bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proximity labeling reveals new insights into the relationships between meiotic recombination proteins inS. cerevisiae
Authors: Voelkel-Meiman Karen , Poppel Alex J. , Liddle Jennifer C. , Balsbaugh Jeremy L. , MacQueen Amy J. 
Published: September 2023

AbstractSeveral protein ensembles facilitate MutSγ crossover recombination and the associated process of synaptonemal complex (SC) assembly during meiosis, but the physical and functional relationships between the components involved remain obscure. We have employed proximity labeling as a phenotypic tool to discern functional relationships between meiotic recombination and SC proteins inS. cerevisiae, and to gain deeper insight into molecular deficits of crossover-defective mutants. We find that recombination initiation (Spo11) and the Mer3 helicase are dispensable for proximity labeling of the Zip3 E3 ligase by components of the ZZS ensemble (Zip2, Zip4 and Spo16) but are required for proximity labeling of Zip3 by Msh4, consistent with the possibility that MutSγ joins Zip3 only after a specific recombination intermediate has been generated. Proximity labeling analysis of crossover-defectivezip1mutants suggests a key shared defect is a failure to assemble an early recombination ensemble where ZZS can properly engage Zip3. We furthermore discovered that Zip3’s abundance within the meiotic cell is uniquely dependent on the presence of Zip1, and that the post-translational modification of Zip3 is promoted by most MutSγ pathway proteins but countered by Zip1. Based on this and additional data, we propose a model whereby Zip1 stabilizes a functional, unmodified form of Zip3 until intermediate steps in recombination are complete. We also find that SC structural protein Ecm11 is proximity labeled by ZZS complex proteins in a Zip4-dependent manner, but by Zip3 and Msh4, at least in part, via a distinct pathway. Finally, streptavidin pulldowns followed by mass spectrometry on eleven different proximity labeling strains uncovers shared proximity targets of MutSγ-associated proteins, some with known meiotic functions and others not yet implicated in a meiotic activity, highlighting the potential power of proximity labeling as a discovery tool.
Controlled experiment finds no detectable citation bump from Twitter promotion
Authors: Branch Trevor A. , Cȏté Isabelle M. , David Solomon R. , Drew Joshua A. , LaRue Michelle , Márquez Melissa C. , Parsons E. Chris M. , Rabaiotti D. , Shiffman David , Steen David A. , Wild Alexander L. 
Published: September 2023

AbstractMultiple studies across a variety of scientific disciplines have shown that the number of times that a paper is shared on Twitter (now called X) is correlated with the number of citations that paper receives. However, these studies were not designed to answer whether tweeting about scientific papers causes an increase in citations, or whether they were simply highlighting that some papers have higher relevance, importance or quality and are therefore both tweeted about more and cited more. The authors of this study are leading science communicators on Twitter from several life science disciplines, with substantially higher follower counts than the average scientist, making us uniquely placed to address this question. We conducted a three-year-long controlled experiment, randomly selecting five articles published in the same month and journal, and randomly tweeting one while retaining the others as controls. This process was repeated for 10 articles from each of 11 journals, recording Altmetric scores, number of tweets, and citation counts before and after tweeting. Randomization tests revealed that tweeted articles were downloaded 2.6–3.9 times more often than controls immediately after tweeting, and retained significantly higher Altmetric scores (+81%) and number of tweets (+105%) three years after tweeting. However, while some tweeted papers were cited more than their respective control papers published in the same journal and month, the overall increase in citation counts after three years (+7% for Web of Science and +12% for Google Scholar) was not statistically significant (p> 0.15). Therefore while discussing science on social media has many professional and societal benefits (and has been a lot of fun), increasing the citation rate of a scientist’s papers is likely not among them.
LRH-1/NR5A2 Activation Rewires Immunometabolism Blunting Inflammatory Immune Cell Progression in Individuals with Type 1 Diabetes and Enhances Human Islet Function in Mice
Authors: Cobo-Vuilleumier N , Rodríguez-Fernandez S , López-Noriega L , Lorenzo PI , Franco JM , Lachaud CC , Martin Vazquez E , Araujo Legido R , Dorronsoro A , López-Férnandez-Sobrino R , Fernádez-Santos B , Salas-Lloret D , van Overbeek N , Ramos-Rodriguez M , Mateo-Rodríguez C , Hidalgo L. , Nano R , Arroba AI , Campos Caro A , Vertegaal ACO , Martin Montalvo A , Martín F , Aguilar-Diosdado M , Piemonti L , Pasquali L , González Prieto R , García Sánchez MI , Martínez-Brocca MA , Vives-Pi M , Gauthier BR 
Published: September 2023

