gebhart/patrepeval huggingface dataset:
Transcriptional Profiling of Bone Regeneration (2002)

The healing of skeletal fractures is essentially a replay of bone development, involving the closely regulated, interdependent processes of chondrogenesis and osteogenesis. Using a rat femur model of bone healing to determine the degree of transcriptional complexity of these processes, suppressive subtractive hybridization (SSH) was performed between RNA isolated from intact bone to that of callus from post-fracture (PF) days 3, 5, 7, and 10 as a means of identifying up-regulated genes in the regenerative process. Analysis of 3,635 cDNA clones revealed 588 known genes (65.8%, 2392 clones) and 821 expressed sequence tags (ESTs) (31%, 1,127). The remaining 116 cDNAs (3.2%) yielded no homology and presumably represent novel genes. Microarrays were then constructed to confirm induction of expression and determine the temporal profile of all isolated cDNAs during fracture healing. These experiments confirmed that approximately 90 and approximately 80% of the subtracted known genes and ESTs are up-regulated (> or = 2.5-fold) during the repair process, respectively. Clustering analysis revealed subsets of genes, both known and unknown, that exhibited distinct expression patterns over 21 days (PF), indicating distinct roles in the healing process. Additionally, this transcriptional profiling of bone repair revealed a host of activated signaling molecules and even pathways (i.e. Wnt). In summary, the data demonstrate, for the fist time, that the healing process is exceedingly complex, involves thousands of activated genes, and indicates that groups of genes rather than individual molecules should be considered if the regeneration of bone is to be accelerated exogenously.
Field desorption of a potassium-gold film on tungsten (2004)

The formation and destruction of alloys and chemical compounds of gold with potassium occurring in their coadsorption on tungsten have been studied by continuous-mode field-desorption microscopy, field-emission microscopy, and time-of-flight mass analysis of the products of field-induced desorption. The effect of an electric field on these processes was investigated. Monatomic and cluster ions of potassium and its compounds with gold were found to appear in fields too weak for field desorption to set in. Chemical reactions give rise to autooscillations in the field desorption of potassium.
Regulation of glucose transporter expression in cardiac myocytes: p38 MAPK is a strong inducer of GLUT4 (2004)

Spontaneous dedifferentiation of adult rat cardiomyocytes in vitro is associated with downregulation of GLUT4, which can be reversed by treatment with IGF-1. The effect of IGF-1 is mediated by the p38 MAPK/MEF2 axis, which is a strong inducer of GLUT4 expression.
TCP with sender-side intelligence to handle dynamic, large, leaky pipes (2005)

Transmission control protocol Westwood (TCPW) has been shown to provide significant performance improvement over high-speed heterogeneous networks. The key idea of TCPW is to use eligible rate estimation (ERE) methods to intelligently set the congestion window (cwnd) and slow-start threshold (ssthresh) after a packet loss. ERE is defined as the efficient transmission rate eligible for a sender to achieve high utilization and be friendly to other TCP variants. This work presents TCP Westwood with agile probing (TCPW-A), a sender-side only enhancement of TCPW, that deals well with highly dynamic bandwidth, large propagation time/bandwidth, and random loss in the current and future heterogeneous Internet. TCPW-A achieves this goal by adding the following two mechanisms to TCPW. 1) When a connection initially begins or restarts after a timeout, instead of exponentially expanding cwnd to an arbitrary preset sthresh and then going into linear increase, TCPW-A uses agile probing, a mechanism that repeatedly resets ssthresh based on ERE and forces cwnd into an exponential climb each time. The result is fast convergence to a more appropriate ssthresh value. 2) In congestion avoidance, TCPW-A invokes agile probing upon detection of persistent extra bandwidth via a scheme we call persistent noncongestion detection (PNCD). While in congestion avoidance, agile probing is actually invoked under the following conditions: a) a large amount of bandwidth that suddenly becomes available due to change in network conditions; b) random loss during slow-start that causes the connection to prematurely exit the slow-start phase. Experimental results, both in ns-2 simulation and lab measurements using actual protocols implementation, show that TCPW-A can significantly improve link utilization over a wide range of bandwidth, propagation delay, and dynamic network loading.
The role of the cyclic peptide backbone in the anti‐HIV activity of the cyclotide kalata B1 (2004)

