LLukas22/scidocs huggingface dataset:
Misunderstanding in cancer patients: why shoot the messenger?

AIM
We aimed to document the prevalence of misunderstanding in cancer patients and investigate whether patient denial is related to misunderstanding.


PATIENTS AND METHODS
Two hundred forty-four adult cancer outpatients receiving treatment completed a survey assessing levels of understanding and denial. Doctors provided the facts against which patient responses were compared. Multiple logistic regression analyses determined the predictors of misunderstanding.


RESULTS
Most patients understood the extent of their disease (71%, 95% CI: 65%-77%) and goal of treatment (60%, 95% CI: 54%-67%). Few correctly estimated the likelihood of treatment achieving cure (18%, 95% CI: 13%-23%), prolongation of life (13%, 95% CI: 8%-17%) and palliation (18%, 95% CI: 10%-27%). Patient denial predicted misunderstanding of the probability that treatment would cure disease when controlling for other patient and disease variables (OR = 2.20, 95% CI: 0.99-4.88, P = 0.05). Patient ratings of the clarity of information received were also predictive of patient understanding.


CONCLUSIONS
Patient denial appears to produce misunderstanding, however, doctors' ability to communicate effectively is also implicated. The challenge that oncologists face is how to communicate information in a manner which is both responsive to patients' emotional status and sufficiently informative to allow informed decision-making to take place.
Internet of Things Architecture IoTA Project Deliverable D 2 . 2 – Concepts for Modelling IoT-Aware Processes

ion Yes No Partly Availability / Mobility No No No Fault tolerance Partly No Partly Flexibility / Event based Yes Partly Partly Uncertainty of information No No No
Matrix mechanical plasticity regulates cancer cell migration through confining microenvironments

Studies of cancer cell migration have found two modes: one that is protease-independent, requiring micron-sized pores or channels for cells to squeeze through, and one that is protease-dependent, relevant for confining nanoporous matrices such as basement membranes (BMs). However, many extracellular matrices exhibit viscoelasticity and mechanical plasticity, irreversibly deforming in response to force, so that pore size may be malleable. Here we report the impact of matrix plasticity on migration. We develop nanoporous and BM ligand-presenting interpenetrating network (IPN) hydrogels in which plasticity could be modulated independent of stiffness. Strikingly, cells in high plasticity IPNs carry out protease-independent migration through the IPNs. Mechanistically, cells in high plasticity IPNs extend invadopodia protrusions to mechanically and plastically open up micron-sized channels and then migrate through them. These findings uncover a new mode of protease-independent migration, in which cells can migrate through confining matrix if it exhibits sufficient mechanical plasticity. In order to metastasize, cancer cells must migrate through basement membranes and dense stroma, and proteases are thought to be required due to the confining nature of these matrices. Here the authors use synthetic matrices to show that cells can migrate through confining matrices using force generation alone, rather than protease degradation, if the matrices exhibit mechanical plasticity.
Effects of mud therapy on perceived pain and quality of life related to health in patients with knee osteoarthritis.

OBJECTIVE
To analyze the effects of mud therapy on perceived pain, Health Related Quality of Life (HRQL) and drug use in patients diagnosed with knee osteoarthritis.


MATERIAL AND METHODS
A prospective, controlled clinical trial. The sample (n=147) was divided into an experimental group (EG) of 61 subjects (69.13 ± 5,60 years) who received 11 consecutive sessions of peloids in the knee/s affected by the process described and a control group (CG) of 60 subjects (73.08 ± 8,90 years) who continued routine drug treatment. The sample was assessed before and after intervention using the SF-36, Visual Analogue Scale and changes in drug use, setting a significance level of P ≤ .05.


RESULTS
After the intervention, there were statistically significant differences (P<.05) in all parameters analyzed between EG and CG, reduced drug use in the EG versus no change in the CG. The general health, bodily pain and perceived pain are those that show major changes between the two groups.


