gebhart/patrepeval huggingface dataset:
Steric and Electronic Control in the Addition of Hydrazine and Phenylhydrazine to α-[(Dimethylamino)methylene]-β-oxoarylpropanenitriles (1997)

Reaction of hydrazine with α-[(dimethylamino)methylene]-β-oxoarylpropanenitriles 2 gives a mixture of the 4-aroyl-5-aminopyrazoles 3 and the 5-aryl-4-cyanopyrazoles 4. Similarly reaction of 2 with phenylhydrazine gives rise to the 5-amino-4-aroyl-1-phenylpyrazoles 5 and 5-aryl-4-cyano-1-phenylpyrazoles 6. The regioselectivity of addition has been investigated with respect to the electronic nature and steric requirements of the aromatic substitution. The ratio of products was found to be independent of the electronic nature of the substituent. The outcome of the reaction was however very sensitive to steric factors. Substituents in the para- and meta-positions favoured formation of the pyrazole-nitrile products 4 and 6, whereas sterically demanding ortho-substituents favoured the pyrazole-amino ketones 3 and 5.
Fungal cell wall synthesis: the construction of a biological structure. (1988)

The cell wall is of vital importance for the protection of the fungal cell. It consists of structural components, mostly beta-linked polysaccharides, and of interstitial components, usually glycoproteins. Cell shape is determined by the wall and is attained by localized growth. Regulatory mechanisms that act on chitin and beta(1----3) glucan synthetase indicate how localized biosynthesis can be achieved. Whereas structural polysaccharides appear to be exported by vectorial synthesis through the plasma membrane, glycoproteins are manufactured in an assembly line that takes them through several cellular compartments before exocytosis to the periplasmic space. In this space, the last phase of cell wall construction takes place, i.e. branching of structural polysaccharides and linkage between different components.
Hybrid MEMS-IDT-based accelerometer and gyroscope in a single chip (2001)

In this paper, recent advances made on wireless MEMS-IDT (Interdigital Transducer) based accelerometers and gyroscopes at Penn State and HVS are presented. The concept and design principles are based on using surface acoustic waves (SAW) and polysilicon seismic mass for acceleration and proof mass for gyro. By designing the seismic mass of the accelerometer to float just above a high frequency Rayleigh Surface Acoustic Wave Sensor (SAWS), we are able to realize the accuracy and versatility required for the measurement of accelerations from 10<SUP>-6</SUP> g to 100 g. The gyro design is based on the combination of Surface Acoustic Wave Resonator (SAWR) and Surface Acoustic Wave Sensor, which operates at the Rayleigh mode. The transmitter IDT creates SAW that propagates back and forth between the reflectors and forms a standing wave pattern within the cavity space between the IDTs. The particles at the anti-nodes of standing wave pattern experience large amplitude of vibration perpendicular to the plane of the substrate, which serves as the reference vibrating motion for the gyroscope. A number of metallic (proof) masses are strategically positioned at the anti-node locations so that the effect of the Coriolis force can be used to sense the gyroscopic motion.
Generation of a dual RT Env SHIV that is infectious in rhesus macaques (2010)

The objective of this study was to develop and characterize a SHIV recombinant virus for evaluating the efficacy of ART and microbicide products that target both HIV RT and/or Env-mediated entry. RT Env SHIV can productively infect macaques by both the IV and mucosal route, making it a valuable tool for transmission studies.
Sleep Related Problems and Urological Symptoms: Testing the Hypothesis of Bidirectionality in a Longitudinal, Population Based Study (2013)

These data suggest that self-reported sleep related problems and urological symptoms are linked bidirectionally, and that body mass index may be a factor in the relationship between sleep and the development of urological symptoms.
Comment on the Equality Condition for the I-MMSE Proof of Entropy Power Inequality (2017)

The paper establishes the equality condition in the I-MMSE proof of the entropy power inequality (EPI). This is done by establishing an exact expression for the deficit between the two sides of the EPI. Interestingly, a necessary condition for the equality is established by making a connection to the famous Cauchy functional equation.
Curcumin: A Multipurpose Matrix for MALDI Mass Spectrometry Imaging Applications (2013)

