gebhart/patrepeval huggingface dataset:
Surface Structure and Coverage of an Oligonucleotide Probe Tethered onto a Gold Substrate and Its Hybridization Efficiency for a Polynucleotide Target (2001)

A single-stranded oligonucleotide whose 5‘ end is derivatized with a mercaptohexyl tether group was either directly anchored onto a gold surface or attached to a gold surface as part of a mixed self-assembled monolayer that contains mercaptohexanol. The application of these surface-confined DNA oligomers as heterogeneous probes for the detection of polynucleotides (e.g., M13 phage DNA) is considered, with an emphasis on the elucidation of the relationship between the hybridization efficiency and the surface coverage and orientation of the probe molecules. Atomic force microscopy (AFM) and flow-injection quartz crystal microbalance (FI-QCM) were used in tandem to study the immobilization of the probe, to estimate the extent and efficiency of the hybridization of M13 phage DNA (7249 bases), and to examine the effect of using a different alkanethiol to reorient the preformed film for a higher hybridization efficiency. The surface density and the resultant hybridization efficiency were found to be highly dependent on the morphology and surface structure of the gold substrate as well as on the concentration of the solution used for the probe fabrication but much less dependent on the probe immobilization time. The lower limit of the hybridization efficiency was estimated to be about 1.1% which is an underestimate because only the resolvable circular features were included in the estimation. Although the duplex formed at the gold surface covered with only the thiolated DNA probe adopts exclusively the orientation in which the target loop is parallel with respect to the substrate surface, the predominant duplex orientation at the gold substrate modified with mixed self-assembled monolayers is tethered to the surface with a small tilt angle versus the surface normal. Visualization of the duplex orientation allows one to understand whether the Sauerbrey equation is valid for the interpretation of certain FI-QCM results. Although it is probably valid to use the Sauerbrey equation to calculate the amount of a polynucleotide at a surface covered only by the thiolated DNA probe, the practice might be questionable for that at the surface with the DNA/alkanethiol mixed SAM on the basis of our AFM images of the target orientations.
Real-time clothes comparison based on multi-view vision (2008)

In this paper, we present a clothing recognition system that augments clothes recommendation and fashion exploration using the intelligent multi-view vision technology of the responsive mirror, an implicitly controlled human-computer interaction system for clothes fitting rooms. The responsive mirror provides shoppers with real-time ldquoselfrdquo and ldquosocialrdquo clothes comparisons. The system recommends clothing that is ldquosimilarrdquo and ldquodifferentrdquo than the clothing that the person is trying on in the mirror. The goal of the research in this paper is to create a recommendation system that uses a definition of ldquosimilarrdquo and ldquodifferentrdquo that matches human perception. We address the social nature of the recognition problem by conducting a user study to identify the salient clothes factors that people use to determine clothes similarity. We describe the computer vision and machine learning techniques employed to recognize the factors that human eyes perceive in term of clothing similarity from frontal-view outfit images. We describe the key components of the motion-tracking and clothes-recognition systems and evaluate their performance by user study and experiments on a simulated clothes fitting image dataset. The approach and results presented here will benefit designers and developers of similar applications in the future.
A 150pW program-and-hold timer for ultra-low-power sensor platforms (2009)

Lifetime and form factor are two critical concerns for emerging sensor platforms, particularly for applications such as implantable medical devices. The limited energy from power sources, typically either microfabricated batteries or scavenged energy, remains one of the biggest challenges for such platforms. Reducing power consumption can lower system volume and extend lifetime. To achieve very low power consumption aggressive voltage scaling has been applied in recent microsystems. The average power consumption of sensor platforms, which are often low duty cycle, can be greatly reduced by applying strong power gating while idling. A key component in power gating is the timekeeping device while the system is in the idle mode. Since the timer is always active, it is often the dominant source for energy loss and must oscillate at a low frequency (e.g., from sub-Hzto 10Hz).
Modified microdialysis probe for sampling extracellular fluid and administering drugs in vivo (1993)

