bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chern Numbers of Terminal Threefolds
Authors: Cascini Paolo , Chen Hsin-Ku 
Published: November 2024

Abstract
Let $X$ be a smooth complex projective threefold. We show that if $X_{i}\dashrightarrow X_{i+1}$ is a flip which appears in the $K_{X}$-MMP, then $c_{1}(X_{i})^{3}-c_{1}(X_{i+1})^{3}$ is bounded by a constant depending only on $b_{2}(X)$.
Network dynamics investigation of omics-data-driven circadian-hypoxia crosstalk logical model in gallbladder cancer reveals key therapeutic target combinations
Authors: Singh Aakansha , Dwivedi Anjana 
Published: November 2024

Abstract
Recent findings in cancer research have pointed towards the bidirectional interaction between circadian and hypoxia pathways. However, little is known about their crosstalk mechanism. In this work, we aimed to investigate this crosstalk at a network level utilizing the omics information of gallbladder cancer. Differential gene expression and pathway enrichment analysis were used for selecting the crucial genes from both the pathways, followed by the construction of a logical crosstalk model using GINsim. Functional circuit identification and node perturbations were then performed. Significant node combinations were used to investigate the temporal behavior of the network through MaBoSS. Lastly, the model was validated using published in vitro experimentations. Four new positive circuits and a new axis viz. BMAL1/ HIF1αβ/ NANOG, responsible for stemness were identified. Through triple node perturbations viz.a. BMAL:CLOCK (KO or E1) + P53 (E1) + HIF1α (KO); b. P53 (E1) + HIF1α (KO) + MYC (E1); and c. HIF1α (KO) + MYC (E1) + EGFR (KO), the model was able to inhibit cancer growth and maintain a homeostatic condition. This work provides an architecture for drug simulation analysis to entrainment circadian rhythm and in vitro experiments for chronotherapy-related studies.
Insight Box. Circadian rhythm and hypoxia are the key dysregulated processes which fuels-up the cancer growth. In the present work we have developed a gallbladder cancer (GBC) specific Boolean model, utilizing the RNASeq data from GBC dataset and tissue specific interactions. This work adequately models the bidirectional nature of interactions previously illustrated in experimental papers showing the effect of hypoxia on dysregulation of circadian rhythm and the influence of this disruption on progression towards metastasis. Through the dynamical study of the model and its response to different perturbations, we report novel triple node combinations that can be targeted to efficiently reduce GBC growth. This network can be used as a generalized framework to investigate different crosstalk pathways linked with cancer progression.
Lived experience and lessons learned from the support of two secondary eye care units to improve cataract surgery and refractive services in two regions of Ethiopia: health system-strengthening support
Authors: Alemu Tsegaye , Seyum Dawit , Tesfaye Samson , Sisay Alemayehu , Wardle Andrew , Sorato Mende Mensa 
Published: November 2024

Abstract

Background
Blindness and poor eyesight are significant public health issues globally and specifically in Ethiopia. In Ethiopia, there is limited access to cataract surgery and refractive error treatment centers. Therefore, this study aimed to evaluate the role of health system support in improving access to eye care services, particularly cataract surgery and refractive error treatment services in two secondary eye care units (SECUs).

Methods
A parallel mixed-lived experience study was conducted in two SECUs. A desk review of relevant project documents and health facility activity reports was performed for quantitative data. The study was conducted from 12 December 2022 to 30 January 2023. A total of 21 in-depth interview participants were included.

Results
Overall, 14 106 cataract surgeries were performed during the pilot project implementation period. Assela Teaching and Referral Hospital Eye Care Unit performed cataract surgery 20–30 times per week. Similarly, Debre Tabor Comprehensive Hospital performed cataract surgery 18–24 times per week. The refractive service of the two SECUs was planned to range from 15–30 to 60 per week, and the refractive services were increased from 50–60 per week in both eye care units.

Conclusions
This project has significantly helped the existing health system achieve the 2030 global target and has improved access to eye care services in selected SECUs. The use of cataract surgery and refractive error performance markedly increased from 0 to 100%.
Innovative perspectives on bacteriocins: advances in classification, synthesis, mode of action, and food industry applications
Authors: Bahrami Sara , Andishmand Hashem , Pilevar Zahra , Hashempour-baltork Fataneh , Torbati Mohammadali , Dadgarnejad Manouchehr , Rastegar Hossein , Mohammadi Seyed Ali , Azadmard-Damirchi Sodeif 
Published: November 2024

Abstract
Bacteriocins, natural antimicrobial peptides produced by bacteria, present eco-friendly, non-toxic, and cost-effective alternatives to traditional chemical antimicrobial agents in the food industry. This review provides a comprehensive update on the classification of bacteriocins in food preservation. It highlights the significant industrial potential of pediocin-like and two-peptide bacteriocins, emphasizing chemical synthesis methods like Fmoc-SPPS to meet the demand for bioactive bacteriocins. The review details the mode of action, focusing on mechanisms such as transmembrane potential disruption and pH-dependent effects. Furthermore, it addresses the limitations of bacteriocins in food preservation and explores the potential of nanotechnology-based encapsulation to enhance their antimicrobial efficacy. The benefits of nanoencapsulation, including improved stability, extended antimicrobial spectrum, and enhanced functionality, are underscored. This understanding is crucial for advancing the application of bacteriocins to ensure food safety and quality.
Applying a computer model to evaluate the evolution of resistance by western corn rootworm to multiple Bt traits in transgenic maize
Authors: McCulloch John B , Gassmann Aaron J 
Published: November 2024

Abstract
Western corn rootworm, Diabrotica virgifera virgifera (LeConte) (Coleoptera: Chrysomelidae), is a major pest of maize in the United States. Transgenic maize producing insecticidal toxins from the bacterium Bacillus thuringiensis (Bt) have been used to manage this pest since 2003. Refuges of non-Bt maize have been used to delay resistance to Bt maize by western corn rootworm, and are planted in conjunction with maize producing single or multiple (i.e., pyramids) Bt toxins. Two Bt toxins, Cry3Bb1 and Gpp34/Tpp35Ab1, were used individually before being combined as a pyramid, at which point resistance had already evolved to Cry3Bb1. Pyramids targeting western corn rootworm therefore contained at least one toxin to which resistance had evolved. Western corn rootworm has now evolved resistance to all four commercially available Bt toxins used for rootworm management. We used laboratory and field-generated data to parameterize a deterministic model to simulate the effectiveness of refuges and Bt pyramids to delay resistance to Bt maize in western corn rootworm. Resistance to the pyramid of Cry3Bb1 with Gpp34/Tpp35Ab1 evolved more rapidly when resistance to Cry3Bb1 was already present. This effect arose when model conditions affecting initial resistance allele frequency, inheritance of resistance, and fitness costs were varied. Generally, resistance evolved faster when initial resistance allele frequencies were higher, inheritance of resistance was nonrecessive, and fitness costs were absent, which is consistent with previous models that simulated resistance evolution. We conclude that new transgenic pyramids should pair novel, independently acting toxins with abundant refuges to minimize the risk of rapid resistance evolution.
The role of external-beam radiotherapy for differentiated thyroid cancer
Authors: Kawamoto Terufumi , Shikama Naoto , Nakamura Naoki , Mizowaki Takashi 
Published: November 2024

Abstract
The treatment options for differentiated thyroid cancer (DTC) are surgery, thyroid stimulating hormone suppression, radioactive iodine, and multitargeted tyrosine kinase inhibitors. The role of external-beam radiotherapy (EBRT) for DTC is controversial because of the lack of randomized controlled trials, but prospective single-arm studies and propensity score matching analyses have shown its efficacy and safety. This review discusses the role of EBRT after resection of gross disease, when there is a high risk of locoregional failure, as well as its role for locoregionally gross recurrent and unresectable disease. As in other tumor sites, EBRT has an important role in the palliative management and local control of patients with metastatic DTC, especially with bone and brain metastases.
Deliberation in online political talk: exploring interactivity, diversity, rationality, and incivility in the public spheres surrounding news vs. satire
Authors: Boukes Mark 
Published: November 2024

