bluuebunny/crossref_metadata_2025_split huggingface dataset:
Total Synthesis of Daphniphyllum Alkaloids: (+)-Daphlongamine E, (+)-Calyciphylline R, and (–)-10-Deoxydaphnipaxianine A
Authors: Zhang Yan , Chen Yuye , Xu Jing 
Published: January 2024

AbstractHere, we wish to describe our detailed efforts in the total synthesis of three calyciphylline A-type alkaloids, namely (+)-daphlongamine E, (+)-calyciphylline R, and (–)-10-deoxydaphnipaxianine A. Important steps in our approach include a Pt-catalyzed nitrile hydration, a Babler–Dauben rearrangement, a novel selective amide reduction tactic, and an oxidative Nazarov cyclization via an unfunctionalized tertiary divinyl carbinol (TDC).
Family Perception of OpenNotes in the Neonatal Intensive Care Unit
Authors: McCallie Katherine R. , Balasundaram Malathi , Sarabu Chethan 
Published: January 2024

Abstract
Background OpenNotes, or sharing of medical notes via a patient portal, has been studied extensively in the adult population, but less in pediatric populations, and even more rarely in inpatient pediatric or intensive care settings.
Objectives This study aimed to understand families' interaction with and perception of inpatient hospital notes shared via patient portal in a community Neonatal Intensive Care Unit (NICU).
Methods At the end of the NICU discharge education, completed in the patient portal before discharge, families were offered an anonymous survey on OpenNotes.
Results Out of 446 NICU patients from March 16, 2022 to March 16, 2023, there were 59 respondents (13%). Race was primarily Asian (48%), and English was the predominant language (93%). Most families indicated that the notes were “very or somewhat easy to understand” (93%). Seventy-three percent of respondents felt much better about the doctor(s) after reading the notes, and 53% contacted the physicians about something in the notes. Six (16%) felt that OpenNotes were more confusing than helpful.
Conclusion To the authors' knowledge, this is the first study on NICU families' perceptions of OpenNotes, which indicated positive interactions with the doctors' daily progress notes and gave important suggestions for improvement.
Rare Cause of Soft Tissue Infection: Shewanella algae
Authors: Yılık Ezgi , Akgül Ayşe Hümeyra , Gençeli Mustafa , Akcan Özge Metin , Kan Seda Nur Arazi , Doğan Metin 
Published: January 2024

Abstract
Shewanella algae is a common microorganism in nature, but a rare pathogen in humans. It is a causative agent of skin and soft tissue infections, especially in patients with skin ulcers or trauma. S. algae can enter the body through the eyes, ears, gastrointestinal tract, or respiratory tract. Immunocompromised individuals are at increased risk of developing bacteremia and sepsis from the infection. This report presents a case of posttraumatic soft tissue infection caused by S. algae in an 18-year-old male after swimming in the sea. The bacteria were cultured from the wound site.
From incorporation to emplacement in the cultural sociology of immigration
Authors: Voyer Andrea 
Published: January 2024

AbstractCultural sociology can be useful for uncovering factors facilitating and hindering immigrant incorporation. The process of incorporation blends different logics and pressures, where the work of incorporation is divided between immigrants who pursue incorporation, and social groups (from nations, to communities, and from classrooms to corporations) that facilitate, hinder, and shape trajectories of inclusion. Cultural sociology has much to contribute to our understanding of the relation between immigrants and the role of others in the process of incorporation. In this essay, I first summarize underlying ideas in the cultural sociology of immigration and immigrant incorporation. I argue that incorporation entails two types of agency on the part of immigrants: mastery and change-making. I then bring three books, Elizabeth Becker’s (Mosques in the metropolis: incivility, caste, and contention in Europe. University of Chicago Press, Chicago, 2021), Nancy Foner’s (One quarter of the nation: immigration and the transformation of America. Princeton University Press, Princeton, 2022), and Heba Gowayed’s (Refuge: how the state shapes human potential. Princeton University Press, Princeton, 2022), into conversation with cultural theory, reflecting on how the theory challenges the books, and also how the books challenge the theory. I conclude with a proposal for a new approach to thinking about processes of incorporation as consisting of emplacement and acceptance. Adopting this approach contributes to cultural theory by eliminating the need for an outgroup in the construction of the social solidarity.
The body in pieces: towards a feminist phenomenology of violence
Authors: Kaku Archana 
Published: January 2024

