Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of immune-related features involved in Duchenne muscular dystrophy: A bidirectional transcriptome and proteome-driven analysis

Background We aimed to investigate the biological mechanism and feature genes of Duchenne muscular dystrophy (DMD) by multi-omics and experimental verification strategy. Methods We integrated the transcriptomic and proteomic methods to find the differentially expressed mRNAs (DEMs) and proteins (DEPs) between DMD and Control groups. Weighted gene co-expression network analysis (WGCNA) was then used to identify modules of highly correlated genes and hub genes. In the following steps, the immune and stromal cells infiltrations were accomplished by xCELL algorithm. Furthermore, TF and miRNA prediction were performed with Networkanalyst. ELISA, western blot and external datasets were performed to verify the key proteins/mRNAs in DMD patient and mouse. Finally, a nomogram model was established based on the potential biomarkers. Results 4515 DEMs and 56 DEPs were obtained from the transcriptomic and proteomic study respectively. 14 common genes were identified, which is enriched in muscle contraction and inflammation-related pathways. Meanwhile, we observed 33 significant differences in the infiltration of cells in DMD. Afterwards, a total of 22 miRNAs and 23 TF genes interacted with the common genes, including TFAP2C, MAX, MYC, NFKB1, RELA, hsa-miR-1255a, hsa-miR-130a, hsa-miR-130b, hsa-miR-152, and hsa-miR-17. In addition, three genes (ATP6AP2, CTSS, and VIM) showed excellent diagnostic performance on discriminating DMD in GSE1004, GSE3307, GSE6011 and GSE38417 datasets (all AUC > 0.8), which is validated in patients (10 DMD vs. 10 controls), DMD with exon 55 mutations, mdx mouse, and nomogram model. Conclusion Taken together, ATP6AP2, CTSS, and VIM play important roles in the inflammatory response in DMD, which may serve as diagnostic biomarkers and therapeutic targets.
Autocorrelation function mechanism for pitch salience and cross-correlation function mechanism for sound localization revealed by magnetoencephalography

A model of primary sensations and spatial sensations is proposed by Ando (2001). The model of the auditory-brain system includes the autocorrelation function (ACF), the interaural cross-correlation function (IACF) mechanisms. At present, environmental noises are evaluated by sound level such as equivalent continuous A-weighted sound pressure level (LAeq). However, we sometimes feel annoyed with sound with low sound level because of the quality. Sound quality can be characterized by factors obtained from ACF and IACF of sound. For example, pitch and pitch strength can be characterized by delay time and amplitude of the maximum peak of the ACF. Directional sensation can be characterized by delay time and amplitude of the maximum peak of the IACF. To verify the model, we investigated how ACF and IACF factors are coded in our human brain. The results indicated that delay time and amplitude of the maximum peak of the ACF and IACF are coded by the latency and strength of brain activity.
Immunological role and prognostic value of SPARCL1 in pan-cancer analysis

Background: Secreted protein acidic and rich in cysteine-like 1 (SPARCL1) was a kind of extracellular matrix glycoprotein. SPARCL1 was strongly inhibited in most cancers. However, the potential functions of SPARCL1 in the pan-cancer cohort have not been widely studied. Methods: We evaluated the transcriptional level and the prognostic value of SPARCL1 in 33 types of cancer and revealed the relationship between genetic alterations of SPARCL1 and the tumor mutation burden. Meanwhile, we assessed the correlations between SPARCL1 and tumor-infiltrating lymphocytes across cancers. Results: The transcriptional level of SPARCL1 was inhibited in most cancers. Although SPARCL1 was down-regulated in most cancers, SPARCL1 might play a protective or detrimental role in different cancers. We demonstrated that mutation count was elevated in the altered SPARCL1 group in several cancers. Additionally, we found a significant positive correlation between SPARCL1 and macrophage infiltration levels in most cancers. Especially, marker sets of M2 macrophages were strongly related to SPARCL1 in cholangiocarcinoma, colon adenocarcinoma, rectum adenocarcinoma, and pancreatic adenocarcinoma. Conclusion: Our study found that SPARCL1 might work as a biomarker for prognosis and immune infiltration in pan-cancer analysis.
Variation of blubber thickness for three marine mammal species in the southern Baltic Sea

