Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating Species and Population Level Foraging Variation and Individual Specialization in Pygoscelis Penguins Using Stable Isotope Analysis

vii CHAPTER 1: GENERAL INTRODUCTION.1 LITERATURE CITED.6 CHAPTER 2: SPECIES AND POPULATION LEVEL DIFFERENCES IN SEASONAL CONSISTENCY AND INDIVIDUAL VARIATION OF PYGOSCELIS PENGUIN FORAGING STRATEGIES.1
Presence of Thyroid Disorders in Patients with Autoimmune and Autoinflammatory Rheumatic Diseases

1 Department of Physical Medicine and Rehabilitation, Medical Faculty, Sakarya University, Sakarya, Turkey 2 Department of Physical Medicine and Rehabilitation, Division of Rheumatology, Medical Faculty, Sakarya University, Sakarya, Turkey 3 Department of Physical Medicine and Rehabilitation, Division of Rheumatology, Bolu Training and Research Hospital, Bolu, Turkey 4 Department of Internal Medicine, Division of Hematology, Medical Faculty, Sakarya University, Sakarya, Turkey
Emergency Physicians' Perceived Influence of EHR Use on Clinical Workflow and Performance Metrics

Abstract Objective Over the last decade, electronic health records (EHRs) have shaped clinical practice. In this article, we investigated the perceived effects of EHR use on clinical workflow and meaningful use (MU) performance metrics. Materials and Methods Semistructured interviews were conducted with 20 (n = 20) physicians at two urban emergency departments. Interview questions focused on time spent on EHR use, changes in clinical practices with EHR use, and the effect of MU performance metrics on clinical workflow. Qualitative coding using grounded theory and descriptive analyses were performed to provide descriptive insights. Results Physicians reported that EHRs improved their clinical workflow, especially on MU-related activities including door-to-doctor time and admit decision time. EHR use also affected physicians work efficiency, quality of care provided, and overall patient safety. Conclusion Physicians' perception of EHRs is likely to influence their practices. With negative perceptions of EHR usability problems, positive aspects of EHR use, including the influence on MU performance metrics, may be overridden.
Tanshinone IIA inhibits cell proliferation and tumor growth by downregulating STAT3 in human gastric cancer

Gastric cancer is the third leading cause of cancer-associated deaths worldwide. Research into the underlying mechanisms of gastric cancer is essential for the development of novel therapeutic agents to improve the prognoses of patients with gastric cancer. Tanshinone IIA (Tan IIA) is the pure extract of Danshen root (Salvia miltiorrhiza) and has been report to inhibit the proliferation of gastric cancer cells; however, the intrinsic underlying mechanisms remain unclear. The aim of the present study was to investigate whether Tan IIA has a direct anti-cancer effect in gastric cancer cells and determine the underlying mechanisms responsible. The results revealed that Tan IIA effectively inhibits proliferation in three human gastric cancer cell lines (SNU-638, MKN1 and AGS) in a time- and dose-dependent manner. Furthermore, Tan IIA treatment induced an increase in apoptosis, B-cell lymphoma (Bcl-2)-associated protein X expression and cleaved caspase-3 levels, as well as a decrease in Bcl-2 expression. Treatment with Tan IIA inhibited Furthermore, treatment with Tan IIA significantly inhibited the phosphorylation of signal transducer and activator of transcription 3 (STAT3), which may be responsible for the changes in apoptosis gene expression. However, overexpression of STAT3 significantly ameliorated the Tan IIA-induced suppression of cell growth and apoptosis. A nude mouse xenograft model was constructed and the results revealed that intraperitoneal Tan IIA treatment for 28 days significantly inhibited tumor growth and STAT3 activation. The results of the present study suggest that Tan IIA exerts potent anti-cancer activity in gastric cancer cells and this effect is mediated by the downregulation of STAT3 activation.
Methylation and Expression of Nonclustered Protocadherins Encoding Genes and Risk of Precancerous Gastric Lesions in a High-Risk Population

Nonclustered protocadherins (PCDH) family is a group of cell–cell adhesion molecules. We have found differentially methylated genes in the nonclustered PCDHs family associated with Helicobacter pylori (H. pylori) infection in prior genome-wide methylation analysis. To further investigate the methylation and expression of nonclustered PCDHs encoding genes in H. pylori--related gastric carcinogenesis process, four candidate genes including PCDH7, PCDH10, PCDH17, and PCDH20 were selected, which were reported to be tumor suppressors for digestive cancers. A total of 747 participants with a spectrum of gastric lesions were enrolled from a high-risk population of gastric cancer. Promoter methylation levels of four genes were significantly higher in H. pylori–positive subjects than the negative group (all P < 0.001). Elevated methylation levels of PCDH10 and PCDH17 were observed with the increasing severity of gastric lesions (both Ptrend < 0.001). In the protein expression analysis, PCDH17 expression was inversely associated with gastric lesions; the OR [95% confidence interval (CI)] was 0.49 (0.26–0.95) for chronic atrophic gastritis (CAG), 0.31 (0.15–0.63) for intestinal metaplasia, and 0.38 (0.19–0.75) for indefinite dysplasia and dysplasia, compared with superficial gastritis. In addition, PCDH10 expression was significantly lower in CAG (OR, 0.40; 95% CI, 0.24–0.68). The inverse association between methylation and protein expression of PCDH10 and PCDH17 was further supported when we explored the methylation and mRNA expression in The Cancer Genome Atlas database (all P < 0.001). Our study found elevated promoter methylation and decreased expression of PCDH10 and PCDH17 in advanced gastric lesions, suggesting that elevated PCDH10 and PCDH17 methylation may be an early event in gastric carcinogenesis. Cancer Prev Res; 11(11); 717–26. ©2018 AACR.
Foraging as an evidence accumulation process

A canonical foraging task is the patch-leaving problem, in which a forager must decide to leave a current resource in search for another. Theoretical work has derived optimal strategies for when to leave a patch, and experiments have tested for conditions where animals do or do not follow an optimal strategy. Nevertheless, models of patch-leaving decisions do not consider the imperfect and noisy sampling process through which an animal gathers information, and how this process is constrained by neurobiological mechanisms. In this theoretical study, we formulate an evidence accumulation model of patch-leaving decisions where the animal averages over noisy measurements to estimate the state of the current patch and the overall environment. Evidence accumulation models belong to the class of drift diffusion processes and have been used to model decision making in different contexts especially in cognitive and systems neuroscience. We solve the model for conditions where foraging decisions are optimal and equivalent to the marginal value theorem, and perform simulations to analyze deviations from optimal when these conditions are not met. By adjusting the drift rate and decision threshold, the model can represent different “strategies”, for example an increment-decrement or counting strategy. These strategies yield identical decisions in the limiting case but differ in how patch residence times adapt when the foraging environment is uncertain. To account for sub-optimal decisions, we introduce an energy-dependent utility function that predicts longer than optimal patch residence times when food is plentiful. Our model provides a quantitative connection between ecological models of foraging behavior and evidence accumulation models of decision making. Moreover, it provides a theoretical framework for potential experiments which seek to identify neural circuits underlying patch leaving decisions.
Increased Metabolic Activity on 18F-Fluorodeoxyglucose Positron Emission Tomography–Computed Tomography in Human Immunodeficiency Virus–Associated Immune Reconstitution Inflammatory Syndrome

Background Immune reconstitution inflammatory syndrome (IRIS) represents an unexpected inflammatory response shortly after initiation of antiretroviral therapy (ART) in some human immunodeficiency virus (HIV)-infected patients with underlying neoplasia or opportunistic infections, including tuberculosis. We hypothesized that IRIS is associated with increased glycolysis and that 18F-fluorodeoxyglucose (FDG) positron emission tomography-computed tomography (PET/CT) could help identify high-risk subjects. Methods In this prospective cohort study, 30 HIV-infected patients (CD4+ count <100 cells/µL) underwent FDG-PET/CT scans at baseline and 4-8 weeks after ART initiation. Ten patients developed IRIS (6 mycobacterial). Results At baseline, total glycolytic activity, total lesion volume, and maximum standardized uptake values (SUVs) of pathologic FDG uptake (reflective of opportunistic disease burden) were significantly higher in IRIS vs non-IRIS (P = .010, .017, and .029, respectively) and significantly correlated with soluble inflammatory biomarkers (interferon-γ, myeloperoxidase, tumor necrosis factor, interleukin 6, soluble CD14). Baseline bone marrow (BM) and spleen FDG uptake was higher in mycobacterial IRIS specifically. After ART initiation, BM and spleen mean SUV decreased in non-IRIS (P = .004, .013) but not IRIS subjects. Our results were supported by significantly higher glucose transporter 1 (Glut-1) expression of CD4+ cells and monocytes after ART initiation in IRIS/mycobacterial IRIS compared with non-IRIS patients. Conclusions We conclude that increased pathologic metabolic activity on FDG-PET/CT prior to ART initiation is associated with IRIS development and correlates with inflammatory biomarkers. Abnormally elevated BM and spleen metabolism is associated with mycobacterial IRIS, HIV viremia, and Glut-1 expression on CD4+ cells and monocytes. Clinical Trials Registration NCT02147405.
Conversion surgery with gemcitabine plus nab-paclitaxel for locally advanced unresectable pancreatic cancer: A case report

