gebhart/patrepeval huggingface dataset:
Characterization of an early gene accelerating expression of late genes of the baculovirus Autographa californica nuclear polyhedrosis virus (1988)

The region of the Autographa californica nuclear polyhedrosis virus (AcMNPV) encompassing the EcoRI T fragment (29.0 to 30.1 map units) was characterized by DNA sequencing, transcriptional mapping, and site-directed mutagenesis. The largest transcript from this region, an early 1.7-kilobase (kb) poly(A)+ RNA, encompassed three tandem, nonoverlapping open reading frames (ORFs). The largest of these ORFs, ETL, was proximal to the 5' end of the transcript and had the capacity to encode a 28-kilodalton (kDa) polypeptide. A recombinant virus, vETL beta gal, containing the Escherichia coli beta-galactosidase (beta gal) gene fused to the N-terminal two-thirds of the ETL ORF, produced blue plaques in the presence of a chromogenic indicator of beta gal and wild-type levels of polyhedra in cell culture. This recombinant was also infectious in insect larvae by oral administration of occluded virus. Comparison of vETL beta gal and wild-type viral proteins pulse-labeled at various times postinfection (p.i.) revealed (i) absence of a virus-induced 28-kDa polypeptide, (ii) early expression of a large (approximately 130-kDa) polypeptide which may be the ETL-beta gal fusion protein, (iii) a delay in expression of early 35 and 40-kDa polypeptides, and (iv) a 4- to 6-h delay in the expression of late proteins in vETL beta gal-infected cells. Cycloheximide did not inhibit synthesis of the 1.7-kb RNA but did inhibit its shutoff, which occurs at 12 h p.i. in the absence of inhibitors. Thus, the ETL gene product is apparently an early 28-kDa protein which is necessary, directly or indirectly, for timely expression of many other AcMNPV genes. The promoter-leader regions of the 1.7-kDa transcript showed significant sequence similarities to the leader of the AcMNPV IE-1 gene. The middle ORF within the 1.7-kb transcript, ETM, would encode a hydrophobic polypeptide of 113 amino acid residues. ETS, a small ORF within and proximal to the 3' end of the 1.7-kb transcript, was also transcribed as a set of smaller (approximately 0.5-kb) RNAs initiated heterogeneously in the region between ETL and ETS and persisting throughout infection.
Embryonic implantation in mice is blocked by interleukin-1 receptor antagonist. (1994)

We have investigated the relevance of interleukin-1 receptor type I (IL-1R tI) in the implantation process in vivo in a murine model. Indirect immunofluorescence experiments demonstrate that IL-1R tI is located in mouse endometrial lumenal epithelium with increased intensity in the periimplantation period, whereas IL-1 beta staining is located in the mouse placenta. PMSG/human CG (hCG)-stimulated and mated 12-week-old B6C3F-1 female mice were randomly allocated to three groups: A, control noninjected; B, buffer-injected animals; and C, animals injected ip with 20 micrograms recombinant human IL-1 receptor antagonist (rhIL-1ra) every 12 h beginning on pregnancy day 3. Injections were continued until day 9, and animals were killed 12 h after the last injection. Pregnancy rates in the three groups were: noninjected, 58.8% (10 of 17); buffer-injected, 73.7% (14 of 19); rhIL-1ra-injected, 6.7% (1 of 15), P = 0.0001155, Fisher exact test. To rule out the possibility that pregnancy failure was due to an embryotoxic effect of rhIL-1ra, 2-cell mouse embryos (n = 276) were flushed from the same group of animals used for in vivo experiments and cultured with increasing concentrations of rhIL-1ra: 0 microgram/ml (n = 91), 1 microgram/ml (n = 36), 50 micrograms/ml (n = 36), 100 micrograms/ml (n = 52), and 200 micrograms/ml (n = 61) rhIL-1ra. The percentages of 2-cell mouse embryos reaching the blastocyst stage after 72 h in culture were 85.7%, 91.6%, 94.4%, 96%, and 85.2%, respectively. We further cultured these blastocysts for 5 days on fibronectin-coated plates with or without 200 micrograms/ml rhIL-1ra. In both groups, hatching, attachment to fibronectin, outgrowth, and migration were documented to be similar. Furthermore, our longitudinal morphological study of embryonic implantation in control and rhIL-1ra-injected mice shows that the blockade of IL-1R tI interferes with the attachment of mouse blastocysts to maternal endometrium in vivo. In summary, we demonstrate that blockade of maternal endometrial IL-1R tI with IL-1ra prevents implantation in the mouse by interfering with embryonic attachment, without adverse effects on blastocyst formation, hatching, fibronectin attachment, outgrowth, and migration in vitro.
Effect of fishmeal replacement with spray-dried animal plasma and colistin on intestinal structure, intestinal microbiology, and performance of weanling pigs challenged with Escherichia coli K991 (2003)

We evaluated spray-dried animal plasma (SDAP) as an alternative to antimicrobial medication with colistin sulfate in weanling pigs challenged with Escherichia coli K99. Forty-eight piglets weaned at 24 d of age were distributed into 12 pens, and each pen was assigned to one of four dietary treatments. All the piglets were given an oral dose of 5 x 10(7) cfu of E. coli K99 at weaning. The dietary treatments followed a factorial arrangement with two levels of SDAP (0 and 7%) and two levels of colistin (0 and 300 mg/kg of diet). The ADG and ADFI were measured on d 7 and 14 of trial. Three piglets from each treatment were killed on d 7 and 14 to remove the small intestine, and to obtain ileal and cecal digestive contents. The inclusion of SDAP improved ADG by 68 g (P < 0.05) and ADFI by 41 g (P < 0.10) in wk 1 of trial. During wk 2, SDAP improved ADG by 41 g (P < 0.10) and gain:feed ratio (G:F) by 25% (P < 0.01). On the other hand, whereas colistin had no effect on performance in wk 1, it improved ADG by 102 g (P < 0.01), ADFI by 62 g (P < 0.01), and G:F by 26% (P < 0.01) in wk 2. Over the 14 d of the trial, ADG was improved by 54 (P < 0.05) and 75 g (P < 0.05), and G:F was improved by 35 (P < 0.05) and 32% (P < 0.05) due to SDAP and colistin, respectively. There was interaction between colistin and SDAP for ADFI in wk 2 and between d 0 to 14 (P < 0.05), which indicates that their effects were not additive. The use of colistin was advantageous in the maintenance of the integrity of the intestinal mucosa of the pigs, as suggested by a small intestine that was 93 g heavier (P < 0.10) and with the tallest villi 106 microm longer (P < 0.10) than in pigs without colistin. The inclusion of SDAP in the diet favored the growth of lactobacilli in the ileum (P < 0.10) and the cecum (P < 0.05), whereas colistin reduced the number of enterococci in the cecum (P < 0.05) and of Escherichia coli both in the ileum and the cecum (P < 0.001). These results suggest that SDAP may be an alternative to medicated feed with antibiotics since it provided a level of protection against an experimental challenge with E. coli K99 similar to that obtained with colistin, an antibiotic of proven efficacy. The current situation in which the use of antimicrobials in animal feeding is being questioned should encourage further investigation into the use of SDAP as a means of preventing disease in pigs at weaning.
Aripiprazole versus quetiapine in treatment-resistant obsessive–compulsive disorder: a double-blind clinical trial (2014)

This study shows that treatment-resistant OCD patients may benefit more from addition of quetiapine in comparison with aripiprazole, to their ongoing SRI therapy.
Design patterns for container-based distributed systems (2016)

In the late 1980s and early 1990s, object-oriented programming revolutionized software development, popularizing the approach of building of applications as collections of modular components. Today we are seeing a similar revolution in distributed system development, with the increasing popularity of microservice architectures built from containerized software components. Containers [15] [22] [1] [2] are particularly well-suited as the fundamental “object” in distributed systems by virtue of the walls they erect at the container boundary. As this architectural style matures, we are seeing the emergence of design patterns, much as we did for objectoriented programs, and for the same reason – thinking in terms of objects (or containers) abstracts away the lowlevel details of code, eventually revealing higher-level patterns that are common to a variety of applications and algorithms. This paper describes three types of design patterns that we have observed emerging in container-based distributed systems: single-container patterns for container management, single-node patterns of closely cooperating containers, and multi-node patterns for distributed algorithms. Like object-oriented patterns before them, these patterns for distributed computation encode best practices, simplify development, and make the systems where they are used more reliable.
Circuit Camouflage Integration for Hardware IP Protection (2014)

Circuit camouflage technologies can be integrated into standard logic cell developments using traditional CAD tools. Camouflaged logic cells are integrated into a typical design flow using standard front end and back end models. Camouflaged logic cells obfuscate a circuit's function by introducing subtle cell design changes at the GDS level. The logic function of a camouflaged logic cell is extremely difficult to determine through silicon imaging analysis preventing netlist extraction, clones and counterfeits. The application of circuit camouflage as part of a customer's design flow can protect hardware IP from reverse engineering. Camouflage fill techniques further inhibit Trojan circuit insertion by completely filling the design with realistic circuitry that does not affect the primary design function. All unused silicon appears to be functional circuitry, so an attacker cannot find space to insert a Trojan circuit. The integration of circuit camouflage techniques is compatible with standard chip design flows and EDA tools, and ICs using such techniques have been successfully employed in high-attack commercial and government segments. Protected under issued and pending patents.
Systemic Acquired Resistance (1996)

John A. Ryals, Urs H. Neuenschwander, Michael G. Willits, Antonio Molina, Henry-York Steiner, Michelle D. Hunt, Systemic Acquired Resistance, The Plant Cell, Vol. 8, No. 10, Special Review Issue on Plant-Microbe Interactions (Oct., 1996), pp. 1809-1819
A human beta-actin expression vector system directs high-level accumulation of antisense transcripts. (1987)

We have constructed a mammalian expression vector consisting of 3 kilobases of the human beta-actin gene 5' flanking sequence plus 5' untranslated region and intervening sequence 1 linked at the 3' splice site to a short DNA polylinker sequence containing unique Sal I, HindIII, and BamHI restriction endonuclease sites followed by a simian virus 40 (SV40) polyadenylylation signal. Two derivatives, containing the selection markers obtained from pSV2gpt or pSV2neo, were also generated. We find that the promoter activity of this vector is a great or greater than that of the SV40 early promoter in a variety of human and rodent cells. The vector was used to generate gamma-actin and beta-tubulin antisense transcripts in human fibroblast cell lines. The antisense transcripts accumulate to levels comparable with that of the highly abundant gamma-actin and beta-tubulin mRNAs.
Phospholipid and arachidonic acid metabolism in zymosan‐stimulated human monocytes: Modulation by cAMP (1987)

Receptor-ligand interaction in mononuclear phagocytes is intimately linked to alterations in membrane phospholipids and release of arachidonic acid (AA). In addition, synthesis of bioactive lipids from released AA can result in further modification of cell responses. Upon challenge with opsonized zymosan, [3H]-arachidonic acid ([3H]-AA)-labeled human monocytes released 25 +/- 2% of their incorporated radiolabel within 30 min. Pretreatment of the monocytes with 5 X 10(-4) M isobutylmethylxanthine (IBMX) or 1 X 10(-3) M dibutyryl cyclic AMP (d-cAMP) inhibited total [3H]-AA release in the presence of zymosan by 47% and 42%, respectively. Analysis of incorporated [3H]-AA in cellular phospholipid pools indicated that significant amounts of label were lost from both phosphatidylcholine (PC) and phosphatidylinositol (PI) during zymosan stimulation. Treatment with d-cAMP substantially inhibited the loss of label from PC, but had no affect on PI. HPLC analysis of cell supernatants from zymosan-treated cells indicated that 5-HETE was the predominant metabolite generated from [3H]-AA, and its production was depressed during treatment with d-cAMP. Phospholipase activity in human monocyte homogenates was not effected by d-cAMP or IBMX at the highest concentrations used, whether these were added directly to the homogenate or by pretreatment of whole cells, demonstrating that inhibition required an intact cell. These results suggest that human monocytes exposed to opsonized zymosan release AA via two mechanisms and that modulation by cAMP is indirectly effecting a phospholipase directed towards PC.
Fungal diseases of the sinuses (1990)

With recent advances in medicine, fungal diseases are becoming not only better understood, but also increasingly important in the management of patients with paranasal sinus disease. Fungal sinus diseases run the gamut from allergic fungal rhinitis and allergic fungal sinusitis, through fungus balls, to invasive and fulminant fungal sinusitis. Allergic fungal sinusitis may be thought of as the sinus counterpart of allergic bronchopulmonary fungal disease. Patients typically are first seen with chronic sinusitis. They may be atopic, and the peripheral blood often shows elevated IgE levels and absolute eosinophil counts. Such patients may be managed conservatively, requiring only surgical drainage and corticosteroid therapy. Fungus balls are typified by the so-called "aspergilloma." Although patients often have some predisposing factor, such as local tissue hypoxia or massive fungal exposure, most patients are not immunocompromised. Fungus balls may be treated with the traditional Caldwell-Luc operation or with newer endoscopic procedures. Invasive or fulminant fungal sinusitis generally occurs in immunosuppressed patients and merits aggressive surgical excision and debridement, as well as systemic chemotherapy, usually amphotericin B. In this article, we review fungal disease of the paranasal sinuses and present findings from our review of patients with chronic sinusitis.
Tyrosine Kinase Activity and Transformation Potency of bcr-abl Oncogene Products (1990)

Oncogenic activation of the proto-oncogene c-abl in human leukemias occurs as a result of the addition of exons from the gene bcr and truncation of the first abl exon. Analysis of tyrosine kinase activity and quantitative measurement of transformation potency in a single-step assay indicate that variation in bcr exon contribution results in a functional difference between p210bcr-abl and p185bcr-abl proteins. Thus, foreign upstream sequences are important in the deregulation of the kinase activity of the abl product, and the extent of deregulation correlates with the pathological effects of the bcr-abl proteins.
Comparison of Recombinant Derivatives of Chimeric TNT-3 Antibody for the Radioimaging of Solid Tumors (2003)

Although intact monoclonal antibodies (MAbs) are well suited as therapeutic reagents, their relatively slow clearance rates render them less useful for imaging applications. Over the last several years, our laboratory has developed a unique targeting approach to solid tumors that utilizes MAbs directed against DNA and its components to bind to degenerating cells and necrotic regions of tumors in a specific manner. Because these MAbs have considerable potential for the early diagnosis of cancer and for the monitoring of cytoreductive therapies, the availability of an effective imaging agent is highly desirable. To accomplish this goal, a series of genetically engineered derivatives of MAb chTNT-3 including the single-chain Fv, diabody, triabody, Fab, and F(ab')(2) were generated and expressed in NS0 myeloma cells using the Glutamine Synthetase Amplification System. Initial in vitro studies demonstrated that each of the antibody derivatives maintained its antigen binding in a stable manner. In vivo analyses after radiolabeling were then performed to evaluate their pharmacokinetic, biodistribution, and tumor-imaging properties in solid tumor-bearing mice. The results of these studies showed that compared with intact parental chTNT-3, which has a half-life of 134.2 h, the smaller derivatives were eliminated more rapidly (4.9-8.1 h). Importantly, the smaller derivatives were found to have significantly higher tumor-to-organ ratios, but lower overall uptake levels compared with parental (125)I-chTNT-3 in two different tumor models. A comparison of the five derivatives showed that the F(ab')(2) reagent consistently gave the best results in imaging and biodistribution studies. Based upon these results, further studies are warranted to demonstrate the potential of this reagent for the diagnosis and monitoring of solid tumors using noninvasive imaging techniques such as immunoscintigraphy and positron emission tomography (PET).
Encephalitogenic T cell clones with variant receptor specificity. (1988)

We explored antigenic differences between guinea pig (GP)-basic protein (BP), rat (Rt)-BP, and respective peptides from the encephalitogenic region for Lewis rats by comparing the fine specificity of T lymphocyte lines and clones selected from animals primed with these Ag. Encephalitogenic T cell lines specific for GP-BP or Rt-BP predictably recognized the corresponding 72-89 and to a lesser degree the 72-84 (S55S) amino acid sequence. T cell lines selected from rats primed with GP-S55S responded preferentially to GP-S55S compared to other peptides. A T cell line raised to Rt-S55S, however, initially recognized the S55S and S72-89 peptides but were nearly unresponsive to the intact GP-BP or Rt-BP. T cell clones selected from the Rt-S55S line at that point had two distinct patterns of response: clones that recognized both of the BP and the S55S peptides adoptively transferred delayed-type hypersensitivity and experimental autoimmune encephalomyelitis. These clones also recognized residues 69-81 (S67) but not peptide S75-89. In contrast, T cell clones that responded only to synthetic peptides GP-S55S and Rt-S55S but not to the parent BP adoptively transferred delayed-type hypersensitivity but not disease in Lewis rats. The same clones failed to respond to either the S67 or the S75-89 sequences. These results demonstrate that the encephalitogenic Rt-S55S sequence houses a minimum of two T cell epitopes with differing specificities and functions. One epitope is immuno-dominant and resembles the encephalitogenic region of the intact BP molecule. The second non-encephalitogenic epitope is restricted to the S55S sequences and is not shared by the parent BP, the S67, or the S75-89 sequences. Both types of Rt-S55S-specific clones differ in fine specificity from encephalitogenic clones selected from GP-BP immunized rats, thus indicating that uniformity of T cell recognition of the encephalitogenic epitope is not an absolute condition for T cells to be encephalitogenic.
Pharmacology of long-acting beta-agonists. (1995)

Preclinical studies have shown both salmeterol and formoterol to be potent and selective at beta 2-adrenoceptors but to have different mechanisms and durations of action. The pharmacologic profiles of these drugs result from prolonged activation of beta 2-adrenoceptors, leading to long-lasting bronchodilation (with no evidence of tolerance or tachyphylaxis) and additional nonbronchodilator properties. The long-acting beta 2-agonists represent a therapeutic advance in the management of asthma.
Limited T Cell Receptor Diversity of HCV-specific T Cell Responses Is Associated with CTL Escape (2004)

Escape mutations are believed to be important contributors to immune evasion by rapidly evolving viruses such as hepatitis C virus (HCV). We show that the majority of HCV-specific cytotoxic T lymphocyte (CTL) responses directed against viral epitopes that escaped immune recognition in HCV-infected chimpanzees displayed a reduced CDR3 amino acid diversity when compared with responses in which no CTL epitope variation was detected during chronic infection or with those associated with protective immunity. Decreased T cell receptor (TCR) CDR3 amino acid diversity in chronic infection could be detected long before the appearance of viral escape mutations in the plasma. In both chronic and resolved infection, identical T cell receptor clonotypes were present in liver and peripheral blood. These findings provide a deeper understanding of the evolution of CTL epitope variations in chronic viral infections and highlight the importance of the generation and maintenance of a diverse TCR repertoire directed against individual epitopes.
Evidence that thiosulfate assimilation by Salmonella typhimurium is catalyzed by cysteine synthase B (1983)

Mutants carrying defects in cysteine synthase A or B or both were isolated from Salmonella typhimurium LT2. Parent strains were able to grow on minimal media containing sulfate, sulfite, sulfide, or thiosulfate as sulfur sources. Mutants lacking cysteine synthase B were unable to grow on thiosulfate, whereas mutants lacking cysteine synthase A grew on the four inorganic sulfur sources described above with little difference in their growth rates. Mutants lacking both cysteine synthases failed to grow on media containing any of the inorganic sulfur sources tested. Purification of cysteine synthase B resulted in the copurification of S-sulfocysteine synthase. In addition, the two activities were also cotransduced. These activities appear to be associated with the cysM gene, and this is able to be cotransducted with the cysK gene at a high frequency. From these results, it may be concluded that thiosulfate is assimilated via S-sulfocysteine exclusively with the aid of S-sulfocysteine synthase.
Disruption of the Epithelial Apical-Junctional Complex by Helicobacter pylori CagA (2003)

Helicobacter pylori translocates the protein CagA into gastric epithelial cells and has been linked to peptic ulcer disease and gastric carcinoma. We show that injected CagA associates with the epithelial tight-junction scaffolding protein ZO-1 and the transmembrane protein junctional adhesion molecule, causing an ectopic assembly of tight-junction components at sites of bacterial attachment, and altering the composition and function of the apical-junctional complex. Long-term CagA delivery to polarized epithelia caused a disruption of the epithelial barrier function and dysplastic alterations in epithelial cell morphology. CagA appears to target H. pylori to host cell intercellular junctions and to disrupt junction-mediated functions.
A 79GHz UWB pulse-compression vehicular radar in 90nm CMOS (2012)

A 79GHz UWB pulse-compression (PC) vehicular radar system is presented. A PC waveform is a long pulse with internal modulation. The energy of it can be increased without raising the instantaneous peak power. Meanwhile, a PC waveform preserves an equal bandwidth and the range resolution associated with a single pulse waveform. In addition, the PC technique also allows multiple radars operating simultaneously based on the code division multiple accessing (CDMA). In this work, the internal modulation of the PC waveform is binary phase shift keying (BPSK) with a 31-bit length pseudo noise (PN) sequence. The modulation rate is 1 Gb/s and the maximum pulse width is 31 nsec. The CMOS chip presents a self-contained radar system with the transmitter, receiver, frequency synthesizer, and complete timing circuit fully integrated in a standard 90nm CMOS technology.