bluuebunny/crossref_metadata_2025_split huggingface dataset:
Norms, institutions, and digital veils of uncertainty—Do network protocols need trust anyway?
Authors: Alston Eric 
Published: September 2024

AbstractIn large and complex human groups, social rules reduce individuals' uncertainty about their own choice set, including through these rules' simultaneous influence on the choice set of other individuals. But uncertainty varies as to the extent to which it is knowable and quantifiable ex ante. Therefore, different classes of social rules deal with the future uncertainty of individuals' conduct in structurally distinct ways, with institutions and norms being the hallmark example of this distinction. Institutions, through their costly definition and enforcement by a known organization, require specific delineation of behavior and penalties ex ante, meaning they of necessity confront “known unknowns” (risk), or the conduct of members of an organization that can be predicted ex ante. Norms, in contrast, are only effective in shaping behavior if sufficiently shared within a community, which means their application is automatic in expectation to an individual ordering their conduct considering potential norms. This makes norms apply to ex ante known and unknown situations alike, relative to the precision that the articulation of institutions requires with respect to human behavior. Although digital governance carries the benefits (and costs) of considerable institutional “completeness,” governance by protocol is nonetheless incomplete in the face of the complex set of exogenous shocks and human actions that a given digital networked organization will experience. This means digital institutions need to mimic the adaptability of institutions more generally, through the institutional mechanisms of flexibility detailed in this analysis. More generally, though, the fact that norms can serve as a complementary gap‐filler in contexts where institutions do not reach suggest that digital organization designers cannot avoid simultaneous consideration of the human community of network users that will define the norms that become crucial in periods of true uncertainty for any organization.
Effective use of skin microbiome signatures for fingerprint identification
Authors: Yılmaz Seda Salman , Kuşkucu Mert Ahmet , Çakan Hüseyin , Aygün Gökhan 
Published: September 2024

AbstractBackgroundRecent advances have increased the importance of the human microbiome, including the skin microbiome. Despite the hand microbiome research, the factors affecting the composition of the hand microbiome and their personal characteristics are incompletely known.ObjectivesDespite changing environmental factors and personal variation, we aimed to indicate the interpersonal distinction between skin microbiota using simple and rapid molecular methods.MethodsOver a non‐consecutive 10‐day period, samples were taken from 10 adult individuals, and ribotyping analysis of the 16S and 23S genes of S. epidermidis was performed on each skin sample. Additionally, EcoRI and HindIII enzyme reactions and variable number tandem repeat (VNTR) reactions of S. epidermidis obtained from DNA samples were performed. The skin microbiomes of individuals were evaluated along with the microbiome profiles left on the surfaces they touched.ResultsIn the environmental samples taken, it has been observed that people preserve their core skin microbiota characters and carry them to their environment. It was determined that the highest similarity rate was 77.14%, and the lowest similarity rate was 31.74%.ConclusionOur study showed that the core skin microbiota retains its characteristics and leaves traces in environments. The fact that the personal microbiome remains unchanged despite environmental differences and has characteristic features has shown that it can be used in forensic sciences to distinguish individuals from each other. These results with simple and rapid methods further increased the importance and significance of the study. The findings indicate that personal skin microbiota can provide a significant contribution to criminal investigations by increasing accuracy and reliability, especially in forensic analyses.
Emergency Response Planning: A Framework to Assess Hydrant–Structure Access
Authors: Baik Jiwon , Murray Alan T. 
Published: September 2024

