julilili42/papers huggingface dataset:
11q13 is a susceptibility locus for hormone receptor positive breast cancer
2012-03-29

A recent two-stage genome-wide association study (GWAS) identified five novel breast cancer susceptibility loci on chromosomes 9, 10, and 11. To provide more reliable estimates of the relative risk associated with these loci and investigate possible heterogeneity by subtype of breast cancer, we genotyped the variants rs2380205, rs1011970, rs704010, rs614367, and rs10995190 in 39 studies from the Breast Cancer Association Consortium (BCAC), involving 49,608 cases and 48,772 controls of predominantly European ancestry. Four of the variants showed clear evidence of association (P ≤ 3 × 10(-9) ) and weak evidence was observed for rs2380205 (P = 0.06). The strongest evidence was obtained for rs614367, located on 11q13 (per-allele odds ratio 1.21, P = 4 × 10(-39) ). The association for rs614367 was specific to estrogen receptor (ER)-positive disease and strongest for ER plus progesterone receptor (PR)-positive breast cancer, whereas the associations for the other three loci did not differ by tumor subtype.
Predicting hand function after hemispherotomy: TMS versus fMRI in hemispheric polymicrogyria
2012-03-29

Summary Patients with hemispheric malformations of cortical development (such as polymicrogyria) often develop medically intractable epilepsies for which hemispherotomy can be an excellent treatment option. Transcranial magnetic stimulation (TMS) and functional magnetic resonance imaging (fMRI) are noninvasive methods used to evaluate the sensorimotor system in adults and children before surgery. Preoperative results of both methods and their predictive values regarding hand function after hemispherotomy are described in four boys with hemispheric polymicrogyria, pharmacoresistent epilepsy, and hemiparesis with preserved grasp function of the paretic hand. TMS showing ipsilateral projections from the contralesional hemisphere but no evidence of crossed corticospinal projections from the lesioned hemisphere correctly predicted preserved postoperative grasp function in all four patients. In contrast, the interpretation of sensorimotor fMRI in patients with congenital hemiparesis is more difficult, as ipsilesional activation can occur as it was the case in three of four patients in the current study. This activation might represent contralaterally preserved primary somatosensory (S1) and not primary motor (M1) representation and is apparently not necessary for the paretic hand to still perform grasp movements.
Arresting mantle formation and redirecting embryonic shell gland tissue by platinum2+ leads to body plan modifications in Marisa cornuarietis (Gastropoda, Ampullariidae)
2012-03-29

Abstract To evaluate the threat that anthropogenic substances pose to animals when they are emitted into the environment, tests like the invertebrate embryo toxicity test with the ramshorn snail Marisa cornuarietis have been developed. These tests are used to investigate substances like the heavy metal platinum (Pt) that is used in catalytic converters and is gradually released in car exhausts. In 2010, our group reported that high Pt concentrations cause body plan alterations in snails and prevent the formation of an external shell during M. cornuarietis embryogenesis. Now, this study presents scanning‐electron micrographs and histological sections of platinum 2+ (Pt 2+ )‐treated and untreated M. cornuarietis embryos and compares “normally” developing and “shell‐less” embryos during embryogenesis, to reveal the exact course of events that lead to this body plan shift. Both groups showed similar development until the onset of torsion 70‐ to 82‐h postfertilization. In the Pt 2+ ‐exposed embryos, the rudimentary shell gland (=anlage of both shell gland and mantle, which usually evaginates, grows, and eventually covers the visceral sac) does not spread across the visceral sac but remains on its ventral side. Without the excessive growth of the shell gland, a horizontal rotation of the visceral sac relative to head and foot does not occur, as being normal during the process of torsion. J. Morphol., 2012. © 2012 Wiley Periodicals, Inc.
Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA
2012-03-30

DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5'-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.
Error reactivity in self-paced performance: Highly-accurate individuals exhibit largest post-error slowing
2012-03-30

Reaction time is typically increased following an erroneous response. This post-error slowing is traditionally explained by a strategic adjustment of response threshold towards more conservative behaviour. A recently proposed orienting account provides an alternative explanation for post-error slowing. According to this account, committing an error evokes an orienting response (OR), which inhibits information processing in the subsequent trial, resulting in slow and inaccurate performance. We tested a straightforward prediction of the orienting account in the context of self-paced performance, adopting an individual-differences approach: Post-error slowing should be larger the less frequent an error is. To this end, participants were classified into three groups differing in overall performance accuracy. Larger post-error slowing and stronger post-error accuracy decrease were observed for the high-accuracy group than for the two other groups. Practice pronounced the post-error accuracy decline, especially for the high-accuracy group. The results are consistent with the orienting account of post-error slowing but are problematic for accounts based on strategic evaluation mechanisms.
Proof-Theoretic Semantics, Self-Contradiction, and the Format of Deductive Reasoning
2012-03-30

From the point of view of proof-theoretic semantics, it is argued that the sequent calculus with introduction rules on the assertion and on the assumption side represents deductive reasoning more appropriately than natural deduction. In taking consequence to be conceptually prior to truth, it can cope with non-well-founded phenomena such as contradictory reasoning. The fact that, in its typed variant, the sequent calculus has an explicit and separable substitution schema in form of the cut rule, is seen as a crucial advantage over natural deduction, where substitution is built into the general framework.
The Global Iron Cycle
2012-03-30

This chapter contains sections titled: Overview The inorganic geochemistry of iron: redox and reservoirs Iron in modern biology and biogeochemical cycles Iron through time Summary Acknowledgements References
Axonal transport deficit in a KIF5A –/– mouse model
2012-03-31

Hereditary spastic paraplegia (HSP) is a neurodegenerative disorder preferentially affecting the longest corticospinal axons. More than 40 HSP genetic loci have been identified, among them SPG10, an autosomal dominant HSP caused by point mutations in the neuronal kinesin heavy chain protein KIF5A. Constitutive KIF5A knockout (KIF5A( -/- )) mice die early after birth. In these mice, lungs were unexpanded, and cell bodies of lower motor neurons in the spinal cord swollen, but the pathomechanism remained unclear. To gain insights into the pathophysiology, we characterized survival, outgrowth, and function in primary motor and sensory neuron cultures from KIF5A( -/- ) mice. Absence of KIF5A reduced survival in motor neurons, but not in sensory neurons. Outgrowth of axons and dendrites was remarkably diminished in KIF5A( -/- ) motor neurons. The number of axonal branches was reduced, whereas the number of dendrites was not altered. In KIF5A( -/- ) sensory neurons, neurite outgrowth was decreased but the number of neurites remained unchanged. In motor neurons maximum and average velocity of mitochondrial transport was reduced both in anterograde and retrograde direction. Our results point out a role of KIF5A in process outgrowth and axonal transport of mitochondria, affecting motor neurons more severely than sensory neurons. This gives pathophysiological insights into KIF5A associated HSP, and matches the clinical findings of predominant degeneration of the longest axons of the corticospinal tract.
Classroom Climate and Contextual Effects: Conceptual and Methodological Issues in the Evaluation of Group-Level Effects
2012-04-01

Classroom context and climate are inherently classroom-level (L2) constructs, but applied researchers sometimes—inappropriately—represent them by student-level (L1) responses in single-level models rather than more appropriate multilevel models. Here we focus on important conceptual issues (distinctions between climate and contextual variables; use of classroom L2 rather than student-level L1 measures) and more appropriate multilevel models. To illustrate these issues, we consider the effects of two L2 classroom climate variables and one L2 classroom contextual variable on two L1 student-level outcomes for 2261 students in 128 classes. Through this example, we illustrate how to apply evolving doubly latent multilevel models to (a) evaluate the factor structure of L1 and L2 constructs based on multiple indicators of classroom climate and context measures, (b) control measurement error at L1 and L2, (c) control sampling error in the aggregation of L1 responses to form L2 constructs (the average of student-level responses to form classroom-level constructs), and (d) provide guidelines for appropriate analysis of classroom climate as an L2 construct. [Supplementary materials are available for this article. Go to the publisher's online edition of Educational Psychologist for the following free supplemental resources: Substantive basis of the present investigation and more detailed description of the methodology.]
Effective T‐cell recall responses require the taurine transporter Taut
2012-04-01

T‐cell activation and the subsequent transformation of activated T cells into T ‐cell blasts require profound changes in cell volume. However, the impact of cell volume regulation for T ‐cell immunology has not been characterized. Here we studied the role of the cell‐volume regulating osmolyte transporter T aut for T ‐cell activation in T aut‐deficient mice. T‐cell mediated recall responses were severely impaired in taut −/− mice as shown with B 16 melanoma rejection and hapten‐induced contact hypersensitivity. CD4 + and CD8 + T cells were unequivocally located within peripheral lymph nodes of unprimed taut −/− mice but significantly decreased in taut −/− compared with taut +/+ mice following in vivo activation. Further analysis revealed that T aut is critical for rescuing T cells from activation‐induced cell death in vitro and in vivo as shown with TCR , superantigen, and antigen‐specific activation. Consequently, reduction of CD4 + and CD8 + T cells in taut −/− mice upon antigen challenge resulted in impaired in vivo generation of T ‐cell memory. These findings disclose for the first time that volume regulation in T cells is an element in the regulation of adaptive immune responses and that the osmolyte transporter T aut is crucial for T ‐cell survival and T ‐cell mediated immune reactions.
Changes in Regional Brain Morphology in Neuropsychiatric Systemic Lupus Erythematosus
2012-04-01

Objective. Neuropsychiatric lupus (NPSLE) is a severe and potentially life-threatening condition, reported to occur in 25%–70% of patients with systemic lupus erythematosus (SLE). Brain imaging, especially magnetic resonance imaging, is frequently used to diagnose or exclude overt cerebral pathologies such as edema, hemorrhage, and central thrombosis. More advanced imaging techniques have been applied to demonstrate subtle changes in regional cerebral blood flow and brain structure. We investigated changes in regional gray-matter (GM) volume in SLE patients without neurological manifestations and NPSLE patients at an acute stage of the disease. Methods. Using high-resolution structural images and voxel-based morphometry (VBM), we investigated regional GM volume in 20 NPSLE patients (within 2 weeks of the acute manifestation), 18 SLE patients without neurologic and/or psychiatric manifestations, and 18 healthy controls. Results. VBM analyses revealed several regions of GM atrophy in various parts of the brain in NPSLE and SLE patients. GM atrophy was seen in both groups in the temporal and parietal lobes and was most pronounced in the posterior thalamus bilaterally. Both groups showed an increase in regional GM volume in the posterior parahippocampal gyrus. Conclusion. Our data suggest that changes in regional brain morphology are present in acute NPSLE, but also in SLE (as compared to controls), which might be indicative of a subclinical neurodegenerative process. Further research is needed to investigate whether specific neuropsychiatric symptoms are related to these changes.
The Pharmacogenomics of Sex Hormone Metabolism: Breast Cancer Risk in Menopausal Hormone Therapy
2012-04-01

With women in western countries spending nearly one-third of their lifetime beyond menopause and a substantial number of these women facing severe menopausal symptoms, the goal of sex hormone pharmacogenomics is to promote the safe use of hormone replacement therapy (HRT). This could be achieved by providing molecular predictors for the upfront stratification of women in need of relief from menopausal symptoms into those with a likely benefit from HRT and those with a contraindication due to an HRT-associated breast cancer risk or other adverse effects. An increasing knowledge base of sex hormone metabolism and its variability, HRT outcomes and breast cancer susceptibility, as well as emerging examples of pharmacogenomic predictors, underscore the potential relevance of genetic variations for HRT outcome. The genes responsible for the metabolism, signaling and action of sex hormones are at the heart of this research; however, pharmacogenomic investigation of their therapeutic effects due to the enormous complexity of the biological pathways involved is still in its infancy. This article discusses the current knowledge, challenges and potential future directions towards the goal of genotype-guided safer HRT use.
FLOW CYTOMETRIC LYMPHOCYTE SUBSET ANALYSIS USING MATERIAL FROM FROZEN WHOLE BLOOD
2012-04-01

Multicenter immune monitoring programs commonly rely on storing and shipping cryopreserved peripheral blood mononuclear cells (PBMC), isolated from whole blood before freezing. However, under many conditions in the field, facilities to separate PBMC are absent. Here, we investigate the feasibility of using whole blood (WB) frozen at -80°C as a source of viable lymphocytes for use in immunological studies. We compare the percentage of CD4 and CD8 T lymphocytes and their subsets from frozen WB with results from cryopreserved PBMC in five random healthy blood donors (three female, two male). We report that CD4 and CD8 values in lymphocytes from WB frozen up to 120 days were very similar to those of PBMC frozen up to 10 days. These data suggest that within the limits of parameters investigated in this study, contrary to our original assumptions, whole blood frozen at -80°C may in fact be an appropriate source of viable lymphocytes for T cell enumeration assays in immunological and epidemiological studies.
Microstructure Evolution during Recrystallization in Dual-Phase Steels
2012-04-01

The microstructure and texture of rolled and annealed dual-phase steels with 0.147 wt. % C, 1.868 wt. % Mn, and 0.403 wt. % Si were analyzed using SEM, EDX, and EBSD. Hot rolled sheets showed a ferritic-pearlitic microstructure with a pearlite volume fraction of about 40 % and ferrite grain size of about 6 μm. Ferrite and pearlite were heterogeneously distributed at the surface and distributed in bands at the center of the sheets. The hot rolled sheets revealed a through-thickness texture inhomogeneity with a plane-strain texture with strong α-fiber and γ-fiber at the center and a shear texture at the surface. After cold rolling, the ferrite grains showed elongated morphology and larger orientation gradients, the period of the ferrite-pearlite band structure at the center of the sheets was decreased, and the plane-strain texture components were strengthened in the entire sheet. Recrystallization, phase transformation, and the competition of both processes were of particular interest with respect to the annealing experiments. For this purpose, various annealing techniques were applied, i.e., annealing in salt bath, conductive annealing, and industrial hot-dip coating. The sheets were annealed in the ferritic, intercritical, and austenitic temperature regimes in a wide annealing time range including variation of heating and cooling rates.
Is Patient Education About Adhesions a Requirement in Abdominopelvic Surgery?
2012-04-01

