gebhart/patrepeval huggingface dataset:
The AroQ and PheA Domains of the Bifunctional P-Protein from <i>Xanthomonas campestris</i> in a Context of Genomic Comparison (1997)

The gene (denoted aroQp.pheA) encoding the bifunctional P-protein (chorismate mutase-P/prephenate dehydratase) from Xanthomonas campestris was cloned. aroQp.pheA is essential for L-phenylalanine biosynthesis. DNA sequencing of the smallest subclone capable of functional complementation of an Escherichia coli phenylalanine auxotroph revealed a putative open reading frame (ORF) of 1200 bp that would encode a 43,438-Da protein. AroQp.PheA exhibited 51% amino acid identity with a Pseudomonas stutzeri homologoue and greater than 30% identities with AroQp.PheA proteins from Haemophilus influenzae, Neisseria gonorrhoeae, and a number of enteric bacteria. AroQp.PheA from X. campestris, when expressed in E. coli, possesses a 40-residue amino-terminal extension that is lysine-rich and that is absent in all of the AroQp.PheA homologues known at present. About 95% of AroQp.PheA was particulate and readily sedimented by low-speed centrifugation. Soluble preparations of cloned AroQp.PheA exhibited a native molecular mass of 81,000 Da, indicating that the active enzyme species is a homodimer. These preparations were unstable after purification of about 40-fold, even in the presence of glycerol, which was an effective protectant before fractionation. When AroQp.PheA was overproduced by a T7 translation vector, unusual inclusion bodies having a macromolecular structure consisting of protein fibrils were observed by electron microscopy. Insoluble protein collected at low-speed centrifugation possessed high catalytic activity. The single band obtained via SDS-PAGE was used to confirm the translational start via N-terminal amino acid sequencing. A perspective on the evolutionary relationships of monofunctional AroQ and PheA proteins and the AroQp.PheA family of proteins is presented. A serC gene located immediately upstream of X. campestris aroQp.pheA appears to reflect a conserved gene organization, and both may belong to a single transcriptional unit.
Annulation of Aromatic Imines via Directed C—H Bond Activation. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Predicted Quality-Adjusted Life Years as a Composite Measure of the Clinical Value of Diabetes Risk Factor Control (2007)

Using predicted QALYs to measure value holds promise as a sensitive composite indicator for quality measurement. Complex, evidence-based quality indicators such as these can potentially provide accurate and useful information to health plans, providers, and consumers.
Direct Imaging of Soft−Hard Interfaces Enabled by Graphene (2009)

Direct imaging of surface molecules and the interfaces between soft and hard materials on functionalized nanoparticles is a great challenge using modern microscopy techniques. We show that graphene, a single atomic layer of sp(2)-bonded carbon atoms, can be employed as an ultrathin support film that enables direct imaging of molecular layers and interfaces in both conventional and atomic-resolution transmission electron microscopy. An atomic-resolution imaging study of the capping layers and interfaces of citrate-stabilized gold nanoparticles is used to demonstrate this novel capability. Our findings reveal the unique potential of graphene as an ideal support film for atomic-resolution transmission electron microscopy of hard and soft nanomaterials.
I. AN INTRODUCTION TO THE LIBRARY AND INFORMATION SERVICES OF A PROFESSIONAL INSTITUTION (1950)

The Library and Information department which I represent is a joint one of two professional Institutions, the Institution of Mining and Metallurgy, and the Institution of Mining Engineers. Both Institutions possess Royal Charters and were founded in the late nineteenth century, the former for the advancement of the science of economic geology, mining and extraction metallurgy of all minerals other than coal, and the latter for the advancement of the science of coal and iron ore mining and allied subjects. The Institution of Mining Engineers is slightly the older institution.
Microhotplate temperature sensor calibration and BIST (2011)