AbstractThis article proposes that feminist phenomenology offers an essential set of conceptual tools for analysing forms of violence which destroy the body beyond the point of death. To illustrate the potential utility of this approach, I apply this lens to the 11 September 2001 attack on the World Trade Center in Manhattan, New York City. I identify several distinct modes of bodily transformation from the attack, grouped into three broad categories: vaporised bodies, intermingled remains, and hidden fragments. I describe how these transformations unsettled the relationships between bodies and contexts, and occasioned the formation of new relationships in ways that heightened and extended the violence of the attack. I end with a discussion of attempts to resettle and repair these relationships through the creation of fictive bodies. These fictive bodies aim to repair the specific harms caused by the derangement of bodily relations by re-establishing firm boundaries between heroic, national bodies, and the monstrous body of the attacker. Through rigorous engagement with this case, I illustrate the unique potential of feminist phenomenology to account for the relationships between bodies, objects, and spaces as the site of political meaning-making in the aftermath of violence.
CrossFuse-XGBoost: accurate prediction of the maximum recommended daily dose through multi-feature fusion, cross-validation screening and extreme gradient boosting
Authors: Li Qiang , He Yu , Pan Jianbo 
Published: January 2024

Abstract
In the drug development process, approximately 30% of failures are attributed to drug safety issues. In particular, the first-in-human (FIH) trial of a new drug represents one of the highest safety risks, and initial dose selection is crucial for ensuring safety in clinical trials. With traditional dose estimation methods, which extrapolate data from animals to humans, catastrophic events have occurred during Phase I clinical trials due to interspecies differences in compound sensitivity and unknown molecular mechanisms. To address this issue, this study proposes a CrossFuse-extreme gradient boosting (XGBoost) method that can directly predict the maximum recommended daily dose of a compound based on existing human research data, providing a reference for FIH dose selection. This method not only integrates multiple features, including molecular representations, physicochemical properties and compound–protein interactions, but also improves feature selection based on cross-validation. The results demonstrate that the CrossFuse-XGBoost method not only improves prediction accuracy compared to that of existing local weighted methods [k-nearest neighbor (k-NN) and variable k-NN (v-NN)] but also solves the low prediction coverage issue of v-NN, achieving full coverage of the external validation set and enabling more reliable predictions. Furthermore, this study offers a high level of interpretability by identifying the importance of different features in model construction. The 241 features with the most significant impact on the maximum recommended daily dose were selected, providing references for optimizing the structure of new compounds and guiding experimental research. The datasets and source code are freely available at https://github.com/cqmu-lq/CrossFuse-XGBoost.
Multiomics-integrated deep language model enables in silico genome-wide detection of transcription factor binding site in unexplored biosamples
Authors: Yang Zikun , Li Xin , Sheng Lele , Zhu Ming , Lan Xun , Gu Fei 
Published: January 2024

Abstract

Motivation
Transcription factor binding sites (TFBS) are regulatory elements that have significant impact on transcription regulation and cell fate determination. Canonical motifs, biological experiments, and computational methods have made it possible to discover TFBS. However, most existing in silico TFBS prediction models are solely DNA-based, and are trained and utilized within the same biosample, which fail to infer TFBS in experimentally unexplored biosamples.

Results
Here, we propose TFBS prediction by modified TransFormer (TFTF), a multimodal deep language architecture which integrates multiomics information in epigenetic studies. In comparison to existing computational techniques, TFTF has state-of-the-art accuracy, and is also the first approach to accurately perform genome-wide detection for cell-type and species-specific TFBS in experimentally unexplored biosamples. Compared to peak calling methods, TFTF consistently discovers true TFBS in threshold tuning-free way, with higher recalled rates. The underlying mechanism of TFTF reveals greater attention to the targeted TF’s motif region in TFBS, and general attention to the entire peak region in non-TFBS. TFTF can benefit from the integration of broader and more diverse data for improvement and can be applied to multiple epigenetic scenarios.

