bluuebunny/crossref_metadata_2025 huggingface dataset:
Artificial intelligence for assessment of vascular involvement and tumor resectability on CT in patients with pancreatic cancer
Authors: Bereska Jacqueline I. , Janssen Boris V. , Nio C. Yung , Kop Marnix P. M. , Kazemier Geert , Busch Olivier R. , Struik Femke , Marquering Henk A. , Stoker Jaap , Besselink Marc G. , Verpalen Inez M. ,   for the Pancreatobiliary and Hepatic Artificial Intelligence Research (PHAIR) consortium
Published: February 2024

Objective

This study aimed to develop and evaluate an automatic model using artificial intelligence (AI) for quantifying vascular involvement and classifying tumor resectability stage in patients with pancreatic ductal adenocarcinoma (PDAC), primarily to support radiologists in referral centers. Resectability of PDAC is determined by the degree of vascular involvement on computed tomography scans (CTs), which is associated with considerable inter-observer variability.

Methods

We developed a semisupervised machine learning segmentation model to segment the PDAC and surrounding vasculature using 613 CTs of 467 patients with pancreatic tumors and 50 control patients. After segmenting the relevant structures, our model quantifies vascular involvement by measuring the degree of the vessel wall that is in contact with the tumor using AI-segmented CTs. Based on these measurements, the model classifies the resectability stage using the Dutch Pancreatic Cancer Group criteria as either resectable, borderline resectable, or locally advanced (LA).

Results

We evaluated the performance of the model using a test set containing 60 CTs from 60 patients, consisting of 20 resectable, 20 borderline resectable, and 20 locally advanced cases, by comparing the automated analysis obtained from the model to expert visual vascular involvement assessments. The model concurred with the radiologists on 227/300 (76%) vessels for determining vascular involvement. The model’s resectability classification agreed with the radiologists on 17/20 (85%) resectable, 16/20 (80%) for borderline resectable, and 15/20 (75%) for locally advanced cases.

Conclusions

This study demonstrates that an AI model may allow automatic quantification of vascular involvement and classification of resectability for PDAC.

Relevance statement

This AI model enables automated vascular involvement quantification and resectability classification for pancreatic cancer, aiding radiologists in treatment decisions, and potentially improving patient outcomes.

Key points

• High inter-observer variability exists in determining vascular involvement and resectability for PDAC.

• Artificial intelligence accurately quantifies vascular involvement and classifies resectability for PDAC.

• Artificial intelligence can aid radiologists by automating vascular involvement and resectability assessments.

Graphical Abstract
The effect of a strict facial-mask policy on the spread of COVID-19 in Switzerland during the early phase of the pandemic
Authors: Nussli Emanuel , Hediger Simon , Spohn Meta-Lina , Maathuis Marloes H.
Published: February 2024

During several weeks in the second half of the year 2020, the cantons of Switzerland could choose to adopt the government-determined facial-mask policy, corresponding to mandatory facial-mask wearing on public transport, or a strict facial-mask policy, corresponding to mandatory facial-mask wearing on public transport and in all public or shared spaces where social distancing was not possible. We estimate the effect of introducing the strict facial-mask policy on the spread of COVID-19 in Switzerland during this first phase of the pandemic in 2020, using the cantonal heterogeneity in facial-mask policies. We adjust for social distancing behavior, weather, other non-pharmaceutical policies and further variables. We estimate a significant reduction in the expected spread of COVID-19 in the early pandemic if the strict facial-mask policy is adopted.
A case report of X-linked CDKL5 gene variant in monozygotic twins associated with developmental and epileptic encephalopathy-2
Authors: Gupta Aayushi , Utage Prashant , Utage Aparna Prashant , Aman Nadir , Pujar Akhilesh
Published: February 2024

Background

CDKL5 (Cyclin‐Dependent Kinase Like-5) deficiency disorder (CDD; Online Mendelian Inheritance in Man database 300203, 300672) is a rare neurologic disorder, which is caused by mutation in CDKL5 gene, situated on the X chromosome. Therefore, this condition is inherited in an X-linked dominant pattern. In general, this gene provides instruction for making a protein that is essential for normal brain development and plays an important regulatory role in neuronal function.

Case presentation

We report a case of 2.5-year-old monozygotic twins (female), Twin-1 is found to be affected with CDKL5 deficiency disorder; development and epileptic encephalopathy-2; DEE2. The symptoms started at approximately 4 months of age.

