gebhart/patrepeval huggingface dataset:
Gold Nanoparticle–Fluorophore Complexes: Sensitive and Discerning “Noses” for Biosystems Sensing (2010)

Gold nanoparticles (NPs) efficiently quench adsorbed fluorophores. Upon disruption of such complexes by an analyte, fluorescence turn-on is observed. By judicious choice of the functionalized NP and the fluorophore, these complexes display different responses to analytes, thus leading to versatile yet simple array-based sensor platforms. Using this strategy, we can identify proteins in buffer and serum, distinguish between both different species and different strains of bacteria, and differentiate between healthy, cancerous, and metastatic human and murine cells.
Synthesis of triglycerides from 1,3-dibromopropan-2-ol (1983)

1,3-Dibromopropan-2-ol (I) was converted into an acyl derivative (VI) by reaction with an appropriate acyl chloride in the presence of pyridine. The acyl derivative (VI) was subjected to nucleophilic substitution with 3 mol. equiv. tris(decyl)methylammonium carboxylate in refluxing hexane. This led to symmetrical diacid triglycerides in 90–94% yield. Substitution with an equimolar amount of the carboxylate afforded, predominantly, the 1,2-bisacyloxy-3-bromopropane (VII) which could be easily isolated and further substituted to give unsymmetrical diacid– and triacid–triglycerides in ca. 96% yield. Lipolysis showed the synthetic triglycerides to be ca. 99% pure.
Monoclonal antibodies directed against tick-borne encephalitis virus with neutralizing activity in vivo. (1994)

Monoclonal antibodies (MoAbs) were raised against the tick-borne encephalitis (TBE) virus, strain K23. The reactivities of 14 selected MoAbs were characterized by ELISA, Western blot analysis, haemagglutination inhibition, immunoprecipitation, in vivo protection and in vitro neutralization tests. All MoAbs reacted only with the glycoprotein E. The binding epitope of one MoAb could be delimited by a synthetic peptide to amino acids 306-339 representing one immunodominant loop structure of the glycoprotein E. The MoAbs exhibited individual reactivities against 13 different TBE virus isolates in ELISA and immunoblot test ranging from type-specific reactions to a broad reactivity with all isolates. Four MoAbs also showed a cross-reaction with other flaviviruses like West Nile virus and/or Yellow fever virus in immunoblot analysis. By competition ELISA the MoAbs could be divided into five different reaction patterns. Four MoAbs showed neutralizing activity with titers in the range 1:140 to 1:5,000 in an in vitro assay. These neutralizing activities could be confirmed by an in vivo mouse challenge model. The MoAbs are useful for diagnostic purposes and for differentiation of TBE virus strains and other flaviviruses.
Differential roles of multiple signal peptidases in the virulence of Listeria monocytogenes (2004)

Most bacteria contain one type I signal peptidase (Spase I) for cleavage of signal peptides from exported and secreted proteins. Here, we identified a locus encoding three contiguous Spase I genes in the genome of Listeria monocytogenes. The deduced Sip proteins (denoted SipX, SipY and SipZ) are significantly similar to SipS and SipT, the major SPase I proteins of Bacillus subtilis (38% to 44% peptidic identity). We studied the role of these multiple signal peptidases in bacterial pathogenicity by constructing a series of single- and double-chromosomal knock-out mutants. Inactivation of sipX did not affect intracellular multiplication of L. monocytogenes but significantly reduced bacterial virulence (approximately 100-fold). Inactivation of sipZ impaired the secretion of phospholipase C (PC-PLC) and listeriolysin O (LLO), restricted intracellular multiplication and almost abolished virulence (LD(50) of 10(8.3)), inactivation of sipY had no detectable effects. Most importantly, a mutant expressing only SipX was impaired in intracellular survival and strongly attenuated in the mouse (LD(50) of 10(7.2)), whereas, a mutant expressing only SipZ behaved like wild-type EGD in all the assays performed. The data establish that SipX and SipZ perform distinct functions in bacterial pathogenicity and that SipZ is the major Spase I of L. monocytogenes. This work constitutes the first report on the differential role of multiple Spases I in a pathogenic bacterium and suggests a possible post-translational control mechanism of virulence factors expression.
Re-ID Driven Localization Refinement for Person Search (2019)

