Miracle-dz/UniFAR-FTUs huggingface dataset:
Providing foraging resources for solitary bees on farmland: current schemes for pollinators benefit a limited suite of species

1. Changes in agricultural practice across Europe and North America have been associated with range contractions and a decline in the abundance of wild bees. Concerns at these declines has led to the development of flower-rich agri-environment schemes as a way to enhance bee diversity and abundance. Whilst the effect of these schemes on bumblebee species (Bombus spp.) has been well studied, their impact on the wider bee community is poorly understood. 2. We used direct observations of foraging bees and pollen load analysis to quantify the relative contribution that sown flowers (i.e. those included in agri-environment scheme seed mixes) make to the pollen diets of wild solitary bees on Higher Level Stewardship farms (HLS) implementing pollinator-focused schemes and on Entry Level Stewardship farms (ELS) without such schemes in southern England, UK. 3. HLS management significantly increased floral abundance, and as the abundance of sown flowers increased these sown plants were utilised for pollen by a greater proportion of the solitary bee species present. However, the overall proportion of pollen collected from sown plants was low for both direct observations (27.0%) and pollen load analysis (23.3%). 4. At most only 25 of the 72 observed species of solitary bee (34.7%) were recorded utilising sown plants to a meaningful degree. The majority of solitary bee species did not collect pollen from flower species sown for pollinators. 5. Total bee species richness was significantly associated with plant species richness, but there was no difference in the total species richness of either bee or flowering plant species between HLS and ELS farms. 6. Synthesis and applications. These results show that the majority of solitary bee species present on farmland in the south-east of England collect the majority of their pollen from plants that persist unaided in the wider environment, not from those included in agri-environment schemes focused on pollinators. If diverse bee communities are to be maintained on farmland, existing schemes should contain an increased number of flowering plant species and additional schemes that increase the diversity of flowering plants in complementary habitats should be studied and trialled.
Uncertainty propagation and analysis of image-guided surgery

A successful image-guided surgical intervention requires accurate measurement of coordinate systems. Uncertainty is introduced every time a pose is measured by the optical tracking system. When we transform a measured pose into a different coordinate system, the covariance (which encodes the uncertainty of the pose) must be propagated to this new coordinate system. In this paper, we describe a method for propagating covariances estimated from registration, tracking, and instrument calibration into the tip of the surgical tool. This is clinically important, since it is at the tool tip that the clinician cares about uncertainty. We demonstrate that the propagation method, which is computed in real time as the tool moves through space, reliably computes the propagated covariance by comparing our estimate to true covariances from Monte Carlo simulations.
Stability analysis for a partial element equivalent circuit (PEEC) model of neutral type

This paper is concerned with the robust stability analysis problem for a partial element equivalent circuit (PEEC) model of neutral type. Based on the Lyapunov stability theory and a linear matrix inequality (LMI) approach, some sufficient delay-dependent stability conditions are derived. A numerical example shows that the result using the method in the paper is less conservative than that using some existing methods in the literature.
Fresh-Squeezed Orange Juice Properties Before and During In Vitro Digestion as Influenced by Orange Variety and Processing Method.

