Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive analysis of gene expression profiles provides insight into the pathogenesis of Crohn's disease

Crohn's disease (CD) is a type of inflammatory bowel disease that cannot be fully cured by medication or surgery. In the present study, the aim was to understand the underlying mechanisms of CD. Two CD microarray datasets were downloaded from The Gene Expression Omnibus database: GSE36807 (13 CD and 7 normal samples) and GSE59071 (8 CD and 11 normal samples). A series of bioinformatics analyses were conducted, including weighted gene co-expression network analysis to identify stable modules, and analysis of differentially expressed genes (DEGs) between CD and normal samples. The common DEGs in the GSE36807 and GSE59071 datasets were screened. Subsequently, overlapping genes in the stable modules and the DEGs were selected to construct a protein-protein interaction (PPI) network using Cytoscape software. Enrichment analysis of genes in the network was performed to explore their biological functions. A total of 10 stable modules and 927 DEGs were identified, of which 234 genes were shared in the stable modules and the DEGs. After removal of 32 uncharacterized genes, 202 genes were selected to build the PPI network. Low density lipoprotein receptor (LDLR), toll-like receptor 2 (TLR2), lipoprotein lipase (LPL), forkhead box protein M1 (FOXM1) and neuropeptide Y (NPY) were revealed as key nodes with high degree. Pathway enrichment analysis demonstrated that LPL was enriched in the peroxisome proliferator-activated receptor (PPAR) signaling pathway. In conclusion, LDLR, TLR2, FOXM1 and NPY, as well as LPL in the PPAR signaling pathway may serve critical roles in the pathogenesis of CD.
Candidate genes and microRNAs for glioma pathogenesis and prognosis based on gene expression profiles

Glioma is the most common malignant brain tumor, and the incidence of glioma demonstrates an upward trend. It is vital to elucidate the pathogenesis of glioma and seek effective therapies. The aim of the present study was to identify the potential gene markers associated with glioma based on GSE31262 gene expression profiles, and to explore the underlying mechanism of glioma progression by analyzing the gene markers. The microarray dataset GSE31262 was downloaded and neural stem cell samples (control group) and glioma samples (glioma group) were analyzed to identify the differentially expressed genes (DEGs) between the two groups. Gene Ontology functional and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using DAVID software. Subsequently, a protein-protein interaction (PPI) network was constructed and important modules were extracted from this network. Additionally, the miRNA-target regulatory network was established. In total, 1377 DEGs with P<0.01 and |log2 fold change| ≥2 were identified between the control and glioma groups. The DEGs that were upregulated in glioma samples compared with controls were primarily associated with functions such as the M phase and cell cycle pathway, while the downregulated genes were associated with functions such as nerve impulse and the axon guidance pathway. The results also indicated that certain DEGs, including cyclin-dependent kinase 1 (CDK1) and cadherin 1 (CDH1), had important roles in the PPI network. The MCODE tool in Cytoscape software was used to identify upregulated and downregulated modules in the PPI network, and 5 upregulated and 2 downregulated modules were extracted. Furthermore, the WebGestal online tool was used to identify potential interactions of the upregulated and downregulated genes with microRNAs (miRNA/miR), and miR-135A/B and its two targets, discs large MAGUK scaffold protein 2 and forkhead box O1 (FOXO1), had the highest number of connections in the miRNA-target regulatory network. In addition, cell division cycle 20 and FOXO1 were confirmed to be upregulated in U87 glioma cells compared with normal human astrocytes (HA1800) by reverse transcription-quantitative polymerase chain reaction. In conclusion, M phase function and the axon guidance pathway may be vital for glioma progression. In addition, CDK1 and CDH1 may be associated with the process of glioma. Furthermore, miR-135A/B, and the target FOXO1, may be potential therapy targets for glioma treatment.
Variation of Bandwidth with Modulation Index in Frequency Modulation

