Miracle-dz/UniFAR-FTUs huggingface dataset:
Lessons on Applying Automated Recommender Systems to Information-Seeking Tasks

Automated recommender systems predict user preferences by applying machine learning techniques to data on products, users, and past user preferences for products. Such systems have become increasingly popular in entertainment and e-commerce domains, but have thus far had little success in information-seeking domains such as identifying published research of interest. We report on several recent publications that show how recommenders can be extended to more effectively address information-seeking tasks by expanding the focus from accurate prediction of user preferences to identifying a useful set of items to recommend in response to the user's specific information need. Specific research demonstrates the value of diversity in recommendation lists, shows how users value lists of recommendations as something different from the sum of the individual recommendations within, and presents an analytic model for customizing a recommender to match user information-seeking needs.
Monocyte heterogeneity in obesity and subclinical atherosclerosis.

AIMS Monocytes and monocyte-derived macrophages have been recognised as the cellular hallmark of atherosclerosis decades ago. Recently, they have also been shown to play a pivotal role in obesity. Monocytes display immunophenotypic heterogeneity with functionally distinct subpopulations. We initiated the I LIKE HOMe study to examine monocyte heterogeneity in obesity and subclinical atherosclerosis. METHODS AND RESULTS We assessed carotid intima media thickness (IMT), body mass index (BMI), and other cardiovascular risk factors in 622 healthy volunteers. Using flow-cytometry, we differentiated monocytes into CD14(++)CD16(-) and CD16(+) cells, which we further subdivided into CD14(++)CD16(+) and CD14((+))CD16(+) cells. Body mass index was significantly correlated with carotid IMT. High CD16(+) monocyte counts were significantly associated with both higher BMI and increased carotid IMT. Adjustment for CD16(+) monocyte counts weakened the correlation between BMI and carotid IMT, suggesting that the increase in CD16(+) monocyte numbers in obesity may partly explain the association between obesity and IMT. CONCLUSION Our results reveal a significant univariate association between CD16(+) monocytes and both obesity and subclinical atherosclerosis in low-risk individuals. They are in line with recent observations that CD16(+) monocytes show high endothelial affinity and a potent capacity to invade vascular lesions and to transform into pro-inflammatory cytokine producing macrophages.
Real-Time Task Replication for Fault Tolerance in Identical Multiprocessor Systems

Multiprocessor platforms have been widely adopted in both embedded and server systems. In addition to the performance improvement, multiprocessor systems could have the flexibility in tolerating processor failures via task replication. This paper considers the replication of periodic hard real-time tasks in identical multiprocessor environments. Each task is replicated on K distinct processors, where K is a user-determined integer for fault tolerance to improve system reliability. When the objective is to minimize the maximum utilization in a system with a specified number of processors, we present a greedy algorithm with a 2-approximation ratio, and a polynomial-time approximation scheme is developed. For the minimization of the number of processors required to derive feasible schedules with task replication, we develop greedy algorithms with a 2-approximation ratio and an asymptotic polynomial-time approximation scheme
Synthetic Lethal Screen Demonstrates That a JAK2 Inhibitor Suppresses a BCL6-dependent IL10RA/JAK2/STAT3 Pathway in High Grade B-cell Lymphoma*

We demonstrate the usefulness of synthetic lethal screening of a conditionally BCL6-deficient Burkitt lymphoma cell line, DG75-AB7, with a library of small molecules to determine survival pathways suppressed by BCL6 and suggest mechanism-based treatments for lymphoma. Lestaurtinib, a JAK2 inhibitor and one of the hits from the screen, repressed survival of BCL6-deficient cells in vitro and reduced growth and proliferation of xenografts in vivo. BCL6 deficiency in DG75-AB7 induced JAK2 mRNA and protein expression and STAT3 phosphorylation. Surface IL10RA was elevated by BCL6 deficiency, and blockade of IL10RA repressed STAT3 phosphorylation. Therefore, we define an IL10RA/JAK2/STAT3 pathway each component of which is repressed by BCL6. We also show for the first time that JAK2 is a direct BCL6 target gene; BCL6 bound to the JAK2 promoter in vitro and was enriched by ChIP-seq. The place of JAK2 inhibitors in the treatment of diffuse large B-cell lymphoma has not been defined; we suggest that JAK2 inhibitors might be most effective in poor prognosis ABC-DLBCL, which shows higher levels of IL10RA, JAK2, and STAT3 but lower levels of BCL6 than GC-DLBCL and might be usefully combined with novel approaches such as inhibition of IL10RA.
Fully Codon-Optimized luciferase Uncovers Novel Temperature Characteristics of the Neurospora Clock

