Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural Beach Vegetation Coverage and Type Influence the Nesting Habitat of Hawksbill Turtles (Eretmochelys imbricata) in Campeche, Mexico

Abstract The hawksbill turtle (Eretmochelys imbricata) is a critically endangered species with a global distribution and is broadly distributed along the Yucatan Peninsula in the Gulf of Mexico. To complete its life cycle, this species uses sandy beaches with particular environmental conditions that facilitate nesting and hatching. This study aimed to identify if beach physical characteristics influence biological reproductive parameters (hatching and emergence success). Nesting activity was monitored along 18 km of beach in the state of Campeche, Mexico, during 2014. Seventy-eight nests were recorded, 12 physical and environmental variables were measured in the nests and contiguous areas, and the hatching and emergence success of each nest was determined. Beach slope and width had no significant relationship to nest site selection. Nest depth and nest distance to highest tide and vegetation, including vegetation type, did influence hatching and emergence success. Herbaceous and bushy plants were positively correlated with reproductive parameters, highlighting the importance of preserving beach vegetation cover. This parameter was a central structural component of hawksbill nesting habitat, possibly because it influenced nest shading, preventing egg overheating and possible embryo death. Preservation and restoration of vegetation structure on hawksbill nesting beaches is clearly vital to enhancing the reproductive success of this species.
Veterans’ Experiences With Diabetes: A Qualitative Analysis

Purpose The purpose of the study was to explore an understanding of the psychosocial-behavioral impact of diabetes self-management among veterans with diabetes. Methods Twenty-six veterans participated in 1 of 9 focus groups that were conducted following a group diabetes self-management education class and prior to a mindfulness intervention as part of a feasibility pilot study. Discussions were guided by open-ended questions that addressed the overarching research question, “How do attitudes and experiences with diabetes inform psychosocial-educational approaches to diabetes self-management education and care for veterans? ” Focus groups were audio-recorded and transcribed. The data was then independently coded and thematically analyzed by 2 coders. Results Five main themes that reflect veterans’ perceptions of their experiences with diabetes and diabetes self-management were identified: (1) distress and negative emotions, (2) social isolation, (3) perceived lack of control, (4) attitudes toward diabetes support, and (5) desire for information about stress, diabetes, health, and behavior. Conclusions Veterans experience emotional distress and have unmet psychosocial needs related to diabetes self-management. Insight gained from these veteran perspectives suggests a framework for integrating psycho-educational interventions like mindfulness into diabetes care that emphasize stress reduction, person-centered communication, and opportunities for peer support.
Genetics of clear cell renal cell carcinoma : new tumor suppressor genes and aberrant chromatin regulation

De korte arm van chromosoom 3 bevat verschillende genen die een rol kunnen spelen bij de ontwikkeling van de meest voorkomende soort nierkanker: heldercellige niercelcarcinomen (ccRCCs). Dat blijkt uit onderzoek van promovendus Gerben Duns. Bij heldercellige niercelcarcinomen is de korte arm van chromosoom 3 vaak afwezig. Dit is een aanwijzing dat dit deel van het genoom genen bevat die deze vorm van kanker onderdrukken. Voor Duns was dit aanleiding om het betreffende chromosoom te onderzoeken met behulp van de technieken GINI en targeted exome sequencing. Duns identificeerde vier genen die betrokken zijn bij het ontstaan van ccRCC’s. Verschillende van deze genen coderen voor eiwitten die een rol spelen bij het modificeren van histonen en het modelleren van chromatine, zo laat de promovendus verder zien. Hij concludeert dat verstoring van de regulatie van chromatine een essentiele gebeurtenis lijkt in de ontwikkeling van ccRCCs. Hiermee heeft Duns aangrijpingspunten gevonden voor nader onderzoek naar deze ziekte. Wellicht kunnen de opgedane inzichten bijdragen aan de ontwikkeling van een nieuw medicijn.
A Point-of-Care Immunosensor Based on a Quartz Crystal Microbalance with Graphene Biointerface for Antibody Assay