Conclusion

Current study aims to stratify risk using NGS (next generation sequencing) in both the parents and Twin-2. This case highlights the importance of genetic testing in patients with genetic disorder for proper diagnosis, for better treatment/management and to understand the prognosis of the condition. Together with the clinical and genetic information, genetic counselling of the patient/patient’s parents can help them in taking informed decision.
Does preoperative bone marrow edema affect clinical outcomes after medial open-wedge high tibial osteotomy?
Authors: Kim Hee-June , Shin Ji-Yeon , Lee Hyun-Joo , Kim Dong-Hyun , Jo Yeonggwon , Kim Joon-Woo , Oh Chang-Wug , Kyung Hee-Soo
Published: February 2024

Purpose

The aim of this study is to evaluate the results of high tibial osteotomy (HTO) in patients with bone marrow edema (BME) and assess the effect of factors on the subsequent results.

Methods

A total of 138 patients who underwent medial open-wedge HTO using locking plate were included in this study. BME was observed in 108 patients using preoperative magnetic resonance imaging. Clinical results were evaluated before HTO and postoperatively at 12 months. Moreover, we evaluated the factors affecting the clinical results.

Results

The clinical scores were all significantly improved regardless of the presence of BME. There were no differences in improvement of clinical scores between patients with BME and without BME. Patients with BME showed higher postoperative Western Ontario and McMaster Universities Arthritis Index (WOMAC) stiffness scores than patients without BME. Furthermore, patients with BME on both the femur and tibia showed lower Knee Society function scores than patients with BME on either the femur or the tibia. Patients with large BME lesions exhibited a lower Hospital for Special Surgery score and WOMAC pain scores, postoperatively. In patients with BME, patients with undercorrection showed significantly lower improvement in WOMAC pain scores compared with patients with acceptable correction.

Conclusions

The clinical improvement after HTO in patients with varus and medial osteoarthritis was not different regardless of the presence or absence of BME. However, accurate alignment should be considered essential for achieving better clinical outcomes in patients with preoperative BME.
Significance of OCT3/4 and SOX2 antigens expression by leukemic blast cells in adult acute leukemia
Authors: Aref Salah , Khaled Omnyia , Menshawy Nadia El , Azmy Emad , Aref Mohamed , Salama Osama , Khaled Nada
Published: February 2024

Objective

This study aimed to address the prognostic impact of SOX2 and OCT3/4 expression on adult acute leukemia patients’ outcomes.

Methods

SOX2 and OCT3/4 expression by blast cells were evaluated by flow cytometry in 80 acute leukemia patients and 8 healthy controls.

Results

Baseline SOX2 and OCT3/4 expression were significantly higher in both ALL (P = < 0.001, P = 0.005 respectively) and AML patients (P < 0.001, P = 0.003 respectively) as compared to control, and decline at complete remission (CR) and elevated again at relapse. High SOX2 and OCT3/4 levels were significantly correlated with the presence of adverse risk stratification parameters.

Conclusion

Our findings indicated that both SOX2 and OCT3/4 could serve as biomarkers that could improve risk stratification of acute leukemia patients. Also, both SOX2 and OCT3/4 might be a therapeutic target, especially in resistant acute leukemia.
Pharmaceutical significance of Schiff bases: an overview
Authors: Mushtaq Irfan , Ahmad Maqbool , Saleem Muhammad , Ahmed Adnan
Published: February 2024

Schiff bases are a diverse group of organic compounds with great pharmaceutical importance due to the presence of carbon–nitrogen double bonds (–C=N–). These compounds are synthesized by the condensation reaction between a primary amine and an aldehyde or ketone in a suitable solvent such as methanol. These compounds have shown antibacterial, antifungal, antiviral, anti-inflammatory, and antioxidant activities, which have garnered the attention of organic chemists in synthesizing these compounds. Recent advances have been summarized in this review paper mainly including compounds with potential antibacterial, antifungal, and antiviral activities. Synthetic schemes are included to provide a better understanding of the Schiff base synthesis mechanism. This review paper will provide a way forward for the pharmaceutical chemist to synthesize new compounds with potential biological activities.

Graphical abstract
Patient-derived organoids in human cancer: a platform for fundamental research and precision medicine
Authors: Qu Shanqiang , Xu Rongyang , Yi Guozhong , Li Zhiyong , Zhang Huayang , Qi Songtao , Huang Guanglong
Published: February 2024

