gebhart/patrepeval huggingface dataset:
Semi-quantitative Determination of Protein Expression Using Immunohistochemistry Staining and Analysis: An Integrated Protocol (2019)

Semi-quantitative IHC is a powerful method for investigating protein expression and localization within tissues. The semi-quantitative immunohistochemistry (IHC) involves using software such as free software ImageJ Fiji to conduct deconvolution and downstream analysis. Currently, there is lack of an integrated protocol that includes a detailed procedure of how to measure or compare protein expression. Publications that use semi-quantification methods to quantify protein expression often don't provide enough details in their methods section, which makes it difficult for the reader to reproduce their data. The current protocol for the first time provides a detailed, step-by-step instruction of conducting semi-quantitative analysis of IHC images using ImageJ Fiji software so that researchers would be able to follow this single protocol to conduct their research. The protocol uses semi-quantitative IHC of organic anion transporting polypeptide (OATP1B1) as an example, and gives detailed steps on how to deconvolute IHC images stained with hematoxylin and 3, 3 - diaminobenzidine (DAB) and how to quantify their expression using ImageJ Fiji. The protocol includes clear steps for a reader so that this method can be applied to many different proteins. We anticipate this method will provide a practical guidance to the reader and make semi-quantification of proteins an easier task to include in publications.
Molecular cloning of the S-layer protein gene of Campylobacter rectus ATCC 33238 (1994)

A genomic DNA library of Campylobacter rectus (Wolinella recta) ATCC 33238 was constructed using bacteriophage lambda EMBL3 as a vector. One clone expressing the S-layer protein was identified immunologically with the antiserum to the S-layer protein of C. rectus ATCC 33238. Western immunoblotting using monoclonal antibodies directed against the S-layer protein showed a single blot of recombinant protein at 150 kDa, suggesting that this clone contained the entire coding region of the S-layer protein gene. Additionally, the S-layer protein gene was subcloned into plasmid vector pUC18. Southern hybridization revealed that the S-layer protein gene was present on the chromosome of C. rectus as a single-copy gene, and that there were minor heterogeneities among the S-layer protein genes of clinical isolates. Moreover, a spontaneous stable mutant strain, which has no S-layer expression, also conserved the full-length gene of the S-layer protein.
Study of the Heat-Treated Human Albumin Stabilization by Caprylate and Acetyltryptophanate (2002)

Sodium salt of N-acetyl-DL-tryptophan (AT) and octanoic acid (caprylic acid CA) individually and in combination were studied as thermal stabilizer with different concentrations in heat treatment of human albumin solution. HPLC protein profiles before pasteurization of albumin showed less than 1% polymer. In free stabilizer albumin solution during pasteurization visible clot was formed . But by using variation of the above mentioned stabilizers , the amount of polymer was increased to about 4% during pasteurization (60° C, 10 h). By increasing the heat to the visible clot formation point , the most effective stabilizer against visible clot formation was found to be CA. However, in drug formulation it is important to choose the variety and concentrati on of stabilizers in accordance with regulations. Iran. Biomed. J. 6 (4): 135-140, 2002
The Effect of Kurosaka Screw Divergence on the Holding Strength of Bone-Tendon-Bone Grafts (1995)

Fresh-frozen porcine knees were used to demonstrate the effects of diverging Kurosaka screw placement on linear load to failure in simulated anterior cruciate ligament reconstructions. Screws, placed anteromedially (rear-entry or tibial type) or intraarticularly (endoscopic femoral type) into each tibia, were directed at 0 degree, 15 degrees, or 30 degrees divergence angles relative to a guide wire. Grafts were axially loaded to failure to determine holding strength. Hierarchical analysis of variance was used to analyze differences between tibial side and endoscopic femoral type screw placement and the angles of divergence. Overall, the difference in pullout strength between rear-entry (or tibial side) and endoscopic femoral type fixation was shown to be statistically significant (P < 0.001). Anteromedially placed screws showed a statistically significant decrease in holding strength at 15 degrees and 30 degrees compared with 0 degree of divergence (P < 0.05). Intraarticular screw placement resulted in a statistically significant decrease in holding strength only at 30 degrees of divergence (P < 0.05). This study supports the importance of accurate screw placement within the tibia to ensure optimal interference fixation and suggests that endoscopic screw placement may offer significant added security when there are minor degrees of divergence.
Efficient clustering of identity-by-descent between multiple individuals (2013)

