gebhart/patrepeval huggingface dataset:
Performance enhancement of InGaN light-emitting diodes by laser lift-off and transfer from sapphire to copper substrate (2004)

Laser lift-off technique was employed to carry out transfer of prefabricated InGaN multiple-quantum-well light-emitting diodes (LEDs) from sapphire onto Cu substrate. Silver epoxy was used as the bonding material. Characterization results showed tremendous device improvements in terms of maximum allowable current, light output power, and reliability from the use of conductive Cu substrate. LEDs on Cu could withstand a maximum current of 530 mA before breakdown while those on sapphire could only withstand 350 mA. At 40 mA, light output power of LEDs on sapphire and Cu was 0.74 and 0.95 mW, respectively. In addition, reliability test at constant current of 300 mA showed improvement in light output power for LEDs on Cu whereas LEDs on sapphire suffered deterioration with time.
Huntingtin Modulates Transcription, Occupies Gene PromotersIn Vivo, and Binds Directly to DNA in a Polyglutamine-Dependent Manner (2008)

Transcriptional dysregulation is a central pathogenic mechanism in Huntington's disease, a fatal neurodegenerative disorder associated with polyglutamine (polyQ) expansion in the huntingtin (Htt) protein. In this study, we show that mutant Htt alters the normal expression of specific mRNA species at least partly by disrupting the binding activities of many transcription factors which govern the expression of the dysregulated mRNA species. Chromatin immunoprecipitation (ChIP) demonstrates Htt occupation of gene promoters in vivo in a polyQ-dependent manner, and furthermore, ChIP-on-chip and ChIP subcloning reveal that wild-type and mutant Htt exhibit differential genomic distributions. Exon 1 Htt binds DNA directly in the absence of other proteins and alters DNA conformation. PolyQ expansion increases Htt-DNA interactions, with binding to recognition elements of transcription factors whose function is altered in HD. Together, these findings suggest mutant Htt modulates gene expression through abnormal interactions with genomic DNA, altering DNA conformation and transcription factor binding.
Improved Secretory Production of Recombinant Proteins by Random Mutagenesis of hlyB , an Alpha-Hemolysin Transporter from Escherichia coli (2005)

Fusion proteins with an alpha-hemolysin (HlyA) C-terminal signal sequence are known to be secreted by the HlyB-HlyD-TolC translocator in Escherichia coli. We aimed to establish an efficient Hly secretory expression system by random mutagenesis of hlyB and hlyD. The fusion protein of subtilisin E and the HlyA signal sequence (HlyA(218)) was used as a marker protein for evaluating secretion efficiency. Through screening of more than 1.5 x 10(4) E. coli JM109 transformants, whose hlyB and hlyD genes had been mutagenized by error-prone PCR, we succeeded in isolating two mutants that had 27- and 15-fold-higher levels of subtilisin E secretion activity than the wild type did at 23 degrees C. These mutants also exhibited increased activity levels for secretion of a single-chain antibody-HlyA(218) fusion protein at 23 and 30 degrees C but unexpectedly not at 37 degrees C, suggesting that this improvement seems to be dependent on low temperature. One mutant (AE104) was found to have seven point mutations in both HlyB and HlyD, and an L448F substitution in HlyB was responsible for the improved secretion activity. Another mutant (AE129) underwent a single amino acid substitution (G654S) in HlyB. Secretion of c-Myc-HlyA(218) was detected only in the L448F mutant (AE104F) at 23 degrees C, whereas no secretion was observed in the wild type at any temperature. Furthermore, for the PTEN-HlyA(218) fusion protein, AE104F showed a 10-fold-higher level of secretion activity than the wild type did at 37 degrees C. This result indicates that the improved secretion activity of AE104F is not always dependent on low temperature.
Isolation and characterization of the cDNA for murine granulocyte colony-stimulating factor. (1986)

