bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting wrong sign Yukawa coupling of type II two-Higgs-doublet model in light of recent LHC data *
Authors: Wang Lei , Wang Hong-Xin , Han Xiao-Fang 
Published: June 2020

Abstract
In light of the recently obtained LHC Higgs data, we examine the parameter space of the type II two-Higgs-doublet model, in which the 125 GeV Higgs bosons exhibit wrong sign Yukawa couplings. Combining the relevant theoretical and experimental limits, we find that the LHC Higgs data exclude most of the parameter space of the wrong sign Yukawa coupling. For

600 GeV, the allowed samples are mainly distributed across several corners and narrow bands of

GeV, 30

GeV, 240 GeV

GeV, 380 GeV

GeV, and 480 GeV

GeV. For

600 GeV,

is required to be lower than 470 GeV. The light pseudo-scalar with a mass of 20 GeV is still permitted in the case of the wrong sign Yukawa coupling of 125 GeV Higgs bosons.
Effect of agricultural system on seed selection in the Rappang Sidenreng Regency
Authors: Fitriani R , Wulandary A , Mursalat A , Dagong M I A 
Published: June 2020

Abstract
Increased grain production is strongly influenced by the irrigation system owned by farmers. With optimal irrigation system then the farmer will dare to buy more expensive seeds. Farmers will be willing to take greater risks because of grain production to be acquired greater. According to the Data Collection Guidelines for Food Crops and Horticulture, Ministry of Agriculture, several factors can affect the rise and fall of the average rice production per hectare is the problem of soil fertility, use of fertilizers, seeds, how to grow crops, pests and many more. The purpose of this study to determine the effect of agricultural systems on seed selection in Sidrap. This study was conducted in 11 districts in Sidrap, using 99 samples. To answer the purposes of this study, the research institute using logistic regression data analysis is an approach to create predictive models such as linear regression, or commonly referred to as Ordinary Least Squares (OLS). The results showed that a good irrigation system such as the system of irrigation the farmers are more willing to take the risk to buy seed expensive that have good quality, unlike the case with rainfed and pumping which tends to farmers choose to use seed that relatively cheaper, because farmers do not dare to take the risk of failure of grain production because irrigation systems are less supportive. The conclusion of the research is that good irrigation will have an impact on farmers’ preferences to use better seedlings and be prepared to take risks.
Factor analysis in the adopting of utilization of rice straw waste as feed in South Bontonompo district, Gowa regency
Authors: Sudrajat E , Baba S , Amrawaty A A 
Published: June 2020

Abstract
This study aims to analyze the barriers of farmers in adopting the utilization of rice straw waste as feed. The study was conducted in South Bontonompo District, Gowa Regency, South Sulawesi Province, Indonesia. The type of research was a quantitative descriptive research using Factor Analysis tool. The variables measured in this study were 11 variables. Sample was drawn through simple random technique resulting in 55 farmers as respondents. The research data were collected by conducting a survey using the interview technique with a questionnaire. The results showed that the extraction of 11 variables indicated that all of them fulfilled the requirements for Factor Analysis, resulting in 3 formation factors. The variables included in factor 1 are knowledge about waste utilization (X5), waste management skills (X7), land ownership (X8), labor availability (X9), inability to pay for labor (X10) and age (X11). Variables included in factor 2 are difficulties in transporting feed (X3), non-intensive maintenance system (X4) and number of livestock ownership (X6). Meanwhile, the variables included in factor 3 are storage warehouse (X1) and processing equipment (X2). Factor 1 is named the intrinsic constraints because it is an internal part of breeders, factor 2 is named livestock business constraints because it is related to the situation of cattle farmers in carrying out cattle business activities, while factor 3 is named infrastructure constraints because it is a supporting factor in the cattle business.
Nonlinear optics of MXene in laser technologies
Authors: Jhon Young In , Jhon Young Min , Lee Ju Han 
Published: June 2020

