gebhart/patrepeval huggingface dataset:
Antifibrotic Effects ofN-Acetyl-Seryl-Aspartyl-Lysyl-Proline on the Heart and Kidney in Aldosterone-Salt Hypertensive Rats (2001)

N-acetyl-seryl-aspartyl-lysyl-proline (Ac-SDKP) inhibits not only hematopoietic cell proliferation but also fibroblast proliferation and collagen synthesis in vitro. Ac-SDKP also prevents collagen deposition and cell proliferation in the left ventricle (LV) in rats with renovascular hypertension (renin dependent). However, it is not clear whether Ac-SDKP has similar effects in a model of renin-independent hypertension (aldosterone-salt). Using a hypertensive rat model of cardiac and renal fibrosis created by chronic elevation of circulating aldosterone (ALDO) levels, we examined the effect of Ac-SDKP on blood pressure, cardiac and renal fibrosis and hypertrophy, and proliferating cell nuclear antigen (PCNA) expression in the LV and left kidney. Uninephrectomized rats were divided into 4 groups: (1) controls that received tap water, (2) rats that received ALDO (0.75 microgram/h SC) and 1% NaCl/0.2% KCl in drinking water (ALDO-salt), (3) rats that received ALDO-salt plus Ac-SDKP 400 microgram. kg(-1). day(-1) SC, and (4) rats that received ALDO-salt plus Ac-SDKP 800 microgram. kg(-1). d(-1) SC. After 6 weeks of treatment, the ALDO-salt group was found to have significantly increased blood pressure with decreased body weight and plasma renin concentration (P<0.05), LV and renal hypertrophy as well as renal injury, significantly increased collagen content in both ventricles and kidney as well as increased collagen volume fraction in the LV (P<0.0001), and significantly increased interstitial and perivascular PCNA-positive cells in the LV and kidney (P<0.0001). Ac-SDKP at 800 microgram. kg(-1). d(-1) markedly prevented cardiac and renal fibrosis (P<0.005) without affecting blood pressure or organ hypertrophy. It also suppressed PCNA expression in the LV and kidney in a dose-dependent manner. We concluded that Ac-SDKP prevents increased collagen deposition and cell proliferation in the heart and kidney in ALDO-salt hypertensive rats. Because ACE inhibitors increase plasma and tissue Ac-SDKP and decrease cardiac and renal fibrosis, we speculate that Ac-SDKP may participate in the antifibrotic effect of ACE inhibitors.
Multiplex PCR for TCR delta rearrangements: a rapid and specific approach for the detection and identification of immature and mature rearrangements in ALL (1998)

The preferential occurrence of immature T-cell receptor (TCR) delta rearrangements (i.e. incomplete Ddelta2-Ddelta3 and Vdelta2-Ddelta3) in B-cell precursor acute lymphoblastic leukaemia (BCP ALL) and of predominantly mature rearrangements (incomplete Ddelta2-Jdelta1, complete Vdelta1, Vdelta2, Vdelta3 to Jdelta1) in T-lineage ALL prompted us to establish two separate multiplex PCR systems for the identification of clonal TCRdelta rearrangements. PCR products of the expected size for the specific rearrangements were detectable from a dilution of 100-1000 clonal cells in 150000 polyclonal cells. Both multiplex PCR systems were used to analyse samples from 86 childhood BCPALLs and 30 T-lineage ALLs. The results of the multiplex PCRs were controlled by standard PCR analyses for the individual rearrangements and Southern blots, which were identical. Only immature TCRdelta rearrangements were detected in BCP ALL (59%), whereas no rearrangement was found in the remaining BCP leukaemias, thus confirming the exclusive presence of immature TCRdelta rearrangements in B-lineage cells. 50% of the T-lineage ALLs contained mature rearrangements, but no immature rearrangements were found. These two multiplex PCR techniques appear to be reliable and fast aids in the analysis of clonal TCRdelta rearrangements in ALL.
A design of a nanometer size metal particle generator: Thermal decomposition of metal carbonyls (1999)

We have developed a method which can produce both pure and alloy nanometer size metal particles in a large scale. This method combines a thermal decomposition of metal carbonyls with a collision induced clustering. Metal carbonyls are thermally decomposed with a hot filament and resultant bare metal atoms undergo collisions to produce nanometer size metal particles. This method requires a very simple experimental setup even though it is a high efficiency production method. Using this method, we have produced, high purity Fe, Mo, and alloy Fe/Mo nanometer size metal particles.
Common regions of deletion in chromosome regions 3p12 and 3p14.2 in primary clear cell renal carcinomas. (1994)

Nearly all clear cell renal cell carcinomas (RCCs) exhibit loss of alleles on the short arm of chromosome 3. Loss and mutation at the von Hippel-Lindau (VHL) gene at 3p25 probably occurs in most RCCs and, since the VHL gene was recently cloned, data on VHL involvement in RCCs is accumulating. However, the region 3p14-p12, a region that contains the familial RCC-associated t(3;8)(p14.2;q24) chromosome translocation and the small cell lung carcinoma-associated homozygous deletion at 3p13-12, has also been reported to exhibit allele loss in a large fraction of RCCs. In order to focus future studies on potential suppressor genes in the 3p14-p12 region, we have studied allele loss in 30 RCCs with 9 polymorphic simple sequence repeat markers spanning 3p21.1-p12. Partial losses in the 3p21-p12 region were observed, allowing determination of common regions of loss of heterozygosity overlap in 15 RCCs. Results suggested that most RCCs exhibit loss in a region which brackets the t(3;8) familial chromosome translocation at 3p14.2, and some show additional deletions within the U2020 small cell lung carcinoma deletion at 3p12.
A Functionally Diverse Enzyme Superfamily that Abstracts the α Protons of Carboxylic Acids (1995)

Mandelate racemase and muconate lactonizing enzyme are structurally homologous but catalyze different reactions, each initiated by proton abstraction from carbon. The structural similarity to mandelate racemase of a previously unidentified gene product was used to deduce its function as a galactonate dehydratase. In this enzyme superfamily that has evolved to catalyze proton abstraction from carbon, three variations of homologous active site architectures are now represented: lysine and histidine bases in the active site of mandelate racemase, only a lysine base in the active site of muconate lactonizing enzyme, and only a histidine base in the active site of galactonate dehydratase. This discovery supports the hypothesis that new enzymatic activities evolve by recruitment of a protein catalyzing the same type of chemical reaction.
Ablation of Uroplakin III Gene Results in Small Urothelial Plaques, Urothelial Leakage, and Vesicoureteral Reflux (2000)

Urothelium synthesizes a group of integral membrane proteins called uroplakins, which form two-dimensional crystals (urothelial plaques) covering >90% of the apical urothelial surface. We show that the ablation of the mouse uroplakin III (UPIII) gene leads to overexpression, defective glycosylation, and abnormal targeting of uroplakin Ib, the presumed partner of UPIII. The UPIII-depleted urothelium features small plaques, becomes leaky, and has enlarged ureteral orifices resulting in the back flow of urine, hydronephrosis, and altered renal function indicators. Thus, UPIII is an integral subunit of the urothelial plaque and contributes to the permeability barrier function of the urothelium, and UPIII deficiency can lead to global anomalies in the urinary tract. The ablation of a single urothelial-specific gene can therefore cause primary vesicoureteral reflux (VUR), a hereditary disease affecting approximately 1% of pregnancies and representing a leading cause of renal failure in infants. The fact that VUR caused by UPIII deletion seems distinct from that caused by the deletion of angiotensin receptor II gene suggests the existence of VUR subtypes. Mutations in multiple gene, including some that are urothelial specific, may therefore cause different subtypes of primary reflux. Studies of VUR in animal models caused by well-defined genetic defects should lead to improved molecular classification, prenatal diagnosis, and therapy of this important hereditary problem.
Easy and Efficient Bonding of Biomolecules to an Oxide Surface of Silicon (2004)

A new method is described to attach biological molecules to the surface of silicon. Semiconductors such as Si modified with surface-bound capture molecules have enormous potential for use in biosensors for which an ideal detection platform should be inexpensive, recognize targets rapidly with high sensitivity and specificity, and possess superior stability. In this process, a self-assembled film of an organophosphonic acid is bonded to the native or synthesized oxide-coated Si surface as a film of the corresponding phosphonate. The phosphonate film is functionalized to enable covalently coupling biological molecules, ranging in size from small peptides to large multi-subunit proteins, to the Si surface. Surface modification and biomolecule coupling procedures are easily accomplished: all reactions can proceed in air, and most take place under ambient conditions. The biomolecule-modified surfaces are stable under physiological conditions, are selective for adhesion of specific cells types, and are reusable.
Development of an electromagnetic micro-generator (2001)

A design methodology for linear micro-generators is developed, and is applied to the design of a mm scale electromagnetic micro-generator. The fabrication of a prototype device is also described using generally available microfabrication techniques, and the results of testing the device on a variable amplitude vibration source, in air and vacuum, are presented. The experimental results confirm the design rules and indicate how the generation of useful power levels might be achieved.
Ultrastructural localization of a platelet-derived growth factor/v-sis-related protein(s) in cytoplasm and nucleus of simian sarcoma virus-transformed cells. (1987)

The subcellular distribution of v-sis-related protein(s) was analyzed in three simian sarcoma virus (SSV)-transformed cell lines with immunofluorescence and protein A-gold labeling techniques using rabbit polyclonal anti-platelet-derived-growth factor (PDGF) antisera. Antigenically reactive proteins were recognized in subcellular organelles related to protein synthesis and processing, including polyribosomes, endoplasmic reticulum, and the Golgi apparatus, as well as on the cytoplasmic surface of plasma membranes. Prominent immunoreactive proteins were also shown in association with nuclear chromatin in intact cells and in isolated nuclei using Lowicryl K4M resin embedding techniques. Protein A-gold labeling was markedly reduced in sections of non-SSV-transformed fibroblasts incubated with anti-PDGF and absent from SSV-transformed cells if Epon resin was substituted for Lowicryl in the embedding process or if sections were with irrelevant antisera. Nuclear localization of v-sis-related antigens was confirmed in a nitrocellulose-based immunoassay using nuclei isolated from SSV-transformed fibroblasts. Thus, polypeptides recognized antigenically as related to the v-sis gene product not only may be found in subcellular organelles associated with protein synthesis and packaging but also may be found in the nucleus of SSV-transformed cells. These results raise the possibility that v-sis- or PDGF-like proteins may function within the nucleus of SSV-transformed cells.
Network architecture for global biomedical monitoring service (2005)

Most of the patients who are in hospitals and, increasingly, patients controlled remotely from their homes, at-home monitoring, are continuously monitored in order to control their evolution. The medical devices used up to now, force the sanitary staff to go to the patients' room to control the biosignals that are being monitored, although in many cases, patients are in perfect conditions. If patient is at home, it is he or she who has to go to the hospital to take the record of the monitored signal. New wireless technologies, such as BlueTooth and WLAN, make possible the deployment of systems that allow the display and storage of those signals in any place where the hospital intranet is accessible. In that way, unnecessary displacements are avoided. This paper presents a network architecture that allows the identification of the biosignal acquisition device as IP network nodes. The system is based on a TCP/IP architecture which is scalable and avoids the deployment of a specific purpose network.
CD137 Induces Proliferation and Endomitosis in Monocytes (1999)

Peripheral monocytes are short-lived and are replenished from hematopoietic stem cells whose proliferation is believed to be confined to the bone marrow. Human peripheral monocytes are assumed not to be able to proliferate. In this study we show that CD137 (ILA/4-1BB), a member of the tumor necrosis factor receptor family, induces a widespread and profound proliferation of human peripheral monocytes. Macrophage colony-stimulating factor and granulocyte-macrophage colony-stimulating factor are essential, but not sufficient for proliferation. Additional soluble autocrine factors induced by CD137 are required. Induction of proliferation is mediated via reverse signaling through a CD137 ligand, expressed constitutively by peripheral monocytes. The ability of CD137 to induce proliferation in human peripheral monocytes is not shared by any other known molecule.
Photoplethysmography and its application in clinical physiological measurement (2007)

