Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative relations among causality measures with applications to pulse-output nonlinear network reconstruction

The causal connectivity of a network is often inferred to understand the network function. It is arguably acknowledged that the inferred causal connectivity relies on the causality measure one applies, and it may differ from the network’s underlying structural connectivity. However, the interpretation of causal connectivity remains to be fully clarified, in particular, how causal connectivity depends on causality measures and how causal connectivity relates to structural connectivity. Here, we focus on nonlinear networks with pulse signals as measured output, e.g., neural networks with spike output, and address the above issues based on four intensively utilized causality measures, i.e., time-delayed correlation coefficient, time-delayed mutual information, Granger causality, and transfer entropy. We theoretically show how these causality measures are related to one another when applied to pulse signals. Taking the simulated Hodgkin-Huxley neural network and the real mouse brain network as two illustrative examples, we further verify the quantitative relations among the four causality measures and demonstrate that the causal connectivity inferred by any of the four well coincides with the underlying network structural connectivity, therefore establishing a direct link between the causal and structural connectivity. We stress that the structural connectivity of networks can be reconstructed pairwise without conditioning on the global information of all other nodes in a network, thus circumventing the curse of dimensionality. Our framework provides a practical and effective approach for pulse-output network reconstruction. Significance Statement Inferring network connectivity is a key challenge in many diverse scientific fields. We investigate networks with pulse signal as measured output and solve the above reverse-engineering issue by establishing a direct link between the network’s causal connectivity and structural connectivity. Here, the causal connectivity can be inferred by any one of the four causality measures, i.e., time-delayed correlation coefficient, time-delayed mutual information, Granger causality, and transfer entropy. We analytically reveal the relationship among these four measures and show that they are equally effective to fully reconstruct the network connectivity pairwise. Our work provides a practical framework to reconstruct the structural connectivity in general pulse-output nonlinear networks or subnetworks.
Soundanism

Soundanism is an interactive sound installation exploring possible relationships between music, breathing, masturbation and sex. The visitor, after putting on a helmet and a mask with a small electret microphone, takes part into a feedback system: he provokes all the sounds he perceives. The microphone picks up the sounds generated by his breathing, which are then digitally processed and transmitted through 14 small loudspeakers placed in the interior of the helmet. Additionally, information collected from the real-time analysis of the respiration is compared to the characteristics of thousands of sounds (connected in different degrees of obviousness with the idea of sex) that the visitor triggers and transforms, voluntarily or involuntarily, through his breathing. Soundanism questions the notion of control in an interactive system. Located at the borderline between public and intimate, consciousness and dream, the work evades established categories such as installation, performance and instrument. It proposes an invitation: you can try to control and dominate the system, or relax and just breath.
Carvacrol prevents acrylamide-induced oxidative and inflammatory liver damage and dysfunction in rats

Background: Acrylamide causes hepatotoxicity with the effect of oxidative stress and inflammatory processes. Carvacrol is a monoterpenic phenol with antioxidant and anti-inflammatory properties. Aims: To determine the effects of carvacrol on oxidative liver injury induced by acrylamide administration in rats. Methods: Rats were divided into three groups of six animals each: healthy group acrylamide group (ACR), and acrylamide + carvacrol group (TACR). First, carvacrol (50 mg/kg) was administered intraperitoneally to the CACR group. One hour later, acrylamide (20 mg/kg) was given orally to the ACR and CACR groups. This procedure was performed for 30 days, after which the animals were sacrificed. The malondialdehyde (MDA) and total glutathione (tGSH) levels, total oxidant (TOS) and total antioxidant status (TAS), tumor necrosis factor-alpha (TNF-α), interleukin-1beta (IL-1β), and nuclear factor kappa b (NF-κB) were measured in the excised liver tissues. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels were determined in blood serum samples. Liver tissues were also examined histopathologically. Results: In the ACR group, malondialdehyde, TOS, ALT, AST levels, and NF-κB, IL-1β, and TNF-α levels were found to be high, and tGSH and total antioxidant status levels were low. In addition, diffuse degenerative changes and necrosis in hepatocytes, and moderate inflammation in the portal region were detected in the liver tissues of the ACR group. While carvacrol prevented the biochemical changes induced by acrylamide, it also alleviated the damage in the histological structure. Conclusion: Carvacrol may be used for liver damage caused by acrylamide.
THE OPTICAL FORM OF THE BIPOLAR PREPLANETARY NEBULA IRAS 09371+1212

CCD images of IRAS 09371 + 1212 were taken during two different observing runs at the 1.5-m telescope at La Silla, Chile. The characteristics of the bipolar Frosty Leo Nebula indicate that it is a transitional object belonging to the relatively small class of preplanetary nebulae. It is unique among known objects in two respects: it has the only circumstellar outflow in which crystalline ice dominates the long-wavelength emission spectrum, and it is unique among preplanetary nebulae in having point-reflection-symmetric deviations from axial symmetry. The interpretation offered for this symmetry is that the bipolar outflow is directed by a precessing disk.
The value of 7 peripheral blood serum ratios in diagnosis and prediction of disease activity of patients within inflammatory bowel disease individuals

Objective In recent years, a number of studies have suggested that inflammation-based biomarkers can be applied in the diagnostics and prognostic testing of disease. However, the association between these ratios and inflammatory bowel disease (IBD) remains unclear. We aimed to investigate the role of these inflammation-based ratios in patients with IBD. Methods Retrospective analysis of 362 patients with IBD and 100 healthy individuals from January 2016 and December 2021. The receiver operating characteristic curve and logistic regression analysis was applied to explore the diagnostic and predictive performance of the seven ratio markers [neutrophil- to-albumin ratio (NAR), neutrophil-to-pre-albumin ratio (NPAR), albumin-to-alkaline-phosphatase ratio (AAPR), albumin-to-globulin ratio (AGR), albumin-to-fibrinogen ratio (AFR), fibrinogen-to-pre-albumin ratio (FPR), and Prognostic Nutritional Index (PNI)] regarding to disease activity in IBD individuals. Results Compared with healthy controls, patients with Crohn’s disease (CD) or ulcerative colitis (UC) exhibited higher levels of NAR, NPAR, FPR (P < 0.001), lower levels of AAPR, and PNI (P < 0.001). Multivariate logistic regression showed that the level of NPAR (OR = 1.12, 95%CI: 1.02–1.23, P = 0.016) and AGR (OR = 1.01, 95%CI: 1.01–1.12, P < 0.001) was an independent risk factor of IBD. Then, we found the level of NPAR (OR = 1.10, 95%CI: 1.01–1.20, P = 0.02) and PNI (OR = 0.83, 95%CI: 0.71–0.96, P = 0.01) was independently associated with disease activity. Besides, a positive association was observed between the level of NPAR and two clinical scores [Harvey Bradshaw index (HBI) in patients with CD, Mayo score in patients with UC]. Finally, the level of NPAR (P = 0.002) and PNI (P = 0.003) showed a significant difference in the IBD-associated neoplasia group and IBD without neoplasia group. Conclusion Our data first suggests NPAR as a putative biomarker for diagnosing and predicting disease activity in patients with IBD. Investigations involving a larger number of IBD individuals are necessary to validate its use as an easily obtained peripheral blood biomarker of IBD.
State-of-the-art review and update of in vivo models of necrotizing enterocolitis

NEC remains one of the most common causes of mortality and morbidity in preterm infants. Animal models of necrotizing enterocolitis (NEC) have been crucial in improving our understanding of this devastating disease and identifying biochemical pathways with therapeutic potential. The pathogenesis of NEC remains incompletely understood, with no specific entity that unifies all infants that develop NEC. Therefore, investigators rely on animal models to manipulate variables and provide a means to test interventions, making them valuable tools to enhance our understanding and prevent and treat NEC. The advancements in molecular analytic tools, genetic manipulation, and imaging modalities and the emergence of scientific collaborations have given rise to unique perspectives and disease correlates, creating novel pathways of investigation. A critical review and understanding of the current phenotypic considerations of the highly relevant animal models of NEC are crucial to developing novel therapeutic and preventative strategies for NEC.
Comparison of the application of high-flow nasal oxygen with two different oxygen concentrations in infant and child laryngotracheal surgery

Background This study aimed to compare the use of the STRIVE Hi technique with 70 and 100% oxygen concentrations in children with 1st or 2nd degree laryngeal obstruction undergoing suspension laryngoscopic surgery. Methods Children aged 1 month to 6 years scheduled for suspension laryngoscopic surgery with spontaneous respiration were randomly divided into the 70% oxygen concentration group (HFNO70% group) and the 100% oxygen concentration group (HFNO100% group). The data recorded for all the patients included age and sex, comorbidities, preoperative physiological status, methods of induction and maintenance of anesthesia, course of the disease and surgical options, and duration of operation. The primary endpoint was the lowest oxygen saturations during the surgery. The secondary endpoints included the partial pressure of oxygen PaO2, the arterial pressure of carbon dioxide PaCO2, the peak transcutaneous carbon dioxide PtcCO2, and the incidence of desaturation (defined as SpO2 < 90%) or hypercarbia (PtcCO2 > 65 mmHg). Results A total of 80 children with 1st or 2nd degree laryngeal obstruction were included in the analysis. The median [IQR (range)] duration of spontaneous ventilation using STRIVE Hi was 52.5 [40–60 (30–170)]min and 62.5 [45–81 (20–200)]min in the HFNO 70% and HFNO 100% groups, respectively (p = 0.99); the lowest oxygen saturation recorded during the operation was 97.8 ± 2.1% and 96.8 ± 2.5%, respectively (p = 0.053); the mean PaO2 at the end of surgery was 184.6 ± 56.3 mmHg and 315.2 ± 101.3 mmHg, respectively (p < 0.001); and the peak transcutaneous CO2 was 58.0 ± 13.0 mmHg and 60.4 ± 10.9 mmHg, respectively (p = 0.373), despite a long operation time. Conclusion STRIVE Hi had a positive effect on children undergoing tubeless laryngeal surgery with spontaneous ventilation, and for children with 1st or 2nd degree laryngeal obstruction, there was no significant difference in maintaining the intraoperative oxygenation between the 70 and 100% oxygen concentration groups. The 100% oxygen concentration group showed significant hyperoxia, which has been proven to be associated with multiple organ damage. Using a relatively lower oxygen concentration of 70% can effectively reduce the hazards associated with hyperoxia compared to 100% oxygen concentration. Clinical trial registration [www.chictr. org.cn], identifier [CHICTR2200064500].
The role of linguistic and cognitive skills in reading Chinese as a second language: A path analysis modeling approach

This study examined the role of basic linguistic skills (vocabulary, syntax, orthography, and morphological awareness), basic cognitive skills (working memory), and higher-order cognitive skills (inference making and reading monitoring) in reading Chinese as a second language (L2). A total of 252 international students from Pakistan, Indonesia, Malaysia, and Laos were recruited, and a range of measures including a Chinese reading comprehension test (HSK level 3), four linguistic knowledge tests on Chinese lexical, syntactic, and orthographic knowledge as well as morphological awareness, a reading span test, an inference making task, and an inconsistency detection test. The results of hierarchical multiple regressions showed that the measured linguistic skills and cognitive skills explained 80% of the variances in L2 Chinese reading, among which morphological awareness made the largest contribution. The path analysis revealed that linguistic skills and working memory contributed indirectly to reading comprehension via inference making and comprehension monitoring, while the two higher-order cognitive skills made direct contributions. Overall, this study demonstrates that inference making and comprehension monitoring contributed directly to reading comprehension, while linguistic skills and working memory functioned indirectly via the higher-order cognitive skills It also highlights the importance of morphological awareness in a hierarchical model of L2 Chinese reading.
ARPEGE/ALADIN : A numerical weather prediction model for Central-Europe with the participation of the Hungarian Meteorological Service