ABSTRACT We report the complete reconstruction of the firefly luciferase gene, fully codon optimized for expression in Neurospora crassa. This reporter enhances light output by approximately 4 log orders over that with previously available versions, now producing light that is visible to the naked eye and sufficient for monitoring the activities of many poorly expressed genes. Time lapse photography of strains growing in race tubes, in which the frq or eas/ccg-2 promoter is used to drive luciferase, shows the highest levels of luciferase activity near the growth front and newly formed conidial bands. Further, we have established a sorbose medium colony assay that will facilitate luciferase-based screens. The signals from sorbose-grown colonies of strains in which the frq promoter drives luciferase exhibit the properties of circadian rhythms and can be tracked for many days to weeks. This reporter now makes it possible to follow the clock in real time, even in strains or under conditions in which the circadian rhythm in conidial banding is not expressed. This property has been used to discover short, ca. 15-h period rhythms at high temperatures, at which banding becomes difficult to observe in race tubes, and to generate a high-resolution temperature phase-response curve.
A comparison of Bayesian hierarchical modeling with group‐based exposure assessment in occupational epidemiology

We build a Bayesian hierarchical model for relating disease to a potentially harmful exposure, by using data from studies in occupational epidemiology, and compare our method with the traditional group‐based exposure assessment method through simulation studies, a real data application, and theoretical calculation. We focus on cohort studies where a logistic disease model is appropriate and where group means can be treated as fixed effects. The results show a variety of advantages of the fully Bayesian approach and provide recommendations on situations where the traditional group‐based exposure assessment method may not be suitable to use. Copyright © 2013 John Wiley & Sons, Ltd.
Implications of Resveratrol on Glucose Uptake and Metabolism

Resveratrol—a polyphenol of natural origin—has been the object of massive research in the past decade because of its potential use in cancer therapy. However, resveratrol has shown an extensive range of cellular targets and effects, which hinders the use of the molecule for medical applications including cancer and type 2 diabetes. Here, we review the latest advances in understanding how resveratrol modulates glucose uptake, regulates cellular metabolism, and how this may be useful to improve current therapies. We discuss challenges and findings regarding the inhibition of glucose uptake by resveratrol and other polyphenols of similar chemical structure. We review alternatives that can be exploited to improve cancer therapies, including the use of other polyphenols, or the combination of resveratrol with other molecules and their impact on glucose homeostasis in cancer and diabetes.
Land Surface Air Temperature Data Are Considerably Different Among BEST‐LAND, CRU‐TEM4v, NASA‐GISS, and NOAA‐NCEI

