Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Application of Circulating Tumor DNA in the Genetic Analysis of Patients with Advanced GIST

Gastrointestinal stromal tumors (GIST) are the most common mesenchymal tumor of digestive tract. In the past, tissue biopsy was the main method for the diagnosis of GISTs. Although, circulating tumor DNA (ctDNA) detection by next-generation sequencing (NGS) may be a feasible and replaceable method for diagnosis of GISTs. We retrospectively analyzed the data for ctDNA and tissue DNA detection from 32 advanced GIST patients. We found that NGS obviously increased the positive rate of ctDNA detection. ctDNA detection identified rare mutations that were not detected in tissue DNA detection. Tumor size and Ki-67 were significant influencing factors of the positive rate of ctDNA detection and concordance between ctDNA and tissue DNA detection. In all patients, the concordance rate between ctDNA and tissue DNA detection was 71.9%, with moderate concordance, but the concordance was strong for patients with tumor size > 10 cm or Ki-67 > 5%. Tumor size, mitotic figure, Ki-67, and ctDNA mutation type were the significant influencing factors of prognosis, but only tumor size and ctDNA mutation type, were the independent prognostic factors for advanced GIST patients. We confirmed that ctDNA detection by NGS is a feasible and promising method for the diagnosis and prognosis of advanced GIST patients. Mol Cancer Ther; 17(1); 290–6. ©2017 AACR.
Scalable Production in Human Cells and Biochemical Characterization of Full-Length Normal and Mutant Huntingtin

Huntingtin (Htt) is a 350 kD intracellular protein, ubiquitously expressed and mainly localized in the cytoplasm. Huntington’s disease (HD) is caused by a CAG triplet amplification in exon 1 of the corresponding gene resulting in a polyglutamine (polyQ) expansion at the N-terminus of Htt. Production of full-length Htt has been difficult in the past and so far a scalable system or process has not been established for recombinant production of Htt in human cells. The ability to produce Htt in milligram quantities would be a prerequisite for many biochemical and biophysical studies aiming in a better understanding of Htt function under physiological conditions and in case of mutation and disease. For scalable production of full-length normal (17Q) and mutant (46Q and 128Q) Htt we have established two different systems, the first based on doxycycline-inducible Htt expression in stable cell lines, the second on “gutless” adenovirus mediated gene transfer. Purified material has then been used for biochemical characterization of full-length Htt. Posttranslational modifications (PTMs) were determined and several new phosphorylation sites were identified. Nearly all PTMs in full-length Htt localized to areas outside of predicted alpha-solenoid protein regions. In all detected N-terminal peptides methionine as the first amino acid was missing and the second, alanine, was found to be acetylated. Differences in secondary structure between normal and mutant Htt, a helix-rich protein, were not observed in our study. Purified Htt tends to form dimers and higher order oligomers, thus resembling the situation observed with N-terminal fragments, although the mechanism of oligomer formation may be different.
Oregon's Medicaid Coordinated Care Organizations.

In 2012, the state of Oregon transformed its Medicaid program by establishing 16 “coordinated care organizations,” or CCOs, to provide comprehensive care for its Medicaid population. Coordinated care organizations can be considered a type of accountable care organization (ACO): they are locally governed; are accountable for access, quality, and health spending; and emphasize primary care medical homes. However, CCOs differ from most Medicare and commercial ACOs in their acceptance of full financial risk in the form of a global budget. Coordinated care organizations are also required to integrate financing and delivery systems for a broad scope of services, including mental health, addiction, and dental services. Approximately 90% of the state’s 1.1 million Medicaid enrollees now receive care through CCOs that take a variety of forms that reflect the local context. These CCOs include a mix of for-profit and not-forprofit organizations and vary in the size of the population covered (from fewer than 11 000 enrollees to more than 200 000 enrollees). Some CCOs were formed out of previous Medicaid managed care organizations, whereas others were created out of new alliances and partnerships. Oregon’s transformation was made possible through a remarkable arrangement with the Centers for Medicare & Medicaid Services (CMS), which, beginning in 2012, would provide a total of $1.9 billion over
Anaphylaxis due to Pachycondyla goeldii ant: a case report.

