gebhart/patrepeval huggingface dataset:
Fluorescence spectroscopy of oral tissue: Monte Carlo modeling with site-specific tissue properties (2009)

A Monte Carlo model with site-specific input is used to predict depth-resolved fluorescence spectra from individual normal, inflammatory, and neoplastic oral sites. Our goal in developing this model is to provide a computational tool to study how the morphological characteristics of the tissue affect clinically measured spectra. Tissue samples from the measured sites are imaged using fluorescence confocal microscopy; autofluorescence patterns are measured as a function of depth and tissue sublayer for each individual site. These fluorescence distributions are used as input to the Monte Carlo model to generate predictions of fluorescence spectra, which are compared to clinically measured spectra on a site-by-site basis. A lower fluorescence intensity and longer peak emission wavelength observed in clinical spectra from dysplastic and cancerous sites are found to be associated with a decrease in measured fluorescence originating from the stroma or deeper fibrous regions, and an increase in the measured fraction of photons originating from the epithelium or superficial tissue layers. The simulation approach described here can be used to suggest an optical probe design that samples fluorescence at a depth that gives optimal separation in the spectral signal measured for benign, dysplastic, and cancerous oral mucosa.
Abstract 4531: Nanoscale Artificial Antigen Presenting Cells for T Cell Immunotherapy. (2013)

Abstract Artificial antigen presenting cells (aAPC), which deliver stimulatory signals to cytotoxic lymphocytes, are a powerful tool for adoptive immunotherapy and in vivo T cell stimulation. Thus far, bead-based aAPC have been synthesized by coupling T cell activating proteins such as CD3 or MHC-peptide to beads several microns in diameter. By reducing the size of aAPC, we anticipated more efficient delivery of these stimulatory signals to tumor and lymph nodes where antigen-specific T cells reside. We thus manufactured aAPC based on two nanoscale particle platforms: biocompatible iron-dextran paramagnetic particles, 50-100 nm in diameter, and avidin-coated quantum dot nanocrystals, less than 20 nm in diameter. Nanoscale aAPC induced antigen-specific T cell proliferation from both TCR transgenic mouse splenocytes and human, polyclonal peripheral blood T cells. In a subcutaneous mouse melanoma model, both iron-dextran particles and quantum dot nanocrystals mediated tumor rejection when injected in vivo. To our knowledge, this is the first description of a nanoscale, particle-based aAPC that induces T cell proliferation in vitro and leads to effective T cell stimulation and tumor rejection in vivo. Furthermore, nano-aAPC represent a novel platform for studying receptor-ligand interactions at the membrane-nanoparticle interface. Citation Format: Karlo Perica, Joan G. Bieler, Andrés De León Medero, Yen-Ling Chiu, Malarvizhi Durai, Michaela Niemöller, Mario Assenmacher, Anne Richter, Mathias Oelke, Jonathan Schneck. Nanoscale Artificial Antigen Presenting Cells for T Cell Immunotherapy. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4531. doi:10.1158/1538-7445.AM2013-4531
INTERFERON α/β SYNTHESIS DURING ACUTE GRAFT-VERSUS-HOST DISEASE (1987)

Graft-versus-host disease (GVHD) is a major obstacle to successful bone marrow transplantation. The role of interferon (IFN) in GVHD is currently unclear. We have previously shown that interferon (IFN) is produced in vitro by alloantigen-stimulated murine bone marrow cells. This study was initiated to examine whether IFN production occurs in vivo during GVHD. Lethally irradiated mice were given bone marrow (10(7)) and/or spleen cells (2 X 10(7)) from either allogeneic or syngeneic mice. Mice given allogeneic spleen cells or bone marrow and spleen cells showed signs of GVHD within 10 days and usually died within 20 days of transplantation. Mice undergoing GVHD were found to have significant levels of IFN activity in their sera. Serum IFN was detected early (day 3) after transplantation with optimal IFN activity (greater than or equal to 80 units) occurring at 5-6 days. The IFN activity present in the sera obtained from mice with GVHD was identified as IFN alpha/beta by using specific antisera against IFN alpha/beta and IFN gamma. In contrast, irradiated mice given T-cell-depleted allogeneic bone marrow and spleen cells failed to develop GVHD and had no detectable serum IFN activity. Irradiated mice given syngeneic bone marrow and spleen cells or only allogeneic bone marrow cells did not develop GVHD and did not produce detectable IFN activity in their sera. These results show that serum IFN activity correlates well with GVHD and opens for speculation the possibility that IFN may be involved in the pathogenesis associated with GVHD.
The Epidemiology of Skin Cancer (1996)

The incidence of skin cancer has reached epidemic proportions. Only through heroic efforts by health care professionals and the general public to prevent the development or progression of skin cancer will this epidemic be abated.
The Influence of Mild Body and Brain Hypothermia on Ischemic Brain Damage (1990)

The influence of brain and body temperature on ischemic brain damage, notably on the density and distribution of selective neuronal vulnerability, was studied in SPF-Wistar rats subjected to 15 min of forebrain ischemia induced by bilateral occlusion of the common carotid arteries combined with arterial hypotension (50 mm Hg) in a room air environment. In one group of animals, the body temperature was maintained at 37 degrees C but no attempt was made to prevent heat losses from the ischemic brain; i.e., the head was not heated during ischemia. Under those conditions the temperature of the caudoputamen and at a subcutaneous site over the skull bone spontaneously fell to approximately 32 degrees C. In four other groups, both the rectal and the subcutaneous skull temperatures were maintained at 38, 37, 35, and 33 degrees C during the ischemia. Our results confirm those recently reported when brain temperature was varied during 20 min of ischemia, with body temperature kept constant. Thus, the histopathological outcome of the brain damage, as assessed after 7 days of recovery, was strongly temperature dependent. Whereas ischemia at 37-38 degrees C consistently caused neuronal necrosis in the hippocampus, neocortex, and caudoputamen, spontaneous cooling of the brain during ischemia at a rectal temperature of 37 degrees C significantly reduced the ischemic damage. Intentional lowering of temperature to 35 degrees C markedly reduced and to 33 degrees C virtually prevented neuronal necrosis in some but not all of the regions studied. While damage to the caudoputamen was extremely temperature sensitive, that affecting the CA1 sector of the hippocampus, and particularly the lateral reticular nucleus of the thalamus, was less so. Our results suggest that whatever biochemical events are responsible for selective neuronal vulnerability, they are temperature sensitive; however, since there are differences in sensitivity between different parts of the brain, more than one mechanism may be involved.
Projecting Individualized Probabilities of Developing Breast Cancer for White Females Who Are Being Examined Annually (1989)

To assist in medical counseling, we present a method to estimate the chance that a woman with given age and risk factors will develop breast cancer over a specified interval. The risk factors used were age at menarche, age at first live birth, number of previous biopsies, and number of first-degree relatives with breast cancer. A model of relative risks for various combinations of these factors was developed from case-control data from the Breast Cancer Detection Demonstration Project (BCDDP). The model allowed for the fact that relative risks associated with previous breast biopsies were smaller for women aged 50 or more than for younger women. Thus, the proportional hazards models for those under age 50 and for those of age 50 or more. The baseline age-specific hazard rate, which is the rate for a patient without identified risk factors, is computed as the product of the observed age-specific composite hazard rate times the quantity 1 minus the attributable risk. We calculated individualized breast cancer probabilities from information on relative risks and the baseline hazard rate. These calculations take competing risks and the interval of risk into account. Our data were derived from women who participated in the BCDDP and who tended to return for periodic examinations. For this reason, the risk projections given are probably most reliable for counseling women who plan to be examined about once a year.
Semi-Supervised Learning in Gigantic Image Collections (2009)

With the advent of the Internet it is now possible to col-lect hundreds of millions of images. These images come with varying degrees of label information. “Clean labels” can be manually obtained on a small fraction, “noisy la-bels ” may be extracted automatically from surrounding text, while for most images there are no labels at all. Semi-supervised learning is a principled framework for combin-ing these different label sources. However, it scales poly-nomially with the number of images, making it impractical for use on gigantic collections with hundreds of millions of images and thousands of classes. In this paper we show how to utilize recent results in ma-chine learning to obtain highly efficient approximations for semi-supervised learning. Specifically, we use the conver-gence of the eigenvectors of the normalized graph Lapla-cian to eigenfunctions of weighted Laplace-Beltrami oper-ators. We combine this with a label sharing framework obtained from Wordnet to propagate label information to classes lacking manual annotations. Our algorithm enables us to apply semi-supervised learning to a database of 80 million images with 74 thousand classes. 1.
Chloride channel and chloride conductance regulator domains of CFTR, the cystic fibrosis transmembrane conductance regulator (1998)

CFTR is a cyclic AMP (cAMP)-activated chloride (Cl-) channel and a regulator of outwardly rectifying Cl- channels (ORCCs) in airway epithelia. CFTR regulates ORCCs by facilitating the release of ATP out of cells. Once released from cells, ATP stimulates ORCCs by means of a purinergic receptor. To define the domains of CFTR important for Cl- channel function and/or ORCC regulator function, mutant CFTRs with N- and C-terminal truncations and selected individual amino acid substitutions were created and studied by transfection into a line of human airway epithelial cells from a cystic fibrosis patient (IB3-1) or by injection of in vitro transcribed complementary RNAs (cRNAs) into Xenopus oocytes. Two-electrode voltage clamp recordings, 36Cl- efflux assays, and whole cell patch-clamp recordings were used to assay for the Cl- channel function of CFTR and for its ability to regulate ORCCs. The data showed that the first transmembrane domain (TMD-1) of CFTR, especially predicted alpha-helices 5 and 6, forms an essential part of the Cl- channel pore, whereas the first nucleotide-binding and regulatory domains (NBD1/R domain) are essential for its ability to regulate ORCCs. Finally, the data show that the ability of CFTR to function as a Cl- channel and a conductance regulator are not mutually exclusive; one function could be eliminated while the other was preserved.
Transcutaneous analyte measuring method (TAMM): a reflective, noninvasive, near-infrared blood chemistry analyzer (1995)

TAMM for Transcutaneous Analyte Measuring Method is a near infrared spectroscopic technique for the noninvasive measurement of human blood chemistry. A near infrared indium gallium arsenide (InGaAs) photodiode array spectrometer has been developed and tested on over 1,000 patients as a part of an SBIR program sponsored by the Naval Medical Research and Development Command. Nine (9) blood analytes have been measured and evaluated during pre-clinical testing: sodium, chloride, calcium, potassium, bicarbonate, BUN, glucose, hematocrit and hemoglobin. A reflective rather than a transmissive invasive approach to measurement has been taken to avoid variations resulting from skin color and sensor positioning. The current status of the instrumentation, neural network pattern recognition algorithms and test results will be discussed.
Control of parallel task granularity by throttling decomposition (2002)

This paper introduces a new mechanism which performs lazy task creation in a novel way for the exposure of large grain parallelism. In lazy task creation, all new-born tasks are provisionally inlined and parallelism is extracted from the inlined information later on demand. Large grain parallelism is achieved by executing the inlined tasks in the current thread unless a new task is demanded. However, the new scheme leaves a self-divisible task called seed instead inlining the task and let further task demands be satisfied by sprouting new tasks from the seed rather than retrospectively reversing the inlining decision of the task. In the scheme, decomposition itself is throttled rather than just the extraction of a task. The scheme makes the serial section clearly separated from the parallel section in an evaluation tree, and this allows the serial section to adopt a sequential algorithm. The performance improvement is significant in divide-and-conquer applications by adoption of sequential algorithms.
Pyridinium oximes: rationale for their selection as causal antidotes against organophosphate poisonings and current solutions for auto-injectors. (2006)

During the last five decades, five pyridinium oximes were found to be worthy of use as antidotes against nerve agents in humans: pralidoxime, in a form of chloride or PAM-2 Cl and mesylate or P2S (against sarin, cyclosarin and VX), trimedoxime or TMB-4 and obidoxime or LüH-6 (both against tabun, sarin and VX), HI-6 (against sarin, soman, cyclosarin and VX) and HLö-7 (against all the five nerve agents). In order to provide the auto-injector with the best and most potent acetylcholinesterase reactivator, the Defence Research and Development Canada (DRDC) received in the 1990s a core funding from the federal government's CBRN research and Technology Initiative (CRTI). Its ultimate result should be three products: (1) 3-in-1 auto-injector (atropine, HI-6 dimethanesulphonate and avizafone, as anticonvulsant), (2) 2-in-1 auto-injector (atropine and HI-6 dimethanesulphonate) and (3) HI-6 dimethanesulphonate in a vial for administration by the medically trained personnel. Previous experimental and clinical experience suggests that, among the oximes mentioned, only trimedoxime and obidoxime can be used for acetylcholinesterase reactivation and antidotal protection against most of the organophosphorus insecticides. The search for an "omnipotent" oxime, effective in reactivation of AChE inhibited with both nerve agents and organophosphorus insecticides, is still ongoing.
Ocular torsion quantification with video images (1994)

The present paper describes a technique to quantify eye rotations about the visual axis (ocular torsion). Two digitized polar transformed images of the iris are displayed on a video monitor in order to facilitate a visual comparison and manual interaction. Emphasis is placed on error analysis and the method's simplicity when applied to static ocular torsion measurement. The implementation, applying averaging over ocular torsion determined in partitioned iris images, yields a theoretical resolution of 5' of arc. In a control experiment with an artificial eye, the accuracy showed to be better than 14' of arc. In practice, the measuring device was validated with the data from the literature by means of an experiment about ocular torsion in humans during tilt and hypergravity conditions (up to 3 g).
Use of a collagen barrier to enhance healing in human periodontal furcation defects. (1992)

Guided tissue regeneration procedures are intended to selectively favor healing by the periodontal ligament tissues. However, in most studies of the efficacy of guided tissue regeneration, nonresorbable barriers and membranes have been used, necessitating their surgical removal after a time. The present study employed a resorbable collagen barrier to treat Class II function invasions. The results of this treatment were compared with the results of conventional therapy. For most clinical parameters, there was no statistically significant difference in the results of treatment with or without collagen membranes. Sites treated with a collagen barrier did exhibit statistically significant improvement in probing depth and horizontal osseous support; however, these findings cannot be attributed entirely to the placement of the collagen membrane.
Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes (2017)

Substantial efforts are being made to optimize the CRISPR/Cas9 system for precision crop breeding. The avoidance of transgene integration and reduction of off-target mutations are the most important targets for optimization. Here, we describe an efficient genome editing method for bread wheat using CRISPR/Cas9 ribonucleoproteins (RNPs). Starting from RNP preparation, the whole protocol takes only seven to nine weeks, with four to five independent mutants produced from 100 immature wheat embryos. Deep sequencing reveals that the chance of off-target mutations in wheat cells is much lower in RNP mediated genome editing than in editing with CRISPR/Cas9 DNA. Consistent with this finding, no off-target mutations are detected in the mutant plants. Because no foreign DNA is used in CRISPR/Cas9 RNP mediated genome editing, the mutants obtained are completely transgene free. This method may be widely applicable for producing genome edited crop plants and has a good prospect of being commercialized.
Incensole acetate, an incense component, elicits psychoactivity by activating TRPV3 channels in the brain (2008)

Burning of Boswellia resin as incense has been part of religious and cultural ceremonies for millennia and is believed to contribute to the spiritual exaltation associated with such events. Transient receptor potential vanilloid (TRPV) 3 is an ion channel implicated in the perception of warmth in the skin. TRPV3 mRNA has also been found in neurons throughout the brain; however, the role of TRPV3 channels there remains unknown. Here we show that incensole acetate (IA), a Boswellia resin constituent, is a potent TRPV3 agonist that causes anxiolytic-like and antidepressive-like behavioral effects in wild-type (WT) mice with concomitant changes in c-Fos activation in the brain. These behavioral effects were not noted in TRPV3(-/-) mice, suggesting that they are mediated via TRPV3 channels. IA activated TRPV3 channels stably expressed in HEK293 cells and in keratinocytes from TRPV3(+/+) mice. It had no effect on keratinocytes from TRPV3(-/-) mice and showed modest or no effect on TRPV1, TRPV2, and TRPV4, as well as on 24 other receptors, ion channels, and transport proteins. Our results imply that TRPV3 channels in the brain may play a role in emotional regulation. Furthermore, the biochemical and pharmacological effects of IA may provide a biological basis for deeply rooted cultural and religious traditions.
Formation of monodisperse bubbles in a microfluidic flow-focusing device (2004)

This letter describes a method for generating monodisperse gaseous bubbles in a microfluidic flow-focusing device. The bubbles can be obtained in a range of diameters from 10 to 1000μm. The volume Vb of the bubbles scales with the flow rate q and the viscosity μ of the liquid, and the pressure p of the gas stream as Vb∝p∕qμ. This method allows simultaneous, independent control of the size of the individual bubbles and volume fraction of the dispersed phase. Under appropriate conditions, bubbles self-assemble into highly ordered, flowing lattices. Structures of these lattices can be adjusted dynamically by changing the flow parameters.
Determination of Stromal Signatures in Breast Carcinoma (2005)

Many soft tissue tumors recapitulate features of normal connective tissue. We hypothesize that different types of fibroblastic tumors are representative of different populations of fibroblastic cells or different activation states of these cells. We examined two tumors with fibroblastic features, solitary fibrous tumor (SFT) and desmoid-type fibromatosis (DTF), by DNA microarray analysis and found that they have very different expression profiles, including significant differences in their patterns of expression of extracellular matrix genes and growth factors. Using immunohistochemistry and in situ hybridization on a tissue microarray, we found that genes specific for these two tumors have mutually specific expression in the stroma of nonneoplastic tissues. We defined a set of 786 gene spots whose pattern of expression distinguishes SFT from DTF. In an analysis of DNA microarray gene expression data from 295 previously published breast carcinomas, we found that expression of this gene set defined two groups of breast carcinomas with significant differences in overall survival. One of the groups had a favorable outcome and was defined by the expression of DTF genes. The other group of tumors had a poor prognosis and showed variable expression of genes enriched for SFT type. Our findings suggest that the host stromal response varies significantly among carcinomas and that gene expression patterns characteristic of soft tissue tumors can be used to discover new markers for normal connective tissue cells.
PDA Security : Incorporating Handhelds into the Enterprise (2003)

FOREWORD ACKNOWLEDGMENTS INTRODUCTION SECTION ONE: INTRODUCTION TO PDA SECURITY IN THE ENTERPRISE Incorporating Handhelds into the Enterprise PDAs in the Enterprise The Power Resource Guide to Understanding Where Security Must be Achieved SECTION TWO: HANDHELDS IN THE ENTERPRISE When a Handheld Becomes Information Technology's Problem The Components of a Measured IT Response The How-To Guide SECTION THREE: THE TECHNOLOGY OF PDA SECURITY: CRYPTOGRAPHY, PASSWORDS, HACKING, AND MORE Understanding Handheld Security is Largely About the Operating System Hacking Threats and Mitigations SECTION FOUR: GRADUATION Handhelds Where Does Device Security Go from Here? INDEX
Converting Tissue Plasminogen Activator to a Zymogen: A Regulatory Triad of Asp-His-Ser (1993)

Unlike most serine proteases of the chymotrypsin family, tissue-type plasminogen activator (tPA) is secreted from cells as an active, single-chain enzyme with a catalytic efficiency only slightly lower than that of the proteolytically cleaved form. A zymogenic mutant of tPA has been engineered that displays a reduction in catalytic efficiency by a factor of 141 in the single-chain form while retaining full activity in the cleaved form. The residues introduced in the mutant, serine 292 and histidine 305, are proposed to form a hydrogen-bonded network with aspartate 477, similar to the aspartate 194-histidine 40-serine 32 network found to stabilize the zymogen chymotrypsinogen.
Anodic Reaction of 2-Furoic Acids. II. Electrolysis of Methyl 5-Acetyl-2-furoate and Its Homologous in Protic Solvents (1972)

Abstract Anodic oxidation of methyl 5-acetyl-2-furoate 4 in methanol leads to ring-opened diesters 8 and 9, and lactone 10 in addition to methyl 5-acetyl-2,5-dimethoxy-2,5-dihydro-2-furoates 7. Formation of 8, 9, and 10 can be rationalized as arising from 7. On the other hand, oxidation of methyl 5-methoxy- and 5-bromo-2-furoates, 5 and 6, also give 9 and 10. The reactions involve initial production of cationic intermediates 13 and 15, which are readily solvolized to give 8, 9, and 10. A mechanism of the formation of the intermediates 13 from 5, 6, and 7 is discussed.