bluuebunny/crossref_metadata_2025_split huggingface dataset:
Group SCAD regression analysis for microarray time course gene expression data
Authors: Wang Lifeng , Chen Guang , Li Hongzhe 
Published: April 2007

AbstractMotivation: Since many important biological systems or processes are dynamic systems, it is important to study the gene expression patterns over time in a genomic scale in order to capture the dynamic behavior of gene expression. Microarray technologies have made it possible to measure the gene expression levels of essentially all the genes during a given biological process. In order to determine the transcriptional factors (TFs) involved in gene regulation during a given biological process, we propose to develop a functional response model with varying coefficients in order to model the transcriptional effects on gene expression levels and to develop a group smoothly clipped absolute deviation (SCAD) regression procedure for selecting the TFs with varying coefficients that are involved in gene regulation during a biological process.Results: Simulation studies indicated that such a procedure is quite effective in selecting the relevant variables with time-varying coefficients and in estimating the coefficients. Application to the yeast cell cycle microarray time course gene expression data set identified 19 of the 21 known TFs related to the cell cycle process. In addition, we have identified another 52 TFs that also have periodic transcriptional effects on gene expression during the cell cycle process. Compared to simple linear regression (SLR) analysis at each time point, our procedure identified more known cell cycle related TFs.Conclusions: The proposed group SCAD regression procedure is very effective for identifying variables with time-varying coefficients, in particular, for identifying the TFs that are related to gene expression over time. By identifying the TFs that are related to gene expression variations over time, the procedure can potentially provide more insight into the gene regulatory networks.Contact: hli@cceb.upenn.eduSupplementary information: http://www.cceb.med.upenn.edu/~hli/gSCAD-Appendix.pdf
An efficient method for the detection and elimination of systematic error in high-throughput screening
Authors: Makarenkov Vladimir , Zentilli Pablo , Kevorkov Dmytro , Gagarin Andrei , Malo Nathalie , Nadon Robert 
Published: April 2007

Abstract
Motivation: High-throughput screening (HTS) is an early-stage process in drug discovery which allows thousands of chemical compounds to be tested in a single study. We report a method for correcting HTS data prior to the hit selection process (i.e. selection of active compounds). The proposed correction minimizes the impact of systematic errors which may affect the hit selection in HTS. The introduced method, called a well correction, proceeds by correcting the distribution of measurements within wells of a given HTS assay. We use simulated and experimental data to illustrate the advantages of the new method compared to other widely-used methods of data correction and hit selection in HTS.
Contact: makarenkov.vladimir@uqam.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Petrous Apex Aspergillosis as a Long‐Term Complication of Cholesterol Granuloma
Authors: Eloy Jean Anderson , Bederson Joshua B. , Smouha Eric E. 
Published: April 2007

AbstractAspergillus infection of the petrous apex is a rare and devastating condition. To date, only two such cases have been reported, which resulted from direct extension of chronic Aspergillus otitis media. We present a case of petrous apex aspergillosis occurring years after surgical drainage of a petrous apex granuloma cyst. Because of the potential lethal nature of this condition, aggressive surgical therapy should be considered early in this illness and may provide the best chance for survival.
The Transnasal Esophagoscopy Documentation Dilemma
Authors: Garner Justin , Schweinfurth John , May Warren , Faust John 
Published: April 2007

