gebhart/patrepeval huggingface dataset:
Altering Retroviral Tropism Using a Random-Display Envelope Library (2002)

Tissue-specific gene delivery is an important aspect of many gene therapy applications. The experiments reported here constitute the first successful demonstration that cell-specific entry can be obtained by screening a random library of retroviral envelope proteins produced from a mammalian cell system. The library consisted of 10(6) different subgroup A feline leukemia virus envelope protein variants with 10 randomly substituted amino acids in the receptor-determining region. Selecting the library for fully functional envelope proteins able to mediate stable gene transfer resulted in the identification of a single envelope protein variant (EF). Subsequent examination of the host range of EF revealed that it was highly specific for D17 canine osteosarcoma cells. This was in contrast to the host ranges of the parental subgroup A and closely related subgroup C envelope proteins. Interference assays on D17 cells further indicated that receptor usage by EF was also altered compared with the A and C envelope proteins. The EF envelope protein thus isolated should be useful for studying gene therapy treatments of osteosarcoma in a large-animal model.
Chardonnay grape seed procyanidin extract supplementation prevents high‐fat diet‐induced obesity in hamsters by improving adipokine imbalance and oxidative stress markers (2008)

Studies reported the effects of polyphenols but not for grape polyphenols towards obesity. We analysed the effects of a polyphenolic grape seed extract (GSE) on obesity and oxidative stress in hamsters receiving a high-fat diet (HFD). Three groups of hamsters received a standard diet (STD), or a HFD plus a daily gavage with water (Control, HFD) or a solution of GSE (HFD + GSE) for 12 wk. Plasma glucose, triglycerides (TG), insulin, leptin and adiponectin were measured. Oxidative stress was assessed by cardiac production of superoxide anion and NAD(P)H oxidase expression. After 12 wk, HFD increased abdominal fat as compared with standards. GSE avoided this feature. HFD led to higher plasma glucose, TG, insulin and greater insulin resistance (HOMA-IR) values. GSE prevented in part these effects, reducing insulinemia and leptinemia by 16.5 and 45%, respectively, whereas adiponectin level increased by 61% compared with obese controls. GSE lowered glycemia and HOMA-IR and strongly prevented cardiac production of superoxide by 74% and NAD(P)H oxidase expression by 30%. This is the first time that chronic consumption of grape phenolics is shown to reduce obesity development and related metabolic pathways including adipokine secretion and oxidative stress.
Autoimmunity and thyroid growth. Where do we stand? (1996)

This issue of European Journal of Endocrinology contains two articles which have in common the study in humans of the involvement of TSH receptor antibodies (TSH-R-ab) and T cells in goitrous conditions such as Graves’ disease and sporadic goitre.
Full-Length cDNA Cloning and Determination of mRNA 5′and 3′Ends by Amplification of Adaptor-Ligated cDNA (1996)

An efficient cDNA amplification procedure is described for determining of the 5′ and 3′ ends of mRNAs and cloning full-length cDNAs. In this approach, a double-stranded (ds) adaptor is ligated to both ends of a library of ds cDNA by T4 DNA ligase. This adaptor-ligated ds cDNA is then used to selectively amplify 5′- or 3′-cDNA fragments by PCR with a combination of gene-specific and adaptor-specific primers. This is a unified method for 5′and 3′rapid amplification of cDNA ends (RACE) from the same adaptor-ligated ds cDNA template. A specially designed adaptor combines features of “vectorette PCR” and “suppression PCR” technologies that significantly reduce background during amplification. The application of “long and accurate PCR” (LA PCR) technology makes possible the amplification of large RACE products and full-length cDNAs with high fidelity to the original mRNA. We investigated efficacy and limitations of this PCR-based approach for cDNA cloning by amplification of 5′- and 3′-RACE fragments and full-length cDNAs of three members of the abundant human actin gene family (1.3–1.9 kb), the medium abundance transferrin receptor mRNA (5.0 kb) and the low-medium abundance insulin-like growth factor II receptor mRNA (9.1 kb).
Kinetic and affinity limits on antibodies produced during immune responses. (1995)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Tissue Engineering: Künstlicher Gewebeersatz aus vitalen Komponenten (1995)

