gebhart/patrepeval huggingface dataset:
Standardized large-scale H-1PV production process with efficient quality and quantity monitoring (2015)

The promising anticancer properties of rodent protoparvoviruses, notably H-1PV, have led to their clinical testing. This makes it necessary to produce highly pure, well-characterized virus batches in sufficient quantity. The present work focused on developing standardized production, purification, and characterization procedures as a basis for exploiting H-1PV both preclinically and in clinical trials for anticancer virotherapy. Two infection and two virus purification strategies were tested and the resulting virus preparations compared for their purity and full-, infectious-, and empty-particle contents. The adopted production process, which involves culturing and infecting NB-324K cells in 10-layer CellSTACK(®) chambers (1×10(3) infectious units per infected cell), is simple, scalable, and reproducible. Downstream processing to eliminate contaminating DNA and protein includes DNAse treatment, filtration, and two Iodixanol density-gradient centrifugations, the first gradient being a step gradient and the second, either a step (1×10(10) PFU/ml) or a continuous gradient (3×10(11) PFU/ml). A procedure was also developed for obtaining infectious particle-free preparations of empty virions for research purposes: cesium chloride density gradient centrifugation followed by UV irradiation (1×10(14) physical particles/ml). For quick, sensitive determination of physical particles (and hence, particle-to-infectivity ratios), a "Capsid-ELISA" was developed, based on a novel monoclonal antibody that specifically targets assembled capsids.
Modification of calcium–phosphate coatings on titanium by recombinant amelogenin (2003)

Amelogenin proteins, the principal components of the developing dental enamel extracellular matrix, have been postulated to facilitate the elongated and oriented growth of the carbonated apatite crystals during enamel formation. We previously reported that amelogenin caused modulation of apatite crystals nucleated on a bioactive glass (Bioglass(R)) in vitro. Here, the effects of amelogenin on the growth morphology of calcium-phosphate crystals nucleated on a titanium surface were investigated in order to gain a better understanding of the role of amelogenins during enamel biomineralization and to explore their potential application in the design and development of novel biomaterials. The dose-dependent effects of a recombinant mouse amelogenin (rM179) were found to be different from those of bovine serum albumin, which significantly inhibited apatite crystal growth and caused the octacalcium phosphate (OCP) crystals to change from a plate-like shape to a curved shape, indicating a general inhibitory effect. The effects of rM179 on the crystal growth of OCP at 12.5-100 microg/mL and of apatite at 50 microg/mL were insignificant while the apatite crystals were remarkably elongated along their c-axes upon the use of 100 microg/mL of rM179. The unique modulation of the calcium-phosphate coatings on titanium by rM179 supports the view that amelogenins have a great potential for applications designed to develop novel biomimetic materials.
Conformation and Dynamics of Interchain Cysteine-Linked Antibody-Drug Conjugates as Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry (2014)

Antibody-drug conjugates (ADCs) are protein therapeutics in which a target specific monoclonal antibody (mAb) is conjugated with drug molecules. The manufacturing of ADCs involves additional conjugation steps, which are carried out on the parent mAbs, and it is important to evaluate how the drug conjugation process impacts the conformation and dynamics of the mAb. Here, we present a comparative study of interchain cysteine linked IgG1 ADCs and the corresponding mAb by hydrogen/deuterium exchange mass spectrometry (HDX-MS). We found that ∼90% of the primary sequence of the ADC conjugated with either monomethyl auristatin E or F (vcMMAE/mcMMAF) displayed the same HDX kinetics as the mAb, indicating the ADCs and mAbs share very similar conformation and dynamics in solution. Minor increases in HDX kinetic rates were observed in two Fc regions in the ADCs relative to the mAb which indicated that both regions become more structurally dynamic and/or more solvent-accessible in the ADCs. The findings led to a subsequent inquiry into whether the local conformational changes were due to the presence of drugs on the interchain cysteine residues or the absence of intact interchain disulfides or both. To address this question, a side-by-side HDX comparison of ADCs, mAbs, reduced mAbs (containing 8 reduced interchain cysteine thiols), and partially reduced mAbs (conjugation process intermediate) was performed. Our results indicated that the slight increase in conformational dynamics detected at the two regions in the ADCs was due to the absence of intact interchain disulfide bonds and not the presence of vcMMAE or mcMMAF on the alkylated interchain cysteine residues. These results highlight the utility of HDX-MS for interrogating the higher-order structure of ADCs and other protein therapeutics.
Applications of terahertz imaging (2002)

