Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating a common covariance matrix for network meta-analysis of gene expression datasets in diffuse large B-cell lymphoma

Estimating gene networks in combination with posthoc analysis based on data from malignant tissue is a major challenge in cancer systems biology as it allows us to improve our understanding of disease pathology and eventually identify new drug targets. Motivated by the need for improving the inherently unstable covariance estimation compounded by noisy gene expression data, we present a hierarchical random covariance model applied as a meta-analysis of gene networks across eleven large-scale gene expression studies of diffuse large B-cell lymphoma (DLBCL). The approach was inspired by traditional meta-analysis using random effects models and we derive and compare basic properties and estimators of the model. Simple inference and interpretation of an introduced parameter measuring the inter-class homogeneity is suggested. The methods are generally applicable where multiple classes are present and believed to share a common covariance matrix of interest that is obscured by class-dependent noise. As such, it provides a basis for meta- or integrative analysis of covariance matrices where the classes are formed by datasets. In a posthoc analysis of the estimated common covariance matrix for the DLBCL data we were able to identify biologically meaningful gene networks of prognostic value. Of particular interest was the identification of a network with the S100 family of calcium-binding proteins as central players which further fuels the indications that knock down of these proteins may improve the immunotherapy strategies and outcome of lymphoma patients.
Relation between big five personality traits and Hofstede's cultural dimensions

Purpose – The purpose of this study is to quantitatively assess the inter‐relational aspects of personality traits, using the five‐factor model of personality, and Hofstede's five dimensions of national culture for work‐related values to evaluate the differences between the US and Indian cultures.Design/methodology/approach – The research method is quantitative and samples include qualified online‐panel respondents, representing educated and experienced business professionals who use the internet. Data analysis includes Pearson correlation and multiple analysis of variance. Sample results show large differences in all five cultural dimensions as compared to Hofstede's 1980 data.Findings – Changes in work‐related values may reflect the influence of advances in communication and internet technologies, offering insight toward problems associated with global multicultural projects. Correlations between personality traits and cultural dimensions exist for certain occupational‐job categories, and provide insigh.
Development of psychopathology: A vulnerability-stress perspective.

Preface Acknowledgments I. OVERVIEW AND FOUNDATIONS 1. Conceptualizing the Role of Stressors in the Development of Psychopathology - Kathryn E. Grant and Susan D. McMahon 2. Vulnerability-Stress Models - Rick E. Ingram and David D. Luxton II. VULNERABILITIES 3. The Role of Emotion Regulation in the Development of Psychopathology - Tara M. Chaplin and Pamela M. Cole 4. Biological Vulnerabilities to the Development of Psychopathology - Robert O. Pihl and Amelie Nantel-Vivier 5. Cognitive Vulnerability-Stress Models of Psychopathology: A Developmental Perspective - Brandon E. Gibb and Meredith E. Coles 6. Interpersonal Factors As Vulnerability to Psychopathology Over the Life Course - Kimberly Van Orden, LaRicka R. Wingate, Kathryn H. Gordon, and Thomas E. Joiner 7. Genetic Vulnerabilities to the Development of Psychopathology - Kathryn S. Lemery and Lisa Doelger 8. Interpreting Personality As a Vulnerability for Psychopathology: A Developmental Approach to the Personality-Psychopathology Relationship - Jennifer L. Tackett and Robert F. Krueger 9. Attachment As Vulnerability to the Development of Psychopathology - Joanne Davila, Melissa Ramsay, Catherine B. Stroud, and Sara J. Steinberg III. DISORDERS 10. Depression From Childhood Through Adolescence and Adulthood: A Developmental Vulnerability and Stress Perspective - Benjamin L. Hankin and John R. Z. Abela 11. Anxiety Disorders: A Developmental Vulnerability-Stress Perspective - Nathan L. Williams, John M. Reardon, Kathleen T. Murray, and Tara M. Cole 12. A Developmental Vulnerability-Stress Model of Eating Disorders: A Cognitive Approach - Myra Cooper 13. The Development of Substance Abuse in Adolescence: Correlates, Causes, and Consequences - Jon D. Kassel, Sally Weinstein, Steven A. Skitch, Jennifer Veilleux, and Robin Mermelstein 14. Development of Behavioral Problems Over The Life Course: A Vulnerability and Stress Perspective - Benjamin L. Hankin, John R. Z. Abela, Randy P. Auerbach, Chad M. McWhinnie, and Steven A. Skitch 15. The Developmental Psychopathology of Personality Disorders - Jeffrey G. Johnson, Pamela G. McGeoch, Vanessa P. Caskey, Sotoodeh G. Abhary, Joel R. Sneed, and Robert F. Bornstein Author Index Subject Index About the Editors About the Contributors
Predictive Biomarkers and Personalized Medicine Ki67Measured after Neoadjuvant Chemotherapy for Primary Breast Cancer

Purpose: The value of Ki67 measured on residual disease after neoadjuvant chemotherapy is not sufficiently described. Experimental Design: Participants of theGeparTrio studywith primary breast cancer randomly received neoadjuvant response-guided [8 cycles TAC (docetaxel/doxorubicin/cyclophosphamide) in responding and TAC-NX (vinorelbine/capecitabine) in nonresponding patients] or conventional (6 cycles TAC) chemotherapy according to interim response assessment. Ki-67 levels were centrally measured immunohistochemically after neoadjuvant treatment if tumor tissue was available. Here, we analyze 1,151 patients having a pathologic complete response (pCR; n, 484), or residual disease with low (0–15%), intermediate (15.1–35%), or high (35.1–100%) posttreatment Ki67 levels in 488, 77, and 102 patients, respectively. Results: Patients with high posttreatment Ki67 levels showed higher risk for disease relapse (P < 0.0001) and death (P < 0.0001) compared with patients with low or intermediate Ki67 levels. Patients with low Ki67 levels showed a comparable outcome to patients with a pCR (P 1⁄4 0.211 for disease-free and P 1⁄4 0.779 for overall survival). Posttreatment Ki67 levels provided more prognostic information than pretreatment Ki67 levels or changes of Ki67 from preto posttreatment. Information on pCR plus posttreatment Ki67 levels surmount the prognostic information of pCR alone in hormone–receptorpositive disease [hazard ratios (HR), 1.82–5.88] but not in hormone–receptor-negative disease (HR: 0.61–1.73). Patients with conventional and response-guided treatment did not show a different distribution of posttreatment Ki67 (P 1⁄4 0.965). Conclusions: Posttreatment Ki67 levels provide prognostic information for patients with hormone– receptor-positive breast cancer and residual disease after neoadjuvant chemotherapy. Levels were not prognostic for outcome after response-guided chemotherapy. High posttreatment Ki67 indicates the need for innovative postneoadjuvant treatments. Clin Cancer Res; 19(16); 4521–31. 2013 AACR.
Serial Frequencies and Clinical Features of Uveitis in Hokkaido, Japan

ABSTRACT Purpose: Environmental and lifestyle changes influence the clinical features of uveitis. This study reviewed the epidemiologic trends of uveitis in the Japanese population. Methods: A retrospective review of the past 80 years of reports from Hokkaido University Hospital. Results: In the 1930s, tuberculosis accounted for 46% and syphilitic uveitis for 31% of cases. The frequency of these diseases decreased to 12% in the 1950s; 8% in 1969; 0.6% in the 1990s; and 0.8% in the 2000s, while the rate of non-infectious uveitis increased. The three most common specific diagnoses were: sarcoidosis, Vogt–Koyanagi–Harada disease, and Behçet disease. Although Behçet disease was the most frequent non-infectious uveitis until the 1980s, sarcoidosis is now the most frequent cause of newly diagnosed non-infectious uveitis. Conclusions: The etiology of uveitis has changed with the times. Tubercular and syphilitic cases have greatly decreased, and sarcoidosis is the most frequent type of uveitis today.
On MAXCUT in strictly supercritical random graphs, and coloring of random graphs and random tournaments

