Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive Association Analysis of the Vitamin D Pathway Genes, VDR, CYP27B1, and CYP24A1, in Prostate Cancer

Genetic variation in vitamin D–related genes has not been investigated comprehensively and findings are equivocal. We studied the association between polymorphisms across the entire vitamin D receptor (VDR) gene and genes encoding for vitamin D activating enzyme 1-α-hydroxylase (CYP27B1) and deactivating enzyme 24-hyroxylase (CYP24A1) and prostate cancer risk among middle-aged men using a population-based case-control study design. DNA samples and survey data were obtained from incident cases (n = 630), 40 to 64 years old, identified through the Seattle-Puget Sound Surveillance, Epidemiology, and End Results cancer registry from 1993 to 1996 and from random controls (n = 565) of similar age without a history of prostate cancer. We selected and genotyped tag single-nucleotide polymorphisms to predict common variants across VDR (n = 22), CYP27B1 (n = 2), and CYP24A1 (n = 14). Haplotypes of VDR and CYP24A1 were not associated with prostate cancer risk. In the genotype analysis, homozygotes at two VDR loci (rs2107301 and rs2238135) were associated with a 2- to 2.5-fold higher risk of prostate cancer compared with the homozygote common allele [odds ratio, 2.47 (95% confidence interval, 1.52-4.00; P = 0.002) and 1.95 (95% confidence interval, 1.17-3.26; P = 0.007), respectively; P value corrected for multiple comparisons for VDR = 0.002]. We found no evidence that the two associated VDR single-nucleotide polymorphisms were modified by age at diagnosis, prostate cancer aggressiveness, first-degree family history of prostate cancer, or vitamin D intake. Genotypes of CYP27B1 and CYP24A1 were not associated with prostate cancer risk. Our findings suggest that polymorphisms in the VDR gene may be associated with prostate cancer risk and, therefore, that the vitamin D pathway might have an etiologic role in the development of prostate cancer. (Cancer Epidemiol Biomarkers Prev 2007;16(10):1990–9)
Simultaneous Power-Based Localization of Transmitters for Crowdsourced Spectrum Monitoring

The current mechanisms for locating spectrum offenders are time consuming, human-intensive, and expensive. In this paper, we propose a novel approach to locate spectrum offenders using crowdsourcing. In such a participatory sensing system, privacy and bandwidth concerns preclude distributed sensing devices from reporting raw signal samples to a central agency; instead, devices would be limited to measurements of received power. However, this limitation enables a smart attacker to evade localization by simultaneously transmitting from multiple infected devices. Existing localization methods are insufficient or incapable of locating multiple sources when the powers from each source cannot be separated at the receivers. In this paper, we first propose a simple and efficient method that simultaneously locates multiple transmitters using the received power measurements from the selected devices. Second, we build sampling approaches to select sensing devices required for localization. Next, we enhance our sampling to also take into account incentives for participation in crowdsourcing. We experimentally evaluate our localization framework under a variety of settings and find that we are able to localize multiple sources transmitting simultaneously with reasonably high accuracy in a timely manner.
VA FitHeart, a Mobile App for Cardiac Rehabilitation: Usability Study

Background Cardiac rehabilitation (CR) improves outcomes for patients with ischemic heart disease or heart failure but is underused. New strategies to improve access to and engagement in CR are needed. There is considerable interest in technology-facilitated home CR. However, little is known about patient acceptance and use of mobile technology for CR. Objective The aim of this study was to develop a mobile app for technology-facilitated home CR and seek to determine its usability. Methods We recruited patients eligible for CR who had access to a mobile phone, tablet, or computer with Internet access. The mobile app includes physical activity goal setting, logs for tracking physical activity and health metrics (eg, weight, blood pressure, and mood), health education, reminders, and feedback. Study staff demonstrated the mobile app to participants in person and then observed participants completing prespecified tasks with the mobile app. Participants completed the System Usability Scale (SUS, 0-100), rated likelihood to use the mobile app (0-100), questionnaires on mobile app use, and participated in a semistructured interview. The Unified Theory of Acceptance and Use of Technology and the Theory of Planned Behavior informed the analysis. On the basis of participant feedback, we made iterative revisions to the mobile app between users. Results We conducted usability testing in 13 participants. The first version of the mobile app was used by the first 5 participants, and revised versions were used by the final 8 participants. From the first version to revised versions, task completion success rate improved from 44% (11/25 tasks) to 78% (31/40 tasks; P=.05), SUS improved from 54 to 76 (P=.04; scale 0-100, with 100 being the best usability), and self-reported likelihood of use remained high at 76 and 87 (P=.30; scale 0-100, with 100 being the highest likelihood). In interviews, patients expressed interest in tracking health measures (“I think it’ll be good to track my exercise and to see what I’m doing”), a desire for introductory training (“Initially, training with a technical person, instead of me relying on myself”), and an expectation for sharing data with providers (“It would also be helpful to share with my doctor, it just being a matter of clicking a button and sharing it with my doctor”). Conclusions With participant feedback and iterative revisions, we significantly improved the usability of a mobile app for CR. Patient expectations for using a mobile app for CR include tracking health metrics, introductory training, and sharing data with providers. Iterative mixed-method evaluation may be useful for improving the usability of health technology.
A Qualitative Analysis of EHR Clinical Document Synthesis by Clinicians

