Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing Alternative Methods for Holding Virgin Honey Bee Queens for One Week in Mailing Cages before Mating

In beekeeping, queen honey bees are often temporarily kept alive in cages. We determined the survival of newly-emerged virgin honey bee queens every day for seven days in an experiment that simultaneously investigated three factors: queen cage type (wooden three-hole or plastic), attendant workers (present or absent) and food type (sugar candy, honey, or both). Ten queens were tested in each of the 12 combinations. Queens were reared using standard beekeeping methods (Doolittle/grafting) and emerged from their cells into vials held in an incubator at 34C. All 12 combinations gave high survival (90 or 100%) for three days but only one method (wooden cage, with attendants, honey) gave 100% survival to day seven. Factors affecting queen survival were analysed. Across all combinations, attendant bees significantly increased survival (18% vs. 53%, p<0.001). In addition, there was an interaction between food type and cage type (p<0.001) with the honey and plastic cage combination giving reduced survival. An additional group of queens was reared and held for seven days using the best method, and then directly introduced using smoke into queenless nucleus colonies that had been dequeened five days previously. Acceptance was high (80%, 8/10) showing that this combination is also suitable for preparing queens for introduction into colonies. Having a simple method for keeping newly-emerged virgin queens alive in cages for one week and acceptable for introduction into queenless colonies will be useful in honey bee breeding. In particular, it facilitates the screening of many queens for genetic or phenotypic characteristics when only a small proportion meets the desired criteria. These can then be introduced into queenless hives for natural mating or insemination, both of which take place when queens are one week old.
ACES: adaptive clock estimation and synchronization using Kalman filtering

Clock synchronization across a network is essential for a large number of applications ranging from wired network measurements to data fusion in sensor networks. Earlier techniques are either limited to undesirable accuracy or rely on specific hardware characteristics that may not be available for certain systems. In this work, we examine the clock synchronization problem in resource-constrained networks such as wireless sensor networks where nodes have limited energy and bandwidth, and also lack the high accuracy oscillators or programmable network interfaces some previous protocols depend on. This paper derives a general model for clock offset and skew and demonstrates its applicability. We design efficient algorithms based on this model to achieve high synchronization accuracy given limited resources. These algorithms apply the Kalman filter to track the clock offset and skew, and adaptively adjust the synchronization interval so that the desired error bounds are achieved. We demonstrate the performance advantages of our schemes through extensive simulations obeying real-world constraints.
Bridging the Resolution Gap: Imaging the Same Transcription Factories in Cryosections by Light and Electron Microscopy

The resolution of conventional light microscopy is limited to ∼200 nm in the x- and y-axes and <500 nm in the z-axis. A simple way of improving z-axis resolution is to analyze thin sections of 100–200 nm. The utility of such an approach is illustrated by reference to transcription sites imaged in cryosections of human nuclei. Cells are permeabilized, allowed to extend nascent transcripts in Br-UTP, fixed, cryosectioned, and Br-RNA-immunolabeled with fluorochromes and gold particles. As expected, physical sectioning improves resolution and brings other advantages. First, sections allow improved antibody access and better immunolabeling. Second, more sites (with a more representative range of intensities) can now be resolved against lower backgrounds, facilitating quantitative analysis. Third, problems associated with chromatic aberration when two differently colored images of the same objects are collected can be sidestepped by refocusing between image collection. Fourth, exactly the same sites can be imaged by light and electron microscopy, allowing direct comparison between the two techniques. Immunogold labeling and electron microscopy provided the most accurate counts of site number. The results confirm that nascent transcripts in the nucleoplasm are confined to several thousand sites, or “factories,” with diameters of ∼40 nm.
Explicit Representation of Antonymy in Language Modeling

