinoline, C15H16N2O2S (7). The amino adduct 7 was prepared via a two-step reaction, starting from the condensation of 2-nitrobenzenesulfonyl chloride (4) with 1,2,3,4-tetrahydroisoquinoline (5), to afford 2-(2′-nitrobenzenesulfonyl)-1,3,4-trihydroisoquinoline, C15H14N2O4S (6), in 82% yield. The catalytic hydrogenation of 6 with hydrogen gas, in the presence of 10% palladium-on-charcoal catalyst, furnished 7. Products 6–8 were characterized by their melting points, IR and NMR (1H and 13C) spectroscopy, and single-crystal X-ray diffraction. The three compounds crystallized in the monoclinic space group, with 7 exhibiting classical intramolecular hydrogen bonds of 2.16 and 2.26 Å. All three crystal structures exhibit centrosymmetric pairs of intermolecular C—H...π(ring) and/or π–π stacking interactions. The docking studies of molecules 6, 7 and 8 with deoxyribonucleic acid (PDB id: 1ZEW) revealed minor-groove binding behaviours without intercalation, with 7 presenting the most favourable global energy of the three molecules. Nonetheless, molecule 8 interacted strongly with the DNA macromolecule, with an attractive van der Waals energy of −15.53 kcal mol−1.
Crystal structure of zwitterionic 3,3′-[1,1′-(butane-1,4-diyl)bis(1H-imidazol-3-ium-3,1-diyl)]bis(propane-1-sulfonate) dihydrate
Authors: Udvardy Antal , De Sourav , Gál Tamás Gyula , Papp Gábor , Czégéni Csilla Enikő , Joó Ferenc
Published: July 2020

The crystal structure of the title compound, C16H26N4O6S2·2H2O, a water-soluble di-N-heterocyclic carbene ligand precursor was determined using a single crystal grown by the slow cooling of a hot N,N-dimethylformamide solution of the compound. The dihydrate crystallizes in the monoclinic space group P21/c, with half of the zwitterionic molecule and one water molecule of crystallization in the asymmetric unit. The remaining part of the molecule is completed by inversion symmetry. In the molecule, the imidazole ring planes are parallel with a plane-to-plane distance of 2.741 (2) Å. The supramolecular network is consolidated by hydrogen bonds of medium strength between the zwitterionic molecules and the water molecules of crystallization, as well as by π–π stacking interactions between the imidazole rings of neighbouring molecules and C—H...O hydrogen-bonding interactions.
The effectiveness of perceived social support in discount stores in Korea
Authors: Song Chanho , Brown Haakon T. , Tameez Rahmatullah Rami
Published: July 2020

Purpose

The purpose of this study is to bridge the gap in literature to examine social support that customers receive from their relationships with frontline service providers in discount stores.

Design/methodology/approach

In total, 381 consumers are accessed through an online survey administered by an online research company in South Korea. The authors use the structural equation model (SEM) technique to test the proposed hypotheses.

Findings

Social support (emotional, instrumental, informational and appraisal) significantly influences customer satisfaction in discount stores. In addition, customer satisfaction significantly influences word of mouth (WOM) and purchase intention.

Originality/value

Very few studies have addressed the relationship between social support and consumer satisfaction in the discount store industry. This research helps to understand that social support is a basic consideration for customers of discount stores when they are shopping.