bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bayesian model to identify multiple expression patterns with simultaneous FDR control for a multi-factor RNA-seq experiment
Authors: Bian Yuanyuan , He Chong , Qiu Jing 
Published: April 2023

Abstract
It is often of research interest to identify genes that satisfy a particular expression pattern across different conditions such as tissues, genotypes, etc. One common practice is to perform differential expression analysis for each condition separately and then take the intersection of differentially expressed (DE) genes or non-DE genes under each condition to obtain genes that satisfy a particular pattern. Such a method can lead to many false positives, especially when the desired gene expression pattern involves equivalent expression under one condition. In this paper, we apply a Bayesian partition model to identify genes of all desired patterns while simultaneously controlling their false discovery rates (FDRs). Our simulation studies show that the common practice fails to control group specific FDRs for patterns involving equivalent expression while the proposed Bayesian method simultaneously controls group specific FDRs at all settings studied. In addition, the proposed method is more powerful when the FDR of the common practice is under control for identifying patterns only involving DE genes. Our simulation studies also show that it is an inherently more challenging problem to identify patterns involving equivalent expression than patterns only involving differential expression. Therefore, larger sample sizes are required to obtain the same target power to identify the former types of patterns than the latter types of patterns.
The influence of CASP8 D302H gene variant in colorectal cancer risk and prognosis
Authors: Cacina Canan , Turan Sürmen Saime , Arıkan Soykan , Pençe Sadrettin , Yaylım İlhan 
Published: April 2023

Abstract

Objectives
Apoptosis is defined as programmed cell death, which regulates cellular functions and various physiological responses. Several studies reported that Caspase genes play important roles in the apoptosis and inflammation process. Caspase-8 (CASP8) is a member of the cysteine protease family and a key regulator gene in the induction of apoptosis. In present study, we aimed to investigate the possible associations between the CASP8; D302H (G>C) gene polymorphism and colorectal cancer risk and prognosis.

Methods
The CASP8; D302H genotypes were determined in 75 colorectal cancer patients and 122 healthy controls. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism method (PCR-RFLP) was used to detect the CASP8; D302H gene variation in the study group.

Results
We found that individuals carrying the GC genotype of CASP8; D302H gene variation had significantly lower colorectal cancer risk compared with those carrying CC and GG genotypes (OR=0.539; p=0.045). In addition, we analyzed the clinicopathological characteristics of patients and noticed a significant correlation between the C allele frequency and moderately differentiated tumor parameter (p<0.05).

Conclusions
The CASP8; D302H gene polymorphism GC genotype might be associated with a reduced risk of colorectal cancer but further studies in a larger population are needed most effective evaluation of the CASP8; D302H gene variation in colorectal cancer development.
The effects of SDS, APG, and DTAB surfactants on the morphology of micro-nano RDX particles prepared in a microfluidic reactor
Authors: Li Ying , Zhang Yifan , Zhan Lewu , Hou Jing , Li Bindong 
Published: April 2023

Abstract
The effects of different surfactants on the morphology of 1,3,5-trinitro-1,3,5-triazinane (RDX) micro-nanoparticles prepared by solvent/non-solvent method in a microfluidic reactor were investigated. Alkyl polyglycoside (APG), sodium dodecyl sulphate (SDS) and dodecyltrimethylammonium bromide (DTAB) were selected as non-solvents. The surface tension and interfacial tension (IFT) properties of SDS, APG and DTAB were investigated. Compared to DTAB and SDS, the APG could effectively reduce the interfacial tension to 10−2 mN/m and exhibited better surface tension. The RDX prepared with different surfactants were analysed by scanning electron microscopy (SEM), X-ray diffractometry (XRD) and Fourier transform infrared spectrometry (FTIR). The results showed that the different surfactants could significantly improve the dispersion effect of RDX and the crystal morphology was uniform and stable.
Perceptual History Biases Are Predicted by Early Visual-Evoked Activity
Authors: Fornaciai Michele , Togoli Irene , Bueti Domenica 
Published: April 2023

