gebhart/patrepeval huggingface dataset:
So you Need a Protein - A Guide to the Production of Recombinant Proteins (2009)

The field of biotechnology owes a great deal to the ability to produce recombinant proteins, which can be made in far greater abundance than many native proteins, and are more easily quality controlled. There is a great need for individual proteins to be produced for research purposes. This review is aimed at researchers who are not experienced at protein expression, but find that they have a need to produce a recombinant protein. We detail the major expression systems that will be commonly used in the laboratory situation- bacterial, yeast and insect cell culture. The application of each, and the relative advantages/disadvantages are discussed.
Quantitation of Muscle Glycogen Synthesis in Normal Subjects and Subjects with Non-Insulin-Dependent Diabetes by13C Nuclear Magnetic Resonance Spectroscopy (1990)

To examine the extent to which the defect in insulin action in subjects with non-insulin-dependent diabetes mellitus (NIDDM) can be accounted for by impairment of muscle glycogen synthesis, we performed combined hyperglycemic-hyperinsulinemic clamp studies with [13C]glucose in five subjects with NIDDM and in six age- and weight-matched healthy subjects. The rate of incorporation of intravenously infused [1-13C]glucose into muscle glycogen was measured directly in the gastrocnemius muscle by means of a nuclear magnetic resonance (NMR) spectrometer with a 15.5-minute time resolution and a 13C surface coil. The steady-state plasma concentrations of insulin (approximately 400 pmol per liter) and glucose (approximately 10 mmol per liter) were similar in both study groups. The mean (+/- SE) rate of glycogen synthesis, as determined by 13C NMR, was 78 +/- 28 and 183 +/- 39 mumol-glucosyl units per kilogram of muscle tissue (wet weight) per minute in the diabetic and normal subjects, respectively (P less than 0.05). The mean glucose uptake was markedly reduced in the diabetic (30 +/- 4 mumol per kilogram per minute) as compared with the normal subjects (51 +/- 3 mumol per kilogram per minute; P less than 0.005). The mean rate of nonoxidative glucose metabolism was 22 +/- 4 mumol per kilogram per minute in the diabetic subjects and 42 +/- 4 mumol per kilogram per minute in the normal subjects (P less than 0.005). When these rates are extrapolated to apply to the whole body, the synthesis of muscle glycogen would account for most of the total-body glucose uptake and all of the nonoxidative glucose metabolism in both normal and diabetic subjects. We conclude that muscle glycogen synthesis is the principal pathway of glucose disposal in both normal and diabetic subjects and that defects in muscle glycogen synthesis have a dominant role in the insulin resistance that occurs in persons with NIDDM.
Transcriptomic versus Chromosomal Prognostic Markers and Clinical Outcome in Uveal Melanoma (2007)

Molecular classification based on gene expression profiling of the primary tumor was superior to monosomy 3 and clinicopathologic prognostic factors for predicting metastasis in uveal melanoma.
Multiperspective panoramas for cel animation (1997)

We describe a new approach for simulating apparent camera motion through a 3D environment. The approach is motivated by a traditional technique used in 2D cel animation, in which a single background image, which we call a multiperspective panorama, is used to incorporate multiple views of a 3D environment as seen from along a given camera path. When viewed through a small moving window, the panorama produces the illusion of 3D motion. In this paper, we explore how such panoramas can be designed by computer, and we examine their application to cel animation in particular. Multiperspective panoramas should also be useful for any application in which predefined camera moves are applied to 3D scenes, including virtual reality fly-throughs, computer games, and architectural walk-throughs. CR Categories: I.3.3 [Computer Graphics]: Picture/Image Generation. Additional
Lambda Gam protein inhibits the helicase and chi-stimulated recombination activities of Escherichia coli RecBCD enzyme (1991)

The lambda Gam protein was isolated from cells containing a Gam-producing plasmid. The purified Gam protein was found to bind to RecBCD without displacing any of its subunits. Gam was shown to inhibit all known enzymatic activities of RecBCD: ATP-dependent single- and double-stranded DNA exonucleases, ATP-independent single-stranded endonuclease, and the ATP-dependent helicase. When produced in vivo, Gam inhibited chi-activated recombination in lambda red gam crosses but had little effect on the host's ability to act as a recipient in conjugational recombination. These experiments suggest that RecBCD possesses an additional "unknown" activity that is resistant to or induced by Gam. Additionally, the expression of Gam in recD mutants sensitizes the host to UV irradiation, indicating that Gam alters one or more of the in vivo activities of RecBC(D-).
The Role of Interdigestive Small Bowel Motility in the Regulation of Gut Microflora, Bacterial Overgrowth, and Bacterial Translocation in Rats (1998)