Cancer is associated with a high degree of heterogeneity, encompassing both inter- and intra-tumor heterogeneity, along with considerable variability in clinical response to common treatments across patients. Conventional models for tumor research, such as in vitro cell cultures and in vivo animal models, demonstrate significant limitations that fall short of satisfying the research requisites. Patient-derived tumor organoids, which recapitulate the structures, specific functions, molecular characteristics, genomics alterations and expression profiles of primary tumors. They have been efficaciously implemented in illness portrayal, mechanism exploration, high-throughput drug screening and assessment, discovery of innovative therapeutic targets and potential compounds, and customized treatment regimen for cancer patients. In contrast to conventional models, tumor organoids offer an intuitive, dependable, and efficient in vitro research model by conserving the phenotypic, genetic diversity, and mutational attributes of the originating tumor. Nevertheless, the organoid technology also confronts the bottlenecks and challenges, such as how to comprehensively reflect intra-tumor heterogeneity, tumor microenvironment, tumor angiogenesis, reduce research costs, and establish standardized construction processes while retaining reliability. This review extensively examines the use of tumor organoid techniques in fundamental research and precision medicine. It emphasizes the importance of patient-derived tumor organoid biobanks for drug development, screening, safety evaluation, and personalized medicine. Additionally, it evaluates the application of organoid technology as an experimental tumor model to better understand the molecular mechanisms of tumor. The intent of this review is to explicate the significance of tumor organoids in cancer research and to present new avenues for the future of tumor research.
LFSPROShiny: An Interactive R/Shiny App for Prediction and Visualization of Cancer Risks in Families With Deleterious Germline TP53 Mutations
Authors: Nguyen Nam H. , Dodd-Eaton Elissa B. , Peng Gang , Corredor Jessica L. , Jiao Wenwei , Woodman-Ross Jacynda , Arun Banu K. , Wang Wenyi
Published: February 2024

PURPOSE

LFSPRO is an R library that implements risk prediction models for Li-Fraumeni syndrome (LFS), a genetic disorder characterized by deleterious germline mutations in the TP53 gene. To facilitate the use of these models in clinics, we developed LFSPROShiny, an interactive R/Shiny interface of LFSPRO that allows genetic counselors (GCs) to perform risk predictions without any programming components and further visualize the risk profiles of their patients to aid the decision-making process.

METHODS

LFSPROShiny implements two models that have been validated on multiple LFS patient cohorts: a competing risk model that predicts cancer-specific risks for the first primary and a recurrent-event model that predicts the risk of a second primary tumor. Starting with a visualization template, we keep regular contact with GCs, who ran LFSPROShiny in their counseling sessions, to collect feedback and discuss potential improvement. On receiving the family history as input, LFSPROShiny renders the family into a pedigree and displays the risk estimates of the family members in a tabular format. The software offers interactive overlaid side-by-side bar charts for visualization of the patients' cancer risks relative to the general population.

RESULTS

We walk through a detailed example to illustrate how GCs can run LFSPROShiny in clinics from data preparation to downstream analyses and interpretation of results with an emphasis on the utilities that LFSPROShiny provides to aid decision making.

CONCLUSION

Since December 2021, we have applied LFSPROShiny to over 100 families from counseling sessions at the MD Anderson Cancer Center. Our study suggests that software tools with easy-to-use interfaces are crucial for the dissemination of risk prediction models in clinical settings, hence serving as a guideline for future development of similar models.
Carotid Intima-Media Thickness in Surgically or Conservatively Managed Patients With Primary Hyperparathyroidism
Authors: Carnevale Vincenzo , Pugliese Flavia , Eller-Vainicher Cristina , Salcuni Antonio S , Nieddu Luciano , Chiodini Iacopo , Scillitani Alfredo
Published: February 2024

Context

Current evidence of cardiovascular (CV) risk in primary hyperparathyroidism (PHPT) is still inconsistent.

Objective

To prospectively investigate changes of early atherosclerosis in patients with PHPT undergoing parathyroidectomy (PTx) or conservative management, according to consensus criteria.

Methods

Biochemical parameters of PHPT, CV risk factors (systolic and diastolic blood pressure, cholesterol [total, high-density, and low-density], triglyceride, HbA1c, HOMA-IR), and carotid intima-media thickness (IMT) and plaque were assessed in 52 consecutive postmenopausal PHPT patients both at baseline and ≥ 24 months after surgery (PTx, n = 22) or conservative management (non-PTx, n = 30).

Results

At baseline, PTx and non-PTx showed comparable age, BMI, renal function, and 25(OH)D levels, and did not differ for CV risk factors, IMT and plaques, or for prevalence of smoking, diabetes mellitus, or antihypertensive or statin therapy, while all parameters characterizing PHPT differed. Follow-up duration in PTx was longer than in non-PTx (P = .004). Parameters characterizing PHPT significantly improved ≥ 24 months after surgery, whereas in non-PTx serum phosphate slightly decreased and parathyroid hormone increased. Systolic and diastolic blood pressure increased at follow-up in both groups, while other CV risk factors did not significantly vary. In PTx, IMT did not significantly vary after surgery (0.85 ± 0.14 to 0.89 ± 0.22 mm, P = .366), whereas it significantly increased in non-PTx (0.80 ± 0.18 to 0.93 ± 0.23 mm, P = .008), even adjusting for blood pressure. Plaque prevalence and incidence did not significantly differ in the 2 groups.

