bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical approach to evaluate the influence of water saturation on the strength of Neogene Tuff in Utsunomiya city, Japan
Authors: Ranaweera Neranjan , Togashi Yota , Osada Masahiko , Kawanoue Ryo 
Published: January 2023

Abstract
Evaluation of the deformation behavior due to drying is crucial in underground construction works. Especially, geological repository for High-Level Radioactive Waste (HLW) shall be carefully selected to act as a natural barrier to prevent radioactive nuclide leaks. Uniaxial Compressive Strength (UCS) is one such governing factors when designing or selecting a suitable location for such underground storage compartments or access tunnels. Since nuclide leakage through geological repositories, intact rocks UCS will vary with the drying conditions. Hence, it is vital to evaluate the behavior of UCS subject to the conditions prescribed. A variety of statistical models has been built to govern the interdependency between UCS and water content. However, there are no significant amount of research have been conducted to emphasize the UCS variation with the degree of saturation under the influence of drying condition. Numerically, Richard’s equation exact solution in Neuman boundary condition has been derived to exploit the degree of saturation with respect to time and position. Experimentally, obtain the UCS variation with the degree of saturation pertaining to the Neogene Tuff in Utsunomiya city, Japan. A best fit statistical model was generated for experimental data between UCS variation and the degree of saturation. Then, the experimental saturation degree was replaced by Richard’s equation exact solution saturation degree values. Surprisingly, produced graphs for experimental data and numerical analysis data for exact solution were perfectly overlapped. Results point out that change of UCS shows similar characteristics, which exponentially decrease, with both experimental saturation values and exact solution saturation values influenced the drying condition. Moreover, it suggests that UCS value can be predicted subject to the time and position in the sedimentary rocks under drying conditions.
Accurate and efficient prediction of vibrational circular dichroism spectra of condensed-phase systems with the generalized energy-based fragmentation method
Authors: Zhao Dongbo , Liao Kang , Hong Benkun , Li Wei , Li Shuhua 
Published: January 2023

Abstract
The vibrational circular dichroism (VCD) spectra could determine the molecular chirality of condensed-phase systems, but their quantum chemistry calculations are costly. The fragment-based methods have not been applied to the VCD spectra of periodic systems yet. In this work, we have extended the generalized energy-based fragmentation (GEBF) approach to accurately and efficiently compute the VCD spectra of chiral molecular crystals under periodic boundary conditions (PBCs) and macromolecules in solutions. In this approach, the Hessian matrices, atomic polar/axial tensors of a target system, are evaluated as a linear combination of the corresponding quantities from a series of small electrostatically embedded subsystems. Comparisons of GEBF and conventional VCD spectra of two large molecules show that this approach can satisfactorily reproduce the conventional computational results. Then, we applied the PBC-GEBF method to calculate the VCD spectra of a chiral molecular crystal and two macromolecules in solutions. Our results show that the experimental VCD spectrum can be roughly reproduced in terms of both band shape and vibrational peaks. The GEBF-VCD and PBC-GEBF-VCD approaches are expected to be practical tools to investigate the chirality of molecular crystals and macromolecules in solutions.
Challenging Folk-Linguistics: Grammatical and Spelling Variation in Students’ Writing in Hebrew on WhatsApp and in Essays
Authors: Finkelstein Shir , Netz Hadar 
Published: January 2023

AbstractWith the increasing use of mobile phones among young people, there is growing public concern about possible detrimental effects of digital writing on learners’ literacy and language skills. We ask whether and to what extent nonstandard forms typical of spoken Hebrew and of digital communication are also found in the formal writing of high-school students. To this end, we compare between two corpora of Modern Hebrew: a naturalistic corpus of 7,120 WhatsApp messages (35,085 words) written by 80 students in three classroom WhatsApp groups and a corpus of 291 school essays (34,700 words) written by 291 students. The findings indicate that a rather clear distinction is maintained between adherence to traditional formal writing in school essays as opposed to a more lenient approach on WhatsApp. The findings thus provide empirical linguistic evidence challenging the predominant folk-linguistic public ideology.
Marrying Collective Wisdom: Researcher-practitioner Collaboration in Developing ELT Textbooks
Authors: Shu Dingfang , Yang Shanshan , Sato Masatoshi 
Published: January 2023

