bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water position sampling on protein structures based on a 3D distribution function using a weighted Monte Carlo method
Authors: Kobayashi Shinpei , Kiyota Yasuomi , Takeda-Shitaka Mayuko 
Published: June 2024

Abstract
To gain a detailed understanding of protein structure, function, and interaction, water molecules around proteins are important. Therefore, computational methods for predicting water positions are required. When a hydration water distribution such as a 3D distribution function is available, methods to predict water positions explicitly from the water distribution are useful. In this paper, we introduce DroPred, a method for predicting water positions based on a 3D distribution function of water oxygen atoms using a weighted Monte Carlo method. The probability density derived from the 3D distribution function is used as weight in the weighted Monte Carlo method. DroPred generates multiple samples from a single 3D distribution function. We evaluated the performance of DroPred by predicting water positions at protein–protein interface structures. By adjusting the weight using an exponential parameter, prediction performance of DroPred in water position sampling was improved. This method will be helpful for understanding protein structure, function, and interaction.
Study on factors affecting quantum yield for the design of improved ortho-nitrobenzyl photoremovable protecting groups
Authors: Nguyen Linh Tran Bao , Abe Manabu 
Published: June 2024

Abstract
The use of photoremovable protecting groups (PPGs) for the protection and deprotection of biologically active substances has become instrumental in elucidating functional mechanisms in cells. However, the development of chromophores responsive to visible and near-infrared (NIR) light often results in reduced quantum yields (Φu) of uncaging reactions. Because a high quantum yield is essential for practical PPGs, it is imperative to understand the factors influencing it and devise strategies to enhance it. In this study, we systematically investigated nitrobiphenyl scaffolds featuring amino substituents as electron donors, potentially serving as visible and NIR excitable chromophores. Among the synthesized structures, PPGs incorporating carbazole and phenothiazine units as amino substituents exhibited the highest Φu values of 0.2 and 0.1, respectively, rendering them promising candidates for physiological studies. Conversely, diphenylamine substituents yielded considerably lower Φu values. Photophysical properties and quantum chemical calculations provided insights into the nature of the lowest excited states and their impact on Φu, highlighting the significance of achieving the balance between local n–π* excitation and charge-transfer excitation for manipulating the uncaging quantum yield in ortho-nitrobenzyl derivatives.
Sulfur atom effect on the photochemical release of benzylamine from caged amines
Authors: Nguyen Hai Dang , Abe Manabu 
Published: June 2024

Abstract
Carbamate linkers are commonly used to attach photolabile protecting groups (PPGs) to amine functional groups. However, the release of amines from the carbamate linkage has low photochemical quantum yields because of the low leaving ability of the carbamic anion. In this study, we synthesized a new coumarin-based thiocarbamate-containing caged amine as a model to study the effect of sulfur on the photocleavage of the amine from the PPG. The release of the amine from the thiocarbamate (−SC(O)NHCH2Ph) linkage was ∼20 times faster than from the carbamate (−OC(O)NHCH2Ph) linkage.
Surface alterations and compound release from aligner attachments in vitro
Authors: Iliadi Anna , Zervou Sevasti-Kiriaki , Koletsi Despina , Schätzle Marc , Hiskia Anastasia , Eliades Theodore , Eliades George 
Published: June 2024

Abstract

Aim
The aim of the present study was to assess the alterations in morphology, roughness, and composition of the surfaces of a conventional and a flowable composite attachment engaged with aligners, and to evaluate the release of resin monomers and their derivatives in an aqueous environment.

Methods
Zirconia tooth-arch frames (n = 20) and corresponding thermoformed PET-G aligners with bonded attachments comprising two composite materials (universal—C and flowable—F) were fabricated. The morphological features (stereomicroscopy), roughness (optical profilometry), and surface composition (ATR-FTIR) of the attachments were examined before and after immersion in water. To simulate intraoral use, the aligners were removed and re-seated to the frames four times per day for a 7-day immersion period. After testing, the eluents were analyzed by LC-MS/MS targeting the compounds Bis-GMA, UDMA, 2-HEMA, TEGDMA and BPA and by LC-HRMS for suspect screening of the leached dental material compounds and their degradation products.

Results
After testing, abrasion-induced defects were found on attachment surfaces such as scratches, marginal cracks, loss of surface texturing, and fractures. The morphological changes and debonding rate were greater in F. Comparisons (before-after testing) revealed a significantly lower Sc roughness parameter in F. The surface composition of the aligners after testing showed minor changes from the control, with insignificant differences in the degree of C = C conversion, except for few cases with strong evidence of hydrolytic degradation. Targeted analysis results revealed a significant difference in the compounds released between Days 1 and 7 in both materials. Insignificant differences were found when C was compared with F in both timeframes. Several degradation products were detected on Day 7, with a strong reduction in the concentration of the targeted compounds.