The word vectors learned by continuous space language models are known to have the property that the vectors of synonymous words have cosine similarities close to one. To date, however, the relation of antonymy has not been captured in these models. In this paper, we demonstrate that by incorporating prior information from a thesaurus as an extra term in the language model objective function, the induced word vectors are useful not only for language modeling, but also for modeling both synonymy and antonymy. The learned vectors have the property that the vectors of antonymous words tend to have cosine similarities close to negative one, while synonymous words retain similarity close to positive one. We show that with a small penalty in language model perplexity, the induced word vectors do very well on a standard GRE test of opposites.
Laboratory Typing Methods for Diagnostic of Salmonella Strains, the “Old” Organism That Continued Challenges

Salmonella are enteric gram negative organisms that are widely dispersed in nature. These organisms can reside as common commensals in the gastrointestinal tracts of animals and man or cause disease states that range from self-limited diarrhea to bacteremia with enteric fever or invasion of vascular structures, bone or other localized sites (Hook, 1990). Organisms can be highly host adapted, where they infect only a limited number of species, or can be much more ubiquitous. The most significant human host-adapted organism is S. typhi, the cause of typhoid fever. Man remains the only known reservoir for these isolates. Similarly, S. pullorum and S. gallinarum are poultry associated organisms that are so hostadapted that even upon transmission to man they usually remain non-pathogenic (Ziprin & Hume, 2001). More frequently, animal host-adapted organisms can be transmitted to man causing symptomatic disease. S. choleraesuis is normally a porcine organism though it can cause gastroenteritis and enteric fever, when transmitted to man (especially in children). Other organisms, such as S. typhimurium, have a broad host range and these serotypes are responsible for the majority of human infections. Thus, Salmonella strains, the well and “old” pathogens, continued threat to public health. In fact, despite that, the incidence of salmonellosis has decreased substantially especially in developed country, recent events and several articles illustrate continued challenges in Salmonella control. The first challenge in Salmonella control is the widespread distribution of food; in fact contaminated food produced in one country may cause illness far away demonstrating the importance of robust control programmes. Likewise, this organism cause substantial economic loss resulting from mortality, morbidity, poor growth of infected animals, poultry and human beings; hazardous of transmitting food poisoning with gastroenteritis to human and so represents a serous problem for the food industry (Khan et al., 2007). The second challenge is traceability, in fact, the complexity of the food supply chains and/ or the lack of identifying markers on foods can make it extremely difficult to trace back to their origin.
The Cellular Ataxia Telangiectasia-Mutated Kinase Promotes Epstein-Barr Virus Lytic Reactivation in Response to Multiple Different Types of Lytic Reactivation-Inducing Stimuli

ABSTRACT The Epstein-Barr virus (EBV) latent-to-lytic switch is mediated by the viral proteins BZLF1 (Z), BRLF1 (R), and BRRF1 (Na). Since we previously showed that DNA-damaging agents (including chemotherapy and irradiation) can induce EBV lytic reactivation and recently demonstrated that wild-type p53 contributes to lytic reactivation, we investigated the role of the ATM kinase during EBV reactivation. ATM phosphorylates and activates p53, as well as numerous other substrates involved in the cellular DNA damage response. Using an ATM inhibitor (KU55933), we found that ATM activity is required for efficient induction of EBV lytic gene expression by a variety of different stimuli, including a histone deacetylase (HDAC) inhibitor, the transforming growth factor β (TGF-β) cytokine, a demethylating agent (5-azacytidine), B cell receptor engagement with anti-IgG antibody, hydrogen peroxide, and the proteosome inhibitor bortezomib. In EBV-infected AGS (gastric) cells, knockdown of ATM, or p53, expression inhibits EBV reactivation. Conversely, treatment of these cells with nutlin-3 (which activates p53 and ATM) robustly induces lytic reactivation in a p53- and ATM-dependent manner. The ability of the EBV R and Na proteins to induce lytic reactivation in EBV-infected AGS cells is ATM dependent. However, overexpression of Z induces lytic gene expression in the presence or absence of ATM activity. Our results suggest that ATM enhances Z promoter activity in the context of the intact EBV genome and that p53 contributes to the ATM effect. Nevertheless, since we found that ATM inhibitors also reduce lytic reactivation in Burkitt lymphoma cells that have no p53, additional ATM substrates must also contribute to the ATM effect.
Integrin expression and function in the response of primary culture hepatic stellate cells to connective tissue growth factor (CCN2)