This paper intends to give a general description of the limited area numerical weather prediction model ARPEGE/ALADIN developed by a collaboration between Meteo-France and some Central- and Eastern-European meteorological services (and also Morocco) including the Hungarian Meteorological Service (HMS). The model is a hydrostatic, spectral limited area model for dynamical adaptation at the limit of the hydrostatic approximation. The main characteristics of the model are discussed like the preparation of initial and lateral boundary conditions, the initialization method, the representation of the meteorological fields, the dynamics, the physics and the post-processing. The first experiences at HMS are discussed in the light of the one year quasi-operational application of the model. Finally, the possible future utilization for nowcasting purposes is mentioned.
Modulation of T-cell function by myeloid-derived suppressor cells in hematological malignancies

Myeloid-derived suppressor cells (MDSCs) are pathologically activated neutrophils and monocytes that negatively regulate the immune response to cancer and chronic infections. Abnormal myelopoiesis and pathological activation of myeloid cells generate this heterogeneous population of myeloid-derived suppressor cells. They are characterized by their distinct transcription, phenotypic, biochemical, and functional features. In the tumor microenvironment (TME), myeloid-derived suppressor cells represent an important class of immunosuppressive cells that correlate with tumor burden, stage, and a poor prognosis. Myeloid-derived suppressor cells exert a strong immunosuppressive effect on T-cells (and a broad range of other immune cells), by blocking lymphocyte homing, increasing production of reactive oxygen and nitrogen species, promoting secretion of various cytokines, chemokines, and immune regulatory molecules, stimulation of other immunosuppressive cells, depletion of various metabolites, and upregulation of immune checkpoint molecules. Additionally, the heterogeneity of myeloid-derived suppressor cells in cancer makes their identification challenging. Overall, they serve as a major obstacle for many cancer immunotherapies and targeting them could be a favorable strategy to improve the effectiveness of immunotherapeutic interventions. However, in hematological malignancies, particularly B-cell malignancies, the clinical outcomes of targeting these myeloid-derived suppressor cells is a field that is still to be explored. This review summarizes the complex biology of myeloid-derived suppressor cells with an emphasis on the immunosuppressive pathways used by myeloid-derived suppressor cells to modulate T-cell function in hematological malignancies. In addition, we describe the challenges, therapeutic strategies, and clinical relevance of targeting myeloid-derived suppressor cells in these diseases.
Lipopolysaccharide structure modulates cationic biocide susceptibility and crystalline biofilm formation in Proteus mirabilis

Chlorhexidine (CHD) is a cationic biocide used ubiquitously in healthcare settings. Proteus mirabilis, an important pathogen of the catheterized urinary tract, and isolates of this species are often described as “resistant” to CHD-containing products used for catheter infection control. To identify the mechanisms underlying reduced CHD susceptibility in P. mirabilis, we subjected the CHD tolerant clinical isolate RS47 to random transposon mutagenesis and screened for mutants with reduced CHD minimum inhibitory concentrations (MICs). One mutant recovered from these screens (designated RS47-2) exhibited ~ 8-fold reduction in CHD MIC. Complete genome sequencing of RS47-2 showed a single mini-Tn5 insert in the waaC gene involved in lipopolysaccharide (LPS) inner core biosynthesis. Phenotypic screening of RS47-2 revealed a significant increase in cell surface hydrophobicity and serum susceptibility compared to the wildtype, and confirmed defects in LPS production congruent with waaC inactivation. Disruption of waaC was also associated with increased susceptibility to a range of other cationic biocides but did not affect susceptibility to antibiotics tested. Complementation studies showed that repression of smvA efflux activity in RS47-2 further increased susceptibility to CHD and other cationic biocides, reducing CHD MICs to values comparable with the most CHD susceptible isolates characterized. The formation of crystalline biofilms and blockage of urethral catheters was also significantly attenuated in RS47-2. Taken together, these data show that aspects of LPS structure and upregulation of the smvA efflux system function in synergy to modulate susceptibility to CHD and other cationic biocides, and that LPS structure is also an important factor in P. mirabilis crystalline biofilm formation.
Tracing timing of growth in cultured molluscs using strontium spiking

