gebhart/patrepeval huggingface dataset:
Identification of Common Germinal-Center B-Cell Precursors in Two Patients with Both Hodgkin's Disease and Non-Hodgkin's Lymphoma (1999)

In two patients with classic Hodgkin's disease and non-Hodgkin's B-cell lymphoma, we identified a common B-cell precursor, probably a germinal-center B-cell, for both lymphomas. This finding suggests that the two types of lymphoma underwent both shared and distinct transforming events and provides proof of the B-cell derivation of Reed-Sternberg cells in classic Hodgkin's disease.
A CMOS 0.8 μm programmable charge pump for the output stage of an implantable pacemaker (2002)

This work proposes a voltage multiplier suitable for a pacemaker pulse generator in a high voltage 0.8 /spl mu/m CMOS technology. The proposed circuit topology can handle the relatively high voltages required to stimulate the heart, while still being able to operate from an almost exhausted pacemaker battery. The circuit can operate with a supply voltage from 2.8 V to 2 V, while the maximum output voltage is about three times the power supply. Fine programmability of the output voltage has been achieved, thus allowing the choice of the optimum trade-off between stimulation efficacy and battery longevity. Moreover the proposed solution takes care of minimizing the parasitic coupling and disturbances between the charge pump and other blocks in the system.
Inhibition of Endothelial Regeneration by Type-Beta Transforming Growth Factor from Platelets (1986)

Damage to the vessel wall is a signal for endothelial migration and replication and for platelet release at the site of injury. Addition of transforming growth factor-beta (TGF-beta) purified from platelets to growing aortic endothelial cells inhibited [3H]thymidine incorporation in a concentration-dependent manner. A transient inhibition of DNA synthesis was also observed in response to wounding; cell migration and replication are inhibited during the first 24 hours after wounding. By 48 hours after wounding both TGF-beta-treated and -untreated cultures showed similar responses. Flow microfluorimetric analysis of cell cycle distribution indicated that after 24 hours of exposure to TGF-beta the cells were blocked from entering S phase, and the fraction of cells in G1 was increased. The inhibition of the initiation of regeneration by TGF-beta could allow time for recruitment of smooth muscle cells into the site of injury by other platelet components.
Generation of cytotoxic T lymphocytes in vitro. V. Response of normal and immune spleen cells to subcellular alloantigens. (1975)

Subcellular particulate membrane fragments prepared from murine lymphoid or tumor cells were used as a cell-free antigen source in order to stimulate the generation of cytolytic thymus-derived effector cells (CTL) in vitro. When cultivated with normal spleen cells as a source of responding lymphocytes, particulate antigen preparations induced only low CTL activities; in contrast, virtually normal responses were observed when immune spleens were used as a source of responding cells. In both cases, results were compared to those responses obtained with intact irradiated (1000 rads) normal spleen cells as stimulating antigen. The effector cells generated with particulate antigen preparations (obtained either by hypotonic shock or by sonication) were shown to be T cells and were characterized with regard to the kinetics of their response and their dose-activity relationship. It was also shown that the responses observed were specific, both at the level of initiation and at the effector level. The results obtained suggest that there exists a fundamental difference between normal and alloimmune spleen cells in their ability to respond in vitro to stimulation by subcellular antigen preparations.
Insulin-like growth factor I receptor activity in human medulloblastomas. (2002)

Medulloblastomas represent about 25% of all pediatric intracranial neoplasms. These highly malignant tumors arise from the cerebellum affecting mainly children between ages 5 and 15. Although the etiology of medulloblastomas has not yet been elucidated, several reports suggest that insulin-like growth factor I (IGF-I) may contribute to the development of these tumors. Results of this study show that the majority of cases examined were characterized by the abundant presence of the receptor for IGF-I (IGF-IR) protein (16 of 20 cases), and its major signaling molecule, insulin receptor substrate 1 (IRS-1; 15 of 20). Protein levels for IGF-IR and IRS-1, determined by Western blot and immunohistochemistry, were significantly higher in medulloblastoma biopsies than in control cerebellar tissue. By immunohistochemistry, 10 of 17 biopsies examined were also positive for the anti-pY1316 antibody staining that specifically recognizes the phosphorylated (active) form of the IGF-IR. These findings correlate with the fact that phosphorylated forms of the downstream-signaling molecules Erk-1, Erk-2, and Akt/protein kinase B were found in medulloblastoma biopsies but not in control cerebellar tissue. Importantly, there is a strong inverse correlation between biopsies that are positive for anti-pY1316 and for anti-Trk-C immunoreactivity. These observations direct our attention to the IGF-IR system as a potential therapeutic target in medulloblastomas and suggest a possibility of using the anti-pY1316 antibody as a potential prognostic marker for medulloblastomas.
Transforming growth factor beta 1 is present at sites of extracellular matrix gene expression in human pulmonary fibrosis. (1991)

Idiopathic pulmonary fibrosis is an inexorably fatal disorder characterized by connective tissue deposition within the terminal air spaces resulting in loss of lung function and eventual respiratory failure. Previously, we demonstrated that foci of activated fibroblasts expressing high levels of fibronectin, procollagen, and smooth muscle actin and thus resembling those found in healing wounds are responsible for the connective tissue deposition and scarring in idiopathic pulmonary fibrosis. Using in situ hybridization and immunohistochemistry, we now demonstrate the presence of transforming growth factor beta 1 (TGF-beta 1), a potent profibrotic cytokine, in the foci containing these activated fibroblasts. These results suggest that matrix-associated TGF-beta 1 may serve as a stimulus for the persistent expression of connective tissue genes. One potential source of the TGF-beta 1 is the alveolar macrophage, and we demonstrate the expression of abundant TGF-beta 1 mRNA in alveolar macrophages in lung tissue from patients with idiopathic pulmonary fibrosis.
The cDNA structure of the porcine pro‐hormone convertase PC2 and the comparative processing by PC1 and PC2 of the N‐terminal glycopeptide segment of porcine POMC (1992)

The complete cDNA structure of the porcine (p) pro-protein and pro-hormone convertase PC2 (pPC2) was obtained from a cDNA library of pituitary neurointermediate lobes mRNA. The deduced amino acid sequence revealed that pPC2 exhibits a 99-97% sequence identity to the human, mouse and rat homologues. The 3' end of the 2.1 kb cDNA is the least conserved segment. On Northern blots of pars intermedia poly A+ RNA two transcripts of 3 and 5 kb were detected. Molecular analysis of the N-terminal glycopeptide products of porcine pro-opiomelanocortin (pPOMC) co-expressed with vaccinia virus recombinants of PC1 or PC2, revealed that in cells devoid or containing secretory granules both convertases can cleave pPOMC with PC1 releasing the 1-80, 1-107 and 1-148 glycopeptide fragments, and PC2 cleaving pPOMC directly into pPOMC 1-107.
Development of robust antibody purification by optimizing protein‐A chromatography in combination with precipitation methodologies (2015)

To be administered to patients, therapeutic monoclonal antibodies must have very high purity, with process related impurities like host-cell proteins (HCPs) and DNA reduced to <100 ppm and <10 ppb, respectively, relative to desired product. Traditionally, Protein-A chromatography as a capture step has been the work horse for clearing a large proportion of these impurities. However, remaining levels of process and product related impurities still present significant challenges on the development of polishing steps further downstream. In this study, we have incorporated high throughput screening to evaluate three areas of separation: (i) Harvest treatment; (ii) Protein-A Chromatography; and (iii) Low pH Viral Inactivation. Precipitation with low pH treatment of cell culture harvest resulted in selective removal of impurities while manipulating the pH of wash buffers used in Protein-A chromatography and incorporating wash additives that disrupt various modes of protein-protein interaction resulted in further and more pronounced reduction in impurity levels. In addition, our study also demonstrate that optimizing the neutralization pH post Protein-A elution can result in selective removal of impurities. When applied over multiple mAbs, this optimization method proved to be very robust and the strategy provides a new and improved purification process that reduces process related impurities like HCPs and DNA to drug substance specifications with just one chromatography column and open avenues for significant decrease in operating costs in monoclonal antibody purification.
A usability study of awareness widgets in a shared workspace groupware system (1996)

Article Free Access Share on A usability study of awareness widgets in a shared workspace groupware system Authors: Carl Gutwin Department of Computer Science, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4 Department of Computer Science, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4View Profile , Mark Roseman Department of Computer Science, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4 Department of Computer Science, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4View Profile , Saul Greenberg Department of Computer Science, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4 Department of Computer Science, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4View Profile Authors Info & Claims CSCW '96: Proceedings of the 1996 ACM conference on Computer supported cooperative workNovember 1996 Pages 258–267https://doi.org/10.1145/240080.240298Published:16 November 1996Publication History 156citation2,195DownloadsMetricsTotal Citations156Total Downloads2,195Last 12 Months103Last 6 weeks16 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Memory bank disambiguation using modulo unrolling for Raw machines (2002)

We present modulo unrolling, a code transformation technique for enabling array references to be accessed through the fast static network on a Raw machine. A Raw machine comprises of a mesh of simple, replicated tiles connected by an interconnect which supports fast, static near-neighbor communication. Like all other resources, memory is distributed across the tiles. Management of the memory can be performed by well known techniques which generate the requisite communication code on distributed address-space architectures. On the other hand, the fast, static network provides the compiler with a simple interface to optimize such communication. This paper addresses the problem of taking advantage of such static communication for memory accesses. The requirement for static memory communication is the compile-time knowledge of the exact communication required for each memory reference. This knowledge, in turn, can be obtained if a memory reference refers exclusively to memory residing on a single processing tile. We introduce modulo unrolling as a technique which allows the static communication of a large class of array accesses. We show how this technique achieves the goal of static communication by using a relatively small unroll factor. For a set of dense matrix scientific applications, we are able to access all the array references on the static network, enabling scalable speedups on the Raw machine.
DATF: a database of Arabidopsis transcription factors (2005)

DATF is freely available at http://datf.cbi.pku.edu.cn
Segregation-mediated capping of Volmer-Weber Cu islands grown onto Ag(111) (2005)

The growth of Cu on an Ag(111) surface is studied using scanning tunneling microscopy at room temperature and for low Cu coverage ranging from 0.02 to 1.5 monolayers. Three-dimensional islands are found to grow at the Ag surface steps. During this Volmer-Weber growth, the erosion of steps and the formation of vacancy domains inside the terraces indicate that a large redistribution of Ag atoms takes place. Moreover, STM images from the top of islands reveal a $(9\ifmmode\times\else\texttimes\fi{}9)$ reconstruction which is well known to occur in the reverse case, where one Ag monolayer is deposited on Cu(111). These findings combined with molecular dynamics simulations allow us to conclude that the Cu islands are capped, from the very beginning of the growth, by one monolayer of Ag atoms diffusing from the eroded regions.
Aligning single-wall carbon nanotubes with an alternating-current electric field (2001)

Single-wall carbon nanotubes (SWCNTs) were highly aligned by an external electric field. The results suggest that the alignment of SWCNTs shows significant dependencies on the frequency and the magnitude of the applied electric field. The electric field with 5 MHz straightened out the SWCNTs and created highly oriented samples with fewer large particles. We also discussed the mechanism and applications.
RNA editing in Newcastle disease virus (1993)

The co-transcriptional editing of the Newcastle disease virus (NDV) P gene has been studied by sequence analysis of cloned viral genomic RNA and mRNA. Evidence has been obtained for the specific insertion of non-templated G nucleotides, the consequence of which is the generation of three populations of P gene-derived mRNAs. The three populations encode proteins (P, V and W) which have a common N-terminal region, but which utilize three different reading frames at their C termini. Paradoxically, NDV edits its P gene mRNA by the insertion of non-templated G residues in a manner similar to Sendai and measles viruses (P-->V editing) despite its apparent closer evolutionary relationship to the simian virus type 5, mumps and related group of viruses which edit a V genomic sequence to generate an mRNA to encode a functional P protein (V-->P editing).
Evaluating the Yield of Medical Tests (1982)

A method is presented for evaluating the amount of information a medical test provides about individual patients. Emphasis is placed on the role of a test in the evaluation of patients with a chronic disease. In this context, the yield of a test is best interpreted by analyzing the prognostic information it furnishes. Information from the history, physical examination, and routine procedures should be used in assessing the yield of a new test. As an example, the method is applied to the use of the treadmill exercise test in evaluating the prognosis of patients with suspected coronary artery disease. The treadmill test is shown to provide surprisingly little prognostic information beyond that obtained from basic clinical measurements.
Effect of duct obstruction on structure, elemental composition, and function of rat submandibular glands. (1989)

Obstruction of salivary glands occurs in association with a number of pathological conditions. It has been suggested that the major changes found in the salivary glands of patients with cystic fibrosis are due to obstruction of the excretory duct by viscous mucus. In the present study, the effect of excretory duct obstruction on structure, elemental composition and function of rat submandibular gland was investigated. Obstruction was effected by infusion of a fast-hardening protein emulsion in the main excretory duct. After 1 week, and more pronounced after 2 weeks of obstruction the number of granular duct cells had decreased in the obstructed gland. X-ray microanalysis showed an increase in Mg, Ca and K, and a decrease in Na levels in the acinar cells, compared to normal glands. The contralateral glands apparently underwent compensatory hypertrophy and showed a similar pattern of changes in elemental composition. The composition of pilocarpine-induced submandibular saliva was neither in the obstructed nor in the contralateral gland significantly different from that in control glands. However, the flow rate was somewhat lower. Hence, increase in cellular Ca levels in submandibular gland acinar cells in cystic fibrosis could be secondary to duct obstruction, but the present study does not support the hypothesis that duct obstruction would result in changes in the composition of saliva.
New insights into haemostasis in liver failure (2003)

The precise mechanisms leading to the coagulopathy of acute liver injury are unclear. To study this further, coagulation and immune changes have been compared in patients with acute liver injury secondary to paracetamol overdose, with chronic cirrhosis, and normal healthy controls. In acute liver injury, coagulation factors II, V, VII and X were reduced to a similar degree, and were significantly lower than factors IX and XI. In cirrhosis, by contrast, these coagulation factors were reduced to similar levels. Factor VIII increased in acute liver injury, but was normal in cirrhosis. Interleukin-6 and tumour necrosis factor-alpha levels increased in both patient groups, but were higher in paracetamol overdose. Thrombin-antithrombin and soluble tissue factor levels increased in those with acute liver injury, but were normal in patients with cirrhosis. Functional antithrombin was reduced in both acute liver injury and cirrhosis. It is hypothesized that in acute paracetamol-induced liver injury, immune activation leads to tissue factor-initiated consumption of factors II, V, VII and X, but that levels of factors IX and XI are better preserved because of inhibition of the thrombin-induced amplification phase of coagulation. These findings have implications for appropriate coagulation factor support for patients with acute liver injury.
Separation of the DNA Replication, Segregation, and Transcriptional Activation Functions of Epstein-Barr Nuclear Antigen 1 (2002)

In latent Epstein-Barr virus infection, the viral EBNA1 protein binds to specific sites in the viral origin of DNA replication, oriP, to activate the initiation of DNA replication, enhance the expression of other viral latency proteins, and partition the viral episomes during cell division. The DNA binding domain of EBNA1 is required for all three function, and a Gly-Arg-rich sequence between amino acids 325 and 376 is required for both the transcriptional activation and partitioning functions. We have used mutational analysis to identify additional EBNA1 sequences that contribute to EBNA1 functions. We show that EBNA1 amino acids 8 to 67 contribute to, but are not absolutely required for, EBNA1 replication, partitioning, and transcriptional activation functions. A Gly-Arg-rich sequence (amino acids 33 to 53) that is similar to that of amino acids 325 to 376 and lies within the 8-to-67 region was not responsible for the functional contributions of residues 8 to 67, since deletion of amino acids 34 to 52 alone did not affect EBNA1 functions. We also found that deletion of amino acids 61 to 83 eliminated the transcriptional activity of EBNA1 without affecting partitioning. This mutant also exhibited an increased replication efficiency that resulted in the maintenance of oriP plasmids at a copy number approximately fourfold higher than for wild-type EBNA1. The results indicate that the three EBNA1 functions have overlapping but different sequence requirements. Transcriptional activation requires residues 61 to 83 and 325 to 376 and is stimulated by residues 8 to 67; partitioning requires residues 325 to 376 and is stimulated by residues 8 to 67; and replication involves redundant contributions of both the 325-to-376 and 8-to-67 regions.
Osteochondral Repair Using Perichondrial Cells: A 1-Year Study in Rabbits (1997)

Articular cartilage repair remains a clinical and scientific challenge with increasing interest focused on the transplantation of chondrogenic cells. This study evaluated the repair response during a 1-year period after implantation of allogenic perichondrium cell polylactic acid composite grafts into 3.7 x 5 mm osteochondral defects drilled into the medial femoral condyles of 82 adult New Zealand White rabbits. The repair tissue was evaluated grossly, histologically, histomorphometrically, biochemically, and biomechanically at 6 weeks, 12 weeks, 6 months, and 1 year after implantation. After gross evaluation, cartilaginous material appeared to fill the defect in 70 experimental knees, for an overall repair frequency of 85%. The histomorphometric results and the histologic appearances were variable. None of the specimens were completely normal at 1 year. Only specimens with subchondral bone reformation displayed a definable cartilage appearing surface with chondrocytes surrounded by dense matrix. Subchondral bone reformation was inconsistent, reaching 50% at 1 year. Biochemically, the repair tissue matured during a 1-year period into a hyaline Type II collagen dominant tissue, whereas glycosaminoglycan content remained low at all time periods. The measured compressive properties of the repair tissue at 1 year were not significantly different from those of the contralateral knee that was not surgically treated. The treatment of osteochondral defects in the rabbit knee with allogenic perichondrium cell polylactic acid composite grafts yielded a high percentage of grossly successful repairs that showed inconsistent subchondral bone reformation. These results suggest that healthy subchondral bone is important to articular cartilage repair. They also highlight that a cartilaginous appearing tissue at gross inspection may not represent structurally normal articular cartilage. Continued multidisciplinary studies on the arthroplastic potential of rib perichondrial cells are needed before human studies, which rarely can extend beyond gross assessment of repair tissue appearance can be undertaken.
Systems biology of transcription control in macrophages (2007)

The study of the mammalian immune system offers many advantages to systems biologists. The cellular components of the mammalian immune system are experimentally tractable; they can be isolated or differentiated from in vivo and ex vivo sources and have an essential role in health and disease. For these reasons, the major effectors cells of the innate immune system, macrophages, have been a particular focus in international genome and transcriptome consortia. Genome-scale analysis of the transcriptome, and transcription initiation has enabled the construction of predictive models of transcription control in macrophages that identify the points of control (the major nodes of networks) and the ways in which they interact.