gebhart/patrepeval huggingface dataset:
Method for Cellular Imaging of Palmitoylated Proteins with Clickable Probes and Proximity Ligation Applied to Hedgehog, Tubulin, and Ras (2014)

Hedgehog protein undergoes post-translational palmitoylation, which is critical for its signaling activity during embryonic development and in adult tissues. Due to a lack of suitable imaging methods, the trafficking route of palmitoylated Hedgehog has remained unclear in secretory cells. Here, we report a novel method for imaging the subcellular distribution of palmitoylated forms of cellular proteins with high resolution. The method utilizes clickable chemical reporters to label the entire palmitoylated proteome, followed by proximity ligation on antibodies to the click-conjugated dye and the protein of interest to reveal the spatial localization of specific palmitoylated proteins, as exemplified by sonic Hedgehog, tubulin, and Ras. Palmitoylated sonic Hedgehog is found in the endoplasmic reticulum, the Golgi apparatus, and at the plasma membrane but not the endosomal system in Hedgehog-secreting cells. Palmitoylated tubulin is found along microtubule tracks and also partially associated with the plasma membrane, while palmitoylated H-Ras is visualized at various cellular locations including the plasma membrane, Golgi apparatus and endoplasmic reticulum. Our method is broadly applicable to imaging the palmitoylation of cellular proteins as well as other protein post-translational modifications that are detectable by clickable chemical reporters.
CLA formation in oils during hydrogenation process as affected by catalyst types, catalyst contents, hydrogen pressure, and oil species (2002)

Abstract The effects of types and amount of catalysts, hydrogen pressure, and kinds of vegetable oils on the formation of CLA isomers were studied during hydrogenation. CLA isomers were identified by using a silver ion‐impregnated high‐performance liquid chromatograph and 100‐m cyano‐capillary column gas chromatograph. A selective catalyst (SP‐7) produced a considerably higher content of CLA in soybean oil than nonselective catalysts. The maximal quantity of CLA produced in soybean oil during hydrogenation increased greatly with increasing amount of catalyst. By increasing the amount of selective catalyst from 0.05 to 0.3%, the quantity of total CLA obtained was about 1.9 times higher. Changes in hydrogen pressure also greatly influenced total CLA formed. By decreasing hydrogen pressure from 0.24 to 0.024 MPa, the quantity of CLA obtained was about 1.3 times higher. With different oil species (soybean, cottonseed, and corn oils), the time to reach the maximal quantity of CLA was different under the same hydrogenation conditions. However, the maximal quantity of CLA and proportion of CLA isomers formed were almost identical, regardless of oil species tested, under the same hydrogenation conditions.
The Use of Injection/Falloff Tests and Pressure Buildup Tests To Evaluate Fracture Geometry and Post-Stimulation Well Performance in the Devonian Shales (1991)

ABSTRACT This paper summarizes a series of experiments performed on the Gilbert Exploration Emma Preece No. 1 well in Martin Co., KY which have led to a better understanding of fracture geometry and post-stimulation well performance in the Devonian Shales. The Preece well, like many Devonian Shale wells, was perforated and stimulated with a single treatment over a large, perforated interval (727 ft). Post-fracture well tests performed after initial completion indicated little improvement over pre-fracture well performance. In 1989, the treated interval was sub-divided into four distinct zones to further evaluate the fracture treatment using isolation, communication, nitrogen injection/falloff, and flow/buildup tests. Results of these tests indicate (1) that the large completion interval was not uniformly stimulated by the fracture treatment and (2) that reservoir quality was different for each perforated interval, indicating the completion interval should be treated as a layered reservoir. These results help explain the apparent short fracture half-length and the less-than-expected flow rates for this well following stimulation.
A semi-automated multiplex high-throughput assay for measuring IgG antibodies against Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) domains in small volumes of plasma (2008)

Using this lyophilized multiplex assay, antibody reactivity levels to twenty eight different recombinant PfEMP1 proteins were simultaneously measured using a single microliter of plasma. Thus, the assay reported here provides a useful tool for rapid and efficient quantification of antibody reactivity against PfEMP1 variants in human plasma.
The apoptosis-associated gamma-ray response of BCL-X(L) depends on normal p53 function. (1996)

