gebhart/patrepeval huggingface dataset:
Preview Control for Vehicle Lateral Guidance in Highway Automation (1991)

Continuous deterministic preview control is applied to the vehicle lateral contol problem. It is shown that the preview control consists of a feedback term and two feedforward terms. If the preview control algorithm is applied on the FSLQ augmented system, the feedback term will be exactly the same as the FSLQ feedback control law. Therefore, the advantages of the FSLQ control law (robustness on measurement noises, including ride quality explicitly in the performance index, etc. see [1]) remain in the preview control law. Frequency-domain analysis and numerical simulation results are presented to show the improvements introduced by utilizing preview control in both the time domain and the frequency domain.
Improved Procedure for Direct Coupling of Carbohydrates to Proteins via Reductive Amination (2008)

Carbohydrate-protein conjugates are utilized extensively in basic research and as immunogens in a variety of bacterial vaccines and cancer vaccines. As a result, there have been significant efforts to develop simple and reliable methods for the construction of these conjugates. While direct coupling via reductive amination is an appealing approach, the reaction is typically very inefficient. In this paper, we report improved reaction conditions providing an approximately 500% increase in yield. In addition to optimizing a series of standard reaction parameters, we found that addition of 500 mM sodium sulfate improves the coupling efficiency. To illustrate the utility of these conditions, a series of high mannose BSA conjugates were produced and incorporated into a carbohydrate microarray. Ligand binding to ConA could be observed and apparent affinity constants ( K ds) measured using the array were in good agreement with values reported by surface plasmon resonance. The results show that the conditions are suitable for microgram-scale reactions, are compatible with complex carbohydrates, and produce biologically active conjugates.
Modeling Human Endometrial Decidualization from the Interaction between Proteome and Secretome (2010)

Proteomic and secretomic have been used as hypothesis-free approaches together with complex bioinformatics to model the human decidual interactome for the first time. We confirm previous knowledge, describe new molecules, and we have built up a model for human in vitro decidualization as invaluable tool for the diagnosis, therapy, and interpretation of biological phenomena.
Identification of cytokeratin 1 as a binding protein and presentation receptor for kininogens on endothelial cells (1998)

A kininogen binding protein(s), a putative receptor, was identified on endothelial cells. A 54-kDa protein was isolated by a biotin-high molecular mass kininogen (HK) affinity column that, on aminoterminal sequencing of tryptic digests, was identified as cytokeratin 1. Multiple antibodies directed to cytokeratin 1 reacted with a 54-kDa band on immunoblot of lysates of endothelial cells. On laser scanning confocal microscopy, cytokeratin 1 antigen was found on the surface of endothelial cells. Cytokeratin 1 antigen also was detected on endothelial cell membranes by flow cytometry. Moreover, an antipeptide antibody to a sequence unique to cytokeratin 1 also specifically bound to nonpermeabilized endothelial cells. Biotin-HK specifically bound to cytokeratin only in the presence of Zn2+, and cytokeratin blocked biotin-HK binding to endothelial cells. Further, HK and low molecular mass kininogen, but not factor XII, blocked biotin-HK binding to cytokeratin, and peptides of each cell binding region of HK on domains 3,4, and 5 blocked biotin-HK binding to cytokeratin. gC1qR and soluble urokinase-like plasminogen activator receptor also inhibited biotin-HK binding to cytokeratin. These investigations identify a new function for cytokeratin 1 as a kininogen binding protein. Cytokeratins, members of the family of intermediate filament proteins, may represent a new class of receptors.
The Effect of Intravesical Mitomycin C on Recurrence of Newly Diagnosed Superficial Bladder Cancer: A Further Report with 7 Years of Followup (1996)

Our analysis confirms the positive benefit of mitomycin C to decrease the number of subsequent recurrences and increase the recurrence-free interval.
Synthesis of new carbon‐11‐labeled 7‐aroyl‐aminoindoline‐1‐sulfonamides as potential PET agents for imaging of tubulin polymerization in cancers (2008)

Abstract The tubulin polymerization is an attractive target for anticancer therapy and in the development of cancer imaging agents for use in biomedical imaging technique positron emission tomography (PET). 7‐Aroyl‐aminoindoline‐1‐sulfonamides are a novel class of potent antitublin agents. Carbon‐11‐labeled 7‐aroyl‐aminoindoline‐1‐sulfonamides have been synthesized as new potential PET agents for imaging of tubulin polymerization in cancers. The target tracers were prepared by O ‐[ 11 C]methylation of their corresponding precursors using [ 11 C]CH 3 OTf and isolated by a simplified solid‐phase extraction purification procedure in 40–55% radiochemical yields based on [ 11 C]CO 2 and decay corrected to the end of bombardment (EOB), 15–20 min overall synthesis time from EOB, &gt;98% radiochemical purity, and 74–111 GBq/µmol specific activity at the end of synthesis. Copyright © 2008 John Wiley &amp; Sons, Ltd.
TES7, a monoclonal antibody targeting B7‐H3, potently inhibits Hs‐700T growth in vivo. (2008)

Human B7‐H3, a member of the B7 family of costimulator molecules, is a ∼110kDa type I membrane protein with 4 extracellular Ig like loops (IgV1‐IgC1‐IgV2‐IgC2), a short cytoplasmic tail, and a putative isoform with only 2 extracellular Ig like loops (IgV2‐IgC2). In this report, we present and characterize TES7, a monoclonal antibody specific to human B7‐H3. We map TES7 binding to the IgV1‐IgC1 portion of B7‐H3, and demonstrate TES7/B7‐H3 interaction to be density and receptor clustering sensitive. Immunohistochemical studies of TES7 show differential staining on normal versus cancerous human tissues (normal pancreas, lung, liver, kidney, and heart were negative, membrane staining observed on colon epithelia; positive staining on 4/4 lung cancer, 4/4 colon cancer, and 6/13 pancreatic cancer samples; 4/4 breast cancer and 3/3 prostate cancers samples were positive). Using TES7 in vivo, we demonstrate growth inhibition of subcutaneously implanted Hs‐700T cells. The data presented are the first demonstration of disease‐associated reorganization of B7‐H3 surface expression, and presents TES7 as a novel tool for the study of B7‐H3 biology and as a potential cancer therapeutic.
Epilepsy and sodium channel blockers (2002)

Epilepsy is one of the most frequent neurological diseases and although most patients nowadays respond well to anti-epileptic drugs (AED), 30 - 40% of them still present seizures despite treatment with 2 or more AED. This illustrates the need for discovery and testing of new molecules designed for specific brain targets. Several voltage-gated Na+ channel gene mutations were shown to be associated with genetic and hereditary epilepsy. Thus, while it is noteworthy that some currently available AED act through Na+ channels, the identified mutations in Na+ channel genes strongly support the development of new Na+ channel blockers used as AED. This review focuses on the pathophysiology of epilepsy and particularly on insight gained from the identification of mutations in idiopathic epilepsy (IE). All of the IE mutations identified concern genes coding for ion channels, suggesting a possible role of these integral membrane proteins in epileptogenesis. The recent identification of mutations in genes encoding the α1, α2 and β1 subunits of the voltage-gated Na+ channel (SCN1A, SCN2A, SCN1B) and their association with febrile seizures (FS) further illustrates the contribution of these channels in epilepsy. Modes of action of AED supposed to act through the voltage-gated Na+ channels are examined in an attempt to propose alternative routes to discover new active compounds.
ADAMs family members as amyloid precursor protein α‐secretases (2003)

In the non-amyloidogenic pathway, the Alzheimer's amyloid precursor protein (APP) is cleaved within the amyloid-beta domain by alpha-secretase precluding deposition of intact amyloid-beta peptide. The large ectodomain released from the cell surface by the action of alpha-secretase has several neuroprotective properties. Studies with protease inhibitors have shown that alpha-secretase is a zinc metalloproteinase, and several members of the adamalysin family of proteins, tumour necrosis factor-alpha convertase (TACE, ADAM17), ADAM10, and ADAM9, all fulfil some of the criteria required of alpha-secretase. We review the evidence for each of these ADAMs acting as the alpha-secretase. What seems to be emerging from numerous studies, including those with mice in which each of the ADAMs has been knocked out, is that there is a team of zinc metalloproteinases able to cleave APP at the alpha-secretase site. We also discuss how upregulation of alpha-secretase activity by muscarinic agonists, cholesterol-lowering drugs, steroid hormones, non-steroidal anti-inflammatory drugs, and metal ions may explain some of the therapeutic actions of these agents in Alzheimer's disease.
Photothermal multispectral image cytometry for quantitative histology of nanoparticles and micrometastasis in intact, stained and selectively burned tissues (2010)

