bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deriving the cone fundamentals: a subspace intersection method
Authors: Wandell Brian A. , Goossens Thomas , Brainard David H. 
Published: February 2024

AbstractTwo ideas, proposed by Thomas Young and James Clerk Maxwell, form the foundations of color science: (1) Three types of retinal receptors encode light under daytime conditions, and (2) color matching experiments establish the critical spectral properties of this encoding. Experimental quantification of these ideas are used in international color standards. But, for many years the field did not reach consensus on the spectral properties of the biological substrate of color matching: the sensitivity of thein situ cones(cone fundamentals). By combining auxiliary data (thresholds, inert pigment analyses), complex calculations, and color matching from genetically analyzed dichromats, the human cone fundamentals have now been standardized.Here we describe a new computational method to estimate the cone fundamentals using only color matching from dichromatic observers. We show that it is not necessary to include data from trichromatic observers in the analysis or to know the primary lights used in the matching experiments. Remarkably, it is even possible to estimate the fundamentals by combining data from experiments using different, unknown primaries. We then suggest how the new method may be applied to color management in modern image systems.
Ca2+-sensor ALG-2 engages ESCRTs to enhance lysosomal membrane resilience to osmotic stress
Authors: Chen Wei , Motsinger Madeline M. , Li Jiaqian , Bohannon Kevin P. , Hanson Phyllis I. 
Published: February 2024

ABSTRACTLysosomes are central players in cellular catabolism, signaling, and metabolic regulation. Cellular and environmental stresses that damage lysosomal membranes can compromise their function and release toxic content into the cytoplasm. Here, we examine how cells respond to osmotic stress within lysosomes. Using sensitive assays of lysosomal leakage and rupture, we examine acute effects of the cathepsin C-metabolized osmotic disruptant glycyl-L-phenylalanine 2-naphthylamide (GPN). Our findings reveal that widely used concentrations of GPN rupture only a small fraction of lysosomes, but surprisingly trigger Ca2+release from nearly all. Chelating cytoplasmic Ca2+using BAPTA makes lysosomes more likely to rupture under GPN-induced stress, suggesting that Ca2+plays a role in protecting or rapidly repairing lysosomal membranes. Mechanistically, we establish that GPN causes the Ca2+-sensitive protein Apoptosis Linked Gene-2 (ALG-2) and interacting ESCRT proteins to redistribute onto lysosomes, improving their resistance to membrane stress created by GPN as well as the lysosomotropic drug chlorpromazine. Furthermore, we show that activating the cation channel TRPML1, with or without blocking the endoplasmic reticulum Ca2+pump, creates local Ca2+signals that protect lysosomes from rupture by recruiting ALG-2 and ESCRTs without any membrane damage. These findings reveal that Ca2+, through ALG-2, helps bring ESCRTs to lysosomes to enhance their resilience and maintain organelle integrity in the face of osmotic stress.SIGNIFICANCEAs the degradative hub of the cell, lysosomes are full of toxic content that can spill into the cytoplasm. There has been much recent interest in how cells sense and repair lysosomal membrane damage using ESCRTs and cholesterol to rapidly fix “nanoscale damage”. Here, we extend understanding of how ESCRTs contribute by uncovering a preventative role of the ESCRT machinery. We show that ESCRTs, when recruited by the Ca2+-sensor ALG-2, play a critical role in stabilizing the lysosomal membrane against osmotically-induced rupture. This finding suggests that cells have mechanisms not just for repairing but also for actively protecting lysosomes from stress-induced membrane damage.
Activation loop phosphorylation and cGMP saturation of PKG regulate egress of malaria parasites
Authors: Koussis Konstantinos , Haase Silvia , Withers-Martinez Chrislaine , Flynn Helen R. , Kunzelmann Simone , Christodoulou Evangelos , Ibrahim Fairouz , Skehel Mark , Baker David A. , Blackman Michael J. 
Published: February 2024

AbstractThe cGMP-dependent protein kinase (PKG) is the sole cGMP sensor in malaria parasites, acting as an essential signalling hub to govern key developmental processes throughout the parasite life cycle. Despite the importance of PKG in the clinically relevant asexual blood stages, many aspects of malarial PKG regulation, including the importance of phosphorylation, remain poorly understood. Here we use genetic and biochemical approaches to show that reduced cGMP binding to cyclic nucleotide binding domain B does not affectin vitrokinase activity but prevents parasite egress. Similarly, we show that phosphorylation of a key threonine residue (T695) in the activation loop is dispensable for kinase activityin vitrobut is essential forin vivoPKG function, with loss of T695 phosphorylation leading to aberrant phosphorylation events across the parasite proteome and changes to the substrate specificity of PKG. Our findings indicate thatPlasmodiumPKG is uniquely regulated to transduce signals crucial for malaria parasite development.
SMCHD1 activates the expression of genes required for the expansion of human myoblasts
Authors: Wong Matthew Man-Kin , Gardner Ed , Megeney Lynn A. , Emerson Charles P. , Gabellini Davide , Dilworth F. Jeffrey 
Published: February 2024