<b>Background:</b> Over the past decades, our knowledge and understanding of adhesions and adhesion-related complications has increasingly grown and it has become evident that adhesions have significant implications for patients, physicians and the healthcare system. The question arises whether this has resulted in greater awareness of adhesion-related problems among practicing physicians and appropriate patient education on this topic in daily practice. The following article provides a brief overview of the important subject of adhesions, discusses current awareness of adhesions among patients and doctors and addresses the consequences of failure to provide patient education and consent from a medical perspective. <b>Methods:</b> Selective literature searches were conducted in PubMed and the Cochrane Library. A patient information and consent form was developed based on several years' experience and expertise in the field of adhesions. <b>Results:</b> Adhesions are the most common type of complication in abdominopelvic surgery today, with devastating consequences for some patients. Surveys investigating the awareness of adhesions among physicians and patients clearly showed that even well-informed physicians fail to educate their patients adequately. Such failure could potentially lead to successful medical malpractice lawsuits against doctors. <b>Conclusion:</b> Considering their clear clinical impact, adhesions and related consequences should always be discussed with patients preoperatively. A newly developed consent form that specifically addresses adhesion formation may serve to thoroughly educate patients preoperatively and to adequately document the process of doing so.
A Deep Embedding of Queries into Ruby
2012-04-01

We demonstrate SWITCH, a deep embedding of relational queries into Ruby and Ruby on Rails. With SWITCH, there is no syntactic or stylistic difference between Ruby programs that operate over in-memory array objects or database-resident tables, even if these programs rely on array order or nesting. SWITCH's built-in compiler and SQL code generator guarantee to emit few queries, addressing long-standing performance problems that trace back to Rails' Active Record database binding. "Looks likes Ruby, but performs like handcrafted SQL, " is the ideal that drives the research and development effort behind SWITCH.
Symmetry Breaking by Electric Discharges in Water and Formation of Light Magnetic Monopoles in an Extended Standard Model (Part III)
2012-04-01

By Lochak (theory) and Urutskoev (experiment) the hypothesis has been suggested that during electric discharges in water light magnetic monopoles can be created and according to Lochak these monopoles should be looked upon as a kind of excited neutrinos. Based on a quantum field theoretic derivation of an extended (effective) Standard Model, which describes the effects of symmetry breaking caused by the discharge, in Part I and Part II (H. Stumpf, Z. Naturforsch. 66a, 205 and 329 (2011)), the possibility was investigated whether under these circumstances magnetic effects can occur. While in the above two parts the focus of the theory was directed to show the evidence of magnetically active neutrinos, in this part the behaviour of the leptonic doublets (v, e ̄) and (v̅ , e + ) is studied under the (symmetry breaking) conditions of such an electric discharge. The results obtained by the quantum field theoretic treatment of this problem are in agreement with symmetry considerations earlier performed by Lochak
Researching religious education journals: methodology and selected results from a German study
2012-04-01

This article is based on a research project concerning the development of religious education as an academic discipline in Germany during the twentieth century. Applying a methodology that has been of growing interest in a number of fields, the project proceeded by analysing major religious education journals published between 1900 and 1975. The present report focuses on the procedures developed and used in this research project in order to make it available to others in other countries. This is why the procedures are described in detail while the material results of the study are presented only selectively, to the degree that they indicate the results that can be reached by the methodology applied, and give readers an impression of how general theories of modernization, professionalization, scientification, etc. can be used for interpreting the development of religious education as an academic discipline. The authors suggest that research of this kind may eventually create a better basis for international comparative research in religious education.
Efficient digital design for automotive mixed-signal ASICs using simulink
2012-04-01

In common design flows of mixed-signal ASICs, the transition from system-level models to implementation-level models is executed in a manual process that carries potential for an efficiency gain by automation. This contribution addresses this aspect by showing and discussing an approach for efficient automated transitions from digital parts of Simulink models representing heterogeneous systems to VHDL and Verilog descriptions. It describes a design flow, in which a Simulink model representing a digital part of a mixed-signal ASIC is checked and optimized for automated generation of design rule compliant and more efficient digital hardware implementations. For this purpose, modeling guidelines and optimizations were implemented and integrated into an easily usable graphical user interface. Thereby, the strategy is based on considering and optimizing the digital part with respect to the surrounding heterogeneous system. An evaluation of the presented design flow is shown by applying the flow to an automotive hardware design.