Miracle-dz/UniFAR-FTUs huggingface dataset:
Land Use, Land Cover, and Pollinator Health: A Review and Trend Analysis

About 35 percent of the world’s food crops depend on pollinators, including managed honey bees, to reproduce. However, pollinators face a number of stressors, such as parasites, poor nutrition, pesticides, and diseases. A literature review indicates that pollinators may benefit from landscapes richer in high-quality forage (pollen and nectar sources) and highlights the different needs of managed honey bees and native (unmanaged)pollinators. This study uses 30 years of data on U.S. land uses to calculate a pollinator forage suitability index. When averaged across the Nation, the forage suitability index increased from 1982 to 2002 and declined slightly from 2002 to 2012—though in important honey bee regions (such as Central North and South Dakota), the decline from 2002 to 2012 is more pronounced. The study also analyzes the economics of providing better pollinator forage, such as assigning property rights for colony placement and voluntary government conservation programs to increase pollinator forage.
Surrogate-assisted feature extraction for high-throughput phenotyping

Objective: Phenotyping algorithms are capable of accurately identifying patients with specific phenotypes from within electronic medical records systems. However, developing phenotyping algorithms in a scalable way remains a challenge due to the extensive human resources required. This paper introduces a high-throughput unsupervised feature selection method, which improves the robustness and scalability of electronic medical record phenotyping without compromising its accuracy. Methods: The proposed Surrogate-Assisted Feature Extraction (SAFE) method selects candidate features from a pool of comprehensive medical concepts found in publicly available knowledge sources. The target phenotype’s International Classification of Diseases, Ninth Revision and natural language processing counts, acting as noisy surrogates to the gold-standard labels, are used to create silver-standard labels. Candidate features highly predictive of the silver-standard labels are selected as the final features. Results: Algorithms were trained to identify patients with coronary artery disease, rheumatoid arthritis, Crohn’s disease, and ulcerative colitis using various numbers of labels to compare the performance of features selected by SAFE, a previously published automated feature extraction for phenotyping procedure, and domain experts. The out-of-sample area under the receiver operating characteristic curve and F-score from SAFE algorithms were remarkably higher than those from the other two, especially at small label sizes. Conclusion: SAFE advances high-throughput phenotyping methods by automatically selecting a succinct set of informative features for algorithm training, which in turn reduces overfitting and the needed number of gold-standard labels. SAFE also potentially identifies important features missed by automated feature extraction for phenotyping or experts.
VKORC1-1639 G>A Polymorphism and the Risk of Non-Variceal Upper Gastrointestinal Bleeding.

BACKGROUND AND AIMS The mutations in the gene that encodes vitamin K epoxide reductase (VKOR) enzyme are responsible for low levels of vitamin K. The purpose of this study was to evaluate whether the presence of the VKORC1 -1639 G> A polymorphism is a risk factor for non-variceal upper gastrointestinal bleeding (UGIB) in patients without concomitant therapy with vitamin K antagonists. METHODS This case-control study comprised 163 consecutive patients diagnosed with UGIB and 178 controls, in whom the diagnosis of UGIB was excluded. The following data were recorded: age, gender, alcohol consumption, smoking, history of UGIB, nonsteroidal anti-inflammatory drugs (NSAIDs) or low-dose aspirin consumption. Genetic analysis included genotyping for the VKORC1 -1639 G>A polymorphism. RESULTS History of UGIB (OR 3.463, CI95% 1.463-8.198, p=0.005), smoking (OR 2.498, CI95% 1.358-4.597, p=0.003), alcohol consumption (OR 3.283, CI95% 1.796-6.000, p<0.001), use of NSAIDs (OR 4.542, CI95% 2.502-8.247, p<0.001) or of low-dose aspirin (OR 2.390, CI95% 1.326-4.310), and the VKORC1 -1639 G> A AA genotype (OR 1.364, CI95% 0.998-1.863, p=0.05) were associated with an increased risk of UGIB. The risk of UGIB was analyzed in patients with genotype AA who used aspirin or NSAIDs. The genotype AA has not kept its status of independent risk factor (p=0.3). In subjects with NSAIDs/aspirin therapy and genotype AA there was a two times higher chance of UGIB compared to those under NSAIDs/aspirin therapy alone (OR 7.6 vs. 3.6, p<0.001). CONCLUSION Patients with non-variceal UGIB caused by the use of NSAIDs or low-dose aspirin are more frequent carriers of the VKORC1 -1639 G>A AA genotype, as compared to those without UGIB.
Phenolic profiling of Portuguese propolis by LC-MS spectrometry: uncommon propolis rich in flavonoid glycosides.

INTRODUCTION Propolis is a chemically complex resinous substance collected by honeybees (Apis mellifera) from tree buds, comprising plant exudates, secreted substances from bee metabolism, pollen and waxes. Its chemical composition depends strongly on the plant sources available around the beehive, which have a direct impact in the quality and bioactivity of the propolis. Being as Portugal is a country of botanical diversity, the phenolic characterisation of propolis from the different regions is a priority. OBJECTIVE Extensive characterisation of the phenolic composition of Portuguese propolis from different continental regions and islands. METHOD Forty propolis ethanolic extracts were analysed extensively by liquid chromatography with diode-array detection coupled to electrospray ionisation tandem mass spectrometry (LC-DAD-ESI-MS(n) ). RESULTS Seventy-six polyphenols were detected in the samples and two groups of propolis were established: the common temperate propolis, which contained the typical poplar phenolic compounds such as flavonoids and their methylated/esterified forms, phenylpropanoid acids and their esters, and an uncommon propolis type with an unusual composition in quercetin and kaempferol glycosides - some of them never described in propolis. CONCLUSION The method allowed the establishment of the phenolic profile of Portuguese propolis from different geographical locations, and the possibility to use some phenolic compounds, such as kaempferol-dimethylether, as geographical markers. Data suggest that other botanical species in addition to poplar trees can be important sources of resins for Portuguese propolis.
Molecular dynamics study of chemically engineered green fluorescent protein mutants: Comparison of intramolecular fluorescence resonance energy transfer rate

Because of its unusual spectroscopic properties, green fluorescent protein (GFP) has become a useful tool in molecular genetics, biochemistry and cell biology. Here, we computationally characterize the behavior of two GFP constructs, designed as bioprobes for enzymatic triggering using intramolecular fluorescence resonance energy transfer (FRET). These constructs differ in the location of an intramolecular FRET partner, an attached chemical chromophore (either near an N‐terminal or C‐terminal site). We apply the temperature replica exchange molecular dynamics method to the two flexible constructs in conjunction with a generalized Born implicit solvent model. The calculated rate of FRET was derived from the interchromophore distance, R, and orientational factor, κ2. In agreement with experiment, the construct with the C‐terminally attached dye was predicted to have higher energy transfer rate than observed for the N‐terminal construct. The molecular basis for this observation is discussed. In addition, we find that the orientational factor, κ2, deviates from the commonly assumed value, the implications of which are also considered. Proteins 2009. © 2008 Wiley‐Liss, Inc.
BQP and the polynomial hierarchy

The relationship between BQP and PH has been an open problem since the earliest days of quantum computing. We present evidence that quantum computers can solve problems outside the entire polynomial hierarchy, by relating this question to topics in circuit complexity, pseudorandomness, and Fourier analysis. First, we show that there exists an oracle relation problem (i.e., a problem with many valid outputs) that is solvable in BQP, but not in PH. This also yields a non-oracle relation problem that is solvable in quantum logarithmic time, but not in AC0. Second, we show that an oracle decision problem separating BQP from PH would follow from the Generalized Linial-Nisan Conjecture, which we formulate here and which is likely of independent interest. The original Linial-Nisan Conjecture (about pseudorandomness against constant-depth circuits) was recently proved by Braverman, after being open for twenty years.
Heparin Has an Inhibitory Effect on Endothelin‐1 Synthesis and Release by Endothelial Cells

