Miracle-dz/UniFAR-FTUs huggingface dataset:
Divergence in cuticular hydrocarbons between parapatric subspecies of the meadow grasshopper,chorthippus parallelus(Orthoptera, Acrididae)

Abstract Two subspecies of the grasshopper Chorthippus parallelus (Orthoptera; Acrididae) meet and form a hybrid zone in the Pyrenees. Here we investigate whether the subspecies differ in the blend of cuticular hydrocarbons. Such differences may function as chemical signals, being detected via contact chemoreception and used during mate choice as in other insects. Gas chromatography shows that the subspecies have diverged in the composition of their cuticular hydrocarbons. This difference between subspecies exists over and above variation in cuticular hydrocarbons among individual populations. The majority of the difference can be attributed to the relative amounts of a small group of compounds present in the cuticle. The possible consequences of this chemical divergence for mating encounters between the subspecies are discussed.
Physical Activity and Body Composition Are Associated With Severity and Risk of Depression, and Serum Lipids

Background Physical activity and a healthy body composition are said to reduce the risk of major depressive disorder. Nonetheless, deeper insight is needed into which specific forms of physical activity (and their relation to body composition) are effective in improving and preventing depressive symptoms. Methods We compared different self-reported physical activities of the Global Physical Activity Questionnaire and body composition measures between patients with a current major depressive episode (MDE; N = 130) and healthy control subjects (N = 61). These parameters were also tested for correlations with depression severity and serum lipid levels in patients and controls. Results Patients with a current MDE reported significantly fewer hours spent on total physical activity, walking or bicycling for travel, and vigorous-intensity activities at leisure than healthy control subjects. More time spent on vigorous-intensity activities at work, less time spent on walking or bicycling for travel, higher body fat mass, and lower body muscle mass correlated significantly with stronger depression severity. Physical activity and body measures correlated significantly with serum lipid levels. Limitations Self-reports of physical activity, only short-term follow-up of 20 days, cross-sectional study design without examination of causal role of exercise. Conclusions More time spent on traveling by foot or by bike is especially associated with a lower risk of and milder depression. These results highlight the differential role of physical activity in depression.
Comparison of Carboplatin With 5-Fluorouracil vs. Cisplatin as Concomitant Chemoradiotherapy for Locally Advanced Head and Neck Squamous Cell Carcinoma

Background: Chemoradiotherapy (CRT) including three cycles of cisplatin is considered the standard of care for locally advanced head and neck squamous cell carcinoma (LA-HNSCC). However, around one-third of the patients cannot complete cisplatin because of toxicity. Carboplatin plus 5-fluorouracil (carbo-5FU) is another accepted treatment option with a different toxicity profile. We compared tolerability and efficacy of concomitant carbo-5FU and cisplatin. Patients and Methods: We conducted a retrospective analysis of LA-HNSCC patients treated with CRT in two Dutch cancer centers between 2007 and 2016. All patients received intensity-modulated radiotherapy. One center routinely administered carboplatin 300–350 mg/m2 at day 1, 22, and 43 followed by 5FU 600 mg/m2/day for 96 h. The other center used cisplatin 100 mg/m2 at day 1, 22, and 43. The primary endpoint of this study was chemotherapy completion rate. Secondary endpoints included overall survival (OS), disease-free survival (DFS), locoregional control (LRC) and distant metastasis–free interval (DMFS), toxicity, and unplanned admissions. Results: In the carbo-5FU cohort (n = 211), 60.2% of the patients completed chemotherapy vs. 76.7% (p < 0.001) of the patients in the cisplatin cohort (n = 223). Univariate analysis showed a higher risk of death in the carbo-5FU cohort [hazard ratio (HR) 1.53, 95% CI, 1.09–2.14, p = 0.01] with a 3-year OS of 65.4 vs. 76.5% for cisplatin. OS was independently associated with T and N stage and p16 status, but not with chemotherapy regimen (HR 1.08, 95% CI, 0.76–1.55, p = 0.65). Three-year DFS was 70.0% for carbo-5FU vs. 78.6% for cisplatin (HR 1.37, 95% CI, 0.93–2.01, p = 0.05). A similar outcome was observed for both LRC (HR 1.27, 95% CI, 0.74–2.09, p = 0.4) and DMFS (HR 1.08, 95% CI 0.62–1.90, p = 0.77). The risk of discontinuation for chemotherapy-associated toxicity was higher in the carbo-5FU cohort than in the cisplatin cohort (relative risk = 1.69). Conclusion: LA-HNSCC patients treated with concomitant carbo-5FU completed chemotherapy less frequently than patients treated with cisplatin. Treatment regimen was not an independent prognostic factor for OS.
Chemoproteomic profiling of itaconation by bioorthogonal probes in inflammatory macrophages.

Itaconate is an anti-inflammatory metabolite involved in pathogen-macrophage interaction, but the mechanisms underlying its effect are not fully understood. Competitive cysteine profiling has been performed to interrogate itaconate's reactivity in cell lysates, however, methods for analyzing targets of itaconation directly in living macrophages are still lacking. Here we developed a specific bioorthogonal probe, itaconate-alkyne (ITalk), for quantitative and site-specific chemoproteomic profiling of itaconation in inflammatory macrophages. ITalk recapitulates the anti-inflammatory property of itaconate and enables biochemical evaluation and proteomic analysis of its direct targets. Our study delineates the widespread landscape of itaconate substrates, providing a versatile tool and comprehensive resource for investigating its function.
Evaluation of multi-antigen serological screening for active tuberculosis among people living with HIV

Better triage tests for screening tuberculosis (TB) disease are needed for people living with HIV (PLHIV). We performed the first evaluation of a previously-validated 8-antigen serological panel to screen PLHIV for pulmonary TB in Kampala, Uganda. We selected a random 1:1 sample with and without TB (defined by sputum culture) from a cohort of PLHIV initiating antiretroviral therapy. We used a multiplex microbead immunoassay and an ensemble machine learning classifier to determine the area under the receiver operating characteristic curve (AUC) for Ag85A, Ag85B, Ag85C, Rv0934-P38, Rv3881, Rv3841-BfrB, Rv3873, and Rv2878c. We then assessed the performance with the addition of four TB-specific antigens ESAT-6, CFP-10, Rv1980-MPT64, and Rv2031-HSPX, and every antigen combination. Of 262 participants (median CD4 cell-count 152 cells/μL [IQR 65–279]), 138 (53%) had culture-confirmed TB. The 8-antigen panel had an AUC of 0.53 (95% CI 0.40–0.66), and the additional 4 antigens did not improve performance (AUC 0.51, 95% CI 0.39–0.64). When sensitivity was restricted to ≥90% for the 8- and 12-antigen panel, specificity was 2.2% (95% CI 0–17.7%) and 8.1% (95% CI 0–23.9%), respectively. A three-antigen combination (Rv0934-P38, Ag85A, and Rv2031-HSPX) outperformed both panels, with an AUC of 0.60 (95% CI 0.48–0.73), 90% sensitivity (95% CI 78.2–96.7%) and 29.7% specificity (95% CI 15.9–47%). The multi-antigen panels did not achieve the target accuracy for a TB triage test among PLHIV. We identified a new combination that improved performance for TB screening in an HIV-positive sample compared to an existing serological panel in Uganda, and suggests an approach to identify novel antigen combinations specifically for screening TB in PLHIV.
Sequential Learning with Endogenous Consideration Sets

We study the problem of a decision maker alternating between exploring existing alternatives and searching for new ones. We show that the decision to search depends on the composition of the consideration set only through the information the latter contains about the probability of finding new alternatives. When the search technology is stationary, or improves over time, search is equivalent to replacement. With deteriorating technologies, instead, alternatives are revisited after search is launched and each expansion is treated as if it were the last one. The analysis yields a formula for pricing new alternatives and/or the option to expand the consideration set in the future. We also show how to accommodate for certain irreversible choices that admit as special case a generalization of Weitzman's (1979) "Pandora's boxes" problem in which the set of boxes is endogenous and each alternative may require multiple explorations before it can be selected.
Minimal clinically important difference for asthma endpoints: an expert consensus report

