bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementing deep learning models for the classification of Echinococcus multilocularis infection in human liver tissue
Authors: Sulyok Mihaly , Luibrand Julia , Strohäker Jens , Karacsonyi Peter , Frauenfeld Leonie , Makky Ahmad , Mattern Sven , Zhao Jing , Nadalin Silvio , Fend Falko , Schürch Christian M. 
Published: January 2023

Abstract
Background
The histological diagnosis of alveolar echinococcosis can be challenging. Decision support models based on deep learning (DL) are increasingly used to aid pathologists, but data on the histology of tissue-invasive parasitic infections are missing. The aim of this study was to implement DL methods to classify Echinococcus multilocularis liver lesions and normal liver tissue and assess which regions and structures play the most important role in classification decisions.

Methods
We extracted 15,756 echinococcus tiles from 28 patients using 59 whole slide images (WSI); 11,602 tiles of normal liver parenchyma from 18 patients using 33 WSI served as a control group. Different pretrained model architectures were used with a 60–20–20% random splitting. We visualized the predictions using probability-thresholded heat maps of WSI. The area-under-the-curve (AUC) value and other performance metrics were calculated. The GradCAM method was used to calculate and visualize important spatial features.

Results
The models achieved a high validation and test set accuracy. The calculated AUC values were 1.0 in all models. Pericystic fibrosis and necrotic areas, as well as germinative and laminated layers of the metacestodes played an important role in decision tasks according to the superimposed GradCAM heatmaps.

Conclusion
Deep learning models achieved a high predictive performance in classifying E. multilocularis liver lesions. A possible next step could be to validate the model using other datasets and test it against other pathologic entities as well, such as, for example, Echinococcus granulosus infection.

Graphical Abstract
Risk assessment for colorectal cancer via polygenic risk score and lifestyle exposure: a large-scale association study of East Asian and European populations
Authors: Xin Junyi , Du Mulong , Gu Dongying , Jiang Kewei , Wang Mengyun , Jin Mingjuan , Hu Yeting , Ben Shuai , Chen Silu , Shao Wei , Li Shuwei , Chu Haiyan , Zhu Linjun , Li Chen , Chen Kun , Ding Kefeng , Zhang Zhengdong , Shen Hongbing , Wang Meilin 
Published: January 2023

Abstract
Background
The genetic architectures of colorectal cancer are distinct across different populations. To date, the majority of polygenic risk scores (PRSs) are derived from European (EUR) populations, which limits their accurate extrapolation to other populations. Here, we aimed to generate a PRS by incorporating East Asian (EAS) and EUR ancestry groups and validate its utility for colorectal cancer risk assessment among different populations.

Methods
A large-scale colorectal cancer genome-wide association study (GWAS), harboring 35,145 cases and 288,934 controls from EAS and EUR populations, was used for the EAS-EUR GWAS meta-analysis and the construction of candidate EAS-EUR PRSs via different approaches. The performance of each PRS was then validated in external GWAS datasets of EAS (727 cases and 1452 controls) and EUR (1289 cases and 1284 controls) ancestries, respectively. The optimal PRS was further tested using the UK Biobank longitudinal cohort of 355,543 individuals and ultimately applied to stratify individual risk attached by healthy lifestyle.

Results
In the meta-analysis across EAS and EUR populations, we identified 48 independent variants beyond genome-wide significance (P < 5 × 10−8) at previously reported loci. Among 26 candidate EAS-EUR PRSs, the PRS-CSx approach-derived PRS (defined as PRSCSx) that harbored genome-wide variants achieved the optimal discriminatory ability in both validation datasets, as well as better performance in the EAS population compared to the PRS derived from known variants. Using the UK Biobank cohort, we further validated a significant dose-response effect of PRSCSx on incident colorectal cancer, in which the risk was 2.11- and 3.88-fold higher in individuals with intermediate and high PRSCSx than in the low score subgroup (Ptrend = 8.15 × 10−53). Notably, the detrimental effect of being at a high genetic risk could be largely attenuated by adherence to a favorable lifestyle, with a 0.53% reduction in 5-year absolute risk.

Conclusions
In summary, we systemically constructed an EAS-EUR PRS to effectively stratify colorectal cancer risk, which highlighted its clinical implication among diverse ancestries. Importantly, these findings also supported that a healthy lifestyle could reduce the genetic impact on incident colorectal cancer.
Generalizable transfer learning of automated tumor segmentation from cervical cancers toward a universal model for uterine malignancies in diffusion-weighted MRI
Authors: Lin Yu-Chun , Lin Yenpo , Huang Yen-Ling , Ho Chih-Yi , Chiang Hsin-Ju , Lu Hsin-Ying , Wang Chun-Chieh , Wang Jiun-Jie , Ng Shu-Hang , Lai Chyong-Huey , Lin Gigin 
Published: January 2023

Abstract
Purpose
To investigate the generalizability of transfer learning (TL) of automated tumor segmentation from cervical cancers toward a universal model for cervical and uterine malignancies in diffusion-weighted magnetic resonance imaging (DWI).