Abstract
Recently, two-dimension transition metal carbides, carbonitrides, and nitrides called MXenes have attracted huge attention due to their outstanding physical properties in various fields. Here we highlight the enormous potential of MXenes as nonlinear optical materials in the laser technologies, which includes ultrafast laser pulse generation, laser frequency modulation based on four-wave mixing, and photonic diodes with time reversal symmetry breaking. Emphasis is placed on the wide spectral applicability of metallic MXene saturable absorbers in passively mode-locked femtosecond laser technologies, allowing for operation in the visible to mid-infrared range. The Z-scan analysis reveals that Ti3C2Tx MXene has a large nonlinear optical absorption coefficient and a negative nonlinear refractive index, and notably it also possesses the higher threshold for light-induced damage with 50% increase in nonlinear transmittance. The MXene/C60 stacked modules enable the achievement of nonreciprocal transmission of laser pulses for photonic rectification. We strongly believe that MXenes will play a significant role in advanced laser technologies such as optical information processing, molecular spectroscopy, and micromachining, while providing many insightful electro-optical applications.
Identification of conserved evolutionary trajectories in tumors
Authors: Hodzic Ermin , Shrestha Raunak , Malikic Salem , Collins Colin C , Litchfield Kevin , Turajlic Samra , Sahinalp S Cenk 
Published: June 2020

Abstract

Motivation
As multi-region, time-series and single-cell sequencing data become more widely available; it is becoming clear that certain tumors share evolutionary characteristics with others. In the last few years, several computational methods have been developed with the goal of inferring the subclonal composition and evolutionary history of tumors from tumor biopsy sequencing data. However, the phylogenetic trees that they report differ significantly between tumors (even those with similar characteristics).

Results
In this article, we present a novel combinatorial optimization method, CONETT, for detection of recurrent tumor evolution trajectories. Our method constructs a consensus tree of conserved evolutionary trajectories based on the information about temporal order of alteration events in a set of tumors. We apply our method to previously published datasets of 100 clear-cell renal cell carcinoma and 99 non-small-cell lung cancer patients and identify both conserved trajectories that were reported in the original studies, as well as new trajectories.

Availability and implementation
CONETT is implemented in C++ and available at https://github.com/ehodzic/CONETT.

Supplementary information
Supplementary data are available at Bioinformatics online.
iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters
Authors: Amin Ruhul , Rahman Chowdhury Rafeed , Ahmed Sajid , Sifat Md Habibur Rahman , Liton Md Nazmul Khan , Rahman Md Moshiur , Khan Md Zahid Hossain , Shatabda Swakkhar 
Published: June 2020

Abstract

Motivation
Promoter is a short region of DNA which is responsible for initiating transcription of specific genes. Development of computational tools for automatic identification of promoters is in high demand. According to the difference of functions, promoters can be of different types. Promoters may have both intra- and interclass variation and similarity in terms of consensus sequences. Accurate classification of various types of sigma promoters still remains a challenge.

Results
We present iPromoter-BnCNN for identification and accurate classification of six types of promoters—σ24,σ28,σ32,σ38,σ54,σ70. It is a CNN-based classifier which combines local features related to monomer nucleotide sequence, trimer nucleotide sequence, dimer structural properties and trimer structural properties through the use of parallel branching. We conducted experiments on a benchmark dataset and compared with six state-of-the-art tools to show our supremacy on 5-fold cross-validation. Moreover, we tested our classifier on an independent test dataset.

Availability and implementation
Our proposed tool iPromoter-BnCNN web server is freely available at http://103.109.52.8/iPromoter-BnCNN. The runnable source code can be found https://colab.research.google.com/drive/1yWWh7BXhsm8U4PODgPqlQRy23QGjF2DZ.

Supplementary information
Supplementary data are available at Bioinformatics online.
Morphometric analysis of dung beetle (Gymnopleurus mopsus: Scarabaeidae: Coleoptera) populations from two different biomes in Mongolia
Authors: Lim Changseob , Kang Ji Hyoun , Park Sung Hwan , Seok Sangwoo , Bayartogtokh Badamdorj , Bae Yeon Jae 
Published: June 2020

