Miracle-dz/UniFAR-FTUs huggingface dataset:
Common and Unique Neural Activations in Autobiographical, Episodic, and Semantic Retrieval

This study sought to explore the neural correlates that underlie autobiographical, episodic, and semantic memory. Autobiographical memory was defined as the conscious recollection of personally relevant events, episodic memory as the recall of stimuli presented in the laboratory, and semantic memory as the retrieval of factual information and general knowledge about the world. Our objective was to delineate common neural activations, reflecting a functional overlap, and unique neural activations, reflecting functional dissociation of these memory processes. We conducted an event-related functional magnetic resonance imaging study in which we utilized the same pictorial stimuli but manipulated retrieval demands to extract autobiographical, episodic, or semantic memories. The results show a functional overlap of the three types of memory retrieval in the inferior frontal gyrus, the middle frontal gyrus, the caudate nucleus, the thalamus, and the lingual gyrus. All memory conditions yielded activation of the left medial-temporal lobe; however, we found a functional dissociation within this region. The anterior and superior areas were active in episodic and semantic retrieval, whereas more posterior and inferior areas were active in autobiographical retrieval. Unique activations for each memory type were also delineated, including medial frontal increases for autobiographical, right middle frontal increases for episodic, and right inferior temporal increases for semantic retrieval. These findings suggest a common neural network underlying all declarative memory retrieval, as well as unique neural contributions reflecting the specific properties of retrieved memories.
Comparison of the effects of a high- and normal-casein breakfast on satiety, ‘satiety’ hormones, plasma amino acids and subsequent energy intake

The present study compared the effects of a high- and normal-casein-protein breakfast on satiety, ‘satiety’ hormones, plasma amino acid responses and subsequent energy intake. Twenty-five healthy subjects (BMI 23·9 (sem 0·3) kg/m2; age 22 (sem 1) years) received a subject-specific standardised breakfast (20 % of daily energy requirements): a custard with casein as the single protein source with either 10, 55 and 35 (normal-casein breakfast) or 25, 55 and 20 (high-casein breakfast) % of energy (En%) from protein, carbohydrate and fat respectively in a randomised, single-blind design. Appetite profile (visual analogue scale; VAS), plasma glucose, insulin, glucagon-like peptide 1, ghrelin and amino acid concentrations were determined for 4 h; here the sensitive moment in time for lunch was determined. Subjects came for a second set of experiments and received the same custards for breakfast, and an ad libitum lunch was offered at 180 min after breakfast; energy intake was assessed. There were increased scores of fullness and satiety after the 25 En% casein-custard compared with the 10 En% casein-custard, particularly at 180 min (26 (sem 4) v. 11 (sem 5) mm VAS; P < 0·01) and 240 min (13 (sem 5) v. − 1 (sem 5) mm VAS; P < 0·01). This coincided with prolonged elevated plasma amino acid concentrations; total amino acids and branched-chain amino acids were higher after the 25 En% casein-custard compared with the 10 En% casein-custard at 180 and 240 min (P < 0·001). There was no difference in energy intake (3080 (sem 229) v. 3133 (sem 226) kJ for 25 En% and 10 En% respectively; NS) from the ad libitum lunch. In conclusion, a breakfast with 25 % of energy from casein is rated as being more satiating than a breakfast with 10 % of energy from casein at 3 and 4 h after breakfast, coinciding with prolonged elevated concentrations of plasma amino acids, but does not reduce subsequent energy intake.
Sliced Inverse Regression with Regularizations

Summary In high‐dimensional data analysis, sliced inverse regression (SIR) has proven to be an effective dimension reduction tool and has enjoyed wide applications. The usual SIR, however, cannot work with problems where the number of predictors, p, exceeds the sample size, n, and can suffer when there is high collinearity among the predictors. In addition, the reduced dimensional space consists of linear combinations of all the original predictors and no variable selection is achieved. In this article, we propose a regularized SIR approach based on the least‐squares formulation of SIR. The L2 regularization is introduced, and an alternating least‐squares algorithm is developed, to enable SIR to work with n < p and highly correlated predictors. The L1 regularization is further introduced to achieve simultaneous reduction estimation and predictor selection. Both simulations and the analysis of a microarray expression data set demonstrate the usefulness of the proposed method.
Modification of Boc-Protected CAN508 via Acylation and Suzuki-Miyaura Coupling

