gebhart/patrepeval huggingface dataset:
Analysis of in vivo dynamics of influenza virus infection in mice using a GFP reporter virus (2010)

Influenza A virus is being extensively studied because of its major impact on human and animal health. However, the dynamics of influenza virus infection and the cell types infected in vivo are poorly understood. These characteristics are challenging to determine, partly because there is no efficient replication-competent virus expressing an easily traceable reporter gene. Here, we report the generation of a recombinant influenza virus carrying a GFP reporter gene in the NS segment (NS1-GFP virus). Although attenuated when compared with wild-type virus, the NS1-GFP virus replicates efficiently in murine lungs and shows pathogenicity in mice. Using whole-organ imaging and flow cytometry, we have tracked the dynamics of influenza virus infection progression in mice. Imaging of murine lungs shows that infection starts in the respiratory tract in areas close to large conducting airways and later spreads to deeper sections of the lungs. In addition to epithelial cells, we found GFP-positive antigen-presenting cells, such as CD11b(+)CD11c(-), CD11b(-)CD11c(+), and CD11b(+)CD11c(+), as early as 24 h after intranasal infection. In addition, a significant proportion of NK and B cells were GFP positive, suggesting active infection of these cells. We next tested the effects of the influenza virus inhibitors oseltamivir and amantadine on the kinetics of in vivo infection progression. Treatment with oseltamivir dramatically reduced influenza infection in all cell types, whereas, surprisingly, amantadine treatment more efficiently blocked infection in B and NK cells. Our results demonstrate high levels of immune cells harboring influenza virus antigen during viral infection and cell-type-specific effects upon treatment with antiviral agents, opening additional avenues of research in the influenza virus field.
Exploiting web search engines to search structured databases (2009)

Web search engines often federate many user queries to relevant structured databases. For example, a product related query might be federated to a product database containing their descriptions and specifications. The relevant structured data items are then returned to the user along with web search results. However, each structured database is searched in isolation. Hence, the search often produces empty or incomplete results as the database may not contain the required information to answer the query. In this paper, we propose a novel integrated search architecture. We establish and exploit the relationships between web search results and the items in structured databases to identify the relevant structured data items for a much wider range of queries.Our architecture leverages existing search engine components to implement this functionality at very low overhead. We demonstrate the quality and efficiency of our techniques through an extensive experimental study.
Conjugation of Monoclonal Antibodies with TETA Using Activated Esters: Biological Comparison of 64 Cu-TETA-1A3 with 64 Cu-BAT-2IT-1A3 (2001)

A simple method for conjugation of monoclonal antibodies (mAbs) with the chelating agent 1,4,8,11-tetraazacyclotetradecane-1,4,8,11-tetraacetic acid (TETA), has been developed using commercially available reagents. This method involved activation of a single carboxyl group of TETA with N-hydroxysulfosuccinimide and 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide. The resulting activated ester of TETA was reacted with the anti-colorectal carcinoma mAb 1A3 at molar ratios ranging from 10:1 to 100:1 to give immunoconjugates modified with an average of 0.4 to 2.0 functional chelators per antibody molecule. The TETA-1A3 conjugate was labeled with 64Cu at specific activities as high as 15.4 microCi/microgram, and the radiolabeled mAb exhibited high in vitro serum stability and minimal loss of immunoreactivity. The biodistribution of 64Cu-labeled TETA-1A3 in hamsters bearing GW39 human colon carcinoma xenografts was compared to that of 64Cu-BAT-2IT-1A3 (BAT = 6-(p-bromoacetamidobenzyl)-1,4,8,11-tetraazacyclotetradecane-1,4,8,11- tetraacetic acid; 2IT = 2-iminothiolane). Both conjugates showed high tumor uptake (6.60-9.05% injected dose/gram) from 24 to 48 h post-injection and generally similar blood clearance and non-target organ uptakes. Human absorbed dose estimates derived from the hamster biodistribution data showed the critical organs for both conjugates to be the large intestine and the red marrow. Our results suggest that the in vitro and in vivo performance characteristics of 64Cu-TETA-1A3 compare favorably with those of 64Cu-BAT-2IT-1A3 and that further evaluation of the diagnostic and therapeutic efficacy of 64Cu-TETA-1A3 is warranted.
Prion-Protein-Specific Aptamer Reduces PrPSc Formation (2002)

The critical initial event in the pathophysiology of transmissible spongiform encephalopathies (TSEs) appears to be the conversion of the cellular prion protein (PrP(C)) into the abnormal isoform PrP(Sc). This isoform forms high-molecular-weight protease K (PK) resistant aggregates that accumulate in the central nervous system of affected individuals. We have selected nuclease-resistant 2'-amino-2'-deoxypyrimidine-modified RNA aptamers which recognize a peptide comprising amino acid residues 90-129 of the human prion protein with high specificity. This domain of prion proteins is thought to be functionally important for the conversion of PrP(C) into its pathogenic isoform PrP(Sc) and is highly homologous among prion proteins of various species including mouse, hamster, and man. Consequently, aptamer DP7 binds to the full-length human, mouse, and hamster prion protein. At low concentrations in the growth medium of persistently prion-infected neuroblastoma cells, aptamer DP7 significantly reduced the relative proportion of de novo synthesized PK-resistant PrP(Sc) within only 16 h. These findings may open the door towards a rational development of a new class of drugs for the therapy or prophylaxis of prion diseases.
Multifocal planes head-mounted displays (2000)

Stereoscopic head-mounted displays (HMD's) provide an effective capability to create dynamic virtual environments. For a user of such environments, virtual objects would be displayed ideally at the appropriate distances, and natural concordant accommodation and convergence would be provided. Under such image display conditions, the user perceives these objects as if they were objects in a real environment. Current HMD technology requires convergent eye movements. However, it is currently limited by fixed visual accommodation, which is inconsistent with real-world vision. A prototype multiplanar volumetric projection display based on a stack of laminated planes was built for medical visualization as discussed in a paper presented at a 1999 Advanced Research Projects Agency workshop (Sullivan, Advanced Research Projects Agency, Arlington, Va., 1999). We show how such technology can be engineered to create a set of virtual planes appropriately configured in visual space to suppress conflicts of convergence and accommodation in HMD's. Although some scanning mechanism could be employed to create a set of desirable planes from a two-dimensional conventional display, multiplanar technology accomplishes such function with no moving parts. Based on optical principles and human vision, we present a comprehensive investigation of the engineering specification of multiplanar technology for integration in HMD's. Using selected human visual acuity and stereoacuity criteria, we show that the display requires at most 27 equally spaced planes, which is within the capability of current research and development display devices, located within a maximal 26-mm-wide stack. We further show that the necessary in-plane resolution is of the order of 5 microm.
Women With and Without Metabolic Disorder Differ in Their Gut Microbiota Composition (2012)

The aim of this study was to investigate whether overweight/obese women in metabolic disorder group (MDG, n = 27) differ in their gut microbiota composition from overweight/obese women in non-metabolic disorder group (NMDG, n = 47) and normal weight women group (NWG, n = 11). Gut microbiota was profiled from fecal samples by 16S rRNA fluorescence in situ hybridization and flow cytometry in 85 premenopausal women. Body composition was measured by bioimpedance, and dietary intakes were collected via food diaries. Standard procedures were used to assess plasma glucose, serum insulin, lipids, and inflammatory status. We found that the proportion of bacteria belonging to Eubacterium rectale-Clostridium coccoides group, indicating efficient energy harvest from nutrients in gut, was higher in MDG compared to NMDG and NWG, while no difference was found between NMDG and NWG. The proportion of Eubacterium rectale-Clostridium coccoides group correlated positively with weight, BMI, total fat, fat mass percentage (FM%), visceral fat area, and serum triglycerides, and negatively with high-density lipoprotein (HDL). Our results indicate that certain members of Eubacterium rectale-Clostridium coccoides group are associated with obesity-related MDs not obesity per se.
Measured electrical performance of V-groove inductors for microprocessor power delivery (2003)

Thin-film V-groove inductors for microprocessor power delivery are discussed. A 10-MHz, 3.3-V to 1.1-V, 7-A dc-dc converter with V-groove inductors has been predicted to have an efficiency of 88% and power density of 60 W of output power per cm/sup 2/ of substrate area. The first prototype inductors with composite granular Co-ZrO/sub 2/ thin-films were fabricated with dimensions smaller than those required for a 7-A converter in order to fabricate them on standard 25-mm silicon wafers. For these prototype devices, we predicted that a 10-MHz, 3.3-V to 1.1-V, 2.1-A dc-dc converter would have 60% efficiency. Measurements on the prototypes indicate that a 2.1-A converter would have 55% efficiency with a power density of 28 W/cm/sup 2/. Measured losses were 23% higher than predicted. We have demonstrated that V-groove inductors can be fabricated with performance close to predicted results.
A high quality MBE-LPC-FE speech coder at 2.4 kbps and 1.2 kbps (2002)

This paper presents a high quality speech coder based on the multi-band excitation (MBE) model operating at 2.4 kb/s and 1.2 kb/s. The features of this coder mainly focus on two aspects. One is an accurate and reliable pitch estimation and voiced/unvoiced decision algorithm. The other is the efficient quantization of the variable dimension spectral amplitude vector. Besides representing the spectral envelope information using an all-pole model, we also encode error vectors of the spectral amplitude vector at several important positions. Informal listening tests indicate that the speech quality of this coder at 2.4 kb/s is comparable and even superior to the INMARSAT-M IMBE 4.15 kb/s coder. The coder has been implemented in real-time on a single TMS320C31 floating point DSP.
Growing kidneys (2001)

The number of kidney transplantations performed per year is restricted by the limited availability of donor organs. One possible solution to this shortage is the use of renal xenografts. However, the transplantation of xenografts is complicated by hyperacute and acute rejection. A second possible solution is to 'grow a kidney' from a transplanted renal anlage. It has been postulated that the host immune response might be attenuated after the transplantation of such an anlage (metanephros) instead of a developed kidney. Transplanted metanephroi become chimeric organs in that their blood supply originates, at least partly, from the host. It is possible to transplant a developing metanephros, without the use of immunosuppression, from one rat to another. Transplanted metanephroi grow, differentiate, become vascularized, and function in host rats. 'Growing kidneys' via the transplantation of metanephroi may hold promise as a novel therapeutic approach to the treatment of chronic renal failure.
Quantitation of MYC gene expression in sporadic breast tumors with a real-time reverse transcription-PCR assay. (1999)

MYC gene overexpression was identified recently as a downstream step at the end of the Wnt/APC/beta-catenin pathway dysregulation observed in colorectal cancer (T-C. He et al., Science (Washington DC), 281: 1509-1512, 1998). It thus appears that an excess of c-myc protein is a primary cause of numerous cancers. In breast cancer, MYC has been studied mostly at the DNA level because of the poor quality of available antibodies against the protein product. The renewed interest in MYC calls for a sensitive and accurate method for analyzing MYC overexpression in breast tumors. We have developed a real-time quantitative reverse transcription-PCR assay based on TaqMan fluorescence methodology to quantify the MYC mRNA copy number. We validated the method on a large series of breast tumors. MYC gene overexpression was observed in 29 of 134 (22%) breast tumor RNAs, ranging from 3.2 to 19 times the level in normal breast tissues. These data imply that dysregulated MYC gene expression is potentially involved in the pathogenesis of breast cancer, especially by favoring local cell proliferation. We also found that MYC gene overexpression was rarely due to an increased MYC gene copy number in breast cancer. This new, simple, rapid, and semiautomated method will be useful for screening cancer patients for MYC overexpression and will prove a powerful tool in large, randomized, prospective, cooperative group trials and in the MYC-based therapy project.
Chimeric mouse-human IgG1 antibody that can mediate lysis of cancer cells. (1987)

A chimeric mouse-human antibody has been created that recognizes an antigen found on the surface of cells from many carcinomas. Immunoglobulin constant (C) domains of the mouse monoclonal antibody L6, C gamma 2a and C kappa, were substituted by the human C gamma 1 and C kappa by recombining cDNA modules encoding variable or C domains. The cDNA constructs were transfected into lymphoid cells for antibody production. The chimeric antibody and mouse L6 antibody bound to carcinoma cells with equal affinity and mediated complement-dependent cytolysis. In the presence of human effector cells, the chimeric antibody gave antibody-dependent cellular cytotoxicity at 100 times lower concentration than that needed for the mouse L6 antibody. The chimeric antibody, but not the mouse L6 antibody, is effective against a melanoma line expressing small amounts of the L6 antigen. The findings point to the usefulness of the chimeric antibody approach for obtaining agents with strong antitumor activity for possible therapeutic use in man.
High-performance, energy-efficient platforms using in-socket FPGA accelerators (2009)

Growing demand for energy-efficient, high-performance systems has resulted in the growth of innovative heterogeneous computing system architectures that use FPGAs. FPGA-based architectures enable designers to implement custom instruction streams executing on potentially thousands of compute elements. Traditionally, FPGAs have been used as compute elements on PCI devices; however, this does not allow the FPGAs to be co-processors. This paper describes a high-performance system architecture that is based on the Intel® Xeon® platform in which one or more FPGAs, acting as application accelerators, replace one or more processors in a dual/multi-processor (DP/MP) platform. The FPGA is thus connected directly to the Front Side Bus (FSB) and enjoys the same privileges as a processor, i.e., full participation in the coherency protocol, unrestricted access to system memory and to other processors via the high bandwidth, and low latency connection to the FSB. In addition, we also describe a software layer called the "Accelerator Abstraction Layer (AAL)", which provides a uniform, hardware- and/or platform-independent application interface. Applications written on AAL can be ported to multiple platforms that have different types of accelerators and the application does not have to be modified. In addition, the AAL also enables the developer/user to reprogram the FPGA on the fly (analogous to an operating system context switch) thereby utilizing the programmable nature of the FPGA. The resulting hardware/software stack creates a flexible and powerful platform for accelerator innovation and deployment.
Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase (1992)

The nucleotide sequence of a 3.1 kb segment carrying the cytosine deaminase gene (codA) from Escherichia coli was determined. The sequence revealed the presence of two open reading frames, the first (codB) specifying a highly hydrophobic polypeptide and the second specifying cytosine deaminase. A two-codon overlap between the two reading frames indicates that they constitute an operon. Transcription of the operon was found to be regulated by exogenous purines. Polypeptides specified by each of the two reading frames were expressed in minicells, and the codB gene product was found to be highly enriched in the membrane fraction. Uptake experiments showed that the CodB protein is required for cytosine transport into the cell and that the intracellular accumulation of cytosine correlated with the codB gene dose. A topological model for the cytosine permease in the cytoplasmic membrane is proposed.
Altered Physiology in Worker Honey Bees (Hymenoptera: Apidae) Infested with the Mite Varroa destructor (Acari: Varroidae): A Factor in Colony Loss During Overwintering? (2004)

The ectoparasitic mite Varroa destructor (Anderson & Trueman) is the most destructive pest of the honey bee, Apis mellifera L., in Europe and the United States. In temperate zones, the main losses of colonies from the mites occur during colony overwintering. To obtain a deeper knowledge of this phenomenon, we studied the mites' impact on the vitellogenin titer, the total protein stores in the hemolymph, the hemocyte characteristics, and the ecdysteroid titer of adult honey bees. These physiological characteristics are indicators of long-time survival and endocrine function, and we show that they change if bees have been infested by mites during the pupal stage. Compared with noninfested workers, adult bees infested as pupae do not fully develop physiological features typical of long-lived wintering bees. Management procedures designed to kill V. destructor in late autumn may thus fail to prevent losses of colonies because many of the adult bees are no longer able to survive until spring. Beekeepers in temperate climates should therefore combine late autumn management strategies with treatment protocols that keep the mite population at low levels before and during the period when the winter bees emerge.
p53 gene mutations in Barrett's epithelium and esophageal cancer. (1991)

Genomic DNA was extracted from archival pathology specimens comprising 10 squamous and 14 adenocarcinomas, including 7 with Barrett's epithelium adjacent to tumor, and corresponding normal esophagus from the resection margin. The polymerase chain reaction was used to amplify selected exons of p53 which were analyzed for mutations using single-strand conformation polymorphism analysis. Mutations were localized to exon 8 for 1 adenocarcinoma and to exon 5 for 1 squamous tumor and 4 of 7 Barrett's specimens. Sequencing confirmed mutations at codons 273 (CGT----CAT; adenocarcinoma) and 176 (TGC----TTC; squamous) and in Barrett's epithelium at codons 152 (CCG----CTG), 155 (ACC----GCC) and 175 (CGC----CAC). Specimens of Barrett's epithelium from separate sites had identical p53 mutations suggesting a clonal origin. Cancers arising in mutant epithelium did not have mutations corresponding to those found in the Barrett's specimens suggesting that other events are required for tumorigenesis.
Systems Biology: Properties of Reconstructed Networks (2006)

Genome sequences are now available that enable us to determine the biological components that make up a cell or an organism. The discipline of systems biology examines how these components interact and form networks, and how the networks generate whole cell functions corresponding to observable phenotypes. This 2006 textbook devoted to systems biology describes how to model networks, how to determine their properties, and how to relate these to phenotypic functions. The prerequisites are some knowledge of linear algebra and biochemistry. Though the links between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, in an associated web site Palsson provides problem sets, projects and Powerpoint slides, and keeps the presentation in the book concrete with illustrative material and experimental results
Improved Adhesion and Proliferation of Human Endothelial Cells on Polyethylene Precoated with Monoclonal Antibodies Directed against Cell Membrane Antigens and Extracellular Matrix Proteins (1991)

Endothelial cell seeding may improve the patency of synthetic vascular grafts provided that platelet reactivity of nonendothelialized sites is not increased. We have investigated if surface-adsorbed monoclonal antibodies directed against endothelial cell membrane proteins and against extracellular matrix proteins promote the adhesion and proliferation of cultured human endothelial cells, without causing platelet deposition at non-endothelialized sites. Adhesion of endothelial cells onto polyethylene coated with monoclonal antibodies directed against endothelial cell-specific membrane antigens, integrin receptors and glycoprotein CD31 was equal to or higher than adhesion onto fibronectin-coated polyethylene. Endothelial cells did not proliferate on these surface-adsorbed antibodies. However, pre-coating of polyethylene with mixtures of endothelial cell-specific monoclonal antibodies and monoclonal antibodies directed against fibronectin or von Willebrand factor, resulted in relatively high adhesion and optimal proliferation. Platelet reactivity of the polyethylene surface was found to significantly increase after adsorption of fibronectin, endothelial cell-specific monoclonal antibody or its Fc fragments. In contrast, adsorption of F(ab')2 fragments of endothelial cell-specific monoclonal antibody did not promote platelet deposition. Therefore, it is concluded that coating of vascular graft materials with mixtures of F(ab')2 fragments of monoclonal antibodies specifically directed against endothelial cells and against extracellular matrix proteins may be an effective way to both promote the growth of seeded endothelial cells and limit platelet-graft interaction.