AbstractStudying the phenotypic variation of organisms along environmental gradients can provide insight into the influences of specific environmental factors. Mongolia, which is distributed across three different biomes, is an ideal location for studying the mechanisms that underlie such phenotypic variation over a large range of climate. The present study examined the variation in shape and size of the body in a ball-rolling dung beetle, Gymnopleurus mopsus (Pallas), in Mongolia and investigated the effects of climate on the species’ morphology. A total of 290 individuals were collected from seven sites and were analysed using multivariate and regression approaches, as well as geometric morphometrics. Body shape and size varied across the study sites and between the different biomes. Populations from the desert-steppe region had thinner bodies and longer heads than those from the steppe region, possibly to facilitate burrowing. Variation in the species’ body size followed a pattern that was the converse of Bergmann’s rule and, thus, might increase heat capacity and enhance thermoregulation ability in the desert-steppe region. Accordingly, the results of the present study provide novel insight into the influence of climate on the variation of dung beetle phenotypes.
Spatiotemporal expression of aquaporin 9 is critical for the antral growth of mouse ovarian follicles†
Authors: Lee Sungeun , Kang Hee-Gyoo , Ryou Chongsuk , Cheon Yong-Pil 
Published: June 2020

Abstract
Although a few aquaporins (AQPs) expressed in granulosa cells have been postulated to mediate fluid passage into the antrum, the specific expression of AQPs in different follicle cell types and stages and their roles have not been evaluated extensively. The spatiotemporal expression of aquaporin (Aqp) 7, 8, and 9 and the functional roles of Aqp9 in antral growth and ovulation were examined using a superovulation model and 3-dimensional follicle culture. Aqp9 was expressed at a high level in the rapid growth phase (24–48 h post equine chorionic gonadotropin (eCG) for superovulation induction) compared to Aqp7 (after human chorionic gonadotropin (hCG)) and Aqp8 (8–24 h post eCG and 24 h post hCG). A dramatic increase in the expression and localization of Aqp9 mRNA in theca cells was observed, as evaluated using quantitative reverse transcription-polymerase (RT-PCR) coupled with laser capture microdissection and immunohistochemistry. AQP9 was located primarily on the theca cells of the tertiary and preovulatory follicles but not on the ovulated follicles. In phloretin-treated mice, the diameter of the preovulatory follicles and the number of ovulated oocytes decreased. Consistent with these findings, knocking down Aqp9 expression with an Aqp9 siRNA inhibited follicle growth (0.28:1 = siRNA:control) and decreased the number of ovulated follicles (0.36:1 = siRNA:control) during in vitro growth and ovulation induction. Based on these results, the expression of AQPs is under the control of the physiological status, and AQP9 expression in theca during folliculogenesis is required for antral growth and ovulation in a tissue-specific and stage-dependent manner.
Matrix-variate logistic regression with measurement error
Authors: Fang Junhan , Yi Grace Y 
Published: June 2020

Summary
Measurement error in covariates has been extensively studied in many conventional regression settings where covariate information is typically expressed in a vector form. However, there has been little work on error-prone matrix-variate data, which commonly arise from studies with imaging, spatial-temporal structures, etc. We consider analysis of error-contaminated matrix-variate data. We particularly focus on matrix-variate logistic measurement error models. We examine the biases induced from naive analysis which ignores measurement error in matrix-variate data. Two measurement error correction methods are developed to adjust for measurement error effects. The proposed methods are justified both theoretically and empirically. We analyse an electroencephalography dataset with the proposed methods.
Crop wild phylorelatives (CWPs): phylogenetic distance, cytogenetic compatibility and breeding system data enable estimation of crop wild relative gene pool classification
Authors: Viruel Juan , Kantar Michael B , Gargiulo Roberta , Hesketh-Prichard Peri , Leong Nathan , Cockel Christopher , Forest Félix , Gravendeel Barbara , Pérez-Barrales Rocío , Leitch Ilia J , Wilkin Paul 
Published: June 2020

