Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of aerobic exercise frequencies on liver fibrosis, α-fetoprotein and cytokeratin 19 in experimental type 2 diabetes-induced rats: an immunohistochemistry study

ABSTRACT We investigated using immunohistochemistry the effects of frequency of aerobic exercise on liver fibrosis and measured the expression of the oval cell marker, alpha fetoprotein (AFP), and the hepatocellular carcinoma marker, CK 19, in rats with early-period induced type 2 diabetes (T2DM). Rats were divided into four groups: control sedentary rats, diabetic sedentary rats, diabetic rats with continuous exercise (30 min/day, 5 days/week) and diabetic rats with short periods of exercise (3 x 10 min/day, 5 days/week). T2DM was induced using an intraperitoneal (i.p.) injection of nicotinamide (NA) and streptozotocin (STZ). Liver samples were obtained 8 weeks after injection. Tissue sections were stained with hematoxylin and eosin, periodic acid-Schiff and Masson’s trichrome. We also used immunochemical staining for AFP, smooth muscle actin (α-SMA) and CK19. Continuous and short periods of aerobic exercise produced similar effects during the early period of liver damage in the STZ-NA model, i.e., decreased blood glucose levels and improved body weight, improved liver histology and reduced fibrosis, necrosis and steatosis; and reduced expression of AFP and α-SMA. Moderate aerobic exercise for 150 min/week appeared to reduce early liver damage in a rat model of T2DM.
Association between tumor necrosis factor-α -308 Gauss/A polymorphism and risk of silicosis and coal workers pneumoconiosis in Chinese population

Abstract Background: Many studies have attempted to clarify the association between TNF-a -308G/A polymorphism and pneumoconiosis, but there has been no definite consensus to date. To further assess the effects of TNF-a -308G/A polymorphism on the risk of pneumoconiosis, a meta-analysis was performed in Chinese population. Methods: We searched the related literature in PubMed and Chinese databases through June 2018. The strength of the associations was assessed used pooled odds ratios (ORs) and 95% confidence intervals (CIs). Results: Nine case–control studies including 730 silicosis cases, 457 coal workers pneumoconiosis cases and 2429 controls were identified according to the inclusion criteria. In the total analyses, a significantly elevated risk was found in allelic model (OR = 1.41, 95% CI = 1.16–1.71). In the subgroup analyses by geographic area and type of pneumoconiosis, significant results were found both in North China (A versus G, OR = 1.33, CI = 1.05–1.69) and South China (A versus G, OR = 1.56, CI = 1.14–2.15); significant results were also found in silicosis (A versus G, OR = 1.40, CI = 1.11–1.78) and coal worker pneumoconiosis (A versus G, OR = 1.42, CI = 1.03–1.96). Conclusion: This meta-analysis suggested that TNF-a gene -308 G/A polymorphism is associated with increased silicosis and coal workers pneumoconiosis risk in the Chinese population, and further studies in other ethnic groups are required for definite conclusions.
Multilevel MDA-Lite Paris Traceroute

Since its introduction in 2006--2007, Paris Traceroute and its Multipath Detection Algorithm (MDA) have been used to conduct well over a billion IP level multipath route traces from platforms such as M-Lab. Unfortunately, the MDA requires a large number of packets in order to trace an entire topology of load balanced paths between a source and a destination, which makes it undesirable for platforms that otherwise deploy Paris Traceroute, such as RIPE Atlas. In this paper we present a major update to the Paris Traceroute tool. Our contributions are: (1) MDA-Lite, an alternative to the MDA that significantly cuts overhead while maintaining a low failure probability; (2) Fakeroute, a simulator that enables validation of a multipath route tracing tool's adherence to its claimed failure probability bounds; (3) multilevel multipath route tracing, with, for the first time, a Traceroute tool that provides a router-level view of multipath routes; and (4) surveys at both the IP and router levels of multipath routing in the Internet, showing, among other things, that load balancing topologies have increased in size well beyond what has been previously reported as recently as 2016. The data and the software underlying these results are publicly available.
Osteocalcin Ameliorates Motor Dysfunction in a 6-Hydroxydopamine-Induced Parkinson’s Disease Rat Model Through AKT/GSK3β Signaling