Several groups routinely produce gridded land surface air temperature (LSAT) data sets using station measurements to assess the status and impact of climate change. The Intergovernmental Panel on Climate Change Fifth Assessment Report suggests that estimated global and hemispheric mean LSAT trends of different data sets are consistent. However, less attention has been paid to the intercomparison at local/regional scales, which is important for local/regional studies. In this study we comprehensively compare four data sets at different spatial and temporal scales, including Berkley Earth Surface Temperature land surface air temperature data set (BEST‐LAND), Climate Research Unit Temperature Data Set version 4 (CRU‐TEM4v), National Aeronautics and Space Administration Goddard Institute for Space Studies data (NASA‐GISS), and data provided by National Oceanic and Atmospheric Administration National Center for Environmental Information (NOAA‐NCEI). The mean LSAT anomalies are remarkably different because of the data coverage differences, with the magnitude nearly 0.4°C for the global and Northern Hemisphere and 0.6°C for the Southern Hemisphere. This study additionally finds that on the regional scale, northern high latitudes, southern middle‐to‐high latitudes, and the equator show the largest differences nearly 0.8°C. These differences cause notable differences for the trend calculation at regional scales. At the local scale, four data sets show significant variations over South America, Africa, Maritime Continent, central Australia, and Antarctica, which leads to remarkable differences in the local trend analysis. For some areas, different data sets produce conflicting results of whether warming exists. Our analysis shows that the differences across scales are associated with the availability of stations and the use of infilling techniques. Our results suggest that conventional LSAT data sets using only station observations have large uncertainties across scales, especially over station‐sparse areas. In developing future LSAT data sets, the data uncertainty caused by limited and unevenly distributed station observations must be reduced.
Cell adhesion and cell surface topography in aggregates of 3T3 and SV40- virus-transformed 3T3 cells. Visualization of interior cells by scanning electron microscopy

A technique for exposing the interior of aggregates of cultured cells has been developed and is described in this report. Using this technique, we have examined for the first time, by scanning electron microscopy, cell morphology and cell contact ultrastructure in the interior of aggregates of BALB/c 3T3 and SV40-transformed 3T3 cells. The 3T3 cells make initial intercellular contact by means of microvillar processes. Over a period of 3-8 h, some of these microvillar contacts are replaced by broader projections. In contrast, the SV40-transformed cells make initial intercellular contact by means of blebs or blunt projections which are also broadened and extended over a period of 3-8 h. For both 3T3 and SV40-3T3 cells, the surfaces of the cells which form the outer layer of the aggregate resemble the surfaces of single cells fixed in suspension, regardless of how long the aggregates have been cultured. Thse cells are covered with many cellular processes and are roughly hemispherical in profile. The surfaces of the internal cells of the aggregates, however, lose many of their cellular processes, develop smooth patches, and many become irregular in shape. This smooth morphology was also observed on the interior surfaces of the peripheral cell layer. From these observations we conclude that: (a) the stabilization of adhesive contacts is a slow process which takes at least 3-8 h; (b) the outer surfaces of peripheral cells differ significantly from the surfaces of interior cells; and (c) clear differences in surface topography exist between nonmalignant 3T3 cells and their malignant SV40 transformants.
Cardiac Transcriptome and Dilated Cardiomyopathy Genes in Zebrafish

Background—Genetic studies of cardiomyopathy and heart failure have limited throughput in mammalian models. Adult zebrafish have been recently pursued as a vertebrate model with higher throughput, but genetic conservation must be tested. Methods and Results—We conducted transcriptome analysis of zebrafish heart and searched for fish homologues of 51 known human dilated cardiomyopathy–associated genes. We also identified genes with high cardiac expression and genes with differential expression between embryonic and adult stages. Among tested genes, 30 had a single zebrafish orthologue, 14 had 2 homologues, and 5 had ≥3 homologues. By analyzing the expression data on the basis of cardiac abundance and enrichment hypotheses, we identified a single zebrafish gene for 14 of 19 multiple-homologue genes and 2 zebrafish homologues of high priority for ACTC1. Of note, our data suggested vmhc and vmhcl as functional zebrafish orthologues for human genes MYH6 and MYH7, respectively, which are established molecular markers for cardiac remodeling. Conclusions—Most known genes for human dilated cardiomyopathy have a corresponding zebrafish orthologue, which supports the use of zebrafish as a conserved vertebrate model. Definition of the cardiac transcriptome and fetal gene program will facilitate systems biology studies of dilated cardiomyopathy in zebrafish.
A review of CO2 and associated carbon dynamics in headwater streams: A global perspective