Methods
In this retrospective multicenter study, we analyzed pelvic DWI data from 169 and 320 patients with cervical and uterine malignancies and divided them into the training (144 and 256) and testing (25 and 64) datasets, respectively. A pretrained model was established using DeepLab V3 + from the cervical cancer dataset, followed by TL experiments adjusting the training data sizes and fine-tuning layers. The model performance was evaluated using the dice similarity coefficient (DSC).

Results
In predicting tumor segmentation for all cervical and uterine malignancies, TL models improved the DSCs from the pretrained cervical model (DSC 0.43) when adding 5, 13, 26, and 51 uterine cases for training (DSC improved from 0.57, 0.62, 0.68, 0.70, p < 0.001). Following the crossover at adding 128 cases (DSC 0.71), the model trained by combining data from adding all the 256 patients exhibited the highest DSCs for the combined cervical and uterine datasets (DSC 0.81) and cervical only dataset (DSC 0.91).

Conclusions
TL may improve the generalizability of automated tumor segmentation of DWI from a specific cancer type toward multiple types of uterine malignancies especially in limited case numbers.
Transfer of mesenchymal stem cell mitochondria to CD4+ T cells contributes to repress Th1 differentiation by downregulating T-bet expression
Authors: Akhter Waseem , Nakhle Jean , Vaillant Loïc , Garcin Geneviève , Le Saout Cécile , Simon Matthieu , Crozet Carole , Djouad Farida , Jorgensen Christian , Vignais Marie-Luce , Hernandez Javier 
Published: January 2023

Abstract
Background
Mesenchymal stem/stromal cells (MSCs) are multipotent cells with strong tissue repair and immunomodulatory properties. Due to their ability to repress pathogenic immune responses, and in particular T cell responses, they show therapeutic potential for the treatment of autoimmune diseases, organ rejection and graft versus host disease. MSCs have the remarkable ability to export their own mitochondria to neighboring cells in response to injury and inflammation. However, whether mitochondrial transfer occurs and has any role in the repression of CD4+ Th1 responses is unknown.

Methods and results
In this report we have utilized CD4+ T cells from HNT TCR transgenic mice that develop Th1-like responses upon antigenic stimulation in vitro and in vivo. Allogeneic bone marrow-derived MSCs reduced the diabetogenic potential of HNT CD4+ T cells in vivo in a transgenic mouse model of disease. In co-culture experiments, we have shown that MSCs were able to reduce HNT CD4+ T cell expansion, expression of key effector markers and production of the effector cytokine IFNγ after activation. This was associated with the ability of CD4+ T cells to acquire mitochondria from MSCs as evidenced by FACS and confocal microscopy. Remarkably, transfer of isolated MSC mitochondria to CD4+ T cells resulted in decreased T cell proliferation and IFNγ production. These effects were additive with those of prostaglandin E2 secreted by MSCs. Finally, we demonstrated that both co-culture with MSCs and transfer of isolated MSC mitochondria prevent the upregulation of T-bet, the master Th1 transcription factor, on activated CD4+ T cells.

Conclusion
The present study demonstrates that transfer of MSC mitochondria to activated CD4+ T cells results in the suppression of Th1 responses in part by downregulating T-bet expression. Furthermore, our studies suggest that MSC mitochondrial transfer might represent a general mechanism of MSC-dependent immunosuppression.
Politics of reproduction: a view from Israel on the Dobbs decision
Authors: Shalev Carmel 
Published: January 2023

Abstract
Background
This opinion piece looks at the recent decision of the United States Supreme Court in Dobbs v. Jackson Women's Health Organization and then compares the law on abortion in the USA to the law in Israel on reproductive medicine in general.
The Dobbs decision validated a Mississippi state law that restricted access to abortion, while overruling the landmark precedent of Roe v. Wade on women's constitutional right to safe abortion. It declared that the US constitution does not confer upon women any right to abortion, whether pre- or post-viability, sending shockwaves throughout the world. It also had an immediate effect on women's reproductive health in the US.

Main body
Women's right to reproductive freedom and to make decisions about their lives and their bodies is key to their hard-won equality. Still, abortion remains in ongoing controversy worldwide with legal barriers that impact upon the most vulnerable. In Israel, abortion is relatively available, accessible, affordable, and acceptable, in both law and practice. This is because of the lenient and nuanced stance of rabbinical authorities in the Jewish law tradition. This stance, together with Israel's post-Holocaust biblical culture of "be fruitful and multiply", also underlies its high rates of medically assisted reproduction for the treatment of infertility, including preimplantation genetic diagnosis of fertilized eggs. Women's bodies mediate all these repro-genetic technologies, in most cases for the benefit of others, not because of their own health needs. There is also concern about global practices and market forces that objectify women's bodies, exploit women and are harmful to their health, wellbeing, and dignity, carrying on outdated patriarchal patterns.