ABSTRACTAccessibility between fire hydrants and buildings is paramount in emergency response, significantly influencing the efficiency and effectiveness of firefighting operations in the event of an incident. However, assessing this relationship within a geographic information system (GIS) framework presents challenges on two fronts. Obtaining the path avoiding building and parcel obstructions to hydrants is not trivial. Further, determining the furthest extent around a building exterior from hydrants is complicated, yet it is critically important given the spatial limitations of equipment reach. To assess furthest extent, an analytical framework is introduced based on the Euclidean shortest path problem. The proposed approach offers a comprehensive, automated GIS‐based methodology tailored to evaluate the dynamic relationship between hydrants and buildings. The developed methods are able to accurately and precisely identify the furthest point around a building structure from hydrant, facilitating risk assessment as well as fire code compliance. This enables a comprehensive evaluation of potential loss and structure vulnerability at property, street, neighborhood, and regional levels.
The genetic basis of leaf hair development in upland cotton (Gossypium hirsutum)
Authors: Wang Xiaoyang , Dai Panhong , Li Hongge , Wang Jingjing , Gao Xu , Wang Zhenzhen , Peng Zhen , Tian Chunyan , Fu Guoyong , Hu Daowu , Chen Baojun , Xing Aishuang , Tian Yuan , Nazir Mian Faisal , Ma Xinli , Rong Junkang , Liu Fang , Du Xiongming , He Shoupu 
Published: September 2024

SUMMARYTrichomes, which originate from the epidermal cell of aerial organs, provide plants with defense and secretion functions. Although numerous genes have been implicated in trichome development, the molecular mechanisms underlying trichome cell formation in plants remain incompletely understood. Here, we using genome‐wide association study (GWAS) across 1037 diverse accessions in upland cotton (Gossypium hirsutum) to identify three loci associated with leaf pubescence (hair) amount, located on chromosome A06 (LPA1), A08 (LPA2) and A11 (LPA3), respectively. GhHD1, a previously characterized candidate gene, was identified on LPA1 and encodes an HD‐Zip transcription factor. For LPA2 and LPA3, we identified two candidate genes, GhGIR1 and GhGIR2, both encoding proteins with WD40 and RING domains that act as inhibitors of leaf hair formation. Expression analysis revealed that GhHD1 was predominantly expressed in hairy accessions, whereas GhGIR1 and GhGIR2 were expressed in hairless accessions. Silencing GhHD1 or overexpressing GhGIR1 in hairy accessions induced in a hairless phenotype, whereas silencing GhGIR2 in hairless accessions resulted in a hairy phenotype. We also demonstrated that GhHD1 interact with both GhGIR1 and GhGIR2, and GhGIR1 can interact with GhGIR2. Further investigation indicated that GhHD1 functions as a transcriptional activator, binding to the promoters of the GhGIR1 and GhGIR2 to active their expression, whereas GhGIR1 and GhGIR2 can suppress the transcriptional activation of GhHD1. Our findings shed light on the intricate regulatory network involving GhHD1, GhGIR1 and GhGIR2 in the initiation and development of plant epidermal hairs in cotton.
ERFVII‐controlled hypoxia responses are in part facilitated by MEDIATOR SUBUNIT 25 in Arabidopsis thaliana
Authors: Schippers Jos H. M. , von Bongartz Kira , Laritzki Lisa , Frohn Stephanie , Frings Stephanie , Renziehausen Tilo , Augstein Frauke , Winkels Katharina , Sprangers Katrien , Sasidharan Rashmi , Vertommen Didier , Van Breusegem Frank , Hartman Sjon , Beemster Gerrit T. S. , Mhamdi Amna , van Dongen Joost T. , Schmidt‐Schippers Romy R. 
Published: September 2024

SUMMARYFlooding impairs plant growth through oxygen deprivation, which activates plant survival and acclimation responses. Transcriptional responses to low oxygen are generally associated with the activation of group VII ETHYLENE‐RESPONSE FACTOR (ERFVII) transcription factors. However, the exact mechanisms and molecular components by which ERFVII factors initiate gene expression are not fully elucidated. Here, we show that the ERFVII factors RELATED TO APETALA 2.2 (RAP2.2) and RAP2.12 cooperate with the Mediator complex subunit AtMED25 to coordinate gene expression under hypoxia in Arabidopsis thaliana. Respective med25 knock‐out mutants display reduced low‐oxygen stress tolerance. AtMED25 physically associates with a distinct set of hypoxia core genes and its loss partially impairs transcription under hypoxia due to decreased RNA polymerase II recruitment. Association of AtMED25 with target genes requires the presence of ERFVII transcription factors. Next to ERFVII protein stabilisation, also the composition of the Mediator complex including AtMED25 is potentially affected by hypoxia stress as shown by protein‐complex pulldown assays. The dynamic response of the Mediator complex to hypoxia is furthermore supported by the fact that two subunits, AtMED8 and AtMED16, are not involved in the establishment of hypoxia tolerance, whilst both act in coordination with AtMED25 under other environmental conditions. We furthermore show that AtMED25 function under hypoxia is independent of ethylene signalling. Finally, functional conservation at the molecular level was found for the MED25‐ERFVII module between A. thaliana and the monocot species Oryza sativa, pointing to a potentially universal role of MED25 in coordinating ERFVII‐dependent transcript responses to hypoxia in plants.
Triboinformatics Approach for Prediction of High-Stress Abrasive Wear and Coefficient of Friction in Al/TiC Nanocomposites Using Machine Learning Techniques
Authors: Golla Chitti Babu , Narasimha Rao R. , Ismail Syed 
Published: September 2024

