gebhart/patrepeval huggingface dataset:
Effect of solution pH on protein transmission and membrane capacity during virus filtration (2007)

Although virus filtration is now an integral part of the overall viral clearance strategy for the purification of many commercial therapeutic proteins, there is currently little understanding of the factors controlling the performance of the virus filters. The objective of this study was to examine the effects of solution pH on protein transmission and capacity during virus filtration. Data were obtained using bovine serum albumin as a model protein with Viresolve 180 membranes oriented with both the skin-side up and skin-side down. Membranes were also characterized using dextran sieving measurements both before and after protein filtration. Membrane capacity and protein yield were minimal at the protein isoelectric point, which was due to the greater degree of concentration polarization associated with the smaller protein diffusion coefficient at this pH. In contrast, the actual protein sieving coefficient was maximum at the protein isoelectric point due to the absence of any strong electrostatic exclusion under these conditions. The yield and capacity were both significantly greater when the membrane was oriented with the skin-side down. These results provide important insights into the effects of solution conditions on the performance of virus filtration membranes for protein purification.
RAIM Availability for GPS Augmented with Barometric Altimeter Aiding and Clock Coasting1 (1993)

In late 1991, the FAA formed a group called the Satellite Operational Implementation Team to accelerate the introduction of satellite navigation and communications into the National Airspace System (NAS). Since then, the team has been addressing major technical and operational issues that need to be resolved before GPS is used in instrument flight rules (IFR) operations in the NAS. One of the most critical criteria for the operational approval of near-term use of GPS in the NAS is availability of receiver autonomous integrity monitoring (RAIM) detection and identification functions. To improve RAIM availability, SOFT members suggested that relatively simple GPS augmentations in the form of barometric altimeter aiding and clock coasting be considered. This paper analyzes GPS RAIM availability with these augmentations and presents the technical analyses used by the team to support its recommendations.
Parallelizing serial code for a distributed processing environment with an application to high frequency electromagnetic scattering (1991)

This thesis investigates the parallelization of existing serial programs in computational electromagnetics for use in a parallel environment. Existing Algorithms for calculating the radar cross section of a object are covered, and a ray-tracing code is chosen for implementation on a parallel machine. Current parallel architectures are introduced and a suitable parallel machine is selected for the implementation of the chosen ray tracing algorithm. The standard techniques for the parallelization of serial code are discussed, including load balancing and decomposition considerations, and appropriate methods for the parallelization effort are selected. A load balancing algorithm is modified to increase the efficiency of the application, and a high level design of the structure of the serial program is presented. A detailed design of the modifications for the parallel implementation is also included, with both the high level and the detailed design specified in a high level design language called UNITY. The correctness of the design is proven using UNITY and standard logic operations. The theoretical and empirical results show that is possible to achieve and efficient parallel application of a serial computational electromagnetic program where the characteristics of the algorithm and the target architecture critically influence the development of such a implementation.
Langerhans cell sarcoma arising from chronic lymphocytic lymphoma/small lymphocytic leukemia: lineage analysis and braf v600e mutation study (2013)

LCS can be transdifferentiated from CLL/SLL and BRAF V600E mutation may provide the foundation for alternative therapy of LCS.
A platelet alpha-granule membrane protein (GMP-140) is expressed on the plasma membrane after activation. (1985)

We have previously characterized a monoclonal antibody, S12, that binds only to activated platelets (McEver, R.P., and M.N. Martin, 1984, J. Biol. Chem., 259:9799-9804). It identifies a platelet membrane protein of Mr 140,000, which we have designated as GMP-140. Using immunocytochemical techniques we have now localized this protein in unstimulated and thrombin-stimulated platelets. Polyclonal antibodies to purified GMP-140 were used to enhance the sensitivity of detection. Nonpermeabilized, unstimulated platelets, incubated with anti-GMP-140 antibodies, and then with IgG-gold probes, showed very little label for GMP-140 along their plasma membranes. In contrast, thrombin-stimulated platelets exhibited at least a 50-fold increase in the amount of label along the plasma membrane. On frozen thin sections of unstimulated platelets we observed immunogold label along the alpha-granule membranes. We also employed the more sensitive technique of permeabilizing with saponin unstimulated platelets in suspension, and then incubating the cells with polyclonal anti-GMP-140 antibodies and Fab-peroxidase conjugate. Alpha-granule membranes showed heavy reaction product, but no other intracellular organelles were specifically labeled. These results demonstrate that GMP-140 is an alpha-granule membrane protein that is expressed on the platelet plasma membrane during degranulation.
Growth of gallium oxide thin films from gallium acetylacetonate by atomic layer epitaxy (1996)

Gallium oxide thin films have been deposited by atomic layer epitaxy (ALE) using Ga(acac)3(acac = pentane-2,4-dionate) and either water or ozone as precursors. Films were grown on silicon (100), soda lime and Corning glass substrates. The influence of the deposition parameters (e.g. pulse duration, growth and source temperatures) on film growth were studied and by a proper choice of the parameters a self-controlled growth was demonstrated around 370°C. Spectrophotometry, X-ray diffraction (XRD), Rutherford back-scattering spectroscopy (RBS) and X-ray photoelectron spectroscopy (XPS) were used to determine the refractive index, thickness, crystallinity and stoichiometry of the films. All the films were amorphous and highly uniform with only small thickness variations. The films deposited with water contained a considerable amount of carbon as an impurity whereas ozone as an oxidizer gave stoichiometric Ga2O3 films.
Understanding Reuse, Performance, and Hardware Cost of DNN Dataflow (2019)

The data partitioning and scheduling strategies used by DNN accelerators to leverage reuse and perform staging are known as dataflow, which directly impacts the performance and energy efficiency of DNN accelerators. An accelerator micro architecture dictates the dataflow(s) that can be employed to execute layers in a DNN. Selecting a dataflow for a layer can have a large impact on utilization and energy efficiency, but there is a lack of understanding on the choices and consequences of dataflow, and of tools and methodologies to help architects explore the co-optimization design space.
Citation Analysis as a Tool in Journal Evaluation (1972)

As a communications system, the network of journals that play a paramount role in the exchange of scientific and technical information is little understood. Periodically since 1927, when Gross and Gross published their study (1) of references in 1 year’s issues of the Journal of the American Chemical Socie/y, pieces of the network have been illuminated by the work of Bradford (2), Allen (3), Gross and Woodford (4), Hooker (5), Henkle (6), Fussier (7), Brown (8), and others (9). Nevertheless, there is still no map of the journal network as a whok. To date, studies of the network and of the interrelation of its components have been limited in the number of journak, the areas of scientific study, and the periods of time their authors were able to consider, Such shortcomings have not been due to any lack of purpose, insight, or energy on the part of investigators, but to the practical difficulty of compiling and manipulating manually the enormous amount of necessary data. A solution to this problem of data is available in the data base used to produce the Science Citation Index ( SCI ) (10). The coverage of the SCI is international and multidisciplinary; it has grown from 600 journals in 1964 to 2400 journals in 1972, and now includes the world’s most important scientific and technical journals in mow disciplines. The SCI is published quarterly and is cumulated annually and quinquennially, but the data base from which the volumes are compiled is maintained on magnetic tape and is updated weekly. At the end of 1971, this data base contained more than 27 mi[tion references to about 10 million different published items. These references appeared over the past decade in the footnotes and bibliographies of more than 2 million journal articles, communications, letters, and so on. The data base is, thus, not only multidisciplinary, it covers a substantial period of time and, being in machine-readable form, is amenable to extensive manipulation by computer. In 1971, the Institute for Scientfic Information (1S1) decided to undertake a systematic analysis of journal citation patterns across the whole of science and technology. It began by extracting from the data base all references pobIished during the last quarter of 1969 in the 2200 journals then covered by the SCL The resultant sample was about 1 million citations of journals, books, reports, theses, and so forth. To test whether this 3-month sample was representative of the year as a whole, it was matched against another sample made by selecting every 27th reference from the approximately 4 million references collected over the entire year. The two samples were similar enough in scope (number of diflerent items cited) and detail (relative frequency of their citation by different journals) to
Regulators of cyclin-dependent kinases are crucial for maintaining genome integrity in S phase (2010)

Maintenance of genome integrity is of critical importance to cells. To identify key regulators of genomic integrity, we screened a human cell line with a kinome small interfering RNA library. WEE1, a major regulator of mitotic entry, and CHK1 were among the genes identified. Both kinases are important negative regulators of CDK1 and -2. Strikingly, WEE1 depletion rapidly induced DNA damage in S phase in newly replicated DNA, which was accompanied by a marked increase in single-stranded DNA. This DNA damage is dependent on CDK1 and -2 as well as the replication proteins MCM2 and CDT1 but not CDC25A. Conversely, DNA damage after CHK1 inhibition is highly dependent on CDC25A. Furthermore, the inferior proliferation of CHK1-depleted cells is improved substantially by codepletion of CDC25A. We conclude that the mitotic kinase WEE1 and CHK1 jointly maintain balanced cellular control of Cdk activity during normal DNA replication, which is crucial to prevent the generation of harmful DNA lesions during replication.
Quantitative Comparison of Global Carbohydrate Structures of Glycoproteins Using LC−MS and In-Source Fragmentation (1997)

A comparative method for the quantitative analysis of the ratio of oxonium fragment (reporter) ions derived from sialic acid and N-acetylhexosamine residues on a large intact glycoprotein, the B domain of recombinant human factor VIII (rhFVIII), was developed. The method utilized liquid chromatography-electrospray ionization mass spectrometry (LC-ESI MS) on a single-quadrupole instrument. During development, systematic approaches such as full-matrix and simplex strategies were used for the optimization of the signal-to-noise ratio by controlling source temperature and cone voltage. The method was found to be precise (RSD = 0.84%), sensitive (capable of differentiating 1 sialic acid residue change among at least 29 sialic acids on a 103-kDa glycoprotein that is 38% carbohydrate), applicable to a wide range of loading (11.6-372 micrograms of FVIII), and accurate according to a comparison to matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. Combining the method with enzymatic removal of N-glycans, selective O-glycan analysis was also performed leading to differential fragment ion analysis ascribed to N- and O-glycans. Quantitative ESI in-source dissociation MS combined with LC can generally be used for glycoproteins, as one of the indicators, to compare the distribution of carbohydrate residues over N- and O-glycans, to investigate their isoforms, and compare batch-to-batch characteristics of biopharmaceuticals.
Isolation, characterisation and expression of the bacterioferritin gene of Rhodobacter capsulatus (1996)

The nucleotide sequence of the Rhodobacter capsulatus bacterioferritin gene (bfr) was determined and found to encode a protein of 161 amino acids with a predicted molecular mass of 18 174 Da.The molecular mass of the purified protein was estimated to be 18 176.06f 0.80 Da by electrospray mass spectrometry.The bfr gene was introduced into an expression vector, and bacterioferritin was produced to a high level in Escherichia coli.The amino acids which are involved in haem ligation, and those which provide ligands in the binuclear metal centre in bacterioferritin from E. coli are conserved in the R. capsulatus protein.The sequences of bactetiofenitins, ferritin-like proteins, and proteins similar to Dps of E. coli are compared, and membership of the bacterioferritin family re-evaluated.
Shape Deposition Manufacturing With Microcasting: Processing, Thermal and Mechanical Issues (1998)

Shape deposition manufacturing (SDM) is a solid freeform fabrication (SFF) methodology for automatically building up material layers to form three-dimensional, complex-shaped, multi-material structures. Microcasting is a molten metal droplet deposition process which is able to create fully dense metal layers with controlled microstructures. SDM combines microcasting with other intermediate processing operations, such as CNC machining and shot peening, to create high quality metal parts. In this paper, a description is given of SDM and the microcasting process. An overview of thermal and mechanical issues associated with SDM and microcasting is presented, including the control of interlayer metallurgical bonding through substrate remelting, the control of cooling rates of both the substrate and the deposited material and the minimization of residual thermal stress effects. Thermal models are used to study the issue of localized remelting of previously deposited material by newly deposited molten droplets to achieve metallurgical bonding. Mechanical modeling provides insight into residual stress build-up during part manufacture and residual stress-driven debonding between deposited layers.
Docking of Glycosaminoglycans to Heparin-Binding Proteins:  Validation for aFGF, bFGF, and Antithrombin and Application to IL-8 (1999)

