Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Akt activator SC-79 is a potential treatment for alcohol-induced osteonecrosis of the femoral head

Alcohol is a leading risk factor for osteonecrosis of the femoral head (ONFH). We explored the molecular mechanisms underlying alcohol-induced ONFH and investigated the protective effect of the novel Akt activator SC-79 against this disease. We found that ethanol inhibited expression of the osteogenic genes RUNX2 and OCN, downregulated osteogenic differentiation, impaired the recruitment of Akt to the plasma membrane, and suppressed Akt phosphorylation at Ser473, thereby inhibiting the Akt/GSK3β/β-catenin signaling pathway in bone mesenchymal stem cells. To assess SC-79′s ability to counteract the inhibitory effect of ethanol on Akt-Ser73 phosphorylation, we performed micro-computerized tomography and immunofluorescent staining of osteopontin, osteocalcin and collagen type 1 in a rat model of alcohol-induced ONFH. We found that SC-79 injections inhibited alcohol-induced osteonecrosis. These results show that alcohol-induced ONFH is associated with suppression of p-Akt-Ser473 in the Akt/GSK3β/β-catenin signaling pathway in bone mesenchymal stem cells. We propose that SC-79 treatment to rescue Akt activation could be tested in the clinic as a potential therapeutic approach to preventing the development of alcohol-induced ONFH.
Spectrum Sensing With Multiple Primary Users Over Fading Channels

We investigate the impact of multiple primary users (PUs) and fading on the spectrum sensing of a classical energy detector (ED). Specifically, we present the novel closed-form expressions for the false-alarm and detection probabilities in a multiple PUs environment, assuming the Nakagami-m fading and complex Gaussian PUs transmitted signals. The results reveal the importance of taking into consideration the wireless environment, when evaluating the ED spectrum sensing performance and selecting the ED threshold.
The Cutting Simulation of Austenitic Stainless Steel Based on ANSYS/LS-DYNA

The austenitic stainless steel cutting process was stimulated by general-purpose finite element software ANSYS/LS-DYNA.The results are as follows:The mechanism of chip separation is that the workpiece shear stresses on both sides of the tool tip are relatively large,but in the opposite direction;the largest equivalent stress is extended to the below of the machined surface during the cutting process,which is one of the reasons of work hardening;the shear plane temperature is almost equal; in the vertical to the shear plane direction,the temperature gradient is large,temperature distribution at the bottom of chip is uniform.
Intracellular localisation of proteins to specific cellular areas by nanocapsule mediated delivery

Abstract Nanocapsules are promising carriers with great potential for intracellular protein transport. Although many studies have intended to improve cell uptake efficacy, there is an increasing interest in understanding of subcellular distribution of cargoes inside cells, which is essential for purposeful delivery of biomolecules into specific sites within cells. Herein, we interrogate the intracellular localisation of exogenous proteins, including fluorescein isothiocyanate (FITC)-labelled bovine serum albumin (BSA) and green fluorescent protein (GFP), mediated by specially designed nanocapsules. The results show that the designed nanocapsules can deliver the two types of fluorescent proteins into different cellular destinations (cytosol, nucleus or the whole cell), depending on the composition of nanocapsules. Meanwhile, several impact factors that influence the distribution of proteins in cells have also been investigated, and the results suggest that the localisation of capsule-mediated proteins in cells is strongly affected by the surface properties of nanocapsules, the types of stabilisers and proteins, and environmental temperatures. The rational control of intracellular localised delivery of exogenous proteins as we demonstrated in this study might open new avenues to obtain desired magnitude of drug effects for modulating cell activity.
The Challenge of using Map-reduce to Query Open Data

For transparency and democracy reasons, a few years ago Public Administrations started publishing data sets concerning public services and territories. These data sets are called open, because they are publicly available through many web sites. Due to the rapid growth of open data corpora, both in terms of number of corpora and in terms of open data sets available in each single corpus, the need for a centralized query engine arises, able to select single data items from within a mess of heterogeneous open data sets. We gave a first answer to this need in (Pelucchi et al., 2017), where we defined a technique for blindly querying a corpus of open data. In this paper, we face the challenge of implementing this technique on top of the Map-Reduce approach, the most famous solution to parallelize computational tasks in the Big Data world.
Synbiotic preparation with Lactic acid bacteria and inulin as a functional food: In vivo evaluation of microbial activities, and preneoplastic aberrant crypt foci