Tissue engineering as a new field of research has gained increasing importance in recent years. The interdisciplinary field combines, biomaterials cell biology, and cell culture bio-engineering technology. The main focus of tissue engineering is the synthesis of artificial constructs or tissues based on vital cells or cell matrix. Biomaterials provide a three-dimensional structure to shape or guide tissue development. Isolated cartilage cells from a patient can form new tissues when suspended in non-woven resorbable polymers for reconstructive surgery. To achieve sufficient amounts of autologous cells for transplant formation, cells from biopsies have to be multiplied in monolayer culture. Dedifferentiated and undifferentiated mesenchymal cells may be used for bone and cartilage engineering. High cell densities in three-dimensional cultures require perfusion techniques to stabilize culture conditions. Morphogenetic factors such as BMP (bone morphogenetic protein) are thought to play a key role in inducing and controlling phenotypic tissue formation. In conclusion, modern in vitro approaches open new avenues for the development of vital tissue replacements for the clinic. Tissues can be repaired with the patient's own cells eventually leaving no residual artificial materials. Tissue engineering further provides new approaches for in vitro models of the extracellular matrix or diseases which mainly affect this matrix such as rheumatoid arthritis or osteoarthritis. This article describes recent developments in connective tissue engineering and discusses the potential for human tissue repair and reconstructive surgery.
Tamper Evident Microprocessors (2010)

Most security mechanisms proposed to date unquestioningly place trust in microprocessor hardware. This trust, however, is misplaced and dangerous because microprocessors are vulnerable to insider attacks that can catastrophically compromise security, integrity and privacy of computer systems. In this paper, we describe several methods to strengthen the fundamental assumption about trust in microprocessors. By employing practical, lightweight attack detectors within a microprocessor, we show that it is possible to protect against malicious logic embedded in microprocessor hardware. We propose and evaluate two area-efficient hardware methods - TrustNet and DataWatch - that detect attacks on microprocessor hardware by knowledgeable, malicious insiders. Our mechanisms leverage the fact that multiple components within a microprocessor (e.g., fetch, decode pipeline stage etc.) must necessarily coordinate and communicate to execute even simple instructions, and that any attack on a microprocessor must cause erroneous communications between micro architectural subcomponents used to build a processor. A key aspect of our solution is that TrustNet and DataWatch are themselves highly resilient to corruption. We demonstrate that under realistic assumptions, our solutions can protect pipelines and on-chip cache hierarchies at negligible area cost and with no performance impact. Combining TrustNet and DataWatch with prior work on fault detection has the potential to provide complete coverage against a large class of microprocessor attacks.
Clinical comparison of human and canine atopic dermatitis using human diagnostic criteria (Japanese Dermatological Association, 2009): Proposal of provisional diagnostic criteria for canine atopic dermatitis (2011)

Atopic dermatitis (AD) is a common skin disease encountered in both humans and dogs. Canine AD can be used in the analysis of naturally occurring AD; however, details of clinical comparison have been lacking. The purpose of this study is to compare those clinical features using the human diagnostic criteria (Japanese Dermatological Association, 2009). Fifty-one dogs with canine AD were evaluated by the human criteria. Prior to this study, canine AD was basically diagnosed by the fulfillment of two authentic canine AD criteria and a positive reaction against Dermatophagoides farinae in serum immunoglobulin E levels and/or in intradermal tests. Among the human AD criteria items, behavior corresponding to pruritus was observed in all 51 dogs. Skin lesions corresponding to eczematous dermatitis were seen in 50 dogs, and symmetrical distribution of skin lesions was noted in all 51 dogs. A chronic or chronically relapsing course was observed in 50 dogs. Based on these results, the concordance rate for the criteria was 96% (49/51). Differential diagnoses of AD were also investigated in the same manner. The concordance rate for the criteria was 0% (0/69) in scabies, 2% (1/50) in pyoderma, 0% (0/50) in demodicosis, 0% (0/9) in cutaneous lymphoma, 0% (0/2) in ichthyosis, 25% (2/7) in flea allergy, 48% (24/50) in seborrheic dermatitis and 75% (3/4) in food allergy. Canine AD is thus indicated as a valuable counterpart to human AD in clinical aspects. In addition, the human AD criteria could be applicable, with some modification, as provisional diagnostic criteria for canine AD.
Gamma-range oscillations in backward-masking functions and their putative neural correlates. (2000)

Backward-masking functions have been hitherto categorized into two types, commonly named Type A and Type B. The analysis of a model of Retino-Cortical Dynamics produces the prediction that spatially localized stimuli should reveal an oscillatory metacontrast function. The predicted new type of metacontrast masking function was investigated in a psychophysical experiment. The results show oscillatory metacontrast functions with significant power in the gamma range (30-70 Hz). A marked decrease in the oscillations is observed when the spatial extent of the stimuli is increased. The theoretical basis of the study relates the oscillations found in the metacontrast function to gamma-range oscillations observed in scalp and intracerebral recordings. The qualitative agreement between the model and data provides support for this putative relationship.
Effector and Regulatory T-cell Subsets in Autoimmunity and Tissue Inflammation (2010)

Many autoimmune diseases are driven by self-reactive T helper cells. Until recently, organ-specific autoimmune diseases were primarily associated with Th1 cells but not Th2 cells. However, the discovery of a number of new effector T-cell subsets, like Th17 and Th9 cells, and regulatory T cells, like Tregs and Tr1 cells, has changed the way we view and understand autoimmunity at cellular and molecular levels. In recent years, IL-17-producing Th17 cells have emerged as major players in autoimmunity. The complicated relationship between Th1 and Th17 cells, as well as the intricate balance between Tregs and Th17 cells, provides a basis for understanding the immunological mechanisms that induce and regulate autoimmunity. Here, we give an overview of the interplay between different effector T-cell subsets and regulatory T-cell subsets, and how they contribute to the development of autoimmunity and tissue inflammation.
Biomedical and Biochemical Applications of Self-Assembled Metallacycles and Metallacages (2013)

Metal ions and metal complexes with organic molecules are ubiquitous in nature. Bulk metal ions of Na, K, Mg, and Ca constitute as much as 1% of human body weight. The remaining trace ions, most commonly of Fe, Ni, Cu, Mn, Zn, Co, Mo, and V, make up ∼0.01% by weight, but their importance in biological processes cannot be overstated. Although nature is limited to the use of bioavailable metal ions, many rarer transition metals can elicit novel biological responses when they interact with biomolecules. For this reason, metal-biomolecule complexes are of interest in medicinal applications. A well-known example is cisplatin, which contains Pt, rare in nature, but highly effective in this context as an anticancer drug in the form of cis-Pt(NH3)2Cl2 and analogous Pt(II) complexes. This and other examples have led to strong interest in discovering new metalloanticancer drugs. In this Account, we describe recent developments in this area, particularly, using coordination-driven self-assembly to form tunable supramolecular coordination complexes (SCCs) with biomedical applications. Coordination-driven self-assembly describes the spontaneous formation of metal-ligand bonds in solution, transforming molecular building blocks into single, 2D metallacycles, or 3D metallacages depending on the directionality of the precursors used. Such SCCs have well-defined internal cavities and simple pre- or post-self-assembly functionalizations. They are highly tunable both spatially and electronically. Metal ions are necessary structural elements for the directional bonding approach, which can be exploited to provide biological activity to an SCC, particularly for Pt- and Ru-based structures. Since these two metals are not only among the most commonly used for coordination-driven self-assembly but are also the basis for a number of small molecule anticancer agents, researchers have evaluated a growing number of SCCs for their antitumor properties. The biological application of SCCs is still an emergent field of study, but the examples discussed in this Account confirm that supramolecular scaffolds have relevance to a wide variety of biochemical and biomedical targets. SCCs can serve as anticancer agents, act as selective sensors for biologically important analytes, or interact with DNA and proteins. The myriad of possible SCCs and their almost limitless modularity and tunability without significant synthetic penalty suggests that the biological applications of such species will continue along this already promising path.
Determination of the dipole moments of RNAse SA wild type and a basic mutant (2011)

In this study, we report the effects of acidic to basic residue point mutations (5K) on the dipole moment of RNAse SA at different pHs. Dipole moments were determined by measuring solution capacitance of the wild type (WT) and the 5K mutant with an impedance analyzer. The dipole moments were then (1) compared with theoretically calculated dipole moments, (2) analyzed to determine the effect of the point mutations, and (3) analyzed for their contribution to overall protein-protein interactions (PPI) in solution as quantitated by experimentally derived second virial coefficients. We determined that experimental and calculated dipoles were in reasonable agreement. Differences are likely due to local motions of residue side chains, which are not accounted for by the calculated dipole. We observed that the proteins' dipole moments increase as the pH is shifted further from their isoelectric points and that the wild-type dipole moments were greater than those of the 5K. This is likely due to an increase in the proportion of one charge (either negative or positive) relative to the other. A greater charge disparity corresponded to a larger dipole moment. Finally, the larger dipole moments of the WT resulted in greater attractive overall PPI for that protein as compared to the 5K.
Design of Retroviral Expression Vectors (2003)

Several characteristics of amphotropic murine retroviruses have made them useful as vectors for gene transfer with some distinct advantages over other methods of transduction. First, the normal replication cycle of retroviruses includes integration of the viral genome into the host’s chromosomal DNA, and these viruses have evolved a very efficient mechanism of stable gene transfer for this purpose. Second, because the integration machinery uses the termini of the viral DNA as substrate, insertion of viral DNA takes place in a predictable manner with the long terminal repeat (LTR) sequences flanking the genes they carry. Third, retroviruses have a broad host range, which allows gene transfer and expression of foreign genes in many cell types, even including some cell types that are refractory to gene transfer by other means. Fourth, a cytopathic effect on infected cells is lacking, which is especially important for gene expression studies and the generation of stable cell lines. Fifth, all retrovial proteins required for the assembly of infectious virions can be supplied in trans, thereby enabling the expression of exogenous genes up to approx 8 kbp. Finally, retroviral vectors can be conveniently manipulated in plasmid form and, as discussed below, are somewhat flexible in terms of vector design.
Expression of cyclooxygenase-2 in human lung carcinoma. (1998)

Epidemiological studies indicate that the use of aspirin decreases incidence of and mortality from gastrointestinal cancers. A major target of aspirin and other nonsteroid anti-inflammatory drugs is cyclooxygenase (Cox), the rate-limiting enzyme in the conversion of arachidonic acid to prostanoids. Two Cox genes have been cloned (Cox-1 and Cox-2), of which Cox-2 has recently been found to be expressed in several human carcinomas. We have now studied the expression of Cox-2 mRNA and protein in human lung adenocarcinoma, squamous cell carcinoma, and small cell lung cancer. Cox-2 mRNA steady-state levels were high in well-differentiated adenocarcinoma samples, but low in poorly differentiated adenocarcinoma, squamous cell carcinoma, and small cell lung cancer, as detected by Northern blot analysis. Immunohistochemistry showed Cox-2 staining in 19 of 21 adenocarcinomas. However, well-differentiated adenocarcinomas contained more Cox-2 staining than the poorly differentiated ones. Expression of the Cox-2 protein was also seen in all 11 squamous cell carcinomas studied, although the level of staining seemed to be less than that in the adenocarcinomas. Small cell lung cancer specimens (n = 4) stained with a relatively weak intensity. Interestingly, atypical alveolar epithelium, which associates with asbestosis and idiopathic fibrosing alveolitis and is considered to be a precursor lesion for lung cancer, expressed the Cox-2 protein. Our data, thus, suggest that Cox-2 is expressed in human lung carcinomas and in precursor lesions leading to this malignancy.
A cell cycle study of human mammary epithelial cells. (1993)