The plant cyclotides, the largest known family of circular proteins, have tightly folded structures and a range of biological activities that lend themselves to potential pharmaceutical and agricultural applications. Based on sequence homology, they are classified into the bracelet and Möbius subfamilies. The bracelet subfamily has previously been shown to display anti-HIV activity. We show here that a member of the Möbius subfamily, kalata B1, also exhibits anti-HIV activity despite extensive sequence differences between the subfamilies. In addition, acyclic permutants of kalata B1 displayed no anti-HIV activity, suggesting that this activity is critically dependent on an intact circular backbone.
Small Molecule Modulators of Keap1‐Nrf2‐ARE Pathway as Potential Preventive and Therapeutic Agents (2012)

Kelch-like ECH-associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor 2 (Nrf2)-antioxidant response elements (ARE) pathway represents one of the most important cellular defense mechanisms against oxidative stress and xenobiotic damage. Activation of Nrf2 signaling induces the transcriptional regulation of ARE-dependent expression of various detoxifying and antioxidant defense enzymes and proteins. Keap1-Nrf2-ARE signaling has become an attractive target for the prevention and treatment of oxidative stress-related diseases and conditions including cancer, neurodegenerative, cardiovascular, metabolic, and inflammatory diseases. Over the last few decades, numerous Nrf2 inducers have been developed and some of them are currently undergoing clinical trials. Recently, overactivation of Nrf2 has been implicated in cancer progression as well as in drug resistance to cancer chemotherapy. Thus, Nrf2 inhibitors could potentially be used to improve the effectiveness of cancer therapy. Herein, we review the signaling mechanism of Keap1-Nrf2-ARE pathway, its disease relevance, and currently known classes of small molecule modulators. We also discuss several aspects of Keap1-Nrf2 interaction, Nrf2-based peptide inhibitor design, and the screening assays currently used for the discovery of direct inhibitors of Keap1-Nrf2 interaction.
Treatment of Chronic Hepatitis D with Interferon Alfa-2a (1994)

In about half the patients with chronic hepatitis D treated with high doses of interferon alfa-2a (9 million units three times a week for 48 weeks), the serum alanine aminotransferase level becomes normal, HDV RNA becomes undetectable in serum, and there is histologic improvement. However, a relapse is common after treatment has been stopped.
Influence of Dose on Regeneration of Murine Hematopoietic Stem Cells after Total Body Irradiation and 5-Fluorouracil (1992)

The regeneration of murine bone marrow stem cells after treatment with 5-fluorouracil (5-FU) and total body irradiation (TBI) was investigated by means of the spleen colony assay. 5-FU was given intraperitoneally in doses ranging from 75 to 225 mg/kg body weight. TBI was administrated as a single fraction in the dose range 0.75-3.50 Gy. The frequency of stem cells declined rapidly and reached a minimum (nadir) on day 1-2 after either of the 2 treatments. Their number returned to near-pretreatment values by day 7-10. Increasing the dose of either 5-FU or TBI resulted in a lower nadir in stem cell survival and a higher regeneration rate of the stem cells. The maximal regeneration rate corresponded to a doubling time of 19 h. The time to complete regeneration was constant and neither influenced by the treatment modality nor by the dose. Both this work and previous studies on cyclophosphamide and combined 5-FU and TBI may indicate that the regeneration rate of bone marrow stem cells after a cytotoxic assault is influenced primarily by the stem cell surviving the treatment rather than the treatment modality.
Two-way chemical signaling in Agrobacterium-plant interactions (1992)