Osteoblasts derived osteocalcin (OCN) is recently reported to be involved in dopaminergic neuronal development. As dopaminergic neuronal injury in the substantia nigra (SN) is a pathological hallmark of Parkinson’s disease (PD), we investigated whether OCN could exert protective effects on 6-hydroxydopamine (6-OHDA)-induced PD rat model. Our data showed that the OCN level in the cerebrospinal fluid (CSF) in PD rat models was significantly lower than that in controls. Intervention with OCN could improve the behavioral dysfunction in PD rat models and reduce the tyrosine hydroxylase (TH) loss in the nigrostriatal system. In addition, OCN could inhibit the astrocyte and microglia proliferation in the SN of PD rats. In vitro studies showed that OCN significantly ameliorated the neurotoxicity of 6-OHDA through the AKT/GSK3β signaling pathway. In summary, OCN plays a protective role against parkinsonian neurodegeneration in the PD rat model, suggesting a potential therapeutic use of OCN in PD.
Meckel's diverticulum in the adult: surgical treatment

Abstract Introduction: Management of asymptomatic Meckel’s diverticulum (MD) incidentally discovered in adults remains controversial. The aim of this study was to determine if incidental diverticula should be removed. Materials and methods: We reviewed a consecutive series of patients surgically managed from January 1994 to December 2016. Patients were divided into two groups according to symptomatic or asymptomatic diverticula, and characteristics were compared. Results: The study included 66 patients: 30 in the symptomatic group (45%) and 36 in the incidental group (55%). We found 12 females (18.2%), and the ratio male:female was higher in the symptomatic group (14:1 vs. 2.6:1). Patients in the symptomatic group were significantly younger: 41.7 ± 18.1 vs. 54.7 ± 19.8 years (p = .007). MD in the symptomatic group tended to be longer (3.8 ± 1.9 vs. 2.6 ± 0.9 cm; p = .003). A MD-associated malignancy was present in three patients (4.5%), all neuroendocrine tumours. Major postoperative complications occurred in 6.6% of symptomatic patients and 0% within the incidental group, without specific morbidity related to prophylactic surgery. No mortality was observed. Conclusion: Resection of incidentally found Meckel’s diverticulum can be made because of benefits outweigh the risks in this high-risk area for cancer.
Childhood-onset craniopharyngioma: latest insights into pathology, diagnostics, treatment, and follow-up

ABSTRACT Introduction: Childhood-onset craniopharyngiomas are rare embryonic tumors of low-grade histological malignancy. Severe obesity, physical fatigue, and psychosocial deficits due to hypothalamic tumor involvement have negative impact on quality of life. Initial pretreatment involvement of hypothalamic structures and/or treatment-related lesions result in sequelae clinically associated with impaired social and physical functionality and severe neuroendocrine deficiencies. Overall and progression-free survival rates are not associated with the degree of surgical resection. However, reduced overall survival rates were observed in patients with primary hypothalamic tumor involvement. Areas covered: This review discusses new perspectives on diagnostics, treatment, and follow-up of patients with childhood-onset craniopharyngioma, which were mostly published after 2010 and presented at the 5th International Multidisciplinary Postgraduate Course on Childhood Craniopharyngioma, 19–22 April 2018, at Bad Zwischenahn, Germany. Expert commentary: Percutaneous radio-oncological treatment options are effective in prevention of relapses and tumor progressions. Initial experience with proton beam therapy in childhood-onset craniopharyngioma patients shows promising results in terms of more protective radiological treatment. Recent reports on the molecular pathogenesis of craniopharyngioma open perspectives on the possibility of testing novel treatments targeting pathogenic pathways. As long as effective treatment options for hypothalamic syndrome are not available, hypothalamus-sparing treatment strategies are recommended.
NeuroImage: Clinical Microstructural brain changes track cognitive decline in mild cognitive impairment

