gebhart/patrepeval huggingface dataset:
Ultrahigh-resolution Optical Coherence Tomography with the Frequency-sweeping the Broadened Spectrum of a fs Cr:forsterite Laser (2007)

We demonstrate a swept-source optical coherence tomography system, including a broadband frequency sweeping light source with the central wavelength around 1250 nm, to achieve an axial resolution of 2.4 microns in tissue.
Restriction of substrate specificity of subtilisin E by introduction of a side chain into a conserved glycine residue (1996)

Substitution of the conserved Gly127 for residues having a side chain markedly changed the substrate specificity of subtilisin E from Bacillus subtilis. The crystallographic findings suggested that Gly127 is responsible for accepting even the large P1 substrates, and the marked change of specificity was attributed to the introduction of a side chain in this position. To test this hypothesis, Gly127 was replaced with 3 non-charged amino acids, Ala, Ser and Val. When assayed with synthetic peptide substrates, all mutants purified from the periplasmic space in Escherichia coli showed a marked preference for small P1 substrate up to 150-fold relative to the wild-type. The kinetic data and molecular modeling analysis suggest that large hydrophobic P1 residues were unable to access the binding pocket due to steric hindrance.
Sequence‐dependent hydrolysis of RNA using modified oligonucleotide splints and RNase H (1987)

To cleave RNA molecules using RNase H in a site-specific manner, a short deoxyoligonucleotide (3-5mer) joining with 2'-O-methyl oligonucleotide(s) was designed as a DNA splint to be used. Model experiments were carried out using ribooligonucleotide substrates (9 and 18 mer). It was found that the use of this type of splints (9 mer) causes a unique cleavage by RNase H. For example, when 3'm (GA)d(AGAA)m(GGU)5' was used as a hybridization strand, 32pUCUUUCUUCUUCCAGGAU was cleaved specifically between U11 and C12 to yield 32pUCUUUCUUCUU. This method will have a variety of applications for the study of RNA.
Effect of low‐power laser irradiation on the mechanical properties of bone fracture healing in rats (1998)

Background and Objective Low-power laser irradiation (LPLI) has been found to have a positive effect on bone fracture healing in animal models, based on morphogenic, biochemical, roentgenographic, and electron microscopic measurements. We investigated the effect of LPLI on bone fracture healing in rats using biomechanical methods. Study Design/Materials and Methods: Two groups of male Wistar rats, divided in a randomized block design in a blinded fashion, each consisting of 25 animals, were subjected to anesthesia and tibial bone fracture with internal fixation. The first group was treated with LPLI (HeNe laser 632.8 nm, 35 mW), applied transcutaneously over 30 minutes to the area of the fracture daily for 14 days. The second group served as a control. After 4 weeks, the tibia was removed and tested at tension up to failure (by a Lloyd LR 50K testing apparatus, U.K.) in 16 rats from group I and 15 from group II. The maximal load at failure, the structural stiffness of the tibia (callus stiffness), and the extension maximal load were measured. Results The maximal load at failure and the structural stiffness of the tibia were found to be elevated significantly in the irradiated group (P = .014 and P = .0023, respectively), whereas the extension maximal load was reduced (P = .015). In addition, gross non-union was found in four fractures in the control group, compared to none in the irradiated group. Conclusion These results suggest that LPLI treatment may play a role in enhancing bone healing. Lasers Surg. Med. 22:97–102, 1998. © 1998 Wiley-Liss, Inc.
User-Friendly Expression Plasmids Enable the Fusion of VHHs to Application-Specific Tags (2012)

One of the advantages of using recombinant instead of conventional antibodies is that these can be easily manipulated by means of standard molecular biology techniques. Therefore this opportunity can be exploited to prepare fusion constructs composed of VHHs and suitable tags. According to the applications in which the antibodies will be applied, molecules such as fluorescent probes, biotin, and PEG can be either covalently or non-covalently linked to the antibodies. Within this chapter, practical tips for the choice and expression of the most appropriate among the available plasmids are listed, keeping in mind the experimental conditions in which usually the fusion antibodies will be applied.
DEFLATE Compressed Data Format Specification version 1.3 (1996)