What we see in the present is affected by what we saw in the recent past. Serial dependence, a bias making a current stimulus appear more similar to a previous one, has been indeed shown to be ubiquitous in vision. At the neural level, serial dependence is accompanied by a signature of stimulus history (i.e., past stimulus information) emerging from early visual-evoked activity. However, whether this neural signature effectively reflects the behavioral bias is unclear. Here we address this question by assessing the neural (electrophysiological) and behavioral signature of stimulus history in human subjects (both male and female), in the context of numerosity, duration, and size perception. First, our results show that while the behavioral effect is task-dependent, its neural signature also reflects task-irrelevant dimensions of a past stimulus, suggesting a partial dissociation between the mechanisms mediating the encoding of stimulus history and the behavioral bias itself. Second, we show that performing a task is not a necessary condition to observe the neural signature of stimulus history, but that in the presence of an active task such a signature is significantly amplified. Finally, and more importantly, we show that the pattern of brain activity in a relatively early latency window (starting at ∼35-65 ms after stimulus onset) significantly predicts the behavioral effect. Overall, our results thus demonstrate that the encoding of past stimulus information in neural signals does indeed reflect serial dependence, and that serial dependence occurs at a relatively early level of visual processing.SIGNIFICANCE STATEMENTWhat we perceive is determined not only by the information reaching our sensory organs, but also by the context in which the information is embedded. What we saw in the recent past (perceptual history) can indeed modulate the perception of a current stimulus in an attractive way, a bias that is ubiquitous in vision. Here we show that this bias can be predicted by the pattern of brain activity reflecting the encoding of past stimulus information, very early after the onset of a stimulus. This in turn suggests that the integration of past and present sensory information mediating the attractive bias occurs early in the visual processing stream, and likely involves early visual cortices.
Evidence for low nanocompaction of heterochromatin in living embryonic stem cells
Authors: Dupont Claire , Chahar Dhanvantri , Trullo Antonio , Gostan Thierry , Surcis Caroline , Grimaud Charlotte , Fisher Daniel , Feil Robert , Llères David 
Published: April 2023

AbstractDespite advances in the identification of chromatin regulators and genome interactions, the principles of higher‐order chromatin structure have remained elusive. Here, we applied FLIM‐FRET microscopy to analyse, in living cells, the spatial organisation of nanometre range proximity between nucleosomes, which we called “nanocompaction.” Both in naive embryonic stem cells (ESCs) and in ESC‐derived epiblast‐like cells (EpiLCs), we find that, contrary to expectations, constitutive heterochromatin is much less compacted than bulk chromatin. The opposite was observed in fixed cells. HP1α knockdown increased nanocompaction in living ESCs, but this was overridden by loss of HP1β, indicating the existence of a dynamic HP1‐dependent low compaction state in pluripotent cells. Depletion of H4K20me2/3 abrogated nanocompaction, while increased H4K20me3 levels accompanied the nuclear reorganisation during EpiLCs induction. Finally, the knockout of the nuclear cellular‐proliferation marker Ki‐67 strongly reduced both interphase and mitotic heterochromatin nanocompaction in ESCs. Our data indicate that, contrary to prevailing models, heterochromatin is not highly compacted at the nanoscale but resides in a dynamic low nanocompaction state that depends on H4K20me2/3, the balance between HP1 isoforms, and Ki‐67.
The Ebola virus VP40 matrix layer undergoes endosomal disassembly essential for membrane fusion
Authors: Winter Sophie L , Golani Gonen , Lolicato Fabio , Vallbracht Melina , Thiyagarajah Keerthihan , Ahmed Samy Sid , Lüchtenborg Christian , Fackler Oliver T , Brügger Britta , Hoenen Thomas , Nickel Walter , Schwarz Ulrich S , Chlanda Petr 
Published: April 2023

AbstractEbola viruses (EBOVs) assemble into filamentous virions, whose shape and stability are determined by the matrix viral protein 40 (VP40). Virus entry into host cells occurs via membrane fusion in late endosomes; however, the mechanism of how the remarkably long virions undergo uncoating, including virion disassembly and nucleocapsid release into the cytosol, remains unknown. Here, we investigate the structural architecture of EBOVs entering host cells and discover that the VP40 matrix disassembles prior to membrane fusion. We reveal that VP40 disassembly is caused by the weakening of VP40–lipid interactions driven by low endosomal pH that equilibrates passively across the viral envelope without a dedicated ion channel. We further show that viral membrane fusion depends on VP40 matrix integrity, and its disassembly reduces the energy barrier for fusion stalk formation. Thus, pH‐driven structural remodeling of the VP40 matrix acts as a molecular switch coupling viral matrix uncoating to membrane fusion during EBOV entry.
A tiny loop in the Argonaute PIWI domain tunes small RNA seed strength
Authors: Xiao Yao , Liu TingYu M , MacRae Ian J 
Published: April 2023

AbstractArgonaute (AGO) proteins use microRNAs (miRNAs) and small interfering RNAs (siRNAs) as guides to regulate gene expression in plants and animals. AGOs that use miRNAs in bilaterian animals recognize short (6–8 nt.) elements complementary to the miRNA seed region, enabling each miRNA to interact with hundreds of otherwise unrelated targets. By contrast, AGOs that use miRNAs in plants employ longer (> 13 nt.) recognition elements such that each miRNA silences a small number of physiologically related targets. Here, we show that this major functional distinction depends on a minor structural difference between plant and animal AGO proteins: a 9‐amino acid loop in the PIWI domain. Swapping the PIWI loop from human Argonaute2 (HsAGO2) into Arabidopsis Argonaute10 (AtAGO10) increases seed strength, resulting in animal‐like miRNA targeting. Conversely, swapping the plant PIWI loop into HsAGO2 reduces seed strength and accelerates the turnover of cleaved targets. The loop‐swapped HsAGO2 silences targets more potently, with reduced miRNA‐like targeting, than wild‐type HsAGO2 in mammalian cells. Thus, tiny structural differences can tune the targeting properties of AGO proteins for distinct biological roles.
1H-MRS to evaluate improved triglyceride accumulation in idiopathic triglyceride deposit cardiomyovasculopathy after CNT-01 (tricaprin/trisdecanoin) administration
Authors: Aikawa Tatsuro , Sai Eiryu , Kudo Ayako , Kawaguchi Yuko O , Takamura Kazuhisa , Hiki Makoto , Yokoyama Takayuki , Miyazaki Tetsuro , Fujimoto Shinichiro , Shimada Kazunori , Hirano Ken-ichi , Daida Hiroyuki , Minamino Tohru 
Published: April 2023

Summary
Triglyceride deposit cardiomyovasculopathy (TGCV) is an intractable disease characterized by massive triglyceride (TG) accumulation in the myocardium and coronary arteries caused by genetic or acquired dysfunction of adipose TG lipase (ATGL). A phase IIa trial has been conducted involving patients with idiopathic TGCV using CNT-01 (tricaprin/trisdecanoin) by the Japan TGCV study group, which showed that CNT-01 improved myocardial lipolysis as demonstrated by iodine-123-beta-methyl iodophenyl-pentadecanoic acid (BMIPP) scintigraphy. We evaluated changes in myocardial TG content using proton magnetic resonance spectroscopy (1H-MRS) before/after CNT-01. This report describes a male patient with hypertension, diabetes, angina pectoris, repeated percutaneous coronary intervention, chest pain, and exertional dyspnea that persisted despite standard medications and nitroglycerin. Idiopathic TGCV was diagnosed based on a remarkably reduced washout rate (WR) for BMIPP scintigraphy, high myocardial TG content on 1H-MRS, and no ATGL mutation. After an 8-week, 1.5 g/day CNT-01 administration, the WR of BMIPP increased from 5.1 to 13.3% and the myocardial TG content decreased from 8.4 to 5.9%, with no adverse effects. CNT-01 corrected myocardial lipolysis and subsequently reduced TG content in idiopathic TGCV as evaluated using 1H-MRS, which may be a useful, noninvasive evaluation of therapeutic efficacy.

Learning points

Triglyceride deposit cardiomyovasculopathy (TGCV) is an intractable disease characterized by massive triglyceride accumulation in the myocardium and coronary arteries, caused by genetic or acquired dysfunction of adipose triglyceride lipase.

Japan TGCV Study Group developed a specific treatment for idiopathic TGCV using CNT-01 (tricaprin/trisdecanoin), a type of medium-chain fatty acid.

CNT-01 corrected myocardial lipolysis and reduced TG content in idiopathic TGCV using proton magnetic resonance spectroscopy, which may be a useful noninvasive evaluation of therapeutic efficacy.
Gamification Elements in the Process of Ukrainian Language Training of Pedagogy Specialists
Authors: Humeniuk Iryna 
Published: April 2023

The article studies the problem of using gamification elements in the process of training future preschool and primary school teachers on the example of the methodology of teaching Ukrainian Language for Professional Purposes. The necessity of improving the methodology of teaching the language to students of different age groups while taking into account the main educational trends and public demand has been substantiated. According to the goal, the essence of the "gamification" concept has been defined regarding the modern education sector. The peculiarities of using gamification, which have a great impact on the effectiveness of teaching students at pedagogical institutions of higher education, have been determined.
It is emphasized that the growth of the number of game means in the methodology of teaching Ukrainian Language for Professional Purposes is not always directly proportional to the increase of success. Since gamification is impossible without using information and communications technology, consideration of the factor of appropriate technological support is necessary. The age factor manifests itself rather in the information and technological skills and abilities of certain age groups than the effectiveness of completed tasks on the condition of unhindered mastery of the technology. In the process of gamification, the element of novelty has a significant impact, as well as the temporal and motivational dependence of the interest of the performers on the duration or algorithmization of the tasks. The psychological factor is manifested through gender, which substantiates the inefficiency of using gamification with elements of competition or open ranking of results for female audience. In the context of training pedagogy specialists, the process of gamification during the study of a certain discipline has a dual purpose: increasing the motivation and therefore the effectiveness of training, formation of necessary competencies of future teachers; mastering completed gamified tasks as possible ways and means of teaching the Ukrainian language in future professional activity.
Based on the analysis of the information space of the problem, a system of tasks with gamification elements has been developed and adapted to the content of the Ukrainian Language for Professional Purposes academic discipline.
Interwar Period in Polish History Handbooks of the Fifty Years (1945 – 1994)
Authors: Wagner Barbara 
Published: April 2023

The article presents the theoretical aspects of teaching Polish history at schools from 1945 to 1994. The author emphasizes that the Poles undeniably are a nation whose identity and national character have been shaped to a great extent by tradition and history education. It has been proven that the national character is formed in the course of history and the factors contributing to it may be easily recognized. When the national character manages to specify itself it tends to stability and rejection or assimilation destructive influence. It turned out that of great importance is that the national character is never exclusively unique or uncommon; it is rather a combination of widespread features typical for many nations. These two trends of historical influence existed side by side despite their contrary character which was especially clear within fifty years. The formation of the historical consciousness of the contemporary Poles has been proudly influenced by the image of the interwar period of 1918-1939. The author concludes that the expansion of history propaganda function did not result in a change in social awareness of history. People rejected the official history (even reliably presented facts) since they still had in mind the practice of the Stalin period and the faults of the recent history; instead, they resorted to 'private' history which was frequently based on books of the 19th-century authors.
Peculiarities of Future Educators’ Training for the Forming of the Fundamentals of National Consciousness in Children of Older Preschool Age
Authors: Marchii-Dmytrash Tamara , Boryn Halyna 
Published: April 2023

The peculiarities of professional training of future educators for the forming of older preschool-age children’s national consciousness are substantiated in the article. The main tasks, directions, and means of national education of children of older preschool age are analyzed. The main ethnographical means that contribute to the forming of the fundamentals of the national consciousness of children in the sixth year of life are specified and characterized, and the content of pedagogical activities aimed at expanding their horizons with specific ethnographical knowledge and ideas about important social phenomena and events is determined. All this can be realized with the help of various genres of oral folk art, traditions and customs of the Ukrainian people, folk games and toys, folk industries and crafts, and national symbols. All the ethnographical means listed above in figurative and rhythmic forms reflect real life in all its diversity (everyday life, social phenomena, work, human relationships) and contribute to national education, forming of the fundamentals of the national consciousness of older preschool-age children.
It was established that preschool national education should help the child to form and apply the acquired social knowledge, and contribute to the forming of the skills of spiritual perception of national and cultural heritage. The result of national education should be reflected in the children's acquisition of social experience, the inheritance of the spiritual and moral values of the Ukrainian people, the achievement of a high level of national consciousness, as well as in the forming of a personality as a patriot of one's country. It is worth noting that national feelings are the basis of national consciousness and they do not arise by themselves, but only as a result of long-term educational influence on the personality, starting from the older preschool age.
The future IPE teachers’ training for the development of national consciousness in children of older preschool age should be aimed at self-realization and the disclosure of their individual creative abilities. Gradually, the student’s vocabulary is enriched with everyday words, proverbs, sayings, tongue twisters, riddles, and other works of oral folk creativity, they learn to dramatize fragments of familiar Ukrainian fairy tales, make toys, decorate national dishes, clothes, and other household items. A systematic approach in work promotes the development of higher education getters’ interests in ethnography.
Effect of strain amplitude and confining pressure on the velocity and attenuation of <i>P</i> and <i>S</i> waves in dry and water-saturated sandstone: an experimental study
Authors: Mashinskii E. I. 
Published: April 2023

In rock physics, much attention has been paid to the study of the processes of strain of natural materials at small strains. Experiments using high-precision measurements have allowed new knowledge at micro/nano level to be acquired. The microplasticity of solids is studied in materials science, but there is also data regarding some rocks. The property of microplasticity of natural materials is still little studied. The study was carried out on rock samples. The effect of strain amplitude and confining pressure on the velocity and attenuation of P and S waves in dry and water-saturated sandstone has been studied. The method of reflected waves was used in the frequency range of 0.5–1.4 MHz at four strain amplitudes (0.5–1.67)·10−6 Amplitude cycling causes an open and closed hysteresis effect for wave velocity and attenuation. This has been observed for both dry and water-saturated sandstone. The hysteresis loop overlaps in both states. The amplitude changes in the velocity of P-wave in dry sandstone is 1.12 %, and the attenuation of P-wave in dry sandstone is 5.43 %. As for S-wave, its maximum attenuation in dry sandstone reaches 8.81 %. The behavior of a wave velocity and attenuation can be explained by the combined effect of viscoelasticity and microplasticity. Elastoplastic transition strongly depends on the details of the microstructure, its defectiveness, and other parameters. The characteristics of the complications of wave parameters can be the signs of the internal structure of the subject.
Stress factors for patients undergoing cardiac surgery.
Authors: Franca Lisboa Gois Cristiane Franca , Aguillar Olga Maimoni , Santos Valmira dos Santos , Rodríguez Eliana Ofelia Llapa 
Published: April 2023

Objective. To describe the stress factors related to cardiac surgery and to the environment in an Intensive Care Unit (ICU).
Methodology. Exploratory, descriptive and qualitative study based on the statements of patients undergoing cardiac surgery. The data was collected through semi-structured interviews and reviewed using thematic content analysis.
Results. Four categories emerged: 1) Surgical experience: overcoming fear; 2) the ICU environment and the postoperative period: a difficult experience; 3) unpleasant experiences: thirst, intubation and pain; and 4) relationship with health care professionals: impersonality, professional presence representing safety and comfort, orientation and information representing safety and clarification.
Conclusion. Two groups of stress factors were identified: the intra personal (thirst, pain and others) and extra personal related to the environment.