Conclusions
The use of aligners affects the surface characteristics and degradation rate of composite attachments in an aqueous environment, releasing monomers, and monomer hydrolysates within 1-week simulated use.
Extracellular vesicles
Authors: Wang Juan , Barr Maureen M , Wehman Ann M 
Published: June 2024

Abstract
Extracellular vesicles (EVs) encompass a diverse array of membrane-bound organelles released outside cells in response to developmental and physiological cell needs. EVs play important roles in remodeling the shape and content of differentiating cells and can rescue damaged cells from toxic or dysfunctional content. EVs can send signals and transfer metabolites between tissues and organisms to regulate development, respond to stress or tissue damage, or alter mating behaviors. While many EV functions have been uncovered by characterizing ex vivo EVs isolated from body fluids and cultured cells, research using the nematode Caenorhabditis elegans has provided insights into the in vivo functions, biogenesis, and uptake pathways. The C. elegans EV field has also developed methods to analyze endogenous EVs within the organismal context of development and adult physiology in free-living, behaving animals. In this review, we summarize major themes that have emerged for C. elegans EVs and their relevance to human health and disease. We also highlight the diversity of biogenesis mechanisms, locations, and functions of worm EVs and discuss open questions and unexplored topics tenable in C. elegans, given the nematode model is ideal for light and electron microscopy, genetic screens, genome engineering, and high-throughput omics.
The chromatin-associated 53BP1 ortholog, HSR-9, regulates recombinational repair and X chromosome segregation in the Caenorhabditis elegans germ line
Authors: Li Qianyan , Hariri Sara , Calidas Aashna , Kaur Arshdeep , Huey Erica , Engebrecht JoAnne 
Published: June 2024

Abstract
53BP1 plays a crucial role in regulating DNA damage repair pathway choice and checkpoint signaling in somatic cells; however, its role in meiosis has remained enigmatic. In this study, we demonstrate that the Caenorhabditis elegans ortholog of 53BP1, HSR-9, associates with chromatin in both proliferating and meiotic germ cells. Notably, HSR-9 is enriched on the X chromosome pair in pachytene oogenic germ cells. HSR-9 is also present at kinetochores during both mitotic and meiotic divisions but does not appear to be essential for monitoring microtubule–kinetochore attachments or tension. Using cytological markers of different steps in recombinational repair, we found that HSR-9 influences the processing of a subset of meiotic double-stranded breaks into COSA-1-marked crossovers. Additionally, HSR-9 plays a role in meiotic X chromosome segregation under conditions where X chromosomes fail to pair, synapse, and recombine. Together, these results highlight that chromatin-associated HSR-9 has both conserved and unique functions in the regulation of meiotic chromosome behavior.
The (im)possibility of personal and industrial (machine-generated) data to be subject to property rights
Authors: Nekit Kateryna 
Published: June 2024

Abstract
Discussions surrounding the possibility of expanding the legal regime of ownership to data have been ongoing for several decades. Proponents of recognizing the right of ownership to data motivate their position by the needs of the data economy and the need to protect the interests of data subjects. However, specific properties of data cause contradictions with the concept of property rights. This paper examines data in a system of related categories, such as information and knowledge, aiming to determine their correlation and answer the question of whether personal and industrial (machine-generated) data can be objects of ownership. The category of digital data is analysed; its specific features, which make it possible to equate them with a type of property, are determined. The paper reveals correlation between concepts of digital ownership and data ownership and answers the question of why there is no room for personal and industrial data in the ownership paradigm.
Afghan Women Are Under Threat from the Taliban: A Great Test of the Turkish Government and the Courts
Authors: Kaya Hülya 
Published: June 2024

Abstract
This article examines how Türkiye evaluates the protection requirements of Afghan women fleeing from persecution in Afghanistan. It considers whether Türkiye grants refugee status to Afghan women as members of a ‘particular social group’ or on other Refugee Convention grounds. It analyses the jurisprudence of Türkiye’s Administrative Courts and Regional Administrative Courts concerning international protection claims lodged by Afghan women between August 2021 and June 2023 to determine whether Türkiye follows a gender-sensitive interpretation of the Refugee Convention and respects the principle of non-refoulement.
Sumset Estimates in Convex Geometry
Authors: Fradelizi Matthieu , Madiman Mokshay , Zvavitch Artem 
Published: June 2024