The MMC is an important mechanism controlling bacterial growth in the upper small bowel. Its disruption with morphine promotes duodenal bacterial overgrowth and bacterial translocation.
Online Video Object Segmentation via Convolutional Trident Network (2017)

A semi-supervised online video object segmentation algorithm, which accepts user annotations about a target object at the first frame, is proposed in this work. We propagate the segmentation labels at the previous frame to the current frame using optical flow vectors. However, the propagation is error-prone. Therefore, we develop the convolutional trident network (CTN), which has three decoding branches: separative, definite foreground, and definite background decoders. Then, we perform Markov random field optimization based on outputs of the three decoders. We sequentially carry out these processes from the second to the last frames to extract a segment track of the target object. Experimental results demonstrate that the proposed algorithm significantly outperforms the state-of-the-art conventional algorithms on the DAVIS benchmark dataset.
Improved mammalian vectors for high expression of G418 resistance. (1987)

Cell lines, such as those of teratocarcinoma and embryonic stem cells, fail to support high G418 resistance after transfection of neo vectors. To alleviate this, we modified pSV2-neo in two steps, first with tandem promoters of SV40 early genes and HSVtk, then by removing an improper met codon located immediately upstream of the authentic initiator codon in the mRNA sequence. In the final product, pSTneoB, the neo transcription unit has XhoI sites at both ends. pSTneoB yields G418-resistant transformants of teratocarcinoma cells at dramatically higher efficiencies than pSV2-neo. This vector extends the application of G418 selection in gene transfer to a wider range of cell types.
Nanoparticle-Aptamer Bioconjugates (2004)

Nucleic acid ligands (aptamers) are potentially well suited for the therapeutic targeting of drug encapsulated controlled release polymer particles in a cell- or tissue-specific manner. We synthesized a bioconjugate composed of controlled release polymer nanoparticles and aptamers and examined its efficacy for targeted delivery to prostate cancer cells. Specifically, we synthesized poly(lactic acid)-block-polyethylene glycol (PEG) copolymer with a terminal carboxylic acid functional group (PLA-PEG-COOH), and encapsulated rhodamine-labeled dextran (as a model drug) within PLA-PEG-COOH nanoparticles. These nanoparticles have the following desirable characteristics: (a) negative surface charge (-50 +/- 3 mV, mean +/- SD, n = 3), which may minimize nonspecific interaction with the negatively charged nucleic acid aptamers; (b) carboxylic acid groups on the particle surface for potential modification and covalent conjugation to amine-modified aptamers; and (c) presence of PEG on particle surface, which enhances circulating half-life while contributing to decreased uptake in nontargeted cells. Next, we generated nanoparticle-aptamer bioconjugates with RNA aptamers that bind to the prostate-specific membrane antigen, a well-known prostate cancer tumor marker that is overexpressed on prostate acinar epithelial cells. We demonstrated that these bioconjugates can efficiently target and get taken up by the prostate LNCaP epithelial cells, which express the prostate-specific membrane antigen protein (77-fold increase in binding versus control, n = 150 cells per group). In contrast to LNCaP cells, the uptake of these particles is not enhanced in cells that do not express the prostate-specific membrane antigen protein. To our knowledge, this represents the first report of targeted drug delivery with nanoparticle-aptamer bioconjugates.
Fungal Infections in Solid-Organ Transplantation (1993)

Journal Article Fungal Infections in Solid-Organ Transplantation Get access Carlos V. Paya Carlos V. Paya From the Divisions of Infectious Diseases and Experimental Pathology, Mayo Clinic/Foundation, Rochester, Minnesota Reprints or correspondence: Dr. Carlos V. Paya, Division of Infectious Diseases, Mayo Clinic/Foundation, Rochester, Minnesota 55905. Search for other works by this author on: Oxford Academic PubMed Google Scholar Clinical Infectious Diseases, Volume 16, Issue 5, May 1993, Pages 677–688, https://doi.org/10.1093/clind/16.5.677 Published: 01 May 1993 Article history Received: 20 August 1992 Revision received: 30 November 1992 Published: 01 May 1993
Molecular genetic analysis of the V kappa Ser group associated with two mouse light chain genetic markers. Complementary DNA cloning and southern hybridization analysis. (1985)

