Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromobox Homolog 8 (CBX8) in Human Tumor Carcinogenesis and Prognosis: A Pancancer Analysis Using Multiple Databases

Some emerging studies have suggested that chromobox homolog 8 (CBX8) may play a critical role in carcinogenesis and prognosis in human cancer. Based on The Cancer Genome Atlas (TCGA)’s available data and the Gene Expression Omnibus (GEO) database, we conducted a systematic analysis of the carcinogenic effects of the CBX8 gene. We used TIMER2, GEPIA2, UALCAN, cBioPortal, Kaplan-Meier plotter, OncoLnc, STRING, HPA, and Oncomine data analysis websites and R data analysis software to analyze available data. The results show that the level of expression of CBX8 was significantly different among 27 different types of tumors and adjacent normal tissues. Moreover, we found that CBX8 expression had a close relationship with prognosis in some kinds of cancers. The phosphorylation level of some protein sites (such as S256) was significantly increased in tumors. CD8 + T-cell, B-cell and cancer-associated fibroblast infiltration levels were associated with CBX8 expression. The results of enrichment analysis indicated that the main biological activities of CBX8 are connected to gene transcription and repair of DNA damage. In conclusion, the level of expression of CBX8 was closely related to carcinogenesis and prognosis of some kinds of tumors, which needs further experimental verification.
Individual and Interactive Effects of Ocean Warming and Acidification on Adult Favites colemani

Tropical coral reefs are threatened by local-scale stressors that are exacerbated by global ocean warming and acidification from the post-industrial increase of atmospheric CO2 levels. Despite their observed decline in the past four decades, little is known on how Philippine coral reefs will respond to ocean warming and acidification. This study explored individual and synergistic effects of present-day (pH 8.0, 28°C) and near-future (pH 7.7, 32°C) scenarios of ocean temperature and pH on the adult Favites colemani, a common massive reef-building coral in Bolinao-Anda, Philippines. Changes in seawater temperature drive the physiological responses of F. colemani, whereas changes in pH create an additive effect on survival, growth, and photosynthetic efficiency. Under near-future scenarios, F. colemani showed sustained photosynthetic competency despite the decline in growth rate and zooxanthellae density. F. colemani exhibited specificity with the Cladocopium clade C3u. This coral experienced lower growth rates but survived projected near-future ocean warming and acidification scenarios. Its pH-thermal stress threshold is possibly a consequence of acclimation and adaptation to local environmental conditions and past bleaching events. This research highlights the importance of examining the susceptibility and resilience of Philippine corals to climate-driven stressors for future conservation and restoration efforts in the changing ocean.
Motion Polytopes in Virtual Reality for Shared Control in Remote Manipulation Applications

In remote applications that mandate human supervision, shared control can prove vital by establishing a harmonious balance between the high-level cognition of a user and the low-level autonomy of a robot. Though in practice, achieving this balance is a challenging endeavor that largely depends on whether the operator effectively interprets the underlying shared control. Inspired by recent works on using immersive technologies to expose the internal shared control, we develop a virtual reality system to visually guide human-in-the-loop manipulation. Our implementation of shared control teleoperation employs end effector manipulability polytopes, which are geometrical constructs that embed joint limit and environmental constraints. These constructs capture a holistic view of the constrained manipulator’s motion and can thus be visually represented as feedback for users on their operable space of movement. To assess the efficacy of our proposed approach, we consider a teleoperation task where users manipulate a screwdriver attached to a robotic arm’s end effector. A pilot study with prospective operators is first conducted to discern which graphical cues and virtual reality setup are most preferable. Feedback from this study informs the final design of our virtual reality system, which is subsequently evaluated in the actual screwdriver teleoperation experiment. Our experimental findings support the utility of using polytopes for shared control teleoperation, but hint at the need for longer-term studies to garner their full benefits as virtual guides.
Mitochondrial Genome of Eleutheronema rhadinum With an Additional Non-coding Region and Novel Insights Into the Phylogenetics

