gebhart/patrepeval huggingface dataset:
Precision of Heavy–Light Peptide Ratios Measured by MALDI-TOF Mass Spectrometry (2012)

We have investigated the precision of peptide quantitation by MALDI-TOF mass spectrometry (MS) using six pairs of proteotypic peptides (light) and same-sequence stable isotope labeled synthetic internal standards (heavy). These were combined in two types of dilution curves spanning 100-fold and 2000-fold ratios. Coefficients of variation (CV; standard deviation divided by mean value) were examined across replicate MALDI spots using a reflector acquisition method requiring 100 000 counts for the most intense peak in each summed spectrum. The CV of light/heavy peptide centroid peak area ratios determined on four replicate spots per sample, averaged across 11 points of a 100-fold dilution curve and over all six peptides, was 2.2% (ranging from 1.5 to 3.7% among peptides) at 55 fmol total (light + heavy) of each peptide applied per spot, and 2.5% at 11 fmol applied. The average CV of measurements at near-equivalence (light = heavy, the center of the dilution curve) for the six peptides was 1.0%, about 17-fold lower CV than that observed when five peptides were ratioed to a sixth peptide (i.e., a different-sequence internal standard). Response curves across the 100-fold range were not completely linear but could be closely modeled by a power law fit giving R(2) values >0.998 for all peptides. The MALDI-TOF MS method was used to determine the endogenous level of a proteotypic peptide (EDQYHYLLDR) of human protein C inhibitor (PCI) in a plasma digest after enrichment by capture on a high affinity antipeptide antibody, a technique called stable isotope standards and capture by anti-peptide antibodies (SISCAPA). The level of PCI was determined to be 770 ng/mL with a replicate measurement CV of 1.5% and a >14 000-fold target enrichment via SISCAPA-MALDI-TOF. These results indicate that MALDI-TOF technology can provide precise quantitation of high-to-medium abundance peptide biomarkers over a 100-fold dynamic range when ratioed to same-sequence labeled internal standards and enriched to near purity by specific antibody capture. The robustness and throughput of MALDI-TOF in comparison to conventional nano-LC-MS technology could enable currently impractical large-scale verification studies of protein biomarkers.
Optically referenced double comb interferometry: applications and technological needs (2011)

Interferogram chirping to enhance the quality of dual comb interferometry is discussed, along with the associated trade with multiplicative noise. It is also shown that the signal providing the optical path difference axis is not oscillating at the carrier frequency of the optical signal. Applications less affected by the limited spectral range are proposed.
<i>In vivo</i>characterization of a polymeric nanoparticle platform with potential oral drug delivery capabilities (2008)

Nanotechnology has enabled significant advances in the areas of cancer diagnosis and therapy. The field of drug delivery is a sterling example, with nanoparticles being increasingly used for generating therapeutic formulations of poorly water-soluble, yet potent anticancer drugs. Whereas a number of nanoparticle-drug combinations are at various stages of preclinical or clinical assessment, the overwhelming majorities of such systems are injectable formulations and are incapable of being partaken orally. The development of an oral nano-delivery system would have distinct advantages for cancer chemotherapy. We report the synthesis and physicochemical characterization of orally bioavailable polymeric nanoparticles composed of N-isopropylacrylamide, methylmethacrylate, and acrylic acid in the molar ratios of 60:20:20 (designated NMA622). Amphiphilic NMA622 nanoparticles show a size distribution of <100 nm (mean diameter of 80 +/- 34 nm) with low polydispersity and can readily encapsulate a number of poorly water-soluble drugs such as rapamycin within the hydrophobic core. No apparent systemic toxicities are observed in mice receiving as much as 500 mg/kg of the orally administered void NMA622 for 4 weeks. Using NMA622-encapsulated rapamycin ("nanorapamycin") as a prototype for oral nano-drug delivery, we show favorable in vivo pharmacokinetics and therapeutic efficacy in a xenograft model of human pancreatic cancer. Oral nanorapamycin leads to robust inhibition of the mammalian target of rapamycin pathway in pancreatic cancer xenografts, which is accompanied by significant growth inhibition (P < 0.01) compared with control tumors. These data indicate that NMA622 nanoparticles provide a suitable platform for oral delivery of water-insoluble drugs like rapamycin for cancer therapy.
Immobilized Marasmius oreades agglutinin: use for binding and isolation of glycoproteins containing the xenotransplantation or human type B epitopes (2003)

