gebhart/patrepeval huggingface dataset:
Early aging–associated phenotypes in Bub3/Rae1 haploinsufficient mice (2006)

Aging is a highly complex biological process that is believed to involve multiple mechanisms. Mice that have small amounts of the mitotic checkpoint protein BubR1 age much faster than normal mice, but whether other mitotic checkpoint genes function to prevent the early onset of aging is unknown. In this study, we show that several aging-associated phenotypes appear early in mice that are double haploinsufficient for the mitotic checkpoint genes Bub3 and Rae1 but not in mice that are single haploinsufficient for these genes. Mouse embryonic fibroblasts (MEFs) from Bub3/Rae1 haploinsufficient mice undergo premature senescence and accumulate high levels of p19, p53, p21, and p16, whereas MEFs from single haploinsufficient mice do not. Furthermore, although BubR1 hypomorphic mice have less aneuploidy than Bub3/Rae1 haploinsufficient mice, they age much faster. Our findings suggest that early onset of aging-associated phenotypes in mice with mitotic checkpoint gene defects is linked to cellular senescence and activation of the p53 and p16 pathways rather than to aneuploidy.
COMPLEMENT ACTIVATION ASSOCIATES WITH SACCULAR CEREBRAL ARTERY ANEURYSM WALL DEGENERATION AND RUPTURE (2006)

These data suggests that complement activation and MAC formation are involved in SCAA wall degeneration and rupture.
Acceleration of Full-thickness Wound Healing in Porcine Model by Autologous Platelet Gel. (2007)

Controversy over efficacy of many wound treatments, particularly autologous platelet gel (APG), is common. The objective of this study was to determine if autologous platelet gel would accelerate the healing process of full-thickness cutaneous wounds in a porcine model. Autologous platelet gel with a ratio of 10:4 was created using 10 cc platelet-rich plasma and 4 cc autologous thrombin rich plasma. A punch was used to create 24 full-thickness, cutaneous round wounds on each flank of a neutered pig and were treated with APG on 1 side versus 0.9% saline (control) on the other side. The wounds were then covered with transparent vapor permeable film dressing. On Day 14 and Day 28 post-injury, all 24 wounds were photographed and digital imaging system tracings determined the area of each wound. Biopsy specimens from each wound were obtained. On Day 14, the specimens were taken from 9- and 3 o'clock positions at the edge of the round wounds, and on Day 28 the specimens were taken from 12- and 6 o'clock positions of the round wounds. This was done to reduce bias from variations in thickness of the pig skin. Sections were stained with hematoxylin and eosin for histological study, which included microscopic review and dermal thickness measurement. The mean size of wounds treated with APG was consistently smaller than contralateral wounds treated with saline alone. On Days 14 and 28 post-injury, APG-treated wounds were 23% and 25% smaller in area than the control wounds (P < 0.001), respectively. Histological study revealed thicker dermis on APG-treated wounds and more normal anatomic skin structures on the APG side. Higher magnification revealed leukocytes consistently more prevalent in granulation tissue on the control side, indicating a delayed healing process.
Methodological approach to minimal residual disease detection by flow cytometry in adult B-lineage acute lymphoblastic leukemia. (2006)

A flow cytometric approach to minimal residual disease (MRD) monitoring useful in childhood B-lineage acute lymphoblastic leukemia (ALL) is discussed here in the context of ALL in adults. Of 64 leukemia samples analyzed, 95.3% had at least one abnormal phenotype (57.3% had two or more) as compared to physiologic B-cell precursors in adult bone marrow. The method was sensitive enough to detect one leukemic cell among 10,000 normal cells in 16/19 experiments (84.2%). Blast phenotypes were stable in culture and at relapse, and were useful for MRD monitoring in patients. Marker combinations for childhood ALL are also applicable to adult cases.
A unique signature identifies a family of zinc‐dependent metallopeptidases (1989)

The primary sequence motif HExxH has been found in many zinc-dependent endopeptidases. We show that a larger signature comprising this sequence is common to most of the known zinc-dependent endopeptidases, and that the presence of the signature can be indicative of membership in the family. A search of the protein sequence databases for entries containing the signature retrieved several unexpected potential zinc endopeptidases.
Electrospinning and Porosity Measurements of Nylon-6/Poly(ethylene oxide) Blended Nonwovens (2007)

A simple method was used to prepare a nonwoven fabric of intimately co-mingled Nylon-6 and Polyethylene oxide (PEO) electrospun fibers by spinning fibers onto a rotating collector. Electrospinning parameters for each polymer were independent. Fiber mixture and distribution was uniform throughout the depth of the fabric. Porosity and pore size distribution of the materials were measured before and after a washing treatment. The PEO component was removed during the washing step to create increased pore size in the remaining fabric. This study indicates a simple method to create nanofiber nonwovens of multiple dissimilar polymers and provides a strategy for controlling pore size distribution independently from fiber formation.
A computer-aided design system for microelectromechanical systems (MEMCAD) (1992)

The authors describe the MIT microelectromechanical computer-aided design system (MEMCAD), in which selected commercial software packages are linked with specialized database and numerical programs to allow designers to quickly perform both mechanical and electrical analyses of structures either described directly, or derived from the design specification (mask data plus process flow). The system architecture, the various modules, and their present status are described, and present system performance is demonstrated with several examples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cell surface fibronectin and oncogenic transformation (1979)

Fibronectin is a large glycoprotein at the cell surface of many different cell types; a related protein is present in plasma. Fibronectin is a dimer of 230,000-dalton subunits and also occurs in larger aggregates; it forms fibrillar networks at the cell surface, between cells and substrata and between adjacent cells, and it is not a typical membrane protein. Cell surface fibronectin is reduced in amount or absent on transformed cells and in many cases its loss correlates with acquisition of tumorigenicity and, in particular, metastatic ability. Exceptions to the correlations with transformation and tumorigenicity exist. Loss of fibronectin and the resulting reduced adhesion appear to be involved in pleiotropic alterations in cell behavior and may be responsible for several aspects of the transformed phenotype in vitro. Fibronectin interacts with other macromolecules (collagen/gelatin, fibrin/fibrinogen, proteoglycans) and is apparently connected to microfilaments inside the cell.
Effect of Levetiracetam on Epilepsy‐Related Quality of Life (2000)

Addition of LEV to standard medication seems to have a positive impact on health-related quality of life, particularly among responders in this short-term study. These exploratory analyses require additional studies to evaluate long-term changes in a larger population.
Elastic impedance (1999)

It is now commonplace for 3-D data sets to be processed as partial offset volumes to exploit the AVO information in the data. However, there has been significant asymmetry in the way these volumes could be calibrated and inverted. The amplitudes of near-offset, or intercept, stacks relate to changes in acoustic impedance and can be tied to well logs using synthetics based on acoustic impedance (AI) or inverted, to some extent, back to AI using poststack inversion algorithms. However, there have been no simple analogous processes for far-offset stacks.
On Regularized Losses for Weakly-supervised CNN Segmentation (2018)

Minimization of regularized losses is a principled approach to weak supervision well-established in deep learning, in general. However, it is largely overlooked in semantic segmentation currently dominated by methods mimicking full supervision via "fake" fully-labeled training masks (proposals) generated from available partial input. To obtain such full masks the typical methods explicitly use standard regularization techniques for "shallow" segmentation, e.g. graph cuts or dense CRFs. In contrast, we integrate such standard regularizers directly into the loss functions over partial input. This approach simplifies weakly-supervised training by avoiding extra MRF/CRF inference steps or layers explicitly generating full masks, while improving both the quality and efficiency of training. This paper proposes and experimentally compares different losses integrating MRF/CRF regularization terms. We juxtapose our regularized losses with earlier proposal-generation methods using explicit regularization steps or layers. Our approach achieves state-of-the-art accuracy in semantic segmentation with near full-supervision quality.
Preparation and characterization of new fluoroxy compounds. Bis(fluoroxy)perfluoro alkanes (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and characterization of new fluoroxy compounds. Bis(fluoroxy)perfluoro alkanesPhillip Gerhard. Thompson and Julianne H. PragerCite this: J. Am. Chem. Soc. 1967, 89, 10, 2263–2267Publication Date (Print):May 1, 1967Publication History Published online1 May 2002Published inissue 1 May 1967https://doi.org/10.1021/ja00986a005Request reuse permissionsArticle Views89Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (635 KB) Get e-Alertsclose Get e-Alerts
Pseudotyping of Glycoprotein D-Deficient Herpes Simplex Virus Type 1 with Vesicular Stomatitis Virus Glycoprotein G Enables Mutant Virus Attachment and Entry (2000)

ABSTRACT The use of herpes simplex virus (HSV) vectors for in vivo gene therapy will require the targeting of vector infection to specific cell types in certain in vivo applications. Because HSV glycoprotein D (gD) imparts a broad host range for viral infection through recognition of ubiquitous host cell receptors, vector targeting will require the manipulation of gD to provide new cell recognition specificities in a manner designed to preserve gD's essential role in virus entry. In this study, we have determined whether an entry-incompetent HSV mutant with deletions of all Us glycoproteins, including gD, can be complemented by a foreign attachment/entry protein with a different receptor-binding specificity, the vesicular stomatitis virus glycoprotein G (VSV-G). The results showed that transiently expressed VSV-G was incorporated into gD-deficient HSV envelopes and that the resulting pseudotyped virus formed plaques on gD-expressing VD60 cells, albeit at a 50-fold-reduced level compared to that of wild-type gD. This reduction may be related to differences in the entry pathways used by VSV and HSV or to the observed lower rate of incorporation of VSV-G into virus envelopes than that of gD. The rate of VSV-G incorporation was greatly improved by using recombinant molecules in which the transmembrane domain of HSV glycoprotein B or D was substituted for that of VSV-G, but these recombinant molecules failed to promote virus entry. These results show that foreign glycoproteins can be incorporated into the HSV envelope during replication and that gD can be dispensed with on the condition that a suitable attachment/entry function is provided.
A supersecondary structure library and search algorithm for modeling loops in protein structures (2006)

We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105,950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed phi/psi main chain dihedral angle propensities. Confidence Z-score cut-offs were determined for each loop length that identify those predicted fragments that outperform a competitive ab initio method. A web server implements the method, regularly updates the fragment library and performs prediction. Predicted segments are returned, or optionally, these can be completed with side chain reconstruction and subsequently annealed in the environment of the query protein by conjugate gradient minimization. The prediction method was tested on artificially prepared search datasets where all trivial sequence similarities on the SCOP superfamily level were removed. Under these conditions it is possible to predict loops of length 4, 8 and 12 with coverage of 98, 78 and 28% with at least of 0.22, 1.38 and 2.47 A of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5:1 ratio an earlier developed database search method.
Olanzapine Use for the Adjunctive Treatment of Adolescents with Anorexia Nervosa (2011)

Despite our best attempts at matching olanzapine-treated subjects with a control sample, analysis revealed significant differences between groups, suggesting greater illness severity in those augmented with olanzapine. Given these inherent differences, we were unable to draw any firm conclusions regarding the potential efficacy of olanzapine. Factors associated with the prescription of adjunctive pharmacotherapy in this cohort appear to be linked to illness severity, acuity, and associated comorbidity. The observed side-effect profile indicates the need for more consistent predrug screening and for closer monitoring during treatment.
Cloning and Sequencing of the Alkaline Protease cDNA fromAspergillus oryzae (1988)

Journal Article Cloning and Sequencing of the Alkaline Protease cDNA from Aspergillus oryzae Get access Hiroki Tatsumi, Hiroki Tatsumi Research and Development Division, Kikkoman Corporation, 399 Noda, Noda-shi, Chiba 278, Japan Search for other works by this author on: Oxford Academic Google Scholar Manabu Ohsawa, Manabu Ohsawa Research and Development Division, Kikkoman Corporation, 399 Noda, Noda-shi, Chiba 278, Japan Search for other works by this author on: Oxford Academic Google Scholar Ryohei F Tsuji, Ryohei F Tsuji Research and Development Division, Kikkoman Corporation, 399 Noda, Noda-shi, Chiba 278, Japan Search for other works by this author on: Oxford Academic Google Scholar Seiji Murakami, Seiji Murakami Research and Development Division, Kikkoman Corporation, 399 Noda, Noda-shi, Chiba 278, Japan Search for other works by this author on: Oxford Academic Google Scholar Eiichi Nakano, Eiichi Nakano Research and Development Division, Kikkoman Corporation, 399 Noda, Noda-shi, Chiba 278, Japan Search for other works by this author on: Oxford Academic Google Scholar Hiroshi Motai, Hiroshi Motai Research and Development Division, Kikkoman Corporation, 399 Noda, Noda-shi, Chiba 278, Japan Search for other works by this author on: Oxford Academic Google Scholar Atsushi Masaki, Atsushi Masaki Research Division, The Green Cross Corporation, 2–1180–1 Shodai Ohtani, Hirakata-shi, Osaka 573, Japan Search for other works by this author on: Oxford Academic Google Scholar Yutaka Ishida, Yutaka Ishida Research Division, The Green Cross Corporation, 2–1180–1 Shodai Ohtani, Hirakata-shi, Osaka 573, Japan Search for other works by this author on: Oxford Academic Google Scholar Kohji Murakami, Kohji Murakami Research Division, The Green Cross Corporation, 2–1180–1 Shodai Ohtani, Hirakata-shi, Osaka 573, Japan Search for other works by this author on: Oxford Academic Google Scholar Haruhide Kawabe, Haruhide Kawabe Research Division, The Green Cross Corporation, 2–1180–1 Shodai Ohtani, Hirakata-shi, Osaka 573, Japan Search for other works by this author on: Oxford Academic Google Scholar ... Show more Hirofumi Arimura Hirofumi Arimura Research Division, The Green Cross Corporation, 2–1180–1 Shodai Ohtani, Hirakata-shi, Osaka 573, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 52, Issue 7, 1 July 1988, Pages 1887–1888, https://doi.org/10.1080/00021369.1988.10868950 Published: 01 July 1988 Article history Received: 14 April 1988 Published: 01 July 1988
ALBINO3, an Arabidopsis Nuclear Gene Essential for Chloroplast Differentiation, Encodes a Chloroplast Protein That Shows Homology to Proteins Present in Bacterial Membranes and Yeast Mitochondria (1997)

Eva Sundberg, Jacoba G. Slagter, Ingela Fridborg, Suzanne P. Cleary, Colin Robinson, George Coupland, ALBINO3, an Arabidopsis Nuclear Gene Essential for Chloroplast Differentiation, Encodes a Chloroplast Protein That Shows Homology to Proteins Present in Bacterial Membranes and Yeast Mitochondria, The Plant Cell, Vol. 9, No. 5 (May, 1997), pp. 717-730
Macrophage Metalloelastase Mediates Acute Cigarette Smoke–induced Inflammation via Tumor Necrosis Factor-α Release (2003)

The cells and proteases that mediate cigarette smoke-induced emphysema are controversial, with evidence favoring either neutrophils and neutrophil-derived serine proteases or macrophages and macrophage-derived metalloproteases as the important effectors. We recently reported that both macrophage metalloelastase (MMP-12) and neutrophils are required for acute cigarette smoke-induced connective tissue breakdown, the precursor of emphysema. Here we show how these disparate observations can be linked. Both wild-type (MMP-12 +/+) mice and mice lacking MMP-12 (MMP-12 -/-) demonstrated rapid increases in whole-lung nuclear factor-kappaB activation and gene expression of proinflammatory cytokines after cigarette smoke exposure, indicating that a lack of MMP-12 does not produce a global failure to upregulate inflammatory mediators. However, only MMP-12 +/+ mice demonstrated increased whole-lung tumor necrosis factor-alpha (TNF-alpha) protein or release of TNF-alpha from cultured alveolar macrophages exposed to smoke in vitro. Levels of whole-lung E-selectin, an endothelial activation marker, were increased in only MMP-12 +/+ mice. These findings suggest that, acutely, MMP-12 mediates smoke-induced inflammation by releasing TNF-alpha from macrophages, with subsequent endothelial activation, neutrophil influx, and proteolytic matrix breakdown caused by neutrophil-derived proteases. TNF-alpha release may be a general mechanism whereby metalloproteases drive cigarette smoke-induced inflammation.
Homography-based visual servo tracking control of a wheeled mobile robot (2004)

A visual servo tracking controller is developed in this paper for a monocular camera system mounted on an underactuated wheeled robot (WMR) subject nonholonomic motion constraints (i.e., the camera-in-hand problem). A prerecorded image sequence (e.g., a video) of three target points is used to define a desired trajectory for the WMR. By comparing the target points from the prerecorded sequence with the corresponding target points in the live image, projective geometric relationships are exploited to construct a Euclidean homography. The information obtained by decomposing the Euclidean homography is used to develop a kinematic controller. A Lyapunov-based analysis is used to develop an adaptive update law to actively compensate for the lack of depth information required for the translation error system.
Requirement for vascular endothelial growth factor in wound- and inflammation-related corneal neovascularization. (1998)

These data are the first to demonstrate that VEGF may be required for inflammatory neovascularization of the rat cornea and to identify VEGF as a functional endogenous corneal angiogenic factor.
Stimulation of CD8+ T cell responses to MAGE-3 and Melan A/MART-1 by immunization to a polyvalent melanoma vaccine (1997)

A critical requirement for cancer vaccines is that they stimulate CD8+ T cell responses. In this study, we tested the ability of a polyvalent melanoma vaccine to induce CD8+ T cell responses to the melanoma associated antigens MAGE-3 and Melan A/MART-1. Fifteen HLA-A2+ patients with resected malignant melanoma were immunized with the vaccine s.c. every 2-3 weeks. CD8+ T cells in peripheral blood reacting to HLA-A2 restricted epitopes on MAGE-3 (FLWGPRALV) and Melan A/MART-1/(AAGIGILTV) were quantitated using a filter spot assay at baseline and following 4 immunizations. Vaccine immunization induced CD8+ T cells reacting to one or both of these peptides in 9 of the 15 (60%) patients. These cells were CD8+ and HLA-A2 restricted, as reactivity was abrogated by monoclonal antibodies (MAbs) to CD8 and class I HLA, but not by anti-CD4. All responding patients remained recurrence-free for at least 12 months (median 15 months, range 12 to >21 months), whereas melanoma recurred within 3-5 months in non-responders. The differences in outcome were unrelated to differences in disease severity or overall immunological competence between responders and non-responders. Our results demonstrate directly that MAGE-3 and Melan A/MART-1 can stimulate CD8+ T cell responses in humans, and suggest that these responses are protective and surrogate markers of vaccine efficacy.