Host microbiome and metabolome are associated with the incidence of colorectal cancer (CC), one of the major health problems in developed countries. The pro and prebiotic supplementation helps to improve the host health. Inulin is one such prebiotic used for the enhancement of naive probiotic bacterial population. This paper explains the impact of inulin (PRE) extracted from Jerusalem artichoke (JA), Lactobacillus plantarum HII11 (PRO), and synbiotic (SYN; inulin + L. plantarum HII11) preparation on Azoxymethane mediated CC induced rat model with respect to changes in microbial load, microbial enzymes, and preneoplastic aberrant crypt foci. The results suggested that the PRE and SYN supplementation effectively reduced the selected pathogenic bacteria (Salmonella spp., and Escherichia coli), microbial enzymes and increased the probiotic load. The intervention of SYN significantly reduced the colonic ACF in CC model. The study results revealed that the supplementation of SYN diet (inulin and L. plantarum HII11) protects the AOM-mediated colon cancer induced host.
Isolation and Characterization of a New Cyanobacterial Strain with a Unique Fatty Acid Composition

A new cyanobacterial strain was isolated and purified from salt Lake Balkhash, Kazakhstan. According to its morphological and ultrastructural characteristics, 16S rRNA sequence and the fatty acid profile, the strain has been classified as Cyanobacterium spp. and assigned as Cyanobacterium sp. IPPAS B-1200. The strain is characterized by a non-temperature inducible Δ9-desaturation system, and by high relative amounts of myristic (14:0—30%) and myristoleic (14:1Δ9—10%) acids. The total amount of C14 fatty acids reaches 40%, which is unusually high for cyanobacteria, and it has never been reported before. The remaining fatty acids are represented mainly by palmitic (16:0) and palmitoleic (16:1Δ9) acids (the sum reaches nearly 60%). Such a fatty acid composition, together with a relatively high speed of growth, makes this newly isolated strain a prospective candidate for biodiesel production.
Design Study for Creating Pathfinder: A Visualization Tool for Generating Software Test Plans using Model based Testing

Model Based Testing (MBT) is a popularly used software testing technique in the software industry. However, there still exists a gap between the awareness of benefits of MBT and its adoption in the industry, specifically in the Computer Aided Design (CAD) or Computer Aided Engineering (CAE) domains. This can be predominantly attributed to the learning curve of using many of the existing MBT tools. To address this gap in the CAD/CAE industry, we propose Pathfinder an MBT tool, with a Graphical User Interface (GUI), for guiding a software tester in generating test plans for a system-under-test (SUT). The goal of using Pathfinder is for obtaining consistency and reproducibility in the generated test plans across a team of software testers. Our tool introduces a novel representation of the SUT as a High-level Model (HLM), and the use of graph visualization for test plan generation from the HLM. We have designed the GUI to be intuitive for the tester to generate test plans and select relevant tests, which precedes the test execution done outside of our tool. Here, we discuss the design decisions we adopted towards creating Pathfinder, and demonstrates its usage with two case studies.
Re-ranking using compression-based distance measure for Content-based Commercial Product Image Retrieval

With the prevalence of E-Commerce sites such as eBay, Content-based Commercial Product Image Retrieval (CBCPIR) has become an emerging application-oriented field of Content-based Image Retrieval (CBIR). Though a number of traditional CBIR techniques and evaluation criterions have been applied directly or with minor modifications, they tend to neglect one critical factor that greatly affects user experience: users usually care about the exact ranks of the results, especially few top ones, which should share very high similarity with the query image. In this work, we propose a novel two-stage retrieval framework that uses a compression-based re-ranking method and a new subjective retrieval evaluation criterion to address such a problem. More specifically, we extend the state-of-art texture descriptor Campana-Keogh (CK) method from data mining in several aspects and validate the superiority of our framework via extensive experiments and real-world user feedback. We also make our code and CBCPIR dataset publicly available. The number of images of the latter is much larger than current freely accessible ones and better represents real-world commercial product images.
Refill-Based Medication Use Quality Measures in Kidney Transplant Recipients: Examination of Proportion of Days Covered and Medication Possession Ratio