The complete mitochondrial genome of Eleutheronema rhadinum was determined for the first time. The E. rhadinum mitogenome was 16,718 bp in length, comprising 13 protein coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), 1 control region (CR), and 1 L-strand replication origin (OL). The genome organization, and base composition were similar to other teleosts. An additional non-coding region detected in the HSL cluster, was with significant similarity to the nearby tRNA-Leu (CUN), which could be a useful marker for identifying E. rhadinum and Eleutheronema tetradactylum. Furthermore, phylogenetic analysis showed species in the family Polynemidae were well clustered together. But sister relationships between Polynemidae and Sciaenidae, Menidae plus Lactariidae were refused by present study.
Integrating Genetic and Transcriptomic Data to Reveal Pathogenesis and Prognostic Markers of Pancreatic Adenocarcinoma

Pancreatic adenocarcinoma (PAAD) is one of the deadliest malignancies and mortality for PAAD have remained increasing under the conditions of substantial improvements in mortality for other major cancers. Although multiple of studies exists on PAAD, few studies have dissected the oncogenic mechanisms of PAAD based on genomic variation. In this study, we integrated somatic mutation data and gene expression profiles obtained by high-throughput sequencing to characterize the pathogenesis of PAAD. The mutation profile containing 182 samples with 25,470 somatic mutations was obtained from The Cancer Genome Atlas (TCGA). The mutation landscape was generated and somatic mutations in PAAD were found to have preference for mutation location. The combination of mutation matrix and gene expression profiles identified 31 driver genes that were closely associated with tumor cell invasion and apoptosis. Co-expression networks were constructed based on 461 genes significantly associated with driver genes and the hub gene FAM133A in the network was identified to be associated with tumor metastasis. Further, the cascade relationship of somatic mutation-Long non-coding RNA (lncRNA)-microRNA (miRNA) was constructed to reveal a new mechanism for the involvement of mutations in post-transcriptional regulation. We have also identified prognostic markers that are significantly associated with overall survival (OS) of PAAD patients and constructed a risk score model to identify patients’ survival risk. In summary, our study revealed the pathogenic mechanisms and prognostic markers of PAAD providing theoretical support for the development of precision medicine.
Phylogenetic Comparison and Splicing Analysis of the U1 snRNP-specific Protein U1C in Eukaryotes

As a pivotal regulator of 5’ splice site recognition, U1 small nuclear ribonucleoprotein (U1 snRNP)-specific protein C (U1C) regulates pre-mRNA splicing by interacting with other components of the U1 snRNP complex. Previous studies have shown that U1 snRNP and its components are linked to a variety of diseases, including cancer. However, the phylogenetic relationships and expression profiles of U1C have not been studied systematically. To this end, we identified a total of 110 animal U1C genes and compared them to homologues from yeast and plants. Bioinformatics analysis shows that the structure and function of U1C proteins is relatively conserved and is found in multiple copies in a few members of the U1C gene family. Furthermore, the expression patterns reveal that U1Cs have potential roles in cancer progression and human development. In summary, our study presents a comprehensive overview of the animal U1C gene family, which can provide fundamental data and potential cues for further research in deciphering the molecular function of this splicing regulator.
Chromosome Identification and Cytogenetic Map Construction of Zhikong Scallop (Chlamys farreri) Based on Fluorescence in situ Hybridization

Zhikong scallop (Chlamys farreri) is a bivalve species with broad economic and biological value, and an essential species of aquaculture in North China. Recently, efforts have been made to improve knowledge of genome, genetics, and cytogenetics, which is devoted to develop the molecular breeding project for the scallop. In this study, we constructed a cytogenetic map and identified all chromosomes of C. farreri using fluorescence in situ hybridization (FISH). A total of 100 Bacterial Artificial Chromosome (BAC) clones and 27 fosmid clones, including 58 microsatellite marker-anchored BAC clones, 4 genes-anchored BAC clones, 38 random BAC clones, 22 repetitive sequences-anchored fosmid clones, and 5 gene-anchored fosmid clones, were tested as probes, and 69 of them produced specific and stable signal on one pair of chromosomes. Then, multiple co-hybridizations were conducted to distinguish all the submetacentric and subtelocentric chromosomes with similar morphology by the abovementioned chromosome-specific markers. On this basis, a cytogenetic map of C. farreri containing 69 clones was constructed by co-hybridization and karyotype analysis. The markers covered all 19 pairs of chromosomes, and the average number of markers on each chromosome was 3.6. The cytogenetic map provides a platform for genetic and genomic analysis of C. farreri, which facilitates the molecular breeding project of C. farreri and promotes the comparative studies of chromosome evolution in scallops and even bivalves.
Everyday Life Meaningfulness for the Community-Dwelling Oldest Old During the COVID-19 Pandemic

In many countries, the COVID-19 pandemic has led to strong restrictions and changed the everyday lives of older people. In Finland, people aged 70 and over were instructed to stay at home under quarantine-like conditions. Existing studies from other countries have reported increases in negative experiences and symptoms as a result of such restrictions, including psychosocial stress. However, little focus has been given to older people’s experiences of meaningfulness during the pandemic. Using survey and interview data, we ask to what extent have community-dwelling oldest old (80+) experienced meaningfulness during the pandemic, what background factors are associated with meaningfulness and what factors have contributed to everyday life meaningfulness during the pandemic. The data was collected as part of the COVID-19 sub-study of the third follow-up of the Cardiovascular Risk Factors, Aging and Dementia (CAIDE85+) study, a Finnish population-based cohort study carried out in the eastern part of the country. In the quantitative analyses, meaningfulness was assessed as part of the Experiences of Social Inclusion Scale. The association of meaningfulness with different background factors (gender, age, living alone, self-chosen quarantine or physical isolation, self-rated health, physical functioning, and cognitive capacity) was explored with the Chi-square test. The quantitative findings indicate that the majority of the participants experienced meaningfulness during the pandemic. Participants who did not practice any physical isolation measures and participants with higher self-rated health experienced more meaningfulness. There was no evidence for difference in the prevalence of meaningfulness and other background factors. The qualitative data was analyzed using thematic analysis. The findings indicated that factors contributing to meaningfulness in everyday life were social contacts, daily chores and activities, familiar places and seasonal changes. The small sample size does not provide possibilities for generalizing the results into the wider population of older adults. However, the results provide new understanding of the oldest old’s experiences of meaningfulness in everyday life during the global pandemic. The findings may help find ways to support older people’s meaningfulness in challenging times.
Application of Central Composite Design in the Adsorption of Ca(II) on Metakaolin Zeolite

Metakaolin zeolite-A was synthesized from thermally activated kaolin clay and characterized by Fourier Transform Infrared Spectroscopy and X-Ray Diffraction Spectroscopy. The effects of pH (2–10), contact time (10–180 min), initial concentration (5–120 mgL−1), and dosage (0.1–2 g) and their interactions were investigated using response surface methodology following a central composite design. Optimum removal (87.70%) was obtained at pH 6, contact time 180 min, initial concentration 40.0 mgL−1, and adsorbent dosage 1.0 g by Excel Solver using the GRG solving method. The adsorption data fitted best to the Langmuir model with correlation coefficient and Chi-square value . The Freundlich isotherm gave a correlation coefficient and . The adsorption process followed the pseudo-second-order model. The calculated thermodynamic parameters showed that the adsorption process was endothermic and not thermodynamically spontaneous. The studied zeolite-A can therefore be used as a promising adsorbent for the removal of Ca(II) ions from aqueous solutions.
Aerobic Respiration and Its Regulation in the Metal Reducer Shewanella oneidensis

