Miracle-dz/UniFAR-FTUs huggingface dataset:
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

Integrative multi-species prediction (IMP) is an interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions and networks. The system provides a framework for biologists to analyze their candidate gene sets in the context of functional networks, as they expand or focus these sets by mining functional relationships predicted from integrated high-throughput data. IMP integrates prior knowledge and data collections from multiple organisms in its analyses. Through flexible and interactive visualizations, researchers can compare functional contexts and interpret the behavior of their gene sets across organisms. Additionally, IMP identifies homologs with conserved functional roles for knowledge transfer, allowing for accurate function predictions even for biological processes that have very few experimental annotations in a given organism. IMP currently supports seven organisms (Homo sapiens, Mus musculus, Rattus novegicus, Drosophila melanogaster, Danio rerio, Caenorhabditis elegans and Saccharomyces cerevisiae), does not require any registration or installation and is freely available for use at http://imp.princeton. edu.
Prevalence of tick-borne viruses in Ixodes ricinus assessed by high-throughput real-time PCR

Ticks are one of the principal arthropod vectors of human and animal infectious diseases. Whereas the prevalence of tick-borne encephalitis virus in ticks in Europe is well studied, there is less information available on the prevalence of the other tick-borne viruses (TBVs) existing worldwide. The aim of this study was to improve the epidemiological survey tools of TBVs by the development of an efficient high-throughput test to screen a wide range of viruses in ticks.In this study, we developed a new high-throughput virus-detection assay based on parallel real-time PCRs on a microfluidic system, and used it to perform a large scale epidemiological survey screening for the presence of 21 TBVs in 18 135 nymphs of Ixodes ricinus collected from five European countries. This extensive investigation has (i) evaluated the prevalence of four viruses present in the collected ticks, (ii) allowed the identification of viruses in regions where they were previously undetected.In conclusion, we have demonstrated the capabilities of this new screening method that allows the detection of numerous TBVs in a large number of ticks. This tool represents a powerful and rapid system for TBVs surveillance in Europe and could be easily customized to assess viral emergence.
Diffusion into New Markets: Economic Returns Required by Households to Adopt Rooftop Photovoltaics

While the U.S. residential solar market is growing quickly, costs for acquiring customers are high--and this indicates the value of efforts to identify new market segments and predict areas ripe for adoption. To better understand how the next wave of solar diffusion could occur, we explore the range of economic thresholds that households without PV would require to consider solar adoption, finding that these households require more attractive payback times by 1-3 years to achieve comparable market share as current adopters. In contrast, non-adopters indicate they would be satisfied with equal or lower returns when the benefits of solar are expressed in terms of their monthly bill savings—as is the case for third-party owned systems. If true, this suggests that the leasing model fundamentally inverts the assumption that later adopters require higher economic benefits. Adopters, both buyers and leasers, are compared to their non-adopting peers across a range of demographic and attitudinal factors. We find that leasers appear to be more highly influenced by installer advertising (radio, TV) and marketing, while buyers were more influenced by personal contacts. Environmental concern, once a preeminent reason for adopting is decreasing in relative importance, whereas lowering total electricity costs and protecting one’s household from future increases in prices are now the two more important reasons. Understanding these dynamics, and how they are changing, offers installers low-cost opportunities to attract new customers and expand their market base.
The Fine Art of Destruction: A Guide to In‐Depth Glycoproteomic Analyses—Exploiting the Diagnostic Potential of Fragment Ions

The unambiguous mass spectrometric identification and characterization of glycopeptides is crucial to elucidate the micro‐ and macroheterogeneity of glycoproteins. Here, combining lower and stepped collisional energy fragmentation for the in‐depth and site‐specific analysis of N‐ and O‐glycopeptides is proposed. Using a set of four representative and biopharmaceutically relevant glycoproteins (IgG, fibrinogen, lactotransferrin, and ribonuclease B), the benefits and limitations of the developed workflow are highlighted and a state‐of‐the‐art blueprint for conducting high‐quality in‐depth N‐ and O‐glycoproteomic analyses is provided. Further, a modified and improved version of cotton hydrophilic interaction liquid chromatography‐based solid phase extraction for glycopeptide enrichment is described. For the unambiguous identification of N‐glycopeptides, the use of a conserved yet, rarely employed‐fragmentation signature [Mpeptide+H+0,2X GlcNAc]+ is proposed. It is shown for the first time that this fragmentation signature can consistently be found across all N‐glycopeptides, but not on O‐glycopeptides. Moreover, the use of the relative abundance of oxonium ions to retrieve glycan structure information, for example, differentiation of hybrid‐ and high‐mannose‐type N‐glycans or differentiation between antenna GlcNAc and bisecting GlcNAc, is systematically and comprehensively evaluated. The findings may increase confidence and comprehensiveness in manual and software‐assisted glycoproteomics.
Open Questions for Building Optimal Operation Policies for Dam Management Using Factored Markov Decision Processes