A cDNA sequence coding for murine granulocyte colony-stimulating factor (G-CSF) has been isolated from a cDNA library prepared with mRNA derived from murine fibrosarcoma NFSA cells, which produce G-CSF constitutively. Identification of murine G-CSF cDNA was based on the cross-hybridization with human G-CSF cDNA under a low-stringency condition. The cDNA can encode a polypeptide consisting of a 30-amino acid signal sequence, followed by a mature G-CSF sequence of 178 amino acids with a calculated Mr of 19,061. The nucleotide sequence and the deduced amino acid sequence of murine G-CSF cDNA were 69.3% and 72.6% homologous, respectively, to the corresponding sequences of human G-CSF cDNA. The murine G-CSF cDNA, when introduced into monkey COS cells under the simian virus 40 promoter, could direct the synthesis of a protein that can stimulate the granulocyte colony formation from mouse bone marrow cells and support the proliferation of murine NFS-60 myeloid leukemia cells.
Advanced Glycation End Product (AGE)–Mediated Induction of Tissue Factor in Cultured Endothelial Cells Is Dependent on RAGE (1997)

Activation of ECs and induction of tissue factor by AGE albumin in ECs is dependent on RAGE.
Mechanics of finger-tip electronics (2013)

Tactile sensors and electrotactile stimulators can provide important links between humans and virtual environments, through the sensation of touch. Soft materials, such as low modulus silicones, are attractive as platforms and support matrices for arrays sensors and actuators that laminate directly onto the fingertips. Analytic models for the mechanics of three dimensional, form-fitting finger cuffs based on such designs are presented here, along with quantitative validation using the finite element method. The results indicate that the maximum strains in the silicone and the embedded devices are inversely proportional to the square root of radius of curvature of the cuff. These and other findings can be useful in formulating designs for these and related classes of body-worn, three dimensional devices.
A surface component on GH3 pituitary cells that recognizes transforming growth factor-beta, activin, and inhibin. (1988)

We have examined the ability of various forms of activin and inhibin, which are structurally related to transforming growth factor-beta (TGF-beta), to interact with various types of cell surface TGF-beta binding sites. Activin AB, inhibin A, and inhibin B were unable to compete with 125I-TGF-beta 1 for binding to the TGF-beta receptor types I, II, or III that coexist in human skin fibroblasts, rat liver epithelial cells, and mink lung epithelial cells. In contrast, activins and inhibins effectively competed for TGF-beta 1 binding to GH3 rat pituitary tumor cells. Binding of TGF-beta 1 to GH3 cells was mediated by about 2700 sites/cell with a Kd = 90 pM. Affinity labeling of these GH3 binding sites by cross-linking to 125I-TGF-beta 1 yielded 70-74-kDa labeled complexes distinct from previously identified TGF-beta binding components. Labeling of these 70-74-kDa components with 125I-TGF-beta 1 was inhibited by TGF-beta 1, TGF-beta 2, activin AB, and inhibin B at concentrations in the high picomolar to low nanomolar range, but it was not significantly affected by other polypeptide hormones and growth factors tested. The 70-74-kDa labeled GH3 components represent a novel type of cell surface TGF-beta binding protein that is unique in its ability to recognize various other members of the TGF-beta family of bioactive polypeptides.
Molecular Interactions between the Specialist HerbivoreManduca sexta (Lepidoptera, Sphingidae) and Its Natural Host Nicotiana attenuata. II. Accumulation of Plant mRNAs in Response to Insect-Derived Cues (2001)

The transcriptional changes in Nicotiana attenuata Torr. ex Wats. elicited by attack from Manduca sexta larvae were previously characterized by mRNA differential display (D. Hermsmeier, U. Schittko, I.T. Baldwin [2001] Plant Physiol 125: 683-700). Because herbivore attack causes wounding, we disentangled wound-induced changes from those elicited by M. sexta oral secretions and regurgitant (R) with a northern analysis of a subset of the differentially expressed transcripts encoding threonine deaminase, pathogen-induced oxygenase, a photosystem II light-harvesting protein, a retrotransposon homolog, and three unknown genes. R extensively modified wound-induced responses by suppressing wound-induced transcripts (type I) or amplifying the wound-induced response (type II) further down-regulating wound-suppressed transcripts (type IIa) or up-regulating wound-induced transcripts (type IIb). It is interesting that although all seven genes displayed their R-specific patterns in the treated tissues largely independently of the leaf or plant developmental stage, only the type I genes displayed strong systemic induction. Ethylene was not responsible for any of the specific patterns of expression. R collected from different tobacco feeding insects, M. sexta, Manduca quinquemaculata, and Heliothis virescens, as well as from different instars of M. sexta were equally active. The active components of M. sexta R were heat stable and active in minute amounts, comparable with real transfer rates during larval feeding. Specific expression patterns may indicate that the plant is adjusting its wound response to efficiently fend off M. sexta, but may also be advantageous to the larvae, especially when R suppress wound-induced plant responses.
Heparan Sulfate Proteoglycans Modulate Monocyte Migration across Cerebral Endothelium (2003)

