Miracle-dz/UniFAR-FTUs huggingface dataset:
LncRNA PVT1 promotes exosome secretion through YKT6, RAB7, and VAMP3 in pancreatic cancer

Pancreatic cancer (PC) is one of the deadliest cancers worldwide. Cancer cells secrete excessive numbers of exosomes that play essential roles in tumorigenesis. Long non-coding RNAs (lncRNAs) are essential non-coding RNAs for cancer progression. However, the role of lncRNA plasmacytoma variant translocation 1 (PVT1) in exosome secretion of PC remains to be comprehensively investigated. Thus, nanoparticle tracking analysis and transmission electron microscopy were performed to determine exosome secretion. Confocal microscopy, western blots, real-time PCR, immunofluorescence, pull-down and RNA immunoprecipitation assays, and rescue experiments were applied to investigate the mechanism underlying the role of PVT1 in exosome secretion. The results showed that PVT1 was upregulated in PC cells, along with increased levels of YKT6 v-SNARE homolog (YKT6), ras-related protein Rab-7 (RAB7), and vesicle-associated membrane protein 3 (VAMP3). Also, PVT1 promoted the transportation of multivesicular bodies (MVBs) towards the plasma membrane. In addition, PVT1 promoted the docking of MVBs by altering RAB7 expression and localization. Moreover, PVT1 promoted the fusion of MVBs with the plasma membrane through regulating YKT6 and VAMP3 colocalization and the palmitoylation of YKT6. Taken together, the results suggest that PVT1 promoted exosome secretion of PC cells and thus, can expand the understanding of PVT1 in tumor biology.
Investigation of novel indole-based HIV-1 protease inhibitors using virtual screening and text mining

Abstract Human immunodeficiency virus type 1 protease (HIV-1 PR) inhibitors have been used as possible therapeutic agents for HIV-1 infection in clinical study. Most of the HIV therapy-related problems usually stem from long-term opioid usage. The rapid development of drug-resistant variants limits the long-term effectiveness of current inhibitors as therapeutic agents. In addition, different side effects were reported. Further drug development is required to design new compounds which have similar efficacy as the drugs currently used in HIV infection but without having undesirable side effects. Indole derivatives were considered as one of the effective HIV inhibitors. Indole is an important fragment used in many FDAapproved medicines and used in various diseases. For this purpose, in this study the molecules containing” indole” keywords in their fragments are taken from the Specs-SC database which includes 212520 small molecules. 5194 molecules that include indole keywords are selected. These selected molecules are then screened against HIV-1 PR target protein using molecular docking simulations. Then the molecules are ranked according to the their docking scores. Top docking poses of ten ligands and FDA approved drug Amprenavir are subjected to 100 ns Molecular Dynamics (MD) simulations. Thus, by using combination of text mining and integrated molecular modeling approaches, we identified novel indole-based hits against HIV-1 PR. Communicated by Ramaswamy H. Sarma
Leadership Perceptions and Practices of Hospitality in Senior Care

Senior care providers are increasingly focused on hospitality to distinguish themselves from competitors. A mixed-methods approach was used to examine perceptions of hospitality from leadership (i.e., administrators of nursing homes and assisted living facilities) and use of hospitality practices across settings and lines of service. Results indicated that hospitality practices readily exist in senior care settings (i.e., nursing homes, assisted living facilities), but may be referred to by names other than hospitality. There also appear to be more similarities than differences in practices across long-term care service lines (i.e., short- and long-stay nursing home residents, assisted living), suggesting that, regardless of provider type, hospitality in senior care is becoming part of the expected culture and cadre of services for residents. Overall, findings suggest hospitality practices are related to providers’ census, payer mix, and organizational performance.
Shock wave impact on the viability of MDA-MB-231 cells