Production of connective tissue growth factor (CCN2, also known as CTGF) is a hallmark of hepatic fibrosis. This study examined early primary cultures of hepatic stellate cells (HSC) for (i) CCN2 regulation of its cognate receptor integrin subunits; and (ii) interactions between CCN2 and integrin α5β1, heparan sulphate proteoglycans (HSPG) or fibronectin (FN) in supporting cell adhesion. HSC were isolated from healthy male Balb/c mice. mRNA levels of CCN2 or α5, β1, αv or β3 integrin subunits were measured in days 1–7 primary culture HSC, and day 3 or day 7 cells treated with recombinant CCN2 or CCN2 small interfering RNA. Interactions between CCN2 and integrin α5β1, HSPG or FN were investigated using an in vitro cell adhesion assay. Co‐incident with autonomous activation over the first 7 days, primary culture HSC increasingly expressed mRNA for CCN2 or integrin subunits. Addition of exogenous CCN2 or knockdown of endogenous CCN2 differentially regulated integrin gene expression in day 3 versus day 7 cells. Either full length CCN2 (‘CCN21–4’) or residues 247–349 containing module 4 alone (‘CCN24’) supported day 3 cell adhesion in an integrin α5β1‐ and HSPG‐dependent fashion. Adhesion of day 3 cells to FN was promoted in an integrin α5β1‐dependent manner by CCN21–4 or CCN24, whereas FN promoted HSPG‐dependent HSC adhesion to CCN21–4 or CCN24. These findings suggest CCN2 regulates integrin expression in primary culture HSC and supports HSC adhesion via its binding of cell surface integrin α5β1, a novel CCN2 receptor in primary culture HSC which interacts co‐operatively with HSPG or FN.
Interfirm Mobility, Wages, and the Returns to Seniority and Experience in the U.S.

Much of the research in labor economics during the 1980s and the early 1990s was devoted to the analysis of changes in the wage structure across many of the world's economies. Only recently, has research turned to the analysis of mobility in its various guises. From the life cycle perspective, decreased wage mobility and increased job instability, makes the phenomenon of increasing wage inequality more severe than it appears to be at first sight. In general, workers' wages may change through two channels: (a) return to their firm-specific human capital (seniority); or (b) inter-firm wage mobility. Our theoretical model gives rise to three equations: (1) a participation equation; (2) a wage equation; and (3) an interfirm mobility equation. In this model the wage equation is estimated simultaneously with the two decision equations. We use the Panel Study of Income Dynamics (PSID) to estimate the model for three education groups. Our main finding is that returns to seniority are quite high for all education groups. On the other hand, the returns to experience appear to be similar to those previously found in the literature.
Opus: University of Bath Online Publication Store Advanced Mathematical Study and the Development of Conditional Reasoning Skills

This version is made available in accordance with publisher policies. Please cite only the published version using the reference above. Abstract Since the time of Plato, philosophers and educational policy-makers have assumed that the study of mathematics improves one's general 'thinking skills'. Today, this argument, known as the 'Theory of Formal Discipline' is used in policy debates to prioritize mathematics in school curricula. But there is no strong research evidence which justifies it. We tested the Theory of Formal Discipline by tracking the development of conditional reasoning behavior in students studying post-compulsory mathematics compared to post-compulsory English literature. In line with the Theory of Formal Discipline, the mathematics students did develop their conditional reasoning to a greater extent than the literature students, despite them having received no explicit tuition in conditional logic. However, this development appeared to be towards the so-called defective conditional understanding, rather than the logically normative material conditional understanding. We conclude by arguing that Plato may have been correct to claim that studying advanced mathematics is associated with the development of logical reasoning skills, but that the nature of this development may be more complex than previously thought. Copyright: ß 2013 Attridge, Inglis. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
The Reliability and Validity of the Psychopathy Checklist–Revised in a Sample of Female Offenders

The reliability and validity of the Psychopathy Checklist–Revised (PCL–R) was examined in a sample of 528 nonpsychotic female offenders participating in a study assessing the generalizability of the instrument to females using personality, attitudinal, and laboratory behavioral measures. Results showed good interrater reliability and adequate internal consistency. Correlations with a number of self-report validity measures and previous criminal behavior provide support for the convergent validity of the instrument. A lack of association with general psychopathology provides support for the discriminant validity of the instrument. However, significant correlations with anxiety, negative affectivity, and intelligence run counter to expectations and to findings with male offenders. Furthermore, the low base rate of psychopathy in this sample, relative to base rates among male prisoners, raises the concern that either psychopathy is less prevalent in females than in males or the PCL–R is not adequately assessing the construct in female offenders.
Inflammation in Benign Prostate Tissue and Prostate Cancer in the Finasteride Arm of the Prostate Cancer Prevention Trial

Background: A previous analysis of the placebo arm of the Prostate Cancer Prevention Trial (PCPT) reported 82% overall prevalence of intraprostatic inflammation and identified a link between inflammation and higher-grade prostate cancer and serum PSA. Here, we studied these associations in the PCPT finasteride arm. Methods: Prostate cancer cases (N = 197) detected either on a clinically indicated biopsy or on protocol-directed end-of-study biopsy, and frequency-matched controls (N = 248) with no cancer on an end-of-study biopsy were sampled from the finasteride arm. Inflammation in benign prostate tissue was visually assessed using digital images of hematoxylin and eosin–stained sections. Logistic regression was used for statistical analysis. Results: In the finasteride arm, 91.6% of prostate cancer cases and 92.4% of controls had at least one biopsy core with inflammation in benign areas (P < 0.001 for difference compared with placebo arm). Overall, the odds of prostate cancer did not differ by prevalence [OR, 0.90; 95% confidence interval (CI), 0.44–1.84] or extent (P trend = 0.68) of inflammation. Inflammation was not associated with higher-grade disease (prevalence: OR, 1.07; 95% CI, 0.43–2.69). Furthermore, mean PSA concentration did not differ by the prevalence or extent of inflammation in either cases or controls. Conclusion: The prevalence of intraprostatic inflammation was higher in the finasteride than placebo arm of the PCPT, with no association with higher-grade prostate cancer. Impact: Finasteride may attenuate the association between inflammation and higher-grade prostate cancer. Moreover, the missing link between intraprostatic inflammation and PSA suggests that finasteride may reduce inflammation-associated PSA elevation. Cancer Epidemiol Biomarkers Prev; 25(3); 463–9. ©2015 AACR.
For personal use. Only reproduce with permission from The Lancet Publishing Group. Effect of sunlight and season on serotonin turnover in the brain

Background Thiomersal is a preservative containing small amounts of ethylmercury that is used in routine vaccines for infants and children. The effect of vaccines containing thiomersal on concentrations of mercury in infants' blood has not been extensively assessed, and the metabolism of ethylmercury in infants is unknown. We aimed to measure concentrations of mercury in blood, urine, and stools of infants who received such vaccines.
An Efficient Synthesis of Spiro[indoline-3,9′-xanthene]trione Derivatives Catalyzed by Magnesium Perchlorate

A simple and efficient method for the synthesis of spiro[indoline-3,9′-xanthene]trione derivatives by means of condensation between isatins and 1,3-cyclohexanedione in the presence of a catalytic amount of magnesium perchlorate at 80 °C in 50% aqueous ethanol medium has been described. Notably, the present method offers desirable advantages of good yields, simplicity of workup procedure, easy purification, and reduced reaction times.
Neuromyelitis Optica

