bluuebunny/crossref_metadata_2025 huggingface dataset:
Harnessing generative AI to decode enzyme catalysis and evolution for enhanced engineering
Authors: Xie Wen Jun , Warshel Arieh
Published: December 2023

Enzymes, as paramount protein catalysts, occupy a central role in fostering remarkable progress across numerous fields. However, the intricacy of sequence-function relationships continues to obscure our grasp of enzyme behaviors and curtails our capabilities in rational enzyme engineering. Generative artificial intelligence (AI), known for its proficiency in handling intricate data distributions, holds the potential to offer novel perspectives in enzyme research. Generative models could discern elusive patterns within the vast sequence space and uncover new functional enzyme sequences. This review highlights the recent advancements in employing generative AI for enzyme sequence analysis. We delve into the impact of generative AI in predicting mutation effects on enzyme fitness, catalytic activity and stability, rationalizing the laboratory evolution of de novo enzymes, and decoding protein sequence semantics and their application in enzyme engineering. Notably, the prediction of catalytic activity and stability of enzymes using natural protein sequences serves as a vital link, indicating how enzyme catalysis shapes enzyme evolution. Overall, we foresee that the integration of generative AI into enzyme studies will remarkably enhance our knowledge of enzymes and expedite the creation of superior biocatalysts.
Evolution of Chronic Lesion Tissue in RRMS patients: An association with disease progression
Authors: Klistorner Samuel , Barnett Michael H , Parratt John , Yiannikas Con , Klistorner Alexander
Published: December 2023

Background and Objective

This study examines the long-term changes in Chronic Lesion Tissue (CLT) among relapsing and remitting MS (RRMS) patients, focusing on its impact on clinical and radiological disease progression indicators.

Methods

The study involved 72 MS patients with at least a 5-year follow-up. Annual assessments used 3D FLAIR, pre- and post-contrast 3D T1, and diffusion-weighted MRI. Lesion segmentation was conducted using iQ-MSTMsoftware, while brain structures were segmented using AssemblyNet. Volumetric changes in CLT were tracked using a custom-designed pipeline.

Results

Throughout the follow-up period, the volume of CLT in the entire cohort increased continuously and steadily, averaging 7.75±8.2% or 315±465 mm³ per year. Patients with expanding CLT experienced significantly faster brain atrophy, affecting both white and grey matter, particularly in the brain’s central area. Expanded CLT was also associated with higher and worsening EDSS scores, in contrast to the stable CLT group, where EDSS remained unchanged.

Conclusion

This study demonstrates that, over a period of up to 7 years, patient-specific enlargement of CLT, where present, progresses at a constant rate and significantly influences disease progression.
AncestryGrapher toolkit: Python command-line pipelines to visualize global– and local– ancestry inferences from the RFMix2 software
Authors: Lisi Alessandro , Campbell Michael C.
Published: December 2023

Admixture is a fundamental process that has shaped patterns of genetic variation and the risk for disease in human populations. Here, we introduce the AncestryGrapher toolkit for visualizing inferred global– and local– ancestry by theRFMix v.2software. Currently, there is no straightforward method to summarize population ancestry results fromRFMixanalysis.

Results

To demonstrate the utility of our method, we applied the AncestryGrapher toolkit to the output files ofRFMixv.2 to visualize the global and local ancestry of individuals in the Mozabite Berber population from North Africa. Our results showed that the Mozabite Berbers derived their ancestry from the Middle East, Europe, and sub-Saharan Africa (global ancestry). Furthermore, we found that the population origin of ancestry varied considerably along chromosomes. More specifically, we observed variance in ancestry along chromosome 2 (local ancestry), in the genomic region containing the common genetic polymorphisms associated with lactase persistence, a trait known to be under strong positive selection. This finding indicates that the demographic process of admixture has influenced patterns of allelic variation in addition to natural selection. Overall, the AncestryGrapher toolkit facilitates the exploration, interpretation, and reporting of ancestry patterns in human populations.

Availability and implementation

The AncestryGrapher toolkit is free and open source onhttps://github.com/alisi1989/RFmix2-Pipeline-to-plot.
Auditory training alters the cortical representation of both learned and task irrelevant sound features
Authors: Atilgan Huriye , Walker Kerry M , King Andrew J. , Schnupp Jan W. , Bizley Jennifer K.
Published: December 2023

Auditory learning is supported by long-term changes in the neural processing of sound. We mapped neural sensitivity to timbre, pitch and location in animals trained to discriminate the identity of artificial vowels based on their spectral timbre in a two-alternative forced choice (T2AFC, n=3, female ferrets) or to detect changes in fundamental frequency or timbre of repeating artificial vowels in a go/no-go task (n=2 female ferrets). Neural responses were recorded under anaesthesia in two primary cortical fields and two tonotopically organised non-primary fields. Responses were compared these data to that of naïve control animals. We observed that in both groups of trained animals the overall sensitivity to sound timbre was reduced across three cortical fields but enhanced in non-primary field PSF. Neural responses in trained animals were able to discriminate vowels that differed in either their first or second formant frequency unlike control animals whose sensitivity was mostly driven by changes in the second formant. Neural responses in the T2AFC animals, who were required to generalise across pitch when discriminating timbre, became less modulated by fundamental frequency, while those in the go/no-go animals were unchanged relative to controls. Finally, both trained groups showed increased spatial sensitivity and altered tuning. Trained animals showed an enhanced representation of the midline, where the speaker was located in the experimental chamber. Overall, these results demonstrate training elicited widespread changes in the way in which auditory cortical neurons represent complex sounds with changes in how both task relevant and task-irrelevant features were represented.
A Comprehensive Survey of Scoring Functions for Protein Docking Models
Authors: Shirali Azam , Stebliankin Vitalii , Shi Jimeng , Narasimhan Giri
Published: December 2023

The protein-protein docking problem is fundamental to our understanding of how proteins interact. It is also important because of its relevance to drug discovery and vaccine design. Docking methods typically involve two steps. The first step generates many possible candidate conformations, while the second step evaluates the candidates using some scoring function. Despite numerous experiments with many innovative scoring functions, a good scoring function for docking remains elusive. Deep learning models offer alternatives to using explicit empirical or mathematical functions for scoring protein-protein complexes. In this study, we perform a comprehensive survey of the state-of-the-art scoring functions by considering the most popular and highly performant approaches for scoring protein-protein complexes, evaluating their strengths and weaknesses to aid researchers in understanding progress made in this field. Our survey compares the state-of-the-art in classical and deep learning-based scoring methods.
Collective Impacts of Demographic and Clinical Factors on Psycho-emotional States of Patients with Hepatocellular Carcinoma: A Cross-Sectional Study
Authors: Liang Crystal Chia-Chun , Pan I-Ju
Published: December 2023

Background

To appraise comprehensively the demographic and clinical factors that may collectively contribute to demoralization, depression and negative meaning of life in patients with cancer, employing hepatocellular carcinoma (HCC) as the representative investigative subject.

Purpose

To appraise comprehensively the demographic and clinical factors that collectively contribute to demoralization, depression and negative meaning of life in patients with cancer, employing hepatocellular carcinoma (HCC) as the representative malignancy for investigation in a Taiwanese population.

Design

A retrospective cross-sectional study from 2019–2020 on 250 HCC patients in hospitalized and following the STROBE guidelines.

Methods

Prevalence was estimated by G-power; and associations between demographic or clinical factors and scores of Mandarin versions of Demoralization Scale (DS-MV), Center for Epidemiologic Studies Depression Scale (CES-D) or Meaning in Life Scale (MiLs) were evaluated by Chi-square test or Pearson’s product-moment correlation.

Results

Factors with DS-MV scores higher than 30 included marital status, children as primary caregiver, gender and metastasis. Factors with CES-D scores higher than 16 included marital status, children as primary caregiver, age, monthly financial support and cancer comorbidity. Factors with MiLs scores less than 7 included marital status, and recurrence or duration of cancer.

Conclusions

Marital status is a major contributing factor to all three psychological states. Children as primary caregiver impacts more critically than spouse on both demoralization and depression; gender and metastasis are akin to demoralization; age, monthly financial support and cancer comorbidity contribute to depression; and recurrence and duration of cancer impact on negative meaning of life.

Impact

This is first time that collective demographic and clinical factors on the mental health of patients with liver cancer are identified. Our findings would encourage clinical nurses to be more conscious of the contribution of these factors on the emotional states of patients with cancer when performing their daily duties.
First cleavage is a manifestation of the geometry of the unfertilized oocyte: implications for monozygotic twinning in mice
Authors: Nolte Thomas , Halabian Reza , Israel Steffen , Suzuki Yutaka , Fuellen Georg , Makalowski Wojtek , Boiani Michele
Published: December 2023

A long-standing question in mammalian embryology is whether regional differences of oocyte composition matter for the properties of blastomeres receiving those regions after fertilization. A hitherto untested hypothesis is that allocation depends on the orientation of 1stcleavage. However, the orientation is influenced by the site of sperm entry, which can be almost anywhere on the membrane of oocytes when these are inseminated. This variability undermines consistency and reproducibility of studies. Therefore, we harnessed the intracytoplasmic sperm injection to impose the site of fertilization in three specific ooplasmic regions (animal pole, vegetal pole, equator) in mice. Notwithstanding this categorical distinction, after 1stcleavage, the sister blastomeres differed from each other nearly the same way, as measured by gene expression and twin blastocysts formation following 2-cell embryo splitting. We reasoned that either the oocyte territories did not matter, or their effect was obscured by other factors. To shed light on these possibilities, we immobilized the oocytes on the micromanipulation stage during sperm injection and for 24 h thereafter. Imaging revealed that the orientation of 1stcleavage, instead of varying with the fertilization site, followed the shorter diameter of the unfertilized oocyte. This led in most cases to the segregation of animal and vegetal hemispheres into the sister blastomeres of 2-cell embryos. Since one blastomere received more of the animal materials and the other blastomere more of the vegetal materials, this offers a rationale to explain the distinct properties of monozygotic twins derived from 2-cell embryos in mice.
The effects of cell-cell orientation in modeling the hallmarks of lung cancer in vitro
Authors: Espinoza Andres S. , McVicar Rachael N. , Finlay Darren , Murad Rabi , Vuori Kristiina , Grimmig Bethany A. , Bush Anne , Smith Emily , Mandel-Clausen Thomas , McGee Heather M. , Snyder Evan Y. , Leibel Sandra L.
Published: December 2023

To better understand and develop treatments for lung cancer, it is important to have reliable and physiologically relevant culture models. Traditional methods of growing lung cancer cells in two- dimensional (2D) monolayers have limitations in mimicking the complex architecture and microenvironment of lung tumorsin vivo, limiting their value as reliably informative disease models. In this study, we introduce a new cell culture platform called “tumoroids,” which involves growing HCC827 lung cancer cells in three-dimensional (3D) configurations. By comparing transcriptional profiles of HCC827 cells grown as tumoroids versus the same cells grown in 2D monolayers, we investigate how cell-cell orientation and signaling impact the cancer-driving properties of lung cancer. We examine key features associated with cancer progression, such as epithelial mesenchymal transition, replicative ability, and induction of angiogenesis. Additionally, we assess the functional characteristics of the 3D tumoroid culture system by subjecting the cells to irradiation. Through comparing the gene expression profiles of the 3D tumoroid and 2D cultures with those of primary human lung adenocarcinoma, we find that the 3D tumoroid cultures more closely resemble the characteristics of primary human lung cancer. This suggests that the 3D tumoroid culture platform can serve as a valuablein vitromodel for studying lung cancer, offering greater clinical relevance compared to traditional 2D cultures. Overall, this study highlights the importance of using advanced culture models like 3D tumoroids to improve our understanding of lung cancer and facilitate the development of effective treatments.
Genome-wide characterisation of pathogenicity-related proteins inMycena citricolor,the causal agent of the American Leaf Spot in coffee
Authors: Larke-Mejía N. L. , Arciniegas N. , Di Palma F. , Angel C C. A. , De Vega J. J.
Published: December 2023

Mycena citricoloris a fungus that causes the American Leaf Spot (ALS) disease in multiple hosts, including coffee and avocado. This hemibiotroph penetrates the plant through damage induced by oxalic acid. This can cause 20-90% crop losses in coffee depending on the environmental and production conditions.M. citricoloris the only known pathogenic species in theMycenagenus, a large group of saprophytic mushrooms. Comparing the saprophytic and pathogenic genomes can allow us to identify genetic machinery associated with the pathogen’s genome-wide functional acquisitions to cause disease.

To identify pathogenicity-related genes inM. citricolor, we analysed protein family copy-number variation, secretome prediction, and homology to known virulence factors in twoM. citricolorassemblies, including a newly assembled and annotated long-read genome. We found that the pathogenicM. citricolorhad a higher proportion of secreted genes expanded in copy-number, and expanded gene copies homologous to known virulence factors than the saprophyticMycena. We shortlisted over 300 candidate genes in eachM.citricolorassembly. Focusing on genes strongly regulated during plant interaction, we found over 100 candidates, primarily from multiple copies (up to 4-3 times) of 42 well-known virulence factors (e.g. MFS1, CUTA, NoxA/B, OLE1, NorA), plus a few clade-specific uncharacterised genes.

M.citricolortransition to a pathogenic lifestyle reflected genome-wide functional changes.M.citricolorseems to primarily depend on well-known virulence factors in large copy numbers, suggesting the molecular plant-interaction processes involved are like those of better-studied fungi. Hypothetically, the development of ALS resistance could mirror studied responses to these virulence factors.
Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq
Authors: Tong Gregory , Hah Nasun , Martinez Thomas F.
Published: December 2023

Accurate and comprehensive annotation of microprotein-coding small open reading frames (smORFs) is critical to our understanding of normal physiology and disease. Empirical identification of translated smORFs is carried out primarily using ribosome profiling (Ribo-seq). While effective, published Ribo-seq datasets can vary drastically in quality and different analysis tools are frequently employed. Here, we examine the impact of these factors on identifying translated smORFs. We compared five commonly used software tools that assess ORF translation from Ribo-seq (RibORFv0.1, RibORFv1.0, RiboCode, ORFquant, and Ribo-TISH), and found surprisingly low agreement across all tools. Only ∼2% of smORFs were called translated by all five tools and ∼15% by three or more tools when assessing the same high- resolution Ribo-seq dataset. For larger annotated genes, the same analysis showed ∼72% agreement across all five tools. We also found that some tools are strongly biased against low- resolution Ribo-seq data, while others are more tolerant. Analyzing Ribo-seq coverage as a proxy for translation levels revealed that highly translated smORFs are more likely to be detected by more than one tool. Together these results support employing multiple tools to identify the most confident microprotein-coding smORFs, and choosing the tools based on the quality of the dataset and planned downstream characterization experiments of predicted smORFs.
Centromere inactivation during aging can be rescued in human cells
Authors: Sikder Sweta , Baek Songjoon , McNeil Truman , Dalal Yamini
Published: December 2023

Aging involves a range of genetic, epigenetic, and physiological alterations. A key characteristic of aged cells is the loss of global heterochromatin, accompanied by a reduction in canonical histone levels. In this study, we track the fate of centromeres during aging in human cells. Our findings reveal that the centromeric histone H3 variant CENP-A is downregulated in aged cells, in a p53-dependent manner. We observe repression of centromeric noncoding transcription through an epigenetic mechanism via recruitment of a lysine-specific demethylase 1 (LSD1/KDM1A) to centromeres. This suppression results in defective de novo CENP-A loading at aging centromeres. By dual inhibition of p53 and LSD1/KDM1A in aged cells, we mitigate the reduction in centromeric proteins and centromeric transcripts, leading to mitotic rejuvenation of these cells. These results offer insights into a novel mechanism for centromeric inactivation during aging and provide potential strategies to reactivate centromeres.
Peptide fibrils as vaccine: a proof of concept
Authors: Zabrodskaya Yana , Sivak Konstantin , Sergeeva Maria , Aleksandrov Andrey , Kalinina Elena , Taraskin Alexandr , Eropkin Mikhail , Eropkina Elena , Egorov Vladimir
Published: December 2023

The potential of amyloid-like fibrils formed by peptides as vaccine candidates was investigated using a fragment of the Ebola virus glycoprotein. Peptide in fibrillar form were found to induce an immune response to the full-length protein without causing cellular toxicity or significant changes in hematological studies. The ability of the studied peptide fragment to oligomerize and form amyloid-like fibrils and intermediates suggests potential implications for the virus’s mechanisms of action on cells, particularly those of the immune system. Additionally, if native GP2 epitopes are retained in the peptide fibrils, they may serve as effective immunization agents due to their autoadjuvant properties; however, it is important to consider the possibility of cross-reactivity with human proteins. These findings provide valuable insights into the potential use of amyloid-forming peptide as vaccine candidates and highlight the need for further research into their immunogenic and adjuvant properties.
Quality 4.0: results from a systematic literature review
Authors: Oliveira Diana , Alvelos Helena , Rosa Maria J.
Published: December 2023

Purpose

Quality 4.0 is being presented as the new stage of quality development. However, its overlying concept and rationale are still hard to define. To better understand what different authors and studies advocate being Quality 4.0, a systematic literature review was undertaken on the topic. This paper presents the results of such review, providing some avenues for further research on quality management.

Design/methodology/approach

The documents for the systematic literature review have been searched on the Scopus database, using the search equation: [TITLE-ABS-KEY (“Quality 4.0”) OR TITLE-ABS-KEY (Quality Management” AND (“Industry 4.0” OR “Fourth Industr*” OR i4.0))]. Documents were filtered by language and by type. Of the 367 documents identified, 146 were submitted to exploratory content analysis.

Findings

The analyzed documents essentially provide theoretical discussions on what Quality 4.0 is or should be. Five categories have emerged from the content analysis undertaken: Industry 4.0 and the Rise of a New Approach to Quality; Motivations, Readiness Factors and Barriers to a Quality 4.0 Approach; Digital Quality Management Systems; Combination of Quality Tools and Lean Methodologies and Quality 4.0 Professionals.

Research limitations/implications

It was hard to find studies reporting how quality is actually being managed in organizations that already operate in the Industry 4.0 paradigm. Answers could not be found to questions regarding actual practices, methodologies and tools being used in Quality 4.0 approaches. However, the research undertaken allowed to identify in the literature different ways of conceptualizing and analyzing Quality 4.0, opening up avenues for further research on quality management in the Industry 4.0 era.

Originality/value

This paper offers a broad look at how quality management is changing in response to the affirmation of the Industry 4.0 paradigm.
Natural Rights, Constituent Power, and the Stain of Constitutionalism
Authors: Fasel Raffael N.
Published: December 2023

The power to make constitutions (the so‐called constituent power) is predominantly understood today as a legally unlimited power belonging to the people. This understanding sits uncomfortably with constitutionalism: the idea that public powers are legally limited. Would such a power not leave an indelible blemish on constitutions that are otherwise committed to constitutionalism? This article shows that this problem, which I call the Stain of Constitutionalism, stems from a misapprehension of what constituent power was originally understood to be. Focusing closely on the writings of Emmanuel Joseph Sieyès, Thomas Paine, and the Marquis de Condorcet, I demonstrate that, far from adopting it, these founding fathers of constituent power theory rejected the notion of unlimited constituent power. Instead, they defended a natural rights approach according to which constituent power is legally limited by considerations such as freedom and equality.
Female mate choice is affected by male condition but not female condition in an assassin bug
Authors: Asakura Shoichi , Kiyose Katsuya , Suzaki Yû , Okada Kensuke , Katsuki Masako
Published: December 2023

Sexual selection theory predicts that females prefer males in good condition because mating with them provides more resources such as sperm, ejaculates and nuptial gifts. The female's condition also affects her mating decisions, and condition‐dependent mate choice may allow her to gain more resources from a mate in the context of fluctuating resource availability.

We here investigated how female mating decisions and their fitness consequences varied in the assassin bug Amphibolus venator when the conditions of potential mates and/or the females differed (good or poor condition).

Females in both good and poor conditions preferred males in good condition, and females that mated with males in good condition produced more eggs with higher hatch rates. This increase in fitness may be attributed to the males in good condition transferring more ejaculate to the females.

In contrast, female mate preference, fecundity and hatch rates were not affected by their own condition. This suggests that females do not choose mates according to their own condition in A. venator. However, the females in good condition laid larger eggs than females in poor condition, implying that females in good condition may invest more per egg to improve their reproductive success.

To understand the evolution of female mate choice, it is necessary to investigate the effects of the condition of both sexes on female mating decision and their fitness. In A. venator, male condition may affect mate choice more than female condition.
Artificial light at night affects fish passage rates in two small‐sized Cypriniformes fish
Authors: Tarena Fabio , Comoglio Claudio , Candiotto Alessandro , Nyqvist Daniel
Published: December 2023

An increasing presence of instream structures such as weirs, dams, culverts and reservoirs degrades habitats, fragments rivers and blocks fish movements worldwide. Longitudinal river movements are fundamental for many fish species and the most widespread solution to restore longitudinal connectivity is the implementation of different fish passage solutions. Fishway functionality, however, is highly variable. To design a functional fishway, several aspects of the fish's interaction with its environment need to be taken into consideration. Artificial light at night (ALAN) can affect a range of different behaviours in fish, from activity and movement to feeding and predator–prey relationships. In a fish passage setting, fish are exposed to artificial light at night (ALAN) in the form of light pollution, but, sometimes, also as part of the fish passage solution. Although likely highly species specific, the effect of artificial light on fish passage behaviour has been little explored. Here we study the passage behaviour of two small‐sized fish species, European gudgeon (Gobio gobio) and Italian riffle dace (Telestes muticellus), over a scaled deep side notch weir in a hydraulic flume in three different light conditions: daylight, darkness and ALAN. Although both species passed the obstacle at high efficiencies under all light conditions, their passage behaviours were influenced by light, particularly at the higher levels. While ALAN reduced passage success and resulted in delayed passage for gudgeon, riffle dace passed at higher rates under the artificial light compared to night treatment. Both results indicate a risk of negative effects from ALAN on passage performance at real fishways—or movement rates in lit areas of natural streams—for both species. Independent of light conditions, individuals of both species also passed faster after repeated trials, demonstrating learning in a fish passage context.
Revitalizing a Traditional Market Space in Ile-Ife, Nigeria: An Analysis of Environmental Quality Indicators and Policy Implications
Authors: Fajoye Oluwafemi Samson , Taiwo Amos Oluwole , Odunsi Oluwafemi Michael , Dada Olanrewaju Timothy , Adebara Temitope Muyiwa
Published: December 2023

Traditional market settings in Nigeria have been observed to be poor in environmental quality and less conducive for human physical and economic wellbeing. The physical conditions of the markets have been used to draw conclusions in livability of the space. Policy options to revitalize the overall environmental quality of market spaces require users’ inputs. The study, therefore, examined the environmental quality of a traditional market space in Nigeria, specifically focusing on Odo-Ogbe in Ile-Ife, and explored the potential for policy interventions to revitalize the market. The study was carried out among everyday users of the market. Information obtained through questionnaire administration was the users’ socio-economic backgrounds and twenty-three variables having social, economic and environmental characteristics. Physical observation was also carried out for an all-inclusive environment assessment of the market. Using systematic random and purposive sampling techniques, 119 market users were selected for the survey. Results showed that, the majority of the users were married (64.7%), females (74.8%), who had one form of educational qualification or the other (89.9%). Using an index tagged “Users’ Environmental Quality Index” (UEQI), sixteen environmental quality indicators were rated to be important. Among these were “availability of electricity (UEQI=4.68)”, “availability of water (UEQI=4.52)”, and “clean and healthy environment (UEQI=4.18)”. The study recommended that the government concerned with city administration should pull financial and human resources together to provide facilities and services related to users’ environmental quality indicator data for effective revitalization of the market space.
An Almost Unbiased Regression Estimator: Theoretical Comparison and Numerical Comparison in Portland Cement Data
Authors: Ng Set Foong
Published: December 2023

Multicollinearity is the problem when there is linear dependency among the independent variables. The Ordinary least squares estimator (OLSE) that is commonly adopted is not suitable for the linear regression model when the independent variables are correlated. This is due to the high variance in OLSE and hence the accuracy of OLSE reduces in the presence of multicollinearity. Hence, the estimator named k-almost unbiased regression estimator (KAURE) was proposed as an alternative to OLSE in this paper. KAURE was developed by using the definition of an almost unbiased estimator to further reduce the bias of Liu-type estimator-special case (LTESC). The properties of KAURE including bias, variance-covariance and mean squared error (MSE) were derived. Theoretical comparison and real-life data comparison were carried out to evaluate the performance of the KAURE based on the MSE criterion. The application of the real-life data supported the theoretical comparison that showed the superiority of KAURE over OLSE and LTESC. The results revealed that KAURE could be considered as an alternative estimator for the linear regression model to combat the problem of multicollinearity.
MYH13, a superfast myosin expressed in extraocular, laryngeal and syringeal muscles
Authors: Schiaffino Stefano , Hughes Simon M. , Murgia Marta , Reggiani Carlo
Published: December 2023