The type B-specific lectin from the mushroom Marasmius oreades was immobilized onto Sepharose 4B. The immobilized lectin bound murine laminin and bovine thyroglobulin, glycoproteins that contain the Galalpha1,3Galbeta1,4GlcNAc epitope. This epitope is responsible for hyperacute rejection of xenotransplants from lower mammals to humans, Old World monkeys, or apes. The immobilized lectin also bound a fraction of serum proteins from type B human serum but little or none from type A or O(H) serum. The major protein bound from human B serum was a portion of the alpha2-macroglobulin. Treatment of this fraction with N-glycosidase F resulted in decreased molecular weight of bands associated with alpha2-macroglobulin and loss of their M. oreades lectin reactivity, whereas on treatment with coffee bean alpha-galactosidase, this bound fraction also lost reactivity with M. oreades lectin but became reactive with Ulex europaeus I lectin, suggesting the presence of L-fucosyl-alpha1,2-terminated structures. The presence of blood group epitopes on alpha2-macroglobulin has been detected previously by immunological methods, but this is the first isolation and characterization of the specifically glycosylated fraction of this serum protein. The immobilized lectin also bound a number of proteins from pig, rabbit, and rat serum that were distinct in electrophoretic mobility from the human B-serum components and presumably contain the xenotransplantation epitope among their glycan structures. This report further demonstrates the utility of immobilized lectins in isolating and characterizing glycan structures of naturally occurring glycoproteins.
Characterization of N,N(Me)2-Dmt-Tic-OH, a delta selective opioid dipeptide antagonist (2000)

N,N(Me)2-Dimethyl-tyrosine-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid-OH (N,N(Me)2-Dmt-Tic-OH) is a very selective delta opioid dipeptide with elevated antagonist activity. We have radiolabelled this compound by catalytic tritiation of the N,N(Me)2-Dmt(3',5'-I2)-Tic-OH precursor. The ligand labelled rat brain membranes with a Kd value of 0.42 nM and a Bmax of 63.12 fmol/mg protein. The new tritiated ligand showed high affinity for the delta opioid receptor whereas its binding at mu and kappa opioid receptors was weak. N,N(Me)2-Dmt-Tic-OH was able to inhibit the agonist-stimulated binding of the non-hydrolysable GTP analogue ¿35SGTPgammaS, thus attenuating the activation of G proteins via opioid receptors. This simple opioid dipeptide in both normal and labelled form may serve as a useful tool to study delta opioid receptors in vitro and in vivo.
A self-organizing network for computing a posteriori conditional class probability (1993)

A neural network architecture whose goal is the computation of a posteriori conditional class probabilities for input vectors that belong to one of two input classes is described. The network architecture has been designed to adaptively produce Voronoi tessellation partitions of the input vectors in R/sup n/ based on the Euclidean distance metric, without regard to the actual a priori class probabilities of the input vectors. These prior probabilities are then used by the network to adaptively compute the a posteriori conditional class probability for the two classes for each tessellation partition. The network presented is thus a connectionist model for vector quantization clustering and includes the process of automatic node creation necessary for many unsupervised learning applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Thread-Mounted Thermocouple (1988)

Thread-mounted thermocouple developed to accurately measure temperature of surrounding material. Comprised of threaded rod or bolt drilled along length, dual-hole ceramic insulator rod, thermocouple wire, optional ceramic filler, and epoxy resin. In contact with and takes average temperature of, surrounding material. Fabricated easily in size and metal to suit particular application. Because of simplicity and ability to measure average temperature, widespread use of design foreseen in varity of applications.
A new DRAM architecture and its control method for the system power consumption (2014)

