Miracle-dz/UniFAR-FTUs huggingface dataset:
Agricultural Landscape and Pesticide Effects on Honey Bee (Hymenoptera: Apidae) Biological Traits

Abstract Sixteen honey bee (Apis mellifera L.) colonies were placed in four different agricultural landscapes to study the effects of agricultural landscape and exposure to pesticides on honey bee health. Colonies were located in three different agricultural areas with varying levels of agricultural intensity (AG areas) and one nonagricultural area (NAG area). Colonies were monitored for their performance and productivity for one year by measuring colony weight changes, brood production, and colony thermoregulation. Palynological and chemical analyses were conducted on the trapped pollen collected from each colony and location. Our results indicate that the landscape’s composition significantly affected honey bee colony performance and development. Colony weight and brood production were significantly greater in AG areas compared to the NAG area. Better colony thermoregulation in AG areas’ colonies was also observed. The quantities of pesticides measured in the trapped pollen were relatively low compared to their acute toxicity. Unexplained queen and colony losses were recorded in the AG areas, while colony losses because of starvation were observed in the NAG area. Our results indicate that landscape with high urban activity enhances honey bee brood production, with no significant effects on colony weight gain. Our study indicates that agricultural crops provide a valuable resource for honey bee colonies, but there is a trade-off with an increased risk of exposure to pesticides.
Efficacy and safety of paritaprevir/ritonavir, ombitasvir, and dasabuvir with ribavirin for the treatment of HCV genotype 1b compensated cirrhosis in patients aged 70 years or older

Abstract Advanced age has been a major limitation of interferon-based treatment for chronic hepatitis C virus (HCV) infection because of its poor response and tolerability. Direct-acting antiviral (DAA) drug regimens are safe and highly effective, allowing administration of treatment also in elderly. This study aims to assess the efficacy and safety of paritaprevir/ritonavir, ombitasvir, and dasabuvir (PrOD) with ribavirin for the treatment of patients aged ≥70 years with HCV genotype 1b compensated cirrhosis. A total of 1008 patients with HCV genotype 1b compensated cirrhosis were prospectively treated with PrOD + ribavirin for 12 weeks, between December 2015 and July 2016. Sustained virologic response 12 weeks after the end of treatment (SVR12), adverse effects (AEs), comorbidities, discontinuation, and death rates were recorded. Efficacy and safety of therapy were assessed in patients aged ≥70 years and compared with data from patients <70 years. There were 117 patients aged ≥70 years, preponderantly females (58.9%), mean age 73.3 ± 2.8 years (range 70–82), and 37 (31.6%) were treatment-experienced. Comorbidities were reported in 60.6% of patients ≥70 years and in 39.8% of those <70 years (P < .001). SVR12 rates based on intention-to-treat and per-protocol analyses were 97.4% and 100%, respectively, in patients ≥70 years, compared to 97.8% and 99.6%, respectively, in patients <70 years (P = ns and P = ns). Severe AEs were reported in 4 (3.4%) patients ≥70 years, compared to 23 (2.6%) in those <70 years (P = ns). One death was recorded in a patient aged 79 years (0.9%) and 6 deaths (0.8%) in those <70 years (P = ns). Treatment with PrOD + ribavirin in patients 70 years of age or older with HCV genotype 1b compensated cirrhosis proved as effective, safe, and well tolerated, as it did in younger patients.
The nucleotide‐free state of heterotrimeric G proteins α‐subunit adopts a highly stable conformation