In vivo microdialysis provides an important new tool for investigating changes in extracellular fluid levels of endogenous compounds in vivo. Delivery of drugs via the microdialysis probe can be used to study local release and metabolism of neurotransmitters, but the dialysis membrane limits diffusion of substances between the perfusate and the extracellular fluid. Thus there may be considerable delay in responses, drug concentrations at the effector sites are less than those in the probe, and high-molecular-weight substances cannot traverse the membrane at all. This report describes a simple modification of commercially available microdialysis probes. A cannula is glued to the external surface of the probe. When glycine was administered via the cannula into the striatum of conscious rats, increments in microdialysate concentrations of dopamine were at least 10 times greater than when glycine was administered via the dialysis fluid in the probe. The threshold glycine dose for behavioral (turning) effects was also decreased by approximately 60-fold, and the time to the peak neurochemical and behavioral effects was markedly decreased. The modified probe did not destroy local catecholaminergic cells, as indicated by tyrosine hydroxylase immunofluorescence. Use of the modified microdialysis probe should facilitate pharmacological and neuroendocrine studies in behaving animals.
Reply to “Speaker identification by speech spectrograms: some further observations” [R.H. Bolt, F.S. Cooper, E.E. David, P.B. Denes, J.M. Pickett, and K.N. Stevens, J. Acoust. Soc. Am. <b>54</b>, 531–534 (1973)] (1973)

In their letter to the editor, “Speaker identification by speech spectrograms: some further observations,” Bolt et al. [J. Acoust. Soc. Am. 54, 531–534 (1973)] express an opinion on voice identification as produced in real-life cases by specially trained professional examiners using a combined aural and visual examination of speaker samples. The opinion of these authors is not based on personal experience or even on a direct observation of these examinations. In addition, they disregard crucial facts that strongly interact with the reliability of those positive decisions produced by professional, full-time examiners, such as their special training and responsibility, the five possible decisions they are entitled to produce after each examination, the number of samples, and the length of time used to perform each examination. It is our contention that opinions based on feelings other than in actual experience are of little value, irrespective of the scientific authority of those who produce such an opinion.
Application of in‐gel protease assay in a biological sample: Characterization and identification of urokinase‐type plasminogen activator (uPA) in secreted proteins from a prostate cancer cell line PC‐3 (2004)

A considerable problem in proteomics is to separate and identify functional proteins that participate in specific biological processes. To expedite the analysis of active proteases, we have developed a substrate-specific, sensitive in-gel trypsin activity assay after two-dimensional (2-D) separation in a sodium dodecyl sulphate (SDS)-polyacrylamide gel [22]. Using this method, we detected and characterized Arg-specific protease activity in the secreted protein sample of a prostate cancer cell line, PC-3, in 1-D and 2-D gels. Mass spectrometry (MS) identified the protease as urokinase-type plasminogen activator (uPA). Western blotting using anti-uPA antibody and protease inhibition tests confirmed the identification. Since no antibody was involved in the procedure, the result clearly demonstrates the feasibility of this method for identifying novel proteases in biological samples.
Location of the Two Genes Encoding Glutaconate Coenzyme A‐Transferase at the Beginning of the Hydroxyglutarate Operon in <i>Acidaminococcus fermentans</i> (1994)

Glutaconate coenzyme A-transferase (Gct) from Acidaminococcus fermentans consists of two subunits (GctA, 35725 Da and GctB, 29168 Da). The N-termini sequences of both subunits were determined. DNA sequencing of a subgenomic fragment of A. fermentans revealed that the genes encoding glutaconate CoA-transferase (gctAB) are located upstream of a gene cluster formed by gcdA, hgdC, hgdA and hgdB in this order. Further upstream of gctA, a DNA sequence was detected showing significant similarities to sigma 70-type promoters from Escherichia coli. Primer-extension analysis revealed that this specific DNA sequence was indeed the location of transcription initiation in A. fermentans. The entire gene cluster, 7.3 kb in length, comprising gctAB, gcdA and hgdCAB, has tentatively been named the hydroxyglutarate operon, since the enzymes encoded by these genes are involved in the conversion of (R)-2-hydroxyglutarate to crotonyl-CoA in the pathway of glutamate fermentation by A. fermentans. The genes gctAB were expressed together in E. coli. Cell-free extracts of a transformant E. coli strain contained glutaconate CoA-transferase at a specific activity of up to 30 U/mg protein. The recombinant enzyme was purified to homogeneity with a specific activity of 130 U/mg protein by ammonium sulfate fractionation and crystallisation. The amino acid residue directly involved in catalysis was tentatively identified as E54 of the small subunit of the enzyme (GctB).
Aerobic granulation (2000)

