bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deeply integrating latent consistent representations in high-noise multi-omics data for cancer subtyping
Authors: Cai Yueyi , Wang Shunfang 
Published: March 2024

Abstract
Cancer is a complex and high-mortality disease regulated by multiple factors. Accurate cancer subtyping is crucial for formulating personalized treatment plans and improving patient survival rates. The underlying mechanisms that drive cancer progression can be comprehensively understood by analyzing multi-omics data. However, the high noise levels in omics data often pose challenges in capturing consistent representations and adequately integrating their information. This paper proposed a novel variational autoencoder-based deep learning model, named Deeply Integrating Latent Consistent Representations (DILCR). Firstly, multiple independent variational autoencoders and contrastive loss functions were designed to separate noise from omics data and capture latent consistent representations. Subsequently, an Attention Deep Integration Network was proposed to integrate consistent representations across different omics levels effectively. Additionally, we introduced the Improved Deep Embedded Clustering algorithm to make integrated variable clustering friendly. The effectiveness of DILCR was evaluated using 10 typical cancer datasets from The Cancer Genome Atlas and compared with 14 state-of-the-art integration methods. The results demonstrated that DILCR effectively captures the consistent representations in omics data and outperforms other integration methods in cancer subtyping. In the Kidney Renal Clear Cell Carcinoma case study, cancer subtypes were identified by DILCR with significant biological significance and interpretability.
scAMAC: self-supervised clustering of scRNA-seq data based on adaptive multi-scale autoencoder
Authors: Tan Dayu , Yang Cheng , Wang Jing , Su Yansen , Zheng Chunhou 
Published: March 2024

Abstract
Cluster assignment is vital to analyzing single-cell RNA sequencing (scRNA-seq) data to understand high-level biological processes. Deep learning-based clustering methods have recently been widely used in scRNA-seq data analysis. However, existing deep models often overlook the interconnections and interactions among network layers, leading to the loss of structural information within the network layers. Herein, we develop a new self-supervised clustering method based on an adaptive multi-scale autoencoder, called scAMAC. The self-supervised clustering network utilizes the Multi-Scale Attention mechanism to fuse the feature information from the encoder, hidden and decoder layers of the multi-scale autoencoder, which enables the exploration of cellular correlations within the same scale and captures deep features across different scales. The self-supervised clustering network calculates the membership matrix using the fused latent features and optimizes the clustering network based on the membership matrix. scAMAC employs an adaptive feedback mechanism to supervise the parameter updates of the multi-scale autoencoder, obtaining a more effective representation of cell features. scAMAC not only enables cell clustering but also performs data reconstruction through the decoding layer. Through extensive experiments, we demonstrate that scAMAC is superior to several advanced clustering and imputation methods in both data clustering and reconstruction. In addition, scAMAC is beneficial for downstream analysis, such as cell trajectory inference. Our scAMAC model codes are freely available at https://github.com/yancy2024/scAMAC.
Dynamic models augmented by hierarchical data: an application of estimating HIV epidemics at sub-national level
Authors: Le Bao , Niu Xiaoyue , Brown Tim , Imai-Eaton Jeffrey W 
Published: March 2024

Summary
Dynamic models have been successfully used in producing estimates of HIV epidemics at the national level due to their epidemiological nature and their ability to estimate prevalence, incidence, and mortality rates simultaneously. Recently, HIV interventions and policies have required more information at sub-national levels to support local planning, decision-making and resource allocation. Unfortunately, many areas lack sufficient data for deriving stable and reliable results, and this is a critical technical barrier to more stratified estimates. One solution is to borrow information from other areas within the same country. However, directly assuming hierarchical structures within the HIV dynamic models is complicated and computationally time-consuming. In this article, we propose a simple and innovative way to incorporate hierarchical information into the dynamical systems by using auxiliary data. The proposed method efficiently uses information from multiple areas within each country without increasing the computational burden. As a result, the new model improves predictive ability and uncertainty assessment.
The Construction of Capital Among Family Members of People in Prison
Authors: Umamaheswar Janani 
Published: March 2024