The recent advances involving imaging with sub-picosecond terahertz pulses have opened up a wide range of possibilities in the applications of far-infrared technology. For the first time, a commercially viable terahertz imaging spectrometer seems a realizable prospect. However, several substantial engineering research challenges remain to be overcome before this goal can be achieved. One of these involves the necessity for a femtosecond laser system, required for gating the emitter and receiver antennas used in the THz-TDS system. The demonstration experiments performed to date have employed rather crude signal processing algorithms. The shortcomings of these are evident in some of the results presented here, highlighting the need for a more sophisticated treatment.
Pneumococcal Conjugate Vaccine for Adults: A New Paradigm (2012)

A 13-valent pneumococcal conjugate vaccine has been studied in adults aged ≥ 50 years to compare the immune response to that induced by the 23-valent pneumococcal polysaccharide vaccine, which has been the standard of care over the past 30 years. The results demonstrate that adults, regardless of whether they are naive or previously vaccinated with the polysaccharide vaccine, have an overall superior antibody response when vaccinated with the conjugate vaccine compared with the pneumococcal polysaccharide vaccine. More importantly, the nature of the response is indicative of a T-cell-dependent response that elicits immunological memory and, therefore, primes the immune system for either natural exposure or subsequent booster vaccination with either conjugate or polysaccharide vaccine. The conjugate vaccine, which has been successful in reducing pneumococcal disease in children, now provides a new approach to preventing pneumococcal disease, including community-acquired pneumonia, in adults.
Bistable Deformable Mirror Device (1988)

The bistable DMD is the digital version of a class of reflective, micromechanical spatial light modulators (SLMs) known as deformable mirror devices (DMDs). In its earliest form the DMD was a hybrid SLM consisting of a metalized polymer mirror bonded to an underlying silicon address circuit[1,2].
Preparation Of Antithrombin, High Activity Heparin And A Heparin-Antithrombin Complex By A Rapid Two-Step Affinity Method (1981)

The tight binding affinity of antithrombin for heparin makes possible a relatively selective purification scheme based on salt elution from heparin-Sepharose. We have found, however, that purity can often be greatly increased if the elution is carried out with soluble heparin instead. This heparin can be removed from the antithrombin, either in whole or part, by a second affinity step on Concanavalin A Sepharose. The antithrombin, which binds to the matrix through its glycosidic moieties, retains its ability to bind heparin at physiological ionic strengths. Thus, the complex of antithrombin and heparin is readily isolated free of unbound heparin species. The complex can be eluted intact with low ionic strength buffers containing sugars which compete for binding to the lectin. Alternatively, the high activity heparin (400–500 units/mg) can be obtained separately by a 1 M NaCl wash which is then followed by a carbohydrate wash to obtain the purified antithrombin. We have made certain preliminary biochemical and anticoagulant characterizations of these materials. Not unexpectedly, both the high activity heparin and its complex with antithrombin show significantly greater in vitro potency in comparison to unfractionated heparin. In vivo anticoagulant efficacy, as evaluated in a rabbit infusion model, confirmed the in vitro findings and further suggests some potential therapeutic benefit may be derived from infusion of a preformed heparin-antithrombin complex.
Automated perfusion‐weighted MRI using localized arterial input functions (2006)

Automated CBF calculation using local AIFs is feasible and appears to produce more useful CBF maps.
Demonstration of long lengths of longitudinally uniform hollow core Photonic Bandgap fibre and their demonstration for low latency data transmission (2015)