In this paper we describe a novel long-term microhotplate temperature sensor calibration technique suitable for Built-In Self Test (BIST). The microhotplate thermal resistance (thermal efficiency) and the thermal voltage from an integrated platinum-rhodium thermocouple were calibrated against a freshly calibrated four-wire polysilicon microhotplate-heater temperature sensor (heater) that is not stable over long periods of time when exposed to higher temperatures. To stress the microhotplate, its temperature was raised to around 400 °C and held there for days. The heater was then recalibrated as a temperature sensor, and microhotplate temperature measurements were made based on the fresh calibration of the heater, the first calibration of the heater, the microhotplate thermal resistance, and the thermocouple voltage. This procedure was repeated 10 times over a period of 80 days. The results show that the heater calibration drifted substantially during the period of the test while the microhotplate thermal resistance and the thermocouple-voltage remained stable to within about plus or minus 1 °C over the same period. Therefore, the combination of a microhotplate heater-temperature sensor and either the microhotplate thermal resistance or an integrated thin film platinum-rhodium thermocouple can be used to provide a stable, calibrated, microhotplate-temperature sensor, and the combination of the three sensor is suitable for implementing BIST functionality. Alternatively, if a stable microhotplate-heater temperature sensor is available, such as a properly annealed platinum heater-temperature sensor, then the thermal resistance of the microhotplate and the electrical resistance of the platinum heater will be sufficient to implement BIST. It is also shown that aluminum- and polysilicon-based temperature sensors, which are not stable enough for measuring high microhotplate temperatures (>220 °C) without impractically frequent recalibration, can be used to measure the silicon substrate temperature if never exposed to temperatures above about 220 °C.
A Rectangle-Intersection Algorithm with Limited Resource Requirements (2010)

It is demonstrated that power-efficient software also requires simplicity and the use of elementary data structures in addition to asymptotically optimal CPU and memory requirements. Though in the past few decades much effort has been devoted to reporting all k intersecting pairs in a planar set of n iso-oriented rectangles, all the known algorithms using elementary data structures, such as linked lists, are either not optimal, report some intersections repeatedly or fail to report some altogether. A simpler algorithm is proposed that uses only linear arrays and that takes O(n log n + k) time and O(n) space, which are the best possible under the algebraic RAM model of computation. The algorithm is designed for systems with limited resources, such as mobile 3D graphics, and can be implemented in less than 100 lines of Java code.
Environmental Impact of Deepwater Sewage Discharge off Sydney (1993)

A comprehensive monitoring program (the EMP) was put in place to assess the environmental impacts of Sydney's new deep water outfalls. The EMP involves studies of environmental impacts on fish and macro invertebrate community structures, on water quality in the ocean and at the beaches, and of accumulation of contaminants in marine organisms and sediments. Comprehensive computer models (including 3-D) were developed, supported by oceanographic experiments. Since commencement of sewage discharge in deep water, both the extent and frequency of faecal bacterial contamination at Sydney's beaches have reduced. In the ocean, bacteria levels have increased, but numbers remain relatively low. The disappearance of the major shoreline sewage plumes have resulted in reduced contaminant concentrations in shoreline biota. No evidence of a build-up of concentrations of contaminants in the surface sediments at the sampling sites has yet been detected. The micro layer concentrations found in the EMP work at all three shoreline outfalls were considerably lower than those found in the overseas studies. Computer modelling is playing the major role in providing an understanding of the physical processes in the ocean, and behaviour of the deep water plumes, to assist in the interpretation of the impact monitoring. Indications to date are that conditions along the Sydney shoreline have considerably improved, compared to those previously existing. The final assessment is yet to be made.
Performance analysis of efficient concatenated coding scheme for ARQ protocols (1991)

Benelli investigated the performance of two concatenated coding schemes for ARQ protocols. The two schemes differ in their strategies of retransmission. It was shown that the two schemes proposed by Benelli provide a significant improvement in throughput efficiency of ARQ protocols with respect to other similar schemes. The analysis presented by Benelli is complicated. An alternative analysis is provided. Some implementation problems of the Benelli's schemes are also discussed. An efficient retransmission strategy which avoids unnecessary retransmissions and maintains a fixed decoding complexity is proposed.
Secular Trend of Hospital‐Acquired Candidemia among Intensive Care Unit Patients in the United States during 1989–1999 (2002)