Conclusion
Reproductive health policy ought to be based on an ethic of care and responsibility first and foremost for the women, as well as the children they choose to bring to life, in the spirit of the Jewish tradition that her life is of greater value than the fetus'. Women deserve control of their bodies and their lives and respect for the choices they make to the best of their judgment, which when it comes to abortion are mostly hard ones. They have a right to reproductive choice, freedom, autonomy, and dignity.
The views expressed in this perspective are those of the author.
Assessing social competence and antisocial behaviors in children: item response theory analysis of the home and community social behavior scales
Authors: Hukkelberg Silje Sommer , Andersson Björn 
Published: January 2023

Abstract
Background
The Home and Community Social Behavior Scales (HCSBS) is a rating scale that assesses social competence and antisocial behavior among children and youths between ages 5–18. The present study aimed to investigate the psychometric properties of the HCSBS by applying item response theory (IRT).

Methods
The HCSBS was completed by parents of 551 Norwegian children refereed to three independent interventions towards problem behaviors. Data used in this study was collected before the interventions started. IRT was carried out in R version 4.0.0 to investigate HCSBS items, subscales and main scales.

Results
The results showed that the two-dimensional IRT models for social competence and antisocial behavior were the most appropriate. The measurement precision of the scales was high for a large range of the latent spectrum, and estimated reliabilities were satisfactory. Model evaluations indicated that the overall model fit for the scales were acceptable, but some misfit existed with respect to specific item pairs.

Conclusion
The results indicate that the HCSBS is a reliable measurement instrument although there is still a potential for improvement by revising some of the items.
Virtual cleaning of works of art using a deep generative network: spectral reflectance estimation
Authors: Maali Amiri Morteza , Messinger David W. 
Published: January 2023

Abstract
Generally applied to a painting for protection purposes, a varnish layer becomes yellow over time, making the painting undergo an appearance change. Upon this change, the conservators start a process that entails removing the old layer of varnish and applying a new one. As widely discussed in the literature, helping the conservators through supplying them with the probable outcome of the varnish removal can be of great value to them, aiding in the decision making process regarding varnish removal. This help can be realized through virtual cleaning, which in simple terms, refers to simulation of the cleaning process outcome. There have been different approaches devised to tackle the problem of virtual cleaning, each of which tries to develop a method that virtually cleans the artwork in a more accurate manner. Although successful in some senses, the majority of them do not possess a high level of accuracy. Prior approaches suffer from a range of shortcomings such as a reliance on identifying locations of specific colors on the painting, the need to access a large set of training data, or their lack of applicability to a wide range of paintings. In this work, we develop a Deep Generative Network to virtually clean the artwork. Using this method, only a small area of the painting needs to be physically cleaned prior to virtual cleaning. Using the cleaned and uncleaned versions of this small area, the entire unvarnished painting can be estimated. It should be noted that this estimation is performed in the spectral reflectance domain and herein it is applied to hyperspectral imagery of the work. The model is first applied to a Macbeth ColorChecker target (as a proof of concept) and then to real data of a small impressionist panel by Georges Seurat (known as ‘Haymakers at Montfermeil’ or just ‘Haymakers’). The Macbeth ColorChecker is simulated in both varnished and unvarnished forms, but in the case of the ‘Haymakers’, we have real hyperspectral imagery belonging to both states. The results of applying the Deep Generative Network show that the proposed method has done a better job virtually cleaning the artwork compared to a physics-based method in the literature. The results are presented through visualization in the sRGB color space and also by computing Euclidean distance and spectral angle (calculated in the spectral reflectance domain) between the virtually cleaned artwork and the physically cleaned one. The ultimate goal of our virtual cleaning algorithm is to enable pigment mapping and identification after virtual cleaning of the artwork in a more accurate manner, even before the process of physical cleaning.
Living on the edge: morphological, karyological and genetic diversity studies of the Hungarian Plantago maxima populations and established ex situ collection
Authors: Kovács Zsófia , Mlinarec Jelena , Höhn Mária 
Published: January 2023

