gebhart/patrepeval huggingface dataset:
Receptor-ligand interactions between serum amyloid P component and model soluble immune complexes. (1993)

We report here that isolated human serum amyloid P (SAP) binds aggregates of human IgG (AAg), which are model soluble immune complexes. The binding interaction was specific with regard to AAg compared to monomeric IgG, saturable, of high affinity, and reversible. With SAP adsorbed to microtiter plate wells, protein binding assays of AAg preparations with m.w. values of 1.05 to 2.25 x 10(6) were performed. The assay results yielded binding isotherms and estimates of the dissociation constant values of SAP:AAg binding ranging between 0.60 and 1.9 nM. Using the same method, the dissociation constant of SAP binding of biotinylated AAg was estimated to be approximately 3.0 nM. Competitive protein binding assays using biotinylated AAg and unlabeled AAg or monomeric IgG were performed to determine the relative affinity (IC50) of SAP binding. The IC50 values ranged from 22 to 51 nM for different sizes of AAg. The IC50 determined for monomeric IgG was 10 microM, demonstrating a relative specificity of SAP binding for AAg. The binding interaction was reversible, the SAP:AAg complexes dissociating with a t1/2 of 125 min. AAg binding to solid phase-adsorbed SAP was not dependent upon the presence of several cations, including calcium, but was not supported by cuprous ion. The differential binding of AAg vs monomeric IgG reported here for SAP is similar to the other human immune complex binding proteins C1q, rheumatoid factor, and cellular Ig C-region receptors. These results indicate that SAP:AAg binding has the hallmarks of a receptor:ligand interaction and may have implications for the disposal of immune complexes in vivo.
Proteomic-Based Discovery and Characterization of Glycosylated Eosinophil-Derived Neurotoxin and COOH-Terminal Osteopontin Fragments for Ovarian Cancer in Urine (2006)

Specific elevated posttranslationally modified urinary EDN and osteopontin COOH-terminal fragments in ovarian cancer might lead to potential noninvasive screening tests for early diagnosis. Urine with less complexity than serum and relatively high thermodynamic stability of peptides or metabolites is a promising study medium for discovery of the novel biomarkers which may present in many non-urinary tract neoplastic diseases.
Learning the speech front-end with raw waveform CLDNNs (2015)

Learning an acoustic model directly from the raw waveform has been an active area of research.However, waveformbased models have not yet matched the performance of logmel trained neural networks.We will show that raw waveform features match the performance of log-mel filterbank energies when used with a state-of-the-art CLDNN acoustic model trained on over 2,000 hours of speech.Specifically, we will show the benefit of the CLDNN, namely the time convolution layer in reducing temporal variations, the frequency convolution layer for preserving locality and reducing frequency variations, as well as the LSTM layers for temporal modeling.In addition, by stacking raw waveform features with log-mel features, we achieve a 3% relative reduction in word error rate.
Adversarial Discriminative Domain Adaptation (2017)

Adversarial learning methods are a promising approach to training robust deep networks, and can generate complex samples across diverse domains. They can also improve recognition despite the presence of domain shift or dataset bias: recent adversarial approaches to unsupervised domain adaptation reduce the difference between the training and test domain distributions and thus improve generalization performance. However, while generative adversarial networks (GANs) show compelling visualizations, they are not optimal on discriminative tasks and can be limited to smaller shifts. On the other hand, discriminative approaches can handle larger domain shifts, but impose tied weights on the model and do not exploit a GAN-based loss. In this work, we first outline a novel generalized framework for adversarial adaptation, which subsumes recent state-of-the-art approaches as special cases, and use this generalized view to better relate prior approaches. We then propose a previously unexplored instance of our general framework which combines discriminative modeling, untied weight sharing, and a GAN loss, which we call Adversarial Discriminative Domain Adaptation (ADDA). We show that ADDA is more effective yet considerably simpler than competing domain-adversarial methods, and demonstrate the promise of our approach by exceeding state-of-the-art unsupervised adaptation results on standard domain adaptation tasks as well as a difficult cross-modality object classification task.
High strength graphene oxide/polyvinyl alcohol composite hydrogels (2011)