The cyclin-dependent kinase inhibitor, CAN508, was protected with di-tert-butyl dicarbonate to access the amino-benzoylated pyrazoles. The bromo derivatives were further arylated by Suzuki-Miyaura coupling using the XPhos Pd G2 pre-catalyst. The coupling reaction provided generally the para-substituted benzoylpyrazoles in the higher yields than the meta-substituted ones. The Boc groups were only utilized as directing functionalities for the benzoylation step and were hydrolyzed under conditions of Suzuki-Miyaura coupling, which allowed for elimination of the additional deprotection step.
Evolving Clonal Adaptive Resonance Theory based on ECOS theory

The present work describes an evolution of the hybrid immune approach called Clonart (Clonal Adaptive Resonance Theory) using ECOS (Evolving Connectionist Systems) architectures. Some improvements were developed to allow the control of the growth of the clusters. Clonart's architecture is an Evolutionary Algorithm biologically inspired on the use of the Clonal Selection Principle. Therefore, a technique inspired on ART 1 network was combined to store the best antibodies. However, these strategies may create a lot of clusters due to the ART behavior. For that reason, techniques of insertion, aggregation and pruning inspired on ECOS operation were used to control the amount of clusters in Clonart. In this way, old and unnecessary clusters may confuse the Clonart and increase the learning error rate. This behavior was especially important, because many problems need constant retraining. The effectiveness of this approach was evaluated using ten databases from UCI Machine Learning Repository.
MHC Multimer-Guided and Cell Culture-Independent Isolation of Functional T Cell Receptors from Single Cells Facilitates TCR Identification for Immunotherapy

Adoptive therapy using T cells redirected to target tumor- or infection-associated antigens is a promising strategy that has curative potential and broad applicability. In order to accelerate the screening process for suitable antigen-specific T cell receptors (TCRs), we developed a new approach circumventing conventional in vitro expansion-based strategies. Direct isolation of paired full-length TCR sequences from non-expanded antigen-specific T cells was achieved by the establishment of a highly sensitive PCR-based T cell receptor single cell analysis method (TCR-SCAN). Using MHC multimer-labeled and single cell-sorted HCMV-specific T cells we demonstrate a high efficacy (approximately 25%) and target specificity of TCR-SCAN receptor identification. In combination with MHC-multimer based pre-enrichment steps, we were able to isolate TCRs specific for the oncogenes Her2/neu and WT1 even from very small populations (original precursor frequencies of down to 0.00005% of CD3+ T cells) without any cell culture step involved. Genetic re-expression of isolated receptors demonstrates their functionality and target specificity. We believe that this new strategy of TCR identification may provide broad access to specific TCRs for therapeutically relevant T cell epitopes.
Cultural Configuration of Wikipedia: measuring Autoreferentiality in Different Languages

Among the motivations to write in Wikipedia given by the current literature there is often coincidence, but none of the studies presents the hypothesis of contributing for the visibility of the own national or language related content. Similar to topical coverage studies, we outline a method which allows collecting the articles of this content, to later analyse them in several dimensions. To prove its universality, the tests are repeated for up to twenty language editions of Wikipedia. Finally, through the best indicators from each dimension we obtain an index which represents the degree of autoreferentiality of the encyclopedia. Last, we point out the impact of this fact and the risk of not considering its existence in the design of applications based on user generated content.
Neuroanatomic substrates of semantic memory impairment in Alzheimer's disease: Patterns of functional MRI activation

Impairment in semantic processing occurs early in Alzheimer's disease (AD) and differential impact on subtypes of semantic relations have been reported, yet there is little data on the neuroanatomic basis of these deficits. Patients with mild AD and healthy controls underwent 3 functional MRI auditory stimulation tasks requiring semantic or phonological decisions (match–mismatch) about word pairs (category–exemplar, category–function, pseudoword). Patients showed a significant performance deficit only on the exemplar task. On voxel-based fMRI activation analyses, controls showed a clear activation focus in the left superior temporal gyrus for the phonological task; patients showed additional foci in the left dorsolateral prefrontal and bilateral cingulate areas. On the semantic tasks, predominant activation foci were seen in the inferior and middle frontal gyrus (left greater than right) in both groups but patients showed additional activation suggesting compensatory recruitment of locally expanded foci and remote regions, for example, right frontal activation during the exemplar task. Covariance analyses indicated that exemplar task performance was strongly related to signal increase in bilateral medial prefrontal cortex. The authors conclude that fMRI can reveal similarities and differences in functional neuroanatomical processing of semantic and phonological information in mild AD compared to healthy elderly, and can help to bridge cognitive and neural investigations of the integrity of semantic networks in AD. (JINS, 1999, 5, 377–392.)
A third tal-1 promoter is specifically used in human T cell leukemias

A common feature of T cell acute lymphoblastic leukemias (T-ALLs) is the presence of structural alteration of the 5' part of the tal-1 locus, localized on chromosomal band 1p32. These alterations consist of either a t(1;14)(p32;q11) chromosomal translocation (3% of T-ALLs) or tald submicroscopic deletion (12-25% additional T-ALLs). We have characterized a case of T-ALL with t(1;14)(p32;q11) in which, unlike the majority of t(1;14), the recombination with the T cell receptor delta elements affected the 3' side of the tal-1 locus. In this case, tal-1 transcription is initiated from a promoter located within the fourth exon similarly to the DU 528 cell line. In a T-ALL bearing a t(1;14) affecting the 5' part of tal-1, two types of tal-1 transcripts were observed, namely those probably initiated from the D delta region juxtaposed to tal-1 by the translocation, and those from the exon 4 promoter. It is interesting that this exon 4 promotion was also found in leukemic T cell lines and T-ALL samples without apparent tal-1 genomic alteration. In contrast, no transcript initiated from the exon 4 promoter was found in T-ALL with tald1 or tald2 deletion. In these cells, tal-1 is expressed via SIL-tal-1 fused transcripts. Finally, this exon 4 initiation was detected neither in normal bone marrow, nor in malignant cells from the erythroid/megakaryocytic lineages. Taken as a whole, these data suggest that the exon 4 promoter is specifically active in T cell lineage.
Number of Cervical Examinations and Risk of Intrapartum Maternal Fever

OBJECTIVE: To estimate the association between number of cervical examinations and risk of maternal fever during term labor and delivery. METHODS: Within a 4-year retrospective cohort study of all consecutive term (37 weeks of gestation or more) singleton deliveries reaching the second stage of labor, we identified women who developed an intrapartum fever and compared them with women who remained afebrile through 6 hours postpartum. Primary exposure was number of digital cervical examinations. Extensive data were collected from the medical record, including obstetric and medical history, cervical examinations and timing, admitting diagnoses, and outcomes. Time-to-event analyses were used to account for length of labor. Cox proportional hazard models were developed adjusting for potentially confounding factors. RESULTS: Of 2,395 women who were afebrile at admission, 174 (7.2%) developed an intrapartum fever. Women were examined one to 14 times. There was no significant association between increasing number of examinations and risk of fever. Even for the 505 women who had more than seven examinations during labor, there was no statistically significant increased risk of fever (hazard ratio 0.9, 95% confidence interval 0.4–2.0) compared with those with one to three examinations. Subanalyses by labor type and examinations after rupture of membranes also showed no significant association between number of cervical examinations and risk of intrapartum fever. CONCLUSION: During term labor management, maternal fever risk is not significantly increased by the number of cervical examinations. LEVEL OF EVIDENCE: II
The Problem of Handwritten Mathematical Expression Recognition Evaluation

We discuss in this paper some issues related to the problem of mathematical expression recognition. The very first important issue is to define how to ground truth a dataset of handwritten mathematical expressions, and next we have to face the problem of benchmarking systems. We propose to define some indicators and the way to compute them so as they reflect the actual performances of a given system.
Regional and Ultrastructural Immunolocalization of Copper-Zinc Superoxide Dismutase in Rat Central Nervous System

We examined the distribution of copper-zinc superoxide dismutase (CuZn-SOD) in adult rat central nervous system by light and electron microscopic immunocytochemistry, using an affinity-purified polyclonal antibody. The enzyme appeared to be exclusively localized in neurons. No immunoreactivity was seen in non-neuronal cells. The staining intensity was variable, depending on the brain region and, within the same region, on the neuron type. Highly immunoreactive elements included cortical neurons evenly distributed in the different layers, hippocampal interneurons, neurons of the reticular thalamic nucleus, and Golgi, stellate, and basket cells of the cerebellar cortex. Other neurons, i.e., pyramidal cells of the neocortex and hippocampus, Purkinje and granule cells of the cerebellar cortex, and the majority of thalamic neurons, showed much weaker staining. In the spinal cord, intense CuZnSOD immunoreactivity was present in many neurons, including motor neurons. Pre-embedding immunoelectron microscopy of the neocortex, hippocampus, reticular thalamic nucleus, and cerebellar cortex showed cytosolic and nucleoplasmic labeling. Moreover, single membrane-limited immunoreactive organelles identified as peroxisomes were often found, even in neurons that appeared weakly stained at the light microscopic level. In double immunogold labeling experiments, particulate CuZn-SOD immunoreactivity co-localized with catalase, a marker enzyme for peroxisomes, thus demonstrating that in neural tissue CuZnSOD is also present in peroxisomes.
Effect of Tomato Nutrient Complex on Blood Pressure: A Double Blind, Randomized Dose–Response Study

Oxidative stress is implicated in the pathogenesis of essential hypertension, a risk factor for cardiovascular morbidity and mortality. Tomato carotenoids such as lycopene and the colorless carotenoids phytoene and phytofluene induce the antioxidant defense mechanism. This double-blind, randomized, placebo-controlled study aimed to find effective doses of Tomato Nutrient Complex (TNC) to maintain normal blood pressure in untreated hypertensive individuals. The effect of TNC treatment (5, 15 and 30 mg lycopene) was compared with 15 mg of synthetic lycopene and a placebo over eight weeks. Results indicate that only TNC treatment standardized for 15 or 30 mg of lycopene was associated with significant reductions in mean systolic blood pressure (SBP). Treatment with the lower dose standardized for 5 mg of lycopene or treatment with 15 mg of synthetic lycopene as a standalone had no significant effect. To test carotenoid bioavailability, volunteers were treated for four weeks with TNC providing 2, 5 or 15 mg lycopene. The increase in blood levels of lycopene, phytoene, and phytofluene was dose dependent. Results suggest that only carotenoid levels achieved by the TNC dose of 15 mg lycopene or higher correlate to a beneficial effect on SBP in hypertensive subjects while lower doses and lycopene alone do not.
Suggested Shape for a First Generation Endovascular Untethered Microdevice Prototype

Shape design optimization for an untethered microdevice meant to navigate in the human bloodstream is studied based on previous variational finite element (FE) work done. The suggested shape for a first generation prototype is a prolate spheroid design, which enables to minimize the drag force and to maximize the use of the MRI's magnetic gradients
Nonexpansive pyramid for image coding using a nonlinear filterbank

A nonexpansive pyramidal decomposition is proposed for low-complexity image coding. The image is decomposed through a nonlinear filterbank into low- and highpass signals and the recursion of the filterbank over the lowpass signal generates a pyramid resembling that of the octave wavelet transform. The structure itself guarantees perfect reconstruction and we have chosen nonlinear filters for performance reasons. The transformed samples are grouped into square blocks and used to replace the discrete cosine transform (DCT) in the Joint Photographic Expert Group (JPEG) coder. The proposed coder has some advantages over the DCT-based JPEG: computation is greatly reduced, image edges are better encoded, blocking is eliminated, and it allows lossless coding.
The Regulatory Effects of Tropomyosin and Troponin-I on the Interaction of Myosin Loop Regions with F-actin*