Conclusion

Our results suggest that in postmenopausal patients with PHPT, subclinical atherosclerosis could be halted by PTx, whereas it worsens over time in nonoperated patients with milder disease.
The terrestrial gastropods in three Dodecanese islands, Rhodes, Symi, Chalki (Aegean Sea, Greece)
Authors: Maroulis Leonidas , Karakasi Danae , Bitzilekis Eleftherios , Dalias Panagiotis , Mylonas Moisis , Vardinoyannis Katerina
Published: February 2024

Rhodes, Symi and Chalki are three islands with different characteristics in the southeastern part of the Aegean Sea. In this work, we present their complete land snail fauna based on recent survey, samples from the collections of the Natural History Museum of Crete and a thorough bibliographic review. We report 67 land snail species from Rhodes, 34 species from Symi, and 32 from Chalki, with 4, 20 and 9 new records for each island, respectively. Also, one species has been added to the malacofauna of Greece, while many names, which were mentioned mainly in the 19th century, have been clarified, synonymised or abolished from the lists of the islands. Our results once again demonstrate the importance of the reproductive system as a tool for reliable assessment of the taxonomy of Aegean land snails, and that sampling during the rainy season should be the preferred methodological approach for collecting land snails in the Greek islands.
What type of social media posts about sustainable construction is better for audience engagement?
Authors: Primožič Lea , Dolezal Franz , Prislan Rok , Kutnar Andreja
Published: February 2024

Background In an effort to move to a sustainable society, new concepts and findings related to sustainable construction are being developed. With ambition to transfer newly developed knowledge to society, various communication paths are being used. In this study we investigated what kind of messages shared on institutional social media channels (Facebook, Twitter (now renamed to X), and LinkedIn) about sustainable construction create more audience engagement. Methods The study consisted of two phases of weekly social media posts. In each phase, 15 posts were published on the same day and time, while engagement was monitored. Three different types of posts were created, that were sequential cycling each week. Type 1 was written informative content related to research activities; type 2 was image content related to the research activities and equipment, with a short text caption of the image; and type 3 was image content with people – scientists working on research activities with a short text caption of the image. Results Poisson regression analysis revealed that type 3 posts result in the most audience engagement on LinkedIn, suggesting that using images of people in combination with short text captions is the most effective way to engage social media audiences. These findings can help organizations to use social media to promote sustainable construction and other sustainability-related research. The engagement was lower on Facebook and Twitter (X). Conclusions As the science is aiming to be closer to the society, these findings deliver an important insight of science communication through the social media. Although the study delivered several lessons learnt related to science communication through social media studies, it provides an important bases for further studies. Conclusions can support research organizations in improving their science communication.
Translation Notes: Heidegger, Derrida, and the Chance for (a) Philosophy
Authors: Nardelli Elena
Published: February 2024

This paper aims to show that translation is not only a fully-fledged philosophical problem, but also a specific philosophical praxis and a test bed for extracting the core of different philosophical frameworks. For this purpose, I will take into consideration the respective philosophies of Martin Heidegger and Jacques Derrida. Even if Heidegger often practices translation from the Greek in his own works and adds a few remarks towards an original investigation of this activity, he ultimately understands translation as a ‘makeshift’ or as a shipwreck. Throughout his contestation of Heidegger’s position, Derrida shows the trap of the endless appropriation of the experience of the origin structure. He also frees up the discourse by putting the hierarchical polarization between the original and the translation into question. Thus, translation becomes a chance for philosophy, even for Derrida’s deconstruction, a chance to generate new paths for investigation and to keep its question open
The genome sequence of a stiletto fly, Thereva unica (Harris, 1780)
Authors: Drake Martin , Spilling Chris ,   Natural History Museum Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,   Wellcome Sanger Institute Scientific Operations: Sequencing Operations,   Wellcome Sanger Institute Tree of Life Core Informatics team,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: February 2024

We present a genome assembly from an individual female Thereva unica (a stiletto fly; Arthropoda; Insecta; Diptera; Therevidae). The genome sequence is 910.1 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.66 kilobases in length.
Fluctuation Theory of Continuous-Time, Skip-Free Downward Markov Chains with Applications to Branching Processes with Immigration
Authors: Loeffen Ronnie , Patie Pierre , Wang Jian
Published: February 2024

We develop a comprehensive methodology for the fluctuation theory of continuous-time, skip-free Markov chains, extending and improving the recent work of Choi and Patie for discrete-time, skip-free Markov chains. As a significant application, we use it to derive a full set of fluctuation identities regarding exiting a finite or infinite interval for Markov branching processes with immigration, thereby uncovering many new results for this classic family of continuous-time Markov chains. The theory also allows us to recover in a simple manner fluctuation identities for skip-free downward compound Poisson processes.
The first report of Candida auris infection in Vietnam
Authors: Dang-Vu Thong , Lam-Quoc Dung , Duong-Minh Ngoc , Vu Ha , Nguyen-Ho Lam , Truong-Thien Phu , Nguyen-Dang Khoa
Published: February 2024