Shock waves are gaining interests in biological and medical applications. In this work, we investigated the mechanical characteristics of shock waves that affect cell viability. In vitro testing was conducted using the metastatic breast epithelial cell line MDA-MB-231. Shock waves were generated using a high-power pulse laser. Two different coating materials and different laser energy levels were used to vary the peak pressure, decay time, and the strength of subsequent peaks of the shock waves. Within the testing capability of the current study, it is shown that shock waves with a higher impulse led to lower cell viability, a higher detached cell ratio, and a higher cell death ratio, while shock waves with the same peak pressure could lead to different levels of cell damage. The results also showed that the detached cells had a higher cell death ratio compared to the attached cells. Moreover, a critical shock impulse of 5 Pa·s was found to cause the cell death ratio of the detached cells to exceed 50%. This work has demonstrated that, within the testing range shown here, the impulse, rather than the peak pressure, is the governing shock wave parameter for the damage of MDA-MB-231 breast cancer cells. The result suggests that a lower-pressure shock wave with a longer duration, or multiple sequential low amplitude shock waves can be applied over a duration shorter than the fundamental response period of the cells to achieve the same impact as shock waves with a high peak pressure but a short duration. The finding that cell viability is better correlated with shock impulse rather than peak pressure has potential significant implications on how shock waves should be tailored for cancer treatments, enhanced drug delivery, and diagnostic techniques to maximize efficacy while minimizing potential side effects.
A Novel Retrovirus (Gunnison’s Prairie Dog Retrovirus) Associated With Thymic Lymphoma in Gunnison’s Prairie Dogs in Colorado, USA

As part of research and wildlife disease surveillance efforts, we performed necropsy examinations of 125 free-ranging (n = 114) and captive (n = 11) prairie dogs in Colorado from 2009 to 2017. From these cases, we identified three cases of thymic lymphoma in free-ranging Gunnison’s prairie dogs (Cynomys gunnisoni), and we identified a novel retroviral sequence associated with these tumors. The viral sequence is 7700 nucleotides in length and exhibits a genetic organization that is consistent with the characteristics of a type D betaretrovirus. The proposed name of this virus is Gunnison’s prairie dog retrovirus (GPDRV). We screened all 125 prairie dogs for the presence of GPDRV using PCR with envelope-specific primers and DNA extracted from spleen samples. Samples were from Gunnison’s prairie dogs (n = 59), black-tailed prairie dogs (Cynomys ludovicianus) (n = 40), and white-tailed prairie dogs (Cynomys leucurus) (n = 26). We identified GPDRV in a total of 7/125 (5.6%) samples including all three of the prairie dogs with thymic lymphoma, as well as spleen from an additional four Gunnison’s prairie dogs with no tumors recognized at necropsy. None of the GPDRV-negative Gunnison’s prairie dogs had thymic lymphomas. We also identified a related, apparently endogenous retroviral sequence in all prairie dog samples. These results suggest that GPDRV infection may lead to development of thymic lymphoma in Gunnison’s prairie dogs.
A High-Throughput System for Cyclic Stretching of Precision-Cut Lung Slices During Acute Cigarette Smoke Extract Exposure

Rationale Precision-cut lung slices (PCLSs) are a valuable tool in studying tissue responses to an acute exposure; however, cyclic stretching may be necessary to recapitulate physiologic, tidal breathing conditions. Objectives To develop a multi-well stretcher and characterize the PCLS response following acute exposure to cigarette smoke extract (CSE). Methods A 12-well stretching device was designed, built, and calibrated. PCLS were obtained from male Sprague-Dawley rats (N = 10) and assigned to one of three groups: 0% (unstretched), 5% peak-to-peak amplitude (low-stretch), and 5% peak-to-peak amplitude superimposed on 10% static stretch (high-stretch). Lung slices were cyclically stretched for 12 h with or without CSE in the media. Levels of Interleukin-1β (IL-1β), matrix metalloproteinase (MMP)-1 and its tissue inhibitor (TIMP1), and membrane type-MMP (MT1-MMP) were assessed via western blot from tissue homogenate. Results The stretcher system produced nearly identical normal Lagrangian strains (Exx and Eyy, p > 0.999) with negligible shear strain (Exy < 0.0005) and low intra-well variability 0.127 ± 0.073%. CSE dose response curve was well characterized by a four-parameter logistic model (R2 = 0.893), yielding an IC50 value of 0.018 cig/mL. Cyclic stretching for 12 h did not decrease PCLS viability. Two-way ANOVA detected a significant interaction between CSE and stretch pattern for IL-1β (p = 0.017), MMP-1, TIMP1, and MT1-MMP (p < 0.001). Conclusion This platform is capable of high-throughput testing of an acute exposure under tightly-regulated, cyclic stretching conditions. We conclude that the acute mechano-inflammatory response to CSE exhibits complex, stretch-dependence in the PCLS.
Cytotoxicity of IFN-γ and TNF-α for Vascular Endothelial Cell Is Mediated by Nitric Oxide☆

Abstract Endothelial cell injury is a critical event in tissue damage accompanying inflammation, in which both inflammatory cytokines and reactive oxygen species may play pivotal roles, although the exact mechanism has not yet been clarified. We found that combined stimulation with interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α) induced both cytotoxicity to murine vascular endothelial cell line F-2 and an increase in nitric oxide (NO). Therefore, in the present study, the implication of NO in cytotoxicity was examined. A potent iNOS-specific inhibitor ONO-1714 completely blocked both cytokine-induced cytotoxicity and NO production. NO scavengers such as carboxy-PTIO and hemoglobin blocked cytotoxicity. Moreover, exogenous NO from NOC 18 also caused cytotoxicity. These results together demonstrated that cytotoxicity of IFN-γ and TNF-α for endothelial cell F-2 was mediated by NO, suggesting a pathogenic role of cytokine-induced NO production in endothelial damage under inflammatory conditions.
Bootstrapping and Plug-and-Play Operations on Software Defined Networks: A Case Study on Self-configuration using the SONAr Architecture

The autonomous network concept has gained strength with the growing complexity of the current networks, especially after the definition of 5G requirements and their key performance indicators. This concept is challenging to implement in legacy networks, and it has become feasible with the emergence of network softwarization, which enables the deployment of functionalities through a logically centralized control plane abstraction. The network softwarization simplifies the management process, reduces operational costs (OPEX), enhances protection against failures, and enables complex requirements such as high-performance indicators and IoT support. The Self-Organizing Networks Architecture (SONAr) project uses cutting-edge technologies and concepts such as SDN, NFV, and Machine Learning. It proposes a new architecture aimed at the design of self-management in computer networks, oriented by declarative intents. In this work, we introduce the SONAr project by describing its components and specifications. We also present a case study that shows the self-configuration property that includes bootstrapping and plug-and-play operations using SONAr components focusing on strategies applicable to OpenFlow based networks. We explain the decisions made in the implementation and present comparative results between them.
Draft Genome Sequence of the Astaxanthin-Producing Microalga Haematococcus lacustris Strain NIES-144

Haematococcus lacustris is an industrially important eukaryotic microalga that is thought to be a great source of natural astaxanthin with strong antioxidant activity. Here, we report the draft assembly and annotation results of the genome of H. lacustris NIES-144. These data will expand our knowledge of the molecular biological features of this microalga. ABSTRACT Haematococcus lacustris is an industrially important eukaryotic microalga that is thought to be a great source of natural astaxanthin with strong antioxidant activity. Here, we report the draft assembly and annotation results of the genome of H. lacustris NIES-144. These data will expand our knowledge of the molecular biological features of this microalga.
Cell-of-Origin Subtyping of Diffuse Large B-Cell Lymphoma by Using a qPCR-based Gene Expression Assay on Formalin-Fixed Paraffin-Embedded Tissues

