LLukas22/scidocs huggingface dataset:
Rac and Rho GTPases in cancer cell motility control

Rho GTPases represent a family of small GTP-binding proteins involved in cell cytoskeleton organization, migration, transcription, and proliferation. A common theme of these processes is a dynamic reorganization of actin cytoskeleton which has now emerged as a major switch control mainly carried out by Rho and Rac GTPase subfamilies, playing an acknowledged role in adaptation of cell motility to the microenvironment. Cells exhibit three distinct modes of migration when invading the 3 D environment. Collective motility leads to movement of cohorts of cells which maintain the adherens junctions and move by photolytic degradation of matrix barriers. Single cell mesenchymal-type movement is characterized by an elongated cellular shape and again requires extracellular proteolysis and integrin engagement. In addition it depends on Rac1-mediated cell polarization and lamellipodia formation. Conversely, in amoeboid movement cells have a rounded morphology, the movement is independent from proteases but requires high Rho GTPase to drive elevated levels of actomyosin contractility. These two modes of cell movement are interconvertible and several moving cells, including tumor cells, show an high degree of plasticity in motility styles shifting ad hoc between mesenchymal or amoeboid movements. This review will focus on the role of Rac and Rho small GTPases in cell motility and in the complex relationship driving the reciprocal control between Rac and Rho granting for the opportunistic motile behaviour of aggressive cancer cells. In addition we analyse the role of these GTPases in cancer progression and metastatic dissemination.
Uncertainty in Deep Learning

Deep learning has attracted tremendous attention from researchers in various fields of information engineering such as AI, computer vision, and language processing [Kalchbrenner and Blunsom, 2013; Krizhevsky et al., 2012; Mnih et al., 2013], but also from more traditional sciences such as physics, biology, and manufacturing [Anjos et al., 2015; Baldi et al., 2014; Bergmann et al., 2014]. Neural networks, image processing tools such as convolutional neural networks, sequence processing models such as recurrent neural networks, and regularisation tools such as dropout, are used extensively. However, fields such as physics, biology, and manufacturing are ones in which representing model uncertainty is of crucial importance [Ghahramani, 2015; Krzywinski and Altman, 2013]. With the recent shift in many of these fields towards the use of Bayesian uncertainty [Herzog and Ostwald, 2013; Nuzzo, 2014; Trafimow and Marks, 2015], new needs arise from deep learning. In this work we develop tools to obtain practical uncertainty estimates in deep learning, casting recent deep learning tools as Bayesian models without changing either the models or the optimisation. In the first part of this thesis we develop the theory for such tools, providing applications and illustrative examples. We tie approximate inference in Bayesian models to dropout and other stochastic regularisation techniques, and assess the approximations empirically. We give example applications arising from this connection between modern deep learning and Bayesian modelling such as active learning of image data and data efficient deep reinforcement learning. We further demonstrate the method’s practicality through a survey of recent applications making use of the suggested tools in language applications, medical diagnostics, bioinformatics, image processing, and autonomous driving. In the second part of the thesis we explore its theoretical implications, and the insights stemming from the link between Bayesian modelling and deep learning. We discuss what determines model uncertainty properties, analyse the approximate inference analytically in the linear case, and theoretically examine various priors such as spike and slab priors.
Impact of renal function of patients with advanced urothelial cancer on eligibility for first-line chemotherapy and treatment outcomes.

OBJECTIVE
The aim of the study is to clarify the clinical effects of first-line chemotherapy regimens for advanced urothelial cancer on clinical responses and survival of patients grouped by renal function.


METHODS
In this multicenter retrospective cohort study, 345 urothelial cancer patients received systemic chemotherapy for metastatic or unresectable disease in 17 centers (2004-10).


RESULTS
Two hundred and forty-one patients were treated with methotrexate, vinblastine, doxorubicin and cisplatin/methotrexate, epirubicin and cisplatin (n = 136) or gemcitabine and cisplatin (n = 105) followed by carboplatin-based treatments, non-platinum treatments or other regimens. After 2008, gemcitabine and cisplatin was the most frequently used regimen in patients with an estimated glomerular filtration rate < 60 ml/min/1.73 m(2) and in those with estimated glomerular filtration rate ≥ 60 ml/min/1.73 m(2). The gemcitabine and cisplatin patients' complete response rate was 10.5% and their response rate was 52.4%, which was highest among all regimens. Gemcitabine and cisplatin demonstrated a better 3-year overall survival when the estimated glomerular filtration rate was ≥ 60 ml/min/1.73 m(2) (31.4%), but it tended to be worse when the estimated glomerular filtration rate was < 60 ml/min/1.73 m(2) (14.1%). In the latter cases, the dose reduction rate of gemcitabine and cisplatin was high (43.9%). Among the patients with estimated glomerular filtration rate < 60 ml/min/1.73 m(2), the 1-year overall survival of the patients treated with a reduced dose of gemcitabine and cisplatin was significantly lower than that of those treated with standard-dose gemcitabine and cisplatin (26.2 vs. 60.3%, respectively, P = 0.0108).


CONCLUSIONS
Gemcitabine and cisplatin provided favorable responses and survival in patients with estimated glomerular filtration rate ≥ 60 ml/min/1.73 m(2) but unsatisfactory oncological outcomes in patients with estimated glomerular filtration rate < 60 ml/min/1.73 m(2), especially when treated with a reduced dose. Alternative regimens might be optimal rather than reduced-dose gemcitabine and cisplatin in patients with estimated glomerular filtration rate < 60 ml/min/1.73 m(2).
Feasibility of management of high-grade cervical lesions in a single visit: a randomized controlled trial.

CONTEXT
The incidence of cervical cancer is higher among low-income and minority women who have never undergone a conventional Papanicolaou test or who do not follow up after testing. Screening has been shown to reduce cervical cancer incidence rates.


OBJECTIVES
To determine the feasibility and acceptability of immediately treating women with severely abnormal Papanicolaou test results by using a single-visit cervical cancer screening and treatment program and to compare treatment rates and 12-month follow-up rates with those of women who received usual care.


DESIGN, SETTING, AND PARTICIPANTS
Randomized controlled trial conducted among 3521 women aged 18 years or older recruited between January 1999 and April 2002 at US community health centers located in predominantly Latino underserved areas.


INTERVENTIONS
Women randomized to usual care (n = 1805) were discharged immediately after examination. Women randomized to the single-visit group (n = 1716) remained at the clinic until the results of their conventional Papanicolaou test were available. Large loop electrosurgical excision procedure was performed in single-visit patients with either a diagnosis of a high-grade squamous intraepithelial lesion (HGSIL)/atypical glandular cells of undetermined significance (AGUS) or suspicion of carcinoma. All other patients with abnormal Papanicolaou test results were referred to abnormal cytology clinics or elected to receive follow-up care outside the study's medical system.


MAIN OUTCOME MEASURES
Treatment rates for HGSIL/AGUS at 6 months, follow-up rates at 6 months for lower-grade lesions, and 1-year follow-up rates for all patients.


RESULTS
The rate of abnormal Papanicolaou test results was 4.1%. One percent of results showed high-grade lesions. In the single-visit group, the mean visit time was 2.8 hours and the mean time for delivery and processing of the Papanicolaou tests was 66 minutes. Six months after randomization, 14 (88%) of 16 single-visit and 10 (53%) of 19 usual care patients with HGSIL/AGUS had completed treatment. Fifty percent in the single-visit program and 53% of usual care with less abnormal Papanicolaou tests completed treatment within 6 months. Overall, 36% in each group presented for a follow-up Papanicolaou test 1 year later. Women in the single-visit group with high-grade lesions (10/16; 63%) were significantly more likely to attend follow-up for Papanicolaou tests 12 months later than women with similar lesions in the usual care group (4/19; 21%).


CONCLUSIONS
For cervical cancer screening, the single-visit program was feasible and the degree of acceptability was high in this underserved population. Single visit programs provide an opportunity to increase the rate of immediate treatment and follow-up of women with severely abnormal Papanicolaou test results. This strategy did not improve follow-up rates for women with less-abnormal results. Trial Registration http://ClinicalTrials.govIdentifier: NCT00237562.
The mushroom Agaricus Blazei Murill in combination with metformin and gliclazide improves insulin resistance in type 2 diabetes: a randomized, double-blinded, and placebo-controlled clinical trial.

BACKGROUND
Complementary and alternative medicine use in adults with type 2 diabetes is popular. Although most of the herbs and supplements appear to be safe, there is still insufficient evidence that demonstrates their definitive beneficial effects. This study was done to determine whether the supplement of Agaricus blazei Murill extract improves insulin resistance in type 2 diabetes.


MATERIALS AND METHODS
This study was a clinical randomized, double-blind, placebo-controlled trial. Of a population of 536 registered diabetes patients with 72 subjects (1) aged between 20 and 75 years, (2) being Chinese, (3) having type 2 diabetes for more than 1 year, and (4) having been taking gliclazide and metformin for more than 6 months were enrolled in this study. The enrolled patients were randomly assigned to either receiving supplement of Agaricus blazei Murill (ABM) extract or placebo (cellulose) 1500 mg daily for 12 weeks. Homeostasis model assessment for insulin resistance (HOMA-IR) was used as the major outcome measurement.


RESULTS
At the end of the study, subjects who received supplement of ABM extract (n = 29) showed significantly lower HOMA-IR index (3.6[standard deviation, 2.5] versus 6.6[standard deviation, 7.4], p = 0.04) than the control group (n = 31). The plasma adiponectin concentration increased 20.0(standard deviation, 40.7)% in the ABM group after 12 weeks of treatment, but decreased 12.0(20.0)% among those taking the placebo (p < 0.001).


CONCLUSIONS
Supplement of ABM extract improves insulin resistance among subjects with type 2 diabetes. The increase in adiponectin concentration after taking AMB extract for 12 weeks might be the mechanism that brings the beneficial effect. Studies with longer periods of follow-up should be conducted in the future.
Quality Risk in Outsourcing : Noncontractible Product Quality and Private Quality Cost Information

This article addresses the concept of quality risk in outsourcing. Recent trends in outsourcing extend a contract manufacturer’s (CM’s) responsibility to several functional areas, such as research and development and design in addition to manufacturing. This trend enables an original equipment manufacturer (OEM) to focus on sales and pricing of its product. However, increasing CM responsibilities also suggest that the OEM’s product quality is mainly determined by its CM. We identify two factors that cause quality risk in this outsourcing relationship. First, the CM and the OEM may not be able to contract on quality; second, the OEM may not know the cost of quality to the CM. We characterize the effects of these two quality risk factors on the firms’ profits and on the resulting product quality. We determine how the OEM’s pricing strategy affects quality risk. We show, for example, that the effect of noncontractible quality is higher than the effect of private quality cost information when the OEM sets the sales price after observing the product’s quality. We also show that committing to a sales price mitigates the adverse effect of quality risk. To obtain these results, we develop and analyze a three-stage decision model. This model is also used to understand the impact of recent information technologies on profits and product quality. For example, we provide a decision tree that an OEM can use in deciding whether to invest in an enterprise-wide quality management system that enables accounting of quality-related activities across the supply chain. © 2009 Wiley Periodicals, Inc. Naval Research Logistics 56: 669–685, 2009
Caregiver burden and coping strategies in caregivers of patients with Alzheimer’s disease

BACKGROUND
Alzheimer's disease (AD) causes considerable distress in caregivers who are continuously required to deal with requests from patients. Coping strategies play a fundamental role in modulating the psychologic impact of the disease, although their role is still debated. The present study aims to evaluate the burden and anxiety experienced by caregivers, the effectiveness of adopted coping strategies, and their relationships with burden and anxiety.


METHODS
Eighty-six caregivers received the Caregiver Burden Inventory (CBI) and the State-Trait Anxiety Inventory (STAI Y-1 and Y-2). The coping strategies were assessed by means of the Coping Inventory for Stressful Situations (CISS), according to the model proposed by Endler and Parker in 1990.