The standard treatment for locally advanced unresectable (UR-LA) pancreatic ductal adenocarcinoma (PDAC) is chemo-radiotherapy. Surgery following chemo-radiotherapy (conversion surgery), has been considered a useful strategy and has been used for UR-LA PDAC. The current study presents the case of a 43-year-old woman who complained of back pain. A radiological examination revealed a pancreatic tumor in contact with >270 degrees of the superior mesenteric artery (SMA) perimeter, with invasion extending from the superior mesenteric vein (SMV) to the portal vein (PV). An endoscopic ultrasonography-guided fine needle aspiration biopsy revealed adenocarcinoma as the pathological diagnosis and the patient was diagnosed with UR-LA PDAC. Following 12 courses of combined gemcitabine plus nab-paclitaxel (GnP) for 9 months, the extent of tumor invasion to the SMA and SMV was improved and the level of cancer antigen (CA) 19-9 decreased. A pancreatoduodenectomy with PV resection and reconstruction using a left renal vein graft were performed. Pathological examination revealed that the operative outcome was R0 (no residual tumor) resection and the patient was alive 19 months after the initial treatment (9 months post surgery), however, there was local tumor recurrence. Between March 2015 and February 2016 a total of 10 cases of UR-LA PDAC were encountered at the Department of General Surgery, Chiba University Hospital (Chiba, Japan), in which GnP therapy was performed. Including the present case, 6 of the 11 cases (55%) underwent conversion surgery with curative resection. Kaplan-Meier analysis revealed that patients treated with conversion surgery presented significantly longer overall survival (OS) than those treated with no conversion surgery (median OS, 22.5 vs. 11 months; P=0.047, Wilcoxon test). The minimum reduction of CA19-9 was 67%. In conclusion, conversion surgery following GnP therapy is a desirable option for UR-LA PDAC. A significant reduction in the CA19-9 levels may be useful in determining the timing of changeover from medicine to surgery in patients with UR-LA PDAC in whom conversion surgery is being considered.
Managerial Incentives to Increase Risk Provided by Debt, Stock, and Options

We measure a manager’s risk-taking incentives as the total sensitivity of the manager’s debt, stock, and option holdings to firm volatility. We compare this measure with the option vega and with the relative measures used by the prior literature. Vega does not capture risk-taking incentives from managers’ stock and debt holdings and does not reflect the fact that employee options are warrants. The relative measures do not incorporate the sensitivity of options to volatility. Our new measure explains risk choices better than vega and the relative measures and should be useful for future research on managers’ risk choices. Data and the online appendix are available at https://doi.org/10.1287/mnsc.2017. 2811. This paper was accepted by Shiva Rajgopal, accounting.
Scale Exploiting Minimal Solvers for Relative Pose with Calibrated Cameras