Equations are derived for the carrier and side-frequency amplitudes which are obtained when a carrier wave is frequency-modulated by a complex audio signal. The bandwidth occupied by such a frequency-modulated wave is defined as the distance between the two frequencies beyond which none of the side frequencies is greater than 1 per cent of the carrier amplitude obtained when the modulation is removed. Curves are given to show the amount this bandwidth exceeds the extremes of deviation for a range of modulation indexes from 0.1 to 10,000, for sinusoidal, square, rectangular, and triangular modulation. For more precise definitions of bandwidth, curves are also given for side-frequency amplitude limits of 0.1 per cent and 0.01 per cent of the carrier-wave amplitude. For complex modulatlon the total bandwidth can be estimated by computing the bandwidth that would be required by each audio-frequency component, if it were on separately, and adding the results.
BioContainers on Purdue Clusters

Container technologies such as Docker, Kubernetes, and SingularityCE have been receiving an increasing level of attention in academic institutions. Containers wrap up the application into an isolated file system containing everything it needs to run, such as compiler, libraries and dependencies. This enables containers to always run the same, regardless of the environment in which they are running, promoting container technology as a critical tool for reproducible research. In high-performance computing (HPC) context, containers gain popularity because they can significantly reduce the administrators’ work of deploying applications. On Purdue University HPC clusters, several hundred SingularityCE containers have been deployed. Here, we will introduce how SingularityCE containers are used to create the bioinformatic tool collection (biocontainers). Due to the ease of deployment and portability, biocontainers have been deployed in Purdue’s 6 HPC clusters as well as XSEDE Anvil, providing a reliable and reproducible computing environment for life science researchers.
Risk Factors and Outcomes of Revision Arthroscopic Posterior Shoulder Capsulolabral Repair

Background: Risk factors and outcomes of revision arthroscopic posterior capsulolabral repair of the shoulder are currently not well defined. Hypothesis: Athletes who require revision arthroscopic posterior unidirectional capsulolabral repair will have poorer outcomes and return to play when compared with those undergoing primary procedures, with risk factors including younger age, injury size, bone loss, and anchor number. Study Design: Case-control study; Level of evidence, 3. Methods: A total of 297 shoulders that underwent arthroscopic posterior capsulolabral repair at minimum 2-year follow-up were reviewed. In addition to surgical data, the American Shoulder and Elbow Surgeons scoring system with subjective stability, range of motion, strength, and pain scores as well as return to sport were compared pre- and postoperatively between those who did and did not require revision surgery. Magnetic resonance arthrogram measurements of glenoid labral, chondral, and bone version and labral and bone width were also compared. Results: Nineteen shoulders required revision surgery (6.4%) at 8.9-year follow-up. Significant risk factors included female sex (P = .001), dominant shoulder (P = .005), and concomitant rotator cuff injury (P = .029). Patients with ≤3 anchors were more likely to require revision (odds ratio = 3.48). Smaller glenoid bone width was a risk factor for requiring future revision surgery (P < .001), but glenoid labral, chondral, and bone version and labral width were not risk factors. All patients had significant improvements in American Shoulder and Elbow Surgeons, pain, range of motion, and strength scores after the original surgery; however, those who required revision surgery had less improvement (P < .05). Stability improved significantly for nonrevisions (P < .001) but did not for revisions (P = .662). In the nonrevision group, 64.3% returned to sport at the same level, which was significantly higher than the 15.4% of the revision group (P = .004). Overall, 78.6% of the nonrevision group and 61.6% of the revision group returned to sport at some level (P = .280). Conclusion: Athletes underwent revision arthroscopic posterior capsulolabral repair at an incidence of 6.4%. Revision patients had significantly poorer outcome scores and return to play when compared with those who did not undergo revision surgery with risk factors being dominant shoulder surgery, female sex, concomitant rotator cuff injury, the use of 3 or fewer anchors, and smaller glenoid bone width. These data are essential for patient selection, optimal treatment techniques, and patient education as posterior shoulder instability failure requiring revision has not previously been evaluated.
Oppositional Defiant Disorder dimensions and aggression: The moderating role of hostile bias and sex

