Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Architecture Characterizes Tumor Progression Paths and Fate in Breast Cancer Patients

This study demonstrates the relation among structural genomic alterations, molecular subtype, and clinical behavior and shows that an objective score of genomic complexity can provide independent prognostic information in breast cancer. Form and Malfunction Breast cancer is an iniquitous disease with a panoply of predisposing genetic and environmental causes, the details of which have yet to be fully understood. One of every four women will be diagnosed with breast cancer, hence the early and accurate identification of specific tumor features that may affect overall survival is imperative in achieving an optimal prognosis. A widely appreciated taxonomy in the breast cancer field has enabled the molecular discernment of five pathological subtypes; however, as research dives deeper into the chromosomal underpinnings of the disease, new classifiers are needed to augment what is known with key structural details to create a more vivid tumor landscape. Now, Russnes and colleagues have generated new algorithms that can estimate the specific genomic region as well as the architectural type of rearrangement—gains or losses of chromosome arms. A cohort of breast tumors was scored using this method, and all tumors with complex rearrangements had more whole chromosome arms affected than those without complex rearrangement. Moreover, there was an overlapping correlation with the molecular subtyping features of the tumors, and the score could confer prognostic power. Distinct molecular subtypes of breast carcinomas have been identified, but translation into clinical use has been limited. We have developed two platform-independent algorithms to explore genomic architectural distortion using array comparative genomic hybridization data to measure (i) whole-arm gains and losses [whole-arm aberration index (WAAI)] and (ii) complex rearrangements [complex arm aberration index (CAAI)]. By applying CAAI and WAAI to data from 595 breast cancer patients, we were able to separate the cases into eight subgroups with different distributions of genomic distortion. Within each subgroup data from expression analyses, sequencing and ploidy indicated that progression occurs along separate paths into more complex genotypes. Histological grade had prognostic impact only in the luminal-related groups, whereas the complexity identified by CAAI had an overall independent prognostic power. This study emphasizes the relation among structural genomic alterations, molecular subtype, and clinical behavior and shows that objective score of genomic complexity (CAAI) is an independent prognostic marker in breast cancer.
Development of a clinical measure of turning for older adults.

OBJECTIVE The purpose of this study was to identify the characteristics present and observable when older adults safely and efficiently turn while walking and to develop and evaluate a clinical measure of turning based on these characteristics. DESIGN This was a validation study of balance and mobility tests using a three-group sample of convenience. RESULTS The reliability of a turn measure consisting of nine movement items was identified. Five of the turn measure items were able to discriminate between multiple faller and the other two groups. The two items dichotomously rated as yes or no were "seems steady throughout the turn" and "moves fluently without hesitation between turn and walk when exiting the turn. " Three other items were, total turn score, the time taken to turn, and turn step number. These last two items also achieved strong correlation with existing balance measures and high sensitivity for identifying multiple fallers. These items form an easy-to-use clinical measure of turning for older adults. CONCLUSIONS The turn measure developed in this investigation was found to be a reliable and valid clinical measure of turning while walking for older adults. Specific turn items were found to discriminate between groups of healthy and impaired older adults and had good sensitivity for identifying multiple fallers. The turn measure is relatively quick to administer and score and uses equipment readily available in most clinical settings.
Response to Intervention Screening and Progress–Monitoring Practices in 41 Local Schools

This study describes response to intervention (RTI) screening and progress–monitoring instruments and procedures in 41 local school settings. For screening the schools most often used published reading assessments or commercial products; a three–times–per–year screening schedule was most prevalent. For progress monitoring schools most often relied on published reading assessments; a weekly progress monitoring schedule was most prevalent. The variability between local school practices is discussed with regard to efficiency, equity, and viability of RTI.
If only I had taken my usual route… : Age-related differences in counter-factual thinking

ABSTRACT Previous research suggests that young adults can shift between rational and experiential modes of thinking when forming social judgments. The present study examines whether older adults demonstrate this flexibility in thinking. Young and older adults completed an If-only task adapted from Epstein, Lipson, and Huh's (1992, Journal of Personality and Social Psychology, 62, 328) examination of individuals' ability to adopt rational or experiential modes of thought while making a judgment about characters who experience a negative event that could have been avoided. Consistent with our expectations for their judgments of the characters, young adults shifted between experiential and rational modes of thought when instructed to do so. Conversely, regardless of the mode of thought being used or the order with which they adopted the different modes of thought (i.e., shifting from experiential to rational in Study 1 and from rational to experiential in Study 2), older adults consistently offered judgments and justifications that reflected a preference for experiential-based thought.
Cultivating sources of competitive advantage: Opportunities for small-scale African farmers in global value chains