Minimal clinically important difference (MCID) can be defined as the smallest change or difference in an outcome measure that is perceived as beneficial and would lead to a change in the patient's medical management. The aim of the current expert consensus report is to provide a “state-of-the-art” review of the currently available literature evidence about MCID for end-points to monitor asthma control, in order to facilitate optimal disease management and identify unmet needs in the field to guide future research. A series of MCID cut-offs are currently available in literature and validated among populations of asthmatic patients, with most of the evidence focusing on outcomes as patient reported outcomes, lung function and exercise tolerance. On the contrary, only scant and partial data are available for inflammatory biomarkers. These clearly represent the most interesting target for future development in diagnosis and clinical management of asthma, particularly in view of the several biologic drugs in the pipeline, for which regulatory agencies will soon require personalised proof of efficacy and treatment response predictors. Minimal clinically important difference (MCID) cut-offs in asthma are validated for patient reported outcomes and lung function, but not for inflammatory biomarkers. MCID represents a key target for future development in asthma management. http://bit.ly/33hcWIe
Soil Amendment Effects on Growth and Sprouting Success in a Pennsylvania Northern Red Oak Stand on Extremely Acidic Soils

Abstract On the Laurel Hill, anecdotal accounts reported coppice regeneration of oaks to be limited. Possible causes of poor sprouting success were large stump size, deer browsing, season of cutting and poor tree vigor. Our study site had been partially cut three years before this study to salvage some northern red oak (Quercus rubra L.) which had died. We attempted to increase Q. rubra vigor, as measured by increasing basal area growth, with soil amendments of 6,600 kg/h dolo-mitic lime, 110 kg/h K2O equivalents and 220 kg/h P2O5 equivalents while accounting for other growth variables. The objective was to improve overall Q. rubra sprouting success by increasing vigor prior to harvest. The soil amendments increased soil available calcium (Ca), magnesium (Mg), potassium (K) and phosphorus (P) and reduced available aluminum (Al). Foliar concentrations of Ca, Mg and K were increased. Basal area increment of treated Q. rubra trees increased by 10 percent and terminal elongation increased by nearly 100 percent. Two years after treatment, the trees were cut during the dormant season and all stumps were protected from deer browsing. After two years, 80 percent of the stumps had sprouted. No effect of lime and fertilizer on the sprouts was found.
Comparative vegetative anatomy and systematics of Cymbidium (Cymbidieae: Orchidaceae)

The genus Cymbidium (Orchidaceae) exhibits distinctive ecological diversification and occurs in terrestrial, epiphytic, and lithophytic life forms. One species, Cymbidium macrorhizon, lacks foliage leaves and has a strongly mycoparasitic existence. Correlation between habitat differentiation and anatomical characters was tested for 21 species of Cymbidium and its putative sister groups. Although hypostomaty characterizes the genus, C. canaliculatum shows amphistomaty. Ecological preference of this species indicates that amphistomaty is likely adapted to intensive insolation. Four types of subepidermal foliar sclerenchyma were found. Two forest floor species, C. goeringii and C. lancifolium as well as the mycoparasitic C. macrorhizon, do not have this sclerenchyma. In this genus, development of sclerenchyma is correlated with the degree of epiphytism. Palisade mesophyll evolved in Cymbidium section Cymbidium. As members of this section grow on isolated trees in tropical lowland forests or on rocks, the differentiation of palisade tissue is probably correlated with immigration to high light habitats. With the exception of C. macrorhizon, stegmata were found in leaves and stems of Cymbidium. Furthermore, a few epiphytic species have stegmata in their roots; this is a curious feature rarely found in vascular plants. Subterranean rhizomes characterize terrestrial species, while ageotropic roots are found in some epiphytic species. Cymbidium macrorhizon shows peculiar features such as degeneration of stomata, anomocytic stomata, and lack of stegmata and sclerenchyma. This set of character transformations is probably correlated with the evolution of mycoparasitic existence. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society, 2002, 138, 383–419.
Association Analysis as a Strategy for Improvement of Quantitative Traits in Plants

Association analysis is a method potentially useful for detection of marker-trait associations based on linkage disequilibrium, but little information is available on the application of this technique to plant breeding populations. With appropriate statistical methods, valid association analysis can be done in plant breeding populations; however, the most significant marker may not be closest to the functional gene. Bias can arise from (i) covariance among markers and QTL, frequently related to population structure or intense selection and (ii) differences in initial frequencies of marker alleles in the population, such that exclusive alleles tend to be in higher association. The potentials and limitations of germplasm bank collections, synthetic populations, and elite germplasm are compared, as experimental materials for association analysis integrated with plant breeding practice. Synthetics offer a favorable balance of power and precision for association analysis and would allow mapping of quantitative traits with increasing resolution through cycles of intermating. A model to describe the association between markers and genes as conditional probabilities in synthetic populations under recurrent selection is proposed, which can be computed on the basis of assumptions related to the history of the population. This model is useful for predicting the potential of different populations for association analysis and forecasting the response to marker-assisted selection.
Prey preference and feeding behaviour of the diplogastrid predator Mononchoides gaugleri (Nematoda: Diplogastrida)

Prey preference and feeding behaviour of Mononchoides gaugleri were studied using 11 phytoparasitic nematode species as prey. A full range of prey preferences were detected in no choice and paired choice predator-prey experiments. Meloidogyne incognita , Heterodera mothi and Anguina tritici juveniles (coefficient of preference = 0.92-1.00) were highly preferred as prey by M. gaugleri in all tests. The second tier of prey preference was occupied by the adult Hirschmanniella oryzae , Tylenchorhynchus mashhoodi , Xiphinema americanum and Paratrichodorus christiei (coefficient of preference = 0.19-0.67), and the third tier by Longidorus attenuatus and Helicotylenchus indicus (coefficient of preference = −0.15-−0.57). Hemicriconemoides mangiferae and Hoplolaimus indicus were not preyed upon. Mononchoides gaugleri attacked H. mothi and A. tritici (maximum strike rate (SR)= 92-94%), which has resulted in maximal prey wounding (encounters resulted in wounding (EW) = 46-47%). Longidorus attenuatus was attacked minimally (SR = 42%) with fewest casualties (EW = 21%). Hirschmanniella oryzae , H. mothi and M. incognita were most susceptible (prey susceptibility (PS) = 87.5-93.5%), whereas X. americanum and P. christiei were highly resistant prey species (prey resistance (PR) = 66.7-74.2%). Temperature and prey density governed predator feeding activities, with optimal search duration at 20-30°C and 150-225 prey. The shortest and longest feeding durations of Mononchoides gaugleri were recorded for M. incognita and L. attenuatus , respectively. Predation was density-dependent.
Bat flies (Diptera: Nycteribiidae) from Mount Makiling, Luzon Island: new host and distribution records, with a checklist of species found in the Philippines

Our survey in Mount Makiling Forest Reserve, Luzon Island, Philippines from April to May 2011 revealed new host records of bat fly species (Diptera: Nycteribiidae), including: Eucampsipoda philippinensis Ferris , Cyclopodia garrula Maa , C. horsfieldi de Mejeire , Phthiridium brachyacantha (Theodor) and Penicillidia acuminata Theodor . We also report C. garrula as a new record for Luzon Island. A checklist of the species known from the Philippines with the known distribution and bat host species was also provided.
TNF-α–Induced Tolerance to Ischemic Injury Involves Differential Control of NF-κB Transactivation: The Role of NF-κB Association with p300 Adaptor

Preconditioning with sublethal ischemia results in natural tolerance to ischemic stress, where multiple mediators of ischemic damage are simultaneously counteracted. Tumor necrosis factor alpha (TNF-α) has been implicated in development of ischemic tolerance. Using cellular models of ischemic tolerance, we have demonstrated that an effector of TNF-α– induced preconditioning is ceramide, a sphingolipid messenger in TNF-α signaling. TNF-α/ceramide-induced preconditioning protected cultured neurons against ischemic death and cultured astrocytes against proinflammatory effects of TNF-α. TNF-α activates a transcription factor NF-κB that binds promoters of multiple genes, thus ensuring pleiotropic effects of TNF-α. We describe here a mechanism that allows selective suppression of TNF-α/NF-κB–induced harmful genes in preconditioned cells while preserving cytoprotective responses. We demonstrate that in astrocytes activation of an adhesion molecule ICAM-1 by TNF-α is regulated through association of the phosphorylated p65 subunit of NF-κB with an adapter protein, p300, and that in preconditioned cells p65 remains unphosphorylated and ICAM-1 transcription is inhibited. However, TNF-α–activated transcription of a protective enzyme, MnSOD, does not depend on p300 and does not become inhibited in preconditioned cells. This new understanding of TNF-α–induced adaptation to ischemic stress and inflammation could suggest novel avenues for clinical intervention during ischemic and inflammatory diseases.
Interactive Learning with Proactive Cognition Enhancement for Crowd Workers