We present efﬁcient minimal solvers for the estimation of relative pose between two calibrated images. The proposed method exploits known scale ratios of feature matches which are intrinsically provided by scale invariant feature detectors with scale-space pyramids ( e.g . SIFT). Since we are using scale, the number of required feature matches is reduced and consequently fewer inliers are needed. In our paper, we derive two solvers each related to one of the two possible minimal sets: Our 1 + 3 point algorithm estimates relative pose from four feature matches with one known scale, while our 2 + 1 point al-gorithm computes relative pose from three feature matches with two known scales. We embed the proposed methods into RANSAC with two inlier classes, and present an ef-ﬁcient RANSAC modiﬁcation for less reliable scales. Finally, we analyze performance and robustness in synthetic data, and evaluate our RANSAC approach on real data in comparison to RANSAC based on the ﬁve point algorithm.
The MAPK kinase BcMkk1 suppresses oxalic acid biosynthesis via impeding phosphorylation of BcRim15 by BcSch9 in Botrytis cinerea

The mitogen-activated protein kinase (MAPK) cassette of the cell wall integrity (CWI) pathway is primarily responsible for orchestrating changes of cell wall. However, functions of this cassette in other cellular processes are not well understood. Here, we found that the Botrytis cinerea mutant of MAPK kinase (BcMkk1) displays more serious defects in mycelial growth, conidiation, responses to cell wall and oxidative stresses, but possesses less reduced virulence than the mutants of its upstream (BcBck1) and downstream (BcBmp3) kinases. Interestingly, BcMkk1, but not BcBck1 and BcBmp3, negatively regulates production of oxalic acid (OA) and activity of extracellular hydrolases (EHs) that are proposed to be virulence factors of B. cinerea. Moreover, we obtained evidence that BcMkk1 negatively controls OA production via impeding phosphorylation of the Per-Arnt-Sim (PAS) kinase BcRim15 by the Ser/Thr kinase BcSch9. In addition, the fungal Pro40 homolog BcPro40 was found to interact simultaneously with three MAPKs, implying that BcPro40 is a scaffold protein of the CWI pathway in B. cinerea. Taken together, results of this study reveal that BcMkk1 negatively modulates virulence via suppressing OA biosynthesis in B. cinerea, which provides novel insight into conserved and species-specific functions of the MAPK kinase in fungi.
Designing Incentive Systems for Truthful Forecast Information Sharing Within a Firm

We consider a firm where the sales division (Sales) is responsible for demand forecasting and the operations division (Operations) is responsible for ordering. Sales has better information about the demand than Operations and sends a nonbinding demand forecast to Operations. To incentivize truthful information sharing, we include a forecast error penalty in the incentive system of Sales. Besides monetary payoffs, we also add behavioral factors to the utility function of Sales. We model the setting as a signaling game and derive the Pareto-dominant separating equilibria of the game. In laboratory experiments, we observe human behavior that is in line with the predictions of the behavioral model but deviates substantially from expected-payoff-maximizing behavior. We use the behavioral model to design incentive systems for truthful information sharing and validate the approach in an experiment with out-of-sample treatments and out-of-sample subjects. We conduct additional experiments to provide further robus.
Explaining nurses’ experiences of caring for brain dead patients: a content analysis

Background Caring for patients with brain death diagnosis is the heaviest of duties for nurses, and, due to the complexities and stressors, it is the biggest challenge of nursing in an intensive care unit. Objective This qualitative research aimed to disclose the nurses’ experience of caring for brain-dead patients. Methods The present study was a qualitative research using a content analysis, where the data collection process included 21 semi-structured and in-depth interviews with intensive care nurses, physicians, head nurses, a transplantation committee coordinator, and the authority of the organ procurement unit. Adequate data were collected from March 2014 until the saturation point was reached in June 2016. Data were analyzed simultaneously with data collection using qualitative content analysis with a conventional approach. Results Qualitative content analysis of data resulted in two themes and eight subthemes, reflecting the analysis of nurses’ experiences of caring for brain-dead patients. The themes included “Challenges of right and duty requirement,” and “turbulent confrontation with successive chains of tension”. Finally, the main themes of “resonance of stress and internal conflict in care” were abstracted. Conclusion The findings deepened our understanding and knowledge of the issue. Despite all the stress, nurses care for potential organ donors, and this results in preserving the organs’ viability for donation. Nurses’ problems and challenges in this caring process should be considered by policymakers of health and treatment systems and a supportive model be designed for nurses in the intensive care unit.
Experimental Study of Wireless Monitoring of Human Respiratory Movements Using UWB Impulse Radar Systems

This paper analyzes and discusses the capability of human being detection using impulse ultra-wideband (UWB) radar with an improved detection algorithm. The multiple automatic gain control (AGC) technique is employed to enhance the amplitudes of human respiratory signals. Two filters with seven values averaged are used to further improve the signal-to-noise ratio (SNR) of the human respiratory signals. The maximum slope and standard deviation are used for analyzing the characteristics of the received pulses, which can provide two distance estimates for human being detection. Most importantly, based on the two distance estimates, we can accurately judge whether there are human beings in the detection environments or not. The data size can be reduced based on the defined interested region, which can improve the operation efficiency of the radar system for human being detection. The developed algorithm provides excellent performance regarding human being detection, which is validated through comparison with several well-known algorithms.
Sleep onset latency is related with reduced bone mineral density in elderly people with insomnia: a retrospective study

Purpose Inconsistent outcome about association between insufficient sleep and bone mineral density (BMD) has been reported. The present study aimed to determine whether BMD was associated with score of Pittsburgh Sleep Quality Index (PSQI). Methods A total of 410 patients (mean age 81.6±5.9 years) attending our hospital for evaluation of sleep were retrospectively studied. Dual-Energy X-ray Absorptiometry was used to measure BMD and T-score at femoral neck and lumbar spines over L2–L4 regions. Subjective sleep status was evaluated by the PSQI questionnaires. The Mann–Whitney U test and chi-square analysis were used to compare continuous variables and categorical variables, respectively. Spearman correlation test was conducted to find the relationship between BMD and other clinical factors. Multinomial logistic regressions analysis was performed to analyze independent factors predicting BMD. Results Majority of the participants with osteoporosis (OP) were female and had lower body mass index (BMI) and higher sleep onset latency score. Spearman correlation test showed that gender, BMI, score of total PSQI, and sleep onset latency were significantly related to BMD and T-score in femoral neck and lumbar region L2–L4. Finally, multinomial logistic regression analysis demonstrated that gender and age were independent factors for OP and osteopenia and that after adjustment for gender, age, and BMI, sleep onset latency of <15 minutes (OR: 0.38; 95% CI: 0.15–0.96; P=0.04) and 16–30 minutes (OR: 0.37; 95% CI: 0.17–0.79; P=0.01) were less likely to have reduced BMD. Conclusion There was a significant association between BMD and sleep onset latency, suggesting that, in elderly patients with sleep problem, BMD measurement and intervention for OP might be valuable.
Treatment preferences among Japanese women with dysmenorrhea: results from a discrete choice experiment study

Purpose To examine patient preferences for oral and intrauterine system treatments for dysmenorrhea in Japan. Patients and methods A discrete choice experiment was conducted to assess the willingness to accept trade-offs among hypothetical treatment profiles. An internet-based survey was administered to women 18–49 years of age who self-reported a dysmenorrhea diagnosis or experienced dysmenorrhea at least once in the past 6 months (N=309). Choice questions included pairs of treatments presented with different attributes: mode of administration, reduction in bleeding after 6 months, chance of symptoms becoming “improved”, nausea, weight gain, irregular bleeding, and risk of venous thromboembolism. Relative importance (RI) estimates were computed. Results The mean respondent age was 35.8 years (standard deviation =7.0), and 85 women (27.5%) reported that they had previously used hormonal therapy for dysmenorrhea. Treatment preference was most strongly associated with mode of administration (RI=49.8%), followed by chance of irregular bleeding (RI=17.3%). In contrast, treatment preference was most weakly associated with chance of weight gain (RI=2.4%) and reduction in bleeding after 6 months (RI=0.8%). Respondents preferred oral treatments: for twice-daily regimen, odds ratio (OR)=4.90; for once-daily fixed cyclic regimen, OR=4.20; and for once-daily flexible extended regimen, OR=2.44; whereas for intrauterine system, OR=0.02 (p<0.001 for all). Those with prior hormonal therapy experience exhibited the same pattern. Conclusion Mode of administration factored heavily in dysmenorrhea treatment preferences. Women of reproductive age preferred oral medication, especially twice-daily regimen and once-daily fixed cyclic regimen. Findings can potentially help to improve physician–patient communication and treatment decision making. Physicians should consider factors that can influence patient preference to optimize treatment acceptance and adherence.