Heparan sulfate proteoglycans (HSPGs) are known to participate in a wide range of biological events, including cellular trafficking. In this study we report that in situ cerebral blood vessels highly express HSPGs. Of the syndecan family, syndecan-2 is highly expressed on virtually all brain vessels and syndecan-1 and -3 are only present on larger blood vessels. These endothelial HSPGs have a functional role in monocyte diapedesis across brain endothelium, as assessed in our in vitro adhesion and migration assays. Our data indicate that heparin prevents monocyte adhesion to brain endothelium by interacting solely with the monocyte. Transendothelial migration of monocytes can be prevented by preincubation of brain endothelium with heparin by enzymatic removal of heparan sulphate side chains or by inhibition of cellular sulfation. Blocking of G-protein-dependent signaling in the monocytes prevented monocyte adhesion and migration to similar extent, suggesting that G-dependent signaling may be involved in HSPG-mediated monocyte adhesion and transendothelial migration. Our data demonstrate that brain endothelial HSPGs have a modulatory role in the transendothelial migration of monocytes in a direct and indirect fashion and may therefore contribute to the formation of neuroinflammatory lesions.
Stereotactic Delivery of a Recombinant Adenovirus into a C6 Glioma Cell Line in a Rat Brain Tumor Model (1994)

The dismal results of conventional therapy for primary malignant brain tumors has justified exploring gene therapy approaches for this disease. Transduction of animal brain tumor models in vivo has been reported previously with retroviruses and herpes viruses. Because adenoviruses have the advantage of transducing quiescent and actively dividing tumor cells, they may prove to be more effective in such therapy. We used a replication-deficient recombinant adenovirus bearing the Escherichia coli beta-galactosidase gene in a rat C6 glioma tumor model. Transduced cells were detected by X-5-bromo-4-chloro-3-indolyl beta-D-galactoside staining to reveal beta-galactosidase activity. Initial experiments in vitro showed 50% and 90% transduction at vector titers of approximately 10(7) and 10(8) plaque-forming units/ml, respectively. Although no cytopathic effects were seen at 10(7) plaque-forming units/ml, more than 50% reduction in tumor cell growth was noted at 10(8) plaque-forming units/ml both in vitro and in vivo. Stereotactic delivery of the recombinant adenovirus into the frontal lobe of normal rat brains resulted in intense staining of all cell types, that is, neurons, astrocytes, and ependymal cells. Stereotactic injection into C6 glioma brain tumors in rats stained 25 to 30% of the tumor cells. We conclude that adenovirus vectors can be used to transfer genes to central nervous system tumors in vivo. Using stereotactic delivery, adenovirus vectors can transfer genes into the central nervous system intended for tumor therapy.
Role of Kupffer cells in pathogenesis of sepsis‐induced drug metabolizing dysfunction (2011)

The present study aimed to determine the role of Kupffer cells (KCs) in cytochrome P450 (CYP) isozyme activity and the expression of its gene during polymicrobial sepsis. For ablation of KCs, rats were pretreated with gadolinium chloride (GdCl(3)) at 48 and 24 h before cecal ligation and puncture (CLP). The depletion of KCs was confirmed by measuring the mRNA level of the KC marker gene CD163. Serum aminotransferase levels and lipid peroxidation showed an increase and hepatic glutathione content showed a decrease at 24 h after CLP. These changes were prevented by GdCl(3) pretreatment. Catalytic activities of CYP1A1, 1A2 and 2E1 showed a significant reduction at 24 h after CLP but were prevented by GdCl(3). A reduction in the levels of CYP2E1 protein and CYP2B1 and CYP2E1 mRNA expression was prevented by GdCl(3). Phosphorylation of CYP1A1/1A2 markedly increased 24 h after CLP, which was prevented by GdCl(3). The increased serum level of high mobility group box 1, hepatic level of Toll-like receptors 2 and 4, and inducible nitric oxide synthase protein expression were prevented by GdCl(3). In addition, elevated serum concentrations of tumor necrosis factor-α and interleukin-6, and increased hepatic mRNA levels of tumor necrosis factor-α and interleukin-6 were decreased by depletion of KCs. Our findings suggest that ablation of KCs protects against hepatic drug-metabolizing dysfunction by modulation of the inflammatory response.
Composite Model Checking: Verification with Type-Specific Symbolic Representations (1999)

