gebhart/patrepeval huggingface dataset:
Acetylcholine receptors in regenerating muscle accumulate at original synaptic sites in the absence of the nerve. (1979)

We examined the role of nerve terminals in organizing acetylcholine receptors on regenerating skeletal-muscle fibers. When muscle fibers are damaged, they degenerate and are phagocytized, but their basal lamina sheaths survive. New myofibers form within the original basal lamina sheaths, and they become innervated precisely at the original synaptic sites on the sheaths. After denervating and damaging muscle, we allowed myofibers to regenerate but deliberately prevented reinnervation. The distribution of acetylcholine receptors on regenerating myofibers was determined by histological methods, using [125I] alpha-bungarotoxin or horseradish peroxidase-alpha-bungarotoxin; original synaptic sites on the basal lamina sheaths were marked by cholinesterase stain. By one month after damage to the muscle, the new myofibers have accumulations of acetylcholine receptors that are selectively localized to the original synaptic sites. The density of the receptors at these sites is the same as at normal neuromuscular junctions. Folds in the myofiber surface resembling junctional folds at normal neuromuscular junctions also occur at original synaptic sites in the absence of nerve terminals. Our results demonstrate that the biochemical and structural organization of the subsynaptic membrane in regenerating muscle is directed by structures that remain at synaptic sites after removal of the nerve.
Tourette Syndrome: A Hereditary Neuropsychiatric Spectrum Disorder (1994)

The objective was to determine if the high frequency of behavioral problems in Tourette syndrome (TS) probands is the result of the pleiotrophic expression of the Gts genes or due to ascertainment bias. It was possible to distinguish between these two hypotheses by comparing the frequency of these behaviors in nonproband relatives with TS to relatives without TS. Twenty behavioral problems were prospectively assessed in a consecutive series of 361 TS probands, 113 nonproband TS relatives, 380 relatives without TS, and 68 controls, by the administration of a questionnaire based on the Diagnostic Interview Schedule and the DSM-III-R. Significance was set at a very conservative level of p < or = .001. Except for problems with smoking, reading and compulsive eating, all other behaviors were significantly more common in nonproband TS relatives than in relatives without TS. The relatives were also dichotomized on the basis of each of the behavioral problems. Regardless of the behavioral trait used, there was a higher frequency of all other behaviors in those who were positive versus those who were negative for that behavior. Ranking according to the number of behaviors that were significant indicated that mania, obsessive-compulsive behaviors and schizoid behaviors represented higher degrees of expression of the Gts genes than chronic tics. These results indicate that the Gts genes cause a spectrum of behavioral disorders in addition to chronic tics, indicate that TS is a behavioral spectrum disorder, and emphasize the role of genetic factors in a wide range of human behaviors.
The human immunodeficiency virus gp120 binding site on CD4: delineation by quantitative equilibrium and kinetic binding studies of mutants in conjunction with a high-resolution CD4 atomic structure. (1992)

The first immunoglobulin V-like domain of CD4 contains the binding site for human immunodeficiency virus gp120. Guided by the atomic structure of a two-domain CD4 fragment, we have examined gp120 interaction with informative CD4 mutants, both by equilibrium and kinetic analysis. The binding site on CD4 appears to be a surface region of about 900 A2 on the C" edge of the domain. It contains an exposed hydrophobic residue, Phe43, on the C" strand and four positively charged residues, Lys29, Lys35, Lys46, and Arg59, on the C, C', C", and D strands, respectively. Replacement of Phe43 with Ala or Ile reduces affinity for gp120 by more than 500-fold; Tyr, Trp, and Leu substitutions have smaller effects. The four positively charged side chains each make significant contributions (7-50-fold). This CD4 site may dock into a conserved hydrophobic pocket bordered by several negatively charged residues in gp120. Class II major histocompatibility complex binding includes the same region on CD4; this overlap needs to be considered in the design of inhibitors of the CD4-gp120 interaction.
Oxygen saturation and breathing patterns in infancy. 1: Full term infants in the second month of life. (1991)