Neuromyelitis optica is an autoimmune disorder that affects the nerves of the eyes and the central nervous system, which includes the brain and spinal cord. Autoimmune disorders occur when the immune system malfunctions and attacks the body's own tissues and organs. In neuromyelitis optica, the autoimmune attack causes inflammation of the nerves, and the resulting damage leads to the signs and symptoms of the condition.
A Common Cortical Circuit Mechanism for Perceptual Categorical Discrimination and Veridical Judgment

Perception involves two types of decisions about the sensory world: identification of stimulus features as analog quantities, or discrimination of the same stimulus features among a set of discrete alternatives. Veridical judgment and categorical discrimination have traditionally been conceptualized as two distinct computational problems. Here, we found that these two types of decision making can be subserved by a shared cortical circuit mechanism. We used a continuous recurrent network model to simulate two monkey experiments in which subjects were required to make either a two-alternative forced choice or a veridical judgment about the direction of random-dot motion. The model network is endowed with a continuum of bell-shaped population activity patterns, each representing a possible motion direction. Slow recurrent excitation underlies accumulation of sensory evidence, and its interplay with strong recurrent inhibition leads to decision behaviors. The model reproduced the monkey's performance as well as single-neuron activity in the categorical discrimination task. Furthermore, we examined how direction identification is determined by a combination of sensory stimulation and microstimulation. Using a population-vector measure, we found that direction judgments instantiate winner-take-all (with the population vector coinciding with either the coherent motion direction or the electrically elicited motion direction) when two stimuli are far apart, or vector averaging (with the population vector falling between the two directions) when two stimuli are close to each other. Interestingly, for a broad range of intermediate angular distances between the two stimuli, the network displays a mixed strategy in the sense that direction estimates are stochastically produced by winner-take-all on some trials and by vector averaging on the other trials, a model prediction that is experimentally testable. This work thus lends support to a common neurodynamic framework for both veridical judgment and categorical discrimination in perceptual decision making.
A Heuristic Algorithm for Deriving Compact Models of Processor Instruction Sets

Finding a compact formal representation of a processor instruction set is important for easier comprehension by the designer, as well as for synthesis of an efficient hardware implementation of the processor's microcontroller. We present a new heuristic algorithm for deriving compact models of processor instruction sets. The algorithm is based on finding similarities between pairs of instructions and assigning similar opcodes (using a Hamming distance metric) to similar instructions (using a newly introduced instruction similarity metric). We demonstrate that this heuristic produces results with an average overhead, in terms of area, of 7.8% in comparison to the global optimum on the benchmarks we studied (subsets of instructions of ARM Cortex M0+, Texas Instruments MSP430 and Intel 8051 processors). The algorithm is implemented as an open-source plugin for the Workcraft framework and is validated on a case study of a subset of 61 (out of 68) instructions of ARM Cortex M0+ processor. We compare the presented algorithm against a number of other available implementations.
Proteasome inhibition causes nigral degeneration with inclusion bodies in rats

Structural and functional defects in 26/20S proteasomes occur in the substantia nigra pars compacta and may underlie protein accumulation, Lewy body formation and dopaminergic neuronal death in Parkinson's disease. We therefore determined the pathogenicity of proteasomal impairment following stereotaxic unilateral infusion of lactacystin, a selective proteasome inhibitor, into the substantia nigra pars compacta of rats. These animals became progressively bradykinetic, adopted a stooped posture and displayed contralateral head tilting. Administration of apomorphine to lactacystin-treated rats reversed behavioral abnormalities and induced contralateral rotations. Lactacystin caused dose-dependent degeneration of dopaminergic cell bodies and processes with the cytoplasmic accumulation and aggregation of &agr;-synuclein to form inclusion bodies. These findings support the notion that failure of the ubiquitin-proteasome system to degrade and clear unwanted proteins is an important etiopathogenic factor in Parkinson's disease.