ABSTRACTSMCHD1 is an epigenetic regulatory protein known to modulate the targeted repression of large chromatin domains. Diminished SMCHD1 function in muscle fibers causes Facioscapulohumeral Muscular Dystrophy (FSHD2) through derepression of theD4Z4chromatin domain, an event which permits the aberrant expression of the disease-causing geneDUX4. Given that SMCHD1 plays a broader role in establishing the cellular epigenome, we examined whether loss of SMCHD1 function might affect muscle homeostasis through additional mechanisms. Here we show that acute depletion of SMCHD1 results in a DUX4-independent defect in myoblast proliferation. Genomic and transcriptomic experiments determined that SMCHD1 associates with enhancers of genes controlling cell cycle to activate their expression. Amongst these cell cycle regulatory genes, we identified LAP2 as a key target of SMCHD1 required for the expansion of myoblasts, where the ectopic expression of LAP2 rescues the proliferation defect of SMCHD1-depleted cells. Thus, the epigenetic regulator SMCHD1 can play the role of a transcriptional co-activator for maintaining the expression of genes required for muscle progenitor expansion. This DUX4-independent role for SMCHD1 in myoblasts suggests that the pathology of FSHD2 may be a consequence of defective muscle regeneration in addition to the muscle wasting caused by spurious DUX4 expression.Chromatin modifier SMCHD1 regulates the proliferation of human myoblastsSMCHD1 binds to enhancers of cell cycle regulatory genes to activate their expressionLap2 is an SMCHD1 direct target gene that regulates the expansion of human myoblasts.
A neutral process of genome reduction in marine bacterioplankton
Authors: Wang Xiaojun , Xie Mei , Ho Kaitlyn Elizabeth Yee Kei , Sun Ying , Chu Xiao , Zhang Shuangfei , Ringel Victoria , Wang Hui , Zhang Xiao-Hua , Shao Zongze , Zhao Yanlin , Brinkhoff Thorsten , Petersen Jörn , Wagner-Döbler Irene , Luo Haiwei 
Published: February 2024

AbstractMarine bacterioplankton communities are dominated by cells equipped with small genomes. Streamlining selection has been accepted as the main force driving their genome reduction. Here, we report that a neutral evolutionary mechanism governs genome reduction in the Roseobacter group that represents 5-20% of the bacterioplankton cells in coastal waters. Using representative strains that fall into three genome size groups (2-3, 3-4, and 4-5 Mbp), we measured their genomic mutation rates (μ) through long-term mutation accumulation experiments followed by genome sequencing the resulting 437 mutant lines. We further calculated their effective population sizes (Ne) based on μ and the neutral genetic diversity of the studied species, the latter estimated based on multiple genome sequences of natural isolates collected from global oceans with their population structure considered. A surprising finding is thatNescales positively with genome size, which is the opposite of the expectation from the streamlining selection theory. As the strength of random genetic drift is the inverse ofNe, this result instead suggests drift as the primary driver of genome reduction. Additionally, we report a negative scaling between μ and genome size, which is the first experimental evidence for the long-lasting hypothesis that mutation rate increases play a part in marine bacterial genome reduction. As μ scales inversely withNe, genetic drift appears to be the ultimate cause of genome reduction in these Roseobacters. Our finding discounts, but is insufficient to reject, the streamlining theory because streamlining process is expected to be more effective in oligotrophic open ocean waters.
Pathogen genomics and One Health: a scoping review of current practices in zoonotic disease research
Authors: Catalano Stefano , Battelli Francesca , Traore Zoumana I , Raghwani Jayna , Faust Christina L , Standley Claire J 
Published: February 2024

ABSTRACTWhole-genome sequencing has revolutionised the field of infectious disease surveillance, enabling near real-time detection of pathogens and tracking how infections may spread. We performed a scoping review of studies that have applied genomic epidemiology to zoonotic disease transmission across One Health domains (human, animal, and environment). We identified 114 records published between 2005 and 2022 which reported original multi-domain genomic data of zoonotic pathogens integrated into phylogenetic models. Most studies investigated bacterial pathogens, highlighting key knowledge gaps for other zoonotic agents, particularly arboviruses. Sampling and sequencing efforts vastly varied across domains: the median number and range of pathogen genomes analysed were highest for humans (23; 1-29,586) and lowest for the environment domain (13; 1-956). Infectious disease genomics was leveraged to track zoonotic disease outbreaks and cross-domain transmission, to enhance pathogen surveillance, and to disentangle evolutionary dynamics driving lineage diversification and virulence. Our study informs effective study design for future genomic applications to multi-domain and cross-species transmission of zoonoses, with the potential to identify key infection sources and inform interventions for local and global health security.
QGSJET-III model of high energy hadronic interactions: The formalism
Authors: Ostapchenko Sergey 
Published: February 2024

The physics content of the QGSJET-III Monte Carlo generator of high energy hadronic collisions is described. In particular, a phenomenological implementation of higher twist corrections to hard parton scattering processes is discussed in some detail. Additionally addressed is the treatment of the so-called “color fluctuation” effects related to a decomposition of hadron wave functions into a number of Fock states characterized by different spatial sizes and different parton densities. Selected model results regarding the energy dependence of the total, elastic, and diffractive proton-proton cross sections are presented.

Published by the American Physical Society
2024
Role of the National Archives of South Africa in promoting human rights
Authors: Netshakhuma Nkholedzeni Sidney 
Published: February 2024

Purpose
This paper aims to explore the role played by the National Archives of South Africa in human rights promotion and protection. The study examined the challenges that archivists encounter when undertaking archival functions, such as acquisition, appraisal and access provision, that contribute to forming documentary archives crucial for human rights promotion and protection.

Design/methodology/approach
A review of literature dealing with acquisition, appraisal and access was used in this research. It was supplemented with interviews.

Findings
This paper provides recommendations of benefits in the field of archives management with a focus on the areas of acquisition, appraisal and access. The transformational discourse in the jurisdiction of archives management challenges archival institutions to be active players in selecting historical and cultural archives’ significance that is significant in human rights protections. However, despite judicial requirements that recommend the importance of archives, there is evidence that archival functions such as appraisal, acquisition and access are not being fully used, resulting in national archives institutions that are subject to irregularities that contribute to an unbalanced archives collection.

Research limitations/implications
The paper was limited only to the National Archives of South Africa.

Practical implications
The paper makes practical implications concerning the acquisition, appraisal and providing access to human rights records.

Social implications
Sufficient funding resource allocation ought to be provided to advance human rights promotion.

Originality/value
This paper offers informed recommendations to address the challenges of acquisition, appraisal and access provision of archive materials. The availability of archives materials reinforces the community by aiding to protect legal rights and prevent human rights violations. It was, thus, necessary to establish whether the National Archives of South Africa is actively building the archives collections that are important for human rights promotion and protection.
Winner-takes-all or competitive coexistence? Research on the co-opetition relationships between platform owners and complementors
Authors: Pei Lijuan 
Published: February 2024

Purpose
The purpose of this study is to explore the coopetition relationships between platform owners and complementors in complementary product markets. Drawing on the coopetition theory, the authors examined the evolutionary trends of the coopetition relationships between platform owners and complementors and explore the main influence factors.

Design/methodology/approach
The authors used Lotka–Volterra model to analyze the coopetition relationship between platform owners and complementors, including the evolutionary trends as well as the results. Considering the feasibility of sample data collection, simulation is used to verify the effects of different factors on the evolution of coopetition relationships.

Findings
The results show that there are four possible results of the competition in the complementary products market. That comprises “winner-take-all for platform owners,” “winner-take-all for complementors,” “stable competitive coexistence” and “unstable competitive coexistence,” where “stable competitive coexistence” is the optimal evolutionary state. Moreover, the results of competitive evolution are determined by innovation subjects’ interaction parameters. However, the natural growth rate, the initial market benefits of the two innovators and the overall benefits of the complementary product markets influence the time to reach a steady state.

Originality/value
The study provides new insights into the entry of platform owners into complementary markets, and the findings highlight the fact that in complementary product markets, platform owners and complementors should seek “competitive coexistence” rather than “winner-takes-all.” Moreover, the authors also enrich the coopetition theory by revealing the core factors that influence the evolution of coopetition relationships, which further enhance the analysis of the evolutionary process of coopetition relationships.
Optimizing IRE targeting using multi-electrode structure and biomedical multi-output generator
Authors: López-Alonso Borja , Briz Pablo , Sarnago Hector , Burdio José M. , Lucia Oscar 
Published: February 2024

Purpose
This paper aims to study the feasibility of proposed method to focus the electroporation ablation by mean of multi-output multi-electrode system.

Design/methodology/approach
The proposed method has been developed based on a previously designed electroporation system, which has the capabilities to modify the electric field distribution in real time, and to estimate the impedance distribution. Taking into consideration the features of the system and biological tissues, the problem has been addressed in three phases: modeling, control system design and simulation testing. In the first phase, a finite element analysis model has been proposed to reproduce the electric field distribution within the hepatic tissue, based on the characteristics of the electroporation system. Then, a control strategy has been proposed with the goal of ensuring complete ablation while minimizing the affected volume of healthy tissue. Finally, to check the feasibility of the proposal, several representative cases have been simulated, and the results have been compared with those obtained by a traditional system.

Findings
The proposed method achieves the proposed goal, as part of a complex electroporation system designed to improve the targeting, effectiveness and control of electroporation treatments and serve to demonstrate the feasibility of developing new electroporation systems capable of adapting to changes in the preplanning of the treatment in real-time.

Originality/value
The work presents a thorough study of control method to multi-output multi-electrode electroporation system by mean of a rigorous numerical simulation.
Game evolution analysis of BIM application willingness of prefabricated construction parties
Authors: Zhang Chi , He Kun , Zhang Wenjie , Jin Ting , Ao Yibin 
Published: February 2024

PurposeTo further promote application of BIM technology in construction of prefabricated buildings, influencing factors and evolution laws of willingness to apply BIM technology are explored from the perspective of willingness of participants.Design/methodology/approachIn this paper, a tripartite game model involving the design firm, component manufacturer and construction firm is constructed and a system dynamics method is used to explore the influencing factors and game evolution path of three parties' application of BIM technology, from three perspectives, cost, benefit and risk.FindingsThe government should formulate measures for promoting the application of BIM according to different BIM application willingness of the parties. When pursuing deeper BIM application, the design firm should pay attention to reducing the speculative benefits of the component manufacturer and the construction firm. The design firm and the component manufacturer should pay attention to balancing the cost and benefit of the design firm while enhancing collaborative efforts. When the component manufacturer and the construction firm cooperate closely, it is necessary to pay attention to balanced distribution of interests of both parties and lower the risk of BIM application.Originality/valueThis study fills a research gap by comprehensively investigating the influencing factors and game evolution paths of willingness of the three parties to apply BIM technology to prefabricated buildings. The research helps to effectively improve the building quality and construction efficiency, and is expected to contribute to the sustainability of built environment in the context of circular economy in China.
Community resilience in Bondo community, Southern Malawi: balancing energy, water and biodiversity
Authors: Mwale Vincent Dodoma , To Long Seng , Gogoda Chrispin , Ngonda Tiyamike , Nkhoma Richard 
Published: February 2024

Purpose
This study aims to investigate the intricate relationships between a community energy system, water resources and biodiversity conservation, with a specific focus on augmenting community energy resilience in Bondo. The primary objective is to gain an in-depth understanding of how community members perceive and experience the challenges related to balancing the often-conflicting demands of energy, water and biodiversity conservation within this context.

Design/methodology/approach
The research uses a qualitative approach to unravel the multifaceted dynamics of community energy systems, water resources and biodiversity conservation in Bondo. Data were collected through focus groups and direct observations, enabling a nuanced exploration of community perspectives and lived experiences. The subsequent analysis of this qualitative data follows established thematic analysis procedures.

Findings
The study's findings shed light on the formidable barriers that impede rural communities in Malawi from accessing electricity effectively. Even in communities fortunate enough to have electricity connections, the lack of knowledge regarding productive electricity use results in community energy systems operating at significantly reduced load factors. Furthermore, the intricate challenge of managing a biodiversity hotspot persists, exacerbated by the densely populated peripheral communities' continued reliance on forest, land and water resources. These activities, in turn, contribute to ecosystem degradation.

Originality/value
In a context where government-led management of forest reserves and game reserves has not yielded the expected results due to a multitude of factors, there arises a compelling need for innovative approaches. One such innovation involves fostering partnerships between the government and experienced trusts as lead organisations, providing a fresh perspective on addressing the complex interplay between community energy systems, water resources and biodiversity conservation. This novel approach opens doors to explore alternative pathways for achieving the delicate balance between human energy needs and the preservation of vital ecosystems.
Raising pre-service English language teachers’ awareness of sustainable development goals through literary texts
Authors: Arikan Arda , Zorba Mehmet Galip 
Published: February 2024

Purpose
This study aims to examine the outcome of an online project to inform preservice English language teachers regarding the United Nations’ Sustainable Development Goals (SDGs).

Design/methodology/approach
A qualitative research method was used to understand participants’ overall knowledge. In total, 30 preservice teachers were selected from a larger pool after considering their grade point averages, sex, university affiliations and geographical backgrounds to ensure a balanced distribution and diversity. Qualitative data were collected through written productions, video recordings and a postproject survey.

Findings
Findings revealed that preservice teachers deepened their understanding of SDGs and adopted a positive attitude toward SDGs while increasing their pedagogical awareness and knowledge of teaching English in response to SDGs. They also regarded literary texts as a valuable resource for teaching SDGs.

Originality/value
This study contributes to the literature by demonstrating that literary works are valuable for educating preservice teachers on integrating SDGs. A detailed overview of the project and its outcomes can guide practitioners and teacher educators in integrating SDGs into their education programs and English language teaching.