Terrestrial carbon export via inland aquatic systems is a key process in the global carbon cycle. It includes loss of carbon to the atmosphere via outgassing from rivers, lakes, or reservoirs and carbon fixation in the water column as well as in sediments. This review focuses on headwater streams that are important because their stream biogeochemistry directly reflects carbon input from soils and groundwaters. Major drivers of carbon dioxide partial pressures (pCO2) in streams and mechanisms of terrestrial dissolved inorganic, organic and particulate organic carbon (DIC, DOC, and POC) influxes are summarized in this work. Our analysis indicates that the global river average pCO2 of 3100 ppmV is more often exceeded by contributions from small streams when compared to rivers with larger catchments (> 500 km2). Because of their large proportion in global river networks (> 96% of the total number of streams), headwaters contribute large—but still poorly quantified—amounts of CO2 to the atmosphere. Conservative estimates imply that globally 36% (i.e., 0.93 Pg C yr−1) of total CO2 outgassing from rivers and streams originate from headwaters. We also discuss challenges in determination of CO2 sources, concentrations, and fluxes. To overcome uncertainties of CO2 sources and its outgassing from headwater streams on the global scale, new investigations are needed that should include groundwater data. Such studies would also benefit from applications of integral CO2 outgassing isotope approaches and multiscale geophysical imaging techniques.
Chain of Custody and Evidence Integrity Verification Using Blockchain Technology

The validity and integrity of digital evidence and the chain of custody are crucial to all digital forensic investigations. All new evidence and access logs of the original evidence should be logged in a document called the ‘chain of custody’. This document shows the timeline of any piece of evidence from the time it was recorded until the end of the investigation. In a traditional digital investigation, trusted parties, such as an investigator, are allowed access to the digital evidence and follow a strict process when dealing with data. These trusted parties have the capability to alter the data making the evidence inadmissible in a court of law. Alternatively, these trusted parties may also alter the data accidentally or with malicious intent, due to a lack of transparency and non-repudiation. Blockchain technology can solve this issue, however, existing research shows that adopting blockchain does not provide adequate transparent access control mechanisms. Consequently, this makes blockchain difficult to adopt due to the one-to-one mapping and the inability to easily validate the chain of custody and evidence admissibility. Current methodologies rely on an external off-chain access control mechanism, which, regrettably, remains susceptible to potential breaches that could compromise its integrity and validity. This paper proposes an enhanced model to provide access control through smart contracts, ensuring immutability, flexibility, transparency, and non-repudiation of both the access control mechanisms and the digital evidence itself. This is achieved by moving the access control mechanism to the blockchain. This tracks any changes made through the access control mechanism, further ensuring transparency and integrity. This smart contract-based access control builds off role-based access control, allowing for more complex hierarchies to be used. This model aims to allow for both modularity, making adoption easier for existing digital forensic tools, and encouraging digital investigation and litigation to become more streamlined. Existing tools can easily integrate with the proposed model adding an extra layer of non-repudiation, transparency, and integrity.
Reversible Inhibitors of Fatty Acid Amide Hydrolase That Promote Analgesia: Evidence for an Unprecedented Combination of Potency and Selectivity

Fatty acid amide hydrolase (FAAH) is the primary catabolic regulator of several bioactive lipid amides in vivo, including the endogenous cannabinoid anandamide and the sleep-inducing substance oleamide. Inhibitors of FAAH are considered a potential therapeutic approach for the treatment of several nervous system disorders, including pain, anxiety, and insomnia. However, for FAAH inhibitors to achieve clinical utility, they must not only display efficacy in vivo but also selectivity for this enzyme relative to the numerous other serine hydrolases present in mammalian proteomes. Here, we report a general strategy for evaluating the pharmacological activity and target specificity of FAAH inhibitors and its implementation to develop the first class of selective reversible inhibitors of this enzyme that are highly efficacious in vivo. Using a series of functional proteomics, analytical chemistry, and behavioral pharmacology assays, we have identified a class of α-keto-heterocycles that show unprecedented selectivity for FAAH relative to other mammalian hydrolases, and, when administered to rodents, raise central nervous system levels of anandamide and promote cannabinoid receptor 1-dependent analgesia in several assays of pain sensation. These studies provide further evidence that FAAH may represent an attractive therapeutic target and describe a general route by which inhibitors of this enzyme can be optimized to achieve exceptional potency, selectivity, and efficacy in vivo.
Human Sec31B: a family of new mammalian orthologues of yeast Sec31p that associate with the COPII coat