We have investigated the effect of DNA damage on the expression of BCL-X, a member of the BCL-2 family. BCL-X mRNA levels were found to increase upon exposure human cells to ionizing radiation (IR). The Bcl-X(L) protein, but not Bcl-X(S), was identified to be induced by IR. Like BAX, another member of the BCL-2 family and a p53-regulated gene, the induction of BCL-X(L) was dependent on normal p53 function and required that cells have an apoptosis-susceptible phenotype. The induction of BCL-X(L) was rapid, transient and dose-dependent. The mRNA level peaked at 4 h and returned to baseline by 24 h post-irradiation. In agreement with the increased transcript level, Bcl-X(L) protein level was also observed to increase in cells with wild-type p53 where IR triggered apoptosis. In addition, a survey of the BCL-X(L) mRNA basal levels in human cells with known apoptotic responses showed that low basal levels of BCL-X(L) mRNA in cells were highly correlated with a strong ability of cells to undergo IR-induced apoptosis. On the other hand, high levels of basal BCL-X(L) were correlated with the resistance of cells to IR-induced apoptosis regardless of p53 status. These results indicate that BCL-2 and BCL-X(L) behave differently in response to DNA damage treatment even though they both are able to protect cells from p53-mediated apoptosis; along with down-regulation of BCL-2, BCL-X(L) was up-regulated by IR in human cells with wild-type p53 and susceptibility to IR-induced apoptosis. We speculate that the physiological function of increased BCL-X(L) protein would be expected to probably limit the severity and length of BAX effect in order to maintain a proper threshold for apoptosis and to complete cell cycle arrest activated by p53.
The glutamate‐enriched cortical and thalamic input to neurons in the subthalamic nucleus of the rat: Convergence with GABA‐positive terminals (1995)

Neurons of the subthalamic nucleus play a key role in the normal physiology and the pathophysiology of the basal ganglia. In order to understand better how the activity of subthalamic neurons and hence the output of the basal ganglia are controlled, we have reexamined the topography and examined in detail the synaptology and neurochemical nature of the two major excitatory projections to the subthalamic nucleus, that from the cortex and from the parafascicular nucleus of the thalamus. The approach was to use anterograde neuronal tracing and postembedding immunocytochemistry for amino acid transmitters. In confirmation of previous findings the cortical and thalamic projections were topographically organized, although the topography was more finely organized, and the projections more extensive, than previously demonstrated. Cortical and thalamic terminals made asymmetrical synaptic contacts with the dendrites and spines of subthalamic neurons. The thalamic terminals contacted larger postsynaptic targets, and therefore presumably more proximal regions of subthalamic neurons, than did the cortical terminals. Quantitative analysis of the postembedding immunolabelled sections revealed that the cortical and thalamic terminals were significantly enriched in glutamate-immunoreactivity when compared to identified gamma-aminobutyric acid (GABA)-positive terminals, supporting physiological studies that suggest that these projections use glutamate as their neurotransmitter. In addition a small population of nonanterogradely labelled terminals that formed asymmetrical synapses and were immunopositive for GABA were identified. A larger population of terminals that formed symmetrical synapses were also immunopositive for GABA and were probably derived from the globus pallidus. The latter type of terminal was found to make convergent synaptic input with cortical or thalamic terminals on the dendrites and spines of subthalamic neurons, indicating that the "indirect pathways" by which information flows through the basal ganglia converge at the level of individual neurons in the subthalamic nucleus.
Analysis of the Organization and Nucleotide Sequence of the Chromosomal Gene for the β-Subunit of Rat Thyrotropin (1986)

The gene for the beta-subunit of rat thyrotropin has been isolated from a library of rat DNA fragments cloned in bacteriophage lambda. The complete nucleotide sequence of the gene has been determined including a portion of 5'- and 3'-flanking regions. The rat TSH-beta gene contains approximately 4879 nucleotides which ultimately lead to the production of a mRNA of about 554 nucleotides, exclusive of the 3' poly(A) tract. The first exon which represents only 5' untranslated sequences of the mRNA, is separated from the second exon by a very large, 3.9-kbp intervening sequence. The second and third exons are separated by a small, 377-bp intervening sequence. Southern blot analysis of total genomic DNA demonstrated that the rat genome contains sequences similar to the cloned gene, suggesting that no rearrangements occurred during the cloning process.
Distribution of Mud Induced Damage Around Horizontal Wellbores (1998)