In this paper, we present the conceptual model of a realworld application of Markov Decision Processes to dam management. The idea is to demonstrate that it is possible to efficiently automate the construction of operation policies by modelling the problem as a sequential decision problem that can be easily solved using stochastic dynamic programming. We will explain the problem domain and provide an analysis of the resulting value and policy functions. We will also present a useful discussion about the issues that will appear when the conceptual model to be extended into a real-world application.
Hormone Replacement Therapy: Would it be Possible to Replicate a Functional Ovary?

Background: Throughout history, menopause has been regarded as a transition in a woman’s life. With the increase in life expectancy, women now spend more than a third of their lives in menopause. During these years, women may experience intolerable symptoms both physically and mentally, leading them to seek clinical advice. It is imperative for healthcare providers to improve the quality of life by reducing bothersome menopausal symptoms and preventing disorders such as osteoporosis and atherosclerosis. The current treatment in the form of hormone replacement therapy (HRT) is sometimes inadequate with several limitations and adverse effects. Objective and rationale: The current review aims to discuss the need, efficacy, and limitations of current HRT; the role of other ovarian hormones, and where we stand in comparison with ovary-in situ; and finally, explore towards the preparation of an HRT model by regeneration of ovaries tissues through stem cells which can replicate a functional ovary. Search methods: Four electronic databases (MEDLINE, Embase, Web of Science and CINAHL) were searched from database inception until 26 April 2018, using a combination of relevant controlled vocabulary terms and free-text terms related to ‘menopause’, ‘hormone replacement therapy’, ‘ovary regeneration’, ‘stem cells’ and ‘ovarian transplantation’. Outcomes: We present a synthesis of the existing data on the efficacy and limitations of HRT. HRT is far from adequate in postmenopausal women with symptoms of hormone deprivation as it fails to deliver all hormones secreted by naïve ovarian tissue. Moreover, the pharmacokinetics of synthetic hormones makes them substantially different from natural ones. Not only does the number and type of hormones given in HRT matter, but the route of delivering and their release in circulation are also imperative. The hormones are delivered either orally or topically in a non-physiological uniform manner, which brings along with it several side effects. These identify the need for a hormone delivery system which replicates, integrates and reacts as per the requirement of the female body. Wider implications: The review outlines the strengths and weaknesses of HRT and highlights the potential areas for future research. There is a tremendous potential for research in this field to understand the collective roles of the various ovarian hormones and to devise an auto-regulated hormone delivery system which replicates the normal physiology. Its clinical applications can prove to be transformative for postmenopausal women helping them to lead a healthy and productive life.
T cell receptor β‐chain repertoire analysis of tumor‐infiltrating lymphocytes in pancreatic cancer

Pancreatic cancer is lethal due to lack of perceptible symptoms and effective treatment methods. Immunotherapy may provide promising therapeutic choices for malignant tumors like pancreatic cancer. Tumor‐infiltrating lymphocytes (TIL) in tumor mesenchyme could recognize peptide antigens presented on the surface of tumor cells. The present study aimed to test the relationship between the T cell receptor (TCR) β repertoire of the tumor and peripheral blood, and also to investigate the intra‐tumor spatial heterogeneity of the TCR β repertoire in pancreatic cancer. To the best of our knowledge, this is the first study to evaluate the clonal composition of TCR β repertoire in TIL across the spatial extent of pancreatic cancer. In this study, we studied 5 patients who were diagnosed with primary pancreatic cancer. Ultra‐deep sequencing was used to assess the rearrangement of the TCR β‐chain (TCR β) gene. HE staining and immunohistochemistry of CD3, CD4, CD8 and HLA class I were used to show histopathology and immune conditions macroscopically. TIL repertoire showed that different regions of the same tumor showed a greater number of repertoire overlaps between each other than between peripheral blood, which suggested that T cell clones in pancreatic cancer might be quite different from those in peripheral blood. In contrast, intra‐tumoral TCR β repertoires were spatially homogeneous between different regions of a single tumor tissue. Based on these results, we speculated that the cellular adaptive immune response in pancreatic cancer was spatially homogeneous; this may pave the way for immunotherapy for the treatment of pancreatic cancer patients.
Toward Emotional Well-Being: Staying Calm with ECG Feedback

Recently, recognizing emotion through physiological information has ﬂourished. Next research interest is how such information feedback inﬂuences user’s emotion, because controlling emotions is a key to emotional well-being. Aiming at effective feedback in real-time and daily-usable system, we studied the inﬂuence of physiological information feedback on user’s emotion using standardized emotional movie clips. We built real-time Electrocardiogram (ECG) visualization sys-tem and studied the inﬂuence of the feedback. Subjects watched ﬁve movie clips while wearing three-lead ECG sensor and the emotions were assessed using a semantic self-report scale. Conditions without-ECG and with-ECG feedback are compared. We found that Heart Rate Variability (HRV) differs signiﬁcantly when feed-back is given. We believe that this study offers implications when designing real-time physiological information feedback system. Finally, a possible study direction toward augmenting emotion with wireless ECG sensor is discussed.
Metal Organic Frameworks Based Materials for Heterogeneous Photocatalysis

The increase in environmental pollution due to the excessive use of fossil fuels has prompted the development of alternative and sustainable energy sources. As an abundant and sustainable energy, solar energy represents the most attractive and promising clean energy source for replacing fossil fuels. Metal organic frameworks (MOFs) are easily constructed and can be tailored towards favorable photocatalytic properties in pollution degradation, organic transformations, CO2 reduction and water splitting. In this review, we first summarize the different roles of MOF materials in the photoredox chemical systems. Then, the typical applications of MOF materials in heterogeneous photocatalysis are discussed in detail. Finally, the challenges and opportunities in this promising field are evaluated.
Unsupervised Rating Prediction based on Local and Global Semantic Models

Current recommendation engines attempt to answer the same question: given a user with some activity in the system, which is the next entity, be it a restaurant, a book or a movie, that the user should visit or buy next. The presumption is that the user would favorably review the item being recommended. The goal of our project is to predict how a user would rate an item he/she never rated, which is a generalization of the task recommendation engines perform. Previous work successfully employs machine learning techniques, particularly statistical methods. However, there are some outlier situations which are more difﬁcult to predict, such as new users. In this paper we present a rating prediction approach targeted for entities for which little prior information exists in the database. We put forward and test a number of hypotheses, exploring recommendations based on nearest neighbor-like methods. We adapt existing common sense topic modeling methods to compute similarity measures between users and then use a relatively small set of key users to predict how the target user will rate a given business. We implemented and tested our system for recommending businesses using the Yelp Academic Dataset. We report initial results for topic-based rating predictions, which perform consistently across a broad range of parameters.
Comparative Effects of Coenzyme Q10 or n-3 Polyunsaturated Fatty Acid Supplementation on Retinal Angiogenesis in a Rat Model of Oxygen-Induced Retinopathy

Neonatal intermittent hypoxia (IH) or apnea afflicts 70% to 90% of all preterm infants <28 weeks gestation, and is associated with severe retinopathy of prematurity (ROP). We tested the hypotheses that coenzyme Q10 (CoQ10) or omega-3 polyunsaturated fatty acids (n-3 PUFAs) supplementation during neonatal IH reduces the severity of oxygen-induced retinopathy (OIR). Newborn rats were exposed to two IH paradigms: (1) 50% O2 with brief hypoxia (12% O2); or (2) 21% O2 with brief hypoxia, until postnatal day 14 (P14), during which they received daily oral CoQ10 in olive oil, n-3 PUFAs in fish oil, or olive oil only and compared to room air (RA) treated groups. Pups were examined at P14, or placed in RA until P21. Retinal angiogenesis, histopathology, and morphometry were determined. Both IH paradigms produced severe OIR, but these were worsened with 50/12% O2 IH. CoQ10 and n-3 PUFAs reduced the severity of OIR, as well as ocular growth factors in both IH paradigms, but CoQ10 was more effective in 50/12% O2 IH. Supplementation with either CoQ10 or n-3 PUFAs targeting IH-induced retinal injury is individually effective for ameliorating specific characteristics consistent with ROP. Given the complexity of ROP, further studies are needed to determine whether combined CoQ10 and n-3 PUFAs supplementation would optimize their efficacy and result in a better outcome.
Effect of Diet Supplementation with Quinoa Seed and/or Linseed on Immune Response, Productivity and Meat Quality in Merinos Derived Lambs