Infection caused by Candida auris has rapidly become a global health threat. C. auris created a significant healthcare burden due to various complicating factors, including misidentification by commercial identification methods, potent antifungal resistance, high mortality rates and the possibility of nosocomial outbreaks through direct contact. In Vietnam, there are currently no clinical reports on C. auris infections. Here, we present four clinical cases of C. auris infections in the Department of Pulmonary Medicine of Cho Ray Hospital in southern Vietnam. Through this report, we aim to highlight the attention to the emergence of C. auris in Vietnam. Further research on C. auris infections is warranted, focusing on newly observed clinical characteristics present in all cases in this report, including hypoalbuminaemia and corticosteroid usage. Moreover, one case of resistance to amphotericin B has been identified, possibly due to prior exposure to this antifungal agent.
Does mild chronic obstructive pulmonary disease need a standard pulmonary rehabilitation program? A case report
Authors:   School of Physical Therapy, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen Province, Thailand, Kosura Nimit , Aung Nwe Aung ,   School of Physical Therapy, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen Province, Thailand, Chumpangern Worawat ,   Department of Medicine Faculty of Medicine, Khon Kaen University, Khon Kaen Province, Thailand, Sriya Kongrit ,   Senior Family Medicine, Namphong Hospital, Khon Kaen Province, Thailand, Phimphasak Chatchai ,   School of Physical Therapy, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen Province, Thailand, Ubolsakka-Jones Chulee ,   School of Physical Therapy, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen Province, Thailand
Published: February 2024

Background: Patients with mild chronic obstructive pulmonary disease (COPD) are usually not recommended for a standard pulmonary rehabilitation (PR)program based on the GOLD guideline in mild COPD GOLD A classification. Especially, the scientific evidence on exercise capacity that can be identified for recruitment in PR programs has been less reported. Thus, a preliminary case study to identify the exercise capacity under cardiopulmonary responses by aerobic exercise testing among patients in mild COPD GOLD A classification was the aim of this study. Objective: To evaluate the cardiopulmonary responses from exercise capacity testing in individual COPD patients with mild COPD GOLD A Classification. Materials and methods: Four participants with mild COPD GOLD A performed an exercise endurance capacity test at home using Spot Marching Exercise Test (SMT), marching on the spot with high hip and arm raising. The load of SMT was indicated by a controlled stepping rate at 70, 80, 90, 100, and 110 steps/min. Every participant performed Incremental SMT (ISMT) with every 3 min incremental load, and the Constant SMT (CSMT) at the peak load. Both exercise tests were terminated at symptom limit. Resting time between ISMT and CSMT was at least 30 minutes. Cardiopulmonary exercise responses, Borg perceived breathlessness (RPB) and exertion (RPE) were monitored every minute during the exercise test. The duration of exercises was recorded. Results: Peak exercise capacity using ISMT was low with the end exercise load at 70, 80, 80, and 90 steps/min which is equivalent to moderate to high intensity at 81%, 62%, 65% and 93% of age-predicted maximum heart rate (HRmax). The exercise test was stopped by breathlessness at RPB 7, 8, 6, and 5. Respiratory rates (RR) were 36, 26, 38, and 38 breaths/min. With CSMT, the results showed very short exercise duration 1.78, 4.60, 2.15, and 2.47 mins with RPB 7, 8, 5, and 5 and RR of 33, 27, 34, and 41 breaths/min respectively. Conclusion: This preliminary report reveals that all four mild COPD GOLD A show low exercise capacity and very poor exercise endurance that should identify the appropriated standard PR program in the future.
I was easier for him to control when I was drunk: women’s experiences of substance use and domestic abuse victimisation
Authors: Fox Sarah , Holly Jennifer , Allwright Lucy
Published: February 2024

Many women who are victims of domestic abuse also experience problematic substance use; yet there is a gap in knowledge concerning the interplay of both issues from the perspective of women. While some may use substances to cope with the impact of abuse, their use of substances can also be used against them by the perpetrator as a means of control. This narrative study seeks to reduce the gap in knowledge regarding women’s substance use and victimisation experiences by presenting findings from interviews with women who have experienced the co-occurring issues. Reflecting on the definition of coercive control, and exploring women’s narratives, this article demonstrates how perpetrators may use a woman’s substance use as justification to increase dependency, isolate them from sources of support, reduce their independence and regulate their everyday behaviour. This is an important finding, evidencing how substances are a tactic of coercive control. Conversely, the narratives also illustrate how women may use their substance use to be in control in an uncontrollable situation. Initial recommendations highlight the need to explore the nuance of experience among women with co-occurring substance use and domestic abuse, so that support is provided that is reflective of their lived experience.
Noninvasive hemoglobin quantification across different cohorts using a wearable diffuse reflectance spectroscopy system
Authors: Chen Ying-Yu , Lai Guan-Hua , Chen Chia-Te , Cheng Hsiu-Chi , Tseng Sheng-Hao
Published: February 2024

