Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of prognostic immune-related genes in rhabdoid tumor of kidney based on TARGET database analysis

Background: Malignant rhabdoid tumor of the kidney (RTK) is a rare and highly aggressive pediatric malignancy. Immune system dysfunction is significantly correlated with tumor initiation and progression. Methods: We integrated and analyzed the expression profiles of immune-related genes (IRGs) in 65 RTK patients based on the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Prognostic related IRGs in RTK patients were analyzed using univariate and multivariate analysis, based on which a prognostic model with IRGs was constructed. Correlation analysis between the risk score of our model and tumor-infiltrating cell were also investigated. Results: Twenty two IRGs were significantly associated with the clinical outcomes of RTK patients. Gene ontology (GO) analysis revealed that inflammatory pathways were most frequently implicated in RTK. A prognostic model was constructed using 7 IRGs (MMP9, SERPINA3, FAM19A5, CCR9, PLAUR, IL1R2, PRKCG), which were independent prognostic indices that could differentiate patients based on their survival outcomes. Furthermore, the risk scores from our prognostic model was positively associated with cancer-associated fibroblasts (CAFs). Conclusions: We screened seven IRGs of clinical significance to distinguish patients with different survival outcomes. This may enhance our understanding of the immune microenvironment of RTK, and could use to design individualized treatments for RTK patients. Background: Malignant rhabdoid tumor of the kidney (RTK) is a rare and highly aggressive pediatric malignancy. Immune system dysfunction is significantly correlated with tumor initiation and progression. Methods: We integrated and analyzed the expression profiles of immune-related genes (IRGs) in 65 RTK patients based on the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Prognostic related IRGs in RTK patients were analyzed using univariate and multivariate analysis, based on which a prognostic model with IRGs was constructed. Correlation analysis between the risk score of our model and tumor-infiltrating cell were also investigated. Results: Twenty two IRGs were significantly associated with the clinical outcomes of RTK patients. Gene ontology (GO) analysis revealed that inflammatory pathways were most frequently implicated in RTK. A prognostic model was constructed using 7 IRGs (MMP9, SERPINA3, FAM19A5, CCR9, PLAUR, IL1R2, PRKCG), which were independent prognostic indices that could differentiate patients based on their survival outcomes. Furthermore, the risk scores from our prognostic model was positively associated with cancer-associated fibroblasts (CAFs). Conclusions: We screened seven IRGs of clinical significance to distinguish patients with different survival outcomes. This may enhance our understanding of the immune microenvironment of RTK and could use to design individualized treatments for RTK patients.
Extended low-frequency phase of the distortion-product otoacoustic emission in human newborns

At constant f2/f1 ratios, the phase of the nonlinear distortion component of the 2f1−f2 distortion-product otoacoustic emission (DPOAE) has a steep low-frequency segment and a flat high-frequency segment in adults and newborns. In adults, recent work found that a third segment characterizes the phase at even lower frequencies. The present study tests whether the same is true of the newborn DPOAE phase. Newborn and adult phase curves are generally similar. However, as previously reported, phase-gradient delays at mid frequencies (the region of steepest phase slope) are 50% longer in newborns.
De novo sequence redesign of a functional Ras‐binding domain globally inverted the surface charge distribution and led to extreme thermostability

To acquire extremely thermostable proteins of given functions is challenging for conventional protein engineering. Here we applied ABACUS, a statistical energy function we developed for de novo amino acid sequence design, to globally redesign a Ras‐binding domain (RBD), and obtained an extremely thermostable RBD that unfolds reversibly at above 110°C, the redesigned RBD experimentally confirmed to have expected structure and Ras‐binding interface. Directed evolution of the redesigned RBD improved its Ras‐binding affinity to the native protein level without excessive loss of thermostability. The designed amino acid substitutions were mostly at the protein surface. For many substitutions, strong epistasis or significantly differentiated effects on thermostability in the native sequence context relative to the redesigned sequence context were observed, suggesting the globally redesigned sequence to be unreachable through combining beneficial mutations of the native sequence. Further analyses revealed that by replacing 38 of a total of 48 non‐interfacial surface residues at once, ABACUS redesign was able to globally “invert” the protein's charge distribution pattern in an optimized way. Our study demonstrates that computational protein design provides powerful new tools to solve challenging protein engineering problems.
Pectin Methylesterases Modulate Plant Homogalacturonan Status in Defenses against the Aphid Myzus persicae[OPEN]