Heparin−protein interactions play an important role in many steps of the immune system. Here, we evaluated the search capabilities of three widely used programsGRID, DOCK, and AutoDockfor heparin binding sites. Because of the weak surface complementarity and the high charge density of the sulfated sugar chain, the docking of heparin to its protein partners presents a challenging task for computational docking. Our protocols were tested on antithrombin and acidic and basic fibroblast growth factor, the only three proteins for which structures of their complexes with heparin are available. With all three programs, the heparin binding site for these test cases was determined correctly. We then used these protocols to predict the heparin binding site on Interleukin-8, a chemokine with a central role in the human immune response. The results indicate that His18, Lys20, Arg60, Lys64, and Arg68 in interleukin-8 bind to heparin.
Differences in the Transcriptional Response to Fulvestrant and Estrogen Deprivation in ER-Positive Breast Cancer (2014)

The transcriptional response to fulvestrant has much in common with estrogen deprivation, but is stronger with distinctions potentially attributable to arrest of estrogen-independent ERα activity and involvement of AR signaling. Genes responding differently to fulvestrant may have predictive utility. These data are consistent with the clinical efficacy of fulvestrant versus anastrozole and higher dosing regimens.
The Absolute Bioavailability of Oral Melatonin (2000)

The absolute bioavailability of oral melatonin tablets was studied in 12 normal healthy volunteers. Subjects were administered, in a randomized crossover fashion, melatonin 2 mg intravenously and 2 and 4 mg orally. Blood was sampled over approximately eight (estimated) half-lives. Both the 2 and the 4 mg oral dosages showed an absolute bioavailability of approximately 15%. No difference in serum half-life was seen in any of the study phases. Oral melatonin tablets in dosages of 2 and 4 mg show poor absolute bioavailability, either due to poor oral absorption, large first-pass metabolism, or a combination of both. Further studies examining larger doses, in an attempt to saturate first-pass metabolism if it occurs, may be warranted.
An Arabidopsis myb Homolog Is Induced by Dehydration Stress and Its Gene Product Binds to the Conserved MYB Recognition Sequence (1993)

Takeshi Urao, Kazuko Yamaguchi-Shinozaki, Satomi Urao, Kazuo Shinozaki, An Arabidopsis myb Homolog Is Induced by Dehydration Stress and Its Gene Product Binds to the Conserved MYB Recognition Sequence, The Plant Cell, Vol. 5, No. 11 (Nov., 1993), pp. 1529-1539
A rotary electrostatic micromotor 1×8 optical switch (1999)

This paper describes a 1/spl times/8 rotary electrostatic micromotor optical switch fabricated using high-aspect-ratio micromachining technology to produce silicon or nickel components which are subsequently assembled to form a switch. The switch consists of a salient-pole micromotor with 1-mm-diameter 200-/spl mu/m-thick rotor that supports up to a 500-/spl mu/m-tall, 900-/spl mu/m-wide mirror. Typical switches were actuated at 50 V, operated for extended periods in room air, and found to have a rapid rotation with an average optical switching time between two neighboring fiber ports of 18 ms. Optical testing was performed at wavelength of 1310 nm in single- and multimode, and at 850 nm in multimode. The optical beam was propagated in free space with minimal divergence through the use of externally mounted collimating gradient-index lenses. With an aluminum coating, the mirror and external optics exhibited an input to output coupling loss as low as 0.96 dB in multimode and 2.32 dB in single-mode. Interchannel crosstalk was less than -45 dB.
Urinary Biomarkers TIMP-2 and IGFBP7 Early Predict Acute Kidney Injury after Major Surgery (2015)

Urinary [TIMP-2]×[IGFBP7] test sufficiently detect patients with risk of AKI after major non-cardiac surgery. Due to its rapid responsiveness it extends the time frame for intervention to prevent development of AKI.
Evidence that botulinum C2 toxin has two dissimilar components (1980)