Demands have been placed on dynamic random access memory (DRAM) to not only increase memory capacity and data transfer speed but also to reduce operating and standby currents. When a system uses DRAM, the restricted data retention time necessitates a re-write operation because each bit of the DRAM is stored as an amount of electrical charge in a storage capacitor. Power consumption for the refresh operation increases in proportion to memory capacity. According to a new proposed method the refresh operation frequency and its power consumption reduce to 1/(2 to the Nth) (N=1, 2, 3, 4) when full memory capacity is not required, by effectively extending the refresh operation interval. The proposal includes the conversion from 1 cell/bit to (2 to the Nth) cells/bit, which reduces the variation of retention times among memory cells. This leads the refresh operation frequency from 1/(2 to the Nth) to 1/(2 to the Nth) X 1/(2 to the Nth), while it accompanies the additional charging power for the composed memory cell. A system can select the best way of 1 cell/bit and (2 to the Nth) cells/bit from the total viewpoint, while all conventional functions and operations in the full array access mode are fully compatible.
Monolithic W-band seven-stage low noise amplifier/detectorforradiometric imaging array application (1994)

The authors have demonstrated, for the first time, a monolithic W-band seven-stage low noise amplifier (LNA)/detector as a complete direct-detection receiver for application in millimetre-wave radiometric imaging array systems. The LNA has achieved a noise figure of 3.8 dB with an associated gain of 34 dB over the band from 92 to 96 GHz. A field radiometric image taken by the device in stepping push-broom mode shows excellent results.
Real-time rendering on a power budget (2016)

With recent advances on mobile computing, power consumption has become a significant limiting constraint for many graphics applications. As a result, rendering on a power budget arises as an emerging demand. In this paper, we present a real-time, power-optimal rendering framework to address this problem, by finding the optimal rendering settings that minimize power consumption while maximizing visual quality. We first introduce a novel power-error, multi-objective cost space, and formally formulate power saving as an optimization problem. Then, we develop a two-step algorithm to efficiently explore the vast power-error space and leverage optimal Pareto frontiers at runtime. Finally, we show that our rendering framework can be generalized across different platforms, desktop PC or mobile device, by demonstrating its performance on our own OpenGL rendering framework, as well as the commercially available Unreal Engine.
Gain competition in dual wavelength quantum cascade lasers (2010)

We investigated dual wavelength mid-infrared quantum cascade lasers based on heterogeneous cascades. We found that due to gain competition laser action tends to start in higher order lateral modes. The mid-infrared mode with the lower threshold current reduces population inversion for the second laser with the higher threshold current due to stimulated emission. We developed a rate equation model to quantitatively describe mode interactions due to mutual gain depletion.
Ka-band deployable mesh reflector antenna compatible with the deep space network (2017)

This paper presents a novel deployable Ka-band antenna folding in a 1.5U (10×10×15cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) stowage volume suitable for 6U (10×20×30cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) class CubeSats. This antenna is designed for telecommunication and is compatible with the NASA's Deep Space Network (DSN) at Ka-band frequencies (uplink: 34.2-34.7 GHz and downlink: 31.8-32.3 GHz). Detailed simulations, considering all aspects of the circularly-polarized mesh deployable reflector antenna including the feed, show that 42.0-dBi gain and 57% aperture efficiency is achievable at 32GHz. The mechanical deployment mechanism is thoroughly described as it is a critical component of the deployable CubeSat antenna.
Certifiably Robust Interpretation via Renyi Differential Privacy (2021)

Motivated by the recent discovery that the interpretation maps of CNNs could easily be manipulated by adversarial attacks against network interpretability, we study the problem of interpretation robustness from a new perspective of \Renyi differential privacy (RDP). The advantages of our Renyi-Robust-Smooth (RDP-based interpretation method) are three-folds. First, it can offer provable and certifiable top-$k$ robustness. That is, the top-$k$ important attributions of the interpretation map are provably robust under any input perturbation with bounded $\ell_d$-norm (for any $d\geq 1$, including $d = \infty$). Second, our proposed method offers $\sim10\%$ better experimental robustness than existing approaches in terms of the top-$k$ attributions. Remarkably, the accuracy of Renyi-Robust-Smooth also outperforms existing approaches. Third, our method can provide a smooth tradeoff between robustness and computational efficiency. Experimentally, its top-$k$ attributions are {\em twice} more robust than existing approaches when the computational resources are highly constrained.
Dual targeting of salt inducible kinases and CSF1R uncouples bone formation and bone resorption (2021)

