gebhart/patrepeval huggingface dataset:
Monoclonal antibodies specific for elongation factor Tu and complete nucleotide sequence of the tuf gene in Mycobacterium tuberculosis (1992)

Monoclonal antibodies against mycobacterial antigens were produced by immunizing LOU/C rats with live Mycobacterium bovis BCG. The antibodies were characterized by an enzyme-linked immunosorbent assay and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by Western blotting (immunoblotting). One antibody, MAMB 2, reactive with a 47-kDa protein was used to screen a lambda gt11 M. tuberculosis gene library (R. A. Young, B. R. Bloom, C. M. Grosskinsky, J. Ivanji, D. Thomas, and R. W. Davis, Proc. Natl. Acad. Sci. USA 82:2583-2587, 1985). Three recombinant phages reactive with MAMB 2 in plaque lysates were isolated, and part of the insert was sequenced. The mycobacterial inserts were all expressed as proteins fused with beta-galactosidase when the phages were induced as lysogens in Escherichia coli. The entire M. tuberculosis tuf gene was obtained by screening the lambda gt11 library with a DNA probe specific for the primary clones. A phage isolated from this screening was able to express the native protein in E. coli when introduced as a lysogen. A comparison of the entire gene sequence and the deduced protein sequence with the EMBL DNA and Swiss-Prot protein data libraries revealed strong homologies with elongation factors of bacteria, yeast mitochondria, and a plant chloroplast.
An Official American Thoracic Society Workshop Report: Features and Measurements of Experimental Acute Lung Injury in Animals (2011)

Acute lung injury (ALI) is well defined in humans, but there is no agreement as to the main features of acute lung injury in animal models. A Committee was organized to determine the main features that characterize ALI in animal models and to identify the most relevant methods to assess these features. We used a Delphi approach in which a series of questionnaires were distributed to a panel of experts in experimental lung injury. The Committee concluded that the main features of experimental ALI include histological evidence of tissue injury, alteration of the alveolar capillary barrier, presence of an inflammatory response, and evidence of physiological dysfunction; they recommended that, to determine if ALI has occurred, at least three of these four main features of ALI should be present. The Committee also identified key "very relevant" and "somewhat relevant" measurements for each of the main features of ALI and recommended the use of least one "very relevant" measurement and preferably one or two additional separate measurements to determine if a main feature of ALI is present. Finally, the Committee emphasized that not all of the measurements listed can or should be performed in every study, and that measurements not included in the list are by no means "irrelevant." Our list of features and measurements of ALI is intended as a guide for investigators, and ultimately investigators should choose the particular measurements that best suit the experimental questions being addressed as well as take into consideration any unique aspects of the experimental design.
Urokinase receptor antibody can reduce tumor volume and detect the presence of occult tumor metastases in vivo. (2002)

The serine protease urinary plasminogen activator or urokinase (uPA), produced in abundance by many malignancies, plays a key role in tumor cell invasion and metastasis. uPA is localized within the malignant cell milieu via its cell surface receptor [uPA receptor (uPAR)], which is expressed by tumor and tumor-associated cells. In the present study, we have used a syngeneic model of rat breast cancer to directly evaluate the role of uPAR as a diagnostic and therapeutic target in metastatic breast cancer. A polyclonal antibody against the ligand-binding NH(2)-terminal domain of rat uPAR (ruPAR) was developed. This antibody recognizes ruPAR by both immunofluorescence and Western blot analysis. Recombinant ruPAR and ruPAR IgG displaced the binding of (125)I-labeled ruPAR IgG to rat prostate cancer cells (Dunning R3227 Mat Ly Lu) and breast cancer cells (Mat B-III) overexpressing ruPAR (Mat B-III-uPAR). ruPAR IgG also blocked the invasive capacity of these tumor cells in a dose-dependent manner. Mat B-III-uPAR cells were inoculated s.c. into the mammary fat pad of syngeneic female Fischer rats. On day 10 after tumor cell inoculation, animals were injected with (125)I-labeled preimmune or ruPAR IgG and then sacrificed at timed intervals. Maximum (125)I uptake was observed in primary tumors and in tissues commonly affected by tumor metastases (liver, spleen, lungs, and lymph nodes) at 12 h. Injection of (125)I-labeled preimmune or ruPAR IgG into normal non-tumor-bearing animals resulted in minimal basal levels of uPAR expression and established the specificity of the ruPAR IgG. Similar results were obtained by Northern blot and PCR analysis of mRNA isolated from tissues of normal and tumor-bearing animals. To evaluate the effectiveness of this antibody in tumor progression, ruPAR IgG (50-100 microg/day) was injected s.c. for 7 days (day 1-7) at the site of tumor cell inoculation (mammary fat pad), and animals were sacrificed at various time points for evaluation of tumor growth and metastases. Animals receiving ruPAR IgG showed a marked decrease in tumor growth and metastases as compared with control tumor-bearing animals receiving the same dose of preimmune rabbit IgG. Histological analysis of experimental primary tumors showed marked tumor necrosis that was due to increased tumor cell apoptosis as determined by terminal deoxynucleotidyl transferase-mediated nick end labeling assay. Together, these studies demonstrate the ability of anti-uPAR antibody to decrease tumor volume and detect the presence of microscopic occult tumor metastases in malignancies where uPA/uPAR play a key role in tumor progression.
Inhibition of cell growth in CaCO2 cells by the polyamine analogue N1,N12-bis(ethyl)spermine is preceded by a reduction in MYC oncoprotein levels (1998)