BACKGROUND: The Pharmacy Quality Alliance’s definition of proportion of days covered (PDC) and medication possession ratio (MPR) have not been examined as potential quality measures in the kidney transplant recipient population. OBJECTIVES: To (a) describe the frequency distribution of MPR and PDC using mycophenolic acid products in a real-world kidney transplant recipient population and (b) evaluate associations between MPR and PDC with late (> 90 days after transplantation) biopsy-proven acute rejection (BPAR). METHODS: This was a retrospective cohort study combining data from the Wisconsin Allograft Recipient Database with University of Wisconsin (UW) Health Specialty Pharmacy prescription claims and dispensing data from March 10, 2006, to June 30, 2012. Patients who met criteria for persistence filling mycophenolic acid prescriptions at UW Health Specialty Pharmacy in the first year following discharge from kidney transplantation surgery hospitalization were included. Patients were excluded if they were enrolled in a clinical trial, if they had BPAR within 90 days of transplantation, or if they did not have panel reactive antibody data available. PDC and MPR were calculated over 360 days after discharge, and multivariable analyses were performed to determine if there were associations between PDC or MPR with late BPAR within 3 years. RESULTS: This study included 388 patients. The incidence of 3-year late BPAR was 5.1% (n = 20). Characteristics of patients who experienced late BPAR were largely consistent with those who did not experience late BPAR, with the exception of number of hospital readmissions, which was higher among patients who experienced late BPAR. The frequency distribution of PDC and MPR exhibited a skewed left distribution, with a median PDC of 0.972 and a median MPR of 1.000. Higher PDC was associated with lower odds of late BPAR (OR = 0.041, 95% CI = 0.004-0.417) in multivariable analysis, as was a higher MPR (OR = 0.041, 95% CI = 0.004-0.419). CONCLUSIONS: MPR and PDC may be calculated from data available to pharmacies and health plans, and each was associated with 3-year late BPAR among patients who did not experience early BPAR. However, the construct validity of these medication adherence measures requires further study.
Virtual reality support for teleoperation using online grasp planning

Classic telepresence approaches allow a human to interact with a remote or a virtual reality environment (VR) with force feedback. Coupling with a remote robot can be used to work in dangerous environments without the human being on-site. The coupling with a VR system can be used for training and verification of task sequences or robotic actions.training and verification of task sequences or robotic actions. We present an enhanced telepresence system that uses the advantages of VR to perform manipulation tasks in remote environments with multifingered hands.It provides the user with an intuitive interface that visualizes the knowledge of the robot about its environment; and the combination of VR, telepresence and shared autonomy facilitates object manipulation for the user.
Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages

Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.
Identifying auditory cortex encoding abnormalities in schizophrenia: The utility of low-frequency versus 40 Hz steady-state measures.

Magnetoencephalography (MEG) and EEG have identified poststimulus low frequency and 40 Hz steady-state auditory encoding abnormalities in schizophrenia (SZ). Negative findings have also appeared. To identify factors contributing to these inconsistencies, healthy control (HC) and SZ group differences were examined in MEG and EEG source space and EEG sensor space, with better group differentiation hypothesized for source than sensor measures given greater predictive utility for source measures. Fifty-five HC and 41 chronic SZ were presented 500 Hz sinusoidal stimuli modulated at 40 Hz during simultaneous whole-head MEG and EEG. MEG and EEG source models using left and right superior temporal gyrus (STG) dipoles estimated trial-to-trial phase similarity and percent change from prestimulus baseline. Group differences in poststimulus low-frequency activity and 40 Hz steady-state response were evaluated. Several EEG sensor analysis strategies were also examined. Poststimulus low-frequency group differences were observed across all methods. Given an age-related decrease in left STG 40 Hz steady-state activity in HC (HC > SZ), 40 Hz steady-state group differences were evident only in younger participants' source measures. Findings thus indicated that optimal data collection and analysis methods depend on the auditory encoding measure of interest. In addition, whereas results indicated that HC and SZ auditory encoding low-frequency group differences are generally comparable across modality and analysis strategy (and thus not dependent on obtaining construct-valid measures of left and right auditory cortex activity), 40 Hz steady-state group-difference findings are much more dependent on analysis strategy, with 40 Hz steady-state source-space findings providing the best group differentiation.
Impaired cohesion and homologous recombination during replicative aging in budding yeast

How does the genome become unstable during aging? The causal relationship between genomic instability and replicative aging is unclear. We reveal here that genomic instability at the budding yeast ribosomal DNA (rDNA) locus increases during aging, potentially due to the reduced cohesion that we uncovered during aging caused by the reduced abundance of multiple cohesin subunits, promoting increased global chromosomal instability. In agreement, cohesion is lost during aging at other chromosomal locations in addition to the rDNA, including centromeres. The genomic instability in old cells is exacerbated by a defect in DNA double-strand break (DSB) repair that we uncovered in old yeast. This was due to limiting levels of key homologous recombination proteins because overexpression of Rad51 or Mre11 reduced the accumulation of DSBs and largely restored DSB repair in old cells. We propose that increased rDNA instability and the reduced DSB repair capacity of old cells contribute to the progressive accumulation of global chromosomal DNA breaks, where exceeding a threshold of genomic DNA damage ends the replicative life span.
Event-level analyses of sex-risk and injection-risk behaviors among nonmedical prescription opioid users

ABSTRACT Background: Nonmedical prescription opioid use has been linked to hepatitis C virus (HCV) infection among people who inject drugs and with using high dead space syringes that retain more blood and transfer more HIV if shared. Little is known regarding its effects on sex-risk behaviors. Objectives: This paper examines event-level associations between nonmedical prescription opioid use and sharing high dead space syringes (injection risk) and unprotected intercourse (sex risk) behaviors. Methods: We recruited 1,985 participants from two overlapping risk groups—drug users and men who have sex with men (MSM)—and their sex partners. Participants completed an interview that included event-level sex questions with recent sex partners and injection questions with recent injection partners. We used multivariable generalized estimating equations (GEE) to assess the associations between nonmedical prescription opioid use and unprotected intercourse during sexual encounters and sharing syringes during injection episodes, while adjusting for within-person correlations. Results: When both partners used nonmedical prescription opioids, its use was independently associated with unprotected intercourse in sexual encounters (OR = 2.24; 95% CI = 1.12, 4.49). The use of nonmedical prescription opioids was also associated with sharing high dead space syringes during injection episodes (OR = 6.57; 95% CI = 1.63, 26.51). Conclusion: Nonmedical prescription opioid use is associated with an increase in the risk of unprotected sex and sharing high dead space syringes. HIV and HCV prevention interventions for nonmedical prescription opioid users should address sex-risk behaviors and encourage the use of acceptable low dead space needles and syringes.
Therapeutic Potential of Afatinib for Cancers with ERBB2 (HER2) Transmembrane Domain Mutations G660D and V659E.

We previously reported on a family with hereditary lung cancer, in which a germline mutation in the transmembrane domain (G660D) of avian erythroblastic leukemia viral oncogene homolog 2 (erb-b2 receptor tyrosine kinase 2) (ERBB2; human epidermal growth factor receptor 2 [HER2]) seemed to be responsible for the cancer predisposition. Although few data are available on treatment, anti-ERBB2 therapeutic agents may be effective for ERBB2-mutant cancers. The familial lung cancer patient in one of the authors' institutes developed bone metastasis with enlarging lung tumors and was treated with the ERBB2 inhibitor afatinib. We also encountered a patient with ampullary adenocarcinoma with ERBB2 G660D and S310F comutations in another institute of the authors', revealed by comprehensive genomic profiling. This patient was then treated with afatinib and also achieved transitory response. We also searched for ERBB2 transmembrane mutations in various types of cancers in PubMed, The Cancer Genome Atlas (TCGA), and the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) database. Besides our two cases, two patients with V659E mutations were found via PubMed. Three potential patients were found in TCGA. In addition, MSK-IMPACT allowed identification of three additional urothelial carcinomas with G660D mutations and two lung adenocarcinomas with V659E mutations. Our experience suggests that establishing a database of integrated information regarding the clinical genome and therapeutic outcome of patients with recurrent but less common mutations is essential to implement precision oncology. KEY POINTS Rare but targetable mutations such as avian erythroblastic leukemia viral oncogene homolog 2 (erb-b2 receptor tyrosine kinase 2) (ERBB2; human epidermal growth factor receptor 2 [HER2]) transmembrane domain (TMD) mutations can be detected by comprehensive genomic profiling.Afatinib may be effective for patients with cancer with ERBB2 (HER2) TMD mutations.In order to implement precision oncology, it is important to establish a database of integrated information regarding the clinical genomes and therapeutic outcomes of patients with recurrent but less common mutations.
On a learning curve for shared decision making: Interviews with clinicians using the knee osteoarthritis Option Grid

RATIONAL Tools used in clinical encounters to illustrate to patients the risks and benefits of treatment options have been shown to increase shared decision making. However, we do not have good information about how these tools are viewed by clinicians and how clinicians think patients would react to their use. OBJECTIVE Our aim was to examine clinicians' views about the possible and actual use of tools designed to support patients and clinicians to collaborate and deliberate about treatment options, namely, Option Grid decision aids. METHOD We conducted a thematic analysis of qualitative interviews embedded in the intervention phase of a trial of an Option Grid decision aid for osteoarthritis of the knee. Interviews were conducted with 6 participating clinicians before they used the tool and again after clinicians had used the tool with 6 patients. RESULTS In the first interview, clinicians voiced concerns that the tool would lead to an increase in encounter duration, patient resistance regarding involvement in decision making, and potential information overload. At the second interview, after minimal training, the clinicians reported that the tool had changed their usual way of communicating, and it was generally acceptable and helpful to integrate it into practice. DISCUSSION AND CONCLUSIONS After experiencing the use of Option Grids, clinicians became more willing to use the tools in their clinical encounters with patients. How best to introduce Option Grids to clinicians and adopt their use into practice will need careful consideration of context, workflow, and clinical pathways.