Clinicians utilize electronic health record (EHR) systems during time-constrained patient encounters where large amounts of clinical text must be synthesized at the point of care. Qualitative methods may be an effective approach for uncovering cognitive processes associated with the synthesis of clinical documents within EHR systems. We utilized a think-aloud protocol and content analysis with the goal of understanding cognitive processes and barriers involved as medical interns synthesized patient clinical documents in an EHR system to accomplish routine clinical tasks. Overall, interns established correlations of significance and meaning between problem, symptom and treatment concepts to inform hypotheses generation and clinical decision-making. Barriers identified with synthesizing EHR documents include difficulty searching for patient data, poor readability, redundancy, and unfamiliar specialized terms. Our study can inform recommendations for future designs of EHR clinical document user interfaces to aid clinicians in providing improved patient care.
Radiocarbon and stable‐isotope geochemistry of organic and inorganic carbon in Lake Superior

We present a lake‐wide investigation of Lake Superior carbon and organic matter biogeochemistry using radiocarbon, stable isotope, and carbon concentrations. Dissolved inorganic carbon (DIC) abundance in the lake was 121–122 Tg C, with offshore concentration andδ13C values being laterally homogenous and tightly coupled to the physical and thermal regime and biochemical processes. Offshore Δ14C of DIC (50–65‰) exhibited lateral homogeneity and was more 14C enriched than co‐occurring atmospheric CO2 (∼38‰); nearshore Δ14C of DIC (36–38‰) was similar to atmospheric CO2. Dissolved organic carbon (DOC) abundance was 14.2–16.4 Tg C. DOC's concentration and δ13C were homogenous in June (mixed lake), but varied laterally during August (stratification) possibly due to spatial differences in lake productivity. Throughout sampling, DOC had modern radiocarbon values (14–58‰) indicating a semilabile nature with a turnover time of ≤60 years. Lake particulate organic carbon (POC, 0.9–1.3 Tg C) was consistently 13C depleted relative to DOC. The δ15N of epilimnetic particulate organic nitrogen shifted to more negative values during stratification possibly indicating greater use of nitrate (rather than ammonium) by phytoplankton in August. POC's radiocarbon was spatially heterogeneous (Δ14C range: 58‰ to −303‰), and generally 14C depleted relative to DOC and DIC. POC 14C depletion could not be accounted for by black carbon in the lake but, because of its spatial and temporal distribution, is attributed to sediment resuspension. The presence of old POC within the epilimnion of the open lake indicates possible benthic‐pelagic coupling in the lake's organic carbon cycle; the ultimate fate of this old POC bears further investigation.
Attitude estimation and stabilization of a rigid body using low-cost sensors

We consider the attitude and gyro-bias estimation as well as the attitude stabilization problem of a rigid body in space using low-cost sensors. We assume that a biased measurement of the angular velocity of the rigid body is provided by a low-cost gyroscope, and the attitude measurements are obtained using low-cost (low-pass) sensors such as accelerometers and magnetometers. We provide an attitude and gyro-bias estimation algorithm using the biased gyro measurement and the attitude measurements - which represent the true attitude only at low frequencies - provided by the low-cost attitude sensors. Finally, the proposed estimation algorithm is coupled with a quaternion-based attitude stabilization scheme, and simulation results are provided to show the effectiveness of the proposed algorithm.
Advanced transaction models in workflow contexts