We describe the annual incidence of primary bloodstream infection (BSI) associated with Candida albicans and common non-albicans species of Candida among patients in intensive care units that participated in the National Nosocomial Infections Surveillance system from 1 January 1989 through 31 December 1999. During the study period, there was a significant decrease in the incidence of C. albicans BSI (P<.001) and a significant increase in the incidence of Candida glabrata BSI (P=.05).
Deletions in herpes simplex virus glycoprotein D define nonessential and essential domains (1990)

Herpes simplex virus glycoprotein D (gD) is a major component of the virion envelope and infected cell membranes and is essential for virus entry into cells. We have recently shown that gD interacts with a limited number of cell surface receptors which are required for virus penetration into cells. To define domains of gD which are required for aspects of virus replication including receptor binding, deletion mutations of 5 to 14 amino acids were constructed by using oligonucleotide-directed mutagenesis. Plasmids containing mutant genes for gD were assayed for the ability to rescue a recombinant virus, F-gD beta, in which beta-galactosidase sequences replace gD-coding sequences. Effects on global folding and posttranslational processing of the molecules were assessed by using a panel of monoclonal antibodies which recognize both continuous and discontinuous epitopes. A region near the amino terminus (residues 7 to 21) of gD which is recognized by monoclonal antibodies able to neutralize herpes simplex virus in the absence of complement was not essential for function. In addition, virtually all of the cytoplasmic domain of gD and an extracellular domain close to the membrane were dispensable. In contrast, deletion mutations in the central region of the molecule, save for one exception, led to alterations in global folding of the molecule and maturation of the protein was inhibited.
Relations of mechanical properties to density and CT numbers in human bone (1995)

Mechanical properties of cortical and cancellous bone from eight human subjects were determined using an ultrasonic transmission technique. Raw computerized tomography (CT) values obtained from scans of the bones in water were corrected to Hounsfield units. The correlations between CT numbers and mechanical property estimated from cortical bone were found to be low (r2 < 0.2), while these relationships for cancellous bone were found to be higher (r2 > 0.6). These results suggest that CT values may be useful in predicting mechanical properties only for cancellous bone. Poor correlations were found between modulus in the radial or circumferential direction and modulus in the superior-inferior direction for cortical bone, whereas good correlations were found between modulus in the anterior-posterior direction or medial-lateral direction and modulus in the S-I direction for cancellous bone. These results indicate that modulus in the radial or circumferential direction could not be predicted from modulus in the S-I direction for cortical bone, but could be predicted for cancellous bone. The predictive capabilities of linear and power models evaluated for cancellous bone alone were approximately equal. However, the power function gives a better fit of data at the low and high density values. The specific relationships, depending on the types of bone, that predict elastic modulus from density and CT numbers were suggested for human cortical and cancellous bone. These specific correlations may help a number of researchers develop more accurate models; however, these hypotheses should be proven by further study.
Hierarchical Convolutional Neural Networks for Segmentation of Breast Tumors in MRI With Application to Radiogenomics (2018)

Breast tumor segmentation based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a challenging problem and an active area of research. Particular challenges, similarly as in other segmentation problems, include the class-imbalance problem as well as confounding background in DCE-MR images. To address these issues, we propose a mask-guided hierarchical learning (MHL) framework for breast tumor segmentation via fully convolutional networks (FCN). Specifically, we first develop an FCN model to generate a 3D breast mask as the region of interest (ROI) for each image, to remove confounding information from input DCE-MR images. We then design a two-stage FCN model to perform coarse-to-fine segmentation for breast tumors. Particularly, we propose a Dice-Sensitivity-like loss function and a reinforcement sampling strategy to handle the class-imbalance problem. To precisely identify locations of tumors that underwent a biopsy, we further propose an FCN model to detect two landmarks located at two nipples. We finally selected the biopsied tumor based on both identified landmarks and segmentations. We validate our MHL method on 272 patients, achieving a mean Dice similarity coefficient (DSC) of 0.72 which is comparable to mutual DSC between expert radiologists. Using the segmented biopsied tumors, we also demonstrate that the automatically generated masks can be applied to radiogenomics and can identify luminal A subtype from other molecular subtypes with the similar accuracy with the analysis based on semi-manual tumor segmentation.
Provenance research: Torridonian and Wealden (1991)

