gebhart/patrepeval huggingface dataset:
Crystal Structure of an Active Form of BACE1, an Enzyme Responsible for Amyloid β Protein Production (2008)

BACE1 (beta-secretase) is a transmembrane aspartic protease that cleaves the beta-amyloid precursor protein and generates the amyloid beta peptide (Abeta). BACE1 cycles between the cell surface and the endosomal system many times and becomes activated interconvertibly during its cellular trafficking, leading to the production of Abeta. Here we report the crystal structure of the catalytically active form of BACE1. The active form has novel structural features involving the conformation of the flap and subsites that promote substrate binding. The functionally essential residues and water molecules are well defined and play a key role in the iterative activation of BACE1. We further describe the crystal structure of the dehydrated form of BACE1, showing that BACE1 activity is dependent on the dynamics of a catalytically required Asp-bound water molecule, which directly affects its catalytic properties. These findings provide insight into a novel regulation of BACE1 activity and elucidate how BACE1 modulates its activity during cellular trafficking.
A 900 bp genomic region from the mouse dystrophin promoter directs lacZ reporter expression only to the right heart of transgenic mice (1997)

In order to study the regulatory mechanism of developmental and tissue-specific expression of the muscle type dystrophin gene in mice, transgenic mice were generated carrying the 900 bp genomic fragment derived from the muscle type dystrophin promoter region fused to the bacterial lacZ gene. Six independent transgenic mouse lines showed specific reporter gene expression in the right heart, but not in skeletal or smooth muscle. The reporter gene expression was first detected in the presumptive right ventricle of the embryos at 8.5 days post coitum and the expression continued only in the right ventricle throughout the development and at the adult stage. The results indicate that the 900 bp genomic fragment contains the regulatory element required for expression of dystrophin only in the right heart, suggesting that distinct elements are responsible for the expression in the left and right compartments of the heart, and/or in skeletal and smooth muscle cells. Based on these findings, the relationship between defects in muscle type promoter and the diseases caused by abnormal dystrophin expression is discussed.
Tangible Holographic 3D Objects with Virtual Touch (2015)

This poster describes the design of a display and interaction device that allows a natural mid-air manipulation and feedback of floating, true 3D objects. This so called virtual touch will create a natural feeling of manipulating and touching of the virtual 3D object for the user. The 3D display system allows users to reach into the viewing volume to touch virtual objects, and even feel gradients of haptic feedback as the hands penetrate into virtual objects. True 3D objects are dynamically relit according to the real-world environment captured by cameras, which is reflected on shiny virtual surfaces to reach more realistic user experience. On the other hand, 3D virtual objects can cast real shadows on the real workspace. In case the virtual objects are defined as light-emitting, glows can also be projected onto the desk and the real objects. These techniques together form the basis of an ultra-realistic visualization and interaction system that will find its way into many technical and educational uses.
Human cingulate cortex and autonomic control: converging neuroimaging and clinical evidence (2003)

Human anterior cingulate function has been explained primarily within a cognitive framework. We used functional MRI experiments with simultaneous electrocardiography to examine regional brain activity associated with autonomic cardiovascular control during performance of cognitive and motor tasks. Using indices of heart rate variability, and high- and low-frequency power in the cardiac rhythm, we observed activity in the dorsal anterior cingulate cortex (ACC) related to sympathetic modulation of heart rate that was dissociable from cognitive and motor-related activity. The findings predict that during effortful cognitive and motor behaviour the dorsal ACC supports the generation of associated autonomic states of cardiovascular arousal. We subsequently tested this prediction by studying three patients with focal damage involving the ACC while they performed effortful cognitive and motor tests. Each showed abnormalities in autonomic cardiovascular responses with blunted autonomic arousal to mental stress when compared with 147 normal subjects tested in identical fashion. Thus, converging neuroimaging and clinical findings suggest that ACC function mediates context-driven modulation of bodily arousal states.
Functional groups on ‘Z’ DNA recognized by monoclonal antibodies (1984)

Both brominated poly[d(GC)] and poly[d( Gm5C )] form stable left-handed Z-DNA structures at physiological ionic strengths. These two antigens were used to prepare monoclonal antibodies from immunized mice. The specificity of the antibodies was studied in detail with a solid-phase radioimmune assay as well as by means of competition experiments. Both immunogens produced several relatively non-specific antibodies but two types of very specific antibody were also distinguished. The first binds poly[d( Gm5C )] but not brominated poly[d(GC)] while the other has the opposite specificity and will only bind the brominated polymer.
Fluorescence Imaging Creates A Window On The Cell (1994)

RETURN TO ISSUEPREVNewsNEXTFluorescence Imaging Creates A Window On The CellROGER Y. TSIENView Author Information Howard Hughes Medical Institute, University of California, San DiegoCite this: Chem. Eng. News 1994, 72, 29, 34–44Publication Date (Print):July 18, 1994Publication History Published online11 November 2010Published inissue 18 July 1994https://doi.org/10.1021/cen-v072n029.p034Copyright © 1994 American Chemical SocietyArticle Views25Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) SUBJECTS:Cations,Fluorescence,Fluorescence imaging,Imaging agents,Molecules Get e-Alerts
Expression of baculovirus P35 prevents cell death in Drosophila (1994)

The baculovirus P35 protein functions to prevent apoptotic death of infected cells. We have expressed P35 in the developing embryo and eye of the fly Drosophila melanogaster. P35 eliminates most, if not all, normally occurring cell death in these tissues, as well as X-irradiation-induced death. Excess pupal eye cells that are normally eliminated by apoptosis develop into pigment cells when their death is prevented by P35 expression. Our results suggest that one mechanism by which viruses prevent the death of the host cell is to block a cell death pathway that mediates normally occurring cell death. Identification of molecules that interact biochemically or genetically with P35 in Drosophila should provide important insights into how cell death is regulated.
Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons (2016)

Clarifying gene expression in narrowly defined neuronal populations can provide insight into cellular identity, computation, and functionality. Here, we used next-generation RNA sequencing (RNA-seq) to produce a quantitative, whole genome characterization of gene expression for the major excitatory neuronal classes of the hippocampus; namely, granule cells and mossy cells of the dentate gyrus, and pyramidal cells of areas CA3, CA2, and CA1. Moreover, for the canonical cell classes of the trisynaptic loop, we profiled transcriptomes at both dorsal and ventral poles, producing a cell-class- and region-specific transcriptional description for these populations. This dataset clarifies the transcriptional properties and identities of lesser-known cell classes, and moreover reveals unexpected variation in the trisynaptic loop across the dorsal-ventral axis. We have created a public resource, Hipposeq (http://hipposeq.janelia.org), which provides analysis and visualization of these data and will act as a roadmap relating molecules to cells, circuits, and computation in the hippocampus.
Correlation between tumor vascularity, vascular endothelial growth factor production by tumor cells, serum vascular endothelial growth factor levels, and serum angiogenic activity in patients with breast carcinoma. (1999)

Angiogenesis is an important prognostic factor in invasive breast carcinoma. We analyzed sera and tumor samples from 36 patients with primary breast carcinomas to determine the relationship between tumor vascularity, vascular endothelial growth factor (VEGF) production by tumor cells, levels of circulating VEGF (measured by ELISA assay), and levels of endothelial growth factors analyzed by a functional test of human umbilical vein endothelial cells (HUVEC) proliferation. Tumor vascularity was correlated directly with VEGF production by the tumor, indicating that VEGF production is a relevant factor in determining angiogenesis in primary tumor. No correlation was found either between the number of vessels in the tumor or the production of VEGF by tumor cells and the levels of serum angiogenic factors including VEGF. On the contrary, the two serum tests correlated together because a high serum level of VEGF is more frequent in cases with the presence of HUVEC-stimulating growth factors. These data indicate that the principal source of factors stimulating angiogenesis in the primary tumor is the tumor itself. This is an important issue in the context of anti-angiogenic therapeutic approaches, which should be planned to interfere with tumor production of angiogenic factors rather than with circulating angiogenic factors. In conclusion, whereas the vessel count and VEGF production by tumor cells are parameters that give direct information on tumor angiogenesis, long-term follow-up is necessary to determine the clinical significance of the determination of serum HUVEC-stimulating factors in the progression of breast carcinoma.
Proteolysis and fusion of low density lipoprotein particles independently strengthen their binding to exocytosed mast cell granules. (1994)

Abstract Contact between low density lipoproteins (LDL) and exocytosed mast cell granules, the leads to binding of LDL to the granule remnants via ionic interactions between the apolipoprotein B-100 (apoB-100) component of LDL and the heparin proteoglycan component of the granule remnants. Upon incubation at 37 degrees C, the heparin proteoglycan-bound apoB-100 is progressively proteolyzed by remnant chymase and carboxypeptidase A, which are also bound to the heparin proteoglycans. Thereupon, the LDL particles fuse, and their binding to the granule remnants strengthens, as defined by the decreased ability of NaCl to release LDL from the remnants. We now have examined separately the effects of proteolysis and fusion on LDL binding. Proteolysis without fusion was induced by lowering the incubation temperature to 15 degrees C, and proteolysis-independent fusion was induced by treating granule remnant-bound LDL with sphingomyelinase in the presence of protease inhibitors. It was found that degradation of the heparin proteoglycan-bound apoB-100, even without accompanying particle fusion, increased the strength of LDL binding to the granule remnants, suggesting exposure of buried heparin binding regions of apoB-100. When such proteolyzed LDL particles were allowed to fuse, the strength of their binding to the granule remnants increased still further, probably because of an increase in the number of apoB-100 fragments in the enlarged particles. Proteolysis-independent fusion, induced by sphingomyelinase treatment of granule remnant-bound LDL, also increased the strength of binding. The results show that proteolytic degradation and fusion, the two modifications of granule remnant-bound LDL subsequent to action by chymase and carboxypeptidase A of the granule remnants, represent two separate mechanisms by which LDL particles become tightly bound to the heparin proteoglycans of exocytosed mast cell granules. Since the formation of an atheroma, the hallmark of atherosclerosis, is characterized by accumulation in the proteoglycan matrix of the arterial intima of extracellular lipid droplets resembling the fused LDL particles on the granule remnant surfaces, the modifications of LDL described in this study may provide a clue to the actual processes by which the lipid droplets are anchored to the arterial intima.
Liquid Lenses and Driving Mechanisms: A Review (2012)

Abstract In this paper, we discuss liquid lenses driven by various mechanisms. By properly designing the device structure and choosing the optimal materials, the liquid lenses offer great potential for practical uses. The driving mechanism dictates the application and performance of the liquid lenses. Here we categorize the driving mechanisms into mechanical and electrical ones. In general, mechanical driving with an elastic membrane and an external pump drives liquids in a cavity by controlling the hydraulic pressure. The mechanical driving method can be applied to most of the liquids, but the application of the electrical driving method would be limited by the conductivity or the permittivity of the liquids. Therefore, the properties of the different liquids, e.g., dielectric liquids, liquid crystal molecules, and conductive liquids, deeply affect the mechanism we may choose to realize a liquid lens. Among various electrical methods, dielectrophoresis (DEP), electrostatic forces, and electrowetting-on-dielectric (EWOD) are emphasized here for driving dielectric liquids, liquid crystal molecules, and conductive liquids, respectively. DEP deforms the liquid lenses when the permittivities are different between the liquid and the medium. Electrostatic force orients the liquid crystal molecules to follow the applied electric field. Electrowetting-driven liquid lenses change their focal lengths by altering the contact angle. Here we show the designs and the structures of liquid lenses to describe their mechanisms, performances and feasibilities. It is worth mentioning that the liquid lenses using electrowetting have been commercialized. No moving parts would be the most important reason to use electrical manipulations rather than mechanical ones.
Effects of transdermal testosterone application on the ovarian response to FSH in poor responders undergoing assisted reproduction technique—a prospective, randomized, double-blind study (2006)

No significant beneficial effects of androgen administration on the ovarian response to FSH could be demonstrated. However, subsequent clinical trials are needed to determine whether an optimal dose and/or a longer duration of testosterone administration may be helpful.
Inhibitory effect of igm rheumatoid factor on immune complex solubilization capacity and inhibition of immune precipitation (1984)

Abstract Purified IgM rheumatoid factors (RF; 3 monoclonal and 2 polyclonal) were shown to inhibit, in a dosedependent manner, 2 complement‐mediated functions, i.e., the immune complex solubilization capacity and the inhibition of immune precipitation. Inhibition of immune complex solubilization capacity occurred only if RF was added at the same time as, but not after, addition of the complement source. Experimental evidence suggests that the effects of RFs were not related to their anticomplementary activity, but rather required the attachment of RF to the Fc region of the IgG molecule. Although no clinical data are available so far, it might be plausible that these newly described properties of RF have biologic relevance.
Effective Thermal Conductivities of a Novel Fuzzy Fiber-Reinforced Composite Containing Wavy Carbon Nanotubes (2014)

This article deals with the investigation of the effect of carbon nanotube (CNT) waviness on the effective thermal conductivities of a novel fuzzy fiber-reinforced composite (FFRC). The distinctive feature of the construction of this novel FFRC is that wavy CNTs are radially grown on the circumferential surfaces of the carbon fibers. Effective thermal conductivities of the FFRC are determined by developing the method of cells (MOCs) approach in conjunction with the effective medium (EM) approach. The effect of CNT waviness is studied when wavy CNTs are coplanar with either of the two mutually orthogonal planes of the carbon fiber. The present study reveals that (i) if CNT waviness is parallel to the carbon fiber axis then the axial (K1) and the transverse (K2) thermal conductivities of the FFRC are improved by 86% and 640%, respectively, over those of the base composite when the CNT volume faction present in the FFRC is 16.5% and the temperature is 400 K, (ii) the effective value of K1 of the FFRC containing wavy CNTs being coplanar with the carbon fiber axis is enhanced by 75% over that of containing straight CNTs for the fixed CNT volume faction when the temperature is 400 K, and (iii) the CNT/polymer matrix interfacial thermal resistance does not affect the effective thermal conductivities of the FFRC. The present work also reveals that for a particular value of the CNT volume fraction, optimum values of the CNT waviness parameters, such as the amplitude and the wave frequency of the CNT for improving the effective thermal conductivities of the FFRC can be estimated.
Enzootic nasal tumour of goats: demonstration of a type D-realated retrovirus in nasal fluids and tumours (1991)

Nasal exudate and tumour tissue from goats with enzootic nasal tumours were shown to contain a reverse transcriptase activity associated with a particle of buoyant density typical of retroviruses. The same particle contained a 25,000 Mr protein that cross-reacted with the p27 of Mason-Pfizer monkey virus (MPMV) and with p25 of sheep pulmonary adenomatosis retrovirus. It also contained a low Mr protein related to p10-12 of MPMV.
Self-contained, tetracycline-regulated retroviral vector system for gene delivery to mammalian cells (1996)

Retroviral vectors that contain the tetracycline-inducible (Tet) system were developed. The two components of the Tet system were organized within the vectors in a manner that stringently maintains tetracycline-dependent regulation. Regulated expression of an indicator gene inserted into the retroviral vectors was examined in several different cell types. In infected NIH 3T3 cells, levels of induction in the absence of tetracycline were observed to be as much as 336-fold higher than levels in the presence of tetracycline, which were extremely low. Tetracycline-dependent regulation was observed in all other transduced cell types and ranged from 24- to 127-fold. The generation of retroviral vectors containing regulatory elements that allow for the regulated expression of heterologous genes and that have the ability to infect virtually all dividing target cells should greatly facilitate the biochemical and genetic examination of a broad range of genes. Moreover, these inducible retroviral vectors should prove useful in gene therapy applications.
Studies on Syntheses of Coumarin Derivatives. XIV (1963)

The Reimer-Tiemann reaction of 5-nitroresorcinol monomethyl ether (I) and addition of aniline to the ether-soluble product gave N-(2-hydroxy-4-nitro-6-methoxy-benzylidene) aniline (II), m.p. 143-144°, whose hydrolysis afforded 4-nitro-6-methoxy-salicylaldehyde (III), m.p. 97-98.5°. III formed a 2, 4-dinitrophenylhydrazone (IV) of m.p. 242-243°, whose reaction with piperidine and diethyl malonate in ethanol afforded ethyl 5-methoxy-7-nitro-3-coumarincarboxylate (V), m.p. 163.5-165°. Catalytic reduction of V over palladium-carbon gave ethyl 5-methoxy-7-amino-3-coumarincarboxylate (VI), m.p. 214-215.5°, whose diazotization followed by hydrolysis produced 5-methoxy-7-hydroxy-3-coumarincarboxylic acid (VII), m.p. 264°. 5-Methoxy-7-nitro-3-coumarincarboxylic acid (VIII), m.p. 172°, was obtained by heating V with dil. hydrochloric acid while heating of V with hydrobromic acid (d=1.48) gave 5-hydroxy-7-nitro-3-coumarincarboxylic acid (IX), m.p. 250-252°.
The Use of Treatment Wetlands for Petroleum Industry Effluents (1999)

Although the use of treatment wetlands is well established for wastewater categories such as municipal waste, stormwater, and acid mine drainage water, their use in treating a variety of industrial and agricultural wastewaters is less well developed. Several large-scale wetland projects currently exist at oil refineries, and numerous pilot studies of constructed treatment wetlands have been conducted at terminals, gas and oil extraction and pumping stations, and refineries. This paper reviews treatment wetland performance for chemical oxygen demand, biochemical oxygen demand, trace organics, metals, toxicity, total suspended solids, nitrogen, and phosphorus. All of these contaminants can be reliably removed from wastewater by treatment wetlands. Pollutant removal is highly dependent on hydraulic loading and influent concentration and to a lesser extent on internal plant communities, water depth, and hydraulic efficiency. In most cases, data from petroleum industry wetland studies indicate that treatment wetlands are equally or more effective at removing pollutants from petroleum industry wastewaters than from other types of wastewater. Until industry-specific data are more complete, this finding can be used along with published rate constants from other wastewater categories to provide conservative estimates for sizing petroleum industry treatment wetlands.
Wide bandwidth and high coupling efficiency Si_3N_4-on-SOI dual-level grating coupler (2014)

We propose and experimentally demonstrate fiber-to-chip grating couplers with aligned silicon nitride (Si(3)N(4)) and silicon (Si) grating teeth for wide bandwidths and high coupling efficiencies without the use of bottom reflectors. The measured 1-dB bandwidth is a record 80 nm, and the measured peak coupling efficiency is -1.3 dB, which is competitive with the best Si-only grating couplers. The grating couplers are integrated in a Si(3)N(4) on silicon-on-insulator (SOI) integrated optics platform with aligned waveguides in both the Si(3)N(4) and Si, and we demonstrate a 1 × 4 tunable multiplexer/demultiplexer using the Si(3)N(4)-on-SOI dual-level grating couplers and thermally-tuned Si microring resonators.
Analysis of a diagnostic strategy for patients with suspected tumors of unknown origin. (1995)

The limited diagnostic evaluation used in this study identified patients with treatable malignancies and increased the survival duration of a population of suspected UPT patients. Primary malignancies with the best survival can be diagnosed through careful pathologic review and focused evaluations for breast and ovarian cancer in women.