The discovery in 1977 that Agrobacterium species can transfer a discrete segment of oncogenic DNA (T-DNA) to the genome of host plant cells has stimulated an intense interest in the molecular biology underlying these plant-microbe associations. This attention in turn has resulted in a series of insights about the biology of these organisms that continue to accumulate at an ever-increasing rate. This excitement was due in part to the notion that this unprecedented interkingdom DNA transfer could be exploited to create transgenic plants containing foreign genes of scientific or commercial importance. In the course of these discoveries, Agrobacterium became one of the best available models for studying the molecular interactions between bacteria and higher organisms. One extensively studied aspect of this association concerns the exchange of chemical signals between Agrobacterium spp. and host plants. Agrobacterium spp. can recognize no fewer than five classes of low-molecular-weight compounds released from plants, and other classes probably await discovery. The most widely studied of these are phenolic compounds, which stimulate the transcription of the genes needed for infection. Other compounds include specific monosaccharides and acidic environments which potentiate vir gene induction, acidic polysaccharides which induce one or more chromosomal genes, and a family of compounds called opines which are released from tumorous plant cells to the bacteria as nutrient sources. Agrobacterium spp. in return release a variety of chemical compounds to plants. The best understood is the transferred DNA itself, which contains genes that in various ways upset the balance of phytohormones, ultimately causing neoplastic cell proliferation. In addition to transferring DNA, some Agrobacterium strains directly secrete phytohormones. Finally, at least some strains release a pectinase, which degrades a component of plant cell walls.
Synergistic antitumor effect of interferon and anti-idiotype monoclonal antibody in murine lymphoma. (1986)

Both IFN-alpha and anti-idiotype monoclonal antibody therapy have significant antitumor activity in vivo in a murine B cell lymphoma model. Combination therapy with syngeneic anti-idiotype antibody of the IgG2a or IgG2b isotype (a single i.p. injection of 100 micrograms) and recombinant human hybrid interferon-alpha A/D (10(4) to 10(6) U three times weekly for 3 wk) synergistically increased median survival time in mice challenged with a lethal dose of tumor cells compared with the sum of the median survival times of the two individual treatments. IFN-alpha has direct antiproliferative activity against 38C13 in vitro and enhances in vitro macrophage anti-idiotype antibody-specific cytolysis for IgG2a, IgG2b, and IgG1 isotypes.
Contact angle hysteresis: a different view and a trivial recipe for low hysteresis hydrophobic surfaces (2010)

Contact angle hysteresis is addressed from two perspectives. The first is an analysis of the events that occur during motion of droplets on superhydrophobic surfaces. Hysteresis is discussed in terms of receding contact line pinning and the tensile failure of capillary bridges. The sign of the curvature of the solid surface is implicated as playing a key role. The second is the report of a new method to prepare smooth low hysteresis surfaces. The thermal treatment of oxygen plasma-cleaned silicon wafers with trimethylsilyl-terminated linear poly(dimethylsiloxane) (PDMS - commercial silicone oils) in disposable glass vessels is described. This treatment renders silicon/silica surfaces that contain covalently attached PDMS chains. The grafted layers of nanometre scale thickness are liquid-like (rotationally dynamic at room temperature), decrease activation barriers for contact line motion and minimize water contact angle hysteresis. This simple method requires neither sophisticated techniques nor substantial laboratory skills to perform.
Human immunodeficiency virus type-1 reverse transcription can be inhibited in vitro by oligonucleotides that target both natural and synthetic tRNA primers (2000)

Reverse transcription of human immunodeficiency virus type-1 is primed by cellular tRNA(Lys3), which is selectively packaged into viral particles where it is bound at its 3' terminus to a complementary sequence of viral RNA termed the primer binding site (PBS). Since cellular tRNA(Lys3) is highly conserved, it might conceivably serve as a good target for novel antagonists to block reverse transcriptase (RT) activity. In this study, we have examined a number of antisense oligodeoxyribonucleotides (ODNs) that are complementary to different parts of the tRNA primer and, therefore, may interfere with the initiation of RT-mediated DNA synthesis. We found that the stability of complexes between synthetic tRNA(Lys3 )and ODNs was significantly increased when binding occurred via sequences involved in tertiary interactions of the tRNA. In particular, ODNs with complementarity to both the variable and TPsiC stem-loop of tRNA(Lys3 )bound with high affinity to both free tRNA(Lys3 )as well as to the binary tRNA(Lys3)/RNA complex. As a result, the initiation of DNA synthesis was severely compromised under these conditions. Moreover, RT-associated RNase H activity recognized the tRNA within this ternary tRNA(Lys3)/RNA/ODN complex as an RNA template and initiated its degradation. Both this RNase H degradation of tRNA(Lys3 )as well as the altered structure of the tRNA/RNA complex, due to the binding of the ODN, contributed to the inhibition of synthesis of viral DNA. The initiation of RT activity was almost completely blocked when using ODNs that interfered with intermolecular tRNA/RNA interactions that involved both the PBS and sequences outside the PBS. Similar findings were obtained with natural preparation of tRNA(Lys3).
Structural symmetry of the extracellular domain of the Cytokine/Growth hormone/Prolactin receptor family and Interferon receptors revealed by Hydrophobic Cluster Analysis (1991)

Sequence comparison based on Hydrophobic Cluster Analysis procedures shows that the extracellular ≈ 200 amino acids domains of cytokines receptors belonging to the Cytokine/Growth hormone/Prolactin receptor family and to the Interferon one are organized in two homologous subdomains. Further, comparison of the subdomains of 32 independent sequences and of a lot of already recognized homologous domains with data bases could lead to the hypothesis that these ≈ 100 amino acids subdomains could possess the overall fold of the constant immunoglobulin domains and so could belong to the immunoglobulin superfamily.
Identification and characterization of RP1 Tra1 cistrons involved in pilus function and plasmid mobilization (1993)

Transfer-defective mutants of the Tra1 region of RP1 were isolated. Complementation studies involving stable heterozygotes combined with the mapping of Tn5 insertion mutations revealed two pilus cistrons, pilA and pilB, at positions 46.9 to 48.2 kb and 46.0 to 46.4 kb, respectively. All pilB mutants were Dps- (i.e., resistant to donor-specific phages PR4 and PRR1), whereas pilA mutants were Dps- (promoter-proximal mutations), Dps+/- (sensitive only to PR4 [more centrally located mutations]), or Dps+ (sensitive to both phages [promoter-distal mutations]). The correlation between the site mutated and the Dps phenotype, together with the finding that certain Dps+ pilA mutants continued to mobilize nonconjugative plasmids, suggested that pilA is bifunctional, contributing both to pilus function (at the promoter-proximal end) and to RP1 mobilization. It was also shown that the 43.5- to 49.5-kb region that includes pilA and pilB encodes all of the Tra1 pilus functions required for propagation of donor-specific phages and hence, probably, for pili that are active in conjugation. Finally, three cistrons that specifically affect RP1 mobilization were identified. Two of these, mobA and mobB, occur immediately anticlockwise to oriT and probably correspond to the traJ and traI genes characterized by other workers. The third cistron, mobC, occurs clockwise to oriT and may be a new mobilization gene, since its function can be substituted by IncP beta plasmids, a feature different from that of the traK mobilization gene which occurs in the same region but is RP1 specific. None of the mob cistrons was required for mobilization of nonconjugative plasmids, except for mobB, which was required by pVS99.
A Comparison of Alternative Serum Biomarkers With Creatinine for Predicting Allograft Function After Kidney Transplantation (2010)

Scyc outperforms Scr as a predictor of early graft function after deceased-donor kidney transplant.
The Menkes copper transporter is required for the activation of tyrosinase (2000)

Menkes disease is an X-linked recessive copper deficiency disorder caused by mutations in the ATP7A (MNK) gene. The MNK gene encodes a copper-transporting P-type ATPase, MNK, which is localized predominantly in the trans-Golgi network (TGN). The MNK protein relocates to the plasma membrane in cells exposed to elevated copper where it functions in copper efflux. A role for MNK at the TGN in mammalian cells has not been demonstrated. In this study, we investigated whether the MNK protein is required for the activity of tyrosinase, a copper-dependent enzyme involved in melanogenesis that is synthesized within the secretory pathway. We demonstrate that recombinant tyrosinase expressed in immortalized Menkes fibroblast cell lines was inactive, whereas in normal fibroblasts known to express MNK protein there was substantial tyrosinase activity. Co-expression of the Menkes protein and tyrosinase from plasmid constructs in Menkes fibroblasts led to the activation of tyrosinase and melanogenesis. This MNK-dependent activation of tyrosinase was impaired by the chelation of copper in the medium of cells and after mutation of the invariant phosphorylation site at aspartic acid residue 1044 of MNK. Collectively, these findings suggest that the MNK protein transports copper into the secretory pathway of mammalian cells to activate copper-dependent enzymes and reveal a second copper transport role for MNK in mammalian cells. These findings describe a single cell-based system that allows both the copper transport and trafficking functions of MNK to be studied. This study also contributes to our understanding of the molecular basis of pigmentation in mammalian cells.
Single Molecule Epigenetic Analysis in a Nanofluidic Channel (2010)

Epigenetic states are governed by DNA methylation and a host of modifications to histones bound with DNA. These states are essential for proper developmentally regulated gene expression and are perturbed in many diseases. There is great interest in identifying epigenetic mark placement genome wide and understanding how these marks vary among cell types, with changes in environment or according to health and disease status. Current epigenomic analyses employ bisulfite sequencing and chromatin immunoprecipitation, but query only one type of epigenetic mark at a time, DNA methylation, or histone modifications and often require substantial input material. To overcome these limitations, we established a method using nanofluidics and multicolor fluorescence microscopy to detect DNA and histones in individual chromatin fragments at about 10 Mbp/min. We demonstrated its utility for epigenetic analysis by identifying DNA methylation on individual molecules. This technique will provide the unprecedented opportunity for genome wide, simultaneous analysis of multiple epigenetic states on single molecules.
Photochemistry of aliphatic imides. Synthesis of azetidine-2,4-diones via photochemical isomerization of succinimides and N-formyl-N-methyl .alpha.,.beta.-unsaturated amides (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemistry of aliphatic imides. Synthesis of azetidine-2,4-diones via photochemical isomerization of succinimides and N-formyl-N-methyl .alpha.,.beta.-unsaturated amidesKazuhiro Maruyama, Takeshi Ishitoku, and Yasuo KuboCite this: J. Org. Chem. 1981, 46, 1, 27–34Publication Date (Print):January 1, 1981Publication History Published online1 May 2002Published inissue 1 January 1981https://pubs.acs.org/doi/10.1021/jo00314a006https://doi.org/10.1021/jo00314a006research-articleACS PublicationsRequest reuse permissionsArticle Views1543Altmetric-Citations38LEARN 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
Improved low-density parity-check codes using irregular graphs (2001)

We construct new families of error-correcting codes based on Gallager's (1973) low-density parity-check codes. We improve on Gallager's results by introducing irregular parity-check matrices and a new rigorous analysis of hard-decision decoding of these codes. We also provide efficient methods for finding good irregular structures for such decoding algorithms. Our rigorous analysis based on martingales, our methodology for constructing good irregular codes, and the demonstration that irregular structure improves performance constitute key points of our contribution. We also consider irregular codes under belief propagation. We report the results of experiments testing the efficacy of irregular codes on both binary-symmetric and Gaussian channels. For example, using belief propagation, for rate 1/4 codes on 16000 bits over a binary-symmetric channel, previous low-density parity-check codes can correct up to approximately 16% errors, while our codes correct over 17%. In some cases our results come very close to reported results for turbo codes, suggesting that variations of irregular low density parity-check codes may be able to match or beat turbo code performance.
Quantitative Evaluation of the Relative Cell Permeability of Peptoids and Peptides (2007)

We evaluated quantitatively the relative cell permeability of peptoids and peptides using a cell-based reporter gene-based assay. Generally, peptoids were much more cell permeable than the corresponding peptides, though the difference decreased with increasing length. These results suggest that peptoids may be useful reagents for manipulating the activities of intracellular proteins.