gebhart/patrepeval huggingface dataset:
RETRACTED: Structure of vaccinia complement protein in complex with heparin and potential implications for complement regulation (2004)

Vaccinia virus complement control protein (VCP), a homolog of the regulators of the complement activation family of proteins, inhibits complement activation through mechanisms similar to human fluid-phase complement regulators factor H and C4b-binding protein. VCP has a heparin-binding activity that assists vaccinia in host interactions. Interaction with cell-surface polyanions like heparin is centrally important in the functioning of fluid-phase complement regulators and is the basis of host-target discrimination by the alternative pathway. We report the structure of VCP in complex with a heparin decasaccharide, which reveals changes in VCP that might be pertinent to complement regulation. Properties that VCP shares with fluid-phase complement regulators suggest that such conformational changes may be of relevance in the functioning of other complement regulators. Additionally, comparison of VCP-heparin interactions with potentially similar interactions in factor H might enable understanding of the structural basis of familial hemolytic uremic syndrome, attributed to mutational disruption of heparin and C3b binding by factor H.
Hardware Implementation Analysis of the MD5 Hash Algorithm (2005)

Hardware implementation aspects of the MD5 hash algorithm are discussed in this paper. A general architecture for MD5 is proposed and several implementations are presented. An extensive study of effects of pipelining on delay, area requirements and throughput is performed, and finally certain architectures are recommended and compared to other published MD5 designs. The designs were implemented on a Xilinx Virtex-II XC2V4000-6 FPGA and a throughput of 586 Mbps was achieved with logic requirements of only 647 slices and 2 BlockRAMs. Methods to increase the throughput to gigabit-level were also studied and an implementation of parallel MD5 blocks achieving a throughput of over 5.8 Gbps was introduced. At least to the authors' knowledge, MD5 designs presented in this paper are the fastest published FPGA-based architectures at the time of writing.
Microchips as Controlled Drug-Delivery Devices (2000)

Controlled-release systems are common in a number of product areas, including foods, cosmetics, pesticides, and paper. Microencapsulated systems, for example, are used for the release of flavors and vitamins in foods, fragrances in perfumes, and inks in carbonless copy paper. Controlled-release systems for drug delivery first appeared in the 1960s and 1970s. In the past three decades, the number and variety of controlled release systems for drug-delivery applications has increased dramatically. Many of these use polymers having particular physical or chemical characteristics such as biodegradability, biocompatibility, or responsiveness to pH or temperature changes. However, recent advances in the field of microfabrication have created the possibility of a new class of controlled-release systems for drug delivery, namely, that of small, programmable devices. Their small size, potential for integration with microelectronics, and ability to store and release chemicals on demand could make controlled-release microchips useful in a number of areas, including medical diagnostics, analytical chemistry, chemical detection, industrial process monitoring and control, combinatorial chemistry, microbiology, and fragrance delivery. More importantly, drug-delivery microchips resulting from this convergence of controlled release and microfabrication technologies may provide new treatment options to clinicians in their fight against disease.
Preparation of high titer lambda phage lysates (1987)

Journal Article Preparation of high titer lambda phage lysates Get access Thomas A. Patterson, Thomas A. Patterson Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael Dean Michael Dean 1Program Resources, Inc.Frederick, MD 21701–1013, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 15, Issue 15, 11 August 1987, Page 6298, https://doi.org/10.1093/nar/15.15.6298 Published: 11 August 1987 Article history Received: 27 June 1987 Published: 11 August 1987
Neuroticismo, fortaleza yoica, apoyo social y eventos de vida (ESTRÉS): hacia una teoría de la inteligencia psicosocial (1998)

Although aortic valve anatomy is three-dimensionally complex, careful echocardiographic investigation can yield surgically relevant information. The promise of intravascular and transesophageal imaging is in yielding the raw data of sufficient resolution to make the three-dimensional reconstruction clinically meaningful. (ECHOCARDIOGRAPHY, Volume 13, May 1996)
Biodegradable Nanoellipsoidal Artificial Antigen Presenting Cells for Antigen Specific T‐Cell Activation (2015)

Non-spherical nanodimensional artificial antigen presenting cells (naAPCs) offer the potential to systemically induce an effective antigen-specific immune response. In this report it is shown biodegradable ellipsoidal naAPCs mimic the T-Cell/APC interaction better than equivalent spherical naAPCs. In addition, it is demonstrated ellipsoidal naAPCs offer reduced non-specific cellular uptake and a superior pharmacokinetic profile compared to spherical naAPCs.
Mouse GATA-4: a retinoic acid-inducible GATA-binding transcription factor expressed in endodermally derived tissues and heart. (1993)

We report the cDNA cloning and characterization of mouse GATA-4, a new member of the family of zinc finger transcription factors that bind a core GATA motif. GATA-4 cDNA was identified by screening a 6.5-day mouse embryo library with oligonucleotide probes corresponding to a highly conserved region of the finger domains. Like other proteins of the family, GATA-4 is approximately 50 kDa in size and contains two zinc finger domains of the form C-X-N-C-(X17)-C-N-X-C. Cotransfection assays in heterologous cells demonstrate that GATA-4 trans activates reporter constructs containing GATA promoter elements. Northern (RNA) analysis and in situ hybridization show that GATA-4 mRNA is expressed in the heart, intestinal epithelium, primitive endoderm, and gonads. Retinoic acid-induced differentiation of mouse F9 cells into visceral or parietal endoderm is accompanied by increased expression of GATA-4 mRNA and protein. In vitro differentiation of embryonic stem cells into embryoid bodies is also associated with increased GATA-4 expression. We conclude that GATA-4 is a tissue-specific, retinoic acid-inducible, and developmentally regulated transcription factor. On the basis of its tissue distribution, we speculate that GATA-4 plays a role in gene expression in the heart, intestinal epithelium, primitive endoderm, and gonads.
Evaluation of a Delivery System Providing Long-term Release of Cyclosporine (1996)

The device produces sustained intravitreal levels of cyclosporine. Although it was associated with reversible toxic effects in the rabbit, it was well tolerated in primates. Sustained-release implants are a promising new treatment for chronic uveitis.
Rate Variation Among Nuclear Genes and the Age of Polyploidy in Gossypium (2003)

Molecular evolutionary rate variation in Gossypium (cotton) was characterized using sequence data for 48 nuclear genes from both genomes of allotetraploid cotton, models of its diploid progenitors, and an outgroup. Substitution rates varied widely among the 48 genes, with silent and replacement substitution levels varying from 0.018 to 0.162 and from 0.000 to 0.073, respectively, in comparisons between orthologous Gossypium and outgroup sequences. However, about 90% of the genes had silent substitution rates spanning a more narrow threefold range. Because there was no evidence of rate heterogeneity among lineages for any gene and because rates were highly correlated in independent tests, evolutionary rate is inferred to be a property of each gene or its genetic milieu rather than the clade to which it belongs. Evidence from approximately 200,000 nucleotides (40,000 per genome) suggests that polyploidy in Gossypium led to a modest enhancement in rates of nucleotide substitution. Phylogenetic analysis for each gene yielded the topology expected from organismal history, indicating an absence of gene conversion or recombination among homoeologs subsequent to allopolyploid formation. Using the mean synonymous substitution rate calculated across the 48 genes, allopolyploid cotton is estimated to have formed circa 1.5 million years ago (MYA), after divergence of the diploid progenitors about 6.7 MYA.
Neoadjuvant therapy for advanced head and neck cancer with allopurinol-modulated high dose 5-fluorouracil and cisplatin a phase I-II study (1987)

The combination of cisplatin (100 mg/m2) and 5-fluorouracil (5-FU) by continuous infusion (1 g/m2/day for 5 days) has been reported to produce a high response rate as neoadjuvant therapy for advanced squamous cell head and neck cancer. We sought to improve the response rate by increasing the dose of 5-FU to 1.5 g/m2/day and 2.0 g/m2/day with allopurinol modulation to reduce toxicity. The overall response rate in the 30 patients who received three courses of chemotherapy was 100% with a 50% complete response (CR) rate. A 50% CR rate was observed in patients with T3 (six of 12) and N3 (four of eight) disease. Six patients (four with CR) did not complete subsequent treatment as planned. Seven of 11 (63.6%) chemotherapy complete responders and three of 12 (25%) partial responders (one lost to follow-up) who received all planned treatment are free of disease. The major toxicity encountered was stomatitis (severe in 32%) followed by leukopenia. The maximum tolerated dose of 5-FU in this combination with allopurinol protection was 1.5 g/m2/day. Cisplatin plus high dose 5-FU does not appear to be associated with a higher CR rate than that reported with conventional doses of 5-FU and is more toxic.
Empirical Guidance on Scatterplot and Dimension Reduction Technique Choices (2013)

To verify cluster separation in high-dimensional data, analysts often reduce the data with a dimension reduction (DR) technique, and then visualize it with 2D Scatterplots, interactive 3D Scatterplots, or Scatterplot Matrices (SPLOMs). With the goal of providing guidance between these visual encoding choices, we conducted an empirical data study in which two human coders manually inspected a broad set of 816 scatterplots derived from 75 datasets, 4 DR techniques, and the 3 previously mentioned scatterplot techniques. Each coder scored all color-coded classes in each scatterplot in terms of their separability from other classes. We analyze the resulting quantitative data with a heatmap approach, and qualitatively discuss interesting scatterplot examples. Our findings reveal that 2D scatterplots are often 'good enough', that is, neither SPLOM nor interactive 3D adds notably more cluster separability with the chosen DR technique. If 2D is not good enough, the most promising approach is to use an alternative DR technique in 2D. Beyond that, SPLOM occasionally adds additional value, and interactive 3D rarely helps but often hurts in terms of poorer class separation and usability. We summarize these results as a workflow model and implications for design. Our results offer guidance to analysts during the DR exploration process.
2SNP: scalable phasing based on 2-SNP haplotypes (2005)

2SNP software package implements a new very fast scalable algorithm for haplotype inference based on genotype statistics collected only for pairs of SNPs. This software can be used for comparatively accurate phasing of large number of long genome sequences, e.g. obtained from DNA arrays. As an input 2SNP takes genotype matrix and outputs the corresponding haplotype matrix. On datasets across 79 regions from HapMap 2SNP is several orders of magnitude faster than GERBIL and PHASE while matching them in quality measured by the number of correctly phased genotypes, single-site and switching errors. For example, 2SNP requires 41 s on Pentium 4 2 Ghz processor to phase 30 genotypes with 1381 SNPs (ENm010.7p15:2 data from HapMap) versus GERBIL and PHASE requiring more than a week and admitting no less errors than 2SNP.
The Ki-67 protein: From the known and the unknown (2000)

The expression of the human Ki-67 protein is strictly associated with cell proliferation. During interphase, the antigen can be exclusively detected within the nucleus, whereas in mitosis most of the protein is relocated to the surface of the chromosomes. The fact that the Ki-67 protein is present during all active phases of the cell cycle (G(1), S, G(2), and mitosis), but is absent from resting cells (G(0)), makes it an excellent marker for determining the so-called growth fraction of a given cell population. In the first part of this study, the term proliferation marker is discussed and examples of the applications of anti-Ki-67 protein antibodies in diagnostics of human tumors are given. The fraction of Ki-67-positive tumor cells (the Ki-67 labeling index) is often correlated with the clinical course of the disease. The best-studied examples in this context are carcinomas of the prostate and the breast. For these types of tumors, the prognostic value for survival and tumor recurrence has repeatedly been proven in uni- and multivariate analysis. The preparation of new monoclonal antibodies that react with the Ki-67 equivalent protein from rodents now extends the use of the Ki-67 protein as a proliferation marker to laboratory animals that are routinely used in basic research. The second part of this review focuses on the biology of the Ki-67 protein. Our current knowledge of the Ki-67 gene and protein structure, mRNA splicing, expression, and cellular localization during the cell-division cycle is summarized and discussed. Although the Ki-67 protein is well characterized on the molecular level and extensively used as a proliferation marker, the functional significance still remains unclear. There are indications, however, that Ki-67 protein expression is an absolute requirement for progression through the cell-division cycle.
Antiaminic agents derived from thieno[2,3-c]-2-benzothiepin: 4-(1-Methyl-4-piperidylidene)-4,9-dihydrothieno[2,3-c]-2-benzothiepin and some related compounds (1983)

In the reaction of thieno[2,3 c ]-2-benzothiepin-4(9 H )-one ( VI ) with 1-methyl-4-piperidylmagnesium chloride 7-(1-methyl-4-piperidyl)thieno[2,3- c ]-2-benzothiepin-4(9 H )-one ( VIII ) is formed in addition to the expected amino alcohol VII . The title compound I was obtained by the acid catalyzed dehydration of the pure alcohol VII . Compound I (pipethiadene) has outstanding antihistamine, antiserotonin, antireserpine and anticataleptic activity and was recommended to clinical trials as a potential antimigraine agent. For pharmacokinetic and metabolic studies there were prepared the NC 2 H 3 analogue of pipethiadene IV and further, as potential metabolites, the demethyl analogue III , S-oxide X , demethyl S-oxide XI , N-oxide XIII and N,S-dioxide XIV . The Witting reaction of the ketone VI with 3-dimethylaminopropylidenetriphenylphosphorane resulted in a mixture of geometric isomers of 4-(3-dimethylamino-propylidene)-4,9-dihydrothieno[2,3- c ]-2-benzothiepin with the strongly predominating Z -isomer XVI which was isolated from the mixture by crystallization of the hydrogen maleate. The mixture with the predominating Z -isomer XVI was converted by the treatment with 80% sulfuric acid and dilution with water to a mixture with the predominating E -isomer XV (dithiadene) which was isolated by crystallization of the hydrogen sulfate. Some further new thieno[2,3- c ]-2-benzothiepin derivatives were synthesized as potential intermediates.
A new technique of “Marlex®‐peritoneal sandwich” in the repair of large incisional hernias (1991)

Repair of a large abdominal wall incisional hernia is a difficult surgical problem with recurrence being a common complication. In addition, other complications such as hematomas, seromas, and sinus formation result from the use of foreign material. A new technique to obviate these complications was used in 60 patients with large incisional hernias repaired over the last 15 years. Marlex polypropylene mesh was used for repair, sandwiched between 2 layers of peritoneum of the overstretched hernia sac. There was no operative mortality and no recurrence in follow up from 3 years to 7 years. Postoperative complications encountered could be managed conservatively, without necessitating any major surgical procedure or mesh removal.
SIFT Flow: Dense Correspondence across Scenes and Its Applications (2010)

While image alignment has been studied in different areas of computer vision for decades, aligning images depicting different scenes remains a challenging problem. Analogous to optical flow, where an image is aligned to its temporally adjacent frame, we propose SIFT flow, a method to align an image to its nearest neighbors in a large image corpus containing a variety of scenes. The SIFT flow algorithm consists of matching densely sampled, pixelwise SIFT features between two images while preserving spatial discontinuities. The SIFT features allow robust matching across different scene/object appearances, whereas the discontinuity-preserving spatial model allows matching of objects located at different parts of the scene. Experiments show that the proposed approach robustly aligns complex scene pairs containing significant spatial differences. Based on SIFT flow, we propose an alignment-based large database framework for image analysis and synthesis, where image information is transferred from the nearest neighbors to a query image according to the dense scene correspondence. This framework is demonstrated through concrete applications such as motion field prediction from a single image, motion synthesis via object transfer, satellite image registration, and face recognition.
Induction of Antitumor Immunity by Vaccination of Dendritic Cells Transfected with MUC1 RNA (2000)

Dendritic cells (DC) are potent APCs. In this study, murine bone marrow-derived DC were transfected with RNA encoding the MUC1 Ag that is aberrantly overexpressed in human breast and other carcinomas. The MUC1 RNA-transfected DC exhibited cell surface expression of MUC1 and costimulatory molecules. After injection at the base of the tail, the transfected DC were detectable in inguinal lymph nodes by dual immunochemical staining. Vaccination of wild-type mice with MUC1 RNA-transfected DC induced anti-MUC1 immune responses against MUC1-positive MC38/MUC1, but not MUC1-negative, tumor cells. Mice immunized with the transfected DC were protected against challenge with MC38/MUC1 tumor cells. Furthermore, mice with established MC38/MUC1 tumors were eliminated after receiving the vaccination. CTLs isolated from mice immunized with the transfected DC exhibited specific cytolytic activity against MC38/MUC1 tumor cells. In contrast to these findings, there was little if any anti-MUC1 immunity induced with the transfected DC in MUC1 transgenic (MUC1.Tg) mice. However, coadministration of the transfected DC and IL-12 reversed the unresponsiveness to MUC1 Ag in MUC1.Tg mice and induced MUC1-specific immune responses. These findings demonstrate that vaccination of DC transfected with MUC1 RNA and IL-12 reverses tolerance to MUC1 and induces immunity against MUC1-positive tumors.
Rigor-type mutation in the kinesin-related protein HsEg5 changes its subcellular localization and induces microtubule bundling (1998)

HsEg5 is a human kinesin-related motor protein essential for the formation of a bipolar mitotic spindle. It interacts with the mitotic centrosomes in a phosphorylation-dependent manner. To investigate further the mechanisms involved in targetting HsEg5 to the spindle apparatus, we expressed various mutants of HsEg5 in HeLa cells. All these mutants share a mutation of Thr-112 in the N-terminal motor domain, resulting in the inactivation of the ATP binding domain. In vitro, the HsEg5-T112N mutant motor domain showed a nucleotide-independent microtubule association, typical of a kinesin protein binding to microtubules in a rigor state. In vivo, overexpression of the HsEg5 rigor mutant in HeLa cells induced, in interphase, microtubule bundling, and, in mitosis, the formation of monopolar mitotic spindles similar to those observed after microinjection of anti-HsEg5 antibodies. Localization of the HsEg5 rigor mutant on cytoplasmic microtubules did not require the C-terminal tail domain but was lost when the stalk domain was also deleted. Sucrose gradient centrifugation experiments showed that microtubule bundling was most likely caused by the binding of HsEg5 mutants in a dimeric state. These results demonstrate that the precise subcellular localization of HsEg5 in vivo is regulated not only by the phosphorylation of the tail domain but also by the oligomeric state of the protein.
Quantifying the Semiconducting Fraction in Single-Walled Carbon Nanotube Samples through Comparative Atomic Force and Photoluminescence Microscopies (2009)

A new method was used to measure the fraction of semiconducting nanotubes in various as-grown or processed single-walled carbon nanotube (SWCNT) samples. SWCNT number densities were compared in images from near-IR photoluminescence (semiconducting species) and AFM (all species) to compute the semiconducting fraction. The results show large variations among growth methods and effective sorting by density gradient ultracentrifugation. This counting-based method provides important information about SWCNT sample compositions that can guide controlled growth methods and help calibrate bulk characterization techniques.
A hardware platform for B-ISDN services multiplexing: design and performances of AAL and ATM layers (2002)

The ATM technique has been identified as adequate to transport a wide variety of high-speed data services; moreover, the need of high-performance leads to a hardware implementation of the AAL and ATM protocol layers. A generic customer premises network (CPN) with capabilities of multiplexing and adapting different data services (The CPN can be addressed as a service multiplexer as well as an interworking unit), is examined. In particular a hardware architecture with centralized AAL 3/4 (common part) and ATM protocol functions is considered: all data services share both the AAL and ATM buffers while they keep separate upper layers. The mixed data flows are controlled by a shaping function, located into the ATM layer; this function ensures that the ATM cells are transmitted according to the parameters describing the traffic behavior of each VP/VC circuits, as shown in CCTT Rec. I.371. Two different architectures have been analyzed: one based on a unique AAL/ATM shared buffer, the other based on two separate buffers (one for each layer); the performances of these two models are given. The work is being carried out in the framework of the Italtel activity on ATM (started since the 1980s from the EEC RACE experiences) whose major objective is the introduction of the ATM switching in the public TLC domain (a flexible ATM cross connect UTXC is being developed).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sensitive Ligand-Based Protein Quantification Using Immuno-PCR: A Critical Review Of Single-Probe And Proximity Ligation Assays (2014)

Quantitative PCR (qPCR) of reverse-transcribed mRNA has revolutionized gene expression analyses. qPCR analysis is based on the prevalent assumption that mRNA transcript numbers provide an adequate measure of specific biomarker expression. However, taking the complexity of protein turnover into account, there is a need to correlate qPCR-derived transcriptional patterns with protein translational patterns so as to not leave behind important pathobiological details. One emerging approach in protein analysis is PCR-coupled protein quantification, often denoted as immuno-PCR (iPCR), which targets soluble proteins. Here we review recent trends and applications in iPCR assays that may bridge the gap between classical enzyme-linked immunosorbent assays and mass spectrometry methodologies in terms of sensitivity and multiplexing.