The polyamine analogue N1,N12bis(ethyl)spermine (BESpm) is a potent inhibitor of cell proliferation and is representative of a class of agents currently in clinical trials. Previous studies have demonstrated that BESpm treatment can produce a decrease in the mRNA levels of the protooncogene c-myc resulting from decreased transcription. Investigation into the mechanism of the antiproliferative effect of BESpm in the colon cancer cell line CaCO2 indicated that significant reduction in MYC protein, but not c-myc mRNA levels, preceded cytostasis. Specificity of the downregulation of MYC expression by BESpm treatment was demonstrated by comparison to effects on the polyamine catabolic enzyme spermidine/spermine N1-acetyltransferase (SSAT) and the polyamine biosynthetic enzyme ornithine decarboxylase (ODC). SSAT activity rapidly increased while levels of ODC activity decreased after BESpm treatment. Measurement of intracellular polyamines demonstrated significant uptake of the analogue after 24 hours, which was concurrent with a reduction of spermine and spermidine levels. Thus, cellular uptake of BESpm mediated a reduction of polyamine levels that was associated with a decrease of MYC protein at the post-transcriptional level. J. Cell. Physiol. 174:380–386, 1998. © 1998 Wiley-Liss, Inc.
Reduction of α-Ketoglutarate by Homogeneous Lactic Dehydrogenase X of Testicular Tissue (1969)

Abstract Lactic dehydrogenase X, an isozyme found thus far only in mature sperm of mammals and birds, has been purified to homogeneity from rat tissue. A molecular weight of 125,000 ± 4,000 was determined. In addition to its ability to catalyze the pyridine nucleotide-linked interconversion of pyruvate and lactate, the enzyme exhibits substantial activity for the similar interconversions of α-ketoglutarate and α-hydroxyglutarate, a property not present in other isozymes of lactic dehydrogenase. Pyruvate reduction was strongly inhibited by excess substrate, whereas the α-ketoglutarate saturation curve was essentially hyperbolic.
T-Cell Lymphoma in a Dog with Cutaneous Lesions (1983)

皮膚に結節および潰瘍の多発した4歳, 雌の雑種犬を精査した. 皮膚結節の生検においては, 真皮における腫瘍性リンパ系細胞の著明な増生が認められ, 剖検時, 各臓器に同様な細胞の浸潤, 増生が認められた. 皮膚結節の腫瘍細胞は, ヒト赤血球Eロゼット形成および表面免疫グロブリンの検査所見でT細胞の形質を示し, 本例をT細胞リンパ腫と診断した.
Antisperm antibodies: diagnosis and treatment (1996)

During the onset of spermatogenesis at puberty, new developmental antigens make their appearance on the sperm surface (Ishahakia, 1988). Because immune tolerance for self-antigens is expressed neonatally, these newly appearing sperm antigens may be immunogenic. It has been theorized that sequestration of developing sperm by the blood–testis barrier prevents the generation of autoantibodies to sperm (Dym, 1973). Additional evidence has recently been presented that certain testicular auto-antigens exist outside the blood–testis barrier and are accessible to circulating antibodies and immune processing cells. A population of suppressor T lymphocytes has also been identified in the epididymis, suggesting that active immune suppression may play a role in preventing the development of autoimmunity to sperm (El-Demiry & James, 1988).
Hypomethylation of Intragenic LINE-1 Represses Transcription in Cancer Cells through AGO2 (2011)

In human cancers, the methylation of long interspersed nuclear element -1 (LINE-1 or L1) retrotransposons is reduced. This occurs within the context of genome wide hypomethylation, and although it is common, its role is poorly understood. L1s are widely distributed both inside and outside of genes, intragenic and intergenic, respectively. Interestingly, the insertion of active full-length L1 sequences into host gene introns disrupts gene expression. Here, we evaluated if intragenic L1 hypomethylation influences their host gene expression in cancer. First, we extracted data from L1base (http://l1base.molgen.mpg.de), a database containing putatively active L1 insertions, and compared intragenic and intergenic L1 characters. We found that intragenic L1 sequences have been conserved across evolutionary time with respect to transcriptional activity and CpG dinucleotide sites for mammalian DNA methylation. Then, we compared regulated mRNA levels of cells from two different experiments available from Gene Expression Omnibus (GEO), a database repository of high throughput gene expression data, (http://www.ncbi.nlm.nih.gov/geo) by chi-square. The odds ratio of down-regulated genes between demethylated normal bronchial epithelium and lung cancer was high (p<1E(-27); OR = 3.14; 95% CI = 2.54-3.88), suggesting cancer genome wide hypomethylation down-regulating gene expression. Comprehensive analysis between L1 locations and gene expression showed that expression of genes containing L1s had a significantly higher likelihood to be repressed in cancer and hypomethylated normal cells. In contrast, many mRNAs derived from genes containing L1s are elevated in Argonaute 2 (AGO2 or EIF2C2)-depleted cells. Hypomethylated L1s increase L1 mRNA levels. Finally, we found that AGO2 targets intronic L1 pre-mRNA complexes and represses cancer genes. These findings represent one of the mechanisms of cancer genome wide hypomethylation altering gene expression. Hypomethylated intragenic L1s are a nuclear siRNA mediated cis-regulatory element that can repress genes. This epigenetic regulation of retrotransposons likely influences many aspects of genomic biology.
Handbook of stereoisomers: therapeutic drugs (1989)

VOLUME I: Introduction. a-Adrenergic Drugs. Antirrhythmic Drugs. Antihypertensive Drugs. Anticoagulant Drugs. Anti-Inflammatory Drugs. Antihistaminic Drugs. Antiallergic Drugs. Index. VOLUME II: Antibiotic and Antimicrobial Drugs. Antimalarial Drugs. Antineoplastic Drugs. Opioid Analgesic Drugs. Psychotropic Drugs.
Light and Scanning Electron Microscopy of Nasal Biopsy Material from Patients with Naturally Acquired Common Colds (1984)

As our knowledge of the histopathology of common colds is very limited, we have undertaken a blind quantitative examination by scanning electron microscopy and light microscopy of 56 nasal biopsies, taken from 29 volunteers with naturally acquired colds. In agreement with earlier reports we found evidence of sloughing of epithelial cells, but in contrast to in vitro experiments, this did not result in a destruction of the epithelial lining, which by and large remained continuous, with structurally normal cell borders. There was a significant increase in the number of neutrophils, both in epithelium and in lamina propria, already on the 2nd day of the disease, and the hypothesis is advanced that the virus infection itself is the cause of the local neutrophilia. The only other abnormality demonstrated was an increased number of extracellular erythrocytes in the acute stage. The histological picture was not suggestive of an involvement of epithelial mast cells in the inflammation.
Transthyretin mutations in hyperthyroxinemia and amyloid diseases (2001)

Over 80 different disease-causing mutations in transthyretin (TTR) have been reported. The vast majority are inherited in an autosomal dominant manner and are related to amyloid deposition, affecting predominantly peripheral nerve and/or the heart. A small portion of TTR mutations are apparently non-amyloidogenic. Among these are mutations responsible for hyperthyroxinemia, presenting high affinity for thyroxine (a TTR ligand). Compound heterozygotic individuals for TTR mutants have been described; noteworthy is the clinically protective effect exerted by a non-pathogenic over a pathogenic mutation. Current TTR mutations and their significance are briefly reviewed here.
Fluorescent Cardiac Imaging (2007)

The impairment of myocardial perfusion in response to increased coronary stenosis severity and total vessel occlusion can be quantitatively assessed by FCI and correlates well with results obtained by fluorescent microsphere.
Involvement of Enterotoxins G and I in Staphylococcal Toxic Shock Syndrome and Staphylococcal Scarlet Fever (1999)

We investigated the involvement of the recently described staphylococcal enterotoxins G and I in toxic shock syndrome. We reexamined Staphylococcus aureus strains isolated from patients with menstrual and nonmenstrual toxic shock syndrome (nine cases) or staphylococcal scarlet fever (three cases). These strains were selected because they produced none of the toxins known to be involved in these syndromes (toxic shock syndrome toxin 1 and enterotoxins A, B, C, and D), enterotoxin E or H, or exfoliative toxin A or B, despite the fact that superantigenic toxins were detected in a CD69-specific flow cytometry assay measuring T-cell activation. Sets of primers specific to the enterotoxin G and I genes (seg and sei, respectively) were designed and used for PCR amplification. All of the strains were positive for seg and sei. Sequence analysis confirmed that the PCR products, corresponded to the target genes. We suggest that staphylococcal enterotoxins G and I may be capable of causing human staphylococcal toxic shock syndrome and staphylococcal scarlet fever.
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System (2015)

The microbial adaptive immune system CRISPR mediates defense against foreign genetic elements through two classes of RNA-guided nuclease effectors. Class 1 effectors utilize multi-protein complexes, whereas class 2 effectors rely on single-component effector proteins such as the well-characterized Cas9. Here, we report characterization of Cpf1, a putative class 2 CRISPR effector. We demonstrate that Cpf1 mediates robust DNA interference with features distinct from Cas9. Cpf1 is a single RNA-guided endonuclease lacking tracrRNA, and it utilizes a T-rich protospacer-adjacent motif. Moreover, Cpf1 cleaves DNA via a staggered DNA double-stranded break. Out of 16 Cpf1-family proteins, we identified two candidate enzymes from Acidaminococcus and Lachnospiraceae, with efficient genome-editing activity in human cells. Identifying this mechanism of interference broadens our understanding of CRISPR-Cas systems and advances their genome editing applications.
Beating the Photon-Number-Splitting Attack in Practical Quantum Cryptography (2005)

We propose an efficient method to verify the upper bound of the fraction of counts caused by multiphoton pulses in practical quantum key distribution using weak coherent light, given whatever type of Eve's action. The protocol simply uses two coherent states for the signal pulses and vacuum for the decoy pulse. Our verified upper bound is sufficiently tight for quantum key distribution with a very lossy channel, in both the asymptotic and nonasymptotic case. So far our protocol is the only decoy-state protocol that works efficiently for currently existing setups.
[Determination of acceptability of 2 cutaneous estradiol gels, in a dose of 1.5 mg daily]. (2000)

A better acceptability of the 0.1% estradiol gel and of its packaging compared to that of the 0.06% estradiol gel in this new formulation and packaging is observed in this study.
Mutations in the RET proto-oncogene are associated with MEN 2A and FMTC (1993)

Multiple endocrine neoplasia type 2A (MEN 2A) and familial medullary thyroid carcinoma (FMTC) are dominantly inherited conditions which predispose to the development of endocrine neoplasia. Evidence is presented that sequence changes within the coding region of the RET proto-oncogene, a putative transmembrane tyrosine kinase, may be responsible for the development of neoplasia in these inherited disorders. Single strand conformational variants (SSCVs) in exons 7 and 8 of the RET proto-oncogene were identified in eight MEN 2A and four FMTC families. The variants were observed only in the DNA of individuals who were either affected or who had inherited the MEN2A or FMTC allele as determined by haplotyping experiments. The seven variants identified were sequenced directly. All involved point mutations within codons specifying cysteine residues, resulting in nonconservative amino acid changes. Six of the seven mutations are located in exon 7. A single mutation was found in exon 8. Variants were not detected in four MEN 2B families studied for all exon assays available, nor were they detectable in 16 cases of well documented sporadic medullary thyroid carcinoma or pheochromocytoma that were tested for exon 7 variants. Coinheritance of the mutations with disease and the physical and genetic proximity of the RET proto-oncogene provide evidence that RET is responsible for at least two of the three inherited forms of MEN 2. Neither the normal function, nor the ligand of RET are yet known. However, its apparent involvement in the development of these inherited forms of neoplasia as well as in papillary thyroid carcinoma suggest an important developmental or cell regulatory role for the protein.
Nondestructive Direct Determination of Heroin in Seized Illicit Street Drugs by Diffuse Reflectance near-Infrared Spectroscopy (2008)

A new method has been developed for the fast and nondestructive direct determination of heroin in seized street illicit drugs using partial least-squares regression analysis of diffuse reflectance near-infrared spectra. Data were obtained from untreated samples placed in standard glass chromatography vials. A heterogeneous population of 31 samples, previously analyzed by a reference method, was employed to build the calibration model and to have a separated validation set. Based on the use of zero-order data for a calibration set of 21 samples, after standard normal variate and quadratic linear removed baseline correction (detrending), in the wavelength range from 1111 to 1647 nm, 8 PLS factors were enough to obtain a root-mean-square error of prediction of 1.3% w/w, with a quality coefficient of 10% for the estimation of the accuracy error in the prediction of heroin concentration in unknown samples and a residual predictive deviation of 5.4.
Intracellular bacteria of porcine proliferative enteropathy: cultivation and maintenance in vitro (1993)

An obligate intracellular bacterium was isolated from the intestines of all 10 cases of porcine proliferative enteropathy from four different pig farms. The organism grew in a rat enterocyte cell line (IEC-18) and was maintained over 20 passages. The growth of the bacteria was assessed by immunostaining of cells exposed to infection. Infection was not associated with morphological cell change, and growth was confined to cells infected at the time of each transfer of infection and the progeny of these cells. The bacterium is a microaerophilic, cell dependent, curved or rod-shaped, gram-negative bacillus that multiplies freely in the enterocyte cytoplasm. Cell cultures containing the intracellular bacteria appear to be free of other microorganisms, including chlamydiae and viruses.
AD-Frustum: Adaptive Frustum Tracing for Interactive Sound Propagation (2008)

We present an interactive algorithm to compute sound propagation paths for transmission, specular reflection and edge diffraction in complex scenes. Our formulation uses an adaptive frustum representation that is automatically sub-divided to accurately compute intersections with the scene primitives. We describe a simple and fast algorithm to approximate the visible surface for each frustum and generate new frusta based on specular reflection and edge diffraction. Our approach is applicable to all triangulated models and we demonstrate its performance on architectural and outdoor models with tens or hundreds of thousands of triangles and moving objects. In practice, our algorithm can perform geometric sound propagation in complex scenes at 4-20 frames per second on a multi-core PC.
Biodegradable microspheres containing adriamycin in the treatment of proliferative vitreoretinopathy. (1992)

The use of biodegradable polymer microspheres containing adriamycin for the treatment of proliferative vitreoretinopathy (PVR) in an experimental rabbit model was investigated. A single injection of microspheres containing 10 micrograms of adriamycin effectively decreased traction retinal detachment to 10% (n = 10), whereas 50% of eyes injected with blank microspheres (n = 10) developed retinal detachment (P < 0.05). A single injection of microspheres, containing 3 micrograms of adriamycin, did not suppress retinal detachment. Electroretinographic and histologic studies confirmed that the 10 micrograms injection of adriamycin in microspheres was not toxic to the retina, although the injection of the same amount of free adriamycin caused retinal necrosis and detachment. Thus, microspheres containing adriamycin hold promise as a new treatment modality for PVR.
Amplification, up‐regulation and over‐expression of DVL‐1, the human counterpart of the Drosophila disheveled gene, in primary breast cancers (2003)

Wnt proteins form a family of highly conserved, secreted signaling molecules that regulate cell-to-cell interactions during embryogenesis. Wnt genes and Wnt signaling are also implicated in cancer. It has been shown that Wnt proteins bind to receptors of the frizzled family on the cell surface. Through several cytoplasmic relay components including DVL-1, the human counterpart of the Drosophila disheveled gene, the signal is transduced to beta-catenin, which then enters the nucleus and forms a complex with T-cell factor (TCF) to activate transcription of Wnt target genes. We describe here the amplification of DVL-1 in 13 of 24 primary breast cancers examined, and increased expression of this gene in 11 of those tumors in comparison to corresponding non-cancerous breast tissues. Immunohistochemical staining demonstrated that DVL-1 protein was prominent in the cytoplasm of cancer cells, but not in normal epithelial cells of the mammary duct or in myoepithelial cells. These data indicate that amplification and increased expression of the DVL-1 gene may play some role in human breast carcinogenesis through derangement of the Wnt signaling pathway.