Miracle-dz/UniFAR-FTUs huggingface dataset:
What “The Cancer Genome Atlas” database tells us about the role of ATP-binding cassette (ABC) proteins in chemoresistance to anticancer drugs

ABSTRACT Introduction: Chemotherapy remains the only option for advanced cancer patients when other alternatives are not feasible. Nevertheless, the success rate of this type of therapy is often low due to intrinsic or acquired mechanisms of chemoresistance. Among them, drug extrusion from cancer cells through ATP-binding cassette (ABC) proteins plays an important role. ABC pumps are primary active transporters involved in the barrier and secretory functions of many healthy cells. Areas covered: In this review, we have used The Cancer Genome Atlas (TCGA) database to explore the relationship between the expression of the major ABC proteins involved in cancer chemoresistance in the most common types of cancer, and the drugs used in the treatment of these tumors that are substrates of these pumps. Expert opinion: From unicellular organisms to humans, several ABC proteins play a major role in detoxification processes. Cancer cells exploit this ability to protect themselves from cytostatic drugs. Among the ABC pumps, MDR1, MRPs and BCRP are able to export many antitumor drugs and are expressed in several types of cancer, and further up-regulated during treatment. This event results in the enhanced ability of tumor cells to reduce intracellular drug concentrations and hence the pharmacological effect of chemotherapy.
Ovarian cancer and the evolution of subtype classifications using transcriptional profiling†

Abstract Ovarian cancer is a complex disease with multiple subtypes, each having distinct histopathologies and variable responses to treatment. This review highlights the technological milestones and the studies that have applied them to change our definitions of ovarian cancer. Over the past 50 years, technologies such as microarrays and next-generation sequencing have led to the discovery of molecular alterations that define each of the ovarian cancer subtypes and has enabled further subclassification of the most common subtype, high-grade serous ovarian cancer (HGSOC). Improvements in mutational profiling have provided valuable insight, such as the ubiquity of TP53 mutations in HGSOC tumors. However, the information derived from these technological advances has also revealed the immense heterogeneity of this disease, from variation between patients to compositional differences within single masses. In looking forward, the emerging technologies for single-cell and spatially resolved transcriptomics will allow us to better understand the cellular composition and structure of tumors and how these contribute to the molecular subtypes. Attempts to incorporate the complexities ovarian cancer has resulted in increasing sophistication of model systems, and the increased precision in molecular profiling of ovarian cancers has already led to the introduction of inhibitors of poly (ADP-ribose) polymerases as a new class of treatments for ovarian cancer with DNA repair deficiencies. Future endeavors to define increasingly accurate classification strategies for ovarian cancer subtypes will allow for confident prediction of disease progression and provide important insight into potentially targetable molecular mechanisms specific to each subtype. Summary Sentence Advances in technologies to define the transcriptional profile of ovarian cancers has resulted in continuing evolution of subtype classification, improvements in preclinical animal models and a greater appreciation for the complexity of these tumors.
Evolution of UHF Body Imaging in the Human Torso at 7T

Abstract The potential value of ultrahigh field (UHF) magnetic resonance imaging (MRI) and spectroscopy to biomedical research and in clinical applications drives the development of technologies to overcome its many challenges. The increased difficulties of imaging the human torso compared with the head include its overall size, the dimensions and location of its anatomic targets, the increased prevalence and magnitude of physiologic effects, the limited availability of tailored RF coils, and the necessary transmit chain hardware. Tackling these issues involves addressing notoriously inhomogeneous transmit B1 (B1+) fields, limitations in peak B1+, larger spatial variations of the static magnetic field B0, and patient safety issues related to implants and local RF power deposition. However, as research institutions and vendors continue to innovate, the potential gains are beginning to be realized. Solutions overcoming the unique challenges associated with imaging the human torso are reviewed as are current studies capitalizing on the benefits of UHF in several anatomies and applications. As the field progresses, strategies associated with the RF system architecture, calibration methods, RF pulse optimization, and power monitoring need to be further integrated into the MRI systems making what are currently complex processes more streamlined. Meanwhile, the UHF MRI community must seize the opportunity to build upon what have been so far proof of principle and feasibility studies and begin to further explore the true impact in both research and the clinic.
CROSS-PROPERTY CONNECTION BETWEEN HEAT AND FORCE NETWORKS IN THERMALLY-ASSISTED COMPACTION OF GRANULAR MATERIALS