Abstract
The need for collaboration between researchers and practitioners to address the research-practice gap is a long-debated topic in applied linguistics. Little is known, however, about how researchers and practitioners can collaboratively develop teaching materials, as a potential venue to narrow the gap. This study explored how two groups of professionals in China worked together to develop textbook materials and achieved bi-directional knowledge flow. In addition, the textbooks were analyzed in light of how participants contributed to the co-authored product. Interviews with four researchers and three practitioners along with their written reflections revealed relatively equal and constructive collaborative relationships in which multi-directional knowledge flow, co-creation of new knowledge, and positive emotional interactions emerged. Though subtle, the collaboration was reflected on the nature of the developed textbooks. With a nuanced interpretation of the complexity of researcher-practitioner collaboration, we highlight the emotional dimension of collaboration and the need to pay attention to the person in the collaboration when examining a research-practice relationship.
Applications of transformer-based language models in bioinformatics: a survey
Authors: Zhang Shuang , Fan Rui , Liu Yuti , Chen Shuang , Liu Qiao , Zeng Wanwen 
Published: January 2023

AbstractSummaryThe transformer-based language models, including vanilla transformer, BERT and GPT-3, have achieved revolutionary breakthroughs in the field of natural language processing (NLP). Since there are inherent similarities between various biological sequences and natural languages, the remarkable interpretability and adaptability of these models have prompted a new wave of their application in bioinformatics research. To provide a timely and comprehensive review, we introduce key developments of transformer-based language models by describing the detailed structure of transformers and summarize their contribution to a wide range of bioinformatics research from basic sequence analysis to drug discovery. While transformer-based applications in bioinformatics are diverse and multifaceted, we identify and discuss the common challenges, including heterogeneity of training data, computational expense and model interpretability, and opportunities in the context of bioinformatics research. We hope that the broader community of NLP researchers, bioinformaticians and biologists will be brought together to foster future research and development in transformer-based language models, and inspire novel bioinformatics applications that are unattainable by traditional methods.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
UPP2: fast and accurate alignment of datasets with fragmentary sequences
Authors: Park Minhyuk , Ivanovic Stefan , Chu Gillian , Shen Chengze , Warnow Tandy 
Published: January 2023

Abstract

Motivation
Multiple sequence alignment (MSA) is a basic step in many bioinformatics pipelines. However, achieving highly accurate alignments on large datasets, especially those with sequence length heterogeneity, is a challenging task. Ultra-large multiple sequence alignment using Phylogeny-aware Profiles (UPP) is a method for MSA estimation that builds an ensemble of Hidden Markov Models (eHMM) to represent an estimated alignment on the full-length sequences in the input, and then adds the remaining sequences into the alignment using selected HMMs in the ensemble. Although UPP provides good accuracy, it is computationally intensive on large datasets.

Results
We present UPP2, a direct improvement on UPP. The main advance is a fast technique for selecting HMMs in the ensemble that allows us to achieve the same accuracy as UPP but with greatly reduced runtime. We show that UPP2 produces more accurate alignments compared to leading MSA methods on datasets exhibiting substantial sequence length heterogeneity and is among the most accurate otherwise.

Availability and implementation
https://github.com/gillichu/sepp.

Supplementary information
Supplementary data are available at Bioinformatics online.
Decreased water exchange rate across blood–brain barrier in hereditary cerebral small vessel disease
Authors: Li Yingying , Ying Yunqing , Yao Tingyan , Jia Xuejia , Liang Huilou , Tang Weijun , Jia Xiuqin , Song Haiqing , Shao Xingfeng , Wang Danny J J , Wang Chaodong , Cheng Xin , Yang Qi 
Published: January 2023