Introduction Growth experiments present a powerful tool for determining the effect of environmental parameters on growth and carbonate composition in biogenic calcifiers. For successful proxy calibration and biomineralization studies, it is vital to identify volumes of carbonate precipitated by these organisms at precise intervals during the experiment. Here, we investigate the use of strontium labelling in mollusc growth experiments. Methods Three bivalve species (Cerastoderma edule, Mytilus edulis and Ostrea edulis) were grown under monitored field conditions. The bivalves were regularly exposed to seawater with elevated concentrations of dissolved strontium chloride (SrCl2). In addition, the size of their shells was determined at various stages during the experiment using calliper measurements and digital photography. Trace element profiles were measured in cross sections through the shells of these molluscs using laser ablation ICPMS and XRF techniques. Results Our results show that doses of dissolved strontium equivalent to 7-8 times the background marine value (~0.6 mmol/L) are sufficient to cause reproducible peaks in shell-incorporated strontium in C. edule and M. edulis shells. No negative effects were observed on shell calcification rates. Lower doses (3-5 times background values) resulted in less clearly identifiable peaks, especially in M. edulis. Strontium spiking labels in shells of O. edulis are more difficult to detect, likely due to their irregular growth. Discussion Strontium spiking is a useful technique for creating time marks in cultured shells and a reproducible way to monitor shell size during the growing season while limiting physical disturbance of the animals. However, accurate reconstructions of growth rates at high temporal resolution require frequent spiking with high doses of strontium.
Precision pointing of scientific instruments on space station: The LFGGREC perspective

An application of Lyapunov function-gradient-generated robustness-enhancing control (LFGGREC) is explored. The attention is directed to a reduced-complexity representation of the pointing problem presented by the system composed of the Space Infrared Telescope Facility gimbaled to a space station configuration. Uncertainties include disturbance forces applied in the crew compartment area and control moments applied to adjacent scientific payloads (modeled as disturbance moments). Also included are uncertainties in gimbal friction and in the structural component of the system, as reflected in the inertia matrix, the damping matrix, and the stiffness matrix and the effect of the ignored vibrational dynamics of the structure. The emphasis is on the adaptation of LFGGREC to this particular configuration and on the robustness analysis. <<ETX>>
Identification of new immune subtypes of renal injury associated with anti-neutrophil cytoplasmic antibody–associated vasculitis based on integrated bioinformatics analysis

Background: Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a systemic autoimmune disease that may lead to end-stage renal disease. However, few specifific biomarkers are available for AAV-related renal injury. The aim of this study was to identify important biomarkers and explore new immune subtypes of AAV-related renal injury. Methods: In this study, messenger RNA expression profiles for antibody-associated vasculitis and AAV-associated kidney injury were downloaded from the Gene Expression Omnibus database. Weighted gene co-expression network analysis (WGCNA) was performed to identify the most relevant module genes to AAV. Key module genes from WGCNA were then intersected with AAV- and nephropathy-related genes from the Genecards database to identify key genes for AAV-associated kidney injury. Subsequently, the expression of key genes was validated in independent datasets and the correlation of genes with clinical traits of kidney injury was verified by the Nephroseq database. Finally, non-negative matrix factorization (NMF) clustering was performed to identify the immune subtypes associated with the key genes. Results: Eight co-key genes (AGTR2, ANPTL2, BDKRB1, CSF2, FGA, IL1RAPL2, PCDH11Y, and PGR) were identifified, and validated the expression levels independent datasets. Receiver operating characteristic curve analysis revealed that these eight genes have major diagnostic value as potential biomarkers of AAV-related renal injury. Through our comprehensive gene enrichment analyses, we found that they are associated with immune-related pathways. NMF clustering of key genes identified two and three immune-related molecular subtypes in the glomerular and tubular data, respectively. A correlation analysis with prognostic data from the Nephroseq database indicated that the expression of co-key genes was positively co-related with the glomerular filtration rate. Discussion: Altogether, we identifified 8 valuable biomarkers that firmly correlate with the diagnosis and prognosis of AAV-related renal injury. These markers may help identify new immune subtypes for AAV-related renal injury.