Quantifying hemoglobin is vital yet invasive through blood draws. We developed a wearable diffuse reflectance spectroscopy device comprising control and sensor boards with photodiodes and light-emitting diodes to noninvasively determine hemoglobin. Neural networks enabled recovery of optical parameters for chromophore fitting to calculate hemoglobin. Testing healthy and elderly subjects revealed strong correlation (r=0.9) between our system and invasive methods after data conversion. Bland-Altman analysis demonstrated tight 95% limits of agreement from −1.98 to 1.98 g/dL between the DRS and invasive hemoglobin concentrations. By spectroscopically isolating hemoglobin absorption, interference from melanin was overcome. Our device has the potential for future integration into wearable technology, enabling hemoglobin level tracking.
Continuous tuning of pulse parameters in a soliton fiber laser by adjusting the effect of nonlinear polarization rotation: publisher’s note
Authors: Zhang Xintong , Guo Haozhe , He Wenbin , Wang Xiaocong , Huang Qi , Zheng Yu , Yin Ruochen , Huang Zhiyuan , Jiang Xin , Xu Lixin , Leng Yuxin , Pang Meng
Published: February 2024

This publisher’s note contains a correction to Opt. Lett. 49, 674 (2024)10.1364/OL.509981.
Accounting for isoform expression increases power to identify genetic regulation of gene expression
Authors: LaPierre Nathan , Pimentel Harold
Published: February 2024

A core problem in genetics is molecular quantitative trait locus (QTL) mapping, in which genetic variants associated with changes in the molecular phenotypes are identified. One of the most-studied molecular QTL mapping problems is expression QTL (eQTL) mapping, in which the molecular phenotype is gene expression. It is common in eQTL mapping to compute gene expression by aggregating the expression levels of individual isoforms from the same gene and then performing linear regression between SNPs and this aggregated gene expression level. However, SNPs may regulate isoforms from the same gene in different directions due to alternative splicing, or only regulate the expression level of one isoform, causing this approach to lose power. Here, we examine a broader question: which genes have at least one isoform whose expression level is regulated by genetic variants? In this study, we propose and evaluate several approaches to answering this question, demonstrating that “isoform-aware” methods—those that account for the expression levels of individual isoforms—have substantially greater power to answer this question than standard “gene-level” eQTL mapping methods. We identify settings in which different approaches yield an inflated number of false discoveries or lose power. In particular, we show that calling an eGene if there is a significant association between a SNP and any isoform fails to control False Discovery Rate, even when applying standard False Discovery Rate correction. We show that similar trends are observed in real data from the GEUVADIS and GTEx studies, suggesting the possibility that similar effects are present in these consortia.
Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis
Authors: Baer Lachlan , Barthelson Karissa , Postlethwait John H. , Adelson David L. , Pederson Stephen M. , Lardelli Michael
Published: February 2024

In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when the effects of homozygosity for recessive mutations are studied in non-isogenic backgrounds, genes located proximal to the mutation on the same chromosome often appear over-represented among those genes identified as differentially expressed (DE). One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect functional responses to the mutation but, instead, result from an unequal distribution of expression quantitative trait loci (eQTLs) between sample groups of mutant or wild-type genotypes. This is problematic because eQTL expression differences are difficult to distinguish from genes that are DE due to functional responses to a mutation. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) are also observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between those sample groups subjected to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting-based approaches. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. Our method for DAR analysis requires only RNA-sequencing data, facilitating its application across new and existing datasets.
Trends and driving forces of agricultural carbon emissions: A case study of Anhui, China
Authors: Qi Yanwei , Liu Huailiang , Zhao Jianbo , Zhang Shanzhuang , Zhang Xiaojin , Zhang Weili , Wang Yakai , Xu Jiajun , Li Jie , Ding Yulan
Published: February 2024

To facilitate accurate prediction and empirical research on regional agricultural carbon emissions, this paper uses the LLE-PSO-XGBoost carbon emission model, which combines the Local Linear Embedding (LLE), Particle Swarm Algorithm (PSO) and Extreme Gradient Boosting Algorithm (XGBoost), to forecast regional agricultural carbon emissions in Anhui Province under different scenarios. The results show that the regional agricultural carbon emissions in Anhui Province generally show an upward and then downward trend during 2000–2021, and the regional agricultural carbon emissions in Anhui Province in 2030 are expected to fluctuate between 11,342,100 tones and 14,445,700 tones under five different set scenarios. The projections of regional agricultural carbon emissions can play an important role in supporting the development of local regional agriculture, helping to guide the input and policy guidance of local rural low-carbon agriculture and promoting the development of rural areas towards a resource-saving and environment-friendly society.
Immediate crossover fatigue after unilateral submaximal eccentric contractions of the knee flexors involves peripheral alterations and increased global perceived fatigue
Authors: Gioda Jennifer , Da Silva Flavio , Monjo Florian , Corcelle Baptiste , Bredin Jonathan , Piponnier Enzo , Colson Serge S.
Published: February 2024

After a unilateral muscle exercise, the performance of the non-exercised contralateral limb muscle can be also impaired. This crossover fatigue phenomenon is still debated in the literature and very few studies have investigated the influence of eccentric contractions. This study was designed to assess neuromuscular adaptations involved in the crossover fatigue of the non-exercised contralateral knee flexor muscles. Seventeen healthy young men performed a unilateral submaximal eccentric exercise of the right knee flexors until a 20% reduction in maximal voluntary isometric contraction torque was attained in the exercised limb. Before (PRE), immediately after exercise cessation (POST) and 24 hours later (POST24), neuromuscular function and perceived muscle soreness were measured in both the exercised limb and non-exercised limb. In addition, global perceived fatigue was assessed at each measurement time. At POST, significant reductions in maximal voluntary isometric contraction were observed in the exercised limb (-28.1%, p < 0.001) and in the non-exercised limb (-8.5%, p < 0.05), evidencing crossover fatigue. At POST, voluntary activation decreased in the exercised limb only (-6.0%, p < 0.001), while electrically evoked potentiated doublet torque was impaired in both the exercised limb and the non-exercised limb (-11.6%, p = 0.001). In addition, global perceived fatigue significantly increased at POST (p < 0.001). At POST24, all measured variables returned to PRE values, except for perceived muscle soreness scores exhibiting greater values than PRE (p < 0.05). A possible cumulative interaction between peripheral alterations and global perceived fatigue may account for the immediate crossover fatigue observed in the non-exercised limb.
Ensemble learning based transmission line fault classification using phasor measurement unit (PMU) data with explainable AI (XAI)
Authors: Bin Akter Simon , Sarkar Pias Tanmoy , Rahman Deeba Shohana , Hossain Jahangir , Abdur Rahman Hafiz
Published: February 2024

A large volume of data is being captured through the Phasor Measurement Unit (PMU), which opens new opportunities and challenges to the study of transmission line faults. To be specific, the Phasor Measurement Unit (PMU) data represents many different states of the power networks. The states of the PMU device help to identify different types of transmission line faults. For a precise understanding of transmission line faults, only the parameters that contain voltage and current magnitude estimations are not sufficient. This requirement has been addressed by generating data with more parameters such as frequencies and phase angles utilizing the Phasor Measurement Unit (PMU) for data acquisition. The data has been generated through the simulation of a transmission line model on ePMU DSA tools and Matlab Simulink. Different machine learning models have been trained with the generated synthetic data to classify transmission line fault cases. The individual models including Decision Tree (DT), Random Forest (RF), and K-Nearest Neighbor (K-NN) have outperformed other models in fault classification which have acquired a cross-validation accuracy of 99.84%, 99.83%, and 99.76% respectively across 10 folds. Soft voting has been used to combine the performance of these best-performing models. Accordingly, the constructed ensemble model has acquired a cross-validation accuracy of 99.88% across 10 folds. The performance of the combined models in the ensemble learning process has been analyzed through explainable AI (XAI) which increases the interpretability of the input parameters in terms of making predictions. Consequently, the developed model has been evaluated with several performance matrices, such as precision, recall, and f1 score, and also tested on the IEEE 14 bus system. To sum up, this article has demonstrated the classification of six scenarios including no fault and fault cases from transmission lines with a significant number of training parameters and also interpreted the effect of each parameter to make predictions of different fault cases with great success.
A phase-shifting anterior-posterior network organizes global phase relations
Authors: Menceloglu Melisa , Grabowecky Marcia , Suzuki Satoru
Published: February 2024

Prior research has identified a variety of task-dependent networks that form through inter-regional phase-locking of oscillatory activity that are neural correlates of specific behaviors. Despite ample knowledge of task-specific functional networks, general rules governing global phase relations have not been investigated. To discover such general rules, we focused on phase modularity, measured as the degree to which global phase relations in EEG comprised distinct synchronized clusters interacting with one another at large phase lags. Synchronized clusters were detected with a standard community-detection algorithm, and the degree of phase modularity was quantified by the index q. Notably, we found that the mechanism controlling phase modularity is remarkably simple. A network comprising anterior-posterior long-distance connectivity coherently shifted phase relations from low-angles (|Δθ| < π/4) in low-modularity states (bottom 5% in q) to high-angles (|Δθ| > 3π/4) in high-modularity states (top 5% in q), accounting for fluctuations in phase modularity. This anterior-posterior network may play a fundamental functional role as (1) it controls phase modularity across a broad range of frequencies (3–50 Hz examined) in different behavioral conditions (resting with the eyes closed or watching a silent nature video) and (2) neural interactions (measured as power correlations) in beta-to-gamma bands were consistently elevated in high-modularity states. These results may motivate future investigations into the functional roles of phase modularity as well as the anterior-posterior network that controls it.
Cointegrations in house price dynamics and ageing population risks
Authors: Cheung William M.
Published: February 2024

