gebhart/patrepeval huggingface dataset:
Serine 132 Is the C3 Covalent Attachment Point on the CH1 Domain of Human IgG1 (2001)

The covalent binding of C3 (complement component C3) to antigen-antibody complexes (Ag.Ab; immune complexes (ICs)) is a key event in the uptake, transport, presentation, and elimination of Ag in the form of Ag.Ab.C3b (IC.C3b). Upon interaction of C3 with IgG.IC, C3b.C3b.IgG covalent complexes are formed that are detected on SDS-polyacrylamide gel electrophoresis by two bands corresponding to C3b.C3b (band A) and C3b.IgG (band B) covalent complexes. This allows one to evaluate the covalent binding of C3b to IgG antibodies. It has been described that C3b can attach to both the Fab (on the CH1 domain) and the Fc regions of IgG. Here the covalent interaction of C3b to the CH1 domain, a region previously described spanning residues 125-147, has been studied. This region of the CH1 domain is exposed to solvent and contains a cluster of six potential acceptor sites for ester bond formation with C3b (four Ser and two Thr). A set of 10 mutant Abs were generated with the putative acceptor residues substituted by Ala, and we studied their covalent interaction with C3b. Single (Ser-131, Ser-132, Ser-134, Thr-135, Ser-136, and Thr-139), double (positions 131-132), and multiple (positions 134-135-136, 131-132-134-135-136, and 131-132-134-135-136-139) mutants were produced. None of the mutants (single, double, or multiple) abolished completely the ability of IgG to bind C3b, indicating the presence of C3b binding regions other than in the CH1 domain. However, all mutant Abs, in which serine at position 132 was replaced by Ala, showed a significant decrease in the ability to form C3b.IgG covalent complexes, whereas the remaining mutants had normal activity. In addition we examined ICs using the F(ab')2 fragment of the mutant Abs, and only those containing Ala at position 132 (instead of Ser) failed to bind C3b. Thus Ser-132 is the binding site for C3b on the CH1 domain of the heavy chain, in the Fab region of human IgG.
Novel Systemic Drugs for Cutaneous T-Cell Lymphoma (2010)

For the last few years new therapeutic options for primary cutaneous T-cell lymphoma (CTCL) have been recently introduced into clinical trials, particularly for patients with advanced stage and refractory disease. Systemic treatment uses biological response modifiers, such as fusion molecules, rexinoids, interferons as well as monoclonal antiobodies, and new antiproliferative drugs, such as histone deacetylase inhibitors, proteasome inhibitors or forodesine. This review focuses on recent advances in the development of systemic agents for CTCL including both novel patented compounds and novel therapeutic protocol of intervention.
Kidney function and the use of nitrofurantoin to treat urinary tract infections in older women (2015)

In this study, the presence of mild or moderate reductions in estimated glomerular filtration rate did not justify avoidance of nitrofurantoin.
Sorting and Searching (1973)

Chapter 5 is concerned with sorting into order, internal sorting and external sorting. Chapter 6 deals with the problem of searching for specified items in tables or files. It is subdivided into methods which search sequentially, or by comparison of keys, or by digital properties, or by'hashing.'It then discusses the more difficult problem of secondary key retrieval
Alternative BCR/ABL Splice Variants in Philadelphia Chromosome–Positive Leukemias Result in Novel Tumor-Specific Fusion Proteins that May Represent Potential Targets for Immunotherapy Approaches (2007)

Imatinib currently represents the standard treatment in the early chronic phase of chronic myelogenous leukemia (CML), thanks to the high percentage of cytogenetic complete remission achieved, but it is yet unclear to what extent it can eradicate leukemia. Therefore, different vaccination strategies have been suggested, mainly based on the exploitment of the junctional peptides spanning the fusion region of the Bcr/Abl proteins. To identify new potential immunologic targets, 63 Philadelphia chromosome-positive patients and 6 BCR/ABL-positive cell lines were tested in nested reverse transcriptase PCR to detect the presence of BCR/ABL transcripts arising from the alternative splicing of the main BCR/ABL transcripts. We could detect BCR/ABL transcripts with junctions between BCR exon 1, 13, or 14 and ABL exon 4 in approximately 80% of patients and 84% of cell lines, beside the main fusion transcripts. Translation products of these transcripts were characterized at their COOH terminus by a large amino acid portion derived from the out of frame (OOF) reading of ABL gene. These proteins were detected in BCR/ABL-positive cell lines by immunoprecipitation and immunohistochemistry. Finally, we determined whether OOF-specific CD8+ T cells could be found in the peripheral blood of CML patients and whether they could acquire effector function following in vitro sensitization with OOF-derived peptides predicted to bind to human leucocyte antigen (HLA)-A2 and HLA-A3 molecules. We detected the presence of OOF-specific CD8+ T cells in four of four patients studied, and in one case, these T cells exhibited specific cytotoxic activity against both peptide-pulsed targets and autologous primary CML cells.
Expression of the wild-type p53 antioncogene induces guanine nucleotide-dependent stem cell division kinetics. (1995)

The predominant type of cell division in adult mammals is renewal growth. Renewing stem cells in somatic tissues undergo continuous asymmetric divisions. One new daughter cell retains the division potential of the original stem cell, while the other differentiates into a functional constituent of the tissue. Disruptions of this process lead to the development of human cancers. We show that through a guanine nucleotide-dependent mechanism, the p53 antioncogene can induce exponentially dividing cells to switch to an asymmetric stem cell growth pattern. This finding suggests that the observed high frequency of p53 mutations in human cancers reflects a critical function in the regulation of somatic renewal growth.
Isolation in mixed-signal systems using a novel electromagnetic bandgap (EBG) structure (2005)

This work presents an efficient isolation method in mixed-signal systems using a novel electromagnetic bandgap (EBG) structure called the alternating impedance EBG (AI-EBG) for isolating sensitive RF/analog circuits from noisy digital circuits. This EBG structure shows excellent isolation by suppressing almost all possible electromagnetic modes in bandgap frequencies. Measurements on a practical mixed-signal system show the feasibility of using this EBG structure to reduce noise coupling between RF/analog circuits and digital circuits, especially where a common power supply is used. To the best of our knowledge, this is the first example of a realistic mixed-signal system employing an EBG-based noise suppression scheme.
ACCESS TO TRANSMISSION PERFORMANCE MARGINS THROUGH PRE-EMPHASIS ADJUSTMENT IN WDM SYSTEMS (1998)

A met,hod to evaluate the transmission performance margins of WDM systems, based on multiplex pre- emphasis opthisation, has been experimentally validated.
Pleuropneumonia of swine caused by Haemophilus parahaemolyticus. Studies on the protection obtained by vaccination. (1976)

Sixty-six pigs were vaccinated with formaldehyde-killed 24-hour or 6-hour culture of H. parahaemolyticus with Freund's incomplete adjuvant (1:1 or 3:1) or 15 per cent Alhydrogel. The vaccine was injected subcutaneously when the pigs were 9 weeks old. A booster injection was given 2 weeks later. Two weeks after the booster injection the pigs were challenged by intranasal inoculation of 10(10) organisms. The efficacy of the vaccine was evaluated by clinical observations and autopsy findings. Vaccines with Alhydrogel adjuvant: With 24-hour culture 25 per cent of the pigs were protected. With 6-hour culture the protection reached 67 per cent. Vaccines with Freund's incomplete adjuvant: With 24-hour culture 67 per cent of the vaccinates were protected. With 6-hour culture 90 per cent were protected. It is concluded that a 6-hour culture of H. parahaemolyticus is superior to an older culture in immunizing power. Vaccine with Freund's incomplete adjuvant caused severe local reaction with persistent granuloma formation. For that reason it is questionable whether this vaccine will be accepted for field use. H. parahaemolyticus could be found in the respiratory tract, also of animals that were protected by vaccination. Further studies on the significance and duration of the carrier state in this infection are required.
Investigation of three new mouse mammary tumor cell lines as models for transforming growth factor (TGF)-β and Neu pathway signaling studies: identification of a novel model for TGF-β-induced epithelial-to-mesenchymal transition (2004)

We suggest that the BRI-JM04 and BRI-JM05 cell lines can be used to investigate Neu oncogene driven mammary tumorigenesis, whereas the BRI-JM01 cell line will be useful for studying TGF-beta1-induced EMT.
Layer-by-Layer-Coated Gelatin Nanoparticles as a Vehicle for Delivery of Natural Polyphenols (2009)

Natural polyphenols with previously demonstrated anticancer potential, epigallocatechin gallate (EGCG), tannic acid, curcumin, and theaflavin, were encased into gelatin-based 200 nm nanoparticles consisting of a soft gel-like interior with or without a surrounding LbL shell of polyelectrolytes (polystyrene sulfonate/polyallylamine hydrochloride, polyglutamic acid/poly-l-lysine, dextran sulfate/protamine sulfate, carboxymethyl cellulose/gelatin, type A) assembled using the layer-by-layer technique. The characteristics of polyphenol loading and factors affecting their release from the nanocapsules were investigated. Nanoparticle-encapsulated EGCG retained its biological activity and blocked hepatocyte growth factor (HGF)-induced intracellular signaling in the breast cancer cell line MBA-MD-231 as potently as free EGCG.
Identification of a tissue-specific putative transcription factor in breast tissue by serological screening of a breast cancer library. (2001)

Application of SEREX (serological analysis of recombinant tumor cDNA expression libraries) to different tumor types has led to the identification of several categories of human tumor antigens. In this study, the analysis of a breast cancer library with autologous patient serum led to the isolation of seven genes, designated NY-BR-1 through NY-BR-7. NY-BR-1, representing 6 of 14 clones isolated, showed tissue-restricted mRNA expression in breast and testis but not in 13 other normal tissues tested. Among tumor specimens, NY-BR-1 mRNA expression was found in 21 of 25 breast cancers but in only 2 of 82 nonmammary tumors. Structural analysis of NY-BR-1 cDNA and the corresponding genomic sequences in the recently released working draft of human genome indicated that NY-BR-1 is composed of 37 exons and has an open reading frame of 4.0-4.2 kb, encoding a peptide of Mr 150,000-160,000. A bipartite nuclear localization signal motif indicates a nuclear site for NY-BR-1, and the presence of a bZIP site (DNA-binding site followed by leucine zipper motif) suggests that NY-BR-1 is a transcription factor. Additional structural features include five tandem ankyrin repeats, implying a role for NY-BR-1 in protein-protein interactions. NY-BR-1 thus represents a breast tissue-specific putative transcription factor with autoimmunogenicity in breast cancer patients. In addition to NY-BR-1, a homologous gene, NY-BR-1.1, was identified in this study. NY-BR-1.1 shares 54% amino acid homology with NY-BR-1 and also shows tissue-restricted mRNA expression. However, unlike NY-BR-1, NY-BR-1.1 mRNA is expressed in brain, in addition to breast and testis. The exon structure of NY-BR-1.1 remains to be defined. Using human genome database, NY-BR-1 was localized to chromosome 10p11-p12, and NY-BR-1.1 was tentatively localized to chromosome 9.
Cryptococcal Meningitis and Sarcoidosis (2002)

This report describes a patient with cryptococcal meningitis and newly diagnosed sarcoidosis not taking corticosteroids. Sarcoidosis is an independent risk factor for cryptococcal infection; most patients with sarcoidosis who develop cryptococcal infection are not on immunosuppressive drugs. Cryptococcal meningitis in sarcoid patients often presents clinically with non-specific features, and should be excluded in patients with sarcoidosis and neurological disturbances.
Rate-distortion efficiency of subband coding with integer coefficient filters (2002)

Discusses efficient image compression algorithms that are suitable for low-complexity implementation in deep space probes. Subband coding or equivalent wavelet transforms provide some advantages over traditional block transforms in terms of rate distortion performance under the mean square-error criterion and according to subjective visual evaluation. Furthermore, the possibility of choosing a desired resolution, independently in the time or frequency domain, is important to preserve the specific features that are most relevant for substantiating scientific findings. A low-complexity version of a JPEG-like algorithm based on the integer cosine transform (ICT), is being implemented in software on the Galileo spacecraft. The most promising candidate for improving the current ICT-based algorithm is a subband coding method that uses quadrature mirror filters (QMF) with lattice structure and integer coefficients. Lattice QMF filters are paraunitary perfect reconstruction (PR) filters. This provides a simple method to obtain PR filters with integer coefficients, without the need for any additional constraint to be satisfied for guaranteeing the PR property. Similarly, orthonormal wavelet transforms can be easily implemented by de signing a two-channel paraunitary QMF bank and then using a tree structure. This means that the wavelet orthonormality properties can be retained even when the coefficients are quantized or subject to certain constraints.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Novel Pharmacologic Candidates for Treatment of Primary Open-Angle Glaucoma. (2017)

Primary open-angle glaucoma (OAG) affects approximately 45 million people worldwide and more than 2.5 million people aged 40 years or older in the United States. Pharmacologic treatment for glaucoma is directed towards lowering intraocular pressure (IOP) to slow disease progression and delay visual field loss. Current medical treatment options for the lowering of IOP include the following classes of topical medications: beta-adrenergic antagonists, alpha-adrenergic agonists, cholinergic agonists, carbonic anhydrase inhibitors, and prostaglandin analogs. Issues with existing drugs include failure to achieve target IOP with monotherapy, drug-related side effects, and low patient compliance with multiple daily administration of eye drops. In recent years, the scientific and medical community has seen encouraging development of novel classes of drugs for primary OAG, the majority of which lower IOP by targeting the trabecular meshwork outflow pathway to increase aqueous humor outflow. Among the most promising new pharmacologic candidates are rho kinase inhibitors including ripasudil (K-115), netarsudil (AR-13324), and AMA0076; adenosine receptor agonists including trabodenoson (INO-8875); and modified prostaglandin analogs including latanoprostene bunod (LBN, BOL-303259-X) and ONO-9054. This study aims to systematically review and summarize the most recent developments in clinical trials for new pharmacologic options for the treatment of primary open-angle glaucoma.
Regulation of Protein Tyrosine Kinase Activation by the T-cell Antigen Receptor Chain (1992)

Resting antigen-specific T lymphocytes in the G0 stage of the cell cycle encounter antigenic peptides bound to major histocompatibility complex (MHC) molecules on the surfaces of antigen-presenting cells. These T cells are activated to proliferate and exhibit a variety of differentiated functions. This complex cellular interaction involves a large number of plasma membrane molecules on the T cell and the antigen presenting cell. However, the T-cell antigen receptor (TCR) must play a central role in directing the initiation of antigen-specific responses.
A Novel Spike Distance (2001)

The discrimination between two spike trains is a fundamental problem for both experimentalists and the nervous system itself. We introduce a measure for the distance between two spike trains. The distance has a time constant as a parameter. Depending on this parameter, the distance interpolates between a coincidence detector and a rate difference counter. The dependence of the distance on noise is studied with an integrate-and-fire model. For an intermediate range of the time constants, the distance depends linearly on the noise. This property can be used to determine the intrinsic noise of a neuron.
In vitro biosynthesis of three sulfated glycoproteins of murine zonae pellucidae by oocytes grown in follicle culture. (1983)

The zona pellucida is an extracellular glycocalyx that surrounds the growing oocyte and mediates specific biological functions essential to early mammalian development. We have isolated by a novel technique intact zonae pellucidae from a murine follicle culture system which mimics in vivo granulosa cell-oocyte interactions. Using radioactive precursors we have demonstrated that all three zona proteins, ZP-1, ZP-2, and ZP-3, are sulfated glycoproteins. Incubation of the follicle culture with tunicamycin (0.5 microgram/ml), an antibiotic that blocks N-glycosylation, inhibits new protein deposition in the zona. Under these same conditions overall protein synthesis is decreased only 30%. Biosynthetic studies indicate that after 6 days in culture the zona proteins are produced at 0.4 pg/oocyte/h, which represents 2-3% of the total oocyte protein synthesis. This synthesis stops at or before ovulation and the extremely long half-life (greater than 100 h) of the zona may be essential to preserve its known biological functions, all of which occur after ovulation.
The Benefits of Powered Liposuction Versus Traditional Liposuction: A Paired Comparison Analysis (2001)