Abstract
Researchers have documented the harms of imprisonment on family life, but much less is known about how family members seek support to cope with the challenges of familial imprisonment. In this article, I draw on 8 months of ethnographic observations of a virtual family support group and in-depth interviews with 27 family members of people in prison to explore participants’ need for, and construction of, communities of support. Drawing on Bourdieu’s concepts of social and cultural capital, I reveal how family members cultivated and leveraged networks of support to develop the social connections, knowledge, skills and resources needed to cope with familial imprisonment. I argue, however, that the persistence of participants’ struggles underscores the intractable nature of the inequality produced by familial imprisonment.
Investigation of the risk factors in the development of radionecrosis in patients with brain metastases undergoing stereotactic radiotherapy
Authors: Doğan Bedriye , Demir Harun , Işık Naciye , Gunalp Gun , Günbey Hediye Pınar , Yaprak Gökhan 
Published: March 2024

Abstract

Objective
To investigate the incidence, timing, and the factors predictors radionecrosis (RN) development in brain metastases (BMs) undergoing stereotactic radiotherapy (SRT).

Methods
The study evaluated 245 BMs who exclusively received SRT between 2010 and 2020. RN was detected pathologically or radiologically.

Results
The median of follow-up was 22.6 months. RN was detected in 18.4% of the metastatic lesions, and 3.3% symptomatic, 15.1% asymptomatic. The median time of RN was 22.8 months (2.5-39.5), and the rates at 6, 12, and 24 months were 16.8%, 41.4%, and 66%, respectively. Univariate analysis revealed that Graded Prognostic Assessment (P = .005), Score Index of Radiosurgery (P = .015), Recursive Partitioning Analysis (P = .011), the presence of primary cancer (P = .004), and localization (P = .048) significantly increased the incidence of RN. No significant relationship between RN and brain-gross tumour volume doses, planning target volume, fractionation, dose (P &gt; .05). Multivariate analysis identified SIR &gt; 6 (OR: 1.30, P = .021), primary of breast tumour (OR: 2.33, P = .031) and supratentorial localization (OR: 3.64, P = .025) as risk factors.

Conclusions
SRT is used effectively in BMs. The incidence of RN following SRT is undeniably frequent. It was observed that the incidence rate increased as the follow-up period increased. We showed that brain-GTV doses are not predictive of RN development, unlike other publications. In study, a high SIR score and supratentorial localization were identified as factors that increased the risk of RN.

Advances in knowledge
RN is still a common complication after SRT. Symptomatic RN is a significant cause of morbidity. The causes of RN are still not clearly identified. In many publications, brain dose and volumes have been found to be effective in RN. But, with this study, we found that brain dose volumes and fractionation did not increase the incidence of RN when brain doses were taken into account. The most important factor in the development of RN was found to be related to long survival after SRT.
A rare case of De Garengeot hernia: CT findings
Authors: Iovino Maria , D’Elia Anna Chiara , Rispo Maurizio , Rispo Alfonso , Brunetti Arturo , Sandomenico Fabio 
Published: March 2024

Abstract
We report a case of “De Garengeot’s hernia” (DGH), a rare condition that occurs when the inflamed appendix is localized inside a femoral hernia. The appendix may be involved in inflammatory or necrotic processes and the treatment is emergency surgery. It is usually discovered by chance during surgery. It occurs in 0.5%-5% of all femoral hernias. In 0.08%-0.13% of cases, the appendix can present inflammatory or necrotic processes due to the narrowness of the neck of the femoral canal; in these cases, an emergency surgery is required through a no standard surgical procedure. In the other cases, it is usually found accidentally during surgical repair of the hernia or more rarely diagnosed preoperatively by CT. Therefore, the purpose of our study is to report a case of DGH describing CT main findings in order to improve the preoperative diagnosis.
Exploring the Relationship between Ethical Conflicts and Psychological Distress among Social Workers: The Role of Social and Economic Exchange and Burnout
Authors: Kagan Maya , Zychlinski Ester , Lev Sagit 
Published: March 2024