Polyvinyl alcohol (PVA) hydrogels have been proposed for use as promising biomaterials in biomedical and tissue engineering but their poor mechanical and water-retention properties have hindered their development. Graphene oxide (GO), an excellent nanofiller, was added to PVA to make GO/PVA composite hydrogels by a freeze/thaw method. The mechanical properties of the GO/PVA hydrogels were significantly improved. Compared to pure PVA hydrogels, a 132% increase in tensile strength and a 36% improvement of compressive strength were achieved with the addition of 0.8 wt% of GO, which suggests an excellent load transfer between the GO and the PVA matrix. The incorporation of certain amount of GO into composite hydrogels does not affect the toxicity of PVA to osteoblast cells.
Technical considerations for supporting data rates beyond 100 Gb/s (2012)

As traffic demands continue to grow, supporting data rates beyond 100 Gb/s will be required to increase optical channel capacity and support higher-rate client interfaces. Advanced modulation formats that adapt to optimize spectral efficiency over a range of channel signal-tonoise ratio conditions are required. Channels can be constructed by varying parameters such as symbol rate, bits per symbol, number of polarizations, and number of optical and electrical subcarriers. Channel capacity can also be increased using advanced techniques such as optical time-division multiplexing, and fibers that support multiple cores and modes. Many channel designs can support higher data rates, but there are trade-offs between complexity, spectral efficiency, and optical reach.
Autocorrelation - a new differentiating domain for multiple access wireless communications (2003)

Existing multiple access methods, such as TDMA, CSMA/CA, FDMA, and CDMA, require transmitters be coordinated in order to assure multiple access signals to be separable based on the difference in time domain, frequency domain, or code domain, respectively. These coordinative multiple access methods may suffer co-channel interferences badly from non-coordinative transmitters. In this paper, a new differentiating domain, the autocorrelation of the transmitted signals, is exploited, and a new random multiple access method, based on the principle of Autocorrelation Matching (AM), is developed on top of it. The advantages of having autocorrelation as the differentiation factor for multiple access communications systems include, among others, (1) one FIR vector filter automatically does both the equalization of the designated FIR channel for the purpose of detecting the desired signal and the suppression of all other signals; (2) no training signal is needed for equalization; and (3) the equalization and suppression performance is independent of the noise level.
Effects of Etomidate and Hypothermia on Cerebral Metabolism and Blood Flow in a Canine Model of Hypoperfusion (1993)

Etomidate is a nonbarbiturate hypnotic agent which, like the barbiturates, decreases the cerebral metabolic rate of oxygen consumption (CMRO2) 35-50%. The present studies assessed whether etomidate decreased CMRO2 through temperature-dependent mechanisms and whether the combination of etomidate and moderate hypothermia (28 degrees C) decreased CMRO2 more than hypothermia alone. Nineteen anesthetized dogs were treated with saline, etomidate (burst-suppressive doses), etomidate with hypothermia, or hypothermia alone. Etomidate did not affect (p > 0.05) the mean arterial pressure (MAP, mm Hg) but modestly lowered the heart rate [HR; 124 +/- 6 to 105 +/- 14, (mean +/- SEM); p < 0.05] whereas hypothermia (without or with etomidate) lowered (p < 0.05) both MAP (141 +/- 4 to 116 +/- 5 and 135 +/- 6 to 81 +/- 7) and HR (135 +/- 14 to 84 +/- 3 and 135 +/- 10 to 69 +/- 5, respectively). Etomidate administration did not result in a change (p > 0.05) in the esophageal, brain parenchymal, or subdural temperature. CMRO2 (ml/100 g/min) decreased (p < 0.05) during etomidate administration (3.2 +/- 0.4 to 1.7 +/- 0.2) and hypothermia (3.5 +/- 0.2 to 1.1 +/- 0.2), but the addition of etomidate to hypothermia did not further reduce CMRO2 in the animals (3.1 +/- 0.5 to 1.3 +/- 0.2) despite decreasing their brain hemispheric electrical activity from 9 +/- 1 Hz to a burst-suppressive state.(ABSTRACT TRUNCATED AT 250 WORDS)
Process development for a recombinant Chinese hamster ovary (CHO) cell line utilizing a metal induced and amplified metallothionein expression system (2004)

