Miracle-dz/UniFAR-FTUs huggingface dataset:
A glycolysis-related gene pairs signature predicts prognosis in patients with hepatocellular carcinoma

Background Hepatocellular carcinoma (HCC) is one of the most universal malignant liver tumors worldwide. However, there were no systematic studies to establish glycolysis‑related gene pairs (GRGPs) signatures for the patients with HCC. Therefore, the study aimed to establish novel GRGPs signatures to better predict the prognosis of HCC. Methods Based on the data from Gene Expression Omnibus, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium databases, glycolysis-related mRNAs were used to construct GRGPs. Cox regression was applied to establish a seventeen GRGPs signature in TCGA dataset, which was verified in two validation (European and American, and Asian) datasets. Results Seventeen prognostic GRGPs (HMMR_PFKFB1, CHST1_GYS2, MERTK_GYS2, GPC1_GYS2, LDHA_GOT2, IDUA_GNPDA1, IDUA_ME2, IDUA_G6PD, IDUA_GPC1, MPI_GPC1, SDC2_LDHA, PRPS1_PLOD2, GALK1_IER3, MET_PLOD2, GUSB_IGFBP3, IL13RA1_IGFBP3 and CYB5A_IGFBP3) were identified to be significantly progressive factors for the patients with HCC in the TCGA dataset, which constituted a GRGPs signature. The patients with HCC were classified into low-risk group and high-risk group based on the GRGPs signature. The GRGPs signature was a significantly independent prognostic indicator for the patients with HCC in TCGA (log-rank P = 2.898e−14). Consistent with the TCGA dataset, the patients in low-risk group had a longer OS in two validation datasets (European and American: P = 1.143e−02, and Asian: P = 6.342e−08). Additionally, the GRGPs signature was also validated as a significantly independent prognostic indicator in two validation datasets. Conclusion The seventeen GRGPs and their signature might be molecular biomarkers and therapeutic targets for the patients with HCC.
Computational perspectives revealed prospective vaccine candidates from five structural proteins of novel SARS corona virus 2019 (SARS-CoV-2)

Background The present pandemic COVID-19 is caused by SARS-CoV-2, a single-stranded positive-sense RNA virus from the Coronaviridae family. Due to a lack of antiviral drugs, vaccines against the virus are urgently required. Methods In this study, validated computational approaches were used to identify peptide-based epitopes from six structural proteins having antigenic properties. The Net-CTL 1.2 tool was used for the prediction of CD8+ T-cell epitopes, while the robust tools Bepi-Pred 2 and LBtope was employed for the identification of linear B-cell epitopes. Docking studies of the identified epitopes were performed using HADDOCK 2.4 and the structures were visualized by Discovery Studio and LigPlot+. Antigenicity, immunogenicity, conservancy, population coverage and allergenicity of the predicted epitopes were determined by the bioinformatics tools like VaxiJen v2.0 server, the Immune Epitope Database tools and AllerTOP v.2. 0, AllergenFP 1.0 and ElliPro. Results The predicted T cell and linear B-cell epitopes were considered as prime vaccine targets in case they passed the requisite parameters like antigenicity, immunogenicity, conservancy, non-allergenicity and broad range of population coverage. Among the predicted CD8+ T cell epitopes, potential vaccine targets from surface glycoprotein were; YQPYRVVVL, PYRVVVLSF, GVYFASTEK, QLTPTWRVY, and those from ORF3a protein were LKKRWQLAL, HVTFFIYNK. Similarly, RFLYIIKLI, LTWICLLQF from membrane protein and three epitopes viz; SPRWYFYYL, TWLTYTGAI, KTFPPTEPK from nucleocapsid phosphoprotein were the superior vaccine targets observed in our study. The negative values of HADDOCK and Z scores obtained for the best cluster indicated the potential of the epitopes as suitable vaccine candidates. Analysis of the 3D and 2D interaction diagrams of best cluster produced by HADDOCK 2.4 displayed the binding interaction of leading T cell epitopes within the MHC-1 peptide binding clefts. On the other hand, among linear B cell epitopes the majority of potential vaccine targets were from nucleocapsid protein, viz; 59−HGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLS−105, 227−LNQLE SKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATK−266, 3−DNGPQNQRNAPRITFGGP−20, 29−GERSGARSKQRRPQGL−45. Two other prime vaccine targets, 370−NSASFSTFKCYGVSPTKLNDLCFTNV−395 and 260−AGAAAYYVGYLQPRT−274 were identified in the spike protein. The potential B-cell conformational epitopes were predicted on the basis of a higher protrusion index indicating greater solvent accessibility. These conformational epitopes were of various lengths and belonged to spike, ORF3a, membrane and nucleocapsid proteins. Conclusions Taken together, eleven T cell epitopes, seven B cell linear epitopes and ten B cell conformational epitopes were identified from five structural proteins of SARS-CoV-2 using advanced computational tools. These potential vaccine candidates may provide important timely directives for an effective vaccine against SARS-CoV-2.
Maximization of Non-Opioid Multimodal Analgesia in Ambulatory Surgery Centers