Overnight 12 hour tape recordings were made of arterial oxygen saturation (SaO2, pulse oximeter in the beat to beat mode) and abdominal wall breathing movement on 67 healthy, full term infants between the ages of 29 and 54 (median 39) days. The median baseline SaO2 during regular breathing was 99.8% (range 97.0-100%). Fifty four infants (81%) had shortlived episodes during which SaO2 fell to 80% or less (desaturation); the median rate was 0.9 desaturations/hour, and the median duration of each desaturation was 1.2 seconds. The 97th centile value for the duration of all episodes in which SaO2 fell to less than or equal to 80% was 4.0 seconds. The frequency of desaturations was significantly higher, and their duration significantly longer, when the breathing pattern was non-regular rather than regular. The percentage of apnoeic pauses (greater than or equal to 4 seconds in duration) followed by a desaturation was higher during non-regular than regular breathing; it was particularly high during periodic breathing. A knowledge of normal variability of baseline measurements of oxygenation and of the relationship between oxygenation and breathing patterns in infants is essential to the use of pulse oximetry in clinical practice.
An Evaluation of the Novel Selective Estrogen Receptor Modulator, Idoxifene, for Effects on Reproduction in Rats and Rabbits (1998)

Idoxifene, a tissue-specific selective estrogen receptor modulator, was evaluated in male and female rats and female rabbits after oral administration for effects on fertility and/or embryo-fetal development. In all studies, adult toxicity was evident at doses >/=0.03 mg/kg/day in rats and >/=0.1 mg/kg/day in rabbits as evidenced by decreased body weight and/or food consumption. In the male fertility study, rats were treated with 0.003, 0.3, or 3.0 mg/kg/day for 64 to 68 days. Doses >/=0.3 mg/kg/day decreased seminal vesicle and prostate weights and impaired posttesticular sperm development, resulting in decreased epididymal sperm count and weight, but did not affect male fertility. In the female fertility study, rats were treated for 2 weeks prior to mating until insemination with 0.003, 0.03, or 3.0 mg/kg/day. Disrupted estrous cycles, impaired fertility, increased preimplantation loss, and increased vaginal fluid at necropsy were evident at >/=0.03 mg/kg/day. In the early embryonic development study, pregnant female rats were treated from days 0 to 6 postcoitus (pc) with 0.003, 0.03, or 3.0 mg/kg/day idoxifene. Partial or complete preimplantation loss was seen at 0.03 and 3.0 mg/kg/day, respectively. In the embryo-fetal development study, pregnant rats were treated from days 6 to 17 pc with 0.003, 0.03, or 3.0 mg/kg/day. At 3.0 mg/kg/day there was maternal lethality, excess vaginal fluid, embryo-fetal death, generalized fetal edema, and developmental delays. Excess vaginal fluid but no fetal effects were seen at 0.03 mg/kg/day. There were no treatment-related effects at 0.003 mg/kg/day in any rat reproduction study performed. In the rabbit embryo-fetal development study, pregnant New Zealand White rabbits were treated from days 6 to 20 pc with 0.01, 0.1, or 1.0 mg/kg/day idoxifene. At 1.0 mg/kg/day there was maternal lethality, vaginal or uterine bleeding, abortion/premature deliveries, and embryolethality. Vaginal or uterine bleeding was seen at 0.1 mg/kg/day. No treatment-related effects were observed at 0.01 mg/kg/day. Although systemic toxicity was evident in all the studies, the effects of idoxifene on rat and rabbit reproduction were considered to be due to the pharmacological activity of the compound.
Evidence for a Role of CRM1 in Signal-Mediated Nuclear Protein Export (1997)

Chromosome maintenance region 1 (CRM1), a protein that shares sequence similarities with the karyopherin beta family of proteins involved in nuclear import pathway, was shown to form a complex with the leucine-rich nuclear export signal (NES). This interaction was inhibited by leptomycin B, a drug that prevents the function of the CRM1 protein in yeast. To analyze the role of the CRM1-NES interaction in nuclear export, a transport assay based on semipermeabilized cells was developed. In this system, which reconstituted NES-, cytosol-, and energy-dependent nuclear export, leptomycin B specifically blocked export of NES-containing proteins. Thus, the CRM1 protein could act as a NES receptor involved in nuclear protein export.
Current Protocols in Immunology (2018)