Person search aims at localizing and identifying a query person from a gallery of uncropped scene images. Different from person re-identification (re-ID), its performance also depends on the localization accuracy of a pedestrian detector. The state-of-the-art methods train the detector individually, and the detected bounding boxes may be sub-optimal for the following re-ID task. To alleviate this issue, we propose a re-ID driven localization refinement framework for providing the refined detection boxes for person search. Specifically, we develop a differentiable ROI transform layer to effectively transform the bounding boxes from the original images. Thus, the box coordinates can be supervised by the re-ID training other than the original detection task. With this supervision, the detector can generate more reliable bounding boxes, and the downstream re-ID model can produce more discriminative embeddings based on the refined person localizations. Extensive experimental results on the widely used benchmarks demonstrate that our proposed method performs favorably against the state-of-the-art person search methods.
The Paternal Effect of Campylobacter jejuni Colonization in Ceca in Broilers (2008)

Campylobacter jejuni is one of the most common causes of acute enteritis worldwide. Chickens are believed to be the main reservoir of C. jejuni. The role that host genetics play in resistance/susceptibility to C. jejuni colonization in broilers is still not clear. Day-old broilers from 2 parental lines (A and B) and their F(1) reciprocal crosses (C and D) were challenged orally with 10(5) cfu of C. jejuni to address the role of genetics in determining resistance/susceptibility to C. jejuni colonization in broilers. Cloacal swabs were collected on 6, 10, and 13 d postinoculation (dpi), and cecal contents cultured for C. jejuni on 7 and 14 dpi. The number of C. jejuni colonies in the cloacal swabs and cecal contents of each bird were recorded at each time point. Significantly fewer bacteria were found in the cecal contents from line A than B (P < 0.05) and cross D (A male x B female) when compared with cross C (A female x B male) at both 7 and 14 dpi. There was a significant correlation between C. jejuni counts in cloacal swabs and those in cecal contents. The results indicated that a paternal effect might be one of the important genetic factors influencing resistance to C. jejuni colonization in broilers.
Multi-channel transmit/receive metal detector coil design for vehicular applications (2014)

Metal detector coil design has been matured to great extent over the years. However, vehicle mounted or remotely operated metal detectors require different specifications and these specifications dictate multiple transmit and receive coils operating in various settings. Unlike handheld operation, detector is more susceptible to metallic body of the vehicle. Moreover, ground calibration is also different than handheld devices. Coil geometries and intercoupling between them play a significant role in system design and performance. In this study, we study different coil geometries for vehicular applications. Starting from well-known coil geometries, we placed coils on dry, wet and ferrous soil to understand the interaction mechanism. Simulation studies are performed in frequency domain but the results are all applicable to time domain pulse based detector systems.
Large-scale application of IBM Design Thinking and Agile development for IBM z14 (2018)

In this paper, we describe the application of IBM Design Thinking and Agile development for the IBM z14 project. We discuss the adoption of IBM Design Thinking practices and its impact on the development and client reception of IBM z14. Furthermore, we show how the design direction of the IBM z14 system was iteratively shaped by involving key members of client organizations (“sponsor users”) early in the development process. Next, we discuss how applying Agile practices in a hardware/firmware environment—with iterative development and test, playbacks, and continuous integration—allowed for faster course correction and delivery on a challenging schedule. This paper provides a case study for the adoption of IBM Design Thinking and Agile practices, which were originally designed for small team operations, and the challenge of applying them to a large-scale development organization such as the IBM team developing the z14 with more than 1,000 engineers.
Multirotor drone sizing and trajectory optimization within Modelon Impact (2023)

The design of multirotor drones often relies on optimizing its performance in terms of maximum speed requirements and hover time. This is well suited to undefined tasks. In the case of repetitive tasks, the drone trajectory can be added as a third degree of freedom. This paper focuses on the use of Modelon Impact and its dynamic optimization capabilities to reach a multirotor drone design and 1-D trajectory optimization. In comparison to other options investigated by the authors in a separate publication, Modelon Impact based optimization proved to be much simpler, more robust, and faster – for this use case.
Attachment of Norovirus to Histo Blood Group Antigens: A Cooperative Multistep Process (2015)