Bone formation and resorption are typically coupled, such that the efficacy of anabolic osteoporosis treatments may be limited by bone destruction. The multi-kinase inhibitor YKL-05-099 potently inhibits salt inducible kinases (SIKs) and may represent a promising new class of bone anabolic agents. Here, we report that YKL-05-099 increases bone formation in hypogonadal female mice without increasing bone resorption. Postnatal mice with inducible, global deletion of SIK2 and SIK3 show increased bone mass, increased bone formation, and, distinct from the effects of YKL-05-099, increased bone resorption. No cell-intrinsic role of SIKs in osteoclasts was noted. In addition to blocking SIKs, YKL-05-099 also binds and inhibits CSF1R, the receptor for the osteoclastogenic cytokine M-CSF. Modeling reveals that YKL-05-099 binds to SIK2 and CSF1R in a similar manner. Dual targeting of SIK2/3 and CSF1R induces bone formation without concomitantly increasing bone resorption and thereby may overcome limitations of most current anabolic osteoporosis therapies.
Nitrile Hydratase Gene from<i>Rhodococcus</i>sp. N-774 Requirement for Its Downstream Region for Efficient Expression (1994)

For improvement of the production of nitrile hydratase (NHase) from Rhodococcus sp. N-774 by recombinant DNA techniques, several plasmids, each of which had a deletion of the upstream or downstream region of the genes encoding the alpha and beta subunits of NHase, were constructed. Enzyme assays of recombinant R. rhodochrous and Escherichia coli cells showed that a downstream region of the NHase genes was indispensable for the production of active NHase in both cells, but for the production of the active amidase, no genes other than the amidase structural gene were required. The nucleotide sequence of the downstream region contained a single open reading frame (Orf1188) with 396 amino acids. Orf1188 showed similarity in amino acid sequence to P47K, an open reading frame found downstream of the NHase genes from Pseudomonas chlororaphis B23, and also to the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans. Because the distance between the TGA stop codon for the NHase beta-subunit and the ATG codon for Orf1188 is only 98 bp, and because production of both Orf1188 and NHase is dependent on a promoter upstream of the amidase gene, these genes appear to be co-transcribed in a polycistronic manner, forming an operon. By optimization of the culture conditions of R. rhodochrous carrying pKRNH2, which contained the amidase, NHase, and Orf1188 genes, the transformant showed the NHase activity 6-fold higher than that of the original strain, Rhodococcus sp. N-774.
The K121Q variant of the human PC-1 gene is not associated with insulin resistance or type 2 diabetes among Danish Caucasians. (2000)

The human plasma-cell membrane differentiation antigen-1 (PC-1) has been shown to inhibit insulin receptor tyrosine kinase activity. Recently, a K121Q polymorphism in the human PC-1 gene was found in a Sicilian population and was shown to be strongly associated with insulin resistance. The objectives of the present investigation were to examine in the Danish Caucasian population whether the K121Q variant was associated with type 2 diabetes or, in glucose-tolerant subjects, with impaired whole-body insulin sensitivity. We genotyped 404 Danish type 2 diabetic patients and found that the allele frequency of the variant was 0.14 (95% CI 0.12-0.16), whereas the allele frequency was 0.16 (95% CI 0.13-0.19) among 237 matched glucose-tolerant control subjects (P = 0.6). In the control subjects, there were no significant differences among wild-type, heterozygous, or homozygous subjects in regard to 1) serum insulin and plasma glucose levels at fasting, 60 min, or 120 min during an oral glucose tolerance test (OGTT) or 2) the estimates of insulin resistance obtained from the homeostasis model assessment (HOMA). Furthermore, we investigated the impact of the variant in 2 other Danish population samples that comprised 356 young healthy subjects and 226 glucose-tolerant offspring of type 2 diabetic probands, respectively. In all of the study populations, the polymorphism was not associated with an altered insulin sensitivity index as estimated from an intravenous glucose tolerance test in combination with an intravenous injection of tolbutamide. In addition, among the 226 offspring, the variations in serum insulin and serum C-peptide responses measured during an OGTT were not related to the PC-1 genotype. In conclusion, the K121Q polymorphism of the human PC-1 gene is not associated with type 2 diabetes or insulin resistance among Danish Caucasians.
Pregnancy Rates Per Artificial Insemination for Cows and Heifers Inseminated at a Synchronized Ovulation or Synchronized Estrus (1997)