Availability and implementation
We provide a web server (https://tftf.ibreed.cn/) for users to utilize TFTF model. Users can train TFTF model and discover TFBS with their own data.
Multiple genes in the Pate5–13 genomic region contribute to ADAM3 processing
Authors: Noda Taichi , Shinohara Hina , Kobayashi Sumire , Taira Ayumu , Oura Seiya , Tahara Duri , Tokuyasu Midori , Araki Kimi , Ikawa Masahito 
Published: January 2024

Abstract
Sperm proteins undergo post-translational modifications during sperm transit through the epididymis to acquire fertilizing ability. We previously reported that the genomic region coding Pate family genes is key to the proteolytic processing of the sperm membrane protein ADAM3 and male fertility. This region contains nine Pate family genes (Pate5–13), and two protein-coding genes (Gm27235 and Gm5916), with a domain structure similar to Pate family genes. Therefore, in this study, we aimed to identify key factors by narrowing the genomic region. We generated three knockout (KO) mouse lines using CRISPR/Cas9: single KO mice of Pate10 expressed in the caput epididymis; deletion KO mice of six caput epididymis-enriched genes (Pate5–7, 13, Gm27235, and Gm5916) (Pate7-Gm5916 KO); and deletion KO mice of four genes expressed in the placenta and epididymis (Pate8, 9, 11, and 12) (Pate8–12 KO). We observed that the fertility of only Pate7-Gm5916 KO males was reduced, whereas the rest remained unaffected. Furthermore, when the caput epididymis-enriched genes, Pate8 and Pate10 remained in Pate7-Gm5916 KO mice were independently deleted, both KO males displayed more severe subfertility due to a decrease in mature ADAM3 and a defect in sperm migration to the oviduct. Thus, our data showed that multiple caput epididymis-enriched genes within the region coding Pate5–13 cooperatively function to ensure male fertility in mice.
The Epworth sleepiness scale may have more advantages than the multiple sleep latency test in assessing sleepiness in patients with obstructive sleep apnea
Authors: Sun Yuangfeng , Li Taomei , Li Jing , Zou Ke , Tang Xiangdong 
Published: January 2024

Abstract
This study aimed to analyze the brain function of severe obstructive sleep apnea patients with various sleepiness assessment methods and explore the brain imaging basis for the differences between these methods. This study included 30 severe obstructive sleep apnea patients and 19 healthy controls. Obstructive sleep apnea patients were divided into a subjective excessive daytime sleepiness group and a subjective non-excessive daytime sleepiness group according to the Epworth sleepiness scale. Moreover, they were divided into an objective excessive daytime sleepiness group and an objective non-excessive daytime sleepiness group according to the multiple sleep latency test. The fractional amplitude of low-frequency fluctuation was used to assess the features of brain function. Compared with healthy controls, participants in the subjective excessive daytime sleepiness group exhibited higher fractional amplitude of low-frequency fluctuation signals in the right thalamus, left cerebellar lobe 6, left putamen, and pallidum. Participants in the objective excessive daytime sleepiness group showed higher fractional amplitude of low-frequency fluctuation signals in the right thalamus and lower fractional amplitude of low-frequency fluctuation signals in the right superior frontal gyrus, the dorsolateral and superior frontal gyrus, and the medial orbital. We concluded that the thalamus may be involved in subjective and objective sleepiness regulation. Functional abnormalities in the putamen and pallidum may be involved in subjective sleepiness, whereas the frontal lobe may be involved in objective sleepiness.
Investigation of causal relationships between cortical structure and osteoporosis using two-sample Mendelian randomization
Authors: Li Long-Jun , Zhong Xian-Xing , Tan Guo-Zhi , Song Ming-Xi , Li Pian , Liu Zhen-Xin , Xiong Si-Cheng , Yang Da-Qi , Liang Zu-Jian 
Published: January 2024