AbstractEnabling food security requires access to a broad range of genetic resources to facilitate crop breeding. This need is increased in a climate change scenario, which will require the production of novel crops adapted to new conditions. However, many major crops have reduced genetic diversity due to the genetic bottlenecks that they have experienced during their domestication and subsequent breeding. Crop wild relatives (CWRs) remain underexploited in plant breeding programmes, mostly because of the lack of knowledge of their cross-compatibility with crops. In this study, we use a combination of phylogenetic distance metrics, cytogenetic compatibility data (e.g. chromosome number and ploidy) and information about breeding systems to predict interspecific cross-compatibility between crop and wild species and hence identify crop wild phylorelatives (CWPs) (i.e. CWRs that can breed with the crop). We illustrate this concept using cultivated asparagus as a model by integrating previous cross-compatibility knowledge and CWR classifications into a phylogenetic framework reconstructed using available sequence data. Our approach aims to reinforce the use of the gene pool classification system of CWRs of Harlan and De Wet, since CWPs are estimated to belong to the secondary gene pool and non-CWPs to the tertiary gene pool. Identifying CWPs unlocks novel uses of genetic resources, although such data are available for less than half of the known CWRs (43.4% with sequence data and 32.5% with known ploidy). The need to conserve plants that provide or enhance provisioning ecosystem services, including CWRs, is clear if we are to rise to the global challenge of ensuring food security for all. However, basic knowledge about their conservation status is still lacking, with only c. 20% of CWRs assigned an IUCN red list assessment, 23% of which are Data Deficient (DD). Using the CWP classification presented here to define CWRs will contribute towards helping to prioritize CWRs for IUCN assessments and, where prioritised, conservation.
A case report of isolated right ventricular lymphocytic myocarditis
Authors: Indraratna Praveen , Sivasubramaniam Vanathi , Davidson Trent , Eggleton Simon 
Published: June 2020

Abstract

Background
Lymphocytic myocarditis is an uncommon condition with a variety of clinical presentations. Isolated involvement of the right ventricle (RV) is very rare. We present a case of a young woman who developed right ventricular dysfunction and arrhythmias as a consequence of this condition, which appeared to be chronic at diagnosis.

Case summary
A 26-year-old lady was admitted to hospital following routine echocardiography, requested for screening of pulmonary hypertension in the context of known hypersensitivity pneumonitis. This echocardiogram demonstrated severe right ventricular dilatation and impairment. She was also experiencing atrial fibrillation and non-sustained, symptomatic episodes of ventricular tachycardia. Endomyocardial biopsy revealed lymphocytic myocarditis. She was managed with azathioprine and prednisone, as well as sotalol and apixaban for her atrial fibrillation, and has had no complications in the 12 months since discharge.

Discussion
Lymphocytic myocarditis isolated to the RV has only been reported in two previous cases, both of which were acute, dramatic presentations. This is the first report of a chronic example of this disease process. Due to her intercurrent immunosuppression, this patient may have been pre-disposed to the condition either by re-activation of a latent viral infection or partial treatment of a true autoimmune lymphocytic myocarditis.
Atrial fibrillation: a risk factor for unfavourable outcome in COVID-19? A case report
Authors: Schnaubelt Sebastian , Breyer Marie-Kathrin , Siller-Matula Jolanta , Domanovits Hans 
Published: June 2020

Abstract

Background
Fulminant cardiac involvement in COVID-19 patients has been reported; the underlying suspected mechanisms include myocarditis, arrhythmia, and cardiac tamponade. In parallel, atrial fibrillation is common in the elderly population which is at particularly high risk for COVID-19 morbidity and mortality.

Case summary
A 72-year-old male SARS-CoV2-positive patient was admitted to the intensive care unit due to delirium and acute respiratory failure. Atrial fibrillation known from history was exacerbated, and made complex rate and rhythm control necessary. Progressive heart failure with haemodynamic deterioration and acute kidney injury with the need for continuous renal replacement therapy were further aggravated by pericardial tamponade.

Discussion
Treatment of acute heart failure in COVID-19 patients with a cytokine storm complicated by tachycardic atrial fibrillation should include adequate rate or rhythm control, and potentially immunomodulation.
Effect of atorvastatin on muscle symptoms in coronary heart disease patients with self-perceived statin muscle side effects: a randomized, double-blinded crossover trial
Authors: Kristiansen Oscar , Vethe Nils Tore , Peersen Kari , Wang Fagerland Morten , Sverre Elise , Prunés Jensen Elena , Lindberg Morten , Gjertsen Erik , Gullestad Lars , Perk Joep , Dammen Toril , Bergan Stein , Husebye Einar , Otterstad Jan Erik , Munkhaugen John 
Published: June 2020

Abstract

Aims
To estimate the effect of atorvastatin on muscle symptom intensity in coronary heart disease (CHD) patients with self-perceived statin-associated muscle symptoms (SAMS) and to determine the relationship to blood levels of atorvastatin and/or metabolites.