We present a sensitive and low-cost immunoassay, based on a customized open-source quartz crystal microbalance coupled with graphene biointerface sensors (G-QCM), to quantify antibodies in undiluted patient serum. We demonstrate its efficacy for a specific antibody against the phospholipase A2 receptor (anti-PLA2R), which is a biomarker in primary membranous nephropathy. A novel graphene–protein biointerface was constructed by adsorbing a low concentration of denatured bovine serum albumin (dBSA) on the reduced graphene oxide (rGO) sensor surface. The dBSA film prevents the denaturation of the protein receptor on the rGO surface and serves as the cross-linker for immobilization of the receptor for anti-PLA2R antibodies on the surface. The detection limit and selectivity of this G-QCM biosensor was compared with a commercial QCM system. The G-QCM immunoassay exhibited good specificity and high sensitivity toward the target, with an order of magnitude better detection limit (of 100 ng/mL) compared to the commercial system, at a fraction of the cost and with considerable time saving. The results obtained from patient sera compared favorably with those from enzyme-linked immunosorbent assay, validating the feasibility of use in clinical applications. The multifunctional dBSA-rGO platform provides a promising biofunctionalization method for universal immunoassay and biosensors. With the advantages of inexpensive, rapid, and sensitive detection, the G-QCM sensor and instrument form an effective autoimmune disease screening tool.
Overview of the 8th Author Profiling Task at PAN 2020: Profiling Fake News Spreaders on Twitter

First of all we thank the participants: 66 this year, record in terms of participants at PAN Lab since 2009! We have to thank also Martin Potthast, Matti Wiegmann, and Nikolay Kolyada to help with the 66 Virtual Machines in the TIRA platform. We thank Symanto for sponsoring the ex aequo award for the two best performing systems at the author profiling shared task of this year. The work of Paolo Rosso was partially funded by the Spanish MICINN under the research project MISMIS-FAKEnHATE on Misinformation and Miscommunication in social media: FAKE news and HATE speech (PGC2018-096212-B-C31). The work of Anastasia Giachanou is supported by the SNSF Early Postdoc Mobility grant under the project Early Fake News Detection on Social Media, Switzerland (P2TIP2 181441).
Foot fat pad: Characterization by mesenchymal stromal cells in rats

Foot fat pad (FFP) is a highly functionalized fat depot of great significance for weight bearing in the foot. Mesenchymal stromal cells (MSCs) in subcutaneous adipose tissues are widely studied for regenerative potentials. MSCs in FFP, which may contribute to the physiological and pathological conditions of the foot, have not been characterized. In this study, MSCs were isolated from FFP (designated as MSCs‐ffp) and subcutaneous adipose tissue (designated as MSCs‐sub) from rats. The cell surface markers, proliferation, and efficiency of colony formation were compared between MSCs‐ffp and MSCs‐sub. In addition, MSCs‐ffp were induced for osteogenic, chondrogenic, and adipogenic differentiation. The tri‐lineage differentiation potentials were compared between MSCs‐ffp and MSCs‐sub by the expression of Runx2, Sox9, and proliferator‐activated receptor gamma (PPAR‐γ), respectively, using quantitative polymerized chain reaction. The expression of elastin and associated genes by MSCs‐ffp were also evaluated. MSCs‐ffp, like MSCs‐sub, expressed CD44, CD73, and CD90. MSCs‐ffp and MSCs‐sub proliferated at similar rates but MSCs‐ffp formed more colonies than MSCs‐sub. MSCs‐ffp were capable of differentiating into osteogenic, chondrogenic, and adipogenic lineages. Under the conditions of osteogenic and adipogenic differentiation, MSCs‐sub expressed more Runx2 and PPAR‐γ, respectively, than MSCs‐ffp. The undifferentiated MSCs‐ffp upregulated the expression of fibulin‐5. In conclusion, MSCs‐ffp shared common biology with MSCs‐sub but were more efficient in colony formation, less adipogenic and osteogenic, and participated in elastogenesis. The unique features of MSCs‐ffp may relate to their roles in the physiological functions of FFP.
Genetic analyses of agronomic traits of tef (Eragrostis tef) genotypes.