Abstract
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) and heterozygous HTRA1 mutation-related cerebral small vessel disease (CSVD) are the two types of dominant hereditary CSVD. Blood–brain barrier (BBB) failure has been hypothesized in the pathophysiology of CSVD. However, it is unclear whether there is BBB damage in the two types of hereditary CSVD, especially in heterozygous HTRA1 mutation-related CSVD.
In this study, a case-control design was used with two disease groups including CADASIL (n = 24), heterozygous HTRA1 mutation-related CSVD (n = 9) and healthy controls (n = 24). All participants underwent clinical cognitive assessments and brain MRI. Diffusion-prepared pseudo-continuous arterial spin labelling was used to estimate the water exchange rate across the BBB (kw). Correlation and multiple linear regression analyses were used to examine the association between kw and disease burden and neuropsychological performance, respectively.
Compared with the healthy controls, kw in the whole brain and multiple brain regions was decreased in both CADASIL and heterozygous HTRA1 mutation-related CSVD patients (Bonferroni-corrected P &lt; 0.007). In the CADASIL group, decreased kw in the whole brain (β = −0.634, P = 0.001), normal-appearing white matter (β = −0.599, P = 0.002) and temporal lobe (β = −0.654, P = 0.001) was significantly associated with higher CSVD score after adjusting for age and sex. Reduced kw in the whole brain was significantly associated with poorer neuropsychological performance after adjusting for age, sex and education in both CADASIL and heterozygous HTRA1 mutation-related CSVD groups (β = 0.458, P = 0.001; β = 0.884, P = 0.008).
This study showed that there was decreased water exchange rate across the BBB in both CADASIL and heterozygous HTRA1 mutation-related CSVD patients, suggesting a common pathophysiological mechanism underlying the two types of hereditary CSVD. These results highlight the potential use of kw for monitoring the course of CADASIL and heterozygous HTRA1 mutation-related CSVD, a possibility which should be tested in future research.
Bone involvement in primary cutaneous diffuse large B-cell lymphoma, leg-type
Authors: Laurent Claire , Ram-Wolff Caroline , Ingen-Housz-Oro Saskia , Beylot-Barry Marie , Barete Stephane , Saillard Clemence , Dupuy Alain , Bagot Martine , Adamski Henri 
Published: January 2023

Abstract
Primary cutaneous diffuse large B-cell lymphoma, leg-type (PCDLBCL-LT) is an aggressive cutaneous lymphoma. Bone involvement is rare and poorly described. We present five cases of PCDLBCL-LT with bone localization. In four cases, the bone involvement was diagnosed during the initial staging with positron emission tomography (PET) or computed tomography (CT) scan, and in the fifth case after tibial fracture during treatment with rituximab (RTX) and polychemotherapy (PCT). PCDLBCL-LT can be asymptomatic and involve bone sites distant from cutaneous lesions. None had other extracutaneous involvement. In our series, all patients received RTX-PCT as first-line chemotherapy and all had early relapses or progression. Second-line treatments had poor efficacy. Our series shows that bone involvement seems to be associated with poor prognosis in PCDLBCL-LT. Bone localization is not diagnosed with initial thoracic–abdominal–pelvic CT when asymptomatic and affecting the limbs only. If there is a suspicion of PCDLBCL-LT, patients should undergo systematic investigation with alternative imaging techniques, including PET, both at baseline and if there is any concern during follow-up.
A Deep Learning Model for Energy-Aware Task Scheduling Algorithm Based on Learning Automata for Fog Computing
Authors: Ebrahim Pourian Reza , Fartash Mehdi , Akbari Torkestani Javad 
Published: January 2023

Abstract
This paper presents an artificial intelligence deep learning model for an energy-aware task scheduling algorithm based on learning automata (LA) in the Fog Computing (FC) Applications. FC is a distributed computing model that serves as an intermediate layer between the cloud and Internet of Things (IoT) to improve the quality of service. The IoT is the closest model to the wireless sensor network (WSN). One of its important applications is to create a global approach to health care system infrastructure development that reflects recent advances in WSN. The most influential factor in energy consumption is task scheduling. In this paper, the issue of reducing energy consumption is investigated as an important challenge in the fog environment. Also, an algorithm is presented to solve the task scheduling problem based on LA and measure the makespan (MK) and cost parameters. Then, a new artificial neural network deep model is proposed, based on the presented LA task scheduling fog computing algorithm. The proposed neural model can predict the relation among MK, energy and cost parameters versus VM length for the first time. The proposed model results show that all of the desired parameters can be predicted with high precision.
Persistence or regression of prediabetes and coronary artery calcification among adults without diabetes
Authors: Cho Yoosun , Chang Yoosoo , Ryu Seungho , Kim Yejin , Jung Hyun-Suk , Kang Jeonggyu , Choi In Young , Kim Chan-won , Oh Hyungseok , Wild Sarah H , Byrne Christopher D 
Published: January 2023

Abstract

Objective
The effect of changes in glycemic status on subclinical atherosclerosis is uncertain. We assessed the association of persistence, regression, or progression of prediabetes with coronary artery calcium score (CACS) as a measure of subclinical atherosclerosis.