Methods and results
A randomized multi-centre trial consecutively identified 982 patients with previous or ongoing atorvastatin treatment after a CHD event. Of these, 97 (9.9%) reported SAMS and 77 were randomized to 7-week double-blinded treatment with atorvastatin 40 mg/day and placebo in a crossover design. The primary outcome was the individual mean difference in muscle symptom intensity between the treatment periods, measured by visual-analogue scale (VAS) scores. Atorvastatin did not affect the intensity of muscle symptoms among 71 patients who completed the trial. Mean VAS difference (statin-placebo) was 0.31 (95% CI: −0.24 to 0.86). The proportion with more muscle symptoms during placebo than atorvastatin was 17% (n = 12), 55% (n = 39) had the same muscle symptom intensity during both treatment periods whereas 28% (n = 20) had more symptoms during atorvastatin than placebo (confirmed SAMS). There were no differences in clinical or pharmacogenetic characteristics between these groups. The levels of atorvastatin and/or metabolites did not correlate to muscle symptom intensity among patients with confirmed SAMS (Spearman’s rho ≤0.40, for all variables).

Conclusion
Re-challenge with high-intensity atorvastatin did not affect the intensity of muscle symptoms in CHD patients with self-perceived SAMS during previous atorvastatin therapy. There was no relationship between muscle symptoms and the systemic exposure to atorvastatin and/or its metabolites. The findings encourage an informed discussion to elucidate other causes of muscle complaints and continued statin use.
Postadmixture Selection on Chileans Targets Haplotype Involved in Pigmentation, Thermogenesis and Immune Defense against Pathogens
Authors: Vicuña Lucas , Klimenkova Olga , Norambuena Tomás , Martinez Felipe I , Fernandez Mario I , Shchur Vladimir , Eyheramendy Susana 
Published: June 2020

Abstract
Detection of positive selection signatures in populations around the world is helping to uncover recent human evolutionary history as well as the genetic basis of diseases. Most human evolutionary genomic studies have been performed in European, African, and Asian populations. However, populations with Native American ancestry have been largely underrepresented. Here, we used a genome-wide local ancestry enrichment approach complemented with neutral simulations to identify postadmixture adaptations underwent by admixed Chileans through gene flow from Europeans into local Native Americans. The top significant hits (P = 2.4×10−7) are variants in a region on chromosome 12 comprising multiple regulatory elements. This region includes rs12821256, which regulates the expression of KITLG, a well-known gene involved in lighter hair and skin pigmentation in Europeans as well as in thermogenesis. Another variant from that region is associated with the long noncoding RNA RP11-13A1.1, which has been specifically involved in the innate immune response against infectious pathogens. Our results suggest that these genes were relevant for adaptation in Chileans following the Columbian exchange.
Characteristics and Management of Male Breast Parenchymal Cysts
Authors: Maimone Santo , Ocal Idris T , Robinson Kristin A , Wasserman Martha C , Maxwell Robert W 
Published: June 2020

Abstract

Objective
Parenchymal breast cysts are considered to be rare in men and are sparsely described in the literature. The purpose of this study was to review our institution’s experience with male breast cysts in an effort to improve overall understanding and management of this rare entity.

Methods
An institutional review board–exempt retrospective study was performed. Radiology reports for males who underwent mammogram and/or breast ultrasound at any of our institution’s primary or satellite locations from January 1995 to January 2020 were screened to find males with breast cysts. If cysts were reported and images were available, case review was performed to confirm parenchymal breast cyst(s) and patient characteristics were collated.

Results
Of 5425 male cases presenting for breast imaging, 19 (0.4%) cases of male breast cysts were confirmed, with a mean patient age of 41.6 years (range: 2–81 years). The most common indication leading to cyst discovery was a palpable lump, corresponding to the site of the cyst in 5 (26.3%) patients and near the site where cyst(s) were ultimately discovered in 7 (36.8%) patients. There were 8 (42.1%) instances of cysts without concurrent gynecomastia. Three (15.8%) men underwent needle sampling. There were no cases of atypia or malignancy on needle biopsy or on subsequent clinical follow-up, with median clinical follow-up of 70.3 months (range: 3.3–259.4 months).

Conclusion
Male breast parenchymal cysts are rare, but their prevalence is likely underestimated. If detected incidentally or upon targeted evaluation, biopsy may be averted if classic benign cyst features are identified.