Abstract
Sumset estimates, which provide bounds on the cardinality of sumsets of finite sets in a group, form an essential part of the toolkit of additive combinatorics. In recent years, probabilistic or entropic forms of many of these inequalities were introduced. We study analogues of these sumset estimates in the context of convex geometry and the Lebesgue measure on ${\mathbb{R}}^{n}$. First, we observe that, with respect to Minkowski summation, volume is supermodular to arbitrary order on the space of convex bodies. Second, we explore sharp constants in the convex geometry analogues of variants of the Plünnecke-Ruzsa inequalities. In the last section of the paper, we provide connections of these inequalities to the classical Rogers-Shephard inequality.
Acceptance and forage utilization responses of steers consuming low-quality forage and supplemented black soldier fly larvae as a novel feed
Authors: Tasci Kayra D , Wickersham Tryon A , Drewery Merritt L 
Published: June 2024

Abstract
As the insect-rearing industry scales in the United States and other developed nations, it has the potential to create multiple product streams (e.g., oil and protein-rich biomass) for existing markets. Black soldier fly larvae (BSFL; Hermetia illucens) has been identified as a potential livestock feed because it is not expected to compete in the human food sector and its production has a lesser environmental footprint than that of conventional feeds. Existing research on BSFL as feed focuses on full-fat BSFL for poultry and aquaculture. Therefore, the objective of our experiment was to evaluate the viability of defatted BSFL as an alternative protein source for beef cattle consuming forage. Procedures were approved by Texas State University IACUC (#7726). Two experiments were conducted using ruminally cannulated beef steers fed low-quality forage in 5 × 5 Latin squares. Experiment 1 assessed consumption of BSFL as a protein supplement and included five 5-d periods with 3-d for washout and 2-d for measurement of supplement intake and preference. There were five treatments delivered in addition to the basal forage: 100% soybean meal (SBM); 75% SBM/25% BSFL; 50% SBM/50% BSFL; 25% SBM/75% BSFL; and 100% BSFL. Supplement and forage intake did not differ between treatments (P ≥ 0.45) nor was there a treatment × day interaction (P ≥ 0.45). Experiment 2 evaluated the effect of BSFL supplementation on forage (5.3% crude protein) intake and digestion and included five 14-d periods with 8-d for treatment adaptation, 5-d for measurement of intake and digestion, and 1-d for determination of ruminal fermentation. There were four treatments of supplemental BSFL provided at graded N levels: 0, 50, 100, or 150 mg N/kg BW and one level of SBM at 100 mg N/kg BW. Increasing provision of BSFL linearly increased forage organic matter (OM) intake (P = 0.04), total OM intake (P &lt; 0.01), total digestible OM intake (P &lt; 0.01), dry matter digestibility (P = 0.01), and OM digestibility (P = 0.02). There were no significant differences (P ≥ 0.17) in intake or digestibility between levels of BSFL and SBM. Ultimately, defatted BSFL has potential to replace conventional feeds as a protein supplement without sacrificing forage utilization.
Changes in the trends of initial treatment for newly diagnosed prostate cancer in Japan: a nationwide multi-institutional study
Authors: Kawai Taketo , Onozawa Mizuki , Taguchi Satoru , Shiota Masaki , Sakamoto Shinichi , Yamamoto Yoshiyuki , Kitagawa Yasuhide , Nakagawa Tohru , Hinotsu Shiro , Kume Haruki ,   Japan Study Group of Prostate Cancer (J-CaP)
Published: June 2024

Abstract

Background
In previous large-scale studies conducted through 2010, androgen deprivation therapy (ADT) was the most common initial treatment for prostate cancer patients in Japan. However, recent advancements in treatment technologies have significantly affected the management of prostate cancer in Japan. This study analyzed the trends in initial treatments for prostate cancer based on two nationwide surveys.

Methods
Two Japan-wide multi-institutional surveys, J-CaP2010 and J-CaP2016, were conducted to enroll patients newly histologically diagnosed with prostate cancer in 2010 and 2016–18, respectively. Both surveys included age at diagnosis, initial PSA level, ISUP Grade Group, TNM classification, and initial treatment for prostate cancer.

Results
J-CaP2010 included data from 8192 patients across 140 institutions, whereas J-CaP2016 included data from 21 841 patients across 186 institutions. In J-CaP2016, the proportion of radical prostatectomy (RP) and radiation therapy (RT) in the initial treatment increased (from 32% to 36% and 21% to 26%, respectively), whereas the proportion of ADT decreased (from 40% to 29%) compared with those in J-CaP2010. The increase in RP or RT was noticeable in patients aged 75 years and older (from 20% to 38%) and those with high-risk localized cancer (from 58% to 74%) or locally advanced cancer (from 38% to 56%). The proportion of active surveillance or watchful waiting increased in patients with low-risk localized cancer (from 21% to 41%). The proportion of robot-assisted RP within all RPs and the proportion of intensity-modulated RT within all RTs increased remarkably (from 2.3% to 78% and 20% to 50%, respectively).