Gülşad Küçük, Marcial Gonzalez and Alberto M. Cuitiño 3 1Department of Mechanical and Aerospace Engineering, Rutgers University, Piscataway, NJ, 08854, USA, gulsad@gmail.com 2School of Mechanical Engineering Purdue University 585 Purdue Mall West Lafayette, IN 47907-2088, marcialgonzalez@purdue.edu 3Department of Mechanical and Aerospace Engineering, Rutgers University, Piscataway, NJ, 08854, USA, cuitino@jove.rutgers. edu
Diagnosis of Papillary Breast Lesions on Core Needle Biopsy: Upgrade Rates and Interobserver Variability

The histologic distinction between papillary breast lesions remains challenging, especially with core biopsy (CB) specimens. A retrospective review of the clinical, imaging, and histologic findings was performed for patients with papillary breast lesions on CB from 2013 to 2017. The interpretation accuracy was expressed as upgrade rate relative to the excision diagnosis. Diagnostic reproducibility with and without immunohistochemistry was analyzed as interobserver variability among 3 board-certified pathologists. Among 57 papillary lesions with biopsies and excisions available for review, the upgrade rates were 0% for benign papilloma, 30% for papilloma with atypical ductal hyperplasia, and 25% for papilloma with ductal carcinoma in situ, resulting in an overall upgrade rate of 11.1%. There were no statistical differences between patients in an upgrade group and others, when comparing the patient age, clinical presentation, BI-RADS (Breast Imaging Reporting and Database System) category, location, and histologic grade. The overall interobserver variability of the 60 consecutive core biopsies of papillary breast lesions by morphology alone was in the “substantial” agreement range (κ = 0.79, 86% agreement), with an excellent κ score of 0.88 for papilloma (92% agreement). “Substantial” and “fair” κ values were seen for papilloma with atypical ductal hyperplasia/ductal carcinoma in situ (0.74, 84% agreement) and invasive carcinoma (0.40, 60% agreement). Use of immunohistochemical stains improved the κ values into “excellent” range (0.92, 94% agreement). Our study favors a conservative approach in the management of benign papillomas, at least in cases of good radiologic-pathologic concordance. Papillary breast lesions with atypia/malignancy show lower diagnostic reproducibility on CB, and utility of immunohistochemistry is recommended in challenging cases.
Risk of Lameness in Dairy Cows with Paratuberculosis Infection

Simple Summary Johne’s disease (JD) is an important disease affecting cows in the UK dairy industry, as is lameness, and both cause milk production losses and cows losing weight. The aim of this work was to see if cows with JD were more likely to be lame and if so, what the order of occurrence of these two events is. We looked at the JD and lameness records of two farms and paired 98 JD cows (half of them with a high response to the test for JD) and compared them with herd mates. We evaluated the timing and the proportion of lameness in JD-positive cows compared to their controls and proportion of lameness before and after the first JD-positive test. JD cows turn lame on average three months earlier and are lame 2.7 times more often than non-JD cows. Further, high positive cows were 2.8 times more likely to develop lameness after JD diagnosis compared to medium positive cows. Results of this study suggest that there is a link between JD and lameness and that JD precedes lameness. The underlying mechanisms for this association remain unknown and were not the scope of this study. Abstract Johne’s disease (JD) is an important disease affecting the UK dairy industry, as is cattle lameness. An association between JD and lameness has been suggested; however, little evidence exists to support this. The purpose of this study was to determine if cows affected by JD were more likely to be lame and if so, what the temporal association is. Retrospective dairy cow mobility and JD status (based on milk ELISA) data were obtained from two farms of 98 JD cows (49 high and 49 medium positive) and their matched controls. We evaluated the timing and the proportion of (chronic) lameness in JD-positive cows versus controls and proportion of lameness before and after the first ELISA positive test. Compared to their controls, JD cows are lame more often (Odds Ratio = 2.7 (95% Confidence Interval = 1.2–6.0) p = 0.017) and became lame on average three months earlier (p = 0.010). High positive cows were more likely to develop lameness after seroconversion (OR = 2.8 (95% CI = 1.1–7.5), p = 0.038) versus medium positive cows. Results of this study suggest that there is a link between JD and lameness and that JD precedes lameness. The underlying mechanisms for this association remain unknown and were not the scope of this study.
Advances in the development and application of an open source model server for building information