This study aims to analyze the influence of processing and orange variety on initial quality, antioxidant activity, total polyphenol content (TPC), and ascorbic acid content of fresh-squeezed orange juice during in vitro digestion. Fresh-squeezed orange juice was made from Fukumoto Navel, Lane Late Navel, Olinda Nucellar Valencia, and Campbell Valencia oranges, and was processed thermally and nonthermally. Antioxidant activity (FRAP and ABTS assays), TPC (Folin-Ciocalteu method), and ascorbic acid were analyzed before and after gastrointestinal digestion. Bioaccessibility was calculated by comparing the measured values after digestion with the initial value for each juice. Orange variety significantly influenced pH, acidity, and total soluble solids (P < 0.0001). Antioxidant activity by FRAP was significantly higher (P < 0.0001) in Fukumoto Navel orange juice (16.0 ± 0.4 mM Trolox) than the other juices (range: 9.1 to 10 mM Trolox). TPC was significantly influenced by orange variety (P < 0.0001) and ranged from 521 ± 6 (Campbell Valencia) to 800 ± 11 mg gallic acid/L (Lane Late Navel). Processing method did not influence antioxidant and polyphenol bioaccessibility (P > 0.05). However, antioxidant activity by ABTS and ascorbic acid bioaccessibility were significantly influenced by orange variety (P < 0.0001). These results indicate that fruit variety and nutrient bioaccessibility should be considered to optimize processing and formulation parameters. PRACTICAL APPLICATION Processing method and variety of fruit during beverage manufacturing may influence its nutrient bioaccessibility. We present a detailed examination of the influence of orange variety, harvest time, and processing method on initial quality parameters and antioxidant bioaccessibility. It is recommended that nutritional analysis of beverages take into consideration both the bioaccessibility of nutrients and the initial nutrient content of the beverage. These results can be used for juice processors to take into consideration the harvest season and produce variety to manufacture beverages with higher nutritional quality.
Invited Review Vitamin D and skin cancer

Vitamin D signaling plays a key role in various important processes, including cellular proliferation, differentiation, and apoptosis, immune regulation, hormone secretion, and skeletal health. Further, vitamin D production and supplementation have been shown to exert protective effects via an unknown signaling mechanism involving the vitamin D receptor (VDR) in several diseases and cancer types, including skin cancer. With over 3.5 million new diagnoses in 2 million patients annually, skin cancer is the most common cancer type in the United States. While ultraviolet B (UVB) radiation is the main etiologic factor for non-melanoma skin cancer (NMSC), UVB also induces cutaneous vitamin D production. This paradox has been the subject of contradictory findings in the literature in regards to amount of sun exposure necessary for appropriate vitamin D production, as well as any beneficial or detrimental effects of vitamin D supplementation for disease prevention. Further clinical and epidemiological studies are necessary to elucidate the role of vitamin D in skin carcinogenesis.
The Neuroscience of Stigma and Stereotype Threat

This article reviews social neuroscience research on the experience of stigma from the target's perspective. More specifically, we discuss several research programs that employ electroencephalography, event-related potentials, or functional magnetic resonance imaging methods to examine neural correlates of stereotype and social identity threat. We present neuroimaging studies that show brain activation related to the experience of being stereotyped and ERP studies that shed light on the cognitive processes underlying social identity processes. Among these are two projects from our own lab. The first project reveals the important role of the neurocognitive conflict-detection system in stereotype threat effects, especially as it pertains to stereotype threat `spillover'. The second project examines the role of automatic ingroup evaluations as a neural mediator between social identity threats and compensatory ingroup bias. We conclude with a discussion of the benefits, limitations, and unique contributions of social neuroscience to our understanding of stigma and social identity threat.
CD10-positive mantle cell lymphoma: clinicopathologic and prognostic study of 30 cases

Mantle cell lymphoma is usually negative for CD10 which is useful in distinguishing MCL from other CD10 + B cell lymphomas. Here we assessed the clinicopathologic features of 30 cases of CD10+ MCL, the largest series to date in the English literature, and compared them with a group of 212 typical MCL cases (CD5+, CD10-negative, CD23-negative, cyclin D1+). The 30 patients with CD10+ MCL included 17 men and 13 women with a median age of 68 years. Compared with CD10-negative MCL, patients with CD10+ MCL showed a lower male predominance (p = 0.01), more often had a diffuse growth pattern (p = 0.04) and blastoid/pleomorphic morphology (p < 0.0001), and more often showed BCL6 expression (p = 0.009). In all MCL patients, CD10 expression was not associated with overall survival (OS) (p = 0.16). However, in more aggressive subsets of MCL patients including those with high Ki67 (> 60%), blastoid/pleomorphic morphology, or high MCL International Prognostic Index (MIPI), CD10 expression was associated with a worse OS (p = 0.003, 0.04, and 0.001, respectively). High Ki67 (> 60%), blastoid/pleomorphic morphology, and high MIPI were also been identified as poor prognostic factors patients with in CD10+ MCL (p = 0.001, 0.0003, and 0.01, respectively). In summary, CD10+ MCL more often has a diffuse growth pattern, blastoid/pleomorphic morphology, and BCL6 expression. In MCL patients with a high Ki-67 (> 60%), blastoid/pleomorphic morphology, or high MIPI, CD10 expression contributes to an even worse prognosis. MCL should be included in the differential diagnosis of CD10 + B cell lymphomas.
Boredom Begs to Differ: Differentiation From Other Negative Emotions