Background: Hostile Attributional Bias (HAB) has been related to conduct problems. The common and unique associations between the different dimensions of Oppositional Defiant Disorder (ODD) symptoms, specific components of HAB, sex and types of aggression (overt and relational) in a community sample of 491 7‐year‐old children are investigated. Method: Teachers rated the children's ODD symptoms and aggression and the children self‐reported about HAB. Multiple linear regressions showed that ODD dimensions were directly associated with both types of aggression. Results: Boys were more overtly aggressive and girls more relational. Emotional distress was directly associated with relational aggression. The relational component of HAB uniquely moderated the influence of the oppositional dimension on relational aggressive behaviour. Conclusions: The assessment of social cognition variables is necessary to approach specific interventions in the presence of ODD symptoms, as this may help to identify a subset of children prone to aggressive reactions. &NA; Dimensiones del Trastorno Negativista Desafiante y la agresión: el rol moderador del sesgo hostil y el sexo. Antecedentes: el sesgo hostil atribucional (SHA) se ha relacionado con los problemas de conducta. Método: este trabajo investiga asociaciones comunes y específicas entre las diferentes dimensiones del Trastorno Negativista Desafiante (TND), el sexo y diferentes tipos de agresividad (abierta y relacional) en una muestra comunitaria de 491 participantes de 7 años de edad. Los profesores informaron sobre los síntomas de TND y la agresividad de los participantes y estos autoinformaron sobre su SHA. Regresiones lineales múltiples mostraron que todas las dimensiones de TND estaban directamente asociadas con ambos tipos de agresividad. Resultados: los chicos mostraron más agresividad abierta y las chicas más agresividad relacional. El malestar emocional se asoció directamente con la agresividad relacional. El componente relacional del SHA moderó de manera específica la influencia de la dimensión oposicionista sobre la conducta de agresividad relacional. Conclusiones: la evaluación de variables de cognición social en presencia de síntomas de TND es necesaria, ya que podría ayudar a identificar un subgrupo de niños proclive a las reacciones agresivas y contribuir al diseño de intervenciones específicas.
Roof-Inhabiting Cousins of Rock-Inhabiting Fungi: Novel Melanized Microcolonial Fungal Species from Photocatalytically Reactive Subaerial Surfaces

Subaerial biofilms (SAB) are an important factor in weathering, biofouling, and biodeterioration of bare rocks, building materials, and solar panel surfaces. The realm of SAB is continually widened by modern materials, and the settlers on these exposed solid surfaces always include melanized, stress-tolerant microcolonial ascomycetes. After their first discovery on desert rock surfaces, these melanized chaetothyrialean and dothidealean ascomycetes have been found on Mediterranean monuments after biocidal treatments, Antarctic rocks and solar panels. New man-made modifications of surfaces (e.g., treatment with biocides or photocatalytically active layers) accommodate the exceptional stress-tolerance of microcolonial fungi and thus further select for this well-protected ecological group. Melanized fungal strains were isolated from a microbial community that developed on highly photocatalytic roof tiles after a long-term environmental exposure in a maritime-influenced region in northwestern Germany. Four of the isolated strains are described here as a novel species, Constantinomyces oldenburgensis, based on multilocus ITS, LSU, RPB2 gene phylogeny. Their closest relative is a still-unnamed rock-inhabiting strain TRN431, here described as C. patonensis. Both species cluster in Capnodiales, among typical melanized microcolonial rock fungi from different stress habitats, including Antarctica. These novel strains flourish in hostile conditions of highly oxidizing material surfaces, and shall be used in reference procedures in material testing.
E-cigarette adverts and children’s perceptions of tobacco smoking harms: an experimental study and meta-analysis

Objectives Children exposed to electronic cigarette (e-cigarette) adverts may perceive occasional tobacco smoking as less harmful than children not exposed to e-cigarette adverts. Given the potential cross-cueing effects of e-cigarette adverts on tobacco smoking, there is an urgent need to establish whether the effect found in prior research is robust and replicable using a larger sample and a stronger control condition. Design A between-subjects experiment with one independent factor of two levels corresponding to the advertisements to which participants were exposed: glamorous adverts for e-cigarettes, or adverts for objects unrelated to smoking or vaping. Participants English school children aged 11–16 (n=1449). Outcomes Perceived harm of occasional smoking of one or two tobacco cigarettes was the primary outcome. Secondary outcomes included: perceived harm of regular tobacco smoking, susceptibility to tobacco smoking and perceived prevalence of tobacco smoking in young people. Perceptions of using e-cigarettes were gauged by adapting all the outcome measures used to assess perceptions of tobacco smoking. Results Tobacco smokers and e-cigarette users were excluded from analyses (final sample n=1057). Children exposed to glamorous e-cigarette adverts perceived the harms of occasional smoking of one or two tobacco cigarettes to be lower than those in the control group (Z=−2.13, p=0.033). An updated meta-analysis comprising three studies with 1935 children confirmed that exposure to different types of e-cigarette adverts (glamorous, healthful, flavoured, non-flavoured) lowers the perceived harm of occasional smoking of one or two tobacco cigarettes (Z=3.21, p=0.001). Conclusions This study adds to existing evidence that exposure to e-cigarette adverts reduces children’s perceptions of the harm of occasional tobacco smoking.
Distortion Tests by the Intermodulation Method

Although the term "intermodulation" has been used for a long time to describe a form of distortion, only recently has simplified testing equipment been made available which permits the commercial testing of audio, radio, and general sound-recording equipment by this method. In this paper there is described a compact piece of apparatus which is being used for routine maintenance tests on the sound recording and reproducing systems. A comparison is made between the harmonic and intermodulation methods of making such tests to show the advantage of the latter method. Circuits and descriptions of the apparatus for generating and analyzing the intermodulation test tone needed in making the tests are given. Tests on radio transmission systems, sound disk and film recording apparatus, iron-core coupling devices, and general sound systems are described which show how the intermodulation method of measuring distortion is in many cases a more adequate indication of equipment performance than other methods commonly used, as well as being less laborious.
Parameter Estimation of Signal-Dependent Random Noise in CMOS/CCD Image Sensor Based on Numerical Characteristic of Mixed Poisson Noise Samples

Parameter estimation of Poisson-Gaussian signal-dependent random noise in the complementary metal-oxide semiconductor/charge-coupled device image sensor is a significant step in eliminating noise. The existing estimation algorithms, which are based on finding homogeneous regions, acquire the pair of the variances of noise and the intensities of every homogeneous region to fit the linear or piecewise linear curve and ascertain the noise parameters accordingly. In contrast to the existing algorithms, in this study, the Poisson noise samples of all homogeneous regions in every block image are pieced together to constitute a larger sample following the mixed Poisson noise distribution; then, the mean and variance of the mixed Poisson noise sample are deduced. Next, the mapping function among the noise parameters to be estimated—variance of Poisson-Gaussian noise and that of Gaussian noise corresponding to the stitched region in every block image—is constructed. Finally, the unbiased estimations of noise parameters are calculated from the mapping functions of all the image blocks. The experimental results confirm that the proposed method can obtain lower mean absolute error values of estimated noise parameters than the conventional ones.
Schwann cell O-GlcNAcylation promotes peripheral nerve remyelination via attenuation of the AP-1 transcription factor JUN

Significance Schwann cells (SCs), the ensheathing glia of the peripheral nervous system, promote nerve repair/regeneration. Defects in these SC injury responses potentially contribute to the pathogenesis of diabetic neuropathy, the most prevalent form of peripheral neuropathy. Here, we show that O-GlcNAcylation, a posttranslational modification controlled by the metabolic state of the cell, influences SC injury responses and nerve repair. The transcription factor JUN, an essential regulator of the SC injury program, is O-GlcNAcylated at multiple sites, and loss of this modification leads to increased activity and ineffective repair SC function. These results demonstrate that O-GlcNAcylation regulates SC injury responses via modulation of JUN activity and broaden our understanding of how changes in metabolism, such as occur in diabetes, affect nerve repair. Schwann cells (SCs), the glia of the peripheral nervous system, play an essential role in nerve regeneration. Upon nerve injury, SCs are reprogrammed into unique “repair SCs,” and these cells remove degenerating axons/myelin debris, promote axonal regrowth, and ultimately remyelinate regenerating axons. The AP-1 transcription factor JUN is promptly induced in SCs upon nerve injury and potently mediates this injury-induced SC plasticity; however, the regulation of these JUN-dependent SC injury responses is unclear. Previously, we produced mice with a SC-specific deletion of O-GlcNAc transferase (OGT). This enzyme catalyzes O-GlcNAcylation, a posttranslational modification that is influenced by the cellular metabolic state. Mice lacking OGT in SCs develop a progressive demyelinating peripheral neuropathy. Here, we investigated the nerve repair process in OGT-SCKO mutant mice and found that the remyelination of regenerating axons is severely impaired. Gene expression profiling of OGT-SCKO SCs revealed that the JUN-dependent SC injury program was elevated in the absence of injury and failed to shut down at the appropriate time after injury. This aberrant JUN activity results in abnormalities in repair SC function and redifferentiation and prevents the timely remyelination. This aberrant nerve injury response is normalized in OGT-SCKO mice with reduced Jun gene dosage in SCs. Mechanistically, OGT O-GlcNAcylates JUN at multiple sites, which then leads to an attenuation of AP-1 transcriptional activity. Together, these results highlight the metabolic oversight of the nerve injury response via the regulation of JUN activity by O-GlcNAcylation, a pathway that could be important in the neuropathy associated with diabetes and aging.
Functionalized Hydrophilic Superparamagnetic Iron Oxide Nanoparticles for Magnetic Fluid Hyperthermia Application in Liver Cancer Treatment

In this work, we report the synthesis of hydrophilic and surface-functionalized superparamagnetic iron oxide nanoparticles (SPIOs) to utilize them as nanomedicines for treating liver cancer via magnetic fluid hyperthermia (MFH)-based thermotherapy. For this purpose, initially, we have synthesized the SPIOs through co-precipitation/thermolysis methods, followed by in situ surface functionalization with short-chained molecules, such as 1,4-diaminobenzene (14DAB), 4-aminobenzoic acid (4ABA) and 3,4-diaminobenzoic acid (34DABA) and their combination with terephthalic acid (TA)/2-aminoterephthalic acid (ATA)/trimesic acid (TMA)/pyromellitic acid (PMA) molecules. The as-prepared SPIOs are investigated for their structure, morphology, water dispersibility, and magnetic properties. The heating efficacies of the SPIOs are studied in calorimetric MFH (C-MFH) with respect to their concentrations, surface coatings, dispersion medium, and applied alternating magnetic fields (AMFs). Although all of the as-prepared SPIOs have exhibited superparamagnetic behavior, only 14DAB-, 4ABA-, 34DABA-, and 4ABA-TA-coated SPIOs have shown higher magnetization values (Ms = 55–71 emu g–1) and good water dispersibility. In C-MFH studies, 34DABA-coated SPIO-based aqueous ferrofluid (AFF) has revealed faster thermal response to the applied AMF and reached therapeutic temperature even at the lowest concentration (0.5 mg mL–1) compared with 14DAB-, 4ABA-, and 4ABA-TA-coated SPIO-based AFFs. Moreover, 34DABA-coated SPIO-based AFF has exhibited high heating efficacies (i.e., specific absorption rate/intrinsic loss power values of 432.1 W gFe–1/5.2 nHm2 kg–1 at 0.5 mg mL–1), which could be mainly due to (i) enhanced π–π conjugation paths of surface-attached 34DABA coating molecules because of intrafunctional group attractions and (ii) improved anisotropy from the formation of clusters/linear chains of the SPIOs in ferrofluid suspensions, owing to interfunctional group attractions/interparticle interactions. Moreover, the 34DABA-coated SPIOs have demonstrated (i) very good cytocompatibility for 24/48 h incubation periods and (ii) higher killing efficiency of 61–88% (via MFH) in HepG2 liver cancer cells as compared to their treatment with only AMF/water-bath-based thermotherapy. In summary, the 34DABA-coated SPIOs are very promising heat-inducing agents for MFH-based thermotherapy and thus could be used as effective nanomedicines for cancer treatments.