Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge Maintenance Heresies: Meta-Knowledge Complicates KM

The role of a discussion paper is to provoke discussion. Hence, my comments will be heretical rather than theoretical. For the theory, see [19]. Today I want to say two things. Firstly, the knowledge maintenance (KM) problem is our next big challenge. A common method for tackling the KM problem is to use some type of meta-knowledge to represent expected/unexpected or good/bad knowledge. This metaknowledge takes many forms including architectures [26], patterns [12], problem solving methods (PSMs) [29, 31], or ontologies [13]. Elsewhere [20], I have argued that patterns of design and architecture are very similar to PSMs and ontologies:
Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image Guided Neurosurgery

We aimed to study the performance of a parallel implementation of an intraoperative nonrigid registration algorithm that accurately simulates the biomechanical properties of the brain and its deformations during surgery. The algorithm was designed to allow for improved surgical navigation and quantitative monitoring of treatment progress in order to improve the surgical outcome and to reduce the time required in the operating room. We have applied the algorithm to two neurosurgery cases with promising results. High performance computing is a key enabling technology that allows the biomechanical simulation to be executed quickly enough for the algorithm to be practical. Our parallel implementation was evaluated on a symmetric multi-processor and two clusters and exhibited similar performance characteristics on each. The implementation was sufficiently fast to be used in the operating room during a neurosurgery procedure. It allowed a three-dimensional volumetric deformation to be simulated in less than ten seconds.
Female Autonomy and Education of the Subsequent Generation: Evidence from India

The paper uses discrete time duration models and a latent factor structural model to look at the influence of female autonomy on the age at which children enrol in school. Female autonomy is defined as the extent to which a woman can influence decisions taken by the household she lives in. Data come from the third round of the National Family Health Survey for India, 2005/2006. A woman’s autonomy is found to positively influence her children’s enrolment. This effect is particularly pronounced in the northern states of India, which are characterised both by lower enrolment rates and lower female autonomy.
Recent Advances in Understanding Competitive Markets

The Arrow-Debreu model of competitive markets has proven to be a remarkably rich and °exible foundation for studying an array of important economic problems, ranging from social security reform to the determinants of long-run growth. Central to the study of such questions are many of the extensions and modi ̄cations of the classic Arrow-Debreu framework that have been advanced over the last 40 years. These include dynamic models of exchange over time, as in overlapping generations or continuous time, and under uncertainty, as in incomplete ̄nancial markets. Many of the most interesting and important recent advances have been spurred by questions about the role of markets in allocating resources and providing opportunities for risksharing arising in ̄nance and macroeconomics. This article is intended to give an overview of some of these more recent developments in theoretical work involving competitive markets, and highlight some promising areas for future work.
Electrostatic Control and Chloride Regulation of the Fast Gating of ClC-0 Chloride Channels

The opening and closing of chloride (Cl−) channels in the ClC family are thought to tightly couple to ion permeation through the channel pore. In the prototype channel of the family, the ClC-0 channel from the Torpedo electric organ, the opening-closing of the pore in the millisecond time range known as “fast gating” is regulated by both external and internal Cl− ions. Although the external Cl− effect on the fast-gate opening has been extensively studied at a quantitative level, the internal Cl− regulation remains to be characterized. In this study, we examine the internal Cl− effects and the electrostatic controls of the fast-gating mechanism. While having little effect on the opening rate, raising [Cl−]i reduces the closing rate (or increases the open time) of the fast gate, with an apparent affinity of >1 M, a value very different from the one observed in the external Cl− regulation on the opening rate. Mutating charged residues in the pore also changes the fast-gating properties—the effects are more prominent on the closing rate than on the opening rate, a phenomenon similar to the effect of [Cl−]i on the fast gating. Thus, the alteration of fast-gate closing by charge mutations may come from a combination of two effects: a direct electrostatic interaction between the manipulated charge and the negatively charged glutamate gate and a repulsive force on the gate mediated by the permeant ion. Likewise, the regulations of internal Cl− on the fast gating may also be due to the competition of Cl− with the glutamate gate as well as the overall more negative potential brought to the pore by the binding of Cl−. In contrast, the opening rate of the fast gate is only minimally affected by manipulations of [Cl−]i and charges in the inner pore region. The very different nature of external and internal Cl− regulations on the fast gating thus may suggest that the opening and the closing of the fast gate are not microscopically reversible processes, but form a nonequilibrium cycle in the ClC-0 fast-gating mechanism.
Parallel Loss-of-Function at the RPM1 Bacterial Resistance Locus in Arabidopsis thaliana