Deciphering the mechanism of activation of heterotrimeric G proteins by their cognate receptors continues to be an intriguing area of research. The recently solved crystal structure of the ternary complex captured the receptor‐bound α‐subunit in an open conformation, without bound nucleotide has improved our understanding of the activation process. Despite these advancements, the mechanism by which the receptor causes GDP release from the α‐subunit remains elusive. To elucidate the mechanism of activation, we studied guanine nucleotide‐induced structural stability of the α‐subunit (in response to thermal/chaotrope‐mediated stress). Inherent stabilities of the inactive (GDP‐bound) and active (GTP‐bound) forms contribute antagonistically to the difference in conformational stability whereas the GDP‐bound protein is able to switch to a stable intermediate state, GTP‐bound protein loses this ability. Partial perturbation of the protein fold reveals the underlying influence of the bound nucleotide providing an insight into the mechanism of activation. An extra stable, pretransition intermediate, ‘empty pocket’ state (conformationally active‐state like) in the unfolding pathway of GDP‐bound protein mimics a gating system – the activation process having to overcome this stable intermediate state. We demonstrate that a relatively more complex conformational fold of the GDP‐bound protein is at the core of the gating system. We report capturing this threshold, ‘metastable empty pocket’ conformation (the gate) of α‐subunit of G protein and hypothesize that the receptor activates the G protein by enabling it to achieve this structure through mild structural perturbation.
Redshift-Space Clustering of SDSS Galaxies — Luminosity Dependence, Halo Occupation Distribution, and Velocity Bias

We present the measurements and modelling of the small-to-intermediate scale (� 0.1‐ 25h 1 Mpc) projected and three-dimensional (3D) redshift-space two-point correlation functions (2PCFs) of local galaxies in the Sloan Digital Sky Survey (SDSS) Data Release 7. We find a clear dependence of galaxy clustering on luminosity in both projected and redshift spaces, generally being stronger for more luminous samples. The measurements are successfully interpreted within the halo occupation distribution (HOD) framework with central and satellite velocity bias parameters to describe galaxy kine matics inside haloes and to model redshift-space distortion (RSD) effects. In agreement wit h previous studies, we find that more luminous galaxies reside in more massive haloes. Including the redshift-space 2PCFs helps tighten the HOD constraints. Moreover, we find that luminous central galaxies are not at rest at the halo centres, with the velocity dispersion about 30% that of the dark matter. Such a relative motion may reflect the consequence of galaxy and halo me rgers, and we find that central galaxies in lower mass haloes tend to be more relaxed with respect to their host haloes. The motion of satellite galaxies in luminous samples is consist ent with their following that of the dark matter. For faint samples, satellites tends to have slo wer motion, with velocity dispersion inside haloes about 85% that of the dark matter. We discuss possible applications of the velocity bias constraints on studying galaxy evolution and cosmology. In the appendix, we characterize the distribution of galaxy redshift measurement errors, which is well described by a Gaussian-convolved double exponential distribution.
Role of Anterior Intralaminar Nuclei of Thalamus Projections to Dorsomedial Striatum in Incubation of Methamphetamine Craving

Relapse to methamphetamine (Meth) seeking progressively increases after withdrawal from drug self-administration (incubation of Meth craving). We previously demonstrated a role of dorsomedial striatum (DMS) dopamine D1 receptors (D1Rs) in this incubation. Here, we studied the role of afferent glutamatergic projections into the DMS and local D1R–glutamate interaction in this incubation in male rats. We first measured projection-specific activation on day 30 relapse test by using cholera toxin b (retrograde tracer) + Fos (activity marker) double-labeling in projection areas. Next, we determined the effect of pharmacological reversible inactivation of lateral or medial anterior intralaminar nuclei of thalamus (AIT-L or AIT-M) on incubated Meth seeking on withdrawal day 30. We then used an anatomical asymmetrical disconnection procedure to determine whether an interaction between AIT-L→DMS glutamatergic projections and postsynaptic DMS D1Rs contributes to incubated Meth seeking. We also determined the effect of unilateral inactivation of AIT-L and D1R blockade of DMS on incubated Meth seeking, and the effect of contralateral disconnection of AIT-L→DMS projections on nonincubated Meth seeking on withdrawal day 1. Incubated Meth seeking was associated with selective activation of AIT→DMS projections; other glutamatergic projections to DMS were not activated. AIT-L (but not AIT-M) inactivation or anatomical disconnection of AIT-L→DMS projections decreased incubated Meth seeking. Unilateral inactivation of AIT-L or D1R blockade of the DMS had no effect on incubated Meth craving, and contralateral disconnection of AIT-L→DMS projections had no effect on nonincubated Meth seeking. Our results identify a novel role of AIT-L and AIT-L→DMS glutamatergic projections in incubation of drug craving and drug seeking. SIGNIFICANCE STATEMENT Methamphetamine seeking progressively increases after withdrawal from drug self-administration, a phenomenon termed incubation of methamphetamine craving. We previously found that D1R-mediated dopamine transmission in the dorsomedial striatum plays a critical role in this incubation phenomenon. Here, we used neuroanatomical and neuropharmacological methods in rats to demonstrate that an interaction between the glutamatergic projection from the lateral anterior intralaminar nuclei of the thalamus to the dorsomedial striatum and local dopamine D1 receptors plays a critical role in relapse to methamphetamine seeking after prolonged withdrawal. Our study identified a novel motivation-related thalamostriatal projection critical to relapse to drug seeking.
Predicting the cardiac toxicity of drugs using a novel multiscale exposure–response simulator