This specification defines a lossless compressed data format that compresses data using a combination of the LZ77 algorithm and Huffman coding, with efficiency comparable to the best currently available general-purpose compression methods. The data can be produced or consumed, even for an arbitrarily long sequentially presented input data stream, using only an a priori bounded amount of intermediate storage. The format can be implemented readily in a manner not covered by patents.
Human B cell-inducing factor(s) for production of IgM, IgG and IgA: independence from IL 2. (1984)

Human peripheral blood B cells are stimulated into proliferation by killed Staphylococcus aureus bacteria strain Cowan I (Sac). T lymphocytes in the presence of a T cell mitogen induce high numbers of immunoglobulin-secreting cells (ISC) in these Sac-stimulated B cells. The T cells can be largely replaced by a lymphokine factor. We describe here the 11000-fold purification of this B cell-inducing factor (BIF). BIF preparations that are free of IL 2 do not require IL 2 for optimal induction of ISC. This was shown by the lack of effect of IL 2 alone or with suboptimal or optimal concentrations of BIF on the induction of ISC and by the absence of IL 2 production in the purified B cell population which, with other controls, excludes significant T cell contamination. BIF, purified through four fractionation steps and free of IL 2, induces IgM, IgG, and IgA-ISC in approximately the same ratio as unfractionated lymphokine. Because we have not yet attained a pure BIF preparation, the possibility of separate factors for the production of each immunoglobulin isotype cannot be ruled out.
Spontaneous solubilization of membrane-bound human testis angiotensin-converting enzyme expressed in Chinese hamster ovary cells. (1991)

The testis isozyme of angiotensin-converting enzyme (ACE; EC 3.4.15.1) is a membrane-bound protein that, apart from the first 35 N-terminal residues, is identical to the C-terminal half of somatic ACE and contains the same putative C-terminal membrane anchor. Stable transfection of Chinese hamster ovary (CHO) cells with an expression vector containing the full-length human testis ACE cDNA results in the expression of two forms of recombinant human testis ACE (hTACE): membrane-bound ACE and, surprisingly, large quantities (up to 3 mg/liter) of soluble hTACE in the conditioned medium. Both forms are fully active and are physicochemically similar. However, by phase separation in Triton X-114, the soluble enzyme is hydrophilic, as is an anchor-minus mutant hTACE recovered from the medium of CHO cells transfected with a vector that contains a 3'-truncated testis ACE cDNA lacking the sequence encoding the membrane anchor. In contrast, the membrane-bound hTACE is amphipathic but is converted to a hydrophilic form on treatment with trypsin. The data establish that in ACE the hydrophobic sequence near the C terminus is necessary for membrane anchoring. Moreover, in CHO cells, membrane-bound hTACE is apparently solubilized by proteolytic cleavage of this anchor. A similar mechanism may account for the release of endothelial ACE in vivo to generate serum ACE and more generally for the constitutive processing and solubilization of analogously anchored proteins such as the amyloid precursor protein, among others. The release of membrane-bound ACE in CHO cells may, therefore, provide a useful system for the study of membrane-protein-solubilizing proteases.
NRG-3 in human breast cancers: activation of multiple erbB family proteins. (1998)

Ligands of the EGF/Heregulin family control the growth of epithelial cells by binding to receptors of the erbB family. By searching a large database of cDNA sequences at Human Genome Sciences Inc. we have identified a new encoded protein sequence containing all the conserved elements of the EGF/Heregulin family. The same sequence has recently been independently identified as NRG-3. The EGF-like domain of NRG-3 was generated as a recombinant protein in E. coli and used to test the specificity of receptor binding. In human breast cancer cells and in 32D cells transfected by erbB family members, NRG-3 activated multiple erbB family members. These include EGF receptor (erbB1) and erbB4 when expressed individually and erbB2 and erbB3 when expressed together. Recombinant NRG-3 altered the growth of human breast cancer cells growing in vitro. NRG-3 was expressed in cell lines derived from breast cancer. These results indicate that NRG-3 is a potential regulator of normal and malignant breast epithelial cells in vivo.
Immunotherapy for cancer: the use of lymphokine activated killer (LAK) cells. (1987)