Heterotrophic aerobic granular sludge was cultivated in a sequencing batch airlift reactor (SBAR). A steady state operation, at a COD loading of 2.3 kg COD/(m3· d), was run for 50 days after which the experiment was terminated. The granules obtained were smooth, 1.0 mm in diameter and had a density of 48 g/l. Selection of dense granules occurred by applying a short settling time. Slow settling s ludge was washed out with the effluent and only the granules with good settling properties settled fast enough (vmin&gt;16.2 m/h) to be retained in the reactor. Nitrification and almost complete denitrification occurred in the fully aerobic SBAR without any optimization of the process conditions. Compared to a sequencing batch bubble column (SBBC) much more dense granules with a smaller diameter were obtained in the SBAR at the same substrate loading rate and the same mixing intensity. Compared to granules formed in a, continuous fed, biofilm airlift suspension (BAS) reactor much more dense granules were obtained in the SBAR as well. The diameter of the granules in the BAS reactor was smaller than in the SBAR. Possible reasons for the better quality of the sludge granules in the SBAR are discussed.
Exploring the bounds of web latency reduction from caching and prefetching (1997)

Prefetching and caching are techniques commonly used in I/O systems to reduce latency. Many researchers have advocated the use of caching and prefetching to reduce latency in the Web. We derive several bounds on the performance improvements seen from these techniques, and then use traces of Web proxy activity taken at Digital Equipment Corporation to quantify these bounds. We found that for these traces, local proxy caching could reduce latency by at best 26%, prefetching could reduce latency by at best 57%, and a combined caching and prefetching proxy could provide at best a 60% latency reduction. Furthermore, we found that how far in advance a prefetching algorithm was able to prefetch an object was a significant factor in its ability to reduce latency. We note that the latency reduction from caching is significantly limited by the rapid changes of objects in the Web. We conclude that for the workload studied caching offers moderate assistance in reducing latency. Prefetching can of...
Optimizing multiplex CRISPR/Cas9-based genome editing for wheat (2016)

Abstract Background CRISPR/Cas9-based genome editing holds great promise to accelerate the development of new crop varieties by providing a powerful tool to modify the genomic regions controlling major agronomic traits. To diversify the set of tools available for wheat genome engineering, we have established a tRNA-based multiplex gene editing strategy for hexaploid wheat. Results The functionality of the various CRISPR/Cas9 components was assessed using the transient expression in the wheat protoplasts followed by next-generation sequencing (NGS) of the targeted genomic regions. The efficiency of wheat codon-optimized Cas9 for targeted gene editing in wheat was validated. Multiple single guide RNAs (gRNAs) were evaluated for the ability to edit the homoeologous copies of four genes affecting some important agronomic traits in wheat. Low correspondence was found between the gRNA efficiency predicted bioinformatically and that assessed in the transient expression assay. A multiplex gene editing construct with several gRNA-tRNA units under the control of a single promoter for the RNA polymerase III generated indels at the targets sites with the efficiency comparable to that obtained for a single gRNA construct. Conclusions By integrating the protoplast transformation assay with multiplexed NGS, it is possible to perform fast functional screens for a large number of gRNAs and to optimize constructs for effective editing of multiple independent targets in the wheat genome. The multiplexing capacity of the tandemly arrayed tRNA–gRNA construct is well suited for the simultaneous editing of the redundant gene copies in the allopolyploid genomes or genomic regions beneficially affecting multiple agronomic traits. A polycistronic gene construct that can be quickly assembled using the Golden Gate reaction along with the wheat codon optimized Cas9 will further expand the set of tools available for engineering the wheat genome.
A Symmetrical Analog Wide-band Multiplier IC Operating Up To 8Gb/s (1991)