ABSTRACTThe intricate etiology of type 1 diabetes mellitus (T1D), marked by a detrimental cross-talk between the immune system and insulin-producing β-cells, has impeded effective disease-modifying therapies. The discovery that pharmacological activation of the nuclear receptor LRH-1/NR5A2 can reverse hyperglycemia in mouse models of T1D by attenuating the autoimmune attack coupled to β-cell survival/regeneration, prompted us to investigate whether immune tolerization could be achieved in individuals with T1D by LRH-1/NR5A2 activation as well as improving islet function/survival after xenotransplantation in mice. Pharmacological activation of LRH-1/NR5A2 induced a coordinated genetic and metabolic reprogramming of T1D macrophages and dendritic cells, shifting them from a pro-to an anti-inflammatory/tolerogenic phenotype. Regulatory T-cells were also expanded resulting in the impediment of cytotoxic T-cell proliferation. LRH-1/NR5A2 activation enhanced human islet engraftment and function in hyperglycemic immunocompetent mice. In summary our findings demonstrate the feasibility of re-establishing immune tolerance within a pro-inflammatory environment, opening a new therapeutic venue for T1D.
Identifying key urban design attributes for enhanced sense of safety – the case of El-Sherouk city in Cairo
Authors: Aly Toka Fahmy , Ehab Salma , Lotfi Yomna Amr 
Published: September 2023

PurposeSafety, one of the basic human needs for existence, is a very important factor in achieving a successful urban space. A lack of its presence could make it challenging for residents of a place to live and function effectively. Therefore, this study aims to identify the urban design attributes that would potentially enhance the perceived sense of safety, mainly focusing on two case studies in El-Sherouk neighborhood in Cairo. The two selected case studies are considered car-oriented due to their reduced levels of safety.Design/methodology/approachThis study was conducted through a set of data collection phases from field surveys and survey questionnaires that infer the influence of the surrounding urban environment on a specific target group. Statistical Package for the Social Sciences (SPSS) statistical analysis tool was used to analyze data collected from survey questionnaires.FindingsFinally, by the end of this research, a set of urban design qualities vital for achieving the desired levels of safety were introduced. The findings of this study revealed key urban design qualities that can potentially contribute to enhancing the perceived sense of safety as they showed a strong positive correlation: (1) imageability, (2) transparency, (3) complexity and (4) human scale and enclosure. Moreover, multiple linear regression indicates that urban design qualities are strong predictors of perceived safety.Originality/valueThis study presents a holistic approach to studying the relationship between urban design and perceived safety by examining two case studies located in El-Sherouk City in Cairo, Egypt. While previous research has focused on one theory of safety design such as crime prevention, defensible space theory, eyes on the street or safer city centers, this article tries to fill in the gap in the literature by analyzing all aspects of urban design and its correlation to an enhanced perceived safety. In addition, most of the previous studies have tackled the safety aspects of old urban settlements. However, this study tackles a new urban settlement.
Factors influencing mobile phone usage awareness for accessing agricultural marketing information by grape smallholder farmers in Dodoma, Tanzania
Authors: Nyagango Alex I. , Sife Alfred S. , Kazungu Isaac 
Published: September 2023

Purpose
There is a contradictive debate on factors influencing mobile phone usage awareness among scholars. This study aims to examine factors influencing mobile phone usage awareness for accessing agricultural marketing information.

Design/methodology/approach
A descriptive cross-sectional research design was used with 400 smallholder grape farmers. The use of structured questionnaires, focus group discussions and key informant interviews helped to collect primary data. Data analysis was subjected to descriptive, ordinal logistic regression and thematic approaches.