Abstract This paper presents the results of an experimental study on the extent, depth, and distribution of mud induced formation damage around a horizontal wellbore. This investigation aims at addressing the question of how much damage is caused in the bottom, middle, and upper portions of the heel and toe when a horizontal well is drilled. Our simulated borehole consists of a 5" diameter pipe rotating inside a 7" diameter pipe. Three core holders are placed at the top, middle and bottom of the simulated borehole. The fluid loss rate and the permeability of 4 different sections of the core are measured as mud is circulated in the annulus and the inside pipe is rotated. The formation damage and the fluid loss data for the top, middle and bottom of the wellbore are measured for different drill-in fluids, axial velocities and pipe rotation rates. It is found that when the drill pipe is concentric the fluid loss rate is symmetrical and independent of axial fluid velocity and rotational speed of drill pipe, over the range of rpms and velocities studied. For eccentric annuli (as might be expected in horizontal wellbores) the extent of damage and fluid loss vary azimuthally with the most damage occurring in the bottom portion of the hole. The extent and depth of damage are related to the speed of drill pipe rotation and the time of exposure to the mud. Erosion of the mud cake at the bottom of the hole plays an important role in the distribution of formation damage around the hole. Both the drill-in fluids tested, sized calcium carbonate and sized salt, were found to be relatively non-damaging. However, the presence of drill solids in the mud induces significant damage. P. 441
An analysis of XML compression efficiency (2007)

XML simplifies data exchange among heterogeneous computers, but it is notoriously verbose and has spawned the development of many XML-specific compressors and binary formats. We present an XML test corpus and a combined efficiency metric integrating compression ratio and execution speed. We use this corpus and linear regression to assess 14 general-purpose and XML-specific compressors relative to the proposed metric. We also identify key factors when selecting a compressor. Our results show, XMill or WBXML may be useful in some instances, but a general-purpose compressor is often the best choice.
Structure-Function Analysis of Inositol Hexakisphosphate-induced Autoprocessing in Clostridium difficile Toxin A (2009)

The action of Clostridium difficile toxins A and B depends on inactivation of host small G-proteins by glucosylation. Cellular inositol hexakisphosphate (InsP6) induces an autocatalytic cleavage of the toxins, releasing an N-terminal glucosyltransferase domain into the host cell cytosol. We have defined the cysteine protease domain (CPD) responsible for autoprocessing within toxin A (TcdA) and report the 1.6 A x-ray crystal structure of the domain bound to InsP6. InsP6 is bound in a highly basic pocket that is separated from an unusual active site by a beta-flap structure. Functional studies confirm an intramolecular mechanism of cleavage and highlight specific residues required for InsP6-induced TcdA processing. Analysis of the structural and functional data in the context of sequences from similar and diverse origins highlights a C-terminal extension and a pi-cation interaction within the beta-flap that appear to be unique among the large clostridial cytotoxins.
Harnessing Competing Endocytic Pathways for Overcoming the Tumor-Blood Barrier: Magnetic Resonance Imaging and Near-Infrared Imaging of Bifunctional Contrast Media (2009)

Ovarian cancer is the most lethal gynecologic malignancy, often diagnosed at advanced stage leading to poor prognosis. In the study reported here, magnetic resonance imaging and near-infrared reflectance imaging were applied for in vivo analysis of two competing endocytic pathways affecting retention of bifunctional daidzein-bovine serum albumin (BSA)-based contrast media by human epithelial ovarian carcinoma cells. Suppression of caveolae-mediated uptake using nystatin or by BSA competition significantly enhanced daidzein-BSA-GdDTPA/CyTE777 uptake by tumor cells in vitro. In vivo, perivascular myofibroblasts generated an effective perivascular barrier excluding delivery of BSA-GdDTPA/CyTE777 to tumor cells. The ability to manipulate caveolae-mediated sequestration of albumin by perivascular tumor myofibroblasts allowed us to effectively overcome this tumor-stroma barrier, increasing delivery of daidzein-BSA-GdDTPA/CyTE777 to the tumor cells in tumor xenografts. Thus, both in vitro and in vivo, endocytosis of daidzein-BSA-GdDTPA/CyTE777 by ovarian carcinoma cells was augmented by albumin or by nystatin. In view of the cardinal role of albumin in affecting the availability and pharmacokinetics of drugs, this approach could potentially also facilitate the delivery of therapeutics and contrast media to tumor cells.
Performance Analysis of RSS-AoA-Based Key Generation Scheme for Mobile Wireless Nodes (2017)

By exploiting the reciprocity and randomness properties of wireless channels, physical-layer-based key generation provides a stable secrecy channel even when the main channel suffers from a bad condition. Even though the channel variation due to the mobility of nodes in wireless channels provides an improvement of key generation rate (KGR), it decreases the key consistency probability (KCP) between the node pairs. Inspired by the received signal strength(RSS)-angle of arrival(AoA)-based geolocation research, in this work, we analyze the performance of the key extraction using the RSS and AoA. We aim to identify a way to utilize the high KGR of the AoA-based method to overcome the major drawback of having a low KGR in the most common RSS-based scheme. Specifically, we derive the KCP and KGR of the RSS-AoA-based key generation scheme. Further, we propose a new performance metric called effective key generation rate (EKGR), to evaluate the designed key generation scheme in practical scenarios. Finally, we provide numerical results to verify the accuracy of the presented theoretical analysis.
The Development of Domino Reactions Incorporating the Heck Reaction: The Formation of N‐Heterocycles (2011)

Abstract The methodological development of a series of domino or cascade reactions affording a series of N‐heterocycles is described. The rapid formation of these ring systems is in each case associated with the incorporation of a Heck reaction at either an early or a late stage of the domino process. A range of catalytic conditions and substrate modifications for optimisation of domino Tsuji–Trost/Heck, Buchwald–Hartwig/Heck and Heck/carbopalladation reaction sequences are reported.
Der Vergleich der Spannungsreihen in verschiedenen Solventien. II (1960)

Abstract Die bisher vorgeschlagenen McThoden [1] für einen brauchbaren Anschluß der Spannungsreihen in nichtwäßrigen Lösungsmitteln an diejenige des Wassers (E 0 H (H 2 O) = 0) werden um ein weiteres Verfahren vermehrt. Das Redoxnormalpotential geeignet ausgewählter Redoxsysteme kann näherungsweise als unabhängig von der Art des Lösungsmittels angenommen werden. Damit ist dann eine Möglichkeit gegeben, die Spannungsreihen aneinander anzuschließen. Die verschiedenen Anforderungen, die an ein hierzu geeignetes Redoxsystem gestellt werden müssen, werden von den untersuchten Systemen am besten von Ferrocen/Ferrociniumion (Cyclopentadienyl‐Eisen‐II bzw. ‐Eisen‐III) erfüllt. Als gleich brauchbar erweist sich das Kobaltanaloge des Ferrocens. Einige weitere Eisen‐ und Osmiumkomplexe sind wenigstens in einigen Lösungsmitteln anwendbar. Die Redoxnormalpotentiale wurden in den Lösungsmitteln Wasser, Methanol, Acetonitril und Formamid bestimmt. Die erhaltenen Ergebnisse stimmen befriedigend mit der verbesserten, von Plesskow [2] vorgeschlagenen Rubidiummethode überein. Ferner wurde der Gang der freien Solvatationsenergie des Silberions mit dem Molenbruch des Lösungsmittelgemisches Wasser‐Acetonitril bestimmt.
Comparative performance of reference laboratory tests and in-clinic tests for Giardia in canine feces (2018)

Of the tests evaluated here, the SNAP test had the highest sensitivity and specificity. The SNAP test had the highest percent positive and percent negative agreement when compared to the microtiter plate format ELISA and the O&P assay.
Functions of and interactions between the A and B blocks in adenovirus type 2-specific VARNA1 gene. (1986)

The internal transcriptional control region (ITCR) of VARNA1 gene consists of a 33-base-pair (bp) interblock sequence and two 12-bp sequence blocks that are highly conserved in most of the genes transcribed by RNA polymerase III. To define the functions of and study the interactions between the two blocks, we have constructed mutants with altered interblock sequence or spacing for transcription. The results of transcription efficiencies and competing strengths indicated that the interblock sequence was dispensable and the A and B blocks were essential for transcription control. One of the major functions of the interblock sequence was to maintain an optimal spacing for an intimate interaction between the two essential blocks. Shortening or elongating the interblock spacing in the mutants beyond this range drastically decreased the transcription efficiencies and competing strengths of these mutated genes. To further study how the interaction between the two blocks leads to initiation, the start sites and sizes of RNA products of the mutants were determined. When the interblock spacing was less than 105 bp, the wild-type start site was dictated by the A block after an interaction with the B block through proteins. However, when the interblock spacing was longer than 105 bp, several new start sites located closer to the B block were preferentially used. This suggests that new start sites may be dictated by the B block when its interaction with the A block is weakened by longer spacing. The mechanisms of interaction between the bipartite domain in this gene leading to initiation are different from those in tRNAs and Alu-family RNA genes.
A fully implantable 96-channel neural data acquisition system (2009)

A fully implantable neural data acquisition system is a key component of a clinically viable brain-machine interface. This type of system must communicate with the outside world and obtain power without the use of wires that cross through the skin. We present a 96-channel fully implantable neural data acquisition system. This system performs spike detection and extraction within the body and wirelessly transmits data to an external unit. Power is supplied wirelessly through the use of inductively coupled coils. The system was implanted acutely in sheep and successfully recorded, processed and transmitted neural data. Bidirectional communication between the implanted system and an external unit was successful over a range of 2 m. The system is also shown to integrate well into a brain-machine interface. This demonstration of a high channel-count fully implanted neural data acquisition system is a critical step in the development of a clinically viable brain-machine interface.
Natuur van en voor de burger (2004)

De afgelopen jaren is op veel verschillende manieren geprobeerd sturing te geven aan natuurbeleid. Op basis van een analyse van de verschillende vormen van sturing pleiten de auteurs voor een benadering waarin participatie, verbreding en leerprocessen een hoofdrol spelen. Daarvoor is een goed samenspel nodig tussen overheidsbeleid en lokale participatie, en tussen de natuur van burgers en die van ecologen
Non-viral and viral hematopoietic progenitor cell gene therapy (2015)

The pluripotent characteristic of hematopoietic stem cells (HSCs) makes them a good candidate for gene therapy. The safety drawbacks of the commonly used viral gene transfer system have made the search for alternative gene transfer methods such as non-viral or hybrid gene transfer systems became increasingly appealing in the field. One such system is the Sleeping Beauty (SB) transposon-mediated gene transfer system. Using a non-viral approach to delivery SB plasmids we were able to significantly increase the efficiency of stable gene up to 20-fold higher than previously published data by incrementally optimizing each element of the SB transposon system. In vivo studies demonstrated that SB-modified human CD34+ cells were engrafted in NOD/SCID/yC(null) (NSG) mice and differentiated into multi-lineage cell types with stable transgene expression. Transgene expression remained persistent in the secondary transplanted NSG mice indicating a long-term stable integration achieved by HSB-transposon system. Non-integrating lentiviral (NIL) vectors were also investigated as another method for SB plasmid delivery. Combining the stable integration of the SB transposon system with the delivery efficiency of NIL, termed NILting beauty, could produce a hybrid vector system that synergizes the advantages of both viral and non-viral vector systems and provide a more effective and safer approach to genetically modify HSCs. The feasibility and potential of utilizing NILting beauty to achieve stable transgene integration was evaluated using K562 and human HSCs. Up to 7% stable transgene expression was achieved in K562 cells and around 1% for human CD34+ cells when transduced with NILting beauty vectors. The other approach to increase long-term transgene expression with relatively minimal adverse effects in clinical HSC gene therapy is using non-myeloablative conditioning regimen.