We have cloned human brain and testis Sec31B protein (also known as secretory pathway component Sec31B-1 or SEC31-like 2; GenBank accession number AF274863). Sec31B is an orthologue of Saccharomyces cerevisiae Sec31p, a component of the COPII vesicle coat that mediates vesicular traffic from the endoplasmic reticulum. Sec31B is widely expressed and enriched in cerebellum and testis. Its predicted sequence of 1180 residues (expected molecular mass 128,711 Da) shares 47.3% and 18.8% similarity to human Sec31A (also known as Sec31; GenBank accession number AF139184) and yeast Sec31p, respectively. The gene encoding Sec31B is located on chromosome 10q24 and contains 29 exons. PCR analysis of exon utilization reveals massive alternative mRNA splicing of Sec31B, with just 16 exons being constitutively utilized in all transcripts. The presence of a stop codon in exon 13 generates two families of Sec31B gene products (each displaying additional patterns of mRNA splicing): a group of full-length proteins (hereafter referred to as Sec31B-F) and also a group of truncated proteins (hereafter referred to as Sec31B-T), distinguished by their utilization of exon 13. Sec31B-F closely resembles Sec31p and Sec31A, with canonical WD repeats in an N-terminal domain that binds Sec13 and a proline-rich C-terminal region that presumably binds Sec23/24. The Sec31B-T group (molecular mass 52,983 Da) contains a preserved WD-repeat domain but lacks the C-terminal proline-rich region. When expressed as a fusion protein with eYFP in cultured cells, Sec31B-F associates with the endoplasmic reticulum and with vesicular-tubular clusters, displays restricted intracellular movement characteristic of COPII vesicle dynamics, co-distributes on organelles with Sec13, Sec31A and Sec23 (markers of the COPII coat), and concentrates with ts045-VSV-G-CFP (VSV-G) when examined early in the secretory pathway or after temperature or nocodazole inhibition. The role of the truncated form Sec31B-T appears to be distinct from that of Sec31B-F and remains unknown. We conclude that Sec31B-F contributes to the diversity of the mammalian COPII coat, and speculate that the Sec31 cage, like Sec24, might be built with isoforms tuned to specific types of cargo or to other specialized functions.
Offsets and prioritizing the selection of new elements in search displays: More evidence for attentional capture in the preview effect

The preview effect refers to the finding that new elements in a search display are prioritized over old elements. Donk and Theeuwes (2001) suggest that this prioritization is due to bottom-up attentional capture, as new elements that abruptly appear with increases in luminance produce a preview effect whereas new elements that are equiluminant to the background do not. The present study extends this research by examining if new elements that appear from offsets, with and without luminance changes, yield similar findings to onsets. This was indeed the case, as equiluminant offsets did not produce a preview effect but offsets with corresponding increases or decreases in luminance did show the prioritization of new elements over old elements. These findings show that the prioritization of new elements is sensitive to changes in luminance but not to the direction of such changes.
Darwin's mistake: Explaining the discontinuity between human and nonhuman minds

Abstract Over the last quarter century, the dominant tendency in comparative cognitive psychology has been to emphasize the similarities between human and nonhuman minds and to downplay the differences as “one of degree and not of kind” (Darwin 1871). In the present target article, we argue that Darwin was mistaken: the profound biological continuity between human and nonhuman animals masks an equally profound discontinuity between human and nonhuman minds. To wit, there is a significant discontinuity in the degree to which human and nonhuman animals are able to approximate the higher-order, systematic, relational capabilities of a physical symbol system (PSS) (Newell 1980). We show that this symbolic-relational discontinuity pervades nearly every domain of cognition and runs much deeper than even the spectacular scaffolding provided by language or culture alone can explain. We propose a representational-level specification as to where human and nonhuman animals' abilities to approximate a PSS are similar and where they differ. We conclude by suggesting that recent symbolic-connectionist models of cognition shed new light on the mechanisms that underlie the gap between human and nonhuman minds.