CONCLUSIONS
Mud therapy in patients diagnosed with knee osteoarthritis attains immediate effects on perceived pain and HRQOL, reducing the consumption of specific drugs. Studies are needed to evaluate the scientific evidence from the effects of such intervention.
Poetry, Politics and Popcorn : Angels in America at the National Theatre. Performance Review

Critique theâtrale d’Angels in America de Tony Kushner et mis-en-scene par Marianne Elliott au National Theatre (London, UK), mai - aout 2017.
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods

MOTIVATION
Biomarker discovery is an important topic in biomedical applications of computational biology, including applications such as gene and SNP selection from high-dimensional data. Surprisingly, the stability with respect to sampling variation or robustness of such selection processes has received attention only recently. However, robustness of biomarkers is an important issue, as it may greatly influence subsequent biological validations. In addition, a more robust set of markers may strengthen the confidence of an expert in the results of a selection method.


RESULTS
Our first contribution is a general framework for the analysis of the robustness of a biomarker selection algorithm. Secondly, we conducted a large-scale analysis of the recently introduced concept of ensemble feature selection, where multiple feature selections are combined in order to increase the robustness of the final set of selected features. We focus on selection methods that are embedded in the estimation of support vector machines (SVMs). SVMs are powerful classification models that have shown state-of-the-art performance on several diagnosis and prognosis tasks on biological data. Their feature selection extensions also offered good results for gene selection tasks. We show that the robustness of SVMs for biomarker discovery can be substantially increased by using ensemble feature selection techniques, while at the same time improving upon classification performances. The proposed methodology is evaluated on four microarray datasets showing increases of up to almost 30% in robustness of the selected biomarkers, along with an improvement of approximately 15% in classification performance. The stability improvement with ensemble methods is particularly noticeable for small signature sizes (a few tens of genes), which is most relevant for the design of a diagnosis or prognosis model from a gene signature.


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Measuring engagement in fourth to twelfth grade classrooms: the Classroom Engagement Inventory.

Research on factors that may promote engagement is hampered by the absence of a measure of classroom-level engagement. Literature has suggested that engagement may have 3 dimensions--affective, behavioral, and cognitive. No existing engagement scales measure all 3 dimensions at the classroom level. The Classroom Engagement Inventory (CEI) was developed to fill this gap. In Study 1, exploratory and confirmatory factor analyses were conducted on data from 3,481 students from the 4th to 12th grade. The results suggested a 4-factor model of the CEI. Using these results, in Study 2 several items were revised and data were collected 1 year later from 4th to 12th grade students in the same school district as Study 1. Analyses were conducted on data from 3,560 students after data cleaning. A series of potential models was tested. The final results suggest a 5-factor 24-item CEI: (1) Affective Engagement, (2) Behavioral Engagement-Compliance, (3) Behavioral Engagement-Effortful Class Participation, (4) Cognitive Engagement, and (5) Disengagement. Results advance understanding of the construct of classroom engagement. The CEI fills a significant gap in measurement of engagement. The CEI is classroom level, measures multiple dimensions of engagement, uses self-report, is relatively short, and can be readily administered in classrooms from the 4th to 12th grade.
CREDIT RISK SCORING MODELS

Credit scoring models play a fundamental role in the risk management practice at most banks. They are used to quantify credit risk at counterparty or transaction level in the different phases of the credit cycle (e.g. application, behavioural, collection models). The credit score empowers users to make quick decisions or even to automate decisions and this is extremely desirable when banks are dealing with large volumes of clients and relatively small margin of profits at individual transaction level (i.e. consumer lending, but increasingly also small business lending). In this article, we analyze the history and new developments related to credit scoring models. We find that with the new Basel Capital Accord, credit scoring models have been remotivated and given unprecedented significance. Banks, in particular, and most financial institutions worldwide, have either recently developed or modified existing internal credit risk models to conform with the new rules and best practices recently updated in the market. Moreover, we analyze the key steps of the credit scoring model’s lifecycle (i.e. assessment, implementation, validation) highlighting the main requirement imposed by Basel II. We conclude that banks that are going to implement the most advanced approach to calculate their capital requirements under Basel II will need to increase their attention and consideration of credit scoring models in the next future. JEL classification: G17; G21
A systematic literature review of empirical evidence on computer games and serious games

This paper examines the literature on computer games and serious games in regard to the potential positive impacts of gaming on users aged 14 years or above, especially with respect to learning, skill enhancement and engagement. Search terms identified 129 papers reporting empirical evidence about the impacts and outcomes of computer games and serious games with respect to learning and engagement and a multidimensional approach to categorizing games was developed. The findings revealed that playing computer games is linked to a range of perceptual, cognitive, behavioural, affective and motivational impacts and outcomes. The most frequently occurring outcomes and impacts were knowledge acquisition/content understanding and affective and motivational outcomes. The range of indicators and measures used in the included papers are discussed, together with methodological limitations and recommendations for further work in this area. 2012 Published by Elsevier Ltd.
Male circumcision, penile human papillomavirus infection, and cervical cancer in female partners.

BACKGROUND
It is uncertain whether male circumcision reduces the risks of penile human papillomavirus (HPV) infection in the man and of cervical cancer in his female partner.


METHODS
We pooled data on 1913 couples enrolled in one of seven case-control studies of cervical carcinoma in situ and cervical cancer in five countries. Circumcision status was self-reported, and the accuracy of the data was confirmed by physical examination at three study sites. The presence or absence of penile HPV DNA was assessed by a polymerase-chain-reaction assay in 1520 men and yielded a valid result in the case of 1139 men (74.9 percent).


RESULTS
Penile HPV was detected in 166 of the 847 uncircumcised men (19.6 percent) and in 16 of the 292 circumcised men (5.5 percent). After adjustment for age at first intercourse, lifetime number of sexual partners, and other potential confounders, circumcised men were less likely than uncircumcised men to have HPV infection (odds ratio, 0.37; 95 percent confidence interval, 0.16 to 0.85). Monogamous women whose male partners had six or more sexual partners and were circumcised had a lower risk of cervical cancer than women whose partners were uncircumcised (adjusted odds ratio, 0.42; 95 percent confidence interval, 0.23 to 0.79). Results were similar in the subgroup of men in whom circumcision was confirmed by medical examination.


CONCLUSIONS
Male circumcision is associated with a reduced risk of penile HPV infection and, in the case of men with a history of multiple sexual partners, a reduced risk of cervical cancer in their current female partners.
Performance of prostate cancer antigen 3 (PCA3) and prostate-specific antigen in Prescreened men: reproducibility and detection characteristics for prostate cancer patients with high PCA3 scores (≥ 100).

BACKGROUND
Prostate cancer antigen 3 (PCA3) is considered to be prostate cancer (PCa) specific and highly overexpressed in cancer. Therefore a high PCA3 score should result in a high positive predictive value (PPV) and specificity for a positive biopsy.


OBJECTIVE
Our aim was to reevaluate, retest PCA3, and rebiopsy men with an initial PCA3 ≥ 100 and no PCa detected and compare the results with a random cohort of men with an initial PCA3<100.


DESIGN, SETTING, AND PARTICIPANTS
We invited men 63-75 yr of age with a PCA3 ≥100 for retesting and a control group with an initial PCA3 < 100 to participate in the European Randomized Study of Screening for Prostate Cancer, section Rotterdam.


INTERVENTIONS
Blood and urine sampling were used to determine prostate-specific antigen (PSA) and PCA3. Prostate biopsies were performed if the PSA was ≥2.5 ng/ml and/or the PCA3 score was ≥ 35.


MEASUREMENTS
We correlated the initial and reevaluated PCA3 scores. Our assessment of the PPV after rebiopsy was based on the newly determined PCA3 score.


