gebhart/patrepeval huggingface dataset:
Gain-of-Function Mutants of the Cytokinin Receptors AHK2 and AHK3 Regulate Plant Organ Size, Flowering Time and Plant Longevity (2017)

The phytohormone cytokinin is a regulator of numerous processes in plants. In Arabidopsis (<i>Arabidopsis thaliana</i>), the cytokinin signal is perceived by three membrane-located receptors named ARABIDOPSIS HISTIDINE KINASE2 (AHK2), AHK3, and AHK4/CRE1. How the signal is transmitted across the membrane is an entirely unknown process. The three receptors have been shown to operate mostly in a redundant fashion, and very few specific roles have been attributed to single receptors. Using a forward genetic approach, we isolated constitutively active gain-of-function variants of the <i>AHK2</i> and <i>AHK3</i> genes, named <i>repressor of cytokinin deficiency2</i> (<i>rock2</i>) and <i>rock3</i>, respectively. It is hypothesized that the structural changes caused by these mutations in the sensory and adjacent transmembrane domains emulate the structural changes caused by cytokinin binding, resulting in domain motion propagating the signal across the membrane. Detailed analysis of lines carrying <i>rock2</i> and <i>rock3</i> alleles revealed how plants respond to locally enhanced cytokinin signaling. Early flowering time, a prolonged reproductive growth phase, and, thereby, increased seed yield suggest that cytokinin regulates various aspects of reproductive growth. In particular, it counteracts the global proliferative arrest, a correlative inhibition of maternal growth by seeds, an as yet unknown activity of the hormone.
One-dimensional behavior and high thermoelectric power factor in thin indium arsenide nanowires (2015)

Electrical conductivity and Seebeck coefficient of quasi-one-dimensional indium arsenide (InAs) nanowires with 20 nm diameter are investigated. The carrier concentration of the passivated nanowires was modulated by a gate electrode. A thermoelectric power factor of 1.7 × 10−3 W/m K2 was measured at room temperature. This value is at least as high as in bulk-InAs and exceeds by far typical values of thicker InAs nanowires with three-dimensional properties. The interpretation of the experimental results in terms of power-factor enhancement by one-dimensionality is supported by model calculations using the Boltzmann transport formalism.
A Resource Allocation Framework for Network Slicing (2018)

Telecommunication networks are converging to a massively distributed cloud infrastructure interconnected with software defined networks. In the envisioned architecture, services will be deployed flexibly and quickly as network slices. Our paper addresses a major bottleneck in this context, namely the challenge of computing the best resource provisioning for network slices in a robust and efficient manner. With tractability in mind, we propose a novel optimization framework which allows fine-grained resource allocation for slices both in terms of network bandwidth and cloud processing. The slices can be further provisioned and auto-scaled optimally based on a large class of utility functions in real-time. Furthermore, by tuning a slice-specific parameter, system designers can trade off traffic-fairness with computing-fairness to provide a mixed fairness strategy. We also propose an iterative algorithm based on the alternating direction method of multipliers (ADMM) that provably converges to the optimal resource allocation and we demonstrate the method's fast convergence in a wide range of quasi-stationary and dynamic settings.
Immunoisolation of Tumor Cells: Generation of Antitumor Immunity Through Indirect Presentation of Antigen (1997)

In recent years, a number of cancer therapies have been developed based on the augmentation of the immune response in the tumor-bearing individual. We have developed a novel approach to such therapies, using a membrane-bound immunoisolation device containing tumor cells to enhance the immune response of mice to the adenocarcinoma, MCA-38. Use of an immunoisolation device for cancer immunotherapy has several advantages. First, safety is enhanced because the reintroduced tumor cells are sequestered within the device. Second, the immunoisolation device permits introduction and maintenance of live cells that can stimulate the immune system for extended periods. Finally, the cells can be quantitatively removed at the end of the treatment period. Cells derived from the murine adenocarcinoma cell line MCA-38 were implanted into mice within a membrane-enclosed (immunoisolation) device. After 3 weeks, the animals were challenged by injection of free tumor cells. All of the control animals (lacking implants or with empty devices) developed tumor at the challenge site, whereas all of the animals that received devices containing tumor cells remained tumor free. The animals also remained tumor free after a second challenge. It is our hypothesis that antigens shed from tumor cells within the device are taken up by antigen-presenting cells of the host and thus indirectly initiate the activation of the immune system.
Biophysical Characterization of gp41 Aggregates Suggests a Model for the Molecular Mechanism of HIV-associated Neurological Damage and Dementia (2000)