Curcumin, 1,7-bis-(4-hydroxy-3-methoxy-phenyl)-hepta-1,6-diene-3,5-dione, is a polyphenolic compound naturally present in the Curcuma longa plant, also known as tumeric. Used primarily as a coloring agent and additive in food, curcumin has also long been used for its therapeutic properties in a number of medical scenarios. Here, we report on an entirely novel use of curcumin; its extended structure of conjugated double bonds suggested the potential of this compound to be a good matrix assisted laser desorption ionization mass spectrometry (MALDI MS) matrix candidate. In the quest for novel and more efficient MALDI MS matrices, curcumin is revealed to be a versatile and multipurpose matrix. It has been applied successfully for the analysis of pharmaceuticals and drugs, for imaging lipids in skin and lung tissues, and for the analysis of a number of compound classes in fingermarks. In each case, the use of curcumin is shown to promote analyte ionization very efficiently as well as provide excellent mass spectral image quality.
Tree-Guided Group Lasso for Multi-Task Regression with Structured Sparsity (2018)

We consider the problem of learning a sparse multi-task regression, where the structure in the outputs can be represented as a tree with leaf nodes as outputs and internal nodes as clusters of the outputs at multiple granularity. Our goal is to recover the common set of relevant inputs for each output cluster. Assuming that the tree structure is available as prior knowledge, we formulate this problem as a new multi-task regularized regression called tree-guided group lasso. Our structured regularization is based on a grouplasso penalty, where groups are defined with respect to the tree structure. We describe a systematic weighting scheme for the groups in the penalty such that each output variable is penalized in a balanced manner even if the groups overlap. We present an efficient optimization method that can handle a largescale problem. Using simulated and yeast datasets, we demonstrate that our method shows a superior performance in terms of both prediction errors and recovery of true sparsity patterns compared to other methods for multi-task learning.
Business Rules Based Agile ERP Systems Development (2009)

Business rules are relatively new addition in the field of Enterprise Resource Planning (ERP) systems, which are kind of business information systems, development. Recently some relevant enhancements of existing business information systems engineering methods were introduced, although there are still open issues of how business rules may be used and improve qualitative and quantitative attributes of such kind of information systems. The paper discusses existing business information systems engineering issues arising out of using business rules approach. The paper also introduces several ways of business rule involvement aiming at ensuring ERP systems development agility based on running researches in the field also carried out by the authors.
Questioned Document Examination Using CEDAR-FOX (2018)

Handwriting verification casework often involves comparing the writing in a questioned document with samples of known writing. This paper describes the use of CEDAR-FOX, a software tool for questioned document examination, in a case involving extended writing. The different steps involved from scanning the documents to obtaining a nine-point qualitative measure are described. The various algorithms used, along with a demonstration of its. functionalities on the case are also described. The paper serves two purposes: a guide to using a stateof- the-art software system for a quantitative analysis of handwriting, and an introduction to the science and technology of the software.&#x0D; Purchase Article - $10
Glycoengineering of Therapeutic Antibodies with Small Molecule Inhibitors (2021)

Monoclonal antibodies (mAbs) are one of the cornerstones of modern medicine, across an increasing range of therapeutic areas. All therapeutic mAbs are glycoproteins, i.e., their polypeptide chain is decorated with glycans, oligosaccharides of extraordinary structural diversity. The presence, absence, and composition of these glycans can have a profound effect on the pharmacodynamic and pharmacokinetic profile of individual mAbs. Approaches for the glycoengineering of therapeutic mAbs-the manipulation and optimisation of mAb glycan structures-are therefore of great interest from a technological, therapeutic, and regulatory perspective. In this review, we provide a brief introduction to the effects of glycosylation on the biological and pharmacological functions of the five classes of immunoglobulins (IgG, IgE, IgA, IgM and IgD) that form the backbone of all current clinical and experimental mAbs, including an overview of common mAb expression systems. We review selected examples for the use of small molecule inhibitors of glycan biosynthesis for mAb glycoengineering, we discuss the potential advantages and challenges of this approach, and we outline potential future applications. The main aim of the review is to showcase the expanding chemical toolbox that is becoming available for mAb glycoengineering to the biology and biotechnology community.
Role of Presenilin-1 in Aggressive Human Melanoma (2022)

Presenilin-1 (PS-1), a component of the gamma (γ)-secretase catalytic complex, has been implicated in Alzheimer's disease (AD) and in tumorigenesis. Interestingly, AD risk is inversely related to melanoma, suggesting that AD-related factors, such as PS-1, may affect melanomagenesis. PS-1 has been shown to reduce Wnt activity by promoting degradation of beta-catenin (β-catenin), an important Wnt signaling partner. Since Wnt is known to enhance progression of different cancers, including melanoma, we hypothesized that PS-1 could affect Wnt-associated melanoma aggressiveness. Western blot results showed that aggressive melanoma cells expressed significantly lower levels of both PS-1 and phosphorylated-β-catenin (P-β-catenin) than nonaggressive melanoma cells. Immunohistochemistry of human melanoma samples showed significantly reduced staining for PS-1 in advanced stage melanoma compared with early stage melanoma. Furthermore, γ-secretase inhibitor (GSI) treatment of aggressive melanoma cells was followed by significant increases in PS-1 and P-β-catenin levels, suggesting impaired Wnt signaling activity as PS-1 expression increased. Finally, a significant reduction in cell migration was associated with the higher levels of PS-1 and P-β-catenin in the GSI-treated aggressive melanoma cells. We demonstrate for the first time that PS-1 levels can be used to assess melanoma aggressiveness and suggest that by enhancing PS-1 expression, Wnt-dependent melanoma progression may be reduced.
Phase transformation and magnetic properties of NiFe thin films on Si(100) wafer and SiO2/Si(100) substrate by co-sputtering (2010)

Si(100) wafer와 <TEX>$SiO_2$</TEX>/Si(100) 웨이퍼에 증착된 NiFe 합금 박막의 결정상과 자기적 특성을 비교하고자 동시 스퍼터링법을 이용하여 두 기판 위에 150 nm의 박막을 제조하여 그의 상변화와 자기적 특성을 XRD, FE-SEM, VSM으로 비교하였다. 두 기판 위에 증착된 NiFe 박막은 BCC상으로 증착되었으나 <TEX>$400^{\circ}C$</TEX>에서 2시간 열처리를 한 결과 BCC에서 FCC로의 상전이가 일어나는 것을 관찰 할 수 있었으며 Si(100) wafer위에 증착된 박막에서는 <TEX>$500^{\circ}C$</TEX>에서 열처리 후에도 BCC와 FCC가 혼재하여 나타나는 것을 알 수 있었다. <TEX>$450^{\circ}C$</TEX>에서 열처리 하였을 때 각형비가 가장 높았으며 포화자화는 0.0118 emu로 나타나고 있었다. <TEX>$500^{\circ}C$</TEX> 이상의 온도에서는 상전이로 인해 포화자화가 급격히 감소하는 것을 볼 수 있었다. Ni-Fe alloys have various applications such as thin film inductor, thin film transformer, magnetic head's shield case, etc. Magnetic properties of Ni-Fe thin films depend on the process parameters such as thickness, contents, deposition rate, substrates, etc. In this study, NiFe films with a thickness of about 150nm were deposited on Si(100) wafer and <TEX>$SiO_2$</TEX>/Si(100) substrate at room temperature by a DC magnetron co-sputtering using Fe and Ni targets. Their phase formation and magnetic properties as a function of annealing temperature were investigated with XRD, FE-SEM and VSM. The assputtered films have BCC structure. With increasing annealing temperature, NiFe thin film for <TEX>$SiO_2$</TEX>/Si(100) substrate transformed completely from BCC to FCC phase above <TEX>$500^{\circ}C$</TEX>, but some BCC phase remained above <TEX>$500^{\circ}C$</TEX> on Si(100) wafer. For samples annealed at <TEX>$450^{\circ}C$</TEX>, squareness ratio of NiFe thin film shows peak value and its saturation magnetization is around 0.0118 emu, which means that the optimum annealing temperature of NiFe thin film seems to be <TEX>$450^{\circ}C$</TEX>. The saturation magnetization of films decreased rapidly above the annealing temperature of <TEX>$500^{\circ}C$</TEX> due to phase transformation from BCC to FCC phase.
An Intrinsically Linear 13-Level Capacitive DAC for Delta Sigma Modulators (2022)

Mismatch of the digital-to-analog converter (DAC) elements is the major limitation for Signal to Noise and Distortion Ratio (SNDR) and Spurious Free Dynamic Range (SFDR) in multi-bit Delta Sigma Modulators (DSM). In this brief we extend a previously introduced technique to build an intrinsically linear 13 level DAC. An exemplary Switched-Capacitor (SC) 13-levels 20 kHz discrete-time DSM employing this technique is simulated and achieves an SFDR higher than 100 dBc on circuit level in presence of considerable capacitor mismatch. The presented DAC architecture is not limited to be used in a discrete-time modulator, but could also be employed in a Continuous-Time DSM (CTDSM).
Entropy-Driven High Reactivity of Formaldehyde in Nucleophilic Attack by Enolates on Oxide Surfaces (2018)

CH<sub>3</sub>OH dehydrogenation on a metal function occurs in tandem with C-C coupling of HCHO with enolates derived from alkanals or alkanones on acid-base pairs at anatase TiO<sub>2</sub> surfaces with very high specificity for nucleophilic attack by enolates on HCHO over larger carbonyl molecules. The measured rate constants for enolate coupling with HCHO are >10<sup>3</sup>-fold larger than for its coupling with acetone. Free energies derived from theoretical treatments of reactions between C<sub>2</sub>-C<sub>4</sub> bound enolates and carbonyls show that such specificity for nucleophilic attack on HCHO reflects smaller entropy losses upon formation of the transition state (TS), instead of enthalpic effects caused by weaker steric effects or the stronger electrophilic character of HCHO compared with larger carbonyls. The easier steric access and higher electrophilicity of the carbonyl C atom of HCHO in C-C coupling with enolates are compensated by a later TS and by stronger van der Waals contacts for the corresponding reactions of the larger carbonyls. The preeminence of entropic effects over enthalpic stabilization reflects the greater structural organization imposed by surfaces on TS structures compared with similar reactions and structures in gaseous or liquid media. Such organization imposes significant entropic penalties that become least consequential for smaller electrophiles, thus enabling highly selective routes for sequential addition of C<sub>1</sub> groups at nucleophilic C atoms in co-reactants using HCHO, whether added or formed in situ from CH<sub>3</sub>OH, as the monomer source. Such entropy-driven specificity is therefore a unique and unrecognized characteristic of reactions catalyzed by surfaces.
New Cytotoxic 1-Azaanthraquinones and 3-Aminonaphthoquinone from the Stem Bark of Goniothalamus marcanii (1999)

Guided by brine shrimp toxicity and human tumor cell toxicity, fractionation of the alcoholic extract from the stem bark of Goniothalamus marcanii led to the isolation of four new 1-azaanthraquinones: marcanines B (3), C (4), D (5), and E (6), along with two known derivatives: marcanine A and dielsiquinone. A new 5-hydroxy-3-amino-2-aceto-1,4-naphthoquinone (7), a possible 1-azaanthraquinone biosynthetic precursor, was also isolated. The structures of the compounds were elucidated by spectroscopic analyses, mainly 1D and 2D NMR techniques ((1)H, (13)C, NOEDS, COSY, HMQC, and HMBC), as well as comparison with literature data. All the compounds except 6 were evaluated for cytotoxic activity. They exhibited significant cytotoxicity against several human tumor cell lines, A-549, HT-29, MCF7, RPMI, and U251 with the ED(50) in the range of 0.04-3.03 microM.
Condensation Heat Transfer of Mixed Refrigerants inside a Horizontal Tube. (1998)

Experimental and analytical studies of condensation heat transfer were performed for pure, binary and ternary mixtures of HFC32, HFC125 and HFC134a. These heat transfer coefficients were measured inside a horizontal smooth tube 5.8mm ID and 8m long. The refrigerant mixture in the test section was cooled by water flowing through an annulus around the tube. The refrigerant temperature was 40°C and the mass flux was varied between 150 and 400 kg/m2s for all the experiments. The heat transfer conefficients for nonazeotropic binary and ternary mixtures was about 20% lower than that for HFC134a at low mass flux conditions. A new predictive model for condensation heat transfer of multicomponent mixtures is proposed, in which the heat transfer deterioration due to the mass transfer effect is taken into account both in forced-convection condensation and in free-convection condensation. The predicted results are in good agreement with the experimental ones.
Chromosome Aberrations Resulting From Double-Strand DNA Breaks at a Naturally Occurring Yeast Fragile Site Composed of Inverted Ty Elements Are Independent of Mre11p and Sae2p (2009)

Genetic instability at palindromes and spaced inverted repeats (IRs) leads to chromosome rearrangements. Perfect palindromes and IRs with short spacers can extrude as cruciforms or fold into hairpins on the lagging strand during replication. Cruciform resolution produces double-strand breaks (DSBs) with hairpin-capped ends, and Mre11p and Sae2p are required to cleave the hairpin tips to facilitate homologous recombination. Fragile site 2 (FS2) is a naturally occurring IR in Saccharomyces cerevisiae composed of a pair of Ty1 elements separated by approximately 280 bp. Our results suggest that FS2 forms a hairpin, rather than a cruciform, during replication in cells with low levels of DNA polymerase. Cleavage of this hairpin results in a recombinogenic DSB. We show that DSB formation at FS2 does not require Mre11p, Sae2p, Rad1p, Slx4p, Pso2p, Exo1p, Mus81p, Yen1p, or Rad27p. Also, repair of DSBs by homologous recombination is efficient in mre11 and sae2 mutants. Homologous recombination is impaired at FS2 in rad52 mutants and most aberrations reflect either joining of two broken chromosomes in a "half crossover" or telomere capping of the break. In support of hairpin formation precipitating DSBs at FS2, two telomere-capped deletions had a breakpoint near the center of the IR. In summary, Mre11p and Sae2p are not required for DSB formation at FS2 or the subsequent repair of these DSBs.
Magnetic field sensing scheme using CoFeB∕MgO∕CoFeB tunneling junction with superparamagnetic CoFeB layer (2006)

The authors investigated the tunneling magnetoresistance (TMR) of CoFeB∕MgO∕CoFeB tunnel junctions by varying the thickness (tCoFeB) of the top CoFeB layer. Linear and hysteresis-free switching was observed in junctions with tCoFeB⩽10Å, while normal tunneling behavior occurred for tCoFeB&amp;gt;10Å. The field sensitivity and the sensing field range were found to be controlled by varying the thickness of the sensing layer. This finding means that the magnetic tunneling junction (MTJ) provides a scheme for magnetic field sensing, which has a simple sensor design and low power consumption. The magnetic properties of the sensing layer with tCoFeB⩽10Å were found to show the characteristics of superparamagnetism. Although the detailed mechanism of TMR in MTJs with a superparamagnetic layer is not fully understood at present, this phenomenon is observed repeatedly. Therefore, this sensing scheme would be an alternative method for overcoming the problems in magnetic sensors with a crossed magnetization pattern.
Chasing the flux: selecting target pathways through flux analysis of carbon metabolism (2011)

One of the goals of Systems Biology is to develop and utilise high-throughput methods for the measurement of parameters and concentrations on a genome-wide scale, while at the same time generating predictive models for system behaviour. In studying genome-scale metabolic networks, the task of exhaustively assaying and measuring all reaction components can be daunting, because hundreds or even thousands of enzymes (activities and concentrations) need to be considered for the construction of a full-scale, detailed model. There is a clear need for strategies that allow us to systematically select the subsets of pathways and reactions which should be prioritized when studying metabolism. We present a methodology for selecting those reactions that carry the overwhelming majority of the carbon flux through the metabolic network. The recent community-driven reconstruction of the metabolic network of baker’s yeast [1] provides the basis for our analysis. Flux Balance Analysis provides a theoretical flux distribution. Results are constrained with GC-MS exometabolomic measurements of the carbon flux. Flux calculations can also be improved by using 13C measurements to determine intracellular metabolic fluxes. The solution of the constrained FBA problem gives us a ranked list of reactions, based on the amount of carbon flux through each reaction. We improve the specificity of the method further by performing an Elementary Flux Mode analysis, which provides us with target pathways consisting of the reactions that carry the most carbon flux. Our methodology allows us to cover more than 95% of the carbon flux by studying but a small subset of the reactions of the genome-scale metabolic network of baker’s yeast.
Flow parameters associated with hydrodynamic cell injury (1994)

Two flow parameters are proposed for the analysis of flows that have potential to damage animal cells. They are the state of stress (characterized by the second invariant of the stress tensor) and the flow classification parameter R(D) (which is related to the possibility of stress relaxation). We consider the flow that occurs when a 1.7-mm bubble collapses at a liquid interface. Using these two parameters, we show the regions in which the flow is strong in terms of high hydrodynamic stresses and elongation characteristics.
Characterization of bacterial growth and the influence of antibiotics by means of UV resonance Raman spectroscopy (2006)

In this work we monitor the bacterial growth of a Bacillus pumilus batch culture by means of UV resonance Raman spectroscopy. Excitation with a wavelength of 244 nm especially enhances the Raman scattering of the aromatic amino acids and the nucleic acid bases and therefore is a good method to track the metabolic changes that occur during bacterial growth. Furthermore, a drug from the fluoroquinolone group is added to the bacterial suspension at the beginning of the exponential growth phase. With the help of chemometrical methods such as hierarchical cluster analysis (HCA) and principal component analysis (PCA) it is possible to visualize the small changes that occur in the UV resonance Raman spectra due to the interaction of the drug with its biological targets DNA and the enzyme gyrase within the bacterial cell.