Two synchronization protocols were tested for lactating dairy cows and heifers. Nulliparous dairy heifers (13 to 23 mo; n = 155) and primiparous and multiparous dairy cows (60 to 289 d postpartum; n = 310) were assigned randomly to two treatments. Controls received 25 mg of PGF2 alpha and were artificially inseminated according to the a.m.-p.m. rule following detected estrus. All controls that were not detected in estrus were injected with 25 mg of PGF2 alpha at 14-d intervals until artificial insemination (AI) at a detected estrus or until timed AI at 72 to 80 h after a third sequential injection of PGF2 alpha. Treated cows and heifers received a protocol that used GnRH and PGF2 alpha to synchronize ovulation (Ovsynch). Cows and heifers that were treated with Ovsynch were injected i.m. with 100 micrograms of GnRH at a random stage of the estrous cycle. Seven days later, cows and heifers in this group received 25 mg of PGF2 alpha followed by a second injection of 100 micrograms of GnRH 30 to 36 h later. Subsequently, the treated cows and heifers received AI 16 to 20 h after the second injection of GnRH. Pregnancy rates per AI were similar (38.9% vs. 37.8%) for control cows and cows treated with the Ovsynch protocol, respectively. However, pregnancy rate per AI was greater for control heifers (74.4%) than for heifers treated with Ovsynch (35.1%). Evaluation of serum progesterone concentrations at each hormonal injection indicated that the first injection of GnRH synchronized luteal function of lactating dairy cows but not of heifers. In summary, one fixed-time AI at a synchronized ovulation provided similar pregnancy rates per AI as did AI following the a.m-p.m. rule after estrus had been induced by PGF2 alpha in lactating cows, but the fixed-time AI was not effective for heifers because of the lack of synchronization.
Initiation of Bladder Voiding with Epidural Stimulation in Paralyzed, Step Trained Rats (2014)

The inability to control timely bladder emptying is one of the most serious challenges among the several functional deficits that occur after a complete spinal cord injury. Having demonstrated that electrodes placed epidurally on the dorsum of the spinal cord can be used in animals and humans to recover postural and locomotor function after complete paralysis, we hypothesized that a similar approach could be used to recover bladder function after paralysis. Also knowing that posture and locomotion can be initiated immediately with a specific frequency-dependent stimulation pattern and that with repeated stimulation-training sessions these functions can improve even further, we reasoned that the same two strategies could be used to regain bladder function. Recent evidence suggests that rats with severe paralysis can be rehabilitated with a multisystem neuroprosthetic training regime that counteracts the development of neurogenic bladder dysfunction. No data regarding the acute effects of locomotion on bladder function, however, were reported. In this study we show that enabling of locomotor-related spinal neuronal circuits by epidural stimulation also influences neural networks controlling bladder function and can play a vital role in recovering bladder function after complete paralysis. We have identified specific spinal cord stimulation parameters that initiate bladder emptying within seconds of the initiation of epidural stimulation. The clinical implications of these results are substantial in that this strategy could have a major impact in improving the quality of life and longevity of patients while simultaneously dramatically reducing ongoing health maintenance after a spinal cord injury.
Hardware method of synchronising processes without using a clock (1983)

A system of asynchronous logic is described whose purpose is to keep operations taking place in several different devices in step with one another. The description includes details of control waveforms on the three bus lines that interconnect the devices, a suggested implementation and a state table showing how it operates.