Editorial. rappel historique sur la recherche d'une immunotherapie du cancer. Etapes des travaux experimentaux sur l'immunotherapie adoptive et active des tumeurs (du tube digestif surtout). Perspectives d'avenir concernant les cellules LAK
Surface modification of polymers. V. Biomaterial applications (1990)

Abstract Polyethylene films were surface grafted with glycidyl methacrylate (GMA) by UV irradiating the film for 5 min together with benzophenone. Poly(ethylene glycol) (PEG) was attached to the grafted surface through reaction with the epoxy groups. This yielded a surface which consisted of 95% PEG as measured with ESCA. The adsorption of human transferrin onto this film was significantly reduced as compared with a pure polyethylene film. Heparin was also reacted with a GMA grafted PE surface. ESCA showed that heparin was grafted to the surface, and in vitro blood clotting tests on the heparinized PE surface showed a reduced thrombus formation. GMA grafted polystyrene wells were reacted with carbohydrazide, to the formed carbohydrazide surface a rabbit antibody raised against mouse urinary protein (RaMUP) was covalently coupled. The RaMUP coupled surfaces was used in the detection of mouse urinary protein (MUP) at low concentrations (ca. 1 ng/mL) with an ELISA technique.
O-GalNAc Glycans (2009)

O-glycosylation is a common covalent modification of serine and threonine residues of mammalian glycoproteins. This chapter describes the structures, biosynthesis, and functions of glycoproteins that are often termed mucins. In mucins, O-glycans are covalently α-linked via an N-acetylgalactosamine (GalNAc) moiety to the -OH of serine or threonine by an O-glycosidic bond, and the structures are named mucin O-glycans or O-GalNAc glycans. The focus of this chapter is on mucins and mucin-like glycoproteins that are heavily O-glycosylated, although glycoproteins that carry only one or a few O-GalNAc glycans are also briefly discussed. There are also several types of nonmucin O-glycans, including α-linked O-fucose, β-linked O-xylose, α-linked O-mannose, β-linked O-GlcNAc (N-acetylglucosamine), α- or β-linked O-galactose, and α- or β-linked O-glucose glycans (discussed in Chapters 12 and 16–18). In this chapter, however, the term O-glycan refers to mucin O-glycans, unless otherwise specified. Mucin glycoproteins are ubiquitous in mucous secretions on cell surfaces and in body fluids.
When to treat myelodysplastic syndromes. (2011)

The myelodysplastic syndromes represent a heterogeneous series of clonal hematologic neoplasms characterized by morphologic dysplasia, aberrant hematopoiesis and a variable risk of progression to acute myeloid leukemia. These syndromes have a complex pathobiology, and ineffective hematopoiesis is a well-recognized feature of all of them. Normal blood cell maturation, differentiation, function, and survival are impaired, and these abnormalities contribute to the development of peripheral blood pancytopenia. The majority of patients succumb to complications of either bone marrow failure or leukemic progression. The fact that the majority of patients are elderly and have other comorbidities complicates therapeutic decision making and necessitates the development of individualized treatment strategies.
STAT 3 as a Target for Cancer Drug Discovery (2008)

Stat-3 (Signal Transduction and Activator of Transcription) is a member of the Stat family of latent, cytosolic transcription factors that directly relate signals from the plasma membrane to the nucleus. This protein is constitutively activated by aberrant upstream tyrosine kinase activities in a broad spectrum of human tumors, and it has been identified as a promising target for cancer drug discovery. This review deals with the recent developments of peptides and peptidomimetics or even non-peptidic small molecules, able to bind to the SH2 domain of Stat-3, thus blocking its functions. Moreover, several compounds able to alter the Stat-3 pathway by inhibition of kinases upstream to Stat-3, or even with unknown targets, were reviewed. Keywords: Antitumor agents, Stat-3, Peptide-based antagonists, Small molecules, Natural compounds
Pseudopotential calculations of electron and hole addition spectra of InAs, InP, and Si quantum dots (2000)