Ambulatory surgery centers aid the healthcare system by not only providing a cost-effective option for delivery of care but also by helping to reduce overwhelming case volumes at inpatient facilities. While outpatient protocols have been designed for an increasing number of surgical procedures, the inpatient to outpatient transition of surgery remains limited by both procedure type and patient comorbidities. This limitation stems in part from the heavy emphasis on accelerated discharge following outpatient procedures, given that prolonged recovery time is associated with delayed turnover and increased nursing care demands. Since its inception, enhanced recovery after surgery (ERAS) has aimed to primarily reduce the disruption of physiologic homeostasis that occurs secondary to surgery. More recently, the aim of ERAS has evolved to help transition inpatient procedures to outpatient settings and may even be useful in more emergent cases. It should be noted, however, that outpatient surgery even in combination with ERAS is not the best option for all patients, and the use of ERAS protocols should be complemented with predictive assessments of patient risk. Beyond augmenting the efficiency of outpatient surgery, ERAS protocols, when used in eligible patients and especially when combined with regional anesthetic techniques, are effective in delivering opioid-sparing pain management while increasing overall outcomes and patient satisfaction rates.
The relationship between individual phenotype and the division of labour in naked mole-rats: it’s complicated

Background The naked mole-rat (Heterocephalus glaber) is among the most social mammals on the planet, living in eusocial groups of up to 300 individuals that contain a single reproductive female and up to three reproductive males. A critical aspect of their complex social system is the division of labour that allows non-breeders to form an effective workforce. Age- or weight-based polyethisms are widely cited as explanations for how labour is divided, but evidence in support of these hypotheses has been equivocal. Methods To assess the extent to which individual working behaviour is determined by sex, age, weight and social rank, we studied the behaviours of 103 animals from eight captive colonies. We performed focal sampling and ran mixed-effects models to assess which factors explained variation in working behaviour during six ten-minute observation periods per individual. Results Contrary to widely-held beliefs, we found that working behaviour did not decrease linearly with weight, although polynomial regressions indicated younger and medium-sized individuals worked most frequently, while high-ranking individuals worked for the shortest periods of time. Working behaviour and its relationship with individual characteristics also varied between colonies. Conclusions While age- or size-based polyethisms may have some influence on working behaviour, we argue that other characteristics of the individual and colony are also important. In particular, the interactions of individual, social and environmental factors must be considered in order to understand the emergence and effectiveness of the division of labour that is so critical to many social organisms.
Immersive Surgical Anatomy of the Craniocervical Junction

With the advent and increased usage of posterior, lateral, and anterior surgical approaches to the craniocervical junction (CCJ), it is essential to have a sound understanding of the osseous, ligamentous, and neurovascular layers of this region as well as their three-dimensional (3D) orientations and functional kinematics. Advances in 3D technology can be leveraged to develop a more nuanced and comprehensive understanding of the CCJ, classically depicted via dissections and sketches. As such, this study aims to illustrate - with the use of 3D technologies - the major anatomical landmarks of the CCJ in an innovative and informative way. Photogrammetry, structured light scanning, and 3D reconstruction of medical images were used to generate these high-resolution volumetric models. A clear knowledge of the critical anatomical structures and morphometrics of the CCJ is crucial for the diagnosis, classification, and treatment of pathologies in this transitional region.
Isolation and characterization of a motility-defective mutant of Euglena gracilis

Euglena gracilis is a green photosynthetic microalga that swims using its flagellum. This species has been used as a model organism for over half a century to study its metabolism and the mechanisms of its behavior. The development of mass-cultivation technology has led to E. gracilis application as a feedstock in various products such as foods. Therefore, breeding of E. gracilis has been attempted to improve the productivity of this feedstock for potential industrial applications. For this purpose, a characteristic that preserves the microalgal energy e.g., reduces motility, should be added to the cultivars. The objective of this study was to verify our hypothesis that E. gracilis locomotion-defective mutants are suitable for industrial applications because they save the energy required for locomotion. To test this hypothesis, we screened for E. gracilis mutants from Fe-ion-irradiated cell suspensions and established a mutant strain, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${\mathrm{M}}_{3}^{-}$\end{document}M3−ZFeL, which shows defects in flagellum formation and locomotion. The mutant strain exhibits a growth rate comparable to that of the wild type when cultured under autotrophic conditions, but had a slightly slower growth under heterotrophic conditions. It also stores 1.6 times the amount of paramylon, a crystal of β-1,3-glucan, under autotrophic culture conditions, and shows a faster sedimentation compared with that of the wild type, because of the deficiency in mobility and probably the high amount of paramylon accumulation. Such characteristics make E. gracilis mutant cells suitable for cost-effective mass cultivation and harvesting.
Identification of ATP8B1 as a Tumor Suppressor Gene for Colorectal Cancer and Its Involvement in Phospholipid Homeostasis

Homeostasis of membrane phospholipids plays an important role in cell oncogenesis and cancer progression. The flippase ATPase class I type 8b member 1 (ATP8B1), one of the P4-ATPases, translocates specific phospholipids from the exoplasmic to the cytoplasmic leaflet of membranes. ATP8B1 is critical for maintaining the epithelium membrane stability and polarity. However, the prognostic values of ATP8B1 in colorectal cancer (CRC) patients remain unclear. We analyzed transcriptomics, genomics, and clinical data of CRC samples from The Cancer Genome Atlas (TCGA). ATP8B1 was the only potential biomarker of phospholipid transporters in CRC. Its prognostic value was also validated with the data from the Gene Expression Omnibus (GEO). Compared to the normal group, the expression of ATP8B1 was downregulated in the tumor group and the CRC cell lines, which declined with disease progression. The lower expression level of ATP8B1 was also significantly associated with worse survival outcomes in both the discovery samples (359 patients) and the validation samples (566 patients). In multivariate analyses, low ATP8B1 levels predicted unfavorable OS (adjusted HR 1.512, 95% CI: 1.069-2.137; P = 0.019) and were associated with poor progress-free interval (PFI) (adjusted HR: 1.62, 95% CI: 1.207-2.174; P = 0.001). The pathway analysis results showed that the underexpression of ATP8B1 was negatively associated with phospholipid transport, phospholipid metabolic process, and cell-cell adherent junction and positively associated with the epithelial-mesenchymal transition in CRC. Our analysis suggests that ATP8B1 is a potential cancer suppressor in CRC patients and may offer new strategies for CRC therapy.
Bigfin reef squid demonstrate capacity for conditional discrimination and projected future carbon dioxide levels have no effect on learning capabilities

Anthropogenic carbon dioxide (CO2) emissions are being absorbed by the oceans, a process known as ocean acidification, and risks adversely affecting a variety of behaviours in a range of marine species, including inhibited learning in some fishes. However, the effects of elevated CO2 on learning in advanced invertebrates such as cephalopods are unknown. Any impacts to the learning abilities of cephalopods could have far-reaching consequences for their populations and the communities they inhabit. Cephalopods have some of the most advanced cognitive abilities among invertebrates and are one of the few invertebrate taxa in which conditional discrimination has been demonstrated, though the trait has not been demonstrated in any species of squid. Here, we tested for the first time the capacity for conditional discrimination in a squid species (Sepioteuthis lessoniana). Furthermore, we investigated the effects of projected future CO2 levels (1,084 µatm) on conditional discrimination and learning more generally. A three-task experiment within a two-choice arena was used to test learning and conditional discrimination. Learning was measured by improvements in task completion in repeated trials over time and the number of trials required to pass each task. Squid exhibited significant learning capabilities, with an increase in correct choices over successive trials and a decrease in the number of trials needed to complete the successive tasks. Six of the 12 squid tested successfully passed all three tasks indicating a capacity for conditional discrimination in the species. Elevated CO2 had no effect on learning or on the capacity for conditional discrimination in squid. This study highlights the remarkable cognitive abilities of S. lessoniana, demonstrated by their capacity for conditional discrimination, and suggests that ocean acidification will not compromise learning abilities. However, other behavioural traits in the species have been shown to be altered at comparable elevated CO2 conditions. It is not clear why some ecologically important behaviours are altered by elevated CO2 whereas others are unaffected. Future research should focus on the physiological mechanism responsible for altered behaviours in squid at elevated CO2.
Adrenal and Hematological Responses to Stress in Juvenile Green Turtles (Chelonia mydas) with and without Fibropapillomas