How does the riskiness of an ageing population change with house price dynamics of rural areas? Why do rural house prices increase faster than cities despite their ageing populations? Life cycle theory predicts working age households have higher demand for housing than retirement households. An issue that has seen much less attention in the literature is that rural house prices have been increasing despite their populations age rapidly. To answer these issues, our paper introduces an empirical cointegration-based framework designed to be flexible for empirical settings. Our cointegration framework reveals crucial information about rural housing and ageing which has not been found previously: the short-term deviation of house prices from cointegration restrictions is a strong predictor of future rural house prices and migration rate from 1 to 4 year ahead. This is not the case for urban areas nor where cointegration restrictions are being ignored. Rural house prices, not urban ones, are the key to understand this cointegration restriction. Our framework is pertinent to most ageing societies with available housing and demographic data. When a government formulates macroprudential policies internalizing these cointegration restrictions and supporting rural developments, migration into rural areas and population increases are possible. Our evidence highlights the importance of cointegration-based long-run ageing risks for rural housing markets.
A comparison of Bartonella henselae infection in immunocompetent and immunocompromised mice
Authors: Bullard Rebekah L. , Cheslock Mercedes , Goud Gadila Shiva Kumar , Maggi Ricardo G. , Breitschwerdt Edward B. , Saied Ahmad A. , Embers Monica E.
Published: February 2024

Bartonellosis refers to disease caused by the Bartonella genus of bacteria. The breadth of disease manifestations associated with Bartonella is currently expanding and includes regional lymphadenopathy, rheumatic, ocular, and neurological disorders. The dearth of knowledge regarding diagnosis, treatment and pathogenesis of this disease can be partially attributed to the lack of a reliable small animal model for the disease. For this study, Bartonella henselae, the most common species associated with human disease, was injected into Swiss Webster (SW) mice. When the outcome indicated that productive infection did not occur, SCID/Beige (immune compromised) mice were inoculated. While SW mice may potentially harbor an acute infection, less than 10 days in length, the SCID/Beige model provided a sustained infection lasting up to 30-days. These data indicate that SCID/Beige mice can provide a model to study Bartonella infection, therapeutics, and vector dynamics in the future.
The CSR perspective: Interplay of technological innovation, ethical leadership and government regulations for sustainable financial performance
Authors: Zhu Yongming , Salman Muhammad , Kiran Saima , Sajjad Faisal , Sibt-e-Ali Muhammad , Sherwani Shahid , Wajid Kamran Muhammad
Published: February 2024

The financial performance of Chinese public and private sector banks is changing over time. There is no stability in the financial performance of Chinese banks which hurts businesses and the market. The purpose of current research was to determine the influence of corporate social responsibility (CSR) on driving the sustainable financial performance of Chinese banks. From methodological perspective, data was collected from 329 banking sector employees from China to partial least square–structural equation model (PLS-SEM) is employed for data analysis. The research used SPSS 24 and Smart PLS 4 as statistical analysis tools. This research confirmed that achieving sustainability in financial performance for Chinese banks can be achieved with CSR influenced by technological innovation, ethical leadership, and government regulations. This research has statistically confirmed that transformational leadership leading to CSR with technological innovation, ethical leadership, and government regulations can make significant improvements in financial performance. The framework developed by current research is a novel contribution to the literature. The findings of this research improve the literature on the banking sector and advanced performance. Furthermore, this research has highlighted significant ways that can help the banking sector employees to improve their financial performance with sustainability.
Cross-border dual-channel supply chain decision-making under random demand and tariff conditions
Authors: Li Fuchang , Yang Zhongwei , Hu Xiaohui
Published: February 2024

Given the cross-border e-commerce import tariff and random demands, this study establishes a pricing decision model for cross-border e-commerce dual-channel supply chain, which is composed of domestic manufacturers and overseas retailers, so as to analyze the effects of import tariff and random demand on the pricing, demand and profit of cross-border e-commerce. According to the research, import tariffs have a positive correlation with retailers’ retail prices and a negative correlation with manufacturers’ direct prices, wholesale prices, demand and profit from direct channels, and profit from retail channels. The export tax rebate policy will lessen the negative effects of import tariffs and maximize the best choices made by manufacturers and retailers.