In human immunodeficiency virus (HIV)-infected individuals, the level of the HIV envelope protein gp41 in brain tissue is correlated with neurological damage and dementia. In this paper we show by biochemical methods and electron microscopy that the extracellular ectodomain of purified HIV and simian immunodeficiency virus gp41 (e-gp41) forms a mixture of soluble high molecular weight aggregate and native trimer at physiological pH. The e-gp41 aggregate is shown to be largely alpha-helical and relatively stable to denaturants. The high molecular weight form of e-gp41 is variable in size ranging from 7 to 70 trimers, which associate by interactions at the interior of the aggregate involving the loop that connects the N- and C-terminal helices of the e-gp41 core. The trimers are predominantly arranged with their long axes oriented radially, and the width of the high molecular weight aggregate corresponds to the length of two e-gp41 trimers (approximately 200 A). Using both light and electron microscopy combined with immunohistochemistry we show that HIV gp41 accumulates as an extracellular aggregate in the brains of HIV-infected patients diagnosed with dementia. We postulate that the high molecular weight aggregates of e-gp41 are responsible for HIV-associated neurological damage and dementia, consistent with known mechanisms of encephalopathy.
A Ground Fault Location Method for DC Railway Systems (2023)

The application of Direct Current (DC) railway systems is more and more noticeable as they conform most of urban tram feeding systems and, step-by-step, it is being introduced in high-speed train power systems. Despite of their high efficiency, the risk of ground faults is latent due to environmental problems and aging in the catenary. These faults can interrupt the service for hours until it is repaired, then a quick maintenance is needed. In order to help in this issue, this paper proposes a ground fault location method for catenaries in DC railway systems based on the DC voltage and earth current measurement in each DC traction substation (TS). The normalized currents respecting the global fault current are compared with a model-based data pool allowing the method to locate the fault along the protected catenary. To corroborate the method, simulations have been performed in a three-TS DC railway model in Matlab-Simulink obtaining promising results.
NKp30 isoforms and NKp46 transcripts in metastatic melanoma patients: Unique NKp30 pattern in rare melanoma patients with favorable evolution (2016)

Given the NK cell-based immunosurveillance of melanoma, we investigated the prognostic value of NKp46 transcript and NKp30 isoform (NKp30A, NKp30B and NKp30C) profiling in blood of 187 melanoma patients including 13 long survivors (LS), metastatic patients that have controlled the disease. Compared to healthy volunteers (HV), patients had reduced amounts of transcripts of the three NKp30 isoforms (NKp30 A, B and C) but similar ratios between NKp30 isoforms (ΔAB, ΔAC, ΔBC). Stratification of patients according to disease stage showed higher NKp30C and lower NKp46 transcripts in stage IV patients. Furthermore, patients with previous history of conventional chemotherapy displayed reduced NKp30A transcripts. The expression levels of NKp30 isoforms failed to predict survival from sampling of patients, while NKp46 expression predicted melanoma outcome. LS patients displayed elevated NKp30A levels, accordingly high ΔAB and ΔBC ratios, and a unique pattern of rare allelic variants of NKp30 SNPs. Moreover, NK cells from LS displayed correlated NKp30/NKp46 membrane expression, high spontaneous and NKp30- or NKp46-triggered degranulation. These data outline the impact of NKp30 and NKp46 transcripts on melanoma evolution and identify unique genetic features of NKp30 associated with higher NK activation in rare LS melanoma patients that control a metastatic disease.
Protein binding and signaling properties of RIN1 suggest a unique effector function (1997)

Human RIN1 was first characterized as a RAS binding protein based on the properties of its carboxyl-terminal domain. We now show that full-length RIN1 interacts with activated RAS in mammalian cells and defines a minimum region of 434 aa required for efficient RAS binding. RIN1 interacts with the "effector domain" of RAS and employs some RAS determinants that are common to, and others that are distinct from, those required for the binding of RAF1, a known RAS effector. The same domain of RIN1 that binds RAS also interacts with 14-3-3 proteins, extending the similarity between RIN1 and other RAS effectors. When expressed in mammalian cells, the RAS binding domain of RIN1 can act as a dominant negative signal transduction blocker. The amino-terminal domain of RIN1 contains a proline-rich sequence similar to consensus Src homology 3 (SH3) binding regions. This RIN1 sequence shows preferential binding to the ABL-SH3 domain in vitro. Moreover, the amino-terminal domain of RIN1 directly associates with, and is tyrosine phosphorylated by, c-ABL. In addition, RIN1 encodes a functional SH2 domain that has the potential to activate downstream signals. These data suggest that RIN1 is able to mediate multiple signals. A differential pattern of expression and alternate splicing indicate several levels of RIN1 regulation.
In Situ Bioprinting of Autologous Skin Cells Accelerates Wound Healing of Extensive Excisional Full-Thickness Wounds (2019)

The early treatment and rapid closure of acute or chronic wounds is essential for normal healing and prevention of hypertrophic scarring. The use of split thickness autografts is often limited by the availability of a suitable area of healthy donor skin to harvest. Cellular and non-cellular biological skin-equivalents are commonly used as an alternative treatment option for these patients, however these treatments usually involve multiple surgical procedures and associated with high costs of production and repeated wound treatment. Here we describe a novel design and a proof-of-concept validation of a mobile skin bioprinting system that provides rapid on-site management of extensive wounds. Integrated imaging technology facilitated the precise delivery of either autologous or allogeneic dermal fibroblasts and epidermal keratinocytes directly into an injured area, replicating the layered skin structure. Excisional wounds bioprinted with layered autologous dermal fibroblasts and epidermal keratinocytes in a hydrogel carrier showed rapid wound closure, reduced contraction and accelerated re-epithelialization. These regenerated tissues had a dermal structure and composition similar to healthy skin, with extensive collagen deposition arranged in large, organized fibers, extensive mature vascular formation and proliferating keratinocytes.
Elastoplastic Micromechanical Modeling of Two-Dimensional Irregular Convex and Nonconvex (Re-entrant) Hexagonal Foams (1998)

A nonlinear micromechanical model for two-dimensional irregular hexagonal foams has been developed that allows for anisotropy in morphology and/or material. Based upon the orientation, cross section, length, and material properties of each strut, the resulting microlevel beam behavior within the unit cell determines its structural properties. Nonlinearity is introduced as coupled elastoplastic beam behavior, where the elastoplastic behavior of each beam is considered. The analytical. formulation for the stiffness matrix of the general elastoplastic unit cell is. found by considering compatibility and equilibrium of the unit cell. The structural properties of the elastoplastic unit cell are embedded in a continuum finite element model as material properties, thus capturing the microstructure of the foam in an accurate and efficient model. Structural nonlinearity is therefore directly linked to localized plasticity and its evolution at the microlevel. Elastic analyses investigated the degree of anisotropy in structural properties that was induced by various morphological changes. The differences in stress and deformation behavior between a regular hexagonal foam and a re-entrant foam were also demonstrated. Plastic analyses showed how structural nonlinearity could be explained by localized microstructural behavior. The advantage of this micromechanical model is that it allows a study of the effects of morphology and/or material anisotropies on the overall foam behavior.
Asymmetric patterns of gap junctional communication in developing chicken skin (1993)