The need for Building Information Model (BIM) servers to facilitate collaboration has been repeatedly reported in literature and stated by industry practitioners. To date, only a few commercial implementations of model servers are available. However, these applications are either limited to vendorspecific, proprietary data models or their complexity and pricing structure imposes a considerable threshold to their adoption by SMEs. The academic, standardization and development communities suffer a lack of open platforms that allows the integration and evaluation of research results and prototypes in a larger context. Although promising efforts aiming the creation of free and open platforms for a larger audience have been made in the past (Kiviniemi et al, 2005), none of these initiatives is still in existence to date. In this paper we report on the progress of the bimserver.org project, a collective effort to create a software framework that serves both as an open, low-cost entry into collaboration using shared building models for SMEs and as a test bed for research and development. We introduce conceptual, methodological and implementation specific advancements that have been made compared to earlier publications. Based on a series of interviews and a survey we report on user experiences that have been made by a diverse audience of architectural, engineering, project management companies as well as educational projects in academic environments and third party developers. A discussion of future research and development directions concludes this paper. Among these prospective additions to the framework are customizations and tailored solutions of external parties that use the open nature of the platform to suit their specific needs.
Adsorption of Adenine and Thymine and Their Radicals on Single-Wall Carbon Nanotubes

The adsorption of adenine, thymine, and their radicals on the surfaces of metallic and semiconducting single-wall carbon nanotubes are studied by local density approximation within density functional theory. The energies and equilibrium distances for several configurations are obtained after relaxation of the entire system. The changes of the molecular bonds and angles before and after adsorption are also calculated. We find that all molecules are physisorbed due to the interaction of their π-orbitals and the π-orbitals of the nanotubes. The electronic structure of both metallic and semiconducting nanotubes is not changed significantly upon adsorption, and thus only small changes in the carbon nanotube properties are expected. The results from these studies can be used as a model of DNA interaction with the surfaces of carbon nanotubes.
Exploring the Functional and Geometric Bias of Spatial Relations Using Neural Language Models

The challenge for computational models of spatial descriptions for situated dialogue systems is the integration of information from different modalities. The semantics of spatial descriptions are grounded in at least two sources of information: (i) a geometric representation of space and (ii) the functional interaction of related objects that. We train several neural language models on descriptions of scenes from a dataset of image captions and examine whether the functional or geometric bias of spatial descriptions reported in the literature is reflected in the estimated perplexity of these models. The results of these experiments have implications for the creation of models of spatial lexical semantics for human-robot dialogue systems. Furthermore, they also provide an insight into the kinds of the semantic knowledge captured by neural language models trained on spatial descriptions, which has implications for image captioning systems.
Vehicle Rebalancing for Mobility-on-Demand Systems with Ride-Sharing