Learning from crowds often performs in an active learning paradigm, aiming to improve learning performance quickly as well as to reduce labeling cost by selecting proper workers to (re)label critical instances. Previous active learning methods for learning from crowds do not have any proactive mechanism to effectively improve the reliability of workers, which prevents to obtain steadily rising learning curves. To help workers improve their reliability while performing tasks, this paper proposes a novel Interactive Learning framework with Proactive Cognitive Enhancement (ILPCE) for crowd workers. The ILPCE framework includes an interactive learning mechanism: When crowd workers perform labeling tasks in active learning, their cognitive ability to the specific domain can be enhanced through learning the exemplars selected by a psychological model-based machine teaching method. A novel probabilistic truth inference model and an interactive labeling scheme are proposed to ensure the effectiveness of the interactive learning mechanism and the performance of learning models can be simultaneously improved through a fast and low-cost way. Experimental results on three real-world learning tasks demonstrate that our ILPCE significantly outperforms five representative state-of-the-art methods.
Fat and body condition in migrating Redwings Turdus iliacus

During the night of 29-30 October 1995, over 600 Redwings Turdus iliacus died as a result of flying into the lighthouse at Bardsey, Gwynedd, North Wales. These migrating birds were used to investigate fat levels in relation to age, sex, biometrics and pectoral muscle mass. Wing length was the best single linear measure of size and mean wing length of males was 2.5 mm greater than that of females. Body mass of the casualties declined during the night and the mean body mass of birds arriving towards the end of the night was 1.5 g lower than that of the first arrivals. Fat deposits at different body sites were significantly correlated with each other and with body mass, and, by extrapolation, the mass of intra-abdominal fat remaining would be significant when other fat deposits have been depleted. Fat in the tracheal pit (the claviculo-coracoid fat body) demonstrated the best correlation with body mass and was linearly correlated with visual fat scores. Fat was also present in the pectoral muscle but did not make a significant contribution to overall body mass. Two-thirds of the variation in body mass was accounted for by wing length, the mass of claviculo-coracoid fat and the lean-dry mass of pectoral muscle. Claviculo-coracoid fat and lean pectoral-muscle mass contributed independently to overall body mass. These data support the view that increase in fat in relation to migration is accompanied by an increase in protein or lean muscle mass, but suggest that these are controlled independently.
Sensory Quality of Cherry Tomatoes in Relation to 1-MCP Treatment and Storage Duration

1-MCP (1-methylcyclopropene), the ethylene receptors blocker, is used in horticultural practice for prolonging shelf-life of several species of fruits and vegetables. The objective of this study was to determine the effect of 1-MCP treatment on sensory characteristics of cherry type tomatoes ( Solanum lycopersicum L. var . cerasiforme ) after 4-week storage. In the experiment the fruits were harvested at pink and light-red fruit stages (3rd and 5th stage, according to USDA classification), and stored for 3 and 4 weeks at 12 o C, then moved to 20 sup>oC for 2 days to obtain marketable maturity. 1-MCP was applied after harvest in concentration of 1 ppm, for 12 hours at 18 o C. The plants belonging to the Dasher F 1 cultivar were grown in a greenhouse in rockwool slabs and fruits were harvested in June. Sensory analysis was performed in expert panel with Quantitative Descriptive Analysis (QDA), using 12 sensory descriptors concerning smell, taste, flavour and texture of the fruits. Also semi-consumer test of liking was carried out. As the control freshly harvested red fruits at optimal consumer's maturity were used. The 1-MCP treated fruits harvested in the light-red stage were of better sensory quality than the untreated ones, similar to freshly harvested, but in the case of the pink fruits, the quality was rated lower. It can be concluded that 1-MCP treatment was effective in delaying ripening of the fruits by better keeping their firmness and colour, however in the case of fruits harvested in earlier stage, overall sensory quality and consumer acceptance was scored lower than for the freshly harvested ones, mainly due to more intensive sour taste and lower sweetness.