The suspension Chinese Hamster Ovary cell line, 13-10-302, utilizing the metallothionein (MT) expression system producing recombinant human growth hormone (hGH) was studied in a serum-free and cadmium-free medium at different fermentation scales and modes of operation. Initial experiments were carried out to optimize the concentration of metal addition to induce the MT promoter. Subsequently, the cultivation of the 13-10-302 cell line was scaled up from spinner flasks into bioreactors, and the cultivation duration was extended with fed-batch and perfusion strategies utilizing 180 microM zinc to induce the promoter controlling expression of recombinant hGH. It was shown that a fed-batch process could increase the maximum cell numbers twofold, from 3.3 to 6.3 x 10(6) cell/mL, over those obtained in normal batch fermentations, and this coupled with extended fermentation times resulted in a fourfold increase in final hGH titer, from 135 +/- 15 to 670 +/- 70 mg/L at a specific productivity q(hGH) value of 12 pg cell(-1)d(-1). The addition of sodium butyrate increased the specific productivity of hGH in cells to a value of approximately 48 pg cell(-1)d(-1), resulting in a final hGH titer of over a gram per liter during fed-batch runs. A BioSep acoustic cell recycler was used to retain the cells in the bioreactor during perfusion operation. It was necessary to maintain the specific feeding rates (SFR) above a value of 0.2 vvd/(10(6) cell/mL) to maintain the viability and productivity of the 13-10-302 cells; under these conditions the viable cell number increased to over 10(7) cell/mL and resulted in a volumetric productivity of over 120 mg(hGH) L(-1)d(-1). Process development described in this work demonstrates cultivation at various scales and sustained high levels of productivity under cadmium free condition in a CHO cell line utilizing an inducible metallothionein expression system.
Antibodies against Erythropoietin and Other Protein‐Based Therapeutics: An Overview (2005)

Many factors influence the immunogenicity of protein-based therapeutics. At present, it is inconceivable to manufacture a biopharmaceutical without the risk of this adverse effect. Thus, the detection and characterization of antibodies against protein-based therapeutics is a significant task. Only clinical studies and careful monitoring of the market can be used to conclusively demonstrate rates of immunogenicity in humans for protein therapeutics. Fully validated, reliable, and robust in vitro assays, in combination with sensitive bioassays, should be used to address these topics.
Digital rights management on open and semi-open networks (2002)

Gives an overview of how the openness of the future Internet affects digital rights management (DRM). There will be open and semi-open parts in the future Internet. DRM systems enable many important features of information product distribution on the Internet. At the same time, these systems have significant costs: how should content distributors maintain user friendliness and solve revenue-earning difficulties? While DRM systems enable efficient charging possibilities, it is a challenge to implement DRM in the open Internet in a way that attracts customers and really adds value to their experience. Plausibly, there will be many competing DRM solutions. They should, however, be standardized and interoperable enough to enable customers to use information products on different platforms. DRM systems must be appropriately applicable to both open and semi-open networks. It may be technically easier to implement a DRM system in a semi-open environment, but that is not a sufficient solution for a longer-term view. DRM system providers should at least have roadmaps of how to develop their products to work in an open network and on multiple platforms.
CTLA4 Blockade Induces Frequent Tumor Infiltration by Activated Lymphocytes Regardless of Clinical Responses in Humans (2011)

CTLA4 blockade induces frequent increases in ITI by T cells despite which only a minority of patients have objective tumor responses.
Probing the ArcA-P Modulon of Escherichia coli by Whole Genome Transcriptional Analysis and Sequence Recognition Profiling (2004)

The ArcB/ArcA two-component signal transduction system of Escherichia coli regulates gene expression in response to the redox conditions of growth. Over the years, genetic screens have lead to the identification of about 30 ArcA-P-controlled operons that are involved in redox metabolism. However, the discovery of 3 targets that are not implicated in respiratory metabolism (the tra operon for plasmid conjugation, psi site for Xer-based recombination, and oriC site for chromosome replication) suggests that the Arc modulon may comprise additional operons that are involved in a myriad of functions. To identify these operons, we derived the ArcA-P-dependent transcription profile of E. coli using oligonucleotide-based microarray analysis. The findings indicated that 9% of all open reading frames in E. coli are affected either directly or indirectly by ArcA-P. To identify which operons are under the direct control of ArcA-P, we developed the ArcA-P recognition weight matrix from footprinting data and used it to scan the genome, yielding an ArcA-P sequence affinity map. By overlaying both methods, we identified 55 new Arc-regulated operons that are implicated in energy metabolism, transport, survival, catabolism, and transcriptional regulation. The data also suggest that the Arc response pathway, which translates into a net global downscaling of gene expression, overlaps partly with the FNR regulatory network. A conservative but reasonable assessment is that the Arc pathway recruits 100-150 operons to mediate a role in cellular adaptation that is more extensive than hitherto anticipated.
A new route to high yield sugars from biomass: phosphoric–sulfuric acid (2009)

We have developed a simple and effective route for the high yield extraction of sugars from cellulosic based biomass. This process uses a combination of a cellulose decrystallization step with a mixture of phosphoric and sulfuric acid, followed by a hydrolysis step producing sugars (xylose and glucose) with yields of approximately 90%.
Search for optimal age for weaning. Ten-year prospective study. (1993)

The effect of infant nutrition on some clinical and biochemical parameters was studied from birth in a longitudinal prospective study. The data covering the period up to 7 years were reported previously. At the age 10 years 80 children were examined. Two children have been regularly followed up because of high blood pressure. Both had been breast-fed for less than one week and are obese at present. Surprisingly serum total cholesterol was the highest in the group breast-fed for more than 6 months. There were no pronounced differences in the levels of lipoprotein cholesterol carriers. The incidence of a high (over 6.0) atherogenic index (total chol - HDL chol) x APOB/APOA1 x HDL chol) and cholesterolemia over 4.8 mmol/l was significantly (chi 2 test) higher in the group breast-fed for over 6 months. Thyroid function parameters were not affected by the duration of breast-feeding. We conclude that besides undoubtedly favorable effects of breast-feeding, some functions might be also adversely affected if it lasts for more than 6 months. For justified recommendation of optimal duration of breast-feeding all aspects should be considered and more data collected.
α-Keto Acid Chain Elongation Reactions Involved in the Biosynthesis of Coenzyme B (7-Mercaptoheptanoyl Threonine Phosphate) in Methanogenic Archaea (1998)

The biochemistry of the 13 steps involved in the conversion of alpha-ketoglutarate and acetylCoA to alpha-ketosuberate, a precursor to the coenzymes coenzyme B (7-mercapto heptanoylthreonine phosphate) and biotin, has been established in Methanosarcina thermophila. These series of reactions begin with the condensation of alpha-ketoglutarate and acetylCoA to form trans-homoaconitate. The trans-homoaconitate is then hydrated and dehydrated to cis-homoaconitate with (S)-homocitrate serving as an intermediate. Rehydration of the cis-homoaconitate produces (-)-threo-isohomocitrate [(2R,3S)-1-hydroxy-1,2, 4-butanetricarboxylic acid], which undergoes a NADP+-dependent oxidative decarboxylation to produce alpha-ketoadipate. The resulting alpha-ketoadipate then undergoes two consecutive sets of alpha-ketoacid chain elongation reactions to produce alpha-ketosuberate. In each of these sets of reactions, it has been shown that the homologues of cis-homoaconitate, homocitrate, and (-)-threo-isohomocitrate serve as intermediates. The protein product of the Methanococcus jannaschii MJ0503 gene aksA (AksA) was found to catalyze the condensation of alpha-ketoglutarate and acetylCoA to form trans-homoaconitate. This gene product also catalyzed the condensation of alpha-ketoadipate or alpha-ketopimelate with acetylCoA to form, respectively, the (R)-homocitrate homologues of (R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and (R)-2-hydroxy-1,2, 6-hexanetricarboxylic acid. The alpha-ketosuberate resulting from this series of reactions then undergoes a nonoxidative decarboxylation to form 7-oxoheptanoic acid, a precursor to coenzyme B, and an oxidative decarboxylation to form pimelate, the precursor to biotin. Of the 13 intermediates in this pathway, eight have not previously been reported as occurring in biological systems.
Rapid Disuse Atrophy of Diaphragm Fibers in Mechanically Ventilated Humans (2008)

The combination of 18 to 69 hours of complete diaphragmatic inactivity and mechanical ventilation results in marked atrophy of human diaphragm myofibers. These findings are consistent with increased diaphragmatic proteolysis during inactivity.
Photonic ring resonance is a versatile platform for performing multiplex immunoassays in real time (2017)

Photonic ring resonance is a property of light where in certain circumstances specific wavelengths are trapped in a ring resonator. Sensors based on silicon photonic ring resonators function by detecting the interaction between light circulating inside the sensor and matter deposited on the sensor surface. Binding of biological material results in a localized change in refractive index on the sensor surface, which affects the circulating optical field extending beyond the sensor boundary. That is, the resonant wavelength will change when the refractive index of the medium around the ring resonator changes. Ring resonators can be fabricated onto small silicon chips, allowing development of a miniature multiplex array of ring based biosensors. This paper describes the properties of such a system when responding to the refractive index changed in a simple and precise way by changing the ionic strength of the surrounding media, and in a more useful way by the binding of macromolecules to the surface above the resonators. Specifically, a capture immunoassay is described that measures the change of resonant wavelength as a patient serum sample with anti-SS-A autoantibodies is flowed over a chip spotted with SS-A antigen and amplified with anti-IgG. The technology has been miniaturized and etched into a 4×6mm silicon chip that can measure 32 different reactions in quadruplicate simultaneously. The variability between 128 rings on a chip as measured by 2M salt assays averaged 0.6% CV. The output of the assays is the average shift per cluster of 4 rings, and the assays averaged 0.5% CV between clusters. The variability between chips averaged 1.8%. Running the same array on multiple instruments showed that after some improvements to the wavelength referencing system, the upper boundary of variation was 3% between 13 different instruments. The immunoassay displayed about 2% higher variability than the salt assays. There are several outstanding features of this system. The amount of antigen used on the chip for each test is around 200 picograms, only a few microliters of sample is necessary, and the assays take <10min.
Synthesis and Characterization of Carbon Nanotube–Polymer Multilayer Structures (2011)

We develop lightweight, multilayer materials composed of alternating layers of poly dimethyl siloxane (PDMS) polymer and vertically aligned carbon nanotube (CNT) arrays, and characterize their mechanical response in compression. The CNT arrays used in the assembly are synthesized with graded mechanical properties along their thickness, and their use enables the creation of multilayer structures with low density (0.12-0.28 g/cm(3)). We test the mechanical response of structures composed of different numbers of CNT layers partially embedded in PDMS polymer, under quasi-static and dynamic loading. The resulting materials exhibit a hierarchical, fibrous structure with unique mechanical properties: They can sustain large compressive deformations (up to ∼0.8 strain) with a nearly complete recovery and present strain localization in selected sections of the materials. Energy absorption, as determined by the hysteresis observed in stress-strain curves, is found to be at least 3 orders of magnitude larger than that of natural and synthetic cellular materials of comparable density. Conductive bucky paper is included within the polymer interlayers. This allows the measurement of resistance variation as a function of applied stress, showing strong correlation with the observed strain localization in compression.
High-Throughput Bioanalytical LC/MS/MS Determination of Benzodiazepines in Human Urine:  1000 Samples per 12 Hours (1999)

The analytical capabilities of liquid chromatography tandem mass spectrometry for sensitive and highly selective determination of target compounds in complex biological samples makes it well suited for high-throughput analysis. We report the fast separation of six benzodiazepines isolated from human urine via selected reaction monitoring liquid chromatography/mass spectrometry using short dwell times to accommodate fast-eluting chromatographic peaks. The analytes were extracted from human urine samples along with their deuterium-labeled internal standards by a simple liquid-liquid extraction in 96-well plates. Using four autosamplers coupled to one chromatographic column and one tandem mass spectrometer operated in the turbo ion spray mode with positive ion detection, 1152 samples (12 96-well plates) were analyzed in less than 12 h. Through an electronic switching box designed and constructed in-house, the autosamplers were synchronized with the mass spectrometer so that injections were made as soon as the mass spectrometer was ready to collect data. Each run required 30 s to complete with another 7-8 s for the data system to load the next data file to be collected. Chromatographic integrity and ion current response remained relatively constant for the duration of the analyses. The results show acceptable precision and accuracy and demonstrate the feasibility of using fast separations with tandem mass spectrometry for high-throughout analysis of biological samples containing multiple analytes.