gebhart/patrepeval huggingface dataset:
Impact of checkpoint latency on overhead ratio of a checkpointing scheme (1997)

Checkpointing reduces loss of computation in the presence of failures. Two metrics characterize a checkpointing scheme: checkpoint overhead and checkpoint latency. The paper shows that a large increase in latency is acceptable if it is accompanied by a relatively small reduction in overhead. Also, for equidistant checkpoints, optimal checkpoint interval is shown to be typically independent of checkpoint latency.
The Golgin GCC88 Is Required for Efficient Retrograde Transport of Cargo from the Early Endosomes to theTrans-Golgi Network (2007)

Retrograde transport pathways from early/recycling endosomes to the trans-Golgi network (TGN) are poorly defined. We have investigated the role of TGN golgins in retrograde trafficking. Of the four TGN golgins, p230/golgin-245, golgin-97, GCC185, and GCC88, we show that GCC88 defines a retrograde transport pathway from early endosomes to the TGN. Depletion of GCC88 in HeLa cells by interference RNA resulted in a block in plasma membrane-TGN recycling of two cargo proteins, TGN38 and a CD8 mannose-6-phosphate receptor cytoplasmic tail fusion protein. In GCC88-depleted cells, cargo recycling was blocked in the early endosome. Depletion of GCC88 dramatically altered the TGN localization of the t-SNARE syntaxin 6, a syntaxin required for endosome to TGN transport. Furthermore, the transport block in GCC88-depleted cells was rescued by syntaxin 6 overexpression. Internalized Shiga toxin was efficiently transported from endosomes to the Golgi of GCC88-depleted cells, indicating that Shiga toxin and TGN38 are internalized by distinct retrograde transport pathways. These findings have identified an essential role for GCC88 in the localization of TGN fusion machinery for transport from early endosomes to the TGN, and they have allowed the identification of a retrograde pathway which differentially selects TGN38 and mannose-6-phosphate receptor from Shiga toxin.
Use of an Orthotopic Xenograft Model for Assessing the Effect of Epidermal Growth Factor Receptor Amplification on Glioblastoma Radiation Response (2006)

Our results indicate that EGFR amplification, as a biomarker, is not singularly predictive of glioblastoma response to radiation therapy, nor does the inhibition of EGFR enhance the intrinsic radiation responsiveness of glioblastoma tumors. However, efficacious EGFR inhibitor and radiation monotherapy regimens can be used in combination to achieve additive antitumor effect against a subset of glioblastoma.
The ABCG2 transporter is an efficient Hoechst 33342 efflux pump and is preferentially expressed by immature human hematopoietic progenitors (2002)

A promising and increasingly exploited property of hematopoietic stem cells is their ability to efflux the fluorescent dye Hoechst 33342. The Hoechst-negative cells are isolated by fluorescence-activated cell sorting as a so-called side "population" (SP) of bone marrow. This SP from bone marrow, as well as other tissues, is reported to contain immature stem cells with considerable plasticity. Some cell lines also efflux Hoechst and generate SP profiles. Reverse transcription-polymerase chain reaction (RT-PCR) and efflux inhibition studies with the lung carcinoma cell line, A549, implicated the ABCG2 transporter as a Hoechst efflux pump. Furthermore, it is shown that transient expression of ABCG2 generates a robust SP phenotype in human embryonic kidney (HEK293) cells. The results allow the conclusion that ABCG2 is a potent Hoechst efflux pump. Semiquantitative RT-PCR was used to characterize the developmental pattern of expression of ABCG2 in hematopoiesis. It is expressed at relatively high levels in putative hematopoietic stem cells (isolated as SP, 34+/38- or 34+/KDR+ populations) and drops sharply in committed progenitors (34+/38+, 34+/33+, or 34+/10+). Expression remains low in most maturing populations, but rises again in natural killer cells and erythroblasts. Comparison of messenger RNA (mRNA) levels for the 3 major multidrug-resistant efflux pumps, MDR1, MRP1, and ABCG2, in bone marrow SP cells reveals that ABCG2 is the predominant form in these cells. These data suggest that ABCG2 contributes significantly to the generation of the SP phenotype in hematopoietic stem cells. Furthermore, the sharp down-regulation of ABCG2 at the stage of lineage commitment suggests that this gene may play an important role in the unique physiology of the pluripotent stem cell.
Dose-Dependent Effects of Testosterone on Sexual Function, Mood, and Visuospatial Cognition in Older Men (2005)

Different aspects of male behavior respond differently to testosterone. When considered together with previous data from young men, these data indicate that testosterone dose-response relationships for sexual function and visuospatial cognition differ in older and young men.
Monolithic Bioreactor Immobilizing Trypsin for High-Throughput Analysis (2005)

A miniaturized trypsin reactor was prepared by coating a trypsin-containing gel on a porous silica monolith. The trypsin-encapsulated gel was prepared by the sol-gel method. The sol-gel reaction was optimized so that the sol solution containing trypsin forms a thin film on the sol-gel monolith. The trypsin was encapsulated into the gel matrix without losing its activity. The silica monolith was fabricated to fit into a 96-well microtiter plate well and could then be easily removed. The trypsin-immobilized monolith was reacted in the 96-well microtiter plate. After the reaction, the monolith was removed, and the enzymatic activity was measured. The large surface area of the monolith enabled the immobilized trypsin to achieve a high catalytic turnover rate. Furthermore, the kinetic parameter of the immobilized trypsin indicates the absence of diffusional limitations. The durability and repeatability of the fabricated trypsin-coated monolith was tested and found to be satisfactory. The encapsulated trypsin exhibits an increased stability even after continuous use compared with that in free solution. Furthermore, this on-plate bioreactor was applicable to the digestion of protein with multiple cleavage sites.
Cross-species receptor binding characteristics of human and mouse leukemia inhibitory factor suggest a complex binding interaction. (1994)

Leukemia inhibitory factor (LIF) is a pleiotropic cytokine whose activities appear to be mediated through a single heterodimeric receptor complex. Human LIF (hLIF) can bind to and activate mouse LIF (mLIF) receptors but mLIF is unable to bind to hLIF receptors. Cross-species competition of mLIF and hLIF for binding to the mLIF receptor was found to be dependent on which ligand was used as the radioactive tracer (Layton, M. J., Cross, B. A., Metcalf, D., Ward, L. D., Simpson, R. J., and Nicola, N. A. (1992) Proc. Natl. Acad. Sci. U. S. A. 89, 8616-8620), and this phenomenon was investigated in the present study. We found that hLIF bound to the low affinity mLIF receptor with a 100-500-fold higher primary affinity and lower kinetic dissociation rate than mLIF, but both ligands displayed a single rate of ligand dissociation. In contrast, the binding of hLIF to low and high affinity hLIF receptors revealed two classes of binding site. The observed tracer-dependent phenomena suggested that both mLIF and hLIF interfere with the binding of each other to the mLIF receptor. A model is presented in which hLIF binds to two sites on mLIF and hLIF receptors, one of which interferes with the common site for mLIF. This model may reconcile some of the observed complexities of LIF/LIF receptor interactions.
Alanine-scanning Mutagenesis of α-Helix D Segment of Interleukin-13 Reveals New Functionally Important Residues of the Cytokine (2002)

We documented that alpha-helices A, C, and D in human interleukin-13 (IL13) participate in interaction with its respective receptors. We hypothesized that alpha-helix D is the site II of the cytokine that binds IL13Ralpha1, a component of the normal tissue heterodimeric signaling IL13/4 receptor (IL13/4R), and that alpha-helix D independently binds a monomeric IL13Ralpha2 receptor, which is a non-signaling glioma-restricted receptor for IL13. Therefore, we alanine-scanned mutagenized helix D of IL13 to identify the residues involved in the respective receptors interaction. Recombinant muteins of IL13 were produced in Escherichia coli, and their structural integrity and identity were verified. The alanine mutants were tested in functional cellular assays, in which IL13 interaction with IL13Ralpha2 (glioma cells) or an ability to functionally stimulate IL13/4R (TF-1 cells) were examined, and also in binding assays. We found that residues 105, 106, and 109 of the d-helix of IL13 are responsible for interacting with the glioma-associated receptor. Moreover, glutamic acids at positions 92 and 110, and leucine at position 104 was found to be important for IL13/4R stimulation. Thus, alpha-helix D of IL13 is the primary site responsible for interaction with the IL13 binding proteins. We propose a model that illustrates the binding mode of IL13 with cancer-related IL13Ralpha2 and physiological IL13/4R.
Human homologue of mouse lymph node homing receptor: evolutionary conservation at tandem cell interaction domains. (1989)

A cDNA clone homologous to the mouse lymph node homing receptor core protein (mLHRc) was isolated from a cDNA library derived from stimulated human peripheral blood lymphocytes. Human RNA blot analysis shows a tissue and cell-line distribution of transcript expression generally parallel to that seen in the mouse, with expression confined to lymphoid tissues and some cell lines. Genomic DNA analysis suggests a low-copy gene under high-stringency conditions. The complete nucleotide sequence predicts a mature protein of 334 amino acids, identical in length to mLHRc. The protein shows striking conservation globally between human and mouse sequences. In particular, all three genre of protein interaction domains identified in the mouse--an animal lectin domain, an epidermal growth factor (EGF)-like domain, and two homologous repeat units preserving the motif of complement regulatory proteins (CRP)--are present in the human protein (hLHRc), and maintain the same tandem arrangement. The lectin and EGF-like regions are the most homologous, while the CRP domains are less conserved between species. The two CRP units in hLHRc are distinct from those in mLHRc in that they are homologous to one another rather than identical, suggesting strong pressure for maintenance of two repeats in this molecule. hLHRc is distinct from other kinds of lymphocyte adhesion molecules represented by VLA-4 (integrin) or CD44/gp90Hermes and, together with mLHRc and two other recently described molecules having a similar domain motif, defines a novel class of adhesion molecules exhibiting distinct evolutionary features. We propose that hLHRc likely represents the protein core of the human homologue of mLHRc functionally as well as structurally.
The Chlamydomonas reinhardtii cia3 Mutant Lacking a Thylakoid Lumen-Localized Carbonic Anhydrase Is Limited by CO2 Supply to Rubisco and Not Photosystem II Function in Vivo (2003)

The Chlamydomonas reinhardtii cia3 mutant has a phenotype indicating that it requires high-CO(2) levels for effective photosynthesis and growth. It was initially proposed that this mutant was defective in a carbonic anhydrase (CA) that was a key component of the photosynthetic CO(2)-concentrating mechanism (CCM). However, more recent identification of the genetic lesion as a defect in a lumenal CA associated with photosystem II (PSII) has raised questions about the role of this CA in either the CCM or PSII function. To resolve the role of this lumenal CA, we re-examined the physiology of the cia3 mutant. We confirmed and extended previous gas exchange analyses by using membrane-inlet mass spectrometry to monitor(16)O(2),(18)O(2), and CO(2) fluxes in vivo. The results demonstrate that PSII electron transport is not limited in the cia3 mutant at low inorganic carbon (Ci). We also measured metabolite pools sizes and showed that the RuBP pool does not fall to abnormally low levels at low Ci as might be expected by a photosynthetic electron transport or ATP generation limitation. Overall, the results demonstrate that under low Ci conditions, the mutant lacks the ability to supply Rubisco with adequate CO(2) for effective CO(2) fixation and is not limited directly by any aspect of PSII function. We conclude that the thylakoid CA is primarily required for the proper functioning of the CCM at low Ci by providing an ample supply of CO(2) for Rubisco.
Sequence analysis of the Hendra virus nucleoprotein gene: comparison with other members of the subfamily Paramyxovirinae. (1998)

The nucleoprotein (N) gene of Hendra virus (HeV), an unclassified member of subfamily Paramyxovirinae in the family Paramyxoviridae previously known as equine morbillivirus, was cloned and sequenced. The majority of the deduced amino acid sequence was further confirmed by direct sequencing of peptide fragments of the N protein derived from purified virions. The 3' untranslated sequence of the HeV N gene mRNA was 568 nt and was much longer than that observed in other Paramyxovirinae. The N protein was 532 amino acids in length with a molecular mass of 58.5 kDa. Although the HeV N protein had a slightly higher amino acid sequence identity to those of the genus Morbillivirus than to those of other Paramyxovirinae genera, the level of identity was much lower than that observed within the morbilliviruses. Our results indicated that HeV could not confidently be classified as a member of the genus Morbillivirus, Paramyxovirus or Rubulavirus and suggest that the virus be classified in a new genus within the Paramyxovirinae.
An Improved Synthesis and Resolution of 3-Amino-1,3-dihydro-5-phenyl-2H- 1,4-benzodiazepin-2-ones (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn Improved Synthesis and Resolution of 3-Amino-1,3-dihydro-5-phenyl-2H- 1,4-benzodiazepin-2-onesRonald G. Sherrill and Elizabeth E. SuggCite this: J. Org. Chem. 1995, 60, 3, 730–734Publication Date (Print):February 1, 1995Publication History Published online1 May 2002Published inissue 1 February 1995https://pubs.acs.org/doi/10.1021/jo00108a044https://doi.org/10.1021/jo00108a044research-articleACS PublicationsRequest reuse permissionsArticle Views857Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Potential antidepressants: 2-(Methoxy- and hydroxyphenylthio)benzylamines as selective inhibitors of 5-hydroxytryptamine re-uptake in the brain (1989)

2-, 3- and 4Methoxythiophenol, and 2,4-, 2,5- and 3,4-dimethoxythiophenol were transformed in two steps to the corresponding 2-(methoxyphenylthio)benzoyl chlorides XIII which were reacted with ammonia, methylamine, diethylamine, dipropylamine, and di(2-propyl)amine to give the amides XIV-XIX . These were reduced mostly with lithium aluminium hydride to the amines II-VII . These methoxylated amines were demethylated mostly either by heating with pyridine hydrochloride or by treatment with boron tribromide. Some of the 2-(methoxy- and hydroxy-phenylthio)benzylamines prepared, especially compounds II, III, XXI , and XXII , indicated properties of potential antidepressants being highly active and selective inhibitors of 5-hydroxytryptamine re-uptake in the brain structures and having the typical antireserpine activity. The most interesting compound of the series is XXIb (hydrogen maleate VUFB-15 468) which is undergoing preclinical studies. On the basis of its structure, some further compounds ( XXVII–XXIX, XXXIX-XLI ) were prepared by various methods.
Effects of Robot-Assisted Therapy on Upper Limb Recovery After Stroke: A Systematic Review (2007)

As a result of marked heterogeneity in studies between distal and proximal arm robotics, no overall significant effect in favor of robot-assisted therapy was found in the present meta-analysis. However, subsequent sensitivity analysis showed a significant improvement in upper limb motor function after stroke for upper arm robotics. No significant improvement was found in ADL function. However, the administered ADL scales in the reviewed studies fail to adequately reflect recovery of the paretic upper limb, whereas valid instruments that measure outcome of dexterity of the paretic arm and hand are mostly absent in selected studies. Future research into the effects of robot-assisted therapy should therefore distinguish between upper and lower robotics arm training and concentrate on kinematical analysis to differentiate between genuine upper limb motor recovery and functional recovery due to compensation strategies by proximal control of the trunk and upper limb.
In vitro pharmacologic restoration of CFTR-mediated chloride transport with sodium 4-phenylbutyrate in cystic fibrosis epithelial cells containing delta F508-CFTR. (1997)

The most common cystic fibrosis transmembrane conductance regulator mutation, delta F508-CFTR, is a partially functional chloride channel that is retained in the endoplasmic reticulum and degraded. We hypothesize that a known transcriptional regulator, sodium 4-phenylbutyrate (4PBA), will enable a greater fraction of delta F508-CFTR to escape degradation and appear at the cell surface. Primary cultures of nasal polyp epithelia from CF patients (delta F508 homozygous or heterozygous), or the CF bronchial epithelial cell line IB3-1 (delta F508/W1282X) were exposed to 4PBA for up to 7 d in culture. 4PBA treatment at concentrations of 0.1 and 2 mM resulted in the restoration of forskolin-activated chloride secretion. Protein kinase A-activated, linear, 10 pS chloride channels appeared at the plasma membrane of IB3-1 cells at the tested concentration of 2.5 mM. Treatment of IB3-1 cells with 0.1-1 mM 4PBA and primary nasal epithelia with 5 mM 4PBA also resulted in the appearance of higher molecular mass forms of CFTR consistent with addition and modification of oligosaccharides in the Golgi apparatus, as detected by immunoblotting of whole cell lysates with anti-CFTR antisera. Immunocytochemistry in CF epithelial cells treated with 4PBA was consistent with increasing amounts of delta F508-CFTR. These data indicate that 4PBA is a promising pharmacologic agent for inducing correction of the CF phenotype in CF patients carrying the delta F508 mutation.
Nucleotide sequence analysis of human tpr cDNA clones. (1992)

In this study we have characterized cDNA clones corresponding to a gene, called tpr, that has been implicated in the activation of the met and raf proto-oncogenes. Sequencing of tpr clones isolated from an HT1080 human fibrosarcoma cell line cDNA library identified an open reading frame (ORF) of 726 amino acids. In addition we have established that alternative splicing can result in the deletion of a 30 bp sequence that spans the translation termination site of this ORF. This modification generates mRNAs encoding a tpr protein that has an extended C-terminal domain. The 726 amino acid tpr protein is predicted to have extensive regions of alpha-helix and has three stretches of a heptad repeat motif that is characteristic of proteins adopting a coiled-coil conformation. The tpr protein exhibits weak homology (28-39%) to the alpha-helical domains of several proteins including tropomyosin, spectrin, laminin B1, the Drosophila glued protein and the tail region of myosin heavy chain.
A Modified Thromboelastographic Method for Monitoring c7E3 Fab in Heparinized Patients (1997)

The monoclonal antibody, c7E3 Fab, binds to the platelet surface fibrinogen receptor (GPIIb/IIIa), inhibiting platelet aggregation and clot retraction.We performed an in vitro study to assess the ability of a modification of the thromboelastograph (MTEG) to detect inhibition of clot strength by c7E3 Fab and its reversal with platelet-rich plasma (PRP). In the modified assay (MTEG), thrombin was added to whole blood (WB) and platelet-poor plasma (PPP) and the resultant maximum amplitude (MA) was measured, MAWB and MAPPP, respectively. Anticoagulated blood samples from 17 patients scheduled for cardiac surgery were collected for a dose response (Part I; n = 5) and c7E3 Fab reversal (Part II; n = 12) study. Clot strength was reduced in a dose-dependent manner by c7E3 Fab. Ecteola cellulose effectively reversed the effect of heparin on the thrombin time and the addition of PRP significantly increased the MAWB (P < 0.0001) and MAWB-ppp (P < 0.0001). Subtracting the MAPPP from MAWB significantly magnified the response of MA to the addition of c7E3 Fab (P = 0.002) and its reversal with PRP (P = 0.005). This in vitro study indicates that the MTEG is a responsive assay demonstrating that inhibition by the antiplatelet c7E3 Fab is reversible with PRP. (Anesth Analg 1997;84:31-8)
A Study of the Reaction of Hydroxide Ion with B20H18-2 (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Study of the Reaction of Hydroxide Ion with B20H18-2M. Frederick Hawthorne, Richard L. Philling, and Philip M. GarrettCite this: J. Am. Chem. Soc. 1965, 87, 21, 4740–4746Publication Date (Print):November 1, 1965Publication History Published online1 May 2002Published inissue 1 November 1965https://pubs.acs.org/doi/10.1021/ja00949a013https://doi.org/10.1021/ja00949a013research-articleACS PublicationsRequest reuse permissionsArticle Views93Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts