bluuebunny/crossref_metadata_2025_split huggingface dataset:
FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval
Authors: Qi Junhai , Feng Chenjie , Shi Yulin , Yang Jianyi , Zhang Fa , Li Guojun , Han Renmin 
Published: January 2024

Abstract
The release of AlphaFold2 has sparked a rapid expansion in protein model databases. Efficient protein structure retrieval is crucial for the analysis of structure models, while measuring the similarity between structures is the key challenge in structural retrieval. Although existing structure alignment algorithms can address this challenge, they are often time-consuming. Currently, the state-of-the-art approach involves converting protein structures into three-dimensional (3D) Zernike descriptors and assessing similarity using Euclidean distance. However, the methods for computing 3D Zernike descriptors mainly rely on structural surfaces and are predominantly web-based, thus limiting their application in studying custom datasets. To overcome this limitation, we developed FP-Zernike, a user-friendly toolkit for computing different types of Zernike descriptors based on feature points. Users simply need to enter a single line of command to calculate the Zernike descriptors of all structures in customized datasets. FP-Zernike outperforms the leading method in terms of retrieval accuracy and binary classification accuracy across diverse benchmark datasets. In addition, we showed the application of FP-Zernike in the construction of the descriptor database and the protocol used for the Protein Data Bank (PDB) dataset to facilitate the local deployment of this tool for interested readers. Our demonstration contained 590,685 structures, and at this scale, our system required only 4–9 s to complete a retrieval. The experiments confirmed that it achieved the state-of-the-art accuracy level. FP-Zernike is an open-source toolkit, with the source code and related data accessible at https://ngdc.cncb.ac.cn/biocode/tools/BT007365/releases/0.1, as well as through a webserver at http://www.structbioinfo.cn/.
Promoting a healthy lifestyle: exploring the role of social media and fitness applications in the context of social media addiction risk
Authors: Liu Junfeng 
Published: January 2024

Abstract
The popularity of social networks turns them into a legal method for promoting a healthy lifestyle, which benefits not only people but also different countries’ governments. This research paper aimed to examine the Keep fitness app integrated into WeChat, Weibo and QQ as regards long-term improvements in health-related behaviors (physical activity, nutrition, health responsibility, spiritual growth, interpersonal relationships and stress management) and assess the associated risk of increased social media addiction. Students from Lishui University in China (N = 300) participated in this study, and they were formed into control and experimental groups. The Healthy Lifestyle Behavior Scale and Social Media Disorder Scale were used as psychometric instruments. The Keep app was found to improve respondents’ scores on the parameters of physical activity, nutrition and health responsibility (P = 0.00). However, the level of dependence on social media did not change in either the control or the experimental group during the year of research (P ≥ 0.05). It is concluded that fitness apps can be an effective tool to promote healthy lifestyles among young people in China and other countries. The feasibility of government investment in fitness apps to promote healthy lifestyles is substantiated.
‘A profound effect on how I see myself and the world around me’: what students found meaningful about taking an academic course intended to reduce campus sexual violence
Authors: Lederer Alyssa M , Liddell Jessica L , Johnson Katherine M , Sheffield Sydney 
Published: January 2024

Abstract
Sexual violence is common on US college campuses and can result in negative health and academic outcomes. Credit-bearing courses are a possible innovative intervention, but few have been studied, and little is known about enrolled students’ experiences. Our institution, located in the Southern United States, developed a semester-long class as a curricular intervention after our institutional climate survey results showed high rates of sexual violence among undergraduate students. Students enrolled in the course wrote a final reflection paper on what they found meaningful about the class (N = 62). Qualitative conventional content analysis was used to examine what students found most salient. Three overarching categories emerged: course content, course delivery and course impact, each with multiple themes. For course content, students wrote about 22 different topics from the class. For course delivery, students discussed the open forum to discuss sexuality, the importance of taking the course in their first year of college and the course structure. For course impact, students discussed gaining new knowledge, questioning prior assumptions, experiencing personal transformation and feeling empowered to act. Results indicated that students had a powerful class experience and that this kind of educational intervention has the potential to positively impact enrolled students.
The performance of the amplitude-based model for complex phase retrieval
Authors: Xia Yu , Xu Zhiqiang 
Published: January 2024