Previous studies (21) have shown that two mouse kappa light (L) chain variable (V) region polymorphisms, the IB-peptide and Efla markers, reflect expression of a characteristic group of V kappa regions, called V kappa Ser, by some inbred strains and not others. Expression of V kappa Ser is controlled by a locus on chromosome 6, the chromosome that contains the kappa locus. To further characterize this V kappa group and begin to analyze the basis for its strain-specific expression, full-length complementary DNA (cDNA) copies were produced of L chain mRNA from the M75 myeloma that had been induced in the C.C58 strain of mice, and which produces a V kappa Ser L chain. The C.C58 strain is congenic with BALB/cAn, differing in the region of chromosome 6 that controls expression of the V kappa polymorphisms and the Lyt-2 and Lyt-3 T cell alloantigens. The complete nucleotide sequence of this cloned cDNA was determined and compared with the nucleotide sequences the most closely related BALB/c myeloma L chains known. Results indicated significant differences throughout the variable region, but particularly toward the 5' portion of the sequence. A probe corresponding to 200 bp of the 5' end of the cloned V kappa Ser cDNA was used in Southern hybridizations of restriction digests of liver DNA from a number of inbred, recombinant, and recombinant inbred strains. Under stringent hybridization conditions, one strongly-hybridizing fragment was observed in Bam HI, Hind III, and Eco RI digests, and based on the size of the fragments, strains could be organized into two groups. The presence of strongly hybridizing Bam HI, Hind III, and Eco RI fragments of 3.2, 2.8, and 2.1 kb, respectively, was found to correlate completely with expression by the strain of the IB-peptide and Efla markers. All nonexpressor strains yielded hybridizing fragments of 7.8, 8.4, and 2.8 kb, respectively. Possible explanations for strain-specific expression of V kappa Ser-associated phenotypic markers are discussed.
Selectivity of action of an antiherpetic agent, 9-(2-hydroxyethoxymethyl)guanine (1977)

A guanine derivative with an acyclic side chain, 2-hydroxyethoxymethyl, at position 9 has potent antiviral activity [dose for 50% inhibition (ED(50)) = 0.1 muM] against herpes simplex virus type 1. This acyclic nucleoside analog, termed acycloguanosine, is converted to a monophosphate by a virus-specified pyrimidine deoxynucleoside (thymidine) kinase and is subsequently converted to acycloguanosine di- and triphosphates. In the uninfected host cell (Vero) these phosphorylations of acycloguanosine occur to a very limited extent. Acycloguanosine triphosphate inhibits herpes simplex virus DNA polymerase (DNA nucleotidyltransferase) 10-30 times more effectively than cellular (HeLa S3) DNA polymerase. These factors contribute to the drug's selectivity; inhibition of growth of the host cell requires a 3000-fold greater concentration of drug than does the inhibition of viral multiplication. There is, moreover, the strong possibility of chain termination of the viral DNA by incorporation of acycloguanosine. The identity of the kinase that phosphorylates acycloguanosine was determined after separation of the cellular and virus-specified thymidine kinase activities by affinity chromatography, by reversal studies with thymidine, and by the lack of monophosphate formation in a temperature-sensitive, thymidine kinase-deficient mutant of the KOS strain of herpes simplex virus type 1 (tsA1).
Essential Role of β-Catenin in Postnatal Bone Acquisition (2005)

Mutations in the Wnt co-receptor LRP5 alter bone mass in humans, but the mechanisms responsible for Wnts actions in bone are unclear. To investigate the role of the classical Wnt signaling pathway in osteogenesis, we generated mice lacking the beta-catenin or adenomatous polyposis coli (Apc) genes in osteoblasts. Loss of beta-catenin produced severe osteopenia with striking increases in osteoclasts, whereas constitutive activation of beta-catenin in the conditional Apc mutants resulted in dramatically increased bone deposition and a disappearance of osteoclasts. In vitro, osteoblasts lacking the beta-catenin gene exhibited impaired maturation and mineralization with elevated expression of the osteoclast differentiation factor, receptor activated by nuclear factor-kappaB ligand (RANKL), and diminished expression of the RANKL decoy receptor, osteoprotegerin. By contrast, Apc-deficient osteoblasts matured normally but demonstrated decreased expression of RANKL and increased osteoprotegerin. These findings suggest that Wnt/beta-catenin signaling in osteoblasts coordinates postnatal bone acquisition by controlling the differentiation and activity of both osteoblasts and osteoclasts.
Batch micropackaging by compression-bonded wafer-wafer transfer (1999)