Abstract A common but serious side effect of many drugs is torsades de pointes, a rhythm disorder that can have fatal consequences. Torsadogenic risk has traditionally been associated with blockage of a specific potassium channel and an increased recovery period in the electrocardiogram. However, the mechanisms that trigger torsades de pointes remain incompletely understood. Here we establish a computational model to explore how drug-induced effects propagate from the single channel, via the single cell, to the whole heart level. Our mechanistic exposure–response simulator translates block-concentration characteristics for arbitrary drugs into three-dimensional excitation profiles and electrocardiogram recordings to rapidly assess torsadogenic risk. For the drug of dofetilide, we show that this risk is highly dose-dependent: at a concentration of 1x, QT prolongation is 55% but the heart maintains its regular sinus rhythm; at 5.7x, QT prolongation is 102% and the heart spontaneously transitions into torsades de points; at 30x, QT prolongation is 132% and the heart adapts a quasi-depolarized state with numerous rapidly flickering local excitations. Our simulations suggest that neither potassium channel blockage nor QT interval prolongation alone trigger torsades de pointes. The underlying mechanism predicted by our model is early afterdepolarization, which translates into pronounced U waves in the electrocardiogram, a signature that is correctly predicted by our model. Beyond the risk assessment of existing drugs, our exposure–response simulator can become a powerful tool to optimize the co-administration of drugs and, ultimately, guide the design of new drugs toward reducing life threatening drug-induced rhythm disorders in the heart.
TAP-DLND 1.0 : A Corpus for Document Level Novelty Detection

Detecting novelty of an entire document is an Artificial Intelligence (AI) frontier problem that has widespread NLP applications, such as extractive document summarization, tracking development of news events, predicting impact of scholarly articles, etc. Important though the problem is, we are unaware of any benchmark document level data that correctly addresses the evaluation of automatic novelty detection techniques in a classification framework. To bridge this gap, we present here a resource for benchmarking the techniques for document level novelty detection. We create the resource via event-specific crawling of news documents across several domains in a periodic manner. We release the annotated corpus with necessary statistics and show its use with a developed system for the problem in concern.
Microscopy of Stained Urethral Smear in Male Urethritis; Which Cutoff Should be Used?

Background The microscopical diagnosis of male urethritis was recently questioned by Rietmeijer and Mettenbrink, lowering the diagnostic criteria of the diagnosis to ≥2 polymorphonuclear leucocytes (PMNL) per high power field (HPF), and adopted by Centers for Disease Control and Prevention in their 2015 STD Treatment Guidelines. The European Non-Gonococcal Urethritis Guideline advocates a limit of ≥5 PMNL/HPF. Objective To determine if syndromic treatment of urethritis should be considered with a cutoff value of ≥2 PMNL/HPF in urethral smear. Methods The design was a cross-sectional study investigating the presence and degree of urethritis relative to specific infections in men attending an STI clinic as drop-in patients. Results The material included 2 cohorts: a retrospective study of 13,295 men and a prospective controlled study including 356 men. We observed a mean chlamydia prevalence of 2.3% in the 0–9 stratum, and a 12-fold higher prevalence (27.3%) in the strata above 9. Of the chlamydia cases, 89.8% were diagnosed in strata above 9. For Mycoplasma genitalium, the prevalence was 1.4% in the 0–9 stratum and 11.2% in the stratum ≥10, and 83.6% were diagnosed in strata above 9. For gonorrhea, a significant increase in the prevalence occurred between the 0–30 strata and >30 strata from 0.2% to 20.7%. The results of the prospective study were similar. Conclusions Our data do not support lowering the cutoff to ≥2 PMNL/HPF. However, a standardization of urethral smear microscopy seems to be impossible. The cutoff value should discriminate between low and high prevalence of chlamydia, mycoplasma, and gonorrhea to include as many as possible with a specific infection in syndromic treatment, without overtreating those with few PMNL/HPF and high possibility of having nonspecific or no urethritis.
Analysis of the nonlinear dynamics of daily broiler growth and feed intake.

Daily BW velocity (BWV) and acceleration (BWA) of individual birds have been demonstrated to be oscillatory. Daily feed intake velocity (FIV) and acceleration (FIA) were hypothesized to be oscillatory and to have a positive relationship with BWV and BWA, respectively. Forty-eight male broiler chicks were individually caged and provided a commercial starter feed ad libitum for 49 d. BW and feed intake (FI) were measured daily. Experiment 1 confirmed that, on a daily basis, BWV, BWA, FIV, and FIA were oscillatory. There was a positive correlation between BW and FI, BWV and FIV, and BWA and FIA. A Kohonen neural network (KNN) clustered BWV and FIV into two and three sequential phases. BWA and FIA analysis did not make definitive clusters. In experiment 2, it was hypothesized that correlation between BWV and FIV would increase with feeding of grower and finisher rations. It was hypothesized that KNN three phase clusters may provide more biologically ideal times of ration change (TORC) for starter, grower, and finisher rations. For 49 d, five treatments, nine birds per treatment, were fed starter, grower, and finisher rations singly or together with dietary changes according to an industry or KNN-determined TORC. Evaluation was made of BW, FI, and carcass characteristics. No significant mean differences were found. Compared to the industry group, the KNN group demonstrated significantly improved uniformity (i.e., smaller SD) of BW (bled out), FI, dressing percentage, and some of the carcass characteristics. Differences between KNN and industry TORC results might have been related to the length of time the birds were fed the starter, grower, and finisher diets.
Ocean acidification affects coral growth by reducing skeletal density

Significance Ocean acidification (OA) threatens coral reef futures by reducing the concentration of carbonate ions that corals need to construct their skeletons. However, quantitative predictions of reef futures under OA are confounded by mixed responses of corals to OA in experiments and field observations. We modeled the skeletal growth of a dominant reef-building coral, Porites, as a function of seawater chemistry and validated the model against observational data. We show that OA directly and negatively affects one component of the two-step growth process (density) but not the other (linear extension). Combining our growth model with Global Climate Model output, we show that skeletal density of Porites corals could decline by up to 20.3% over the 21st century solely due to OA. Ocean acidification (OA) is considered an important threat to coral reef ecosystems, because it reduces the availability of carbonate ions that reef-building corals need to produce their skeletons. However, while theory predicts that coral calcification rates decline as carbonate ion concentrations decrease, this prediction is not consistently borne out in laboratory manipulation experiments or in studies of corals inhabiting naturally low-pH reefs today. The skeletal growth of corals consists of two distinct processes: extension (upward growth) and densification (lateral thickening). Here, we show that skeletal density is directly sensitive to changes in seawater carbonate ion concentration and thus, to OA, whereas extension is not. We present a numerical model of Porites skeletal growth that links skeletal density with the external seawater environment via its influence on the chemistry of coral calcifying fluid. We validate the model using existing coral skeletal datasets from six Porites species collected across five reef sites and use this framework to project the impact of 21st century OA on Porites skeletal density across the global tropics. Our model predicts that OA alone will drive up to 20.3 ± 5.4% decline in the skeletal density of reef-building Porites corals.
Thermo-Mechanical Behavior of Polymer Composites Exposed to Fire

One of the most critical issues for Polymer Matrix Composites (PMCs) in naval applications is the structural performance of composites at high temperature such as that experienced in a fire. A three-dimensional model including the effect of orthotropic viscoelasticity and decomposition is developed to predict the thermo-mechanical behavior and compressive failure of polymer matrix composites (PMCs) subjected to heat and compressive load. An overlaid element technique is proposed for incorporating the model into commercial finite element software ABAQUS. The technique is employed with the user subroutines to provide practicing engineers a convenient tool to perform analysis and design studies on composite materials subjected to combined fire exposure and mechanical loading. The resulting code is verified and validated by comparing its results with other numerical results and experimentally measured data from the one-sided heating of composites at small (coupon) scale and intermediate scale. The good agreement obtained indicates the capability of the model to predict material behavior for different composite material systems with different fiber stacking sequences, different sample sizes, and different combined thermo-mechanical loadings. In addition, an experimental technique utilizing Vacuum Assisted Resin Transfer Molding (VARTM) is developed to manufacture PMCs with a hypodermic needle inserted for internal pressure measurement. One-sided heating tests are conducted on the glass/vinyl ester composites to measure the pressure at different locations through thickness during the decomposition process. The model is employed to simulate the heating process and predict the internal pressure due to the matrix decomposition. Both predicted and measured results indicate that the range of the internal pressure peak in the designed test is around 1.1-1.3 atmosphere pressure.
Studies with corn-soya laying diets. 8. Requirements for limiting amino acids--the basal diet and the requirements for isoleucine, lysine and tryptophan.

Abstract LIMITED experimental data are available to document proposed amino acid requirement standards for laying pullets (National Research Council, 1966). The expression of requirements in terms of percent of the diet is becoming increasingly complex as new relationships among amino acids and between amino acids and other nutrients are recognized. For example, a favorable balance of amino acids tends to reduce the dietary protein requirement as demonstrated by Johnson and Fisher (1959). Since it is unlikely that the requirements for all amino acids vary in the same manner relative to the level of protein in the diet, the most useful requirement data for future reference will be those determined with amino acid-adequate diets that contain low levels of protein. In previous reports it was shown that corn-soya diets must contain 12% or less of protein to depress the performance of pullets during either long-term or short-term assays (Bray and Morrissey, 1962;…
Potential for Sulfoxaflor to Improve Conservation Biological Control of Aphis glycines (Hemiptera: Aphididae) in Soybean

Abstract Soybean aphid, Aphis glycines Matsumura, is one of the most important insect pests of soybean in the north central United States. Management of A. glycines currently relies on applications of broad-spectrum insecticides. However, broad-spectrum insecticides can negatively impact the natural enemies associated with aphids. Selective insecticides, on the other hand, are promising control tactics for reducing the negative impact of insecticide applications. Here, we compared the effects of sulfoxaflor (a new selective insecticide) and broad-spectrum insecticides on A. glycines and predators in a two-year field experiment. We sampled A. glycines and aphid predator populations using visual whole-plant inspection. In addition, sweep-net sampling was performed to monitor predator populations. To evaluate the toxicity of the insecticides on predator populations, laboratory bioassays were performed on Hippodamia convergens Guérin-Méneville, Orius insidiosus (Say), and Chrysoperla rufilabris (Burmeister). Field results showed that sulfoxaflor was as effective as the broad-spectrum insecticide in suppressing soybean aphid populations and was less impactful on predator populations. The laboratory bioassays showed that sulfoxaflor was moderately harmful to O. insidiosus, harmless to slightly harmful to H. convergens, and harmless to C. rufilabris. These studies suggest that sulfoxaflor holds promise for improving integration of chemical and biological controls for A. glycines management.