gebhart/patrepeval huggingface dataset:
thrombosis in mice without increased risk of bleeding Selective depletion of plasma prekallikrein or coagulation factor XII inhibits (2012)

ABSTRACT Recent studies indicate that the plasma contact system plays an important role in thrombosis, despite being dispensable for hemostasis. For example, mice deficient in coagulation factor XII (fXII) are protected from arterial thrombosis and cerebral ischemia-reperfusion injury. We demonstrate that selective reduction of prekallikrein (PKK), another member of the contact system, using antisense oligonucleotide (ASO) technology results in an antithrombotic phenotype in mice. The effects of PKK deficiency were compared to those of fXII deficiency produced by specific ASO-mediated reduction of fXII. Mice with reduced PKK had ~3-fold higher plasma levels of fXII, and reduced levels of fXIIa-serpin complexes, consistent with fXII being a substrate for activated PKK in vivo . PKK or fXII deficiency reduced thrombus formation in both arterial and venous thrombosis models, without an apparent effect on hemostasis. The amount of reduction of PKK and fXII required to produce an antithrombotic effect differed between venous and arterial models, suggesting that these factors may regulate thrombus formation by distinct mechanisms. Our results support the concept that fXII and PKK play important and perhaps non-redundant roles in pathogenic thrombus propagation, and highlight a novel, specific and safe pharmaceutical approach to target these contact system proteases. From bloodjournal.hematologylibrary.org by guest on November 6, 2012. For personal use only.
Synthesis of Nonluminescent Lanthanide(III) Chelates Tethered to an Aminooxy Group and Their Applicability to Biomolecule Derivatization (2002)

Synthesis of nonluminescent lanthanide(III) chelates tethered to an aminooxy group (i.e., 1-[4-(6-aminooxyhexamido)benzyl]diethylenetriaminetetraacetic acid lanthanides(III), 6a-d, where Ln(3+) is Eu, Dy, Sm, and Tb) is described. Their applicability to biomolecule derivatization is demonstrated by allowing them to react with a synthetic oligopeptide, a protein, two synthetic drugs, and a steroid. The oligopeptide and protein were linked to 6 after preoxidation of their N-terminal serine residues, while the drugs and the steroid reacted via their ketone functionality. Also some application data is included.
System and method for stimulated emission depletion projection stereolithography (2023)

The present disclosure relates to a system for forming a three dimensional (3D) part. The system may incorporate a beam delivery subsystem for generating optical signals, and a mask subsystem that receives the optical signals and generates optical images therefrom. A first one of the optical images activates a polymerization species of a photo-sensitive resin in accordance with illuminated areas thereof, to thus cause polymerization of select portions of the photo-sensitive resin to help form a layer of the 3D part. A second one of the optical images causes stimulated emission depletion of subportions of the polymerization species, simultaneously, over various areas of the layer, to enhance resolution of at least one subportion of the select portions of the photo-sensitive resin.
Pd(II)-catalyzed carboxylation of aromatic C─H bonds with CO 2 (2023)

The carboxylation of nonactivated C─H bonds provides an attractive yet hitherto largely elusive chemical process to synthesize carboxylic acids by incorporation of CO<sub>2</sub> into the chemical value chain. Here, we report on the realization of such a reaction using simple and nonactivated arenes as starting materials. A computationally designed Pd(II) complex acts as organometallic single-component catalyst, and apart from a base, necessary for thermodynamic stabilization of the intermediates, no other additives or coreagents are required. Turnover numbers up to 10<sup>2</sup> and high regioselectivities are achieved. The potential of this catalytic reaction for "green chemistry" is demonstrated by the synthesis of veratric acid, an intermediate for pharmaceutical production, from CO<sub>2</sub> and veratrol.
Inducing swift nucleation morphology control for efficient planar perovskite solar cells by hot-air quenching (2016)

We introduce a pin-hole free CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3−x</sub>Cl<sub>x</sub> perovskite layer by using heated airflow during the nucleation stage. We control the nucleation stage which gives a pin-hole free planar perovskite with large grains, resulting in a maximum power point (MPP) efficiency of 14.3% and a high efficiency of 19.0% with reproducibility.
Design issues and insights for low-voltage high-density SOI DRAM (1998)

A physics-based study of floating-body effects on the operation of SOI DRAM is described. The study, which is based on device and circuit simulations using a physical SOI MOSFET model calibrated to an actual partially-depleted (PD) SOI DRAM technology, addresses the performance of the peripheral circuitry, e.g., the sense amplifier, as well as the dynamic retention of the data storage cell. Design insight for low-voltage high-density SOI DRAM is attained. Double cell design is shown to yield a dynamic retention time long enough for gigabit memories, and crude body-source ties for nMOS, with pMOS bodies floating, are shown to effectively suppress instabilities in the sense amplifier.
Efficient FPGA architecture for oriented 1-D opening and pattern spectrum (2012)

This paper deals with a dedicated hardware architecture for 1-D morphological opening and pattern spectrum. These operators allow extraction and measurement of 1-D features in images that is a commonly used technique in image analysis and texture classification. The architecture is based on a recently proposed opening algorithm and makes it possible to obtain arbitrary-oriented opening and granulometry at the same time. Respecting a sequential data access, several instances with different orientation can run in parallel on a single input dataflow, increasing thus the performance (experimentally 414 Mpx/s per opening). It opens applicability of traditionally costly operators in embedded, industrial applications.
Detection, Monitoring, and Management of Trastuzumab-Induced Left Ventricular Dysfunction: An Actual Challenge (2012)

The antibody trastuzumab, targeted to inhibit the signalling of ErbB2, a tyrosine kinase receptor overexpressed in 20-30% of breast cancers, improves the prognosis in women affected by this tumour, but produces cardiotoxicity, since ErbB2 is also involved in myocardial homeostasis. In this review, we discuss the pathophysiology of trastuzumab cardiomyopathy and the complex interplay between ErbB2 inhibition and anthracyclines, and we focus on the actual challenges of detecting, monitoring, and managing trastuzumab cardiotoxicity: the research of new, sensitive markers of early trastuzumab toxicity, before the ejection fraction is reduced, is an active field of research.
Differences between bisphosphonates in binding affinities for hydroxyapatite (2009)

Bisphosphonates (BPs) inhibit bone resorption and are widely used for the treatment of bone diseases, including osteoporosis. BPs are also being studied for their effects on hydroxyapatite (HAP)-containing biomaterials. There is a growing appreciation that there are hitherto unexpected differences among BPs in their mineral binding affinities that affect their pharmacological and biological properties. To study these differences, we have developed a method based on fast performance liquid chromatography using columns of HAP to which BPs and other phosphate-containing compounds can adsorb and be eluted by using phosphate buffer gradients at pH 6.8. The individual compounds emerge as discrete and reproducible peaks for a range of compounds with different affinities. For example, the peak retention times (min; mean +/- SEM) were 22.0 +/- 0.3 for zoledronate, 16.16 +/- 0.44 for risedronate, and 9.0 +/- 0.28 for its phosphonocarboxylate analog, NE10790. These results suggest that there are substantial differences among BPs in their binding to HAP. These differences may be exploited in the development of biomaterials and may also partly explain the extent of their relative skeletal retention and persistence of biological effects observed in both animal and clinical studies.
ChemInform Abstract: Synthesis of Two 6′α‐Fluorocarbocyclic Nucleosides and Incorporation into Short Segments of DNA. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Seed biotechnology: translating promise into practice. (2007)

In recent years, biotechnology has come to be synonymous with the use of recombinant DNA techniques to introduce genes into plant or animal genomes. Biotechnology has been applied to modify the composition of seeds as foods or raw products to improve their nutritional, flavour, postharvest or processing characteristics. Genetic changes to improve the production of seeds or their performance as propagules can also be achieved using biotechnology. Proof of concept has been demonstrated for many applications of seed biotechnology. However, the only biotechnology products that have achieved wide commercialization are targeted towards insect and weed management, rather than towards enhancement of the biological or nutritional aspects of seeds. The application of biotechnology to enhance seed production, performance and composition has thus far been stymied in practice by the regulatory requirements and economic risk associated with introducing such products into the commercial marketplace.
Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites (2013)

Transcription activator-like (TAL) effectors are injected into host plant cells by Xanthomonas bacteria to function as transcriptional activators for the benefit of the pathogen. The DNA binding domain of TAL effectors is composed of conserved amino acid repeat structures containing repeat-variable diresidues (RVDs) that determine DNA binding specificity. In this paper, we present TALgetter, a new approach for predicting TAL effector target sites based on a statistical model. In contrast to previous approaches, the parameters of TALgetter are estimated from training data computationally. We demonstrate that TALgetter successfully predicts known TAL effector target sites and often yields a greater number of predictions that are consistent with up-regulation in gene expression microarrays than an existing approach, Target Finder of the TALE-NT suite. We study the binding specificities estimated by TALgetter and approve that different RVDs are differently important for transcriptional activation. In subsequent studies, the predictions of TALgetter indicate a previously unreported positional preference of TAL effector target sites relative to the transcription start site. In addition, several TAL effectors are predicted to bind to the TATA-box, which might constitute one general mode of transcriptional activation by TAL effectors. Scrutinizing the predicted target sites of TALgetter, we propose several novel TAL effector virulence targets in rice and sweet orange. TAL-mediated induction of the candidates is supported by gene expression microarrays. Validity of these targets is also supported by functional analogy to known TAL effector targets, by an over-representation of TAL effector targets with similar function, or by a biological function related to pathogen infection. Hence, these predicted TAL effector virulence targets are promising candidates for studying the virulence function of TAL effectors. TALgetter is implemented as part of the open-source Java library Jstacs, and is freely available as a web-application and a command line program.
On Abnormality Detection in Spuriously Populated Data Streams (2005)

In recent years, advances in hardware technology have made it increasingly easy to collect large amounts of multidimensional data in an automated way. Such databases continuously grow over time, and are referred to as data streams. The behavior of such streams is sensitive to the underlying events which create the stream. In many applications, it is useful to predict abnormal events in the stream in a fast and online fashion. This is often a difficult goal in a fast data stream because of the time criticality of the detection process. Furthermore, the rare events may often be embedded with other spurious abnormalities, which affect the stream in similar ways. Therefore, it is necessary to be able to distinguish between different kinds of events in order to create a credible detection system. This paper discusses a method for supervised abnormality detection from multi-dimensional data streams, so that high specificity of abnormality detection is achieved. We present empirical results illustrating the effectiveness of our method.
Computational study on flow around an automobile. (1987)

In recent years, computational fluid dynamics and computer graphics have become important and useful to visualize three-dimensional wake structures. This paper shows the flow around a one-box vehicle, which is calculated with a third-order-upwind scheme. A CRAY X/MP12 was used for the computation and an IRIS3130, graphic workstation, for the visualization.Computational results were visualized by stream lines and time lines, which show the wake structure clearly. It is concluded that the third-order-upwind scheme is effective for the flow analysis around the vehicle and that the graphic workstation helps us easily understand the flow field.
A Preliminary Discussion About Introduction of New Varieties of Chinese Herbal Medicines from Separate Regions and Their Domestication from Wildness (2003)

After analyzing cultivation factors influencing quality of Chinese herbal medicines, expatiate on means of introducing varieties from separate regions and domesticating rare wild ones, procedures and related advertent problems.
PHOTOTOXIC AND PHOTOCHEMICAL PROPERTIES OF SANGUINARINE* (1992)

Sanguinarine, a commercial drug exhibiting antimicrobial and antitumor properties, was studied with respect to its basic photochemical characteristics and also with regard to its phototoxicity to mosquito larvae (Aedes atropalpus). Sanguinarine proved to be clearly phototoxic to larvae, with an LD50 of 0.096 mg/mL with near UV exposure as compared with 23.3 mg/mL without. Flash photolysis experiments enabled the study of the triplet state of sanguinarine to be undertaken. Quenching by oxygen occurs with a rate constant of 6 x 10(9) M-1s-1 and time-resolved emission studies indicate that sanguinarine produces a significant amount of singlet oxygen (phi delta = 0.16) as does the isoquinoline alkaloid, berberine (phi delta = 0.25). These values represent the first direct quantitative measurements of photosensitization parameters of these compounds. Additionally, sanguinarine exhibits efficient electron donation properties, undergoing reaction with methyl viologen with a rate constant greater than 10(10) M-1s-1, but is a poor electron acceptor. Phototoxicity of sanguinarine can thus be explained in terms of its photosensitization properties.
The explanation of why the level of UMF varies in manuka honey (2008)

A few years ago many beekeepers kindly supplied samples of manuka honey, from the spring 2001 season, directly from hives in various specific locations so that a study could be conducted to investigate the possible reasons why there is variation in the level of UMF in manuka honey.
Precision spectroscopy of hydrogen and femtosecond laser frequency combs (2005)

Precision spectroscopy of the simple hydrogen atom has inspired dramatic advances in optical frequency metrology: femtosecond laser optical frequency comb synthesizers have revolutionized the precise measurement of optical frequencies, and they provide a reliable clock mechanism for optical atomic clocks. Precision spectroscopy of the hydrogen 1S-2S two-photon resonance has reached an accuracy of 1.4 parts in 10(14), and considerable future improvements are envisioned. Such laboratory experiments are setting new limits for possible slow variations of the fine structure constant alpha and the magnetic moment of the caesium nucleus mu(Cs) in units of the Bohr magneton mu(B).
System Design Considerations for Thermoelectric Energy Recovery (2016)

The case for the application of thermoelectric methods to waste heat recovery (WHR) is firmly based on the quantity and value of energy that can be reasonably recovered. The evaluation is application specific, but can begin with a thermodynamic analysis of the potential of the energy sources to support WHR. From this initial work, closed-form solutions for the power output from a thermoelectric generator (TEG) can be used to predict approximately the power output of the device under different operating conditions. As a design for the TEG proceeds, and options are considered, a progressively more detailed modelling process can support the integration choices. As a first step, models based on the physical parameters and empirical correlations for the heat exchange processes give a reliable basis for design choices. Numerical models supported by experimental validation provide the next level of refinement. The result of modelling methods and their experimental validation is the formulation of design guidelines and a developing understanding of the relationship between different types of design. The plate-fin heat exchange is the benchmark architecture. Other architectures may be compared with this standard to establish their feasibility. Initial work with TEG designs of a polygonal cross-section show that an octagonal cross-section can form the basis for a family of designs that are comparable in performance with the plate-fin standard and offer other functionality alongside the important WHR functions. Early work in the investigation of heat exchange architectures suggest an initial and simple design guide but one that will be elaborated as experience in the application of TEGs grows and develops.
The reduced [2Fe-2S] clusters in adrenodoxin and Arthrospira platensis ferredoxin share spin density with protein nitrogens, probed using 2D ESEEM (2009)

We have used X-band ESEEM to study the reduced [2Fe-2S] cluster in adrenodoxin and Arthrospira platensis ferredoxin. By use of a 2D approach (HYSCORE), we have shown that the cluster is involved in weak magnetic interactions with several nitrogens in each protein. Despite substantial differences in the shape and orientational dependence of individual cross-peaks, the major spectral features in both proteins are attributable to two peptide nitrogens (N1 and N2) with similar hyperfine couplings approximately 1.1 and approximately 0.70 MHz. The couplings determined represent a small fraction (0.0003-0.0005) of the unpaired spin density of the reduced cluster transferred to these nitrogens over H-bond bridges or the covalent bonds of cysteine ligands. Simulation of the HYSCORE spectra has allowed us to estimate the orientation of the nuclear quadrupole tensors of N1 and N2 in the g-tensor coordinate system. The most likely candidates for the role of N1 and N2 have been identified in the protein environment by comparing magnetic-resonance data with crystallographic structures of the oxidized proteins. A possible influence of redox-linked structural changes on ESEEM data is analyzed using available structures for related proteins in two redox states.
The Impact of Size on Particulate Vaccine Adjuvants (2014)

Particulate adjuvants have been successful at inducing increased immune responses against many poorly immunogenic antigens. However, the mechanism of action of these adjuvants often remains unclear. As more potential vaccine targets are emerging, it is becoming necessary to broaden our knowledge on the factors involved in generating potent immune responses to recombinant antigens with adjuvants. While composition of adjuvants is integral in defining the overall performance of an adjuvant, some physical parameters such as particle size, surface charge and surface modification may also contribute to the potency. In this review, we will try to highlight the role of particle size in controlling the immune responses to adjuvanted vaccines, with a focus on insoluble aluminum salts, oil-in-water emulsions, polymeric particles and liposomes.
No hasty solutions for African swine fever (2020)

African swine fever vaccines could pose risk of causing disease and spreading the virus further
Faculty Opinions recommendation of External antigen uptake by Langerhans cells with reorganization of epidermal tight junction barriers. (2010)

Outermost barriers are critical for terrestrial animals to avoid desiccation and to protect their bodies from foreign insults. Mammalian skin consists of two sets of barriers: stratum corneum (SC) and tight junctions (TJs). How acquisition of external antigens (Ags) by epidermal Langerhans cells (LCs) occur despite these barriers has remained unknown. We show that activation-induced LCs elongate their dendrites to penetrate keratinocyte (KC) TJs and survey the extra-TJ environment located outside of the TJ barrier, just beneath the SC. Penetrated dendrites uptake Ags from the tip where Ags colocalize with langerin/Birbeck granules. TJs at KC-KC contacts allow penetration of LC dendrites by dynamically forming new claudin-dependent bicellular- and tricellulin-dependent tricellular TJs at LC-KC contacts, thereby maintaining TJ integrity during Ag uptake. Thus, covertly under keratinized SC barriers, LCs and KCs demonstrate remarkable cooperation that enables LCs to gain access to external Ags that have violated the SC barrier while concomitantly retaining TJ barriers to protect intra-TJ environment. PMID: 19995951
Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS (2019)

Small RNA (sRNA) regulators promote efficient responses to stress, but the mechanisms for prioritizing target mRNA regulation remain poorly understood. This study examines mechanisms underlying hierarchical regulation by the sRNA SgrS, found in enteric bacteria and produced under conditions of metabolic stress. SgrS posttranscriptionally coordinates a nine-gene regulon to restore growth and homeostasis. An in vivo reporter system quantified SgrS-dependent regulation of target genes and established that SgrS exhibits a clear target preference. Regulation of some targets is efficient even at low SgrS levels, whereas higher SgrS concentrations are required to regulate other targets. In vivo and in vitro analyses revealed that RNA structure and the number and position of base pairing sites relative to the start of translation impact the efficiency of regulation of SgrS targets. The RNA chaperone Hfq uses distinct modes of binding to different SgrS mRNA targets, which differentially influences positive and negative regulation. The RNA degradosome plays a larger role in regulation of some SgrS targets compared to others. Collectively, our results suggest that sRNA selection of target mRNAs and regulatory hierarchy are influenced by several molecular features and that the combination of these features precisely tunes the efficiency of regulation of multi-target sRNA regulons.