The electron and hole addition energies, the quasiparticle gap, and the optical gap of InAs, InP, and Si quantum dots are calculated using microscopic pseudopotential wave functions. The effects of the dielectric mismatch between the quantum dot and the surrounding material are included using a realistic profile for the dielectric constant $\ensuremath{\epsilon}(\mathbf{r}).$ We find that the addition energies and the quasiparticle gap depend strongly on the dielectric constant of the environment ${\ensuremath{\epsilon}}_{\mathrm{out}},$ while the optical gap is rather insensitive to ${\ensuremath{\epsilon}}_{\mathrm{out}}.$ We compare our results with recent tunneling spectroscopy measurements for InAs nanocrystals, finding excellent agreement. Our calculations for the addition energies and the quasiparticle gap of InP and Si nanocrystals serve as predictions for future experiments.
High permittivity thin film nanolaminates (2000)

Thin (∼10 nm) films comprising of Ta2O5–HfO2, Ta2O5–ZrO2, and ZrO2–HfO2 nanolaminates were deposited and characterized for possible gate dielectric applications. These films were deposited on silicon substrates using atomic layer deposition. The dielectric constants of these films were in 12–14 range and the leakage currents in 2.6×10−8–4.2×10−7 A/cm2 range at 1 MV/cm electric field. It was found that as these films were made thinner, the value of their dielectric constant dropped compared to their bulk values. The dominant leakage current mechanism at low electric fields was determined to be Schottky emission, whereas Poole–Frenkel emission dominated at higher fields.
A Comparison of the Accuracy of an Electromagnetic and a Hybrid Ultrasound-Inertia Position Tracking System (2001)

Results of a comparison study of the tracking accuracy of two commercially available wide-range position tracking systems suitable for CAVEs are presented. An experiment was conducted with Flock of Birds and IS-900 tracking systems installed in the same CAVE environment to compare their accuracy. Another experiment was performed with a newly deployed IS-900 to investigate the impact of different ultrasound emitter configurations on the accuracy of the location tracking. The results show that the IS-900 has a much better accuracy over a larger range of operation than does the Flock of Birds; however, it is sensitive to the optimality of the ultrasound emitters configuration.
Isolation and characterization of cDNA clones for the 35-kDa pulmonary surfactant-associated protein. (1986)

A group of 35,000-dalton sialoglycoproteins is the major non-serum protein component of pulmonary surfactant. Tryptic fragments of these proteins were sequenced, and oligonucleotide probes were synthesized based on the amino acid sequences. A human lung cDNA library was then screened using the oligonucleotide probes, and clones coding for these proteins were identified and characterized. By in vitro transcription-translation experiments we have associated individual clones with particular proteins. The data suggest that co-translational modifications of two primary translation products account for many of the isoforms observed by two-dimensional gel electrophoresis in the precursors of 35,000-dalton sialoglycoproteins.
Substrate-Independent Approach for the Generation of Functional Protein Resistant Surfaces (2011)

A new route for coating various substrates with antifouling polymer layers was developed. It consisted in deposition of an amino-rich adhesion layer by means of RF magnetron sputtering of Nylon 6,6 followed by the well-controlled, surface-initiated atom transfer radical polymerization of antifouling polymer brushes initiated by bromoisobutyrate covalently attached to amino groups present in the adhesion layer. Polymer brushes of hydroxy- and methoxy-capped oligoethyleneglycol methacrylate and carboxybetaine acrylamide were grafted from bromoisobutyrate initiator attached to a 15 nm thick amino-rich adhesion layer deposited on gold, silicon, polypropylene, and titanium-aluminum-vanadium alloy surfaces. Well-controlled polymerization kinetics made it possible to control the thickness of the brushes at a nanometer scale. Zero fouling from single protein solutions and a reduction of more than 90% in the fouling from blood plasma observed on the uncoated surfaces was achieved. The feasibility of functionalization with bioactive compounds was tested by covalent attachment of streptavidin onto poly(oligoethylene glycol methacrylate) brush and subsequent immobilization of model antibodies and oligonucleotides. The procedure is nondestructive and does not require any chemical preactivation or the presence of reactive groups on the substrate surface. Contrary to current antifouling modifications, the developed coating can be built on various classes of substrates and preserves its antifouling properties even in undiluted blood plasma. The new technique might be used for fabrication of biotechnological and biomedical devices with tailor-made functions that will not be impaired by fouling from ambient biological media.
Natural alleles at a tomato fruit size quantitative trait locus differ by heterochronic regulatory mutations (2002)