Dimorphism at the Resistance to Pseudomonas syringae pv. maculicola 1 (RPM1) locus is well documented in natural populations of Arabidopsis thaliana and has been portrayed as a long-term balanced polymorphism. The haplotype from resistant plants contains the RPM1 gene, which enables these plants to recognize at least two structurally unrelated bacterial effector proteins (AvrB and AvrRpm1) from bacterial crop pathogens. A complete deletion of the RPM1 coding sequence has been interpreted as a single event resulting in susceptibility in these individuals. Consequently, the ability to revert to resistance or for alternative R-gene specificities to evolve at this locus has also been lost in these individuals. Our survey of variation at the RPM1 locus in a large species-wide sample of A. thaliana has revealed four new loss-of-function alleles that contain most of the intervening sequence of the RPM1 open reading frame. Multiple loss-of-function alleles may have originated due to the reported intrinsic cost to plants expressing the RPM1 protein. The frequency and geographic distribution of rpm1 alleles observed in our survey indicate the parallel origin and maintenance of these loss-of-function mutations and reveal a more complex history of natural selection at this locus than previously thought.
Power issues related to branch prediction

This paper explores the role of branch predictor organization in power/energy/performance tradeoffs for processor design. We find that as a general rule, to reduce overall energy consumption in the processor it is worthwhile to spend more power in the branch predictor if this results in more accurate predictions that improve running time. Two techniques, however, provide substantial reductions in power dissipation without harming accuracy. Banking reduces the portion of the branch predictor that is active at any one time. And a new on-chip structure, the prediction probe detector (PPD), can use pre-decode bits to entirely eliminate unnecessary predictor and branch target buffer (BTB) accesses. Despite the extra power that must be spent accessing the PPD, it reduces local predictor power and energy dissipation by about 45% and overall processor power and energy dissipation by 5-6%.
Evaluation of Microarray Preprocessing Algorithms Based on Concordance with RT-PCR in Clinical Samples

Background Several preprocessing algorithms for Affymetrix gene expression microarrays have been developed, and their performance on spike-in data sets has been evaluated previously. However, a comprehensive comparison of preprocessing algorithms on samples taken under research conditions has not been performed. Methodology/Principal Findings We used TaqMan RT-PCR arrays as a reference to evaluate the accuracy of expression values from Affymetrix microarrays in two experimental data sets: one comprising 84 genes in 36 colon biopsies, and the other comprising 75 genes in 29 cancer cell lines. We evaluated consistency using the Pearson correlation between measurements obtained on the two platforms. Also, we introduce the log-ratio discrepancy as a more relevant measure of discordance between gene expression platforms. Of nine preprocessing algorithms tested, PLIER+16 produced expression values that were most consistent with RT-PCR measurements, although the difference in performance between most of the algorithms was not statistically significant. Conclusions/Significance Our results support the choice of PLIER+16 for the preprocessing of clinical Affymetrix microarray data. However, other algorithms performed similarly and are probably also good choices.
Significant Role for ladC in Initiation of Legionella pneumophila Infection

ABSTRACT Previously, we identified ladC in a cohort of genes that were present in Legionella pneumophila but absent in other Legionella species. Here we constructed a ladC mutant of L. pneumophila and assessed its ability to replicate in mammalian cell lines and Acanthamoeba castellanii. The ladC mutant was recovered in significantly lower numbers than wild-type L. pneumophila at early time points, which was reversed upon transcomplementation with ladC but not ladCN430A/R434A, encoding a putative catalytically inactive derivative of the protein. In fact, complementation of ladC::Km with ladCN430A/R434A resulted in a severe replication defect within human and amoeba cell models of infection, which did not follow a typical dominant negative phenotype. Using differential immunofluorescence staining to distinguish adherent from intracellular bacteria, we found that the ladC mutant exhibited a 10-fold reduction in adherence to THP-1 macrophages but no difference in uptake by THP-1 cells. When tested in vivo in A/J mice, the competitive index of the ladC mutant dropped fivefold over 72 h, indicating a significant attenuation compared to wild-type L. pneumophila. Although localization of LadC to the bacterial inner membrane suggested that the protein may be involved in signaling pathways that regulate virulence gene expression, microarray analysis indicated that ladC does not influence the transcriptional profile of L. pneumophila in vitro or during A. castellanii infection. Although the mechanism by which LadC modulates the initial interaction between the bacterium and host cell remains unclear, we have established that LadC plays an important role in L. pneumophila infection.
Elevated left and reduced right orbitomedial prefrontal fractional anisotropy in adults with bipolar disorder revealed by tract-based spatial statistics.

CONTEXT Diffusion tensor imaging (DTI) studies in adults with bipolar disorder (BD) indicate altered white matter (WM) in the orbitomedial prefrontal cortex (OMPFC), potentially underlying abnormal prefrontal corticolimbic connectivity and mood dysregulation in BD. OBJECTIVE To use tract-based spatial statistics (TBSS) to examine WM skeleton (ie, the most compact whole-brain WM) in subjects with BD vs healthy control subjects. DESIGN Cross-sectional, case-control, whole-brain DTI using TBSS. SETTING University research institute. PARTICIPANTS Fifty-six individuals, 31 having a DSM-IV diagnosis of BD type I (mean age, 35.9 years [age range, 24-52 years]) and 25 controls (mean age, 29.5 years [age range, 19-52 years]). MAIN OUTCOME MEASURES Fractional anisotropy (FA) longitudinal and radial diffusivities in subjects with BD vs controls (covarying for age) and their relationships with clinical and demographic variables. RESULTS Subjects with BD vs controls had significantly greater FA (t > 3.0, P <or= .05 corrected) in the left uncinate fasciculus (reduced radial diffusivity distally and increased longitudinal diffusivity centrally), left optic radiation (increased longitudinal diffusivity), and right anterothalamic radiation (no significant diffusivity change). Subjects with BD vs controls had significantly reduced FA (t > 3.0, P <or= .05 corrected) in the right uncinate fasciculus (greater radial diffusivity). Among subjects with BD, significant negative correlations (P < .01) were found between age and FA in bilateral uncinate fasciculi and in the right anterothalamic radiation, as well as between medication load and FA in the left optic radiation. Decreased FA (P < .01) was observed in the left optic radiation and in the right anterothalamic radiation among subjects with BD taking vs those not taking mood stabilizers, as well as in the left optic radiation among depressed vs remitted subjects with BD. Subjects having BD with vs without lifetime alcohol or other drug abuse had significantly decreased FA in the left uncinate fasciculus. CONCLUSIONS To our knowledge, this is the first study to use TBSS to examine WM in subjects with BD. Subjects with BD vs controls showed greater WM FA in the left OMPFC that diminished with age and with alcohol or other drug abuse, as well as reduced WM FA in the right OMPFC. Mood stabilizers and depressed episode reduced WM FA in left-sided sensory visual processing regions among subjects with BD. Abnormal right vs left asymmetry in FA in OMPFC WM among subjects with BD, likely reflecting increased proportions of left-sided longitudinally aligned and right-sided obliquely aligned myelinated fibers, may represent a biologic mechanism for mood dysregulation in BD.
Attachment and abandonment : a study of factors contributing to, or hindering, the development of trust and functional family behaviour

This research examines the lives of individual children and adults of diverse ages and ethnicities, who suffer common and uncommon abandonment. The study employs a naturalistic “inquiry from the inside” approach and involves intensive participant observation on the part of the researcher. This allows a form of research to emerge that is longitudinal and dialogical. It includes the collection and analysis of the life histories of participants and allows for comparisons and shared experiences. The depth of involvement of the researcher in the participants’ lives, together with analysis of their experiences, combine to form a unique methodological model, generating a deeper and more nuanced understanding than commonly available of how the abandoned person views their world, while moving toward relational connection. Analysis of the life histories, field notes, observations and interviews, in concert with ethnographic field data, yield a progressive pattern of trust and development of relationship. In this process, the language, stages and steps of a non-clinical model of intervention emerges within the life experiences of the individual participants. The resulting paradigm applies most directly to individuals challenged by abandonment, and to their family structure, with the potential application for social agencies (governmental and nongovernmental) and institutional models of care. The research offers two contributions to the field of study addressing the lived experience of formerly abandoned children and their families including: (1) extended understanding of the phenomenon of attachment through a holistic and dynamic approach to the attachment process, involving life history and ethnographic examination and (2) a coherent model of intervention revealing the development from abandonment to relational connection. This includes responses of the participant to availability and empathy, and reveals a progression from survival through vulnerability and trust, to authenticity and relational connection.
#SarcasmDetection Is Soooo General! Towards a Domain-Independent Approach for Detecting Sarcasm

Automatic sarcasm detection methods have traditionally been designed for maximum performance on a specific domain. This poses challenges for those wishing to transfer those approaches to other existing or novel domains, which may be typified by very different language characteristics. We develop a general set of features and evaluate it under different training scenarios utilizing in-domain and/or out-of-domain training data. The best-performing scenario, training on both while employing a domain adaptation step, achieves an F1 of 0.780, which is well above baseline F1-measures of 0.515 and 0.345. We also show that the approach outperforms the best results from prior work on the same target domain.
Molecular cloning and characterization of a 21 kDa protein secreted from Trichinella pseudospiralis

Recombinant protein was produced from the cDNA library of Trichinella pseudospiralis, which seemed to form part of the excretory–secretory (ES) products. The library was constructed from cDNA of muscle larvae at 1 month post-infection, and immunoscreened with antibody against T. pseudospiralis ES products. A clone, designated Tp21-3, contained a cDNA transcript of 657 bp in length with a single open reading frame, which encoded 172 amino acids (19617 Da in the estimated molecular mass). The predicted amino acid sequence of clone Tp21-3 had a similarity of 76% to that of clone ORF 17.20 (GenBank under accession number U88239) from T. spiralis. The recombinant fusion proteins encoded by clone Tp21-3 were produced in an Escherichia coli expression system and affinity purified. On Western blotting analysis, Tp21-3 recombinant proteins migrated at 40 kDa and reacted to antibody against T. pseudospiralis ES products and T. pseudospiralis-infected sera. Sera were developed against Tp 21-3 recombinant proteins, which reacted to a single band migrating at 21 kDa in crude worm extract and ES products from T. pseudospiralis on Western blotting analysis, and reacted with stichocytes of T. pseudospiralis on immunohistochemical staining.
Negative symptoms: a path analytic approach to a double-blind, placebo- and haloperidol-controlled clinical trial with olanzapine.

OBJECTIVE The authors investigated whether primary negative symptoms of schizophrenia are enduring or treatment-responsive. METHODS Previously, a double-blind, random-assignment trial of the novel antipsychotic olanzapine (in low, medium, and high dose ranges), placebo, or haloperidol (10-20 mg/day) for 335 schizophrenic inpatients was conducted for up to 52 weeks. Changes in the treatment groups from baseline to endpoint in summary scores on the Scale for the Assessment of Negative Symptoms (SANS) and several secondary measures were compared. This article describes a path analysis to determine to what extent the total treatment effect on negative symptoms was direct or indirect (i.e., mediated by differential effects on positive symptoms, extrapyramidal symptoms, or mood). RESULTS Significantly greater improvement was achieved with high-dose olanzapine than with placebo or haloperidol. Olanzapine had a significantly greater direct effect than placebo on all SANS dimensions except anhedonia-asociality. Olanzapine also demonstrated a significantly greater direct effect than haloperidol on negative symptoms, especially on the dimensions of affective flattening and avolition-apathy. Olanzapine's superior effects were replicated in a subgroup with SANS-defined prominent negative symptoms (N = 116) and a subgroup with a BPRS-defined cross-sectional proxy for the deficit state (N = 117). CONCLUSIONS These results suggest that the negative symptoms of schizophrenia are directly responsive to treatment. The significantly greater direct and indirect effects of olanzapine than of haloperidol on negative symptoms are likely related to olanzapine's pleotrophic pharmacology, which includes dopaminergic, serotonergic, muscarinic, and adrenergic activities. The results contribute to the hypothesis that negative symptoms may be under the influence of several neurotransmitters within one or more neuroanatomic circuits.
Procedural Metacognition and False Belief Understanding in 3- to 5-Year-Old Children

Some studies, so far limited in number, suggest the existence of procedural metacognition in young children, that is, the practical capacity to monitor and control one’s own cognitive activity in a given task. The link between procedural metacognition and false belief understanding is currently under theoretical discussion. If data with primates seem to indicate that procedural metacognition and false belief understanding are not related, no study in developmental psychology has investigated this relation in young children. The present paper aims, first, to supplement the findings concerning young children’s abilities to monitor and control their uncertainty (procedural metacognition) and, second, to explore the relation between procedural metacognition and false belief understanding. To examine this, 82 3- to 5-year-old children were presented with an opt-out task and with 3 false belief tasks. Results show that children can rely on procedural metacognition to evaluate their perceptual access to information, and that success in false belief tasks does not seem related to success in the task we used to evaluate procedural metacognition. These results are coherent with a procedural view of metacognition, and are discussed in the light of recent data from primatology and developmental psychology.
Chromothripsis in Hodgkin lymphoma

Chromosomal rearrangements are common features of most cancers, where they contribute to deregulated gene expression. Chromothripsis is a recently described oncogenic mechanism whereby small genomic pieces originating from one chromosomal region undergo massive rearrangements in a single step. Here, we document chromothripsis in Hodgkin lymphoma (HL) cell lines by genomic profiling, showing alternating amplicons of defined chromosomal regions. In L‐1236 cells, fluorescent in situ hybridization analyses identified aberrations affecting amplified chromosomal segments that derived from the long arm regions of chromosomes 3 and 9 and that colocalized to a derivative chromosome 6, indicating the cataclysmic origin of this mutation. The ABL1 gene at 9q34 was targeted by these rearrangements leading to its overexpression in L‐1236 cells, correlating with pharmacological resistance to treatment with the kinase inhibitor dasatinib. Collectively, we identified and characterized chromothriptic rearrangements in HL cell lines to serve as models for analyzing this novel oncogenomic mechanism. © 2013 Wiley Periodicals, Inc.
17β‐estradiol (E2) induces cdc25A gene expression in breast cancer cells by genomic and non‐genomic pathways

Cdc25A is a potent tyrosine phosphatase that catalyzes specific dephosphorylation of cyclin/cyclin‐dependent kinase (cdk) complexes to regulate G1 to S‐phase cell cycle progression. Cdc25A mRNA levels are induced by 17β‐estradiol (E2) in ZR‐75 breast cancer cells, and deletion analysis of the cdc25A promoter identified the −151 to −12 region as the minimal E2‐responsive sequence. Subsequent mutation/deletion analysis showed that at least three different cis‐elements were involved in activation of cdc25A by E2, namely, GC‐rich Sp1 binding sites, CCAAT motifs that bind NF‐Y, and E2F sites that bind DP/E2F1 proteins. Studies with inhibitors and dominant negative expression plasmids show that E2 activates cdc25A expression through activation of genomic ERα/Sp1 and E2F1 and cAMP‐dependent activation of NF‐YA. Thus, both genomic and non‐genomic pathways of estrogen action are involved in induction of cdc25A in breast cancer cells. J. Cell. Biochem. © 2006 Wiley‐Liss, Inc.