To study the pattern of gap junctional communication in chicken skin and feather development, we injected Lucifer Yellow into single cells and monitored the transfer of the fluorescent dye through gap junctions. Dye coupling is present between cells of the epithelium as well as between cells of the mesoderm. However, dye transfer did not occur equally in all directions and showed several consistent patterns and asymmetries, including: (1) no dye coupling between mesoderm and epithelium, (2) partial restriction of dye coupling at the feather bud/interbud boundary during early feather bud development, (3) preferential distribution of Lucifer Yellow along the anteroposterior axis of the feather placode and (4) absence of dye coupling in some epithelial cells. These results suggest the presence of preferential pathways of communication that may play a role in the patterning of chicken skin.
Demonstration of bend-induced nonlinearities in large-mode-area fibers (2007)

We present what we believe to be the first direct measurements of enhanced nonlinearities in large-mode-area fibers due to bend induced reductions in effective area. Both Raman scattering and self-phase modulation are observed to increase in tightly coiled fibers. The measured increase in nonlinearity compares well with predictions from simulations of the modal effective area.
Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation (2013)

Recombineering in bacteria is a powerful technique for genome reconstruction, but until now, it was not generally applicable for development of small-molecule producers because of the inconspicuous phenotype of most compounds of biotechnological relevance. Here, we establish recombineering for Corynebacterium glutamicum using RecT of prophage Rac and combine this with our recently developed nanosensor technology, which enables the detection and isolation of productive mutants at the single-cell level via fluorescence-activated cell sorting (FACS). We call this new technology RecFACS, which we use for genomic site-directed saturation mutagenesis without relying on pre-constructed libraries to directly isolate L-lysine-producing cells. A mixture of 19 different oligonucleotides was used targeting codon 81 in murE of the wild-type, at a locus where one single mutation is known to cause L-lysine production. Using RecFACS, productive mutants were screened and isolated. Sequencing revealed 12 different amino acid exchanges in the targeted murE codon, which caused different L-lysine production titers. Apart from introducing a rapid genome construction technology for C. glutamicum, the present work demonstrates that RecFACS is suitable to simply create producers as well as genetic diversity in one single step, thus establishing a new general concept in synthetic biology.
Shared and distinctive neighborhoods of emerin and LBR revealed by proximity labeling and quantitative proteomics (2022)

Abstract Emerin and LBR are abundant transmembrane proteins of the nuclear envelope (NE) that are concentrated at the inner nuclear membrane (INM). Although both proteins interact with chromatin and nuclear lamins, they have distinctive biochemical and functional properties. Here we have deployed proximity labeling using the engineered biotin ligase TurboID (TbID) and quantitative proteomics to compare the neighborhoods of emerin and LBR in cultured mouse embryonic fibroblasts (MEFs). Our analysis revealed 232 high confidence proximity partners (HCPP) that interact selectively with emerin and/or LBR, 49 of which are shared by both. These included previously characterized NE-concentrated proteins, as well as a host of additional proteins not previously linked to emerin or LBR functions. Many of these are TM proteins of the ER and include two E3 ubiquitin ligases. Using the proximity ligation assay as an orthogonal approach, we validated the interactions described by proximity labeling for 11/12 proteins analyzed, supporting the robustness of our analysis. Overall, this work presents methodology that may be used for large-scale mapping of the landscape of the INM and reveals a group of new proteins with potential functional connections to emerin and LBR.
Supplemental Figures 1 - 4 from Genome-Wide Identification and Characterization of Novel Factors Conferring Resistance to Topoisomerase II Poisons in Cancer (2023)

&lt;p&gt;Figure S1: Keap1, SMARCB1, SMARCA4 and ARID1A regulate resistance to doxorubicin. Figure S2: Keap1 controls expression of NQO1 through Nrf2. Figure S3: C9orf82 regulates DNA double strand break repair. Figure S4: Expression of SWI/SNF complex subunits correlates to clinical outcome.&lt;/p&gt;
High-resolution imaging using ultrasound-modulated optical tomography (2004)

