gebhart/patrepeval huggingface dataset:
Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions (2006)

Riboswitches are structured RNAs typically located in the 5' untranslated regions of bacterial mRNAs that bind metabolites and control gene expression. Most riboswitches sense one metabolite and function as simple genetic switches. However, we found that the 5' region of the Bacillus clausii metE messenger RNA includes two riboswitches that respond to S-adenosylmethionine and coenzyme B12. This tandem arrangement yields a composite gene control system that functions as a two-input Boolean NOR logic gate. These findings and the discovery of additional tandem riboswitch architectures reveal how simple RNA elements can be assembled to make sophisticated genetic decisions without involving protein factors.
Zeolite ZSM-5 membranes grown on porous α-Al2O3 (1995)

ZSM-5 membranes with good permeation selectivity for n-butane–isobutane are grown hydrothermally from a clear solution on horizontally-held porous α-Al_2O_3 disks.
Fibrodysplasia Ossificans Progressiva in the Cat (1992)

Clinical, radiographic, electromyographic, and pathologic findings in a cat with fibrodysplasia ossificans progressiva are described. The features of five previously reported cases of this feline disorder are also presented. This disorder affects young adult to middle-aged cats of both sexes. Characteristic clinical features include progressive stiffness of gait, with enlargement of proximal limb musculature. Radiography reveals multiple mineralized densities within the affected musculature. The clinical course is rapid, with development of severe disability within 2 weeks to several months. Electromyographic and pathologic findings suggest that this is a disorder of connective tissue, affecting primarily the epimysium, tendons, and fasciae, and results in marked proliferation of fibrovascular connective tissue, with associated chondroid and osseous metaplasia.
The Blood-brain barrier : cellular and molecular biology (1993)

Part 1 Cell-cell interactions: brain microvessels and microvascular cells in vitro, John Laterra and Gary W. Goldstein brain endothelial-astrocyte interactions, P.A. Cancilla, et al antigen presentation at the cerebral microvasculature, Zsusanna Fabry and Michael N. Hart lymphocyte traffic to the brain, Hartmut Wekerle cell-cell adhesion molecules of the blood-brain barrier, Ronald L. Heimark. Part 2 Subcellular organelle function: tight junctions of brain endothelium and epithelium, M.W. Brightman and J.H. Tao-cheng microvascular pericytes in development and disease, Ira M. Herman morphological evidence of the functional polarization of brain microvascular endothelium, Andrzej W. Vorbrodt a cell biological perspective for the transcytosis of peptides and proteins through the mammalian blood-brain fluid barriers, Richard D. Broadwell and William A. Banks lysosomes of brain and other vascular endothelia, Kenneth L. Audus and Thomas J. Raub. Part 3 Signal transcution mechanisms: receptor-mediated transport of peptides and proteins across the blood-brain barrier, Phillip M. Friden brain microvascular vasoactive agents - receptors and mechanisms of action, Christian Frelin and Paul Vigne brain microvascular cyclic nucleotides and protein phosphorylation, Ferenc Joo phosphoinositide turnover in the brain microvasculature, Lester R. Drewes oxygen free radicals and the brain microvasculature, A. Lorris Betz. Part 4 Gene expression: subtraction cloning of genes selectively expressed at the blood-brain barrier, Hartmut Weiler-Guettler, et al gamma-glutamyl transpeptidase - molecular cloning and structural and functional features of a blood-brain barrier market protein, Andreas Frey molecular cloning of a blood-brain barrier cell surface glycoprotein, Harald Seulberger and Werner Risau molecular cloning and regulation of gene expression of glood-brain barrier glucose transporter, William M. Pardridge and Ruben J. Boado molecular cloning of choroid plexus-specific transport proteins, Gerhard Schreiber, et al.
Neuropsychological Prediction of Decline to Dementia in Nondemented Elderly (1999)

This study examined whether baseline neuropsychological performance in elderly assessed at a research clinic could accurately predict subsequent decline to dementia. Logistic regression analyses were applied to (1) 213 nondemented elderly with a Global Deterioration Scale (GDS) score of 1, 2, or 3, of whom 74 (35%) subsequently declined to any diagnosis of dementia, and (2) a diagnostically more restricted subset of this sample (N = 179), of whom 56 (31%) declined to a diagnosis of probable Alzheimer's disease (AD). The mean follow-up intervals were 3.8 and 3.7 years, respectively. A small set of baseline neuropsychological measures (especially a Paragraph Delayed Recall Test) significantly differentiated decliners from nondecliners to dementia or AD, after accounting for the contribution of age, sex, education, follow-up interval, and the rating of global clinical status. When examined in combination with the other factors or alone, the cognitive tests produced reasonably high specificities (91%-97%) and sensitivities (73%-89%). Using the obtained regression model, a similar level of classification accuracy was replicated on an independent sample of 119 nondemented elderly. A subanalysis of the high-risk GDS 3 subgroup indicated that cut scores from the paragraph test distinguished nondecliners from decliners (overall accuracies 87%-91%), implying that this assessment may accurately predict future cognitive status in elderly with mild cognitive impairment.
B Cells Induce Tolerance by Presenting Endogenous Peptide-IgG on MHC Class II Molecules via an IFN-γ-Inducible Lysosomal Thiol Reductase-Dependent Pathway (2008)

We have previously demonstrated that splenic B cells, transduced with peptide-IgG fusion proteins, are efficient tolerogenic APCs in vivo. Specific hyporesponsiveness to epitopes encoded in the peptide-IgG fusion protein has been achieved to over one dozen Ags, and clinical efficacy has been established in animal models for several autoimmune diseases and hemophilia. Previous studies also demonstrated that tolerance in this system requires MHC class II expression by the transduced B cells. Yet, the mechanisms of this B cell tolerogenic processing pathway remain unclear. In this study, we show that MHC class II molecules on tolerogenic B cells present epitopes derived from endogenous, but not exogenous (secreted), peptide-IgG fusion protein. These class II epitopes from the IgG fusion protein are processed in lysosomes/endosomes in an IFN-gamma-inducible lysosomal thiol reductase-dependent manner. We suggest that the MHC class II presentation of endogenously produced fusion protein epitopes represents a novel mechanism for tolerance induced by peptide-IgG-transduced B cells. An understanding of this process might provide insights into central and peripheral tolerance induced by other professional and nonprofessional APCs.
Identification of an amino acid that defines the fusogenicity of mumps virus (1993)

Recombinant cDNA clones representing the fusion (F) and hemagglutinin-neuraminidase (HN) proteins of two mumps virus strains different in fusogenicity were constructed. Upon transfection of COS7 cells, extensive cell fusion was observed only when cells expressed the F protein of the fusing strain together with the HN protein derived from either strain. Mutational analyses further showed that the amino acid at position 195 of the F protein plays a critical role in determining the extent of cell fusion induced by mumps virus, since replacement of Ser-195 by Tyr significantly reduced the fusion inducibility of otherwise fusion-competent F protein.
Spermatid-specific expression of protamine 1 in transgenic mice. (1987)

Protamines are abundant basic proteins involved in the condensation of sperm chromatin. In the mouse, protamine genes are transcribed postmeiotically in round spermatids. We have cloned and sequenced the mouse protamine 1 gene. Ten lines of transgenic mice harboring marked protamine 1 sequences were generated by microinjection of fertilized eggs. Transcription of the transgene is restricted to round spermatids and in several cases exceeds that of the endogenous gene. The cis-acting sequences required for tissue-specific protamine expression reside on a 2.4-kilobase restriction fragment. Prospects for using transgenic mice to address fundamental questions of male germ-cell development are discussed.
hsp82 Is an Essential Protein That Is Required in Higher Concentrations for Growth of Cells at Higher Temperatures (1989)

hsp82 is one of the most highly conserved and abundantly synthesized heat shock proteins of eucaryotic cells. The yeast Saccharomyces cerevisiae contains two closely related genes in the HSP82 gene family. HSC82 was expressed constitutively at a very high level and was moderately induced by high temperatures. HSP82 was expressed constitutively at a much lower level and was more strongly induced by heat. Site-directed disruption mutations were produced in both genes. Cells homozygous for both mutations did not grow at any temperature. Cells carrying other combinations of the HSP82 and HSC82 mutations grew well at 25 degrees C, but their ability to grow at higher temperatures varied with gene copy number. Thus, HSP82 and HSC82 constitute an essential gene family in yeast cells. Although the two proteins had different patterns of expression, they appeared to have equivalent functions; growth at higher temperatures required higher concentrations of either protein. Biochemical analysis of hsp82 from vertebrate cells suggests that the protein binds to a variety of other cellular proteins, keeping them inactive until they have reached their proper intracellular location or have received the proper activation signal. We speculate that the reason cells require higher concentrations of hsp82 or hsc82 for growth at higher temperatures is to maintain proper levels of complex formation with these other proteins.
State and Civil Society in Conflict (1997)

The awakening of civic institutions like an empowered parliament, an independent judiciary, a free press and public opinion forums, private thinktanks, human-rights groups, dynamic educational institutions, energetic research organisations and other non-governmental organisations providing institutional restraints on a growing elitist state have added to the forces of despondency in various cross-sections of the society. While the state authorities were involved in corruption and coercive activities or suffered from inertia, the public waited for a messiah to deliver them from oppression. With a diminished belief in the administrative set-up, polarisation between rich and poor increased and the demographically youthful society turned to guns and drugs on a horrendous scale. The interventionist role of the army and monopolisation of power by the bureaucracy made the civil institutions mere appendages of a state which suffered from a dual crisis in mandate and legitimacy. The way in which civil society was gradually beleaguered can be understood in terms of the administrative and economic priorities of the state as reflected in the annual budgetary allocations which have led to a weakening of institutional civic foundations.
Effect of von Willebrand factor coexpression on the synthesis and secretion of factor VIII in Chinese hamster ovary cells. (1989)

In plasma, antihemophilic factor (factor VIII) exists as a 200-kilodalton heavy-chain polypeptide in a metal ion association with an 80-kilodalton light-chain polypeptide. This complex is bound by hydrophobic and hydrophilic interactions to a large multimeric glycoprotein, von Willebrand factor (vWF). Accumulation of secreted human factor VIII activity expressed in Chinese hamster ovary cells requires the addition of serum in the growth medium, which provides vWF. Here we report that coexpression of vWF with factor VIII in Chinese hamster ovary cells resulted in increased stable accumulation of factor VIII activity in the absence of serum in the growth medium. In the coexpressing cells, the vWF cDNA transcription unit was transcribed to yield mRNA which was efficiently translated. vWF was properly processed and secreted to yield disulfide-bonded high-molecular-weight multimers similar to those observed in vWF secreted from human endothelial cells. Nuclear run-on assays showed that the factor VIII gene was transcribed at a level similar to that of the vWF gene, but the mRNA did not accumulate to high levels in the cytoplasm. In addition, although the translation efficiency of the factor VIII mRNA was similar to that of vWF, the processing and secretion of the factor VIII primary translation product was dramatically reduced compared with vWF. These results demonstrate that in Chinese hamster ovary cells both factor VIII mRNA accumulation and the processing and secretion of the primary factor VIII translation product are inefficient processes.
Reframing the Problem: New Institutionalism and Exclusionary Discipline in Schools (2013)

This Article in Response to Controversy is brought to you for free and open access by Western CEDAR. It has been accepted for inclusion in Journal of
Cancer Cell-Derived Clusterin Modulates the Phosphatidylinositol 3′-Kinase-Akt Pathway through Attenuation of Insulin-Like Growth Factor 1 during Serum Deprivation (2008)

