bluuebunny/crossref_metadata_2025_split huggingface dataset:
SexAnnoDB, a knowledgebase of sex-specific regulations from multi-omics data of human cancers
Authors: Yang Mengyuan , Feng Yuzhou , Liu Jiajia , Wang Hong , Wu Sijia , Zhao Weiling , Kim Pora , Zhou Xiaobo 
Published: August 2024

Abstract
Background
Sexual differences across molecular levels profoundly impact cancer biology and outcomes. Patient gender significantly influences drug responses, with divergent reactions between men and women to the same drugs. Despite databases on sex differences in human tissues, understanding regulations of sex disparities in cancer is limited. These resources lack detailed mechanistic studies on sex-biased molecules.

Methods
In this study, we conducted a comprehensive examination of molecular distinctions and regulatory networks across 27 cancer types, delving into sex-biased effects. Our analyses encompassed sex-biased competitive endogenous RNA networks, regulatory networks involving sex-biased RNA binding protein-exon skipping events, sex-biased transcription factor-gene regulatory networks, as well as sex-biased expression quantitative trait loci, sex-biased expression quantitative trait methylation, sex-biased splicing quantitative trait loci, and the identification of sex-biased cancer therapeutic drug target genes. All findings from these analyses are accessible on SexAnnoDB (https://ccsm.uth.edu/SexAnnoDB/).

Results
From these analyses, we defined 126 cancer therapeutic target sex-associated genes. Among them, 9 genes showed sex-biased at both the mRNA and protein levels. Specifically, S100A9 was the target of five drugs, of which calcium has been approved by the FDA for the treatment of colon and rectal cancers. Transcription factor (TF)-gene regulatory network analysis suggested that four TFs in the SARC male group targeted S100A9 and upregulated the expression of S100A9 in these patients. Promoter region methylation status was only associated with S100A9 expression in KIRP female patients. Hypermethylation inhibited S100A9 expression and was responsible for the downregulation of S100A9 in these female patients.

Conclusions
Comprehensive network and association analyses indicated that the sex differences at the transcriptome level were partially the result of corresponding sex-biased epigenetic and genetic molecules. Overall, SexAnnoDB offers a discipline-specific search platform that could potentially assist basic experimental researchers or physicians in developing personalized treatment plans.
Potential processes leading to winter reddening of young Douglas-fir Pseudotsuga menziesii Mirb. Franco. in Europe
Authors: Van Rooij Mahaut , Améglio Thierry , Baubet Olivier , Bréda Nathalie , Charrier Guillaume 
Published: August 2024

Abstract
Key message
Winter reddening of young Douglas-fir (Pseudotsuga menziesii Mirb. Franco), triggered by large thermal fluctuations in late winter, is a critical problem for European forestry. A literature review identified certain climatic conditions that are characteristic of ‘reddening’ years, including warm daily temperatures, high daily temperature amplitude, low relative humidity, moderate wind speeds, as well as the occurrence of freeze-thaw cycles with cold night temperatures.
By describing the triggering environmental and stand factors, we propose three hypotheses for the physiological processes leading to winter reddening, namely (i) hydraulic failure due to winter drought stress, (ii) photo-oxidative stress in shade-acclimated trees, and (iii) early cold deacclimation during warm periods.
i) Low soil temperature, by reducing root water uptake, combined with anticyclonic conditions, by increasing water losses, can induce hydraulic failure in the xylem. Hydraulic failure may be further accelerated by night frosts.
ii) Winter reddening can occur when low temperature and high irradiance coincide, disrupting photostasis. Overwhelming of winter photo-protection may lead to photodamage and subsequent reddening.
iii) Warm periods, by inducing cold deacclimation, make trees susceptible to frost damage.
Finally, the three processes may interact under atypical anticyclonic conditions in late winter (e.g. cold or dry soils, warm days, high irradiance and/or freezing nights). Indeed, trees under water stress would develop a higher sensitivity to freezing night and photooxidative stress. We therefore proposed mitigation actions to avoid exposing trees to stressful conditions based on e.g. stand characteristics, understorey vegetation and planting.
Archaeometa: leveraging blockchain for secure and scalable virtual museums in the metaverse
Authors: Aziz Omer , Farooq Muhammad Shoaib , khelifi Adel , Shoaib Mahdia 
Published: August 2024

Abstract
The rapid evolution of the digital landscape has catalyzed the integration of blockchain technology within the domain of cultural heritage, particularly in virtual museums within the Metaverse. This study introduces ArchaeoMeta, a novel framework designed to leverage blockchain technology to enhance security, authenticity, and visitor interaction in a virtual museum environment. Utilizing smart contracts deployed on the Ethereum Sepolia testnet, the framework manages visitor interactions and secures digital artifacts, addressing challenges associated with scalability and user experience under varying loads. The performance evaluation involved simulating user interactions, scaling up to ten thousand concurrent users, to assess the impact on transaction latency, gas usage, and blockchain size. Findings reveal significant scalability challenges, as transaction latency and blockchain size increased with the number of users, highlighting areas for optimization in managing high user traffic within the blockchain infrastructure. This study contributes to the understanding of blockchain applications in cultural heritage, suggesting that while ArchaeoMeta offers a robust platform for virtual museums, enhancements in scalability through layer-2 solutions or alternative blockchain platforms are essential for its practical implementation. The framework sets a precedent for future research in the convergence of blockchain technology and cultural heritage preservation, promising a transformative impact on how digital cultural experiences are curated and consumed.
Revealing ancient technology: a high-energy X-ray computed tomography examination of a Mesopotamian copper alloy head
Authors: de Lapérouse J.-F. , Eppihimer M. , Flisch A. , Zboray R. 
Published: August 2024

Abstract
Although the origins of lost wax casting extend back into the 5th millennium BCE, it was not until the development of hollow core casting that life-sized metal sculptures could be produced. Based on existing evidence, the earliest adoption of this technique, which involves the inclusion of a clay core within a wax model, occurred in Iraq (Mesopotamia) during the Early Dynastic III period (ca. 2600–2350 BCE). To date, only one hollow core casting from the succeeding Akkadian period (ca. 2350–2150 BCE)—the Sargon Head in the collection of the Iraq Museum—has been studied from a technical point of view. The recent attribution of The Metropolitan Museum of Art's Head of a ruler to this formative period of hollow core lost wax casting provided the impetus for its examination by high-energy X-ray computed tomography—the most practical technique for an object that is continuously on display that could image in 3D the interior morphology of this sculpture given the considerable thickness of its metal walls. This scan revealed a markedly different style of production than the Sargon Head. Although further research on early castings is required to determine the chronological implications of the differences observed and to elucidate more generally the early development of hollow casting technology, the scan of the Head of a ruler provides evidence of some of the challenges encountered and problem-solving strategies used in the casting process.
Antioxidants as adjuvant therapy in the treatment of community-acquired pneumonia
Authors: Youssef Fatma Makram , Elmokadem Eman Mohamed , Samy Amir Eskander Hanna , Ateyya Hayam 
Published: August 2024

Abstract
Background
Community-acquired pneumonia remains a major health concern, characterized by significant morbidity and mortality. The underlying pathophysiology of community-acquired pneumonia involves substantial oxidative stress and inflammation, which contribute to lung tissue damage and impaired immune function.

Main body
Variations in oxidative metabolism contribute to the inflammatory cascade which triggers pneumonia to commence and evolve, whereas oxidative stress as well as inflammatory processes is strongly related. Understanding the underlying immunological dysregulation and unbalanced redox that heighten vulnerability to a variety of illnesses has improved over the past several decades attributable to research. One of the key strategies for addressing oxidative stress is to lower the reactive oxygen species creation in the mitochondrion which is one of the main sites of their generation by using antioxidants, where they prevent oxidants from transferring electrons to other molecules. Consequently, antioxidants either directly or indirectly reduce the risk of damage and preserve the redox equilibrium. Therefore, antioxidants, due to their ability to neutralize reactive oxygen species and modulate inflammatory processes, have been explored as potential adjuvant therapies to enhance the treatment outcomes of community-acquired pneumonia. Where recent research has explored the potential of antioxidants as adjuvant therapy in the treatment of community-acquired pneumonia, aiming to mitigate these detrimental effects. Antioxidants such as N-acetylcystein, vitamin C, vitamin E, astaxanthin, and zinc have shown promising results in both preclinical and clinical studies.

