Miracle-dz/UniFAR-FTUs huggingface dataset:
A Preclinical Systematic Review of Curcumin for Protecting the Kidney with Ischemia Reperfusion Injury

Renal ischemia-reperfusion injury (RIRI) refers to a phenomenon associated with dysfunction of the kidney and tissue damage. Unfortunately, no specific drugs have been found that effectively prevent and treat RIRI. Curcumin (Cur), a polyphenol extracted from turmeric, possesses a variety of biological activities involving antioxidation, inhibition of apoptosis, inhibition of inflammation, and reduction of lipid peroxidation. Eight frequently used databases were searched using prespecified search strategies. The CAMARADES 10-item quality checklist was used to evaluate the risk of bias of included studies, and the RevMan 5.3 software was used to analyze the data. The risk of bias score of included studies ranged from 3 to 6 with an average score of 5.22. Compared with the control group, Cur significantly alleviated renal pathology, reduced blood urea nitrogen and serum creatinine levels, and improved inflammatory indexes, oxidant, and apoptosis in RIRI animal models. Despite the heterogeneity of the response to Cur in terms of serum creatinine, BUN, TNF-alpha, and SOD, its effectiveness for improving the injury of RIRI was remarkable. In the mouse model subgroup of serum creatinine, the effect size of the method of unilateral renal artery ligation with contralateral nephrectomy and shorter ischemic time showed a greater effect than that of the control group. No difference was seen in the methods of model establishment, mode administration, or medication times. The preclinical systematic review provided preliminary evidence that Cur partially improved RIRI in animal models, probably via anti-inflammatory, antioxidant, antiapoptosis, and antifibrosis activities and via improving microperfusion. ARRIVE guidelines are recommended; blinding and sample size calculation should be focused on in future studies. These data suggest that Cur is a potential renoprotective candidate for further clinical trials of RIRI.
eDBLP: visualizing scientific publications

In this paper we describe an approach for visualizing the textual information archived in the DBLP and the static and dynamic relations contained in it. Those relations are existing between authors and co-authors, between keywords, but also between authors and keywords. Visually representing them provides a way to quickly get an overview about emerging or disappearing topics as well as researchers and researcher groups. To reach our goal we apply node-link diagrams, word clouds, heatmaps, and area plots to the preprocessed and transformed DBLP data. All visualizations are equipped with interaction techniques and are built by using the functionality of the Bokeh library in Python, which enables the users to run the eDBLP in a web browser and to explore the dataset in an interactive and intuitive way. Finally, we discuss limitations and scalability issues of our approach.
Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis

A 25-gene expression signature associates with progression of fibrosing steatohepatitis in independent NAFLD cohorts. Gene expression during disease progression Nonalcoholic fatty liver disease (NAFLD) manifests as an array of conditions ranging from hepatic fat buildup to liver inflammation and scarring. Govaere et al. detected a signature of 25 genes whose expression in diseased tissue associated with worsening of histologically defined NAFLD severity in two independent cohorts of patients. Protein expression of GDF15, a member of the transforming growth factor–β superfamily, also associated with ballooning, inflammation, and fibrosis in NAFLD serum samples. Together, these studies provide a comprehensive analysis of gene expression during human NAFLD progression. The mechanisms that drive nonalcoholic fatty liver disease (NAFLD) remain incompletely understood. This large multicenter study characterized the transcriptional changes that occur in liver tissue across the NAFLD spectrum as disease progresses to cirrhosis to identify potential circulating markers. We performed high-throughput RNA sequencing on a discovery cohort comprising histologically characterized NAFLD samples from 206 patients. Unsupervised clustering stratified NAFLD on the basis of disease activity and fibrosis stage with differences in age, aspartate aminotransferase (AST), type 2 diabetes mellitus, and carriage of PNPLA3 rs738409, a genetic variant associated with NAFLD. Relative to early disease, we consistently identified 25 differentially expressed genes as fibrosing steatohepatitis progressed through stages F2 to F4. This 25-gene signature was independently validated by logistic modeling in a separate replication cohort (n = 175), and an integrative analysis with publicly available single-cell RNA sequencing data elucidated the likely relative contribution of specific intrahepatic cell populations. Translating these findings to the protein level, SomaScan analysis in more than 300 NAFLD serum samples confirmed that circulating concentrations of proteins AKR1B10 and GDF15 were strongly associated with disease activity and fibrosis stage. Supporting the biological plausibility of these data, in vitro functional studies determined that endoplasmic reticulum stress up-regulated expression of AKR1B10, GDF15, and PDGFA, whereas GDF15 supplementation tempered the inflammatory response in macrophages upon lipid loading and lipopolysaccharide stimulation. This study provides insights into the pathophysiology of progressive fibrosing steatohepatitis, and proof of principle that transcriptomic changes represent potentially tractable and clinically relevant markers of disease progression.
A decision support framework for security resource allocation under ambiguity