Abstract
This study highlights the importance of Al–Fe–Si alloys in modern engineering for their enhanced hardness, strength, and wear resistance, improving fuel efficiency in the aerospace and automotive sectors. Data-driven analysis and machine learning methods can help understand tribological occurrences by identifying links between material characteristics and tribological behavior. The research examined TiC reinforcement in aluminum nanocomposites synthesized via ultrasonic-assisted stir casting, creating five composites with TiC weight percentages from 0% to 8%. Tests conducted using pin-on-disc equipment under various conditions, including loads of 5–15 N, sliding velocities of 0.5–1.5 m/s, sliding distances of 80–120 m, and abrasive grit sizes of 80–150 µm, revealed significant findings. The Al–6TiC nanocomposite demonstrated an 18% reduction in wear-rate at 80 µm, 28.2% at 120 µm, and 24.5% at 150 µm under a 15 N load and 120 m sliding distance compared to the pure alloy. There was also a 22% friction coefficient reduction with increased loads and grit sizes. Scanning electron microscope (SEM) analysis of the worn surfaces and abrasive papers was conducted. Wear-rate data were analyzed using six machine learning models, with the gradient boosting regressor (GBR) identified as the most accurate, achieving an R2 value of 0.95. This study emphasizes the impact of the TiC content, loading conditions, and hardness on wear and friction coefficient, and shows how machine learning techniques can predict and optimize advanced aluminum nanocomposite design for engineering applications.
Surrogate Modeling of Brain Trauma Risks Associated With Soccer Ball Headers
Authors: Perkins Richard A. , Bakhtiarydavijani Amirhamed , Sharma Gehendra , Nellippallil Anand , Hammi Youssef , Robinson Thomas , Prabhu Raj K. 
Published: September 2024

Abstract
This study presents a coupled mathematical surrogate modeling and finite element analysis to quantify the risk of brain injury resulting from contact between a soccer ball and a player's head. Our approach implements a previously developed and validated regulation size finite element soccer ball and a 50th percentile adult male head model to inform the surrogate models regarding the positioning of the soccer ball's impact, inbound velocity, and the role of the activation of the neck musculature. Surrogate models are developed using injury metrics such as HIC15 and BrIC, which can be correlated to clinical assessments. The surrogate models predict occipital-temporal impacts as the highest risk of injury along a perpendicular axis and highlight the risk of increased velocity and passive neck musculature. The surrogate model predicts the worst-case scenarios to produce HIC15 and BrIC values of approximately 80 and 0.65, which correlate to 4.27% of a minor head injury (AIS1) and 71% of a moderate head injury (AIS2), respectively. These models are also used to develop a graphical user interface that may be used to supplement existing clinical knowledge of soccer headings to improve the head health of athletes participating in the game of soccer.
Efficient Neural Hybrid System Learning and Interpretable Transition System Abstraction for Dynamical Systems
Authors: Yang Yejiang , Mo Zihao , Xiang Weiming 
Published: September 2024

Abstract
This article proposes a neural network hybrid modeling framework for dynamics learning to promote an interpretable, computationally efficient method of dynamics learning and system identification. First, a low-level model is trained to learn the system dynamics, which utilizes multiple simple neural networks to approximate the local dynamics generated from data-driven partitions. Then, based on the low-level model, a high-level model is trained to abstract the low-level neural hybrid system model into a transition system that allows computational tree logic (CTL) verification to promote model’s ability to handle human interaction and verification efficiency.
Investigating Microstructure and Wear Characteristics of Alloy Steels Used as Wear Plates in Ballast Cleaning Operation in Railways
Authors: Pandey Manas , Kumar Nikhil 
Published: September 2024

