gebhart/patrepeval huggingface dataset:
Functional characterization of the DnaK chaperone system from the archaeon Methanothermobacter thermautotrophicusΔH (2009)

We characterized the biochemical and functional properties of the DnaK system from the archaeon Methanothermobacter thermautotrophicus DeltaH. In contrast to the eubacterial chaperone components the archaeal Hsp70 system shows thermal transitions only slightly above the optimal environmental temperature (65 degrees C). Nevertheless, it prevents aggregation of luciferase in the physiological temperature range of the organism, but is also fully functional at 30 degrees C in luciferase refolding. Additionally, GrpE(M.th.) and DnaJ(M.th.) substitute their eubacterial counterparts whereas DnaK(M.th.) is only functional with its native cochaperones which could be attributed to a functional specialization of the eubacterial chaperones during evolution.
Solution‐state structure by NMR of zinc‐substituted rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus (1992)

The three-dimensional solution-state structure is reported for the zinc-substituted form of rubredoxin (Rd) from the marine hyperthermophilic archaebacterium Pyrococcus furiosus, an organism that grows optimally at 100 degrees C. Structures were generated with DSPACE by a hybrid distance geometry (DG)-based simulated annealing (SA) approach that employed 403 nuclear Overhauser effect (NOE)-derived interproton distance restraints, including 67 interresidue, 124 sequential (i-j = 1), 75 medium-range (i-j = 2-5), and 137 long-range (i-j > 5) restraints. All lower interproton distance bounds were set at the sum of the van Der Waals radii (1.8 A), and upper bounds of 2.7 A, 3.3 A, and 5.0 A were employed to represent qualitatively observed strong, medium, and weak NOE cross peak intensities, respectively. Twenty-three backbone-backbone, six backbone-sulfur (Cys), two backbone-side chain, and two side chain-side chain hydrogen bond restraints were include for structure refinement, yielding a total of 436 nonbonded restraints, which averages to > 16 restraints per residue. A total of 10 structures generated from random atom positions and 30 structures generated by molecular replacement using the backbone coordinates of Clostridium pasteurianum Rd converged to a common conformation, with the average penalty (= sum of the square of the distance bounds violations; +/- standard deviation) of 0.024 +/- 0.003 A2 and a maximum total penalty of 0.035 A2. Superposition of the backbone atoms (C, C alpha, N) of residues A1-L51 for all 40 structures afforded an average pairwise root mean square (rms) deviation value (+/- SD) of 0.42 +/- 0.07 A. Superposition of all heavy atoms for residues A1-L51, including those of structurally undefined external side chains, afforded an average pairwise rms deviation of 0.72 +/- 0.08 A. Qualitative comparison of back-calculated and experimental two-dimensional NOESY spectra indicate that the DG/SA structures are consistent with the experimental spectra. The global folding of P. furiosus Zn(Rd) is remarkably similar to the folding observed by X-ray crystallography for native Rd from the mesophilic organism C. pasteurianum, with the average rms deviation value for backbone atoms of residues A1-L51 of P. furiosus Zn(Rd) superposed with respect to residues K2-V52 of C. pasteurianum Rd of 0.77 +/- 0.06 A. The conformations of aromatic residues that compose the hydrophobic cores of the two proteins are also similar. However, P. furiosus Rd contains several unique structural elements, including at least four additional hydrogen bonds and three potential electrostatic interactions.(ABSTRACT TRUNCATED AT 400 WORDS)
Short Communications: Human Immunodeficiency Virus Type 1 Nef Mediates Activation of STAT3 in Immature Dendritic Cells (2002)