Improved characterization of the microstructural brain changes occurring in the early stages of Alzheimer's disease may permit more timely disease detection. This study examined how longitudinal change in brain microstructure relates to cognitive decline in aging and prodromal Alzheimer's disease. At baseline and two-year follow-up, 29 healthy controls and 21 individuals with mild cognitive impairment or mild Alzheimer's disease underwent neuropsychological evaluation and restriction spectrum imaging (RSI). Microstructural change in the hippocampus, entorhinal cortex, and white matter tracts previously shown to be vulnerable to Alzheimer's disease, was compared between healthy controls and impaired participants. Partial correlations and stepwise linear regressions examined whether baseline RSI metrics predicted subsequent cognitive decline, or change in RSI metrics correlated with cognitive change. In medial temporal gray and white matter, restricted isotropic diffusion and crossing fibers were lower, and free water diffusion was higher, in impaired participants. Restricted isotropic diffusion in the hippocampus declined more rapidly for cognitively impaired participants. Baseline hippocampal restricted isotropic diffusion predicted cognitive decline, and change in hippocampal and entorhinal restricted isotropic diffusion correlated with cognitive decline. Within controls, changes in white matter restricted oriented diffusion and crossing fibers correlated with memory decline. In contrast, there were no correlations between rates of cortical atrophy and cognitive decline in the full sample or within controls. Changes in medial temporal lobe microarchitecture were associated with cognitive decline in prodromal Alzheimer's disease, and these changes were distinct from microstructural changes in normal cognitive aging. RSI metrics of brain microstructure may hold value for predicting cognitive decline in aging and for monitoring the course of Alzheimer's disease.
The mechanistic insight of a specific interaction between 15d-Prostaglandin-J2 and eIF4A suggests an evolutionary conserved role across species

ABSTRACT 15-deoxy-delta 12,14-prostaglandin J2 (15d-PGJ2) is an anti-inflammatory/anti-neoplastic prostaglandin that functions through covalent binding to cysteine residues of various target proteins. We previously showed that 15d-PGJ2 mediated anti-inflammatory responses are dependent on the translational inhibition through its interaction with eIF4A (Kim et al., 2007). Binding of 15d-PGJ2 to eIF4A specifically blocks the interaction between eIF4G and eIF4A, which leads to the formation of stress granules (SGs), which then cluster mRNAs with inhibited translation. Here, we show that the binding between 15d-PGJ2 and eIF4A specifically blocks the interaction between the MIF4G domain of eIF4G and eIF4A. To reveal the mechanism of this interaction, we used computational simulation-based docking studies and identified that the carboxyl tail of 15d-PGJ2 could stabilize the binding of 15d-PGJ2 to eIF4A through arginine 295 of eIF4A, which is the first suggestion that the 15d-PGJ2 tail plays a physiological role. Interestingly, the putative 15d-PGJ2 binding site on eiF4A is conserved across many species, suggesting a biological role. Our data propose that studying 15d-PGJ2 and its targets may uncover new therapeutic approaches in anti-inflammatory drug discovery. Summary: The tail region of 15d-PGJ2 plays a important role in modulating the activity of eIF4A protein across species. This implies that the tail region of this prostaglandins can be adapted to design new drugs.
Advertisement calls and DNA sequences reveal a new species of Scinax (Anura: Hylidae) on the Pacific lowlands of Ecuador

Scinax is a speciose genus of Neotropical hylid frogs. We describe a new species from western Ecuador (elevations between 0 and 1207 m) using morphology, vocalizations, and DNA sequences. We also present a new phylogeny for Scinax based on mitochondrial DNA genes 12S rRNA, Cytochrome Oxidase sub-unit I, Cytochrome B, 16S rRNA, NADH dehydrogenase subunit 1, and adjacent tRNAs. The new species, Scinax tsachila sp. nov. was previously confused with S. quinquefasciatus, a morphologically similar sympatric species. They differ by having markedly different advisement calls, distinct skin texture in the dorsum, and different bone coloration. The new species is sister to S. elaeochroa, a species that differs in advertisement call and color pattern. We provide an updated species account for Scinax quinquefasciatus and a redescription of its holotype.
Confidence Inference for Focused Learning in Stereo Matching