There is a rapidly growing interest in the advanced analysis of histological data and the development of appropriate detection technologies in particular for mapping of nanoparticle distributions in tissue in nanomedicine applications. We evaluated photothermal (PT) scanning cytometry for color-coded imaging, spectral identification, and quantitative detection of individual nanoparticles and abnormal cells in histological samples with and without staining. Using this tool, individual carbon nanotubes, gold nanorods, and melanoma cells with intrinsic melanin markers were identified in unstained (e.g. sentinel lymph nodes) and conventionally-stained tissues. In addition, we introduced a spectral burning technique for histology through selective laser bleaching areas with nondesired absorption background and nanobubble-based PT signal amplification. The obtained data demonstrated the promise of PT cytometry in the analysis of low-absorption samples and mapping of various individual nanoparticles' distribution that would be impossible with existing assays. Comparison of PT cytometry and photoacoustic (PA) cytometry previously developed by us, revealed that these methods supplement each other with a sensitivity advantage (up to 10-fold) of contactless PT technique in assessment of thin (≤100 μm) histological samples, while PA imaging provides characterization of thicker samples which, however, requires an acoustic contact with transducers. A potential of high-speed integrated PT-PA cytometry for express histology and immunohistochemistry of both intact and stained heterogeneous tissues with high sensitivity at the zepromolar concentration level is further highlighted.
Dynamic Spring Mediated Cranioplasty in an Experimental Model With Resorbable Foot Plates (2007)

Craniofacial surgery continues to be progressive in its approach to maximize function and aesthetic appearance while minimizing risks and complications. Dynamic springs are one way to minimize invasiveness while achieving favorable results. The purpose of this study was to show the safety and efficacy of dynamic springs with resorbable foot plates for treatment of metopic suture abnormalities in a swine model. The study population consisted of twelve 20 kg Chester swine. The swine were divided into two treatment groups: four in the sham surgery group and eight in the stainless steel spring group. Postoperative analysis consisted of evaluation of the skull growth over time and integrity of the foot plates and underlying dura. The swine, killed at 8 weeks, were examined for spring location in the foot plates, ease of removal of the spring, and postmortem histologic analysis of the bone growth. No morbidity or mortality occurred in the immediate perioperative period secondary to the surgery. Postmortem histologic analysis revealed no infections or complications related to the surgery. Statistical analysis using a mixed linear model with an unstructured variance-covariance matrix was fit. In conclusion, this study confirms the efficacy and safety of the spring-mediated cranioplasty at the metopic suture with use of resorbable foot plates in a swine model.
An activation-collision mechanism for cholesterol transfer between membranes. (1988)

We report the results of experiments which show that cholesterol transfer between membranes cannot proceed by aqueous diffusion, as widely held, but must involve a more complex mechanism. (a) The rate of transfer of [3H]cholesterol from red blood cells was found to vary inversely with the size of the acceptor particle (ghosts, vesicles of ghosts, liposomes, and plasma lipoproteins). (b) The transfer of [3H]cholesterol from red blood cells to ghosts was accelerated by the presence of plasma, even though the plasma competed with the ghosts as an acceptor. (c) The rate of transfer of [3H]cholesterol from red blood cells to ghosts decreased to zero with increasing dilution but was not simply second-order. (d) The cholesterol in retinal rod disc membranes is not at equilibrium with plasma lipoproteins in that disc cholesterol increased when the homogenates were incubated in vitro with plasma. (e) The kinetics of cholesterol transfer cannot be limited by unstirred layer effects since the transfer of lysolecithin in the same system was faster than that of cholesterol by 3 orders of magnitude. The simplest model compatible with all the data suggests a two-step pathway involving a first-order followed by a second-order process. The first step could be a unimolecular activation event, perhaps the movement of the sterol in the donor particle to a more exposed (hydrated) position. In the second step, the activated sterol would be transferred during transient collisions between donor and acceptor particles. When collision is not rate-limiting, the overall process would appear to be simply first-order, hence kinetically indistinguishable from the aqueous diffusion mechanism. The activation-collision model thus not only rationalizes our data but is also consistent with the simpler kinetics previously reported for the transfer of both membrane phospholipids and sterols.
L-DNAs as potenital antimessenger oligonucleotides: a reassessment (1993)

Unnatural L-2'-deoxyribonucleosides L-T, L-dC, L-dA and L-dG were prepared from L-arabinose and assembled, by solution or solid phase synthesis, to give L-oligonucleotides (L-DNAs), which contain all four natural bases. The affinity of these modified oligomers for complementary D-ribo- and D-deoxyribo-oligomers was studied with NMR, UV and CD spectroscopies and mobility shift assay on native PAGE. All experimental results indicate that L-DNAs do not, in general, recognize single-stranded, natural DNA and RNA. Hence, contrary to previous suggestions, it is not possible to envisage their use as wide scope antimessenger agents in the selective control of gene expression.
Cellular Responses to Viral Infection in Humans: Lessons from Epstein-Barr Virus (2007)

Epstein-Barr virus (EBV) provides a useful model to study cellular immunity to a genetically stable, persistent human virus. Different sets of proteins expressed during EBV's lytic and cell transforming infections induce qualitatively different cellular immune responses. The factors governing immunodominance hierarchies and the biological effectiveness of these different responses are now being revealed. Analysis of infectious mononucleosis (IM), a clinical syndrome that can arise during primary EBV infection, has allowed the evolution of the responses to be tracked over time, giving an understanding of the immune response kinetics and of those determinants affecting selection into memory. Furthermore, following IM, expression of the receptor for the homeostatic cytokine IL-15 on NK and T cells is lost within these individuals. This experiment of nature provides a system to advance understanding of immunological homeostasis in humans, illustrating how data obtained from the study of EBV have wider significance to the immunological community.
Actomyosin contractility controls cell surface area of oligodendrocytes (2009)

In summary, our results establish a novel connection between endocytosis, cell surface extension and actomyosin contractility. These findings open up new possibilities of how to promote the morphological differentiation of oligodendrocytes in a non-permissive growth environment. See related minireview by Bauer and ffrench-Constant: http://www.jbiol.com/content/8/8/78.
A Non-AUG-Defined Alternative Open Reading Frame of the Intestinal Carboxyl Esterase mRNA Generates an Epitope Recognized by Renal Cell Carcinoma-Reactive Tumor-Infiltrating Lymphocytes In Situ (1999)

A number of Ags recognized by tumor-reactive T cells have been characterized, including nonmutated gene products and a variety of epitopes shown to arise from either mutated or alternatively processed transcripts. Here, we report that the screening of a cDNA library with an HLA-B7-restricted renal cell carcinoma-reactive T cell clone derived from tumor-infiltrating lymphocytes (TILs) that were clonally amplified in vivo (as assessed by TCRBV complementarity determining region-3 length distribution analysis) resulted in the isolation of a nonamer encoded by an alternative open reading frame (ORF) (a +1 frameshift) of the intestinal carboxyl esterase gene. This peptide binds HLA-B*0702-presenting molecules as assessed in an immunofluorescence-based peptide binding assay using transfected T2 cells. Constitutive expression of this alternative ORF protein was observed in all transformed HLA-B7+ renal cell lines that were recognized in cytotoxicity assays by the TILs. The intestinal carboxyl esterase gene is transcribed in renal cell carcinoma tumors as well as in normal liver, intestinal, or renal tissues. Mutation of the natural ATG translation initiation site did not alter recognition, indicating that frameshifting (i.e., slippage of the ribosome forward) and recoding are not involved. In addition, a point mutation of the three AUG codons that may be used as alternative translation initiation sites in the +1 ORF did not abolish recognition, whereas mutation of an upstream ACG codon did, indicating that the latter codon initiates the translation of the alternative ORF. These results further extend the types of Ags that can be recognized by tumor-reactive TILs in situ (i.e., leading to clonal T cell expansion).
Liposome-encapsulated superparamagnetic iron oxide particles as markers in an MRI-guided search for tumor-specific drug carriers. (1997)

