gebhart/patrepeval huggingface dataset:
Identification by mass spectrometry of the phosphorylated residue responsible for activation of the catalytic domain of myosin I heavy chain kinase, a member of the PAK/STE20 family (1997)

Myosin I heavy chain kinase from Acanthamoeba castellanii is activated in vitro by autophosphorylation (8-10 mol of P per mol). The catalytically active C-terminal domain produced by trypsin cleavage of the phosphorylated kinase contains 2-3 mol of P per mol. However, the catalytic domain expressed in a baculovirus-insect cell system is fully active as isolated without autophosphorylation in vitro. We now show that the expressed catalytic domain is inactivated by incubation with acid phosphatase and regains activity upon autophosphorylation. The state of phosphorylation of all of the hydroxyamino acids in the catalytic domain were determined by mass spectrometry of unfractionated protease digests. Ser-627 was phosphorylated in the active, expressed catalytic domain, lost its phosphate when the protein was incubated with phosphatase, and was rephosphorylated when the dephosphorylated protein was incubated with ATP. No other residue was significantly phosphorylated in any of the three samples. Thus, phosphorylation of Ser-627, which is in the same position as the Ser and Thr residues that are phosphorylated in many other kinases, is necessary and sufficient for full activity of the catalytic domain. Ser-627 is also phosphorylated when full-length, native kinase is activated by autophosphorylation.
Conversion from Farnesyl Diphosphate Synthase to Geranylgeranyl Diphosphate Synthase by Random Chemical Mutagenesis (1996)

Prenyltransferases catalyze the consecutive condensation of isopentenyl diphosphate (IPP) with allylic diphosphates to produce prenyl diphosphates whose chain lengths are absolutely determined by each enzyme. In order to investigate the mechanisms of the consecutive reaction and of the determination of ultimate chain length, a random mutational approach was planned. The farnesyl diphosphate (FPP) synthase gene of Bacillus stearothermophilus was subjected to random mutagenesis by NaNO2 treatment to construct libraries of mutated FPP synthase genes on a high-copy plasmid. From the libraries, the mutants that showed the activity of geranylgeranyl diphosphate (GGPP) synthase were selected by the red-white screening method (Ohnuma, S.-i., Suzuki, M., and Nishino, T. (1994) J. Biol. Chem. 268, 14792-14797), which utilized carotenoid synthetic genes, phytoene synthase, and phytoene desaturase, to visualize the formation of GGPP in vivo. Eleven red positive clones were identified from about 24,300 mutants, and four (mutant 1, 2, 3, and 4) of them were analyzed for the enzyme activities. Results of in vitro assays demonstrated that all these mutants produced (all-E)-GGPP although the amounts were different. Each mutant was found to contain a few amino acid substitutions: mutant 1, Y81H and L275S; mutant 2, L34V and R59Q; mutant 3, V157A and H182Y; mutant 4, Y81H, P239R, and A265T. Site-directed mutagenesis showed that Y81H, L34V, or V157A was essential for the expression of the activity of GGPP synthase. Especially, the replacement of tyrosine 81 by histidine is the most effective because the production ratios of GGPP to FPP in mutant 1 and 4 are the largest. Based on prediction of the secondary structure, it is revealed that the tyrosine 81 situates on a point 11 approximately 12 A apart from the first DDXXD motif, whose distance is similar to the length of hydrocarbon moiety of FPP. These data might suggest that the aromatic ring of tyrosine 81 blocks the chain elongation longer than FPP. Comparisons of kinetic parameters of the mutated and wild type enzymes revealed several phenomena that may relate with the change of the ultimate chain length. They are a decrease of the total reaction rate, increase of Kmfor dimethylallyl diphosphate, decrease of Vmax for dimethylallyl diphosphate, and allylic substrate dependence of Km for IPP.
Losartan inhibits collagen I synthesis and improves the distribution and efficacy of nanotherapeutics in tumors (2011)

The dense collagen network in tumors significantly reduces the penetration and efficacy of nanotherapeutics. We tested whether losartan--a clinically approved angiotensin II receptor antagonist with noted antifibrotic activity--can enhance the penetration and efficacy of nanomedicine. We found that losartan inhibited collagen I production by carcinoma-associated fibroblasts isolated from breast cancer biopsies. Additionally, it led to a dose-dependent reduction in stromal collagen in desmoplastic models of human breast, pancreatic, and skin tumors in mice. Furthermore, losartan improved the distribution and therapeutic efficacy of intratumorally injected oncolytic herpes simplex viruses. Finally, it also enhanced the efficacy of i.v. injected pegylated liposomal doxorubicin (Doxil). Thus, losartan has the potential to enhance the efficacy of nanotherapeutics in patients with desmoplastic tumors.
Growth Hormone Binding Affinity for Its Receptor Surpasses the Requirements for Cellular Activity (1998)

The human growth hormone (hGH)-receptor interaction was used to study the relationship between hormone-receptor affinity and bioactivity. hGH has two nonequivalent sites, called site 1 and site 2, that bind two molecules of receptor in a sequential fashion. We produced both site 1 and site 2 high-affinity hGH variants either by combining alanine mutants previously found to improve affinity at site 1 or by random mutagenesis of residues in site 2 followed by phage display and receptor binding selections. The two high-affinity variants, as well as one which combined them, were used in cell proliferation assays with FDC-P1 cells expressing the hGH receptor. Interestingly, none of these variants produced a change in the EC50 for cell proliferation or the levels of JAK2 tyrosine kinase phosphorylation. Next we studied the effect of a reduction in site 1 affinity on cell proliferation. A systematic series of hGH mutants were produced in which affinity for site 1 was reduced from 5- to 500-fold. Surprisingly, the EC50 for cell proliferation was unaffected until affinity was reduced about 30-fold from wild-type hGH. Thus, native hGH-receptor affinity is much higher than it needs to be for maximal JAK2 phosphorylation or cell proliferation. These studies begin to define basic functional tolerances for receptor activation that need to be considered in the design of hGH mimics.
Reviews of Books (1991)

Reviews of Books Nascent Proletarians: Class Formation in Post-Revolutionary France By Michael P. HanaganOxford: Basil Blackwell. 1989. x + 243 pp. £ 29.50. ISBN 1-557686-041-6. PETER BURKE PETER BURKE University of Nottingham Search for other works by this author on: Oxford Academic Google Scholar French History, Volume 5, Issue 3, September 1991, Pages 385–386, https://doi.org/10.1093/fh/5.3.385 Published: 01 September 1991
Poly(l-lactide) (PLLA)/Multiwalled Carbon Nanotube (MWCNT) Composite:  Characterization and Biocompatibility Evaluation (2006)

Much effort has been directed at the fabrication of carbon nanotubes (CNTs)/polymer composites and the characterization of their physical properties. Among them, composites comprising CNTs and the biocompatible polymers are of special interest due to their potential for specific biomedical applications. we report the preparation of the MWCNT/poly(L-lactide) composite and the corresponding spectroscopic (Raman) and the microscopic (SEM, TEM) characterization. The electronic transport, thermal properties, and biocompatibility of this composite have also been investigated. The Raman spectroscopic analysis suggests the interaction between PLLA and MWCNT occurs mainly through the hydrophobic C-CH3 functional groups. The DC conductivity of the composite increases as the MWCNT loading is increased. Such behavior can be described by a percolation mechanism in which a percolation threshold at about 14 wt % MWCNT loading is observed with the maximum end conductivity of 0.1 S x cm(-1). The DSC study of the PLLA/MWCNT composite reveals that the MWCNTs in the composite have the effect of inducing crystallization and plasticizing the polymer matrix. The results from the cell culture test suggest that the presence of MWCNT in the composite inhibits the growth of the fibroblast cells.
Degradation of atrazine by Pseudomonas: N-dealkylation and dehalogenation of atrazine and its metabolites (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDegradation of atrazine by Pseudomonas: N-dealkylation and dehalogenation of atrazine and its metabolitesRam M. Behki and Shahamat U. KhanCite this: J. Agric. Food Chem. 1986, 34, 4, 746–749Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://pubs.acs.org/doi/10.1021/jf00070a039https://doi.org/10.1021/jf00070a039research-articleACS PublicationsRequest reuse permissionsArticle Views763Altmetric-Citations169LEARN 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
Template Synthesis of Bismuth Telluride Nanowires (1999)

Thermoelectric materials have the ability to convert heat to electricity and are currently used in Peltier cooling devices. Here is reported the combination of electrodeposition with template synthesis to prepare thermoelectric bismuth telluride nanowires within the pores of an alumina template membrane. The individual nanowires can be isolated by removal of the template membrane (see Figure).
A Global Perspective on Spinal Cord Injury Epidemiology (2004)

Spinal cord injury (SCI) is a devastating condition often affecting young and healthy individuals around the world. This debilitating condition not only creates enormous physical and emotional cost to individuals but also is a significant financial burden to society at large. This review was undertaken to understand the global impact of SCI on society. We also attempted to summarize the worldwide demographics and preventative strategies for SCI in varying economic and climatic environments and to evaluate how cultural and economic differences affect the etiology of SCI. A PUBMED database search was performed in order to identify clinical epidemiological studies of SCI within the last decade. In addition, World Bank and World Health Organization websites were used to obtain demographics, economics, and health statistics of countries of interest. A total of 20 manuscripts were selected from 17 countries. We found that SCI varies in etiology, male-to-female ratios, age distributions, and complications in different countries. Nations with similar economies tend to have similar features and incidences in all the above categories. However, diverse methods of classifying SCI were found, making comparisons difficult. Based upon these findings, it is clear that the categorization and evaluation of SCI must be standardized. The authors suggest improved methods of reporting in the areas of etiology, neurological classification, and incidence of SCI so that, in the future, more useful global comprehensive studies and comparisons can be undertaken. Unified injury prevention programs should be implemented through methods involving the Internet and international organizations, targeting the different etiologies of SCI found in different countries.
Characterization of a phosphorylated pentasaccharide isolated from Hansenula holstii NRRL Y-2448 phosphomannan (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharacterization of a phosphorylated pentasaccharide isolated from Hansenula holstii NRRL Y-2448 phosphomannanR. K. Bretthauer, G. J. Kaczorowski, and M. J. WeiseCite this: Biochemistry 1973, 12, 7, 1251–1256Publication Date (Print):March 27, 1973Publication History Published online1 May 2002Published inissue 27 March 1973https://doi.org/10.1021/bi00731a002Request reuse permissionsArticle Views147Altmetric-Citations64LEARN 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 InReddit PDF (703 KB) Get e-Alertsclose Get e-Alerts
Involvement of FAN in TNF-induced apoptosis (2001)

TNF-alpha is a pleiotropic cytokine activating several signaling pathways initiated at distinct intracellular domains of the TNF receptors. Although the C-terminal region is believed to be responsible for apoptosis induction, the functions of more membrane-proximal domains, including the domain that couples to neutral sphingomyelinase activation, are not yet fully elucidated. The roles of this region and of the associated adapter protein FAN (factor associated with neutral SMase activation) in the cytotoxic response to TNF have been investigated. We have now shown that stable expression in human fibroblasts of a dominant negative form of FAN abrogates TNF-induced ceramide generation from sphingomyelin hydrolysis and reduces caspase processing, thus markedly inhibiting TNF-triggered apoptosis. However, the cytotoxic responses to daunorubicin and exogenous ceramide remain unaltered, as do the TNF-induced p42/p44 MAPK activation and CD54 expression. Fibroblasts from FAN-knockout mice also proved to be resistant to TNF toxicity. These findings highlight the previously unrecognized role of the adapter protein FAN in signaling cell death induction by TNF.
Chemotherapy in Patients with Penile Carcinoma (2009)

The prognosis of patients with advanced penile carcinoma is poor. There are only few studies, mostly with a low number of patients, which show a low response rate with severe toxicity. While adjuvant and palliative chemotherapy for penile cancer is universally characterized by low efficacy, neoadjuvant approaches for patients with fixed lymph node metastases have shown some response. Overall, recent experiences with new chemotherapeutic approaches (i.e. taxane-based combinations) have shown some encouraging results. Therefore, these combinations should be investigated in larger and multi-center studies.
Protection of chickens vaccinated with combinations of commercial live infectious bronchitis vaccines containing Massachusetts, Dutch and QX-like serotypes against challenge with virulent infectious bronchitis viruses 793B and IS/1494/06 Israel variant 2 (2016)

Infectious bronchitis virus (IBV) is a coronavirus which affects chickens of all ages. IBV mainly causes respiratory disease but can also result in reduced weight gain, reduced egg production, increased frequency of abnormal eggs and increased rates of mortality. Vaccination is the most important way to control the disease. Nevertheless, novel strains of infectious bronchitis (IB) continue to emerge in the field. In order to respond promptly, combinations of existing IB vaccines are frequently tested to see whether they can provide cross-protection. The efficacy of a combination of vaccines based on Massachusetts, Dutch and QX-like IB strains against emerging IB Israel variant 2 and IB 793B strains was assessed by means of four challenge studies. At least 80% of the birds vaccinated with IB H120 (Mass type) combined with IB D274 (Dutch type) followed by a QX-like IB vaccine booster or vaccinated with a combination of IB H120, IB D274 and QX-like IB were protected against a challenge with IB 793B. In addition, IB 1263 (Mass type) boosted by QX-like IB showed an 85% protection following challenge with IB 793B. A combination of IB H120 and IB D274 boosted by QX-like IB vaccine conferred 70% protection whilst H120 and IB D274 combination on its own showed 61.1% protection against Israel variant 2 challenge. IB 1263 boosted by a QX-like IB vaccine showed 50% protection against IB Israel variant 2. Therefore, it can be concluded that a combination of the IB H120, IB D274 and QX-like IB confers broad protection against different non-related virulent IB strains.
Apoptosis, necrosis and cellular senescence: chaperone occupancy as a potential switch (2003)

Chaperone function plays a key role in repairing proteotoxic damage and in the maintenance of cell survival. Here we compare the regulatory role of molecular chaperones (heat shock proteins, stress proteins) in cellular senescence, apoptosis and necrosis. We also review the current data on chaperone level and function in aging cells, and list some possible therapeutic interventions. Finally, we postulate a hypothesis, that increasing chaperone occupancy might be an important event which forces cells out of the normal cell cycle towards senescence. In the case of severe stress, this may lead to apoptosis or, following lethal stress, to cell necrosis.
Effect of Al-diffusion-induced positive flatband voltage shift on the electrical characteristics of Al-incorporated high-k metal-oxide-semiconductor field-effective transistor (2009)

We systematically studied what effect Al diffusion from high-k dielectrics had on the flatband voltage (Vfb) of Al-incorporated high-k gate stacks. An anomalous positive shift fin Vfb with the decreasing equivalent oxide thickness (EOT) of high-k gate stacks is reported. As the SiO2 interfacial layer is aggressively thinned in Al-incorporated HfxAl1−xOy gate stacks with a metal-gate electrode, the Vfb first lies on the well known linear Vfb-EOT plot and deviates toward the positive-voltage direction (Vfb roll-up), followed by shifting toward negative voltage (Vfb roll-off). We demonstrated that the Vfb roll-up behavior remarkably decreases the threshold voltage (Vth) of p-type metal-oxide-semiconductor field-effect transistors (p-MOSFETs), and does not cause severe degradation in the characteristics of hole mobility. The Vfb roll-up behavior, which is independent of gate materials but strongly dependent on high-k dielectrics, was ascribed to variations in fixed charges near the SiO2/Si interface, which are caused by Al diffusion from HfxAl1−xOy through SiO2 to the SiO2/Si interface. These results indicate that anomalous positive shift in Vfb, i.e., Vfb roll-up, should be taken into consideration in quantitatively adjusting Vfb in thin EOT regions and that it could be used to further tune Vth in p-MOSFETs.
Cell immobilization using PVA crosslinked with boric acid (1992)

A new cell immobilization technique is described in which polyvinyl alcohol is crosslinked with boric acid, with the addition of a small amount of calcium alginate. The presence of the calcium alginate improves the surface properties of the beads, preventing agglomeration. A pure culture of phenol-degrading Pseudomonas was immobilized in the PVA-alginate beads. Phenol was successfully degraded in a fluidized bed of the beads, indicating that cell viability was maintained following the immobilization procedure. The PVA-alginate beads proved to be very strong and durable, with no noticeable degradation of the beads after 2 weeks of continuous operation of the fluidized bed.
Structure, function, and regulation of STAT proteins (2006)

The Signal Transducer and Activator of Transcription (STAT) family of proteins was first discovered in the 1990's as key proteins in cytokine signaling. Since then, the field has greatly advanced in the past 15 years, providing significant insight into the structure, function, and regulation of STATs. STATs are latent cytoplasmic transcription factors consisting of seven mammalian members. They are Tyr phosphorylated upon activation, a post-translational modification critical for dimerization, nuclear import, DNA binding, and transcriptional activation. In recent years, unphosphorylated STATs have also been observed to dimerize and drive transcription, albeit by yet an obscure mechanism. In addition, the function of cytoplasmic STATs is beginning to emerge. Here, we describe the structure, function, and regulation of both unphosphorylated and phosphorylated STATs. STAT isoforms from alternative splicing or proteolytic processing, and post-translational modifications affecting STAT activities are also discussed.
Nucleic‐Acid Analogs with Restricted Conformational Flexibility in the Sugar‐Phosphate Backbone (‘Bicyclo‐DNA’). Part 5. Synthesis, Characterization, and Pairing Properties of Oligo‐α‐D‐(bicyclodeoxynucleotides) of the Bases Adenine and Thymine (α‐Bicyclo‐DNA) (1995)

Abstract A conformational analysis of the (3′S,5′R)‐2′‐deoxy‐3′,5′‐ethano‐α‐ D ‐ribonucleosides (a‐D‐bicyclodeoxynucleosides) based on the X‐ray analysis of N 4 ‐benzoyl‐α‐ D ‐(bicyclodeoxycytidine) 6 and on 1 H‐NMR analysis of the α‐ D ‐bicyclodeoxynucleoside derivatives 1 ‐ 7 reveals a rigid sugar structure with the furanose units in the l′‐exo/2′‐endo conformation and the secondary OH groups on the carbocyclic ring in the pseudoequatorial orientation. Oligonucleotides consisting of α‐ D ‐bicyclothymidine and α‐ D ‐bicyclodeoxyadenosine were successfully synthesized from the corresponding nucleosides by phosphoramidite methodology on a DNA synthesizer. An evaluation of their pairing properties with complementary natural RNA and DNA by means of UV/melting curves and CD spectroscopy show the following characteristics: i) α‐bcd(A 10 ) and α‐bcd(T 10 ) (α = short form of α‐ D )efficiently form complexes with complementary natural DNA and RNA. The stability of these hybrids is comparable or slightly lower as those with natural β‐d(A 10 ) or β‐d(T 10 )( β = short form ofβ‐ D ). ii) The strand orientation in α‐bicyclo‐DNA/β‐DNA duplexes is parallel as was deduced from UV/melting curves of decamers with nonsymmetric base sequences. iii) CD Spectroscopy shows significant structural differences between α‐bicyclo‐DNA/β‐DNA duplexes compared to α‐DNA/β‐DNA duplexes. Furthermore, α‐bicyclo‐DNA is ca. 100‐fold more resistant to the enzyme snake‐venom phosphodiesterase with respect to β‐DNA and about equally resistant as α‐DNA.