gebhart/patrepeval huggingface dataset:
Antitumor Effect of the Idiotypic Cascade Induced by an Antibody Encapsulated in Poly(d, l‐lactide‐co‐glycolide) Microspheres (2001)

A major difficulty encountered during development of antibody vaccines is their weak immunogenicity. In this study, a monoclonal antibody CS20.5 to human breast cancer antigen CA15.3 was coencapsulated in poly(d,l-lactide-co-glycolide) microspheres with monophosphoryl lipid A. The antitumor effect of this formulation was investigated in a murine model. The induced Ab2 biologically mimics antigen as it competed with CA15.3 for the same idiotope on Ab1. Ab3 induction was also observed. After five sequential administrations of encapsulated antibody, mice showed statistically significant tumor regression. These results indicate that this formulation may serve as a potential treatment for breast cancer.
Differential influence of nerve growth factor on neuropeptide expression in vivo: a novel role in peptide suppression in adult sensory neurons (1995)

In this study the actions of NGF in regulating peptide expression were examined in vivo in adult rat primary sensory neurons. The hypothesis that NGF might tonically inhibit expression of some peptides was tested specifically. In situ hybridization and immunohistochemistry were used to detect presence or absence of alpha-CGRP, beta-CGRP, SP, SOM, VIP, CCK, NPY, and GAL as well as their mRNAs. In neurons in normal lumbar DRG alpha-CGRP, beta-CGRP, SP, and SOM are abundantly and heterogeneously expressed whereas few neurons have detectable VIP, CCK, NPY, or GAL. Two weeks following sciatic nerve transection, concentrations of alpha-CGRP, beta-CGRP, SP, and SOM plus their mRNAs have decreased to background in all but a few neurons. In contrast, VIP, CCK, NPY, and GAL are now synthesized in many neurons. Delayed intrathecal infusion of NGF (125 ng/microliter/hr) for 7 d, starting 2 weeks after injury counteracted the decrease in expression of alpha-CGRP, beta-CGRP and SP expression, but not SOM. This lack of influence of NGF on SOM is consistent with the absence of high-affinity NGF receptors and trk mRNA in SOM-positive neurons. Delayed infusion of NGF also reduced the number of neurons expressing VIP, CCK, NPY, and GAL after injury by approximately one-half in each subpopulation. Therefore, we suggest that NGF suppresses expression of these four peptides but only if the neurons also have NGF receptors. The results show that NGF can regulate peptide expression differentially and may also be part of the signal that allows reversion to normal of responses to injury as axons regenerate.
THE REACTION MECHANISM OF HUMAN C5 IN IMMUNE HEMOLYSIS (1970)

The data presented here indicate that the C5 reaction step may proceed via the specific attachment of C5 to EAC1,4,2,3 and the formation of a hemolytically active C5 intermediate complex. During this process only a minor proportion (less than 4%) of C5 offered to EAC1,4,2,3 becomes bound, although the remaining C5 also participates in the reaction as evidenced by its inactivation in the fluid phase. Once bound, C5 is exceptionally efficient in producing hemolysis, requiring less than seven specifically bound molecules per cell for the production of a hemolytic lesion. The extent of formation of the C5 intermediate complex is primarily dependent on the number of molecules of C4, 2 and C3 present on the cells employed for its generation. In these respects, the mode of action of C5 is completely analogous to that of the other components of complement thus far investigated. The C5 step differs, however, in other aspects. The binding of C5 is influenced by C6 and C7, components which are thought to act subsequent to it in the complement sequence. In addition, the hemolytic activity of the isolated C5 intermediate complex is exceedingly labile, having an average half-life at 30 degrees C of only 9 min. This characteristic distinguishes the C5 step, along with the C2 step, as potentially rate-limiting in the complement reaction. However, unlike C2, C5 remains firmly cell-bound during the decay process and apparently undergoes an alteration in situ which renders it hemolytically unreactive. Finally, C5 is unique in that it readily adsorbs in native form to unsensitized erythrocytes. This nonspecifically bound C5 remains firmly attached, although it may be specifically utilized as a source of C5 by an ongoing complement reaction. The significance of the marked affinity of native C5 for cell-surface receptors remains to be determined.
MRI compatibility and visibility assessment of implantable medical devices (1999)