Conclusion
Outcomes of several in vitro as well as in vivo antioxidant studies have demonstrated the antioxidants' promising potential as an adjunct pneumonia therapy. For an assessment of its effectiveness in this therapeutic context, more research involving humans will be required.
Polarization-entangled photon-pair source with van der Waals 3R-WS2 crystal
Authors: Feng Jiangang , Wu Yun-Kun , Duan Ruihuan , Wang Jun , Chen Weijin , Qin Jiazhang , Liu Zheng , Guo Guang-Can , Ren Xi-Feng , Qiu Cheng-Wei 
Published: August 2024

AbstractUltracompact entangled photon sources are pivotal to miniaturized quantum photonic devices. Van der Waals (vdW) nonlinear crystals promise efficient photon-pair generation and on-chip monolithic integration with nanophotonic circuitry. However, it remains challenging to generate maximally entangled Bell states of photon pairs with high purity, generation rate, and fidelity required for practical applications. Here, we realize a polarization-entangled photon-pair source based on spontaneous parametric down conversion in an ultrathin rhombohedral tungsten disulfide (3R-WS2) crystal. This vdW entangled photonic source exhibits a high photon-pair purity with a coincidence-to-accidental ratio of above 800, a generation rate of 31 Hz, and two maximally polarization-entangled Bell states with fidelities exceeding 0.93 and entanglement degree over 0.97. These results stem from scalable optical nonlinearity, enhanced second-order susceptibility by electronic transitions, and a well-defined symmetry-enabled selection rule inherent in 3R-WS2. Our polarization entangled photon source can be integrated with photonic structures for generating more complex entangled states, thus paving an avenue for advanced quantum photonic systems toward computation and metrology.
Deep learning reveals a damage signalling hierarchy that coordinates different cell behaviours driving wound re-epithelialisation
Authors: Turley Jake , Robertson Francesca , Chenchiah Isaac V. , Liverpool Tanniemola B. , Weavers Helen , Martin Paul 
Published: August 2024

ABSTRACT
One of the key tissue movements driving closure of a wound is re-epithelialisation. Earlier wound healing studies describe the dynamic cell behaviours that contribute to wound re-epithelialisation, including cell division, cell shape changes and cell migration, as well as the signals that might regulate these cell behaviours. Here, we have used a series of deep learning tools to quantify the contributions of each of these cell behaviours from movies of repairing wounds in the Drosophila pupal wing epithelium. We test how each is altered after knockdown of the conserved wound repair signals Ca2+ and JNK, as well as after ablation of macrophages that supply growth factor signals believed to orchestrate aspects of the repair process. Our genetic perturbation experiments provide quantifiable insights regarding how these wound signals impact cell behaviours. We find that Ca2+ signalling is a master regulator required for all contributing cell behaviours; JNK signalling primarily drives cell shape changes and divisions, whereas signals from macrophages largely regulate cell migration and proliferation. Our studies show deep learning to be a valuable tool for unravelling complex signalling hierarchies underlying tissue repair.
Ukrainian Civil Society: Past Lessons and Future Possibilities
Authors: Volovchuk Nataliia 
Published: August 2024

In Ukrainian academia, the last decades have seen growing interest in the concept of civil society, which has been studied from different disciplinary angles. Commentators disagree on the level of development it has reached in Ukraine. They emphasize its absence in Soviet times, and the general lack of organizational initiative in contemporary Ukraine. In this essay, I show that, although these critiques of Ukrainian civil society are crucial for comprehending its historical evolution, the history of Ukrainian civil society can also help us understand how it might evolve in the future, both during and, hopefully after, the current war. In my analysis, I focus on two particular lines. The first is the interaction between civil society and the state, which shifted from an anti-state attitude to a model of partnership. The second, which operates in the background, is how civil society has struggled with different utopian ideas, over the 20th and early 21st centuries. Analyzing this relationship to different utopian ideas helps us understand how the relations between civil society and the state changed over time. I conclude with a question about European challenges.
Clinical and Genetic Aspects of Pompe Disease: A Review of Current Knowledge
Authors: Konopka Agata , Sitkiewicz Milena , Szczepaniak Zuzanna , Wdowiak Natalia , Adamska Kinga 
Published: August 2024