The role of homogalacturonan status modulated by PME/PMEI13 is a central component of the early defense responses of Arabidopsis against infestation by the green peach aphid, Myzus persicae. Because they suck phloem sap and act as vectors for phytopathogenic viruses, aphids pose a threat to crop yields worldwide. Pectic homogalacturonan (HG) has been described as a defensive element for plants during infections with phytopathogens. However, its role during aphid infestation remains unexplored. Using immunofluorescence assays and biochemical approaches, the HG methylesterification status and associated modifying enzymes during the early stage of Arabidopsis (Arabidopsis thaliana) infestation with the green peach aphid (Myzus persicae) were analyzed. Additionally, the influence of pectin methylesterase (PME) activity on aphid settling and feeding behavior was evaluated by free choice assays and the Electrical Penetration Graph technique, respectively. Our results revealed that HG status and HG-modifying enzymes are significantly altered during the early stage of the plant-aphid interaction. Aphid infestation induced a significant increase in total PME activity and methanol emissions, concomitant with a decrease in the degree of HG methylesterification. Conversely, inhibition of PME activity led to a significant decrease in the settling and feeding preference of aphids. Furthermore, we demonstrate that the PME inhibitor AtPMEI13 has a defensive role during aphid infestation, since pmei13 mutants are significantly more susceptible to M. persicae in terms of settling preference, phloem access, and phloem sap drainage.
ReMOT Control Delivery of CRISPR-Cas9 Ribonucleoprotein Complex to Induce Germline Mutagenesis in the Disease Vector Mosquitoes Culex pipiens pallens (Diptera: Culicidae)

Abstract The wide distribution of Culex (Cx.) pipiens complex mosquitoes makes it difficult to prevent the transmission of mosquito-borne diseases in humans. Gene editing using CRISPR/Cas9 is an effective technique with the potential to solve the growing problem of mosquito-borne diseases. This study uses the ReMOT Control technique in Culex pipiens pallens (L.) to produce genetically modified mosquitoes. A microinjection system was established by injecting 60 adult female mosquitoes—14 µl injection mixture was required, and no precipitation occurred with ≤1 µl of endosomal release reagents (chloroquine or saponin). The efficiency of delivery of the P2C-enhanced green fluorescent protein-Cas9 (P2C-EGFP-Cas9) ribonucleoprotein complex into the ovary was 100% when injected at 24 h post-bloodmeal (the peak of vitellogenesis). Using this method for KMO knockout, we found that gene editing in the ovary could also occur when P2C-Cas9 RNP complex was injected into the hemolymph of adult Cx. pipiens pallens by ReMOT Control. In the chloroquine group, of the 2,251 G0 progeny screened, 9 individuals showed with white and mosaic eye phenotypes. In the saponin group, of the 2,462 G0 progeny screened, 8 mutant individuals were observed. Sequencing results showed 13 bp deletions, further confirming the fact that gene editing occurred. In conclusion, the successful application of ReMOT Control in Cx. pipiens pallens not only provides the basic parameters (injection parameters and injection time) for this method but also facilitates the study of mosquito biology and control.
Investigating the Psychometric Properties of the Pieper-Zulkowski Pressure Ulcer Knowledge Test among Nurses in Iran

ABSTRACT OBJECTIVE To evaluate the psychometric properties of the Pieper-Zulkowski Pressure Ulcer Knowledge Test (PZ-PUKT) in Iranian nurses. METHODS A convenience sample of 323 nurses and 161 nursing students from the Ardabil University of Medical Sciences in Iran agreed to participate in the study. To determine the psychometric properties of the PZ-PUKT content and differential validity, item analysis (difficulty and discriminative indices), internal consistency, and test-retest were performed. RESULTS Because the total PZ-PUKT score for critical care nurses (39.84 ± 7.10) was higher compared with general nurses (37.01 ± 8.47) and nursing students (24.59 ± 12.95), the differential validity of the tool was confirmed. The mean difficulty indices of questions with and without considering the “I don’t know” option were 0.53 and 0.65, respectively, and 0.27 and 0.13 for discriminative index. Cronbach α coefficient was . 92 for the 72-item test. The correlation coefficient between test and retest for 30 nurses was 0.81. CONCLUSIONS This study showed that the Persian version of the PZ-PUKT is valid and reliable for use in Iran. It can be used in education and research to assess nurses’ knowledge as well as to evaluate the effectiveness of training programs on prevention and care of pressure injuries.
Thymus variants on imaging in patients with rheumatoid arthritis-Clinical and immunological significance.

