Miracle-dz/UniFAR-FTUs huggingface dataset:
Corticopulvinar connections of areas V5, V4, and V3 in the macaque monkey: A dual model of retinal and cortical topographies

The connection zones of cortical areas V3, V4, and V5 (MT) with the thalamic pulvinar nucleus in the macaque monkey were identified. A combination of single‐ and dual‐tracer techniques was used to study their topography and to establish whether these zones occupy separate or overlapping pulvinar territories. In each case, the retinotopic distribution of tracer in the pulvinar was charted by reference to its parallel distribution within the maps of cortical areas V1 and V2. Each of the areas V3, V4, and V5 were found to connect with both the 1° and the 2° maps located within the inferior and lateral pulvinar nuclei and to respect the previously identified topographies of these maps. However, V5 connects to a narrow zone lining the rostrolateral margin of the lateral and inferior pulvinar and V4 to a broader zone within the body of these two nuclei, which is adjacent to but separate from the V5 zone; the V3 zone overlaps both. Focal injections into cortex produce columns of pulvinar label whose trajectory defines a line of isorepresentation. The lines of isorepresentation in the 1° and 2° maps are approximately linear and parallel and adopt a rostrolateral to caudomedial axis; in the 1° map, this axis is roughly perpendicular to the facet of the inferior pulvinar that lies adjacent to the lateral geniculate nucleus. The connections of V5 and V4 can be modelled as successive zones along the axis of isorepresentation, with registered visual topographies. The scheme is extended by existing reports that inferotemporal cortex connects to the caudomedial pole of this axis—reflecting an occipitotemporal cortical gradient, in that V1 and other prestriate areas, e.g., V3, connect to the opposite pole. Thus a simple model of the mapped volume in the pulvinar arises, in which a unidimensional cortical topography is represented orthogonally to retinal topography. Adjoining this volume medially, within the inferior and medial pulvinar, is a second, heavier zone of V5 connectivity, which is poorly topographic. Both the medial and the rostrolateral zones of V5 connectivity may overlap with previously identified regions of tectal input to the pulvinar.J. Comp. Neurol. 439:469–490, 2001. © 2001 Wiley‐Liss, Inc.
DNA Gyrase-mediated Wrapping of the DNA Strand Is Required for the Replication Fork Arrest by the DNA Gyrase-Quinolone-DNA Ternary Complex*

The ability of DNA gyrase (Gyr) to wrap the DNA strand around itself allows Gyr to introduce negative supercoils into DNA molecules. It has been demonstrated that the deletion of the C-terminal DNA-binding domain of the GyrA subunit abolishes the ability of Gyr to wrap the DNA strand and catalyze the supercoiling reaction (Kampranis, S. C., and Maxwell, A. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 14416–14421). By using this mutant Gyr, Gyr (A59), we have studied effects of Gyr-mediated wrapping of the DNA strand on its replicative function and its interaction with the quinolone antibacterial drugs. We find that Gyr (A59) can support oriC DNA replication in vitro. However, Gyr (A59)-catalyzed decatenation activity is not efficient enough to complete the decatenation of replicating daughter DNA molecules. As is the case with topoisomerase IV, the active cleavage and reunion activity of Gyr is required for the formation of the ternary complex that can arrest replication fork progression in vitro. Although the quinolone drugs stimulate the covalent Gyr (A59)-DNA complex formation, the Gyr (A59)-quinolone-DNA ternary complexes do not arrest the progression of replication forks. Thus, the quinolone-induced covalent topoisomerase-DNA complex formation is necessary but not sufficient to cause the inhibition of DNA replication. We also assess the stability of ternary complexes formed with Gyr (A59), the wild type Gyr, or topoisomerase IV. The ternary complexes formed with Gyr (A59) are more sensitive to salt than those formed with either the wild type Gyr or topoisomerase IV. Furthermore, a competition experiment demonstrates that the ternary complexes formed with Gyr (A59) readily disassociate from the DNA, whereas the ternary complexes formed with either the wild type Gyr or topoisomerase IV remain stably bound. Thus, Gyr-mediated wrapping of the DNA strand is required for the formation of the stable Gyr-quinolone-DNA ternary complex that can arrest replication fork progression.
Early and Sustained Changes in Bone Metabolism After Severe Burn Injury.

CONTEXT Severe burn injury causes a massive stress response, consecutively heightened serum levels of acute phase proteins, cortisol, and catecholamines with accompanying disturbance in calcium metabolism. OBJECTIVE Evaluation of early and prolonged changes of serum bone turnover markers (BTMs) and regulators of bone metabolism. DESIGN Longitudinal observational design. SETTING University clinic. PATIENTS A total of 32 male patients with a median age of 40.5 years and a median burned total body surface area of 40% (83% patients with full thickness burn injury). INTERVENTIONS None. MAIN OUTCOME MEASURES Comparison of changes of BTM/regulators of bone metabolism in the early (d 2–7) and prolonged (d 7–56) phases after trauma. RESULTS All investigated BTM/regulators significantly changed. During the early phase, pronounced increases were observed for serum type 1 collagen cross-linked C-telopeptide, intact N-terminal propeptide of type I procollagen, sclerostin, Dickkopf-1, bone-specific alkaline phosphatase, fibroblast growth factor 23, and intact parathyroid hormone levels, whereas 25-hydroxyvitamin D, albumin, serum, and ionized calcium levels decreased. Changes of osteoprotegerin, osteocalcin, and phosphate were less pronounced but remained significant. In the prolonged phase, changes of intact N-terminal propeptide of type I procollagen were most pronounced, followed by elevated sclerostin, osteocalcin, bone-specific alkaline phosphatase, and lesser changes for albumin levels. Calcium and ionized calcium levels tardily increased and remained within the limit of normal. In contrast, levels of intact parathyroid hormone, fibroblast growth factor 23, C-reactive protein, and to a lesser extent serum type 1 collagen cross-linked C-telopeptide and phosphate levels declined significantly during this phase of investigation. CONCLUSIONS Ongoing changes of BTM and regulators of bone metabolism suggest alterations in bone metabolism with a likely adverse influence on bone quality and structure in male patients with severe burn injuries.
OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale

The Open Microscopy Environment (OME) has built and released Bio-Formats, a Java-based proprietary file format conversion tool and OMERO, an enterprise data management platform under open source licenses. In this report, we describe new versions of Bio-Formats and OMERO that are specifically designed to support large, multi-gigabyte or terabyte scale datasets that are routinely collected across most domains of biological and biomedical research. Bio- Formats reads image data directly from native proprietary formats, bypassing the need for conversion into a standard format. It implements the concept of a file set, a container that defines the contents of multi-dimensional data comprised of many files. OMERO uses Bio-Formats to read files natively, and provides a flexible access mechanism that supports several different storage and access strategies. These new capabilities of OMERO and Bio-Formats make them especially useful for use in imaging applications like digital pathology, high content screening and light sheet microscopy that create routinely large datasets that must be managed and analyzed.
Unsatisfying Walks : Solving False QBFs with Local Search

In the past few years, we have seen significant progress in the area of Boolean satisfiability (SAT) solving and its applications. More recently, new effo rts have focused on developing solvers for Quantified Boolean Formulas (QBFs). Recent QBF e valuation results show that developing practical QBF solvers is more challenging than o ne might expect. Even relatively small QBF problems are sometimes beyond the reach of current QBF solvers. We present a new approach for solving unsatisfiable two-alternation QBF s. Our approach is able to solve hard random QBF formulas that other current algorithms cann ot handle. Our solverWalkMinQBF combines the power of stochastic local search methods and co mplete SAT solvers. The solver is incomplete, in that it outpu ts unsat if a certificate forunsatisfiability is found, otherwise it outputs unknown. We test our solver on the model for random formulas introduced in [3] and the Models A and B intro duced in [8]. We compare WalkMinQBF with the state-of-the-art QBF solvers Ssolve andQuBE-BJ. We show that WalkMinQBF outperformsSsolve andQuBE-BJ in time and in the number of formulas solved. We believe our work provides new heuristic insights t at should be useful in complete QBF solvers. As a side result we have developed a stochastic l ocal search algorithm for the minimum unsatisfiability problem (MIN-SAT).
ViPER: augmenting automatic information extraction with visual perceptions

In this paper we address the problem of unsupervised Web data extraction. We show that unsupervised Web data extraction becomes feasible when supposing pages that are made up of repetitive patterns, as it is the case, e.g., for search engine result pages. Hereby the extraction rules are generated automatically without any training or human interaction, by means of operating on the DOM tree respectively the flat tag token sequence of a single page.Our contribution to automatic data extraction through this paper is twofold. First, we identify and rank potential repetitive patterns with respect to the user's visual perception of the Web page, well aware that location and size of matching elements within a Web page constitute important criteria for defining relevance. Second, matching sub-sequences of the pattern with the highest weightiness are aligned with global multiple sequence alignment techniques. Experimental results show that our system is able to achieve high accuracy in distilling and aligning regularly structured objects inside complex Web pages.
Inactivation of Both FHIT and p53 Cooperate in Deregulating Proliferation-Related Pathways in Lung Cancer

Introduction: FHIT and p53 are the two most commonly altered tumor suppressor genes in lung cancer, and their molecular status regulates sensitivity to anticancer drugs. Although their functions are independent, there is evidence that their pathways might be interconnected, but little is known at the molecular level. Methods: Microarray profiling of FHIT-transduced lung cancer cells and modulation of FHIT levels by RNA interference in human bronchial cells were used to generate a signature of FHIT-regulated transcripts. Expression of these genes was evaluated by real-time polymerase chain reaction in 55 primary lung cancer samples characterized for FHIT and p53 expression by immunehistochemistry. Results: A signature of FHIT-transcripts, particularly enriched in genes involved in cell cycle control, was identified. This signature showed overlap with p53-regulated genes, indicating possible crosstalk between these proteins. Consistently, transcriptional deregulation after FHIT modulation was higher in p53-negative cells. In primary lung cancers, inactivation of either gene was detected in 48 of 55 cases (87%) and both genes in 23 of 55 (42%) cases, confirming the central role of these pathways. Primary tumors with inactivation of both FHIT and p53 displayed the strongest deregulation of growth-related pathways with high levels of expression of CCNB1, BUB1, CDC6, TOP2A, MCM6, and CENPF. Conclusions: FHIT and p53 seem to rely on common mediators, and inactivation of both genes results in prominent deregulation of growth-related pathways in lung cancer cell lines and primary tumors. This reveals crosstalk between these proteins and suggests a possible distinctive phenotype for tumors with inactivation of both genes.
Influence of Deformability of Human Red Cells upon Blood Viscosity

The viscosity of blood at high rates of shear is unusually low compared to other suspensions of similar concentration. The underlying mechanisms were studied by rotational viscometry, red cell filtration, viscometry of packed cells and direct microscopic observation of red cells under flow in a transparent cone plate viscometer. Deformability of red cells was altered osmotically or abolished by aldehyde fixation. The normal red cells under isosmotic conditions passed easily through filter pores (5 to 14 μ diameter). After osmotic crenation, deformability of cells in pore flow was reduced. Normal cells were deformed into a variety of shapes at high rates of shear, while crenated cells tumbled undeformed. Suspensions of these normal cells showed more pronounced shear thinning (reduction of viscosity with increasing shear rate) than suspensions of crenated cells. Suspensions of rigid cells showed greatly increased viscosity and a shear thickening as a function of shear rate and shear time. The physiological deformability is of critical importance to blood flow at high rates of shear. This is possible through a fluid transition of the erythrocyte caused by a rotation of the membrane with and around the cell contents. This phenomenon is the prime cause of the progressive reduction in viscosity with increasing shear.
Standard English, the National Curriculum, and linguistic disadvantage :a sociolinguistic account of the careful speech of Tyneside adolescents

This study investigates adolescents' use of standard English in situations requiring careful speech. An account is given of the historical, political, linguistic and educational development of the concept of standard English, with particular emphasis on spoken standard English. Popular conceptions of 'correct speech' are also considered, and all of these are related to requirements in the National Curriculum for England and Wales for the teaching of spoken standard English. This is related to a specific case, namely that of Tyneside English. This variety is described, and an account is given of the area and its main social and econornIc characteristics. Twenty four adolescents are chosen from two schools which contrast highly in terms of socioeconomic profile. The individuals are also selected to provide a spread of levels of attainment, and both sexes are equally represented. M Phonological, grammatical, lexical and discourse variables are quantified using Labovian quantification techniques and approaches which involve counting non-standard variants over a period of time. Principal linguistic variables are: glottalised variants of (p) (t) and (k); non standard verb and pronoun forms; non-standard lexical items, and certain kinds of discourse markers. This process provides evidence of the extent to which young people use or do not use spoken standard English. It is shown that in more careful speech young people from more and less privileged backgrounds use only small frequencies of non-standard variants, but that within this relatively small number differences do exist: certain items are used mainly by less privileged boys, others mainly by girls, others by more privileged individuals in general. Use of non-standard speech is shown to differ for different groups at different linguistic levels. Important differences in gender and in social class emerge, but attainment also appears to have a significant bearing on children's use of spoken standard English. The study concludes by discussing pedagogical approaches which might increase awareness of issues associated with standard English.
Turnover of Fatty Acids during Natural Senescence of Arabidopsis, Brachypodium, and Switchgrass and in Arabidopsis β-Oxidation Mutants1[C][W][OA]

During leaf senescence, macromolecule breakdown occurs and nutrients are translocated to support growth of new vegetative tissues, seeds, or other storage organs. In this study, we determined the fatty acid levels and profiles in Arabidopsis (Arabidopsis thaliana), Brachypodium distachyon, and switchgrass (Panicum virgatum) leaves during natural senescence. In young leaves, fatty acids represent 4% to 5% of dry weight and approximately 10% of the chemical energy content of the leaf tissues. In all three species, fatty acid levels in leaves began to decline at the onset of leaf senescence and progressively decreased as senescence advanced, resulting in a greater than 80% decline in fatty acids on a dry weight basis. During senescence, Arabidopsis leaves lost 1.6% of fatty acids per day at a rate of 2.1 μg per leaf (0.6 μg mg−1 dry weight). Triacylglycerol levels remained less than 1% of total lipids at all stages. In contrast to glycerolipids, aliphatic surface waxes of Arabidopsis leaves were much more stable, showing only minor reduction during senescence. We also examined three Arabidopsis mutants, acx1acx2, lacs6lacs7, and kat2, which are blocked in enzyme activities of β-oxidation and are defective in lipid mobilization during seed germination. In each case, no major differences in the fatty acid contents of leaves were observed between these mutants and the wild type, indicating that several mutations in β-oxidation that cause reduced breakdown of reserve oil in seeds do not substantially reduce the degradation of fatty acids during leaf senescence.
Handbook of bereavement research: Consequences, coping, and care