Botulinum C2 toxin produced by most toxigenic and nontoxigenic strains of Clostridium botulinum types C and D contains two distinct protein components, and these were separated by ion-exchange chromatography and gel filtration. Neither of these components manifested the original toxicity, but the original toxicity was restored when the two components were mixed together and trypsinized. This indicates that C2 toxin consists of two dissimilar protein components and that the cooperation of the two is required to elicit toxicity.
Direct observation of shear piezoelectricity in poly-l-lactic acid nanowires (2017)

Piezoelectric polymers are capable of interconverting mechanical and electrical energy, and are therefore candidate materials for biomedical applications such as sensors, actuators, and energy harvesters. In particular, nanowires of these materials are attractive as they can be unclamped, flexible and sensitive to small vibrations. Poly-l-lactic acid (PLLA) nanowires have been investigated for their use in biological applications, but their piezoelectric properties have never been fully characterised, even though macroscopic films and fibres have been shown to exhibit shear piezoelectricity. This piezoelectric mode is particularly interesting for in vivo applications where shear forces are especially relevant, and is similar to what has been observed in natural materials such as bone and DNA. Here, using piezo-response force microscopy (PFM), we report the first direct observation of shear piezoelectricity in highly crystalline and oriented PLLA nanowires grown by a novel template-wetting method. Our results are validated using finite-element simulations and numerical analysis, which importantly and more generally allow for accurate interpretation of PFM signals in soft nanostructured materials. Our work opens up the possibility for the development of biocompatible and sustainable piezoelectric nanogenerators and sensors based on polymer nanowires.
The eight human “canonical” ribonucleases: Molecular diversity, catalytic properties, and special biological actions of the enzyme proteins (2010)

Human ribonucleases (RNases) are members of a large superfamily of rapidly evolving homologous proteins. Upon completion of the human genome, eight catalytically active RNases (numbered 1-8) were identified. These structurally distinct RNases, characterized by their various catalytic differences on different RNA substrates, constitute a gene family that appears to be the sole vertebrate-specific enzyme family. Apart from digestion of dietary RNA, a wide variety of biological actions, including neurotoxicity, angiogenesis, immunosuppressivity, and anti-pathogen activity, have been recently reported for almost all members of the family. Recent evolutionary studies suggest that RNases started off in vertebrates as host defence or angiogenic proteins.
Contiguous Four‐guanosine Sequence in c‐myc Antisense Phosphorothioate Oligonucleotides Inhibits Cell Growth on Human Lung Cancer Cells: Possible Involvement of Cell Adhesion Inhibition (1997)

A contiguous four‐guanosine (4G) sequence in c‐myc antisense phosphorothioate oligonucleotides caused an antiproliferative effect in smooth muscle cells. To investigate the antiproliferative effect of c‐myc antisense oligonucleotides on human lung cancer cell lines, we synthesized oligonucleotides of various lengths and sequences, focusing on the contiguous four‐guanosine (4G) sequence. While a c‐myc antisense oligonucleotide (20AS1 (4G)) targeted to the translation initiation codon of c‐myc mRNA inhibited cell growth of A549 cells by 69% at 10 μM, a scrambled oligonucleotide (20SCR1 (4G)) containing the contiguous four‐guanosine (4G) sequence also inhibited cell growth by 72% at the same dose. Although treatment with either 20AS1 (4G) or 20SCR1 (4G) inhibited cell adhesion by 70% at 10 μM, expression of c‐myc protein was significantly suppressed only by 20AS1 (4G) (62%), and was only weakly inhibited by 20SCR1 (4G) (32%). Furthermore, a small cell lung carcinoma cell line, Lu65, which can grow in suspension form, was highly resistant to 20AS1 (4G) treatment (IC 50 &gt;20 μM). These results suggest that the cell growth inhibition by C‐myc antisense oligonucleotides containing the contiguous four‐guanosine (4G) sequence was possibly correlated with inhibition of cell adhesion, but not with inhibition of c‐myc protein expression, via a sequence‐specific non‐antisense mechanism.
Effect of Vessel Size on Creation of Hepatic Radiofrequency Lesions in Pigs (2002)

There appears to be a narrow transition zone for hepatic vessels at 2-4 mm, beyond which the heat sink effect was seen consistently and substantial vascular injury was rare.