Findings
This study found that farmers were mostly aware of voice calls helping to access buyers and price information. Education, age and sex were the critical factors influencing mobile phone usage awareness among grape smallholder farmers.

Originality/value
This study contributes to scientific knowledge by providing an understanding of the perceived factors on mobile phone usage awareness within the grape subsector to inform policymakers.
Exploring the barriers to ESG adoption using modified TISM approach
Authors: Parameswar Nakul , Hasan Zuby , Shri Charu , Saini Neha 
Published: September 2023

PurposeThe study explores the barriers to ESG adoption and develops a hierarchical relationship between identified barriers to determine the driving and dependence power.Design/methodology/approachThrough literature and unstructured interviews nine barriers affecting the adoption of ESG reporting were identified and examined using the modified Total Interpretive Structural Modelling (m-TISM) approach. Further, MICMAC analysis is used to analyse the driver-dependence power amongst the barriers.FindingsIn this analysis, the variable lying at the lowest level of hierarchy are considered to be the critical factor and lack of clarity around regulatory and reporting standards is found to be very critical for ESG adoption. To address impediments to ESG adoption, the government should make ESG disclosure mandatory and clearly explain the rules, regulations and advantages associated with ESG implementation.Originality/valueThe current study is very few among examining the barriers to ESG adoption and steppingstone towards the mandatory implementation of ESG disclosures in current scenario.
Cause for caution: Response to Forum Contribution by van der Meer and Folmer
Authors: Piersma Theunis , Koolhaas Anita , van Gils Jan A. , Dekinga Anne 
Published: September 2023

Abstract

Triggered by the disappearance of the bivalve‐eating red knots Calidris canutus from feeding areas in the western Dutch Wadden Sea after these intertidal flats were exposed to the harvesting of edible cockles Cerastoderma edule by shallow‐draft suction dredging vessels, the admission of such dredging practices in this state nature monument, RAMSAR‐site and area designated protection under the EC Habitat and Bird Directives became an issue of politicized and heated societal debate in the 1990s and early 2000s. In the absence of focussed scientific research yielding peer‐reviewed papers, the few published studies on the issue were ‘side‐products’ of a long‐term study on foraging ecology and population dynamics of red knots.

In their contribution, van der Meer and Folmer criticized some of the statistical analyses in, what they consider, key papers leading to the closure of these forms of shellfish‐harvesting in the Dutch Wadden Sea.

The material provided by van der Meer and Folmer represents useful hindsight, further analytical sophistication and a (in our view biased) literature review, and thus raises new issues of concern, while leaving intact the arguments for concern about harmful ecological effects of large‐scale suction‐dredging in protected intertidal areas.

Policy implications. We conclude that, even in the light of the statistical concerns expressed by van der Meer and Folmer, there is still reasonable doubt on an absence of harmful ecological effects of suction‐dredging. This means that the eventual precautionary ruling on suction‐dredging for cockles in the protected Dutch Wadden Sea would remain perfectly valid.
Telocytes protect against lung tissue fibrosis through hexokinase 2‐dependent pathway by secreting hepatocyte growth factor
Authors: Zhang Shaoyuan , Sun Linyi , Chen Borong , Lin Siyun , Gu Jianmin , Tan Lijie , Lin Miao 
Published: September 2023

