bluuebunny/crossref_metadata_2025 huggingface dataset:
Associations between low serum levels of ANRIL and some common gene SNPs in Iranian patients with premature coronary artery disease
Authors: Taheri Bajgan Elham , Zahedmehr Ali , Shakerian Farshad , Maleki Majid , Bakhshandeh Hooman , Mowla Seyed Javad , Malakootian Mahshid
Published: January 2024

Coronary artery disease (CAD) is the major cause of mortality in the world. Premature development of CAD can be attributed to women under 55 and men under 45. Many genetic factors play a part in premature CAD. Among them, ANRIL, a long noncoding RNA is located at the 9p21 risk locus, and its expression seems to be correlated with CAD. In the current study, premature CAD and control blood samples, with and without Type 2 Diabetes (T2D), were genotyped for six SNPs at the 9p21 locus. Additionally, ANRIL serum expression was assessed in both groups using real-time PCR. It was performed using different primers targeting exons 1, 5–6, and 19. The χ2 test for association, along with t-tests and ANOVA, was employed for statistical analysis. In this study, we did not find any significant correlation between premature coronary artery disease and rs10757274, rs2383206, rs2383207, rs496892, rs10757278 and rs10738605. However, a lower ANRIL expression was correlated with each SNP risk genotype. Despite the correlation between lower ANRIL expression and CAD, Type 2 diabetes was associated with higher ANRIL expression. Altogether, the correlation between ANRIL expression and the genotypes of the studied SNPs indicated that genetic variants, even those in intronic regions, affect long noncoding RNA expression levels. In conclusion, we recommend combining genetic variants with expression analysis when developing screening strategies for families with premature CAD. To prevent the devastating outcomes of CAD in young adults, it is crucial to discover noninvasive genetic-based screening tests.
Isatin-tethered halogen-containing acylhydrazone derivatives as monoamine oxidase inhibitor with neuroprotective effect
Authors: Kumar Sunil , Oh Jong Min , Prabhakaran Prabitha , Awasti Abhimanyu , Kim Hoon , Mathew Bijo
Published: January 2024

Sixteen isatin-based hydrazone derivatives (IS1–IS16) were synthesized and assessed for their ability to inhibit monoamine oxidases (MAOs). All the molecules showed improved inhibitory MAO-B activity compared to MAO-A. CompoundIS7most potently inhibited MAO-B with an IC50value of 0.082 μM, followed byIS13andIS6(IC50 = 0.104 and 0.124 μM, respectively). CompoundIS15most potently inhibited MAO-A with an IC50value of 1.852 μM, followed byIS3(IC50 = 2.385 μM). CompoundIS6had the highest selectivity index (SI) value of 263.80, followed byIS7andIS13(233.85 and 212.57, respectively). In the kinetic study, the Kivalues ofIS6,IS7, andIS13for MAO-B were 0.068 ± 0.022, 0.044 ± 0.002, and 0.061 ± 0.001 μM, respectively, and that ofIS15for MAO-A was 1.004 ± 0.171 μM, and the compounds were reversible-type inhibitors. The lead compounds were central nervous system (CNS) permeable, as per parallel artificial membrane permeability assay (PAMPA) test results. The lead compounds were examined for their cytotoxicity and potential neuroprotective benefits in hazardous lipopolysaccharide (LPS)-exposed SH-SY5Y neuroblastoma cells. Pre-treatment with lead compounds enhanced anti-oxidant levels (SOD, CAT, GSH, and GPx) and decreased ROS and pro-inflammatory cytokine (IL-6, TNF-alpha, and NF-kB) production in LPS-intoxicated SH-SY5Y cells. To confirm the promising effects of the compound, molecular docking, dynamics, and MM-GBSA binding energy were used to examine the molecular basis of theIS7-MAO-B interaction. Our findings indicate that lead compounds are potential therapeutic agents to treat neurological illnesses, such as Parkinson's disease.
Glioblastoma multiforme influence on the elemental homeostasis of the distant organs: the results of inter-comparison study carried out with TXRF method
Authors: Wilk Aleksandra , Setkowicz Zuzanna , Banas Dariusz , Fernández-Ruiz Ramón , Marguí Eva , Matusiak Katarzyna , Wrobel Pawel , Wudarczyk-Mocko Jolanta , Janik-Olchawa Natalia , Chwiej Joanna
Published: January 2024

Glioblastoma (GBM) is a fast-growing and aggressive brain tumor which invades the nearby brain tissue but generally does not spread to the distant organs. Nonetheless, if untreated, GBM can result in patient death in time even less than few months from the diagnosis. The influence of the tumor progress on organs other than brain is obvious but still not well described. Therefore, we examined the elemental abnormalities appearing in selected body organs (kidney, heart, spleen, lung) in two rat models of GBM. The animals used for the study were subjected to the implantation of human GBM cell lines (U87MG and T98G) characterized by different levels of invasiveness. The elemental analysis of digested organ samples was carried out using the total reflection X-ray fluorescence (TXRF) method, independently, in three European laboratories utilizing various commercially available TXRF spectrometers. The comparison of the data obtained for animals subjected to T98G and U87MG cells implantation showed a number of elemental anomalies in the examined organs. What is more, the abnormalities were found for rats even if neoplastic tumor did not develop in their brains. The most of alterations for both experimental groups were noted in the spleen and lungs, with the direction of the found element changes in these organs being the opposite. The observed disorders of element homeostasis may result from many processes occurring in the animal body as a result of implantation of cancer cells or the development of GBM, including inflammation, anemia of chronic disease or changes in iron metabolism. Tumor induced changes in organ elemental composition detected in cooperating laboratories were usually in a good agreement. In case of elements with higher atomic numbers (Fe, Cu, Zn and Se), 88% of the results were classified as fully compliant. Some discrepancies between the laboratories were found for lighter elements (P, S, K and Ca). However, also in this case, the obtained results fulfilled the requirements of full (the results from three laboratories were in agreement) or partial agreement (the results from two laboratories were in agreement).
Association between serum heavy metal levels and diabetic retinopathy in NHANES 2011–2020
Authors: Zhang Yan , Liu Xuekui , Zhang Xia , Li Lin , Li Qing , Geng Houfa , Shi Li , Wang Ben , Qiu Qinqin , Yu Tianpei , Sang Yiquan , Wang Liying , Liang Jun , Xu Wei
Published: January 2024

The present study utilized the National Health and Nutrition Examination Survey (NHANES) database to examine the relationship between serum levels of heavy metals and Diabetic retinopathy (DR) in individuals aged over 30 years with type 2 diabetes mellitus (T2DM) in the United States. A cross-sectional analysis was conducted on 1583 individuals with T2DM from the NHANES 2011–2020, including 331 individuals in the DR group and 1252 individuals in the non-DR group. We collected data on serum levels of heavy metals, DR, and serum albumin for descriptive statistics, linear regression, and logistical regression analysis. After adjusting for age, gender, race and other factors, there was no statistically significant association between blood cadmium, selenium, mercury, or lead and DR. However, serum manganese (Mn) and DR had a significant negative association (β = − 0.2045, 95% CI = − 0.3484, − 0.0606). Serum albumin partially modulated the indirect influence of serum Mn on the incidence of DR, accounting for 12.80% of the association between serum Mn and DR. There was a negative association between serum Mn levels and the prevalence of DR in people with T2DM. Mn intake at least in this study has a little influence on the onset and development of DR.
Synthesis of mono Cytochrome P450 in a modified CHO-CPR cell-free protein production platform
Authors: Knauer Jan Felix , Schulz Christian , Zemella Anne , Wüstenhagen Doreen A. , Walter Ruben Magnus , Küpper Jan-Heiner , Kubick Stefan
Published: January 2024

Cytochromes P450 (CYPs) are a group of monooxygenases that can be found in almost all kinds of organisms. For CYPs to receive electrons from co-substrate NADPH, the activity of NADPH-Cytochrome-P450-oxidoreductase (CPR) is required as well. In humans, CYPs are an integral part of liver-based phase-1 biotransformation, which is essential for the metabolization of multiple xenobiotics and drugs. Consequently, CYPs are important players during drug development and therefore these enzymes are implemented in diverse screening applications. For these applications it is usually advantageous to use mono CYP microsomes containing only the CYP of interest. The generation of mono-CYP containing mammalian cells and vesicles is difficult since endogenous CYPs are present in many cell types that contain the necessary co-factors. By obtaining translationally active lysates from a modified CHO-CPR cell line, it is now possible to generate mono CYPs in a cell-free protein synthesis process in a straightforward manner. As a proof of principle, the synthesis of active human CYPs from three different CYP450 gene families (CYP1A2, CYP2B6 and CYP3A4), which are of outstanding interest in industry and academia was demonstrated. Luciferase based activity assays confirm the activity of the produced CYPs and enable the individual adaptation of the synthesis process for efficient cell-free enzyme production. Furthermore, they allow for substrate and inhibitor screenings not only for wild-type CYPs but also for mutants and further CYP isoforms and variants. As an example, the turnover of selected CYP substrates by cell-free synthesized CYPs was demonstrated via an indirect luciferase assay-based screening setup.
Trpv4-mediated apoptosis of Leydig cells induced by high temperature regulates sperm development and motility in zebrafish
Authors: Yamamoto Yasuhiro , Hishikawa Daisuke , Ono Fumihito
Published: January 2024

Exposure of testes to high-temperature environment results in defective spermatogenesis. Zebrafish exposed to high temperature exhibited apoptosis not only in germ cells but also in Leydig cells, as expected from studies using mice or salmon. However, the role of testicular somatic cells in spermatogenesis defects remains unclear. We found that in Leydig cells the Trpv4 gene encoding the temperature sensitive ion channel was specifically upregulated in high temperature. High temperature also reduced hormone synthesis in Leydig cells and led to a prompt downregulation of sperm motility. In the Trpv4 null mutant, neither Leydig cell-specific apoptosis nor decreased sperm motility was observed under high temperature. These results indicate that Leydig cell specific-apoptosis is induced via Trpv4 by high temperature. Notably this Trpv4-dependent mechanism was specific to Leydig cells and did not operate in germ cells. Because sperm exposed to high temperature exhibited compromised genome stability, we propose that temperature sensing leading to apoptosis in Leydig cells evolved to actively suppress generation of offspring with unstable genome.
Compromise or choose: shared movement decisions in wild vulturine guineafowl
Authors: Papageorgiou Danai , Nyaguthii Brendah , Farine Damien R.
Published: January 2024

Shared-decision making is beneficial for the maintenance of group-living. However, little is known about whether consensus decision-making follows similar processes across different species. Addressing this question requires robust quantification of how individuals move relative to each other. Here we use high-resolution GPS-tracking of two vulturine guineafowl (Acryllium vulturinum) groups to test the predictions from a classic theoretical model of collective motion. We show that, in both groups, all individuals can successfully initiate directional movements, although males are more likely to be followed than females. When multiple group members initiate simultaneously, follower decisions depend on directional agreement, with followers compromising directions if the difference between them is small or choosing the majority direction if the difference is large. By aligning with model predictions and replicating the findings of a previous field study on olive baboons (Papio anubis), our results suggest that a common process governs collective decision-making in moving animal groups.
Magnetic fluid film enables almost complete drag reduction across laminar and turbulent flow regimes
Authors: Stancanelli Laura Maria , Secchi Eleonora , Holzner Markus
Published: January 2024

In the race to curb energy and oil consumption, zeroing of wall frictional forces is highly desirable. The turbulent skin friction drag at the solid/liquid interface is responsible for substantial energy losses when conveying liquids through hydraulic networks, contributing approximately 10% to the global electric energy consumption. Despite extensive research, efficient drag reduction strategies effectively applicable in different flow regimes are still unavailable. Here, we use a wall-attached magnetic fluid film to achieve a wall drag reduction of up to 90% in channel flow. Using optical measurements supported by modelling, we find that the strong damping of wall friction emerges from the co-existence of slip and waviness at the coating interface, and the latter is a key factor to obtain almost complete wall drag reduction across laminar and turbulent flow regimes. Our magnetic fluid film is promising and ready to be applied in energy-saving and antifouling strategies in fluid transport and medical devices.
Multi-resolution partial differential equations preserved learning framework for spatiotemporal dynamics
Authors: Liu Xin-Yang , Zhu Min , Lu Lu , Sun Hao , Wang Jian-Xun
Published: January 2024

Traditional data-driven deep learning models often struggle with high training costs, error accumulation, and poor generalizability in complex physical processes. Physics-informed deep learning (PiDL) addresses these challenges by incorporating physical principles into the model. Most PiDL approaches regularize training by embedding governing equations into the loss function, yet this depends heavily on extensive hyperparameter tuning to weigh each loss term. To this end, we propose to leverage physics prior knowledge by “baking” the discretized governing equations into the neural network architecture via the connection between the partial differential equations (PDE) operators and network structures, resulting in a PDE-preserved neural network (PPNN). This method, embedding discretized PDEs through convolutional residual networks in a multi-resolution setting, largely improves the generalizability and long-term prediction accuracy, outperforming conventional black-box models. The effectiveness and merit of the proposed methods have been demonstrated across various spatiotemporal dynamical systems governed by spatiotemporal PDEs, including reaction-diffusion, Burgers’, and Navier-Stokes equations.
First principles studies on the adsorption of rare base-pairs on the surface of B/N atom doped γ-graphyne
Authors: Li Ruirui , Zeng Xia , Lv Mengdan , Zhang Ruiying , Zhang Shengrui , Zhang Tianlei , Yu Xiaohu , Li Chen , Jin Lingxia , Zhao Caibin
Published: January 2024

Translocation time values are different for each rare base-pair based on substrate. Pure and B/N substituted γ-GY nanosheets can detect each base-pair from the translocation time. Our results are expected to provide new biosensor assemblies for experimental scientists.
Exciton dynamics from the mapping approach to surface hopping: comparison with Förster and Redfield theories
Authors: Runeson Johan E. , Fay Thomas P. , Manolopoulos David E.
Published: January 2024

The mapping approach to surface hopping captures the Förster and Redfield limits of excitation energy transfer, and everything in between.
Terbium alginate encapsulated CsPbI3@Pb-MOF: a ratiometric fluorescent bead for detection and adsorption of Fe3+
Authors: Hou Yangwen , Feng Hua , He Jingting , Meng Fanfei , Sun Jing , Li Xiao , Wang Xinlong , Su Zhongmin , Sun Chunyi
Published: January 2024

Sodium alginate gel using Tb3+ as a cross-linker encapsulated powdered CsPbI3@Pb-MOF to construct a ratiometric fluorescent sensing platform for sensitive detection and efficient adsorption of Fe3+.
Revealing microscopic dynamics: in situ liquid-phase TEM for live observations of soft materials and quantitative analysis via deep learning
Authors: Sun Yangyang , Zhang Xingyu , Huang Rui , Yang Dahai , Kim Juyeong , Chen Junhao , Ang Edison Huixiang , Li Mufan , Li Lin , Song Xiaohui
Published: January 2024

By leveraging liquid-phase TEM and deep learning, this work explores quantitative aspects of soft matter dynamics-encompassing phenomena such as surfactant molecule nucleation, polymer self-assembly, and Au nanoparticle ripening in solution.
Multimode adaptive logic gates based on temperature-responsive DNA strand displacement
Authors: Chen Zhekun , Xie Chun , Chen Kuiting , Hu Yingxin , Xu Fei , Pan Linqiang
Published: January 2024

A temperature-responsive three-state switching DNA nanosystem that performs holding, reacting, and resetting at three different temperatures.
Design, synthesis and characterization of hierarchical porous stacked thin films based on MOFs and ordered mesoporous oxides
Authors: Arcidiácono Melina , Allegretto Juan A. , Azzaroni Omar , Angelomé Paula C. , Rafti Matías
Published: January 2024

Integration of mesoporous thin films and metal–organic frameworks as stacked bilayers, towards hierarchical porous 1D photonic crystals.
Optimising digital signal processor‐based defect detection in smart manufacturing with lightweight convolutional neural networks
Authors: Yue Han , Wang Rucen , Gao Yi , Xia Ailing , Su Kaikai , Zhang Jianhua
Published: January 2024

Industrial defect detection is an important part of intelligent manufacturing, and Internet of things (IoT)‐based defect detection is receiving more and more attention. Although deep learning (DL) can help defect detection reduce the cost and improve the accuracy of traditional manual quality inspection, DL requires huge computational resources and is difficult to be simply deployed on IoT devices with limited computational power and memory resources. Digital signal processor (DSP) is an important IoT device with small size, high performance and low energy consumption, which has been widely used in intelligent manufacturing. In order to perform accurate defect detection on DSP, the authors proposed various optimisation strategies and then used a parallel scheme to scale the model to execute on multiple cores. The authors’ method evaluated it on Northeastern University Surface Defect Dataset, Magnetic Tile Defect Dataset, Rail Surface Defect Dataset and Silk Cylinder Defect Dataset, and the experimental results showed that the authors’ method obtains faster speeds without accuracy loss compared to running the same Convolutional Neural Networks model on a mainstream desktop CPU. This means that the authors’ method can realise efficient and accurate defect detection on IoT devices with limited computational power and memory resources, which opens up new possibilities for future development in the field of smart manufacturing.
A task‐driven sampling method based on graph convolution for 3D point cloud compression
Authors: Yang Yakun , Wang Anhong , Bu Donghan , Jing Hao
Published: January 2024

The previous point cloud compression methods only consider reducing the amount of data. However, in applications such as autonomous driving, the compression methods not only require smooth transmission, but also ensure the efficiency of downstream tasks. To this end, a task‐driven sampling network based on graph convolution is proposed to achieve point cloud compression and recovery. First, a downsampling network is presented to simplify and compress the point cloud, in order to optimize the compressed point cloud for downstream tasks, the task loss is added to loss function for end‐to‐end training. Then, an upsampling network with residual correction unit is presented to recover and reconstruct the point cloud. Experiments for point cloud classification task on ModelNet40 dataset show that the compressed point cloud obtained through our network can achieve higher classification accuracy compared to other similar methods, and the reconstructed point cloud can further improve classification accuracy.
Far field radiated emissions prediction of a flyback adapter with curved cables utilizing electromagnetic simulation method
Authors: He Junping , Wang Cong , Wang Weixin , Shu Junhua , Cao Lingling
Published: January 2024

Radiated emissions (RE) testing has long been a challenge in the development of a switched mode power supply (SMPS) with respect to electromagnetic compatibility performance. Accurate far‐field RE prediction can effectively help SMPS designers reveal and understand the mechanisms of radiation generation, and reasonably suppress it. In this paper, a model for predicting the radiation from a single excitation source and a parasitic radiator for a flyback adapter are proposed after analysing the common mode voltage and current paths. Then, novel methods are proposed to predict the far‐field RE of the flyback adapter based on measurements and electromagnetic simulations. Using these methods, the 10‐m far‐field radiation of the flyback adapter under the curved cables layout is accurately predicted and verified by experiments. Then, the characteristics and influencing factors of the radiation are analysed, including the far‐field patterns, the load volume, and the sag degree of the output cable. Finally, a suppression design of the capacitor‐inductor (CL) notch filter is designed for the frequency points that are above the standard limits, and the RE are reduced to less than 30 dBµV/m from 30 to 300 MHz. The research methods proposed in this paper have good reference significance for radiation analysis and prediction of power electronic devices.
The Prince and the Pauper: Evidence for the early high-redshift formation of the Galactic α-poor disc population
Authors: Gent Matthew Raymond , Eitner Philipp , Serenelli Aldo , Friske Jennifer K. S. , Koposov Sergey E. , Laporte Chervin F. P. , Buck Tobias , Bergemann Maria
Published: January 2024

Context. The presence of [α/Fe]–[Fe/H] bi-modality in the Milky Way disc has intrigued the Galactic archaeology community over more than two decades.

Aims. Our goal is to investigate the chemical, temporal, and kinematical structure of the Galactic discs using abundances, kinematics, and ages derived self-consistently with the new Bayesian framework SAPP.

Methods. We employed the public Gaia-ESO spectra, as well as Gaia EDR3 astrometry and photometry. Stellar parameters and chemical abundances are determined for 13 426 stars using NLTE models of synthetic spectra. Ages were derived for a sub-sample of 2898 stars, including subgiants and main-sequence stars. The sample probes a large range of Galactocentric radii, ∼3 to 12 kpc, and extends out of the disc plane to ±2 kpc.

Results. Our new data confirm the known bi-modality in the [Fe/H]–[α/Fe] space, which is often viewed as the manifestation of the chemical thin and thick discs. The over-densities significantly overlap in metallicity, age, and kinematics and none of them offer a sufficient criterion for distinguishing between the two disc populations. In contrast to previous studies, we find that the α-poor disc population has a very extended [Fe/H] distribution and contains ∼20% old stars with ages of up to ∼11 Gyr.

Conclusions. Our results suggest that the Galactic thin disc was in place early, at lookback times corresponding to redshifts of z ∼ 2 or more. At ages of ∼9 to 11 Gyr, the two disc structures shared a period of co-evolution. Our data can be understood within the clumpy disc formation scenario that does not require a pre-existing thick disc to initiate the formation of the thin disc. We anticipate that a similar evolution can be realised in cosmological simulations of galaxy formation.
Discovery of thiofulminic acid with the QUIJOTE line survey: A study of the isomers of HNCS and HNCO in TMC-1
Authors: Cernicharo J. , Agúndez M. , Cabezas C. , Tercero B. , Fuentetaja R. , Marcelino N. , de Vicente P.
Published: January 2024

We present the first detection of HCNS (thiofulminic acid) in space with the QUIJOTE line survey in the direction of TMC-1. We performed a complete study of the isomers of CHNS and CHNO, including NCO and NCS. The derived column densities for HCNS, HNCS, and HSCN are (9.0 ± 0.5) × 109, (3.2 ± 0.1) × 1011, and (8.3 ± 0.4) × 1011 cm−2, respectively. The HNCS/HSCN abundance ratio is 0.38. The abundance ratios HNCO/HNCS, HCNO/HCNS, HOCN/HSCN, and NCO/NCS are 34 ± 4, 8.3 ± 0.7, 0.18 ± 0.03, and 0.78 ± 0.07, respectively. These ratios cannot be correctly reproduced by our gas-phase chemical models, which suggests that formation paths for these species are missing, and/or that the adopted dissociative recombination rates for their protonated precursors have to be revised. The isotopologues H15NCO, DNCO, HN13CO, DCNO, H34SCN, and DSCN have also been detected with the ultrasensitive QUIJOTE line survey.
Heart Rate Variability as a Prognostic Tool for Gastroschisis Infants in the Neonatal Intensive Critical Unit
Authors: Moneme Chioma , Kausch Sherry L. , Belmonte Briana M. , Fleming II Mark A. , Levin Daniel E. , Sullivan Brynne A.
Published: January 2024

Objective Gastroschisis is the most common congenital abdominal wall defect, with an increasing incidence. It results in extrusion of abdominal contents with associated delayed intestinal motility. Abnormal heart rate characteristics (HRCs) such as decreased variability occur due to the inflammatory response to sepsis in preterm infants. This study aimed to test the hypothesis that infants with gastroschisis have decreased heart rate variability (HRV) after birth and that this physiomarker may predict outcomes.

Study Design We analyzed heart rate data from and clinical variables for all infants admitted with gastroschisis from 2009 to 2020.

Results Forty-seven infants were admitted during the study period and had available data. Complex gastroschisis infants had reduced HRV after birth. For those with sepsis and necrotizing enterocolitis, abnormal HRCs occurred early in the course of illness.

Conclusion Decreased HRV was associated with complex gastroschisis. Infants in this group experienced complications that prolonged time to full enteral feeding and time on total parenteral nutrition.

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

Here, 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

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

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

Cultural 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

This 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

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

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

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

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

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

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 < 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 < 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

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

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.