fw2.2 is a major quantitative trait locus that accounts for as much as 30% of the difference in fruit size between wild and cultivated tomatoes. Evidence thus far indicates that fw2.2 alleles modulate fruit size through changes in gene regulation rather than in the FW2.2 protein itself. To investigate the nature of these regulatory changes and the manner in which they may affect fruit size, a pair of nearly isogenic lines has been subjected to detailed developmental, transcriptional, mitotic, and in situ hybridization studies. The results indicate that the large- and small-fruited alleles of fw2.2 differ in peak transcript levels by approximately 1 week. Moreover, this difference in timing of expression is associated with concomitant changes in mitotic activity in the early stage of fruit development. The changes in timing of gene expression (heterochronic allelic variation), combined with overall differences in total transcript levels, are sufficient to account for a large portion phenotypic differences in fruit weight associated with the two alleles.
Breath alkanes determination in ulcerative colitis and Crohn's disease (1999)

An excess of lipid peroxidation is probably an important pathogenetic factor in inflammatory bowel diseases, and this may be assessed through a noninvasive method. Because this method previously also has been shown to be able to evaluate disease activity, it could be a useful tool for studying patients with inflammatory bowel diseases.
Effector-attenuating Substitutions That Maintain Antibody Stability and Reduce Toxicity in Mice (2017)

The antibody Fc region regulates antibody cytotoxic activities and serum half-life. In a therapeutic context, however, the cytotoxic effector function of an antibody is often not desirable and can create safety liabilities by activating native host immune defenses against cells expressing the receptor antigens. Several amino acid changes in the Fc region have been reported to silence or reduce the effector function of antibodies. These earlier studies focused primarily on the interaction of human antibodies with human Fc-γ receptors, and it remains largely unknown how such changes to Fc might translate to the context of a murine antibody. We demonstrate that the commonly used N297G (NG) and D265A, N297G (DANG) variants that are efficacious in attenuating effector function in primates retain potent complement activation capacity in mice, leading to safety liabilities in murine studies. In contrast, we found an L234A, L235A, P329G (LALA-PG) variant that eliminates complement binding and fixation as well as Fc-γ-dependent, antibody-dependent, cell-mediated cytotoxity in both murine IgG2a and human IgG1. These LALA-PG substitutions allow a more accurate translation of results generated with an "effectorless" antibody between mice and primates. Further, we show that both human and murine antibodies containing the LALA-PG variant have typical pharmacokinetics in rodents and retain thermostability, enabling efficient knobs-into-holes bispecific antibody production and a robust path to generating highly effector-attenuated bispecific antibodies for preclinical studies.
ABO-INCOMPATIBLE MARROW TRANSPLANTS (1982)

We analyzed data from 81 ABO-incompatible marrow transplants performed between 1972 and 1980. Patients with high anti-red blood cell antibody levels pretransplant had a significantly increased probability of antibody return post-transplant. This was true for IgG and for IgM as independent variables. However, the return of antibody post-transplant had no effect on engraftment, survival, or blood product requirements posttransplant. Patients who received ABO-incompatible marrow had a similar time to engraftment, survival, and incidence of rejection and graft-versus-host disease as patients receiving ABo-compatible transplants. Neither pretransplant treatment regimen nor the development of graft-versus-host disease had an effect on post-transplant antibody levels. ABO-incompatible marrow transplants can be performed with no greater morbidity or mortality than ABO-compatible grafts. The procedures for antibody removal may be useful in other organ transplant settings.
Expressive speech-driven facial animation (2005)

Speech-driven facial motion synthesis is a well explored research topic. However, little has been done to model expressive visual behavior during speech. We address this issue using a machine learning approach that relies on a database of speech-related high-fidelity facial motions. From this training set, we derive a generative model of expressive facial motion that incorporates emotion control, while maintaining accurate lip-synching. The emotional content of the input speech can be manually specified by the user or automatically extracted from the audio signal using a Support Vector Machine classifier.