AbstractBackgroundThe analysis of genetic diversity of protected plant species can greatly support conservation efforts.Plantago maximaJuss. ex Jacq. is a perennial species distributed along the Eurasian steppe. The westernmost range edge of the species’ distribution is located in the Pannonian basin, in Hungary where it is represented by a few, fragmented and highly endangered populations. We studied population diversity of all Hungarian range edge, natural populations, and one established ex situ population. One population from the centre of distribution (Kazakhstan) was implemented in the cpDNA haplotype study to compare the peripheral vs. central populations. We performed morphometric trait-based analysis, chromosome studies (morphometric analyses and FISH) and genetic diversity evaluations using inter simple sequence repeats (ISSR) and cpDNA trnL-trnF to evaluate differences between the in situ and ex situ populations as well as central vs. peripheral populations.ResultsOur results showed no obvious morphological differences among the in situ and ex situ populations in the period between 2018 and 2020. One ex situ subpopulation develops flowers three years in a row from 2019, which is a favourable indicator of the introduction success. Hungarian populations are exclusively diploids (2n = 2x = 12). The karyogram consists of 5 metacentric and 1 acrocentric chromosome pair.Plantago maximahas one 35S and two 5S rDNA loci, located on the acrocentric chromosome pair. Eight variable ISSR primers yielded 100 fragments, of which 74.6% were polymorphic (mean He = 0.220). A high level of genetic variation within population was observed (92%) while the genetic differentiation among the populations was only 8%. STRUCTURE analysis revealed that the largest Kunpeszér population separated from the rest of the Hungarian populations, indicating a high rate of admixture among the other ones. Based on the trnL-trnF sequence analysis the Hungarian populations represent a single haplotype, which can indicate a reduced diversity due to isolation and recent population decline. By contrast, Kazakh population represents a distinct haplotype compared to the Hungarian samples.ConclusionsThe present study draws the attention to the high conservation value of thePlantago maximapopulations from the westernmost range edge of the species’ distribution.
Doctoral advisor selection processes in science, math, and engineering programs in the United States
Authors: Artiles Mayra S. , Knight David B. , Matusovich Holly M. 
Published: January 2023

AbstractAlthough advising relationships are key for doctoral student success, little research has addressed how they form. Understanding the formation of advising relationships can help contextualize their later development and ultimately support a student’s decision to persist in the doctorate. To understand relationship formation, the purpose of this qualitative study is to identify and describe the types of advisor–advisee selection processes that exist in engineering, science, and math doctoral programs and examine patterns across disciplines within those fields. We conducted interviews with doctoral program directors and engaged in document analysis of graduate student handbooks from 55 doctoral programs in the aforementioned fields in high research institutions across the United States. Using principal–agent theory as a theoretical lens, our findings showed that engineering programs tend to decentralize the advisor selection process by funding students across different funding sources upon enrollment. Contrariwise, science and math programs tended to fund all students in a cohort from a common funding source, which allowed students to have more time to gather information, meet, and select an advisor. These findings also show important nuances when comparing graduate education in these programs that directly impact the doctoral student experience and reiterates the necessity to study these fields separately.
Conscious connected breathing with breath retention intervention in adults with chronic low back pain: protocol for a randomized controlled pilot study
Authors: Pratscher Steven D. , Sibille Kimberly T. , Fillingim Roger B. 
Published: January 2023

AbstractBackgroundChronic pain is a major source of human suffering, and chronic low back pain (cLBP) is among the most prevalent, costly, and disabling of pain conditions. Due to the significant personal and societal burden and the complex and recurring nature of cLBP, self-management approaches that can be practiced at home are highly relevant to develop and test. The respiratory system is one of the most integrated systems of the body, and breathing is bidirectionally related with stress, emotion, and pain. Thus, the widespread physiological and psychological impact of breathing practices and breathwork interventions hold substantial promise as possible self-management strategies for chronic pain. The primary aim of the current randomized pilot study is to test the feasibility and acceptability of a conscious connected breathing with breath retention intervention compared to a sham control condition.MethodsThe rationale and procedures for testing a 5-day conscious connected breathing with breath retention intervention, compared to a deep breathing sham control intervention, in 24 adults (18–65 years) with cLBP is described. Both interventions will be delivered using standardized audio recordings and practiced over 5 days (two times in-person and three times at-home), and both are described as Breathing and Attention Training to reduce possible expectancy and placebo effects common in pain research. The primary outcomes for this study are feasibility and acceptability. Feasibility will be evaluated by determining rates of participant recruitment, adherence, retention, and study assessment completion, and acceptability will be evaluated by assessing participants’ satisfaction and helpfulness of the intervention. We will also measure other clinical pain, psychological, behavioral, and physiological variables that are planned to be included in a follow-up randomized controlled trial.DiscussionThis will be the first study to examine the effects of a conscious connected breathing with breath retention intervention for individuals with chronic pain. The successful completion of this smaller-scale pilot study will provide data regarding the feasibility and acceptability to conduct a subsequent trial testing the efficacy of this breathing self-management practice for adults with cLBP.Trial registrationClinicaltrials.gov, identifierNCT04740710. Registered on 5 February 2021.