Recent developments in Mobility-on-Demand (MoD) systems have demonstrated the potential of road vehicles as an efficient mode of urban transportation Newly developed algorithms can compute vehicle routes in real-time for batches of requests and allow for multiple requests to share vehicles. These algorithms have primarily focused on optimally producing vehicle schedules to pick up and drop off requests. The redistribution of idle vehicles to areas of high demand, known as rebalancing, on the contrary has received little attention in the context of ride-sharing. In this paper, we present a method to rebalance idle vehicles in a ride-sharing enabled MoD fleet. This method consists of an algorithm to optimally partition the fleet operating area into rebalancing regions, an algorithm to determine a real-time demand estimate for every region using incoming requests, and an algorithm to optimize the assignment of idle vehicles to these rebalancing regions using an integer linear program. Evaluation with historical taxi data from Manhattan shows that we can service 99.8% of taxi requests in Manhattan using 3000 vehicles with an average waiting time of 57.4 seconds and an average in-car delay of 13.7 seconds. Moreover, we can achieve a higher service rate using 2000 vehicles than prior work achieved with 3000. Furthermore, with a fleet of 3000 vehicles, we reduce the average travel delay by 86%, the average waiting time by 37%, and the amount of ignored requests by 95% compared to earlier work at the expense of an increased distance travelled by the fleet.
Sex differences in neonatal mouse brain injury after hypoxia‐ischemia and adaptaquin treatment

Hypoxia‐inducible factor prolyl 4‐hydroxylases (HIF‐PHDs) are important targets against oxidative stress. We hypothesized that inhibition HIF‐PHD by adaptaquin reduces hypoxic‐ischemic brain injury in a neonatal mouse model. The pups were treated intraperitoneally immediately with adaptaquin after hypoxia‐ischemia (HI) and then every 24 h for 3 days. Adaptaquin treatment reduced infarction volume by an average of 26.3% at 72 h after HI compared to vehicle alone, and this reduction was more pronounced in males (34.8%) than in females (11.7%). The protection was also more pronounced in the cortex. The subcortical white matter injury as measured by tissue loss volume was reduced by 24.4% in the adaptaquin treatment group, and this reduction was also more pronounced in males (28.4%) than in females (18.9%). Cell death was decreased in the cortex as indicated by Fluoro‐Jade labeling, but not in other brain regions with adaptaquin treatment. Furthermore, in the brain injury area, adaptaquin did not alter the number of cells positive for caspase‐3 activation or translocation of apoptosis‐inducing factor to the nuclei. Adaptaquin treatment increased glutathione peroxidase 4 mRNA expression in the cortex but had no impact on 3‐nitrotyrosine, 8‐hydroxy‐2 deoxyguanosine, or malondialdehyde production. Hif1α mRNA expression increased after HI, and adaptaquin treatment also stimulated Hif1α mRNA expression, which was also more pronounced in males than in females. However, nuclear translocation of HIF1α protein was decreased after HI, and adaptaquin treatment had no influence on HIF1α expression in the nucleus. These findings demonstrate that adaptaquin treatment is neuroprotective, but the potential mechanisms need further investigation.
ProvSQL: Provenance and Probability Management in PostgreSQL

This demonstration showcases ProvSQL, an open-source module for the PostgreSQL database management system that adds support for computation of provenance and probabilities of query results. A large range of provenance formalisms are supported, including all those captured by provenance semirings, provenance semirings with monus, as well as where-provenance. Probabilistic query evaluation is made possible through the use of knowledge compilation tools, in addition to standard approaches such as enumeration of possible worlds and Monte-Carlo sampling. ProvSQL supports a large subset of non-aggregate SQL queries.
Effects of Back Massages on Stress Observed in Students Preparing for the National License Examination

We measured serum level of cortisol and lactate, the stiffness of trapezius, skin blood flow and VAS before and after the back massages of 25 senior college students, who had sent stressful days for 11 months starting from April, preparing for the national license examination. These students usually had complaints of stiffness of shoulder and/or lumber. Back massages significantly reduced the level of serum cortisol from 8.85 ± 0.78 to 5.95 ± 0.68 μg/dl, without affecting that of lactate. The treatment also improved the stiffness of the trapezius of students with complaints from 63.24 ± 0.78 to 59.12 ± 0.78 after the treatment without affecting skin blood flow (SKBF). In addition, back massages reduced the VAS value at the same time. These results indicate that back massages of the student are effective to improve the physical and psychological conditions of the students.
A multi-targeting natural compound with growth inhibitory and anti-angiogenic properties re-sensitizes chemotherapy resistant cancer

Targeted therapies have become the focus of much of the cancer therapy research conducted in the United States. While these therapies have made vast improvements in the treatment of cancer, their results have been somewhat disappointing due to acquired resistances, high cost, and limited populations of susceptible patients. As a result, targeted therapeutics are often combined with other targeted therapeutics or chemotherapies. Compounds which target more than one cancer related pathway are rare, but have the potential to synergize multiple components of therapeutic cocktails. Natural products, as opposed to targeted therapies, typically interact with multiple cellular targets simultaneously, making them a potential source of synergistic cancer treatments. In this study, a rare natural product, deacetylnemorone, was shown to inhibit cell growth in a broad spectrum of cancer cell lines, selectively induce cell death in melanoma cells, and inhibit angiogenesis and invasion. Combined, these results demonstrate that deacetylnemorone affects multiple cancer-related targets associated with tumor growth, drug resistance, and metastasis. Thus, the multi-targeting natural product, deacetylnemorone, has the potential to enhance the efficacy of current cancer treatments as well as reduce commonly acquired treatment resistance.
Using Linked Library Data in Working Research Notes

We describe how we are experimenting with using linked library data to connect the organizational infrastructures of libraries, archives, and special collections with those of researchers who use them. The site of this experimentation is Editors’ Notes, an open-source hosted service for organizing the library and archives-based research of documentary editors. We report on an initial trial of incorporating linked data from libraries and other sources into Editors’ Notes, and describe how that trial has informed our current effort to usefully exploit linked data to benefit researchers. We conclude with an overview of the potential benefits.
Supplementary Material : Retrospective Encoders for Video Summarization

Shot boundaries detection As mentioned in section 3 and 4 of the main text, when B is not given (which is the case in the datasets [5, 14, 16] in our experiments), we learn a shot-boundary detection model to infer the boundaries of the shots. In this paper, shot boundaries for each video are predicted by a pre-trained LSTM. By thresholding the predicted confidence for each frame, we get the shot boundaries for each video. The optimal shot boundaries are determined by the summarization performance on the validation set. The average shot durations are 45, 75, and 35 frames for SumMe, TVSum, and VTW respectively. This is also consistent with the prior knowledge that videos of TVSum are much longer than ones of the other two datasets.
RACK: a time-based fast loss detection algorithm for TCP

This document presents a new TCP loss detection algorithm called RACK ("Recent ACKnowledgment"). RACK uses the notion of time, instead of packet or sequence counts, to detect losses, for modern TCP implementations that can support per-packet timestamps and the selective acknowledgment (SACK) option. It is intended to replace the conventional DUPACK threshold approach and its variants, as well as other nonstandard approaches.
Understanding intellectual disability and autism spectrum disorders from common mouse models: synapses to behaviour

Normal brain development is highly dependent on the timely coordinated actions of genetic and environmental processes, and an aberration can lead to neurodevelopmental disorders (NDDs). Intellectual disability (ID) and autism spectrum disorders (ASDs) are a group of co-occurring NDDs that affect between 3% and 5% of the world population, thus presenting a great challenge to society. This problem calls for the need to understand the pathobiology of these disorders and to design new therapeutic strategies. One approach towards this has been the development of multiple analogous mouse models. This review discusses studies conducted in the mouse models of five major monogenic causes of ID and ASDs: Fmr1, Syngap1, Mecp2, Shank2/3 and Neuroligins/Neurnexins. These studies reveal that, despite having a diverse molecular origin, the effects of these mutations converge onto similar or related aetiological pathways, consequently giving rise to the typical phenotype of cognitive, social and emotional deficits that are characteristic of ID and ASDs. This convergence, therefore, highlights common pathological nodes that can be targeted for therapy. Other than conventional therapeutic strategies such as non-pharmacological corrective methods and symptomatic alleviation, multiple studies in mouse models have successfully proved the possibility of pharmacological and genetic therapy enabling functional recovery.