Abstract
The mutual interaction between bone characteristics and brain had been reported previously, yet whether the cortical structure has any relevance to osteoporosis is questionable. Therefore, we applied a two-sample bidirectional Mendelian randomization analysis to investigate this relationship. We utilized the bone mineral density measurements of femoral neck (n = 32,735) and lumbar spine (n = 28,498) and data on osteoporosis (7300 cases and 358,014 controls). The global surficial area and thickness and 34 specific functional regions of 51,665 patients were screened by magnetic resonance imaging. For the primary estimate, we utilized the inverse-variance weighted method. The Mendelian randomization-Egger intercept test, MR-PRESSO, Cochran’s Q test, and “leave-one-out” sensitivity analysis were conducted to assess heterogeneity and pleiotropy. We observed suggestive associations between decreased thickness in the precentral region (OR = 0.034, P = 0.003) and increased chance of having osteoporosis. The results also revealed suggestive causality of decreased bone mineral density in femoral neck to declined total cortical surface area (β = 1400.230 mm2, P = 0.003), as well as the vulnerability to osteoporosis and reduced thickness in the Parstriangularis region (β = −0.006 mm, P = 0.002). Our study supports that the brain and skeleton exhibit bidirectional crosstalk, indicating the presence of a mutual brain–bone interaction.
Comparison of different estimated glomerular filtration rates for monitoring of kidney function in oncology patients
Authors: Vermassen Tijl , Geboes Karen , Lumen Nicolaas , Van Praet Charles , Rottey Sylvie , Delanghe Joris 
Published: January 2024

ABSTRACT

Background
Tyrosine kinase inhibitors (TKIs) are associated with kidney function deterioration. A shift is ongoing towards glomerular filtration rate (GFR) equations based on other protein markers, such as cystatin C (CSTC) and β-trace protein (BTP). We evaluated various GFR equations for monitoring of kidney function in actively treated oncology patients.

Methods
We monitored 110 patients receiving a TKI. Blood and urine were collected during therapy. Serum analysis included creatinine (Cr), CSTC and BTP; for consequent GFR determination. Urine was analysed for protein, albumin, immunoglobulin G, and α-1-microglobulin. A similar analysis was done in a patient subgroup receiving immune checkpoint inhibitors (ICI) as prior or subsequent line of therapy.

Results
Cr remained constant during TKI treatment (P = 0.7753), whereas a significant decrease in CSTC (from week 2 onward, P &lt; 0.0001) and BTP (at weeks 2 and 4, P = 0.0100) were noticed. Consequently, GFR estimations, using CSTC and/or BTP as a biochemical parameter, showed an apparent increase in GFR, whereas this was not observed for Cr-related GFR estimations. As a result, the GFR gap (ΔGFR) was significantly different from week 2 onward between Cr-based and CSTC-based GFR and between BTP-based and CSTC-based GFR. Glomerular damage was noticed with significant increase in urine protein-to-creatinine ratio, albumin-to-creatinine ratio and immunoglobulin G (all P &lt; 0.0001). No change in α-1-microglobulin was seen. ICI treatment had no effect on Cr (P = 0.2262), CSTC (P = 0.7341), and BTP concentrations (P = 0.3592).

Conclusion
GFR equations, in which CSTC is incorporated, fail to correctly estimate the GFR in oncology patients treated with TKIs. As TKI-treated patients show clear signs of glomerular injury, further assessment is needed on how to correctly monitor the kidney function in actively treated oncology patients.
The influence of resourcefulness on the family functioning of young- and middle-aged lymphoma patients in China: a cross-sectional study
Authors: Wang Ruibo , Tang Han , Cui Panpan , Du Ruofei , Wang Panpan , Sun Qiaozhi , Fu Hang , Lu Hongmei , Li Xuekun , Zhang Tiange , Chen Changying 
Published: January 2024

Abstract

Background
Lymphoma has become 1 of the 10 most common cancers with increased prevalence in young- and middle-aged adults in China. This poses a tremendous burden on patients and their families and brings great challenges to maintaining the balance of family functioning in young- and middle-aged patients.

Objective
This cross-sectional study aimed to analyse the influence of resourcefulness on the family functioning of Chinese young- and middle-aged lymphoma patients.

Methods
A total of 172 Chinese young- and middle-aged patients with lymphoma were recruited from the oncology departments of two tertiary hospitals in Zhengzhou, Henan, China. They were invited to complete a survey that included a demographic questionnaire, the Resourcefulness Scale and the Chinese Version Family Adaptability and Cohesion Scale II. Multiple linear regression was used to analyse the related factors for family functioning.

Results
The multiple regression analysis revealed that the main influencing factors of family cohesion were resourcefulness (β = 0.338, 95% CI (0.072, 0.173)), spouse caregiver (β = 0.376, 95% CI (1.938, 10.395)), and cancer stage (β = –0.274, 95% CI (–3.219, –1.047)). Resourcefulness (β = 0.438, 95% CI (0.096, 0.181)), spouse caregiver (β = 0.340, 95% CI (1.348, 8.363)), and family per capita monthly income (β = 0.157, 95% CI (0.066, 2.243)) were the influencing factors of family adaptability.