We present an implementation of ultrasound-modulated optical tomography that has the potential to provide high resolution images of tissue structures at a penetration depth of several millimeters. Light and pulsed ultrasound are focused on an approximately 100 &mu;m wide area below the sample surface. With this configuration, the length of the ultrasonic pulses determines the axial resolution, and the lateral resolution results from the width of the ultrasonic beam at the focus. Diffuse light reflected from the sample is collected into a fiber and the modulated component is separated from the background by a confocal Fabry-Perot interferometer. Using this setup, high contrast images are obtained of 100 &mu;m wide pieces of hair that are buried one millimeter below the surface of the tissue-mimicking sample. It is the first time, to the authors' knowledge, that images with such high resolution have been obtained using ultrasound-modulated optical tomography in the reflection mode.
Integrated optical components in silicon for high speed analog-to-digital conversion (2007)

Advances in femtosecond lasers and laser stabilization have led to the development of sources of ultrafast optical pulse trains that show jitter on the level of a few femtoseconds over tens of milliseconds and over seconds if referenced to atomic frequency standards. These low jitter sources can be used to perform opto-electronic analog to digital conversion that overcomes the bottleneck set by electronic jitter when using purely electronic sampling circuits and techniques. Electronic Photonic Integrated Circuits (EPICs) may enable in the near future to integrate such an opto-electronic analog-to-digital converters (ADCs) completely. This presentation will give an overview of integrated optical devices such as low jitter lasers, electro-optical modulators, Si-based filter banks, and high-speed Si-photodetectors that are compatible with standard CMOS processing and which are necessary for the implementation of EPIC-chips for advanced opto-electronic ADCs.
Milk casein: inhibitor of lipoxygenase-catalyzed lipid peroxidation (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMilk casein: inhibitor of lipoxygenase-catalyzed lipid peroxidationSimo Laakso and Esa Matti LiliusCite this: J. Agric. Food Chem. 1982, 30, 5, 913–916Publication Date (Print):September 1, 1982Publication History Published online1 May 2002Published inissue 1 September 1982https://pubs.acs.org/doi/10.1021/jf00113a026https://doi.org/10.1021/jf00113a026research-articleACS PublicationsRequest reuse permissionsArticle Views88Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Detecting Bacillus cereus spores on a mail sorting system using Raman spectroscopy (2004)

Abstract The ability of Raman spectroscopy to detect anthrax‐causing spores as they pass through a mail sorting system was investigated. A pump was connected to an existing vacuum manifold on a commercial sorter, and a filter designed to capture 0.5–3 µm particles was placed in‐line. A standard business letter containing 0.23 g of Bacillus cereus spores, a Bacillus anthracis surrogate, was placed in a stack of 20 letters and passed through the system. Raman spectra of the filter positively identified the captured material as bacterial spores by the dominant calcium dipicolinate Raman spectral bands associated with the spore core. A limit of detection, using 400 mW of 785 nm laser excitation for a 1‐s acquisition, is estimated at 4.5 mg. The ability of a Raman spectroscopy based system to detect and prevent the distribution of a letter containing gram levels of anthrax spores is discussed. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Supplementary Table 1-3 from MicroRNA-Related Genetic Variants Associated with Clinical Outcomes in Early-Stage Non–Small Cell Lung Cancer Patients (2023)

&lt;p&gt;Supplementary Table 1-3 PDF file - 162K, Supplementary tables 1 and 2 include effect of selected SNPs on overall survival or recurrence in early stage NSCLC patients; Supplementary table 3 includes all the SNPs selected in the analysis&lt;/p&gt;
An N-heterocyclic carbene iridium catalyst with metal-centered chirality for enantioselective transfer hydrogenation of imines (2017)

A cyclometalating N-heterocyclic carbene iridium complex featuring metal-centered chirality was designed and used for the asymmetric transfer hydrogenation (ATH) of imines. Four strongly σ-donating carbon-based substituents (2 carbenes and 2 phenyl moieties), a chirality transfer directly from the stereogenic metal center to the C[double bond, length as m-dash]N bond of substrates, as well as a restriction of catalyst deactivation by steric demanding substituents, render the new complex one of the most efficient catalysts for ATH of cyclic N-sulfonylimines (down to 0.01 mol% cat., 24 examples, 94-98% ee).