gebhart/patrepeval huggingface dataset:
The Free Hormone Hypothesis Distinction from the Free Hormone Transport Hypothesis (1992)

I. The free hormone transport hypothesis: distinction from the free hormone hypothesis. II. The free hormone hypothesis: importance of the rate-limiting step in tissue uptake. III. Explicit consideration of multiple plasma hormone-binding proteins in transport models. IV. Diffusion barriers in transport models. V. Functions of plasma hormone-binding proteins. VI. Conclusions and areas for future investigation.
Continuous, on-line DNA sequencing using oligodeoxynucleotide primers with multiple fluorophores. (1988)

A method for sequencing DNA by using a difluoresceinated primer and laser excitation is described. Dideoxy protocols have been determined that provide sequences for 600 bases starting with base 1 with less than 1% error in a single load. Electrophoresis is at 20 W and the bands are detected 24 cm from the bottom of the loading well with a scanning fluorescence detector. Bands are imaged on a TV screen in two dimensions. The sequences can be read from the TV screen manually or semiautomatically by using a simple software program. The system allows more bases to be read with a lower error rate than any other reported automated sequencing method.
A Novel, Non-Prostanoid EP2 Receptor-Selective Prostaglandin E2 Agonist Stimulates Local Bone Formation and Enhances Fracture Healing (2003)

A single injection of CP-533,536 at doses of 0.3, 1, or 3 mg/kg to the proximal tibial metaphysis dose-dependently stimulated local lamellar bone formation on trabecular, endocortical, and periosteal surfaces, and thus increased bone mineral content and bone strength at the injected site. Similarly, a single injection of 0.3 mg of CP-533,536 incorporated in PLGH matrix onto the periosteum of the femur induced significantly local bone formation. In the rat femoral fracture model, CP-533,536 in PLGH matrix at doses of 0.05, 0.5, and 5 mg dose-dependently increased callus size, density, and strength compared with PLGH matrix alone. These results show that CP-533,536 stimulates new bone formation on trabecular, endocortical, and periosteal surfaces and enhances fracture healing. These data reveal that EP2 receptor-selective agonists provide therapeutic potential for local bone augmentation, bone repair, and bone healing in humans.
Different appearance of gamma delta T cells during salmonellosis between Ityr and Itys mice (1993)

Ity gene, which is believed to be a single gene on proximal mouse chromosome 1, determines susceptibility to Salmonella infection. We have recently demonstrated that the gamma delta T cells specific for purified protein derivative appear at the early stage after infection with Salmonella choleraesuis strain 31N-1 (avirulent strain) in mice. In the present study, we compared the appearance of the gamma delta T cells in Ityr and Itys mice after infection with S. choleraesuis in an attempt to elucidate the role of the gamma delta T cells in the in vivo effect of the Ity locus on murine salmonellosis. The numbers of gamma delta T cells in the peritoneal cavity and liver were significantly larger in DBA/2 (Ityr) mice than those in BALB/c (Itys) mice after infection with a sublethal dose of S. choleraesuis. C.D2 Ityr mice, which are BALB/c mice with Ityr allele, also showed a significant increase in the number of the gamma delta T cells at the early stage after infection. Similar results in different appearances of the gamma delta T cells could be obtained between BALB/c and DBA/2 mice after infection with Mycobacterium bovis, bacillus Calmette-Guérin. The peritoneal adherent cells of DBA/2 mice infected with S. choleraesuis, which expressed a large amount of heat shock/stress protein (hsp) homologous to the mycobacterial 65-kDa hsp, induced significantly higher level of expansion of the peritoneal gamma delta T cells in normal mice in vivo and in vitro than did those of BALB/c mice infected with S. choleraesuis, which expressed a lesser amount of the hsp. These results suggest that the Ity locus may be closely related to the expression of hsp by macrophages after infection with Salmonella, which in turn stimulate the gamma delta T cells in the host during an early phase of salmonellosis.
Observation of 200th harmonic with fractional linewidth of 10−10 in a microwave frequency comb generated in a tunneling junction (2012)