We have developed a protocol to evaluate the magnetic resonance (MR) compatibility of implantable medical devices. The testing protocol consists of the evaluation of magnetic field-induced movement, electric current, heating, image distortion, and device operation. In addition, current induction is evaluated with a finite element analysis simulation technique that models the effect of radiofrequency fields on each device. The protocol has been applied to several implantable infusion pumps and neurostimulators with associated attachments. Experiments were performed using a 1.5-T whole-body MR system with parameters selected to approximate the intended clinical and worst case configuration. The devices exhibited moderate magnetic field-induced deflection and torque but had significant image artifacts. No heating was detected for any of the devices. Pump operation was halted in the magnetic field, but resumed after removed. Exposure to the magnetic field activated some of the neurostimulators.J. Magn. Reson. Imaging 1999;9:596–603. © 1999 Wiley-Liss, Inc.
Multi-Emissive Difluoroboron Dibenzoylmethane Polylactide Exhibiting Intense Fluorescence and Oxygen-Sensitive Room-Temperature Phosphorescence (2007)

Boron difluoride compounds are light emitting materials with impressive optical properties. Though their strong one- and two-photon absorption and intense fluorescence are well-known and exploited in molecular probes, lasers, and photosensitizers, phosphorescence, in contrast, is typically observed only at low temperatures. Here, we report that unusual room-temperature phosphorescence is achieved by combining a classic boron dye, difluoroboron dibenzoylmethane, BF2dbm, with poly(lactic acid) (PLA), a common biopolymer, resulting in a highly sensitive single-component oxygen sensor. Fluorescence quantum yields are enhanced, and temperature-sensitive delayed fluorescence is also observed. Multi-emissive BF2dbmPLA biomaterials show great promise as multifunctional molecular probes and sensors.
Ibrutinib for the treatment of mantle cell lymphoma (2014)

Mantle cell lymphoma (MCL) is a rare and aggressive form of non-Hodgkin's lymphoma. It can follow a heterogeneous clinical course but generally patients relapse early after standard immunochemotherapy regimens and develop resistance to subsequent therapies. For younger patients, intensive approaches followed by autologous stem cell transplantation offer excellent long-term disease control but with the possible exception of an allogenic stem cell transplant, MCL is an incurable condition. As MCL principally affects older individuals, the majority of patients are not candidates for such intensive approaches. Ibrutinib is an orally active, Bruton's tyrosine kinase inhibitor. It inhibits signaling pathways downstream of Bruton's tyrosine kinase that appear critical for the proliferation and survival of MCL. As a single agent it has shown extremely promising activity in relapsed and refractory MCL patients with an excellent side-effect profile. The exact role for ibrutinib in the treatment of MCL is yet to be established; however, it is likely to fundamentally change the way we treat this disease.
Late MRD response determines relapse risk overall and in subsets of childhood T-cell ALL: results of the AIEOP-BFM-ALL 2000 study (2011)

The prognostic value of MRD in large series of childhood T-ALL has not yet been established. Trial AIEOP-BFM-ALL 2000 introduced standardized quantitative assessment of MRD for stratification, based on immunoglobulin and TCR gene rearrangements as polymerase chain reaction targets: Patients were considered MRD standard risk (MRD-SR) if MRD was negative at day 33 (time point 1 [TP1]) and day 78 (TP2), analyzed by at least 2 sensitive markers; MRD intermediate risk (MRD-IR) if positive either at day 33 or 78 and < 10(-3) at day 78; and MRD high risk (MRD-HR) if ≥ 10(-3) at day 78. A total of 464 patients with T-ALL were stratified by MRD: 16% of them were MRD-SR, 63% MRD-IR, and 21% MRD-HR. Their 7-year event-free-survival (SE) was 91.1% (3.5%), 80.6% (2.3%), and 49.8% (5.1%) (P < .001), respectively. Negativity of MRD at TP1 was the most favorable prognostic factor. An excellent outcome was also obtained in 32% of patients turning MRD negative only at TP2, indicating that early (TP1) MRD levels were irrelevant if MRD at TP2 was negative (48% of all patients). MRD ≥ 10(-3) at TP2 constitutes the most important predictive factor for relapse in childhood T-ALL. The study is registered at http://www.clinicaltrials.gov; "Combination Chemotherapy Based on Risk of Relapse in Treating Young Patients With Acute Lymphoblastic Leukemia," protocol identification #NCT00430118 for BFM and #NCT00613457 for AIEOP.
Construction, Cloning, and Expression of Synthetic Genes Encoding Spider Dragline Silk (1995)

Synthetic genes encoding recombinant spider silk proteins have been constructed, cloned, and expressed. Protein sequences were derived from Nephila clavipes dragline silk proteins and reverse-translated to the corresponding DNA sequences. Codon selection was chosen to maximize expression levels in Escherichia coli. DNA "monomer" sequences were multimerized to encode high molecular weight synthetic spider silks using a "head-to-tail" construction strategy. Multimers were cloned into a prokaryotic expression vector and the encoded silk proteins were expressed in E. coli upon induction with IPTG. Four multimer, ranging in size from 14.7 to 41.3 kDa, were chosen for detailed analysis. These proteins were isolated by immobilized metal affinity chromatography and purified using reverse-phase HPLC. The composition and identity of the purified proteins were confirmed by amino acid composition analysis, N-terminal sequencing, laser desorption mass spectroscopy, and Western analysis using antibodies reactive to native spider dragline silk. Circular dichroism measurements indicate that the synthetic spider silks have substantial beta-sheet structure.
Humanmelanocortin 1 receptorvariants, receptor function and melanocyte response to UV radiation (2002)