Abstract
Political satire is often believed to enrich the public sphere in ways distinct from traditional journalism. This study examines whether deliberative qualities of online political talk in response to satire differ from those in response to regular news or partisan news. The analysis focuses on four normative standards: interactivity, diversity, rationality, and civility. A manual content analysis of YouTube comments (n = 2,447) reveals that the public sphere surrounding political satire shows a notable strength: Less incivility, both in terms of impoliteness and intolerance. Surprisingly, aside from this, satire’s public sphere did not differ much from that of regular news. Comments on partisan news were more opinionated and ideologically diverse. These findings suggest that online political talk prompted by satire is not inferior to that of traditional news. Additionally, this study highlights how the presence of different normative standards is often interconnected.
On the ubiquity of extreme baryon concentrations in the early Universe
Authors: Renzini Alvio 
Published: November 2024

ABSTRACT
Early JWST observations have revealed the ubiquitous presence in the early Universe, up to $z\sim \! 16$, of extreme baryon concentrations, namely forming globular clusters, extremely dense galaxies that may or may not be UV bright, and supermassive black holes in relatively low-mass galaxies. This paper is trying to pinpoint which physical conditions may have favoured the formation of such concentrations, that appear to be very common at high redshifts while their formation being progressively more and more rare at lower redshifts. Building on local globular cluster evidence, it is argued that such conditions can consist in a combination of a ${\sim} \! 10$ Myr extended feedback free time, coupled to low angular-momentum densities in deep local minima of the ISM vorticity field, where baryon concentrations are more likely to form. It is argued that the former condition would follow from more massive stars failing to explode as supernovae, and the latter one from low vorticity prevailing in the early Universe, in contrast to later times with their secular increase of the angular momentum density due to the cumulative effect of tidal interactions.
Integrating Contact Tracing Data to Enhance Outbreak Phylodynamic Inference: A Deep Learning Approach
Authors: Xie Ruopeng , Adam Dillon C , Hu Shu , Cowling Benjamin J , Gascuel Olivier , Zhukova Anna , Dhanasekaran Vijaykrishna 
Published: November 2024

Abstract
Phylodynamics is central to understanding infectious disease dynamics through the integration of genomic and epidemiological data. Despite advancements, including the application of deep learning to overcome computational limitations, significant challenges persist due to data inadequacies and statistical unidentifiability of key parameters. These issues are particularly pronounced in poorly resolved phylogenies, commonly observed in outbreaks such as SARS-CoV-2. In this study, we conducted a thorough evaluation of PhyloDeep, a deep learning inference tool for phylodynamics, assessing its performance on poorly resolved phylogenies. Our findings reveal the limited predictive accuracy of PhyloDeep (and other state-of-the-art approaches) in these scenarios. However, models trained on poorly resolved, realistically simulated trees demonstrate improved predictive power, despite not being infallible, especially in scenarios with superspreading dynamics, whose parameters are challenging to capture accurately. Notably, we observe markedly improved performance through the integration of minimal contact tracing data, which refines poorly resolved trees. Applying this approach to a sample of SARS-CoV-2 sequences partially matched to contact tracing from Hong Kong yields informative estimates of superspreading potential, extending beyond the scope of contact tracing data alone. Our findings demonstrate the potential for enhancing phylodynamic analysis through complementary data integration, ultimately increasing the precision of epidemiological predictions crucial for public health decision-making and outbreak control.
Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections
Authors: McKinley Lauren N , Meyer McCauley O , Sebastian Aswathy , Chang Benjamin K , Messina Kyle J , Albert Istvan , Bevilacqua Philip C 
Published: November 2024

Abstract
Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally. To address this gap, we developed Cleavage High-Throughput Assay (CHiTA), a high-throughput pipeline utilizing massively parallel oligonucleotide synthesis and next-generation sequencing to test putative ribozymes en masse in a scarless fashion. As proof of principle, we applied CHiTA to a small set of known active and mutant ribozymes. We then used CHiTA to test two large sets of naturally occurring twister ribozymes: over 1600 previously reported putative twisters and ∼1000 new candidate twisters. The new candidates were identified computationally in ∼1000 organisms, representing a massive increase in the number of ribozyme-harboring organisms. Approximately 94% of the twisters we tested were active and cleaved site-specifically. Analysis of their structural features revealed that many substitutions and helical imperfections can be tolerated. We repeated our computational search with structural descriptors updated from this analysis, whereupon we identified and confirmed the first intrinsically active twister ribozyme in mammals. CHiTA broadly expands the number of active twister ribozymes found in nature and provides a powerful method for functional analyses of other RNAs.
EXPRESSO: a multi-omics database to explore multi-layered 3D genomic organization
Authors: Cai Liuyang , Qiao Jun , Zhou Ruixin , Wang Xinyi , Li Yelan , Jiang Lei , Zhou Qiangwei , Li Guoliang , Xu Tao , Feng Yuliang 
Published: November 2024