Current Protocols in Immunology is a three-volume looseleaf manual that provides comprehensive coverage of immunological methods from classic to the most cutting edge, including antibody detection and preparation, assays for functional activities of mouse and human cells involved in immune responses, assays for cytokines and their receptors, isolation and analysis of proteins and peptides, biochemistry of cell activation, molecular immunology, and animal models of autoimmune and inflammatory diseases. Carefully edited, step-by-step protocols replete with material lists, expert commentaries, and safety and troubleshooting tips ensure that you can duplicate the experimental results in your own laboratory.Bimonthly updates, which are filed into the looseleaf, keep the set current with the latest developments in immunology methods.The initial purchase includes one year of updates and then subscribers may renew their annual subscriptions.Current Protocols publishes a family of laboratory manuals for bioscientists, including Molecular Biology, Human Genetics, Protein Science, Cytometry, Cell Biology, Neuroscience, Pharmacology, and Toxicology.
Extraction and Dispersion of Large Gold Nanoparticles in Nonpolar Solvents (2001)

Gold nanoparticles up to 70 nm in diameter could be extracted from aqueous solutions into nonpolar organic solvents by tetrathiolated resorcinarenes 1 and 2. The resorcinarene-coated nanoparticles formed stable dispersions in toluene and chloroform and could be passed through a crosslinked polystyrene column without significant degradation, but exhibited variable resistance to alkanethiol-induced flocculation. Gold nanoparticles encapsulated by resorcinarene 2 were found to be exceptionally stable even in the presence of propanethiol and dodecanethiol, with an approximate dispersion half-life of one month at room temperature.
Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism. (1994)

Basal transcription of many genes in yeast is repressed by Mot1, an essential protein which is a member of the Snf2/Swi2 family of conserved nuclear factors. ADI is an ATP-dependent inhibitor of TATA-binding protein (TBP) binding to DNA that inhibits transcription in vitro. Here we demonstrate that ADI is encoded by the MOT1 gene. Mutation of MOT1 abolishes ADI activity and derepresses basal transcription in vitro and in vivo. Recombinant Mot1 removes TBP from DNA and Mot1 contains an ATPase activity which is essential for its function. Genetic interactions between Mot1 and TBP indicate that their functions are interlinked in vivo. These results provide a general model for understanding the mechanism of action of a large family of nuclear factors involved in processes such as transcription and DNA repair.
GATA-1 expression pattern can be recapitulated in living transgenic zebrafish using GFP reporter gene (1997)

In this study, DNA constructs containing the putative zebrafish promoter sequences of GATA-1, an erythroid-specific transcription factor, and the green fluorescent protein reporter gene, were microinjected into single-cell zebrafish embryos. Erythroid-specific activity of the GATA-1 promoter was observed in living embryos during early development. Fluorescent circulating blood cells were detected in microinjected embryos 24 hours after fertilization and were still present in 2-month-old fish. Germline transgenic fish obtained from the injected founders continued to express green fluorescent protein in erythroid cells in the F1 and F2 generations. The green fluorescent protein expression patterns in transgenic fish were consistent with the pattern of GATA-1 mRNA expression detected by RNA in situ hybridization. These transgenic fish have allowed us to isolate, by fluorescence-activated cell sorting, the earliest erythroid progenitor cells from developing embryos for in vitro studies. By generating transgenic fish using constructs containing other zebrafish promoters and green fluorescent protein reporter gene, it should be possible to visualize the origin and migration of any lineage-specific progenitor cells in a living embryo.
Application of Bacterial Biocathodes in Microbial Fuel Cells (2006)

Abstract This review addresses the development and experimental progress of biocathodes in microbial fuel cells (MFCs). Conventional MFCs consist of biological anodes and abiotic cathodes. The abiotic cathode usually requires a catalyst or an electron mediator to achieve high electron transfer, increasing the cost and lowering the operational sustainability. Such disadvantages can be overcome by biocathodes, which use microorganisms to assist cathodic reactions. Biocathodes are feasible in potentiostat‐poised half cells, but only very few studies have investigated them in complete MFCs. The classification of biocathodes is based on which terminal electron acceptor is available. For aerobic biocathodes with oxygen as the terminal electron acceptor, electron mediators, such as iron and manganese, are first reduced by the cathode (abiotically) and then reoxidized by bacteria. Anaerobic biocathodes directly reduce terminal electron acceptors, such as nitrate and sulfate, by accepting electrons from a cathode electrode through microbial metabolism. Biocathodes are promising in MFCs, and we anticipate a successful application after several breakthroughs are made.
SGN-70, a Humanized Anti-CD70 Antibody, Targets CD70-Expressing Hematologic Tumors. (2006)