A microwave frequency comb with up to 200th harmonic of a laser repetition rate is generated by nonlinear intermodal mixing of 15 fs laser pulses in the junction of a scanning tunneling microscope. The highest harmonic has an output power of −146 dBm at 14.85 GHz with a signal/noise ratio of 20 dB and a measured linewidth of 1.2 Hz, which is still larger than the actual linewidth due to phase noise of the spectrum analyzer. Theory suggests that the harmonics have comparable magnitude up to terahertz frequencies, while the observed roll-off is caused by a shunting capacitance in detection circuitry.
Signal integrity and reliability of a new Multi-Stack Package using a Pressure Conductive Rubber (2008)

A proposed Pressure Conductive Rubber (PCR) is used instead of conventional interconnections such as wire and solder bondings for a Multi-Stack Package (MSP). A PCR for a three-dimensional (3-D) high-density interconnection has a major advantage in that it can replace defective dies with known good dies (KGD). In the structure of the PCR in this study working through external pressure, conductive particles are arranged between insulating rubber. To compare the RF electrical performance of the PCR and the solder interconnection, a test-jig with coplanar waveguide (CPW) was assembled. S-parameters and reliability tests of MSP formations using the PCR and solder interconnection were separately measured in a frequency range from 300 KHz to 8 GHz. The measured results show the insertion loss of 1.72 dB and the return loss of 12.7 dB on a single-layer structure at 8 GHz. Additionally, reliability tests of the PCR show stable electrical performance. These results indicate that the RF electrical performance of the PCR is acceptable for use in DDR3 SDRAM (Double Data Rate 3 Synchronous Dynamic Random Access Memory) applications.
NUMA-aware reader-writer locks (2013)

Non-Uniform Memory Access (NUMA) architectures are gaining importance in mainstream computing systems due to the rapid growth of multi-core multi-chip machines. Extracting the best possible performance from these new machines will require us to revisit the design of the concurrent algorithms and synchronization primitives which form the building blocks of many of today's applications. This paper revisits one such critical synchronization primitive -- the reader-writer lock. We present what is, to the best of our knowledge, the first family of reader-writer lock algorithms tailored to NUMA architectures. We present several variations which trade fairness between readers and writers for higher concurrency among readers and better back-to-back batching of writers from the same NUMA node. Our algorithms leverage the lock cohorting technique to manage synchronization between writers in a NUMA-friendly fashion, binary flags to coordinate readers and writers, and simple distributed reader counter implementations to enable NUMA-friendly concurrency among readers. The end result is a collection of surprisingly simple NUMA-aware algorithms that outperform the state-of-the-art reader-writer locks by up to a factor of 10 in our microbenchmark experiments. To evaluate our algorithms in a realistic setting we also present performance results of the kccachetest benchmark of the Kyoto-Cabinet distribution, an open-source database which makes heavy use of pthread reader-writer locks. Our locks boost the performance of kccachetest by up to 40% over the best prior alternatives.
Physiological functions of endosomal proteolysis (1995)

Research Article| April 15 1995 Physiological functions of endosomal proteolysis T Berg; T Berg Search for other works by this author on: This Site PubMed Google Scholar T Gjøen; T Gjøen Search for other works by this author on: This Site PubMed Google Scholar O Bakke O Bakke Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1995) 307 (2): 313–326. https://doi.org/10.1042/bj3070313 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation T Berg, T Gjøen, O Bakke; Physiological functions of endosomal proteolysis. Biochem J 15 April 1995; 307 (2): 313–326. doi: https://doi.org/10.1042/bj3070313 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1995 The Biochemical Society, London1995 Article PDF first page preview Close Modal You do not currently have access to this content.
An Iron-responsive Element Type II in the 5′-Untranslated Region of the Alzheimer's Amyloid Precursor Protein Transcript (2002)

Iron-responsive elements (IREs) are the RNA stem loops that control cellular iron homeostasis by regulating ferritin translation and transferrin receptor mRNA stability. We mapped a novel iron-responsive element (IRE-Type II) within the 5'-untranslated region (5'-UTR) of the Alzheimer's amyloid precursor protein (APP) transcript (+51 to +94 from the 5'-cap site). The APP mRNA IRE is located immediately upstream of an interleukin-1 responsive acute box domain (+101 to +146). APP 5'-UTR conferred translation was selectively down-regulated in response to intracellular iron chelation using three separate reporter assays (chloramphenicol acetyltransferase, luciferase, and red fluorescent protein reflecting an inhibition of APP holoprotein translation in response to iron chelation. Iron influx reversed this inhibition. As an internal control to ensure specificity, a viral internal ribosome entry sequence was unresponsive to intracellular iron chelation with desferrioxamine. Using RNA mobility shift assays, the APP 5'-UTRs, encompassing the IRE, bind specifically to recombinant iron-regulatory proteins (IRP) and to IRP from neuroblastoma cell lysates. IRP binding to the APP 5'-UTR is reduced after treatment of cells with desferrioxamine and increased after interleukin-1 stimulation. IRP binding is abrogated when APP cRNA probe is mutated in the core IRE domain (Delta4 bases:Delta83AGAG86). Iron regulation of APP mRNA through the APP 5'-UTR points to a role for iron in the metabolism of APP and confirms that this RNA structure can be a target for the selection of small molecule drugs, such as desferrioxamine (Fe chelator) and clioquinol (Fe, Cu, and Zn chelator), which reduce Abeta peptide burden during Alzheimer's disease.
Isolation of a cDNA Clone for Spinach Lipid Transfer Protein and Evidence that the Protein Is Synthesized by the Secretory Pathway (1991)

A cDNA clone encoding a nonspecific lipid transfer protein from spinach (Spinacia oleracea) was isolated by probing a library with synthetic oligonucleotides based on the amino acid sequence of the protein. Determination of the DNA sequence indicated a 354-nucleotide open reading frame which encodes a 118-amino acid residue polypeptide. The first 26 amino acids of the open reading frame, which are not present in the mature protein, have all the characteristics of a signal sequence which is normally associated with the synthesis of membrane proteins or secreted proteins. In vitro transcription of the cDNA and translation in the presence of canine pancreatic microsomes or microsomes from cultured maize endosperm cells indicated that proteolytic processing of the preprotein to the mature form was associated with cotranslational insertion into the microsomal membranes. Because there is no known mechanism by which the polypeptide could be transferred from the microsomal membranes to the cytoplasm, the proposed role of this protein in catalyzing lipid transfer between intracellular membranes is in doubt. Although the lipid transfer protein is one of the most abundant proteins in leaf cells, the results of genomic Southern analysis were consistent with the presence of only one gene. Analysis of the level of mRNA by Northern blotting indicated that the transcript was several-fold more abundant than an actin transcript in leaf and petiole tissue, but was present in roots at less than 1% of the level in petioles.
Neuronal Cell Death Is Preceded by Cell Cycle Events at All Stages of Alzheimer's Disease (2003)

Cell cycle events play a major role in the loss of neurons in advanced Alzheimer's disease (AD). It is currently unknown, however, whether the same is true for the neuronal losses in early disease stages. To explore this issue we analyzed brain autopsy material from individuals clinically categorized with mild cognitive impairment (MCI), many if not most of whom will progress to AD. Immunocytochemistry for three cell cycle-related proteins, proliferating cell nuclear antigen, cyclin D, and cyclin B, was performed on sections from hippocampus, basal nucleus of Meynert, and entorhinal cortex. The results obtained from MCI cases were compared with material from individuals diagnosed with AD and those without cognitive impairment. In both hippocampus and basal nucleus, there was a significant percentage of cell cycle immunopositive neurons in the MCI cases. These percentages were similar to those found in the AD cases but significantly higher than non-cognitively impaired controls. In entorhinal cortex, the density of cell cycle-positive neurons was greater in MCI than in AD. However, we observed large variations in the percentages of immunopositive neurons from individual to individual. These findings lend support to the hypothesis that both the mechanism of cell loss (a cell cycle-induced death) and the rate of cell loss (a slow atrophy over several months) are identical at all stages of the AD disease process. The implication of the findings for human clinical trials is discussed.
On-chip starter circuit for switched-inductor DC-DC harvester systems (2013)