Three different types of liposomes containing superparamagnetic iron oxide particles (SPIOs) as the contrast agent were tested for intratumoral enrichment by magnetic resonance imaging (MRI). The liposome-encapsulated SPIOs were investigated in comparison with AMI-227, dextran-coated SPIOs in two different dosages using the CC531 adenocarcinoma in the liver of WAG/RIJ rats as a model. Reduction of the relative signal intensity (SI) in the tumor in T2-weighted MR images was assumed as a measure of the liposome enrichment in the tumor or adjacent tissue. The samples were tested at dosages with isomolar iron content and at dosages producing the same MR relaxivity R2. For reverse phase evaporation vesicles and small unilamellar vesicles behavior differed remarkably according to the applied dosage. A steady, strong reduction in SI, starting immediately after injection and extending up to 48 h, was observed for small unilamellar vesicles sterically stabilized with polyethylene glycol.
Glass transition temperature of dried lens tissue pretreated with trehalose, maltose, or cyclic tetrasaccharide (2014)

The glass transition temperature was measured for the first time in the dried lens tissues as an example of a whole biological tissue and might provide a basis for tissue preservation in the dried condition.
Herpes Simplex Virus Type 1 Immediate-Early Protein ICP27 Is Required for Efficient Incorporation of ICP0 and ICP4 into Virions (2007)

Early in infection, herpes simplex virus type 1 (HSV-1) immediate-early (IE) proteins ICP0 and ICP4 localize to the nucleus, where they stimulate viral transcription. Later in infection, ICP0 and to a lesser extent ICP4 accumulate in the cytoplasm, but their biological role there is unknown. Previously, it was shown that the cytoplasmic localization of ICP0/4 requires the multifunctional IE protein ICP27, which is itself an activator of viral gene expression. Here, we identify a viral ICP27 mutant, d3-4, which is unable to efficiently localize ICP0 and ICP4 to the cytoplasm but which otherwise resembles wild-type HSV-1 in its growth and viral gene expression phenotypes. These results genetically separate the function of ICP27 that affects ICP0/4 localization from its other functions, which affect viral growth and gene expression. As both ICP0 and ICP4 are known to be minor virion components, we used d3-4 to test the hypothesis that the cytoplasmic localization of these proteins is required for their incorporation into viral particles. Consistent with this conjecture, d3-4 virions were found to lack ICP0 in their tegument and to have greatly reduced levels of ICP4. Thus, the cytoplasmic localization of ICP0 and ICP4 appears to be a prerequisite for the assembly of these important transcriptional regulatory proteins into viral particles. Furthermore, our results show that ICP27 plays a previously unrecognized role in determining the composition of HSV-1 virions.
An advanced read/write channel for magnetic disk storage (2003)

An advanced read channel for magnetic disk recording is proposed. The channel incorporates a (1,7) run-length limited code with partial response equalization and Viterbi detection. The (1,7) code reduces the severe nonlinear effects that plague thin film disk recording at high densities. It is shown through analysis and simulation that the proposed read channel is suitable for user densities of 1.5 to 2.0 and higher, for reasonable SNR and error rates.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
N-Heterocyclic Carbene-Catalyzed Mukaiyama Aldol Reactions (2007)

N-Heterocyclic carbenes were shown to be highly effective catalysts to promote Mukaiyama aldol reactions. In the presence of only 0.5 mol % of N-heterocyclic carbene (5), various aldehydes and 2,2,2-trifluoroacetophenone underwent Mukaiyama aldol reactions in THF with trimethylsilyl ketene acetal (2) at 23 degrees C as well as with trimethylsilyl enol ether (7) at 0 degrees C to afford aldol adducts in good yields. These conditions are extremely mild and operationally simple and tolerate various functional groups. [reaction: see text]
Response to thalidomide in chemotherapy‐resistant mantle cell lymphoma: a case report (2002)

Mantle cell lymphoma is an aggressive B-cell lymphoma with a poor median survival despite conventional therapy. Here, we present the case of a patient with multiply relapsed mantle cell lymphoma, having failed treatment with chemotherapy, steroids and rituximab. He was treated with single-agent thalidomide at a dose of 800 mg daily and entered a good partial remission which was maintained for the next 6 months. There is clearly a need for further studies of thalidomide in mantle cell lymphoma to confirm this promising initial result.