For decades benzoin has been used to enhance the “stickiness” of the skin for improved adherence complementing the protective and functional aspects of well-constructed surgical bandages/dressings. The fully adherent and longer-lasting pressure dressing is both aesthetically pleasing to the patient (and surgeon) and, at the same time, functions to decrease seroma or hematoma formation, enhances antisepsis by blocking transient bacterial contamination, and inhibits traumatic sabotage of surgical wounds due to patient overactivity or inadvertent collision with a door jam, car door, table leg, or grandchild, etc. Also, when the bandage looks good, the patient realizes the operation was a success (at least aesthetically). Although simple, our additional steps of deoiling the skin with acetone, followed by multiple compress/release cycles of gauze to the Mastisol area reaps benefits to the patient and surgeon both in function (adherence) and in the production of a truly “dressy” beautiful and long-lasting dressing. In this way, the dressing “bed” is not only more receptive to one's aesthetically pleasing bandage, but is more tacky, yet refined. This same technique can be utilized prior to application of adhesive strips to healing wounds after sutures have been removed, allowing them to “stay on” longer with potentially better cosmesis and less spreading of the scar.
Cyclin D1 (Bcl-1, PRAD1) protein expression in low-grade B-cell lymphomas and reactive hyperplasia. (1994)

Mantle cell (centrocytic) lymphoma (MCL) and occasional cases of B-cell small lymphocytic lymphoma/chronic lymphocytic leukemia (B-SLL/CLL) show a characteristic translocation, t(11:14)(q13;q32) involving rearrangement of the Bcl-1 region. Recently it was shown that the key Bcl-1 region oncogene is cyclin D1/PRAD1; cyclin D1 mRNA was shown to be overexpressed in cases of MCL. We examined cyclin D1 protein expression in low-grade B-cell lymphomas and reactive lymphoid hyperplasias using polyclonal and monoclonal antibodies to cyclin D1 protein. Definite nuclear staining was seen in 15 of 15 MCLs, 1 of 7 B-SLL/CLLs, 0 of 7 reactive hyperplasias, 0 of 10 follicular lymphomas, and 0 of 4 lymphomas of mucosa-associated lymphoid tissue using immunoperoxidase stains on paraffin-embedded sections. Best results were obtained with the affinity-purified polyclonal antibody on microwave-treated, formalin-fixed, paraffin-embedded tissue. MCLs showed diffuse nuclear staining, whereas the one positive B-SLL/CLL showed dot-like or globular nuclear staining. Nuclear cyclin D1 protein can be detected in all cases of MCL and in rare cases of B-SLL/CLL using an immunohistochemical technique on formalin-fixed, paraffin-embedded tissue, and it does not appear to be detectable in reactive hyperplasias and other low-grade B-cell lymphomas. This protein may be useful in subclassification of low-grade B-cell lymphomas.
Platelet ITAM signaling is critical for vascular integrity in inflammation (2013)

Platelets play a critical role in maintaining vascular integrity during inflammation, but little is known about the underlying molecular mechanisms. Here we report that platelet immunoreceptor tyrosine activation motif (ITAM) signaling, but not GPCR signaling, is critical for the prevention of inflammation-induced hemorrhage. To generate mice with partial or complete defects in these signaling pathways, we developed a protocol for adoptive transfer of genetically and/or chemically inhibited platelets into thrombocytopenic (TP) mice. Unexpectedly, platelets with impaired GPCR signaling, a crucial component of platelet plug formation and hemostasis, were indistinguishable from WT platelets in their ability to prevent hemorrhage at sites of inflammation. In contrast, inhibition of GPVI or genetic deletion of Clec2, the only ITAM receptors expressed on mouse platelets, significantly reduced the ability of platelets to prevent inflammation-induced hemorrhage. Moreover, transfusion of platelets without ITAM receptor function or platelets lacking the adapter protein SLP-76 into TP mice had no significant effect on vascular integrity during inflammation. These results indicate that the control of vascular integrity is a major function of immune-type receptors in platelets, highlighting a potential clinical complication of novel antithrombotic agents directed toward the ITAM signaling pathway.