Boredom research is booming. Nonetheless, a comprehensive understanding of boredom in relation to other negative emotions is lacking. This ambiguity impedes accurate interpretation of boredom’s causes and consequences. To gain more insights into boredom, we examined in detail how it differs from a range of other negative experiences, namely sadness, anger, frustration, fear, disgust, depression, guilt, shame, regret, and disappointment. Our research indicates that the appraisals associated with boredom distinguish it clearly from other negative emotions; conceptually (Study 1), in terms of state experiences (Study 2), and in terms of individual differences in these experiences (Study 3). Our findings suggest that boredom is mild in negative valence, low in arousal, is associated with low perceived challenge and low perceived meaningfulness, and has low relevance to moral judgment and behavior. Boredom also involves low attention given to situations and tasks, and the lack of perceived meaningfulness and attention associated with boredom emerged as particularly distinctive characteristics. The findings underscore the importance of carefully discriminating boredom from other emotions in experimental induction, psychometric assessment, and conceptual discussion.
Study of Al1–xTixB2 Particles Extracted from Al–Ti–B Alloys

Abstract Al1–xTixB2 particles extracted from Al–Ti–B alloys have been investigated by means of a transmission electron microscope equipped with an X-ray energy-dispersive spectroscopic analyser. The solid solubility Al1–xTixB2 was found to be unlimited (0 ≤ x ≤ 1). The composition of boride particles extracted from an Al–Ti–B alloy with a composition within the solid solubility range was widely spread, whereas it was close to TiB2 for Ti concentrations in excess of the TiB2 stoichiometry. The particle size varied from 0.02 to 2 μm. The largest particles were almost pure TiB2 or AlB2, but the small ones were solid solutions of varying compositions. Those small particles tended to form relatively large agglomerates. Due to impurities in the master alloys, vanadium was present in some boride particles, implying that we actually have an Al1–x(Ti1–yVy)xB2 solid solution (0 ≤ x + y ≤ 1). The y value was found to vary within the range 0 ≤ y ≤ 0.07. It was found that master alloys containing boride particles with a narrow size distribution and a composition close to TiB2 gives better grain refinement results than master alloys with wide distributions of particle size and composition.
A new approach for sparse matrix vector product on NVIDIA GPUs

The sparse matrix vector product (SpMV) is a key operation in engineering and scientific computing and, hence, it has been subjected to intense research for a long time. The irregular computations involved in SpMV make its optimization challenging. Therefore, enormous effort has been devoted to devise data formats to store the sparse matrix with the ultimate aim of maximizing the performance. Graphics Processing Units (GPUs) have recently emerged as platforms that yield outstanding acceleration factors. SpMV implementations for NVIDIA GPUs have already appeared on the scene. This work proposes and evaluates a new implementation of SpMV for NVIDIA GPUs based on a new format, ELLPACK‐R, that allows storage of the sparse matrix in a regular manner. A comparative evaluation against a variety of storage formats previously proposed has been carried out based on a representative set of test matrices. The results show that, although the performance strongly depends on the specific pattern of the matrix, the implementation based on ELLPACK‐R achieves higher overall performance. Moreover, a comparison with standard state‐of‐the‐art superscalar processors reveals that significant speedup factors are achieved with GPUs. Copyright © 2010 John Wiley & Sons, Ltd.
Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties

Abstract Genomic islands are genomic fragments of alien origin in bacterial and archaeal genomes, usually involved in symbiosis or pathogenesis. In this work, we described Zisland Explorer, a novel tool to predict genomic islands based on the segmental cumulative GC profile. Zisland Explorer was designed with a novel strategy, as well as a combination of the homogeneity and heterogeneity of genomic sequences. While the sequence homogeneity reflects the composition consistence within each island, the heterogeneity measures the composition bias between an island and the core genome. The performance of Zisland Explorer was evaluated on the data sets of 11 different organisms. Our results suggested that the true-positive rate (TPR) of Zisland Explorer was at least 10.3% higher than that of four other widely used tools. On the other hand, the new tool did not lose overall accuracy with the improvement in the TPR and showed better equilibrium among various evaluation indexes. Also, Zisland Explorer showed better accuracy in the prediction of experimental island data. Overall, the tool provides an alternative solution over other tools, which expands the field of island prediction and offers a supplement to increase the performance of the distinct predicting strategy. We have provided a web service as well as a graphical user interface and open-source code across multiple platforms for Zisland Explorer, which is available at http://cefg.uestc. edu.cn/Zisland_Explorer/ or http://tubic.tju. edu.cn/Zisland_Explorer/.
Can asexuality confer a short-term advantage? Investigating apparent biogeographic success in the apomictic triploid fern Myriopteris gracilis.

PREMISE OF THE STUDY Although asexual taxa are generally seen as evolutionary dead ends, asexuality appears to provide a short-term benefit in some taxa, including a wider geographic distribution compared to sexual relatives. However, this may be an illusion created by multiple, morphologically cryptic, asexual lineages, each occupying a relatively small area. In this study we investigate the role of multiple lineages in the biogeography of Myriopteris gracilis Fée (Pteridaceae), a North American apomictic triploid fern species with a particularly large range. METHODS Range-wide asexuality was assessed by counting spores/sporangium in 606 Myriopteris gracilis specimens from across the species range, and lineage structure was assessed with both plastid DNA sequence and Genotyping By Sequencing (GBS) SNP datasets. KEY RESULTS Spore counting of >600 specimens identified no sexual populations, establishing that Myriopteris gracilis is exclusively asexual. The plastid data estimated the crown age of M. gracilis at ca. 2.5 mya and identified two lineages, each largely confined to the eastern or western portions of the range. These groups were further subdivided by the GBS data, revealing at least seven asexual lineages of varying geographic distributions, each occupying a relatively small portion of the total range of M. gracilis. CONCLUSIONS Although maintained exclusively through asexual reproduction, the broad distribution of Myriopteris gracilis is a compilation of numerous, independently formed asexual lineages. Since no single asexual lineage occupies the full extent of the species distribution, recurrent lineage formation should be considered when evaluating the short-term benefit of asexuality in this taxon and others.
MicroRNA-124 suppresses Slug-mediated lung cancer metastasis.

OBJECTIVE Non-small cell lung cancer (NSCLC) is the most common type of lung cancer but its carcinogenesis remains not completely elucidated. Dysregulation of microRNAs (miRNAs) is involved in the development of various cancers, including NSCLC, whereas a role of miR-124 in the pathogenesis of NSCLC has not been reported. Here we addressed these questions. PATIENTS AND METHODS We examined the levels of Slug and miR-124 in NSCLC tissue, compared to the adjacent non-tumor tissue. We also examined the relationship between miR-124 and Slug. The levels of miR-124 were then modified in NSCLC cells, and then the effects on cell invasion were evaluated. RESULTS We detected significantly higher levels of Slug and significantly lower levels of miR-124 in NSCLC tissue, compared to the adjacent non-tumor tissue, and the values of miR-124 and Slug were inversely correlated. Moreover, the low miR-124 levels in NSCLC specimens were associated with poor survival of the patients. In vitro, overexpression of miR-124 significantly inhibited cell invasion, while depletion of miR-124 increased cell invasion in NSCLC cells. The effects of miR-124 on cell growth appeared to result from its regulation of Slug. CONCLUSIONS Our study highlights miR-124 as a previously unrecognized factor that controls NSCLC invasiveness, and the findings here may be important for developing an innovative therapeutic treatment for NSCLC.
OPPOSING NATURAL SELECTION FROM HERBIVORES AND PATHOGENS MAY MAINTAIN FLORAL‐COLOR VARIATION IN CLAYTONIA VIRGINICA (PORTULACACEAE)

