gebhart/patrepeval huggingface dataset:
117 IS AKAP-4 A NOVEL CANCER TESTIS ANTIGEN FOR MULTIPLE MYELOMA? (2007)

Purpose Immunotherapy promises to be a more gentle and successful cancer treatment when compared with current standard treatments. Multiple myeloma (MM) is still a fatal hematologic malignancy that represents approximately 1% of all cancers and 2% of all cancer deaths. Approximately 50,000 Americans currently have MM. The research to discover new suitable cancer targets is needed to improve the effects of immunotherapy. The AKAP family9s protein provides an organizing center about which various protein kinases and phosphatases can be assembled to create solid-state signaling devices that can signal, be modulated, and be trafficked within the cell. A member of this family, AKAP-4, is the focus of our study. Human AKAP-4 is a structural protein of the sperm fibrous sheath that also functions to anchor protein kinase A to this structure via the regulatory subunit of the kinase, and seems to be involved in sperm motility. Our aim was to investigate the presence of AKAP-4 as a novel cancer testis antigen target in MM patients. Methods We evaluated the expression of AKAP-4 mRNA in a normal panel of tissues and in 15 MM patients either by PCR and immunocytochemistry. The normal control investigated tissues were kidney, ovary, skeletal muscle, mammary, brain, heart, colon, stomach, liver, lung, pancreas, spleen, trachea, and bone marrow. Summary The analysis of the mRNA expression of AKAP-4 showed that none of the normal tissues produced any positive band signals, whereas 6 of the 15 investigated patients (40%) showed a positive band signal. The immunohistochemical approach to the normal tissue panel showed no staining in any of the evaluated organs, except for the control, the testis. Five of the 15 MM investigated cases (33.3%) showed positive cytoplasmic staining. Conclusion To our knowledge, we established for the first time that AKAP-4 is expressed at the transcriptional level in MM cases, with a rate of 40%, whereas it is not expressed in normal tissues. Immunocytochemical data confirmed the PCR observations even if with a slightly lower percentage rate (33.3%). Since AKAP-4 has yet not been studied in MM, this is the first study that gives evidence of its aberrant expression in MM and suggests its use as possible novel cancer testis antigen target in MM.
X-linked Angelman-like syndrome caused by Slc9a6 knockout in mice exhibits evidence of endosomal–lysosomal dysfunction (2011)

Mutations in solute carrier family 9 isoform 6 on chromosome Xq26.3 encoding sodium-hydrogen exchanger 6, a protein mainly expressed in early and recycling endosomes are known to cause a complex and slowly progressive degenerative human neurological disease. Three resulting phenotypes have so far been reported: an X-linked Angelman syndrome-like condition, Christianson syndrome and corticobasal degeneration with tau deposition, with each characterized by severe intellectual disability, epilepsy, autistic behaviour and ataxia. Hypothesizing that a sodium-hydrogen exchanger 6 deficiency would most likely disrupt the endosomal-lysosomal system of neurons, we examined Slc9a6 knockout mice with tissue staining and related techniques commonly used to study lysosomal storage disorders. As a result, we found that sodium-hydrogen exchanger 6 depletion leads to abnormal accumulation of GM2 ganglioside and unesterified cholesterol within late endosomes and lysosomes of neurons in selective brain regions, most notably the basolateral nuclei of the amygdala, the CA3 and CA4 regions and dentate gyrus of the hippocampus and some areas of cerebral cortex. In these select neuronal populations, histochemical staining for β-hexosaminidase activity, a lysosomal enzyme involved in the degradation of GM2 ganglioside, was undetectable. Neuroaxonal dystrophy similar to that observed in lysosomal disease was observed in the cerebellum and was accompanied by a marked and progressive loss of Purkinje cells, particularly in those lacking the expression of Zebrin II. On behavioural testing, Slc9a6 knockout mice displayed a discrete clinical phenotype attributable to motor hyperactivity and cerebellar dysfunction. Importantly, these findings show that sodium-hydrogen exchanger 6 loss of function in the Slc9a6-targeted mouse model leads to compromise of endosomal-lysosomal function similar to lysosomal disease and to conspicuous neuronal abnormalities in specific brain regions, which in concert could provide a unified explanation for the cellular and clinical phenotypes in humans with SLC9A6 mutations.
Lipid-free apolipoproteins A-I and A-II promote remodeling of reconstituted high density lipoproteins and alter their reactivity with lecithin:cholesterol acyltransferase (1999)

We examined the effect of lipid-free apolipoprotein A-I (apoA-I) and apoA-II on the structure of reconstituted high density lipoproteins (rHDL) and on their reactivity as substrates for lecithin:cholesterol acyltransferase (LCAT). First, homogeneous rHDL were prepared with either apoA-I or apoA-II using palmitoyloleoylphosphatidylcholine (POPC) and cholesterol. Lipid-free apoA-I and apoA-II were labeled with the fluorescent probe dansyl chloride (DNS). The binding kinetics of apoA-I-DNS to A-II-POPCrHDL and of apoA-II-DNS to A-I-POPCrHDL were monitored by fluorescence polarization, adding the lipid-free apolipoproteins to the rHDL particles in a 1:1 molar ratio. For both apolipoproteins, the binding to rHDL was rapid, occurring within 5 min. Next, the effect on rHDL structure and particle size was determined after incubations of lipid-free apolipoproteins with homogeneous rHDL at 37 degrees C from 0.5 to 24 h. The products were analyzed by non-denaturing gradient gel electrophoresis followed by Western blotting. The effect of apoA-I or apoA-II on 103 A A-II-POPCrHDL was a rearrangement into 78 A particles containing apoA-I and/or apoA-II, and 90 A particles containing only apoA-II. The effect of apoA-I or apoA-II on 98 A A-I-POPCrHDL was a rearrangement into complexes ranging in size from 78 A to 105 A containing apoA-I and/or apoA-II, with main particles of 78 A, 88 A, and 98 A. Finally, the effect of lipid-free apoA-I and apoA-II on rHDL as substrates for LCAT was determined. The addition of apoA-I to A-II-POPCrHDL increased its reactivity with LCAT 24-fold, reflected by a 4-fold increase in apparent V(m)ax and a 6-fold decrease in apparent K(m), while the addition of apoA-II to A-II-POPCrHDL had no effect on its minimal reactivity with LCAT. In contrast, the addition of apoA-II to A-I-POPCrHDL decreased the reaction with LCAT by about one-half. The inhibition was due to a 2-fold increase in apparent K(m); there was no significant change in apparent V(m)ax. Likewise, the addition of apoA-I to A-I-POPCrHDL inhibited the reaction with LCAT to about two-thirds that of A-I-POPCrHDL without added apoA-I. In summary, both lipid-free apoA-I and apoA-II can promote the remodeling of rHDL into hybrid particles of primarily smaller size. Both apoA-I and apoA-II affect the reactivity of rHDL with LCAT, when added to the reaction in lipid-free form. These results have important implications for the roles of lipid-free apoA-I and apoA-II in HDL maturation and metabolism.
<title>Classical and neural methods of image sequence interpolation</title> (2001)

An image interpolation problem is often encountered in many areas. Some examples are interpolation for coding/decoding process for transmission purposes, reconstruction a full frame from two interlaced sub-frames in normal TV or HDTV, or reconstruction of missing frames in old destroyed cinematic sequences. In this paper an overview of interframe interpolation methods is presented. Both direct as well as motion compensated interpolation techniques are given by examples. The used methodology can also be either classical or based on neural networks depending on demand of a specific interpolation problem solving person.
Effect of omeprazole on serum gastrin levels: influence of age and sex. (1990)

Serum gastrin levels were determined in 120 consecutive patients (43 females, 77 males) with peptic disease 24 h post dose after 4 weeks continuous omeprazole (40 mg daily) treatment. Serum gastrin levels were elevated in 33 (28%) but exceeded the twice normal range in only 6 patients (5%). Age and sex did not influence the magnitude of gastrin levels. Gastrin increments induced by omeprazole compared to pretreatment with H2-blockers in 60 cases were similar in both males (42 +/- 10 pg/ml) and females (44 +/- 9 pg/ml). It is concluded that the magnitude of gastrin increases observed during omeprazole therapy are small and independent of age and sex.
Effect of Age and Cytoskeletal Elements on the Indentation-Dependent Mechanical Properties of Chondrocytes (2013)

Articular cartilage chondrocytes are responsible for the synthesis, maintenance, and turnover of the extracellular matrix, metabolic processes that contribute to the mechanical properties of these cells. Here, we systematically evaluated the effect of age and cytoskeletal disruptors on the mechanical properties of chondrocytes as a function of deformation. We quantified the indentation-dependent mechanical properties of chondrocytes isolated from neonatal (1-day), adult (5-year) and geriatric (12-year) bovine knees using atomic force microscopy (AFM). We also measured the contribution of the actin and intermediate filaments to the indentation-dependent mechanical properties of chondrocytes. By integrating AFM with confocal fluorescent microscopy, we monitored cytoskeletal and biomechanical deformation in transgenic cells (GFP-vimentin and mCherry-actin) under compression. We found that the elastic modulus of chondrocytes in all age groups decreased with increased indentation (15-2000 nm). The elastic modulus of adult chondrocytes was significantly greater than neonatal cells at indentations greater than 500 nm. Viscoelastic moduli (instantaneous and equilibrium) were comparable in all age groups examined; however, the intrinsic viscosity was lower in geriatric chondrocytes than neonatal. Disrupting the actin or the intermediate filament structures altered the mechanical properties of chondrocytes by decreasing the elastic modulus and viscoelastic properties, resulting in a dramatic loss of indentation-dependent response with treatment. Actin and vimentin cytoskeletal structures were monitored using confocal fluorescent microscopy in transgenic cells treated with disruptors, and both treatments had a profound disruptive effect on the actin filaments. Here we show that disrupting the structure of intermediate filaments indirectly altered the configuration of the actin cytoskeleton. These findings underscore the importance of the cytoskeletal elements in the overall mechanical response of chondrocytes, indicating that intermediate filament integrity is key to the non-linear elastic properties of chondrocytes. This study improves our understanding of the mechanical properties of articular cartilage at the single cell level.
Type 1 protein secretion in bacteria, the ABC-transporter dependent pathway (Review) (2005)

The relatively simple type 1 secretion system in gram-negative bacteria is nevertheless capable of transporting polypeptides of up to 800 kDa across the cell envelope in a few seconds. The translocator is composed of an ABC-transporter, providing energy through ATP hydrolysis (and perhaps the initial channel across the inner membrane), linked to a multimeric Membrane Fusion Protein (MFP) spanning the initial part of the periplasm and forming a continuous channel to the surface with an outer membrane trimeric protein. Proteins targeted to the translocator carry an (uncleaved), poorly conserved secretion signal of approximately 50 residues. In E. coli the HlyA toxin interacts with both the MFP (HlyD) and the ABC protein HlyB, (a half transporter) triggering, via a conformational change in HlyD, recruitment of the third component, TolC, into the transenvelope complex. In vitro, HlyA, through its secretion signal, binds to the nucleotide binding domain (NBD or ABC-ATPase) of HlyB in a reaction reversible by ATP that may mimic initial movement of HlyA into the translocation channel. HlyA is then transported rapidly, apparently in an unfolded form, to the cell surface, where folding and release takes place. Whilst recent structural studies of TolC and MFP-like proteins are providing atomic detail of much of the transport path, structural analysis of the HlyB NBD and other ABC ATPases, have revealed details of the catalytic cycle within an NBD dimer and a glimpse of how the action of HlyB is coupled to the translocation of HlyA.
Electrochemically Directed Self-Assembly on Gold (2000)

Selectively, and in less than a minute, self-assembled monolayers (SAMs) form by oxidizing alkyl thiosulfates and trapping the resulting intermediate or product on gold electrodes. This approach allows SAMs to be formed on specific electrodes held at a sufficiently high potential to oxidize the precursor. The picture shows, using fluorescence microscopy, a selectively modified electrode (B) and an unmodified electrode (A) on an alumina substrate. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2000/z14044_s.pdf or from the author. 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.
In silico investigation of ADAM12 effect on TGF-β receptors trafficking (2009)

In this work, confronting differential models with qualitative biological observations, we obtained predictions giving new insights into the role of ADAM12 in TGF-beta signaling and hepatic fibrosis process.
Stem Cell Research in Stroke (2011)

Stem cell-based approaches hold much promise as potential novel treatments to restore function after stroke. Studies in animal models have shown that stem cell transplantation can improve function by replacing neurons or by trophic actions, modulation of inflammation, promotion of angiogenesis, remyelination and axonal plasticity, and neuroprotection. Endogenous neural stem cells are also potential therapeutic targets because they produce new neurons after stroke. Clinical trials are ongoing but there is currently no proven stem cell-based therapy for stroke. Preclinical studies and clinical research will be needed to optimize the therapeutic benefit and minimize the risks of stem cells in stroke.
Combined In vivo Effect of A12, a Type 1 Insulin-Like Growth Factor Receptor Antibody, and Docetaxel against Prostate Cancer Tumors (2006)

Our findings suggest that targeting type 1 insulin-like growth factor receptor can enhance the therapeutic effect of docetaxel on advanced prostate cancer. Our findings also suggest a potential mechanism to improve the treatment efficacy of docetaxel in prostate cancer.
Über einige Derivate des 2‐Aminothiazols (1949)

Abstract 2‐Amino‐5‐n‐propylthiazol und 2‐Amino‐4‐n‐butylthiazol wurden synthetisiert und auf ihre biologische Wirkung untersucht.
Nanowires as building blocks for nanoelectronics and nanophotonics (2004)

First, a general framework for the growth of single crystal nanowire building blocks is reviewed, with an emphasis on illustrating the level of control possible in defining composition, diameter, and electronic properties. Second, investigations of electrical transport properties of individual nanowires and nanowire heterostructures are discussed. Third, and as an example of a nanotechnology enabled application, we describe the use of nanowire field-effect devices as ultra-sensitive chemical and biological sensors. Finally, we describe studies of the fundamental optical and opto-electronic properties of compound semiconductor nanowires and nanowire heterostructures. In summary, challenges and goals for realizing nanotechnologies in the future are discussed, including schemes and progress towards highly integrated electronic and photonic systems.
Femtosecond transillumination optical coherence tomography (1993)

We describe a new technique, femtosecond transillumination optical coherence tomography, for time-gated imaging of objects embedded in scattering media. Time gating is performed with a fiber-optic interferometer with femtosecond pulses and coherent heterodyne detection to achieve a 130-dB dynamic range. A confocal imaging arrangement provides additional spatial discrimination against multiply scattered light. By time gating ballistic photons, we achieve 125-microm-resolution images of absorbing objects in media 27 scattering mean free paths thick. We derive a fundamental limit on ballistic imaging thickness based on quantum noise considerations.
Ability of myeloma cells to secrete macrophage inflammatory protein (MIP)‐1α and MIP‐1β correlates with lytic bone lesions in patients with multiple myeloma (2004)

Macrophage inflammatory protein (MIP)-1alpha and MIP-1beta have been identified as candidates for multiple myeloma (MM)-derived bone-resorbing factors. To validate the clinical relevance of these observations, we investigated correlations between the ability of MM cells to secrete these chemokines and the extent of MM bone lesions as well as levels of biochemical bone markers in patients with MM. Patients with multiple bone lesions exhibited higher MIP-1alpha and MIP-1beta secretion from MM cells along with elevated urinary deoxypyridinoline (Dpd), without significant elevation of serum bone-specific alkaline phosphatase (BALP) or osteocalcin compared with those with minimal bone lesions. MIP-1alpha and MIP-1beta levels correlated positively with urinary Dpd and serum BALP but not with serum osteocalcin. These results provide further evidence for a causal role of MIP-1alpha and MIP-1beta in the development of lytic bone lesions, and suggest that MM cells suppress osteoblastic bone formation to cause an imbalance of bone turnover and development of destructive bone lesions.
SUDS: Primitive Mechanisms for Memory Dependence Speculation (1999)

As VLSI chip sizes and densities increase, it becomes possible to put many processing elements on a single chip and connect them together with a low latency communication network. In this paper we propose a software system, SUDS (Software Un-Do System), that leverages these resources using speculation to exploit parallelism in integer programs with many data dependences. We demonstrate that in order to achieve parallel speedups a speculation system must deliver memory request latencies lower than about 30 cycles. We give a cost breakdown for our current working implementation of SUDS that has a memory request latency that is nearly able to meet this goal. In addition, we identify the three primitive runtime operations that are necessary to efficiently parallelize these programs. The subsystems include (1) a fast communication path for true dependences within the program, (2) a method for renaming variables that have anti and output dependences and (3) a memory dependence speculation me...
First cysteine-rich repeat in ligand-binding domain of low density lipoprotein receptor binds Ca2+ and monoclonal antibodies, but not lipoproteins. (1987)

The ligand binding domain of the low density lipoprotein receptor consists of seven cysteine-rich repeats of approximately 40 amino acids each. These repeats, which are located at the NH2 terminus of the protein, are homologous to sequences in complement components C8 and C9. To determine the role of the first repeat (amino acids 2-42), we prepared two plasmids containing expressible low density lipoprotein receptor cDNAs. The first plasmid, p delta R1, lacks only the nucleotides encoding the first repeat. It produced a receptor that bound and internalized lipoproteins and recycled to the cell surface with the same efficiency as the normal receptor. This deleted receptor failed to bind two monoclonal antibodies, IgG-C7 and IgG-15C8, which were shown previously to react with the ligand-binding domain. The second plasmid, pR1, encodes a markedly truncated protein whose extracellular domain consists of the first repeat joined to the transmembrane and cytoplasmic domains. This protein bound the two monoclonal antibodies with the same affinity as the normal receptor, but failed to bind lipoproteins. Binding of IgG-15C8 to the normal receptor and the pR1-encoded protein was Ca2+-dependent, indicating that the first repeat binds Ca2+. We conclude that repeats 2-6 in the ligand-binding domain are sufficient for binding lipoproteins and that the first repeat is highly immunogenic, but is not required for lipoprotein binding.
One‐pot synthesis of hyperbranched glycopolymers by RAFT polymerization (2012)

Abstract Soluble hyperbranched glycopolymers were prepared by copolymerization of glycan monomers with reversible addition‐fragmentation chain transfer polymerization (RAFT) inimers in a simple one‐pot reaction. Two novel RAFT inimers, 2‐(methacryloyloxy)ethyl 4‐cyano‐4‐(phenylcarbonothioylthio)pentanoate (MAE‐CPP) and 2‐(3‐(benzylthiocarbonothioylthio)propanoyloxy)ethyl acrylate (BCP‐EA) were synthesized and used to prepare hyperbranched glycopolymers. Two types of galactose‐based saccharide monomers, 6‐ O ‐methacryloyl‐1,2:3,4‐di‐ O ‐isopropylidene‐ D ‐galactopyranose (proGal‐M) and 6‐ O ‐(2′‐acrylamido‐2′‐methylpropanoate)‐1,2:3,4‐di‐ O ‐isopropylidene‐ D ‐galactopyranose (proGal‐A), containing a methacrylate and an acrylamide group, respectively, were also synthesized and polymerized under the mediation of the MAE‐CPP and BCP‐EA inimers, respectively. In addition, hyperbranched poly(proGal‐M), linear poly(proGal‐A), and hyperbranched poly(proGal‐A) were generated and their polymerization kinetics were studied and compared. An unexpected difference was observed in the kinetics between the two monomers during polymerization: the relationship between polymerization rate and concentration of inimer was totally opposite in the two monomer–inimer systems. Branching analysis was conducted by using degree of branching (DB) as the measurement parameter. As expected, a higher DB occurred with increased inimer content. Furthermore, these polymers were readily deprotected by hydrolysis in trifluoroacetic acid solution resulting in water‐soluble polymers. The resulting branched glycopolymers have potential as biomimetics of polysaccharides. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Yersinia pestis caf1Variants and the Limits of Plague Vaccine Protection (2008)

Yersinia pestis, the highly virulent agent of plague, is a biological weapon. Strategies that prevent plague have been sought for centuries, and immunization with live, attenuated (nonpigmented) strains or subunit vaccines with F1 (Caf1) antigen is considered effective. We show here that immunization with live, attenuated strains generates plague-protective immunity and humoral immune responses against F1 pilus antigen and LcrV. Y. pestis variants lacking caf1 (F1 pili) are not only fully virulent in animal models of bubonic and pneumonic plague but also break through immune responses generated with live, attenuated strains or F1 subunit vaccines. In contrast, immunization with purified LcrV, a protein at the tip of type III needles, generates protective immunity against the wild-type and the fully virulent caf1 mutant strain, in agreement with the notion that LcrV can elicit vaccine protection against both types of virulent plague strains.