Abstract
This paper aims to study the performance of the amplitude-based model $\widehat{{\boldsymbol x}} \in \mathop{\mathrm{argmin}}\limits _{{\boldsymbol x}\in \mathbb{C}^{d}}\sum _{j=1}^{m}\left (|\langle{\boldsymbol a}_{j},{\boldsymbol x}\rangle |-b_{j}\right )^{2}$, where $b_{j}:=|\langle{\boldsymbol a}_{j},{\boldsymbol x}_{0}\rangle |+\eta _{j}$ and ${\boldsymbol x}_{0}\in \mathbb{C}^{d}$ is a target signal. The model is raised in phase retrieval as well as in absolute value rectification neural networks. Many efficient algorithms have been developed to solve it in the past decades. However, there are very few results available regarding the estimation performance in the complex case under noisy conditions. In this paper, we present a theoretical guarantee on the amplitude-based model for the noisy complex phase retrieval problem. Specifically, we show that $\min _{\theta \in [0,2\pi )}\|\widehat{{\boldsymbol x}}-\exp (\mathrm{i}\theta )\cdot{\boldsymbol x}_{0}\|_{2} \lesssim \frac{\|{\boldsymbol \eta }\|_{2}}{\sqrt{m}}$ holds with high probability provided the measurement vectors ${\boldsymbol a}_{j}\in \mathbb{C}^{d},$ $j=1,\ldots ,m,$ are i.i.d. complex sub-Gaussian random vectors and $m\gtrsim d$. Here ${\boldsymbol \eta }=(\eta _{1},\ldots ,\eta _{m})\in \mathbb{R}^{m}$ is the noise vector without any assumption on the distribution. Furthermore, we prove that the reconstruction error is sharp. For the case where the target signal ${\boldsymbol x}_{0}\in \mathbb{C}^{d}$ is sparse, we establish a similar result for the nonlinear constrained $\ell _{1}$ minimization model. To accomplish this, we leverage a strong version of restricted isometry property for an operator on the space of simultaneous low-rank and sparse matrices.
Extracellular symbiont colonizes insect during embryo development
Authors: González Porras Miguel Ángel , Pons Inès , García-Lozano Marleny , Jagdale Shounak , Emmerich Christiane , Weiss Benjamin , Salem Hassan 
Published: January 2024

Abstract
Insects typically acquire their beneficial microbes early in development. Endosymbionts housed intracellularly are commonly integrated during oogenesis or embryogenesis, whereas extracellular microbes are only known to be acquired after hatching by immature instars such as larvae or nymphs. Here, however, we report on an extracellular symbiont that colonizes its host during embryo development. Tortoise beetles (Chrysomelidae: Cassidinae) host their digestive bacterial symbiont Stammera extracellularly within foregut symbiotic organs and in ovary-associated glands to ensure its vertical transmission. We outline the initial stages of symbiont colonization and observe that although the foregut symbiotic organs develop 3 days prior to larval emergence, they remain empty until the final 24 h of embryo development. Infection by Stammera occurs during that timeframe and prior to hatching. By experimentally manipulating symbiont availability to embryos in the egg, we describe a 12-h developmental window governing colonization by Stammera. Symbiotic organs form normally in aposymbiotic larvae, demonstrating that these Stammera-bearing structures develop autonomously. In adults, the foregut symbiotic organs are already colonized following metamorphosis and host a stable Stammera population to facilitate folivory. The ovary-associated glands, however, initially lack Stammera. Symbiont abundance subsequently increases within these transmission organs, thereby ensuring sufficient titers at the onset of oviposition ~29 days following metamorphosis. Collectively, our findings reveal that Stammera colonization precedes larval emergence, where its proliferation is eventually decoupled in adult beetles to match the nutritional and reproductive requirements of its host.
A messaging standard for environmental inspections: is it time?
Authors: Mitchell Clifford S , Callahan Tim , Flynn Eamon 
Published: January 2024

Abstract
Environmental health (EH) services in the United States lag behind other areas of public health and health care with respect to information system interoperability and data sharing. This is partly due to an absence of well-defined use cases, the lack of direct economic drivers and resources to improve, the multiple jurisdictional elements that govern EH services across the United States, and no central organization to drive modernization of EH data. We summarize the status of EH information systems; argue for greater interoperability, including use cases for a messaging standard for environmental inspections; and present recommendations to better align EH services and data modernization efforts currently underway in other areas of public health.
Incorporation of emergent symptoms and genetic covariates improves prediction of aromatase inhibitor therapy discontinuation
Authors: Rattsev Ilia , Stearns Vered , Blackford Amanda L , Hertz Daniel L , Smith Karen L , Rae James M , Taylor Casey Overby 
Published: January 2024

Abstract

Objectives
Early discontinuation is common among breast cancer patients taking aromatase inhibitors (AIs). Although several predictors have been identified, it is unclear how to simultaneously consider multiple risk factors for an individual. We sought to develop a tool for prediction of AI discontinuation and to explore how predictive value of risk factors changes with time.

Materials and Methods
Survival machine learning was used to predict time-to-discontinuation of AIs in 181 women who enrolled in a prospective cohort. Models were evaluated via time-dependent area under the curve (AUC), c-index, and integrated Brier score. Feature importance was analysis was conducted via Shapley Additive Explanations (SHAP) and time-dependence of their predictive value was analyzed by time-dependent AUC. Personalized survival curves were constructed for risk communication.

Results
The best-performing model incorporated genetic risk factors and changes in patient-reported outcomes, achieving mean time-dependent AUC of 0.66, and AUC of 0.72 and 0.67 at 6- and 12-month cutoffs, respectively. The most significant features included variants in ESR1 and emergent symptoms. Predictive value of genetic risk factors was highest in the first year of treatment. Decrease in physical function was the strongest independent predictor at follow-up.

Discussion and Conclusion
Incorporation of genomic and 3-month follow-up data improved the ability of the models to identify the individuals at risk of AI discontinuation. Genetic risk factors were particularly important for predicting early discontinuers. This study provides insight into the complex nature of AI discontinuation and highlights the importance of incorporating genetic risk factors and emergent symptoms into prediction models.
Procedural autonomy of national courts acting as EU trade mark courts—how far can the effectiveness of unitary character of EUTMs be ensured?
Authors: Sztoldman Agnieszka 
Published: January 2024

Abstract
The Court of Justice of the European Union has recently rendered preliminary rulings in two separate European Union trade mark (EUTM) infringement cases, Gemeinde Bodmann-Ludwigshafen (C-256/21) and LM v KP (C-654/21), confirming that a counterclaim for invalidity in an EUTM infringement proceedings is independent in scope and the outcome from the infringement action, reflecting the principle of procedural autonomy of national courts acting as EUTM courts.
Reflecting on the rule of law contestations narratives in the world trading system
Authors: Yenkong Ngangjoh Hodu 
Published: January 2024

Abstract
Contestations have emerged over the nearly three decades of the World Trade Organization (WTO) regarding the narratives on the rule of law (ROL) as a central tenet of the Multilateral Trading System. One of such contestation is whether the idea of ROL was ever internalized in the WTO at its formation or has been exaggerated. This article critically explores this narrative and locates it in the context of the events of the past two decades in the WTO. It challenges the notion of ROL in the world trading system. It argues that although significant progress was made in mainstreaming ROL in the Uruguay Round project, it would be an exaggeration to claim that ROL was embedded in the trading system from its inception. The article concludes that sceptics of the ROL project in the WTO have arguably been vindicated by how things have unfolded in the past two decades.
The Fann, a Genre of Oral Poetry in Antiochian Arabic: Remarks on Form and Performance Practice
Authors: Ağbaht Mahmut , Greve Martin 
Published: January 2024

Abstract
The fann is a genre of oral poetry in the vernacular Arabic of the Alawi community in the Antioch/Hatay province of Turkey. Until recently, it has hardly been mentioned in academic literature. Poetic form and rhythm structure are largely fixed in this genre and it is almost always performed in a similar way; when it comes to the quality of the voice, including a more or less clear melodic shape, there is more left up to the performer. During performances, the rhythmical element dominates the essence of melodic aspects. A preliminary comparison with related genres in the region demonstrates that both the form and performance practice of fann resemble genres in neighbouring Arab countries. Comparison also finds that there is hardly any connection with any Turkish and Kurdish singer-poem tradition as practised in nearby regions. Only recent changes indicate influences from contemporary Turkish music.
Exploring f(T) gravity via strongly lensed fast radio bursts
Authors: Jiang Xinyue , Ren Xin , Li Zhao , Cai Yi-Fu , Er Xinzhong 
Published: January 2024

ABSTRACT
This study aims to investigate the strong gravitational lensing effects in f(T) gravity. We present the theoretical analytic expressions for the lensing effects in f(T) gravity, including deflection angle, magnification, and time delay. On this basis, we also take the plasma lensing effect into consideration. We compare the lensing effects between the General Relativity in a vacuum environment and the f(T) gravity in a plasma environment. From a strongly lensed fast radio burst, the results indicate that in a plasma environment, General Relativity and f(T) gravity can generate indistinguishable image positions, but the magnification and time delay on these positions are significantly different, which can be distinguished by current facilities in principle. Therefore, the discrepancies between observational results and theoretical expectations can serve as clues for a modified gravity theory and provide constraints on f(T) gravity.
Semisynthesis of homogeneous spike RBD glycoforms from SARS-CoV-2 for profiling the correlations between glycan composition and function
Authors: Ye Farong , Li Cheng , Liu Feng-Liang , Liu Xinliang , Xu Peng , Luo Rong-Hua , Song Wenping , Zheng Yong-Tang , Ying Tianlei , Yu Biao , Wang Ping 
Published: January 2024

ABSTRACT
Vaccines have been the primary remedy in the global fight against coronavirus disease 2019 (COVID-19). The receptor-binding domain (RBD) of the spike protein, a critical viral immunogen, is affected by the heterogeneity of its glycan structures and relatively low immunogenicity. Here, we describe a scalable synthetic platform that enables the precise synthesis of homogeneously glycosylated RBD, facilitating the elucidation of carbohydrate structure–function relationships. Five homogeneously glycosylated RBDs bearing biantennary glycans were prepared, three of which were conjugated to T-helper epitope (Tpep) from tetanus toxoid to improve their weak immune response. Relative to natural HEK293-derived RBD, synthetic RBDs with biantennary N-glycan elicited a higher level of neutralising antibodies against SARS-CoV-2 in mice. Furthermore, RBDs containing Tpep elicited significant immune responses in transgenic mice expressing human angiotensin-converting enzyme 2. Our collective data suggest that trimming the N-glycans and Tpep conjugation of RBD could potentially serve as an effective strategy for developing subunit vaccines providing efficient protection.
Paradoxical effects of ZIM3, a CRISPRi effector, on human induced pluripotent stem-cell-derived cardiomyocyte electrophysiology
Authors: Han Julie L , Heinson Yuli W , Pozo Maria R , Li Weizhen , Entcheva Emilia 
Published: January 2024

Abstract
We show that zinc finger imprinted 3 (Zim3), when used as Zim3-KRAB-dCas9 effector in interference CRISPR, without any guide RNAs, paradoxically up-regulates key cardiac ion channel genes in human-induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CMs), responsible for healthy resting membrane potential, repolarization of the action potential, and electrical transmission of signals. These were found to yield expected functional enhancements consistent with a more mature iPSC-CM phenotype, with potentially desirable properties.
The rising authority and agency of public–private partnerships in global health governance
Authors: de Bengy Puyvallée Antoine 
Published: January 2024