AbstractObjective: To determine radiographically the anatomic length difference between the nasal and oral aerodigestive tracts and to clarify gaps in the literature regarding standardized landmark measurements and documentation techniques in transnasal esophagoscopy, as opposed to traditional transoral esophagoscopy.Study Design: This is a prospective radiographic cohort study.Methods: Digital computerized tomography measurement techniques were used to determine the difference in length between the nasal and oral aerodigestive tracts. Using sagittal plane images from consecutive patients, the mean nares‐cricoid (NC) distance, upper incisor‐cricoid (IC) distance, and their mean differences were determined. Male, female, and overall distances and differences were calculated. Standard deviations, 95% confidence intervals, and 90% prediction intervals were also calculated. Mean difference data were applied to reported standard oral esophagoscopy landmark measurements to convert to standard landmark measurements from the nares.Results: Overall mean NC and IC distances were 175.4 mm and 147.5 mm, respectively. For males, these mean distances were 185.5 mm and 155.0 mm, respectively. For females, these mean distances were 165.3 mm and 140.0 mm, respectively. Overall mean NC to IC difference was 27.9 mm. The mean NC to IC difference for males and females was 30.5 mm and 25.2 mm, respectively.Conclusions: Historically, landmark and report measurements in esophagoscopy have been measured and standardized from the upper incisor. This study demonstrates and clarifies the inherent anatomic length difference of the nasal and oral aerodigestive tracts and the resultant documentation dilemma produced by transnasal esophagoscopy techniques. These data provide easy conversion of esophagoscopy measurements reported from the incisors or nares, providing better communication between endoscopists of different disciplines and techniques.
Otopathology in Mohr‐Tranebjærg Syndrome
Authors: Bahmad Fayez , Merchant Saumil N. , Nadol Joseph B. , Tranebjærg Lisbth 
Published: April 2007

AbstractBackground: Mohr‐Tranebjærg syndrome (MTS) is an X‐linked, recessive, syndromic sensorineural hearing loss (HL) characterized by onset of deafness in childhood followed later in adult life by progressive neural degeneration affecting the brain and optic nerves. MTS is caused by mutations in the DDP/TIMM8A gene, which encodes for a 97 amino acid polypeptide; this polypeptide is a translocase of the inner mitochondrial membrane.Objectives: To describe the otologic presentation and temporal bone histopathology in four affected individuals with MTS.Material and Methods: All four subjects belonged to a large, multigenerational Norwegian family and were known to carry a frame shift mutation in the TIMM8A gene. Temporal bones were removed at autopsy and studied by light microscopy. Cytocochleograms were constructed for hair cells, stria vascularis, and cochlear neuronal cells. Vestibular neurons were also counted.Results: All four subjects developed progressive HL in early childhood, becoming profoundly deaf by the age of 10 years. All four developed language, and at least one subject used amplification in early life. Audiometric evaluation in two subjects showed 80‐ to 100‐dB HL by the age of 10 years. The subjects died between the ages of 49 and 67. The otopathology was strikingly similar in that all bones examined showed near‐total loss of cochlear neuronal cells and severe loss of vestibular neurons. When compared with age‐matched controls, there was 90% to 95% loss of cochlear neurons and 75% to 85% loss of vestibular neurons.Conclusions: We infer that the HL in MTS is likely to be the result of a postnatal and progressive degeneration of cochlear neurons and that MTS constitutes a true auditory neuropathy. Our findings have implications for clinical diagnosis of patients with MTS and management of the HL.
Comparison of differential neuronal responsiveness for different regions of the prefrontal cortex in a conditional visual discrimination task
Authors: Xiang J.‐Z. , Brown M. W. 
Published: April 2007

AbstractTo investigate neuronal processing during monkeys' performance of a visual conditional discrimination task, recordings were made from four areas of prefrontal cortex (ventromedial, orbitofrontal, dorsolateral and anterior cingulate) where lesions have been shown to produce impairment of such tasks. Of 1911 recorded neurons, 573 (31%) responded to elements of the task. This proportion was less than the 50% previously reported as responsive in temporal cortex under the same conditions, suggesting sparser encoding in prefrontal than temporal cortex. Of the responsive prefrontal neurons, 165 (29%) responded differently on the different types of trial, so signalling various types of information relevant to task performance and cognition. In line with recent lesion findings, in the dorsolateral region the incidence of such differentially responsive neurons was only an eighth that in the other regions. The relatively high incidence of neuronal responses that encoded a potential instruction cue rather than specific individual stimulus arrangements was consistent with the animals solving the task by using such information, though other neuronal responses could have enabled the task to have been solved by rote learning. Compared to temporal neurons, prefrontal responses more frequently coded information relating to the planned behavioural response rather than perceptual aspects of the task. Population differential response latencies were long (> ∼ 225 ms) in prefrontal cortex. A comparison of such differential latencies between temporal and prefrontal cortex indicated that potential information flow was likely to be primarily from temporal to prefrontal cortex rather than vice versa.
Kynurenic acid blocks nicotinic synaptic transmission to hippocampal interneurons in young rats
Authors: Stone Trevor W. 
Published: April 2007

AbstractThe tryptophan metabolite kynurenic acid can block glutamate at ionotropic receptors, but recent evidence suggests a more potent antagonistic action at α7 nicotinic receptors for acetylcholine on cultured neurons. The present study examines activity of kynurenic acid at those nicotinic receptors, which mediate cholinergic neurotransmission onto interneurons in the rat hippocampus. Intracellular recordings were made from pyramidal cells and interneurons in the presence of atropine, bicuculline methobromide, (3‐aminopropyl)(diethoxymethyl)‐phosphinic acid [CGP35348, to block γ‐aminobutyric acid (GABA)B receptors] and 3‐tropanyl‐3,5‐dichlorobenzoate (MDL 72222, to block 5‐HT3 receptors). In the added presence of glutamate antagonists 2‐amino‐5‐phosphono‐pentanoic acid and 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione, interneurons exhibited a residual excitatory postsynaptic potential (EPSP) that could be blocked by the nicotinic α7 receptor blocker methyl‐lycaconitine, but not by dihydro‐β‐erythroidine which blocks α4β2 receptors. Kynurenic acid reduced the amplitude of these EPSPs with an EC50 of 136 µm. The amplitudes of nicotinic spontaneous miniature EPSPs were also reduced by methyl‐lycaconitine and kynurenic acid. The results show that kynurenic acid is more potent in blocking nicotinic EPSPs compared with the full, glutamate‐mediated EPSPs, but it was substantially less potent than has been reported in cultures, possibly because of differences in the accessibility of synaptic and extrasynaptic receptors. It is suggested that blockade of nicotinic synaptic transmission may be relevant to the actions of kynurenic acid in the hippocampus, but that in the intact brain this activity is likely to be comparable in importance to the blockade of glutamate‐mediated transmission.
Custom and the Courts: Ensuring Women's Rights to Land, Jharkhand, India
Authors: Rao Nitya 
Published: April 2007

ABSTRACTBased on field research in Dumka district, Jharkhand, this article examines the mechanisms through which women operationalize their rights to land. It questions the polarization of legitimation systems into statutory codes and customary practices, as operating independent of each other, and demonstrates the political and temporal situatedness of ‘law’, and the processes of hybridization that allow for the actualization of a legal right, by providing it social recognition and validity. The article explores the choice of different arenas by women for making their claims, with the choice of a particular arena depending not just on access and resource availability, but also on the women's social positionality.
School Choice and the Intergenerational Poverty Trap
Authors: Nishimura Kazuo , Raut Lakshmi K. 
Published: April 2007

AbstractThis paper formulates a dynamic altruistic model of parental choice of school quality and intergenerational social mobility. It shows that when there are many school qualities, the earnings of children as a function of parental schooling investment is a non‐concave function, which leads to multiple steady‐state equilibria. The paper studies the intergenerational dynamics of parental schooling investment and gives conditions on the rate of return from parental schooling investment under which some families are stuck in an intergenerational poverty trap. The policy implications are also discussed.
Exchange Rates, Expectations, and Monetary Policy: a NOEM Perspective*
Authors: Pierdzioch Christian , Stadtmann Georg 
Published: April 2007

AbstractWe use a dynamic general‐equilibrium optimizing two‐country model to analyze how the formation of exchange rate expectations shapes the effects of a monetary policy shock in an open economy. We also provide empirical evidence on how traders in foreign exchange markets form exchange rate expectations. Our model implies that the short‐run output effect of a permanent monetary policy shock diminishes if “technical traders” form the type of regressive exchange rate expectations we find in our empirical analysis. If the influence of technical traders is strong enough, a permanent expansionary monetary policy shock can result in a temporary decline of the output in the country in which it takes place. The output effect of a temporary monetary policy shock is magnified when technical traders form regressive exchange rate expectations.
Cartel Stability and Economic Integration
Authors: Schröder Philipp J. H. 
Published: April 2007

AbstractThis paper revisits the notion that economic integration—modeled as a reduction of trade costs—may be anticompetitive, in the sense that it may reinforce the ability of an international cartel to maintain a collusive understanding about staying out of each other’s markets. The paper is novel in terms of introducing ad valorem and fixed trade costs in addition to the customary unit trade costs. It is shown that an anticompetitive effect, found for reductions in unit trade costs, may disappear once trade costs are ad valorem or fixed.
Trade, Human Capital, and Technology Spillovers: an Industry‐level Analysis
Authors: Wang Yanling 
Published: April 2007

AbstractThis paper studies whether trade promotes North–South and South–South technology spillovers at the industry level, and how the absorptive capacity of the South affects the impact of the technology spillovers. Using data from 16 manufacturing industries in 25 developing countries from 1976 to 1998, the paper shows: (i) North–South trade‐related R&D has a substantial impact on total factor productivity in the South; (ii) South–South trade‐related R&D also promotes technology spillovers but with a smaller magnitude; and (iii) human capital is very important in facilitating North–South and South–South technology spillovers: an increase in human capital could lead to over three times the size of technology spillovers from an increase in trade‐related foreign R&D.
Is conservation tillage suitable for organic farming? A review
Authors: Peigné J. , Ball B. C. , Roger‐Estrade J. , David C. 
Published: April 2007

AbstractConservation tillage covers a range of tillage practices, mostly non‐inversion, which aim to conserve soil moisture and reduce soil erosion by leaving more than one‐third of the soil surface covered by crop residues. Organic farmers are encouraged to adopt conservation tillage to preserve soil quality and fertility and to prevent soil degradation – mainly erosion and compaction. The potential advantages of conservation tillage in organic farming are reduced erosion, greater macroporosity in the soil surface due to larger number of earthworms, more microbial activity and carbon storage, less run‐off and leaching of nutrients, reduced fuel use and faster tillage. The disadvantages of conservation tillage in organic farming are greater pressure from grass weeds, less suitable than ploughing for poorly drained, unstable soils or high rainfall areas, restricted N availability and restricted crop choice. The success of conservation tillage in organic farming hinges on the choice of crop rotation to ensure weed and disease control and nitrogen availability. Rotation of tillage depth according to crop type, in conjunction with compaction control measures is also required. A high standard of management is required, tailored to local soil and site conditions. Innovative approaches for the application of conservation tillage, such as perennial mulches, mechanical control of cover crops, rotational tillage and controlled traffic, require further practical assessment.
Police and policy
Authors: Lévy Yves 
Published: April 2007

‘The French Empire’, wrote one historian, ‘was doubtless the forerunner of the modern police state.’ The same historian wrote elsewhere: ‘The ancien régime was brought down by violence, and the governments which had followed each other in France, since 1789, had been dictatorships : the dictatorship of the ‘Patriots’ in the Constituent Assembly, of the Girondins in the Legislative Assembly, of the Paris Commune after 10 August; then of the Committee of Public Safety; finally the dictatorship of the Directory, which destroyed, by means of coups d'état the majorities in the Legislative Assembly which displeased them.’The police-Empire was not unrelated to the dictatorships which preceded it, and in order to understand it, we must first try to grasp the thread which links these successive dictatorships together.
The Common Market and Conservative Party politics, 1961–2
Authors: Butt Ronald 
Published: April 2007

The Common Market as an issue in domestic British politics under the Macmillan government – and distinct from the negotiations, as such, with the European Economic Community – can be considered under three broad heads. First, there is the question how the decision to seek entry for Britain was taken. How far was it a political decision; how far was it motivated by the views of civil servants; how far was it prompted by interest groups in industry and finance ? Secondly, how did the Conservative Party become converted to the idea of British membership of the European Economic Community and how significant was the opposition to the idea that developed in the party ? The third question is what effect, if any, did domestic political opposition to the Common Market have on the French President's eventual veto of the project ?Except by implication, the third question is excluded from consideration here. Only a close student of French domestic politics is competent to evaluate how far, if at all, the hostility to the European idea in a section of the Conservative Party and the official objections of the Labour Party to British membership of EEC on any terms that then seemed negotiable, made it easier for the French President to impose his final veto. Conceivably, the possibility that a successor labour government might disown any treaty that the conservatives had signed may have played a marginal part in assisting the President's attitude in the final stages.
The European idea and national public opinion
Authors: Rabier Jacques-René 
Published: April 2007

Parallel with the efforts which have been made during the last fifteen or twenty years to build, in Churchill's words (1946) ‘a kind of United States of Europe’, much research has been undertaken to try to find out whether public opinion had followed the movement, or perhaps even anticipated it.I do not intend to recapitulate here in detail all these works, but merely to underline some of the problems which they raise, for the researchers as well as for the men of action and above all for those who, perhaps over-ambitiously, try to reconcile the concerns of the former with those of the latter.
Violent constitutionalism in Uganda
Authors: Engholm G. F. , Mazrui Ali A. 
Published: April 2007

From the country's independence until May 1966 two factors profoundly affected the nature of politics in Uganda. These were, first, a latent violence between groups and, secondly, a vigorous constitutionalism as a style of political contest. Both factors were, inevitably, connected with events and tendencies which went back to well before independence.The possibility of political violence in the country was linked to a few key issues. These included, first, the degree of autonomy to be enjoyed by Buganda as the largest and most developed region in the country; secondly, the unresolved problem of the Lost Counties of Bunyoro; thirdly, relations between the Baganda and other tribes, an issue which later culminated into an alleged Bantu/Nilotic cleavage; and fourthly, the tensions of party allegiances within the parliamentary system. We shall discuss these issues more fully later in this analysis.
Anarchists in Britain Today
Authors: Stafford David 
Published: April 2007

IN 1965 IT WAS POSSIBLE FOR THE AUTHOR OF AN ARTICLE ON THE anarchists in Britain to begin by observing that anarchists no longer figured in the popular consciousness and that the existence of anarchists could occasion as much polite surprise as the continued existence of the Independent Labour Party. This present article and its inclusion in a special issue on Anarchism is perhaps in part a proof that this situation is no longer true, and that anarchism has recently attracted sufficient attention to justify a new and closer look at anarchists in Britain today. It would hardly be rash to argue that whatever else may be true of the Left in Britain in 1970, the anarchists’ presence deserves to provoke much less polite surprise than it may have done five years ago.This article is not, however, a description of the shape and variety of anarchists and anarchist groups to be found in Britain today. It is rather an attempt to describe one particular facet of anarchist thought which has characterized anarchism in the 1960s and to relate this to the ‘anarchhation’ of the New Left described by James Joll in his concluding article. It is to that extent an extrapolation and abstraction from a very wide range of alternatives and undoubtedly presents a picture which many anarchists would not recognize or would repudiate.
The Permanent Representatives Committee and the ‘Deepening’ of the Communities
Authors: Noel Emile , Étienne Henri 
Published: April 2007

THE NINETEEN YEARS DURING WHICH THE TREATY OF PARIS HAS been in force and the thirteen years of the Treaties of Rome have led to a development in the Communities which, in its extent, variety and depth, exceeds anything the signatories could have hoped for. The volume of derived Community legislation has increased considerably and it now governs important sectors of economic activity. The enlargement of the Communities provides the best confirmation of this success.Furthermore, the dynamic force of the Community system has been such that the deepening of the Communities has extended far further than the areas delimited by the Treaty. More and more action has been undertaken in sectors at or beyond the limit of the Communities’ responsibilities – not to speak of decisions taken on ‘foreign policy’, which, since 1970, have led to the introduction of procedures for political co-operation.