bluuebunny/crossref_metadata_2025 huggingface dataset:
Matrix model of two-color one-flavor QCD: The ultrastrong coupling regime
Authors: Acharyya Nirmalendu , Aich Prasanjit , Bandyopadhyay Arkajyoti , Vaidya Sachindeo
Published: September 2024

Using variational methods, we numerically investigate the matrix model for the two-color QCD coupled to a single quark (matrix-QCD2,1) in the limit of ultrastrong Yang-Mills coupling (g=∞). The spectrum of the model has superselection sectors labeled by baryon number B and spin J. We study sectors with B=0, 1, 2 and J=0, 1, which may be organized as mesons, (anti-)diquarks and (anti-)tetraquarks. For each of these sectors, we study the properties of the respective ground states in both chiral and heavy quark limits, and uncover a rich quantum phase transition (QPT) structure. We also investigate the division of the total spin between the glue and the quark and show that glue contribution is significant for several of these sectors. For the (B,J)=(0,0) sector, we find that the dominant glue contribution to the ground state comes from reducible connections. Finally, in the presence of nontrivial baryon chemical potential μ, we construct the phase diagram of the model. For sufficiently large μ, we find that the ground state of the theory may have nonzero spin.

Published by the American Physical Society
2024
Role of local structure in the optical and electronic properties of oxygen vacancies in different crystal phases of
Ga2O3
Authors: Kaewmeechai Chaiyawat , Strand Jack , Shluger Alexander
Published: September 2024

We investigate the structural, electronic, and optical properties of oxygen vacancies (VO) in crystalline α, β, and ε−Ga2O3 using density functional theory (DFT) calculations with the PBE0-TC-LRC functional. Our results reveal that the charge transition levels (CTLs) associated with VO exhibit significant variations depending on the crystal phase and the coordination environment of surrounding atoms. In particular, VOs surrounded by tetrahedral Ga atoms (T-Ga) exhibit deeper CTLs compared to those surrounded by octahedral Ga atoms (O-Ga). We also observe distinct atomic relaxations, with larger displacements of

T

-Ga

atoms compared to O-Ga atoms in the vicinity of VOs. Using linear-response time-dependent DFT, we investigate the optical transitions of VO and identify two distinct types of transitions: defect state to conduction band state and valence band to defect state. These results can be used to better understand the optical properties of VO defects in Ga2O3 films.

Published by the American Physical Society
2024
Pulse instabilities can shape virus-immune coevolution
Authors: Kessler David A. , Levine Herbert
Published: September 2024

Adaptive immune systems engage in an arms race with evolving viruses, trying to generate new responses to viral strains that continually move away from the set of genetically varying strains that have already elicited a functional immune response. It has been argued that this dynamical process can lead to a propagating pulse of an ever-changing viral population and concomitant immune response. Here, we introduce a new stochastic model of viral-host coevolution, taking into account finite-sized host populations and varying processes of immune “forgetting”. Using both stochastic and deterministic calculations, we show that there is indeed a possible pulse solution, but for a large host population size and for finite memory capacity, the pulse becomes unstable to the generation of new infections in its wake. This instability leads to an extended endemic infection pattern, demonstrating that the population-level behavior of virus infections can exhibit a wider range of behavior than had been previously realized.

Published by the American Physical Society
2024
Comment on “Tunneling-tip-induced collapse of the charge gap in the excitonic insulator
Ta2NiSe5
”
Authors: Kim Dowook , Kim So Young , Kim Jun Sung , Baddorf Arthur P. , Li An-Ping , Kim Tae-Hwan
Published: September 2024

In this study, we investigate the discrepancy between the estimate of Q. He [], who observed a remarkable collapse of the exciton gap in Ta2NiSe5 due to the electrostatic field between the scanning tunneling microscope (STM) tip and the sample, and that of a recent angle-resolved photoemission spectroscopy investigation [C. Chen , ]. It is proposed that a critical factor contributing to this discrepancy is due to He 's assumption of a constant work function of the STM tip. This assumption led to an underestimation of the tip-induced electric field. Using a literature value for the sample work function, a more substantial electric field strength is obtained, which resolves the apparent conflict between the doping estimates of these two techniques. Furthermore, our findings highlight the importance of the STM tip condition, which can significantly impact the tip work function and, consequently, influence the doping estimation in experiments involving tip-induced electric fields.

Published by the American Physical Society
2024
Generation of ultrashort ion pulses from ultrafast electron-stimulated desorption
Authors: Chirita Mihaila M. C. , Szabo G. L. , Redl A. , Goldberger M. , Niggas A. , Wilhelm R. A.
Published: September 2024

We present an efficient method to produce laser-triggered proton pulses well below 500 ps pulse width at keV energies. We use femtosecond photoelectron pulses emitted from a cathode to enable ultrafast electron-stimulated desorption of adsorbates on a stainless steel plate under ultrahigh vacuum conditions. While direct photoionization of atoms to form well-timed ion pulses can suffer from a laser-focus-limited large starting volume, in our method the two-dimensional starting plane of the ions is defined with nanometer precision at a solid surface. We clearly outline how the method could be used in the future to efficiently produce ion beam pulses in the (sub)picosecond range for pump-probe experiments with ions.

Published by the American Physical Society
2024
A decision-support system for choosing between traditional and alternative project delivery methods for bundled projects
Authors: Assaf Ghiwa , Assaad Rayan H.
Published: September 2024

Purpose

Project bundling is an innovative practice that groups or bundles several infrastructure projects into a single contract. While project bundling has various benefits, agencies are facing some challenges when bundling their projects, including properly assessing the feasibility (or infeasibility) of project delivery methods (PDMs) of interest. More specifically, project owners face the challenge of properly selecting between traditional and alternative PDMs for their bundled projects. Although some research efforts were devoted to providing guidelines in relation to different aspects related to project bundling, no previous study was conducted to help project owners performing PDMs-related feasibility analysis for bundled projects, which differ from normal, singly delivered projects. To fill this knowledge gap, this paper develops a decision-support tool that assists agencies in deciding whether they should select a traditional or alternative PDM (i.e. whether to go with the Design-Bid-Build (DBB) PDM or not) for their bundled projects.

Design/methodology/approach

An analytical methodology comprised of four main steps was followed in this paper. First, an expert survey was developed and distributed to industry experts to quantify the importance of 25 project bundling objectives. Second, principal component analysis was used to determine the weights for the different project bundling objectives. Third, a series of statistical tests was implemented to identify different feasibility tiers. Fourth, a user-friendly decision-support tool was developed, and its capabilities were demonstrated.

Findings

The results showed that six tiers exist to classify the feasibility (or infeasibility) of traditional PDMs (i.e. the DBB method) for bundled projects. The research outcomes have also reflected that the following five project bundling objectives contribute the most to making traditional PDMs (i.e. the DBB method) more feasible for bundled projects: (1) Having well-defined design features; (2) Requiring prior knowledge or experience with similar project size and scope; (3) Completing the overall project on schedule; (4) Keeping rate of expenditures within cash flow plan; and (5) Acquiring specific legislative, regulatory and jurisdictional requirements early on.

Originality/value

This research adds to the body of knowledge by equipping agencies and project owners with a decision-support system that helps them identify whether traditional or alternative PDMs are more appropriate for the specific objectives of their bundling program(s). By making the right PDM decision, project owners can enhance their bundling practices (especially in relation to the PDM proper selection) and ultimately the performance of their bundled projects.
Monotonic unbounded schemes transformer (MUST): an approach to remove undershoots and overshoots in family of unbounded schemes using finite-volume method
Authors: Yap Y.F. , Chai J.C.
Published: September 2024

Purpose

This paper presents a Monotonic Unbounded Schemes Transformer (MUST) approach to bound/monotonize (remove undershoots and overshoots) unbounded spatial differencing schemes automatically, and naturally. Automatically means the approach (1) captures the critical cell Peclet number when an unbounded scheme starts to produce physically unrealistic solution automatically, and (2) removes the undershoots and overshoots as part of the formulation without requiring human interventions. Naturally implies, all the terms in the discretization equation of the unbounded spatial differencing scheme are retained.

Design/methodology/approach

The authors do not formulate new higher-order scheme. MUST transforms an unbounded higher-order scheme into a bounded higher-order scheme.

Findings

The solutions obtained with MUST are identical to those without MUST when the cell Peclet number is smaller than the critical cell Peclet number. For cell Peclet numbers larger than the critical cell Peclet numbers, MUST sets the nodal values to the limiter value which can be derived for the problem at-hand. The authors propose a way to derive the limiter value. The authors tested MUST on the central differencing scheme, the second-order upwind differencing scheme and the QUICK differencing scheme. In all cases tested, MUST is able to (1) capture the critical cell Peclet numbers; the exact locations when overshoots and undershoots occur, and (2) limit the nodal value to the value of the limiter values. These are achieved by retaining all the discretization terms of the respective differencing schemes naturally and accomplished automatically as part of the discretization process. The authors demonstrated MUST using one-dimensional problems. Results for a two-dimensional convection–diffusion problem are shown in Appendix to show generality of MUST.

Originality/value

The authors present an original approach to convert any unbounded scheme to bounded scheme while retaining all the terms in the original discretization equation.
Project governance: the impact of environmental changes on governance adaptations in large-scale projects
Authors: Ika Lavagnon , Meredith Jack , Zwikael Ofer
Published: September 2024

Purpose

The performance of large-scale projects is often challenged due to major environmental changes that occur during their life. However, literature has paid little attention to the governance adaptations required to respond effectively to these changes. This paper aims to study changes in the project environment over time, the corresponding governance adaptations and their impact on project performance.

Design/methodology/approach

To ensure triangulation between two sources of evidence, we used both primary and secondary data sources and examined 14 projects through 2 studies, the first focused on seven documented, illustrative case projects and the second on interviews with senior and project managers involved in seven additional projects.

Findings

We found the key environmental changes that should trigger appropriate governance adaptations to be market evolutions, technological advancements and sociopolitical events. However, we also found that these necessary governance adaptations are not commonly implemented timely, sufficiently or effectively.

Originality/value

The paper distills the dynamics of large-scale projects in achieving project effectiveness and raises theoretical propositions on the combination of environmental changes and deficient governance adaptations that, over time, turns efficient projects into ineffective projects and discusses implications for theory and practice.
Relational business model for shared responsibility
Authors: Wieland Josef , Geraldo Schwengber Jessica
Published: September 2024

Purpose

This paper aims to contribute to the literature on corporate and leadership responsibility by proposing a relational business model for shared responsibility.

Design/methodology/approach

First, a literature review on corporate and leadership responsibility is presented and discussed. This is followed by an overview of existing public and private regulations and future perspectives that enforce and/or foster corporate and leadership responsibility. Based on the concepts of relational economics, relational leadership and proactive regulation, the theoretical foundations of a relational business model are derived. In addition, a decision model for the empirical application of the relational business model in ethical dilemma situations is developed and presented.

Findings

Theoretical elaboration of a relational business model and an associated relational decision-making approach.

Originality/value

This study contributes to a new way of doing business in terms of shared responsibility. Furthermore, corporate responsibility and leadership responsibility are usually researched as two distinct fields, with the former referring to the meso level and the latter to the micro level. A relational approach, which views leadership as a relational phenomenon, contributes to bridging both concepts.
Effects of escape room game‐based civics education on junior high school students' learning motivation, critical thinking and flow experience
Authors: Chen Hsiu‐Ling , Yohannes Abebayehu , Hung Ning‐Li
Published: September 2024

The escape room game is an example of digital game‐based learning that has become a popular learning tool in recent years. However, not enough is known about enthusiasm for and promising reports of the use of escape rooms in education. The purpose of this study was to investigate the effects of escape room game‐based civics education on eighth grade students' learning motivation, critical thinking and flow experience. To explore the effects, a quasi‐experimental pretest–posttest with a control group design method was employed. The participants were 76 eighth grade students. The subjects were divided into two groups: the experimental group, which used an escape room game, and the control group which used the Google classroom digital platform. The results of the study indicated that there was a significant difference between the two groups in favour of the experimental group in terms of learning motivation. There was a significant difference between the two groups' critical thinking in favour of the experimental group for the ‘assumption’ and ‘interpretation’ subscales of the critical thinking test. Regarding flow experience, the experimental group performed significantly better than the control group. Finally, based on the research results, suggestions are made for the future use of escape room games for teaching and for future research.

Practitioner notes

What is already known about this topic

Escape room games have substantial potential for enhancing learning, motivation and critical thinking.

Studies promoting mental flow, integrating complex skills and using multiple strategies in a game context are limited.

What this paper adds

Students' mind flow experience and critical thinking were enhanced through escape room games.

The escape room game made the learning process more varied, triggered students' interest, and improved their learning motivation.

This study compared the effect of escape room game‐based learning with the Google Classroom platform, not the traditional teaching approach.

Implications for practice and/or policy

Escape room games offer learners innovative opportunities to develop critical thinking skills.

Using an appropriately designed escape room as a game‐based learning environment is an effective and motivating game‐based learning approach.

The realistic and interactive nature of escape room games is an important factor that influences learners' mind‐flow experiences.
Unlocking the multifaceted molecular functions and diverse disease implications of lactylation
Authors: Jing Fengyang , Zhang Jianyun , Zhang Heyu , Li Tiejun
Published: September 2024

In recent years, a significant breakthrough has emerged in biology, the identification of lactylation, a novel post‐translational process. This intriguing modification is not limited to a specific class of proteins but occurs across a diverse range, including histones, signalling molecules, enzymes, and substrates. It can exert a broad regulatory role in various diseases, ranging from developmental anomalies and neurodegenerative disorders to inflammation and cancer. Thus, it presents exciting opportunities for exploring innovative treatment approaches. As a result, there has been a recent surge of research interest, leading to a deeper understanding of the molecular mechanisms and regulatory functions underlying lactylation within physiological and pathological processes. Here, we review the detection and molecular mechanisms of lactylation, from biological functions to disease effects, providing a systematic overview of the mechanisms and functions of this post‐translational modification.
Deep SVBRDF Acquisition and Modelling: A Survey
Authors: Kavoosighafi Behnaz , Hajisharif Saghi , Miandji Ehsan , Baravdish Gabriel , Cao Wen , Unger Jonas
Published: September 2024

Hand in hand with the rapid development of machine learning, deep learning and generative AI algorithms and architectures, the graphics community has seen a remarkable evolution of novel techniques for material and appearance capture. Typically, these machine‐learning‐driven methods and technologies, in contrast to traditional techniques, rely on only a single or very few input images, while enabling the recovery of detailed, high‐quality measurements of bi‐directional reflectance distribution functions, as well as the corresponding spatially varying material properties, also known as Spatially Varying Bi‐directional Reflectance Distribution Functions (SVBRDFs). Learning‐based approaches for appearance capture will play a key role in the development of new technologies that will exhibit a significant impact on virtually all domains of graphics. Therefore, to facilitate future research, this State‐of‐the‐Art Report (STAR) presents an in‐depth overview of the state‐of‐the‐art in machine‐learning‐driven material capture in general, and focuses on SVBRDF acquisition in particular, due to its importance in accurately modelling complex light interaction properties of real‐world materials. The overview includes a categorization of current methods along with a summary of each technique, an evaluation of their functionalities, their complexity in terms of acquisition requirements, computational aspects and usability constraints. The STAR is concluded by looking forward and summarizing open challenges in research and development toward predictive and general appearance capture in this field. A complete list of the methods and papers reviewed in this survey is available at computergraphics.on.liu.se/star_svbrdf_dl/.
Clinicopathological characteristics of low‐dose methotrexate‐induced epidermal dysmaturation: A study of 22 patients
Authors: Aebischer Valentin , Hahn Matthias , Lenders Daniela , Metzler Gisela , Schaller Martin , Silber Toni , Forchhammer Stephan
Published: September 2024

Background and Objective

Erosions of the skin and mucous membranes with epidermal dysmaturation are a known side effect of cytostatic chemotherapy regimens and can also be observed during low‐dose methotrexate (MTX) therapy. The study aimed to delineate the clinical and histopathological alterations.

Patients and Methods

A database search of the archive for dermatopathology was conducted, identifying 22 patients who developed epidermal dysmaturation on low‐dose MTX. Clinical and laboratory changes, along with an array of histologic parameters were analyzed and statistically evaluated using SPSS.

Results

Patients were predominantly female with a mean age of 69.1 years. The main indications were psoriasis vulgaris and rheumatoid arthritis. Clinically, patients mostly presented erosive plaques at the injection site, on mucosal surfaces, and disseminated lesions. Most patients showed normal laboratory values. Histopathologically, key findings included enlarged keratinocytes with pale cytoplasm and enlarged nuclei with prominent nucleoli, along with the degeneration of the basal layer. Consistent observations in the dermal compartment included infiltration of neutrophilic granulocytes, lymphocytes, and histiocytes.

Conclusions

This study proposes clinicopathological criteria for the diagnosis of MTX‐associated skin toxicity, aiming to increase awareness among clinicians and pathologists for early diagnosis. Early recognition can prevent potentially life‐threatening progression.
Cortical oscillations are modified by expertise in dance and music: Evidence from live dance audience
Authors: Poikonen Hanna , Tervaniemi Mari , Trainor Laurel
Published: September 2024

Over the past decades, the focus of brain research has expanded from using strictly controlled stimuli towards understanding brain functioning in complex naturalistic contexts. Interest has increased in measuring brain processes in natural interaction, including classrooms, theatres, concerts and museums to understand the brain functions in the real world. Here, we examined how watching a live dance performance with music in a real‐world dance performance setting engages the brains of the spectators. Expertise in dance or music has been shown to modify brain functions, including when watching dance or listening to music. Therefore, we recorded electroencephalography (EEG) from an audience of dancers, musicians and novices as they watched the live dance performance and analysed their cortical oscillations. We compared intrabrain oscillations when participants watched the performance (with music) or listened to the music alone without the dance. We found that dancers have stronger fronto‐central and parieto‐occipital theta phase synchrony (4–8 Hz) than novices when watching dance, likely reflecting the effects of dance experience on motor imagery, multisensory and social interaction processes. Also, compared with novices, dancers had stronger delta phase synchrony (0.5–4 Hz) when listening to music, and musicians had stronger delta phase synchrony when watching dance, suggesting expertise in music and dance enhances sensitivity or attention to temporal regularities in movement and sound.
L2 discourse marker use in interaction: The case of pues in Spanish
Authors: Dickerson Sydney , Czerwionka Lori
Published: September 2024

While discourse markers (DMs) are crucial for coherence and interactional competence, previous research suggests that learners' usage of DMs differs from L1 speakers. Prior research has taken either a discourse‐functional or interactional approach, yet combining these two methods may provide greater understanding of the unique learner communicative needs that drive the acquisition and use of DMs. This investigation contributes to research on interlanguage DM use by quantitatively investigating the frequency and functional distribution of the Spanish DM pues by L2 and L1 speakers of Spanish from a discourse‐functional perspective and qualitatively examining pues as an interactional resource. Oral interviews with 58 L2 and 14 L1 speakers of Spanish were analyzed, revealing distinct frequency and distributional patterns across groups and unique L2 interactional needs that are supported with the DM pues. Results inform L2 learners and teachers of the importance of DMs for interactions and provide classroom implications.
Recent developments shaping the future of antimicrobial edible food packaging: a review
Authors: Yemenicioğlu Ahmet
Published: September 2024

This article aimed at reviewing recent developments shaping the future of antimicrobial edible food packaging. The main issues discussed in the article are (i) factors (e.g. waste valorisation, sustainability, health and environmental concerns, religious concerns, etc.) causing emerging of alternative hydrocolloids extracted from farming/processing wastes of plants, animals, fungi, insects, snails, etc. as antimicrobial edible packaging material; (ii) emerging methods of manufacturing antimicrobial packaging (e.g. extruded and co‐extruded antimicrobial casings, antimicrobial electrospun mats, and electrosprayed films, coatings and particles); (iii) emerging concepts in using natural antimicrobials in edible packaging such as using narrow‐ or broad‐spectrum antimicrobials, synergetic mixtures, and controlled release strategies based on nanoencapsulation (e.g. Pickering emulsions, nanoemulsions, inclusion complexes, solid lipid nanoparticles and nanostructured lipid carriers). This review helps discovering the future of active edible packaging that is expected to play a central role in improving food safety and quality, human health and environmentally friendly practices.
Work‐Related Strain, Sense of Coherence and Intercultural Sensitivity Among Mental Health Nurses in Qatar: A Cross‐Sectional Study
Authors: Badanapurkar Ashishkumar , Nelson Deborah , Nazarene Ananth , Smith Katja Warwick , Phiri Lazarus , Varghese Sejo , Ramapurath Shiju
Published: September 2024

Migrant nurses face many challenges as they adapt and assimilate into their new working environments. The aim of this cross‐sectional study was to investigate the perceptions of work‐related strain, sense of coherence and intercultural sensitivity among nurses who were employed at a public mental health facility in Qatar. We used three self‐report questionnaires: the work‐related strain inventory, sense of coherence scale and an intercultural sensitivity scale. A cohort of 136 nurses voluntarily engaged in the study. The majority of participants were male, migrated from South Asia and were in their mid‐30s. The study found that both sense of coherence and intercultural sensitivity were inversely proportional to work‐related strain. Work‐related strain was found to be lower than expected; the factors that appear to protect against work‐related strain include longer clinical experience, a high sense of coherence, and intercultural sensitivity. Additionally, greater age and extended clinical experience, combined with a history of work in three or more countries, associated with higher scores on the sense of coherence scale. Lastly, being female, having a postgraduate degree and holding a senior‐level position were associated with increased intercultural sensitivity. As nurses' migration across national and international borders increases in response to global demand, this study has important implications for nursing administrators, educators and policymakers in relation to the development and implementation of strategies to enhance nurses' sense of coherence and intercultural sensitivity and prevent work‐related strain.

Trial Registration number: NCT04196751.
Kinesin‐1‐like protein PSS1 is essential for full‐length homologous pairing and synapsis in rice meiosis
Authors: Zhou Yue , Li Yafei , You Hanli , Chen Jiawei , Wang Bingxin , Wen Minsi , Zhang Yansong , Tang Ding , Shen Yi , Yu Hengxiu , Cheng Zhukuan
Published: September 2024

The pairing and synapsis of homologous chromosomes are crucial for their correct segregation during meiosis. The LINC (Linker of Nucleoskeleton and Cytoskeleton) complex can recruit kinesin protein at the nuclear envelope, affecting telomere bouquet formation and homologous pairing. Kinesin‐1‐like protein Pollen Semi‐Sterility1 (PSS1) plays a pivotal role in male meiotic chromosomal behavior and is essential for fertility in rice. However, its exact role in meiosis, especially as kinesin involved in homologous pairing and synapsis, has not been fully elucidated. Here, we generated three pss1 mutants by genome editing technology to dissect PSS1 biological functions in meiosis. The pss1 mutants exhibit alterations in the radial microtubule organization at pachytene and manifest a deficiency in telomere clustering, which is critical for full‐length homologous pairing. We reveal that PSS1 serves as a key mediator between chromosomes and cytoskeleton, thereby regulating microtubule organization and transmitting the force to nuclei to facilitate homologous chromosome pairing and synapsis in meiosis.
ВЛИЯНИЕ УСЛОВИЙ КУЛЬТИВИРОВАНИЯ НА ПРОДУКЦИЮ ФУКОКСАНТИНА И ПОЛИНЕНАСЫЩЕННЫХ ЖИРНЫХ КИСЛОТ
Authors: Karabekova A. N. , Zayadan B. K.
Published: September 2024

В контексте нутрицевтики и морской фармакологии микроводорослей особый интерес вызывают, жирные кислоты с полиненасыщенные длинными цепями (ЖК-ПНЖК), такие как эйкозапентаеновая (ЭПК, 20:5ω3) и докозагексаеновая кислота (ДГК, 22:6ω3), и каротиноиды, которые синтезируются фотосинтезирующими микроводорослями, включая бурые, золотистые и диатомовые водоросли.
Фукоксантин (Фк) — каротиноиды пигмент из группы ксантофиллов, который составляет примерно 10% от общего количества каротиноидов на Земле. В настоящее время P. tricornutum являктся модельным диатомовым организмом с высокой производительностью фукоксантина (от 2 до 60 мг/г), благодаря своим высоким темпам роста и простоте культивирования.
Однако, несмотря на обширное разнообразие микроводорослей, способных синтезировать фукоксантин, для коммерческого производства изучены лишь несколько видов. Среди множества проблем при интенсивном культивировании микроводорослей важной является обеспечение их минеральными элементами, особенно концентрацией NO₃⁻, а также влиянием спектральных характеристик света.
Цель исследования заключается в проведении скрининга продуцентов фукоксантина в пресноводных фотоавтотрофных микроводорослях, относящихся к классу Pavlovophyceae (Haptophyta) и Chrysophyceae.
Методика исследования включала культивирование коллекционных штаммов D. noctivaga, C. species I и H. magna в среде BBM с различными концентрациями азота (N-NO₃) в 3- и 6-кратном измерении при оптимальной температуре 23℃ и интенсивности тусклого света примерно 230 µмоль м⁻² с⁻¹. Барботаж стерилизованного воздуха, обогащенного CO₂ до 2% (по объему), осуществлялся для обеспечения необходимых условий.
Результаты исследования показали, что среди рассмотренных видов D. noctivaga выделилась наибольшей оптической плотностью (ОП-750 – 3,47 мг/г), концентрацией биомассы (5,35 г/л), сухой массой (10,7 мг) и содержанием Фк (4,0 мг/г сухой биомассы) и ЖК-ПНЖК (37,68 мг/г сухой массы), что превышает значения для других исследованных видов в шесть раз.
Выводы исследования показали, что D. noctivaga в условиях культивирования достигла наибольшей плотности сухой биомассы и высокого содержания длинноцепочечных жирных кислот. Рост был значительным в пальмеллоидной стадии, но прекратился после перехода в стадию агеллят. Важно отметить, что исследование Kanamoto, A. (2021) также выделяет микроводоросль Pavlova spp. (Haptophyta) благодаря высокому содержанию фукоксантина (20,9 мг/г) и тонкой клеточной стенке, что облегчает экстракцию фукоксантина.
ИЗУЧЕНИЕ МЕТАЛЛОПРОТЕАЗ М14 И М42 ШТАММА BACILLUS PARALICHENIFORMIS
Authors: Мадуахасова А.К. , Мусахметов А.С. , Хасенов Б.Б.
Published: September 2024

Протеазы являются ферментами, гидролизующими белки по пептидным связям, и классифицируются на семейства сериновых, цистеиновых, аспартатных и металлопротеаз. Протеазы, в особенности, микробиального происхождения используются в различных отраслях человеческой деятельности. Штаммы-продуценты бациллярных протеаз способны расти на недорогих питательных средах, что имеет немаловажное значение для индустрии. Целью работы являлось получение рекомбинантных металлопротеаз М14 и М42 бацилярного происхождения и изучение их свойств.
На основании последовательности генома штамма Bacillus paralicheniformis (GenBank NCBI под номером доступа CP124861) подобраны праймеры для клонирования генов металлопротеаз М14 и М42 с молекулярными массами 60,6 кДа и 38,2 кДа, соответственно. Гены были клонированы в составе бактериального экспрессионного вектора рЕТ-28с(+) по сайтам BamHI и XhoI и встроены под контроль промотора Т7. Биоинформатический анализ показал, что металлопротеаза М14 содержит сигнальный пептид MNIQKRVQALLAAAAMFAGLMVSDAVHA, который был удален при клонировании.
Путем плазмидной экспрессии в штамме Escherichia coli ArcticExpress(DE3)RP получены рекомбинантные белки rМ14 и rМ42. Индукцию для гетерологичной экспрессии осуществляли путем добавления 0,5 мМ изопропил-β-тиогалактопиранозида. Очистку rМ14 и rМ42 из бактериального лизата осуществляли методом металлоаффинной хроматографии с использованием Ni-NTA сорбента. Очищенный рекомбинантные белки были диализованы на мембране с порогом отсечения 14 кДа. Выход рекомбинантных белков rМ14 и rМ42 составил 27,5 мг и 1,67 мг с 1 литра индуцированной культуры, соответственно.
Изучение биохимических свойств показало, что металлопротеазы rМ14 и rМ42 активны при 50°С в буфере Tris-HCl с рН 7,0. Зимографический анализ на казеине, сополимеризованным с полиакриламидным гелем подтвердил протеолитическую активность rМ14 и rМ42.
Полученными рекомбинантными белками были иммунизированы кролики. Иммунизацию проводили в течение 1 месяца. После подтверждения иммунного ответа, была получена сыворотка, из которой были выделены антитела анти-rM14 и анти-rM42 путем высаливания сульфатом аммония с последующим диализом. С помощью данных антител методом вестерн-блоттинга была проверена секреция металлопротеаз М14 и М42 в энзиматическом экстракте, полученном путем культивирования нативного штамма Bacillus paralicheniformis на перьевой среде. Установлено, что в энзиматическом экстракте штамма Bacillus paralicheniformis присутствует металлопротеаза М14 и отсутствует М42, что можно объяснить определяющей ролью сигнального пептида.
В дальнейшем будет продолжено изучение металлопротеаз rМ14 и rМ42, а полученные антитела rM14 и анти-rM42 будут использованы для определения уровня накопления нативных металлопротеаз в секреторной и внутриклеточной протеоме протеолитических штаммов рода Bacillus при их культивировании на различных субстратах.
MORPHOLOGICAL AND GENETIC CHARACTERISTICS OF POPULATIONS OF THE MAIN CARRIER OF PLAGUE RHOMBOMYS OPIMUS LICHT., 1823 IN THE SOUTH OF KAZAKHSTAN
Authors: Ospan T.B.
Published: September 2024

The great gerbil (Rhombomys opimus, Licht., 1823) is the primary carrier of various bacteriological, viral, and rickettsial diseases in Central Asia, Mongolia, and China. Currently, the systematic position of the great gerbil remains unclear. However, understanding the biology of the species that carry various pathogens is crucial for ensuring public safety. According to classical concepts, plague in nature exists as a complex three-part parasitic system: the causative agent of plague (Yersinia pestis), arthropod carriers or vectors (usually fleas and ticks), and warm-blooded hosts. Modern data suggest the presence of a fourth component - soil invertebrates. The most common parasitic triad in recent outbreaks consists of the causative agent of plague (Yersinia pestis), carried by fleas of the genus Xenopsylla, and the primary carrier, the great gerbil.
Five populations inhabit the South Balkhash basin, with their northern border limited by Lake Balkhash. The colonies of the Taukum’s population are located on the left bank of the lower reaches of the Ili River, in the sands of the Taukum desert. On the right bank of the Ile River, the largest population, Saryesik-Atyrau, is spread out, with the Lyukkum’s population to the east of it, separated by the Karatal River in the west and the Aksu River in the east. Between the Aksu and Lepsy rivers lies the Aralkum’s population, and at the western point of Lake Balkhash lies the Lepsy-Ayaguz’s population. South of the Balkhash group of populations, four populations of the great gerbil are identified, located along the Ili River above the Kapshagai Reservoir: on the right bank, Prialtynemel’s and Karakum’s populations, and on the left bank, Syugatinian’s and Karadala’s populations, separated by the Sharyn River. Another group is the tenth population of the great gerbil – Dzhungarian’s – located southeast of Lake Alakol.
Using morphological methods, craniometric indicators of the above populations were studied, revealing two regional complexes in the Balkhash-Alakol basin: the Balkhash region’s and Dzhungar's. Phylogenetic data combined samples captured in the southern Balkhash region into one cluster. In summary, we have several geographically isolated populations that differ phenotypically and genetically. These populations have evolved alongside specific strains of the plague pathogen and species of flea carriers, resulting in significant differences in resistance to various zoonotic infections.
Draft genome sequence of two
Aspergillus aculeatus
isolated from cashew nuts from coastal Kenya
Authors: Aloo Manase Onyango , Gachanja Pauline Wambui , Muzami Eugene Mwanza , Katua Kyalo , Mukhebi Dennis Wamalabe , Musangi Colletah Rhoda , Juma Bicko Steve , Mbinda Wilton Mwema
Published: September 2024

Aspergillus aculeatus
is a common saprophyte and ubiquitous fungus belonging to section
Nigri
. They produce diverse secondary metabolites which are important in biological processes and industrial applications. We present the draft genome sequences of two
A. aculeatus
isolated from cashew nuts from coastal Kenya.
HCMV detection in Asian gastric cancer RNA-seq data sets and clinical validation in Indian GC patients reveals the HCMV-GC specific gene signatures
Authors: Krishnamoorthy Pandikannan , Raj Athira S. , Das Nilanjana , Chenkual Saia , Pautu Jeremy L. , Ralte Lalengkimi , Senthil Kumar Nachimuthu , Kumar Himanshu
Published: September 2024

Gastric cancer (GC) prevalence is very high in the Asian population. Oncogenic viruses play a crucial role in the progression of different types of cancers. Through reanalysis of clinical RNA-seq data sets derived from Asian GC patients, this study identified the presence of human cytomegalovirus (HCMV) in Asian GC tumors, next to the well-studied association of EBV. Clinical recruitment of the Indian GC cohort and screening for HCMV presence identified a 14.28% occurrence, similar to that observed in the bioinformatics analysis. A combinatorial approach of rank-based meta-analysis and ranking of groups based on an expectation-maximization algorithm identified that the upregulated LINC02864 and MAGEA10 correlated with poor survival of GC patients and downregulated tumor suppressor genes enriching for gastric acid secretion pathway to be associated with HCMV-positive GC patients, revealing the progressive role of HCMV infection in GC. Genes that discriminate between different stages of GC were identified through feature selection implemented in a machine-learning approach. LTF and KLK10 expressions were found to be specifically dysregulated by HCMV and can also indicate the GC stages. The results of this study will guide future studies to identify the functional role of these genes in the HCMV-associated GC.