Abstract The maintenance of floral‐color variation within natural populations is enigmatic because directional selection through pollinator preferences combined with random genetic drift should lead to the rapid loss of such variation. Fluctuating, balancing, and negative frequency‐dependent selection mediated through pollinators have been identified as factors that may contribute to the maintenance of floral‐color variation, and recently it has been suggested that indirect responses to selection on correlated characters through agents of selection other than pollinators may substantially shape the evolution of floral traits. Here, I provide empirical support for this latter view in Claytonia virginica (Portulacaceae) through a multiseason field study, a pollen supplementation study, and an artificial herbivory experiment. These studies show that most individuals fall into one of four discrete color classes, and suggest pollinatormediated selection for increased floral redness in concurrent years. Floral color is also an indirect target of opposing directional selection via herbivores and pathogens that fluctuates through time. Taken together, these data suggest a novel mechanism by which floral‐color variation may be maintained, and illustrate the importance of an inclusive, pluralistic view of selection when investigating the evolution of complex phenotypes.
Audience Costs : Bargaining In The Shadow of Elections

In the spring of 2008, a survey experiment was conducted in which a large sample of Georgian respondents were asked to imagine hypothetical escalation scenarios along the internally-disputed border regions of Abkhazia and South Ossetia. A 2x2 randomization design varied whether Georgia’s then-president, Mikheil Saakashvili, escalated the conflict or was attacked, and whether the military adventure was a success or failure. The situation changed from a hypothetical thought experiment into reality only a few months later, when a war broke out between Georgia and Russia in these regions. A postwar survey found that at least some respondents believe they lived through each of the four experimental conditions in the initial survey experiment. Matching methods show that respondents, reflecting on the events of an actual war, evaluated their leader’s crisis behavior di↵erently than in the survey experiment, and in a manner more consistent with the base assumptions of the audience costs literature. Georgian respondents that believe their president was responsible for baiting the Russians into conflict evaluate his job performance negatively; respondents who believe their leader was merely responding to Russia have higher evaluations of their leader’s performance even if he lost the contest. E↵ects are statistically significant and robust to numerous controls. This is a draft. Please do not cite or circulate.
Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair*

Repair of DNA double strand breaks (DSBs) is key for maintenance of genome integrity. When DSBs are repaired by homologous recombination, DNA ends can undergo extensive processing, producing long stretches of single-stranded DNA (ssDNA). In vivo, DSB processing occurs in the context of chromatin, and studies indicate that histones may remain associated with processed DSBs. Here we demonstrate that histones are not evicted from ssDNA after in vitro chromatin resection. In addition, we reconstitute histone-ssDNA complexes (termed ssNucs) with ssDNA and recombinant histones and analyze these particles by a combination of native gel electrophoresis, sedimentation velocity, electron microscopy, and a recently developed electrostatic force microscopy technique, DREEM (dual-resonance frequency-enhanced electrostatic force microscopy). The reconstituted ssNucs are homogenous and relatively stable, and DREEM reveals ssDNA wrapping around histones. We also find that histone octamers are easily transferred in trans from ssNucs to either double-stranded DNA or ssDNA. Furthermore, the Fun30 remodeling enzyme, which has been implicated in DNA repair, binds ssNucs preferentially over nucleosomes, and ssNucs are effective at activating Fun30 ATPase activity. Our results indicate that ssNucs may be a hallmark of processes that generate ssDNA, and that posttranslational modification of ssNucs may generate novel signaling platforms involved in genome stability.