Photoplethysmography (PPG) is a simple and low-cost optical technique that can be used to detect blood volume changes in the microvascular bed of tissue. It is often used non-invasively to make measurements at the skin surface. The PPG waveform comprises a pulsatile ('AC') physiological waveform attributed to cardiac synchronous changes in the blood volume with each heart beat, and is superimposed on a slowly varying ('DC') baseline with various lower frequency components attributed to respiration, sympathetic nervous system activity and thermoregulation. Although the origins of the components of the PPG signal are not fully understood, it is generally accepted that they can provide valuable information about the cardiovascular system. There has been a resurgence of interest in the technique in recent years, driven by the demand for low cost, simple and portable technology for the primary care and community based clinical settings, the wide availability of low cost and small semiconductor components, and the advancement of computer-based pulse wave analysis techniques. The PPG technology has been used in a wide range of commercially available medical devices for measuring oxygen saturation, blood pressure and cardiac output, assessing autonomic function and also detecting peripheral vascular disease. The introductory sections of the topical review describe the basic principle of operation and interaction of light with tissue, early and recent history of PPG, instrumentation, measurement protocol, and pulse wave analysis. The review then focuses on the applications of PPG in clinical physiological measurements, including clinical physiological monitoring, vascular assessment and autonomic function.
A New Spatiotemporal Regularization Approach for Reconstruction of Cardiac Transmembrane Potential Patterns (2004)

The single-beat reconstruction of electrical cardiac sources from body-surface electrocardiogram data might become an important issue for clinical application. The feasibility and field of application of noninvasive imaging methods strongly depend on development of stable algorithms for solving the underlying ill-posed inverse problems. We propose a novel spatiotemporal regularization approach for the reconstruction of surface transmembrane potential (TMP) patterns. Regularization is achieved by imposing linearly formulated constraints on the solution in the spatial as well as in the temporal domain. In the spatial domain an operator similar to the surface Laplacian, weighted by a regularization parameter, is used. In the temporal domain monotonic nondecreasing behavior of the potential is presumed. This is formulated as side condition without the need of any regularization parameter. Compared to presuming template functions, the weaker temporal constraint widens the field of application because it enables the reconstruction of TMP patterns with ischemic and infarcted regions. Following the line of Tikhonov regularization, but considering all time points simultaneously, we obtain a linearly constrained sparse large-scale convex optimization problem solved by a fast interior point optimizer. We demonstrate the performance with simulations by comparing reconstructed TMP patterns with the underlying reference patterns.
UVA-light and Riboflavin-mediated Corneal Collagen Cross-linking (2011)

Letko, Erik MD; Majmudar, Parag A. MD; Forstot, S. Lance MD; Epstein, Randy J. MD; Rubinfeld, Roy S. MD
Chemical Vapor Deposited Fe2O3 Thin Films Analyzed by XPS (2001)

In the present study, x-ray photoelectron spectroscopy (XPS) was employed to investigate the principal core levels of a Fe2O3 thin film. The sample was deposited on glass in a N2+O2 atmosphere by chemical vapor deposition (CVD), using Fe(acac)3 (Hacac = 2,4-pentanedione) as the source compound. XPS surface data for the Fe 2p3/2, O 1s, and C 1s photoelectrons, obtained by an Al Kα monochromatized excitation source, are reported. Deconvolution of the O 1s signal revealed the presence of –OH groups along with the major component ascribed to lattice oxygen. The relatively high carbon content in the film indicated an incomplete decomposition of the used precursor.
Service Location Protocol, Version 2 (1999)

The Service Location Protocol provides a scalable framework for the discovery and selection of network services. Using this protocol, computers using the Internet need little or no static configuration of network services for network based applications. This is especially important as computers become more portable, and users less tolerant or able to fulfill the demands of network system administration.
Effect of Decompression on Complete Spinal Cord Injury in Rats (2008)

To examine whether spinal cord decompression improves functional recovery and decreases lesion volumes in paraplegic (not paraparetic) rats and, if so, at what postoperative time it is most efficacious. The spinal cords of 63 female rats were compressed at T9 with Yasargil clips. Rats were assigned randomly to five different treatment groups of 3 s, 1 hr, 6 hr, 3 weeks, and 10 weeks. Locomotor behavior scoring was based on the Basso, Beattie, Bresnahan (BBB) Locomotor Rating Scale (Ohio State University, Columbus, OH) motor scores. Comparing five groups, the mean BBB was statistically higher in the 3-s group (P < 0.05). Comparison of progressive changes in BBB in each group revealed statistically meaningful improvement in the 3-s group, too. Spared surface area of spinal cord was 81.5 +/- 4.9% in 3-s group and 10.8 +/- 1.4% in the delayed groups of decompression (P = 0.039). Rats undergoing immediate decompression showed significantly better functional recovery and smaller lesion volumes.
Nucleotide sequence of a 17S (18S) rRNA gene from tomato (1989)

Journal Article Nucleotide sequence of a 17S (18S) rRNA gene from tomato Get access Tamás Kiss, Tamás Kiss Institute of Plant Physiology, Biological Research Center, Hungarian Academy of SciencesH-6701 Szeged, PO Box 521, Hungary Search for other works by this author on: Oxford Academic PubMed Google Scholar Attila Szkukálek, Attila Szkukálek Institute of Plant Physiology, Biological Research Center, Hungarian Academy of SciencesH-6701 Szeged, PO Box 521, Hungary Search for other works by this author on: Oxford Academic PubMed Google Scholar Ferenc Solymosy Ferenc Solymosy Institute of Plant Physiology, Biological Research Center, Hungarian Academy of SciencesH-6701 Szeged, PO Box 521, Hungary Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 5, 11 March 1989, Page 2127, https://doi.org/10.1093/nar/17.5.2127 Published: 11 March 1989 Article history Received: 02 February 1989 Published: 11 March 1989
Fingerprinting to Identify Repeated Sound Events in Long-Duration Personal Audio Recordings (2007)

Body-worn solid-state audio recorders can easily and cheaply capture the bearer's entire acoustic environment throughout the day; we refer to such recordings as "personal audio". Extracting useful information, and providing access and navigation tools for this data is a challenge; in this paper we investigate the use of an audio fingerprinting technique, originally developed for identifying music recordings corrupted by noise, as a tool to rapidly identify recurrent sound events within long (multi-day) recordings. The fingerprinting technique is based on energy peaks in time-frequency, largely removing framing issues and making it intrinsically robust to background noise levels. We show that the technique is very effective at identifying exact repetitions of structured sound (such as jingles and electronic telephone rings) but is unable to find repeats of more 'organic' sound events such as garage door openings.
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages (2016)

We introduce a microfluidic platform that enables off-chip single-cell RNA-seq after multi-generational lineage tracking under controlled culture conditions. We use this platform to generate whole-transcriptome profiles of primary, activated murine CD8+ T-cell and lymphocytic leukemia cell line lineages. Here we report that both cell types have greater intra- than inter-lineage transcriptional similarity. For CD8+ T-cells, genes with functional annotation relating to lymphocyte differentiation and function--including Granzyme B--are enriched among the genes that demonstrate greater intra-lineage expression level similarity. Analysis of gene expression covariance with matched measurements of time since division reveals cell type-specific transcriptional signatures that correspond with cell cycle progression. We believe that the ability to directly measure the effects of lineage and cell cycle-dependent transcriptional profiles of single cells will be broadly useful to fields where heterogeneous populations of cells display distinct clonal trajectories, including immunology, cancer, and developmental biology.
Mechanism of Neutralization by the Broadly Neutralizing HIV-1 Monoclonal Antibody VRC01 (2011)

The structure of VRC01 in complex with the HIV-1 gp120 core reveals that this broadly neutralizing CD4 binding site (CD4bs) antibody partially mimics the interaction of the primary virus receptor, CD4, with gp120. Here, we extended the investigation of the VRC01-gp120 core interaction to the biologically relevant viral spike to better understand the mechanism of VRC01-mediated neutralization and to define viral elements associated with neutralization resistance. In contrast to the interaction of CD4 or the CD4bs monoclonal antibody (MAb) b12 with the HIV-1 envelope glycoprotein (Env), occlusion of the VRC01 epitope by quaternary constraints was not a major factor limiting neutralization. Mutagenesis studies indicated that VRC01 contacts within the gp120 loop D, the CD4 binding loop, and the V5 region were necessary for optimal VRC01 neutralization, as suggested by the crystal structure. In contrast to interactions with the soluble gp120 monomer, VRC01 interaction with the native viral spike did not occur in a CD4-like manner; VRC01 did not induce gp120 shedding from the Env spike or enhance gp41 membrane proximal external region (MPER)-directed antibody binding to the Env spike. Finally, VRC01 did not display significant reactivity with human antigens, boding well for potential in vivo applications. The data indicate that VRC01 interacts with gp120 in the context of the functional spike in a manner distinct from that of CD4. It achieves potent neutralization by precisely targeting the CD4bs without requiring alterations of Env spike configuration and by avoiding steric constraints imposed by the quaternary structure of the functional Env spike.