MYH13 is a unique type of sarcomeric myosin heavy chain (MYH) first detected in mammalian extraocular (EO) muscles and later also in vocal muscles, including laryngeal muscles of some mammals and syringeal muscles of songbirds. All these muscles are specialized in generating very fast contractions while producing relatively low force, a design appropriate for muscles acting against a much lower load than most skeletal muscles inserting into the skeleton. The definition of the physiological properties of muscle fibres containing MYH13 has been complicated by the mixed fibre type composition of EO muscles and the coexistence of different MYH types within the same fibre. A major advance in this area came from studies on isolated recombinant myosin motors and the demonstration that the affinity of actin‐bound human MYH13 for ADP is much weaker than those of fast‐type MYH1 (type 2X) and MYH2 (type 2A). This property is consistent with a very fast detachment of myosin from actin, a major determinant of shortening velocity. The MYH13 gene arose early during vertebrate evolution but was characterized only in mammals and birds and appears to have been lost in some teleost fish. The MYH13 gene is located at the 3′ end of the mammalian fast/developmental gene cluster and in a similar position to the orthologous cluster in syntenic regions of the songbird genome. MYH13 gene regulation is controlled by a super‐enhancer in the mammalian locus and deletion of the neighbouring fast MYH1 and MYH4 genes leads to abnormal MYH13 expression in mouse leg muscles.

image
Experience and Expectation - Digital health implementation in Portugal as present-making via futures imaginations
Authors: Pinto da Costa José Carlos
Published: December 2023

Traditionally, anthropological analysis has placed emphasis on traditions, customs, and cultural heritage, often overlooking the connection between present actions and future aspirations. Acknowledging the reciprocal influence of present actions in shaping the future and the impact of future visions on shaping present actions, this article aims to redress the neglect of future implications on present social practices within anthropological studies. Through an investigation of the implementation of digital health in Portugal, utilizing discourse analysis, qualitative examination, and critical reflection, this study delves into the impact of digitization on sociotechnical systems within healthcare. It also introduces concepts pertinent to the anthropology of the future and methodological propositions for studying the future within the present context. This inquiry explores the sociotechnical imaginaries stemming from the conceptualization of digital health ideals and their realization in present contexts. Aligned with Koselleck's philosophy of historical time, this examination reveals an essential interplay between present actions and future consequences, advocating for an anticipatory approach in anthropology. This method seamlessly integrates future considerations into present realities, augmenting our understanding of social dynamics and fostering a forward-thinking perspective. This perspective is particularly valuable for scrutinizing the intricate political economies of techno-scientific promises fostered within innovation-oriented endeavours. The analysis, conducted across three dimensions—the utilization, reconfiguration, and evolution of the healthcare system through digitalization—highlights the intricate relationship between current healthcare practices, future aspirations, and the transformative impact of digitalization.
Dilated fixed pupils and respiratory failure: a rare clinical course of Lambert-Eaton myasthenic syndrome
Authors: ten Brinck Michelle FM , Verheijen Inge WH , van de Wardt Jaron , van Dijk Gert W , Nijhuis Frouke AP , Verrips Aad
Published: December 2023

Background

Lambert-Eaton myasthenic syndrome (LEMS) is a neuromuscular junction disorder and the clinical triad consists of proximal muscle weakness, autonomic symptoms and reduced tendon reflexes. Sluggish pupillary reflexes are common but dilated fixed pupils are rare.

Case presentation

We report a patient with a rare clinical course of LEMS. The patient was hospitalised due to progressive dyspnoea. She was ambulant and independent of oxygen at hospitalisation. The following day she suffered an in-hospital cardiac arrest based on hypoxia due to sputum stasis. The neurology department was consulted since the patient did not trigger on the ventilator after cessation of sedation. On neurological examination, the patient had dilated and fixed pupils, severe muscle weakness and areflexia, but a normal consciousness. Finally, she was diagnosed with LEMS. In this case report, the clinical course and diagnostic workup including anti-VGCC antibody testing, imaging and the results of electrophysiological studies are discussed. We also emphasise the importance of malignancy screening since the conventional chest CT was negative for lung carcinoma, but PET-CT raised a high suspicion for small-cell lung carcinoma.