Abstract:
Introduction:
Pompe disease is classified as a metabolic myopathy and is a glycogen storage disorder inherited in an autosomal recessive manner due to a mutation in the gene encoding the enzyme α-glucosidase. There are two main forms: infantile and late-onset. The disease progresses chronically, with clinical presentation characterized by progressive muscle weakness and varying degrees of respiratory insufficiency. Although incurable, causative treatment is available in the form of enzyme replacement therapy with alglucosidase alfa, a human recombinant α-glucosidase. Early diagnosis, primarily based on enzyme activity assessment, is crucial as timely treatment can extend and improve patients' quality of life.
Purpose of the work: This study aims to review and characterize the clinical and genetic aspects of Pompe disease.
Materials and methods: A comprehensive analysis of research papers available on PubMed, Google Scholar, Web of Science, Embase and Scopus was undertaken using the searchterms encompassing the following keywords: Pompe disease / lysosomal storage disease / myopathy / acid alpha-1,4-glucosidase / glycogen / newborn screening / enzyme replacement therapy.
Results: Pompe disease is a life-threatening rare condition where prompt diagnosis is essential due to the availability of causative treatment. It is included in newborn screening programs for inherited metabolic disorders in some countries. Unfortunately, in Poland, routine diagnostic screening does not cover this disease. Implementing screening could simplify diagnosis and reduce the need for extensive differential diagnostics. Diagnosing late-onset Pompe disease can be challenging due to its diverse progression and symptoms. Patients with Pompe disease, even those receiving enzyme replacement therapy, require multidisciplinary care involving cardiology, pulmonology, neurology, and physical therapy.
Double-formant PCF-SPR refractive index sensor with ultra-high double-peak-shift sensitivity and a wide detection range
Authors: Luo Xingdi , Lv Jingwei , Liu Wei , Mi Chao , Wang Jianxin , Yang Lin , Chu Paul K. , Liu Chao 
Published: August 2024

A dual-resonance-peak photonic crystal fiber–surface plasmon resonance (PCF-SPR) refractive index (RI) sensor is designed for different wavelength ranges. The first resonance peak of the sensor is distributed in the wavelength range of 700–2350 nm, while the second peak is distributed in the range of 2350–5550 nm. In addition to detecting analytes using the full spectrum of constraint losses (CLs), it is also possible to use a single resonance peak to achieve the detection of analytes. By systematically optimizing the nanowire diameter, the diameter of the inner and outer layer air hole, the width of the groove, the polishing depth, and the distance from the outer layer air hole to the fiber core, the optimal structure of the sensor is finally determined. In this study, the sensor was studied by numerical analysis, and the characteristics of the sensor were evaluated by wavelength detection technology. The results show that within the RI range of 1.24–1.37, the sensor has a maximum wavelength sensitivity (WS) of 54700 nm/RIU for detecting the RI of analytes. Within the above refractive index range, the regression coefficient R2 of the dual-peak-resonance wavelength is 0.99993, ensuring the accuracy of the estimated resonance wavelength of the sensor. In addition, the sensor can also use dual-peak-shift sensitivity (DPSS) to detect the refractive index, which is a relatively new sensing technology. The maximum DPSS of the sensor is 95300 nm/RIU. Due to its high sensitivity and unique dual-peak characteristics, this sensor has wide application prospects in medical diagnosis, environmental monitoring, food safety, and other fields.
Seroprevalence and risk factors for Q fever and Rift Valley fever in pastoralists and their livestock in Afar, Ethiopia: A One Health approach
Authors: Oakley Regina Bina , Gemechu Gizachew , Gebregiorgis Ashenafi , Alemu Ayinalem , Zinsstag Jakob , Paris Daniel Henry , Tschopp Rea 
Published: August 2024

Background
Coxiella burnetii, the causative agent of Q fever, and Rift Valley fever virus are two under-researched zoonotic pathogens in Ethiopia. Potential outbreaks of these diseases, in light of the high dependency of nomadic pastoralists on their livestock, poses a risk to both human and animal health in addition to risking the pastoralists livelihoods. Our study aimed to determine the seroprevalence and associated risk factors for Q fever and Rift Valley fever in pastoral communities in the Afar region of north-eastern Ethiopia.