Abstract
This study examines the association between ethical conflicts and psychological distress among social workers and the role of economic and social exchange in mediating this relationship. It also explores the moderating effect of burnout on the association between ethical conflicts and both social and economic exchange. The sample consisted of 568 Israeli social workers, where the majority were women. A moderated mediation model was employed to analyse the research data. The results indicate that the frequency of ethical conflicts was positively correlated with economic exchange, which in turn was positively correlated with psychological distress. Also, the frequency of ethical conflicts was negatively correlated with social exchange, which was negatively correlated with psychological distress. The effect of the frequency of ethical conflicts on both economic and social exchange was more pronounced at higher levels of burnout. The current study provides valuable insights into the complex processes social workers undergo when faced with ethical conflicts and underscores the importance of addressing burnout and exchanges in the social worker–organisation relationship. The study recommends that policymakers and welfare organisation managers allocate resources towards quality supervision and training programmes, promote teamwork and self-care activities for social workers and create an ethical work environment.
Vaccination with structurally adapted fungal protein fibrils induces immunity to Parkinson’s disease
Authors: Pesch Verena , Flores-Fernandez José Miguel , Reithofer Sara , Ma Liang , Özdüzenciler Pelin , Busch Yannick , Sriraman Aishwarya , Wang YongLiang , Amidian Sara , Kroepel Chiara V M , Müller Laura , Lien Yi , Rudtke Olivia , Frieg Benedikt , Schröder Gunnar F , Wille Holger , Tamgüney Gültekin 
Published: March 2024

Abstract
The pathological misfolding and aggregation of soluble α-synuclein into toxic oligomers and insoluble amyloid fibrils causes Parkinson’s disease, a progressive age-related neurodegenerative disease for which there is no cure.
HET-s is a soluble fungal protein that can form assembled amyloid fibrils in its prion state. We engineered HET-s(218–298) to form four different fibrillar vaccine candidates, each displaying a specific conformational epitope present on the surface of α-synuclein fibrils. Vaccination with these four vaccine candidates prolonged the survival of immunized TgM83+/− mice challenged with α-synuclein fibrils by 8% when injected into the brain to model brain-first Parkinson’s disease or by 21% and 22% when injected into the peritoneum or gut wall, respectively, to model body-first Parkinson’s disease. Antibodies from fully immunized mice recognized α-synuclein fibrils and brain homogenates from patients with Parkinson’s disease, dementia with Lewy bodies and multiple system atrophy.
Conformation-specific vaccines that mimic epitopes present only on the surface of pathological fibrils but not on soluble monomers, hold great promise for protection against Parkinson’s disease, related synucleinopathies and other amyloidogenic protein misfolding disorders.
Atrophy network mapping of clinical subtypes and main symptoms in frontotemporal dementia
Authors: Chu Min , Jiang Deming , Li Dan , Yan Shaozhen , Liu Li , Nan Haitian , Wang Yingtao , Wang Yihao , Yue Ailing , Ren Liankun , Chen Kewei , Rosa-Neto Pedro , Lu Jie , Wu Liyong 
Published: March 2024

Abstract
Frontotemporal dementia (FTD) is a disease of high heterogeneity, apathy and disinhibition present in all subtypes of FTD and imposes a significant burden on families/society. Traditional neuroimaging analysis has limitations in elucidating the network localization due to individual clinical and neuroanatomical variability.
The study aims to identify the atrophy network map associated with different FTD clinical subtypes and determine the specific localization of the network for apathy and disinhibition.
Eighty FTD patients [45 behavioural variant FTD (bvFTD) and 35 semantic variant progressive primary aphasia (svPPA)] and 58 healthy controls at Xuanwu Hospital were enrolled as Dataset 1; 112 FTD patients including 50 bvFTD, 32 svPPA and 30 non-fluent variant PPA (nfvPPA) cases, and 110 healthy controls from the Frontotemporal Lobar Degeneration Neuroimaging Initiative (FTLDNI) dataset were included as Dataset 2. Initially, single-subject atrophy maps were defined by comparing cortical thickness in each FTD patient versus healthy controls. Next, the network of brain regions functionally connected to each FTD patient’s location of atrophy was determined using seed-based functional connectivity in a large (n = 1000) normative connectome.
Finally, we used atrophy network mapping to define clinical subtype-specific network (45 bvFTD, 35 svPPA and 58 healthy controls in Dataset 1; 50 bvFTD, 32 svPPA, 30 nfvPPA and 110 healthy controls in Dataset 2) and symptom-specific networks [combined Datasets 1 and 2, apathy without depression versus non-apathy without depression (80:26), disinhibition versus non-disinhibition (88:68)]. We compare the result with matched symptom networks derived from patients with focal brain lesions or conjunction analysis.
Through the analysis of two datasets, we identified heterogeneity in atrophy patterns among FTD patients. However, these atrophy patterns are connected to a common brain network. The primary regions affected by atrophy in FTD included the frontal and temporal lobes, particularly the anterior temporal lobe. bvFTD connects to frontal and temporal cortical areas, svPPA mainly impacts the anterior temporal region and nfvPPA targets the inferior frontal gyrus and precentral cortex regions. The apathy-specific network was localized in the orbital frontal cortex and ventral striatum, while the disinhibition-specific network was localized in the bilateral orbital frontal gyrus and right temporal lobe. Apathy and disinhibition atrophy networks resemble known motivational and criminal lesion networks, respectively. A significant correlation was found between the apathy/disinhibition scores and functional connectivity between atrophy maps and the peak of the networks.
This study localizes the common network of clinical subtypes and main symptoms in FTD, guiding future FTD neuromodulation interventions.
A hydrodynamic modelling of wave-activated bodies for wavelet marine regions
Authors: Peh J S , Muhieldeen Mohammed W , Shuaib N H 
Published: March 2024

AbstractRecently, most wave energy research has targeted sea areas with high power density under extreme wave conditions for deployment. This trend often leads to higher energy costs for wave power plants. However, many marine areas with low power density, characterized by wavelet conditions and less destructive forces than extreme wave conditions, remain underexplored. Therefore, this study aimed to propose a wave-activated body model for sea regions with wavelet conditions. The wave-activated body design process encompassed site selection, parameter determination, geometry design, comparison and performance evaluation using the ANSYS® AQWA model. The results indicated that the proposed device achieved the desired heave motion, with an amplitude range of 1.2 to –2.5 m, validating its potential for deployment in marine regions with wavelet conditions. Notably, while the proposed design is optimized for wavelet conditions, it was found to have potential limitations in extreme wave environments. This observation emphasizes the challenge of formulating a generalized design suitable for both conditions. Consequently, it is pivotal for wave-activated body designs to be customized based on the specific ocean conditions they target, underscoring the need for specialized designs of wave energy converters that consider the unique wave characteristics of their deployment sites.
Tilted global solar irradiance in Bahrain: an experimental study
Authors: Vasilikos N , Georgantopoulou C , Alajaimi H , Almajed S H , Ahmed M , Mathioulakis D 
Published: March 2024

Abstract
In the present work, tilted global solar irradiance data are presented and analysed, measured for a period of 1 year on the campus of Bahrain Polytechnic, Kingdom of Bahrain, from both a fixed photovoltaic panel and a moving one via a two-axis solar tracker. The fixed panel faces south with an angle of 26° with respect to the horizontal, coinciding with the local geographical latitude. The second panel is moved by two motors, controlled by a global positioning system and suitable software so that the Sun’s rays are perpendicular to the panel surface. A pyranometer is installed on each panel, recording the tilted global solar irradiance, stored by using a data logger. The analysis of the data obtained shows a 33% solar energy gain on an annual basis for the moving panel (2780 versus 2088 kWh/m2 on the fixed panel). More importantly, in June, when the energy demand in Bahrain is elevated due to the increased residential cooling loads, the solar energy received by the moving panel is 54.7% higher compared with that of the fixed panel. On a percentage basis, the increase in solar energy from the moving panel is profound in the early morning and late evening hours. Moreover, the reduction in the solar energy received by the fixed panel from May to June does not appear in the moving panel because of the adjustable orientation of the latter. Throughout the year, the mean daily solar power varies between 0.37 and 0.56 kW/m2 for the fixed panel, and 0.45 and 0.70 kW/m2 for the moving panel. In winter, solar energy fluctuations are elevated due to erratic weather conditions that present a peak standard deviation of 28% of the corresponding mean. The data presented are useful for potential solar investments in Gulf countries.
Optimal site selection for geothermal heated greenhouses in cold climates: a fuzzy logic and geographic information system approach
Authors: Mirabadi Amirhossein , Minaei Saeid , Noorollahi Younes , Almasi Morteza 
Published: March 2024