RESULTS AND LIMITATIONS
After a mean study period of 19 mo, more cases of PCa were detected in rebiopsied men with initial PCA3 scores ≥ 100 than in the controls with PCA3 scores < 100 (30.0% vs 18.8%). Combining initial and rebiopsy data resulted in a PPV of 52.2% in men with PCA3 ≥ 100. Over time, changes in PSA and PCA3 levels were quite different.


CONCLUSIONS
In spite of our rescreened population, PPV and specificity were comparable with all reported studies of men with PCA3 scores ≥ 100. These findings do not explain why these PCA3 scores were excessively high in spite of the absence of biopsy-detectable PCa.
Manipulating perceived social presence through the web interface and its impact on attitude towards online shopping

Electronic commerce typically lacks human warmth and sociability, since it is more impersonal, anonymous and automated than traditional face-to-face commerce. This paper explores how human warmth and sociability can be integrated through the web interface to positively impact consumer attitudes towards online shopping. An empirical study was undertaken to investigate the impact of various levels of socially rich text and picture design elements on the perception of online social presence and its subsequent effect on antecedents of attitudes towards websites. Higher levels of perceived social presence are shown to positively impact the perceived usefulness, trust and enjoyment of shopping websites, leading to more favourable consumer attitudes. Implications of these finding for practitioners and future research are outlined. Crown Copyright r 2007 Published by Elsevier Ltd. All rights reserved.
Synthesis of flexible silica aerogels using methyltrimethoxysilane (MTMS) precursor.

The experimental results on the synthesis of flexible and superhydrophobic silica aerogels using methyltrimethoxysilane (MTMS) precursor by a two-step (acid-base) sol-gel process followed by the supercritical drying, are reported. The effects of various sol-gel parameters on the flexibility of the aerogels have been investigated. The aerogels of different densities were obtained by varying the molar ratio of MeOH/MTMS (S) from 14 to 35, with lower densities for larger S values. It has been observed that the Young's modulus (Y) decreased from 14.11 x 10(4) to 3.43 x 10(4) N/m(2) with the decrease in the density of the aerogels from 100 to 40 kg/m(3). Simultaneously, the aerogels are superhydrophobic with a contact angle as high as 164 degrees . The superhydrophobic aerogels are thermally stable up to a temperature of 530 K, above which they become hydrophilic. The aerogels have been characterized by bulk density, percentage volume shrinkage, and porosity measurements. The microstructures of the aerogels have been studied using the transmission electron microscopy (TEM). The Young's modulus of the aerogels has been determined by an uniaxial compression test. The variation of physical properties of the aerogels has been explained by taking into consideration the hydrolysis, condensation reactions, the resulting colloidal clusters and their network formation.
Leadtime-Inventory Trade-Offs in Assemble-to-Order Systems

This paper studies the trade-off between inventory levels and the delivery leadtime offered to customers in achieving a target level of service. It addresses the question of how much a delivery leadtime can be reduced, per unit increase in inventory, at a fixed fill rate. We show that for a class of assemble-to-order models with stochastic demands and production intervals there is a simple linear trade-off between inventory and delivery leadtime, in a limiting sense, at high fill rates. The limiting slope is easy to calculate and can be interpreted as the approximate marginal rate for trading off inventory against leadtime at a constant level of service. We also investigate how various model features affect the trade-off—in particular, the impact of orders for multiple units of a single item and of orders for multiple units of different items.
On Replenishing Items with Seasonal Intermittent Demand