There has been increasing interest in using Stackelberg game (known as a security game) to allocate limited security resources against different attacker types with a specific probability distribution. However, real problems of this kind often face ambiguous information, such as imprecise, unreliable and absent payoffs, and ambiguous assignments of these payoffs. To this end, based on decision theory and the Dempster–Shafer theory of evidence, this paper proposes a novel framework that can handle these common types of ambiguity. More specifically, this paper deploys the underlying principles of existing rules from decision theory, as a way to characterise different attitudes to ambiguity, during the transformation of ambiguous payoffs into point‐valued payoffs. Hence, our framework holds some good properties: (i) it subsumes traditional security games without ambiguous payoffs, (ii) a uniform margin of error will not affect the results and (iii) the influence of complete ignorance can be minimised. Also, our framework is evaluated by using nine different transformation rules, under various conditions and constraints, against 73,000 randomly generated games (a first comprehensive empirical evaluation to date). The evaluation reveals the benefits of each transformation rule and confirms that different rules can model individuals' different attitudes to ambiguity.
Glycine-based treatment ameliorates NAFLD by modulating fatty acid oxidation, glutathione synthesis, and the gut microbiome

A glycine- and leucine-based tripeptide improves symptoms in a mouse model of nonalcoholic fatty liver disease, which lacks approved treatments. Amino acids alleviate liver disease Glycine is known to be reduced in patients with nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH), diseases with no approved treatments. Rom et al. found that glycine biosynthetic genes showed reduced expression in humans and mice with NAFLD. Conversely, both genetic and dietary reduction of glycine worsened symptoms in the model, suggesting a potential causative role for glycine in NAFLD onset. Administration of glycine or a Gly-Gly-L-Leu tripeptide improved symptoms in a mouse model of NASH by enhancing fatty acid oxidation and glutathione synthesis and modulated the gut microbiome through a potentially indirect effect, indicating the potential of the approach as a treatment. Nonalcoholic fatty liver disease (NAFLD) including nonalcoholic steatohepatitis (NASH) has reached epidemic proportions with no pharmacological therapy approved. Lower circulating glycine is consistently reported in patients with NAFLD, but the causes for reduced glycine, its role as a causative factor, and its therapeutic potential remain unclear. We performed transcriptomics in livers from humans and mice with NAFLD and found suppression of glycine biosynthetic genes, primarily alanine-glyoxylate aminotransferase 1 (AGXT1). Genetic (Agxt1−/− mice) and dietary approaches to limit glycine availability resulted in exacerbated diet-induced hyperlipidemia and steatohepatitis, with suppressed mitochondrial/peroxisomal fatty acid β-oxidation (FAO) and enhanced inflammation as the underlying pathways. We explored glycine-based compounds with dual lipid/glucose-lowering properties as potential therapies for NAFLD and identified a tripeptide (Gly-Gly-L-Leu, DT-109) that improved body composition and lowered circulating glucose, lipids, transaminases, proinflammatory cytokines, and steatohepatitis in mice with established NASH induced by a high-fat, cholesterol, and fructose diet. We applied metagenomics, transcriptomics, and metabolomics to explore the underlying mechanisms. The bacterial genus Clostridium sensu stricto was markedly increased in mice with NASH and decreased after DT-109 treatment. DT-109 induced hepatic FAO pathways, lowered lipotoxicity, and stimulated de novo glutathione synthesis. In turn, inflammatory infiltration and hepatic fibrosis were attenuated via suppression of NF-κB target genes and TGFβ/SMAD signaling. Unlike its effects on the gut microbiome, DT-109 stimulated FAO and glutathione synthesis independent of NASH. In conclusion, impaired glycine metabolism may play a causative role in NAFLD. Glycine-based treatment attenuates experimental NAFLD by stimulating hepatic FAO and glutathione synthesis, thus warranting clinical evaluation.
Systematic Pharmacology and GEO Database Mining Revealed the Therapeutic Mechanism of Xuefu Zhuyu Decoration for Atherosclerosis Cardiovascular Disease