In recent years, numerous transaction models have been proposed to address the problems posed by advanced database applications, but only a few of these models are being used in commercial products. In this paper, we make the case that such models may be too centered around databases to be useful in real environments. Advanced applications raise a variety of issues that are not addressed at all by transaction models. These same issues, however, are the basis for existing workflow systems, which are having considerable success as commercial products in spite of not having a solid theoretical foundation. We explore some of these issues and show that, in many aspects, workflow models are a superset of transaction models and have the added advantage of incorporating a variety of ideas that have so far remained outside the scope of traditional transaction processing.
Elucidation of the Binding Mechanism of Coumarin Derivatives with Human Serum Albumin

Coumarin is a benzopyrone which is widely used as an anti-coagulant, anti-oxidant, anti-cancer and also to cure arthritis, herpes, asthma and inflammation. Here, we studied the binding of synthesized coumarin derivatives with human serum albumin (HSA) at physiological pH 7.2 by using fluorescence spectroscopy, circular dichroism spectroscopy, molecular docking and molecular dynamics simulation studies. By addition of coumarin derivatives to HSA the maximum fluorescence intensity was reduced due to quenching of intrinsic fluorescence upon binding of coumarin derivatives to HSA. The binding constant and free energy were found to be 1.957±0.01×105 M−1, −7.175 Kcal M−1 for coumarin derivative (CD) enamide; 0.837±0.01×105 M−1, −6.685 Kcal M−1 for coumarin derivative (CD) enoate, and 0.606±0.01×105 M−1, −6.49 Kcal M−1 for coumarin derivative methylprop (CDM) enamide. The CD spectroscopy showed that the protein secondary structure was partially unfolded upon binding of coumarin derivatives. Further, the molecular docking studies showed that coumarin derivatives were binding to HSA at sub-domain IB with the hydrophobic interactions and also with hydrogen bond interactions. Additionally, the molecular dynamics simulations studies contributed in understanding the stability of protein-drug complex system in the aqueous solution and the conformational changes in HSA upon binding of coumarin derivatives. This study will provide insights into designing of the new inspired coumarin derivatives as therapeutic agents against many life threatening diseases.
A novel computer test to assess driving-relevant cognitive functions – a pilot study

ABSTRACT Background: The assessment of driving-relevant cognitive functions in older drivers is a difficult challenge as there is no clear-cut dividing line between normal cognition and impaired cognition and not all cognitive functions are equally important for driving. Methods: To support decision makers, the Bern Cognitive Screening Test (BCST) for older drivers was designed. It is a computer-assisted test battery assessing visuo-spatial attention, executive functions, eye–hand coordination, distance judgment, and speed regulation. Here we compare the performance in BCST with the performance in paper and pencil cognitive screening tests and the performance in the driving simulator testing of 41 safe drivers (without crash history) and 14 unsafe drivers (with crash history). Results: Safe drivers performed better than unsafe drivers in BCST (Mann–Whitney U test: U = 125.5; p = 0.001) and in the driving simulator (Student's t-test: t(44) = –2.64, p = 0.006). No clear group differences were found in paper and pencil screening tests (p > 0.05; ns). BCST was best at identifying older unsafe drivers (sensitivity 86%; specificity 61%) and was also better tolerated than the driving simulator test with fewer dropouts. Conclusions: BCST is more accurate than paper and pencil screening tests, and better tolerated than driving simulator testing when assessing driving-relevant cognition in older drivers.
A Sentiment-aligned Topic Model for Product Aspect Rating Prediction

Aspect-based opinion mining has attracted lots of attention today. In this paper, we address the problem of product aspect rating prediction, where we would like to extract the product aspects, and predict aspect ratings simultaneously. Topic models have been widely adapted to jointly model aspects and sentiments, but existing models may not do the prediction task well due to their weakness in sentiment extraction. The sentiment topics usually do not have clear correspondence to commonly used ratings, and the model may fail to extract certain kinds of sentiments due to skewed data. To tackle this problem, we propose a sentiment-aligned topic model(SATM), where we incorporate two types of external knowledge: productlevel overall rating distribution and wordlevel sentiment lexicon. Experiments on real dataset demonstrate that SATM is effective on product aspect rating prediction, and it achieves better performance compared to the existing approaches.
Role of Loc1p in assembly and reorganization of nuclear ASH1 messenger ribonucleoprotein particles in yeast