Most cases of anaphylaxis caused by ants are attributed to ants from the Solenopsis genus [1] but there are many ant species of different genera and their distribution around the world varies. In Brazil, where there are over 2000 catalogued species of ants, all the cases of ant-induced anaphylaxis reported to date have been attributed to Solenopsis species [2,3]. We describe the fi rst case of anaphylaxis caused by Pachycondyla goeldii, an ant from the Ponerinae subfamily. A 52-year-old man developed anaphylaxis after being stung on the hand by an unidentifi ed insect while removing grass from his garden. He felt a tingling sensation and developed generalized urticaria and shortness of breath. He received treatment for anaphylactic shock at the emergency department and recovered within a few hours. Five days later, the patient had recovered completely. At the site of the sting, there was a dark spot surrounded by a red ring. He was receiving treatment for diabetes and hypertension (glimepiride, metformin, and enalapril [5 mg/day]) and he stated that he had not taken any other drugs or eaten any unusual foods. The patient reported that he had been stung twice (40 and 15 days previously) by a black insect like a wasp on his shoulder, which had become swollen and painful. No Solenopsis ants or wasps nests were found during a visit to the patient’s house but black ants measuring 1 cm in length (and popularly known as gambá) were found in the garden. The ants were identifi ed as P goeldii by the Center for the Study of Social Insects (CEIS) at São Paulo State University. The venom was obtained by removing the venom reservoirs with microscissors and squeezing the content into twicedistilled water. The crude venom solution was then lyophilized and maintained at –20oC until needed. The investigation of specifi c immunoglobulin E (IgE) in the patient’s serum (ImmunoCAP, Phadia Uppsala, Sweden) yielded positive results for Solenopsis invicta (class 3) and negative results for Vespula species, Polistes species and Apis mellifera. The total IgE was 49 IU/mL. A positive intradermal skin test was observed with P goeldii venom at a concentration of 0.1 μg/mL and with S invicta extract (IPI-ASAC Laboratory São Paulo, Brazil) at a concentration of 10 μg/mL. The tests performed in 2 nonatopic healthy controls were negative up to 10 μg/mL for both venoms. The venom of P goeldii was subjected to two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis, with the detection of approximately 45 proteins, with a molecular weight of 10 to 66 kDa and an isoelectric point of between 4 and 10 (Figure, A). Immunoassays with the patient’s serum revealed 4 IgE-reactive spots of between 30 and 45 kDa (Figure, B).
Screening for BK Viremia Reduces But Does Not Eliminate the Risk of BK Nephropathy: A Single-Center Retrospective Analysis

Background This study reviewed the outcomes of a screening protocol for BK viremia to determine if early diagnosis, followed by immunosuppression minimization, would prevent progression to nephropathy and graft loss. Methods This review included 369 renal transplant recipients tested for BK virus at serial time points after transplantation. Management included immunosuppression minimization plus cidofovir treatment for BK nephropathy. Results Recipients received tacrolimus-based immunosuppression, with 8% prednisone-free and 6% who received desensitization. With a mean follow-up of 22±10 months, 16% (n=57) of recipients became BK viremia positive. The median (range) time to diagnosis was 3 (1–17) months. Because renal biopsy was performed selectively, 59% of recipients underwent biopsy, with 47% showing BK nephropathy. Seventy-four percent of recipients cleared the virus at a median (range) time of 9 (3–33) months, with four grafts lost to BK nephropathy. Cidofovir-treated recipients displayed a higher viral load at diagnosis but showed equivalent renal function at last evaluation. In multivariate analysis, recipient age, Asian ethnicity, deceased donor, and prednisone use were factors independently associated with BK viremia. Actuarial survival of BK-positive grafts was worse than that of BK-negative grafts (P<0.01, log-rank test). At 9 and 12 months, the mean estimated glomerular filtration rate of the BK-positive group was lower than that of the BK-negative cohort (P=0.02). Conclusions Despite using a screening protocol combined with immunosuppression minimization, BK-positive recipients had a greater risk of graft loss and impaired function than recipients free of infection. Future investigations should focus on practices to prevent BK viremia.
Robust Dictionary Learning with Capped l1-Norm

Expressing data vectors as sparse linear combinations of basis elements (dictionary) is widely used in machine learning, signal processing, and statistics. It has been found that dictionaries learned from data are more effective than off-the-shelf ones. Dictionary learning has become an important tool for computer vision. Traditional dictionary learning methods use quadratic loss function which is known sensitive to outliers. Hence they could not learn the good dictionaries when outliers exist. In this paper, aiming at learning dictionaries resistant to outliers, we proposed capped l1-norm based dictionary learning and an efficient iterative re-weighted algorithm to solve the problem. We provided theoretical analysis and carried out extensive experiments on real word datasets and synthetic datasets to show the effectiveness of our method.
Genetic diversity and breeding system in a group of neotropical epiphytic ferns (Pleopeltis; Polypodiaceae).

Epiphytes are ecologically important components of tropical forests worldwide and yet they have been underrepresented in studies of reproductive biology. Given the presumed ephemeral nature of their substrates, and the importance of dispersal and colonization, epiphytes might be expected to undergo substantial inbreeding to ensure reproductive success, as in weedy terrestrial plants. While there is some evidence for inbreeding in epiphytic angiosperms, the only previous studies of fern epiphytes indicate that they are predominantly outcrossing. The present study reports on the genetic diversity and breeding system of six members of the Neotropical epiphytic fern genus Pleopeltis (Polypodiaceae). A survey of isozyme variability using starch gel electrophoresis revealed high population levels of polymorphism (P = 0.62), allelic diversity (A = 2.3), and individual heterozygosity (Ho = 0.181), but little differentiation among conspecific populations (I ³ 0.98; Gst = 0.048), and high interpopulational gene flow rates (Nm > 1). In addition, there was no indication of homozygote excess within populations that might indicate a history of selfing in these ferns: populations generally conformed to Hardy-Weinberg expected genotype frequencies, and both Wright's inbreeding coefficient (Fis) and Holsinger's intragametophytic selfing rates approached zero. Possible mechanisms limiting inbreeding in these ferns include antheridiogen activity and high levels of genetic load that would lead to inbreeding depression upon selfing.
A TRPV1‐to‐secretagogin regulatory axis controls pancreatic β‐cell survival by modulating protein turnover

Ca2+‐sensor proteins are generally implicated in insulin release through SNARE interactions. Here, secretagogin, whose expression in human pancreatic islets correlates with their insulin content and the incidence of type 2 diabetes, is shown to orchestrate an unexpectedly distinct mechanism. Single‐cell RNA‐seq reveals retained expression of the TRP family members in β‐cells from diabetic donors. Amongst these, pharmacological probing identifies Ca2+‐permeable transient receptor potential vanilloid type 1 channels (TRPV1) as potent inducers of secretagogin expression through recruitment of Sp1 transcription factors. Accordingly, agonist stimulation of TRPV1s fails to rescue insulin release from pancreatic islets of glucose intolerant secretagogin knock‐out(−/−) mice. However, instead of merely impinging on the SNARE machinery, reduced insulin availability in secretagogin−/− mice is due to β‐cell loss, which is underpinned by the collapse of protein folding and deregulation of secretagogin‐dependent USP9X deubiquitinase activity. Therefore, and considering the desensitization of TRPV1s in diabetic pancreata, a TRPV1‐to‐secretagogin regulatory axis seems critical to maintain the structural integrity and signal competence of β‐cells.
Persuasive communication and proenvironmental behaviours: How message tailoring and message framing can improve the integration of behaviours through self-determined motivation.

Public concern about environmental issues has grown substantially in the last two decades. As a consequence, the promotion of environmentally conscious behaviours that are integrated in people’s lifestyle has become an ongoing and important challenge. Persuasive messages are often perceived as the first step in efforts to motivate people to change a specific behaviour. In this article, the authors propose that (a) tailoring messages according to proposed processes underlying behaviour change (i.e., being aware of a problem, deciding what to do, initiating, and implementing a behaviour); and (b) framing these messages in terms of whether they serve intrinsic goals (i.e., health, well-being) as opposed to extrinsic goals (i.e., make or save money, comfort) could make messages more effective by progressively increasing the level of self-determined motivation of the targeted population.
SmartPDR: Smartphone-Based Pedestrian Dead Reckoning for Indoor Localization

Indoor pedestrian tracking extends location-based services to indoor environments where GPS signal is rarely detected. Typical indoor localization method is Wi-Fi-based positioning system, which is practical showing accuracy and extending coverage. However, it involves significant costs of installing and managing wireless access points. A practical indoor pedestrian-tracking approach should consider the absence of any infrastructure or pretrained database. In this paper, we present a smartphone-based pedestrian dead reckoning, SmartPDR, which tracks pedestrians through typical dead reckoning approach using data from inertial sensors embedded in smartphones. SmartPDR does not require any complex and expensive additional device or infrastructure that most existing pedestrian tracking systems rely on. The proposed system was implemented on off-the-shelf smartphones and the performance was evaluated in several buildings. Despite inherent localization errors from low-cost noisy sensors and complicated human movements, SmartPDR successfully tracks indoor user's location, which is confirmed from the experimental results with reasonable location accuracy. Indoor pedestrian tracking system using smartphone inertial sensors can be a promising methodology validating its practical usage through real deployment.
Model Selection Test for the Heavy-Tailed Distributions under Censored Samples with Application in Financial Data

Numerous heavy-tailed distributions are used for modeling financial data and in problems related to the modeling of economics processes. These distributions have higher peaks and heavier tails than normal distributions. Moreover, in some situations, we cannot observe complete information about the data. Employing the efficient estimation method and then choosing the best model in this situation are very important. Thus, the purpose of this article is to propose a new interval for comparing the two heavy-tailed candidate models and examine its suitability in the financial data under complete and censored samples. This interval is equivalent to encapsulating the results of many hypotheses tests. A maximum likelihood estimator (MLE) is used for evaluating the parameters of the proposed heavy-tailed distribution. A real dataset representing the top 30 companies of the Tehran Stock Exchange indices is used to illustrate the derived results.
Microembolic Signal Monitoring in Hemispheric Acute Ischaemic Stroke: A Prospective Study

Background and Purpose: There are few data on the occurrence of microembolic signals (MES) in the acute phase of ischaemic stroke. The objective of our work was to systematically study the frequency of MES in non-selected patients with a first-ever hemispheric transient ischemic attack (TIA) or acute cerebral infarction, and to evaluate the clinical usefulness of MES detection. Methods: 182 consecutive patients with hemispheric TIA or acute cerebral infarction, and 54-age-matched healthy controls were studied. Bilateral transcranial Doppler ultrasound (TCD) monitoring was performed for at least 30 min with a mean time from stroke onset to TCD of 69 h. Stroke severity on admission, early recurrent stroke and dependency on discharge were investigated. Results: MES were detected in 20.5% of patients with arterial sources of embolism, 17.1% of patients with potential sources of cardioembolism and 5% of patients with cryptogenic stroke. They were not registered, however, in lacunar infarctions (p < 0.001). Stroke severity on admission of patients with MES was greater than that of patients without MES (47.1 vs. 19.4% with the Canadian Stroke Scale ≤6.5; p = 0.009). Early recurrent stroke was more frequent in patients with MES (11.8%) than in those without MES (4.2%) although the difference was not statistically significant. Multiple logistic regression analysis showed that MES increased the risk of dependency on discharge (odds ratio, 4.2; 95% CI, 1.2–14.9; p = 0.01) independently of age, stroke severity on admission and presence of an arterial or cardiac embolic source. Conclusions: There is a strong association of MES in the acute phase of stroke with known potential arterial and cardiac embolic sources. MES have an independent predictive value of poor outcome.
The network meta-analytic-predictive approach to non-inferiority trials

In non-inferiority clinical trials, a test treatment is compared to an active-control rather than to placebo. Such designs are considered when placebo is unethical or not feasible. The critical question is whether the test treatment would have been superior to placebo, had placebo been used in the non-inferiority trial. This question can only be addressed indirectly, based on information from relevant historical trials with data on active-control and placebo. The network meta-analytic-predictive approach to non-inferiority trials is based on a network meta-analysis of the data from the historical trials and the non-inferiority trial, and the prediction of the putative test vs. placebo effect in the non-inferiority trial. The approach extends previous work by incorporating between-trial variability for all relevant parameters and focusing on the parameters in the non-inferiority trial rather than on population means. Two prominent examples with binary outcomes are used to illustrate the approach.
Flamelet modelling of non-premixed turbulent combustion with local extinction and re-ignition

Extinction and re-ignition in non-premixed turbulent combustion is investigated. A flamelet formulation accounting for transport along mixture fraction iso-surfaces is developed. A new transport term appears in the flamelet equations, which is modelled by a stochastic mixing approach. The timescale appearing in this model is obtained from the assumption that transport at constant mixture fraction is only caused by changes of the local scalar dissipation rate. The space coordinates appearing in this term can then be replaced by the mixture fraction and the scalar dissipation rate. The dissipation rate of the scalar dissipation rate appears as a diffusion coefficient in the new term. This is a new parameter of the problem and is called the re-ignition parameter. The resulting equations are simplified and stochastic differential equations for the scalar dissipation rate and the re-ignition parameter are formulated. The system of equations is solved using Monte Carlo calculations. The results show that the newly appearing transport term acts by modifying the S-shaped curve such that the lower turning point appears at higher scalar dissipation rate. In an a priori study, predictions using this model are compared with data from a direct numerical simulation of non-premixed combustion in isotropic turbulence simulating extinction and re-ignition.
A Comparison between Two Main Academic Literature Collections: Web of Science and Scopus Databases

Nowadays, the world’s scientific community has been publishing an enormous number of papers in different scientific fields. In such environment, it is essential to know which databases are equally efficient and objective for literature searches. It seems that two most extensive databases are Web of Science and Scopus. Besides searching the literature, these two databases used to rank journals in terms of their productivity and the total citations received to indicate the journals impact, prestige or influence. This article attempts to provide a comprehensive comparison of these databases to answer frequent questions which researchers ask, such as: How Web of Science and Scopus are different? In which aspects these two databases are similar? Or, if the researchers are forced to choose one of them, which one should they prefer? For answering these questions, these two databases will be compared based on their qualitative and quantitative characteristics.
The effect of exogenous melatonin on the histological changes of the ovary induced by Zearalenone

The mycotoxin zearalenone is often found in cereals and animal feeds. The intake of zearalenone through food can result in the hyperestrogenic syndrome, and is related to ovarian structural and functional alterations in mammals. It competitively binds to estrogen receptors and generates oxidative stress. Melatonin is a hormone produced by the pineal gland with a strong effect on reproduction as it inhibits the hypothalamic-pituitary-gonadal axis. It has also direct and indirect antioxidative effects in the ovarian tissues. Our aim was to explore the effect of melatonin on the histological changes of the ovary induced by zearalenone. Forty female Wistar rats were divided into five equal groups and treated for 28 days according to the following scheme: 1. Zearalenone vehiculum (sunflower oil)- treated group, 2. Melatonin vehiculum- (5% ethanol in Ringer) treated control group, 3. group treated with zearalenone (0.3 mg/kg b.w), 4. group treated with melatonin (10 mg/kg b.w) and 5. group of rats treated with zearalenone (0.3 mg/kg b.w) and melatonin (10 mg/kg b.w). Zearalenone induced degenerative changes in all developmental forms of ovarian follicles, hypertrophy of stroma with blood vessel dilatation and hyperemia. The concomitant application of melatonin and zearalenone resulted in milder morphological changes of the ovary, especially of preovulative follicles. Melatonin administration prevents the zaeralenone-induced structural alterations on an ovary. Keywords: zearalenone, melatonin, rat, ovary, histology