Abstract Human noroviruses recognize histo blood group antigens (HBGAs) as cellular attachment factors. Recently, it has been discovered that norovirus infection can be significantly enhanced by HBGA binding. Yet the attachment process and how it promotes host‐cell entry is only poorly understood. The binding of a norovirus protruding (P) domain of a predominant GII.4 Saga strain to HBGAs at atomic resolution was studied. So far, independent and equivalent multiple binding sites were held responsible for attachment. Using NMR experiments we show that norovirus‐HBGA binding is a cooperative multi‐step process, and native mass spectrometry reveals four instead of two HBGA binding sites per P‐dimer. An accompanying crystallographic study has disclosed four instead of two L ‐fucose binding sites per P‐dimer of a related GII.10 strain 1 further supporting our findings. We have uncovered a novel paradigm for norovirus‐HBGA recognition that will inspire further studies into norovirus–host interactions.
ChemInform Abstract: AROMATIC HYDROXYLATION. HYDROXYBENZALDEHYDES FROM BROMOBENZALDEHYDES VIA REACTION OF IN SITU GENERATED, LITHIATED α‐MORPHOLINOBENZYL ALKOXIDES WITH NITROBENZENE (1983)

Abstract Aus dem Brom‐aldehyd (I) erhält man mit Lithium‐morpholid ein Addukt (III), das mit Butyllithium zu (IV) metalliert und dann mit Nitrobenzol zu (V) hydroxyliert wird.
Conformation of chloroplast DNA in wheat leaves (1970)

Sedimentation and electron microscopic studies have provided no evidence for the presence of circular DNA (deoxyribonucleic acid) in chloroplasts from wheat leaves. Electron microscopy of osmotically disrupted chloroplasts has revealed the presence of linear duplex filaments, some with a tertiary helicoidal configuration and possibly monostranded filaments. None of these structures was observed if the chloroplasts were previously treated with DNase (deoxyribonuclease), but the tertiary configuration was somewhat disorganized by RNase (ribonuclease).
Accuracy threshold for concatenated error detection in one dimension (2009)

Estimates of the quantum accuracy threshold often tacitly assume that it is possible to interact arbitrary pairs of qubits in a quantum computer with a failure rate that is independent of the distance between them. None of the many physical systems that are candidates for quantum computing possess this property. Here we study the performance of a concatenated error-detection code in a system that permits only nearest-neighbor interactions in one dimension. We make use of a message-passing scheme that maximizes the number of errors that can be reliably corrected by the code. Our numerical results indicate that arbitrarily accurate universal quantum computation is possible if the probability of failure of each elementary physical operation is below approximately ${10}^{\ensuremath{-}5}$. This threshold is three orders of magnitude lower than the highest known.
Crystal Structures, Phase Stabilities, and Hydrogen Storage Properties of Metal Amidoboranes (2012)

Metal amidoboranes, M(NH2BH3)n (M = alkali metal or alkaline-earth metal), are candidates for on-board hydrogen storage materials with high gravimetric capacity, low H2 release temperature, and the ability to suppress toxic borazine emission. We have used a first-principles density functional theory (DFT) combination with Monte Carlo method to search for crystal structures for a wide array of metal amidoboranes (M = Li, Na, K, Be, Mg, Ca, Sr, and Sc). In cases where the experimental structures are known, the DFT energies of the theoretically predicted LiNH2BH3, NaNH2BH3, KNH2BH3, and Ca(NH2BH3)2 structures are degenerate with the DFT energies computed for the experimental structures [to within 4 kJ/(mol f.u.)], confirming the accuracy of our approach. On the basis of the decomposition reaction pathway, M(NH2BH3)n → MHn + nBN + 2nH2, we compute the H2 release reaction enthalpies and show that the stability of metal amidoboranes obeys the following trend: The metal amidoborane becomes more stable (the decomposition reaction becomes less exothermic) as the metal cation becomes more electropositive, that is, as the metal cation goes down in the periodic table along a given column or as the metal moves to the left along a given row. The only exception to this rule is Mg(NH2BH3)2, which is more stable than Ca(NH2BH3)2. Introducing vibrational entropy effects does not change this exceptional behavior of Mg amidoborane: the phonon contribution serves to shift all reaction enthalpies down by a roughly constant amount, ∼22 kJ/(mol H2) at T = 300 K.
Exploring Similarities Across High-Dimensional Datasets (2011)

Very often, related data may be collected by a number of sources, which may be unable to share their entire datasets for reasons like confidentiality agreements, dataset size, and so forth. However, these sources may be willing to share a condensed model of their datasets. If some substructures of the condensed models of such datasets, from different sources, are found to be unusually similar, policies successfully applied to one may be successfully applied to the others. In this chapter, we propose a framework for constructing condensed models of datasets and algorithms to find similar substructure in pairs of such models. The algorithms are based on the tensor product. We test our framework on pairs of synthetic datasets and compare our algorithms with an existing one. Finally, we apply it to basketball player statistics for two National Basketball Association (NBA) seasons, and to breast cancer datasets. The results are statistically more interesting than results obtained from independent analysis of the datasets.Request access from your librarian to read this chapter's full text.
Examination and determination of 2-methyl-1:4-naphthoquinone (1940)

J. L. Pinder and J. H. Singer, Analyst, 1940, 65, 7 DOI: 10.1039/AN9406500007
Closed-Loop Control of a 3D Printer Gantry (2014)

Thesis (Master's)--University of Washington, 2014
Cryptococcus neoformans: A sugar-coated killer with designer genes (2005)

Cryptococcus neoformans has become a common central nervous system pathogen as the immunocompromised populations enlarge world-wide. This encapsulated yeast has significant advantages for the study of fungal pathogenesis and these include: (1) a clinically important human pathogen; (2) a tractable genetic system; (3) advanced molecular biology foundation; (4) understanding of several virulence phenotypes; (5) well-studied pathophysiology; and (6) robust animal models. With the use of a sequenced genome and site-directed mutagenesis to produce specific null mutants, the virulence composite of C. neoformans has begun to be identified one gene at a time. Studies into capsule production, melanin synthesis, high temperature growth, metabolic pathways and a variety of signaling pathways have led to understandings of what makes this yeast a pathogen at the molecular level. Multiple principles of molecular pathogenesis have been demonstrated in virulence studies with C. neoformans. These include evolutionary differences between the varieties of C. neoformans in their genes for virulence, quantitative impact of genes on the virulence composite, species and site-specific importance of a virulence gene, gene expression correlation with its functional importance or phenotype and the impact of a pathogenesis gene on the host immune response. C. neoformans has now become a primary model to study molecular fungal pathogenesis with the goal of identifying drug targets or vaccine strategies.
Role of Biodiesel-Diesel Blends in Alteration of Particulate Matter Emanated by Diesel Engine (2015)

The current study is focused on the investigation of the role of biodiesel in the alteration of particulate matter (PM) composition emitted from a direct injection-compression ignition. Two important blends of biodiesel with commercial diesel known as B20 (20% biodiesel and 80% diesel by volume) and B50 were used for the comparative analysis of their pollutants with those of 100% or traditional diesel (D). The experiments were performed under the auspices of the Chinese 8-mode steady- state cycle on a test bench by coupling the engine with an AC electrical dynamometer. As per experimental results, over-50 nm aerosols were abated by 8.7-47% and 6-51% with B20 and B50, respectively, on account of lofty nitrogen dioxide to nitrogen oxides (NO2/NO´) ratios. In case of B50, sub-50 nm aerosols and sulphates were higher at maximum load modes of the test, owing to adsorption phenomenon of inorganic nuclei leading to heterogeneous nucleation. Moreover, trace metal emissions (TME) were substantially reduced reflecting the reduction rates of 42-57% and 64-80% with B20 and B50, respectively, relative to baseline measurements taken with diesel. In addition to this, individual elements such as Ca and Fe were greatly minimised, while Na was enhanced with biodiesel blended fuels.
The identification and characterization of an oxalyl-CoA synthetase from grass pea (Lathyrus sativus L.) (2022)