Significance Cytoplasmic mRNA localization is preceded by the formation of nuclear pre-mRNPs. To date the requirement of the nuclear mRNP assembly is not well understood. We used ASH1 mRNA localization from budding yeast to understand the mechanisms of nuclear priming for cytoplasmic mRNA transport. We found that the nuclear factor Loc1p is required to stably and specifically tether the bona fide ASH1 RNA-binding protein She2p to RNA in the nucleus, offering an explanation for the requirement of Loc1p for ASH1 mRNA localization. Because Loc1p is not part of the cytoplasmic ASH1 mRNP, it must be removed before mRNA transport. We show that the cytoplasmic transport factor She3p displaces Loc1p from the ASH1 mRNP, allowing for the maturation of the localizing ASH1 mRNP. Directional transport of mRNA is a universal feature in eukaryotes, requiring the assembly of motor-dependent RNA-transport particles. The cytoplasmic transport of mRNAs is preceded by the nuclear assembly of pre-messenger ribonucleoprotein particles (mRNPs). In budding yeast, the asymmetric synthesis of HO 1 (ASH1) pre-mRNP originates already cotranscriptionally and passes through the nucleolus before its nuclear export. The nucleolar localization of ASH1 mRNA protein 1 (Loc1p) is required for efficient ASH1 mRNA localization. Immunoprecipitation experiments have revealed that Loc1p forms cocomplexes with other components of the ASH1 transport complex. However, it remains unclear how Loc1p is recruited into this mRNP and why Loc1p is important for ASH1 mRNA localization. Here we demonstrate that Loc1p undergoes a direct and specific interaction with the ASH1 mRNA-binding Swi5p-dependent HO expression protein 2 (She2p). This cocomplex shows higher affinity and specificity for RNA bearing localization elements than the individual proteins. It also stabilizes the otherwise transient binding of She2p to ASH1 mRNA, suggesting that cooperative mRNA binding of Loc1p with She2p is the required nuclear function of Loc1p for ASH1 mRNA localization. After nuclear export, myosin-bound She3p joins the ASH1 mRNP to form a highly specific cocomplex with She2p and ASH1 mRNA. Because Loc1p is found only in the nucleus, it must be removed from the complex directly before or after export. In vitro and in vivo experiments indicate that the synergistic interaction of She2p and She3p displaces Loc1p from the ASH1 complex, allowing free Loc1p to rapidly reenter the nucle(ol)us. Together these findings suggest an ordered process of nuclear assembly and reorganization for the maturation of localizing ASH1 mRNPs.
Multiple Forms of Endocytosis In Bovine Adrenal Chromaffin Cells

We studied endocytosis in chromaffin cells with both perforated patch and whole cell configurations of the patch clamp technique using cell capacitance measurements in combination with amperometric catecholamine detection. We found that chromaffin cells exhibit two relatively rapid, kinetically distinct forms of stimulus-coupled endocytosis. A more prevalent “compensatory” retrieval occurs reproducibly after stimulation, recovering an approximately equivalent amount of membrane as added through the immediately preceding exocytosis. Membrane is retrieved through compensatory endocytosis at an initial rate of ∼6 fF/s. Compensatory endocytotic activity vanishes within a few minutes in the whole cell configuration. A second form of triggered membrane retrieval, termed “excess” retrieval, occurs only above a certain stimulus threshold and proceeds at a faster initial rate of ∼248 fF/s. It typically undershoots the capacitance value preceding the stimulus, and its magnitude has no clear relationship to the amount of membrane added through the immediately preceding exocytotic event. Excess endocytotic activity persists in the whole cell configuration. Thus, two kinetically distinct forms of endocytosis coexist in intact cells during perforated patch recording. Both are fast enough to retrieve membrane after exocytosis within a few seconds. We argue that the slower one, termed compensatory endocytosis, exhibits properties that make it the most likely mechanism for membrane recycling during normal secretory activity.
Achieving Turbidity Robustness on Underwater Images Local Feature Detection