Evaluating populational trends of health condition has become an important topic for marine mammal populations under the Marine Strategy Framework Directive (MSFD). In the Baltic Sea, under the recommendation of Helsinki Commission (HELCOM), efforts have been undertaken to use blubber thickness as an indicator of energy reserves in marine mammals. Current values lack geographical representation from the entire Baltic Sea area and a large dataset is only available for grey seals (Halichoerus grypus) from Sweden and Finland. Knowledge on variation of blubber thickness related to geography throughout the Baltic Sea is important for its usage as an indicator. Such evaluation can provide important information about the energy reserves, and hence, food availability. It is expected that methodological standardization under HELCOM should include relevant datasets with good geographical coverage that can also account for natural variability in the resident marine mammal populations. In this study, seasonal and temporal trends of blubber thickness were evaluated for three marine mammal species—harbor seal (Phoca vitulina), grey seal (Halichoerus grypus) and harbor porpoise (Phocoena phocoena)—resident in the southern Baltic Sea collected and investigated under stranding networks. Additionally, the effects of age, season and sex were analyzed. Seasonal variation of blubber thickness was evident for all species, with harbor seals presenting more pronounced effects in adults and grey seals and harbor porpoises presenting more pronounced effects in juveniles. For harbor seals and porpoises, fluctuations were present over the years included in the analysis. In the seal species, blubber thickness values were generally higher in males. In harbor seals and porpoises, blubber thickness values differed between the age classes: while adult harbor seals displayed thicker blubber layers than juveniles, the opposite was observed for harbor porpoises. Furthermore, while an important initial screening tool, blubber thickness assessment cannot be considered a valid methodology for overall health assessment in marine mammals and should be complemented with data on specific health parameters developed for each species.
Evaluation of the cell-free DNA integrity index as a liquid biopsy marker to differentiate hepatocellular carcinoma from chronic liver disease

Background: Hepatocellular carcinoma (HCC) occurs in the majority of patients with underlying chronic liver disease (CLD) of viral and non-viral etiologies, which requires screening for early HCC diagnosis. Liquid biopsy holds great promise now for early detection, prognosis, and assessment of response to cancer therapy. Cell-free DNA (cfDNA) as a liquid biopsy marker can be easily detected by a real-time quantitative PCR (RT-qPCR) assay for a change in its concentration, integrity, and fragmentation in cancer. Methods: Patients with HCC (n = 100), CLD (n = 100), and healthy (n = 30) controls were included in the study. The cfDNA was isolated from serum and real-time quantitative PCR (RT-qPCR) was carried out using primer pairs for large (>205 bp) and small (110 bp) fragments of repetitive elements (ALU and LINE1) and housekeeping genes (β-Actin and GAPDH). Total cfDNA concentrations and integrity index were determined by the absolute quantitation method (L/S ratio or cfDII-integrity). The cfDII as a measure of fragmentation was determined by comparative Ct (2–ΔΔCt) method of relative quantification (cfDII-fragmentation). Using a receiver operating characteristic (ROC) curve, cfDII-integrity and cfDII-fragmentation were used to differentiate HCC from CLD patients or healthy controls. Results: The total cfDNA concentrations in the sera of HCC (244 ng/ml) patients were significantly higher than those of CLD (33 ng/ml) patients and healthy (16.88 ng/ml) controls. HCC patients have shown poor DNA integrity or excess cfDNA fragmentation than CLD patients and healthy controls. The cfDII-integrity of GAPDH and ALU fragment significantly differentiate HCC from CLD at AUROC 0.72 and 0.67, respectively. The cfDII-fragmentation following normalization with cfDNA of healthy control has shown significant differential capabilities of HCC from CLD at AUROC 0.67 using GAPDH and 0.68 using the ALU element. The ROC curve of LINE1 and β-actin cfDII was not found significant for any of the above methods. The cfDII-fragmentation trend in HCC patients of different etiologies was similar indicating increased cfDNA fragmentation irrespective of its etiology. Conclusion: The cfDII measuring both DNA integrity (L/S ratio) and fragmentation of the Alu and GAPDH genes can differentiate HCC from CLD patients and healthy individuals.
Effects of general and corona-specific stressors on mental burden during the SARS-CoV-2 pandemic in Germany