In recent years, there has been a surge of progress in automated verification methods based on state exploration. In areas like hardware design, these technologies are rapidly augmenting key phases of testing and validation. To date, one of the most successful of these methods has been symbolic model checking, in which large finite-state machines are encoded into compact data structures such as binary decision diagrams (BDDs) -- and are then checked for safety and liveness properties. However, these techniques have not realized the same success on software systems. One limitation is their inability to deal with infinite-state programs -- even those with a single unbounded integer. A second problem is that of finding efficient representations for various variable types. We recently proposed a model checker for integer-based systems that uses arithmetic constraints as the underlying state representation. While this approach easily verified some subtle, infinite-state concurrency problems...
Differentiation of myeloid dendritic cells into CD8α-positive dendritic cells in vivo (2000)

Bone marrow-derived dendritic cells (DC) represent a family of antigen-presenting cells (APC) with varying phenotypes. For example, in mice, CD8α+ and CD8α− DC are thought to represent cells of lymphoid and myeloid origin, respectively. Langerhans cells (LC) of the epidermis are typical myeloid DC; they do not express CD8α, but they do express high levels of myeloid antigens such as CD11b and FcγR. By contrast, thymic DC, which derive from a lymphoid-related progenitor, express CD8α but only low levels of myeloid antigens. CD8α+ DC are also found in the spleen and lymph nodes (LN), but the origin of these cells has not been determined. By activating and labeling CD8α− epidermal LC in vivo, it was found that these cells expressed CD8α on migration to the draining LN. Similarly, CD8α− LC generated in vitro from a CD8 wild-type mouse and injected into the skin of a CD8αKO mouse expressed CD8α when they reached the draining LN. The results also show that CD8α+ LC are potent APC. After migration from skin, they localized in the T-cell areas of LN, secreted high levels of interleukin-12, interferon-γ, and chemokine-attracting T cells, and they induced antigen-specific T-cell activation. These results demonstrate that myeloid DC in the periphery can express CD8α when they migrate to the draining LN. CD8α expression on these DC appears to reflect a state of activation, mobilization, or both, rather than lineage.
The Development of a Rapid Prototyping Prosthetic Socket Coated with a Resin Layer for Transtibial Amputees (2010)

This article proposes a type of transtibial socket composed of an inner layer fabricated by a rapid prototyping (RP) machine and an outer layer coated with unsaturated polyester resin. This work integrates contemporary technologies including a handheld scanner and CAD systems, to design a thin primary socket shape and then manufactures the socket using a fused deposition-modeling machine. To prevent breakage caused by the layer-based forming process and to reinforce flexural strength, the current research coats the preliminary RP socket with a layer of unsaturated polyester resin. After shaping the proximal brim of the resin-reinforced RP socket to match the specific stump, this study assembles and aligns a shank and a prosthetic foot to form a prosthesis set. After completing a trial safety walk wearing the prosthesis, which is satisfactory to the amputee and a registered prosthetist, this research measures interface pressures between the stump and the resin-reinforced RP socket. Experiment results demonstrate that the resin-reinforced RP socket is applicable for transtibial amputees. In addition to strengthening the FDM socket and producing consistent socket fit, this study also demonstrates a feasible procedure that employs current technologies to design and manufacture transtibial sockets without plaster moulds.
High-frequency deletional rearrangement of immunoglobulin kappa gene segments introduced into a pre-B-cell line. (1987)

