gebhart/patrepeval huggingface dataset:
Mechanism of Silation of Silica with Hexamethyldisilazane (2000)

The silation of silica with hexamethyldisilazane (HMDS) was examined over the temperature range 150−450 °C. The products and sequence of the reactions at the silica surface were determined. The major products are hexamethyldisiloxane (HMDSO) and ammonia, with lesser amounts of nitrogen and methane. No methane is produced during reactions below 300 °C. Ammonia is the initial product detected, followed by HMDSO. The amount of nitrogen produced increases, and the amount of ammonia and HMDSO produced decreases, with increasing temperature of reaction. A mechanism is proposed. The reaction of HMDS with silica is sequential. Reaction of pendant silyl groups with surface acidic hydroxyls to eliminate methane and the concentration of residual silyl moieties on the silica surface both increase with temperature of reaction.
A biomimetic multicellular model of the airways using primary human cells (2014)

Microfluidic cell cultures enable investigation of complex physiological tissue properties and functionalities. For convenience, they are often implemented with immortalized cell lines, but primary cells more closely approximate the in vivo biology. Our aim was to develop a biomimetic microfluidic model of the human airway using all primary cells. The model is comprised of airway epithelial cells cultured at an air-liquid interface, lung fibroblasts and polarized microvascular endothelial cells, respectively positioned in three vertically stacked, individually accessible compartments separated by nanoporous membranes. We report device fabrication, a gravity fed microfluidic system, and culture medium able to support functional co-cultures of all three primary human cell types. As characterized by imaging and permeability measurements, airway epithelial cells in microfluidic devices displayed mucociliary differentiation and barrier function. Subjacent fibroblasts and microvascular endothelial cells were added under conditions enabling co-culture for at least 5 days. Microfluidic airway models based on primary human cells in a relevant biomimetic configuration will improve physiological relevance and will enable novel disease modeling and drug development studies.
Semiconductor Integrated Circuit Technology and Micromachining (1989)

This chapter contains sections titled: Introduction I. C. Technology Micromachining Conclusion References
The Glycine-Alanine Dipeptide Repeat from C9orf72 Hexanucleotide Expansions Forms Toxic Amyloids Possessing Cell-to-Cell Transmission Properties (2016)

Hexanucleotide expansions, GGGGCC, in the non-coding regions of the C9orf72 gene were found in major frontotemporal lobar dementia and amyotrophic lateral sclerosis patients (C9FTD/ALS). In addition to possible RNA toxicity, several dipeptide repeats (DPRs) are translated through repeat-associated non-ATG-initiated translation. The DPRs, including poly(GA), poly(GR), poly(GP), poly(PR), and poly(PA), were found in the brains and spinal cords of C9FTD/ALS patients. Among the DPRs, poly(GA) is highly susceptible to form cytoplasmic inclusions, which is a characteristic of C9FTD/ALS. To elucidate DPR aggregation, we used synthetic (GA)15 DPR as a model system to examine the aggregation and structural properties in vitro. We found that (GA)15 with 15 repeats fibrillates rapidly and ultimately forms flat, ribbon-type fibrils evidenced by transmission electron microscopy and atomic force microscopy. The fibrils are capable of amyloid dye binding and contain a characteristic cross-β sheet structure, as revealed by x-ray scattering. Furthermore, using neuroblastoma cells, we demonstrated the neurotoxicity and cell-to-cell transmission property of (GA)15 DPR. Overall, our results show the structural and toxicity properties of GA DPR to facilitate future DPR-related therapeutic development.
Zinc fingers (1995)

The term zinc finger was first used to describe a 30‐residue, repeated sequence motif found in an unusually abundant Xenopus transcription factor. It was proposed that each motif is folded around a central zinc ion to form an independent minidomain and that adjacent zinc fingers are combined as modules to make up a DNA‐binding domain with the modules “gripping” the DNA (hence the term finger). We now know that these proposals were correct and that these DNA‐binding motifs are found in many eukaryotic DNA‐binding proteins. More recently, crystal structures of three different complexes between zinc finger domains and their target DNA binding sites have revealed a remarkably simple mode of interaction with DNA. The simplicity of the zinc finger structure, and of its interaction with DNA, is a very striking feature of this protein domain. After the discovery of the zinc finger motif, patterns of potential zinc ligands have been found in several other proteins, some of which also bind to DNA. Structural studies of these domains have revealed how zinc can stabilize quite diverse protein architectures. In total, 10 such small zinc‐binding domains have been studied structurally. These form a diverse collection, but each in turn has been termed a zinc finger motif—although clearly what they have in common is only their zinc‐binding property, which stabilizes an apparently autonomously folded unit.—Klug, A., Schwabe, J. W. R. Zinc fingers. FASEB J. 9, 597‐604 (1995)
An Efficient High-Throughput Screening Method for MYST Family Acetyltransferases, a New Class of Epigenetic Drug Targets (2011)

Epigenetic aberrations are increasingly regarded as key factors in cancer progression. Recently, deregulation of histone acetyltransferases (HATs) has been linked to several types of cancer. Monocytic leukemia zinc finger protein (MOZ) is a member of the MYST family of HATs, which regulate gene expression in cell proliferation and differentiation. Deregulation of these processes through constitutively active MOZ fusion proteins gives rise to the formation of leukemic stem cells, rendering MOZ an excellent target for treating myeloid leukemia. The authors implemented a hit discovery campaign to identify small-molecule inhibitors of MOZ-HAT activity. They developed a robust, homogeneous assay measuring the acetylation of synthetic histone peptides. In a primary screening campaign testing 243 000 lead-like compounds, they identified inhibitors from several chemical classes. Secondary assays were used to eliminate assay-interfering compounds and prioritize confirmed hits. This study establishes a new high-throughput assay for HAT activity and could provide the foundation for the development of a new class of drugs for the treatment of leukemias.
Purification and Properties of the Phosphotriesterase from Pseudomonas diminuta (1989)

The phosphotriesterase produced from the opd cistron of Pseudomonas diminuta was purified 1500-fold to homogeneity using a combination of gel filtration, ion exchange, hydrophobic, and dye matrix chromatographic steps. This is the first organophosphate triesterase or organophosphofluoridate hydrolyzing enzyme to be purified to homogeneity. The enzyme is a monomeric, spherical protein having a molecular weight of 39,000. A single zinc atom is bound to the enzyme and is required for catalytic activity. Incubation with metal chelating compounds, o-phenanthroline, EDTA, or 2,6-pyridine dicarboxylate inactivate the enzyme. The kinetic rate constants, kcat and kcat/Km, for the hydrolysis of paraoxon are 2100 s-1 and 4 x 10(7) M-1 s-1, respectively. The enzyme is inhibited competitively by dithiothreitol, dithioerithritol, and beta-mercaptoethanol. In addition to paraoxon the phosphotriesterase was found to hydrolyze the commonly used organophosphorus insecticides, dursban, parathion, coumaphos, diazinon, fensulfothion, methyl parathion, and cyanophos.
An endothelial growth factor involved in rat renal development. (1998)

In the kidney, there is a close and intricate association between epithelial and endothelial cells, suggesting that a complex reciprocal interaction may exist between these two cell types during renal ontogeny. Thus, we examined whether metanephrogenic mesenchymal cells secrete endothelial mitogens. With an endothelial mitogenic assay and sequential chromatography of the proteins in the media conditioned by a cell line of rat metanephrogenic mesenchymal cells (7.1.1 cells), we isolated a protein whose amino acid analysis identified it as hepatoma-derived growth factor (HDGF). Media conditioned with Cos-7 cell transfected with HDGF cDNA stimulated endothelial DNA synthesis. With immunoaffinity purified antipeptide antibodies, we found that HDGF was widely distributed in the renal anlage at early stages of development but soon concentrated at sites of active morphogenesis and, except for some renal tubules, disappeared from the adult kidney. From a 7.1.1 cells cDNA library, a clone of most of the translatable region of HDGF was obtained and used to synthesize digoxigenin-labeled riboprobes. In situ hybridization showed that during kidney development mRNA for HDGF was most abundant at sites of nephron morphogenesis and in ureteric bud cells while in the adult kidney transcripts disappeared except for a small population of distal tubules. Thus, HDGF is an endothelial mitogen that is present in embryonic kidney, and its expression is synchronous with nephrogenesis.
Iron Loading and Overloading due to Ineffective Erythropoiesis (2010)

Erythropoiesis describes the hematopoietic process of cell proliferation and differentiation that results in the production of mature circulating erythrocytes. Adult humans produce 200 billion erythrocytes daily, and approximately 1 billion iron molecules are incorporated into the hemoglobin contained within each erythrocyte. Thus, iron usage for the hemoglobin production is a primary regulator of plasma iron supply and demand. In many anemias, additional sources of iron from diet and tissue stores are needed to meet the erythroid demand. Among a subset of anemias that arise from ineffective erythropoiesis, iron absorption and accumulation in the tissues increases to levels that are in excess of erythropoiesis demand even in the absence of transfusion. The mechanisms responsible for iron overloading due to ineffective erythropoiesis are not fully understood. Based upon data that is currently available, it is proposed in this review that loading and overloading of iron can be regulated by distinct or combined mechanisms associated with erythropoiesis. The concept of erythroid regulation of iron is broadened to include both physiological and pathological hepcidin suppression in cases of ineffective erythropoiesis.
Arkansas Cotton Variety Test 2004 (2005)

The primary goal of the Arkansas Cotton Variety Test is to provide unbiased data regarding the agronomic performance of cotton varieties and advanced breeding lines in the major cotton-growing areas of Arkansas. This information helps seed companies establish marketing strategies and assists producers in choosing varieties to plant. These annual evaluations will then facilitate the inclusion of new, improved genetic material in Arkansas cotton production. Adaptation of varieties is determined by evaluating the lines at five University of Arkansas System Division of Agriculture research sites (Manila, Keiser, Judd Hill, Marianna, and Rohwer). Entries in the 2019 Arkansas Cotton Variety Test were evaluated in two groups—transgenic and conventional varieties. The 50 entries in the transgenic test included 9 B2XF, 25 B3XF, 13 W3FE, and 3 GLTP lines which were evaluated at all five locations. The conventional test included 15 entries which were evaluated at all locations except Manila. Reported data include lint yield, lint percentage, plant height, percent open bolls, yield component variables, fiber properties, leaf pubescence, stem pubescence, and bract trichome density. All entries in the experiments were evaluated for response to tarnished plant bug and bacterial blight in separate tests at Keiser. This 2019 report includes results of large-plot variety tests in 10 counties that were coordinated by Bill Robertson.
A Carbene-Stabilized Gold(I) Fluoride:  Synthesis and Theory (2005)

The first isolable gold(I) fluoride complex, stabilized by an N-heterocyclic carbene (NHC) ligand, has been isolated in two-coordinate monomeric form. DFT calculations show significant pπ/dπ interactions between fluoride and gold(I) and indicate a substantial negative charge on fluorine.
Role of sphingolipid-mediated cell death in neurodegenerative diseases (1998)

The metazoan nervous system gives rise intradevelopmentally to many more neurons than ultimately survive in the adult. Such excess cells are eliminated through programmed cell death or apoptosis. As is true for cells of other lineages, neuronal survival is sustained by an array of growth factors, such that withdrawal of neurotrophic support results in apoptotic cell death. Apoptosis is therefore believed to represent a beneficial process essential to normal development of central and peripheral nervous system (CNS and PNS) structures. Although the initiation of neuronal apoptosis in response to numerous extracellular agents has been widely reported, the regulatory mechanisms underlying this mode of cell death remain incompletely understood. In recent years, the contribution of lipid-dependent signaling systems, such as the sphingomyelin pathway, to regulation of cell survival has received considerable attention, leading to the identification of lethal functions for the lipid effectors ceramide and sphingosine in both normal and pathophysiological conditions. Moreover, the apoptotic capacities of several cytotoxic receptor systems (e.g., CD120a, CD95) and many environmental stresses (e.g., ionizing radiation, heat-shock, oxidative stress) are now known to derive from the activation of multiple signaling cascades by ceramide or, under some circumstances, by sphingosine. Inappropriate initiation of apoptosis has been proposed to underlie the progressive neuronal attrition associated with various neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and other neurological disorders that are characterized by the gradual loss of specific populations of neurons. In such pathophysiological states, neuronal cell death can result in specific disorders of movement and diverse impairments of CNS and PNS function. In some autoimmune neurological diseases such as Guillain-Barré syndrome, demyelinating polyneuropathy, and motoneuron disease, persistent immunological attack of microvascular endothelial cells by glycolipid-directed autoantibodies may lead to extensive cellular damages, resulting in increased permeability across brain-nerve barrier (BNB) and/or blood-brain barrier (BBB).
Frequent occurrence of deletions and duplications during somatic hypermutation: Implications for oncogene translocations and heavy chain disease (1998)

Human naive and germinal center (GC) B cells were sorted by flow cytometry and rearranged VH region genes were amplified and sequenced from single cells. Whereas no deletions or insertions were found in naive B cells, approximately 4% of in-frame and >40% of out-of-frame rearrangements of GC B cells harbored deletions and/or insertions of variable length. The pattern of deletions/insertions and their restriction to mutated V genes strongly suggests that they result from somatic hypermutation. Deletions and insertions account for approximately 6% of somatic mutations introduced into rearranged VH region genes of GC B cells. These deletions/insertions seem to be the main cause for the generation of heavy chain disease proteins. Furthermore, it appears that several types of oncogene translocations (like c-myc translocations in Burkitt's lymphoma) occur as a byproduct of somatic hypermutation within the GC-and not during V(D)J recombination in the bone marrow as previously thought.
Use of Negative Capacitance to Provide Voltage Amplification for Low Power Nanoscale Devices (2007)

It is well-known that conventional field effect transistors (FETs) require a change in the channel potential of at least 60 mV at 300 K to effect a change in the current by a factor of 10, and this minimum subthreshold slope S puts a fundamental lower limit on the operating voltage and hence the power dissipation in standard FET-based switches. Here, we suggest that by replacing the standard insulator with a ferroelectric insulator of the right thickness it should be possible to implement a step-up voltage transformer that will amplify the gate voltage thus leading to values of S lower than 60 mV/decade and enabling low voltage/low power operation. The voltage transformer action can be understood intuitively as the result of an effective negative capacitance provided by the ferroelectric capacitor that arises from an internal positive feedback that in principle could be obtained from other microscopic mechanisms as well. Unlike other proposals to reduce S, this involves no change in the basic physics of the FET and thus does not affect its current drive or impose other restrictions.
Mass Spectrometry-Based Label-Free Quantitative Proteomics (2009)

In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptide peak areas or peak heights. The second is based on the spectral counting of identified proteins. In this paper, we will discuss the technologies of these label-free quantitative methods, statistics, available computational software, and their applications in complex proteomics studies.
Phosphatidylinositol 3-kinase/Akt signaling in the response of vascular endothelium to ionizing radiation. (2002)

Growth factor enhancement of endothelial cell viability occurs through phosphatidylinositol 3-kinase (PI3K)/Akt-mediated inhibition of apoptosis. The PI3K/Akt signal transduction pathway was activated by both vascular endothelial growth factor and ionizing radiation. Radiation- and vascular endothelial growth factor-induced phosphorylation of Akt was inhibited by PI3K antagonists. To determine whether this signal transduction pathway represents a therapeutic target in tumor vascular endothelium, we examined the effects of the PI3K inhibitors wortmannin and LY294002 on irradiated endothelium. Wortmannin and LY294002 enhanced radiation-induced apoptosis and cytotoxicity in endothelial cells. Tumor vascular window and Doppler ultrasound showed that PI3K antagonists enhanced radiation-induced destruction of tumor blood vessels. Tumor growth delay was significantly increased after treatment with LY294002 followed by irradiation as compared with either agent alone. PI3K in tumor vascular endothelium is a potential therapeutic target to enhance the efficacy of ionizing radiation.
Chronic Obstructive Pulmonary Disease, inflammation and co-morbidity – a common inflammatory phenotype? (2006)

Chronic Obstructive Pulmonary Disease (COPD) is and will remain a major cause of morbidity and mortality worldwide. The severity of airflow obstruction is known to relate to overall health status and mortality. However, even allowing for common aetiological factors, a link has been identified between COPD and other systemic diseases such as cardiovascular disease, diabetes and osteoporosis. COPD is known to be an inflammatory condition and neutrophil elastase has long been considered a significant mediator of the disease. Pro-inflammatory cytokines, in particular TNF-alpha (Tumour Necrosis Factor alpha), may be the driving force behind the disease process. However, the roles of inflammation and these pro-inflammatory cytokines may extend beyond the lungs and play a part in the systemic effects of the disease and associated co-morbidities. This article describes the mechanisms involved and proposes a common inflammatory TNF-alpha phenotype that may, in part, account for the associations.
Production of monoclonal antibodies by genetic immunization. (1994)

Genetic immunization is a simple method for producing polyclonal antibodies in mice. To test if this approach could be used for monoclonal antibody production, biolistic transfection was used to immunize a mouse. High levels of polyclonal antibodies against human growth hormone (hGH) were elicited following three inoculations with the gene for hGH. When hybridoma cells were created from the mouse's splenocytes, approximately 17% secreted antibodies vs. hGH. Of these, some recognized only native or denatured hGH, while most recognized both forms of the protein. These findings demonstrate the utility of genetic immunization as a method to produce monoclonal antibodies.
Reduction of blocking artifacts in image and video coding (1999)

The discrete cosine transform (DCT) is the most popular transform for image and video compression. Many international standards such as JPEG, MPEG, and H.261 are based on a block-DCT scheme. High compression ratios are obtained by discarding information about DCT coefficients that is considered to be less important. The major drawback is visible discontinuities along block boundaries, commonly referred to as blocking artifacts. These often limit the maximum compression ratios that can be achieved. Various postprocessing techniques have been published that reduce these blocking effects, but most of them introduce unnecessary blurring, ringing, or other artifacts. In this paper, a novel postprocessing algorithm based on Markov random fields (MRFs) is proposed. It efficiently removes blocking effects while retaining the sharpness of the image and without introducing new artifacts. The degraded image is first segmented into regions, and then each region is enhanced separately to prevent blurring of dominant edges. A novel texture detector allows the segmentation of images containing both texture and monotone areas. It finds all texture regions in the image before the remaining monotone areas are segmented by an MRF segmentation algorithm that has a new edge component incorporated to detect dominant edges more reliably. The proposed enhancement stage then finds the maximum a posteriori estimate of the unknown original image, which is modeled by an MRF and is therefore Gibbs distributed. A very efficient implementation is presented. Experiments demonstrate that our proposed postprocessor gives excellent results compared to other approaches, from both a subjective and an objective viewpoint. Furthermore, it will be shown that our technique also works for wavelet encoded images, which typically contain ringing artifacts.
Semaphorins and their receptors in vertebrates and invertebrates (2000)

The semaphorins are a family of intercellular signaling proteins that has grown to include 19 identified members in higher vertebrates. Several of its members act as axonal guidance molecules. One participates in signaling in the immune system. The majority, however, do not yet have known biological functions. Recent studies have shown that neuropilins and plexins act as receptors for semaphorins. The most important challenge for the future is to define the biological roles of semaphorins in vivo.