Cancer cells in their respective microenvironments must endure various growth-constraining stresses. Under these conditions, the cancer cell-derived factors are thought to modulate the signaling pathways between cell growth and dormancy. Here, we describe a cancer cell-derived regulatory system that modulates the phosphatidylinositol 3'-kinase (PI3K)-Akt pathway under serum deprivation stress. Through the use of biochemical purification, we reveal that cancer cell-secreted insulin-like growth factor 1 (IGF-1) and clusterin, an extracellular stress protein, constitute this regulatory system. We show that secreted clusterin associates with IGF-1 and inhibits its binding to the IGF-1 receptor and hence negatively regulates the PI3K-Akt pathway during serum deprivation. This inhibitory function of clusterin appears to prefer IGF-1, as it fails to exert any effects on epidermal growth factor signaling. We demonstrate furthermore that the constitutive activation of oncogenic signaling downstream of IGF-1 confers insensitivity to the inhibitory effects of clusterin. Thus, the interplay between cancer cell-derived clusterin and IGF-1 may dictate the outcome of cell growth and dormancy during tumorigenic progression.
Hot-electron-induced degradation in high-voltage submicron DMOS transistors (2002)

The degradation induced by hot-electrons is investigated in small-size lateral and vertical DMOS transistors with voltage rating from 16 to 60 V integrable in a multi-power Bipolar-CMOS-DMOS mixed process with 1.2 /spl mu/m minimum lithography. Dedicated hot-electron tests are necessary to define the maximum operating drain and gate voltage of the devices. An empirical extrapolation model and a simplified scheme for accelerated qualification/reliability tests are proposed allowing one to define the hot-electron-limited safe operating area of DMOS transistors. A quasi-static extension of the model accounts for the hot-electron-induced degradation under a variety of dynamic bias-stress conditions.
B7-H3 Silencing Increases Paclitaxel Sensitivity by Abrogating Jak2/Stat3 Phosphorylation (2011)

In many types of cancer, the expression of the immunoregulatory protein B7-H3 has been associated with poor prognosis. Previously, we observed a link between B7-H3 and tumor cell migration and invasion, and in present study, we have investigated the role of B7-H3 in chemoresistance in breast cancer. We observed that silencing of B7-H3, via stable short hairpin RNA or transient short interfering RNA transfection, increased the sensitivity of multiple human breast cancer cell lines to paclitaxel as a result of enhanced drug-induced apoptosis. Overexpression of B7-H3 made the cancer cells more resistant to the drug. Next, we investigated the mechanisms behind B7-H3-mediated paclitaxel resistance and found that the level of Stat3 Tyr705 phosphorylation was decreased in B7-H3 knockdown cells along with the expression of its direct downstream targets Mcl-1 and survivin. The phosphorylation of Janus kinase 2 (Jak2), an upstream molecule of Stat3, was also significantly decreased. In contrast, reexpression of B7-H3 in B7-H3 knockdown and low B7-H3 expressing cells increased the phosphorylation of Jak2 and Stat3. In vivo animal experiments showed that B7-H3 knockdown tumors displayed a slower growth rate than the control xenografts. Importantly, paclitaxel treatment showed a strong antitumor activity in the mice with B7-H3 knockdown tumors, but only a marginal effect in the control group. Taken together, our data show that in breast cancer cells, B7-H3 induces paclitaxel resistance, at least partially by interfering with Jak2/Stat3 pathway. These results provide novel insight into the function of B7-H3 and encourage the design and testing of approaches targeting this protein and its partners.
[Effect of PCNA antisense oligooxynucleotides and VEGF antisense oligoxynucleotides on growth of hepatocellular carcinoma transplanted in nude mice]. (2001)

The growth of human hepatocellular carcinoma in nude mice can be inhibited by PCNA antisense oligonucleotides and VEGF antisense oligonucleotides respectively. Better inhibitory effect can be obtained if PCNA antisense oligonucleotides and VEGF antisense oligonucleotides are combined in use.
Enhancement of wound tissue expansion and angiogenesis by matrix-embedded fibroblast (dermagraft), a role of hepatocyte growth factor/scatter factor. (1998)

This study examined the effects of matrix-embedded human fibroblasts, a predominant cell type in the injured tissue, on the tissue expansion and angiogenesis. Using a co-culture technique, it was demonstrated that the presence of matrix-embedded fibroblasts (Dermagraft) significantly enhanced the expansion of human wound tissue in a 3D gel system over a period of 10 days. Using a rat aorta ring assay, fibroblasts also significantly stimulated the growth of new vessels from the ring and also enhanced the motility of human vascular endothelial cells. This effect of fibroblasts was neutralised with anti-HGF/SF antibody. HGF/SF protein was detected in both supernatant and cell lysate of the fibroblasts by bioassay and Western blotting, mRNA for HGF/SF was detected in the fibroblasts by RT-PCR. HGF/SF secreted by the fibroblast was able to stimulate the phosphorylation of cMET, HGF/SF receptor. It is thus concluded that matrix embedded fibroblasts are capable of stimulating wound healing and this effect is attributed to HGF/SF, produced by the cell.
Modular Petri net based modeling, analysis and synthesis of dedicated production systems (2004)

Ordinary t-timed Petri nets are used for modeling, analysis and synthesis of random topology production systems and networks. Each production system is first decomposed into production line (transfer chain), assembly, disassembly and parallel machines modules and then their corresponding modular Petri net models are derived. The overall system PN model is obtained via synthesis of the generic modules satisfying system constraints. P- and T-invariants are calculated and given a random topology production system, the total number of the system PN model nodes (places, transitions) is calculated from the corresponding generic PN modules. Results show the applicability of the proposed methodology.
Novel Method Using a Laser Scanning Cytometer for Detection of Mycobacteria in Clinical Samples (2004)

In order to evaluate the capacity of laser scanning cytometry (LSC) to detect acid-fast bacilli directly on clinical samples, a comparison between Kinyoun-stained smears analyzed under light microscopy and propidium iodide-auramine-stained smears analyzed by LSC was performed. The results were compared with those for culture on BACTEC MGIT 960. LSC is a new, reliable methodology to detect MYCOBACTERIA:
High speed full range complex spectral domain optical coherence tomography (2005)

We present a high speed full range spectral domain optical coherence tomography system. By inserting a phase modulator into the reference arm and recording of every other spectrum with a 90 degrees phase shift (introduced by the phase modulator) we are able to distinguish between negative and positive optical path differences with respect to the reference mirror. A modified two-frame algorithm eliminates the problem of suppressing symmetric structure terms in the final image. To demonstrate the performance of our method we present images of the anterior chamber of the human eye in vivo recorded with an A-scan rate of 10000 depth profiles per second.
A neural interface provides long-term stable natural touch perception (2014)

Touch perception on the fingers and hand is essential for fine motor control, contributes to our sense of self, allows for effective communication, and aids in our fundamental perception of the world. Despite increasingly sophisticated mechatronics, prosthetic devices still do not directly convey sensation back to their wearers. We show that implanted peripheral nerve interfaces in two human subjects with upper limb amputation provided stable, natural touch sensation in their hands for more than 1 year. Electrical stimulation using implanted peripheral nerve cuff electrodes that did not penetrate the nerve produced touch perceptions at many locations on the phantom hand with repeatable, stable responses in the two subjects for 16 and 24 months. Patterned stimulation intensity produced a sensation that the subjects described as natural and without "tingling," or paresthesia. Different patterns produced different types of sensory perception at the same location on the phantom hand. The two subjects reported tactile perceptions they described as natural tapping, constant pressure, light moving touch, and vibration. Changing average stimulation intensity controlled the size of the percept area; changing stimulation frequency controlled sensation strength. Artificial touch sensation improved the subjects' ability to control grasping strength of the prosthesis and enabled them to better manipulate delicate objects. Thus, electrical stimulation through peripheral nerve electrodes produced long-term sensory restoration after limb loss.
Simple fabrication method for vertical taper using tensile stress-induced mask and selective etching technique (2003)

A vertical taper structure has a lot of applications for optoelectronic integrated circuits (OEICs). In vertical taper structures, the thickness of the layer must be gradually changed along the device so that special techniques are required. We report on a simple fabrication method for a vertical taper using a tensile stress-induced mask and selective etching technique. We discovered that SiO/sub 2//Cr/Au with a tensile stress could be used for making the vertical taper. Also, the profile could be adjusted by controlling the etching process parameter. For its application, we are making a spot size converter for efficient coupling between a fiber and optical devices.