Abstract
Global public–private partnerships (PPPs) have become prominent in efforts to address global challenges, particularly in the health field. In the scholarly literature, global PPPs have been conceptualized as arenas for voluntary public–private cooperation rather than agents of global governance. This paper challenges this approach, arguing that a sub-class of highly institutionalized partnerships have developed into transnational bureaucracies that, much like international organizations, can draw from their administrative capacities to exercise agency and gain and consolidate authority over time. To substantiate this argument, I present an in-depth analysis of five global health partnerships that played a leading role in the Access to Covid-19 Tools Accelerator (ACT-A), the initiative that sought to coordinate the global response to covid-19. Based on extensive document review and analysis of the ACT-A PPPs —Gavi, the Vaccine Alliance, The Global Fund to Fight AIDS, Tuberculosis and Malaria, The Coalition for Epidemic Preparedness Innovation, Unitaid, and The Foundation for Innovative New Diagnostics — I show how these partnerships’ leadership role during the pandemic emerged from a decade long build-up of PPP agency. These organizations gained administrative capacities that enabled them to increase their authority vis-à-vis their donors, boards, and other external actors through three interlinked strategies: (a) developing greater financial autonomy; (b) expanding their mandates (including toward pandemic preparedness and response); and (c) establishing inter-partnership cooperation and mutual representation to other forums. My analysis suggests the need for future research to consider highly institutionalized PPPs as agents of global governance and to explore empirically and theoretically the consequences of their rising authority.
My first dance
Authors: Franklin Gustavo L 
Published: January 2024

Abstract
Many emotions are generated within a medical consultation. These feelings are often shared among the doctor, patient, and family. In this piece, these emotions are explored as I describe them deeply during my first encounter with a Huntington’s disease patient, bringing the challenges of the situation, mistakes, and the learning that emerged. Understanding the possible sentiments and how to balance these emotions may be essential to prepare the neurologist in training for the challenges inherent in treating a patient with a rare disease.
Abnormal Oculomotor Corollary Discharge Signaling as a Trans-diagnostic Mechanism of Psychosis
Authors: Yao Beier , Rolfs Martin , Slate Rachael , Roberts Dominic , Fattal Jessica , Achtyes Eric D , Tso Ivy F , Diwadkar Vaibhav A , Kashy Deborah , Bao Jacqueline , Thakkar Katharine N 
Published: January 2024

Abstract

Background and Hypothesis
Corollary discharge (CD) signals are “copies” of motor signals sent to sensory areas to predict the corresponding input. They are a posited mechanism enabling one to distinguish actions generated by oneself vs external forces. Consequently, altered CD is a hypothesized mechanism for agency disturbances in psychosis. Previous studies have shown a decreased influence of CD signals on visual perception in individuals with schizophrenia—particularly in those with more severe positive symptoms. We therefore hypothesized that altered CD may be a trans-diagnostic mechanism of psychosis.

Study Design
We examined oculomotor CD (using the blanking task) in 49 participants with schizophrenia or schizoaffective disorder (SZ), 36 bipolar participants with psychosis (BPP), and 40 healthy controls (HC). Participants made a saccade to a visual target. Upon saccade initiation, the target disappeared and reappeared at a horizontally displaced position. Participants indicated the direction of displacement. With intact CD, participants can make accurate perceptual judgements. Otherwise, participants may use saccade landing site as a proxy of pre-saccadic target to inform perception. Thus, multi-level modeling was used to examine the influence of target displacement and saccade landing site on displacement judgements.

Study Results
SZ and BPP were equally less sensitive to target displacement than HC. Moreover, regardless of diagnosis, SZ and BPP with more severe positive symptoms were more likely to rely on saccade landing site.

Conclusions
These results suggest that altered CD may be a trans-diagnostic mechanism of psychosis.