gebhart/patrepeval huggingface dataset:
On the Equivalence of Space-Time Block Coding with Multipath Propagation and/or Cyclic Delay Diversity in OFDM (2002)

The new era of regenerative medicine has led to rapid development of new innovative therapies especially for diseases and tissue/organ defects for which traditional therapies and medicinal products have not provided satisfactory outcome. Although the clinical use and developments of cell-based medicinal products (CBMPs) could be witnessed already for a decade, robust scientific and regulatory provisions for these products have only recently been enacted. The new Regulation for Advanced Therapies (EC) 1394/2007 together with the revised Annex I, Part IV of Directive 2001/83/EC provides the new legal framework for CBMPs. The wide variety of cell-based products and the foreseen limitations (small sample sizes, short shelf life) vs. particular risks (microbiological purity, variability, immunogenicity, tumourigenicity) associated with CBMPs have called for a flexible, case-by-case regulatory approach for these products. Consequently, a risk-based approach has been developed to allow definition of the amount of scientific data needed for a Marketing Authorisation Application (MAA) of each CBMP. The article provides further insight into the initial risk evaluation, as well as to the quality, non-clinical, and clinical requirements of CBMPs. Special somatic cell therapies designed for active immunotherapy are also addressed.
COMPLEMENT DEPOSITION IN EARLY CARDIAC TRANSPLANT BIOPSIES IS ASSOCIATED WITH ISCHEMIC INJURY AND SUBSEQUENT REJECTION EPISODES1 (1999)

Thus, ischemic changes are associated with the activation of complement. Complement activation may in turn promote tissue injury and provide a potential target for future treatment.
5′ untranslated leader sequences of eukaryotic mRNAs encoding heat shock induced proteins (1995)

5' untranslated leaders (5' UTLs) are suggested to play a crucial role in the selective translation of their eukaryotic mRNAs encoding heat shock proteins (HSP) during heat stress conditions. However, the structural features of the HSP mRNAs which cause this effect are mostly unknown. We have compiled the 5' UTLs from about 140 eukaryotic HSP mRNAs including vertebrates, invertebrates, higher and lower plants. A detailed analysis of these sequences according to length, A+T content, context of functional ATGs and presence of upstream non-functional ATGs was made. We observed that all these features were similar to the earlier studies in the literature based on data from HSP as well as non-HSP mRNAs. These observations were reconfirmed by intra-specific comparison of 5' UTLs from HSP and non-HSP genes. Similar to the translation element involved in the selective translation of mRNAs in polioviruses, a search for a short sequence motif complementary to highly conserved 18S rRNA was performed using a HSP mRNA database. The majority of the HSP mRNA sequences (77%) contained one or more small sequence motifs suggesting that they may function as internal ribosome entry sites for selective initiation of translation during heat stress.
PNA-DNA Chimeras Forming Quadruplex Structures (2003)

1H-NMR, CD, and UV spectroscopy have been used to investigate the structure of PNA/DNA chimeras forming quadruplex structures. In particular, we synthesized 5'TGGG3'-t (1) and 5'TGG3'-gt (2), where lower and upper case letters indicate PNA and DNA residues, respectively. CD spectrum and all NMR data of (1) are typical of quadruplexes involving four parallel strands. UV melting profile of (1) indicates that its thermal stability is quite similar to that observed for the reference structure [d(TGGGT)]4. 1H-NMR spectrum for 5'TGG3'-gt (2) shows that this oligonucleotide is not able to fold into a single, well-defined species.
An efficient data-subspace inversion method for 2-D magnetotelluric data (2000)

Abstract There are currently three types of algorithms in use for regularized 2-D inversion of magnetotelluric (MT) data. All seek to minimize some functional which penalizes data misfit and model structure. With the most straightforward approach (exemplified by OCCAM), the minimization is accomplished using some variant on a linearized Gauss-Newton approach. A second approach is to use a descent method [e.g., nonlinear conjugate gradients (NLCG)] to avoid the expense of constructing large matrices (e.g., the sensitivity matrix). Finally, approximate methods [e.g., rapid relaxation inversion (RRI)] have been developed which use cheaply computed approximations to the sensitivity matrix to search for a minimum of the penalty functional. Approximate approaches can be very fast, but in practice often fail to converge without significant expert user intervention. On the other hand, the more straightforward methods can be prohibitively expensive to use for even moderate-size data sets. Here, we present a new and much more efficient variant on the OCCAM scheme. By expressing the solution as a linear combination of rows of the sensitivity matrix smoothed by the model covariance (the “representers”), we transform the linearized inverse problem from the M-dimensional model space to the N-dimensional data space. This method is referred to as DASOCC, the data space OCCAM's inversion. Since generally N ≪ M, this transformation by itself can result in significant computational saving. More importantly the data space formulation suggests a simple approximate method for constructing the inverse solution. Since MT data are smooth and “redundant,” a subset of the representers is typically sufficient to form the model without significant loss of detail. Computations required for constructing sensitivities and the size of matrices to be inverted can be significantly reduced by this approximation. We refer to this inversion as REBOCC, the reduced basis OCCAM's inversion. Numerical experiments on synthetic and real data sets with REBOCC, DASOCC, NLCG, RRI, and OCCAM show that REBOCC is faster than both DASOCC and NLCG, which are comparable in speed. All of these methods are significantly faster than OCCAM, but are not competitive with RRI. However, even with a simple synthetic data set, we could not always get RRI to converge to a reasonable solution. The basic idea behind REBOCC should be more broadly applicable, in particular to 3-D MT inversion.
Insulin Signaling in the Yeast Saccharomyces cerevisiae. 1. Stimulation of Glucose Metabolism and Snf1 Kinase by Human Insulin (1998)

Effects of human insulin on glucose metabolism in the yeast Saccharomyces cerevisiae were studied in this report. Under two conditions of growth limitation (glucose-grown cells during transition to stationary phase or spheroplasts during incubation in synthetic glucose medium), human insulin (10 and 1 microM, respectively) enhanced glycogen accumulation and glycogen synthase activity by 40-60% compared to control cells. Glycogen phosphorylase activity was also increased under the same conditions, but this stimulation was diminished by 35-45% in insulin-treated compared to control cells. Thus, under growth limitation, insulin causes glycogen phosphorylase and glycogen synthase to become more sensitive to inactivation and activation, respectively. In glucose-induced spheroplasts, insulin (1 microM), in addition to glycogen accumulation, led to about 2-fold increases of the rates of ethanol production and glucose oxidation compared to control cells, and the maximal concentration of hexose 6-phosphate was increased by 30-40%. In contrast, glucose transport as well as the levels of the allosteric regulators, fructose 2,6-bisphosphate and cAMP, were not altered at all. Snf1 kinase is assumed to be involved in the regulation of glycogen metabolism in yeast, although it does not seem to be modulated directly by the glucose concentration. Snf1 kinase activity was elevated 5-10-fold in response to insulin both during glucose induction of yeast spheroplasts and during transition to stationary phase of glucose-grown cells. We conclude that Saccharomyces cerevisiae and insulin-sensitive mammalian cells share some parts of the signaling cascades regulating oxidative and nonoxidative glucose metabolism in response to glucose and insulin.
[Expression and pharmacological evaluation of fusion protein FGF21-L-Fc]. (2011)

FGF21 (fibroblast growth factor 21) is a recently described member of the FGF family. It has been previously demonstrated that FGF21 is a potent regulator of glucose homeostasis. To improve stability of FGF21 for better efficacy, a new form of recombinant FGF21 was generated by fusion of a full length FGF21 gene and the Fc fragment of human IgG4 with flexible linker sequence. To examine the glucose regulation activity of FGF21-L-Fc, 3T3-L1 pre-adipocytes were differentiated into adipocytes, and glucose uptake activity of FGF21-L-Fc was examined by glucose oxidase and peroxidase (GOD-POD) assay. The results showed that in comparison with wild type FGF21, FGF21-L-Fc was more potent in stimulation of glucose uptake by 3T3-L1. In vivo studies on the modified protein demonstrated that FGF-L-Fc had a better efficacy in lowering blood glucose of the STZ-induced diabetic animals and controlled glucose level for a longer time. The results provided a sound basis for further studies.
Advancing the preservation of cellular therapy products (2011)

Cell therapies are typically collected in one location, processed in a second location, and then administered in a third location. The ability to preserve the cells is critical to their clinical application. It improves patient access to therapies by increasing the genetic diversity of cells available. In addition, the ability to preserve cells improves the "manufacturability" of a cell therapy product by permitting the cells to be stored until the patient is ready for administration of the therapy, permitting inventory control of products, and improving management of staffing at cell therapy facilities. Finally, the ability to preserve cell therapies improves the safety of cell therapy products by extending the shelf life of a product and permitting completion of safety and quality control testing before release of the product for use. The support of the National Blood Foundation has been critical to our work on improving the quality of frozen and thawed cell therapy products through the development of a microfluidic device to remove dimethlysulfoxide (DMSO). We are also involved in research to replace DMSO with other agents that are less toxic to cells and patients. Finally, the need to advance the preservation of cell therapies was a driving force behind the development of the Biopreservation Core Resource (http://www.biocor.net), a national resource in biopreservation. New interest in translation of cell therapies from the bench to the patient's bedside has the potential to drive the transformation of preservation science, technology, and practice.
Polycrystalline Well-Shaped Blocks of Indium Oxide Obtained by the Sol−Gel Method and Their Gas-Sensing Properties (2003)

Aging-induced aggregation of the nanoparticles in the colloidal solution of indium hydroxide leads to the formation of micrometer particles in the form of well-shaped blocks. As shown by high-resolution transmission electron microscopy and selected area electron diffraction, the well-shaped blocks have a polycrystalline nature composed of small nanounits. After calcination at 400 °C, they consist of cubic and hexagonal In2O3. Semiconducting sensors, composed of well-shaped blocks of cubic and hexagonal In2O3, show high sensitivity to low levels of ozone in the air.
Pictionaire (2010)

This paper introduces an interactive tabletop system that enhances creative collaboration across physical and digital artifacts. Pictionaire offers capture, retrieval, annotation, and collection of visual material. It enables multiple designers to fluidly move imagery from the physical to the digital realm; work with found, drawn and captured imagery; organize items into functional collections; and record meeting histories. These benefits are made possible by a large interactive table augmented with high-resolution overhead image capture. Summative evaluations with 16 professionals and four student pairs validated discoverability and utility of interactions, uncovered emergent functionality, and suggested opportunities for transitioning content to and from the table.
Deletions at chromosome 2q and 12p are early and frequent molecular alterations in bronchial epithelium and NSCLC of long-term smokers (2005)

Most lung cancer is attributed to long-term smoking. In order to define chromosomal regions with an accumulation of smoking-related early molecular damage, we applied 15 microsatellite markers at 8 chromosomal regions (2q35-q36, 3p21.3, 3p14.2, 3p25, 10q11.2, 11p14-15, 12p13.1-p12.3 and 12q14) in an allelotyping study. We studied samples of 42 patients with primary non-small cell lung cancer (NSCLC) (25 squamous cell carcinomas, 13 adenocarcinomas, 2 large cell and 2 bronchioalveolar carcinomas) to compare the frequency of allelic loss in cancer tissue of smokers with matched bronchial epithelium. As a control group we used 11 samples of non-smokers. In NSCLC we found significantly higher frequencies of loss of heterozygosity (LOH) than in matched tumor free bronchial epithelium (p = 0.007). Most frequently, allelic loss was detected in NSCLC at chromosome 3p [3p25 (46%), 3p21.3 (45%), 3p14 (40%)], at 2q35 (24%), 12p12 (29%) and 12q14 (13%), but infrequently at 10q11 (7%) and 11p14-15 (5%). In corresponding histological normal bronchial epithelium, the highest percentage of LOH was found at chromosome 3p [3p21 (17%), 3p25 (12%), 3p14 (9%)] and chromosome 2q (2q35-q36) (17%) and 12p (12p12-p13) (12%). LOH in histologically normal bronchial epithelium was significantly associated with long-term smoking (p = 0.048), especially at chromosome 12p12 (p = 0.018). Our results demonstrate two further deletion hot spots at the chromosomal region 2q35-q36 and 12p12-p13 in tumor tissue of NSCLC and matched histological normal bronchial epithelium of long-term smokers, reflecting a phenomenon referred to as 'field cancerization'. These chromosomal regions represent interesting loci for potential NSCLC associated tumor suppressor genes and could be useful as screening markers for molecular risk assessment of smokers.
Introduction (2012)

This book examines citizen science in the context of the Internet's impact on environmental science, focusing on large citizen science projects that involve monitoring biological and environmental change over broad geographic regions. It discusses the potential of citizen science as a way to study the natural world on broad geographic scales, along with the critical scientific perspectives and tools required to conduct large-scale citizen science research. It also highlights the areas of human endeavor and research that have been integrated with and continue to be influenced by citizen science, especially education. This introduction provides a brief history of citizen science and public participation in citizen science projects, along with an overview of the strategies that have evolved over the years at the Cornell Lab of Ornithology with respect to citizen science, and particularly its projects on birds.
Measles Viruses with Altered Envelope Protein Cytoplasmic Tails Gain Cell Fusion Competence (1998)

The cytoplasmic tail of the measles virus (MV) fusion (F) protein is often altered in viruses which spread through the brain of patients suffering from subacute sclerosing panencephalitis (SSPE). We transferred the coding regions of F tails from SSPE viruses in an MV genomic cDNA. Similarly, we constructed and transferred mutated tail-encoding regions of the other viral glycoprotein hemagglutinin (H) gene. From the mutated genomic cDNAs, we achieved rescue of viruses that harbor different alterations of the F tail, deletions in the membrane-distal half of the H tail, and combinations of these mutations. Viruses with alterations in any of the tails spread rapidly through the monolayer via enhanced cell-cell fusion. Double-tail mutants had even higher fusion competence but slightly decreased infectivity. Analysis of the protein composition of released mutant viral particles indicated that the tails are necessary for accurate virus envelope assembly and suggested a direct F tail-matrix (M) protein interaction. Since even tail-altered glycoproteins colocalized with M protein in intracellular patches, additional interactions may exist. We conclude that in MV infections, including SSPE, the glycoprotein tails are involved not only in virus envelope assembly but also in the control of virus-induced cell fusion.
Identification of the CD163 Protein Domains Involved in Infection of the Porcine Reproductive and Respiratory Syndrome Virus (2009)

Scavenger receptor CD163 is a key entry mediator for porcine reproductive and respiratory syndrome virus (PRRSV). To identify the CD163 protein domains involved in PRRSV infection, deletion mutants and chimeric mutants were created. Infection experiments revealed that scavenger receptor cysteine-rich (SRCR) domain 5 (SRCR 5) is essential for PRRSV infection, while the four N-terminal SRCR domains and the cytoplasmic tail are not required. The remaining CD163 protein domains need to be present but can be replaced by corresponding SRCR domains from CD163-L1, resulting in reduced (SRCR 6 and interdomain regions) or unchanged (SRCR 7 to SRCR 9) infection efficiency. In addition, CD163-specific antibodies recognizing SRCR 5 are able to reduce PRRSV infection.
A new approximate algorithm for image reconstruction in cone-beam spiral CT at small cone-angles (2002)

Presents a new approximate algorithm for image reconstruction with cone-beam spiral CT data at relatively small cone-angles. Based on the algorithm of Wang et al. (1993), our method combines a special complementary interpolation with filtered backprojection. The presented algorithm has three main advantages over Wang's algorithm: (1) It overcomes the pitch limitation of Wang's algorithm. (2) It significantly improves z-resolution when suitable sampling schemes are applied. (3) It avoids the waste of applied radiation dose inherent to Wang's algorithm. Usage of the total applied dose is an important requirement in medical imaging. Our method has been implemented on a standard workstation. Reconstructions of computer-simulated data of different phantoms, assuming sampling conditions and image quality requirements typical to medical CT, show encouraging results.
Interference-mitigating broadband secondary user downlink system: A time-reversal solution (2013)

The spatial and time focusing effects of time-reversal technology make it an ideal candidate for the low interference downlink system to relieve the coexistence issues among different wireless communication systems. The transmitting power would be concentrated at the intended receiver and the leakage to unintended receivers would be automatically suppressed. In this paper, a time-reversal based secondary user downlink system with the coexistence of primary users is proposed. The primary user's performance loss is investigated in terms of effective SINR degradation and achievable data rate deduction. It is illustrated through numerical examples that the time-reversal downlink system relieves the primary user's performance loss as well as achieves satisfying power efficiency compared with the traditional direct transmission.
Multiple transcripts of T-DNA detected in nopaline crown gall tumors. (1982)

Crown gall plant tumors contain neoplastic cells transformed by incorporation of a foreign DNA element, T-DNA, derived from a large tumor-inducing plasmid in the inciting Agrobacterium strain. T-DNA is covalently joined to the nuclear DNA of the tumor cell, and RNA transcripts from T-DNA are present in polyadenylated form on polysomes. This paper presents a detailed analysis of those parts of T-DNA transcribed in a nopaline-type tobacco teratoma, BT37, whose T-DNA has been mapped and cloned. Northern blots of polyA+ RNA were probed with 21 different nick-translated T-DNA fragments, and at least 13 well-defined transcripts were visualized.
Respiratory Viruses Other than Influenza Virus: Impact and Therapeutic Advances (2008)

Though several antivirals have been developed and marketed to treat influenza virus infections, the development of antiviral agents with clinical activity against other respiratory viruses has been more problematic. Here we review the epidemiology of respiratory viral infections in immunocompetent and immunocompromised hosts, examine the evidence surrounding the currently available antivirals for respiratory viral infections other than influenza, highlight those that are in the pipeline, and discuss the hurdles for development of such agents.
The RAGE Axis (2010)

The immunoglobulin superfamily molecule RAGE (receptor for advanced glycation end product) transduces the effects of multiple ligands, including AGEs (advanced glycation end products), advanced oxidation protein products, S100/calgranulins, high-mobility group box-1, amyloid-beta peptide, and beta-sheet fibrils. In diabetes, hyperglycemia likely stimulates the initial burst of production of ligands that interact with RAGE and activate signaling mechanisms. Consequently, increased generation of proinflammatory and prothrombotic molecules and reactive oxygen species trigger further cycles of oxidative stress via RAGE, thus setting the stage for augmented damage to diabetic tissues in the face of further insults. Many of the ligand families of RAGE have been identified in atherosclerotic plaques and in the infarcted heart. Together with increased expression of RAGE in diabetic settings, we propose that release and accumulation of RAGE ligands contribute to exaggerated cellular damage. Stopping the vicious cycle of AGE-RAGE and RAGE axis signaling in the vulnerable heart and great vessels may be essential in controlling and preventing the consequences of diabetes.
Video collage (2007)

In this work, we present Video Collage system, which automatically constructs a compact and visually appealing synthesized collage from a video sequence for efficient video browsing. Given a video, Video Collage is able to select the most representative images, extract salient regions of interest (ROI) from these images and resize ROI according to their saliencies, and seamlessly arrange them on a given canvas while preserving the temporal structure of video content. Furthermore, Video Collage provides a novel user interface that enables users to browse video content in a variety of more efficient ways in contrast to many existing approaches to video browsing.