Source code is available under the GNU Public License http://cs.au.dk/~qianyuxx/EMI/.
A Digital Memory Fuel Controller for Gasoline Engines (1972)

<div class="htmlview paragraph">A digital memory fuel control unit has been developed for otto cycle engines which enables low pollution exhaust emissions to be achieved, coupled with good drivability and mechanical performance. The unit has been tested on a Triumph 2.5 PI vehicle, and the practical results achieved fall just short of the requirements of the 1975 federal and California legislation.</div> <div class="htmlview paragraph">The electronic controller receives signals relating to the engine's instantaneous operating conditions and, by reference to its digital memory, computes the optimum fuel required. The capacity of the controller's memory is effectively increased by an interpolation technique. The controller operates as an on-line process control computer, of cigar box dimensions, which is able to exist in the arduous automotive environment.</div>
Scalpel Sculpturing Techniques for Graft Revision and Dermatologic Surgery (1994)

Scalpel sculpting techniques provide a simple, efficient method of scar revision and removal of superficial skin lesions. The technique reduces operative time and streamlines instrument reprocessing. Because of its simplicity, there is a high degree of patient, nursing, and physician satisfaction.
Heterofucans from Dictyota menstrualis have anticoagulant activity (2004)

Fucan is a term used to denote a family of sulfated L-fucose-rich polysaccharides which are present in the extracellular matrix of brown seaweed and in the egg jelly coat of sea urchins. Plant fucans have several biological activities, including anticoagulant and antithrombotic, related to the structural and chemical composition of polysaccharides. We have extracted sulfated polysaccharides from the brown seaweed Dictyota menstrualis by proteolytic digestion, followed by separation into 5 fractions by sequential acetone precipitation. Gel electrophoresis using 0.05 M 1,3-diaminopropane-acetate buffer, pH 9.0, stained with 0.1% toluidine blue, showed the presence of sulfated polysaccharides in all fractions. The chemical analyses demonstrated that all fractions are composed mainly of fucose, xylose, galactose, uronic acid, and sulfate. The anticoagulant activity of these heterofucans was determined by activated partial thromboplastin time (APTT) using citrate normal human plasma. Only the fucans F1.0v and F1.5v showed anticoagulant activity. To prolong the coagulation time to double the baseline value in the APTT, the required concentration of fucan F1.0v (20 g/ml) was only 4.88-fold higher than that of the low molecular weight heparin Clexane (4.1 g/ml), whereas 80 g/ml fucan 1.5 was needed to obtain the same effect. For both fucans this effect was abolished by desulfation. These polymers are composed of fucose, xylose, uronic acid, galactose, and sulfate at molar ratios of 1.0:0.8:0.7:0.8:0.4 and 1.0:0.3:0.4:1.5:1.3, respectively. This is the fist report indicating the presence of a heterofucan with higher anticoagulant activity from brown seaweed.
The mutational landscape of phosphorylation signaling in cancer (2013)

Somatic mutations in cancer genomes include drivers that provide selective advantages to tumor cells and passengers present due to genome instability. Discovery of pan-cancer drivers will help characterize biological systems important in multiple cancers and lead to development of better therapies. Driver genes are most often identified by their recurrent mutations across tumor samples. However, some mutations are more important for protein function than others. Thus considering the location of mutations with respect to functional protein sites can predict their mechanisms of action and improve the sensitivity of driver gene detection. Protein phosphorylation is a post-translational modification central to cancer biology and treatment, and frequently altered by driver mutations. Here we used our ActiveDriver method to analyze known phosphorylation sites mutated by single nucleotide variants (SNVs) in The Cancer Genome Atlas Research Network (TCGA) pan-cancer dataset of 3,185 genomes and 12 cancer types. Phosphorylation-related SNVs (pSNVs) occur in ~90% of tumors, show increased conservation and functional mutation impact compared to other protein-coding mutations, and are enriched in cancer genes and pathways. Gene-centric analysis found 150 known and candidate cancer genes with significant pSNV recurrence. Using a novel computational method, we predict that 29% of these mutations directly abolish phosphorylation or modify kinase target sites to rewire signaling pathways. This analysis shows that incorporation of information about protein signaling sites will improve computational pipelines for variant function prediction.
Cholinergic Innervation of the Canine and Human Ventricular Conducting System (1974)