In this paper, we present confidence inference approachin an unsupervised way in stereo matching. Deep Neu-ral Networks (DNNs) have recently been achieving state-of-the-art performance. However, it is often hard to tellwhether the trained model was making sensible predictionsor just guessing at random. To address this problem, westart from a probabilistic interpretation of theL1loss usedin stereo matching, which inherently assumes an indepen-dent and identical (aka i.i.d.) Laplacian distribution. Weshow that with the newly introduced dense confidence map,the identical assumption is relaxed. Intuitively, the vari-ance in the Laplacian distribution is large for low confidentpixels while small for high-confidence pixels. In practice,the network learns toattenuatelow-confidence pixels (e.g.,noisy input, occlusions, featureless regions) andfocusonhigh-confidence pixels. Moreover, it can be observed fromexperiments that the focused learning is very helpful in find-ing a better convergence state of the trained model, reduc-ing over-fitting on a given dataset.
Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles

Mutations in the glucosylceramidase beta (GBA) gene are strongly associated with neurodegenerative diseases marked by protein aggregation. GBA encodes the lysosomal enzyme glucocerebrosidase, which breaks down glucosylceramide. A common explanation for the link between GBA mutations and protein aggregation is that lysosomal accumulation of glucosylceramide causes impaired autophagy. We tested this hypothesis directly by measuring protein turnover and abundance in Drosophila mutants with deletions in the GBA ortholog Gba1b. Proteomic analyses revealed that known autophagy substrates, which had severely impaired turnover in autophagy-deficient Atg7 mutants, showed little to no overall slowing of turnover or increase in abundance in Gba1b mutants. Likewise, Gba1b mutants did not have the marked impairment of mitochondrial protein turnover seen in mitophagy-deficient parkin mutants. Proteasome activity, microautophagy, and endocytic degradation also appeared unaffected in Gba1b mutants. However, we found striking changes in the turnover and abundance of proteins associated with extracellular vesicles (EVs), which have been proposed as vehicles for the spread of protein aggregates in neurodegenerative disease. These changes were specific to Gba1b mutants and did not represent an acceleration of normal aging. Western blotting of isolated EVs confirmed the increased abundance of EV proteins in Gba1b mutants, and nanoparticle tracking analysis revealed that Gba1b mutants had six times as many EVs as controls. Genetic perturbations of EV production in Gba1b mutants suppressed protein aggregation, demonstrating that the increase in EV abundance contributed to the accumulation of protein aggregates. Together, our findings indicate that glucocerebrosidase deficiency causes pathogenic changes in EV metabolism and may promote the spread of protein aggregates through extracellular vesicles.
Graph Laplacian Regularized Graph Convolutional Networks for Semi-supervised Learning

Recently, graph convolutional network (GCN) has been widely used for semi-supervised classification and deep feature representation on graph-structured data. However, existing GCN generally fails to consider the local invariance constraint in learning and representation process. That is, if two data points Xi and Xj are close in the intrinsic geometry of the data distribution, then their labels/representations should also be close to each other. This is known as local invariance assumption which plays an essential role in the development of various kinds of traditional algorithms, such as dimensionality reduction and semi-supervised learning, in machine learning area. To overcome this limitation, we introduce a graph Laplacian GCN (gLGCN) approach for graph data representation and semi-supervised classification. The proposed gLGCN model is capable of encoding both graph structure and node features together while maintains the local invariance constraint naturally for robust data representation and semi-supervised classification. Experiments show the benefit of the benefits the proposed gLGCN network.
Arguing Practical Significance in Software Engineering Using Bayesian Data Analysis

This paper provides a case for using Bayesian data analysis (BDA) to make more grounded claims regarding practical significance of software engineering research. We show that using BDA, here combined with cumulative prospect theory (CPT), is appropriate when a researcher or practitioner wants to make clearer connections between statistical findings and practical significance in empirical software engineering research. To illustrate our point we provide an example case using previously published data. We build a multilevel Bayesian model for this data, for which we compare the out of sample predictive power. Finally, we use our model to make out of sample predictions while, ultimately, connecting this to practical significance using CPT. Throughout the case that we present, we argue that a Bayesian approach is a natural, theoretically well-grounded, practical work-flow for data analysis in empirical software engineering. By including prior beliefs, assuming parameters are drawn from a probability distribution, assuming the true value is a random variable for uncertainty intervals, using counter-factual plots for sanity checks, conducting predictive posterior checks, and out of sample predictions, we will better understand the phenomenon being studied, while at the same time avoid the obsession with p-values.
On recovery of signals with single point spectrum degeneracy