Oxalic acid is a small metabolite found in many plants. It serves as protection from herbivores, a chelator of metal ions, a regulator of calcium levels, and additional tasks. However, it is also a strong di-carboxylic acid that can compromise plant viability by reducing cellular pH. Several metabolic pathways have evolved to control oxalate levels in plants by enzymatic degradation. Among them is the pathway that utilizes oxalyl-CoA synthetase (OCS, EC 6.2.1.8) and ATP to convert oxalate to oxalyl-CoA. Oxalyl-CoA can then be degraded to CO<sub>2</sub> or utilized as a precursor for the synthesis of other compounds. In grass pea (<i>Lathyrus sativus</i> L.), a grain legume grown in Asia and Africa for human and animal consumption, the neurotoxic compound β-<i>N</i>-oxalyl-l-α,β-diaminopropionic acid (β-ODAP) is synthesized from oxalyl-CoA and l-α,β-diaminopropionic acid (l-DAPA). Here, we report on the identification and characterization of oxalyl CoA-synthetase from grass pea (<i>Ls</i>OCS). The gene encoding <i>Ls</i>OCS was amplified from grass pea, and then expressed and purified from <i>E. coli</i> cells as an untagged, monomeric protein of 56 kDa. Its catalytic efficiency with oxalate, <i>K</i> <sup>oxalate</sup> <sub>M</sub> = 71.5 ± 13.3 μM, <i>V</i> <sub>max</sub> = 8.2 ± 0.8 μmole min<sup>-1</sup> mg<sup>-1</sup>, was similar to that of OCS homologs from <i>Arabidopsis thaliana</i> (<i>At</i>AAE3) <i>and Medicago truncatula</i> (<i>Mt</i>AAE3). The enzyme was crystalized in complex with AMP and is the first OCS whose structure was determined in the thioester-forming conformation. Finally, we propose that substituting <i>Ls</i>OCS with an oxalate oxidase or decarboxylase may reduce the levels of β-ODAP in grass pea.
B cells for cancer immunotherapy (2014)

We have engineered a novel fusion cytokine named GIFT4 derived from GM-CSF and IL-4, and displaying robust gain-of-function immunostimulatory effects on B cells. GIFT4-programmed B cells have a unique identity and potent capacity to elicit a tumoricidal - cell response, thus comprising a novel B cell-based cancer immunotherapeutic approach.
Neural induction - Dual SMAD inhibition (2014)

Dual SMAD inhibition takes a confluent, feeder free culture of hPSCs and rapidly differentiates them into early neurectoderm (Chambers et al., 2009). This rapid differentiation is caused by blocking the two signaling pathways that utilize SMADs for transduction: BMP and TGFB. Oct4 is extinguished and Pax6 expression has begun by around day 7–8, depending on the line used. This neurectoderm can be passaged to become rosettes or can be patterning to become many other types of neural cells (for example, see Fasano et al., 2010).
Nucleus Basalis of Meynert Stimulation for Dementia: Theoretical and Technical Considerations (2018)

Deep brain stimulation (DBS) of nucleus basalis of Meynert (NBM) is currently being evaluated as a potential therapy to improve memory and overall cognitive function in dementia. Although, the animal literature has demonstrated robust improvement in cognitive functions, phase 1 trial results in humans have not been as clear-cut. We hypothesize that this may reflect differences in electrode location within the NBM, type and timing of stimulation, and the lack of a biomarker for determining the stimulation's effectiveness in real time. In this article, we propose a methodology to address these issues in an effort to effectively interface with this powerful cognitive nucleus for the treatment of dementia. Specifically, we propose the use of diffusion tensor imaging to identify the nucleus and its tracts, quantitative electroencephalography (QEEG) to identify the physiologic response to stimulation during programming, and investigation of stimulation parameters that incorporate the phase locking and cross frequency coupling of gamma and slower oscillations characteristic of the NBM's innate physiology. We propose that modulating the baseline gamma burst stimulation frequency, specifically with a slower rhythm such as theta or delta will pose more effective coupling between NBM and different cortical regions involved in many learning processes.
Adaptability analysis of fault component differential protection in large capacity double-fed wind farm outgoing transmission line protection (2016)

An adaptability problem is existed in fault component differential protection of large capacity double-fed wind farm with low-voltage-ride-through. The working condition is firstly obtained by deducing the basic theory of the fault component differential protection. Then the protection adaptation is analyzed by simulations on MATLAB/Simulink. Different fault's types and fault's positions are dynamically simulated. The research shows that the short-circuit current could not be ignored when the large-scale wind power is integrated into power system and the accurate operation of fault component differential protection would be affected by frequency deviation of the wind power system.