Cutaneous pigmentation is determined by the amounts of eumelanin and pheomelanin synthesized by epidermal melanocytes and is known to protect against sun-induced DNA damage. The synthesis of eumelanin is stimulated by the binding of alpha-melanotropin (alpha-melanocyte-stimulating hormone) to the functional melanocortin 1 receptor (MC1R) expressed on melanocytes. The human MC1R gene is highly polymorphic and certain allelic variants of the gene are associated with red hair phenotype, melanoma and non-melanoma skin cancer. The importance of the MC1R gene in determining skin cancer risk led us to examine the impact of specific polymorphisms in this gene on the responses of human melanocytes to alpha-melanotropin and UV radiation. We compared the ability of human melanocyte cultures, each derived from a single donor, to respond to alpha-melanotropin with dose-dependent stimulation of cAMP formation, tyrosinase activity and proliferation. In each of those cultures the MC1R gene was sequenced, and the eumelanin and pheomelanin contents were determined. Human melanocytes homozygous for Arg160Trp, heterozygous for Arg160Trp and Asp294His, or for Arg151Cys and Asp294His substitutions, but not melanocytes homozygous for Val92Met substitution, in the MC1R demonstrated a significantly reduced response to alpha-melanotropin. Additionally, melanocytes with a non-functional MC1R demonstrated a pronounced increase in their sensitivity to the cytotoxic effect of UV radiation compared with melanocytes expressing functional MC1R. We conclude that loss-of-function mutations in the MC1R gene sensitize human melanocytes to the DNA damaging effects of UV radiation, which may increase skin cancer risk.
Expressed Sequence Tags: Analysis and Annotation<I> (2004)

Expressed sequence tags (ESTs) present a special set of problems for bioinformatic analysis. They are partial and error-prone, and large datasets can have significant internal redundancy. To facilitate analysis of small EST datasets from in-house projects, we present an integrated "pipeline" of tools that take EST data from sequence trace to database submission. These tools also can be used to provide clustering of ESTs into putative genes and to annotate these genes with preliminary sequence similarity searches. The systems are written to use the public-domain LINUX environment and other openly available analytical tools.
The 1.3 Å Crystal Structure of the Flavoprotein YqjM Reveals a Novel Class of Old Yellow Enzymes (2005)

Here we report the crystal structure of YqjM, a homolog of Old Yellow Enzyme (OYE) that is involved in the oxidative stress response of Bacillus subtilis. In addition to the oxidized and reduced enzyme form, the structures of complexes with p-hydroxybenzaldehyde and p-nitrophenol, respectively, were solved. As for other OYE family members, YqjM folds into a (alpha/beta)8-barrel and has one molecule of flavin mononucleotide bound non-covalently at the COOH termini of the beta-sheet. Most of the interactions that control the electronic properties of the flavin mononucleotide cofactor are conserved within the OYE family. However, in contrast to all members of the OYE family characterized to date, YqjM exhibits several unique structural features. For example, the enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers. Moreover, the protein displays a shared active site architecture where an arginine finger (Arg336) at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal Tyr28 instead of a COOH-terminal tyrosine in OYE and its homologs. The structural information led to a specific data base search from which a new class of OYE oxidoreductases was identified that exhibits a strict conservation of active site residues, which are critical for this subfamily, most notably Cys26, Tyr28, Lys109, and Arg336. Therefore, YqjM is the first representative of a new bacterial subfamily of OYE homologs.
Fulvestrant-induced expression of ErbB3 and ErbB4 receptors sensitizes oestrogen receptor-positive breast cancer cells to heregulin β1 (2011)

These findings suggest that although antihormones such as fulvestrant may have potent acute growth-inhibitory activity in ER-positive breast cancer cells, their ability to induce and sensitise cells to growth factors may serve to reduce and ultimately limit their inhibitory activity.
The Effect of Macromolecular Crowding on the Electrostatic Component of Barnase–Barstar Binding: A Computational, Implicit Solvent-Based Study (2014)

Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered ''effective'' solvent dielectric to account for crowding, although the ''best'' effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.
Germanium Nanowire Growth via Simple Vapor Transport (2000)

Germanium nanowires are synthesized in bulk quantities and high purity using a simple vapor transport process. X-ray diffraction, scanning electron microscopy and transmission electron microscopy studies show that these wires are single crystalline with [111] growth direction; they have diameters ranging from 5 to 300 nm, and lengths up to hundreds micrometer. With brief vacuum thermal treatment, the average diameters of the wires can be further reduced to 16 nm.
Solid state Marx generator using series-connected IGBTs (2004)

Pulsed power supplies using solid state switches have been widely studied recently. Use of high power semiconductors such as IGBTs and IGCTs have become an area of interest today. To make this, several type of pulse generators using solid state devices have been adopted and tested in many papers. In this paper, a boost converter array using series-connected switches is presented. The electrical circuit is made of a boost converter array to produce high voltage pulses. To verify the proposed converter, an experimental equipment with a 20 kV, 300 A pulse generator was made and food treatment results are shown.
A novel strategy for generating monoclonal antibodies from single, isolated lymphocytes producing antibodies of defined specificities. (1996)

We report a novel approach to the generation of monoclonal antibodies based on the molecular cloning and expression of immunoglobulin variable region cDNAs generated from single rabbit or murine lymphocytes that were selected for the production of specific antibodies. Single cells secreting antibodies for a specific peptide either from gp116 of the human cytomegalovirus or from gp120 of HIV-1 or for sheep red blood cells were selected using antigen-specific hemolytic plaque assays. Sheep red blood cells were coated with specific peptides in a procedure applicable to any antigen that can be biotinylated. Heavy- and light-chain variable region cDNAs were rescued from single cells by reverse transcription-PCR and expressed in the context of human immunoglobulin constant regions. These chimeric murine and rabbit monoclonal antibodies replicated the target specificities of the original antibody-forming cells. The selected lymphocyte antibody method exploits the in vivo mechanisms that generate high-affinity antibodies. This method can use lymphocytes from peripheral blood, can exploit a variety of procedures that identify individual lymphocytes producing a particular antibody, and is applicable to the generation of monoclonal antibodies from many species, including humans.
Microcarrier Culture Systems (2018)

Animal and human cells can be propagated in vitro in two basically different modes: as anchorage-independent cells growing freely in suspension throughout the bulk of the culture, or as anchorage-dependent cells (ADC) requiring attachment to solid substrate for their propagation (monolayer type of cell growth). This chapter describes the concept of the microcarrier (MC) culture, different commercially and noncommercially developed MCs, and critical parameters which determine their suitability for supporting cell growth and production of biologicals. It also describes the ways in which the MCs are used in the production of biologicals and the main problems and considerations in the scaling up of MC culture reactors. MC cell culture is the method of choice for producing useful products from ADCs, although cell propagators providing large, continuous-surface areas may have value in certain applications. Several kinds of MCs suitable for cultivation of animal and human cells are commercially available from a variety of sources.
Development of a scale to evaluate postoperative pain in dogs (1999)

Behavioral and physiologic measurements can be used reliably to evaluate degree of pain in dogs during the postoperative period and their response to analgesics.
Artificial Genetic Systems: Self‐Avoiding DNA in PCR and Multiplexed PCR (2010)

Discerning in their choice of partner: The DNA of a self-avoiding molecular-recognition system (SAMRS) binds to natural DNA but not to members of the same SAMRS. Multiplexed PCR with an SAMRS based on 2-aminopurine (A*), 2-thiothymine (T*), 2′-hypoxanthine (G*), and N4-ethylcytosine (C*; see examples) showed the benefits of such systems for clinical analysis, which requires many DNA molecules to interact with target DNA but not with each other. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A Gel Mobility Shift Assay for Probing the Effect of Drug–DNA Adducts on DNA-Binding Proteins (2003)

Despite the widespread use of chemotherapeutic drugs in the treatment of various malignancies, in many cases the mechanism of tumor cell kill remains unknown There is, however, much evidence that suggests that DNA is the major cellular target for many of the agents in current clmical use. A number of physicochemical techniques are available to probe the reversrble and nonreversible interactions of these drugs with DNA, and a wealth of information regarding the sequence specificity of these interactions has been documented using these procedures, as well as molecular-biology-based techniques such as DNA and RNA footprinting (,). These studies have also revealed that binding of these compounds to DNA can interfere with various aspects of DNA replrcation, transcription, and translation. Since these intricate processes involve regulatory proteins and cofactors, another approach to characterizing drug-DNA interactions is to ascertain the ability of DNA binding proteins to recognize then drug-modified DNA consensus sequences (, , , ). This approach is particularly relevant because such 5′untranslated regions are unwound when assembled on the nuclear matrix and thus accessrble to drugs during active gene transcription in cells (, , , ). The sequence selectivity of the drug will therefore determine which DNA-binding proteins are affected, thus leading to a broad predictive index of which genes are more likely to be affected, and perhaps, more importantly, being able to identify the critical stage of gene expression at which these agents may be most active.