Abstract Torridonian regional flow-directions are indicated unequivocally by sediment geometries and palaeocurrent structures. In the Wealden more reliance has to be placed on textural and compositional gradients. Flow directions in both guide the search for sourcemassif ‘stumps’: uncovered, covered or inferred. ‘Putting back’ the detritus on to the stumps leads to broad palaeogeographies; but erosional histories, recycling, basin budgets and changes in basinal configuration are major uncertainties. Diagenetic interference with the evidence is minimal. Overlapping opposing flows are consistent with extensional tectonic regimes. Torridonian waste provides evidence on the timing of mantle contributions to the Laurentian crust. Refreshingly new Hercynian petrographies in the Wealden may bear on a similar problem in European Gondwana. Single-grain dating (perhaps to include quartz) and rapid and ultra-precise geochemical and isotopic analysis (including whole-rock) make the prospects for provenance research exciting. Tourmaline, zircon and glauconite have considerable potential for dating and justify fuller investigation of their isotopic and mineral chemistries.
Intramolecular Ion−Ion Interactions in Zwitterionic Metallocene Olefin Polymerization Catalysts Derived from “Tucked-In” Catalyst Precursors and the Highly Electrophilic Boranes XB(C<sub>6</sub>F<sub>5</sub>)<sub>2</sub>(X = H, C<sub>6</sub>F<sub>5</sub>) (1997)

The reactions of so called “tuck-in” permethyl zirconocene compounds Cp*(η5-η1-C5Me4CH2)ZrX (X = Cl (1a), C6H5 (1b), CH3 (1c)) with the highly electrophilic boranes HB(C6F5)2 and B(C6F5)3 are described. The products are zwitterionic olefin polymerization catalysts. Reactions with 1a and 1b yielded single products cleanly, but reactions with tuck-in methyl starting material 1c gave mixtures. Spectroscopic and structural studies showed that the electrophilic zirconium center in the product zwitterions was stabilized by a variety of mechanisms. In the products of reaction between 1a and 1b with HB(C6F5)2, Cp*[η5,η1-C5Me4CH2B(C6F5)2(μ-H)]ZrX (X = Cl (2a), 74%), C6H5 (2b, 62%)), the metal is chelated by a pendant hydridoborate moiety. Chloride product 2a was characterized crystallographically. In the reaction of B(C6F5)3 with 1a, the fluxional zwitterionic product Cp*[η5-C5Me4CH2B(C6F5)3]ZrCl (3a, 84%) is stabilized by a weak donor interaction between one of the ortho fluorine atoms of the −CH2B-(C6F5)3 counterion and the zirconium center (Zr−F = 2.267(5) Å). In the product of the reaction between 1b and B(C6F5)3, Cp*[η5-C5Me4CH2B(C6F5)3]ZrC6H5 (3b, 82%), a similar ortho-fluorine interaction was found in a yellow kinetic product (y-3b), which converted upon heating gently to a thermodynamic orange polymorph (o-3b) in which the zirconium center is compensated via an agostic interaction from an ortho C−H bond of the phenyl group and an interaction between the methylene group of the −CH2B-(C6F5)3 counteranion. These compounds were both characterized by X-ray crystallography. Zwitterion o-3b reacts with H2 to form the zwitterionic hydride Cp*[η5-C5Me4CH2B(C6F5)3]ZrH (4, 77%), characterized by NMR spectroscopy and X-ray crystallography to reveal a return to the ortho-fluorine mode of stabilization. Compounds 2a, 3a, o-3b, and 4 were all found to be active ethlyene polymerization catalysts; the chloride derivatives required minimal amounts of methylaluminoxane (MAO) to alkylate the zirconium center. Polymerization data are discussed in light of the structural findings for the catalysts employed.
FACT Facilitates Transcription-Dependent Nucleosome Alteration (2003)

The FACT (facilitates chromatin transcription) complex is required for transcript elongation through nucleosomes by RNA polymerase II (Pol II) in vitro. Here, we show that FACT facilitates Pol II-driven transcription by destabilizing nucleosomal structure so that one histone H2A-H2B dimer is removed during enzyme passage. We also demonstrate that FACT possesses intrinsic histone chaperone activity and can deposit core histones onto DNA. Importantly, FACT activity requires both of its constituent subunits and is dependent on the highly acidic C terminus of its larger subunit, Spt16. These findings define the mechanism by which Pol II can transcribe through chromatin without disrupting its epigenetic status.
THE BIBLE (1953)

THE BIBLE Get access The Exegetical Method of the Greek Translator of the Book of Job. By DONALD H. GARD. Philadelphia: Society of Biblical Literature, 1952 vi + 107 pages.$1.50. JOHN PATERSON JOHN PATERSON Drew Theological SeminaryMadison, N. J. Search for other works by this author on: Oxford Academic Google Scholar Journal of the American Academy of Religion, Volume XXI, Issue 3, July 1953, Pages 203-a–203, https://doi.org/10.1093/jaarel/XXI.3.203-a Published: 01 July 1953
UNCREATED LIGHT AND DAZZLING DARKNESS: BYZANTIUM OF AVANT-GARDE (2021)

Avant-Garde painters were amazed by fifteenth to sixteenth century “old style” Russian icons, which saw the light of the day in the early twentieth century after two centuries of prohibition. In the seventeenth century, ascetic had been replaced by “Western” mimetic images. Icons had a massive impact on Mikhail Larionov, the founder of Rayonism, who wrote that “Russian icon painters <…> were strongly drawn towards abstraction”. In 1913 he organized an exhibition of his Rayonnist paintings with rays of light reflected from objects. Kazimir Malevich was also influenced by icons. In his theoretical writings, he refers to Gospels. Launching his Suprematism at the “0,10 Exhibition” in 1915, Malevich placed his masterpiece in the “beautiful corner”, as an icon. Alexandre Benois said that the Black Square is a “cult of emptiness, darkness, ‘nothing’”. It will be justified that it was another type of darkness, connected to the concepts of “uncreated light” and “dazzling darkness” in Dionysius the Areopagite and Gregory Palamas’ theology. I refer to Pavel Florensky and Sergey Bulgakov’s philosophy to demonstrate how an application of Palamas’ theory, hesychasm, was reflected in fifteenth-sixteenth-century icon-painting and later in Avant-Garde theory and paintings, in particular by those of Larionov and Malevich.
Emerging role of multikinase inhibitors for refractory thyroid cancer (2012)

Thyroid cancer incidence continues to increase, remaining the most common endocrine malignancy. The need for effective systemic therapies combined with high incidence of driver mutations and overexpression of molecular pathways make refractory thyroid cancer an ideal candidate for treatment with novel agents. Multikinase inhibitors have caused a paradigm shift in the treatment of patients with advanced iodine-refractory thyroid cancer. These agents have shown to be the most effective systemic therapy for this disease not only causing prolonged responses but also improving survival. The activity of these agents inhibiting several pathways simultaneously, such as rearranged during transfection protooncogene, mitogen-activated protein kinase, and angiogenesis, can probably explain the effectiveness in controlling the progression of this malignancy. Several of these agents are currently on clinical studies in patients with differentiated and medullary thyroid cancer and most of them are showing promising clinical activity. With the approval of vandetanib for the treatment of medullary thyroid cancer, a new era in the management of this disease has begun. The molecular rationale for the use of these drugs for thyroid cancer is discussed as well as their promising clinical results.
Composing Software from Multiple Concerns: A Model and Composition Anomalies (2000)

Abstract—Constructing software from components is considered to be a key requirement for managing the complexity of software. Separation of concerns makes only sense if the realizations of these concerns can be composed together effectively into a working program. Various publications have shown that composability of software is far from trivial and fails when components express complex behavior such as constraints, synchroni-zation and history-sensitiveness. We believe that to ad-dress the composability problems, we need to understand and define the situations where composition fails. To this aim, in this paper we (a) introduce a general model of multi-dimensional concern composition, and (b) define so-called composition anomalies. 1.