AbstractPulmonary fibrosis (PF) is one of the common manifestations of end‐stage lung disease. Chronic lung failure after lung transplantation is mainly caused by bronchiolitis obliterans syndrome (BOS) and is mainly characterized by lung tissue fibrosis. Pulmonary epithelial‐mesenchymal transformation (EMT) is crucial for pulmonary fibrosis. Telocytes (TCs), a new type of mesenchymal cells, play a protective role in various acute injuries. For exploring the anti‐pulmonary fibrosis effect of TCs in the BOS model in vitro and the related mechanism, rat tracheal epithelial (RTE) cells were treated with transforming growth factor‐β (TGF‐β) to simulate lung tissue fibrosis in vitro. The RTE cells were then co‐cultured with TCs primarily extracted from rat lung tissue. Western blot, Seahorse XF Analysers and enzyme‐linked immunosorbent assay were used to detect the level of EMT and aerobic respiration of RTE cells. Furthermore, anti‐hepatocyte growth factor (anti‐HGF) antibody was exogenously added to the cultured cells to explore further mechanisms. Moreover, hexokinase 2 (HK2) in RTE cells was knocked down to assess whether it influences the blocking effect of the anti‐HGF antibody. TGF‐β could induce lung tissue fibrosis in RTE cells in vitro. Nevertheless, TCs co‐culture decreased the level of EMT, glucose metabolic indicators (lactate and ATP) and oxygen levels. Furthermore, TCs released hepatocyte growth factor (HGF). Therefore, the exogenous addition of anti‐HGF antibody in the co‐culture system blocked the anti‐lung tissue fibrosis effect. However, HK2 knockdown attenuated the blocking effect of the anti‐HGF antibody. In conclusion, TCs can protect against lung tissue fibrosis by releasing HGF, a process dependent on HK2.
Batch culture analysis to identify potent organic acids for suppressing ruminal methane production
Authors: Yamada Kyouko , Iwamae Keiichiro , Suzuki Yutaka , Koike Satoshi , Kobayashi Yasuo 
Published: September 2023

AbstractWe performed an in vitro rumen batch culture study to screen 11 commercially available organic acids for methane‐suppressing ability and analyzed the rumen microbiota to determine the mode of action of the acids that showed potent methane‐suppressing activity. Nine of the 11 acids showed methane‐suppressing activity. Maleic anhydride, itaconate, citrate, and fumarate, which showed the highest activity, were further examined. These four acids showed methane‐suppressing activity irrespective of the hay‐to‐concentrate ratios of the substrate. Maleic anhydride and itaconate decreased total gas and short‐chain fatty acid production. Maleic anhydride and fumarate increased propionate production, while itaconate increased butyrate production. Maleic anhydride, itaconate, and citrate increased lactate production. Fumarate increased the abundance of bacteria involved in propionate production. Maleic anhydride, itaconate, and citrate increased the abundance of bacteria involved in lactate production. Thus, the results indicate that maleic anhydride, itaconate, and citrate may decrease methane in part by stimulating the acrylate pathway.
Efficacy of gilteritinib in comparison with alectinib for the treatment of ALK‐rearranged non‐small cell lung cancer
Authors: Ando Chihiro , Ichihara Eiki , Nishi Tatsuya , Morita Ayako , Hara Naofumi , Takada Kenji , Nakasuka Takamasa , Watanabe Hiromi , Kano Hirohisa , Nishii Kazuya , Makimoto Go , Kondo Takumi , Ninomiya Kiichiro , Fujii Masanori , Kubo Toshio , Ohashi Kadoaki , Matsuoka Ken‐ichi , Hotta Katsuyuki , Tabata Masahiro , Maeda Yoshinobu , Kiura Katsuyuki 
Published: September 2023

AbstractGilteritinib is a multitarget tyrosine kinase inhibitor (TKI), approved for the treatment of FLT3‐mutant acute myeloid leukemia, with a broad range of activity against several tyrosine kinases including anaplastic lymphoma kinase (ALK). This study investigated the efficacy of gilteritinib against ALK‐rearranged non‐small cell lung cancers (NSCLC). To this end, we assessed the effects of gilteritinib on cell proliferation, apoptosis, and acquired resistance responses in several ALK‐rearranged NSCLC cell lines and mouse xenograft tumor models and compared its efficacy to alectinib, a standard ALK inhibitor. Gilteritinib was significantly more potent than alectinib, as it inhibited cell proliferation at a lower dose, with complete attenuation of growth observed in several ALK‐rearranged NSCLC cell lines and no development of drug tolerance. Immunoblotting showed that gilteritinib strongly suppressed phosphorylated ALK and its downstream effectors, as well as mesenchymal–epithelial transition factor (MET) signaling. By comparison, MET signaling was enhanced in alectinib‐treated cells. Furthermore, gilteritinib was found to more effectively abolish growth of ALK‐rearranged NSCLC xenograft tumors, many of which completely receded. Interleukin‐15 (IL‐15) mRNA levels were elevated in gilteritinib‐treated cells, together with a concomitant increase in the infiltration of tumors by natural killer (NK) cells, as assessed by immunohistochemistry. This suggests that IL‐15 production along with NK cell infiltration may constitute components of the gilteritinib‐mediated antitumor responses in ALK‐rearranged NSCLCs. In conclusion, gilteritinib demonstrated significantly improved antitumor efficacy compared with alectinib against ALK‐rearranged NSCLC cells, which can warrant its candidacy for use in anticancer regimens, after further examination in clinical trial settings.
Quad Mesh Quantization Without a T‐Mesh
Authors: Coudert‐Osmont Yoann , Desobry David , Heistermann Martin , Bommes David , Ray Nicolas , Sokolov Dmitry 
Published: September 2023