Shewanella oneidensis MR-1 is a facultative anaerobe known for its ability to reduce metal oxides. Anaerobic respiration, especially metal reduction, has been the subject of extensive research. In contrast, S. oneidensis aerobic respiration has received less attention. S. oneidensis expresses cbb3- and aa3-type cytochrome c oxidases and a bd-type quinol oxidase. The aa3-type oxidase, which in other bacteria is the major oxygen reductase under oxygen replete conditions, does not appear to contribute to aerobic respiration and growth in S. oneidensis. Our results indicated that although the aa3-type oxidase does not play a role in aerobic growth on lactate, the preferred carbon source for S. oneidensis, it is involved in growth on pyruvate or acetate. These results highlight the importance of testing multiple carbon and energy sources when attempting to identify enzyme activities and mutant phenotypes. Several regulatory proteins contribute to the regulation of aerobic growth in S. oneidensis including CRP and ArcA. The 3',5'-cAMP phosphodiesterase (CpdA) appears to play a more significant role in aerobic growth than either CRP or ArcA, yet the deficiency does not appear to be the result of reduced oxidase genes expression. Interestingly, the ∆cpdA mutant was more deficient in aerobic respiration with several carbon sources tested compared to ∆crp, which was moderately deficient only in the presence of lactate. To identify the reason for ∆cpdA aerobic growth deficiency, we isolated a suppressor mutant with transposon insertion in SO_3550. Inactivation of this gene, which encodes an anti-sigma factor, restored aerobic growth in the cpdA mutant to wild-type levels. Inactivation of SO_3550 in wild-type cells, however, did not affect aerobic growth. The S. oneidensis genome encodes two additional CRP-like proteins that we designated CrpB and CrpC. Mutants that lack crpB and crpC were deficient in aerobic growth, but this deficiency was not due to the loss of oxidase gene expression.
Blood Meals With Active and Heat-Inactivated Serum Modifies the Gene Expression and Microbiome of Aedes albopictus

The Asian “tiger mosquito” Aedes albopictus is currently the most widely distributed disease-transmitting mosquito in the world. Its geographical expansion has also allowed the expansion of multiple arboviruses like dengue, Zika, and chikungunya, to higher latitudes. Due to the enormous risk to global public health caused by mosquitoes species vectors of human disease, and the challenges in slowing their expansion, it is necessary to develop new and environmentally friendly vector control strategies. Among these, host-associated microbiome-based strategies have emerged as promising options. In this study, we performed an RNA-seq analysis on dissected abdomens of Ae. albopictus females from Manhattan, KS, United States fed with sugar and human blood containing either normal or heat-inactivated serum, to evaluate the effect of heat inactivation on gene expression, the bacteriome transcripts and the RNA virome of this mosquito species. Our results showed at least 600 genes with modified expression profile when mosquitoes were fed with normal vs. heat-inactivated-containing blood. These genes were mainly involved in immunity, oxidative stress, lipid metabolism, and oogenesis. Also, we observed bacteriome changes with an increase in transcripts of Actinobacteria, Rhodospirillaceae, and Anaplasmataceae at 6 h post-feeding. We also found that feeding with normal blood seems to particularly influence Wolbachia metabolism, demonstrated by a significant increase in transcripts of this bacteria in mosquitoes fed with blood containing normal serum. However, no differences were observed in the virome core of this mosquito population. These results suggest that heat and further inactivation of complement proteins in human serum may have profound effect on mosquito and microbiome metabolism, which could influence interpretation of the pathogen-host interaction findings when using this type of reagents specially when measuring the effect of Wolbachia in vector competence.
Vertical Canopy Profile and the Impact of Branches on Soybean Seed Composition

Soybean [Glycine max (L.) Merr. ] seeds are of global importance for human and animal nutrition due to their high protein and oil concentrations, and their complete amino acid (AA) and fatty acid (FA) profiles. However, a detailed description of seed composition at different canopy portions (i.e., main stem and branch nodes) is currently lacking in scientific literature. This study aims to (1) characterize seed yield and composition (protein, oil, AA, and FA) at the main stem (exploring a vertical canopy profile) and stem branches and (2) quantify the impact of canopy yield allocation on seed composition, focusing on branches as a potential contributor for higher yields. Four genotypes were field-grown during the 2018 and 2019 seasons, with seeds manually harvested from all the branches and three main stem segments (lower, middle, and upper). Seed samples were analyzed for seed yield (Mg/ha), seed size (mg/seed), protein and oil content (mg/seed) and their respective concentrations (g/kg), and AA and FA concentrations within protein and oil (g/100 g), herein called abundance. The upper main stem produced greater protein (25%) and oil (15%) content relative to the lower section; however, oil concentration increased from top to bottom while protein concentration followed opposite vertical gradient. Limiting AAs (lysine, cysteine, methionine, threonine, and tryptophan) were more abundant in the lower main stem, while the oleic/(linoleic + linolenic) ratio was greater in the upper segment. Overall, branches produced seeds with inferior nutritional quality than the main stem. However, the contribution of branches to yield (%) was positively related to limiting AA abundance and oil concentration across soybean genotypes. Future research studies should consider the morphological process of stem branching as a critical factor intimately involved with soybean seed composition across environments, genotypes, and management practices.
Semantic Predictability Facilitates Comprehension of Degraded Speech in a Graded Manner

Previous studies have shown that at moderate levels of spectral degradation, semantic predictability facilitates language comprehension. It is argued that when speech is degraded, listeners have narrowed expectations about the sentence endings; i.e., semantic prediction may be limited to only most highly predictable sentence completions. The main objectives of this study were to (i) examine whether listeners form narrowed expectations or whether they form predictions across a wide range of probable sentence endings, (ii) assess whether the facilitatory effect of semantic predictability is modulated by perceptual adaptation to degraded speech, and (iii) use and establish a sensitive metric for the measurement of language comprehension. For this, we created 360 German Subject-Verb-Object sentences that varied in semantic predictability of a sentence-final target word in a graded manner (high, medium, and low) and levels of spectral degradation (1, 4, 6, and 8 channels noise-vocoding). These sentences were presented auditorily to two groups: One group (n =48) performed a listening task in an unpredictable channel context in which the degraded speech levels were randomized, while the other group (n =50) performed the task in a predictable channel context in which the degraded speech levels were blocked. The results showed that at 4 channels noise-vocoding, response accuracy was higher in high-predictability sentences than in the medium-predictability sentences, which in turn was higher than in the low-predictability sentences. This suggests that, in contrast to the narrowed expectations view, comprehension of moderately degraded speech, ranging from low- to high- including medium-predictability sentences, is facilitated in a graded manner; listeners probabilistically preactivate upcoming words from a wide range of semantic space, not limiting only to highly probable sentence endings. Additionally, in both channel contexts, we did not observe learning effects; i.e., response accuracy did not increase over the course of experiment, and response accuracy was higher in the predictable than in the unpredictable channel context. We speculate from these observations that when there is no trial-by-trial variation of the levels of speech degradation, listeners adapt to speech quality at a long timescale; however, when there is a trial-by-trial variation of the high-level semantic feature (e.g., sentence predictability), listeners do not adapt to low-level perceptual property (e.g., speech quality) at a short timescale.
VicPred: A Vibrio cholerae Genotype Prediction Tool

Genomic information can be used to predict major pathogenic traits of pathogens without the need for laboratory experimentation. However, no Vibrio cholerae genome-based trait identification tools currently exist. The aim of this study was to develop a web-based prediction tool to identify Vibrio pathogenic traits using publicly available 796 whole-genome sequences of V. cholerae. Using this application, 68 structural O-antigen gene clusters belonging to 49 serogroups of V. cholerae were classified, and the composition of the genes within the O-antigen cluster of each serogroup was identified. The arrangement and location of the CTX prophage and related elements of the seventh cholera pandemic strains were also revealed. With the versatile tool, named VicPred, we analyzed the assemblage of various SXTs (sulfamethoxazole/trimethoprim resistance element) and major genomic islands (GIs) of V. cholerae, and the increasing trend in drug-resistance revealing high resistance of the V. cholerae strains to certain antibiotics. The pathogenic traits of newly sequenced V. cholerae strains could be analyzed based on these characteristics. The accumulation of further genome data will expedite the establishment of a more precise genome-based pathogenic traits analysis tool.