Abstract
The three-dimensional (3D) organization of the human genome plays a crucial role in gene regulation. EXPloration of Regulatory Epigenome with Spatial and Sequence Observations (EXPRESSO) is a novel multi-omics database for exploration and visualization of multi-layered 3D genomic features across 46 different human tissues. Integrating 1360 3D genomic datasets (Hi-C, HiChIP, ChIA-PET) and 842 1D genomic and transcriptomic datasets (ChIP-seq, ATAC-seq, RNA-seq) from the same biosample, EXPRESSO provides a comprehensive resource for studying the interplay between 3D genome architecture and transcription regulation. This database offers diverse 3D genomic feature types (compartments, contact matrix, contact domains, stripes as diagonal lines extending from a genomic locus in contact matrix, chromatin loops, etc.) and user-friendly interface for both data exploration and download. Other key features include REpresentational State Transfer application programming interfaces for programmatic access, advanced visualization tools for 3D genomic features and web-based applications that correlate 3D genomic features with gene expression and epigenomic modifications. By providing extensive datasets and tools, EXPRESSO aims to deepen our understanding of 3D genomic architecture and its implications for human health and disease, serving as a vital resource for the research community. EXPRESSO is freely available at https://expresso.sustech.edu.cn.
Oxygen sensing in the kidney
Authors: Geis Lisa , Kurtz Armin 
Published: November 2024

ABSTRACT
The kidneys fulfil several essential homeostatic functions for the body. One of them is the maintenance of sufficient oxygen supply to the organs. For this purpose, the kidneys control the formation of red blood cells by the production of the hormone erythropoietin. This control of red cell formation is not only relevant to prevent states of oxygen deficiency but also to prevent an unwanted increase of red cell numbers causing thromboembolic risks. The adequate production of erythropoietin requires a sensing of the arterial oxygen content and transduction to hormone production. This oxygen sensing is a two-step process which includes a translation of the arterial oxygen content to respective oxygen tension in the tubulointerstitium and a perception of the resulting local interstitial oxygen tension to translate them into specific cellular responses such as the production of erythropoietin. This contribution will describe these steps of oxygen sensing for the healthy kidney and for the changes occurring during states of chronic renal disease, which are commonly associated with anemia. In this context a special focus will also be set on intrarenal hypoxia and oxygen sensing in the diabetic kidney including the treatment with tubular glucose transport (sodium-glucose cotransporter 2) inhibitors which might influence the oxygen sensing in the kidney. Finally, we will consider the effects of prolyl-hydroxylase inhibitors (HIF-PHIs), which fundamentally interfere with the cellular oxygen sensing and which are meanwhile treatment options in renal anemia.
Monitoring C–C coupling in catalytic reactions via machine-learned infrared spectroscopy
Authors: Yang Li , Zhao Zhicheng , Yang Tongtong , Zhou Donglai , Yue Xiaoyu , Li Xiyu , Huang Yan , Wang Xijun , Zheng Ruyun , Heine Thomas , Sun Changyin , Jiang Jun , Ye Sheng 
Published: November 2024

ABSTRACT
Tracking atomic structural evolution along chemical transformation pathways is essential for optimizing chemical transitions and enhancing control. However, molecule-level knowledge of structural rearrangements during chemical processes remains a great challenge. Here, we couple infrared spectroscopy as a non-invasive method to probe molecular transformations, with a machine-learned protocol to immediately map the spectroscopic fingerprints to atomistic structures. From the theoretical perspective, we demonstrate it here with the example of C–C coupling in catalytic reactions, elucidating various structural conformations along dynamic trajectories. Within the transferable application to the specific CO–CO dimerization reaction, the structural and energetic variations of the critical chemical species could be identified via infrared spectroscopy. This approach extends the power of spectroscopy from fingerprinting chemical configurations to using them for assigning dynamic structural information.
Taleqani’s Last Sermon
Authors: Taleqani Mahmud 
Published: November 2024