Hollow core Photonic Bandgap fibres (HC-PBGFs) are the subject of substantial interest due to their intrinsically low nonlinearity and latency, which represent a substantial advantage over conventional, solid fibres. In this paper, we review recent progress at the ORC towards achieving long lengths of uniform fibre and in particular describe the fabrication of a 11 km long span of HC-PBGF with relatively low loss (~5 dB/km), wide bandwidth (~200 nm) and good longitudinal uniformity. The fibre span was able to support error free transmission at 10 Gbit/s across the entire C-Band. We believe this represents a major stepping stone in the demonstration of the viability of this technology for low-latency data transmission.
Integrated Mobile Health Platform for the Community (2018)

A mobile health platform is proposed as an integrated solution for managing health remotely, using mobile devices. It is based on human-centered design, with the patient at the center, while taking into account the various users of the solution, who have the shared goal of managing the patient's health. These users could be the immediate family, trusted friends, neighbors, community health workers and/or professional care team.
Stretchable Thin‐Film Electronics (2012)

Making stretchable thin-film electronics presents considerable scientific and technological challenges: (i) Can substrates that are inherently extensible support reliable fabrication of thin-film conductor and semiconductor devices? (ii) Can device materials withstand mechanical deformations without compromising their electrical properties? and (iii) Which applications will be enabled with such ultracompliant electronic skins? This chapter illustrates those challenges and potential routes to overcome them. Section 4.2 reviews the physical properties of silicone rubber – the substrate hosting the thin-film devices. Section 4.3 describes the mechanical design to implement and use robust stretchable thin-film circuits. Section 4.4 reviews materials and characteristics of stretchable metallization. Section 4.5 highlights examples of stretchable thin-film devices.
Pulse coupled oscillator synchronization for low power UWB wireless transceivers (2007)

Achieving robust synchronization in low power UWB systems remains a dominant obstacle in the design of these systems. In this paper, we propose using the pulse coupled oscillator (PCO) phenomenon with system feedback as an alternative scheme to conventional master-slave synchronization using power hungry PLL or DLL circuits. Sensor network nodes implementing the PCO state function are mathematically guaranteed to converge towards phase lock, with no need for a PLL, off chip crystal, or continuously operating low noise amplifier. To date, we know of no circuit-level implementation of a PCO based wireless transceiver. We also demonstrate synchronization of a switchable integrated transceiver front-end in the IBM CMOS7RF process, a key first step in design of short-range communications for microwatt power levels.
Diffraction grating lens array (2007)

We have proposed a new type of camera module with a thin structure and distance-detection capability. This camera module has a four-lens-array with diffraction gratings (one for blue, one for red, and two for green). The diffraction gratings on the mold are formed mechanically, and the plastic lens array is fabricated by injection molding. The two green images are compared to detect parallax, and parallax-corrected blue, red and green images are then composed to generate a color image. We have developed new design software and molding technologies for the grating lenses. The depth and period of blazed gratings and the shapes of aspheric lenses are optimized; and blue, red and two green aspheric lenses with gratings are molded as a single four-lens-array. The diffraction gratings on both surfaces of each lens act to improve field curvature and realize wide-angle imaging. However, blazed gratings sometimes cause unnecessary diffraction lights that impede the formation ofhigh-resolution images. We have developed a new method to measure necessary first-order diffraction lights and unnecessary diffraction lights separately. Use of this method allows the relationship between molding conditions and necessary/unnecessary diffraction lights to be shown. Unnecessary diffraction lights can be diminished by employing the optimal molding processes, allowing our grating lenses to be used for image capture.
A Simple Message-Optimal Algorithm for Random Sampling from a Distributed Stream (2016)

We present a simple, message-optimal algorithm for maintaining a random sample from a large data stream whose input elements are distributed across multiple sites that communicate via a central coordinator. At any point in time, the set of elements held by the coordinator represent a uniform random sample from the set of all the elements observed so far. When compared with prior work, our algorithms asymptotically improve the total number of messages sent in the system. We present a matching lower bound, showing that our protocol sends the optimal number of messages up to a constant factor with large probability. We also consider the important case when the distribution of elements across different sites is non-uniform, and show that for such inputs, our algorithm significantly outperforms prior solutions.
Improved processing of ceramic superconductors (1989)

Vacuum calcination of precursor powder under controlled total oxygen pressure has been investigated for synthesizing YBa{sub 2}Cu{sub 3}O{sub x} (YBCO) superconductor. The reaction temperature, {approximately}800{degree}C, is {approximately}100{degree}C lower than that used in ambient-pressure calcination. Since a single calcination results in essentially phase-pure material, total calcination times have been drastically reduced. The vacuum-calcined powder has finer particles and consequently greater sinterability than powders made by conventional methods. Samples made from this powder have critical current densities of {approximately}1000 A/cm{sup 2} at 77 K in zero applied external magnetic field. 14 refs., 4 figs.
A Facile Database Search Engine for Metabolite Identification and Biomarker Discovery in Metabolomics (2016)

ProgenesisTM QI Informatics simplifies the process of metabolite identification and biomarker discovery. Potential biomarkers can be searched in both publicly available and in-house databases for accurate mass, retention time, collision cross section, and fragmentation information. Such an approach is fast and it increases the confidence of metabolite identification in metabolomics experiments
Development of Effective PET and SPECT Imaging Agents for the Serotonin Transporter: Has a Twenty-Year Journey Reached its Destination? (2010)

The serotonin transporter (SERT) has been implicated in a variety of neuropsychiatric disorders including depression, schizophrenia, substance abuse, alcoholism, and Alzheimer's disease. Radiotracer-based in vivo imaging techniques such as Positron Emission Tomography (PET) and Single-Photon Emission Computed Tomography (SPECT) are important tools to investigate the functions of SERT in the living brain under normal conditions and its dysfunction in diseases. In this report we review the development and validation of effective PET and SPECT radiotracers in the last twenty years. First, the requirements for an effective imaging tracer, and factors influencing a tracer's in vivo imaging performance are discussed. PET and SPECT radiotracers for SERT are then categorized and reviewed according to their chemical scaffolds: 1) SSRIs and related compounds; 2) tropane-based ligands; 3) isoquinolines; and 4) substituted diarylsulfides. Critical evaluation and comments are provided for promising radiotracers, if any, emerging from each chemical scaffold. Based on experimental data gathered from radiotracer development for SERT, an examination of the relationship between an imaging tracer's in vitro physicochemical and pharmacological properties and its in vivo performance parameters is provided. Finally, tracers available for imaging applications in humans are assessed and compared in terms of tissue binding kinetics, non-specific binding, and specific binding signals in vivo. From these assessments, we conclude that, after twenty years of development efforts, a number of effective PET and SPECT radiotracers have now been validated and are available for imaging SERT in humans. The applications of these efficacious SERT imaging agents will further advance our understanding of this important transporter in psychiatric and neurodegenerative disorders.
Substrate Preferences for Antiplasmin Cleaving Enzyme Hydrolysis of Peptides Derived from the α2-Antiplasmin Sequence. (2006)

Abstract Antiplasmin cleaving enzyme (APCE) is a proteinase that specifically, but slowly cleaves the Pro-Asn bond in long-form α2-antiplasmin (Met-α2AP) in human plasma. This slow cleavage produces a steady-state plasma mixture of Met-α2AP and an N-terminally shortened form of antiplasmin, Asn-α2AP. The Asn-α2AP form crosslinks to fibrin ~13-fold faster than Met-α2AP. A faster crosslink rate causes a greater number of antiplasmin molecules to become bound during fibrin formation, thereby enhancing resistance to fibrinolysis. Inhibition of plasma APCE may decrease the number of antiplasmin molecules crosslinked and result in clots that are more easily removed during fibrinolysis. Therefore, an inhibitor specific for APCE could potentially be used to regulate fibrinolysis. Human Met-α2AP exists in two polymorphic forms at position six in the mature sequence, with arginine predominant, and tryptophan accounting for a lesser percentage. We have determined the relative cleavage rates of synthetic peptides from a peptide library that span the cleavage site. The peptides contained all common amino acids except cysteine in the polymorphic position (P7 position). Arg was the optimal amino acid in this position with a relative cleavage rate ~5–10-fold faster than other amino acids except Lys, which was ~70% of the Arg rate. The P7 position Arg enhancement was also observed when Arg was in the P6 or P5 position, but no enhancement was observed when Arg was moved to positions P8, P4, P3 or P2. It was also determined that APCE is preferentially an endoproteinase rather than an aminodipeptidase, with a 10-fold greater rate of hydrolysis of the internal Pro-Asn bond in the Met-α2AP 1–17 peptide sequence MEPLGRQLTSGP-NQEQV over the Pro-Asn bond penultimate to the amino-terminal bond in the Met-α2AP 11–27 peptide sequence GP-NQEQVSPLTLLKLGN in peptide hydrolysis experiments. We conclude that APCE inhibitors designed with a positive charge placed upstream of the Pro-X scissile bond equivalent to five to seven amino acid residues may prove to be highly potent and specific. In addition, such inhibitors should also prove useful for blocking the activity of the closely related enzyme fibroblast activation protein. This work was supported by NIH grant HL072995.
Reduction of Number and Duration of Hypoglycemic Events by Glucose Prediction Methods: A Proof-of-Concept In Silico Study (2013)

This in silico proof-of-concept study demonstrates that using predicted rather than measured CGM allows a significant reduction of the number of hypoglycemic events and the time spent in hypoglycemic range both by 75%, stimulating further research and clinical investigation on the generation of preventive hypoglycemic alerts exploiting glucose prediction methods.
Humoral Immune Response against Nontargeted Tumor Antigens after Treatment with Sipuleucel-T and Its Association with Improved Clinical Outcome (2015)

Sipuleucel-T induced humoral antigen spread in patients with mCRPC. IgG responses were associated with improved OS in IMPACT. The methods and results reported may identify pharmacodynamic biomarkers of clinical outcome after sipuleucel-T treatment, and help in clinical assessments of other cancer immunotherapies. See related commentary by Hellstrom and Hellstrom, p. 3581.
Transrectal ultrasound imaging using plane-wave, fan-beam and wide-beam ultrasound: Phantom results (2019)

Plane-wave, fan-beam and wide-beam ultrasound can transmit higher ultrasound energy compared to synthetic-aperture ultrasound, leading to improved signal-to-noise ratios in ultrasound reflection/scattering signals. This is particularly useful for transrectal ultrasound imaging using end-firing transrectal ultrasound probes. We conduct a phantom study to evaluate the capabilities of plane-wave, fan-beam and wide-beam ultrasound for prostate imaging. The penetration depth decreases from plane-wave to fan-beam to wide-beam ultrasound, with increasing imaging areas. We use a transrectal ultrasound prototype consisting of a 256-channel Verasonics Vantage system and a GE intracavitary curved linear array to form plane-wave, fan-beam and wide-beam ultrasound. Our imaging results of a tissue-mimicking prostate phantom show that wide-beam ultrasound produces the best imaging among the three different beams of ultrasound when using the same number of ultrasound incident angles.
3 Chemically Bonded Phosphate Ceramics for Stabilization and Solidification of Mixed Waste (2001)

It exists in various forms in the following proportions: 39% aqueous liquids, 17% inorganic sludges and particulates, 25% heterogeneous debris, 3% soils, and 5% organic liquids. The volume will increase to 1,200,000 since 1994. In addition, the DOE ’s treatment plans currently show a significant number of waste streams that require solidification and stabilization.
<title>Oxygen distributions within tissue by phosphorescence quenching</title> (2002)

Oxygen dependent quenching of phosphorescence is a powerful method for measuring oxygen. Phosphors are now available that absorb and emit in the near IR region of the spectrum, are nontoxic, and remain in the blood, allowing rapid measure of oxygen through out selected tissue volumes. In vivo measurements are non-invasive except for the need to inject phosphor into the blood, and phosphorescence lifetimes can be measured without interference by tissue pigments that absorb or fluorescence at the measurement wavelengths. Phosphorescence quenching is uniquely useful for: (1) imaging oxygen in optically clear media or in the surface layer of the tissue, such as in the retina of the eye; (2) determining the distribution of oxygen in media, such as tissue, which have heterogeneous distributions by deconvoluting phosphorescence decay dat. These can be used to calculate the corresponding oxygen histograms. Measurement in 2D grids can b used to construct contour maps of the fraction of the sampled tissue volume with any selected range of oxygen pressures. These maps accurately show the location and size of any regions of hypoxia within the sampled tissue.