Background: Xuefu Zhuyu decoration (XFZYD), as a traditional Chinese compound recipe, has been used to treat atherosclerosis cardiovascular disease (ASCVD) for thousands of years in China, but its effective compounds and underlying treatment molecular mechanism remains promiscuous, which severely limits its clinical application. Methods: The effective components and their targets of XFZYD were predicted and screened based on the Traditional Chinese Medicine System Pharmacology (TCMSP) database. The candidate therapeutic targets of ASCVD were screened by Pharmacogenomics Knowledgebase (PharmGKB) and Comparative Toxicogenomics Database (CTD). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for target proteins were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) database. Differentially expressed genes were identified using the GEO2R online tool. Molecular docking was performed by Schrodinger software. To assess the efficacy of the prediction, human umbilical vein endothelial cells (HUVECs) treated with the effective compound of XFZYD were used as the in vitro model. Results: A total of 108 effective compounds (including quercetin) and 137 candidate therapeutic targets were identified. Analyzing the relationships among effective compounds, candidate therapeutic targets, and signaling pathways, the therapy mechanisms of XFZYD were mainly reflected in the protection of vascular endothelium, anti-inflammatory, antioxidant stress, etc. Accordingly, we found the effective compound of XFZYD (quercetin) decreased intracellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion molecule 1 (VCAM-1) expressions and pro-inflammatory cytokines in HUVECs treated with lipopolysaccharide (LPS), and reduced the adhesion function of HUVECs with monocytes. The inhibitor of the predicted target protein (PTGS2) could further reduce the expressions of VCAM-1, ICAM-1, and TNF-α induced by LPS, and inhibit the adhesion function of HUVECs with monocytes, while PTGS2 agonists partially counteracted the protective effect of quercetin. Conclusions: In this study, the effective components and potential therapeutic targets of XFZYD for ASCVD treatment were explored from the perspective of systemic pharmacology. The effective component quercetin was verified to protect endothelial cells by reducing endothelial inflammatory response and impeding the attachment of monocytes against the predicted therapeutic target PTGS2.
ScagnosticsViewer: tracking time series patterns via scagnostics meatures

Visual analytics studies the integration of human perceptional ability and the data exploration process. Besides, high dimensional time series has become more and more popular data in daily applications and various domains. It is essential to study visual techniques for this type of data set. This paper is an applied work that extends successes of the scatterplot matrix (SPLOM) for cross-sectional data to the high dimensional temporal data sets. We have built a web-based application that contains various visual techniques to display the temporal data sets by SPLOM at each snapshot and animate the SPLOM to illustrate the evolution of the data sets. Two real data sets in different domains are utilized to demonstrate the advances of this approach.
Buy-many mechanisms

Multi-item mechanisms can be very complex, offering many different bundles to the buyer that could even be randomized. Such complexity is thought to be necessary as the revenue gaps between randomized and deterministic mechanisms, or deterministic and simple mechanisms are huge even for additive valuations. Furthermore, the optimal revenue displays strange properties such as non-continuity: changing valuations by tiny multiplicative amounts can change the optimal revenue by an arbitrarily large multiplicative factor. Our work shows that these strange properties do not apply to most natural situations as they require that the mechanism overcharges the buyer for a bundle while selling individual items at much lower prices. In such cases, the buyer would prefer to break his order into smaller pieces paying a much lower price overall. We advocate studying a new revenue benchmark, namely the optimal revenue achievable by "buy-many" mechanisms, that is much better behaved. In a buy-many mechanism, the buyer is allowed to interact with the mechanism multiple times instead of just once. We show that the optimal buy-many revenue for any n item setting is at most O(log n) times the revenue achievable by item pricing. Furthermore, a mechanism of finite menu-size (n/ε)2O(n) suffices to achieve (1 + ε)-approximation to the optimal buy-many revenue. Both these results are tight in a very strong sense, as any family of mechanisms with description complexity sub-doubly-exponential in n cannot achieve better than logarithmic approximation in revenue. In contrast, for buy-one mechanisms, no simple mechanism of finite menu-size can get a finite-approximation in revenue. Moreover, the revenue of buy-one mechanisms can be extremely sensitive to multiplicative changes in values, while as we show optimal buy-many mechanisms satisfy revenue continuity.
Motion Planning and Iterative Learning Control of a Modular Soft Robotic Snake