We describe an immunoglobulin gene recombination indicator in which a specific rearrangement via deletion results in the acquisition of a dominant phenotype. The indicator consists of the Escherichia coli xanthine/guanine phosphoribosyltransferase (gpt) gene, whose translation is prevented by the presence of an upstream initiation codon out of frame with respect to the gpt coding sequence. Flanking this barrier initiation codon are the heptamer-spacer-nonamer recognition sequences from a kappa chain variable region (V kappa) and from a kappa chain joining region (J kappa). A proper V-J joint results in the deletion of the translational barrier and allows expression of the selectable marker. When tested by transfection into fibroblasts, no rearrangements were detected and the presence of the barrier initiation codon was sufficient to completely abolish gpt expression in these cells. Similarly, no rearrangements were detected after transfer of the test gene into myeloma cells. However, when the construct was introduced into the pre-B-cell line 38B9, greater than 80% of the transfected cells showed evidence of a specific rearrangement. These rearrangements were associated with the translation of gpt, although no selection for its expression was needed. DNA sequence analysis of six different V-J joints revealed that the rearrangement proceeded with a high degree of accuracy. These results indicate that only very minimal DNA sequences (21 base pairs 5' of the V heptamer and 4 base pairs 3' of its nonamer; less than 45 base pairs 5' of the J nonamer and 3' of its heptamer) are required for efficient rearrangement and provide formal proof that kappa gene segments can rearrange by a deletional mechanism.
Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA (2012)

<i>Wolbachia</i> endosymbionts are widespread in arthropods and are generally considered reproductive parasites, inducing various phenotypes including cytoplasmic incompatibility, parthenogenesis, feminization and male killing, which serve to promote their spread through populations. In contrast, <i>Wolbachia</i> infecting filarial nematodes that cause human diseases, including elephantiasis and river blindness, are obligate mutualists. DNA purification methods for efficient genomic sequencing of these unculturable bacteria have proven difficult using a variety of techniques. To efficiently capture endosymbiont DNA for studies that examine the biology of symbiosis, we devised a parallel strategy to an earlier array-based method by creating a set of SureSelect™ (Agilent) 120-mer target enrichment RNA oligonucleotides ("baits") for solution hybrid selection. These were designed from <i>Wolbachia</i> complete and partial genome sequences in GenBank and were tiled across each genomic sequence with 60 bp overlap. Baits were filtered for homology against host genomes containing <i>Wolbachia</i> using BLAT and sequences with significant host homology were removed from the bait pool. Filarial parasite <i>Brugia malayi</i> DNA was used as a test case, as the complete sequence of both <i>Wolbachia</i> and its host are known. DNA eluted from capture was size selected and sequencing samples were prepared using the NEBNext® Sample Preparation Kit. One-third of a 50 nt paired-end sequencing lane on the HiSeq™ 2000 (Illumina) yielded 53 million reads and the entirety of the <i>Wolbachia</i> genome was captured. We then used the baits to isolate more than 97.1 % of the genome of a distantly related <i>Wolbachia</i> strain from the crustacean <i>Armadillidium vulgare</i>, demonstrating that the method can be used to enrich target DNA from unculturable microbes over large evolutionary distances.
Independent component analysis of fMRI data in the complex domain (2002)

In BOLD fMRI a series of MR images is acquired and examined for task-related amplitude changes. These functional changes are small, so it is important to maximize detection efficiency. Virtually all fMRI processing strategies utilize magnitude information and ignore the phase, resulting in an unnecessary loss of efficiency. As the optimum way to model the phase information is not clear, a flexible modeling technique is useful. To analyze complex data sets, independent component analysis (ICA), a data-driven approach, is proposed. In ICA, the data are modeled as spatially independent components multiplied by their respective time-courses. There are thus three possible approaches: 1) the time-courses can be complex-valued, 2) the images can be complex-valued, or 3) both the time-courses and the images can be complex-valued. These analytic approaches are applied to data from a visual stimulation paradigm, and results from three complex analysis models are presented and compared with magnitude-only results. Using the criterion of the number of contiguous activated voxels at a given threshold, an average of 12-23% more voxels are detected by complex-valued ICA estimation at a threshold of /Z/ > 2.5. Additionally, preliminary results from the complex models reveal a phase modulation similar to the magnitude time-course in some voxels, and oppositely modulated in other voxels.