This study reports baseline adrenocortical, hematological, and plasma biochemical values for clinically healthy juvenile green turtles from a discrete population at Kaneohe Bay, island of Oahu, Hawaii. Using a general linear modeling program, we compared mean values for these parameters with mean values of a group afflicted with green turtle fibropapillomas (GTFP). Turtles of similar size classes from both groups were collected under the same conditions in the same study area and season at the same time of the day. Corticosterone, hematological, and enzymatic responses to acute and chronic stress were characterized for each group at four different sampling periods: 0 h (within 2 min of capture), 1 h, 3-4 h, and 24 h postcapture. On the basis of the differences identified between groups and times within a group, we conclude that turtles with GTFP are chronically stressed and immunosuppressed.
Feeding habits of the Pacific bearded brotula Brotula clarkae Hubbs, 1944 (Ophidiidae) along the Pacific coast of Costa Rica, Central America

Summary The present study analyzed the diet composition, ontogenetic shifts and dietary overlap of Brotula clarkae in relation to stage of maturity and sex. Samples were collected from the trawling fishery along the Pacific coast of Costa Rica (2011–2012) at depths ranging from 41.4 to 168.3 m; however, over 80% of the sampled fish were obtained at depths between 50 and 75 m. Size ranged from 14.4 to 98.4 cm total length. Of the 323 analyzed stomachs, 44.3% were from males, 86% were from immature individuals, and 49.8% had at least one prey item. According to the prey-specific index of relative importance (PSIRI), decapod shrimps were the most important prey (57.6% PSIRIi) followed by teleosts (28.2% PSIRIi), stomatopods (10.8% PSIRIi), and crabs (3.3% PSIRIi). Male and female B. clarkae exhibited a high dietary overlap (CH = 0.94). Immature B. clarkae consumed primarily shrimps and crabs (71.5% of stomachs from immature specimens contained shrimps, which accounted for over 66.0% PSIRIi); mature individuals consumed a large proportion of teleosts and stomatopods, which together contributed to over 91.0% PSIRIi. Both immature and mature B. clarkae overlapped spatially with the commercial trawling fishery grounds along the Pacific coast of Costa Rica. However, juveniles feed predominantly on shrimps, suggesting that immature B. clarkae may be subjected to high fishing pressure as by-catch, making them particularly vulnerable to overexploitation.
The effect of maternal overweight and obesity on the viability and metabolism of human oocytes and early embryos

Overweight and obese (OWOB) women are reported to have a lower chance of becoming pregnant. The nutritional enrichment of the periconceptional environment apparent in obese women may be detrimental for embryo viability. This is the first study to examine the development and metabolism of embryos derived from OWOB women compared with those from normal weight women. Measurements of oocyte quality, embryo development and utilisation of exogenous and endogenous metabolites were performed. Results were compared for normal weight and OWOB and examined in relation to blastocyst development and pregnancy outcome. Patients attending the Hull IVF Unit for fertility treatment (n=176) donated supernumerary embryos (n=808) from day 5 to 7/9 of development. Full ethical approval was obtained. Oocytes from overweight or obese women were smaller than those from women of healthy weight, yet post-fertilization they reached the morula stage faster and, as blastocysts, showed reduced glucose consumption and elevated endogenous triglyceride levels. There were no differences in the metabolism of pyruvate or lactate. Amino acid metabolism was more active in embryos generated from OWOB women and significant differences were seen in the turnover of individual amino acids that were also predictive of blastocyst formation and pregnancy outcome. The significant findings were independent of male BMI. In vitro culture supplementation with insulin did not influence glucose consumption, but did appear to modulate developmental progression to the blastocyst stage as well as the utilisation of specific amino acids. Whereas, when the medium was supplemented with l-carnitine (LC), embryos consumed LC from the medium, and at 0.05mM LC addition; embryos showed reduced intracellular triglyceride levels and increased exogenous glucose consumption. However, at 0.5mM LC addition; embryo viability was compromised in cohorts of embryos from women with a BMI <25kg/m2. The data support the hypothesis that embryo viability is compromised in OWOB women. This may reduce not only the chances of conception, but have long-term implications for the health of the offspring in later life.
La mapimite et l'ojuélaïte, deux nouveaux arséniates hydratés de zinc et de fer de la mine Ojuela, Mapimi, Mexique