The well-established cell-of-origin (COO) algorithm categorizes diffuse large B-cell lymphoma (DLBCL) into activated B-cell-like (ABC) and germinal center B-cell-like (GCB) subgroups through gene expression profiling. We aimed to develop and validate a qPCR-based gene expression assay to determine the COO subgroups of DLBCL with formalin-fixed paraffin-embedded (FFPE) tissue. We first established a DLBCL transcriptome database of 1,016 samples retrieved from three published datasets (GSE10846, GSE22470, and GSE31312). With this database, we identified a qPCR-based 32-gene expression signature (DLBCL-COO assay) that is significantly associated with the COO subgroups. The DLBCL-COO assay was further validated in a cohort of 160 Chinese DLBCL patients. Biopsy samples from DLBCL patients with paired FFPE and fresh frozen tissue were collected to assign COO subtypes based on the immunohistochemistry (IHC) algorithm (Han's algorithm), DLBCL-COO assay, and global gene expression profiling with RNA-seq. For 111 paired FFPE and fresh DLBCL samples, the concordance between the IHC, qPCR, and RNA-seq methods was 77.5% and 91.9%, respectively. The DLBCL-COO assay demonstrated a significantly superior concordance of COO determination with the “gold standard” RNA-seq compared with the IHC assignment with Han's algorithm (P = 0.005). Furthermore, the overall survival of GCB patients defined by the DLBCL-COO assay was significantly superior to that of ABC patients (P = 0.023). This effect was not seen when the tumors were classified by the IHC algorithm. The DLBCL-COO assay provides flexibility and accuracy in DLBCL subtype characterization. These findings demonstrated that the DLBCL-COO assay might serve as a useful tool for guiding prognostic and therapeutic options for DLBCL patients.
Performance Analysis of Continuous Binary Data Processing using Distributed Databases within Stream Processing Environments

: Big data applications must process increasingly large amounts of data within ever shorter time. Often a stream processing engine (SPE) is used to process incoming data with minimal latency. While these engines are designed to process data quickly, they are not made to persist and manage it. Thus, databases are still integrated into streaming architectures, which often becomes a performance bottleneck. To overcome this issue and achieve maximum performance, all system components used must be examined in terms of their throughput and latency, and how well they interact with each other. Several authors have already analyzed the performance of popular distributed database systems. While doing so, we focus on the interaction between the SPEs and the databases, as we assume that stream processing leads to changes in the access patterns to the databases. Moreover, our main focus is on the efﬁcient storing and loading of binary data objects rather than typed data, since in our use cases the actual data analysis is not to be performed by the database, but by the SPE. We’ve benchmarked common databases within streaming environments to determine which software combination is best suited for these requirements. Our results show that the database performance differs signiﬁcantly depending on the access pattern used and that different software combinations lead to substantial performance differences. Depending on the access pattern, Cassandra, MongoDB and PostgreSQL achieved the best throughputs, which were mostly the highest when Apache Flink was used.
Assessing an evidence-based intervention for spouse caregivers of persons with Alzheimer’s disease: results of a community implementation of the NYUCI in Israel

Abstract Objectives Alzheimer’s disease (AD) affects not only the person with the illness, but family caregivers as well. The NYU Caregiver Intervention (NYUCI), a psychosocial intervention which has demonstrated both short and long-term benefits for caregivers, has been used widely in the United States and in Australia and England. The Israeli study was a hybrid between a community implementation study and a randomized controlled trial (RCT) of the NYUCI in a non-English speaking country. Method A sample of 100 spouse caregivers participated in trial comparing the NYUCI provided by ten Israeli clinicians (enhanced care), to support group participation (usual care). The major outcome of interest was caregiver depressive symptoms, measured with the Geriatric Depression Scale. A linear random effects regression model controlling for factors associated with depressive symptoms was used to plot the longitudinal trajectories of depressive symptoms over the two-year study period and compare outcomes for the enhanced care and control groups. Results One hundred spouse caregivers enrolled, of whom 81 provided data at baseline and at one or more post intervention assessments. The Israeli adaptation of the NYUCI was effective in reducing depressive symptoms reported by caregivers compared to their counterparts in the control group, b= −1.29 [95%CI (−2.43, −0.15)], p= . 0265. Conclusion While implementing a randomized controlled trial of an intervention developed and tested in traditional research settings using community providers in Israel, posed unique challenges, the study demonstrated benefits to caregivers. As a result, 30 municipalities in Israel are currently implementing an ongoing adaptation of the NYUCI.
Two-stream deep learning architecture for action recognition by using extremely low-resolution infrared thermopile arrays

This paper presents a new method for action recognition using an extremely low-resolution infrared imaging sensor. Thermopile arrays give users privacy but this comes at the price of limited information captured. The question of what methods are applicable to this sensor remains open. In our work, we adopt a two-stream deep learning architecture that accepts both spatial and temporal sequences, processes them based on CNN and stacked GRU layers separately, and finally fuses the features for action classification. To the best of our knowledge, this is the first optical-flow-based method used in combination with extremely low-resolution thermal image sequences. We use a dataset of 16 × 16 pixel image sequences introduced by a related work to directly compare the results and demonstrate the superiority of our method. Experiments show that we are able to achieve a gain of nearly 6% (96.98% vs. 91.07%) in recognition accuracy in 5-classes setup classification.
Examination of group head angle acceleration analysis method for learning evaluation in outdoor education

In the field of outdoor education, learning evaluation is a challenge, as the conventional method, which is subjective evaluation, can be inaccurate. This study attempts to overcome this challenge by evaluating learning using motion sensors. Considering that the moment when a learner moves his or her head during a lecture encompasses important information related to concentration, we measure the concentration of the learner using the angular velocity information of his or her head. However, it is not clear based on the information obtained from only one learner whether the cause of the movement is actually a change in his or her concentration level. Therefore, we propose a method for distinguishing the concentration of learners by comparing head movements in the entire learning group. To confirm the effectiveness of the proposed method, we measured the angular velocity of the learners’ heads in outdoor education by attaching an angular velocity sensor to them. In the lecture-induced gaze direction, the head movement timing of many learners coincided after gaze induction timing. In addition, we found that the learners with higher levels of concentration did not move their heads, except at the time of gaze induction.
Multiple paternity in clutches of snapping turtles (Chelydra serpentina) detected using DNA fingerprints

Female common snapping turtles (Chelydra serpentina) are capable of storing viable sperm for at least several months and are likely to be inseminated by more than one male. Consequently, we tested the hypothesis that multiple paternity occurred within individual clutches of three common snapping turtles from Algonquin Provincial Park, Ontario, Canada, by examining DNA fingerprints. Positive evidence of multiple paternity was detected among samples of offspring from two of the three clutches. In these clutches, the distributions of both paternal DNA fingerprint bands and band-sharing coefficients deviated from those expected under the assumption of a single father, suggesting that paternity was distributed between two or more males in each clutch. Multiple paternity and the ability of females to store sperm make turtles good animals in which to study sperm competition. The mating systems and life-history features of turtles should be studied with the consequences of sperm storage and multiple paternity in .
Diversity and abnormalities of cyclopoid copepods around hydrothermal vent fluids, Kueishantao Island, north-eastern Taiwan

The diversity and abundance of cyclopoid copepods were investigated at four stations along the hydrothermal vent at Kueishantao Island, north-eastern Taiwan. Zooplankton samples were collected by surface tows. Qualitatively, 21 species of cyclopoids belonging to five genera and three families were observed. Our analysis revealed a number of abnormal protrusions (TLAs) on cyclopoid copepods, which were more frequent on the dorsal body surface and in members of the family Corycaeidae. The number of TLAs was highest at the hydrothermal vent plume (HVP) zone and among adult copepods. The potentially high levels of toxic minerals erupting from the hydrothermal vents as well as low pH and high temperatures may weaken the copepods' exoskeletons, thereby increasing susceptibility to infections, indicated by the HVP-related increase of tumoural processes. It is suggested that some of these abnormalities are related to the occurrence of symbiotic tantulocarids, a topic yet to be studied in this interesting environment.
Analysis of Tools for REST Contract Specification in Swagger/OpenAPI

REST is a resource-based architectural style that has emerged as a promising way for designing Web services. A REST API exposes services’ functionalities through a contract that allows consumption by different clients. The contract specifies service’s request and response schemes and related rules the service and the client should comply with. The process of documenting and keeping an API consistent is a time consuming human effort. The documentation should reflect the implementation which may evolve. This work compares different tools for REST APIs specifications. We focused on tools that automatically generate Swagger (Open API in version 3.0), a specification for designing REST APIs. We evaluated the tools using a set of criteria whose results may help software engineers to choose the most appropriate tool, and point out gaps for research initiatives.