jimnoneill/paper-to-field-training huggingface dataset:
Probabilistic nodule filtering in thoracic CT scans

Automated detection of lung nodules in thoracic CT scans is an important clinical challenge. Blood vessels form a major source of false positives in automated nodule detection systems. Hence, the performance of such systems may be improved by enhancing nodules while suppressing blood vessels. Ideally, nodule enhancement filters should enhance nodules while suppressing vessels and lung tissue. A distinction between vessels and nodules is normally obtained through eigenvalue analysis of the Hessian matrix. The Hessian matrix is a second order differential quantity and so is sensitive to noise. Furthermore, by relying on principal curvatures alone, existing filters are incapable of distinguishing between nodules and vessel junctions, and are incapable of handling cases in which nodules touch vessels. In this paper we develop novel nodule enhancement filters that are capable of suppressing junctions and are capable of handling cases in which nodules appear to touch or even overlap with vessels. The proposed filters are based on optimized probabilistic models derived from eigenvalue analysis of the gradient correlation matrix which is a first order differential quantity and so are less sensitive to noise compared with known vessel enhancement filters. The proposed filters are evaluated and compared to known techniques both qualitatively, quantitatively. The evaluation includes both synthetic and actual clinical data.

Topic: Lung Cancer Diagnosis and Treatment
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Concerted Differential Changes of Helical Dynamics\nand Packing upon Ligand Occupancy in a Bacterial Chemoreceptor

Transmembrane\nreceptors are central components of the chemosensory\nsystems by which motile bacteria detect and respond to chemical gradients.\nAn attractant bound to the receptor periplasmic domain generates conformational\nsignals that regulate a histidine kinase interacting with its cytoplasmic\ndomain. Ligand-induced signaling through the periplasmic and transmembrane\ndomains of the receptor involves a piston-like helical displacement,\nbut the nature of this signaling through the &gt;200 Å four-helix\ncoiled coil of the cytoplasmic domain had not yet been identified.\nWe performed single-molecule Förster resonance energy transfer\nmeasurements on Escherichia coli aspartate\nreceptor homodimers inserted into native phospholipid bilayers enclosed\nin nanodiscs. The receptors were labeled with fluorophores at diagnostic\npositions near the middle of the cytoplasmic coiled coil. At these\npositions, we found that the two N-helices of the homodimer were more\ndistant, that is, less tightly packed and more dynamic than the companion\nC-helix pair, consistent with previous deductions that the C-helices\nform a stable scaffold and the N-helices are dynamic. Upon ligand\nbinding, the scaffold pair compacted further, while separation and\ndynamics of the dynamic pair increased. Thus, ligand binding had asymmetric\neffects on the two helical pairs, shifting mean distances in opposite\ndirections and increasing the dynamics of one pair. We suggest that\nthis reflects a conformational change in which differential alterations\nto the packing and dynamics of the two helical pairs are coupled.\nThese coupled changes could represent a previously unappreciated mode\nof conformational signaling that may well occur in other coiled-coil\nsignaling proteins.

Topic: Bacterial Genetics and Biotechnology
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Prevalence of Malnutrition in Eastern Mediterranean Hospitals: Protocol of a Systematic Review and Meta-Analysis

Background: Malnutrition has negative consequences in hospitals, like poor disease recovery, increased mortality, length of hospitalization, readmission, and health care costs.Aims: This review was designed to determine malnutrition prevalence in hospitals located in eastern Mediterranean region (EMR).Study design: To conduct this systematic review, papers, including original articles, related references and conference proceedings on the prevalence of malnutrition in adult hospitalized patients published in international journals and scientific databases from 1 Jan 2017 to 31 Jan 2022 will be included. The following keywords and their alternatives will be used in the literature search: malnutrition, patient, and EMR. The protocol has been registered at PROSPERO (code: CRD42022339426).Methods: After initial screening based on inclusion and exclusion criteria, the full text articles will be read carefully and eligible documents will be selected according to the defined objectives. Afterward, the selected papers will be reviewed for methodological quality and the required information will be extracted. Finally, in case of sufficient data, a meta-analysis will be performed. Screening, selection, quality assessment, and data extraction will be done by at least two independent reviewers.Results: This review is ongoing and will be completed until the end of year 2023.Conclusion: This review aims to provide comprehensive evidence about the prevalence of malnutrition among adult inpatients in EMR hospitals. This can provide regional authorities, health managers and policy makers good information regarding current status to make appropriate decisions for promoting the health status in hospitals.