Abstract Antigens expressed on malignant cells in the absence of significant expression on normal tissues are highly desirable targets for therapeutic antibodies. CD70 is a TNF superfamily member whose normal expression is restricted to activated lymphocytes but is aberrantly expressed in hematologic malignancies and solid tumors including non-Hodgkin’s lymphoma (NHL), Hodgkin’s disease, multiple myeloma (MM), Waldenstrom’s macroglobulinemia, renal cell carcinoma, glioblastoma, and nasopharyngeal carcinoma. To target CD70-expressing hematologic malignancies, we have engineered a humanized IgG1 anti-CD70 antibody that mediates lysis of tumor targets via ADCC and CDC and facilitates antibody dependent cellular phagocytosis in vitro. In vivo, administration of SGN-70 prolonged survival of SCID mice bearing CD70+ disseminated human NHL or MM xenografts. Intravenous injection of the CD70+ MM cell line MM.1S resulted in disease as measured by onset of paralysis, presence of CD138+ MM cells in the bone marrow, and increasing levels of circulating human Ig lambda light chain. SGN-70 treatment of MM.1S-bearing mice significantly delayed onset of paralysis and reduced the monoclonal protein levels detected in serum approximately 4-fold compared to untreated or non-binding antibody control-treated mice. Whereas myeloma cells comprised 32±6.4 % of mononuclear cells in the long bone marrow of control mice, SGN-70 treatment reduced the myeloma cell fraction to 4.9±1.9% of mononuclear cells recovered. SGN-70 treatment also significantly extended the survival of mice bearing disseminated Raji tumors (NHL) compared to control mice. Survival benefit was absent when mice received an Fc-modified antibody deficient in effector functions, confirming that the activity of SGN-70 in these models was dependent upon Fc-FcγR interaction with host immune cells. Together, these data demonstrate that SGN-70 possesses effector cell-mediated antitumor activity and provides rationale for clinical study of SGN-70 in CD70+ hematologic malignancies.
Stable barley chromosomes without centromeric repeats (2005)

The satellite sequences (AGGGAG)(n) and Ty3/gypsy-like retrotransposons are known to localize at the barley centromeres. Using a gametocidal system, which induces chromosomal mutations in barley chromosomes added to common wheat, we obtained an isochromosome for the short arm of barley chromosome 7H (7HS) that lacked the barley-specific satellite sequence (AGGGAG)(n). Two telocentric derivatives of the isochromosome arose in the progeny: 7HS* with and 7HS** without the pericentromeric C-band. FISH analysis demonstrated that both telosomes lacked not only the barley-specific centromeric (AGGGAG)(n) repeats and retroelements but also any of the known wheat centromeric tandem repeats, including the 192-bp, 250-bp, and TaiI sequences. Although they lacked these centromeric repeats, 7HS* and 7HS** both showed normal mitotic and meiotic transmission. Translocation of barley centromeric repeats to a wheat chromosome 4A did not generate a dicentric chromosome. Indirect immunostaining revealed that all tested centromere-specific proteins (rice CENH3, maize CENP-C, and putative barley homologues of the yeast kinetochore proteins CBF5 and SKP1) and histone H3 phosphorylated at serines 10 and 28 localized at the centromeric region of 7HS*. We conclude that the barley centromeric repeats are neither sufficient nor obligatory to assemble kinetochores, and we discuss the possible formation of a novel centromere in a barley chromosome.
Fiber-Optic Microsphere-Based Antibody Array for the Analysis of Inflammatory Cytokines in Saliva (2009)

Antibody microarrays have emerged as useful tools for high-throughput protein analysis and candidate biomarker screening. We describe here the development of a multiplexed microsphere-based antibody array capable of simultaneously measuring 10 inflammatory protein mediators. Cytokine-capture microspheres were fabricated by covalently coupling monoclonal antibodies specific for cytokines of interest to fluorescently encoded 3.1 microm polymer microspheres. An optical fiber bundle containing approximately 50,000 individual 3.1 microm diameter fibers was chemically etched to create microwells in which cytokine-capture microspheres could be deposited. Microspheres were randomly distributed in the wells to produce an antibody array for performing a multiplexed sandwich immunoassay. The array responded specifically to recombinant cytokine solutions in a concentration-dependent fashion. The array was also used to examine endogenous mediator patterns in saliva supernatants from patients with pulmonary inflammatory diseases such as asthma and chronic obstructive pulmonary disease (COPD). This array technology may prove useful as a laboratory-based platform for inflammatory disease research and diagnostics, and its small footprint could also enable integration into a microfluidic cassette for use in point-of-care testing.
A 3.3 V/1 W class D audio power amplifier with 103 dB DR and 90% efficiency (2003)

A single-chip Integrated circuit of 3.3 V/1 W class-D high fidelity and high efficiency audio power amplifier is presented in this paper. The design has been done using a 3.3 V/0.25 /spl mu/m CMOS process. The maximum output power is 1 W before the amplifier saturates. The THD+N at 0.5 W output power is below 0.03% and efficiency is better than 90% thanks to the careful design of the output stage. The dynamic range is more than 100 dB suitable for high fidelity audio applications. A single-loop single-bit third order sigma-delta modulator is used to generate the PWM signal from input audio signal. The PWM signal is then filtered at the output with a second order low pass filter external to the chip to regenerate the input signal.
A Cysteine-String Protein is Expressed in Retina and Brain ofDrosophila (1990)

Antibodies can be used to identify tissue- and stage-specifically expressed genes. A monoclonal antibody MAB ab49 from a hybridoma library screened for immunohistochemical staining in the adult nervous system of Drosophila melanogaster was found to selectively bind to all neuropil regions and to synaptic boutons of motor neurons. In Western blots of homogenized brains the antibody recognizes two proteins of 32 and 34 kD. Using this antibody we have isolated seven cDNA clones that derive from two polyadenylated mRNA splice variants of a gene located at 79E1-2 on polytene chromosomes. The two mRNAs code for two inferred proteins of 249 and 223 amino acids, respectively, which are identical except for their C-terminals and a central deletion of 21 amino acids in the second protein. Both contain a contiguous string of 11 cysteine residues. In situ hybridization to frozen head sections detects expression of this gene in retina and neuronal perikarya. The 32 and 34 kD brain proteins that presumably are localized predominantly in synaptic terminals of photoreceptors and most if not all neurons may correspond to two variant cysteine-string proteins as they are of similar molecular weight and share an antigenic binding site for MAB ab49.
Use of IPsec Transport Mode for Dynamic Routing (2004)

IPsec can secure the links of a multihop network to protect
communication between trusted components, e.g., for a secure virtual
network (VN), overlay, or virtual private network (VPN). Virtual links
established by IPsec tunnel mode can conflict with routing and
forwarding inside VNs because IP routing depends on references to
interfaces and next-hop IP addresses. The IPsec tunnel mode
specification is ambiguous on this issue, so even compliant
implementations cannot be trusted to avoid conflicts. An alternative
to tunnel mode uses non-IPsec IPIP encapsulation together with IPsec
transport mode, which we call IIPtran. IPIP encapsulation occurs as a
separate initial step, as the result of a forwarding lookup of the VN
packet. IPsec transport mode processes the resulting (tunneled) IP
packet with an SA determined through a security association database
(SAD) match on the tunnel header. IIPtran supports dynamic routing
inside the VN without changes to the current IPsec architecture.
IIPtran demonstrates how to configure any compliant IPsec
implementation to avoid the aforementioned conflicts. IIPtran is also
compared to several alternative mechanisms for VN routing and their
respective impact on IPsec, routing, policy enforcement, and
interactions with the Internet Key Exchange (IKE). This memo provides
information for the Internet community.