The paper study recovery problem for discrete time signals with a finite number of missing values. The paper establishes recoverability of these missing values for signals with Z-transform vanishing with a certain rate at a single point. The transfer functions for the corresponding recovering kernels are presented explicitly. Some robustness of the recovery with respect to data truncation or noise contamination is established.
Bayesian modeling of Dynamic Contrast Enhanced MRI data in cerebral glioma patients improves the diagnostic quality of hemodynamic parameter maps

Purpose The purpose of this work is to investigate if the curve-fitting algorithm in Dynamic Contrast Enhanced (DCE) MRI experiments influences the diagnostic quality of calculated parameter maps. Material and methods We compared the Levenberg-Marquardt (LM) and a Bayesian method (BM) in DCE data of 42 glioma patients, using two compartmental models (extended Toft’s and 2-compartment-exchange model). Logistic regression and an ordinal linear mixed model were used to investigate if the image quality differed between the curve-fitting algorithms and to quantify if image quality was affected for different parameters and algorithms. The diagnostic performance to discriminate between high-grade and low-grade gliomas was compared by applying a Wilcoxon signed-rank test (statistical significance p>0.05). Two neuroradiologists assessed different qualitative imaging features. Results Parameter maps based on BM, particularly those describing the blood-brain barrier, were superior those based on LM. The image quality was found to be significantly improved (p<0.001) for BM when assessed through independent clinical scores. In addition, given a set of clinical scores, the generating algorithm could be predicted with high accuracy (area under the receiver operating characteristic curve between 0.91 and 1). Using linear mixed models, image quality was found to be improved when applying the 2-compartment-exchange model compared to the extended Toft’s model, regardless of the underlying fitting algorithm. Tumor grades were only differentiated reliably on plasma volume maps when applying BM. The curve-fitting algorithm had, however, no influence on grading when using parameter maps describing the blood-brain barrier. Conclusion The Bayesian method has the potential to increase the diagnostic reliability of Dynamic Contrast Enhanced parameter maps in brain tumors. In our data, images based on the 2-compartment-exchange model were superior to those based on the extended Toft’s model.
Harnessing CRISPR/Cas 9 System for manipulation of DNA virus genome

The recent development of the Clustered Regularly Interspaced Palindromic Repeat (CRISPR)/CRISPR‐associated protein 9 (Cas9) system, a genome editing system, has many potential applications in virology. The possibility of introducing site specific breaks has provided new possibilities to precisely manipulate viral genomics. Here, we provide diagrams to summarize the steps involved in the process. We also systematically review recent applications of the CRISPR/Cas9 system for manipulation of DNA virus genomics and discuss the therapeutic potential of the system to treat viral diseases.
Response rate profiles for major depressive disorder: Characterizing early response and longitudinal nonresponse

Definition of response is critical when seeking to establish valid predictors of treatment success. However, response at the end of study or endpoint only provides one view of the overall clinical picture that is relevant in testing for predictors. The current study employed a classification technique designed to group subjects based on their rate of change over time, while simultaneously addressing the issue of controlling for baseline severity.
Social Antecedents and Employee Intention to Stay in Selected IT Organizations: A Study in National Capital Region of Delhi

Turbulence in the business environment had made retention of key employees a challenging issue for most organizations. As retention perspectives differ widely from one organization to another, it is difficult for HR heads and industry experts to come out with any prescribed model in order to define employee retention in their organizations. The study explores an under-researched area of the role of social antecedents on employee intention to stay in organizations. The organizations taken into consideration represent selected IT organizations in the NCR of Delhi. The data was collected from 100 employees holding operational and team leader positions in leading IT organizations located in and around the NCR of Delhi. The results of the study indicate that social support, trust and social relationships have substantial roles to play in making employees stay and how different social variables such as co-worker relationship, supervisor relationship, social recognition, trust, collectivism, social networking, anticipation of support and reciprocity are valued while deciding upon the employee’s intention to stay in similar contexts (i.e. sector).