gebhart/patrepeval huggingface dataset:
Interaction of human Rad51 recombination protein with single-stranded DNA binding protein, RPA (1998)

Replication protein A (RPA), a heterotrimeric single-stranded DNA binding protein, is required for recombination, and stimulates homologous pairing and DNA strand exchange promoted in vitro by human recombination protein HsRad51. Co-immunoprecipitation revealed that purified RPA interacts physically with HsRad51, as well as with HsDmc1, the homolog that is expressed specifically in meiosis. The interaction with HsRad51 was mediated by the 70 kDa subunit of RPA, and according to experiments with deletion mutants, this interaction required amino acid residues 169-326. In exponentially growing mammalian cells, 22% of nuclei showed foci of RPA protein and 1-2% showed foci of Rad51. After gamma-irradiation, the percentage of cells with RPA foci increased to approximately 50%, and those with Rad51 foci to 30%. All of the cells with foci of Rad51 had foci of RPA, and in those cells the two proteins co-localized in a high fraction of foci. The interactions of human RPA with Rad51, replication proteins and DNA are suited to the linking of recombination to replication.
Contrast agent-enhanced magnetic resonance imaging of skeletal muscle damage in animal models of muscular dystrophy (2000)

Membrane lesions play an early role in the pathogenesis of muscular dystrophy. Using a new albumin-targeted contrast agent (MS-325), sarcolemmal integrity of two animal models for muscular dystrophy was studied by MRI. Intravenously injected MS-325 does not enter skeletal muscle of normal mice. However, mdx and Sgca-null mutant mice, animal models for Duchenne and sarcoglycan-deficient limb-girdle muscular dystrophy, respectively, showed significant accumulation of MS-325 in skeletal muscle. The results suggest that contrast agent-enhanced MRI could serve as a common, noninvasive imaging procedure for evaluating the localization, extent, and mechanisms of skeletal muscle damage in muscular dystrophy. Furthermore, this method is expected to facilitate assessment of therapeutic approaches in these diseases.
Circadian rhythm abnormalities in totally blind people: incidence and clinical significance. (1992)

When people are completely isolated from environmental time cues, their circadian rhythms free run with a nearly 24-h cycle, generated by an internal body clock. Free-running temperature, cortisol, and melatonin rhythms have also been described in totally blind people, even though they were living in normal society and had access to abundant time cues; thus an intact visual system may be essential for synchronization of the circadian system. However, because of the small numbers of subjects studied, the incidence and clinical significance of circadian rhythm abnormalities among the blind has remained uncertain. In this study, plasma melatonin (n = 20), cortisol (n = 4), and sleep propensity (n = 1) were measured in serial samples taken from totally blind subjects for 24 h. Most totally blind subjects had circadian rhythm abnormalities. In about half of the subjects, the rhythms were free-running. Some blind subjects suffered recurrent insomnia and daytime sleepiness that were maximal when the internal rhythms were out of phase with the preferred sleep times. The high incidence of abnormal circadian rhythms in blind people underscores the importance of the light-dark cycle as an important environmental synchronizer for the human circadian system.
Malignant transformation of human fibroblasts correlates with increased activity of receptor-bound plasminogen activator. (1991)

To determine whether a relationship exists among urokinase plasminogen activator (u-PA) activity, tissue plasminogen activator (t-PA) activity, and the malignant transformation of human fibroblasts, we measured receptor-bound and secreted u-PAs and t-PA activity in fibroblast cell strains of a unique cell lineage and compared the results with the values obtained in human fibrosarcoma-derived cell lines and control cell lines. The lineage consists of four nonmalignant, infinite life span cell strains, clonally derived from a finite life span, neonatal foreskin-derived cell line or one of its derivatives and 10 malignant cell strains clonally derived from that same derivative. Seven of the latter were malignantly transformed by K-, H-, or N-ras oncogene transfection, two were obtained following carcinogen treatment, and one arose spontaneously. All 10 malignant strains in this lineage exhibited significantly higher levels of activity of receptor-bound u-PA than was found in the cell strain from which they arose or the nonmalignant cell strains derived from it. The ras oncogene-transformed malignant strains also exhibited significantly higher levels of activity of receptor-bound t-PA than their cell strain of origin. The other three malignant strains showed undetectable levels, consistent with their attaining the malignant state by an alternate process. The five fully malignant fibrosarcoma-derived cell lines tested also showed high levels of receptor-bound u-PA and t-PA. The majority (greater than or equal to 80%) of the nonmalignant control cell lines did not do so. The 10 malignant cell strains in the lineage also exhibited higher levels of activity of secreted high molecular weight u-PA or t-PA than did their cell strain of origin and the nonmalignant cell strains derived from it, as did the malignant fibrosarcoma-derived cell lines. The data suggest that the malignant state of human fibroblasts is always associated with high levels of activity of receptor-bound u-PA, and in addition cells transformed to the malignant state are very likely to exhibit high levels of receptor-bound t-PA and secreted forms of plasminogen activators.
ADPCM with a multiquantizer for speech coding (1988)

A speech coding algorithm with low complexity and a short processing delay is introduced. The proposed algorithm is ADPCM (adaptive digital pulse code modulation) with a multiquantizer (ADPCM-MQ). The input signal is processed in parallel by multiple ADPCM coders with different characteristics. Then the optimum ADPCM coder with minimum error power is dynamically selected for each frame. A 16-kb/s codec based on this algorithm has been implemented using two general-purpose digital signal processors (MB8764) with 8.3 ms of total processing delay. A segmental SNR of 19-21 dB was achieved at 16 kb/s; with postfiltering the segmental SNR was increased to 23-25 dB. Combined with the time domain compression scheme, the algorithm can be easily applied to 8-kb/s coding. It is also extensible to variable-rate coding.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electronic circuit analysis and design (2001)

This junior-level electronics text provides a foundation for analyzing and designing analog and digital electronic circuits. Computer analysis and design are recognized as significant factors in electronics throughout the book. The use of computer tools is presented carefully, alongside the important hand analysis and calculations. The author, Don Neamen, has many years experience as an enginering educator and an engineer. His experience shines through each chapter of the book, rich with realistic examples and practical rules of thumb.The book is divided into three parts. Part 1 covers semiconductor devices and basic circuit applications. Part 2 covers more advanced topics in analog electronics, and Part 3 considers digital electronic circuits.
Room temperature silicon wafer direct bonding in vacuum by Ar beam irradiation (2002)

We have developed a new method for the direct bonding of silicon wafers at room temperature. In the method Ar fast atom beam etching is used to modify the surface of the specimens, and they are bonded in the vacuum. With the appropriate Ar beam etching, the bonding prepared at room temperature is as strong as that prepared by conventional wet surface modification treatment and high temperature annealing. In the process, pressing load is not necessary when two specimens are mated. Intimate contact at the bonding interface is supposed to be achieved by the attractive force between the surface. Therefore surface roughness of the specimen is quite important in the method. On the other hand, this method does not need ultrahigh vacuum condition. Especially, the influence of inert gas in the vacuum chamber is quite small. Even in the 1000 Pa of Ar, strong bonding can be attained. The applicability of this method to the small area bonding was proved by the bonding of 200 /spl mu/m diameter bumps and 100 /spl mu/m wide lines. These results demonstrate the advantages of this method. This method is promising as a assembling and packaging method for MEMS.
A Preliminary Evaluation of a Recombinant Circumsporozoite Protein Vaccine againstPlasmodium falciparumMalaria (1997)

A recombinant vaccine based on fusion of the circumsporozoite protein and HBsAg plus a potent adjuvant can protect against experimental challenge with P. falciparum sporozoites. After additional studies of protective immunity and the vaccination schedule, field trials are indicated for this new vaccine against P. falciparum malaria.
Oligomerization of hydrophobin SC3 in solution: From soluble state to self‐assembly (2004)

Hydrophobin SC3 is a protein with special self-association properties that differ depending on whether it is in solution, on an air/water interface or on a solid surface. Its self-association on an air/water interface and solid surface have been extensively characterized. The current study focuses on its self-association in water because this is the starting point for the other two association processes. Size-exclusion chromatography was used to fractionate soluble-state SC3. Real-time multiangular light scattering detection of the eluate indicated that SC3 mainly exists as a dimer in buffer, accompanied with a small amount of monomer, tetramer, and larger aggregates. Dimeric SC3 has very likely an elongated shape, as indicated by the hydrodynamic radius determined by using dynamic light scattering (DLS) and fluorescence anisotropy measurements on dansyl-labeled SC3. Size-exclusion chromatography experiments also indicated that the protein oligomerizes very slowly at low temperature (4 degrees C) but rather rapidly at room temperature. Ionic strength plays an important role in the oligomerization; a short-lived monomeric SC3 species could be observed in pure water. Oligomerization was not affected by low pH but was accelerated by high pH. Fluorescence resonance energy transfer showed that dissociation occurred when the protein concentration was lowered; a large population of oligomers, presumably dimers, dissociate when the protein concentration is <4.5 microg/mL. This value is similar to the critical concentration for SC3 self-assembly. Therefore, dimeric SC3 is indicated to be the building block for both aggregation in solution and self-assembly at hydrophobic/hydrophilic interfaces.
The Escherichia coli Chaperonin 60 (groEL) Is a Potent Stimulator of Osteoclast Formation (1998)

Chaperonins (cpns) are intracellular oligomeric protein complexes that fold and refold proteins in a catalytic manner and aid in the transmembrane transport of cellular proteins. We reported previously that the lipopolysaccharide-free recombinant cpn60 of Escherichia coli (groEL) is able to stimulate the breakdown of murine calvarial bone in culture and showed that such resorption is potently inhibited by an inhibitor of the enzyme cyclo-oxygenase and to a lesser extent by inhibitors of 5-lipoxygenase. In this study, we have investigated the effects of groEL on the resorptive activity and formation of osteoclasts in culture. In low density, osteoclast-containing cultures from neonatal rats incubated for 24 or 96 h on dentine discs, groEL (1-1000 ng/ml) stimulated resorption pit formation up to 4-fold, but this effect was essentially dependent on cell number. Using 12-day cultures of mouse bone marrow to assess osteoclast recruitment, groEL (1-1000 ng/ml) caused a dramatic dose-dependent stimulation of the formation of tartrate-resistant acid phosphatase-positive multinucleated cells and the resorption of the dentine on which bone marrow cells were cultured. Osteoclast formation elicited by groEL was almost completely abolished by indomethacin, an inhibitor of cyclo-oxygenase, but was unaffected by inhibitors of 5-lipoxygenase, suggesting that prostaglandins but not leukotrienes may mediate the action of groEL on osteoclastogenesis. It is possible that bacterial cpn60s such as groEL may play a role in the osteolysis associated with bone infections. Whether endogenous ("self") chaperonins have a role in other bone loss disorders, such as osteoporosis, is an intriguing possibility.
Efficient, fair interpolation using Catmull-Clark surfaces (1993)

Article Free Access Share on Efficient, fair interpolation using Catmull-Clark surfaces Authors: Mark Halstead View Profile , Michael Kass View Profile , Tony DeRose View Profile Authors Info & Claims SIGGRAPH '93: Proceedings of the 20th annual conference on Computer graphics and interactive techniquesSeptember 1993 Pages 35–44https://doi.org/10.1145/166117.166121Online:01 September 1993Publication History 220citation1,888DownloadsMetricsTotal Citations220Total Downloads1,888Last 12 Months94Last 6 weeks32 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
The Immunological Synapse Balances T Cell Receptor Signaling and Degradation (2003)

The immunological synapse is a specialized cell-cell junction between T cell and antigen-presenting cell surfaces. It is characterized by a central cluster of antigen receptors, a ring of integrin family adhesion molecules, and temporal stability over hours. The role of this specific organization in signaling for T cell activation has been controversial. We use in vitro and in silico experiments to determine that the immunological synapse acts as a type of adaptive controller that both boosts T cell receptor triggering and attenuates strong signals.
Tools for application-oriented performance tuning (2001)

Application performance tuning is a complex process that requires assembling various types of information and correlating it with source code to pinpoint the causes of performance bottlenecks. Existing performance tools don't adequately support this process in one or more dimensions. We discuss some of the critical utility and usability issues for application-level performance analysis tools in the context of two performance tools, MHSim and HPCView, that we built to support our own work on data layout and optimizing compilers. MHsim is a memory hierarchy simulator that produces source-level information not otherwise available about memory hierarchy utilization and the causes of cache conflicts. HPCView is a tool that combines data from arbitrary sets of instrumentation sources and correlates it with program source code. Both tools report their results in scope-hierarchy views of the corresponding source code and produce their output as HTML databases that can be analyzed portably and collaboratively using a commodity browser. In addition to daily use within our group, the tools are being used successfully by several code development teams in DoD and DoE laboratories.
Dissociation and exchange of the beta 2-microglobulin subunit of HLA-A and HLA-B antigens. (1979)

Human histocompatibility antigens HLA-A, HLA-B, and HLA-C are a complex of two noncovalently associated subunits: a heavy chain glycoprotein (alpha) carrying the genetic polymorphism and an invariant light chain, beta 2-microglobulin (beta 2m). Upon incubation of papain-solubilized HLA with radiolabeled urinary beta 2m, the latter is incorporated into HLA, where it substitutes for the preexisting beta 2m that has dissociated from the complex. The association-dissociation equilibrium that governs this beta 2m exchange reaction was investigated and found to be characterized by a long lifetime of the complex (half-life of 80 min at 37 degrees C) and a relatively low Kd (4 nM). The beta 2m exchange was used as the basis of a radioimmunoassay for HLA antigens with radiolabeled beta 2m as a unique label for all HLA specificities. In a similar fashion, radiolabeled beta 2m can be incorporated into HLA at the cell surface. Although the process is slower and less extensive than in solution, it can be used as a means to tag cells with specific probes for HLA antigens.
A new generation of MPEG-2 video encoder ASIC and its application to new technology markets (1996)

The multimedia era is upon us. The traditional methods used for the storage, signal processing and distribution of video, audio and data are going through significant change. This change is being fuelled by advances in the area of bit-rate reduction technology and in particular the publication of an effective world-wide standard for the compression of video and audio components, the MPEG-2 specification. The paper considers the complexities involved in performing video compression encoding. It introduces newly developed Sony programmable ASICs for performing real time compression encoding of a video source image in compliance with the MPEG-2 Main Profile@Main Level standard. It details the architecture of this newly developed chipset including features that have been implemented within the chipset to identify image complexities, resulting in efficient video compression encoding with high picture quality. The paper also describes how this video compression chipset has been integrated into a new generation MPEG-2 encoder product from Sony and identifies a number of new technology application areas which are being addressed by this new product.
Anti‐VEGFR‐2 scFvs for Cell Isolation. Single‐Chain Antibodies Recognizing the Human Vascular Endothelial Growth Factor Receptor‐2 (VEGFR‐2/flk‐1) on the Surface of Primary Endothelial Cells and Preselected CD34 + Cells from Cord Blood (2001)

Five specific single-chain antibodies recognizing the human vascular endothelial growth factor receptor-2 (VEGFR-2/KDR) were selected from a V-gene phage display library constructed from mice immunized with the extracellular domain of VEGFR-2 (Ig-like domain 1-7). All five scFv antibodies (A2, A7, B11, G3, and H1) bound to the purified native antigen in enzyme-linked immunosorbent assay and Dot Blot, and showed no crossreactivity to the human VEGF-receptor 1 (VEGFR-1). The selected antibodies recognize a conformation-dependent epitope of the native receptor and do not recognize denatured antigen in Western blots, as well as linear overlapping peptides comprising the sequence of the human VEGFR-2. The five scFv antibodies bind to the surface of endothelial cells overexpressing human VEGFR-2 c-DNA (PAE/VEGFR-2 cells) as detected by surface immunofluorescence using confocal microscopy. In addition scFv A7 specifically detected VEGFR-2 expressing endothelial cells in the glomerulus of frozen human kidney tissue sections. Therefore, A7 has potential clinical application as a marker for angiogenesis in cryosections of different human tissues. Additionally, two recombinant scFvs (A2 and A7) very efficiently recognize VEGFR-2 on PAE/VEGFR-2 cells and freshly prepared human umbilical vein endothelial cells by fluorescence-activated cell sorter (FACS) analysis. The scFv fragment A7, which was the most sensitive antibody in FACS analysis, recognizes human CD34+VEGFR-2+ hematopoietic immature cells within the population of enriched CD34+ cells isolated from human cord blood. The dissociation constant of A7 was determined to be K(d) = 3.8 x 10(-9) M by BIAcore analysis. In conclusion, scFv fragment A7 seems to be an important tool for FACS analysis and cell sorting of vascular endothelial cells, progenitor cells and hematopoitic stem cells, which are positive for VEGFR-2 gene expression.
A reversible molecular valve (2005)

In everyday life, a macroscopic valve is a device with a movable control element that regulates the flow of gases or liquids by blocking and opening passageways. Construction of such a device on the nanoscale level requires (i) suitably proportioned movable control elements, (ii) a method for operating them on demand, and (iii) appropriately sized passageways. These three conditions can be fulfilled by attaching organic, mechanically interlocked, linear motor molecules that can be operated under chemical, electrical, or optical stimuli to stable inorganic porous frameworks (i.e., by self-assembling organic machinery on top of an inorganic chassis). In this article, we demonstrate a reversibly operating nanovalve that can be turned on and off by redox chemistry. It traps and releases molecules from a maze of nanoscopic passageways in silica by controlling the operation of redox-activated bistable [2]rotaxane molecules tethered to the openings of nanopores leading out of a nanoscale reservoir.
Mutations producing premature termination of translation and an amino acid substitution in the sterol 27-hydroxylase gene cause cerebrotendinous xanthomatosis associated with parkinsonism (1999)

CTX with parkinsonism is caused by mutations with a severe impact on enzyme function. The two mutations described here are likely to cause loss of function because they are chain terminating or affect an essential site in the protein.
TAC3andTACR3Defects Cause Hypothalamic Congenital Hypogonadotropic Hypogonadism in Humans (2010)

Our data demonstrate the hypothalamic origin of the gonadotropin deficiency in these genetic forms of normosmic CHH. Neurokinin B and NK3R therefore both play a crucial role in hypothalamic GnRH release in humans.
Hydroxyurea attenuates activated neutrophil-mediated sickle erythrocyte membrane phosphatidylserine exposure and adhesion to pulmonary vascular endothelium (2007)

Activated neutrophils increase erythrocyte phosphatidylserine (PS) exposure. PS-exposed sickle red blood cells (SSRBCs) are more adhesive to vascular endothelium than non-PS-exposed cells. An increase in SSRBC fetal hemoglobin (HbF) concentration has been associated with improved rheology and decreased numbers of vasoocclusive episodes. This study examined the effects of HbF, PS-exposed SSRBCs, and chronic hydroxyurea (HU) treatment on activated neutrophil-mediated SSRBC retention/adherence in isolated-perfused rat lungs. Lungs were perfused with erythrocyte suspensions from 1) individuals homozygous for hemoglobin S with 0-7% HbF (SS), 2) with > or =8% HbF (SS + F), and 3) individuals homozygous for hemoglobin S treated with HU therapy for > or =1 yr (SS + HU). Retention of SSRBCs from the SS + HU group was significantly less than that seen in both the SS and SS + F groups. No difference was observed between the SS and SS + F groups. The percentage of HbF and F-cells did not differ between the SS + F and SS + HU groups. At baseline, the proportion of PS-exposed SSRBCs was not different between the SS and SS + HU groups. However, SSRBC treatment with activated neutrophil supernatant caused a twofold increase in PS-exposed SSRBCs in the SS control and no change in the SS + HU group. We conclude that 1) HU attenuates SSRBC retention/adherence in the pulmonary circulation seen in response neutrophil activation, 2) HU stabilizes SSRBC membrane PS, and 3) HU attenuation SSRBC retention/adherence in the pulmonary circulation occurs through a mechanism(s) independent of HbF.