RESULTS
The CBI scores (overall and single sections) were extremely high and correlated with dementia severity. Women, as well as older caregivers, showed higher scores. The trait anxiety (STAI-Y-2) correlated with the CBI overall score. The CISS showed that caregivers mainly adopted task-focused strategies. Women mainly adopted emotion-focused strategies and this style was related to a higher level of distress.


CONCLUSION
AD is associated with high distress among caregivers. The burden strongly correlates with dementia severity and is higher in women and in elderly subjects. Chronic anxiety affects caregivers who mainly rely on emotion-oriented coping strategies. The findings suggest providing support to families of patients with AD through tailored strategies aimed to reshape the dysfunctional coping styles.
Stability estimates for the inverse boundary value problem by partial Cauchy data

In this paper we study the inverse boundary value problem for the Schrödinger equation with a potential and the conductivity equation using partial Cauchy data. We derive stability estimates for these inverse problems.
Beyond Black and White : An Examination of Afrocentric Facial Features and Sex in Criminal Sentencing

This Thesis is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. For more information, please contact pdxscholar@pdx.edu. Recommended Citation Petersen, Amanda Mae, "Beyond Black and White: An Examination of Afrocentric Facial Features and Sex in Criminal Sentencing" (2014). Dissertations and Theses. Paper 1855.
Tilted optic discs: The Beijing Eye Study

PurposeTo determine the prevalence of tilted optic discs and their associations with ocular and general parameters.MethodsThe Beijing Eye Study included 4439 subjects out of 5324 subjects invited to participate (response rate 83.4%) with an age of 40+ years. The present investigation consisted of 4324 (97.4%) subjects for whom readable fundus photographs of at least one eye were available. The main outcome parameter was the presence of tilted optic discs defined as small discs with an oblique orientation and oval disc shape without signs of pathology in eyes without high myopia (defined as >−8 D).ResultsTilted optic discs were detected in 31 eyes (0.36; 95% confidence interval: 0.23, 0.49%) of 23 patients (16 women). Tilted discs were associated with myopia (−6.59±0.68 D vs −0.60±0.02 D, P<0.001), astigmatism (1.55±0.24 D vs 0.59±0.01 D, P<0.001), lower best corrected visual acuity (P<0.001), visual field defects (P<0.001), and small optic disc area (P<0.001).ConclusionsTilted optic discs are present in about four out of 1000 eyes of adult Chinese in Northern China. They are associated with medium myopia, astigmatism, decreased visual acuity, and visual field defects.
Two-year outcomes for interpersonal and social rhythm therapy in individuals with bipolar I disorder.

CONTEXT
Numerous studies have pointed to the failure of prophylaxis with pharmacotherapy alone in the treatment of bipolar I disorder. Recent investigations have demonstrated benefits from the addition of psychoeducation or psychotherapy to pharmacotherapy in this population.


OBJECTIVE
To compare 2 psychosocial interventions: interpersonal and social rhythm therapy (IPSRT) and an intensive clinical management (ICM) approach in the treatment of bipolar I disorder.


DESIGN
Randomized controlled trial involving 4 treatment strategies: acute and maintenance IPSRT (IPSRT/IPSRT), acute and maintenance ICM (ICM/ICM), acute IPSRT followed by maintenance ICM (IPSRT/ICM), or acute ICM followed by maintenance IPSRT (ICM/IPSRT). The preventive maintenance phase lasted 2 years.


SETTING
Research clinic in a university medical center.


PARTICIPANTS
One hundred seventy-five acutely ill individuals with bipolar I disorder recruited from inpatient and outpatient settings, clinical referral, public presentations about bipolar disorder, and other public information activities.


INTERVENTIONS
Interpersonal and social rhythm therapy, an adaptation of Klerman and Weissman's interpersonal psychotherapy to which a social rhythm regulation component has been added, and ICM.


MAIN OUTCOME MEASURES
Time to stabilization in the acute phase and time to recurrence in the maintenance phase.