Design
A cross-sectional study, comprising 126 765 adults, and longitudinal sub-study, comprising 40 622 adults (with baseline and at least 1 follow-up computed tomography scan to assess changes in CACS), were undertaken.

Methods
Changes in glycemic status over 1.5 years (interquartile range, 1.0-2.0) before the first CACS assessment were categorized according to 6 groups: persistent normoglycemia (reference), normoglycemia to prediabetes, normoglycemia to diabetes, prediabetes to normoglycemia, persistent prediabetes, and prediabetes to diabetes. Logistic regression was used to calculate the odds ratios (ORs) and 95% CIs for prevalent coronary artery calcification (CAC). Mixed models with random intercepts and random slopes were used to estimate 5-year CAC progression rates.

Results
Mean (SD) age was 41.3 (7.0) years (74.7% male) (n = 126 765). Multivariable-adjusted OR for prevalent CAC was 1.13 (95% CI, 1.08-1.18) for persistent prediabetes, 1.05 (0.98-1.12) for regression to normoglycemia, and 1.46 (95% CI, 1.27-1.67) for progression from prediabetes to diabetes, compared with persistent normoglycemia. Coronary artery calcification progression increased significantly in all prediabetes groups. Multivariable-adjusted ratio of 5-year CAC progression rates was 1.19 (95% CI, 1.16-1.22) (persistent prediabetes), 1.11 (1.07-1.14) (regression to normoglycemia), and 1.63 (95% CI, 1.26-2.10) (progression from prediabetes to diabetes).

Conclusions
Unfavorable changes in glycemic status, including persistence of prediabetes or progression to diabetes from prediabetes, were associated with increased risk of CAC.
Saline suppression to distinguish the primary aldosteronism subtype: a diagnostic study
Authors: Hashimura Hikaru , Hu Jinbo , Kobayashi Hiroki , Gwini Stella May , Shen Jimmy , Chee Nicholas Y N , Doery James C G , Chong Winston , Fuller Peter J , Abe Masanori , Li Qifu , Yang Jun 
Published: January 2023

Abstract

Objectives
The saline suppression test (SST) serves to confirm the diagnosis of primary aldosteronism (PA), while adrenal vein sampling (AVS) is used to subtype PA as unilateral or bilateral. Criteria that can accurately identify those with bilateral PA based on SST results could reduce the need for AVS. We previously demonstrated that a combination of plasma aldosterone concentration (PAC) &lt; 300 pmol L−1 and a reduction in aldosterone-to-renin ratio (ARR) following recumbent SST had high specificity for predicting bilateral PA in an Australian cohort of 92 patients with PA who have undergone AVS. We sought to validate our predictive criteria in larger, independent cohorts of patients with PA.

Design
An international, multi-centre cohort study.

Methods
Data from 55 patients at Monash Health, Victoria, Australia, 106 patients from the First Affiliated Hospital of Chongqing Medical University, China, and 105 patients from Nihon University Itabashi Hospital, Japan were analysed.

Results
A combination of PAC &lt;300 pmol L−1 and a reduction in ARR following recumbent SST predicted bilateral PA with specificities of 88.2%, 97.0%, and 100.0% in Australian, Chinese, and Japanese cohorts, respectively. This criterion could allow 22%–38% of patients with PA to bypass AVS and proceed directly to medical treatment.