Replication of immunodeficiency viruses (HIV-1 and SIV) in immature dendritic cell (DC)-T cell cocultures is dependent on Nef. In contrast, mature DCs promote the replication of wild-type and nef-defective SIV in concert with CD4(+) T cells. Transcription factor activation occurs on DC maturation and this study aimed to investigate whether Nef triggers similar events in immature DCs, rendering them more like mature DCs. Recombinant HIV nef-expressing adenovirus was used to selectively introduce nef into immature human or macaque DCs. These data provide the first evidence that the expression of HIV nef in immature DCs induced selective activation of STAT3 and, to a lesser extent, NF-kappaB. This highlights how Nef can signal primary immature DCs, suggesting one way in which Nef may modulate immature DCs to drive virus replication in the DC-T cell milieu.
N-(4-hydroxyphenyl)retinamide induces apoptosis of malignant hemopoietic cell lines including those unresponsive to retinoic acid. (1993)

N-(4-Hydroxyphenyl)retinamide (HPR) is a synthetic retinoid of particular clinical interest in cancer chemoprevention. We have examined the in vitro effects of HPR on lymphoid and myeloid malignant cell lines and found that at concentrations between 10(-5) and 3 x 10(-7) M it induces a dose-dependent growth inhibition (the peak plasma concentration in patients treated with HPR is 1 to 2 x 10(-6) M). The antiproliferative effect of HPR was, in all cell lines except K422, more potent than that induced by an equimolar dose of all-trans retinoic acid (RA). Also, this effect was irreversible on HL60 and DoHH2 cells that had been exposed to HPR (3 x 10(-6) M) for 24 h, but reversible on Raji and DHL4 exposed to the retinoid for 48 and 72 h, respectively. Time-course growth analysis showed that HPR at 3 x 10(-6) M or below induces a rapid fall of thymidine uptake and viability (> 90%), whereas between 10(-6) and 3 x 10(-7) M exhibits cytostatic effects. Interestingly, the RA-resistant HL-60R and NB306 cells, characterized by a point mutation in the retinoic acid receptor (RAR) and by the loss of the pml/RAR protein, respectively, were, like the parental RA-inducible HL-60 and NB4 cell lines, fully responsive to HPR, thereby suggesting that HPR and RA could act through different receptors or pathways. DNA flow-cytofluorimetric analysis revealed that HPR does not block cells in a specific phase of the cell cycle but triggers programmed cell death or apoptosis. This phenomenon was evidenced both by the visualization, on gel electrophoresis, of fragmented DNA, and by the "in cell" enzymatic labeling of DNA breaks with fluorescent dUTP. With the latter method, apoptotic cells become detectable by 6 h following exposure to 3 x 10(-6) M HPR. Ultrastructural examination of HPR-treated samples showed cells with chromatin compaction and cytoplasm condensation, characteristic of apoptotic cells. In conclusion, our study demonstrates that HPR suppresses malignant cell growth and induces apoptosis at pharmacologically relevant doses. The differential responsiveness by a number of cell lines, especially HL-60R and NB306, to HPR and RA indicates that these compounds may act through different receptors. The clinical use of HPR, particularly in retinoic acid-unresponsive acute promyelocytic leukemia patients, is suggested.
Characteristics of plums as a raw material with valuable nutritive and dietary properties - a review. (2008)

In Poland plums are an important raw matenal used for desserts and processing. A traditional Polish plum preserve, called powidla being a kind of plum jam, exhibits high nutritive value, due to a considerable degree of raw material concentration, being a rich source of pectins, carotenoids, phenolic compounds and organic acids. Prunes are also products with an advantageous nutritive and dietary value, whose popularity as a wholesome snack has increased considerably in recent years. Plums are a raw material rich in biologically-active substances with antioxidant properties, which is correlated with high contents of phenolic compounds, with the predominance of derivatives of caffeic acid, mainly neochlorogenic and chlorogenic acids, together with smaller amounts of anthocyanins, flavanols and flavonols. Numerous nutritional studies confirm the health-promoting action of plums, e.g. by improving the blood lipid profile, reducing bile acid levels, improving glucose and lipid metabolism or inhibiting osteoporosis.
Incorporating deliverable monitor unit constraints into spot intensity optimization in intensity-modulated proton therapy treatment planning (2013)

The purpose of this study is to investigate the feasibility and impact of incorporating deliverable monitor unit (MU) constraints into spot intensity optimization (SIO) in intensity-modulated proton therapy (IMPT) treatment planning. The current treatment planning system (TPS) for IMPT disregards deliverable MU constraints in the SIO routine. It performs a post-processing procedure on an optimized plan to enforce deliverable MU values that are required by the spot scanning proton delivery system. This procedure can create a significant dose distribution deviation between the optimized and post-processed deliverable plans, especially when small spot spacings are used. In this study, we introduce a two-stage linear programming approach to optimize spot intensities and constrain deliverable MU values simultaneously, i.e., a deliverable SIO (DSIO) model. Thus, the post-processing procedure is eliminated and the associated optimized plan deterioration can be avoided. Four prostate cancer cases at our institution were selected for study and two parallel opposed beam angles were planned for all cases. A quadratic programming based model without MU constraints, i.e., a conventional SIO (CSIO) model, was also implemented to emulate commercial TPS. Plans optimized by both the DSIO and CSIO models were evaluated for five different settings of spot spacing from 3 to 7 mm. For all spot spacings, the DSIO-optimized plans yielded better uniformity for the target dose coverage and critical structure sparing than did the CSIO-optimized plans. With reduced spot spacings, more significant improvements in target dose uniformity and critical structure sparing were observed in the DSIO than in the CSIO-optimized plans. Additionally, better sparing of the rectum and bladder was achieved when reduced spacings were used for the DSIO-optimized plans. The proposed DSIO approach ensures the deliverability of optimized IMPT plans that take into account MU constraints. This eliminates the post-processing procedure required by the TPS as well as the resultant deteriorating effect on ultimate dose distributions. This approach therefore allows IMPT plans to adopt all possible spot spacings optimally. Moreover, dosimetric benefits can be achieved using smaller spot spacings.
Alkyl nitrate nitration of active methylene compounds. VI. Synthesis of .alpha.-nitroalkyl heterocyclics (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkyl nitrate nitration of active methylene compounds. VI. Synthesis of .alpha.-nitroalkyl heterocyclicsHenry Feuer and John P. LawrenceCite this: J. Am. Chem. Soc. 1969, 91, 7, 1856–1857Publication Date (Print):March 1, 1969Publication History Published online1 May 2002Published inissue 1 March 1969https://pubs.acs.org/doi/10.1021/ja01035a049https://doi.org/10.1021/ja01035a049research-articleACS PublicationsRequest reuse permissionsArticle Views240Altmetric-Citations17LEARN 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
Surface plasmon resonance-mediated photocatalysis by noble metal-based composites under visible light (2012)

Harvesting abundant and renewable sunlight in energy production and environmental remediation is an emerging research topic. Indeed, research on solar-driven heterogeneous photocatalysis based on surface plasmon resonance has seen rapid growth and potentially opens a technologically promising avenue that can benefit the sustainable development of global energy and the environment. This review briefly summarizes recent advances in the synthesis and photocatalytic properties of plasmonic composites (e.g., hybrid structures) formed by noble metal (e.g., gold, silver) nanoparticles dispersed on a variety of substrates that are composed of metal oxides, silver halides, graphene oxide, among others. Brief introduction of surface plasmon resonance and the synthesis of noble metal-based composites are given, followed by highlighting diverse applications of plasmonic photocatalysts in mineralization of organic pollutants, organic synthesis and water splitting. Insights into surface plasmon resonance-mediated photocatalysis not only impact the basic science of heterogeneous photocatalysis, but generate new concepts guiding practical technologies such as wastewater treatment, air purification, selective oxidation reactions, selective reduction reactions, and solar-to-hydrogen energy conversion in an energy efficient and environmentally benign approach. This review ends with a summary and perspectives.
Identification of 21 novel human protein kinases, including 3 members of a family related to the cell cycle regulator nimA of Aspergillus nidulans. (1993)

The nimA gene encodes a protein-serine/threonine kinase that is required along with the p34cdc2 kinase for mitosis in Aspergillus nidulans. We have searched for human protein kinases that are related to the NIMA protein kinase using the polymerase chain reaction. Different pairs of degenerate oligonucleotides specific for conserved amino acid motifs in the catalytic domain of NIMA were used as primers in the polymerase chain reaction to amplify partial complementary DNAs (cDNAs) of protein kinases expressed in the promyelocytic leukemia cell line HL-60. Forty-one distinct cDNAs representing a broad spectrum of serine/threonine- and tyrosine-specific protein kinases were identified, and the sequences for 21 of these protein kinases were found to be unique. Three of these cDNAs represent a family of protein kinases whose members are related to NIMA and the murine nimA-related protein kinase Nek1. We discuss the success of this polymerase chain reaction approach with respect to the use of multiple primer pairs, the influence of primer degeneracy, and the tolerance of cDNA amplification to mismatches between primers and template mRNA.
Bayesian Image Reconstruction for Improving Detection Performance of Muon Tomography (2009)

Muon tomography is a novel technology that is being developed for detecting high-Z materials in vehicles or cargo containers. Maximum likelihood methods have been developed for reconstructing the scattering density image from muon measurements. However, the instability of maximum likelihood estimation often results in noisy images and low detectability of high-Z targets. In this paper, we propose using regularization to improve the image quality of muon tomography. We formulate the muon reconstruction problem in a Bayesian framework by introducing a prior distribution on scattering density images. An iterative shrinkage algorithm is derived to maximize the log posterior distribution. At each iteration, the algorithm obtains the maximum a posteriori update by shrinking an unregularized maximum likelihood update. Inverse quadratic shrinkage functions are derived for generalized Laplacian priors and inverse cubic shrinkage functions are derived for generalized Gaussian priors. Receiver operating characteristic studies using simulated data demonstrate that the Bayesian reconstruction can greatly improve the detection performance of muon tomography.
High Linear Voltage References for on-chip CMOS Temperature Sensor (2006)

High linear voltage reference circuitry is designed and implemented in TSMC 0.13μm and 0.18μm CMOS technology. Previous research has proposed the use of MOS transistors operating in the weak inversion region to replace the bipolar devices in conventional PTAT (proportional to absolute temperature) circuits. However, such solutions often have linearity problem in high temperature region due to the current leaking devices in modern deep sub micron and nano-scale CMOS technology. The proposed circuit utilized temperature complementation technique on two voltage references, PTAT and IOAT (independent of absolute temperature) references, to enhance the linearity and produce a more stable IOAT voltage reference. Base on the simulation results, the R-squares of both circuitries are better than 0.999 in a considerable wider temperature range from -55°C to 170°C. Thus, a fully integrated temperature sensor with wider temperature range is designed and easily to integrate to modern system-on-chip designs with minimal efforts.
The Mini-Mental State Examination in Alzheimer’s Disease and Multi-Infarct Dementia (1996)

The aim of this study was to compare the performances on each item of the Mini-Mental State Examination (MMSE) of patients with Alzheimer's disease (AD) and multi-infarct dementia (MID). In order to identify the items that could better distinguish the two groups of patients, 70 AD and 31 MID patients matched for disease severity, age, and education were evaluated. The scores of the 101 patients on each of the MMSE items were entered into a principal component factor analysis using varimax rotation, and two main components were derived. Component 1 was probably representative of recently acquired information, whereas component 2 represented educational level. A score summing the items that loaded on component 1 and the recall item was calculated to generate a measure of episodic memory. Performing analysis of variance and covarying for age and education revealed that this score was statistically different in the two groups, with AD patients having lower values. The data suggest that the MMSE may demonstrate a pattern of impairment of memory that differs between AD and MID. Possible explanations of this finding should take into account the different neuroanatomical impairments and the different degrees of motivation, due to depression or attentional deficits, toward external stimuli.
A meta-analysis on the association of HER-2 overexpression with prognosis in human osteosarcoma (2009)

Various studies examining the relationship between HER-2 overexpression and clinical outcome in patients with osteosarcoma have yielded inconclusive results. The purpose of the current study was to evaluate the relation of HER-2 status with clinical outcome in osteosarcoma. We conducted a meta-analysis of five studies that evaluated the relation between HER-2 status and 2-year survival. DerSimonian-Laird random effects analysis was used to estimate the effects of HER-2 overexpression on 2-year survival. The combined relative risk in patients with osteosarcoma for 2-year survival was 1.26 (95% confidence interval, 0.50-3.14; P = 0.63). HER-2-positive status tended to be associated with a worse 2-year survival, but the overall results were not formally statistically significant. An unfavourable prognostic effect of HER-2 overexpression in osteosarcoma was evident from the meta-analysis. However, because several studies were excluded by the current eligibility criteria, caution is needed in interpreting the results.
Neural interfaces for regenerated nerve stimulation and recording (1998)

A class of implantable, regeneration-type neural interfaces (NI's) for mammalian peripheral nerve recording and stimulation were developed using different fabrication processes and integrating purposely designed components. A typical NI comprises three main components: 1) a microfabricated silicon die incorporating a microelectrode array on multiple through-holes, 2) a polymer guidance channel housing the die, and 3) a flexible flat cable connecting the die to an external electronic circuitry. The design and fabrication of the NI's were aimed at achieving long term, reliable implants by taking into careful account the biological, electrical, and mechanical requirements of the specific implant site. Different versions of the NI were fabricated and implanted between the severed ends of the sciatic nerve in a mammalian animal model (rabbit). Morphological and histological evidence showed that nerves regenerated through the NI's and electrophysiological results demonstrated the recovery of electrical functionality. Moreover, the NI's allowed stimulation of the regenerated nerve producing a visible leg/foot contraction. The NI's presented in this paper are being further improved in the authors' laboratories with the ultimate goal of allowing the control of nerve motor and sensory functions in future prosthetic devices.
A Conditional Random Field for Discriminatively-Trained Finite-State String Edit Distance (2005)

The need to measure sequence similarity arises in information extraction, object identity, data mining, biological sequence analysis, and other domains.This paper presents discriminative string-edit CRFs, a finitestate conditional random field model for edit sequences between strings.Conditional random fields have advantages over generative approaches to this problem, such as pair HMMs or the work of Ristad and Yianilos, because as conditionally-trained methods, they enable the use of complex, arbitrary actions and features of the input strings.As in generative models, the training data does not have to specify the edit sequences between the given string pairs.Unlike generative models, however, our model is trained on both positive and negative instances of string pairs.We present positive experimental results on several data sets.
Targeting SphK1 as a New Strategy against Cancer (2008)

Sphingolipid metabolites have emerged as critical players in a number of fundamental biological processes. Among them, sphingosine-1-phosphate (S1P) promotes cell survival and proliferation, in contrast to ceramide and sphingosine, which induce cell growth arrest and apoptosis. These sphingolipids with opposing functions are interconvertible inside cells, suggesting that a finely tuned balance between them can determine cell fate. Sphingosine kinases (SphKs), which catalyze the phosphorylation of sphingosine to S1P, are critical regulators of this balance. Of the two identified SphKs, sphingosine kinase type 1 (SphK1) has been shown to regulate various processes important for cancer progression and will be the focus of this review, since much less is known of biological functions of SphK2, especially in cancer. SphK1 is overexpressed in various types of cancers and upregulation of SphK1 has been associated with tumor angiogenesis and resistance to radiation and chemotherapy. Many growth factors, through their tyrosine kinase receptors (RTKs), stimulate SphK1 leading to a rapid increase in S1P. This S1P in turn can activate S1P receptors and their downstream signaling. Conversely, activation of S1P receptors can induce transactivation of various RTKs. Thus, SphK1 may play important roles in S1P receptor RTK amplification loops. Here we review the role of SphK1 in tumorigenesis, hormonal therapy, chemotherapy resistance, and as a prognostic marker. We will also review studies on the effects of SphK inhibitors in cells in vitro and in animals in vivo and in some clinical trials and highlight the potential of SphK1 as a new target for cancer therapeutics.