Conclusions
In Japan, RP and RT have increased as initial treatments for prostate cancer, whereas ADT has decreased. Consequently, RP has emerged as the most commonly selected initial treatment, replacing ADT.
Kennington Common, 10 April 1848: The Photographs, the Chartist Crowd, and the Coachman
Authors: Bensimon Fabrice 
Published: June 2024

ABSTRACT
The daguerreotypes of the Chartist meeting on Kennington Common in London on 10 April 1848, often considered as the first crowd photographs, are among the most reproduced photos of the Victorian era. But they have not yet yielded all their secrets. This article discusses the old question of the number of people attending the meeting. Re-examining the daguerreotypes in the light of other sources, it additionally addresses issues relating to the depiction of labour. It looks at what the daguerreotypes tell us about the relationship between the Chartist movement and London’s working class. It attempts to identify places and objects. Finally, it focuses on the place of individuals in the images of this anonymous, faceless, and voiceless crowd. It suggests the name and identity of a little-studied Chartist figure who may be seen on a photo, the coachman, carpenter and builder Henry Cullingham (1791–1873), and considers what we may derive from that.
Optimizing Contrast in Automated 4D STEM Cryotomography
Authors: Seifer Shahar , Kirchweger Peter , Edel Karlina Maria , Elbaum Michael 
Published: June 2024

Abstract
4D STEM is an emerging approach to electron microscopy. While it was developed principally for high-resolution studies in materials science, the possibility to collect the entire transmitted flux makes it attractive for cryomicroscopy in application to life science and radiation-sensitive materials where dose efficiency is of utmost importance. We present a workflow to acquire tomographic tilt series of 4D STEM data sets using a segmented diode and an ultrafast pixelated detector, demonstrating the methods using a specimen of a T4 bacteriophage. Full integration with the SerialEM platform conveniently provides all the tools for grid navigation and automation of the data collection. Scripts are provided to convert the raw data to mrc format files and further to generate a variety of modes representing both scattering and phase contrasts, including incoherent and annular bright field, integrated center of mass, and parallax decomposition of a simulated integrated differential phase contrast. Principal component analysis of virtual annular detectors proves particularly useful, and axial contrast is improved by 3D deconvolution with an optimized point spread function. Contrast optimization enables visualization of irregular features such as DNA strands and thin filaments of the phage tails, which would be lost upon averaging or imposition of an inappropriate symmetry.
Rewiring the Sex-Determination Pathway During the Evolution of Self-Fertility
Authors: Shen Yongquan , Lin Shin-Yi , Harbin Jonathan , Amin Richa , Vassalotti Allison , Romanowski Joseph , Schmidt Emily , Tierney Alexis , Ellis Ronald E 
Published: June 2024

Abstract
Although evolution is driven by changes in how regulatory pathways control development, we know little about the molecular details underlying these transitions. The TRA-2 domain that mediates contact with TRA-1 is conserved in Caenorhabditis. By comparing the interaction of these proteins in two species, we identified a striking change in how sexual development is controlled. Identical mutations in this domain promote oogenesis in Caenorhabditis elegans but promote spermatogenesis in Caenorhabditis briggsae. Furthermore, the effects of these mutations involve the male-promoting gene fem-3 in C. elegans but are independent of fem-3 in C. briggsae. Finally, reciprocal mutations in these genes show that C. briggsae TRA-2 binds TRA-1 to prevent expression of spermatogenesis regulators. By contrast, in C. elegans TRA-1 sequesters TRA-2 in the germ line, allowing FEM-3 to initiate spermatogenesis. Thus, we propose that the flow of information within the sex determination pathway has switched directions during evolution. This result has important implications for how evolutionary change can occur.
Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage
Authors: Wang Mengge , Huang Yuguo , Liu Kaijun , Wang Zhiyong , Zhang Menghan , Yuan Haibing , Duan Shuhan , Wei Lanhai , Yao Hongbing , Sun Qiuxia , Zhong Jie , Tang Renkuan , Chen Jing , Sun Yuntao , Li Xiangping , Su Haoran , Yang Qingxin , Hu Liping , Yun Libing , Yang Junbao , Nie Shengjie , Cai Yan , Yan Jiangwei , Zhou Kun , Wang Chuanchao ,   10K_CPGDP Consortium, He Guanglin , Liu Chao , Wang Mengge , Tang Renkuan , Yun Libing , Yang Junbao , Wang Chuan-Chao , Yan Jiangwei , Zhu Bofeng , Hu Liping , Nie Shengjie , Yao Hongbing , Zhu Bofeng , Liu Chao , He Guanglin 
Published: June 2024

Abstract
Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations.