gebhart/patrepeval huggingface dataset:
Acute exacerbation of idiopathic pulmonary fibrosis: incidence, risk factors and outcome (2010)

Although acute exacerbation of idiopathic pulmonary fibrosis (IPF) has become well recognised, the reported incidence and outcomes are highly variable, and risk factors are unknown. The aim of this study was to estimate the incidence, risk factors and impact of acute exacerbations, and other known causes of rapid deterioration. This was a retrospective review of 461 patients with IPF (269 cases were biopsy-proven). The median follow-up period was 22.9 months. Rapid deterioration requiring hospitalisation occurred in 163 (35.4%) patients, with multiple episodes in 42 patients. Acute exacerbation was the most frequent cause (55.2%), followed by infection. The 1- and 3-yr incidences of acute exacerbation were 14.2 and 20.7%, respectively. Never having smoked and low forced vital capacity (FVC) were significant risk factors. The in-hospital mortality rate was 50.0%, and the 1- and 5-yr survival rates from the initial diagnosis were 56.2 and 18.4%, respectively. Acute exacerbation was a significant predictor of poor survival after the initial diagnosis, along with increased age, low FVC and diffusing capacity of the lung for carbon monoxide, and steroid use with or without cytotoxic therapy. 1- and 3-yr incidences of acute exacerbation were 14.2 and 20.7%, respectively. Never having smoked and low FVC were risk factors. Acute exacerbation had a serious impact on the overall survival of the patients with IPF.
VACUUM-ASSISTED CLOSURE THERAPY AND ORAL ANTICOAGULATION THERAPY (2004)

Steenvoorde, Pascal M.D., M.A.; van Engeland, Anneke M.D.; Oskam, Jacques M.D., Ph.D. Author Information
Exosomes reflect the hypoxic status of glioma cells and mediate hypoxia-dependent activation of vascular cells during tumor development (2013)

Hypoxia, or low oxygen tension, is a major regulator of tumor development and aggressiveness. However, how cancer cells adapt to hypoxia and communicate with their surrounding microenvironment during tumor development remain important questions. Here, we show that secreted vesicles with exosome characteristics mediate hypoxia-dependent intercellular signaling of the highly malignant brain tumor glioblastoma multiforme (GBM). In vitro hypoxia experiments with glioma cells and studies with patient materials reveal the enrichment in exosomes of hypoxia-regulated mRNAs and proteins (e.g., matrix metalloproteinases, IL-8, PDGFs, caveolin 1, and lysyl oxidase), several of which were associated with poor glioma patient prognosis. We show that exosomes derived from GBM cells grown at hypoxic compared with normoxic conditions are potent inducers of angiogenesis ex vivo and in vitro through phenotypic modulation of endothelial cells. Interestingly, endothelial cells were programmed by GBM cell-derived hypoxic exosomes to secrete several potent growth factors and cytokines and to stimulate pericyte PI3K/AKT signaling activation and migration. Moreover, exosomes derived from hypoxic compared with normoxic conditions showed increased autocrine, promigratory activation of GBM cells. These findings were correlated with significantly enhanced induction by hypoxic compared with normoxic exosomes of tumor vascularization, pericyte vessel coverage, GBM cell proliferation, as well as decreased tumor hypoxia in a mouse xenograft model. We conclude that the proteome and mRNA profiles of exosome vesicles closely reflect the oxygenation status of donor glioma cells and patient tumors, and that the exosomal pathway constitutes a potentially targetable driver of hypoxia-dependent intercellular signaling during tumor development.
The AO Ulnar Shortening Osteotomy System Indications and Surgical Technique (2014)

Ulnar shortening osteotomy is an established and frequently performed surgical procedure in wrist surgery. The technical aspects of the procedure have continued to develop in recent years, with instruments and implants being developed specifically for this purpose. Ulnar shortening osteotomy is required for different clinical indications and situations. These varying indications demand different amounts of shortening, but all must be precise and accurate. Controversy exists as to how this can best be achieved in terms of the location for osteotomy, the surgical approach and geometry of the osteotomy, as well as which implant to use to provide optimal stability. The goal of all techniques (besides successfully resolving the underlying problem) is to achieve reliable and rapid bone union without compromising early functional rehabilitation and also to avoid hardware complications. The AO Hand Expert Group has developed a specialized instrumentation system with dedicated and specifically designed implants to ensure exact and accurate cutting with precise and rigid stabilization of the ulna. The matched drill guides and double-blade saws allow accurate completion of the planned amount of shortening together with precise coaptation of the osteotomy fragments. The specific ulnar osteotomy LCP (locking compression plate) combines maximum stability with minimum bulk and soft tissue irritation. The features of the implant, its surgical technique, and early results are described.
Image analysis and platform development for automated phenotyping in cytomics (2013)

&lt;p&gt;&lt;/p&gt;&lt;table&gt;&lt;tbody&gt;&lt;tr&gt;&lt;td&gt;&lt;/td&gt;&lt;td&gt;This thesis is dedicated to the empirical study of image analysis in HT/HC screen study. Often a HT/HC screening produces extensive amounts that cannot be manually analyzed. Thus, an automated image analysis solution is prior to an objective understanding of the raw image data. Compared to general application domain, the efficiency of HT/HC image analysis is highly subjected to image quantity and quality. Accordingly, this thesis will address two major procedures, namely image segmentation and object tracking, in the image analysis step of HT/HC screen study. Moreover, this thesis focuses on expending generic computer science and machine learning theorems into the design of dedicated algorithms for HT/HC image analysis. Additionally, this thesis exemplifies a practical implementation of image analysis and data analysis workflow via empirical case studies with different image modalities and experiment settings. However, the data analysis theorem will be generally illustrated without further expansions. Finally, the thesis will briefly address supplementary infrastructures for end-user interaction and data visualization.&lt;/td&gt;&lt;/tr&gt;&lt;/tbody&gt;&lt;/table&gt;
A phase I and translational study of sequential administration of the topoisomerase I and II inhibitors topotecan and etoposide. (1998)

Because topoisomerase (topo) I- and topo II-targeting agents exert their principal effects on the two major classes of enzymes involved in regulating DNA topology in the cell, there has been considerable interest in evaluating combinations of these classes of agents. In preclinical studies of inhibitors of topo I and topo II in combination, drug scheduling and sequencing have been critical determinants of antitumor activity, with a greater magnitude of cytotoxicity generally occurring when treatment with the topo I inhibitor precedes treatment with the topo II-targeting agent. The underlying mechanism that has been proposed to explain this schedule dependency is compensatory up-regulation of topo II and, therefore, enhanced cytotoxicity of topo II inhibitors in cells treated initially with topo I inhibitors. The feasibility of sequentially administering the topo I inhibitor topotecan (TPT) followed by the topo II inhibitor etoposide to patients with advanced solid malignancies was evaluated in this Phase I and translational laboratory study. Fifty patients with solid neoplasms were treated with TPT doses ranging from 0.17 to 1.05 mg/m2/day as a 72-h continuous (i.v.) infusion on days 1-3 followed by etoposide, 75 or 100 mg/m2/day as a 2-h i.v. infusion daily on days 8-10. The combined rate of severe neutropenia and thrombocytopenia was unacceptably high above the TPT (mg/m2/day)/etoposide (mg/m2/day) dose levels of 0.68/100 and 0.68/75 in minimally and heavily pretreated patients, respectively, and these dose levels are recommended for further disease-directed evaluations of TPT/etoposide on this administration schedule. Successive biopsies of accessible tumors were obtained for quantitation of topo I and II levels prior to and immediately after treatment with TPT and prior to and immediately after treatment with etoposide in seven patients. The results of these limited studies in tumors did not fully support the proposed mechanistic rationale favoring the development of this particular sequential TPT/etoposide regimen, because only two of the six patients' tumors in whom topo I was successively measured had either modest or substantial decrements in topo I levels following treatment with TPT, and the principal effect of interest, up-regulation of topo II following treatment with TPT, was clearly documented in the tumors of only one of six subjects in whom successive measurements of topo I were performed. Even in view of the notable objective antitumor activity in three subjects, including a complete response in a patient with colorectal carcinoma and partial responses in one patient each with non-small cell lung and gastric carcinomas, the toxicity and ancillary laboratory results do not provide substantial evidence that sequential treatment with TPT and etoposide might be more advantageous than either TPT or etoposide administered as a single agent.
Preferential transposition of Drosophila P elements to nearby chromosomal sites. (1993)

Two different schemes were used to demonstrate that Drosophila P elements preferentially transpose into genomic regions close to their starting sites. A starting element with weak rosy+ marker gene expression was mobilized from its location in the subtelomeric region of the 1,300-kb Dp1187 minichromosome. Among progeny lines with altered rosy+ expression, a much higher than expected frequency contained new insertions on Dp1187. Terminal deficiencies were also recovered frequently. In a second screen, a rosy(+)-marked element causing a lethal mutation of the cactus gene was mobilized in male and female germlines, and viable revertant chromosomes were recovered that still contained a rosy+ gene due to an intrachromosomal transposition. New transpositions recovered using both methods were mapped between 0 and 128 kb from the starting site. Our results suggested that some mechanism elevates the frequency 43-67-fold with which a P element inserts near its starting site. Local transposition is likely to be useful for enhancing the rate of insertional mutation within predetermined regions of the genome.
Dual Mechanisms for the Inhibition of E2F Binding to RB by Cyclin-Dependent Kinase-Mediated RB Phosphorylation (1997)

The growth suppression function of RB is dependent on its protein binding activity. RB contains at least three distinct protein binding functions: (i) the A/B pocket, which binds proteins with the LXCXE motif; (ii) the C pocket, which binds the c-Abl tyrosine kinase; and (iii) the large A/B pocket, which binds the E2F family of transcription factors. Phosphorylation of RB, which is catalyzed by cyclin-dependent protein kinases, inhibits all three protein binding activities. We have previously shown that LXCXE binding is inactivated by the phosphorylation of two threonines (Thr821 and Thr826), while the C pocket is inhibited by the phosphorylation of two serines (Ser807 and Ser811). In this report, we show that the E2F binding activity of RB is inhibited by two sets of phosphorylation sites acting through distinct mechanisms. Phosphorylation at several of the seven C-terminal sites can inhibit E2F binding. Additionally, phosphorylation of two serine sites in the insert domain can inhibit E2F binding, but this inhibition requires the presence of the RB N-terminal region. RB mutant proteins lacking all seven C-terminal sites and two insert domain serines can block Rat-1 cells in G1. These RB mutants can bind LXCXE proteins, c-Abl, and E2F even after they become phosphorylated at the remaining nonmutated sites. Thus, multiple phosphorylation sites regulate the protein binding activities of RB through different mechanisms, and a constitutive growth suppressor can be generated through the combined mutation of the relevant phosphorylation sites in RB.
H&E-stained Whole Slide Image Deep Learning Predicts SPOP Mutation State in Prostate Cancer (2016)

A quantitative model to genetically interpret the histology in whole microscopy slide images is desirable to guide downstream immuno-histochemistry, genomics, and precision medicine. We constructed a statistical model that predicts whether or not SPOP is mutated in prostate cancer, given only the digital whole slide after standard hematoxylin and eosin [H&amp;E] staining. Using a TCGA cohort of 177 prostate cancer patients where 20 had mutant SPOP, we trained multiple ensembles of residual networks, accurately distinguishing SPOP mutant from SPOP non-mutant patients (test AUROC=0.74, p=0.0007 Fisher’s Exact Test). We further validated our full metaensemble classifier on an independent test cohort from MSK-IMPACT of 152 patients where 19 had mutant SPOP. Mutants and non-mutants were accurately distinguished despite TCGA slides being frozen sections and MSK-IMPACT slides being formalin-fixed paraffin-embedded sections (AUROC=0.86, p=0.0038). Moreover, we scanned an additional 36 MSK-IMPACT patients having mutant SPOP, trained on this expanded MSK-IMPACT cohort (test AUROC=0.75, p=0.0002), tested on the TCGA cohort (AUROC=0.64, p=0.0306), and again accurately distinguished mutants from non-mutants using the same pipeline. Importantly, our method demonstrates tractable deep learning in this “small data” setting of 20-55 positive examples and quantifies each prediction’s uncertainty with confidence intervals. To our knowledge, this is the first statistical model to predict a genetic mutation in cancer directly from the patient’s digitized H&amp;E-stained whole microscopy slide. Moreover, this is the first time quantitative features learned from patient genetics and histology have been used for content-based image retrieval, finding similar patients for a given patient where the histology appears to share the same genetic driver of disease i.e. SPOP mutation (p=0.0241 Kost’s Method), and finding similar patients for a given patient that does not have have that driver mutation (p=0.0170 Kost’s Method). Significance Statement This is the first pipeline predicting gene mutation probability in cancer from digitized H&amp;E-stained microscopy slides. To predict whether or not the speckle-type POZ protein [SPOP] gene is mutated in prostate cancer, the pipeline (i) identifies diagnostically salient slide regions, (ii) identifies the salient region having the dominant tumor, and (iii) trains ensembles of binary classifiers that together predict a confidence interval of mutation probability. Through deep learning on small datasets, this enables automated histologic diagnoses based on probabilities of underlying molecular aberrations and finds histologically similar patients by learned genetic-histologic relationships. Conception, Writing: AJS, TJF. Algorithms, Learning, CBIR: AJS. Analysis: AJS, MAR, TJF. Supervision: MAR, TJF.
Magnitude and variation of fat-free mass density: a cellular-level body composition modeling study (2003)

The mean density of fat-free mass (FFM) is remarkably stable at 1.10 g/cm(3) in healthy adult humans, and this stability is a cornerstone of the widely applied densitometry-based two-compartment model for estimating total body fat. At present, the usual means of exploring FFM density is by in vitro or in vivo experimental studies. The purpose of the present investigation was to develop a cellular-level body composition model that includes seven factors that determine FFM density. The model, when applied with available empirical coefficients, predicted an FFM density similar to that observed in vivo. An analysis of the seven model components indicates that the ratio of extracellular solids to total body water is a major determinant of individual variation in FFM density. The difference in FFM density across sex, race, and age groups was examined with the developed model. The present study thus provides a conceptual framework for the systematic study of FFM density in humans.
Immunochemical and immunogenic properties of a purified keyhold limpet haemocyanin. (1972)

A highly reproducible method for obtaining a relatively homogeneous preparation of keyhole limpet haemocyanin (KLH) is described. This method employs ion-exchange chromatography on DEAE-cellulose followed by gel filtration on agarose beads. Analysis by immunoelectrophoresis in agar, electrophoresis in polyacrylamide gels, analytical ultracentrifugation and double diffusion in agar indicated that the purified preparation contained one major antigenic component, whereas the crude material contained multiple antigenic components. The crude KLH was found to be a more potent immunogen than the purified preparation upon primary stimulation of rabbits.
Axonopathy and Transport Deficits Early in the Pathogenesis of Alzheimer's Disease (2005)

We identified axonal defects in mouse models of Alzheimer's disease that preceded known disease-related pathology by more than a year; we observed similar axonal defects in the early stages of Alzheimer's disease in humans. Axonal defects consisted of swellings that accumulated abnormal amounts of microtubule-associated and molecular motor proteins, organelles, and vesicles. Impairing axonal transport by reducing the dosage of a kinesin molecular motor protein enhanced the frequency of axonal defects and increased amyloid-beta peptide levels and amyloid deposition. Reductions in microtubule-dependent transport may stimulate proteolytic processing of beta-amyloid precursor protein, resulting in the development of senile plaques and Alzheimer's disease.
Isolation and characterization of a new mutant human cell line unresponsive to alpha and beta interferons. (1991)

Previously we described human cell line 2fTGH, in which expression of guanine phosphoribosyltransferase is tightly controlled by the upstream region of interferon (IFN)-stimulated human gene 6-16. After mutagenesis of 2fTGH and selection with 6-thioguanine and IFN-alpha, we isolated 11.1, a recessive mutant that does not respond to IFN-alpha. We now describe U2, a second recessive mutant, selected similarly, that complements 11.1. U2 had no response to IFN-alpha or IFN-beta, and its response to IFN-gamma was partially defective. Although many genes did respond to IFN-gamma in U2, the 9-27 gene did not and the antiviral response of U2 cells to IFN-gamma was greatly reduced. Band shift assays showed that none of the transcription factors normally induced in 2fTGH cells by IFN-alpha (E and M) or IFN-gamma (G) were induced in U2. However, extracts of untreated U2 cells gave rise to a novel band that was increased by treatment with IFN-gamma but not IFN-alpha. Band shift complementation assays revealed that untreated and IFN-gamma-treated U2 cells lack the functional E gamma subunit of transcription factor E and that IFN-alpha-treated U2 cells do contain the functional E alpha subunit.
Autologous bone marrow transplantation as consolidation therapy for non-Hodgkin's lymphoma patients with poor prognostic features. (1991)

Theoretical considerations and preliminary results of clinical trials support the earlier use of autologous bone marrow transplantation (ABMT) in poor prognosis non-Hodgkin's lymphoma (NHL). A prognostic analysis of 50 patients with intermediate or high grade NHL younger than 60 years, who achieved at least one complete remission and were not treated with BMT, was performed. Patients with bulky tumor at diagnosis and/or serum LDH greater than or equal to 600 U/l do poorly with conventional chemotherapy. Twelve patients with these high-risk initial characteristics in first complete remission (CR) and six patients in second or third CR were treated with cyclophosphamide (60 mg/kg x 2) and total body irradiation (1000-1200 cGy) followed by ABMT. Overall disease-free survival was 65% at a median follow-up of 35 months. No differences were found between the first and later CR patients. The rate of toxic death was 11%. Disease-free survival after first CR was better for 1st CR ABMT patients than for a historical chemotherapy control group with similar poor prognosis features (p = 0.008). These results support the use of ABMT in selected, high-risk NHL patients in first CR.
Expression and functional analysis of the anaplastic lymphoma kinase (ALK) gene in tumor cell lines (2002)

The initial identification of the ALK gene, expressed as C-terminal part of the transforming fusion protein NPM-ALK in the t(2;5)(p23;q35) lymphoma-associated chromosomal translocation, revealed a novel receptor tyrosine kinase (RTK). In order to expand the knowledge on ALK expression in the human system, we examined a panel of human cell lines for ALK expression and found that transcription is completely repressed in cell lines of entodermal origin (0/21). Furthermore, full length receptor expression is absent in cell lines of the hematopoietic system with the exception of t(2;5)-associated anaplastic large cell lymphomas lines (ALCL), which are known to express chimeric NPM-ALK mRNA. Cell lines established from solid tumors of ectodermal origin, including melanoma and breast carcinoma, exhibited widespread mRNA expression of the ALK receptor at a broad range (53/64), an association which was found to be strongest in cell lines derived from neuroblastoma (6/6), glioblastoma (8/8) as well as in cell lines established from Ewing sarcoma (4/4) and retinoblastomas (2/2). Because of the reported involvement of neutrophin tyrosine kinase receptors in autocrine differentiation in neuroblastomas, we analyzed cell lines positive for full length or chimeric ALK protein for the presence of phoshotyrosine residues within the intracellular region of ALK. While the constitutive activation of chimeric NPM-ALK molecules could be shown, no evidence was found for induced or constitutively activated ALK receptors in neuroblastoma, melanoma or breast carcinoma cell lines. Although the receptor could be shown to be consistently expressed with exclusive specificity in tissues developed from the ectoderm, our results do not support any involvement of ALK in the stimulation of tumorigenic cell growth or differentiation so far, indicating that ALK expression is a physiologic rather than a pathologic phenomenon.