bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractAuditory 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.
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

AbstractBackgroundTo 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.PurposeTo 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.DesignA retrospective cross-sectional study from 2019–2020 on 250 HCC patients in hospitalized and following the STROBE guidelines.MethodsPrevalence 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.ResultsFactors 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.ConclusionsMarital 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.ImpactThis 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

AbstractA 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

AbstractTo 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

AbstractMycena 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

SUMMARYAccurate 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

SummaryAging 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

AbstractThe 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

PurposeQuality 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/approachThe 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.FindingsThe 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/implicationsIt 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/valueThis paper offers a broad look at how quality management is changing in response to the affirmation of the Industry 4.0 paradigm.
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

Abstract
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

AbstractAn 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.
MYH13, a superfast myosin expressed in extraocular, laryngeal and syringeal muscles
Authors: Schiaffino Stefano , Hughes Simon M. , Murgia Marta , Reggiani Carlo 
Published: December 2023

AbstractMYH13 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.
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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

BackgroundLambert-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 presentationWe 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.ConclusionsA 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.