Methods to detect local features have been made to be invariant to many transformations. So far, the vast majority of feature detectors consider robustness just to over-land effects. However, when capturing pictures in underwater environments, there are media specific properties that can degrade the visual quality the captured images. Little work has been made in order to study the robustness that the popular feature detectors have to underwater environment image conditions. We develop a new dataset, called TURBID, where we produced real seabed images with different amounts of degradation. On this dataset, we search over multiple feature detectors from the literature to indicate the ones with more robust properties. We concluded that scale-invariant detectors are more robust to degradation of underwater images. Finally, we elected Center Surround Extremas, KAZE, Difference of Gaussians and the Hessian-Laplace as the best detectors for this environment on all tested scenes.
Development of Aggressive Pancreatic Ductal Adenocarcinomas Depends on Granulocyte Colony Stimulating Factor Secretion in Carcinoma Cells

Aggressive PDAC correlates with increased G-CSF production and accumulation of immunosuppressive cells. Treatment of mouse models with gemcitabine and anti–G-CSF was efficacious. Analysis of clinical data indicates a subset of patients for whom this treatment might be effective. The survival rate for pancreatic ductal adenocarcinoma (PDAC) remains low. More therapeutic options to treat this disease are needed, for the current standard of care is ineffective. Using an animal model of aggressive PDAC (Kras/p48TGFβRIIKO), we discovered an effect of TGFβ signaling in regulation of G-CSF secretion in pancreatic epithelium. Elevated concentrations of G-CSF in PDAC promoted differentiation of Ly6G+ cells from progenitors, stimulated IL10 secretion from myeloid cells, and decreased T-cell proliferation via upregulation of Arg, iNOS, VEGF, IL6, and IL1b from CD11b+ cells. Deletion of csf3 in PDAC cells or use of a G-CSF–blocking antibody decreased tumor growth. Anti–G-CSF treatment in combination with the DNA synthesis inhibitor gemcitabine reduced tumor size, increased the number of infiltrating T cells, and decreased the number of Ly6G+ cells more effectively than gemcitabine alone. Human analysis of human datasets from The Cancer Genome Atlas and tissue microarrays correlated with observations from our mouse model experiments, especially in patients with grade 1, stage II disease. We propose that in aggressive PDAC, elevated G-CSF contributes to tumor progression through promoting increases in infiltration of neutrophil-like cells with high immunosuppressive activity. Such a mechanism provides an avenue for a neoadjuvant therapeutic approach for this devastating disease. Cancer Immunol Res; 5(9); 718–29. ©2017 AACR.
Regulation of the neurotensin NT1 receptor in the developing rat brain following chronic treatment with the antagonist SR 48692

The aim of the present study was to investigate the role of neurotensin in the regulation of NT1 receptors during postnatal development in the rat brain. Characterization of the ontogeny of neurotensin concentration and [125I]neurotensin binding to NT1 receptors in the brain at different embryonic and postnatal stages showed that neurotensin was highly expressed at birth, reaching peak levels at postnatal day 5 (P5) and decreasing thereafter. The transient rise in neurotensin levels preceded the maximal expression of NT1 receptors, observed at P10, suggesting that neurotensin may influence the developmental profile of NT1 receptors. Using primary cultures of cerebral cortex neurons from fetal rats, we showed that exposure to the neurotensin agonist JMV 449 (1 nM) decreased (−43%) the amount of NT1 receptor mRNA measured by reverse transcription‐PCR, an effect that was abolished by the nonpeptide NT1 receptor antagonist SR 48692 (1 μM). However, daily injection of SR 48692 to rat pups from birth for 5, 9, or 15 days did not modify [125I]neurotensin binding in brain membrane homogenates. Moreover, postnatal blockade of neurotensin transmission did not alter the density and distribution of NT1 receptors assessed by quantitative autoradiography nor NT1 receptor mRNA expression measured by in situ hybridization in the cerebral cortex, caudate‐putamen, and midbrain. These results suggest that although NT1 receptor expression can be regulated in vitro by the agonist at an early developmental stage, neurotensin is not a major factor in the establishment of the ontogenetic pattern of NT receptors in the rat brain. J. Neurosci. Res. 60:362–369, 2000 © 2000 Wiley‐Liss, Inc.