OBJECTIVES We sought to clarify the presence of radiographic thymus variants using a scoring system, and their association with clinical and immunological features in RA patients. METHODS 387 RA patients randomly selected from all patients visiting our department who underwent chest CT scanning, with exclusion of patients with thymoma or thymic cyst, or age < 30 y. Thymus size and attenuation score in axial CT images were quantitatively interpreted and assessed. Associations between immunophenotype data and clinical and serological features were analysed in a subset of patients. RESULTS Thymic enlargement was found in 76 (19.6%) patients, and a thymus attenuation score ≥ 2 was found in 50 (12.9%) patients. The score was significantly associated with antibodies to citrullinated peptide antigens (ACPA) positivity. Thymic enlargement was significantly associated with the proportions of CD4+ effector memory T cells. CONCLUSION Radiographic thymus variants were frequently observed in RA patients, and may reflect an abnormal immune response involved in the pathogenesis of RA.
Persian Norms for The Stanford Hypnotic Susceptibility Scale, Form C (SHSS:C)

ABSTRACT The Stanford Hypnotic Susceptibility Scale, Form C (SHSS:C), is the most commonly used measure of hypnotizability. In Persian (Farsi), there was a lack of a valid test for hypnotizability. The norms for different language versions of the SHSS:C are important for evaluating the cross-language validity of the measure and determining the ability to compare research findings using the SHSS:C samples of different languages. In this study, a Persian translation of SHSS:C was administered to 321 Farsi-speaking individuals from the cities Tehran and Mashhad. Then, different parameters of the measure, including the distribution, normality, internal consistency, difficulty, and comparison with other SHSS:C norms, have been evaluated and presented. The results indicated that the Persian SHSS:C has good reliability, which is in line with the other language versions of the scale, and the scores from the Persian SHSS:C are comparable to those of the other language versions.
Sex differences in symptom severity, cognition and psychosocial functioning among individuals with at‐risk mental state for psychosis

Sex differences are well documented in schizophrenia, but have been much less studied in at‐risk mental state (ARMS) for psychosis. We aimed to examine sex differences in symptomatology, cognition, social and role functioning in individuals with ARMS, with specific focus on clarifying relationships between sex, negative symptoms and functioning.
A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis[OPEN]

A feedforward loop that controls vascular development was uncovered by identifying a transcriptional network mediated by the receptor kinase PHLOEM INTERCALATED WITH XYLEM. The cambium and procambium generate the majority of biomass in vascular plants. These meristems constitute a bifacial stem cell population from which xylem and phloem are specified on opposing sides by positional signals. The PHLOEM INTERCALATED WITH XYLEM (PXY) receptor kinase promotes vascular cell division and organization. However, how these functions are specified and integrated is unknown. Here, we mapped a putative PXY-mediated transcriptional regulatory network comprising 690 transcription factor-promoter interactions in Arabidopsis (Arabidopsis thaliana). Among these interactions was a feedforward loop containing transcription factors WUSCHEL HOMEOBOX RELATED14 (WOX14) and TARGET OF MONOPTEROS6 (TMO6), each of which regulates the expression of the gene encoding a third transcription factor, LATERAL ORGAN BOUNDARIES DOMAIN4 (LBD4). PXY signaling in turn regulates the WOX14, TMO6, and LBD4 feedforward loop to control vascular proliferation. Genetic interaction between LBD4 and PXY suggests that LBD4 marks the phloem-procambium boundary, thus defining the shape of the vascular bundle. These data collectively support a mechanism that influences the recruitment of cells into the phloem lineage, and they define the role of PXY signaling in this context in determining the arrangement of vascular tissue.
A novel c.1759T>G variant in follicle-stimulating hormone-receptor gene is concordant with male determination in the flathead grey mullet (Mugil cephalus)