New research continues to challenge our assumptions about the fundamental nature and course of grief: its roots in our biology, our emotions, and our social interactions. The "Handbook of Bereavement Research" provides a broad view of diverse contemporary approaches to bereavement, examining both normal adaptation and complicated manifestations of grief. In this volume, leading interdisciplinary scholars focus on three important themes in bereavement research: consequences, coping and care. In exploring the consequences of bereavement, authors examine developmental factors that influence grief both for the individual and the family at different phases of the life cycle. In exploring coping, they describe exciting new empirical studies about how people can and do cope with grief, without professional intervention. People do not grieve alone, so chapters on coping present new ways to understand grief at an interpersonal level as well. Until recently, intervention for the bereaved has not been scientifically guided and has become the subject of challenging differences of opinion and approach. Chapters in the care section of the volume critically examine interventions to date and provide guidance for assessment and more empirically guided treatment strategies. The "Handbook" provides an up-to-date comprehensive review of scientific knowledge about bereavement in an authoritative yet accessible way that should be useful reading for researchers, practitioners and health care professionals in the 21st century.
Iterative kernel principal component analysis for image modeling

In recent years, kernel principal component analysis (KPCA) has been suggested for various image processing tasks requiring an image model such as, e.g., denoising or compression. The original form of KPCA, however, can be only applied to strongly restricted image classes due to the limited number of training examples that can be processed. We therefore propose a new iterative method for performing KPCA, the kernel Hebbian algorithm, which iteratively estimates the kernel principal components with only linear order memory complexity. In our experiments, we compute models for complex image classes such as faces and natural images which require a large number of training examples. The resulting image models are tested in single-frame super-resolution and denoising applications. The KPCA model is not specifically tailored to these tasks; in fact, the same model can be used in super-resolution with variable input resolution, or denoising with unknown noise characteristics, in spite of this, both super-resolution and denoising performance are comparable to existing methods.
Influence of Women's Knowledge on Maternal Health Care Utilization in Southern Laos

This study aims to clarify women's knowledge on obstetric care and to analyse the situation of maternal health care (MHC) utilization in southern Laos. Face to face structured questionnaire and focus group discussions were carried out for 205 mothers aged 29.6 ± 6.7 who had children under the age of five. Three measurements of MHC utilization comprised: 1) antenatal care (ANC), 2) tetanus toxoid (TT) inoculation, and 3) attendance delivery by health professional. Women's knowledge on obstetric care was scored. Women's knowledge was positively correlated with ANC and TT inoculation. It was found that the women with strong superstitious belief were less likely to utilize all three types of MHC than the others. Accessibility to health care facilities strongly affected ANC and attendance delivery. Enhancing women's knowledge on obstetric care and reducing barriers related with sociocultural beliefs are essential to improving maternal health in southern Laos. Asia Pac J Public Health 2001;13(1):13-19
Non-erythroid alpha-spectrin breakdown by calpain and interleukin 1 beta-converting-enzyme-like protease(s) in apoptotic cells: contributory roles of both protease families in neuronal apoptosis.

The cytoskeletal protein non-erythroid alpha-spectrin is well documented as an endogenous calpain substrate, especially under pathophysiological conditions. In cell necrosis (e.g. maitotoxin-treated neuroblastoma SH-SY5Y cells), alpha-spectrin breakdown products (SBDPs) of 150 kDa and 145 kDa were produced by cellular calpains. In contrast, in neuronal cells undergoing apoptosis (cerebellar granule neurons subjected to low potassium and SH-SY5Y cells treated with staurosporine), an additional SBDP of 120 kDa was also observed. The formation of the 120 kDa SBDP was insensitive to calpain inhibitors but was completely blocked by an interleukin 1 beta-converting-enzyme (ICE)-like protease inhibitor, Z-Asp-CH2OC(O)-2,6-dichlorobenzene. Autolytic activation of both calpain and the ICE homologue CPP32 was also observed in apoptotic cells. alpha-Spectrin can also be cleaved in vitro by purified calpains to produce the SBDP doublet of 150/145 kDa and by ICE and ICE homologues [ICH-1, ICH-2 and CPP32(beta)] to produce a 150 kDa SBDP. In addition, CPP32 and ICE also produced a 120 kDa SBDP. Furthermore inhibition of either ICE-like protease(s) or calpain protects both granule neurons and SH-SY5Y cells against apoptosis. Our results suggest that both protease families participate in the expression of neuronal apoptosis.