gebhart/patrepeval huggingface dataset:
MUC1 Expression in Prostate Carcinoma: Correlation with Grade and Stage. (1999)

Mucins have been implicated in the biologic behavior and progression of several types of cancer. The aims of this study were to define the expression pattern of one particular mucin, MUC1, in benign and malignant human prostate tissue and to determine if MUC1 expression correlates with tumor grade and stage. Immunohistochemical staining utilizing an anti-MUC1 monoclonal antibody was performed on 4 fetal prostates, 4 specimens of benign prostatic hyperplasia (BPH), and 34 radical prostatectomy specimens. In human fetal and BPH specimens, there was an apical pattern of MUC1 expression, similar to that reported in other normal and benign tissues. Ninety-four percent of the prostate cancers were MUC1 positive. A high percentage of prostate cancer specimens (62%) demonstrated a diffuse, cytoplasmic staining pattern. There was a statistically significant correlation between diffuse MUC1 staining and Gleason pattern, with a diffuse/total staining percentage of 9% in Gleason 2, 64% in Gleason 3, 80% in Gleason 4, and 100% in Gleason 5. More diffuse staining was also seen in samples from patients with high pathologic stage: 21% in T(2), 75% in T(3), and 67% in N(1) disease. These data indicate that MUC1 expression is prevalent in prostate cancer and that diffuse cytoplasmic staining correlates with advanced Gleason pattern and advanced pathologic stage.
Transcriptional regulation of the ospAB and ospC promoters from Borrelia burgdorferi (2003)

OspA, OspB and OspC are the major outer surface proteins of Borrelia burgdorferi that are differentially synthesized in response to environmental conditions, including culture temperature. We found that DNA was more negatively supercoiled in B. burgdorferi cultures grown at 23 degrees C compared with cultures grown at 35-37 degrees C. We examined the regulation of ospAB and ospC transcription by temperature and DNA supercoiling. DNA supercoiling was relaxed by adding coumermycin A1, an antibiotic that inhibits DNA gyrase. Syntheses of the major outer surface proteins, expression of the ospA and ospC genes and the activities of the ospAB operon and ospC gene promoters were assayed. ospA product levels decreased, whereas ospC product levels increased after shifting from 23 degrees C to 35 degrees C or after adding coumermycin A1. In addition, OspC synthesis was higher in a gyrB mutant than in wild-type B. burgdorferi. Promoter activity was quantified using cat reporter fusions. Increasing temperature or relaxing supercoiled DNA resulted in a decrease in ospAB promoter activity in B. burgdorferi, but not in Escherichia coli, as well as an increase in ospC promoter activity in both bacteria. ospC promoter activity was increased in an E. coli gyrB mutant with an attenuated DNA supercoiling phenotype. These results suggest that B. burgdorferi senses environmental changes in temperature by altering the level of DNA supercoiling, which then affects the expression of the ospAB operon and the ospC gene. This implies that DNA supercoiling acts as a signal transducer for environmental regulation of outer surface protein synthesis.
Burden of Acute Sore Throat and Group A Streptococcal Pharyngitis in School-aged Children and Their Families in Australia (2007)

Group A streptococcal pharyngitis is still common, and the peak incidence occurs in school-aged children. However, the incidence in adults is higher than expected, and the number of secondary cases in families may be an important factor when considering the potential benefits of treatment.
Rough-sea deghosting using a single streamer and a pressure gradient approximation (2002)

Abstract We present a method for receiver ghost correction of towed streamer data that accounts for the rough sea surface. The method explicitly uses the fact that the pressure is zero at the free (sea) surface to estimate the vertical pressure gradient. Continuous elevation measurements of the wave height directly above the hydrophones are required—a measurement which is currently unavailable. The new deghosting method is fundamentally limited to frequencies below the first ghost notch. The lowest-order implementation requires that the streamer is towed no deeper than approximately 6 m and a receiver spatial sampling interval of about 3 m or less. Using the lowest-order and simplest implementation of the new method, the rough-sea error is reduced from 1.5–2.5 dB to about 1–1.5 dB in amplitude and from 20° to 10° in phase, at 50 Hz in a 4-m significant wave height sea. Higher-order terms in the approximation promise to further reduce the error.
Part I: Pathogenetic Role of Peroxynitrite in the Development of Diabetes and Diabetic Vascular Complications: Studies With FP15, A Novel Potent Peroxynitrite Decomposition Catalyst (2002)

The current results demonstrate the importance of endogenous peroxynitrite generation in the pathogenesis of autoimmune diabetes and diabetic cardiovascular complications. Peroxynitrite decomposition catalysts may be of therapeutic utility in diabetes and other pathophysiologic conditions.
The Metabolic Syndrome (2008)

The "metabolic syndrome" (MetS) is a clustering of components that reflect overnutrition, sedentary lifestyles, and resultant excess adiposity. The MetS includes the clustering of abdominal obesity, insulin resistance, dyslipidemia, and elevated blood pressure and is associated with other comorbidities including the prothrombotic state, proinflammatory state, nonalcoholic fatty liver disease, and reproductive disorders. Because the MetS is a cluster of different conditions, and not a single disease, the development of multiple concurrent definitions has resulted. The prevalence of the MetS is increasing to epidemic proportions not only in the United States and the remainder of the urbanized world but also in developing nations. Most studies show that the MetS is associated with an approximate doubling of cardiovascular disease risk and a 5-fold increased risk for incident type 2 diabetes mellitus. Although it is unclear whether there is a unifying pathophysiological mechanism resulting in the MetS, abdominal adiposity and insulin resistance appear to be central to the MetS and its individual components. Lifestyle modification and weight loss should, therefore, be at the core of treating or preventing the MetS and its components. In addition, there is a general consensus that other cardiac risk factors should be aggressively managed in individuals with the MetS. Finally, in 2008 the MetS is an evolving concept that continues to be data driven and evidence based with revisions forthcoming.
Nerve growth factor and the physiology of pain: lessons from congenital insensitivity to pain with anhidrosis (2012)

Congenital insensitivity to pain with anhidrosis (CIPA) is an autosomal recessive genetic disorder characterized by insensitivity to pain, anhidrosis (the inability to sweat) and mental retardation. Nerve growth factor (NGF) is a well-known neurotrophic factor essential for the survival and maintenance of NGF-dependent neurons, including primary afferent neurons with thin fibers and sympathetic postganglionic neurons, during development. NGF is also considered to be an inflammatory mediator associated with pain, itch and inflammation in adults. CIPA results from loss-of-function mutations in the NTRK1 gene-encoding TrkA (tropomyosin-related kinase A), a receptor tyrosine kinase for NGF. Defects in NGF-TrkA signal transduction lead to the failure of survival of various NGF-dependent neurons. As a result, patients with CIPA lack NGF-dependent neurons. Recent studies have revealed that mutations in the NGFB gene-encoding NGF protein also cause congenital insensitivity to pain. Using the pathophysiology of CIPA as a foundation, this review investigates the ways in which NGF-dependent neurons contribute to interoception, homeostasis and emotional responses and, together with the brain, immune and endocrine systems, play crucial roles in pain, itch and inflammation. The NGF-TrkA system is essential for the establishment of neural networks for interoception, homeostasis and emotional responses. These networks mediate reciprocal communication between the brain and the body in humans.
Construction of a potential live oral bivalent vaccine for typhoid fever and cholera-Escherichia coli-related diarrheas (1984)

We used the Salmonella typhi galactose epimerase (galE) mutant strain Ty21a, shown to be a safe, effective, living, attenuated oral typhoid vaccine, as a recipient for a recombinant plasmid containing the gene for production of the nontoxic B subunit of the heat-labile enterotoxin of Escherichia coli. The S. typhi derivative, strain SE12, produced heat-labile enterotoxin subunit B that was structurally and immunologically indistinguishable from heat-labile enterotoxin subunit B produced by strains of E. coli harboring the same plasmid. Tests in mice and guinea pigs showed that strain SE12 was safe when given orally and was capable of inducing a significant antitoxic antibody response when injected parenterally. Moreover, it retained the galactose sensitivity of the parent strain, preserving its utility as a typhoid vaccine. This strain may prove to be a useful live oral bivalent vaccine strain for typhoid fever and cholera-E. coli-related diarrheas.
Anatomy of herpes simplex virus DNA. II. Size, composition, and arrangement of inverted terminal repetitions (1975)

Electron microscope studies on self-annealed intact single strands and on partially denatured molecules show that herpes simplex virus 1 DNA consists of two unequal regions, each bounded by inverted redundant sequences. Thus the region L (70 percent of the contour length of the DNA) separates the left terminal region a1b from its inverted repeat b'a'1, each of which comprises 6 percent of the DNA. The region S (9.4 percent of DNA) separates the right terminal region cas (4.3 percent of the DNA) from its inverted repeat a'sc'. The regions of the two termini which are inverted and repeated itnernally differ in topology. Thus, cas is guanine plus cytosine rich, whereas only the terminal 1 percent of the a1b region, designated as subregion a1, is guanine plus cytosine rich.
Relationship of runoff vessels to results following thrombolysis and revascularization for synthetic graft occlusions. (1995)

The objective of this study was to evaluate the relation between runoff vessels and the prognosis in patients who have had an occlusion of a previously placed peripheral arterial bypass graft. Over a 4-year period 77 occluded synthetic grafts were treated with urokinase and reconstruction after angiographic study. Follow-up ranged from 1 to 1627 days. The cases were divided into three groups according to the number of patent tibial vessels. Group I consisted of patients who had no vessel runoff. Group II consisted of patients who had single vessel runoff. Group III consisted of patients who had two or three runoff vessels. In Group I, the 1, 2, and 3-year patency rates were 35.8%, 8.9%, and 8.9%; and the limb salvage rates were 50.2%, 40.2%, and 40.2% for 1, 2, and 3 years, respectively. The Group II patency rates were 31.2%, 26.0%, and 13.0% and the limb salvage rates were 72.3%, 62.9%, and 62.9%. The Group III patency rates were 50.0%, 26.1%, and 20.9%; and the limb salvage rates were 93.1%, 79.1%, and 79.1%. There is no statistically significant difference in patency rates among any of the groups. The limb salvage rate was significantly increased in Group III, compared to I (P < 0.01) and Group II (P < 0.05), and in Group II, compared to Group I (P < 0.05). These results indicate that the higher rate of limb salvage in this study statistically correlated with the number of runoff vessels.
Sequence database searches viade novo peptide sequencing by tandem mass spectrometry (1997)

A method is described for searching protein sequence databases using tandem mass spectra of tryptic peptides. The approach uses a de novo sequencing algorithm to derive a short list of possible sequence candidates which serve as query sequences in a subsequent homology-based database search routine. The sequencing algorithm employs a graph theory approach similar to previously described sequencing programs. In addition, amino acid composition, peptide sequence tags and incomplete or ambiguous Edman sequence data can be used to aid in the sequence determinations. Although sequencing of peptides from tandem mass spectra is possible, one of the frequently encountered difficulties is that several alternative sequences can be deduced from one spectrum. Most of the alternative sequences, however, are sufficiently similar for a homology-based sequence database search to be possible. Unfortunately, the available protein sequence database search algorithms (e.g. Blast or FASTA) require a single unambiguous sequence as input. Here we describe how the publicly available FASTA computer program was modified in order to search protein databases more effectively in spite of the ambiguities intrinsic in de novo peptide sequencing algorithms.
Histology by magnetic resonance microscopy. (1993)

Magnetic resonance microscopy (MRM) has advanced from a technical challenge to a practical tool in a wide range of basic sciences. This article focuses on the use of MRM as a tool for histological studies. The technical challenges of limited signal to noise have been overcome by improved radio-frequency (rf) coil design and 3DFT encoding with large arrays. Resolution limits imposed by motion in in vivo studies have been overcome by improved physiologic monitoring and control and projection encoding. Integration of technologies now permits routine studies in vivo down to 50 microns. MRM has also been applied to in vitro studies of fixed tissues where absence of motion allows studies down to 10 microns. The nondestructive nature of the technique allows repeated studies of the same sample, retrospective studies through any arbitrary plane, registered studies using different contrast mechanisms, and examination of valuable specimens. The many and unique proton contrasts provided by MRM, i.e., T1, T2, and diffusion weighting, permit direct examination of the state of water in tissues, something not possible with other microscopic techniques. Finally, the inherent three-dimensional nature of MRM allows acquisition of perfectly registered isotropic 3D arrays that, when displayed with appropriate visualization tools, provide new perspectives to histologic examination. The technology of MRM continues to develop rapidly. New pulse sequences are reducing acquisition times. New computer architectures allow larger arrays. A new class of superconducting rf probe has increased the signal to noise ratio by 10 times. These developments promise routine use of MRM in histology studies with resolution to 1 micron in the near future.
Effects of the novel anti‐inflammatory compounds, N‐[2‐(cyclohexyloxy)‐4‐nitrophenyl] methanesulphonamide (NS‐398) and 5‐methanesulphonamido‐6‐(2, 4‐difluorothiophenyl)‐1‐indanone (L‐745, 337), on the cyclo‐oxygenase activity of human blood prostaglandin endoperoxide synthases (1995)

1. We have evaluated the selectivity of ketoprofen and two novel nonsteroidal anti-inflammatory drugs, N-[2-(cyclohexyloxy)-4-nitrophenyl]methanesulphonamide (NS-398) and 5-methanesulphonamido-6-(2,4-difluorothiophenyl)-1-indano ne (L-745,337), in inhibiting the cyclo-oxygenase activity of prostaglandin endoperoxide synthase-2 (PGHS-2) vs PGHS-1 in human blood monocytes and platelets, respectively. 2. Heparinized whole blood samples were drawn from healthy volunteers pretreated with aspirin, 300 mg 48 h before sampling, to suppress the activity of platelet PGHS-1 and incubated at 37 degrees C for 24 h with increasing concentrations of the test compounds in the presence of lipopolysaccharide (LPS, 10 micrograms ml-1). Immunoreactive PGE2 levels were measured in plasma by a specific radioimmunoassay as an index of the cyclo-oxygenase activity of LPS-induced monocyte PGHS-2. 3. The effects of the same inhibitors on platelet PGHS-1 activity were assessed by allowing whole blood samples, drawn from the same subjects in aspirin-free periods, to clot at 37 degrees C for 1 h in the presence of the compounds and measuring immunoreactive thromboxane B2 (TXB2) levels in serum by a specific radioimmunoassay. 4. Under these experimental conditions, ketoprofen enantioselectively inhibited the cyclo-oxygenase activity of both PGHS-1 and PGHS-2 with equal potency (IC50 ratio: approx. 0.5 for both enantiomers), while L-745,337 and NS-398 achieved selective inhibition of monocyte PGHS-2 (IC50 ratio: > 150). L-745,337 and NS-398 did not affect LPS-induced monocyte PGHS-2 biosynthesis to any detectable extent. 5. We conclude that L-745,337 and NS-398 are selective inhibitors of the cyclo-oxygenase activity of human monocyte PGHS-2. These compounds may provide adequate tools to test the contribution of this novel pathway of arachidonate metabolism to human inflammatory disease.
Correlation of primary tumor prostate-specific membrane antigen expression with disease recurrence in prostate cancer. (2003)

This study demonstrates for the first time that overexpression of PSMA in primary PCa correlates with other adverse traditional prognostic factors and independently predicts disease outcome.
A trellis search algorithm for the design of FIR filters with signed-powers-of-two coefficients (1999)

An efficient two-stage algorithm is presented for designing finite-impulse response (FIR) filters that employ sums of signed-powers-of-two (SPT) coefficients. In the first stage, a prototype filter is designed using a fast time-domain approximation. This is followed, in the second stage, where the design problem is formulated as a dynamic-programming-like recursive optimization problem, by a trellis search that optimizes the filter's frequency response. The proposed search algorithm, which iteratively designs filters that employ an increasing number of SPT terms, provides a means to control the filter's implementation complexity. Design examples demonstrate that our algorithm is capable of producing filters having a better frequency response than existing methods while using fewer SPT terms. We also show that the proposed algorithm can be used to design special FIR filters such as matched transmit and receive filters employing sums of signed-powers-of-two coefficients. Also presented is a modified algorithm that further reduces the required number of adders in a filter by exploiting redundancies within the coefficients.
PIES, a Protein Interaction Extraction System (2000)

We consider the problem of extracting, manipulating, and managing biological pathways, especially protein-protein interaction pathways. We discuss here the Protein Interaction Extraction System (PIES). PIES is contructed on top of three main technologies: Kleisli, BioNLP, and Graphviz. Kleisli is a broad-scale data integration system that we use for downloading Medline abstracts and for general manipulation and management of pathway/interaction databases. BioNLP is a natural language-based information extraction module that we use for analysing Medline abstracts and to extract precise protein-protein and other interaction information. Graphviz is a graphical layout package developed for directed graphs that we use for visualization of the extracted pathways. PIES can be augmented with various means for extracting protein interaction information from sequence databases, for example, by using Kleisli's power to integrate sequence comparison tools to detect gene fusion events in sequence databases.
Antiphosphatidylserine antibodies as diagnostic indicators of antiphospholipid syndrome (2014)

Our findings reveal a significant association between aPS and APS, especially when used to diagnosis clinical cases with other negative aPL tests. There is an independent association between aPS and primary APS. In addition, these results demonstrated the advantages of using aPS as a diagnostic test for APS.
Cellular Synthesis of Protein Catenanes (2016)

Direct cellular production of topologically complex proteins is of great interest both in supramolecular chemistry and protein engineering. We describe the first cellular synthesis of protein catenanes through the use of the p53 dimerization domain to guide the intertwining of two protein chains and SpyTag-SpyCatcher chemistry for efficient cyclization. The catenane topology was unambiguously proven by SDS-PAGE, SEC, and partial digestion experiments and was shown to confer enhanced stability toward trypsin digestion relative to monomeric control mutants. The assembly-reaction synergy enabled by protein folding and genetically encoded protein chemistry offers a convenient yet powerful approach for creating mechanically interlocked, complex protein topologies in vivo.
Carcass characteristics and meat quality of once-calved heifers (1991)

Three groups of once-calved (OCH) heifers were slaughtered following the weaning of their calves at 3 (OCH3, n = 32), 5 (OCH5, n = 33) and 7 (OCH7, n = 31) months postcalving. A fourth group of heifers was fed a silage/grain diet and slaughtered at 15 mo of age (C, n = 32). Alternate sides of each carcass were electrically stimulated (ES) at 475 volts for 1 min (20 pulses m −1 , 60 Hz) at 45 min post-stunning. All left sides were dissected into fat, lean and bone and meat quality parameters recorded. Rib eye steaks were evaluated for palatability by a trained panel and for consumer acceptability after an aging period of 6 d. All OCH groups produced heavier carcasses with a higher level of marbling than the C group after adjustment of the data to a constant proportion of carcass fatness, but the proportional yields of lean and bone tissue were similar for all heifer groups. OCH groups produced meat that was darker with a lower drip loss and higher 45 min and 6 d pH than the C group. Consumer acceptability of rib eye steaks was similar for all heifer groups, but the OCH7 (oldest) group had a higher amount of connective tissue when evaluated by a trained panel than other heifer groups. Taste panel evaluations showed that ES increased meat tenderness and overall palatability and reduced the amount of connective tissue when compared to meat from unstimulated carcasses. ES also increased the consumer acceptability of tenderness by 14.3%, flavor by 5.6%, juiciness by 5.2% and overall palatability by 6.7% over meat from unstimulated carcasses. It was concluded that once-calved heifers could produce heavier carcasses of similar composition and meat with similar eating quality to conventionally managed nonpregnant feedlot heifers. Electrical stimulation improved the consumer acceptability of meat primarily through an improvement in meat tenderness. Key words: Beef, carcass, electrical stimulation, meat quality, once-calved heifers