Abstract
This paper presents a comprehensive model for selecting optimal sites for geothermal heated greenhouses in the agricultural industry. The research involves two main componentsf: assessing the geothermal energy resource using geological, geochemical and geophysical indicators; and developing a siting model based on fuzzy logic that considers technical, environmental and socio-economic factors. The study focuses on East Azerbaijan province in Iran—a cold region. The results indicate that ~3.24% of the total area of the province is suitable for constructing geothermal greenhouses, resulting in potential savings of ~148 000 and 745 978 m3 of natural gas in areas with high and very high suitability, respectively.
Development and Validation of a New High-Performance Liquid Chromatography-Ultraviolet Assay for Quantification of Mitoxantrone in Plasma of BALB/c-nu Mice
Authors: Tao Yanru , Zhao Hua , Xiang Yujie , Li Jin , Li Yanting , Hu Jiangling , Wang Hongmei , Jiang Xinhui 
Published: March 2024

Abstract
The concentration of mitoxantrone in the blood of mice was determined by a high-performance liquid chromatography-ultraviolet method with aloe-emodin as the internal standard. The separation was performed on a Hypersil BDS2 column (4.6 × 250 mm, 5 μm) as the analytical column, the mobile Phase A was acetonitrile, and B was 20-mM potassium dihydrogen phosphate (adding 1% triethylamine and adjusting the pH to 2.8 with phosphoric acid) and 4.6-mM sodium octyl sulfonate. The flow rate was 1.0 mL·min−1, the detection wavelength was 243 nm, the column temperature is 25 ± 5°C and the injection amount was 20 μL. Finally, the linear range of mitoxantrone was 5–200 μg·mL−1, and the correlation coefficient was r = 0.9999. The recovery rate of the method was 91.93–105.5%, and the extraction recovery rate was 91.45–105.5%. The intraday precision and interday precision were &lt;3.29% (limit of detection = 0.3 μg·mL−1). The HPLC method established in this paper was simple, rapid, sensitive and accurate, and can be used to determine the content of mitoxantrone in mouse plasma after tail vein injection.
Outcomes in Hematopoietic Cell Transplant and Chimeric Antigen Receptor T-Cell Therapy Recipients With Pre–Cellular Therapy SARS-CoV-2 Infection
Authors: Nimgaonkar Ila , Yoke Leah H , Roychoudhury Pavitra , Flaherty Patrick W , Oshima Masumi Ueda , Weixler Amelia , Gauthier Jordan , Greninger Alexander L , Mielcarek Marco , Boeckh Michael , Liu Catherine , Hill Joshua A 
Published: March 2024

Abstract

Background
Hematopoietic cell transplant (HCT) or chimeric antigen receptor (CAR) T-cell therapy recipients have high morbidity from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. There are limited data on outcomes from SARS-CoV-2 infection shortly before cellular therapy and uncertainty whether to delay therapy.

Methods
We conducted a retrospective cohort study of patients with SARS-CoV-2 infection within 90 days before HCT or CAR-T-cell therapy between January 2020 and November 2022. We characterized the kinetics of SARS-CoV-2 detection, clinical outcomes following cellular therapy, and impact on delays in cellular therapy.

Results
We identified 37 patients (n = 15 allogeneic HCT, n = 11 autologous HCT, n = 11 CAR-T-cell therapy) with SARS-CoV-2 infections within 90 days of cellular therapy. Most infections (73%) occurred between March and November 2022, when Omicron strains were prevalent. Most patients had asymptomatic (27%) or mild (68%) coronavirus disease 2019 (COVID-19). SARS-CoV-2 positivity lasted a median of 20.0 days (interquartile range, 12.5–26.25 days). The median time from first positive SARS-CoV-2 test to cellular therapy was 45 days (interquartile range, 37.75–70 days); 1 patient tested positive on the day of infusion. After cellular therapy, no patients had recrudescent SARS-CoV-2 infection or COVID-19–related complications. Cellular therapy delays related to SARS-CoV-2 infection occurred in 70% of patients for a median of 37 days. Delays were more common after allogeneic (73%) and autologous (91%) HCT compared to CAR-T-cell therapy (45%).

Conclusions
Patients with asymptomatic or mild COVID-19 may not require prolonged delays in cellular therapy in the context of contemporary circulating variants and availability of antiviral therapies.