Wafer-wafer transfer of microstructures is demonstrated by gold bump compression bonding. The process is performed at room temperature; 300/spl deg/C-plus is tolerated subsequently. 4-/spl mu/m bump bonds, transferred polysilicon resonators, vacuum-sealed micropackages, and getter structures have been fabricated, as well as multi-level structures built up by successive aligned transfers. Pull strengths of approximately 7/spl times/10/sup 7/ Pa have been measured. 95% yield has been observed in chip-scale transfers, across multiple designs. Sealed micro-packages tolerate external pressures of at least 7.2/spl times/10/sup 6/ Pa without leakage or observable damage.
The transcription factor AtGRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana (2005)

The development of the flat morphology of leaf blades is dependent on the control of cell proliferation as well as cell expansion. Each process has a polarity with respect to the longitudinal and transverse axes of the leaf blade. However, only a few regulatory components of these processes have been identified to date. We have characterized two genes from Arabidopsis thaliana: ANGUSTIFOLIA3 (AN3), which encodes a homolog of the human transcription coactivator SYT, and GROWTH-REGULATING FACTOR5 (AtGRF5), which encodes a putative transcription factor. AN3 is identical to GRF-INTERACTING FACTOR1 (AtGIF1). The an3 and atgrf5 mutants exhibit narrow-leaf phenotypes due to decreases in cell number. Conversely, cell proliferation in leaf primordia is enhanced and leaves grow larger than normal when AN3 or AtGRF5 is overexpressed. Both genes are expressed in leaf primordia, and in the yeast two-hybrid assay, the gene products were found to interact with each other through their N-terminal domains. These results suggest that AN3 and AtGRF5 act together and are required for the development of appropriate leaf size and shape through the promotion and/or maintenance of cell proliferation activity in leaf primordia.
cis -Acting Sequences Required for NtcB-Dependent, Nitrite-Responsive Positive Regulation of the Nitrate Assimilation Operon in the Cyanobacterium Synechococcus sp. Strain PCC 7942 (1998)

There are three binding sites for NtcA (nirI, nirII, and nirIII), the global nitrogen regulator of cyanobacteria, in the DNA region between the two divergently transcribed operons (nirA and nirB operons) involved in nitrate assimilation in Synechococcus sp. strain PCC 7942. Using the luxAB reporter system, we showed that nirI and nirIII, which are located 23 bp upstream from the -10 promoter element of nirA and nirB, respectively, are required for induction by nitrogen depletion of the nirA and nirB operons, respectively. The induction of nirA operon transcription was a prerequisite for the nitrite-responsive positive regulation of the transcription by NtcB, a LysR-type protein. The NtcA-binding site nirII, located in the middle of the nirA-nirB intergenic region, and a potential binding site for a LysR-type protein (TGCAN5TGCA; designated L1), located between nirI and nirII, were required for the nitrite-responsive, NtcB-dependent enhancement of nirA operon transcription. Although the requirement for the L1 site was consistent with the involvement of the LysR family protein NtcB in transcriptional regulation, NtcB did not bind to the nirA regulatory region in vitro in the presence of nitrite and NtcA, suggesting the involvement of some additional factor(s) in the regulation. An L1-like inverted repeat with the consensus sequence TGCN7GCA was conserved in the nirA promoter region of cyanobacteria, being centered at position -23 with respect to the NtcA-binding site corresponding to nirI, which suggested the common occurrence of nitrite-responsive regulation of the nitrate assimilation operon among cyanobacteria.
Response of VEGF expression to amino acid deprivation and inducers of endoplasmic reticulum stress. (2002)

These results indicate that VEGF is an ER stress-responsive gene and suggest that cells can respond to nutrient deprivation by increasing VEGF expression through both transcriptional and posttranscriptional mechanisms.
Sensitivity of Heterozygous α1,6-Fucosyltransferase Knock-out Mice to Cigarette Smoke-induced Emphysema (2012)

We previously demonstrated that a deficiency in core fucosylation caused by the genetic disruption of α1,6-fucosyltransferase (Fut8) leads to lethal abnormalities and the development of emphysematous lesions in the lung by attenuation of TGF-β1 receptor signaling. Herein, we investigated the physiological relevance of core fucosylation in the pathogenesis of emphysema using viable heterozygous knock-out mice (Fut8(+/-)) that were exposed to cigarette smoke (CS). The Fut8(+/-) mice exhibited a marked decrease in FUT8 activity, and matrix metalloproteinase (MMP)-9 activities were elevated in the lung at an early stage of exposure. Emphysema developed after a 3-month CS exposure, accompanied by the recruitment of large numbers of macrophages to the lung. CS exposure substantially and persistently elevated the expression level of Smad7, resulting in a significant reduction of Smad2 phosphorylation (which controls MMP-9 expression) in Fut8(+/-) mice and Fut8-deficient embryonic fibroblast cells. These in vivo and in vitro studies show that impaired core fucosylation enhances the susceptibility to CS and constitutes at least part of the disease process of emphysema, in which TGF-β-Smad signaling is impaired and the MMP-mediated destruction of lung parenchyma is up-regulated.
New interfaces for popular music performance (2007)

Augmenting performances of live popular music with computer systems poses many new challenges. Here, "popular music" is taken to mean music with a mostly steady tempo, some improvisational elements, and largely predetermined melodies, harmonies, and other parts. The overall problem is studied by developing a framework consisting of constraints and subproblems that any solution should address. These problems include beat acquisition, beat phase, score location, sound synthesis, data preparation, and adaptation. A prototype system is described that offers a set of solutions to the problems posed by the framework, and future work is suggested.
Characterization and Properties of a Modified Human Interferon- -Containing an Additional 18 Amino Acids at the N-Terminus (1983)

A modified human interferon-alpha 2 was produced in Escherichia coli cells infected with phage M13 mp7 containing an interferon-alpha gene. After purification by immunochromatography with the monoclonal antibody NK2, the N-terminal amino acid sequence was determined. The N-terminal methionine was absent but an additional sequence of 18 amino acids at the N-terminus was retained. The modified interferon-alpha 2 was indistinguishable from authentic interferon-alpha 2 in its ability to activate natural killer cells, to slow the growth of Daudi cells, and to confer virus resistance on heterologous cells.
Disaggregated Memory Benefits for Server Consolidation (2011)

Recent architecture research has introduced a new building block - a memory blade - which provides disaggregated memory capacity expansion and sharing for an ensemble of blade servers. In this paper, we examine the systems implications of this new architectural building block. We build a software-based prototype of memory disaggregation and examine how the additional level of indirection provided by the memory blade can provide significantly higher levels of consolidation. We specifically examine the use case of multiple large memory virtual machines (VMs) consolidated onto a single server. We explore content based sharing strategies to maximize the utilization of both local and remote memory. Using an in-memory database workload, our results show significantly higher levels of consolidation versus baseline servers (twice as many VMs than a memory-constrained baseline, providing 47% higher throughput), cost-effective memory expansion (28% better performance-per-dollar versus a large memory baseline), and effective content based sharing (up to 40%).
Cloning and Subcellular Localization of Human Mitochondrial hsp70 (1995)

We report the cloning, nucleotide sequence, and localization of mitochondrial hsp70, a member of the human hsp70 multi-gene family. The human mthsp75 gene was cloned by screening an expression library with monoclonal antibody 3A3 that recognizes three members of the human hsp70 family (hsp70, hsc70, and a 75-kDa protein with characteristics identical to that previously established for mitochondrial hsp70). The identity of the 75-kDa protein was confirmed by subcellular fraction of HeLa cells and the demonstration that the 3A3-reactive 75-kDa protein co-fractionates with mitochondrial localized proteins. The nucleotide sequence of the respective cDNA clone revealed an open reading frame of 679 amino acids with extensive sequence identity with members of the human hsp70 family. The derived amino-terminal pre-sequence shares features common to other mitochondrial targeting sequences. The identity of the cDNA was unequivocally established by introduction of an epitope-tag at the carboxyl terminus of the cloned gene, transfection and analysis by immunofluorescence. The tagged 75-kDa protein localizes to mitochondria, thus providing conclusive evidence that it corresponds to the human mitochondrial hsp70, referred to here as mthsp75.