Topic: Nutrition and Health in Aging
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
Painting as Scotomization: The Rhetoric of a Concealed Image

In Back of a Painting: History Painting No. 12, Doom of 1998–2004, Israeli artist David Ginton paints a back side of a painting with an inscription that describes the painting's alleged recto. The text alludes to a verse from the book of Micah, which unfolds the story of an apprentice who banishes his master. In Ginton's rewriting, the story is displaced to current Israeli politics, yet the charged and disturbing visual content remains hidden, as though painted on the reversed side. Ginton's painting serves for examining a painterly characteristic, in which paintings engage with what cannot be shown directly – endowing this occlusion a significant role. I suggest exploring this characteristic through two texts by Jacques Derrida: Memoire of the Blind of 1993, and his treatise on Valerio Adami's drawing of a back side of a painting in his book The Truth in Painting. A close reading of Derrida's two texts will serve to anchor Ginton's painting in a wider context. As will be shown, Derrida's texts could be read like Ginton's painting, as an exploration of the avoidance of looking and its political consequences. In order to explicate this ambiguous visuality, I turn in what follows to Freud's and Lacan's conceptualizations of the term scotomization regarding the visual field.

Topic: Photography and Visual Culture
Subfield: History
Field: Arts and Humanities
Domain: Social Sciences
Copper-Mediated Trifluoromethylation–Allylation of Arynes

An unprecedented three-component copper-mediated vicinal trifluoromethylation-allylation of arynes is described. A wide range of structurally diverse trifluoromethylated allylarenes can be quickly assembled in one step. The application of the method has been demonstrated in the expedient synthesis of the CF<sub>3</sub>-containing analogue of the antispasmodic drug papaverine. The new reactivity of the [CuCF<sub>3</sub>] reagent, which is generated from the inexpensive industrial byproduct fluoroform, is revealed with unique advantages.

Topic: Fluorine in Organic Chemistry
Subfield: Pharmaceutical Science
Field: Pharmacology, Toxicology and Pharmaceutics
Domain: Life Sciences
132 Corporoplasty with Ossified Plaque Excision and Surgisis Graft

Penile corporoplasty with grafting technique is the preferred surgical treatment for stable Peyronie disease when curvature is >60º or when there is a complex curvature. This technique usually requires plaque incision, but in those cases with ossified plaque it could be necessary to perform plaque excision. We present the case of a 45 year old man, active smoker, with history of spontaneous pneumothorax, who came to our consultation with a 90º dorsal curvature. The disease started one year ago and it has been stable during the last 6 months, preserving the erectile function but being unable to penetrate. On the clinical examination, he presented a huge dorsal ossified plaque of 2 cm x 3 cm so we decided to make excision in it and to use a Surgisis graft. We perform circumcision, penile deglobing and opening of paraurethral Buck’s fascia. Dissection and lifting of the neurovascular bundle. Gittes’ test: dorsal curvature of 100º. We make excision of the ossified plaque. This result in a tunica albuginea defect which is posteriorly closed by a Surgisis graft. New Gittes’ test shows complete correction of the curvature. Finally, closing of Buck’s fascia, dartos and skin. At 12 months of follow up, he presents with complete resolution of the curvature, good erectile function being able to penetrate and refers satisfactory intercourse.

Topic: Sexual function and dysfunction studies
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
1-D numerical simulation of sediment transport in alluvial channel beds

ABSTRACT Quantitative estimate of sediment transport processes is important especially in river-control engineering and for water management projects. In this paper the sediment routing of a 1-D model is presented and applied to some study cases. The procedure simulates the variations of bed roughness conditions due to natural sorting and to generation and migration of bed forms. The suspended-load and the bed-load are treated separately.

Topic: Hydrology and Sediment Transport Processes
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Penetration through the Egg-shell of<i>Pieris brassicae</i>(L.)

The structure of the shell of eggs of Pieris brassicae (L.), together with changes in it and associated membranes during embryonic development, have been investigated in relation to the penetration and toxicity of simple chemicals. The rigid outer shell consists of two proteinaceous layers, covered externally by a relatively hydrofuge cement, by which the egg is attached to the leaf surface. The egg has respiratory pores over its surface, and a single apical micropyle penetrating these layers. The inside of the rigid shell is lined with a layer of unsaturated oil—an unusual feature for an insect egg. When the egg is first laid, the vitelline membrane is directly applied to the inner surface of the solid shell over the region immediately around the micropyle, but within four hours this contact is broken, and the oil layer flows into this region also, and becomes complete. As development proceeds, the vitelline layer is replaced by membranes of embryonic origin, but before eclosion both these epembryonic layers, and also the oil, are resorbed. The egg is remarkably resistant to water-soluble poisons which have no oil-solubility, except during the first four hours of development. This resistance is attributed almost entirely to the oil layer, and the early susceptibility to its absence over the micropylar region. These changes are not reflected in the effect of oil-soluble poisons or fumigants. The solid portions of the shell do not seem to be of great importance in restricting the entry of liquid poisons, even though the cement is comparatively hydrofuge; from experiments with wetting agents and with eggs immersed in poisons under vacuum, it does not appear that the respiratory air spaces in the shell are preferential channels of access; rather, the poisons penetrate through the solid portions of the shell. This penetration, even of oil-soluble materials, is slow, for they can be effectively washed out of the shell again, some considerable time after dipping. On the other hand, non-volatile oily materials can interfere with the respiration of the egg by blocking the air spaces in the shell. The secretion of epembryonic layers does not appear to change the resistance of the egg to water-soluble materials; this is to be expected, for they do not contain lipoid. On the other hand they do add appreciably to the resistance to oil-soluble materials. There is no evidence that poisons are accumulated in these epembryonic membranes, and released during the pre-eclosion period. Experiments with covalent compounds, such as mercuric chloride, suggest that their oil-solubility accounts for their toxicity, whereas electrovalent compounds containing similar heavy metals are only effective while the direct micropylar path of entry is available to them.

Topic: Insect Resistance and Genetics
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Interpretation of the results of the CORA-33 dry core BWR test

All BWR degraded core experiments performed prior to CORA-33 were conducted under ``wet`` core degradation conditions for which water remains within the core and continuous steaming feeds metal/steam oxidation reactions on the in-core metallic surfaces. However, one dominant set of accident scenarios would occur with reduced metal oxidation under ``dry`` core degradation conditions and, prior to CORA-33, this set had been neglected experimentally. The CORA-33 experiment was designed specifically to address this dominant set of BWR ``dry`` core severe accident scenarios and to partially resolve phenomenological uncertainties concerning the behavior of relocating metallic melts draining into the lower regions of a ``dry`` BWR core. CORA-33 was conducted on October 1, 1992, in the CORA tests facility at KfK. Review of the CORA-33 data indicates that the test objectives were achieved; that is, core degradation occurred at a core heatup rate and a test section axial temperature profile that are prototypic of full-core nuclear power plant (NPP) simulations at ``dry`` core conditions. Simulations of the CORA-33 test at ORNL have required modification of existing control blade/canister materials interaction models to include the eutectic melting of the stainless steel/Zircaloy interaction products and the heat of mixing of stainless steel and Zircaloy. The timing and location of canister failure and melt intrusion into the fuel assembly appear to be adequately simulated by the ORNL models. This paper will present the results of the posttest analyses carried out at ORNL based upon the experimental data and the posttest examination of the test bundle at KfK. The implications of these results with respect to degraded core modeling and the associated safety issues are also discussed.

Topic: Nuclear Materials and Properties
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Nosocomial Outbreak of <i>Serratia marcescens</i> in a Neonatal Intensive Care Unit

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Topic: Nosocomial Infections in ICU
Subfield: Critical Care and Intensive Care Medicine
Field: Medicine
Domain: Health Sciences
A Parallel GNFS Integrated with the Block Wiedemann's Algorithm for Integer Factorization

RSA is a very popular public-key based cryptosystem. The security of RSA is relied on the difficulty of large integer factorization. The general number field sieve (GNFS) is an algorithm for factoring very large numbers, especially for integers over 110 digits. It is the asymptotically fastest known factoring algorithm. In this paper, we have successfully implemented the parallel general number field sieve (GNFS) algorithm and integrated with a new method called block Wiedemann's algorithm to solve the large and sparse linear system over GF(2) generated by the GNFS algorithm. The detailed parallel experimental results on a SUN cluster will be presented as well

Topic: Coding theory and cryptography
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Splenic Hematopoietic and Stromal Cells in Cancer Progression

Abstract Tumor-derived secretory factors orchestrate splenic hematopoietic and stromal cells to fuel metastasis. The spleen acts as a reservoir site for hematopoietic stem and progenitor cells, which are rapidly exploited as myeloid-derived suppressor cells at the cost of tumor-reactive lymphoid cells. Splenic erythroid progenitor cells and mesenchymal stromal cells contribute directly and indirectly to both tumor immune escape and the metastatic cascade. Animal models provide valuable mechanistic insights, but their translation to a clinical setting highlights specific challenges and open issues. In this review, we envision the exploitation of the spleen as a source for novel biomarkers and therapeutic approaches.

Topic: Immune cells in cancer
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
∗-GENERALIZED DIFFERENTIAL IDENTITIES OF SEMIPRIME RINGS WITH INVOLUTION

Abstract. The main purpose of this paper is to consider ∗-generalized dif-ferential identities of semiprime ring with involution ∗ of characteristic p ≥ 0. On the one hand, we extend certain results concerning derivations to the context of generalized derivations. On the other hand, we generalize some existing results on prime rings to the case of semiprime rings. 1.

Topic: Advanced Topics in Algebra
Subfield: Algebra and Number Theory
Field: Mathematics
Domain: Physical Sciences
Blackness, Coloniality, and Gender in the Liberation of Occupied France

Abstract: This article will examine the experiences of French colonial women actively engaged in acts of resistance against historical erasure and political oppression during and after the Second World War. The first part of the article looks at the role of literature as a symbol of the intersection where politics, history and fiction converge to interrogate the negotiation between slave and Holocaust narratives. By establishing a certain degree of contiguity between slavery and the Holocaust, Caribbean authors encourage us to reconsider the epistemological correspondences and distinctions that have been formed between Blacks and Jews during these dark chapters of history. The second part chronicles the experiences of women from Guadeloupe and Martinique who joined the French Resistance or the army. They were active participants in various networks and performed crucial tasks toward the liberation of the nation. At the end of the war, however, their contributions to the collective effort were never properly acknowledged or recorded. If scholars have been hesi- tant to examine the particularities revealed by the study of women in the Resistance for fear of undermining established notions of the movement or its modes of operation, this is even more true for the study of colonial women who defied gender or racial expectations. In other words, this article challenges the conventional (gender-based) power dynamics at the heart of the historiography and archival records of the French Resistance to align with postcolonial scholars who are striving to create alternative geographies of survival and liberation.

Topic: African history and culture studies
Subfield: Anthropology
Field: Social Sciences
Domain: Social Sciences
Chronic Intermittent Hypoxia and Hypercapnia Inhibit the Hypothalamic Paraventricular Nucleus Neurotransmission to Parasympathetic Cardiac Neurons in the Brain Stem

Obstructive sleep apnea is associated with chronic intermittent hypoxia/hypercapnia (CIHH) episodes during sleep that heighten sympathetic and diminish parasympathetic activity to the heart. Although one population of neurons in the paraventricular nucleus of the hypothalamus strongly influences sympathetic tone and has increased activity after CIHH, little is known about the role of this pathway to parasympathetic neurons and how this network is altered in CIHH. We hypothesized that CIHH inhibits the excitatory pathway from the paraventricular nucleus of the hypothalamus to parasympathetic cardiac vagal neurons in the brain stem. To test this hypothesis, channelrhodopsin was selectively expressed, using viral vectors, in neurons in the paraventricular nucleus of the hypothalamus and channelrhodopsin-expressing fibers were photoactivated to evoke postsynaptic currents in cardiac vagal neurons in brain stem slices. Excitatory postsynaptic currents were diminished in animals exposed to CIHH. The paired-pulse and prolonged facilitation of the postsynaptic current amplitudes and frequencies evoked by paired and bursts of photoactivation of channelrhodopsin fibers, respectively, occurred in unexposed rats but were blunted in CIHH animals. In response to an acute challenge of hypoxia/hypercapnia, the amplitude of postsynaptic events was unchanged during, but increased after hypoxia/hypercapnia in unexposed animals. In contrast, postsynaptic currents were inhibited during hypoxia/hypercapnia in rats exposed to CIHH. In conclusion, the excitatory pathway to cardiac vagal neurons is diminished in response to both acute and chronic exposures to hypoxia/hypercapnia. This could elicit a reduced cardioprotective parasympathetic activity and an enhanced risk of adverse cardiovascular events in episodes of apnea and chronic obstructive sleep apnea.

Topic: Neuroscience of respiration and sleep
Subfield: Endocrine and Autonomic Systems
Field: Neuroscience
Domain: Life Sciences
Supplementary Figure 2 from Construction and Characterization of Novel, Recombinant Immunotoxins Targeting the &lt;i&gt;Her2/neu&lt;/i&gt; Oncogene Product: &lt;i&gt;In vitro&lt;/i&gt; and &lt;i&gt;In vivo&lt;/i&gt; Studies

Supplementary Figure 2 from Construction and Characterization of Novel, Recombinant Immunotoxins Targeting the &lt;i&gt;Her2/neu&lt;/i&gt; Oncogene Product: &lt;i&gt;In vitro&lt;/i&gt; and &lt;i&gt;In vivo&lt;/i&gt; Studies

Topic: Toxin Mechanisms and Immunotoxins
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
Fertility in India: An Econometric Analysis of a Metropolis

This study analyses household fertility behaviour and attempts to formulate and test several socio-economic hypotheses of fertility in India on the basis of data collected from the metropolitan city of Delhi. Factorial investigations of thirty-four selected variables representing socio-economic, demographic and cultural variables highlight the relative significance of different factors in different aspects of fertility behaviour.

Topic: Demographic Trends and Gender Preferences
Subfield: Gender Studies
Field: Social Sciences
Domain: Social Sciences
Introduction

This chapter sets out the aims of this book, stating the main lines of inquiry. Next, a brief “state of the field” assessment on the historical problem of the Taiwan Strait crises will be made. It will examine how a reevaluation is pertinent with the availability of new sources and how such a new appraisal speaks about the deeper trends of historical questions of Sino-US relations. This is followed by a short content review and a discussion of the usage of Chinese and US sources.

Topic: Chinese history and philosophy
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences