gebhart/patrepeval huggingface dataset:
Autophagy and lysosomal dysfunction as emerging mechanisms of nanomaterial toxicity (2012)

The study of the potential risks associated with the manufacture, use, and disposal of nanoscale materials, and their mechanisms of toxicity, is important for the continued advancement of nanotechnology. Currently, the most widely accepted paradigms of nanomaterial toxicity are oxidative stress and inflammation, but the underlying mechanisms are poorly defined. This review will highlight the significance of autophagy and lysosomal dysfunction as emerging mechanisms of nanomaterial toxicity. Most endocytic routes of nanomaterial cell uptake converge upon the lysosome, making the lysosomal compartment the most common intracellular site of nanoparticle sequestration and degradation. In addition to the endo-lysosomal pathway, recent evidence suggests that some nanomaterials can also induce autophagy. Among the many physiological functions, the lysosome, by way of the autophagy (macroautophagy) pathway, degrades intracellular pathogens, and damaged organelles and proteins. Thus, autophagy induction by nanoparticles may be an attempt to degrade what is perceived by the cell as foreign or aberrant. While the autophagy and endo-lysosomal pathways have the potential to influence the disposition of nanomaterials, there is also a growing body of literature suggesting that biopersistent nanomaterials can, in turn, negatively impact these pathways. Indeed, there is ample evidence that biopersistent nanomaterials can cause autophagy and lysosomal dysfunctions resulting in toxicological consequences.
Application of the Reeb Graph Technique to Vehicle Occupant's Head Detection in Low-resolution Range Images (2007)

In [3], a low-resolution range sensor was investigated for an occupant classification system that distinguish person from child seats or an empty seat. The optimal deployment of vehicle airbags for maximum protection moreover requires information about the occupant's size and position. The detection of occupant's position involves the detection and localization of occupant's head. This is a challenging problem as the approaches based on local shape analysis (in 2D or 3D) alone are not robust enough as other parts of the person's body like shoulders, knee may have similar shapes as the head. This paper discusses and investigate the potential of a Reeb graph approach to describe the topology of vehicle occupants in terms of a skeleton. The essence of the proposed approach is that an occupant sitting in a vehicle has a typical topology which leads to different branches of a Reeb Graph and the possible location of the occupant's head are thus the end points of the Reeb graph. The proposed method is applied on real 3D range images and is compared to Ground truth information. Results show the feasibility of using topological information to identify the position of occupant's head.
Agonistic and antagonistic roles of fibroblasts and cardiomyocytes on viscoelastic stiffening of engineered human myocardium (2018)

Cardiomyocyte and stroma cell cross-talk is essential for the formation of collagen-based engineered heart muscle, including engineered human myocardium (EHM). Fibroblasts are a main component of the myocardial stroma. We hypothesize that fibroblasts, by compacting the surrounding collagen network, support the self-organization of cardiomyocytes into a functional syncytium. With a focus on early self-organization processes in EHM, we studied the molecular and biophysical adaptations mediated by defined populations of fibroblasts and embryonic stem cell-derived cardiomyocytes in a collagen type I hydrogel. After a short phase of cell-independent collagen gelation (30 min), tissue compaction was progressively mediated by fibroblasts. Fibroblast-mediated tissue stiffening was attenuated in the presence of cardiomyocytes allowing for the assembly of stably contracting, force-generating EHM within 4 weeks. Comparative RNA-sequencing data corroborated that fibroblasts are particularly sensitive to the tissue compaction process, resulting in the fast activation of transcription profiles, supporting heart muscle development and extracellular matrix synthesis. Large amplitude oscillatory shear (LAOS) measurements revealed nonlinear strain stiffening at physiological strain amplitudes (>2%), which was reduced in the presence of cells. The nonlinear stress-strain response could be characterized by a mathematical model. Collectively, our study defines the interplay between fibroblasts and cardiomyocytes during human heart muscle self-organization in vitro and underscores the relevance of fibroblasts in the biological engineering of a cardiomyogenesis-supporting viscoelastic stroma. We anticipate that the established mathematical model will facilitate future attempts to optimize EHM for in vitro (disease modelling) and in vivo applications (heart repair).
Phase Performance of an Eight-Channel Wavelength-Division-Multiplexed Analog-Delay Line (2004)

The design of an eight-channel 25 /spl mu/s wavelength-division-multiplexed (WDM) microwave photonic delay line is described. The performance of the delay line was studied by measuring the temperature dependent relative phase drift between channels and the interchannel crosstalk. A simple method for measuring the maximum phase errors produced by the interchannel crosstalk is described and used to measure the maximum error on a channel in this system. The use of polarization interleaving and dispersion compensation to reduce the effects of crosstalk in the system is examined experimentally.
Growth and characterizations of GaN micro-rods on graphene films for flexible light emitting diodes (2014)

We report the growth of GaN micro-rods and coaxial quantum-well heterostructures on graphene films, together with structural and optical characterization, for applications in flexible optical devices. Graphene films were grown on Cu foil by means of chemical vapor deposition, and used as the substrates for the growth of the GaN micro-rods, which were subsequently transferred onto SiO2/Si substrates. Highly Si-doped, n-type GaN micro-rods were grown on the graphene films using metal–organic chemical vapor deposition. The growth and vertical alignment of the GaN micro-rods, which is a critical factor for the fabrication of high-performance light-emitting diodes (LEDs), were characterized using electron microscopy and X-ray diffraction. The GaN micro-rods exhibited promising photoluminescence characteristics for optoelectronic device applications, including room-temperature stimulated emission. To fabricate flexible LEDs, InxGa1–xN/GaN multiple quantum wells and a p-type GaN layer were deposited coaxially on the GaN micro-rods, and transferred onto Ag-coated polymer substrates using lift-off. Ti/Au and Ni/Au metal layers were formed to provide electrical contacts to the n-type and p-type GaN regions, respectively. The micro-rod LEDs exhibited intense emission of visible light, even after transfer onto the flexible polymer substrate, and reliable operation was achieved following numerous cycles of mechanical deformation.
A PRECISE METHOD FOR DETERMINING CONTOURED SURFACES (1982)

Although the petroleum geologist is concerned with analysing three-dimensional data, he relies entirely on two-dimensional portrayals - cross-sections and particularly contour maps of all types. With the advent of digital computers, machine contouring has become increasingly common, but little attention has been directed to the limitations of the various algorithms that can be employed to generate contour maps from a set of control points. For example, it is not widely appreciated that contouring procedures which faithfully honour the value of original control points produce poor predictions at locations where no control is available. Contouring a published set of topographic data shows how this and other limitations lead to approximations and errors in machine-generated contours. A new method based on triangulation interpolation using Delaunay tessellations (deltri analysis) is superior to existing methods. Not only does the method give the most accurate and objective measurement and display of the contoured surface, but it is also computationally efficient. Rapid calculation of volume of closure over contoured structures is possible. The method also allows estimation of the adequacy of the data on which the contouring is based by introducing a measure of 'roughness' of the surface. This is achieved by analysing the directions of normals to triangles surrounding each control point.
A comparison of near-infrared spectroscopy and jugular bulb oximetry in comatose patients resuscitated from a cardiac arrest (1998)

One cause of cerebral damage in comatose patients resuscitated from a cardiac arrest is cerebral ischaemia occurring during the postresuscitation period. Near-infrared spectroscopy has been advocated as a useful monitor of brain oxygenation, but data on clinical use in comatose postarrest patients are not available. Therefore, we compared regional oxygen saturation measured with the INVOS 3100 with global oxygen saturation measured using jugular bulb oximetry in 10 comatose patients successfully resuscitated from an out-of-hospital cardiac arrest. Our data show that, in most patients, there is a significant difference between the two methods. The INVOS 3100 over-read at low jugular bulb saturations (< 60%) and under-read at high jugular bulb saturations (≥ 60%). During hypoventilation we found a significant increase in regional oxygen saturation. This increase was significantly correlated with the rise in cerebral blood flow and cardiac index, indicating that regional oxygen saturation is influenced by both cerebral and extracerebral components. We conclude that regional cerebral oxygen saturation measured with the INVOS 3100 cannot be compared with global cerebral oxygen saturation measured with jugular bulb oximetry in comatose patients resuscitated from a cardiac arrest. This may be due to characteristics of the INVOS 3100 or to the distribution of cerebral blood flow after cardiac arrest.
Side‐chain crystallinity, heat of melting, and thermal transitions in poly[<i>N</i>‐(10‐<i>n</i>‐alkyloxycarbonyl‐<i>n</i>‐decyl)maleimides] (PEMI) (1980)

Abstract The heat of melting, the melting temperature T m , and the sub‐ T g transition temperature have been studied from –120°C to above T m in a series of 11 poly[ N ‐(10‐ n ‐alkyloxycarbonyl‐ n ‐decyl)]‐maleimides (PEMI). Side‐chains from ethyl to n‐docosyl with n even have been included. The contribution to the heat of melting per methylene group shows that the hexagonal paraffin crystal modification is present in these poly( N ‐maleimides), in agreement with x‐ray data for the same compounds. The enthalpy data show that only a part of the outer methylene groups are present in the crystalline aggregates. Furthermore, DSC traces exhibit a typical distribution of crystallite sizes, which become narrower as the side‐chains become longer. The critical chain length needed to form a stable nucleus includes nine methylene groups in the outer part of the n‐alkyl side‐chain. The influence of the side‐chain length and crystallinity on the γ‐transition temperature of these polymers was also investigated. In the range where these polymers are essentially amorphous the sub‐ T g transition temperature decreases continuously as the number of methylene groups in the side‐chain increases. This transition is attributed to internal motion within the external side‐group without any interaction with the main chain. This is presumably made possibly by the partial rotation of the oxycarbonyl group. We suggest that this transition is similar to the well known γ transition which has been attributed to various segmental motions in all ethylene copolymers and in all homopolymers containing a determined number ofCH 2 units in the main‐chain or in the side‐chain. Estimates based on the chemical structure, yield a value for the γ transition of CH 2 similar to that measured by other methods in polyethylene and related materials.
Air-cooled simmered Q-switched Nd: YAG laser with transistor-gated flashlamp pulsing (1984)

Development of high voltage, high current power transistors has opened new vistas in Nd:YAG laser technology. An experimental setup employing photoflash capacitors and transistor-gated flashlamp pulsing instead of conventional pulse circuitry was found to offer substantial advantages.
Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM (2009)

Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding.
Calibration of IQ imbalance in OFDM transceivers (2004)

High rate wireless communication systems require the design of low-cost radio transceivers with low power consumption. The design of direct conversion receivers, which convert the radio frequency directly to baseband, has thus been the subject of active investigation in recent years. However, such architectures introduce certain design challenges of their own, namely DC offsets as well as gain and phase mismatches in the in-phase and quadrature paths. In this paper, we propose novel methods for calibrating the IQ imbalance in the receiver for OFDM communication systems. Relations are derived for the estimation of the gain and phase parameters for AWGN as well as frequency selective fading channels. We will also investigate the statistical properties of the estimated parameters. The calibration procedure is verified for an OFDM system designed based on the IEEE 802.11a standard for wireless local area networks.
Altered Coagulation Protein Content After Albumin Resuscitation (1982)

Previous studies showed that the random addition of supplemental albumin to a resuscitation regimen of blood, salt, and frozen plasma caused a significant (p = less than 0.05) fall in fibrinogen clotting activity (FC) and a rise in prothrombin times (PT) in seriously injured patients; the partial thromboplastin times (PTT) were insignificantly prolonged. Based upon these findings, frozen plasma samples, prospectively collected in 41 non-albumin patients and 35 albumin patients, were analyzed immunologically, in duplicate, for protein content of coagulation factor VIII (VIIIAg), prothrombin (IIAg), fibrinogen (FAg), antithrombin III (ATAg), and fibrin(ogen) split products (FSP). Supplemental albumin resuscitation was associated with a significant fall in FAg (83 +/- 9 versus 124 +/- 10 SE mg/dl), VIIIAg (97 +/- 13 versus 127 +/- 135 SE %), IIAg (54 +/- 3 versus 80 +/- 4 SE %), and ATAg (14 +/- 0.8 +/- 19 +/- 0.8 SE mg%) with no significant changes in FSP. FSP, however, were more than 20 micrograms/ml in 13 of 41 nonalbumin patients versus four of 35 albumin patients (X2 = 4.5, p less than 0.05). Reduced coagulation activity following albumin supplementation seems partly caused by a decrease of coagulation protein content; increased fibrinolysis in the albumin patients is not the cause. Decreased coagulation protein content parallels the fall in coagulation activity and the need for postresuscitation blood transfusions. The role of reduced coagulation synthesis in these changes needs further study.
Mapping of the aspartate and aromatic amino acid aminotransferase genes tyrB and aspC (1977)

Co-transduction experiments using P1-mediated reciprocal and three-factor crosses have been used to map two mutations affecting the aspartate and aromatic amino acid aminotransferases of Escherichia coli. tyrB-, which inactivates the tyrosine-repressible component of these activities is co-transducible with metA and malB; the gene order is metA-malB-tyrB. aspC-, which inactivates the nonrepressible aminotransferase with high activity for aspartate, maps between and is co-transducible with serC and pyrD.
Low-cost method for streamlining marker-assisted selection and breeding line development in rice (Oryza sativa L.) (2009)

Simple and economical microsatellite marker detection is important for successful and widespread adoption of marker technology in various breeding programs. A non-automated but fast, reliable and cost effective protocol for microsatellite marker detection is described that requires only standard molecular laboratory equipment. The protocol consists of a leaf sampling method for 96-well plates, tissue grinding using a bead-based grinder, DNA extraction using a modified heating method, and marker detection using polyacrilamid MegaGel dual vertical electrophoresis. At least 200 data points can be generated by one person in a single day from sample preparation to DNA extraction, PCR run, electrophoresis, and data recording. The cost of consumable chemicals for marker analyses was about U.S. $0.25 per data point. The protocol is adaptable for use in field settings to support marker-assisted selection and breeding line development, as well as for genotyping and mapping purposes. This relatively simple and inexpensive marker detection could expand the participation of small laboratories.  Wider participation from various breeding programs in both developed and developing countries will benefit many crop improvement programs.

	 

	Key words: High throughput, low cost, microsatellite marker, polyacrylamid gel electrophoresis, rice (Oryza sativa), marker-assisted selection, breeding line.
Glycosyl Imidates, 56. Synthesis of the Hexasaccharide Moiety of Pectinioside E (1992)

Abstract The synthesis of the hexasaccharide moiety 2 of pectinioside E ( 1 ), isolated from the whole bodies of the starfish Asterina pectinifera Müller et Troschel, is described. Building block 4 was prepared by a six‐step procedure from D ‐glucose. A reasonable yield was obtained via selective glycosylation of 4 at 2‐OH with donor 5 to give the desired disaccharide 6 which served as an acceptor in the following fucosylation with 9 to afford the crucial trisaccharide 10 . This was easily transformed into trichloroacetimidate 12 . Disaccharide 17 , obtained in high yield by glycosylation of donor 13 with acceptor 14 followed by deacetylation, turned out to be more reactive at 4b‐OH than at 2b‐OH. Thus, the reaction of donor 12 with acceptor 17 gave the desired pentasaccharide 18 β in an acceptable yield; 18 β was readily transformed into the hexasaccharide 20 by glycosylation with donor 15 . Debenzylation of 20 followed by deacylation furnished the target hexasaccharide 2 which was characterized by its per‐ O ‐acetylated product 21 .
The sense of smell: genomics of vertebrate odorant receptors (2002)

Olfactory receptor (OR) proteins interact with odorant molecules in the nose, initiating a neuronal response that triggers the perception of a smell. The OR family is one of the largest known mammalian gene families, with around 900 genes in human and 1500 in mouse. After discounting pseudogenes, the functional repertoire in mouse is more than three times larger than that of human. OR genes encode G-protein-coupled receptors containing seven transmembrane domains. ORs are arranged in clusters of up to 100 genes dispersed in 40-100 genomic locations. Each neuron in the olfactory epithelium expresses only one allele of one OR gene. The mechanism of gene choice is still unknown, but must involve locus, gene, and allele selection. The gene family has expanded mainly by tandem duplications, many of which have occurred since the divergence of the rodent and primate lineages. Interchromosomal segmental duplications including OR genes have also occurred, but more commonly in the human than the mouse family. As a result, many human OR genes have several possible mouse orthologs, and vice versa. Sequence and copy number polymorphisms in OR genes have been described, which may account for interindividual differences in odorant detection thresholds.
Efficient pump wavelengths of erbium-doped fibre optical amplifier (1989)

By choosing pump wavelengths at which excited state absorption does not occur, efficient high gain operation of erbium-doped fibre amplifiers is possible. Practical pump wavelengths of 532 nm and 980 nm are identified as optimal, giving gains as high as 1.35dB/mW and 2.2dB/mW of pump at the two wavelengths, respectively.
Cross-linked Poly (vinyl alcohol) Hydrogel : Study of Swelling and Drug Release Behaviour (2002)

Cross-linked poly {vinyl alcohol) (PVA) is a prolonged-release micromatrix, a hydrophilic polymer and a potentially interesting hydrogel, which is useful for drug delivery applications . As a part of drug development procedure the aim of this study was to investigate the effect of structural changes on drug release (theophylline) from this polymeric network . The studied parameters included: cross-linking agent (glutaraldehyde) concentration, PVA content of the films, theophylline percentage and their overall effect on swelling of the hydrogels, drug loading efficiency, diffusion and release characteristics of theophylline from PVA films . Changes in glutaraldehyde percentage (or cross-linking density) affected the swelling of the films . However, increasing PVA percentage caused more swelling . Drug loading efficiency was higher in gels with higher glutaralde- hyde, PVA and theophylline percentages . Increasing contents of PVA and theo- phylline promoted the diffusion coefficient and drug release rate but glutaralde- hyde had a reverse effect . The pH did not affect the swelling and diffusion coefficient . Water transport and drug release mechanism predominantly followed a Fickian model . It may be concluded that by changing the PVA structural parameters, a rate-controlled drug release is obtained.
Strategies for enhanced drug delivery to the central nervous system (2008)

Treating central nervous system diseases is very challenging because of the presence of a variety of formidable obstacles that impede drug delivery. Physiological barriers like the blood-brain barrier and blood-cerebrospinal fluid barrier as well as various efflux transporter proteins make the entry of drugs into the central nervous system very difficult. The present review provides a brief account of the blood brain barrier, the P-glycoprotein efflux and various strategies for enhancing drug delivery to the central nervous system.