Abstract
Ayatollah Mahmud Taleqani (Iran, 191 1-1979) established a reputation as a reformist within the Shi’i Muslim religious establishment in the early I 960s when he helped to lead (along with Mehdi Bazargan, whose work is also included in this volume) a religious movement aimed at revitalizing both Islamic theory and Iranian politics.’ Arrested and jailed repeatedly by the monarchy for his political opposition, Taleqani was released for the last time in the fall of 1978 and immediately became one of the most respected leaders of the Iranian Revolution. Upon the shah’s fall in early 1979, Taleqani began to chart a course somewhat independent of the official policies of Imam Ruhollah Khomeini, particularly in his defense of Islamic leftists and local elections. The final sermon before his death in September 1979, excerpted here, is famous among Iranian oppositionists for its sharp criticism of religious oppression. The sermon’s reference to Sanandaj (capital of the Kurdish region of northwest Iran) concerns Taleqani’s attempted mediation between Kurds who sought autonomy through local councils-a political structure that Taleqani preferred-and the central government in Tehran, already organizing itself in an authoritarian direction. Taleqani’s mediation failed and the councils were crushed militarily.3 Brief portions of this sermon have been translated in more colorful language by Suroosh lrfani.
Humanity and Islam
Authors: Shari’ati ‘Ali 
Published: November 2024

Abstract
‘Ali Shari’ati (Iran, 1933-1977) may be one of the most popular figures in Iran today. During the Iranian Revolution of 1979, his photograph and his writings appeared through out the country, and the subsequent cold shoulder he received from the clerical leaders of the Islamic Republic of Iran may have served to improve his reputation. Shari’ati was born and raised in northeastern Iran, the son of a religious scholar but educated in secular schools, including the Sorbonne, where he received his doctorate. Upon his return to Iran, Shari’ati launched a career as a lecturer-first at the University of Mashhad, then at the Hosseiniyeh Ershad in Tehran, a religious educational institution, where he built a large following, especially among university students, for his critique of oppressive political and religious establishments. After being tolerated by the Pahlavi regime for several years, he was imprisoned in 1973, and the Hosseiniyeh was shut down. Soon after his release from prison, he died in London. The following lecture from around 1969 defends the concept of free will in lslam. ever since the end of the 19th century, scientists, writers, and thinkers have each evaluated humankind in various ways. Yes, humankind’s position today is shakier than any other period in history.
Extremism
Authors: Al-Qaradawi Yusuf 
Published: November 2024

Abstract
Yusuf Al-Qaradawi (Egypt-Qatar, born 1926), dean of the law school at the University of Qatar, wrote the following essay in 1981 as an attempt to undermine rising Islamic extremism, especially in his home country of Egypt. In particular, AI-Qaradawi’s work is an extended critique of a small radical organization, the Society of Excoriation and Exodus, which kidnapped and killed an Egyptian religious official in 1977. Al-Qaradawi argues that, while extremist religious practices are allowed in Islam, they may not be forced on others.
OSCE Court of Conciliation and Arbitration (CCA)
Authors: Kwiecień Roman 
Published: November 2024

Abstract
This comment presents the activity of the Court of Conciliation and Arbitration within OSCE (CCA) from 1 January 2022 to 31 July 2023. The thirtieth anniversary of the adoption of the Stockholm Convention on Conciliation and Arbitration within OSCE of 1992 provides an opportunity for a realistic review and assessment existing options for the peaceful settlement of disputes offered by the CCA. As thirty years after the conclusion of the Stockholm Convention not one case has been brought before the CCA, in 2022 and until mid-2023 the actions of the CCA were not related to its principal statutory function, i.e., the peaceful settlement of disputes between states. Instead, the CCA’s Bureau took steps to make the Court itself and the procedures it offers more familiar and more attractive to the OSCE participating states. In particular, the Bureau reminded of the Court’s potential role to implement two procedures—conciliation commissions and arbitration tribunals—in a flexible and confidential manner.