RESULTS
We observed no difference between the treatment strategies in time to stabilization. After controlling for covariates of survival time, we found that participants assigned to IPSRT in the acute treatment phase survived longer without a new affective episode (P = .01), irrespective of maintenance treatment assignment. Participants in the IPSRT group had higher regularity of social rhythms at the end of acute treatment (P<.001). Ability to increase regularity of social rhythms during acute treatment was associated with reduced likelihood of recurrence during the maintenance phase (P = .05).


CONCLUSION
Interpersonal and social rhythm therapy appears to add to the clinical armamentarium for the management of bipolar I disorder, particularly with respect to prophylaxis of new episodes.
Colour Me In--an empirical study on consumer responses to the traffic light signposting system in nutrition labelling.

OBJECTIVE
As a means of empowering consumers, nutrition labelling has become a widely discussed topic. Simplicity and uniformity of labelling systems are regarded as the prevailing demands from the consumer side. In the present study, we analyse the effects of the traffic light signposting scheme on consumers' food choices.


DESIGN
In an online survey, respondents first rated the understandability of the traffic light signposting scheme. In a following conjoint experiment, they indicated which products they would select as the healthiest of the presented products, based on the nutritive information provided by the traffic light signposting scheme.


SETTING
A major German university.


SUBJECTS
In total 2002 undergraduate students participated in the survey. Two-thirds (69 %) of the respondents were female and the majority of the respondents (70 %) were between 18 and 24 years old. Seventy-seven per cent of the participants indicated that they had a higher level of education.


RESULTS
Overall, the participants rated the understandability of the traffic light nutrition signposting scheme fairly high (5.9 out of 7). Sugar and fat were found to be the most important attributes of the scheme. Participants placed greater emphases on a change in a product's nutrient characteristic from 'amber to 'red' compared with a change from 'green' to 'amber'.


CONCLUSIONS
Our results confirm the signalling effect of colour coding as it helps reduce the complexity of decision making. Our findings shed new light on the ongoing discussion concerning appropriate and efficient nutrition labelling and provide interesting insights for further research as well as implications for public policy making.
An Ontology-Based Approach for Domain Requirements Elicitation and Analysis

Domain requirements are fundamental for software reuse and are the product of domain analysis. This paper presents an ontology based approach to elicit and analyze domain requirements. An ontology definition is given out. Problem domain is decomposed into several sub problem domains by using subjective decomposition method. The top-down refinement method is used to refine each sub problem domain into primitive requirements. Abstract stakeholders are used instead of real ones when decomposing problem domain and domain primitive requirements are represented by ontology. Not only domain commonality, variability and qualities are presented, but also reasoning logic is used to detect and handle incompleteness and inconsistency of domain requirements. In addition, a case of 'spot and futures transaction' domain is used to illustrate the approach
Influence of technological factors on the resistance of structural materials to hydrogen degradation

The treatment of metals by silicon carbide, forming a thin plastically strained layer, leads to a substantial increase in their resistance to hydrogen at room temperature. For the protection of metals from the action of hydrogen, silver or copper based coatings are usually applied.
Making implicit measures of associations with snack foods more negative through evaluative conditioning.

The present study examined whether implicit measures of associations with snack foods and food consumer behaviour could be changed through a picture-picture evaluative conditioning procedure. In the experimental condition (n=41), female participants completed a conditioning procedure in which pictures of snack foods were paired with images of negatively valenced female body shapes, and pictures of fruits were paired with images of positively valenced body shapes. In a control condition (n=44), snack and fruit stimuli were randomly paired with positively and negatively valenced body shapes. Implicit measures of associations with high-fat snack foods were obtained by using a positive and a negative unipolar single category Implicit Association Test (sc-IAT). A virtual supermarket task was used to assess food consumer behaviour. Results indicated that participants in the experimental condition held a less positive association with high-fat foods on the positive sc-IAT and a more negative association with these foods on the negative sc-IAT as compared to control participants. Opposed to our hypothesis, no behavioural differences were found between the groups. These results imply that this form of associative learning can produce shifts in implicit measures of food evaluations, though behavioural effects were absent.