gebhart/patrepeval huggingface dataset:
A PCR-based assay for the detection of Escherichia coli Shiga-like toxin genes in ground beef (1996)

A detection system based on the PCR has been developed for Escherichia coli strains which harbor the Shiga-like toxin genes. This quantitative detection system involves the 5'-->3' nuclease activity of Thermus aquaticus DNA polymerase, which cleaves an internal oligonucleotide probe that has been labeled with both a fluorescent reporter dye (6-carboxy-fluorescein [FAM]) and a quencher dye (6-carboxytetramethyl-rhodamine [TAMRA]). Parameters which affected the performance of the assay included primer probe distance, probe concentration, and probe target sequence homology. The optimized assay format includes two PCR primers that generate a 497-bp amplicon specific for the sltI gene with the fluorogenic probe located 19 bp from the upstream PCR primer. When the distance between the upstream PCR primer and the probe was reduced from 190 to 19 bp, delta RQ values increased from approximately 1.5 to 3.0. The delta RQ for Shiga-like toxin I probe 102 reached a maximum of 4.15 at concentrations between 25 and 50 nM. The assay is sensitive and can detect approximately 10 +/- 5 CFU per PCR. As few as 0.5 CFU of Shiga-like toxin I-producing E. coli per g could be detected in ground beef with only 12 h of enrichment in modified E. coli broth.
Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex (2005)

Unambiguous indicators of gender in dinosaurs are usually lost during fossilization, along with other aspects of soft tissue anatomy. We report the presence of endosteally derived bone tissues lining the interior marrow cavities of portions of Tyrannosaurus rex (Museum of the Rockies specimen number 1125) hindlimb elements, and we hypothesize that these tissues are homologous to specialized avian tissues known as medullary bone. Because medullary bone is unique to female birds, its discovery in extinct dinosaurs solidifies the link between dinosaurs and birds, suggests similar reproductive strategies, and provides an objective means of gender differentiation in dinosaurs.
Role of Glycosylation in Development (2004)

Researchers have long predicted that complex carbohydrates on cell surfaces would play important roles in developmental processes because of the observation that specific carbohydrate structures appear in specific spatial and temporal patterns throughout development. The astounding number and complexity of carbohydrate structures on cell surfaces added support to the concept that glycoconjugates would function in cellular communication during development. Although the structural complexity inherent in glycoconjugates has slowed advances in our understanding of their functions, the complete sequencing of the genomes of organisms classically used in developmental studies (e.g., mice, Drosophila melanogaster, and Caenorhabditis elegans) has led to demonstration of essential functions for a number of glycoconjugates in developmental processes. Here we present a review of recent studies analyzing function of a variety of glycoconjugates (O-fucose, O-mannose, N-glycans, mucin-type O-glycans, proteoglycans, glycosphingolipids), focusing on lessons learned from human disease and genetic studies in mice, D. melanogaster, and C. elegans.
Phosphate-starvation response in plant cells: de novo synthesis and degradation of acid phosphatases. (1991)

Induction of phosphatase activity is an important component of the plant cell response to phosphate deficiency. Suspension cell cultures of Brassica nigra contain two major inducible acid phosphatase (APase) isozymes; vacuolar phosphoenolpyruvate (PEP) APase and cell wall nonspecific APase. Polyclonal antibodies raised against purified PEP-APase crossreacted specifically with both isozymes. Furthermore, anti-(PEP-APase) IgG detected proteins from a wide range of higher plants, suggesting that the major plant APase isozymes have diverged from a common ancestral form. Quantification on immunoblots indicated that in B. nigra suspension cells experiencing transition from Pi sufficiency to deficiency or vice versa, the amount of total antigenic APase protein correlated closely with total enzyme activity. This was also shown in intact plant roots. Therefore, the activity was governed by the synthesis and degradation of APases. Increases in the amounts of both major APase isozymes occurred simultaneously following Pi deprivation of B. nigra suspension cells, suggesting the involvement of a common regulatory mechanism.
Wide‐field subdiffraction RESOLFT microscopy using fluorescent protein photoswitching (2007)

Subdiffraction fluorescence imaging is presented in a parallelized wide-field arrangement exploiting the principle of reversible saturable/switchable optical transitions (RESOLFT). The diffraction barrier is overcome by photoswitching ensembles of the label protein asFP595 between a nonfluorescent off- and a fluorescent on-state. Relying on ultralow continuous-wave intensities, reversible protein switching facilitates parallelized fast image acquisition. The RESOLFT principle is implemented by illuminating with intensity distributions featuring zero intensity lines that are further apart than the conventional Abbe resolution limit. The subdiffraction resolution is verified by recording live Escherichia coli bacteria labeled with asFP595. The obtained resolution of 50 nm ( approximately lambda/12) is limited only by the spectroscopic properties of the proteins and the imperfections of the optical implementation, but not on principle grounds.
Effect of Histolyticus Infection and Toxin on Transplantable Mouse Tumors. (1947)

SummaryWhen transplantable mouse sarcomas were infected experimentally with Cl. histolyticum, and the infection controlled by systemic injections of histolyticus antitoxin, the life span of some of the animals was prolonged for as long as 20 days beyond that of the non-infected tumor bearers. But in no instance did the infection completely destroy the tumor tissue. All surviving mice, treated eventually with penicillin in order to eradicate residual infection, developed large sarcomas. Under similar conditions, no such temporary regression was observed for transplantable mouse carcinomas.When a study was made of the effect of histolyticus toxin on transplantable mouse tumors, it was found that systemic (intramuscular) injections of toxin were without effect, whereas repeated local injections of toxin, given either directly into the tumor mass or subeutaneously around the base of the tumor, resulted in marked regression of tumor tissue. But for the toxin preparations used, the effective dose approximated, very closely, the lethal dose, particularly when the toxin wras injected directly into the tumor mass. In no instance was there a permanent regression of the tumor.In tissue culture, carcinoma cells were more resistant to the action of histolyticus toxin than sarcoma cells, just as normal epithelium seemed to be more resistant that stroma cells or fibroblasts. But normal and cancerous epithelium were equally resistant to concentrations of toxin that produced severe damage to sarcoma cells.
Differential effects of αCaMKII mutation on hippocampal learning and changes in intrinsic neuronal excitability (2006)

Alpha-calcium/calmodulin-dependent kinase II (alphaCaMKII) is central to synaptic plasticity but it remains unclear whether this kinase contributes to neuronal excitability changes, which are a cellular correlate of learning. Using knock-in mice with a targeted T286A mutation that prevents the autophosphorylation of alphaCaMKII (alphaCaMKII(T286A)), we studied the role of alphaCaMKII signaling in regulating hippocampal neuronal excitability during hippocampus-dependent spatial learning in the Morris water maze. Wild-type control mice showed increased excitability of CA1 pyramidal neurons, as assessed by a reduction in the postburst afterhyperpolarization (AHP), after spatial training in the water maze. Importantly, wild-type mice did not show AHP changes when they were exposed to the water maze without the escape platform and swam the same amount of time as the trained mice (swim controls), thus manifesting learning-specific increases in hippocampal CA1 excitability associated with spatial training. Meanwhile, alphaCaMKII(T286A) mice showed impairments in spatial learning but exhibited reduced levels of AHP that were similar to wild-type controls after water-maze training. Notably, both trained and swim-control groups of alphaCaMKII(T286A) mutants showed similar increased excitability, indicating that swimming by itself is enough to induce changes in excitability in the absence of normal alphaCaMKII function. This result demonstrates dissociation of alphaCaMKII-independent changes in intrinsic neuron excitability from learning and synaptic plasticity mechanisms, suggesting that increases in excitability per se are not perfectly correlated with learning. Our findings suggest that alphaCaMKII signaling may function to suppress learning-unrelated changes during training, thereby allowing hippocampal CA1 neurons to increase their excitability appropriately for encoding spatial memories.
Pharmacological approaches to acute ischaemic stroke: reperfusion certainly, neuroprotection possibly (2007)

Stroke is a major cause of both death and disability. However, there are no pharmacological treatments used in most countries other than recombinant tissue plasminogen activator, a thrombolytic, and this is only used in about 4% of patients presenting after an acute ischaemic stroke. One novel thrombolytic (desmoteplase) has just been reported to have failed in a Phase IIb/III trial, but other thrombolytics and reperfusion agents remain in development. The picture with neuroprotectant agents, that is compounds that act to preserve neurones following an acute cerebral ischaemic insult, is even more bleak. Despite the development of over 1,000 compounds, many proving effective in animal models of stroke, none has demonstrated efficacy in patients in the over 100 clinical trials conducted. This includes NXY-059, which was developed in accordance with the guidelines proposed by an academic-industry roundtable group (STAIR). This review examines the available data on compounds currently in development. It also proposes that the failure of translation between efficacy in preclinical models and patients is likely to terminate most current neuroprotective drug development. It is suggested that animal models must be made more representative of the patient condition (with other co-morbid conditions) and suggests that since stroke is primarily a cardiovascular disease with a neurological outcome, more research on the neurovascular unit would be valuable. New approaches on neuroinflammation, neurorestoration and neurorepair are also likely to gain prominence in the search for new drugs to treat this major clinical problem.
Progress report on amizol (3-amino-1,2,4-triazole) on woody plants (1956)

This new antidandruff thermophobic foam has shown to be more effective than ketoconazole 2% scalp fluid in the treatment of severe dandruff.
Three-dimensional structure of the tryptophan synthase alpha 2 beta 2 multienzyme complex from Salmonella typhimurium. (1988)

The three-dimensional structure of the alpha 2 beta 2 complex of tryptophan synthase from Salmonella typhimurium has been determined by x-ray crystallography at 2.5 A resolution. The four polypeptide chains are arranged nearly linearly in an alpha beta beta alpha order forming a complex 150 A long. The overall polypeptide fold of the smaller alpha subunit, which cleaves indole glycerol phosphate, is that of an 8-fold alpha/beta barrel. The alpha subunit active site has been located by difference Fourier analysis of the binding of indole propanol phosphate, a competitive inhibitor of the alpha subunit and a close structural analog of the natural substrate. The larger pyridoxal phosphate-dependent beta subunit contains two domains of nearly equal size, folded into similar helix/sheet/helix structures. The binding site for the coenzyme pyridoxal phosphate lies deep within the interface between the two beta subunit domains. The active sites of neighboring alpha and beta subunits are separated by a distance of about 25 A. A tunnel with a diameter matching that of the intermediate substrate indole connects these active sites. The tunnel is believed to facilitate the diffusion of indole from its point of production in the alpha subunit active site to the site of tryptophan synthesis in the beta active site and thereby prevent its escape to the solvent during catalysis.
Phase II Evaluation of Nanoparticle Albumin–Bound Paclitaxel in Platinum-Sensitive Patients With Recurrent Ovarian, Peritoneal, or Fallopian Tube Cancer (2009)

Nab-paclitaxel is active in this group of patients with recurrent ovarian, peritoneal, or fallopian tube cancer. The ORR was 64%. Toxicities were manageable. Further studies of nab-paclitaxel in combination with platinum are warranted.
Kilohertz optical resonances in dielectric crystal cavities (2004)

We experimentally demonstrate a crystalline ${\mathrm{CaF}}_{2}$ optical whispering gallery mode resonator characterized by the quality factor $Q&gt;2\ifmmode\times\else\texttimes\fi{}{10}^{10}$ at $\ensuremath{\lambda}=1.319\phantom{\rule{0.3em}{0ex}}\ensuremath{\mu}\mathrm{m}$. We also report the demonstration of ultrahigh-$Q$ resonators of lithium niobate and lithium tantalate $(Q&gt;2\ifmmode\times\else\texttimes\fi{}{10}^{8})$, and sapphire $(Q&gt;{10}^{9})$. We discuss fundamental limits of the $Q$ factor, and application of such resonators for measurement of ultrasmall optical losses in various materials. We further analyze the observation of thermo-optical instability in whispering gallery modes of crystalline resonators.
In vitro studies of transplantation antigens present on bone cells in the rat (1977)

In vitro studies on isolated bone cells were undertaken to investigate the presence of transplantation (histocompatibility) antigens. Bone cells were cultured with allogeneic lymphocytes and exposed to cytotoxic sera containing antibodies against transplantation antigens, to determine their antigenic profile. Preliminary results suggest that bone cells may not express lymphocyte stimulating antigens in an active form, at least after the isolation procedure performed. On the other hand, bone cells were killed by cytotoxic antibodies in a specific way, providing evidence for the presence of serologically defined (SD) transplantation antigens on the cell surface. Additional studies with absorbed sera suggest "sharing" of histocompatibility antigens between bone cells and lymphocytes. The relevance of the surface antigens of bone cells to clinical fields such as bone allotransplantation, susceptibility to various orthopaedic diseases and skeletal sarcomata is discussed.
Determining Reservoir Properties and Flood Performance from Tracer Test Analysis (2009)

Abstract In the last several years a variety of new tools for interpreting interwell tracer tests have been developed. The new methods are based on residence time distributions of the tracer, where much of the previous work used only the mean residence time. Using the distribution of residence times extends the power of moment analysis by allowing for the determination of reservoir properties and flood performance as a function of time. Flow geometry and construction of flow capacity - storage capacity diagrams also follows directly from the analysis. Swept volume vs. time, and sweep efficiency are also determined from the residence time distribution, as is remaining oil saturation. One important key to these new methods is our use of the integrated tracer recovery histories. Estimating residual oil saturation is greatly simplified by our mathematical treatment of slug tracer injection. Examples are presented that show improved saturation estimates even at early times in a tracer test. This paper describes the new analysis methods developed recently and shows by comparisons with analytical and experimental data that the methods are accurate and robust. The method is simple and can be done with a spreadsheet using only produced tracer concentration data; it does not require a reservoir model or numerical simulation. The equations are derived from first principles for a very general case that includes both conservative and partitioning tracers produced from any heterogeneous reservoir.
Human cytomegalovirus inhibits antigen presentation by a sequential multistep process. (1996)

The human cytomegalovirus (HCMV) genomic unique short (US) region encodes a family of homologous genes essential for the inhibition of major histocompatibility complex (MHC) class I-mediated antigen presentation during viral infection. Here we show that US3, the only immediate early (IE) gene within the US region, encodes an endoplasmic reticulum-resident glycoprotein that prevents intracellular transport of MHC class I molecules. In contrast to the rapid degradation of newly synthesized MHC class I heavy chains mediated by the early gene product US11, we found that US3 retains stable MHC class I heterodimers in the endoplasmic reticulum that are loaded with peptides while retained in the ER. Consistent with the expression pattern of US3 and US11, MHC class I molecules are retained but not degraded during the IE period of infection. Our data identify the first nonregulatory role of an IE protein of HCMV and suggest that HCMV uses different T-cell escape strategies at different times during the infectious cycle.
Prospects for use of recombinant BPI in the treatment of gram-negative bacterial infections. (1995)

The bactericidal/permeability-increasing protein (BPI), a potent cytotoxin specific for Gram-negative bacteria and an endotoxin-neutralizing agent, is a major component of the antimicrobial arsenal of mammalian polymorphonuclear leukocytes. The antibacterial and endotoxin-neutralizing activities of the N-terminal portion (approximately 25 kDa) of BPI are at least equal to those of the holoprotein (approximately 50 kDa). Recombinant N-terminal fragments of BPI are antibacterial and inhibit host cell responses to endotoxin in whole blood ex vivo and in animal experiments. BPI administered to both animals and man is apparently nontoxic and nonimmunogenic and acts synergistically with some antibiotics. Thus, the prospects for the therapeutic use of bioactive BPI fragments in serious Gram-negative bacterial infections are highly encouraging.
Role of Mast Cell and Neutrophil Proteases in Airway Secretion (1991)

To investigate the hypothesis that mast cell and neutrophil proteases stimulate airway gland secretion, we studied the effects of two mast cell proteases (tryptase and chymase) and two neutrophil enzymes (human neutrophil elastase and cathepsin G) on secretion of 35S-labeled macro-molecules from cultured bovine airway gland serous cells. Tryptase had no effect, but the other three enzymes stimulated secretion. Threshold concentrations of the enzymes (greater than or equal to 10(-10) M) were lower by two orders of magnitude than other agonists (e.g., histamine, prostaglandins, beta-adrenergic agonists). Only proteases induced maximal secretory response (greater than or equal to 80% depletion of 35S-labeled macromolecules), and these responses were greater than 10-fold larger than those of other agonists. The active catalytic sites of the enzymes are required for their secretory activities. These findings suggest a role for these enzymes in the pathogenesis of inflammatory airway diseases associated with hypersecretion, and they suggest that the use of selective site-directed inhibitors of these enzymes may provide a novel strategy for intervention in inflammatory diseases of the airways associated with hypersecretion (e.g., cystic fibrosis, chronic bronchitis).
In Situ Histochemical Detection of β -Galactosidase Activity in Lung: Assessment of X-Gal Reagent in Distinguishing lacZ Gene Expression and Endogenous β -Galactosidase Activity (1997)

Bacterial lacZ is one of the most commonly used reporter genes for assessing gene transfer to lung. However, lung contains endogenous beta-galactosidase (beta-Gal), which can confound estimation of exogenous lacZ expression by histochemical techniques (i.e., X-Gal) for in situ demonstration of enzyme activity. We investigated several parameters of the X-Gal reaction, including time and temperature of X-Gal exposure as well as lung tissue processing and fixation techniques, and found that none of these could be used to distinguish between endogenous and exogenous beta-Gal activities. The mammalian and bacterial beta-Gal enzymes, however, have pH optima in the acidic and neutral ranges, respectively. Exposing whole lung, lung minces, or mounted frozen sections of lung to X-Gal at mildly alkaline pH (pH 8.0-8.5), minimized detection of endogenous activity in lungs from a variety of species while preserving that resulting from bacterial enzyme activity in a transgenic mouse expressing lacZ. This technique was also useful in distinguishing endogenous activity from that resulting from adenovirus-mediated lacZ gene transfer to diploid lung fibroblasts in primary culture. An appropriate buffer that maintains the desired pH throughout the duration of X-Gal exposure must be used.
Novel Fusion Protein Approach for Efficient High-Throughput Screening of Small Molecule–Mediating Protein-Protein Interactions in Cells and Living Animals (2005)

Networks of protein interactions execute many different intracellular pathways. Small molecules either synthesized within the cell or obtained from the external environment mediate many of these protein-protein interactions. The study of these small molecule-mediated protein-protein interactions is important in understanding abnormal signal transduction pathways in a variety of disorders, as well as in optimizing the process of drug development and validation. In this study, we evaluated the rapamycin-mediated interaction of the human proteins FK506-binding protein (FKBP12) rapamycin-binding domain (FRB) and FKBP12 by constructing a fusion of these proteins with a split-Renilla luciferase or a split enhanced green fluorescent protein (split-EGFP) such that complementation of the reporter fragments occurs in the presence of rapamycin. Different linker peptides in the fusion protein were evaluated for the efficient maintenance of complemented reporter activity. This system was studied in both cell culture and xenografts in living animals. We found that peptide linkers with two or four EAAAR repeat showed higher protein-protein interaction-mediated signal with lower background signal compared with having no linker or linkers with amino acid sequences GGGGSGGGGS, ACGSLSCGSF, and ACGSLSCGSFACGSLSCGSF. A 9 +/- 2-fold increase in signal intensity both in cell culture and in living mice was seen compared with a system that expresses both reporter fragments and the interacting proteins separately. In this fusion system, rapamycin induced heterodimerization of the FRB and FKBP12 moieties occurred rapidly even at very lower concentrations (0.00001 nmol/L) of rapamycin. For a similar fusion system employing split-EGFP, flow cytometry analysis showed significant level of rapamycin-induced complementation.