Conclusion
In patients undergoing the recumbent SST, a post-saline PAC &lt;300 pmol L−1 together with a reduction in ARR can predict bilateral PA with high specificity and may allow targeted treatment to be commenced without AVS in up to a third of patients.
Detection of driver mutations in plasma cell–free nucleic acids in differentiated thyroid neoplasm
Authors: Dutta Susmita , Tarafdar Soham , Mukhopadhyay Pradip , Bhattacharyya Nitai P , Ghosh Sujoy 
Published: January 2023

AbstractImportanceThis proof-of-concept paper demonstrates that driver mutations can be detected in plasma in differentiated thyroid tumors, and we were able to detect mutations in upto 80% malignant thyroid nodules. Additionally, cancer subtypes could also be predicted using a 8-gene panel. In almost 90% follicular adenoma, rat sarcoma virus (RAS) mutations were detectable. There was a strong agreement between driver mutations found in plasma samples, FNAC materials, and histopathology samples. This has potential as a noninvasive, preoperative diagnostic tool (particularly of clinical importance in indeterminate nodules) and may help in detection of residual tumor after surgery. Future research is warranted to test the role of this tool to detect tumor recurrence.ObjectiveUltrasonographic (USG) evaluation and fine-needle aspiration (FNA) are cornerstone for evaluation of thyroid neoplasm. Molecular technique including detection of driver mutation from FNA cytology (FNAC) material is an established modality. In this study, we explored the feasibility of using plasma cell–free nucleic acids to identify known driver mutations in differentiated thyroid neoplasm.DesignPatients presenting with thyroid nodules underwent USG with Thyroid Image Reporting and Data Systems scoring and FNAC (Bethesda classification). All patients in Bethesda 3, 4, 5, 6 underwent surgery and histopathological confirmation. Patients in Bethesda 2 (cosmetic concerns, compressive symptoms) underwent surgery, and rest were presumed benign on the basis of USG, FNAC features, and clinical followup.).SettingEndocrinology clinic.ParticipantsSubjects with thyroid nodule.Intervention(s) or Exposure(s)None.Main Outcome(s) and Measure(s)Plasma sample, FNA, and histopathology material were evaluated for driver mutations (8-gene panel comprising BRAF-V600E, RET/PTC3, RET/PTC1, TERT promoter, HRAS, NRAS, KRAS, and PAX8-PPARG).ResultsA total of 223 subjects were recruited; of these 154 were benign and 69 had differentiated thyroid cancer. We were able to detect driver mutation from plasma in 55 subjects (79.71%) of all malignant patients, and 11 patients in benign category had RAS mutation (follicular adenoma). Rest of the benign nodules did not have any detectable driver mutations.Conclusions and RelevancePlasma might be a viable noninvasive alternative source for detection of driver mutations (8-gene panel) in subjects with differentiated thyroid tumors and may have significant clinical utility.
Disparity in pseudohyphal morphogenic switching response to the quorum sensing molecule 2-phenylethanol in commercial brewing strains ofSaccharomyces cerevisiae
Authors: Britton Scott J , Rogers Lisa J , White Jane S , Neven Hedwig , Maskell Dawn L 
Published: January 2023

AbstractSaccharomyces cerevisiae can undergo filamentous growth in response to specific environmental stressors, particularly nitrogen-limitation, whereby cells undergo pseudohyphal differentiation, a process where cells transition from a singular ellipsoidal appearance to multicellular filamentous chains from the incomplete scission of the mother-daughter cells. Previously, it was demonstrated that filamentous growth in S. cerevisiae is co-regulated by multiple signaling networks, including the glucose-sensing RAS/cAMP-PKA and SNF pathways, the nutrient-sensing TOR pathway, the filamentous growth MAPK pathway, and the Rim101 pathway, and can be induced by quorum-sensing aromatic alcohols, such as 2-phenylethanol. However, the prevalent research on the yeast-pseudohyphal transition and its induction by aromatic alcohols in S. cerevisiae has been primarily limited to the strain Σ1278b. Due to the prospective influence of quorum sensing on commercial fermentation, the native variation of yeast-to-filamentous phenotypic transition and its induction by 2-phenylethanol in commercial brewing strains was investigated. Image analysis software was exploited to enumerate the magnitude of whole colony filamentation in 16 commercial strains cultured on nitrogen-limiting SLAD medium; some supplemented with exogenous 2-phenylethanol. The results demonstrate that phenotypic switching is a generalized, highly varied response occurring only in select brewing strains. Nevertheless, strains exhibiting switching behavior altered their filamentation response to exogenous concentrations of 2-phenylethanol.