The growth regulation of human mammary epithelial cells (HMEC) cultured in a growth factor/hormone-enriched (e.g. EGF, insulin) medium with bovine pituitary extract as the only undefined supplement was studied. The doubling times of the cultures, in which the cells appear in colonies, was 55-72 h, and a considerable intercolonial heterogenecity in proliferative activity could be demonstrated. However, every colony, irrespective of the size of the growth fraction, comprised a sub-population of rapidly growing cells which had a mean generation time of approximately 22 h. When insulin was removed from the culture medium, HMEC proliferation was inhibited. This growth inhibition was shown to be a result of a cell cycle-specific block.
Viral and cellular fos proteins are complexed with a 39,000-dalton cellular protein. (1985)

The structure of viral and cellular fos gene products and their association with a 39,000-dalton cellular protein (p39) were investigated by using antisera raised against synthetic peptides. The first peptide, termed M, corresponded to amino acids 127 to 152 of the v-fos sequence, a region which is identical in c-fos. The second peptide, termed V, corresponded to the nine C-terminal amino acids of v-fos; this region is not present in c-fos. Rabbit antisera were purified by affinity chromatography against their respective peptides before being used for immunoprecipitation. M peptide antisera precipitated p55v-fos and p55c-fos, whereas V peptide antisera precipitated only p55v-fos. This observation confirms the prediction from nucleotide sequence analysis that these proteins are distinct at their C termini. p39 was precipitated in association with p55v-fos and p55c-fos by M and V peptide antisera. However, V peptide antisera did not precipitate p39 from cells expressing p55c-fos, even though the presence of p39 in such cells was demonstrated with M peptide antisera. Denaturation of cell lysates completely abolished the precipitation of p39, whereas the precipitation of p55v-fos was unaffected. Taken together, the data demonstrate that p39 exists in a complex with p55.
Stratal slicing of Miocene-Pliocene sediments in Vermilion Block 50-Tiger Shoal Area, offshore Louisiana (2001)

Many people have viewed modern land surfaces from commercial airplanes and marveled at the form and geometry of geomorphic features such as river channels, deltas, barrier islands, and dune fields. These views represent complete images of the modern time surfaces. We can classify the depositional nature of features on these images by interpreting their planiform geometry and geographic context. In fact, modern 3-D seismic technology has made it possible for us to image similar, but much older, geomorphic or depositional features preserved in the rock record. Unfortunately, although many reservoir-scale (well-to-well scale) features can be detected in vertical seismic lines, few such features can be resolved and interpreted in the vertical perspective because of the data's limited bandwidth. Only in the horizontal perspective are such depositional features large enough to be resolvable when displayed in map view on geologic time surfaces.
Comprehensive Two-Dimensional Gas Chromatography using an On-Column Thermal Modulator Interface (1991)

A thermal desorption modulator prepared on an open-tubular gas chromatographic column continuously generates fast chromatograms sampled from a flowing stream. The output from a slower chromatographic column is a suitable sample stream. Taking the output from one gas chromatographic column as input to a second column through a thermal modulator then generates a set of high-speed chromatograms. One such secondary chromatogram is generated at each point in the primary chromatogram. When plotted in an appropriate two-dimensional form, this set of high-speed chromatograms becomes a comprehensive two-dimensional gas chromatogram. A sample first separated by one column is separated a second time by an independent column. All substances in the sample mixture pass through both columns. Two retention time measures characterize each sample substance. Each substance forms a peak on the two-dimensional plane at a location determined by the interaction of the substance with the two different stationary phases.
A selective insecticidal protein from Pseudomonas for controlling corn rootworms (2016)

The coleopteran insect western corn rootworm (WCR) (Diabrotica virgifera virgifera LeConte) is a devastating crop pest in North America and Europe. Although crop plants that produce Bacillus thuringiensis (Bt) proteins can limit insect infestation, some insect populations have evolved resistance to Bt proteins. Here we describe an insecticidal protein, designated IPD072Aa, that is isolated from Pseudomonas chlororaphis. Transgenic corn plants expressing IPD072Aa show protection from WCR insect injury under field conditions. IPD072Aa leaves several lepidopteran and hemipteran insect species unaffected but is effective in killing WCR larvae that are resistant to Bt proteins produced by currently available transgenic corn. IPD072Aa can be used to protect corn crops against WCRs.