Abstract Various master key regulators (MKRs) that control a binary switch of sex determination (SD) have been found in fish; these provide an excellent model for the study of vertebrate genetic SD. The SD region in flathead grey mullet has been previously mapped to a 1 Mbp region harboring 27 genes, of which one is follicle-stimulating hormone receptor (fshr). Although this gene is involved in gonad differentiation and function, it has not been considered as an MKR of SD. We systematically investigated polymorphism in mullet fshr using DNA shotgun sequences, and compared them between males and females. Capable of encoding nonconservative amino acid substitutions, c.1732G>A and c.1759T>G exhibited association with sex on a population level (N = 83; P ≤ 6.7 × 10−19). Hence, 1732 A and 1759 G represent a male-specific haplotype of the gene, designated as “fshry. ” Additional flanking SNPs showed a weaker degree of association with sex, delimiting the SD critical region to 143 nucleotides on exon 14. Lack of homozygotes for fshry, and the resulting divergence from Hardy–Weinberg equilibrium (N = 170; P ≤ 3.9 × 10−5), were compatible with a male heterogametic model (XY/XX). Capable of replacing a phenylalanine with valine, c.1759T>G alters a conserved position across the sixth transmembrane domain of vertebrate FSHRs. Amino acid substitutions in this position in vertebrates are frequently associated with constant receptor activation and consequently with FSH/FSHR signaling alteration; thus, indicating a potential role of fshr as an MKR of SD.
Effect of Heat Treatment on Color Changes, Dimensional Stability, and Mechanical Properties of Wood

Abstract Properties of fast-growing timbers with low durability can be improved by thermal modification. Thermal modification is an eco-friendly method of improving durability of wood. In this work, specimens of rubberwood (Hevea brasiliensis) and silver oak (Grevillea robusta) were thermally modified in vacuum between 210 to 240°C for 1 to 8 hours, and their weight loss, color, and chemical changes evaluated. Rate of thermal degradation was determined from weight loss data. The color of the modified wood darkened and was uniform throughout. CIE lightness color coordinate (L*) decreased with treatment severity, while chroma coordinates a* and b* increased initially, but later decreased with increased process severity. FTIR analysis showed degradation of cell wall polymers resulting in generation of structures which are responsible for color darkening of thermally modified wood. Mechanical properties (bending strength, MOR, and bending stiffness, MOE) of heat-treated wood decreased. A decrease in hydroxyl groups reduced the hygroscopic nature, resulting in increased dimensional stability of thermally modified wood.
Respiratory and Perceptual Responses to High-Intensity Interval Exercise in Obese Adults

ABSTRACT Purpose Although high-intensity interval exercise (HIIE) has emerged as an attractive alternative to continuous exercise (CE), the effects of HIIE on ventilatory constraints and dyspnea on exertion have not been studied in obese adults, and thus, tolerability of HIIE in obese adults is unknown. The purpose of this study was to examine differences in respiratory and perceptual responses between HIIE and CE in nonobese and obese adults. Methods Ten nonobese (5 men; 24.1 ± 6.2 yr; body mass index, 23.0 ± 1.3 kg·m−2) and 10 obese (5 men; 24.2 ± 3.8 yr; body mass index, 37 ± 4.6 kg·m−2) adults participated in this study. Respiratory and perceptual responses were assessed during HIIE (eight 30-s intervals at 80% maximal work rate, with 45-s recovery periods) and two 6-min sessions of CE, completed below and above ventilatory threshold (Vth). Results Despite similar work rate, HIIE was completed at a higher relative intensity in obese when compared with nonobese participants (68.8% ± 9.4% vs 58.9% ± 5.6% maximal oxygen uptake, respectively; P = 0.01). Expiratory flow limitation and/or dynamic hyperinflation was present during HIIE in 50% of the obese but in none of the nonobese participants. Ratings of perceived breathlessness were highest during HIIE (5.3 ± 2.4), followed by CEaboveVth (2.5 ± 1.6), and CEbelowVth (0.9 ± 0.7; P < 0.05) in obese participants. Unpleasantness associated with breathlessness was higher in obese (4.2 ± 3.0) when compared with nonobese participants (0.6 ± 1.3; P = 0.005) during HIIE. Conclusions HIIE, when prescribed relative to maximal work rate, is associated with greater ventilatory constraints and dyspnea on exertion when compared with CE in obese adults. CE may be more tolerable when compared with HIIE for obese adults.
A computational study of the reaction mechanism involved in the fast cleavage of an unconstrained amide bond assisted by an amine intramolecular nucleophilic attack