Genetic variation, associations, and heritability for grain yield and component traits (days to heading, shoot biomass, 100 seed weight, individual plant above ground biomass, plant seed weight, panicle seed weight, plant height, panicle length and lodging index) were studied in a trial using 18 tef genotypes at two locations in Ethiopia. Highly significant differences were observed among genotypes for most of the traits examined. When correlations between yield component characters were taken into account, most of the values between various character pairs were significant and positive. Lodging index was negatively correlated with harvest index, shoot biomass, above ground plant biomass, plant height and panicle length. Plant seed weight and shoot biomass appeared to contribute substantially to grain yield at the genotypic level. The values for genotypic and phenotypic correlations between the traits were in the same direction indicating that most of the phenotypic correlations were due to genotypic causes. High heritability estimates were observed for days to heading, plant height, and panicle length and intermediate heritability for days to maturity, lodging index, grain yield, panicle seed weight and shoot biomass. Moderately high values for genotypic coefficients of variability, heritability, and genetic advance estimated for grain yield, panicle seed weight and above ground plant biomass may suggest the predominance of additive gene action, and that direct selection based on these traits would be effective for improvement of tef.
Reactions to the opioid epidemic: A text-mining analysis of tweets

Abstract Objective This study analyzed public reactions to the opioid epidemic using Twitter discourse. Methods: One month of unique tweets (n = 26,079) from July 23, 2018 to August 22, 2018 were identified using the keyword “opioid” in conjunction with the words “crisis, epidemic, misuse, prescription, and death. ” Twelve topics, each representing more than 1% of all tweets, together accounted for 17,206 (66%) of identified tweets. Results: The top four tweet topics (representing 38% of the total) addressed lawsuits and public policy, people who use opioids to treat persistent pain, programs to alleviate the opioid epidemic, and one specific initiative, the “#onelesspill” movement. The next seven topics (representing 27% of the total) addressed news articles relating to the opioid epidemic. The 12th topic was a book about the opioid crisis (1.7% of the total tweets). Conclusions: These tweets exhibited polarization of opinions with some people calling for tighter restrictions on opioids and others desperate to preserve their daily use of opioids for alleviation of illnesses characterized by persistent pain. Social media posts can help inform efforts to craft public policy and communication strategies to support optimal opioid stewardship.
Matrix-analytic methods for the analysis of stochastic fluid-fluid models

Abstract Stochastic fluid-fluid models (SFFMs) offer powerful modeling ability for a wide range of real-life systems of significance. The existing theoretical framework for this class of models is in terms of operator-analytic methods. For the first time, we establish matrix-analytic methods for the efficient analysis of SFFMs. We illustrate the theory with numerical examples.
Secondary metabolites profiles and antioxidant activities of germinated brown and red rice

The research aims to investigate the effect of germination on the secondary metabolite profiles and antioxidant activity of brown and red rice. The germination was performed by using a simple laboratory-scale machine that was designed and optimized to provide conditions that support the germination process. The germination was carried out for 2 days in dark conditions at 26°C and 99% humidity. Analysis of the secondary metabolite profile of ungerminated and germinated rice was performed using LC-MS. The antioxidant activities of ungerminated and germinated rice were done by using DPPH method. The results showed that the profiles of secondary metabolites of brown and red rice changed after germination. Some peaks were found to be induced in the germinated rice. However, some peaks were also loss during germination. The antioxidant activity of brown rice was slightly increased due to the germination, from 11.2% to 22.5%. Meanwhile the antioxidant activity of red rice was decreased after germination, from 73.8% to 60.0%.
TIET at CLEF CheckThat! 2020: Verified Claim Retrieval

Internet is the all-singing, all-dancing, multi-pronged tool of modern man, but, for its many beneﬁts it also presents us with daunting challenges. The user is bombarded with tons of information and it is becoming increasingly diﬃcult to tell fact from ﬁction. Consequently, over the past few years research work has intensiﬁed in this regard to better equip the user against false information and indoctrination. In this paper, we propose a system for automatic retrieval of supporting claims given an input claim. Our system uses elasticsearch along with a transformer model to generate a similarity score in two steps. We have submitted our system to CLEF-2020 Check That! Lab’s Task-2: Claim Retrieval and our primary evaluations gave promising results which we will present, analyse and improve henceforth in the paper.
Exploring Argument Retrieval with Transformers

We report on our recent efforts to employ transformer-based models as part of an information retrieval pipeline, using argument retrieval as a benchmark. Transformer models, both causal and bidirectional, are independently used to expand queries using generative approaches as well as to densely embed and retrieve arguments. In particular, we investigate three approaches: (1) query expansion using GPT-2, (2) query expansion using BERT, and orthogonal to these approaches, (3) embedding of documents using Google’s BERT-like universal sentence encoder (USE) combined with a subsequent retrieval step based on a nearest-neighbor search in the embedding space. A comparative evaluation of our approaches at the Touché lab on argument retrieval places our query expansion based on GPT-2 ﬁrst on the leaderboard with a retrieval performance of 0.808 nDCG@5, improving over the task baseline by 6.878%.
Adjustment of Insulin Pump Settings in Type 1 Diabetes Management: Advisor Pro Device Compared to Physicians’ Recommendations

Aims: To compare insulin dose adjustments made by physicians to those made by an artificial intelligence-based decision support system, the Advisor Pro, in people with type 1 diabetes (T1D) using an insulin pump and self-monitoring blood glucose (SMBG). Methods: This was a multinational, non-interventional study surveying 17 physicians from 11 countries. Each physician was asked to provide insulin dose adjustments for the settings of the pump including basal rate, carbohydrate-to-insulin ratios (CRs), and correction factors (CFs) for 15 data sets of pumps and SMBG of people with T1D (mean age 18.4 ± 4.8 years; eight females; mean glycated hemoglobin 8.2% ± 1.4% [66 ± 11mmol/mol]). The recommendations were compared among the physicians and between the physicians and the Advisor Pro. The study endpoint was the percentage of comparison points for which there was an agreement on the direction of insulin dose adjustments. Results: The percentage (mean ± SD) of agreement among the physicians on the direction of insulin pump dose adjustments was 51.8% ± 9.2%, 54.2% ± 6.4%, and 49.8% ± 11.6% for the basal, CR, and CF, respectively. The automated recommendations of the Advisor Pro on the direction of insulin dose adjustments were comparable )49.5% ± 6.4%, 55.3% ± 8.7%, and 47.6% ± 14.4% for the basal rate, CR, and CF, respectively( and noninferior to those provided by physicians. The mean absolute difference in magnitude of change between physicians was 17.1% ± 13.1%, 14.6% ± 8.4%, and 23.9% ± 18.6% for the basal, CR, and CF, respectively, and comparable to the Advisor Pro 11.7% ± 9.7%, 10.1% ± 4.5%, and 25.5% ± 19.5%, respectively, significant for basal and CR. Conclusions: Considerable differences in the recommendations for changes in insulin dosing were observed among physicians. Since automated recommendations by the Advisor Pro were similar to those given by physicians, it could be considered a useful tool to manage T1D.
Repeated Psychosocial Screening of High School Students Using YouthCHAT: Cohort Study

Background Psychosocial problems are common during adolescence and can have long-lasting effects on health and on academic and social functioning. YouthCHAT, an electronic HEEADSSS (home, education, eating, activities, drugs and alcohol, suicide and depression, sexuality and safety)-aligned instrument, has recently been demonstrated to be an acceptable and effective school-based psychosocial screener for 13-year-old (Year 9) high school students. Objective This study aims to compare acceptability and detection rates with repeated YouthCHAT screenings of high school students when they are 13 years old (Year 9) and 14 years old (Year 10). Methods We invited all Year-10 students to complete a YouthCHAT screening in 2018. Rates of positively identified issues were compared between the subset of students screened in both 2017 and 2018. Student acceptability toward YouthCHAT was investigated through focus group sessions. Onward clinical referral rates in 2018 were also investigated to explore the potential referral burden following screening. Data analysis for rates of positively identified issues were conducted with the McNemar test. Chi-square, Fisher exact test, and Kruskal-Wallis test were used to analyze the focus group data. Results Of 141 eligible Year-10 students, 114 (81%) completed a YouthCHAT screening during 2018, and 97 (85%) of them completed it for a second time. Apart from depression, which increased (P=.002), and perceived life stress, which decreased (P=.04), rates of identified issues were broadly similar between 13 and 14 years of age. Repeated screenings via YouthCHAT was acceptable to students and time-efficient (mean, 6 minutes and 32 seconds) but did not reduce the overall number of individuals with identified issues. Onward clinical referrals from positive screens were mostly managed by school-based health services without the need for external referrals. Conclusions Although further evaluation is needed, our results support the value of YouthCHAT as an acceptable and effective instrument with which to achieve routine identification of psychosocial issues and early intervention within a high school environment.
Learning hidden elasticity with deep neural networks

Significance Elastography has been applied to medical imaging to detect cancerous tissues for decades. The conventional elastography based on the assumption of stress uniformity is prone to inaccuracies. Accurately reconstructing elasticity distributions of heterogeneous objects requires solving an inverse problem in elasticity, which is difficult due to its ill-posed nature. By implementing machine learning techniques, we have developed ElastNet, an elastography method for extracting the hidden elasticity of objects based on measured strain distributions. We show that by combining the theory of elasticity with a deep-learning approach, ElastNet can provide rapid and accurate predictions. We validate ElastNet by applying it to various elastography problems with complex elasticity distributions. Elastography is an imaging technique to reconstruct elasticity distributions of heterogeneous objects. Since cancerous tissues are stiffer than healthy ones, for decades, elastography has been applied to medical imaging for noninvasive cancer diagnosis. Although the conventional strain-based elastography has been deployed on ultrasound diagnostic-imaging devices, the results are prone to inaccuracies. Model-based elastography, which reconstructs elasticity distributions by solving an inverse problem in elasticity, may provide more accurate results but is often unreliable in practice due to the ill-posed nature of the inverse problem. We introduce ElastNet, a de novo elastography method combining the theory of elasticity with a deep-learning approach. With prior knowledge from the laws of physics, ElastNet can escape the performance ceiling imposed by labeled data. ElastNet uses backpropagation to learn the hidden elasticity of objects, resulting in rapid and accurate predictions. We show that ElastNet is robust when dealing with noisy or missing measurements. Moreover, it can learn probable elasticity distributions for areas even without measurements and generate elasticity images of arbitrary resolution. When both strain and elasticity distributions are given, the hidden physics in elasticity—the conditions for equilibrium—can be learned by ElastNet.
Differential responses of bone to angiotensin II and angiotensin(1-7): beneficial effects of Ang(1-7) on bone with exposure to high glucose.

Osteoporosis, diabetes and hypertension are common concurrent chronic disorders. This study aimed to explore the respective effect of angiotensin II (Ang II) and angiotensin(1-7) [Ang(1-7)], active peptides in the renin-angiotensin system, on osteoblasts and osteoclasts under high glucose, as well as to investigate the osteo-preservative effects of Ang II type 1 receptor (AT1R) blocker and Ang(1-7) in diabetic spontaneously hypertensive rats (SHR). Ang II and Ang(1-7) respectively decreased and increased the formation of calcified nodules and ALP activity in MC3T3-E1 cells under high glucose, and respectively stimulated and inhibited the number of matured osteoclasts and pit resorptive area in RANKL-induced bone marrow macrophages. Olmesartan and Mas receptor antagonist A779 could abolish those effects. Ang II and Ang(1-7) respectively down-regulated and up-regulated the expressions of osteogenesis factors in MC3T3-E1 cells. Ang II promoted the expressions of cathepsin K and MMP9 in RAW 264.7 cells, while Ang(1-7) repressed these osteoclastogenesis factors. Ang II rapidly increased the phosphorylation of Akt and p38 in RAW 264.7 cells, whereas Ang(1-7) markedly reduced the phosphorylation of p38 and ERK under high glucose. After treatments of diabetic SHR with valsartan and Ang(1-7), a significant increase in trabecular bone area, BMD and mechanical strength was only found in the Ang(1-7)-treated group. Treatment with Ang(1-7) significantly suppressed the increase in renin expression and Ang II content in the bone of SHR. Taken together, Ang II/AT1R and Ang(1-7)/Mas distinctly regulated the differentiation and functions of osteoblasts and osteoclasts upon exposure to high glucose. Ang(1-7) could protect SHR from diabetes-induced osteoporosis.
Characterization of sixteen microsatellite loci from the marine gastropod Monetaria caputdraconis (Gastropoda: Cypraeidae) by next generation sequencing

Easter Island possess a unique marine biodiversity. Monetaria caputdraconis is important among these species due to its cultural and economic importance for the islanders. For this reason, a total of 16 microsatellite loci were characterized for this species. The mean number of alleles per locus in the 76 studied individuals was 11.25 (2-20 alleles per locus) and the observed heterozygosity ranged from 0.08 to 0.88. While none of the loci exhibited significant linkage disequilibrium, 9 showed departures from Hardy-Weinberg equilibrium. The heterozygote deficit observed in M. caputdraconis has been described for other marine invertebrates with planktonic larval development.