The SARS-CoV-2 pandemic turned out to be a serious threat to mental and physical health. However, the relative contribution of corona-specific (DHs) and general stressors (DHg) on mental burden, and specific protective and risk factors for mental health are still not well understood. In a representative sample (N = 3,055) of the German adult population, mental health, potential risk, and protective factors as well as DHs and DHg exposure were assessed online during the SARS-CoV-2 pandemic (June and July 2020). The impact of these factors on mental health was analyzed using descriptive statistics, data visualizations, multiple regressions, and moderation analyses. The most burdensome DHg were financial and sleeping problems, respectively, and DHs corona-media reports and exclusion from recreational activities/important social events. 31 and 24% of total mental health was explained by DHg and DHs, respectively. Both predictors combined explained 36%, resulting in an increase in variance due to DHs of only 5% (R2 adjusted). Being female, older and a lower educational level were identified as general risk factors, somatic diseases as a corona-specific risk factor, and self-efficacy and locus of control (LOC) proved to be corona-specific protective factors. Further analyses showed that older age and being diagnosed with a somatic illness attenuated the positive influence of LOC, self-efficacy, and social support on resilience. Although the data showed that after the first easing restrictions, the stressor load was comparable to pre-pandemic data (with DHs not making a significant contribution), different risk and protective factors could be identified for general and corona-specific stressors. In line with observations from network analysis from other groups, the positive impact of resilience factors was especially diminished in the most vulnerable groups (elderly and somatically ill). This highlights the need to especially target these vulnerable groups to foster their resilience in upcoming waves of the corona pandemic.
Sections of the Matsumoto-Cadavid-Korkmaz Lefschetz fibration

We give a maximal set of disjoint $(-1)$-sections of the well-known Lefschetz fibration constructed by Matsumoto, Cadavid and Korkmaz. In fact, we obtain several such sets for a fixed genus, which implies that the Matsumoto-Cadavid-Korkmaz Lefschetz fibration has more than one supporting minimal Lefschetz pencils. We also determine the diffeomorphism types of the obtained supporting minimal Lefschetz pencils.
Inter-individual responses of post-exercise hypotension in older adults with hypertension: An exploratory analysis of different exercise modalities

Background: Various physical exercise modalities can acutely reduce blood pressure (BP). However, not all individuals respond similarly after an exercise session. Purpose: To measure inter-individual variations in 24-h BP after a single bout of various exercise modalities in older adults with hypertension. Methods: This retrospective study analyzed data from participants with hypertension (≥60 years) previously included in three randomized controlled trials on this topic. BP was assessed using ambulatory BP monitoring. We compared the mean changes in total 24-h, daytime, and nighttime BP after aerobic (AE, n = 19), combined (COMB, n = 19), resistance (RES, n = 23), and isometric handgrip (ISO, n = 18) exercise sessions to a non-exercising control session (C). The minimum detectable changes to classify the participant as a “Responder” for the corresponding exercise protocol were 4 and 2 mmHg for systolic and diastolic BP, respectively. Results: The prevalence of Responders for systolic BP was as follows: AE 24-h: 37%, daytime: 47% and nighttime: 37%; COMB 24-h: 26%, daytime: 21% and nighttime: 32%; RES 24-h: 26%, daytime: 26% and nighttime: 35%; and ISO 24-h: 22%, daytime: 22% and nighttime: 39%. For diastolic BP, the prevalence of Responders was as follows: AE 24-h: 53%, daytime: 53% and nighttime: 31%; COMB 24-h: 26%, daytime: 26% and nighttime: 31%; RES 24-h: 35%, daytime: 22% and nighttime: 52%; and ISO 24-h: 44%, daytime: 33% and nighttime: 33%. Conclusion: There was a high inter-individual variation of BP after a single bout of various exercises in older adults. Responders had higher BP values on the control day without exercise. Various exercise modalities might acutely reduce 24-h BP in older adults with hypertension.
Progression of hepatocellular carcinoma after radiofrequency ablation: Current status of research

