Miracle-dz/UniFAR-FTUs huggingface dataset:
Leaf litter breakdown budgets in streams of various trophic status: effects of dissolved inorganic nutrients on microorganisms and invertebrates

1. We investigated the effect of trophic status on the organic matter budget in freshwater ecosystems. During leaf litter breakdown, the relative contribution of the functional groups and the quantity/quality of organic matter available to higher trophic levels are expected to be modified by the anthropogenic release of nutrients. 2. Carbon budgets were established during the breakdown of alder leaves enclosed in coarse mesh bags and submerged in six streams: two oligotrophic, one mesotrophic, two eutrophic and one hypertrophic streams. Nitrate concentrations were 4.5–6.7 mg L−1 and the trophic status of each stream was defined by the soluble reactive phosphorus concentration ranging from 3.4 (oligotrophic) to 89 μg L−1 (hypertrophic). An ammonium gradient paralleled the phosphate gradient with mean concentrations ranging from 1.4 to 560 μg L−1 NH4-N. The corresponding unionised ammonia concentrations ranged from 0.08 to 19 μg L−1 NH3-N over the six streams. 3. The dominant shredder taxa were different in the oligo-, meso- and eutrophic streams. No shredders were observed in the hypertrophic stream. These changes may be accounted for by the gradual increase in the concentration of ammonia over the six streams. The shredder biomass dramatically decreased in eu- and hypertrophic streams compared with oligo- and mesotrophic. 4. Fungal biomass increased threefold from the most oligotrophic to the less eutrophic stream and decreased in the most eutrophic and the hypertrophic. Bacterial biomass increased twofold from the most oligotrophic to the hypertrophic stream. Along the trophic gradient, the microbial CO2 production followed that of microbial biomass whereas the microbial fine particulate organic matter and net dissolved organic carbon (DOC) did not consistently vary. These results indicate that the microorganisms utilised the substrate and the DOC differently in streams of various trophic statuses. 5. In streams receiving various anthropogenic inputs, the relative contribution of the functional groups to leaf mass loss varied extensively as a result of stimulation and the deleterious effects of dissolved inorganic compounds. The quality/quantity of the organic matter produced by microorganisms slightly varied, as they use DOC from stream water instead of the substrate they decompose in streams of higher trophic status.
Third-Party Certification of Forest Management In Indonesia: Analysing Stakeholders' Recognition and Preferences

The existence of third-party forest and timber certification schemes in Indonesia has created benefits and challenges, mainly for forest industries. In the end, the interests and objectives of those industries will determine whether they decide to get certified and if so, what certification schemes they will use. This study analyses the stakeholder recognition of the competing forest legality and sustainability certification systems and describes the preferences for particular schemes based on stakeholder interests. Online questionnaires were distributed to relevant stakeholders, namely logging companies, wood processing industries, wood processing associations, auditors, academics, environmental organisations and government officials. The results indicate that there are different scheme preferences based on the stakeholder's interests. Sistem verifikasi legalitas kayu (SVLK) is the most frequently preferred scheme due to the simplicity of its requirements and the low cost of its certifying process, while the Forest stewardship council (FSC) is valued for its reputation and very high standards. Furthermore, lembaga ekolabel Indonesia (LEI) was least preferred because of its complexity and because it was unpopular with foreign end buyers, and the programme for the endorsement of forest certification (PEFC) was identified as being a complex scheme that was expensive and subject to high standards, and also appeared to have the least demand. Each scheme should be improved based on stakeholders' expectations, that their popularity with end buyers of timber products should be improved, and that this should be done in a way that allows logging and wood processing industries to choose freely the scheme that is most advantageous to them.
Assessment of diet in young children with an emphasis on fruit and vegetable intake: using CADET – Child and Diet Evaluation Tool

Abstract Objectives To develop a concise, simple tool for use by non-specialists to assess diet in children aged 3–7 years attending primary schools. Design A 24-hour food tick list covering all aspects of the diet and with a focus on fruit and vegetable consumption was developed. This was compared against a 24-hour semi-weighed food diary obtained for the same day as the tick list. Setting Six primary schools with a range of socio-economic and ethnic backgrounds from a large city in the north of England (Leeds). Participants One hundred and eighty children returned completed packs of information; a response rate of 77% of those who were willing to take part, 48% of those approached. Results On average, 2.4 items of fruit including juice (2.1 items as 5-a-day count) were eaten and 1.6 items of vegetables (excluding potato). Twenty-seven per cent and 36% of boys and 23% and 24% of girls reported not eating any fruit or vegetables, respectively, on the recording day. Correlations comparing the diary and tick list were high for both foods (range r = 0.44 to 0.89) and nutrients (range r = 0.41 to 0.68). The level of misclassification was much less than would be expected by chance. Parent and teacher evaluation of the tick list was very positive. Parents felt the tick list was easy and quick to complete. Conclusion The Child and Diet Evaluation Tool (CADET) tick list has been used successfully for rapid collection of food and nutrient information from children aged 3–7 years from diverse social and ethnic backgrounds. The tool has performed better than many food-frequency questionnaires in comparison to a food diary.
Patient perspectives on engagement in shared decision-making for asthma care

Abstract Introduction. Engagement of patient and advocacy group stakeholders is increasingly considered essential to meaningful outcomes research. Patient-centred research benefits from partnership formation between patients, clinicians and research team members. Here, we describe the rationale for engaging patients on a research team and a case study of patient engagement on an asthma shared decision-making study. Methods. Here, we describe a case study of patient engagement in outcomes research and examine the variety of roles patients are engaged in and the associated impact on the study. Results. Patients assisted the project at various levels and were integrated into the research team by (i) advising on study development; (ii) assisting with design and usability of study materials, including the toolkit, patient surveys and dissemination strategies; and (iii) advocacy via membership in external disease-specific organizations and participating in outcomes research conferences. Patients were engaged both individually and as members of a patient advisory board. Primary lessons learned were the importance of building a trusting partnership with patients through understanding perspectives, being aware of clearly explaining patients’ roles, research methods and jargon, providing training, listening to patients’ needs and understanding what the partnership means from a patient perspective. Conclusions. For the case study described, patient engagement directly influenced multiple aspects of the study, including study design, implementation, data analysis and dissemination through incorporation of the patients’ and caregivers’ input and concerns.
Expression of EMT markers and mode of surgery are prognostic in phyllodes tumors of the breast

Phyllodes tumors of the breast are rare neoplasms that account for <1% of all mammary tumors and 2-3% of fibro-epithelial neoplasms of the breast. We evaluated the clinicopathological characteristics of a cohort of 246 Chinese patients in relation to the expression of epithelial-to-mesenchymal (EMT) markers in benign, borderline and malignant tumors and the prognostic value of different surgical regimens. We observed that survival outcomes correlated with the mode of surgical management in the three patient groups. Expression of E-cadherin, Snail, Slug and Twist were higher in epithelial cells from borderline and malignant tumors than those in benign tumors, whereas the expression of N-cadherin was opposite. Levels of the EMT markers Snail and Slug in the stromal compartment increased with the advancing tumor grade. Expression of mesenchymal stem cell markers contributed to the inherent heterogeneity in the malignant tumors. Based on Cox models, surgical management emerged as an independent predictor for disease-free survival, whereas a history of recent growth and tumor grade were independent predictors for overall survival. These findings show that expression of EMT markers, the mode of surgical management, and a history of recent tumor growth had prognostic potential for patients with phyllodes tumors of the breast.
A substrate-integrated-waveguide dual-band bandpass filter based on signal-interference principles

Contrary to conventional RF filtering devices that are based on electromagnetically-coupled resonators, signal-interference microwave filters exploit constructive and destructive interactions of signals that propagate along different electrical paths of the filter volume. To date, most of signal-interference filters have been implemented in planar technologies. However, their operational principles are general and can hence be extrapolated to non transverse-electromagnetic-mode (TEM)/quasi-TEM technologies — either mixed or separate ones —. This paper reports on the design and manufacturing of a C-band signal-interference dual-band bandpass filter based on a half-mode substrate-integrated-waveguide (HMSIW) directional coupler. The obtained experimental results are in close agreement both with the theory and the simulations, which reveals that signal-interference filters can be extended to nonplanar technologies. Their potential for multi-stage higherorder filter realizations is also demonstrated.
Adult Day Center Programs and Their Associated Outcomes on Clients, Caregivers, and the Health System: A Scoping Review

Purpose of the Study Adult day centers (ADCs) offer a heterogeneous group of services that provide for the daily living, care, nutritional, and social needs of older adults. We sought to conceptually map and identify key gaps and findings from literature focused on ADCs, including the types of programs that exist and their associated outcomes on improving health and strengthening health systems. Design and Methods We conducted a scoping review by searching 5 databases for studies evaluating the outcomes of ADCs specifically for community-dwelling older adults. Included studies were conceptually mapped according to the methods used, type of outcome(s) assessed, study population, disease focus, service focus, and health system considerations. The mapping was used to derive descriptive analyses to profile the available literature in the area. Results ADC use has positive health-related, social, psychological, and behavioral outcomes for care recipients and caregivers. There is a substantial amount of literature available on some ADC use outcomes, such as health-related, satisfaction-related and psychological and behavioral outcomes, while less research exists on issues of accessibility and cost-effectiveness. Implications As the population ages, policymakers must carefully consider how ADCs can best serve each user and their caregivers with their unique circumstances. ADCs have the potential to help shape health system interventions, especially those targeting caregivers and people requiring long-term care support. Due to the variation among types of ADC programs, future research on ADCs should consider different characteristics of ADC programs to better contextualize their results.
On breast cancer detection: an application of machine learning algorithms on the wisconsin diagnostic dataset

This paper presents a comparison of six machine learning (ML) algorithms: GRU-SVM[1], Linear Regression, Multilayer Perceptron (MLP), Nearest Neighbor (NN) search, Softmax Regression, and Support Vector Machine (SVM) on the Wisconsin Diagnostic Breast Cancer (WDBC) dataset[2] by measuring their classification test accuracy, and their sensitivity and specificity values. The said dataset consists of features which were computed from digitized images of FNA tests on a breast mass[2]. For the implementation of the ML algorithms, the dataset was partitioned in the following fashion: 70% for training phase, and 30% for the testing phase. The hyper-parameters used for all the classifiers were manually assigned. Results show that all the presented ML algorithms performed well (all exceeded 90% test accuracy) on the classification task. The MLP algorithm stands out among the implemented algorithms with a test accuracy of ≈99.04%.
Fingertip Surface Optimization for Robust Grasping on Contact Primitives

We address the problem of fingertip design by leveraging on the fact that most grasp contacts share a few classes of local geometries. In order to maximize the contact areas for achieving more robust grasps, we first define the concept of Contact Primitive, which represents a set of contacts of similar local geometries. Thereafter, we propose a uniform cost algorithm, which is formulated as a decision making process in a tree structure, to cluster a set of example grasp contacts into a finite set of Contact Primitives. We design fingertips by optimization to match the local geometry of each contact primitive, and then three-dimensionally print them using soft materials to compensate for optimization residuals. For novel objects, we provide an efficient algorithm to generate grasp contacts that match the fingertip geometries while together forming stable grasps. Comparing to a baseline of flat fingertip design, the experiment results show that our design significantly improves grasp stability, and it is more robust against various uncertainties.
Diagnosis and management of iatrogenic cardiac perforation caused by pacemaker and defibrillator leads

Aims Cardiac perforations caused by pacemaker or implantable cardioverter-defibrillator (ICD) leads are uncommon but potentially fatal events. The optimal approach to such cases is unclear. The aim of this study was to identify the optimal imaging modality and management strategy for cardiac perforation. Methods and results All patients presenting to a single institution with cardiac perforation >24 h since implant between 2011 and 2015 were identified retrospectively. Assessment of the diagnostic performance of pre-extraction chest radiography, transthoracic echocardiography (TTE), and computed tomography (CT) was carried out by blinded review. The method of lead extraction and any associated complications were examined. Eighteen cases of cardiac perforation were identified from 426 lead extraction procedures. Sixteen patients had abnormal electrical parameters at device interrogation. In all cases, the perforating lead was an active fixation model, and in four cases, this was an ICD coil. The accuracy of CT imaging for the diagnosis of cardiac perforation was 92.9%, with sensitivity and specificity of 100 and 85.7%, respectively. This was superior to both TTE (accuracy 62.7%, sensitivity and specificity 41.2 and 84.2%, respectively) and chest radiography (accuracy 61.1%, sensitivity and specificity 27.7 and 94.4%, respectively). Transvenous lead extraction (TLE) was performed in 17 patients, and a hybrid surgical approach in 1 patient. Of those who underwent TLE, there was 100% complete procedural success as per Heart Rhythm Society definitions. Conclusion In the setting of cardiac perforation, CT is the imaging modality of choice. Transvenous lead extraction can be recommended as a safe, efficacious, and versatile intervention.
Proteomics and Phylogenetic Analysis of the Cathepsin L Protease Family of the Helminth Pathogen Fasciola hepatica

Cathepsin L proteases secreted by the helminth pathogen Fasciola hepatica have functions in parasite virulence including tissue invasion and suppression of host immune responses. Using proteomics methods alongside phylogenetic studies we characterized the profile of cathepsin L proteases secreted by adult F. hepatica and hence identified those involved in host-pathogen interaction. Phylogenetic analyses showed that the Fasciola cathepsin L gene family expanded by a series of gene duplications followed by divergence that gave rise to three clades associated with mature adult worms (Clades 1, 2, and 5) and two clades specific to infective juvenile stages (Clades 3 and 4). Consistent with these observations our proteomics studies identified representatives from Clades 1, 2, and 5 but not from Clades 3 and 4 in adult F. hepatica secretory products. Clades 1 and 2 account for 67.39 and 27.63% of total secreted cathepsin Ls, respectively, suggesting that their expansion was positively driven and that these proteases are most critical for parasite survival and adaptation. Sequence comparison studies revealed that the expansion of cathepsin Ls by gene duplication was followed by residue changes in the S2 pocket of the active site. Our biochemical studies showed that these changes result in alterations in substrate binding and suggested that the divergence of the cathepsin L family produced a repertoire of enzymes with overlapping and complementary substrate specificities that could cleave host macromolecules more efficiently. Although the cathepsin Ls are produced as zymogens containing a prosegment and mature domain, all secreted enzymes identified by MS were processed to mature active enzymes. The prosegment region was highly conserved between the clades except at the boundary of prosegment and mature enzyme. Despite the lack of conservation at this section, sites for exogenous cleavage by asparaginyl endopeptidases and a Leu-Ser↓His motif for autocatalytic cleavage by cathepsin Ls were preserved.
Allopurinol Dose Escalation and Mortality Among Patients With Gout

Observational data suggest that hyperuricemia and gout are associated with increased mortality, while allopurinol use is associated with reduced mortality. In addition, the protective effect of allopurinol may be dose dependent. The aim of the current study was to determine whether allopurinol dose escalation is associated with cause‐specific mortality in patients with gout.
YSOVAR: MID-INFRARED VARIABILITY AMONG YSOs IN THE STAR FORMATION REGION GGD12-15

We present an IR-monitoring survey with the Spitzer Space Telescope of the star-forming region GGD 12-15. More than 1000 objects were monitored, including about 350 objects within the central 5′, which is found to be especially dense in cluster members. The monitoring took place over 38 days and is part of the Young Stellar Object VARiability project. The region was also the subject of a contemporaneous 67 ks Chandra observation. The field includes 119 previously identified pre-main sequence star candidates. X-rays are detected from 164 objects, 90 of which are identified with cluster members. Overall, we find that about half the objects in the central 5′ are young stellar objects (YSOs) based on a combination of their spectral energy distribution, IR variability, and X-ray emission. Most of the stars with IR excess relative to a photosphere show large amplitude (>0.1 mag) mid-infrared (mid-IR) variability. There are 39 periodic sources, and all but one is found to be a cluster member. Almost half of the periodic sources do not show IR excesses. Overall, more than 85% of the Class I, flat spectrum, and Class II sources are found to vary. The amplitude of the variability is larger in more embedded YSOs. Most of the Class I/II objects exhibit redder colors in a fainter state, which is compatible with time-variable extinction. A few become bluer when fainter, which can be explained with significant changes in the structure of the inner disk. A search for changes in the IR due to X-ray events is carried out, but the low number of flares prevented an analysis of the direct impact of X-ray flares on the IR light curves. However, we find that X-ray detected Class II sources have longer timescales for change in the MIR than a similar set of non-X-ray detected Class IIs.
Population Genetics and Molecular Epidemiology or How to ''débusquer La Bête''

Parasites represent a great proportion of the world's living organisms and are of overwhelming significance because of their impact on hosts (evolutionarily, medically, agronomical and economically). The knowledge of the population biology of such organisms is thus of fundamental importance to population biologists. Most parasites cannot be studied by direct methods and their biology has to be assessed via indirect means, most notably using molecular markers. In this review, we present the molecular tools, the null models employed, the statistical tools available and the kinds of inferences one can make when using molecular markers to study the ecology/epidemiology of host–parasite systems (molecular ecology/molecular epidemiology). We conclude with relevant examples, most issued from our laboratory, to illustrate the pros and cons of such methods for the study of parasites, vectors, micropathogens and their hosts and briefly discuss future needs.
Alcohol consumption and lung cancer risk in never smokers: a pooled analysis of case-control studies

Background Lung cancer is the deadliest cancer in developed countries but the etiology of lung cancer risk in never smokers (LCRINS) is largely unknown. We aim to assess the effects of alcohol consumption, in its different forms, on LCRINS. Methods We pooled six multi-center case-control studies developed in the northwest of Spain. Cases and controls groups were composed of never smokers. We selected incident cases with anatomopathologically confirmed lung cancer diagnoses. All participants were personally interviewed. We performed two groups of statistical models, applying unconditional logistic regression with generalized additive models. One considered the effect of alcohol type consumption and the other considered the quantity of each alcoholic beverage consumed. Results A total of 438 cases and 863 controls were included. Median age was 71 and 66, years, respectively. Adenocarcinoma was the predominant histological type, comprising 66% of all cases. We found that any type of wine consumption posed an OR of 2.20 OR 95%CI 1.12-4.35), and spirits consumption had an OR of 1.90 (95%CI 1.13-3.23). Beer consumption had an OR of 1.33 (95%CI 0.82-2.14). These results were similar when women were analyzed separately, but for men there was no apparent risk for any alcoholic beverage. The dose-response analysis for each alcoholic beverage revealed no clear pattern. Conclusions Wine and spirits consumption might increase the risk of LCRINSs, particularly in females. These results have to be taken with caution given the limitations of the present study.