gebhart/patrepeval huggingface dataset:
Induction of verotoxin sensitivity in receptor-deficient cell lines using the receptor glycolipid globotriosylceramide. (1990)

Verotoxin 1 is an Escherichia coli-derived subunit toxin that specifically binds to the glycolipid globotriosylceramide and is cytotoxic for cells that contain this plasma membrane glycolipid. Glycolipid incorporation experiments have now been performed using human lymphoid cells of the B lineage that lack this receptor, to conclusively demonstrate that globotriosylceramide alone is a functional receptor for this toxin. Globotriosylceramide incorporated into the membrane of toxin-resistant cells provides intracellular access to verotoxin by receptor-mediated endocytosis. Protein synthesis is then inhibited and globotriosylceramide-containing cells are killed.
Mouse cortical collecting duct cells show nonselective cation channel activity and express a gene related to the cGMP-gated rod photoreceptor channel. (1992)

Apical nonselective cation channels with an average single-channel conductance of 34 +/- 2.3 pS were found in M-1 mouse cortical collecting duct cells. Channel activity is increased by depolarization and abolished by cytoplasmic calcium removal. Cytoplasmic application of 0.1 mM cGMP decreases channel open probability by 27%. cDNAs corresponding to approximately 40% of the coding region of the photoreceptor channel were isolated by the polymerase chain reaction from M-1 cells and a rat kidney cDNA library. The rat kidney-derived sequence differs by a single base, and the M-1-cell-derived sequence differs by only two bases, from the photoreceptor sequence. A second clone from M-1 cells differs by 20 out of 426 bases from the photoreceptor sequence. In all three clones, the deduced amino acid sequence is identical to that of the rat photoreceptor channel. Northern blot analysis of poly(A)+ RNA from M-1 cells reveals the presence of a 3.2-kilobase band hybridizing with a retinal cGMP-gated cation channel probe. The results suggest the expression in M-1 cells of more than one gene coding for nonselective cation channels or channel subunits, one of which is identical to the cGMP-gated cation channel gene of rod photoreceptors.
T‐cell receptor Vδ‐Jα rearrangements in human thymocytes: the role of Vδ‐Jα rearrangements in T‐cell receptor‐δ gene deletion (1998)

The differentiation mechanisms that force thymocytes into the T-cell receptor (TCR)-alpha beta or TCR-gamma delta lineage are poorly understood, but rearrangement processes in the TCR-alpha/delta locus are likely to play an important role. It is assumed that the TCR-delta gene is deleted prior to V alpha-J alpha rearrangements by rearrangement of the so-called TCR-delta-deleting elements delta Rec and psi J alpha. However, the TCR-delta gene can also be deleted via V delta-J alpha rearrangements. We studied the different TCR-delta-deleting rearrangements of V delta 1, delta Rec, V delta 2 and V delta 3 to J alpha gene segments in human thymocytes and peripheral blood using polymerase chain reaction analysis. The V delta 1 gene segment is the most upstream V delta gene segment tested and appears to rearrange to almost all J alpha gene segments. In contrast, the delta Rec and V delta 2 gene segments only rearrange to the 5'-located J alpha gene segments, thereby preserving an extensive TCR-alpha combinatorial diversity, because most J alpha gene segments are kept available for subsequent V alpha-J alpha rearrangements. Based on our combined data we hypothesize that the different V delta gene segments and the delta Rec gene segment play different roles in T-cell development with regard to TCR-delta deletion.
Breast Cancer Classification in Histopathological Images using Convolutional Neural Network (2018)

Computer based analysis is one of the suggested means that can assist oncologists in the detection and diagnosis of breast cancer. On the other hand, deep learning has been promoted as one of the hottest research directions very recently in the general imaging literature, thanks to its high capability in detection and recognition tasks. Yet, it has not been adequately suited to the problem of breast cancer so far. In this context, I propose in this paper an approach for breast cancer detection and classification in histopathological images. This approach relies on a deep convolutional neural networks (CNN), which is pretrained on an auxiliary domain with very large labelled images, and coupled with an additional network composed of fully connected layers. The network is trained separately with respect to various image magnifications (40x, 100x, 200x and 400x). The results presented in the patient level achieved promising scores compared to the state of the art methods.
ATM and ATR Substrate Analysis Reveals Extensive Protein Networks Responsive to DNA Damage (2007)

Cellular responses to DNA damage are mediated by a number of protein kinases, including ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3-related). The outlines of the signal transduction portion of this pathway are known, but little is known about the physiological scope of the DNA damage response (DDR). We performed a large-scale proteomic analysis of proteins phosphorylated in response to DNA damage on consensus sites recognized by ATM and ATR and identified more than 900 regulated phosphorylation sites encompassing over 700 proteins. Functional analysis of a subset of this data set indicated that this list is highly enriched for proteins involved in the DDR. This set of proteins is highly interconnected, and we identified a large number of protein modules and networks not previously linked to the DDR. This database paints a much broader landscape for the DDR than was previously appreciated and opens new avenues of investigation into the responses to DNA damage in mammals.
Structural Changes in Bacteriorhodopsin During Ion Transport at 2 Angstrom Resolution (1999)

Crystal structures of the Asp96 to Asn mutant of the light-driven proton pump bacteriorhodopsin and its M photointermediate produced by illumination at ambient temperature have been determined to 1.8 and 2.0 angstroms resolution, respectively. The trapped photoproduct corresponds to the late M state in the transport cycle-that is, after proton transfer to Asp85 and release of a proton to the extracellular membrane surface, but before reprotonation of the deprotonated retinal Schiff base. Its density map describes displacements of side chains near the retinal induced by its photoisomerization to 13-cis,15-anti and an extensive rearrangement of the three-dimensional network of hydrogen-bonded residues and bound water that accounts for the changed pKa values (where Ka is the acid constant) of the Schiff base and Asp85. The structural changes detected suggest the means for conserving energy at the active site and for ensuring the directionality of proton translocation.
Physical mapping and nucleotide sequence of a herpes simplex virus type 1 gene required for capsid assembly (1989)

In this report, we describe some phenotypic properties of a temperature-sensitive mutant of herpes simplex type 1 (HSV-1) and present data concerning the physical location and nucleotide sequence of the genomic region harboring the mutation. The effect of shifts from the permissive to the nonpermissive temperature on infectious virus production by the mutant A44ts2 indicated that the mutated function is necessary throughout, or late in, the growth cycle. At the nonpermissive temperature, no major differences were detected in viral DNA or protein synthesis with respect to the parent A44ts+. On the other hand, electron microscopy of mutant-infected cells revealed that neither viral capsids nor capsid-related structures were assembled at the nonpermissive temperature. Additional analyses employing the Hirt extraction procedure showed that A44ts2 is also unable to mature replicated viral DNA into unit-length molecules under nonpermissive conditions. The results of marker rescue experiments with intact A44ts2 DNA and cloned restriction fragments of A44ts+ placed the lesion in the coordinate interval 0.553 to 0.565 (1,837 base pairs in region UL) of the HSV-1 physical map. No function has previously been assigned to this region, although it is known to be transcribed into two 5' coterminal mRNAs which code in vitro for a 54,000-molecular-weight polypeptide (K. P. Anderson, R. J. Frink, G. B. Devi, B. H. Gaylord, R. H. Costa, and E. K. Wagner, J. Virol. 37:1011-1027, 1981). We sequenced the interval 0.551 to 0.565 and found an open reading frame (ORF) for a 50,175-molecular-weight polypeptide. The predicted product of this ORF exhibits strong homology with the product of varicella-zoster virus ORF20 and lower, but significant, homology with the product of Epstein-Barr virus BORF1. For the three viruses, the corresponding ORFs lie just upstream of the gene coding for the large subunit of viral ribonucleotide reductase. The ORF described here corresponds to the ORF designated UL38 in the recently published nucleotide sequence of the HSV-1 UL region (D. J. McGeoch, M. A. Dalrymple, A. J. Davison, A. Dolan, M. C. Frame, D. McNab, L. J. Perry, J. E. Scott, and P. Taylor, J. Gen. Virol. 69:1531-1574, 1988).
Batch Study of Glycerol Decomposition in One-Stage Supercritical Production of Biodiesel (2009)

The objective of this work was to assess some of the points that need to be elucidated in order to define the economic viability of the noncatalytic supercritical biodiesel process. Net yield of the supercritical process, consumption of methanol, and the quality of the fuel issuing from the reactor were studied. Biodiesel was prepared by reacting refined soy oil with supercritical methanol at T = 280 °C and methanol-to-oil molar ratios of 15 and 20. After the reaction, unreacted methanol, water, and other volatile compounds were removed from the product by stripping with nitrogen at 110 °C. Biodiesel production by the reaction of oils in supercritical methanol under the conditions used in this work produces practically no glycerol byproduct. This fact simplifies the downstream refining of the produced biodiesel. Glycerol is transformed into products of smaller molecular size and water. At first this water reacts with the triglycerides of the reacting mixture to form free fatty acids (FFA), thus increasing the acidity of the product. At longer reaction times the acids are converted into methyl esters again. Glycerol methanolysis reactions increase the methanol consumption. The small amount of glycerides and FFA contaminants in the biodiesel product makes a final step of refining by silica adsorption convenient. No liquid effluents are issued with such a refining step. After the FFA and glycerides are recycled, the yield of the process is 94−96%.
Dipeptidyl Aminopeptidase IV Staining of Cytologic Preparations to Distinguish Benign from Malignant Thyroid Diseases (1991)

Staining for dipeptidyl aminopeptidase IV (DAP IV (EC:3.4.14.5|) activity was applied to aspiration biopsy specimens or imprint preparations of surgical biopsy specimens from thyroid tumors. Material was obtained from 55 patients with histologically proven thyroid diseases: 9 with papillary carcinoma, 5 with follicular carcinoma, 11 with follicular adenoma, 13 with adenomatous goiter, 8 with Hashimoto's thyroiditis, and 9 with other benign conditions. Most tumor cells, follicular lumina in cell clusters, and intranuclear inclusions were strongly positive for DAP IV in all examples of papillary or follicular carcinoma. In contrast, only a few epithelial cells were labeled for DAP IV in follicular adenoma and adenomatous goiter. Some Hiirthle cells in Hashimoto's thyroiditis also were positive for DAP IV. When a DAP IV scoring system based on the percentage of positive cells and staining intensity was used, all benign tissues except one (from a follicular adenoma) were found to have extremely low scores. These results indicate that staining for DAP IV activity is a simple but useful tool to aid in distinguishing benign from malignant thyroid neoplasms.
Identification of a novel retinoid-responsive element in the promoter region of the medium chain acyl-coenzyme A dehydrogenase gene. (1992)

To study the mechanisms involved in regulation of nuclear genes encoding mitochondrial enzymes in oxidative energy pathways, the promoter region of the medium-chain acyl-CoA dehydrogenase (MCAD) gene was analyzed. A series of hexamer sequences known to bind and confer responsiveness to a subset of members of the nuclear receptor superfamily of transcription factors was identified. Cotransfection of an MCAD promoter-chloramphenicol acetyltransferase (CAT) reporter plasmid with retinoic acid receptor (RAR)alpha, beta, or retinoid X receptor alpha (RXR alpha) resulted in 10-15-fold transcriptional activation in response to retinoic acid. The retinoic acid-induced activation was 3-4-fold higher with RXR alpha than with either RAR alpha or RAR beta. Deletional analysis confirmed that a region between -341 and -308 base pairs upstream of the MCAD gene cap site conferred the RA-responsive transcriptional activation to homologous and heterologous promoters. Gel mobility shift assays demonstrated that the MCAD RARE interacted directly with overexpressed receptors. Mutational analysis of the RARE delineated three hexamer binding sequences with unique orientation and spacing compared to other reported retinoid responsive elements. These results indicate that the MCAD gene promoter region contains a novel regulatory element that interacts with members of the retinoid receptor family, with preferential activation by RXR alpha. This element likely plays a role in the transcriptional regulation of this gene and perhaps others involved in oxidative energy metabolism.
Biomass pyrolysis for liquid fuels and chemicals: A review (2007)

volatile matter, 80.0, 74.7; fixed carbon, 19.4, 24.0; and ash, 0.65%, 1.3%. Woody biomass consists of cellulose (C 6 H 10 O 5 ) x , hemicelluloses such as xylan (C 5 H 8 O 4 ) m , and lignin [C 9 H 10 O 3 (OCH 3 ) 0.9-1.7 ] n in trunk, foliage, and bark. Cellulose + hemicellulose contents 15,16 are more in hardwoods (78.8%) than softwoods (70.3%), but lignin is more in softwoods (29.2%) than hardwoods (21.7%). Biomass can be converted to ener gy by physical, biological and thermochemical processes. Physical processes are grinding, drying, filtration, pressing, extraction, and briquetting 17 . Biological processes
Mechanically Strong, Electrically Conductive, and Biocompatible Graphene Paper (2008)

Ultrastrong, smooth, and shiny graphene paper with a layered structure (see figure) is prepared by vacuum filtration of a well-dispersed graphene dispersion. Moderate thermal annealing further enhances its mechanical properties and electrical conductivity. A combination of exceptional mechanical strength, thermal stability, high electrical conductivity, and biocompability makes this unique material promising for many technological applications. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
"Bloodless" rats through the use of artificial blood substitutes. (1975)

Reportnumber: PE 438.829; This document is the result of the preparatory phase of the STOA-project "Making perfect life", that defined the project focus. This resulted in the study document Making Perfect Life: Bio-engineering (in) the 21st century.\nA project plan for the next two phases was developed and a project team was set up. A kick-off meeting with potential project partners was instrumental in discussing and prioritising research themes and issues. This meeting took place on 6 October 2009 at the Royal Academy of Arts and Sciences in Amsterdam.\n"Making perfect life" refers to a new set of engineering capabilities and ambitions that have developed at the beginning of this century. This study explains and illustrates this by looking at four different domains of bio-engineering:\n•\tengineering of the body; \n•\tengineering of living artefacts; \n•\tengineering of the brain; \n•\tengineering of intelligent artefacts. \nThere is a need to reflect from a societal point of view on the new developments in these engineering fields within the life sciences and info-cogno sciences.
Local Hydrogel Release of Recombinant TIMP-3 Attenuates Adverse Left Ventricular Remodeling After Experimental Myocardial Infarction (2014)

An imbalance between matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs (TIMPs) contributes to the left ventricle (LV) remodeling that occurs after myocardial infarction (MI). However, translation of these observations into a clinically relevant, therapeutic strategy remains to be established. The present study investigated targeted TIMP augmentation through regional injection of a degradable hyaluronic acid hydrogel containing recombinant TIMP-3 (rTIMP-3) in a large animal model. MI was induced in pigs by coronary ligation. Animals were then randomized to receive targeted hydrogel/rTIMP-3, hydrogel alone, or saline injection and followed for 14 days. Instrumented pigs with no MI induction served as referent controls. Multimodal imaging (fluoroscopy/echocardiography/magnetic resonance imaging) revealed that LV ejection fraction was improved, LV dilation was reduced, and MI expansion was attenuated in the animals treated with rTIMP-3 compared to all other controls. A marked reduction in proinflammatory cytokines and increased smooth muscle actin content indicative of myofibroblast proliferation occurred in the MI region with hydrogel/rTIMP-3 injections. These results provide the first proof of concept that regional sustained delivery of an MMP inhibitor can effectively interrupt adverse post-MI remodeling.
High-sensitivity Defect Evaluation by a New Preferential Etching Technique for Highly As-doped Si Crystals (1997)

A high-sensitivity preferential etching technique is presented to evaluate crystal defects in a highly As-doped silicon crystal with a resistivity lower than 0.01 Ω· cm. For highly doped n-type Si, a conventional preferential etching technique, such as Secco etching, Wright etching or Dash etching becomes less useful because of a significant decrease in defect detection sensitivity. The new method is quite sensitive to dislocations, stacking faults and oxygen precipitates in highly As-doped crystals with a surface of either (111) or (100). In this method, copper is first decorated at the defect site, then the defect is preferentially etched by a dilute alkaline solution. The technique thus offers us a sensitive and Cr-free method, attractive from an environmental aspect. A correlation between the laser scattering method is also obtained for the oxygen precipitate density.
Physical Polymer Surface Modification Methods and Applications in Food Packaging Polymers (1999)

Continued innovations in the polymer industry have made polymer surface modification methods a subject of intense research. The importance and necessity of surface modification of plastics are explained, and the advantages of physical surface treatments over the less-sophisticated chemical methods are outlined. Currently available physical surface modification methods for food packaging polymers are reviewed from the food packaging perspective. These physical surface modification methods include flame, corona discharge, UV, gamma-ray, electron beam, ion beam, plasma, and laser treatments. The principle of operation of each method is briefly described, and the advantages and disadvantages of each technique are cited. The extent to which each of these methods can produce the specific modifications desired is discussed. Furthermore, the effects of each treatment on barrier, mechanical, and adhesion properties of food packaging polymers are also examined. Finally, an overview of economic aspects of sophisticated surface modification techniques, including ion beam, plasma, and laser treatments, is presented.
Comparison of the biosynthetic and biodegradative ornithine decarboxylases of Escherichia coli (1977)

Biosynthetic ornithine decarboxylase was purified 4300-fold from Escherichia coli to a purity of approximately 85% as judged by polyacrylamide gel electrophoresis. The enzyme showed hyperbolic kinetics with a Km of 5.6 mM for ornithine and 1.0 micronM for pyridoxal phosphate and it was competitively inhibited by putrescine and spermidine. The biosynthetic decarboxylase was compared with the biodegradative ornithine decarboxylase [Applebaum, D., et al. (1975), Biochemistry 14, 3675]. Both enzymes were dimers of 80 000-82 000 molecular weight and exhibited similar kinetic properties. However, they differed significantly in other respects. The pH optimum of the biosynthetic enzyme was 8.1, compared with 6.9 for the biodegradative. Both enzymes were activated by nucleotides, but with different specificity. Antibody to the purified biodegradative ornithine decarboxylase did not cross-react with the biosynthetic enzyme. The evolutionary relationship of these two decarboxylases to the other amino acid decarboxylases of E. coli is discussed.
Camptothecin Accumulation and Variations inCamptotheca (2002)

Camptotheca (Nyssaceae) is a major source of anticancer camptothecin (CPT). It is imperative to understand CPT accumulation and variations in Camptotheca in order to develop CPT production strategies for endangered germplasm. Our study results showed that CPT is primarily accumulated in glandular trichomes of leaves and stems, and CPT content varies among species and varieties but even more significantly within the plant (with different tissues, tissue ages, and seasons). Because of higher CPT yield and desirable biological and ecological features, 'Hicksii' and 'Katie' should be considered the major management germplasm as CPT sources in the future. Young leaves and mature fruits have higher CPT contents than other tissues in the plants. Young photosynthetic leaves and stems contain higher CPT contents than old ones, but 'sink' tissues such as wood, roots, and fruits show different patterns. CPT content also shows a great seasonal change, but is less influenced by tree age. Intact clipping of young leaves and stems should be managed for harvest for CPT production. Preservation and treatment methods influence the CPT extraction. CPT is better preserved in fresh or freeze-dried material than in air or oven-dried material. CPT can be more efficiently extracted after homogenizer treatment of plant materials because more trichome walls can be broken to allow solvent extraction.