Problem statement: There are numerous difficulties associated with replenishing intermittent demand items and these are compounded when the demand distribution(s) vary seasonally. Excess inventories during an “off” season are typical, while shortages frequently occur during the “in” season, especially at the transition points between “seasons”. Approach: Evaluate the extent to which items characterized by non-stationary (seasonal) intermittent demand can be managed with commonly used forecasting and replenishment methods, including existing “intermittent demand” methods. Extensive simulation studies were conducted using combinations of two commonly used forecasting methods and two replenishment policies to evaluate the impact of non-stationary intermittent demand on key inventory performance measures, including average inventory and net profits, including the extent to which combinations of forecasting and replenishment models is adversely impacted by the non-stationary demand distributions. Results: No combination of forecasting and replenishment methods tested consistently outperformed the others and all methods demonstrated a propensity to replace demanded units an average of 10 weeks before the inventory was required to avert a shortage. Conclusion: The inventory performance of the policies tested was consistent with our expectations and offered evidence of the need for further development of forecasting and replenishment models addressing the special characteristics of items with non-stationary intermittent demand.
Intramuscular injection: an integrative research review and guideline for evidence-based practice.

Intramuscular injections (IM) are a common yet complex technique used to deliver medication deep into the large muscles of the body. More than 12 billion IM injections are administered annually throughout the world. However, it is not a benign procedure, and unsafe injection practices are estimated to have significant impacts on patient morbidity and mortality and result in millions of dollars in direct medical costs on an annual basis. Although there is significant research, spanning 8 decades, on the procedure and techniques of administering medications by the IM route, instruction materials and clinician practice do not always reflect research-based practice. An integrative review of the literature has resulted in the development of a guideline for evidence-based practice of IM injections. Use of this guideline can assist the clinician to maximize the therapeutic effects of administered medication while minimizing or eliminating patient injury and discomfort associated with IM injections.
Adversarial Image Translation: Unrestricted Adversarial Examples in Face Recognition Systems

Thanks to recent advances in Deep Neural Networks (DNNs), face recognition systems have achieved high accuracy in classification of a large number of face images. However, recent works demonstrate that DNNs could be vulnerable to adversarial examples and raise concerns about robustness of face recognition systems. In particular adversarial examples that are not restricted to small perturbations could be more serious risks since conventional certified defenses might be ineffective against them. To shed light on the vulnerability of the face recognition systems to this type of adversarial examples, we propose a flexible and efficient method to generate unrestricted adversarial examples using image translation techniques. Our method enables us to translate a source into any desired facial appearance with large perturbations so that target face recognition systems could be deceived. We demonstrate through our experiments that our method achieves about $90\%$ and $30\%$ attack success rates under a white- and black-box setting, respectively. We also illustrate that our generated images are perceptually realistic and maintain personal identity while the perturbations are large enough to defeat certified defenses.
Self-similar groups

Copying and reprinting. Individual readers of this publication, and nonprofit libraries acting for them, are permitted to make fair use of the material, such as to copy a chapter for use in teaching or research. Permission is granted to quote brief passages from this publication in reviews, provided the customary acknowledgment of the source is given. Republication, systematic copying, or multiple reproduction of any material in this publication is permitted only under license from the American Mathematical Society. @ The paper used in this book is acid-free and falls within the guidelines established to ensure permanence and durability. Contents Preface vii Chapter 1. Basic Definitions and Examples 1 1.1. Rooted tree X* and its boundary X^ 1 1.2. Groups acting on rooted trees 2 1.3. Automata 3 1.4. Wreath products 9 1.5. Self-similar actions 10 1.6. The Grigorchuk group 12 1.7. The adding machine and self-similar actions of Z n 16 1.8. Branch groups 17 1.9. Other examples 21 1.10. Bi-reversible automata and free groups 23 Chapter 2. Algebraic Theory 31 2.1. Permutational bimodules 31 2.2. Bases of a covering bimodule and wreath recursions 32 2.3. Tensor products and self-similar actions 33 2.4. The left G-space Wl®" 36 2.5. Virtual endomorphisms 37 2.6. The linear recursion 40 2.7. Invariant subgroups and the kernel of a self-similar action 41 2.8. Recurrent actions 44 2.9. Example: free abelian groups 46 2.10. Rigidity 50 2.11. Contracting actions 57 2.12. Finite-state actions of Z n 62 2.13. Defining relations and word problem 64 Chapter 3. Limit Spaces 71 3.