Abstract
Ballast cleaning machines play a pivotal role in maintaining the stability and safety of railway tracks by transferring and redistributing ballast on the tracks. However, the wear plates used in these machines are subjected to extreme conditions, making the assessment of their wear performance crucial. This study scrutinizes the wear performance of two distinct 31Ni10Cr3Mo6 based alloy steels used as wear plates in the ballast cleaning machines. The study compares the initial microstructure and wear properties of German grade steel (Plasser) wear plate with an indigenous grade steel (RDSO) used as an alternative. The results indicate that the indigenous wear plate consistently exhibits higher weight loss across various loading conditions, whereas the Plasser wear plate demonstrates superior wear resistance, particularly at higher loads. This enhanced performance is attributed to relatively larger amount of high-angle grain boundaries, small grain size, and variations in micro-alloying elements. The compositional analysis indicates low carbon content in both wear plates. The microstructural analysis shows that both samples have a single body-centered cubic crystal structure, with a randomly distributed heterogeneous ferritic and cementite phases in a lath-bainitic microstructure. This comprehensive study provides valuable insights into the wear behavior of these alloy steels, contributing to the optimization of alloying materials and desired microstructure for the wear plates in ballast cleaning machines.
Substrate dependence of transport coupling and phenotype of a small multidrug resistance transporter in
Pseudomonas aeruginosa
Authors: Wegrzynowicz Andrea K. , Heelan William J. , Demas Sydnye P. , McLean Maxwell S. , Peters Jason M. , Henzler-Wildman Katherine A. 
Published: September 2024

ABSTRACT

Small multidrug resistance (SMR) transporters are key players in the defense of multidrug-resistant pathogens to toxins and other homeostasis-perturbing compounds. However, recent evidence demonstrates that EmrE, an SMR from
Escherichia coli
and a model for understanding transport, can also induce susceptibility to some compounds by drug-gated proton leak. This runs down the ∆pH component of the proton-motive force (PMF), reducing the viability of the affected bacteria. Proton leak may provide an unexplored drug target distinct from the targets of most known antibiotics. Activating proton leak requires an SMR to be merely present, rather than be the primary resistance mechanism, and dissipates the energy source for many other efflux pumps. PAsmr, an EmrE homolog from
Pseudomonas aeruginosa
, transports many EmrE substrates in cells and purified systems. We hypothesized that PAsmr, like EmrE, may confer susceptibility to some compounds via drug-gated proton leak. Growth assays of
E. coli
expressing PAsmr displayed substrate-dependent resistance and susceptibility phenotypes, and
in vitro
solid-supported membrane electrophysiology experiments revealed that PAsmr performs both antiport and substrate-gated proton uniport, demonstrating the same functional promiscuity observed in EmrE. Growth assays of
P. aeruginosa
strain PA14 demonstrated that PAsmr contributes resistance to some antimicrobial compounds, but no growth defect is observed with susceptibility substrates, suggesting
P. aeruginosa
can compensate for the proton leak occurring through PAsmr. These phenotypic differences between
P. aeruginosa
and
E. coli
advance our understanding of the underlying resistance mechanisms in
P. aeruginosa
and prompt further investigation into the role that SMRs play in antibiotic resistance in pathogens.

IMPORTANCE

Small multidrug resistance (SMR) transporters are a class of efflux pumps found in many pathogens, although their contributions to antibiotic resistance are not fully understood. We hypothesize that these transporters may confer not only resistance but also susceptibility, by dissipating the proton-motive force. This means to use an SMR transporter as a target; it merely needs to be present (as opposed to being the primary resistance mechanism). Here, we test this hypothesis with an SMR transporter found in
Pseudomonas aeruginosa
and find that it can perform both antiport (conferring resistance) and substrate-gated proton leak. Proton leak is detrimental to growth in
Escherichia coli
but not
P. aeruginosa
, suggesting that
P. aeruginosa
responds differently to or can altogether prevent ∆pH dissipation.
Collaborative learning in the digital age: empowering tuberculosis researchers through virtual training
Authors: Dippenaar Anzaan , Sylvester Taime , Ealand Christopher , Ismail Nabila , Rakotosamimanana Niaina , Miller Michele , Kana Bavesh D. , Warren Rob M. ,   for the FSPI Consortium
Published: September 2024