Snake robotics is an important research topic with a wide range of applications, including inspection in confined spaces, search-and-rescue, and disaster response. Snake robots are well-suited to these applications because of their versatility and adaptability to unstructured and constrained environments. In this paper, we introduce a soft pneumatic robotic snake that can imitate the capabilities of biological snakes, its soft body can provide flexibility and adaptability to the environment. This paper combines soft mobile robot modeling, proprioceptive feedback control, and motion planning to pave the way for functional soft robotic snake autonomy. We propose a pressure-operated soft robotic snake with a high degree of modularity that makes use of customized embedded flexible curvature sensing. On this platform, we introduce the use of iterative learning control using feedback from the on-board curvature sensors to enable the snake to automatically correct its gait for superior locomotion. We also present a motion planning and trajectory tracking algorithm using an adaptive bounding box, which allows for efficient motion planning that still takes into account the kinematic state of the soft robotic snake. We test this algorithm experimentally, and demonstrate its performance in obstacle avoidance scenarios.
Transmission-Mode Ultrasound for Monitoring the Instantaneous Elastic Modulus of the Achilles Tendon During Unilateral Submaximal Vertical Hopping

Submaximal vertical hopping capitalizes on the strain energy storage-recovery mechanism associated with the stretch-shortening cycle and is emerging as an important component of progressive rehabilitation protocols in Achilles tendon injury and a determinant of readiness to return to sport. This study explored the reliability of transmission mode ultrasound in quantifying the instantaneous modulus of elasticity of human Achilles tendon during repetitive submaximal hopping. A custom-built ultrasound transmission device, consisting of a 1 MHz broadband emitter and four regularly spaced receivers, was used to measure the axial velocity of ultrasound in the Achilles tendon of six healthy young adults (mean ± SD; age 26 ± 5 years; height 1.78 ± 0.11 m; weight 79.8 ± 13.6 kg) during steady-state unilateral hopping (2.5 Hz) on a piezoelectric force plate. Vertical ground reaction force and lower limb joint kinematics were simultaneously recorded. The potential sensitivity of the technique was further explored in subset of healthy participants (n = 3) that hopped at a slower rate (1.8 Hz) and a patient who had undergone Achilles tendon rupture-repair (2.5 Hz). Reliability was estimated using the mean-within subject coefficient of variation calculated at each point during the ground-contact phase of hopping, while cross-correlations were used to explore the coordination between lower limb kinematics ground reaction forces and ultrasound velocity in the Achilles tendon. Axial velocity of ultrasound in the Achilles tendon was highly reproducible during hopping, with the mean within-subject coefficient of variation ranging between 0.1 and 2.0% across participants. Ultrasound velocity decreased immediately following touch down (−19 ± 13 ms–1), before increasing by 197 ± 81 ms–1, on average, to peak at 2230 ± 87 ms–1 at 67 ± 3% of ground contact phase in healthy participants. Cross-correlation analysis revealed that ultrasound velocity in the Achilles tendon during hopping was strongly associated with knee (mean r = 0.98, range 0.95–1.00) rather than ankle (mean r = 0.67, range 0.35–0.79) joint motion. Ultrasound velocity was sensitive to changes in hopping frequency in healthy adults and in the surgically repaired Achilles tendon was characterized by a similar peak velocity (2283 ± 13 ms–1) but the change in ultrasound velocity (447 ± 21 ms–1) was approximately two fold that of healthy participants (197 ± 81 ms–1). Although further research is required, the technique can be used to reliably monitor ultrasound velocity in the Achilles tendon during hopping, can detect changes in the instantaneous elastic modulus of tendon with variation in hopping frequency and tendon pathology and ultimately may provide further insights into the stretch-shortening cycle and aid clinical decision concerning tendon rehabilitation protocols and readiness to return to sport.
Altered Insulin Receptor Substrate 1 Phosphorylation in Blood Neuron-Derived Extracellular Vesicles From Patients With Parkinson’s Disease

Introduction Diabetes increases the risk of Parkinson’s disease (PD). The phosphorylation of type 1 insulin receptor substrate (IRS-1) determines the function of insulin signaling pathway. Extracellular vesicles (EVs) are emerging as biomarkers of human diseases. The present study investigated whether PD patients exert altered phosphorylation IRS-1 (p-IRS-1) inside the blood neuron-derived extracellular vesicles (NDEVs). Research Design and Methods In total, there were 94 patients with PD and 63 healthy controls recruited and their clinical manifestations were evaluated. Blood NDEVs were isolated using the immunoprecipitation method, and Western blot analysis was conducted to assess total IRS-1, p-IRS-1, and downstream substrates level in blood NDEVs. Statistical analysis was performed using SPSS 19.0, and p < 0.05 was considered significant. Results The isolated blood EVs were validated according to the presence of CD63 and HSP70, nanoparticle tracking analysis and transmission electron microscopy. NDEVs were positive with neuronal markers. PD patients exerted significantly higher level of p-IRS-1S312 in blood NDEVs than controls. In addition, the p-IRS-1S312 levels in blood NDEVs was positively associated with the severity of tremor in PD patients after adjusting of age, sex, hemoglobin A1c, and body mass index (BMI). Conclusion PD patients exerted altered p-IRS-1S312 in the blood NDEVs, and also correlated with the severity of tremor. These findings suggested the association between dysfunctional insulin signaling pathway with PD. The role of altered p-IRS-1S312 in blood NDEVs as a segregating biomarker of PD required further cohort study to assess the association with the progression of PD.
Testing the Treatment Integrity of the Managing Cancer and Living Meaningfully Psychotherapeutic Intervention for Patients With Advanced Cancer

Introduction The Managing Cancer and Living Meaningfully (CALM) therapy for patients with advanced cancer was tested against a supportive psycho-oncological counseling intervention (SPI) in a randomized controlled trial (RCT). We investigated whether CALM was delivered as intended (therapists’ adherence); whether CALM therapists with less experience in psycho-oncological care show higher adherence scores; and whether potential overlapping treatment elements between CALM and SPI can be identified (treatment differentiation). Methods Two trained and blinded raters assessed on 19 items four subscales of the Treatment Integrity Scale covering treatment domains of CALM (SC: Symptom Management and Communication with Health Care Providers; CSR: Changes in Self and Relationship with Others; SMP: Spiritual Well-being and Sense of Meaning and Purpose; FHM: Preparing for the Future, Sustaining Hope and Facing Mortality). A random sample of 150 audio recordings (75 CALM, 75 SPI) were rated on a three-point Likert scale with 1 = “adherent to some extent,” 2 = “adherent to a sufficient extent,” 3 = “very adherent. ” Results All 19 treatment elements were applied, but in various frequencies. CALM therapists most frequently explored symptoms and/or relationship to health care providers (SC_1: n_applied = 62; 83%) and allowed expression of sadness and anxiety about the progression of disease (FHM_2: n_applied = 62; 83%). The exploration of CALM treatment element SC_1 was most frequently implemented in a satisfactory or excellent manner (n_sufficient or very adherent = 34; 45%), whereas the treatment element SMP_4: Therapist promotes acknowledgment that some life goals may no longer be achievable (n_sufficient or very adherent = 0; 0%) was not implemented in a satisfactory manner. In terms of treatment differentiation, no treatment elements could be identified which were applied significantly more often by CALM therapists than by SPI therapists. Conclusion Results verify the application of CALM treatment domains. However, CALM therapists’ adherence scores indicated manual deviations. Furthermore, raters were not able to significantly distinguish CALM from SPI, implying that overlapping treatment elements were delivered to patients.