Conclusions

A rare course of LEMS, with early respiratory failure and wide, fixed pupils. Regarding repetitive nerve stimulation, it is important to stimulate long enough to see the incremental response. Furthermore, this study illustrated the importance of malignancy screening with PET-CT when there is a high suspicion of small-cell lung carcinoma with negative conventional CT.
Aspects of chemical reaction and mixed convection in ternary hybrid nanofluid with Marangoni convection and heat source
Authors: Abbas Munawar , Khan Nargis , Hashmi M. S. , Inc Mustafa
Published: December 2023

The proposed study examines the effect of inclined magnetic field on a ternary hybrid nanofluid flow that is axisymmetric thermo-solutal Marangoni convective over an infinite disc. Some well-known uses of Marangoni convection include semiconductor production, atomic reactors, crystal growth, fine art mechanisms, melting, thin-film stretching and welding processes. The non-uniform heat generation and viscous dissipation are taken into account. The thermal conductivity and diffusivity coefficient are presumed to vary inversely with linear function of temperature and concentration. The ternary hybrid nanofluid, which consists of silicon dioxide ([Formula: see text]), iron oxide ([Formula: see text]), molybdenum disulfide ([Formula: see text]) and ethylene glycol as base liquid, undergoes an energy transition to improve heat transfer. The system of PDEs is transformed into nonlinear ordinary differential equations (ODEs) by using the appropriate transformations. Using the BVP4C method, this problem is numerically solved. The heat and mass phenomena rates on flow behavior are investigated using tables and graphs to address the impact of several physical and flow parameters on velocity, concentration, and thermal profiles. By increasing the Marangoni convection parameter, the surface tension gradient gets stronger, leading to more efficient heat and mass transfer inside the liquid as well as stronger induced flows. As the temperature and concentration profiles decrease, the outcome is a more consistent dispersion of these properties throughout the liquid.
Dielectric relaxation in solutions chlorobenzene–benzene and chlorobenzene–hexane
Authors: Azizov Samir
Published: December 2023

This paper presents the results of a study of the dielectric constant of solutions of a polar liquid in a nonpolar solvent: chlorobenzene–benzene, chlorobenzene–hexane. The measurements were carried out at a wavelength [Formula: see text][Formula: see text]cm in the temperature range from [Formula: see text]C to [Formula: see text]C. The studies were carried out using the dielectric spectroscopy method. This method allows a more detailed study of the dielectric properties of the objects of study due to the large equilibrium (“static”) dielectric constant of the object. The temperature dependence of the dielectric relaxation time of molecules in the liquid and solid states of the studied solutions is determined. It has been established that with increasing concentration (0.300, 0.562, 0.794, 1.000 for a chlorobenzene–hexane solution and 0.179, 0.368, 0.567, 0.778, 1.000 for a chlorobenzene–benzene solution) of the halogen substituent, the relaxation time increases. The measurement results of dielectric constant [Formula: see text] and absorption coefficient [Formula: see text] obtained for concentrated solutions chlorobenzene–benzene, chlorobenzene–n–hexane at wavelengths [Formula: see text], 80 and [Formula: see text][Formula: see text]cm at temperature [Formula: see text]C are given in the paper. The static dielectric constant is obtained at a frequency of 1[Formula: see text]MHz. The obtained experimental values [Formula: see text], [Formula: see text] and [Formula: see text] of investigated systems in ([Formula: see text], [Formula: see text]) plane locate on the semi-circle the center of which is on [Formula: see text] axis. In this case, the high-frequency limit value of [Formula: see text] dielectric coefficient exceeds the corresponding n2 refraction index square. The macroscopic and molecular relaxation times are calculated on the base of experimental data. The thermodynamic quantities characterizing the process of dielectric relaxation are calculated for solutions of chlorobenzene–benzene, chlorobenzene–hexane. It has been determined that the height of the potential barrier separating the two equilibrium positions of a polar molecule is greatest in the state of a pure polar liquid and decreases with dilution in a nonpolar solvent.
Doping dependence of superconductivity on a honeycomb lattice within the framework of kinetic-energy-driven superconductivity
Authors: Lan Yu , Yu Xian-Feng , Zhang Li-Ting
Published: December 2023

Unconventional superconductivity on a honeycomb lattice has received increasing interest since the discovery of graphene primarily due to the similarities between materials with a honeycomb lattice and cuprate superconductors. Many theoretical studies have been conducted on superconductivity on a honeycomb lattice, however, a consistent picture is still lacking. In this paper, we have extended the theory of kinetic-energy-driven superconductivity, which has been developed to investigate unconventional superconductivity in cuprate superconductors, to explore superconductivity on a honeycomb lattice within the t-J model. Our results demonstrate that the charge-carrier pair gap parameter with [Formula: see text]-wave symmetry exhibits a dome-like shape as a function of doping, with superconductivity emerging at a certain doping concentration and disappearing at high doping levels, similar to what has been observed in cuprate and cobaltate superconductors. Furthermore, the charge-carrier pair gap parameter decreases with increasing the value of [Formula: see text] (the ratio between the antiferromagnetic exchange coupling constant and the nearest-neighbor hopping integral), and approaches zero when [Formula: see text] reaches a sufficiently large value. This indicates that the antiferromagnetic order will suppress the superconducting state and a sufficiently strong exchange coupling will completely destroy the superconductivity. Taking into account our present results together with the corresponding results of cuprate and cobaltate superconductors, it appears that the dome-like shape of the doping dependence of the charge-carrier pair gap parameter may be a common feature in doped Mott insulators.
LQR-Based Suspension for Heavy Vehicles Considering the Time-Varying Characteristics of Vehicle–Road Interaction
Authors: Zhang Buyun , Li Zewei , Tan Chin An , Liu Zhiqiang
Published: December 2023

The rapidly increasing demand for heavy vehicles in the transportation sector has led to more severe road damage and significantly higher road maintenance costs. Investigation of active suspension system incorporating vehicle–road interaction (VRI) can provide effective means to reduce the road damage and improve the ride comfort of vehicles. In this paper, an active vehicle suspension controller based on the strongly stable and robust linear–quadratic regulator (LQR) principle is developed for the time-varying VRI system. The coupled system is modeled by a quarter-car traveling on the road modeled by an Euler–Bernoulli beam resting on a viscoelastic foundation. Two types of road irregularities, deterministic sine wave and random, are considered in the numerical studies. A time-frozen technique, by which the linear time-varying system is converted to a time sequence of time-invariant systems, is applied to solve for the coupled responses. Three variables, the dynamic tire load, vehicle body acceleration, and suspension relative displacement, are used to assess the effectiveness of the LQR-based controller in comparison to the passive suspension system. The performance of the active control is investigated for different vehicle speeds, vehicle loads, and road profiles. Numerical studies show that the controller can effectively reduce the road damage and improve the ride comfort, with a slight increase in the suspension relative displacement. This work lays a useful foundation in the problem formulation and system parameter influences for future vehicle suspension design and road damage mitigation including VRI.
New Analytic Free Vibration Solutions of L-Shaped Moderately Thick Plates by Symplectic Superposition
Authors: Yang Yushi , Xu Dian , Chu Jinkui , Gong Guangping , Chen Yiming , Li Rui
Published: December 2023

L-shaped moderately thick plates have widespread applications in diverse engineering structures. Exploring the benchmark analytic solutions for the free vibration of L-shaped moderately thick plates is important in order to accurately analyze and efficiently design structures. Nevertheless, analytical solutions, which serve as the benchmarks, have been rarely documented in previous literature due to the challenge of finding suitable solutions that satisfy both the governing higher-order partial differential equations (PDEs) and the boundary conditions of the plates. The symplectic superposition method was employed in our recently published study to present the benchmark vibration solutions of clamped rectangular moderately thick plates. In this study, we expand upon this method to solve the free vibration problem of L-shaped moderately thick plates. By employing domain decomposition, we construct an irregular domain by combining multiple rectangular domains. First, the construction of the superposition system is carried out, followed by the import of the sub-problems into the Hamiltonian system, utilizing the fundamental governing equations of the plate. Then, the sub-problems are resolved through the application of the symplectic geometry methodology in an analytical manner. Ultimately, the analytical solutions for frequencies and mode shapes are derived through ensuring the equivalence between the initial problem and the combination of sub-problems. The finite element method is used to validate and present a comprehensive analysis of the natural frequencies and mode shapes obtained from this method. This method possesses the benefits of rapid convergence and accurate precision, rendering it well suited for the analytic modeling of a broader range of plate-related problems.
MRCNet: Multi-Level Residual Connectivity Network for Image Classification
Authors: Ye Mengting , Chen Zhenxue , Guo Yixin , Yu Kaili , Liu Longcheng
Published: December 2023

Computer vision obtains object and environment information by simulating human visual senses and borrowing human sensory activity. As one of the main tasks of computer vision, image classification can be used not only for face recognition, traffic scene recognition, image retrieval, and automatic photo categorization but also as a theoretical basis for target detection and image segmentation. In this paper, we use the existing CNN architecture network-ConvNeXt. By adapting and modifying the residual connectivity and convolutional structure of the network, we achieve a balance between classification accuracy and inference speed. These modifications are able to reduce both computation and memory consumption while keeping accuracy largely unchanged, thus better facilitating network lightweighting.
Vein visualization enhancement by dual-wavelength phase-locked denoising technology
Authors: Ruan Lihua , Yin Zhiqin , Zhou Shibing , Zheng Weibo , Lu Wei , Zhang Tao , Wang Shaowei
Published: December 2023

Visual near-infrared imaging equipment has broad applications in various fields such as venipuncture, facial injections, and safety verification due to its noncontact, compact, and portable design. Currently, most studies utilize near-infrared single-wavelength for image acquisition of veins. However, many substances in the skin, including water, protein, and melanin can create significant background noise, which hinders accurate detection. In this paper, we developed a dual-wavelength imaging system with phase-locked denoising technology to acquire vein image. The signals in the effective region are compared by using the absorption valley and peak of hemoglobin at 700[Formula: see text]nm and 940[Formula: see text]nm, respectively. The phase-locked denoising algorithm is applied to decrease the noise and interference of complex surroundings from the images. The imaging results of the vein are successfully extracted in complex noise environment. It is demonstrated that the denoising effect on hand veins imaging can be improved with 57.3% by using our dual-wavelength phase-locked denoising technology. Consequently, this work proposes a novel approach for venous imaging with dual-wavelengths and phase-locked denoising algorithm to extract venous imaging results in complex noisy environment better.