ABSTRACT

Integrating whole genome sequencing (WGS) of the
Mycobacterium tuberculosis
complex into routine care, surveillance, and research in high tuberculosis burden settings remains challenging due to limited resources and skills. While technological platforms for scaling WGS are emerging, scaling wet lab and analytic components often depends on partnerships where such skills have been established. To address this, a virtual training program was developed. Over 12 weeks, 21 trainees from five Southern African institutes engaged in learning from curated theoretical content and interactive virtual meetings with experienced instructors. The training program, developed by a diverse team of experts in molecular biology, biomedical research, microbiology, and tuberculosis research, provided comprehensive coverage aligned with the latest advancements. Teaching strategies included interactive mentor-led sessions and real-time feedback, together with facilitated knowledge exchange and understanding. The virtual training program yielded several successes. Of note, trainees submitted three scientific articles for peer review, based on their acquired knowledge and its application in research. The program also fostered collaborations on
Mycobacterium tuberculosis
WGS among participants, showcasing the potential for networking and future joint projects. While the virtual training program encountered challenges related to the pandemic, limited resources, trainee engagement, and language barriers, these were creatively mitigated. To improve future training sessions, a platform assessing participant engagement and information retention is recommended. Wider collaborative efforts among experts and institutions in collating resources will lead to more comprehensive training programs. Addressing challenges such as internet connectivity issues and language barriers is crucial for ensuring inclusivity and enhancing the overall learning experience. In conclusion, the virtual training program successfully provided knowledge and skill training in WGS to trainees, leading to scientific article submissions and collaborations. Furthermore, content creators benefited from improved science communication and training opportunities.
Genomic transfer via membrane vesicle: a strategy of giant phage phiKZ for early infection
Authors: Antonova Daria , Nichiporenko Anna , Sobinina Mariia , Wang Yueqi , Vishnyakov Innokentii E. , Moiseenko Andrey , Kurdyumova Inna , Chesnokov Yuri M. , Stepanchikova Elizaveta , Bourkaltseva Maria , Samygina Valeriya R. , Khodorkovskii Mikhail , Sokolova Olga S. , Yakunina Maria V. 
Published: September 2024

ABSTRACT

During infection, the giant phiKZ phage forms a specialized structure at the center of the host cell called the phage nucleus. This structure is crucial for safeguarding viral DNA against bacterial nucleases and for segregating the transcriptional activities of late genes. Here, we describe a morphological entity, the early phage infection (EPI) vesicle, which appears to be responsible for earlier gene segregation at the beginning of the infection process. Using cryo-electron microscopy, electron tomography (ET), and fluorescence microscopy with membrane-specific dyes, we demonstrated that the EPI vesicle is enclosed in a lipid bilayer originating, apparently, from the inner membrane of the bacterial cell. Our investigations further disclose that the phiKZ EPI vesicle contains both viral DNA and viral RNA polymerase (vRNAP). We have observed that the EPI vesicle migrates from the cell pole to the center of the bacterial cell together with ChmA, the primary protein of the phage nucleus. The phage DNA is transported into the phage nucleus after phage maturation, but the EPI vesicle remains outside. We hypothesized that the EPI vesicle acts as a membrane transport agent, efficiently delivering phage DNA to the phage nucleus while protecting it from the nucleases of the bacterium.

IMPORTANCE
Our study shed light on the processes of phage phiKZ early infection stage, expanding our understanding of possible strategies for the development of phage infection. We show that phiKZ virion content during injection is packed inside special membrane structures called early phage infection (EPI) membrane vesicles originating from the bacterial inner cell membrane. We demonstrated the EPI vesicle fulfilled the role of the safety transport unit for the phage genome to the phage nucleus, where the phage DNA would be replicated and protected from bacterial immune systems