In the present work, the fast amide bond cleavage of [3‐((1R,5S,7s)‐3‐azabicyclo[3.3. 1]nonane‐7‐carbonyl)‐3‐azabicyclo[3.3. 1]nonane‐7‐carboxylic acid (bi‐ATDO)], through an intramolecular nucleophilic attack of an amine group is evaluated. First, six possible peptide bond cleavage mechanisms, two of them including a water molecule, are described at the ωB97XD/6–311 + G(d,p)//MP2/6–311 + G(d,p) level of theory. The reaction consisting of an intramolecular nitrogen nucleophilic attack followed by a proton transfer and the amide bond cleavage is determined as the most favorable mechanism. The activation free energy computed for the latter is 20.5 kcal mol−1, which agrees with the reported experimental result of 24.8 kcal mol−1. Inclusion of a water molecule to assist the first step of the reaction results in an activation free energy increase of about 17 kcal mol−1. All the steps in the most favorable mechanism are studied more in detail employing intrinsic reaction coordinate as well as the reaction force and reaction electronic flux analysis.
Developmental Assets of Adolescents and Young Adults With Chronic Illness and Comorbid Depression: Qualitative Study Using YouTube.

BACKGROUND Developmental assets provide a framework for optimizing development among adolescents but have not been studied in adolescents with chronic illness and comorbid depression, which is a group at risk for poor health outcomes. YouTube postings provide valuable insights to understand this understudied population. OBJECTIVE This study aims to explore asset development from the perspectives of adolescents and young adults (AYAs) with chronic illness and comorbid depression. METHODS YouTube was searched using 12 chronic illnesses (eg, diabetes) coupled with "depression" as keywords. Videos were included if they were uploaded by AYAs aged between 11 and 29 years and discussed living with chronic illness and depression during adolescence. Video transcripts were coded deductively for 40 internal and external assets that constitute the Developmental Assets Framework. Categories not captured by deductive coding were identified using conventional content analysis. Categories and their respective assets were labeled as being discussed either negatively or positively. RESULTS In total, 31 videos from 16 AYAs met the inclusion criteria. A total of 7 asset categories, support, constructive use of time, boundaries and expectations (external assets), identity, commitment to learning, positive values, and social competence (internal assets), reflecting 25 (13 internal; 12 external) assets, were discussed. Internal assets, particularly relating to identity, were commonly discussed by AYAs either in a negative way or fluctuated between positive and negative perspectives. CONCLUSIONS In this sample of AYAs with chronic illness and comorbid depression, internal assets were commonly discussed in a negative way. Future research is needed to better understand how assets develop and if the Developmental Assets Framework adequately represents the experiences of this population.
Isolation, Identification, Molecular and Electronic Structure, Vibrational Spectroscopic Investigation, and Anti-HIV-1 Activity of Karanjin Using Density Functional Theory

“Karanjin” (3-methoxy furano-2,3,7,8-flavone) is an anti-HIV drug, and it is particularly effective in the treatment of gastric problems. The method of isolation of “Karanjin” followed the Principles of Green Chemistry (eco-friendly and effortless method). The optimized geometry of the “Karanjin” molecule has been determined by the method of density functional theory (DFT). Using this optimized structure, we have calculated the infrared wavenumbers and compared them with the experimental data. The calculated wavenumbers are in an excellent agreement with the experimental values. On the basis of fully optimized ground-state structure, TDDFT//B3LYP/LANL2DZ calculations have been used to determine the low-lying excited states of Karanjin. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of “Karanjin. ” A complete assignment is provided for the observed FTIR spectra. This is the first report of the isolation, molecular and electronic structure using vibrational spectroscopic investigation, density functional theory, and anti-HIV-1 activity of “Karanjin. ”