&NA; We studied the inhibitory effects of heparin on basal and agonist‐induced endothelin‐1 biosynthesis and release from cultured bovine endothelial cells. Heparin dose‐dependently and similarly inhibited endothelin‐1 release, inositol trisphosphate production, and intracellular free Ca2+ levels stimulated by thrombin. Hirudin fragment had an inhibitory effect on thrombin‐induced endothelin‐1 release, whereas anti‐thrombomodulin antibody had no effect. Heparin completely blocked phorbol ester‐induced endothelin‐1 release, whereas it had a partial inhibitory effect on endothelin‐1 release stimulated by angiotensin and vasopressin. Northern blot analysis using complementary DNA for bovine preproendothelin‐1 as a probe revealed that heparin reduced not only the basal but also the stimulated expression of preproendothelin‐1 messenger RNA by thrombin and phorbol ester. These data suggest that heparin, in addition to its antithrombin effect, has an inhibitory effect on the biosynthesis and release of endothelin‐1, possibly by inhibiting protein kinase C‐dependent pathway. (Hypertension 1993;21:353‐358)
Modeling the Energy Performance of Event-Driven Wireless Sensor Network by Using Static Sink and Mobile Sink

Wireless Sensor Networks (WSNs) designed for mission-critical applications suffer from limited sensing capacities, particularly fast energy depletion. Regarding this, mobile sinks can be used to balance the energy consumption in WSNs, but the frequent location updates of the mobile sinks can lead to data collisions and rapid energy consumption for some specific sensors. This paper explores an optimal barrier coverage based sensor deployment for event driven WSNs where a dual-sink model was designed to evaluate the energy performance of not only static sensors, but Static Sink (SS) and Mobile Sinks (MSs) simultaneously, based on parameters such as sensor transmission range r and the velocity of the mobile sink v, etc. Moreover, a MS mobility model was developed to enable SS and MSs to effectively collaborate, while achieving spatiotemporal energy performance efficiency by using the knowledge of the cumulative density function (cdf), Poisson process and M/G/1 queue. The simulation results verified that the improved energy performance of the whole network was demonstrated clearly and our eDSA algorithm is more efficient than the static-sink model, reducing energy consumption approximately in half. Moreover, we demonstrate that our results are robust to realistic sensing models and also validate the correctness of our results through extensive simulations.
Modelling Grounding and Discourse Obligations Using Update Rules

This paper describes an implementation of some key aspects of a theory of dialogue processing whose main concerns are to provide models of GROUNDING and of the role of DISCOURSE OBLIGATIONS in an agent's deliberation processes. Our system uses the TrindiKit dialogue move engine toolkit, which assumes a model of dialogue in which a participant's knowledge is characterised in terms of INFORMATION STATES which are subject to various kinds of updating mechanisms.
UTA DLNLP at SemEval-2016 Task 12: Deep Learning Based Natural Language Processing System for Clinical Information Identification from Clinical Notes and Pathology Reports

We propose a deep neural network based natural language processing system for clinical information (such as time information, event spans, and their attributes) extraction from raw clinical notes and pathology reports. Our approach uses the context words and their partof-speech tags and shape information as features. We utilize the temporal (1D) convolution neural network to learn the hidden feature representations. In prediction step, we use the Multilayer Perceptron (MLP) to predict event spans. The empirical evaluation demonstrates that our approach significantly outperforms baseline methods.
Going beyond hunger: Linking food supplies to global malnutrition

ABSTRACT International food security and nutrition studies focus mainly on hunger rather than dietary diversity and the nutritional requirements essential for a productive life. The authors present a method that processes Food and Agriculture Organization food supply data into World Health Organization food groups to determine whether national food supply satisfies nutritional requirements for medium energy intake (i.e. c.2200 calories per day) rather than minimum energy intake. They employ a modified version of the International Food Policy Research Institute’s 2013 Global Hunger Index to group nations for comparison. The results show that most nations have a deficit in at least one of four required food groups. However, many developed Mediterranean nations with low levels of hunger display an adequate supply of all food groups. The positioning represents a successful model for managing the nutrition transition from plant-based diets to the consumption of animal protein, oils, fats, and sugars and other carbohydrates. Additionally, the results suggest that health risks associated with overweight and obesity may increase with societal development. Accordingly, the authors conclude that information on medium energy requirements should be combined with complementary socio-economic analysis to inform food and nutrition research and policy.
A step-defined sedentary lifestyle index: <5000 steps/day.

Step counting (using pedometers or accelerometers) is widely accepted by researchers, practitioners, and the general public. Given the mounting evidence of the link between low steps/day and time spent in sedentary behaviours, how few steps/day some populations actually perform, and the growing interest in the potentially deleterious effects of excessive sedentary behaviours on health, an emerging question is "How many steps/day are too few? " This review examines the utility, appropriateness, and limitations of using a reoccurring candidate for a step-defined sedentary lifestyle index: <5000 steps/day. Adults taking <5000 steps/day are more likely to have a lower household income and be female, older, of African-American vs. European-American heritage, a current vs. never smoker, and (or) living with chronic disease and (or) disability. Little is known about how contextual factors (e.g., built environment) foster such low levels of step-defined physical activity. Unfavorable indicators of body composition and cardiometabolic risk have been consistently associated with taking <5000 steps/day. The acute transition (3-14 days) of healthy active young people from higher (>10 000) to lower (<5000 or as low as 1500) daily step counts induces reduced insulin sensitivity and glycemic control, increased adiposity, and other negative changes in health parameters. Although few alternative values have been considered, the continued use of <5000 steps/day as a step-defined sedentary lifestyle index for adults is appropriate for researchers and practitioners and for communicating with the general public. There is little evidence to advocate any specific value indicative of a step-defined sedentary lifestyle index in children and adolescents.
Chimpanzee super strength and human skeletal muscle evolution

Significance Chimpanzee “super strength” has been widely reported since the 1920s although a critical review of the available data suggests that the chimpanzee–human muscular performance differential is only ∼1.5 times. Some hypothesize that this differential reflects underlying differences in muscle mechanics. Here, we present direct measurements of chimpanzee skeletal muscle properties in comparison with those of humans and other terrestrial mammals. Our results show that chimpanzee muscle exceeds human muscle in maximum dynamic force and power output by ∼1.35 times. This is primarily due to the chimpanzee’s higher fast-twitch fiber content, rather than exceptional maximum isometric force or maximum shortening velocities. We suggest that muscular performance capabilities declined during hominin evolution in response to selection for repetitive, low-cost contractile behavior. Since at least the 1920s, it has been reported that common chimpanzees (Pan troglodytes) differ from humans in being capable of exceptional feats of “super strength,” both in the wild and in captive environments. A mix of anecdotal and more controlled studies provides some support for this view; however, a critical review of available data suggests that chimpanzee mass-specific muscular performance is a more modest 1.5 times greater than humans on average. Hypotheses for the muscular basis of this performance differential have included greater isometric force-generating capabilities, faster maximum shortening velocities, and/or a difference in myosin heavy chain (MHC) isoform content in chimpanzee relative to human skeletal muscle. Here, we show that chimpanzee muscle is similar to human muscle in its single-fiber contractile properties, but exhibits a much higher fraction of MHC II isoforms. Unlike humans, chimpanzee muscle is composed of ∼67% fast-twitch fibers (MHC IIa+IId). Computer simulations of species-specific whole-muscle models indicate that maximum dynamic force and power output is 1.35 times higher in a chimpanzee muscle than a human muscle of similar size. Thus, the superior mass-specific muscular performance of chimpanzees does not stem from differences in isometric force-generating capabilities or maximum shortening velocities—as has long been suggested—but rather is due in part to differences in MHC isoform content and fiber length. We propose that the hominin lineage experienced a decline in maximum dynamic force and power output during the past 7–8 million years in response to selection for repetitive, low-cost contractile behavior.
Alum Activates the Bovine NLRP3 Inflammasome

There has been a move away from vaccines composed of whole or inactivated antigens toward subunit-based vaccines, which although safe, provide less immunological protection. As a result, the use of adjuvants to enhance and direct adaptive immune responses has become the focus of much targeted bovine vaccine research. However, the mechanisms by which adjuvants work to enhance immunological protection in many cases remains unclear, although this knowledge is critical to the rational design of effective next generation vaccines. This study aimed to investigate the mechanisms by which alum, a commonly used adjuvant in bovine vaccines, enhances IL-1β secretion in bovine peripheral blood mononuclear cells (PBMCs). Unlike the case with human PBMCs, alum promoted IL-1β secretion in a subset of bovine PBMCs without priming with a toll-like receptor agonist. This suggests that PBMCs from some cattle are primed to produce this potent inflammatory cytokine and western blotting confirmed the presence of preexisting pro-IL-1β in PBMCs from a subset of 8-month-old cattle. To address the mechanism underlying alum-induced IL-1β secretion, specific inhibitors identified that alum mediates lysosomal disruption which subsequently activates the assembly of an NLRP3, ASC, caspase-1, and potentially caspase-8 containing complex. These components form an inflammasome, which mediates alum-induced IL-1β secretion in bovine PBMCs. Given the demonstrated role of the NLRP3 inflammasome in regulating adaptive immunity in murine systems, these results will inform further targeted research into the potential of inflammasome activation for rational vaccine design in cattle.
The cell wall and endoplasmic reticulum stress responses are coordinately regulated in Saccharomyces cerevisiae

The unfolded protein response (UPR) is an intracellular signaling pathway that regulates the cellular response to the accumulation of misfolded proteins in eukaryotes. Our group has demonstrated that cell wall stress activates UPR in yeast through signals transmitted by the cell wall integrity (CWI) mitogen-activated protein (MAP) kinase cascade. The UPR is required to maintain cell wall integrity; mutants lacking a functional UPR have defects in cell wall biosynthesis and are hypersensitive to cell wall-directed antifungal drugs. Since ER stress also activates CWI signaling, we propose that ER and cell wall stress responses are coordinated by CWI and UPR signaling pathways in order to protect cells against these related stressors. Further investigation of the mechanisms of this coordinate regulation may lead to improved cell wall-directed antifungal therapies.
Relative sensitivity of the Montgomery-Asberg Depression Rating Scale, the Hamilton Depression rating scale and the Clinical Global Impressions rating scale in antidepressant clinical trials

Although early antidepressant clinical trials simply relied on a clinician's judgment as to whether a depressed patient clinically improved or not, the Hamilton Depression (HAM-D) rating scale has become the ‘gold standard’ to assess the efficacy of new antidepressants. The alternative Montgomery-Asberg Depression Rating Scale (MADRS) has not achieved general acceptance. However, its ease of use warrants evaluation as to whether it is comparable to HAM-D in its sensitivity in detecting antidepressant-placebo differences in antidepressant clinical trials. A retrospective chart review was performed on the records of 208 depressed adult patients that participated in eight randomized, placebo-controlled, double-blind antidepressant clinical trials at the Northwest Clinical Research Center between 1996 and 2000. We compared the effect sizes of the HAM-D, MADRS and Clinical Impressions Rating Scale (CGI-S for severity and CGI-I for improvement) for patients assigned to placebo or an established antidepressant. The effect size (measured as the mean change in rating with antidepressants minus the mean change for placebo divided by the pooled SD of change, adjusted for age, gender and initial scores) was 0.49 with MADRS, 0.53 with HAM-D, 0.55 with CGI-S and 0.59 with CGI-I. The four rating scales had similar effect sizes regardless of the type of antidepressant evaluated. These data suggest that MADRS is as sensitive an instrument as HAM-D for detecting antidepressant efficacy in clinical trials. Thus, MADRS may be a desirable tool in large-scale, pivotal antidepressant clinical trials.