Methodology/Principal findings
This cross-sectional study screened pastoralists (n = 323) and their livestock (n = 1377) for IgG antibodies to Coxiella burnetii and Rift Valley fever virus. A seroprevalence for Q fever of 25.0% (95%CI 18.6–32.6) was found in pastoralists and 34.3% (95%CI 27.9–41.3) in livestock overall; with 51.9% in goats (95%CI 44.9–58.8), 39.9% in sheep (95%CI 24.6–51.2), 16.3% in camels (95%CI 10.4–24.6) and 8.8% in cattle (95%CI 5.0–15.0). For Rift Valley fever the seroprevalence in pastoralists was 6.1% (95%CI 3.3–11.0) and 3.9% (95%CI 2.6–5.7) in livestock overall; cattle had the highest seroprevalence (8.3%, 95%CI 3.3–19.2), followed by goats (2.7%; 95%CI 1.4–5.1), sheep (2.5%; 95%CI 1.0–5.9) and camels (1.8%; 95%CI 0.4–6.9). Human Q fever seropositivity was found to be associated with goat abortions (OR = 2.11, 95%CI 1.18–3.78, p = 0.011), while Rift Valley fever seropositivity in livestock was found to be associated with cattle abortions (OR = 2.52, 95%CI 1.05–6.08, p = 0.039).

Conclusions/Significance
This study provides evidence for a notable exposure to both Q fever and Rift Valley fever in pastoralists and livestock in Afar. The outbreak potential of these pathogens warrants ongoing integrated human and animal surveillance requiring close collaboration of the human and animal health sectors with community representatives following a One Health approach.
“A whole ball of all-togetherness”: The interwoven experiences of intimate partner violence, brain injury, and mental health
Authors: Toccalino Danielle , Haag Halina (Lin) , Nalder Emily , Chan Vincy , Moore Amy , Colantonio Angela , Wickens Christine M. 
Published: August 2024

Background
Intimate partner violence (IPV) is a global public health crisis, with physical violence leaving IPV survivors at high risk of brain injury (BI). Both BI and IPV have significant physical, psychological, cognitive, and social impacts, including a high risk of mental health concerns, yet there is limited exploration of IPV survivors’ experiences with BI and mental health. This study aimed to explore the BI- and mental health-related needs and experiences of IPV survivors from the perspectives of survivors and service providers with the objective of developing knowledge translation materials to raise awareness and support survivors and service providers in addressing these concerns.

Methods
This qualitative interpretive description study involved 19 semi-structured interviews and two focus group discussions (2–3 participants each) with 24 participants including IPV survivors experiencing BI and mental health concerns as well as IPV, mental health, and BI service providers between October 2020 and February 2021. Three screening questions were used to identify probable BI among survivors. Participants across groups were an average of 48.5±12.7 years old and were predominantly cisgender women (96%), of European origin (75%), with a university degree (71%). Interviews were recorded, transcribed, and thematically analyzed.

Findings
Across interviews, participants spoke about IPV, BI, and mental health as being complex and interrelated experiences that have impacts across the survivor’s life and extend well beyond the abusive relationship. Because of the underrecognized nature of BI in IPV, finding and accessing care requires persistence that survivors spoke of as being like “a full-time job.” The benefit of making meaningful connections, particularly with other survivors, was highlighted.

Conclusions
Recognition of BI as a contributing factor shaping the lived experience of IPV survivors; acknowledgement that the impacts of IPV, BI, and mental health are far reaching and long lasting; and reducing barriers to finding and accessing appropriate care are critical to better supporting IPV survivors with BI and mental health concerns. Clinicians should consider BI and its lingering impacts among the IPV survivors with whom they work. Health and social policy that supports integration of care and the reduction of unnecessary barriers should be a priority.
Ted Lasso and Philosophy: No Question Is into Touch, Marybeth Baggett and David Baggett (eds) (2024)
Authors: Mendez Alex 
Published: August 2024

Review of: Ted Lasso and Philosophy: No Question Is into Touch, Marybeth Baggett and David Baggett (eds) (2024)
Hoboken, NJ: John Wiley & Sons, Inc., 256 pp.,
ISBN 978-1-11989-195-6, e-book, USD 18.00
ISBN: 978-1-119-89193-2, p/bk, USD 21.95