AbstractGrid preserving maps of triangulated surfaces were introduced for quad meshing because the 2D unit grid in such maps corresponds to a sub‐division of the surface into quad‐shaped charts. These maps can be obtained by solving a mixed integer optimization problem: Real variables define the geometry of the charts and integer variables define the combinatorial structure of the decomposition. To make this optimization problem tractable, a common strategy is to ignore integer constraints at first, then to enforce them in a so‐called quantization step. Actual quantization algorithms exploit the geometric interpretation of integer variables to solve an equivalent problem: They consider that the final quad mesh is a sub‐division of a T‐mesh embedded in the surface, and optimize the number of sub‐divisions for each edge of this T‐mesh. We propose to operate on a decimated version of the original surface instead of the T‐mesh. It is easier to implement and to adapt to constraints such as free boundaries, complex feature curves network etc.
Extreme risk dependence between green bonds and financial markets
Authors: Karim Sitara , Lucey Brian M. , Naeem Muhammad A. , Yarovaya Larisa 
Published: September 2023

AbstractThe current study investigates the extreme risk dependence between green bonds and financial markets by employing the dual approaches of time‐varying optimal copula and extreme risk spillover analysis of dynamic conditional Value‐at‐Risk. We report significant symmetric (asymmetric) tail‐dependent copulas in the upper (lower) tails characterizing independent regimes. Green bonds offer sufficient diversification, safe‐haven, and hedging opportunities during stable and distressing times to financial markets. The extreme risk spillovers revealed that COVID‐19 transformed the spillovers between green bonds and financial markets except Bitcoin. We proposed insightful implications for policymakers, governments, investors, and portfolio managers to relish the findings for their investment avenues.
Extended and spatially asynchronous reproductive periodicity in a harvested, warm‐temperate rocky‐reef gastropod (Turbinidae)
Authors: Seinor Kate , Purcell Steven W. , Malcolm Hamish , Smith Stephen D. A. , Benkendorff Kirsten 
Published: September 2023

AbstractTurban snails are targeted for their high‐quality meat and, consequently, are often subjected to heavy harvesting pressure. Managing recreational and small‐scale fisheries is challenging, partly due to a lack of biological data underpinning certain regulatory measures. This study aimed to fill current knowledge gaps on the reproductive cycle of the recreationally and culturally harvested Australian turbinid, Turbo militaris. The objectives were to investigate the reproductive timing of T. militaris in New South Wales (NSW) and identify likely environmental drivers of reproductive periodicity. Oocytes and gonads were sampled from wild animals monthly over 15 months at two sites separated by ~500 km. Analysis of oocyte size frequency and gonadosomatic index revealed that T. militaris has a pattern of extended reproduction, which is synchronous between sexes. Turbo militaris was ripest during summer, and spawning appears to have occurred over multiple events, although primarily during winter. Reproductive timing was associated with environmental explanatory variables, including sea surface temperature, wave height, salinity, phytoplankton and nitrate concentration, together accounting for 81% of the variation in oocyte size frequency and 67% in the gonadosomatic index. Reproductive periodicity was correlated with wave conditions and phytoplankton concentrations inconsistently between sites, indicating that the effect of some environmental conditions may be unpredictable or site‐specific. Reproductive timing was asynchronous between two sites in the NSW fishery, posing challenges for designing seasonal fishing closures and community‐based harvesting rules. Spatial closures for species with spawning over extended timeframes, or spatially asynchronous reproductive cycles, are potentially more suitable for achieving fisheries management objectives.