The N terminus of skeletal myosin light chain 1 and the cardiomyopathy loop of human cardiac myosin have been shown previously to bind to actin in the presence and absence of tropomyosin (Patchell, V. B., Gallon, C. E., Hodgkin, M. A., Fattoum, A., Perry, S. V., and Levine, B. A. (2002) Eur. J. Biochem. 269, 5088–5100). We have extended this work and have shown that segments corresponding to other regions of human cardiac β-myosin, presumed to be sites of interaction with F-actin (residues 554–584, 622–646, and 633–660), likewise bind independently to actin under similar conditions. The binding to F-actin of a peptide spanning the minimal inhibitory segment of human cardiac troponin I (residues 134–147) resulted in the dissociation from F-actin of all the myosin peptides bound to it either individually or in combination. Troponin C neutralized the effect of the inhibitory peptide on the binding of the myosin peptides to F-actin. We conclude that the binding of the inhibitory region of troponin I to actin, which occurs during relaxation in muscle when the calcium concentration is low, imposes conformational changes that are propagated to different locations on the surface of actin. We suggest that the role of tropomyosin is to facilitate the transmission of structural changes along the F-actin filament so that the monomers within a structural unit are able to interact with myosin.
Drug Abuse and Addiction in Medical Illness:: Causes, Consequences, and Treatment

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Efflux Pump Gene Expression in Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolates

Isoniazid (INH) and rifampicin (RIF) are the two most effective drugs in tuberculosis therapy. Understanding the molecular mechanisms of resistance to these two drugs is essential to quickly diagnose multidrug-resistant (MDR) tuberculosis and extensive drug-resistant tuberculosis. Nine clinical Mycobacterium tuberculosis isolates resistant to only INH and RIF and 10 clinical pan-sensitive isolates were included to evaluate the expression of 20 putative drug efflux pump genes and sequence mutations in rpoB (RIF), katG (INH), the inhA promoter (INH), and oxyR-ahpC (INH). Nine and three MDR isolates were induced to overexpress efflux pump genes by INH and RIF, respectively. Eight and two efflux pump genes were induced to overexpress by INH and RIF in MDR isolates, respectively. drrA, drrB, efpA, jefA (Rv2459), mmr, Rv0849, Rv1634, and Rv1250 were overexpressed under INH or RIF stress. Most efflux pump genes were overexpressed under INH stress in a MDR isolates that carried the wild-type katG, inhA, and oxyR-ahpC associated with INH resistance than in those that carried mutations. The expression levels of 11 genes (efpA, Rv0849, Rv1250, P55 (Rv1410c), Rv1634, Rv2994, stp, Rv2459, pstB, drrA, and drrB) without drug inducement were significantly higher (P < 0.05) in nine MDR isolates than in 10 pan-sensitive isolates. In conclusion, efflux pumps may play an important role in INH acquired resistance in MDR M. tuberculosis, especially in those strains having no mutations in genes associated with INH resistance; basal expression levels of some efflux pump genes are higher in MDR isolates than in pan-sensitive isolates and the basal expressional differences may be helpful to diagnose and treat resistant tuberculosis.
Gene expression profiling during the embryo‐to‐larva transition in the giant red sea urchin Mesocentrotus franciscanus

Abstract In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo‐to‐larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins. From these transcripts, ~80% were functionally annotated allowing the identification of ~2,600 functional, structural, and regulatory genes involved in developmental process. Analysis of expression profiles between gastrula and pluteus stages of M. franciscanus revealed 791 differentially expressed genes with 251 GO overrepresented terms. For gastrula, up‐regulated GO terms were mainly linked to cell differentiation and signal transduction involved in cell cycle checkpoints. In the pluteus stage, major GO terms were associated with phosphoprotein phosphatase activity, muscle contraction, and olfactory behavior, among others. Our evolutionary comparative analysis revealed that several of these genes and functional pathways are highly conserved among echinoids, holothuroids, and ophiuroids.