Linear multipliers are key elements in communication sys­tems. The silicon bipolar four-quadrant multiplier presented in this paper was developed for use in the DPSK demodulator of an experimental multi-Gb/s coherent optical-fiber system at the Heinrich Hertz Institute, Berlin. Its features include: dc to 6GHz bandwidth (8 Gb/s) with respect to both inputs and the output, decoupling of all three ports, matched impedance inputs, single -5V power supply, and exact symmetry with respect to both inputs. Other silicon bipolar mixer !Cs operating in the GHz range do not meet the requirements imposed on this analog multiplier.1.2
Analysis of Wireless Power Transfer for Adjustable Power Distribution among Multiple Receivers (2015)

In a multiple-receiver wireless power transfer system, most of the power tends to be transferred to a receiver close to a transmitter. Therefore, it is highly desirable to find a way of providing the required amount of power to each receiver, as well as to improve the overall power transfer efficiency. In this letter, we investigate an impedance matching method of providing adjustable power distribution among receivers while preserving a high overall power transfer efficiency using coupled mode theory and circuit model. We also derive an optimal matching condition and the upper bound of the overall power transfer efficiency, in order to assess the performance of the proposed method. Finally, we perform circuit-level simulations to validate the accuracy of our analysis and the effectiveness of the proposed method.
How I treat patients with thrombotic thrombocytopenic purpura: 2010 (2010)

Thrombotic thrombocytopenic purpura (TTP) is the common name for adults with microangiopathic hemolytic anemia, thrombocytopenia, with or without neurologic or renal abnormalities, and without another etiology; children without renal failure are also described as TTP. The diagnosis of TTP is an indication for plasma exchange treatment, but beginning treatment requires sufficient confidence in the diagnosis to justify the risk of plasma exchange complications. Documentation of a severe deficiency of plasma ADAMTS13 activity, defined as less than 10% of normal, is not essential for the diagnosis of TTP. Some patients without severe ADAMTS13 deficiency may benefit from plasma exchange treatment; in addition, some patients with severe ADAMTS13 deficiency may subsequently be diagnosed with another cause for their clinical features. However, severe acquired ADAMTS13 deficiency does define a subgroup of patients who appear to benefit from treatment with corticosteroids and other immunosuppressive agents in addition to plasma exchange but who have a high risk for relapse. Approximately 80% of patients survive their acute episode, a survival rate that has not changed since the introduction of plasma exchange treatment. Although recovery may appear to be complete, many patients have persistent minor cognitive abnormalities. More effective as well as safer treatment for TTP is needed.
Mitigating congestion in wireless sensor networks (2004)

Network congestion occurs when offered traffic load exceeds available capacity at any point in a network. In wireless sensor networks, congestion causes overall channel quality to degrade and loss rates to rise, leads to buffer drops and increased delays (as in wired networks), and tends to be grossly unfair toward nodes whose data has to traverse a larger number of radio hops.
Correction of iron deficiency in trees by injection with ferric ammonium citrate solution (1986)

Abstract Ferric ammonium citrate is more soluble than iron sulfate, and a very few ml. is all that is needed to supply Fe to trees when injected into trunks of the trees. Ten ml. of a solution with 8% Fe contains enough Fe to increase leaf concentration in 16 kg of leaves by 50 mg kg‐1 expressed on a dry weight basis; this would be a moderately large tree. The technique used is to slant drill holes on two or more sides of a tree and at different elevations, and then add Fe with a syringe corresponding with size of tree. The tree is left to absorb the solution. Control is achieved in days for most species. A few species do not respond. Overtreatment is easy because of the high concentration of Fe. This ferric ammonium citrate method has been used on numerous trees with no injury. Regreening starts to take place within a week. A commercial product is available which has a balance of manganese with some nitrogen. The cost per very large tree for this product is about $0.25 USA. The method is rapid enough for a single operator to do several hundred trees a day. It is suggested that the hole be covered with an asphalt‐base tree‐sealing compound after the Fe solution has been applied. The sterilization of the drill bit, either by alcohol or flame, would be recommended in those areas where bacterial or viral diseases are problems. Since it has been reported that citrus trees absorb fluids poorly, citrus was selected for leaf tissue measurement before and after treatment. About 5 ml. of the ferric ammonium citrate increased the leaf Fe concentration by 50%. The trees used were mature, being about 20 years old. Zinc chelate was tested and found to be effective; DTPA was better than EDTA. Zinc sulfate was ineffective. As a consequence of the zinc treatment, it was found that phosphorus concentrations were elevated.
DNA methylation as a universal biomarker (2010)