Because wireless microsystems can only incorporate tiny batteries, they typically exhaust stored on-board energy quickly. Fortunately, harvesting ambient energy is a viable means of extending their operational lifetimes, except starting and re-starting miniaturized microwatt harvesters from nocharge conditions is difficult. The challenge is drawing usable energy from millivolt signals under micro-scale constraints. This paper proposes a nonlinear on-chip starter that borrows the harvester's steady-state inductor to start the system from nocharge conditions. Simulations show that the starter draws power from 250-500 mV to charge 100 pF to 3 V in 48 μs. The 100-pF temporary supply then powers the harvester's 1-V, 4-μA controller to charge 100 nF by 100 mV in 65-μs cycles until the 100-nF battery charges enough to supply the system.
Nucleoside Specificity in the Carrier IgG-Dependent Induction of Tolerance (1976)

Induction of tolerance to nucleoside haptens in BALB/c mice with isologous IgG conjugates bearing four nucleosides simultaneously (A, G, C, T)-IgG was confirmed. A mixture of separate nucleoside-IgG tolerogens (A-IgG, G-IgG, C-IgG, and T-IgG) was as effective or more effective that the (A, G, C,T)-IgG form in suppressing the response to (A, G, C, T)-KLH. The nucleosides acted independently and simultaneously, since tolerogens with varying combinations of nucleosides caused specific suppression of the respones to only those nucleosides present on the tolerogen. Nucleoside-IgG conjugates did not suppress the response to denatured DNA-methylated bovine serum albumin, in which larger oligonucleotide determinants predominate. In varying combinations, guanosine was the dominant nucleoside both for immunization and for induction of tolerance. After three or four immunizations, control immunized animals made mainly IgG anti-nucleoside antibodies and this IgG antibody formation was preferentially suppressed in tolerogen-treated animals. Tolerance could be established before the primary or secondary immunization and it then persisted for at least 75 days through a fourth course of immunization. The same dosage of tolerogen did not reverse a strongly established anti-nucleoside antibody production after a tertiary response.
Detection caching for faster object detection (2011)

This paper investigates how the speed of an object detector can be rapidly increased through a caching framework when input sequences are quasi-repetitive. In the proposed framework, observed output states are discretized into a large number of classes. Each class induces its own discriminant subspace in the feature space, and is associated with a feature exemplar and a local metric. The feature exemplars and the local metrics are learned online using a novel piecewise linear discriminant analysis. The execution of the original object detector is skipped when the current image feature vector is similar to previously observed feature exemplars, and previously detected object states may simply be recalled. The exemplar recognition is carried via a 1-pass approximate nearest neighbor search in an index tree based on k-means clustering. Preliminary results show up to a 5-fold improvement when applied to the Viola &amp;amp; Jones [23] face detector, improving speeds from 10fps to 50fps. Experiments were done on the standard MPEG-4 testing sequences and real data. 1.1. Detection Caching At the heart of the framework in this paper is the notion that for quasi-repetitive input, it is often much faster recalling previous results from the object detector, than to re-execute the object detector on the same input again. Consider the Viola and Jones face detector [23] which linearly scans through different (x, y, s) states (where s is scale) and evaluates each bounding window to determine whether a face is present or not through a binary classifier. However, if it is possible to identify if a particular image frame (i.e. the entire image frame, not just a particular bounding window) has been previously observed before, the previous (x, y, s) state may simply be recalled – this is multi-class classification, where each parameter state is a separate class (figure 1). Furthermore, the recognition of the image frame may involve a tree-based search in log (rather than linear) number of operations. 1.
Peptide-assisted delivery of steric-blocking antisense oligomers. (2003)

Cationic transport peptides conjugated to steric blocking antisense oligomers (oligos) increase oligo uptake in eukaryotic cell lines, bacteria and mice. Recent reports of arginine-rich transport peptide conjugates strongly suggest that the mechanism of uptake is primarily endocytotic and that previous assay techniques produced confounding artifacts that led to the old non-endocytotic, membrane-penetrating peptide model. The artifacts result from fixing cells for fluorescent microscopy and from using non-trypsinized cells for flow cytometry. Fixing cells redistributes the peptide or peptide-oligo conjugates associated with the outside of cell membranes and trapped in endosomes, giving apparent diffuse cytosolic and nuclear fluorescence. Cationic peptides bound to the outer surface of cells, if not removed, skew fluorescence data obtained by flow cytometry, leading to the earlier conclusions. Upregulation assays now provide a tool for comparing the efficacy of conjugates, measuring oligo uptake by quantitating antisense activity of conjugates. These assays, developed in cell culture and mouse models, are faster and have higher signal-to-noise ratios than downregulation assays. Thus, a convenient and effective method now exists to screen transport peptides.
Cross-Coupling and Dehalogenation Reactions Catalyzed by (N-Heterocyclic carbene)Pd(allyl)Cl Complexes (2004)

A series of well-defined, air- and moisture-stable (NHC)Pd(allyl)Cl (NHC = N-heterocyclic carbene) complexes has been used in several catalytic reactions: Suzuki-Miyaura cross-coupling, catalytic dehalogenation of aryl halides, and aryl amination. The scope of the three processes using various substrates was examined. A general system involving the use of (IPr)Pd(allyl)Cl as catalyst and NaO(t)Bu as base has proven to be highly active for the Suzuki-Miyaura cross-coupling of activated and unactivated aryl chlorides and bromides, for the catalytic dehalogenation of aryl chlorides, and for the catalytic aryl amination of aryl triflates. All reactions proceed in short reaction times and at mild temperatures. The system has also proven to be compatible with the microwave-assisted Suzuki-Miyaura cross-coupling and catalytic dehalogenation processes, affording yields similar to those of the conventionally heated analogous reactions.
Efficient frequency assignment scheme for intermodulationdistortion reduction in fibre-optic microcellular systems (1994)

An efficient and effective frequency assignment scheme for fibre-optic microcellular systems is presented. The scheme is suitable for intermodulation distortion reduction in multichannel transmission systems. The computation time reduction is quite substantial with good intermodulation distortion reduction.
Regulation of urinary ACE2 in diabetic mice (2013)

Angiotensin-converting enzyme-2 (ACE2) enhances the degradation of ANG II and its expression is altered in diabetic kidneys, but the regulation of this enzyme in the urine is unknown. Urinary ACE2 was studied in the db/db model of type 2 diabetes and stretozotocin (STZ)-induced type 1 diabetes during several physiological and pharmacological interventions. ACE2 activity in db/db mice was increased in the serum and to a much greater extent in the urine compared with db/m controls. Neither a specific ANG II blocker, telmisartan, nor an ACE inhibitor, captopril, altered the levels of urinary ACE2 in db/db or db/m control mice. High-salt diet (8%) increased whereas low-salt diet (0.1%) decreased urinary ACE2 activity in the urine of db/db mice. In STZ mice, urinary ACE2 was also increased, and insulin decreased it partly but significantly after several weeks of administration. The increase in urinary ACE2 activity in db/db mice reflected an increase in enzymatically active protein with two bands identified of molecular size at 110 and 75 kDa and was associated with an increase in kidney cortex ACE2 protein at 110 kDa but not at 75 kDa. ACE2 activity was increased in isolated tubular preparations but not in glomeruli from db/db mice. Administration of soluble recombinant ACE2 to db/m and db/db mice resulted in a marked increase in serum ACE2 activity, but no gain in ACE2 activity was detectable in the urine, further demonstrating that urinary ACE2 is of kidney origin. Increased urinary ACE2 was associated with more efficient degradation of exogenous ANG II (10(-9) M) in urine from db/db compared with that from db/m mice. Urinary ACE2 could be a potential biomarker of increased metabolism of ANG II in diabetic kidney disease.
Role of GTP Hydrolysis in Fission of Caveolae Directly from Plasma Membranes (1996)

Caveolae are specialized invaginated cell surface microdomains of undefined function. A cell-free system that reconstituted fission of caveolae from lung endothelial plasma membranes was developed. Addition of cytosol and the hydrolysis of guanosine triphosphate (GTP) induced caveolar fission. The budded caveolae were isolated as vesicles rich in caveolin and the sialoglycolipid GM1 but not glycosyl-phosphatidylinositol (GPI)-anchored proteins. These vesicles contained the molecular machinery for endocytosis and transcytosis. In permeabilized endothelial cells, GTP stimulated, whereas GTPgammaS prevented, caveolar budding and endocytosis of the cholera toxin B chain to endosomes. Thus, caveolae may bud to form discrete carrier vesicles that participate in membrane trafficking.