IMPORTANCE

Nearly 75% of gastric cancer (GC) cases reported globally are from the Asian population. Most existing public databases, such as TCGA, comprise only a fractional portion of data derived from Asian ancestry. This study identified EBV and human cytomegalovirus (HCMV)'s higher detection in GC patients. The presence and role of EBV associated with GC are well-known, and the observation of HCMV prompted us to validate the findings in a small cohort of 40 Indian GC patients. We observed a 14.28% occurrence of HCMV in the Indian cohort, similar to that observed from next-generation sequencing. A combinatorial approach of rank-based meta-analysis and ranking of groups based on an expectation-maximization algorithm identified that the upregulated LINC02864 and MAGEA10 correlated with poor survival of GC patients and downregulated tumor suppressor genes enriching for gastric acid secretion pathway to be associated with HCMV-positive GC patients, revealing the progressive role of HCMV infection in GC.
Water chlorination increases the relative abundance of an antibiotic resistance marker in developing sourdough starters
Authors: Lau Pearson , Jain Swapan , Perron Gabriel G.
Published: September 2024

Multiple factors explain the proper development of sourdough starters. Although the role of raw ingredients and geography, among other things, have been widely studied recently, the possible effect of air quality and water chlorination on the overall bacterial communities associated with sourdough remains to be explored. Here, using
16S rRNA
amplicon sequencing, we show that clean, filtered-air severely limited the presence of lactic acid bacteria in sourdough starters, suggesting that surrounding air is an important source of microorganisms necessary for the development of sourdough starters. We also show that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, using targeted sequencing, which offers a higher resolution, we found that the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic-resistance genes in spoilage and pathogenic bacteria, increased significantly with the level of water chlorination. Although our results suggest that water chlorination might not impact sourdough starters at a deep phylogenetic level, they indicate that it can favor the spread of genetic elements associated with spoilage bacteria.

IMPORTANCE

Proper development of sourdough starters is critical for making tasty and healthy bread. Although many factors contributing to sourdough development have been studied, the effect of water chlorination on the bacterial communities in sourdough has been largely ignored. Researchers used sequencing techniques to investigate this effect and found that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, they discovered that water chlorination could increase the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic resistance genes in spoilage and pathogenic bacteria. This suggests that water chlorination could favor the growth of key spoilage bacteria and compromise the quality and safety of the bread. These findings emphasize the importance of considering water quality when developing sourdough starters for the best possible bread.
Airway management in a child with complete tracheal transection following blunt laryngotracheal trauma
Authors: Joselyn Anita Shirley , Joseph Chris Maria , Vijayanand Nitish
Published: September 2024

Blunt injury to the neck following high-impact trauma can be associated with airway injury. The anaesthesiologist should have a high index of suspicion for the same when the patient presents for any surgical intervention for trauma. A complete evaluation of the tracheobronchial tree using a flexible bronchoscope is essential before instrumenting the airway in a child with suspected laryngotracheal trauma because blind intubation can convert a lesser grade airway trauma into a significant one. We report the airway management in a child belonging to middle childhood, who presented with complete tracheal transection after a blunt laryngotracheal trauma.
Investigation of end-stage kidney disease risk prediction in an ethnically diverse cohort of people with type 2 diabetes: use of kidney failure risk equation
Authors: Goubar Aicha , Mangelis Anastasios , Thomas Stephen , Fountoulakis Nikolaos , Collins Julian , Ayis Salma , Karalliedde Janaka
Published: September 2024

Introduction

The four variable kidney failure (KF) risk equation (KFRE) is recommended to estimate KF risk (ie, need for dialysis or kidney transplantation). Earlier referral to clinical kidney services for people with high-risk of kidney failure can ensure appropriate care, education and support are in place pre-emptively. There are limited data on investigating the performance of KFRE in estimating risk of end-stage kidney disease (ESKD) in people with type 2 diabetes mellitus (T2DM) and chronic kidney disease (CKD). The primary ESKD endpoint event was defined as estimated glomerular filtration rate (eGFR) <10 mL/min/1.73 m2and secondary endpoint eGFR <15 mL/min/1.73 m2.

Research design and methods

We studied 7296 people (30% women, 41% African-Caribbean, 45% Caucasian) with T2DM and CKD (eGFR median (range) 48 (15–59) mL/min/1.73 m2) were included at two hospitals in London (median follow-up 10.2 years). Time to ESKD event was the endpoint and Concordance index (C-index) was used to assess KFRE’s discrimination of those experiencing ESKD from those who did not. Mean (integrated calibration index (ICI)) and 90th percentile (E90) of the difference between observed and predicted risks were used as calibration metrics.

Results

Of the cohort 746 (10.2%) reached ESKD primary event (135 (1.9%) and 339 (4.5%) over 2 and 5 years, respectively). Similarly, 1130 (15.5%) reached the secondary endpoint (270 (3.7%) and 547 (7.5%) over 2 and 5 years, respectively). The C-index for the primary endpoint was 0.842 (95% CI 0.836 to 0.848) and 0.816 (95% CI 0.812 to 0.820) for 2 and 5 years, respectively. KFRE ‘under-predicted’ ESKD risk overall and by ethnic group. Likewise, the C-index for secondary endpoint was 0.843 (0.839–0.847) and 0.801 (0.798–0.804) for 2 and 5 years, respectively. KFRE performance analysis performed more optimally with the primary endpoint with 50% enhancement of the calibration metrics than with the secondary endpoint. KFRE recalibration improved ICI by 50% and E90 by more than 78%.

Conclusions

Although derived for predicting KF, KFRE also demonstrated good discrimination for ESKD outcome. Further studies are needed to identify variables/biomarkers that may improve KFRE’s performance/calibration and to aid the development of other predictive models to enable early identification of people at risk of advanced stages of CKD prior to onset of KF.