Cell-free circulating DNA carries not only tumor-specific changes in its sequence but also distinctive epigenetic marks, namely DNA methylation, in certain GC-rich fragments. These fragments are usually located within the promoters and first exons of many genes, comprising CpG islands. Analysis of DNA methylation using cell-free circulating DNA can facilitate development of very accurate biomarkers for detection, diagnosis, prediction of response to therapy and prognosis of outcomes. Recent data suggest that benign and inflammatory diseases have very specific methylation patterns within cell-free circulating DNA, which are different from the pattern of a malignant tumor of the same organ. In addition, specific methylation patterns have been detected for cancers of different organs, so a differential diagnosis of site-specific cancer appears feasible. Currently, cancer-related applications dominate the field, although methylation-based biomarkers may also be possible for other diseases, including neurodegenerative and psychiatric disorders.
Implication of chromosome 11 in the suppression of neoplastic expression in human cell hybrids. (1986)

Cytogenetic analyses of intraspecies human HeLa X fibroblast hybrid cell populations have provided tentative evidence for the correlation of loss of a single copy of chromosomes 11 and 14 with reexpression of tumorigenicity. In this study paired combinations of nontumorigenic and tumorigenic segregant HeLa X fibroblast hybrid cells from two independent fusion events were examined for the presence or absence of normal chromosomes 11 and 14. In human hybrid cell lines the parental origin of chromosomes can be distinguished on the basis of restriction fragment length polymorphisms. Genes for c-Ha-ras, insulin, and apolipoprotein A-1 on chromosome 11 and a polymorphic locus AW101 on chromosome 14 were used as Southern hybridization probes. Analysis of DNA from the parental fibroblast and HeLa cell lines and their nontumorigenic and tumorigenic hybrids showed the loss of a fibroblast chromosome 11 in four of the tumorigenic segregants and a HeLa chromosome 11 in a fifth hybrid cell line. This latter segregant has, interestingly, also lost a copy of chromosome 14 of fibroblast origin. There was no obvious correlation of loss of a copy of normal chromosome 14 and reexpression of tumorigenicity in any of the other hybrid cell populations. Our conclusion from these observations is that gene(s) that map to normal chromosome 11 might be involved in control of tumorigenic expression in these human hybrid cells.
Fiberless multicolor neural optoelectrode for in vivo circuit analysis (2016)

Maximizing the potential of optogenetic approaches in deep brain structures of intact animals requires optical manipulation of neurons at high spatial and temporal resolutions, while simultaneously recording electrical data from those neurons. Here, we present the first fiber-less optoelectrode with a monolithically integrated optical waveguide mixer that can deliver multicolor light at a common waveguide port to achieve multicolor modulation of the same neuronal population in vivo. We demonstrate successful device implementation by achieving efficient coupling between a side-emitting injection laser diode (ILD) and a dielectric optical waveguide mixer via a gradient-index (GRIN) lens. The use of GRIN lenses attains several design features, including high optical coupling and thermal isolation between ILDs and waveguides. We validated the packaged devices in the intact brain of anesthetized mice co-expressing Channelrhodopsin-2 and Archaerhodopsin in pyramidal cells in the hippocampal CA1 region, achieving high quality recording, activation and silencing of the exact same neurons in a given local region. This fully-integrated approach demonstrates the spatial precision and scalability needed to enable independent activation and silencing of the same or different groups of neurons in dense brain regions while simultaneously recording from them, thus considerably advancing the capabilities of currently available optogenetic toolsets.