Small-scale farmers in developing countries often appropriate little of the value created in global value chains. The farmers typically receive only a fraction of what consumers pay for a certain product. In the current thesis we studied which resources farmers have access to that enable them to appropriate more of the value created. We studied access to resources at both the level of the individual farmer as well as at the level of the collective (the cooperative). Data have been collected among sesame seed farmers in Ethiopia. We learn from our findings that we can explain approximately 30% of the performance differences between ostensibly homogeneous farmers in terms of differences in access to and deployment of so-called strategic resources. We also learn that the potential of collective action currently remains unrealized. The failure to realize this potential is rooted in the neglect of conditions for success of collective action. Farmers in Ethiopia are encouraged to cooperate, but the importance of trust and variances between farmers in ambitions and willingness to take risks, are being neglected. In addition we studied the influence of the institutional environment (rules, norms, values, agreements) on entrepreneurial behavior of farmer cooperatives. We analyzed how certain institutions prescribing entrepreneurial behavior conflict with others institutions dissuading entrepreneurial behavior. The choice for either kind of institution can explain part of the success and failures of farmer cooperatives.
Automatic MRI 2D brain segmentation using graph searching technique

Accurate and efficient segmentation of the whole brain in magnetic resonance (MR) images is a key task in many neuroscience and medical studies either because the whole brain is the final anatomical structure of interest or because the automatic extraction facilitates further analysis. The problem of segmenting brain MRI images has been extensively addressed by many researchers. Despite the relevant achievements obtained, automated segmentation of brain MRI imagery is still a challenging problem whose solution has to cope with critical aspects such as anatomical variability and pathological deformation. In the present paper, we describe and experimentally evaluate a method for segmenting brain from MRI images basing on two‐dimensional graph searching principles for border detection. The segmentation of the whole brain over the entire volume is accomplished slice by slice, automatically detecting frames including eyes. The method is fully automatic and easily reproducible by computing the internal main parameters directly from the image data. The segmentation procedure is conceived as a tool of general applicability, although design requirements are especially commensurate with the accuracy required in clinical tasks such as surgical planning and post‐surgical assessment. Several experiments were performed to assess the performance of the algorithm on a varied set of MRI images obtaining good results in terms of accuracy and stability. Copyright © 2012 John Wiley & Sons, Ltd.
Modelling Changing Lag Structure in U.S. Housing Construction

In this paper, we reconsider the nature of changing lag structure in housing construction. We assume that the U.S. housing construction industry is subject to two regimes determined by the level of housing units under construction: recession and expansion. The econometric model we employ is a generic nonlinear autoregressive distributed lag model. The results imply that builders seem to change the speed of construction depending on whether the construction industry is in a recession or expansion. The mean lag between housing completions and housing starts is significantly shorter in recession periods than in expansion periods. This conclusion is in line with the so-called “accordion effect”.
Reduced Respiratory Control with ADP and Changed Pattern of Respiratory Chain Enzymes as a Result of Selective Deficiency of the Mitochondrial ATP Synthase

The FoF1-ATPase, a multisubunit protein complex of the inner mitochondrial membrane, produces most of the ATP in mammalian cells. Mitochondrial diseases as a result of a dysfunction of ATPase can be caused by mutations in mitochondrial DNA–encoded ATPase subunit a or rarely by an ATPase defect of nuclear origin. Here we present a detailed functional and immunochemical analysis of a new case of selective and generalized ATPase deficiency found in an Austrian patient. The defect manifested with developmental delay, muscle hypotonia, failure to thrive, ptosis, and varying lactic acidemia (up to 12 mmol/L) beginning from the neonatal period. A low-degree dilated cardiomyopathy of the left ventricle developed between the age of 1 and 2 y. A >90% decrease in oligomycin-sensitive ATPase activity and an 86% decrease in the content of the ATPase complex was found in muscle mitochondria. It was associated with a significant decrease of ADP-stimulated respiration of succinate (1.5-fold) and respiratory control with ADP (1.7-fold) in permeabilized muscle fibers, and with a slight decrease of the respiratory chain complex I and compensatory increase in the content of complexes III and IV. The same ATPase deficiency without an increase in respiratory chain complexes was found in fibroblasts, suggesting a generalized defect with tissue-specific manifestation. Absence of any mutations in mitochondrial ATP6 and ATP8 genes indicates a nuclear origin of the defect.
Pricing Strategies of the European Low-Cost Carriers Explained Using Porter's Five Forces Model

In recent decades, the air transport sector has experienced major changes, including the emergence of the low-cost airlines. The strategies adopted by these new companies have given rise to a revitalization of the sector, particularly in Europe and the USA. This article analyses the pricing strategy followed by the low-cost carriers based on Porter's analysis. The research is based on the study of a total of 90 traditional tourist routes between the UK and Spain. As in previous studies, the high level of concentration and advance purchase of fares are the most important components explaining the price dispersion. However, the methodology used (principal component analysis + panel) has generated another series of highly interesting results regarding the role of the Internet and tourism in price setting which require further in-depth study.
Predictability and Variability of Wave and Wind: wave and wind forecasting and diversified energy systems in the Danish North Sea

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MARKETING STRATEGY MAKING: PROSES & AGENDA PENELITIAN

MSM atau Marketing Strategy Making telah berkembang menjadi salah satu kosakata penting dalam pustaka dan penelitian marketing. Studi Menon dkk menunjukkan bahwa konten strategi saja tidaklah cukup untuk menjamin keberhasilan pencapaian kinerja pemasaran, yang tidak kalah penting adalah proses pengembangan strategi itu sendiri. Tulisan ini menyajikan sebuah kerangka kerja berikut agenda penelitian yang relevan.
Characterization of Starch Synthase I and II Expressed in Early Developing Seeds of Kidney Bean (Phaseolus vulgaris L.)

Plant starch synthase (SS) contributes to the elongation of glucan chains during starch biosynthesis and hence plays an essential role in determining the fine structure of amylopectin. To elucidate the role of SS activity in the formation of amylopectin in kidney bean (Phaseolus vulgaris L.), a study was undertaken to isolate cDNA clones for SS and to characterize the enzymatic properties of the coded recombinant enzymes. Two SS cDNAs, designated pvss1 and pvss21, which were isolated from early developing seeds, encoded SSI and SSII (designated PvSSI and PvSSII-1) that displayed significant identity (more than 65%) with other SSI and SSII members, respectively. RNA gel blot analysis indicated that both transcripts accumulate in leaves and developing seeds at the early stage. Immunoblot analysis with antisera raised against both recombinant proteins (rPvSSI and rPvSSII-1) showed that the accumulation of both proteins parallels the gene expression profiles, although both were detectable only in starch-granule fractions. Recombinant enzymes expressed by Escherichia coli cells showed distinct chain-length specificities for the extension of glucan chains. Our results suggest that these SS isozymes for synthesis of transitory starch are also responsible for synthesis of storage starch in early developing seeds of kidney bean.
CFTR Localization in Native Airway Cells and Cell Lines Expressing Wild-type or F508del-CFTR by a Panel of Different Antibodies

The intracellular localization of cystic fibrosis transmembrane conductance regulator (CFTR) in native tissues is a major issue in the study of mutation, processing, and trafficking effects in CFTR and in the evaluation of therapeutic strategies in cystic fibrosis (CF). This work evaluated the applicability of ten different antibodies (Abs) under various fixation techniques for CFTR localization in fresh-brushed nasal epithelial cells collected from CF patients homozygous for F508del and control individuals. In parallel, the same Ab panel was also tested on BHK cell lines overexpressing wild-type or F508del CFTR. The Abs MATG1061, 169, Lis1, MP-CT1, CC24-R, MAB25031, and MAB1660 gave the best detection of CFTR in the apical region (AR) of nasal tall columnar epithelial (TCE) cells. The labeling pattern of these Abs was consistent with the postulated processing defect of F508del CFTR because only a minority of CF TCE cells present CFTR in the AR. In contrast, M3A7, MM13–4, and L12B4 weakly react with the AR and stain almost exclusively a cis-Golgi-like structure in the majority of CF and non-CF airway cells. In BHK cells, all the Abs enabled distinction between wild-type CFTR localization in cell membrane from F508del CFTR, which in these cells is exclusively located in the endoplasmic reticulum.
Neuropathologic confirmation of definitional criteria for human immunodeficiency virus-associated neurocognitive disorders

Research findings have suggested a need for modifications to the original nomenclature for human immunodeficiency virus (HIV)-associated neurocognitive disorders issued in 1991 by the American Academy of Neurology (AAN). The HIV Neurobehavioral Research Center (HNRC) proposed a diagnostic scheme that departs from the AAN 1991 criteria primarily in the inclusion of an asymptomatic neurocognitive impairment (ANI) category that relies on cognitive disturbances as a necessary criterion for diagnosis, without requiring declines in daily functioning, motor, or other behavioral abnormalities. In order to test the predictive validity of these two nomenclatures, the authors compared the correspondence between antemortem neurocognitive diagnoses resulting from AAN and HNRC criteria to a neuropathological diagnosis of HIV encephalitis (HIVE) made at autopsy. Agreement between the two sets of definitional criteria was 79% regarding the classification of cases as either neurocognitively normal or impaired, and 54% with regard to specific neurocognitive diagnoses. When pathological evidence of HIVE was considered as the external indicator of HIV-related brain involvement, 64% of cases were correctly classified by AAN criteria, compared to 72% by HNRC criteria. HNRC criteria had better positive predictive power (95% versus 88%), sensitivity (67% versus 56%), and specificity (92% versus 83%). Three cases with HIVE and were correctly identified by HNRC criteria for ANI but called normal by AAN criteria, supporting inclusion of an asymptomatic neurocognitive condition. The modifications to the AAN 1991 criteria proposed by the HNRC and others in the field have served as a point of departure for a recently revised consensus nomenclature.
Q‐learning for estimating optimal dynamic treatment rules from observational data

The area of dynamic treatment regimes (DTR) aims to make inference about adaptive, multistage decision‐making in clinical practice. A DTR is a set of decision rules, one per interval of treatment, where each decision is a function of treatment and covariate history that returns a recommended treatment. Q‐learning is a popular method from the reinforcement learning literature that has recently been applied to estimate DTRs. While, in principle, Q‐learning can be used for both randomized and observational data, the focus in the literature thus far has been exclusively on the randomized treatment setting. We extend the method to incorporate measured confounding covariates, using direct adjustment and a variety of propensity score approaches. The methods are examined under various settings including non‐regular scenarios. We illustrate the methods in examining the effect of breastfeeding on vocabulary testing, based on data from the Promotion of Breastfeeding Intervention Trial. The Canadian Journal of Statistics 40: 629–645; 2012 © 2012 Statistical Society of Canada
A Comparative Study on the Detection of Covert Attention in Event-Related EEG and MEG Signals to Control a BCI

In brain-computer interface (BCI) applications the detection of neural processing as revealed by event-related potentials (ERPs) is a frequently used approach to regain communication for people unable to interact through any peripheral muscle control. However, the commonly used electroencephalography (EEG) provides signals of low signal-to-noise ratio, making the systems slow and inaccurate. As an alternative noninvasive recording technique, the magnetoencephalography (MEG) could provide more advantageous electrophysiological signals due to a higher number of sensors and the magnetic fields not being influenced by volume conduction. We investigated whether MEG provides higher accuracy in detecting event-related fields (ERFs) compared to detecting ERPs in simultaneously recorded EEG, both evoked by a covert attention task, and whether a combination of the modalities is advantageous. In our approach, a detection algorithm based on spatial filtering is used to identify ERP/ERF components in a data-driven manner. We found that MEG achieves higher decoding accuracy (DA) compared to EEG and that the combination of both further improves the performance significantly. However, MEG data showed poor performance in cross-subject classification, indicating that the algorithm's ability for transfer learning across subjects is better in EEG. Here we show that BCI control by covert attention is feasible with EEG and MEG using a data-driven spatial filter approach with a clear advantage of the MEG regarding DA but with a better transfer learning in EEG.
Separated adaptive control scheme of a rotor-flying manipulator

Rotor flying manipulator (RFM), a new kind of mobile robot system being composed of a rotor flying robot (RFR) and a (several) manipulator(s), has absorbed great attentions in recent years because it enables a RFR to complete active tasks such as mastering and transporting objects. However, steady control of the RFM during both maneuvering and operating is of great difficulty due to the heavy force/moment coupling between the RFR and the manipulator, which introduce high nonlinearity and complexity to the system model. In this paper, a new control scheme of the RFM is proposed to ensure the steady flight. Firstly, the nonlinear mathematical model is derived, which is followed by the coupling analysis to show how the movement of the manipulator influences the whole system's behavior. Subsequently, based on these analyses, a new control scheme is designed with obtainable coupling force/moment. The basic idea of the controller is to take the coupling as a disturbance and separately control the RFR and the manipulator, and the stability is ensured to properly design the controller parameters. Finally, simulations are conducted and the results show the feasibility and validity of the proposed controller.
Effectiveness of Commodity Futures in Curbing Spot Volatility

This study examines the impact of introduction of futures trading on the spot price volatility in the commodity market. The paper considers the United States of America, South Africa and Ethiopian economies. Three commodities i.e. coffee, maize and wheat from New York Mercantile Exchange, South African Futures Exchange and Ethiopian Commodity Exchange are analyzed. ARCH LM test is used to check for heteroskedasticity and GARCH and EGARCH are used to check for the behavior of volatility for the pre- and post-futures periods. For all the three economies, the results indicate presence of the ARCH effect in the log returns. For conditional and unconditional variances; spot price volatility for coffee has decreased after futures trading across all the economies and the EGARCH has also shown reduction in persistence of volatility in the post-futures period in the three economies; while that of maize has reduced for the Ethiopian economy but increased in both the US and South African economies. For wheat, the conditional variance has been found to rise in the post-futures period in all the three economies. These results imply that more positive feedback from futures trading is bound to be seen for maize in the less developed economies as opposed to the developed economies as opposed to the other products. This paper has focused on the overlooked factor by earlier researchers, i.e. of economic-gap amongst countries, in looking at the impact of the futures trading on the spot price variation.