Ces deux nouveaux arseniates hydrates de zinc et de fer, associes a de la scorodite, de l'adamite et de la smithsonite sur une gangue de limonite, proviennent de la mine Ojuela, Mapimi, Etat de Durango, Mexique. Ils ont ete nommes respectivement mapimite et ojuelaite en l'honneur du district minier et de la mine d'origine. Mapimite. — Ce mineral se presente en plaquettes aplaties sur {001} et limitees par {110} ; il est monoclinique Cm avec a = 11,425 ; b = 11,296 ; c = 8,667 A et β = 107° 44', avec Z = 2. Les raies principales du diagramme de poudre sont : 8,24 (100) 001 ; 7,83 (94) 110 ; 4,662 (61) 021 ; 3,883 (46) 22[-1] ; 3,451 (36) 310 ; 3,331 (36) 022 ; 3,217 (41) 22[-2] ; 2,826 (37) 20[-3] ; 2,451 (35) 420. Biaxe positif avec 2V = 50° et np = 1,672 ; nm(b) = 1,678 ; ng = 1,712 ; l'angle a ^ ng est egal a 13°. La dispersion r < v est importante et le pleochroisme fort : jaune clair pâle selon np, bleu de Prusse profond selon ng et jaune verdâtre selon nm La couleur est variable du fait du trichroisme et varie dans les bleus, bleu vert, verts etc. La densite calculee est egale a 3,00 pour une valeur mesuree de 2,95. L'analyse chimique par voie humide a donne : ZnO 15,8 ; FeO 0,9 ; Fe₂O₃ 25,6 ; As₂O₅ 35,6 ; H₂O 21,6 ; total 99,5 % et conduit a la formule Zn₂Fe³⁺₃(AsO₄)₃(OH)₄ • 10 H₂O. La courbe d'ATD, assez complexe, montre deux departs d'eau principaux a 190 et 343 °C, une recristallisation a 638 °C et un phenomene endothermique complexe a 1 000, 1 025 et 1 057 °C marquant la fusion et le depart de As₂O₃ apres reduction. Ojuelaite. — Elle se presente en fibres allongees suivant c et est monoclinique P2₁/c avec a = 10,247 ; b = 9,665 ; c = 5,569 A et β = 94° 22', avec Z = 2. Les raies principales du diagramme de poudre sont : 10,23 (65) 100 ; 7,03 (82) 110 ; 4,83 (78) 020 ; 4,251 (54) 210 ; 4,251 (100) 111 ; 2,901 (62) 221 ; 2,871 (90) 31[-1] ; 2,630 (63) 102. Biaxe positive avec 2Vcalc = 73° et np(b) = 1,696 ; nm = 1,730 et ng(c) = 1,798. La bissectrice de l'angle obtus des axes optiques est selon b. Pleochroique dans les tons jaunes, elle presente une couleur chartreuse (RHS 2-C). Les densites mesurees et calculees sont egales a 3,39. Les resultats de l'analyse chimique par voie humide : ZnO 14,6 ; Fe₂O₃ 27,5 ; As₂O₅ 40,5 ; H₂O 16,8 ; total 99,4% conduisent a la formule ZnFe³⁺₂(AsO₄)₂(OH)₂ • 4H₂O. La courbe d'ATD est similaire a celle de la mapimite : departs d'eau a 198 et 250 °C, recristallisation a 607 °C ; fusion et depart de As₂O₃ a 984 et 1 057 °C.
DIFFERENTIAL CONTRIBUTIONS OF THE TWO CEREBRAL HEMISPHERES TO THE PERCEPTION OF HAPPY AND SAD FACES

FIJU~TIONAI. competencies of the hemispheres in the cognitive realm have been well documented over the past decade [I 31. However, differences between the hemispheres in the perception of affective information and in the production of affective behavior are not well understood. A variety of recent findings are consistent with the hypothesis of differential hemispheric specialization for certain positive and negative affects [4 151. Specifically, the left hemisphere has been implicated as more actively involved in the control of positive affect while the right hemisphere has been associated with the control of negative affect. Most of these findings have focused upon affective experience and expression. While a large body of literature is available on hemispheric specialization for the perception and processing of affect [ 16 203, few of the studies were explicitly concerned with differential hemispheric involvement in the perception of positive YS negative affect [lo. 13, 201 and none has assessed hemispheric asymmetries in the perceptlon of happy and sad human faces. The purpose of the present experiment was to explicitly examine visual field differences in an affective face discrimination task as a function of the nature of the affective expression.