gebhart/patrepeval huggingface dataset:
Association of human lambda light chain V/J/C segments: serologic analysis and primary structure of the lambda VI Bence Jones protein THO. (1986)

The complete amino acid sequence of the human monoclonal lambda VI light chain Bence Jones protein THO was determined. We have found it to have remarkable similarities to the previously sequenced lambda VI Bence Jones protein SUT. Immunochemical analyses demonstrated that both lambda VI chains belong to a V lambda VI sub-subgroup. The 98-residue V gene-encoded segments of proteins THO and SUT are closely homologous and are distinguished from other lambda VI chains by a one-residue deletion at the V-J recombination site. Proteins THO and SUT have identical 13-residue J segments and therefore are encoded by the same J lambda gene. Further, both proteins have identical 105-residue C regions that by sequence represent products of the C lambda 3 (Kern-, Oz+) gene. The primary structure and serologic properties of proteins THO and SUT imply at the protein level of association between certain types of V lambda, J lambda, and C lambda segments.
A Protein Interaction Framework for Human mRNA Degradation (2004)

The degradation of mRNA is an important regulatory step in the control of gene expression. However, mammalian RNA decay pathways remain poorly characterized. To provide a framework for studying mammalian RNA decay, a two-hybrid protein interaction map was generated using 54 constructs from 38 human proteins predicted to function in mRNA decay. The results provide evidence for interactions between many different proteins required for mRNA decay. Of particular interest are interactions between the poly(A) ribonuclease and the exosome and between the Lsm complex, decapping factors, and 5'-->3' exonucleases. Moreover, multiple interactions connect 5'-->3' and 3'-->5' decay proteins to each other and to nonsense-mediated decay factors, providing the opportunity for coordination between decay pathways. The interaction network also predicts the internal organization of the exosome and Lsm complexes. Additional interactions connect mRNA decay factors to many novel proteins and to proteins required for other steps in gene expression. These results provide an experimental insight into the organization of proteins required for mRNA decay and their coupling to other cellular processes, and the physiological relevance of many of these interactions are supported by their evolutionary conservation. The interactions also provide a wealth of hypotheses to guide future research on mRNA degradation and demonstrate the power of exhaustive protein interaction mapping in aiding understanding of uncharacterized protein complexes and pathways.
Selective transmission through very deep zero-order metallic gratings at microwave frequencies (2000)

Zero-order metal grating structures are found to give extraordinary selective transmission at microwave frequencies through the resonant excitation of coupled surface waves. The metal slat structures with dielectric spacings as small as 250 μm strongly transmit wavelengths of several millimeters. A simple interpretation of these novel results which treats the deep grating structures as “filled” Fabry–Perot cavity systems gives model transmissivities which agree very well with the experimental data.
Biotin Reagents for Antibody Pretargeting. Synthesis, Radioiodination, and in Vitro Evaluation of Water Soluble, Biotinidase Resistant Biotin Derivatives (1997)