Simple Summary Stressful conditions can play an important role in affecting welfare, productive performances and meat quality of lambs. The relation between nutrition and immune response has been investigated in the livestock production, particularly in dairy cattle and sheep. Due to costs related to animal feed it is useful to evaluate the proper feeding strategy supplementation for improving animal welfare and lamb meat quality. The present study aimed to evaluate the effects of supplementation with linseed, quinoa seed and their combination on metabolic profile, immune system, and cortisol response in blood and on meat quality of merinos derived lambs. Both linseed and quinoa supplementation enhanced the immune responses of lambs, and showed a hypo cholesterol effect on blood of lambs. Moreover, lambs supplemented with linseed resulted in the lowest level of cortisol secretion during the loading test demonstrating the link between stress and the immune system. In addition, data from the present experiment highlighted that linseed supplementation in lambs enhance meat quality producing a better meat tenderness. These findings should be considered for development of specific strategies aimed at improving the quality of meat and sustaining lambs’ welfare. Abstract In the last years several studies have investigated the strong relation between nutrition and immune response in the livestock production, particularly in dairy cattle and sheep. The aim of this study was to evaluate the effects of supplementation based on linseed, quinoa seeds and their combination on welfare, productivity and quality of meat from merinos derived lambs. 32 weaned lambs were divided into 4 experimental groups: quinoa (Q), linseed (LS) and combination of quinoa and linseed (LS + Q) that received the respective supplementation and control group (C) without supplementation. Lambs from all supplemented groups showed lower plasma urea, creatinine and cholesterol than control. Both linseed and quinoa supplementation enhanced the cell-mediated immune responses of lambs, furthermore, linseed supplementation resulted in the lowest level of cortisol secretion after handling, loading and transport. Meat from lambs supplemented with linseed and LS + Q showed the highest pH, at 1 and 3 h post-mortem, while, meat from all supplemented groups was more tender than meat from control. Results indicated that linseed and quinoa seeds supplementation can help the animal to cope with stressful events due to the close link between stress responses and the immune system and for improving meat quality in terms of better tenderness.
BLocate: A Building Identification Scheme in GPS Denied Environments Using Smartphone Sensors

Indoor localization systems assume that the user’s current building is known by the GPS (Global Positioning System). However, such assumptions do not hold true in GPS denied environments or where the GPS cannot determine the user’s definite location. We present a novel solution to identify the building where the user is present now. The proposed building identification method works on the pervasive magnetic field using a smartphone. The accelerometer data determines the user’s activity of being stationary or walking. An Artificial Neural Network is used to identify the user’s activities and it shows good results. The magnetometer data is used to identify the user’s current building using the fingerprinting approach. Contrary to a traditional fingerprinting approach which stores intensity values, we utilize the patterns formed by the magnetic field strength in the form of a Binary Grid (BG). The BG approach overcomes the limitation of Dynamic Time Warping (DTW) whose performance is degraded when the magnitude of the magnetic data is changed. The experiments are performed with Samsung Galaxy S8 for eight various buildings with different altitudes and number of floors in Yeungnam University, Korea. The results demonstrate that the proposed building identification method can potentially be deployed for building identification. The precision, UAR (Unweighted Average Recall), F score, and Cohen’s Kappa values are used to determine the performance of the proposed system. The proposed systems shows very promising results. The system operates without any aid from any infrastructure dependent technologies like GPS or WiFi. Furthermore, we performed many experiments to investigate the impact of isolated points data to build fingerprint database on system’s accuracy with 1 m and 2 m distance. Results illustrate that by trading off a minor accuracy, survey labor can be reduced by 50 percent.
Cryptotransport: blockchain-powered ride hailing while preserving privacy, pseudonymity and trust

A ride-hailing service, where passengers choose the origin and destination of their ride, preserves location privacy if the origin and destination of the ride are not revealed to anyone other than the driver. Pseudonymity means that the driver and the passenger use a pseudonym and do not reveal their true identity to each other. The service is trusted if a dishonest passenger cannot use the service without paying, and a driver must provide the service to get paid. In this paper, we introduce cryptotrasnport---a ride-hailing service powered by cryptocurrency and blockchain---and we show that it can preserve privacy, pseudonymity, and trust, simultaneously. Furthermore, by using blockchain technology, cryptotransport matches riders with vehicles in a decentralized fashion, without relying on any company or organization to manage the system.