We use a theorem by Ding, Lubetzky, and Peres describing the structure of the giant component of random graphs in the strictly supercritical regime, in order to determine the typical size of MAXCUT of G∼G(n,1+ɛn) in terms of ɛ. We then apply this result to prove the following conjecture by Frieze and Pegden. For every ɛ>0 , there exists ℓɛ such that w.h. p. G∼G(n,1+ɛn) is not homomorphic to the cycle on 2ℓɛ+1 vertices. We also consider the coloring properties of biased random tournaments. A p‐random tournament on n vertices is obtained from the transitive tournament by reversing each edge independently with probability p. We show that for p=Θ(1n) the chromatic number of a p‐random tournament behaves similarly to that of a random graph with the same edge probability. To treat the case p=1+ɛn we use the aforementioned result on MAXCUT and show that in fact w.h. p. one needs to reverse Θ(ɛ3)n edges to make it 2‐colorable.
Mixed discontinuous Galerkin approximation of the Maxwell operator: The indefinite case

We present and analyze an interior penalty method for the numerical discretization of the indefinite time-harmonic Maxwell equations in mixed form. The method is based on the mixed discretization of the curl-curl operator developed in [Houston et al. , J. Sci. Comp. 22 (2005) 325–356] and can be understood as a non-stabilized variant of the approach proposed in [Perugia et al. , Comput. Methods Appl. Mech. Engrg. 191 (2002) 4675–4697]. We show the well-posedness of this approach and derive optimal a priori error estimates in the energy-norm as well as the L 2 -norm. The theoretical results are confirmed in a series of numerical experiments.
Remembering Occupied Warsaw: Polish Narratives of World War II

Offering a rare glimpse into the lives of those who lived through the German occupation of Poland s capital, this important ethnography explores how elderly residents of Warsaw recollect, narrate, and commemorate their experiences, thus showing how the cultural legacies of the occupation reveal themselves in contemporary Polish society.The individuals who are the focus of this study, all long-time residents of the Warsaw neighborhood Zoliborz, responded to the daily deprivations and brutality of the German occupation by joining branches of the Polish underground, ultimately participating in the Warsaw Uprising of 1944 during which their neighborhood was burned, but not destroyed as soldiers, couriers, and medics. Using life histories and ethnographic fieldwork, Tucker examines the ways that her informantsrecovered from the rupture of war, arguing that this process was connected to efforts to rebuild the city itself.Remembering Occupied Warsaw makes an important contribution to studies of collective memory. A moving work of oral history, this book will appeal to scholars and students of anthropology, sociology, and East European studies, as well as general readers interested in Polish history. "
Testing the performance of beta diversity measures based on incidence data: the robustness to undersampling

Aim Researchers measuring beta diversity have rarely concerned themselves with the problems of how complete the species lists of studied communities are, and of how the varying degrees of completeness can actually change estimates of beta diversity. No comprehensive assessment has been made regarding the behaviour of most beta diversity indices when applied to incomplete samples, a situation which is more common than usually recognized. Our objective was to assess the behaviour and robustness of a number of beta diversity measures for incidence data from undersampled communities.
SQUINKY! A Corpus of Sentence-level Formality, Informativeness, and Implicature

We introduce a corpus of 7,032 sentences rated by human annotators for formality, informativeness, and implicature on a 1-7 scale. The corpus was annotated using Amazon Mechanical Turk. Reliability in the obtained judgments was examined by comparing mean ratings across two MTurk experiments, and correlation with pilot annotations (on sentence formality) conducted in a more controlled setting. Despite the subjectivity and inherent difficulty of the annotation task, correlations between mean ratings were quite encouraging, especially on formality and informativeness. We further explored correlation between the three linguistic variables, genre-wise variation of ratings and correlations within genres, compatibility with automatic stylistic scoring, and sentential make-up of a document in terms of style. To date, our corpus is the largest sentence-level annotated corpus released for formality, informativeness, and implicature.
Young, Restless and Creative: Openness to Disruption and Creative Innovations

This paper argues that openness to new, unconventional and disruptive ideas has a first-order impact on creative innovations—innovations that break new ground in terms of knowledge creation. After presenting a motivating model focusing on the choice between incremental and radical innovation, and on how managers of different ages and human capital are sorted across different firms with different degrees of openness to disruption, we provide firm-level, patent level and cross-country evidence consistent with this pattern. Our measures of creative innovations proxy for innovation quality (average number of citations per patent) and creativity (fraction of superstar innovators, the likelihood of a very high number of citations, and generality of patents). Our main proxy for openness to disruption is the age of the manager - based on the idea that only companies or societies open to such disruption will allow the young to rise up within the hierarchy. Using this proxy at the firm, patent and country level, we present robust evidence that openness to disruption is associated with more creative innovations, but we also show that once the effect of the sorting of young managers to firms that are more open to disruption is factored in, the (causal) impact of manager age on creative innovations is small.
Definition of architectural ideotypes for good yield capacity in Coffea canephora.

BACKGROUND Yield capacity is a target trait for selection of agronomically desirable lines; it is preferred to simple yields recorded over different harvests. Yield capacity is derived using certain architectural parameters used to measure the components of yield capacity. METHODS Observation protocols for describing architecture and yield capacity were applied to six clones of coffee trees (Coffea canephora) in a comparative trial. The observations were used to establish architectural databases, which were explored using AMAPmod, a software dedicated to the analyses of plant architecture data. The traits extracted from the database were used to identify architectural parameters for predicting the yield of the plant material studied. CONCLUSIONS Architectural traits are highly heritable and some display strong genetic correlations with cumulated yield. In particular, the proportion of fruiting nodes at plagiotropic level 15 counting from the top of the tree proved to be a good predictor of yield over two fruiting cycles.
Validity of personality measurement in adults with anxiety disorders: psychometric properties of the Spanish NEO-FFI-R using Rasch analyses

The aim of this study was to analyse the psychometric properties of the Spanish NEO Five Factor Inventory–Revised (NEO-FFI-R) using Rasch analyses, in order to test its rating scale functioning, the reliability of scores, internal structure, and differential item functioning (DIF) by gender in a psychiatric sample. The NEO-FFI-R responses of 433 Spanish adults (154 males) with an anxiety disorder as primary diagnosis were analysed using the Rasch model for rating scales. Two intermediate categories of response (‘neutral’ and ‘agree’) malfunctioned in the Neuroticism and Conscientiousness scales. In addition, model reliabilities were lower than expected in Agreeableness and Neuroticism, and the item fit values indicated each scale had items that did not achieve moderate to high discrimination on its dimension, particularly in the Agreeableness scale. Concerning unidimensionality, the five NEO-FFI-R scales showed large first components of unexplained variance. Finally, DIF by gender was detected in many items. The results suggest that the scores of the Spanish NEO-FFI-R are unreliable in psychiatric samples and cannot be generalized between males and females, especially in the Openness, Conscientiousness, and Agreeableness scales. Future directions for testing and refinement should be developed before the NEO-FFI-R can be used reliably in clinical samples.
On the achievable diversity-multiplexing tradeoff in interference channels

We analyze two-user single-antenna fading interference channels with perfect receive channel state information (CSI) and no transmit CSI. For the case of very strong interference, we prove that decoding interference while treating the intended signal as noise, subtracting the result out, and then decoding the desired signal, a process known as “stripping”, achieves the diversity-multiplexing tradeoff (DMT) outer bound derived in Akuiyibo and Lévêque, Int. Zurich Seminar on Commun. , 2008. The proof is constructive in the sense that it provides corresponding code design criteria for DMT optimality. For general interference levels, we compute the DMT of a fixed-power-split Han and Kobayashi type superposition coding scheme, provide design criteria for the corresponding superposition codes, and find that this scheme is DMT-optimal for certain multiplexing rates.
Interactions Among the Brain Default-Mode, Salience, and Central-Executive Networks During Perceptual Decision-Making of Moving Dots

Cognitively demanding goal-directed tasks in the human brain are thought to involve the dynamic interplay of several large-scale neural networks, including the default-mode network (DMN), salience network (SN), and central-executive network (CEN). Resting-state functional magnetic resonance imaging (rsfMRI) studies have consistently shown that the CEN and SN negatively regulate activity in the DMN, and this switching is argued to be controlled by the right anterior insula (rAI) of the SN. However, what remains to be investigated is the pattern of directed network interactions during difficult perceptual decision-making tasks. We recorded fMRI data while participants categorized the left-right motion of moving dots. We defined regions of interest, extracted fMRI time series, and performed directed connectivity analysis using Granger causality techniques. Our analyses demonstrated that the slow oscillation (0.07-0.19 Hz) mediated the interactions within and between the DMN, SN, and CEN nodes both for easier and harder decision-making tasks. We found that the rAI, a key node of the SN, played a causal control over the DMN and CEN for easier decision-making tasks. The combined effort of the rAI and dorsal anterior cingulate cortex of the SN had the causal control over the DMN and CEN for a harder task. These findings provide important insights into how a sensory signal organizes among the DMN, SN, and CEN during sensory information-guided, goal-directed tasks.
Time Course of Early Postadmission Hematoma Expansion in Spontaneous Intracerebral Hemorrhage

Background and Purpose— Early hematoma expansion (EHE) in patients with intracerebral hematoma is a promising treatment target. To date, the time course of EHE has remained poorly described. We prospectively investigated the time course of EHE. Methods— We included consecutive patients presenting spontaneous intracerebral hematoma within 4.5 hours. On admission, patients underwent noncontrast computed tomography (CT) and CT angiography. Serial hematoma volume estimations by transcranial B-mode ultrasound were effected through the contralateral transtemporal bone window by obtaining sagittal, transversal, and coronal diameter and calculating the ABC/2-formula. National Institute of Health Stroke Scale and transcranial B-mode ultrasound were performed consecutively every 30 minutes during the first 6 hours and from 6 to 12 hours every 2 hours. Follow-up CT and ultrasound were performed after ≈24 hours. Results— Twenty-five patients with intracerebral hematoma were included; mean (SD) time from onset to CT was 108.6 (45.7) minutes. Ten (40%) patients had EHE. In patients with a final clinically significant hematoma expansion >12.5 mL, all EHE occurred within 6 hours after admission scan. EHE in spot sign positive patients continued during the first 5 hours after CT angiography. In spot sign–negative patients, no significant EHE was observed (Friedman test, P=0.476). Neurological deterioration occurred in 5 (20%) patients and was well temporally correlated with EHE. Transcranial B-mode ultrasound demonstrated good volume estimation compared with the follow-up CT with a maximum absolute volume deviation within 7 mL and minimal systematic error (mean deviation, 1.3 [confidence interval, −0.1 to 2.6] mL). Conclusions— EHE was reliably reflected by transcranial B-mode ultrasound and mainly occurred within the first 7 to 8 hours after symptom onset. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT01472224.
Characterizing pulmonary blood flow distribution measured using arterial spin labeling

The arterial spin labeling (ASL) method provides images in which, ideally, the signal intensity of each image voxel is proportional to the local perfusion. For studies of pulmonary perfusion, the relative dispersion (RD, standard deviation/mean) of the ASL signal across a lung section is used as a reliable measure of flow heterogeneity. However, the RD of the ASL signals within the lung may systematically differ from the true RD of perfusion because the ASL image also includes signals from larger vessels, which can reflect the blood volume rather than blood flow if the vessels are filled with tagged blood during the imaging time. Theoretical studies suggest that the pulmonary vasculature exhibits a lognormal distribution for blood flow and thus an appropriate measure of heterogeneity is the geometric standard deviation (GSD). To test whether the ASL signal exhibits a lognormal distribution for pulmonary blood flow, determine whether larger vessels play an important role in the distribution, and extract physiologically relevant measures of heterogeneity from the ASL signal, we quantified the ASL signal before and after an intervention (head‐down tilt) in six subjects. The distribution of ASL signal was better characterized by a lognormal distribution than a normal distribution, reducing the mean squared error by 72% (p < 0.005). Head‐down tilt significantly reduced the lognormal scale parameter (p = 0.01) but not the shape parameter or GSD. The RD increased post‐tilt and remained significantly elevated (by 17%, p < 0.05). Test case results and mathematical simulations suggest that RD is more sensitive than the GSD to ASL signal from tagged blood in larger vessels, a probable explanation of the change in RD without a statistically significant change in GSD. This suggests that the GSD is a useful measure of pulmonary blood flow heterogeneity with the advantage of being less affected by the ASL signal from tagged blood in larger vessels. Copyright © 2009 John Wiley & Sons, Ltd.