Augmentation of vagal tone increases ventricular fibrillation threshold (VFT) under nonischemic and ischemic conditions and protects against spontaneous ventricular fibrillation during experimental myocardial infarction. The purpose of this study was to identify the anatomic pathways responsible for this cholinergically-mediated enhanced electrical stability and to determine whether or not these pathways are present in human hearts. Rich cholinergic innervation of the sinoatrial node, atrioventricular node, and atrial myocardium was confirmed in both canine and human hearts. Although sparse cholinergic innervation was present in ventricular myocardium, numerous cholinergic nerve fibers were present in ventricular conduction tissue of both canine and human hearts. To determine whether these cholinergic fibers mediate the protective effects of vagal stimulation, cholinergic fibers to the ventricular conducting system were ablated in dogs. The ablation procedures used resulted in histologic absence of cholinergic nerves in the ventricular conducting system; innervation of the atrium, however, was histologically intact. In these animals vagal stimulation no longer increased VFT but still caused slowing of the sinus rate. The effect of vagal stimulation on VFT was shown to be independent of adrenergic innervation in a group of catecholamine depleted animals (6-hydroxydopamine). We conclude that 1) the enhanced ventricular electrical stability produced by vagal stimulation in dogs is mediated by cholinergic nerve fibers which supply the ventricular conduction system, and 2) this anatomic pathway is present in human hearts.
Maya Blue—Further Perspectives and the Possible Use of Indigo as the Colorant (1982)

A blue pigment having the chemical stability of authentic Maya Blue can be prepared from indigo and attapulgite with the raw materials available to the ancient Maya, and by techniques presumably within their knowledge. The procedure possibly used consists of impregnating attapulgite with an extract of indigo plant leaves and stems and subsequently heating the impregnated clay for an extended period of time at the temperature of boiling water. This procedure would obviate the need for transportation of montmorillonite to areas far removed from its source and would account for the existence of the various types of Maya Blue noted in a previous report.
Long duration impulse withstand capability of SPD (2010)

In low voltage system, there are varity impulse happened with different peak value and time duration due to the lightning and equipment operation or faults. SPD is the main protective device withstanding those impulse, it is widely used in the low power system. However SPD's fault usually lead to big loss in using. Thence SPD's reliability is the focus element concerned by users. To improve the reliability of SPD in using is a very important subject in the field of manufacture and application.
The pulsed wire anemometer: review and further developments (2000)

The purpose of the present paper is to review work that has been done on the pulsed wire anemometer technique and also suggest further developments that could be made in its range of application. The aper discusses the three types of probes that have been used in pulsed wire anemometry: the crossed wire velocity probe, the parallel wire wall shear stress probe and the parallel wire velocity probe. The work shows that the crossed wire and the parallel wire techniques can be used to make velocity, turbulence and wall shear stress measurements in highly turbulent flows without any upper restriction on turbulence level. Comments are also made on the potential of a parallel wire probe for use in highly turbulent flows that would enable higher order velocity cross-product terms to be measured.
Performance bounds for power control supported DCA-algorithms in highway micro cellular radio systems (1995)

To achieve a high spectrum efficiency in cellular radio systems, the radio resource allocation algorithms have to be adaptive to the actual traffic and interference situation. The focus of the paper is on performance bounds of a cellular radio system using dynamic channel assignment (DCA) combined with power control (PC). A trivial upper bound on the performance is identified. The bound is given by the performance of a hypothetical system which is able to use all channels simultaneously in all cells. A lower bound on the performance is derived from a theoretical PC supported DCA-algorithm. For a highway micro cellular system and a deterministic propagation model, numerical results show that the lower and upper bounds are tight. That is, the results indicate that it is possible to use all channels in all cells simultaneously and still provide an acceptable signal-to interference ratio in all assigned communication links.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A cost oriented algorithm for data set allocation in storage hierarchies (1975)

Data set allocation in today's multilevel storage systems is usually based on qualitative, ad hoc decisions. While it would be desirable to obtain an optimal solution to this allocation problem, it is clear that the number of parameters involved makes it intractable to straight-forward solution. In such a situation, we must find a set of assumptions which simplify the problem greatly, but which still provide a basis for considering all significant cost elements. This paper presents such a first, quantitative allocation step. It considers many of the significant detailed costs of system utilization, data storage, data staging, and data migration. Although many avenues of further improvement are available, the present algorithm seems to be usefully accurate. As such, it can aid in quantifying the problems of data set allocation, storage system configuration, and new device designs.
The Chemistry of Silicon‐Sulfur Compounds (1965)

Abstract The preparations, properties, structures, and chemical reactions of silicon‐sulfur compounds are reported. The chain structure of the polymeric silicon disulfide is used as a basis from which the various classes of compounds can be derived: cyclothiasilanes, disilyl sulfides, silanethiols, and organothiosilanes. Infrared data and force constants of the Si‐S bond are discussed.
Simulation of Schottky barrier MOSFETs with a coupled quantum injection/Monte Carlo technique (2000)

A full-band Monte Carlo device simulator has been used to analyze the performance of sub-0.1 /spl mu/m Schottky barrier MOSFETs. In these devices, the source and drain contacts are realized with metal silicide, and the injection of carriers is controlled by gate voltage modulation of tunneling through the source barrier. A simple model treating the silicide regions as metals, coupled with an Airy function approach for tunneling through the barrier, provides injecting boundary conditions for the Monte Carlo procedure. Simulations were carried out considering a p-channel device with 270 /spl Aring/ gate length for which measurements are available. Our results show that in these structures there is not a strong interaction with the oxide interface as in conventional MOS devices and carriers are injected at fairly wide angles from the source into the bulk of the device. The Monte Carlo simulations not only give good agreement with current-voltage (I-V) curves, but also easily reproduce the subthreshold behavior since all the computational power is devoted to simulation of channel particles. The simulations also clarify why these structures exhibit a large amount of leakage in subthreshold regime, due to both thermionic and tunneling emission. Computational experiments suggest ways to modify the doping profile to reduce to some extent the leakage.
A single layer dual band circularly polarized microstrip antenna for GPS applications (2003)

Most current GPS receivers only use the L1 frequency of 1.575 GHz with right hand circular polarization. However, in some applications that need more accurate information, differential GPS is employed and an antenna is required to cover both L1 and L2 (1.227 GHz) bands with CP patterns. Recently, we proposed a square patch antenna with switchable slots for dual band CP operation (see Yang, F. and Rahmat-Samii, Y., Electronics Lett., vol.37, p.1002-3, 2001). It has attractive features of a single layer, a single feed, and small frequency ratio. Hence, such an antenna is proposed for GPS applications. The antenna structure and its design procedure are detailed.
Citicoline Treatment for Experimental Intracerebral Hemorrhage in Mice (1998)

In this animal model of ICH, treatment with citicoline significantly improved functional outcome and reduced the volume of ischemic injury surrounding the hematoma. This study supports a potential role for citicoline in clinical ICH treatment.
Fractionation of Kraft Lignin by Successive Extraction with Organic Solvents. III. Fractionation of Kraft Lignin from Birch (1988)

Article Fractionation of Kraft Lignin by Successive Extraction with Organic Solvents. III. Fractionation of Kraft Lignin from Birch was published on January 1, 1988 in the journal Holzforschung (volume 42, issue 2).
Subcarrier Spreading for ICI Mitigation in OFDM/OFDMA Systems (2010)

Two of the major challenges facing OFDM/OFDMA systems are their sensitivity to frequency selective fading and ICI due to CFO or Doppler shift, especially when the subcarrier spacing becomes smaller. We propose an OFDM transceiver design that employs frequency redundant subcarrier mapping to mitigate frequency selective fading and subcarrier spreading to achieve ICI self cancellation. Both our theoretical analysis and simulation show that such a code-spread-interleaved-redundant OFDM system design offers significant (over 10 dB) improvement in CIR and robust BER performance in different channel conditions.
DNA transposon <i>Hermes</i> inserts into DNA in nucleosome-free regions in vivo (2010)

Transposons are mobile genetic elements that are an important source of genetic variation and are useful tools for genome engineering, mutagenesis screens, and vectors for transgenesis including gene therapy. We have used second-generation sequencing to analyze ≈2 × 10(5) unique de novo transposon insertion sites of the transposon Hermes in the Saccharomyces cerevisiae genome from both in vitro transposition reactions by using purified yeast genomic DNA, to better characterize intrinsic sequence specificity, and sites recovered from in vivo transposition events, to characterize the effect of intracellular factors such as chromatin on target site selection. We find that Hermes transposon targeting in vivo is profoundly affected by chromatin structure: The subset of genome-wide target sites used in vivo is strongly associated (P < 2e-16 by Fisher's exact test) with nucleosome-free chromatin. Our characterization of the insertion site preferences of Hermes not only assists in the future use of this transposon as a molecular biology tool but also establishes methods to more fully determine targeting mechanisms of other transposons. We have also discovered a long-range sequence motif that defines S. cerevisiae nucleosome-free regions.
Analytic Requirements for the Doubly Labeled Water Method (1995)

The doubly labeled water method is the first method that accurately measures total daily energy expenditure in free-living subjects over periods of days to weeks. Validations have indicated that the method can be performed with a coefficient of variation of between 3% and 5%. This precision, however, is dependent on the quality of the isotopic analyses. A recent interlaboratory comparison has indicated that there is a wide variation in the accuracy and precision with which deuterium and 18O enrichments are measured. This reduces the accuracy and precision with which a laboratory will perform the doubly labeled water method and in some cases may limit the application of this technique. Herein we review the analytical requirements for optimal use of the method and some of the potential sources of error in the stable isotope analysis.
In vivo studies on the regeneration kinetics of enriched populations of haemopoietic spleen colony-forming cells from normal bone marrow. (1983)

Functional properties of mouse haemopoietic spleen colony-forming cells, enriched 40- to 80-fold, from normal bone marrow were studied. It was found that: (1) the number of partially purified CFU-s (colony forming unit-spleen) required to rescue lethally irradiated mice was similar to the number of normal unfractionated bone marrow CFU-s giving the same level of protection; (2) the homing of partially purified CFU-s was similar to that of CFU-s from unfractionated bone marrow; (3) the regeneration of CFU-s in spleen was similar for enriched and unfractionated cell populations between 4 and 11 days after transplantation. In contrast, the rate of regeneration of CFU-s in femur was slower with enriched progenitor cells than with unfractionated bone marrow. The growth rate in femur, however, could be restored to normal by injecting freshly isolated syngeneic thymocytes with the enriched CFU-s population. The results indicate that the partially purified CFU-s are by themselves functionally normal and show that the rate of CFU-s repopulation in bone marrow can be affected by cell types other than spleen colony-forming cells.
Stopper-less hybrid low-k/Cu DD structure fabrication combined with low-k CMP (2003)

We demonstrated a stopper-less hybrid of low-k/Cu dual damascene using organic (k=2.65) and inorganic low-k (k=2.6) films for a 0.13-/spl mu/m node to obtain lower effective k and good planarization. An inorganic low-k CMP and dual hard mask process were used. This process had good etching selectivity, a low RC value, and good via yield, and in the case with inorganic low-k CMP, no metal residue remained in the multi-layered structure. Using these technologies, a 5-layered hybrid structure was established.