As part of our development of antibody pretargeting for cancer therapy, an investigation has been conducted to examine the stability of water solubilized, radioiodinated biotin derivatives toward biotinidase degradation in mouse and human serum. Eight new biotin derivatives were synthesized to conduct the study. The biotin derivatives synthesized contained (1) the biotin moiety, (2) a water solubilizing linker moiety, (3) p-iodobenzoate or p-tri-n-butylstannylbenzoate moieties, and (4) in some of the compounds, N-methyl or alpha-methyl containing moieties were added to block biotinidase activity. The linker moiety, 4,7,10-trioxa-1,13-tridecanediamine, 5, was included in the biotin derivatives to improve their water solubility, and it also functioned as a 17 A spacer between the biotin and the benzoyl moieties. Four of the new biotin derivatives (12, 14, 22, and 23) contained a p-tri-n-butylstannylbenzoyl moiety as precursors which could be radioiodinated in the last synthetic step. The other four biotin derivatives (13, 15, 24, and 25) contained p-iodobenzoyl moieties and were used as HPLC reference standards. Initial studies involved radioiodination of 12 to yield [125I]13. Radioiodinated 13, which did not contain a moiety for blocking biotinidase activity, was found to be rapidly degraded in both mouse and human serum at 37 degrees C. Derivatives which were designed to be stable to biotinidase incorporated N-methyl and alpha-methyl moieties adjacent to the biotin carboxylate group. In one set of biotin derivatives (14 and 15), the N-methyl moiety was obtained by incorporating N,N-dimethyl-4,7,10-trioxa-1,13-tridecanediamine, 9, as a linker in the place of 5. In the second set of biotin derivatives (22 and 24), the N-methyl moiety was introduced by incorporating a sarcosine (N-methylglycine) moiety between biotin and 5. The radioiodinated N-methyl containing biotin derivatives [125I]15 and [125I]24 were found to be very stable to biotinidase degradation. An alpha-methyl group was obtained in a pair of biotin derivatives (23 and 25) by incorporating a 3-aminobutyric acid moiety between biotin and 5. The radioiodinated alpha-methyl containing derivative, [125I]25, was found to have an intermediate stability with regards to biotinidase degradation.
Groin Hernia Repair by Laparoscopic Techniques: Current Status and Controversies (2005)

Laparoscopic hernia repair remains controversial, and its position in current hernia surgery remains in flux. In this article we attempt to put the laparoscopic approach in perspective by describing the rationale for its development. We summarize studies comparing it with open repairs, including recent publications, meta-analyses, and systematic reviews; and we then contrast the data with recent findings of the United States Veterans Affairs Cooperative study 456. We discuss the current and future status of the laparoscopic approach to inguinal hernia repair and present an update of our own laparoscopic totally extraperitoneal technique without mesh fixation. From 1994 to 2004 we performed 314 hernia repairs on 224 patients with no intraoperative complications, no conversions to an open procedure, and no mortality. Thirty (14%) minor postoperative complications occurred. There were three herniated lipomas (preperitoneal fat) but no true peritoneal reherniations. We evaluate critical points of laparoscopic hernia repair including extensive preperitoneal dissection, mesh configuration, size and fixation, cost reduction, and the learning curve.
An Autogenously Regulated Expression System for Gene Therapeutic Ocular Applications (2015)

The future of treating inherited and acquired genetic diseases will be defined by our ability to introduce transgenes into cells and restore normal physiology. Here we describe an autogenous transgene regulatory system (ARES), based on the bacterial lac repressor, and demonstrate its utility for controlling the expression of a transgene in bacteria, eukaryotic cells, and in the retina of mice. This ARES system is inducible by the small non-pharmacologic molecule, Isopropyl β-D-1-thiogalactopyranoside (IPTG) that has no off-target effects in mammals. Following subretinal injection of an adeno-associated virus (AAV) vector encoding ARES, luciferase expression can be reversibly controlled in the murine retina by oral delivery of IPTG over three induction-repression cycles. The ability to induce transgene expression repeatedly via administration of an oral inducer in vivo, suggests that this type of regulatory system holds great promise for applications in human gene therapy.
Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6 (2016)

Prokaryotic CRISPR-Cas systems provide an RNA-guided mechanism for genome defense against mobile genetic elements such as viruses and plasmids. In type III-A CRISPR-Cas systems, the RNA-guided multisubunit Csm effector complex targets both single-stranded RNAs and double-stranded DNAs. In addition to the Csm complex, efficient anti-plasmid immunity mediated by type III-A systems also requires the CRISPR-associated protein Csm6. Here we report the crystal structure of Csm6 from Thermus thermophilus and show that the protein is a ssRNA-specific endoribonuclease. The structure reveals a dimeric architecture generated by interactions involving the N-terminal CARF and C-terminal HEPN domains. HEPN domain dimerization leads to the formation of a composite ribonuclease active site. Consistently, mutations of invariant active site residues impair catalytic activity in vitro. We further show that the ribonuclease activity of Csm6 is conserved across orthologs, suggesting that it plays an important functional role in CRISPR-Cas systems. The dimer interface of the CARF domains features a conserved electropositive pocket that may function as a ligand-binding site for allosteric control of ribonuclease activity. Altogether, our work suggests that Csm6 proteins provide an auxiliary RNA-targeting interference mechanism in type III-A CRISPR-Cas systems that operates in conjunction with the RNA- and DNA-targeting endonuclease activities of the Csm effector complex.
Correcting erasure bursts with minimum decoding delay (2011)

Erasure correcting codes are widely used in upper layers of packet-switched networks, where the packet erasures often exhibit bursty patterns. The conventional wisdom to deal with bursty erasures is to apply block interleaving to break down the bursty patterns prior to error correcting coding, or use long-block Reed-Solomon codes. We show that they unnecessarily lead to sub-optimal decoding delay. In this work, with the problem model of multiple erasure bursts present in a coding block, we study the fundamental tradeoff among the rate, decoding delay and burst correction performance of erasure correcting codes. Focusing on a class of codes achieving the Singleton bound, we show that the lowest delay to recover any individual symbol not only depends on the erasure burst patterns correctable by a code, but also on whether the source symbols are encoded causally or non-causally. We also describe a few practical linear code constructions that achieve the performance limit discussed.
An empirical study of real audio traffic (2002)

The delivery of multimedia content is a facet of Internet traffic that is rapidly growing in importance. The new generation of World Wide Web sites rely heavily on extensive multimedia content such as graphics, sound, music and video to attract and retain visitors. While there have been extensive studies on the growth and effects of hyper text transfer protocol (HTTP) traffic used on the Web, little or no work has been performed in analyzing streaming multimedia traffic. We present the results of a brief study to examine the traffic emanating from a popular Internet audio service using the RealAudio program. We found protocol distributions that show a bias towards non-TCP friendly protocols. In addition, we observed consistencies in audio traffic packet sizes and data rate patterns may be useful as a tool for identifying audio data flows. Our results show that audio flows exhibit significant consistency in data rates and are considerably more persistent than HTTP connections.
ZnO Nanotube Based Dye-Sensitized Solar Cells (2007)

We introduce high surface area ZnO nanotube photoanodes templated by anodic aluminum oxide for use in dye-sensitized solar cells (DSSCs). Atomic layer deposition is utilized to coat pores conformally, providing a direct path for charge collection over tens of micrometers thickness. Compared to similar ZnO-based devices, ZnO nanotube cells show exceptional photovoltage and fill factors, in addition to power efficiencies up to 1.6%. The novel fabrication technique provides a facile, metal-oxide general route to well-defined DSSC photoanodes.
An information model of intelligent network services (2022)

This thesis was scanned from the print manuscript for digital preservation and is copyright the author. Researchers can access this thesis by asking their local university, institution or public library to make a request on their behalf. Monash staff and postgraduate students can use the link in the References field.
Plasmacytoid Dendritic Cells Induce CD8+ Regulatory T Cells In Human Ovarian Carcinoma (2005)

To directly dissect the role of each immune component in human tumor immunopathogenesis, we have studied the interaction between dendritic cells and T cells in the tumor environment of patients with ovarian carcinoma. We previously reported that functional plasmacytoid dendritic cells, but not functionally mature myeloid dendritic cells, accumulated in tumor microenvironments. We now show that tumor ascites macrophage-derived dendritic cells induced tumor-associated antigen-specific CD8+ T cells with effector functions. Strikingly, tumor ascites plasmacytoid dendritic cells induced interleukin-10+ CCR7+ CD45RO+ CD8+ regulatory T cells. Four characteristics have been identified in tumor plasmacytoid dendritic cell-induced CD8+ regulatory T cells: (a) induction of CD8+ regulatory T cells is independent of CD4+ CD25+ T cells; (b) CD8+ regulatory T cells significantly suppress myeloid dendritic cell-mediated tumor-associated antigen-specific T cell effector functions through interleukin-10; (c) repetitive myeloid dendritic cell stimulation can recover CD8+ regulatory T cell-mediated poor T cell proliferation, but not T cell effector function; (d) CD8+ regulatory T cells express functional CCR7, and efficiently migrate with lymphoid homing chemokine MIP-3beta. Primary suppressive CCR7+ CD45RO+ CD8+ T cells are found in the tumor environment of patients with ovarian cancers. Thus, tumor-associated plasmacytoid dendritic cells contribute to the tumor environmental immunosuppressive network. Collectively, tumors manipulate tumor microenvironmental dendritic cell subset distribution and function to subvert tumor immunity. The data are relevant to understanding tumor immunopathology as well as reevaluating tumor immunotherapeutic strategies.
Serological Response of Chickens Either Vaccinated or Artificially Infected with Haemophilus paragallinarum (1988)

The serological response of chickens either vaccinated or artificially infected with Haemophilus paragallinarum (Hpg) serovar A or C was investigated using both a specific hemagglutinin (HA) antigen and a common HA antigen. With Hpg serovar A, both vaccinated and artificially infected chickens produced hemagglutination-inhibition (HI) antibodies to Hpg serovar-specific and Hpg common HA antigens. Most chickens vaccinated with Hpg serovar C had detectable HI antibodies to both types of HA antigen by 3 weeks postvaccination, after which titers gradually declined. In contrast, most chickens artificially infected with serovar C produced HI antibodies to only the common HA antigen; very few of these chickens produced HI antibodies to the serovar-specific HA antigen.
Histamine in the brain of insects: a review (1999)

Histamine is the neurotransmitter of photoreceptors in insects and other arthropods. As a photoreceptor transmitter, histamine acts on ligand-gated chloride channels. Another type of histamine receptor has been indicated in the insect central nervous system by binding pharmacology. This receptor is similar to the mammalian H1 receptors, which are G-protein coupled and thus utilize a second messenger system. The distribution of histamine-immunoreactive (HAIR) neurons has been studied in a few insect species: cockroaches, locust, crickets, honey bee, blowflies, and in Drosophila. In addition to its presence in photoreceptor cells, histamine is distributed in a rather small number of neurons in the insect brain. Many of these neurons have extensive bilateral arborizations that innervate several distinct neuropil regions, notably in the protocerebrum. Some patterns of histamine distribution are seen in all the species. On the other hand, the number and morphology of neurons differ between the studied species, and several major neuropils (central body, antennal lobes, mushroom bodies) are supplied by HAIR neurons in some species, but not in others. Thus it appears that there are some species-specific functions of histamine and on others that are preserved between species. Some of the histaminergic neurons may constitute wide field inhibitory systems with functions distinct from those of neurons containing gamma-amino butyric acid (GABA). Novel data are presented for Drosophila and the cockroach Leucophaea maderae and a comparison is made with published data on other insects.
Purification and Characterization of a Novel Erythrose Reductase from Candida magnoliae (2003)

Erythritol biosynthesis is catalyzed by erythrose reductase, which converts erythrose to erythritol. Erythrose reductase, however, has never been characterized in terms of amino acid sequence and kinetics. In this study, NAD(P)H-dependent erythrose reductase was purified to homogeneity from Candida magnoliae KFCC 11023 by ion exchange, gel filtration, affinity chromatography, and preparative electrophoresis. The molecular weights of erythrose reductase determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration chromatography were 38,800 and 79,000, respectively, suggesting that the enzyme is homodimeric. Partial amino acid sequence analysis indicates that the enzyme is closely related to other yeast aldose reductases. C. magnoliae erythrose reductase catalyzes the reduction of various aldehydes. Among aldoses, erythrose was the preferred substrate (K(m) = 7.9 mM; k(cat)/K(m) = 0.73 mM(-1) s(-1)). This enzyme had a dual coenzyme specificity with greater catalytic efficiency with NADH (k(cat)/K(m) = 450 mM(-1) s(-1)) than with NADPH (k(cat)/K(m) = 5.5 mM(-1) s(-1)), unlike previously characterized aldose reductases, and is specific for transferring the 4-pro-R hydrogen of NADH, which is typical of members of the aldo/keto reductase superfamily. Initial velocity and product inhibition studies are consistent with the hypothesis that the reduction proceeds via a sequential ordered mechanism. The enzyme required sulfhydryl compounds for optimal activity and was strongly inhibited by Cu(2+) and quercetin, a strong aldose reductase inhibitor, but was not inhibited by aldehyde reductase inhibitors and did not catalyze the reduction of the substrates for carbonyl reductase. These data indicate that the C. magnoliae erythrose reductase is an NAD(P)H-dependent homodimeric aldose reductase with an unusual dual coenzyme specificity.
The features of myasthenia gravis with autoantibodies to MuSK (2005)

MG patients with antibodies to MuSK have characteristic clinical features that are different from features of the remaining seronegative MG patients. This emphasises the predictive value of anti-MuSK antibody analysis in seronegative MG patients.
Molecular genetics of the LDL receptor gene in familial hypercholesterolemia (1992)

The low density lipoprotein (LDL) receptor is a cell surface transmembrane protein that mediates the uptake and lysosomal degradation of plasma LDL, thereby providing cholesterol to cells. Mutations disrupting the function of this receptor produce autosomal dominant familial hypercholesterolemia (FH). Affected individuals have elevated plasma levels of LDL, which causes premature coronary atherosclerosis. To date, 71 mutations in the LDL receptor gene have been characterized at a molecular level. In this report, we describe 79 additional mutations and review the insights that all 150 mutations have provided into the structure/function relationship of the receptor protein and the clinical manifestations of FH.
Discovery and functional characterization of a novel small molecule inhibitor of the intracellular phosphatase, SHIP2 (2009)

This is the first report of a small molecule inhibitor of SHIP2. This compound will help to elucidate the physiological functions of SHIP2 and its involvement in various diseases, such as type 2 diabetes.
DNA Methylation and Histone Deacetylation in the Control of Gene Expression: Basic Biochemistry to Human Development and Disease (2001)

DNA methylation is a major determinant in the epigenetic silencing of genes. The mechanisms underlying the targeting of DNA methylation and the subsequent repression of transcription are relevant to human development and disease, as well as for attempts at somatic gene therapy. The success of transgenic technologies in plants and animals is also compromised by DNA methylation-dependent silencing pathways. Recent biochemical experiments provide a mechanistic foundation for understanding the influence of DNA methylation on transcription. The DNA methyltransferase Dnmt1, and several methyl-CpG binding proteins, MeCP2, MBD2, and MBD3, all associate with histone deacetylase. These observations firmly connect DNA methylation with chromatin modifications. They also provide new pathways for the potential targeting of DNA methylation to repressive chromatin as well as the assembly of repressive chromatin on methylated DNA. Here we discuss the implications of the methylation-acetylation connection for human cancers and the developmental syndromes Fragile X and Rett, which involve a mistargeting of DNA methylation-dependent repression.
Muscle-specific overexpression of lipoprotein lipase causes a severe myopathy characterized by proliferation of mitochondria and peroxisomes in transgenic mice. (1995)

In extrahepatic tissues lipoprotein lipase (LPL) hydrolyzes triglycerides thereby generating FFA for tissue uptake and metabolism. To study the effects of increased FFA uptake in muscle tissue, transgenic mouse lines were generated with a human LPL minigene driven by the promoter of the muscle creatine kinase gene. In these mice human LPL was expressed in skeletal muscle and cardiac muscle, but not in other tissues. In proportion to the level of LPL overexpression, decreased plasma triglyceride levels, elevated FFA uptake by muscle tissue, weight loss, and premature death were observed in three independent transgenic mouse lines. The animals developed a severe myopathy characterized by muscle fiber degeneration, fiber atrophy, glycogen storage, and extensive proliferation of mitochondria and peroxisomes. This degree of proliferation suggests that FFA play an important role in the biogenesis of these organelles. Our experiments indicate that LPL is rate limiting for the supply of muscle tissue with triglyceride-derived FFA. Improper regulation of muscle LPL can lead to major pathological changes and may be important in the pathogenesis of some human myopathies. Muscle-specific LPL transgenic mouse lines will serve as a useful animal model for the investigation of myopathies and the biogenesis of mitochondria and peroxisomes.