Hepatocellular carcinoma (HCC) remains an important disease for health care systems in view of its high morbidity, mortality, and increasing incidence worldwide. Radiofrequency ablation (RFA) is preferred to surgery as a local treatment for HCC because it is safer, less traumatic, less painful, better tolerated, causes fewer adverse reactions, and allows more rapid postoperative recovery. The biggest shortcoming of RFA when used to treat HCC is the high incidence of residual tumor, which is often attributed to the vascular thermal deposition effect, the wide infiltration zone of peripheral venules, and the distance between satellite foci and the main focus of the cancer. Recurrence and progression of the residual tumor is the most important determinant of the prognosis. Therefore, it is important to be aware of the risk of recurrence and to improve the efficacy of RFA. This review summarizes the relevant literature and the possible mechanisms involved in progression of HCC after RFA. Current studies have demonstrated that multimodal treatments which RFA combined with other anti-cancer approaches can prevent progression of HCC after RFA.
Evaluation of the efficacy of EU-TIRADS and ACR-TIRADS in risk stratification of pediatric patients with thyroid nodules

Background Pediatric thyroid nodules have a lower prevalence but a higher rate of malignancy (ROM) than those in adults. Ultrasound features suspected of malignancy lead to fine needle aspiration biopsy (FNAB) and subsequent cytological determination, upon which management is decided. Based on the characteristics of ultrasound, to standardize clinician decisions and avoid unnecessary FNAB, the European Thyroid Association and the American Radiology College have established guidelines for Thyroid Imaging, Reporting and Data System (EU-TIRADS and ACR-TIRADS) for ROM stratification of thyroid nodules. The aim of this study is to evaluate the diagnostic performance of ACR-TIRADS and EU-TIRADS in pediatric age. Materials and methods Subjects younger than 18 years of age with thyroid nodules greater than 0.5 cm observed in the 2000-2020 period were included. Results Data from 200 subjects were collected. The overall ROM was 13%, rising to 26% if nodules with a diameter >1 cm were considered. Patients with a malignant nodule were more likely to have a higher EU-TIRADS score (p=0.03). Missed cancer diagnoses were 26.9%. Using the EU-TIRADS system, 40% of FNABs could have been avoided, while this scoring system would have resulted in FNAB being performed in 12% of cases where the assessment of ultrasound features would not recommend FNAB. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were 73.1%, 57.1%, 73.1%, and 50%, respectively. Even considering the ACR-TIRADS, a higher score correlated with a higher ROM (p<0.001). This system missed 6 diagnoses of cancer (23.1%). Using the ACR-TIRADS system, 45.3% of FNABs could have been avoided, while FNAB should have been performed in 12% of cases where it was not recommended by ultrasound characteristics. Sensitivity, specificity, PPV and NPV were 76.9%, 50%, 76.9%, and 42.9%, respectively. Conclusion The present study confirms the correspondence of the EU-TIRADS and ACR-TIRADS categories with respect to malignancy but indicates not entirely satisfactory performance compared to FNAB alone. However, the use of the two TIRADS systems should be encouraged in multicentre studies to increase their performance and establish paediatric-specific points in the scoring criteria.
BANDED SURFACES, BANDED LINKS, BAND INDICES AND GENERA OF LINKS

Every link is shown to be presentable as a boundary of an unknotted flat banded surface. A (flat) banded link is defined as a boundary of an unknotted (flat) banded surface. A link's (flat) band index is defined as the minimum number of bands required to present the link as boundaries of an unknotted (flat) banded surface. Banded links of small (flat, respectively) band index are considered here. Some upper bounds are provided for these band indices of a link using braid representatives and canonical Seifert surfaces of the link. The relation between the band indices and genera of links is studied and the band indices of pretzel knots are calculated.
Inhomogeneous Restricted Lattice Walks

We consider inhomogeneous lattice walk models in a half-space and in the quarter plane. For the models in a half-space, we show by a generalization of the kernel method to linear systems of functional equations that their generating functions are always algebraic. For the models in the quarter plane, we have carried out an experimental classification of all models with small steps. We discovered many (apparently) D-finite cases for most of which we have no explanation yet.
Design of novel piecewise uniform scalar quantizer for Gaussian memoryless source

In this paper we propose a novel piecewise uniform scalar quantizer model designed for a Gaussian memoryless source. The segment thresholds of this quantizer model are equidistant while the number of reproduction levels inside segments is determined by optimizing the inner distortion and under the constraint of total number of reproduction levels. For the proposed quantizer model the quantization efficiency and signal to quantization noise ratio (SQNR) is studied. On the basis of the comparison with the efficiency and SQNR of uniform quantizer advantages of the proposed quantizer model are shown. Particularly, it is shown that with the proposed quantizer the correlation between the input signal and the quantization error can be eliminated more than by using the uniform quantizer as well as that the proposed quantizer provides higher level of SQNR.
THE INTERSECTION MOTIVE OF THE MODULI STACK OF SHTUKAS

For a split reductive group $G$ over a finite field, we show that the intersection (cohomology) motive of the moduli stack of iterated $G$-shtukas with bounded modification and level structure is defined independently of the standard conjectures on motivic $t$-structures on triangulated categories of motives. This is in accordance with general expectations on the independence of $\ell$ in the Langlands correspondence for function fields.
Scattering of acoustic waves into Tollmien-Schlichting waves by small streamwise variations in surface geometry

By using the triple-deck scaling of Stewartson (1969) and Messiter (1970) we show that small but relatively sudden surface geometry variations that produce only very weak static pressure variations can nevertheless produce strong, i.e. 0(1), coupling between an externally imposed acoustic disturbance and a spatially growing Tollmien- Schlichting wave. The analysis provides a qualitative explanation of the Leehey & Shapiro (1979) boundary-layer receptivity measurements and is in good quantitative agreement with the Aizin & Polyakov (1979) experiment. It may also explain why small ‘trip wires’ can promote early transition.
Finite-Larmor-radius effects on z–pinch stability

The effect of finite Larmor radius (FLR) on the stability of m = 1 small-axial-wavelength kinks in a z–pinch with purely poloidal magnetic field is investigated. We use the incompressible FLR MHD model; a collisionless fluid model that consistently includes the relevant FLR terms due to ion gyroviscosity, Hall effect and electron diamagnetism. With FLR terms absent, the Kadomtsev criterion of ideal MHD, 2r dp/dr + m2B2/μ0 ≥ 0 predicts instability for internal modes unless the current density is singular at the centre of the pinch. The same result is obtained in the present model, with FLR terms absent. When the FLR terms are included, a normal-mode analysis of the linearized equations yields the following results. Marginally unstable (ideal) modes are stabilized by gyroviscosity. The Hall term has a damping (but not absolutely stabilizing) effect – in agreement with earlier work. On specifying a constant current and particle density equilibrium, the effect of electron diamagnetism vanishes. For a z–pinch with parameters relevant to the EXTRAP experiment, the m = 1 modes are then fully stabilized over the crosssection for wavelengths λ/a ≤ 1, where a denotes the pinch radius. As a general z–pinch result a critical line-density limit Nmax = 5 × 1018 m–1 is found, above which gyroviscous stabilization near the plasma boundary becomes insufficient. This limit corresponds to about five Larmor radii along the pinch radius. The result holds for wavelengths close to, or smaller than, the pinch radius and for realistic equilibrium profiles. This limit is far below the required limit for a reactor with contained alpha particles, which is in excess of 1020 m–1.
Open quantum dynamics via environmental monitoring

A general method is discussed to obtain Markovian master equations which describe the interaction with the environment in a microscopic and non-perturbative fashion. It is based on combining time-dependent scattering theory with the concept of continuous quantum measurements. The applications to the case of a Brownian point particle and to the case of a complex molecule, both in the presence of a gaseous environment, are outlined.
Hele-Shaw flow on weakly hyperbolic surfaces

We consider the Hele-Shaw flow that arises from injection of two-dimensional fluid into a point of a curved surface. The resulting fluid domains are more or less determined implicitly by a mean value property for harmonic functions. We improve on the results of Hedenmalm and Shimorin [8] and obtain essentially the same conclusions while imposing a weaker curvature condition on the surface. Incidentally, the curvature condition is the same as the one that appears in Hedenmalm and Perdomo's paper [7], where the problem of finding smooth area minimizing surfaces for a given curvature form under a natural normalizing condition was considered. Probably there are deep reasons behind this coincidence.