Conclusions
Healthcare professionals and family scholars should value young- and middle-aged lymphoma patients’ family functioning throughout the cancer treatment process, and family interventions should be designed by healthcare providers based on patients’ resourcefulness. Moreover, healthcare providers need to pay attention to the risk factors of patients’ family cohesion and adaptability, such as low family per capita monthly income, and consider employing corresponding measures to help them.
Natural variation in the zinc-finger-encoding exon of Prdm9 affects hybrid sterility phenotypes in mice
Authors: AbuAlia Khawla F N , Damm Elena , Ullrich Kristian K , Mukaj Amisa , Parvanov Emil , Forejt Jiri , Odenthal-Hesse Linda 
Published: January 2024

Abstract
PRDM9-mediated reproductive isolation was first described in the progeny of Mus musculus musculus (MUS) PWD/Ph and Mus musculus domesticus (DOM) C57BL/6J inbred strains. These male F1 hybrids fail to complete chromosome synapsis and arrest meiosis at prophase I, due to incompatibilities between the Prdm9 gene and hybrid sterility locus Hstx2. We identified 14 alleles of Prdm9 in exon 12, encoding the DNA-binding domain of the PRDM9 protein in outcrossed wild mouse populations from Europe, Asia, and the Middle East, 8 of which are novel. The same allele was found in all mice bearing introgressed t-haplotypes encompassing Prdm9. We asked whether 7 novel Prdm9 alleles in MUS populations and the t-haplotype allele in 1 MUS and 3 DOM populations induce Prdm9-mediated reproductive isolation. The results show that only combinations of the dom2 allele of DOM origin and the MUS msc1 allele ensure complete infertility of intersubspecific hybrids in outcrossed wild populations and inbred mouse strains examined so far. The results further indicate that MUS mice may share the erasure of PRDM9msc1 binding motifs in populations with different Prdm9 alleles, which implies that erased PRDM9 binding motifs may be uncoupled from their corresponding Prdm9 alleles at the population level. Our data corroborate the model of Prdm9-mediated hybrid sterility beyond inbred strains of mice and suggest that sterility alleles of Prdm9 may be rare.
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data
Authors: Shah Zafran Hussain , Müller Marcel , Hübner Wolfgang , Wang Tung-Cheng , Telman Daniel , Huser Thomas , Schenck Wolfram 
Published: January 2024

Abstract

Background
Convolutional neural network (CNN)–based methods have shown excellent performance in denoising and reconstruction of super-resolved structured illumination microscopy (SR-SIM) data. Therefore, CNN-based architectures have been the focus of existing studies. However, Swin Transformer, an alternative and recently proposed deep learning–based image restoration architecture, has not been fully investigated for denoising SR-SIM images. Furthermore, it has not been fully explored how well transfer learning strategies work for denoising SR-SIM images with different noise characteristics and recorded cell structures for these different types of deep learning–based methods. Currently, the scarcity of publicly available SR-SIM datasets limits the exploration of the performance and generalization capabilities of deep learning methods.

Results
In this work, we present SwinT-fairSIM, a novel method based on the Swin Transformer for restoring SR-SIM images with a low signal-to-noise ratio. The experimental results show that SwinT-fairSIM outperforms previous CNN-based denoising methods. Furthermore, as a second contribution, two types of transfer learning—namely, direct transfer and fine-tuning—were benchmarked in combination with SwinT-fairSIM and CNN-based methods for denoising SR-SIM data. Direct transfer did not prove to be a viable strategy, but fine-tuning produced results comparable to conventional training from scratch while saving computational time and potentially reducing the amount of training data required. As a third contribution, we publish four datasets of raw SIM images and already reconstructed SR-SIM images. These datasets cover two different types of cell structures, tubulin filaments and vesicle structures. Different noise levels are available for the tubulin filaments.

Conclusion
The SwinT-fairSIM method is well suited for denoising SR-SIM images. By fine-tuning, already trained models can be easily adapted to different noise characteristics and cell structures. Furthermore, the provided datasets are structured in a way that the research community can readily use them for research on denoising, super-resolution, and transfer learning strategies.