gebhart/patrepeval huggingface dataset:
Use of SC54 for the reduction of salmonella in swine (1997)

Infections caused by S. choleraesuis have significant economic impact on pork production in the United States (Wilcock and Schwartz 1992). An avirulent live culture vaccine has been described for the purpose of protecting pigs against infections caused by S. choleraesuis (Kramer, Roof et al. 1992) (Roof and Doitchinoff 1995). Other serotypes of Salmonella have been associated with infections in swine in the United States. These includeS. typhimurium and S. typhisuis (Wilcock and Schwartz 1992), S. heidelberg (Reed, Olander et al. 1985), and S. agona (Fernandez, Duhamel et al. 1993). Two experiments were conducted. Experiment number I was designed to determine the effect of an avirulent live culture vaccine (SC540, NOBL Laboratories, Inc.) in swine on an experimental infection of S. typhimurium. Experiment number 2 was designed to determine the effect of SC540 on Salmonella serogroups within a commercial swine farm.
Integrin Activation (2001)

Summary Integrins are cell surface adhesion receptors that participate in a variety of important processes throughout the vasculature. Here we summarize some recent findings on the regulation of integrin mediated cellular adhesion. Particular emphasis is placed on the regulation of integrin affinity for ligand (activation), although this is just one mechanism by which regulation of integrin-dependent cell adhesion can occur. Also discussed are recent observations on the structural basis of integrin activation, the role of the cytoplasmic domain in integrin affinity regulation, and potential mechanisms by which activation signals are propagated from integrin cytoplasmic domains to the extracellular ligand binding domain.
Space-Based Voice over IP Networks (2007)

In human space exploration missions, there will be a need to provide voice communications services. In this work we focus on the performance of Voice over IP (VoIP) techniques applied to space networks, where long range latencies, simplex links, and significant bit error rates occur. Link layer and network layer overhead issues are examined. We posit that imposing additional speech processing latencies in the form of multiple frames per packet is tolerable in the space regime, and show resulting performance overhead improvements. Furthermore, we find that even with channel bit error rates of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> and 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> , the frame size does not severely degrade the original speech.
Correction: Corrigendum: A polyalanine peptide derived from polar fish with anti-infectious activities (2016)

Scientific Reports 6: Article number: 21385; published online: 26 February 2016; updated: 20 July 2016 In this Article, there is a typographical error in the Results section. “Pa-MAP 1.9 (NH2-LAAKLTKAATKLTAALTKLAAALT-COOH) was designed …” should read: “Pa-MAP 1.9 (NH2-LAAKLTKAATKLTAALTKLAAALTAAAT-COOH) was designed …”
Modeling the Dardanelles strait outflow plume using a coupled model system (2009)

The ADvanced CIRCulation Model, ADCIRC, and the HYbrid Coordinate Ocean Model, HYCOM, are coupled in the Northern Aegean Sea. Over its 62 km, the Dardanelles Strait connects the Aegean Sea to the Marmara Sea. The Dardanelles outflow spreads to the Aegean Sea as a buoyant plume showing seasonal characteristics. The unstructured nature of the ADCIRC mesh provides the resolution necessary to model flow in the narrow strait whose minimum width is about 1 km. During one-way coupling efforts, ADCIRC is initialized using interannual solutions for temperature, salinity, velocity and water surface elevation fields taken from a larger domain HYCOM-AMB model, covering the Aegean, Marmara and Black Seas. Experiments using the one-way coupled model system are targeted at early February and late May of 2003 representing typical winter-spring and summer-fall conditions, respectively.
The effect of a metallic Ni core on charge dynamics in CdS-sensitized p-type NiO nanowire mesh photocathodes (2013)

We report on the synthesis and photoelectrochemical characterization of photocathodes based on CdS-sensitized Ni–NiO core-shell nanowire mesh inverse opals (IOs). Compared to the NiO–CdS nanowire mesh IO electrode, the hole diffusion coefficient of the CdS-sensitized Ni–NiO core-shell nanowire mesh IO photocathode was one order of magnitude larger, indicating that the Ni core facilitated hole transfer in nanostructured p-type electrodes. As a result, the charge-collection efficiency of the Ni–NiO core-shell nanowire mesh IO electrode was shown to be essentially 100%.
In vivo developmental modifications of the expression of genes encoding muscle-specific enzymes in rat. (1986)

cDNA clones for rat muscle-type creatine kinase and glycogen phosphorylase and aldolase A were isolated from a rat muscle cDNA library. An additional clone recognizing an unidentified 2.7-kilobase pair mRNA species was also isolated. These cDNA clones were used as probes to investigate the expression of the corresponding mRNAs during muscle development. Two aldolase A mRNA species were detected, one of 1650 bases expressed in non-muscle tissues, fetal muscle, and adult slow-twitch muscle, the other of 1550 bases was highly specific of adult fast-twitch skeletal muscle differentiation. These aldolase A mRNAs were shown by primer extension to differ by their 5' ends. The accumulation of muscle-type phosphorylase and creatine kinase and muscle-specific aldolase A mRNA accumulation during muscle development seems to be a coordinate process occurring progressively from the 17th day of intrauterine life up to the 30th day after birth. In contrast, the 2.7-kilobase pair RNA species is maximally expressed at the 1st week after birth as is the neonatal form of myosin heavy chain mRNA.
Effect of Nonuniform Deuterium Labeling on Small-Angle Neutron Scattering Results for Polymer Blends (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of Nonuniform Deuterium Labeling on Small-Angle Neutron Scattering Results for Polymer BlendsGlenn C. Reichart, Richard A. Register, William W. Graessley, Ramanan Krishnamoorti, and David J. LohseCite this: Macromolecules 1995, 28, 26, 8862–8864Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/ma00130a021https://doi.org/10.1021/ma00130a021research-articleACS PublicationsRequest reuse permissionsArticle Views135Altmetric-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
Flexible computational photodetectors for self-powered activity sensing (2022)

Abstract Conventional vision-based systems, such as cameras, have demonstrated their enormous versatility in sensing human activities and developing interactive environments. However, these systems have long been criticized for incurring privacy, power, and latency issues due to their underlying structure of pixel-wise analog signal acquisition, computation, and communication. In this research, we overcome these limitations by introducing in-sensor analog computation through the distribution of interconnected photodetectors in space, having a weighted responsivity, to create what we call a computational photodetector. Computational photodetectors can be used to extract mid-level vision features as a single continuous analog signal measured via a two-pin connection. We develop computational photodetectors using thin and flexible low-noise organic photodiode arrays coupled with a self-powered wireless system to demonstrate a set of designs that capture position, orientation, direction, speed, and identification information, in a range of applications from explicit interactions on everyday surfaces to implicit activity detection.
Two methods for auto-organizing personal web history (2003)

Two methods for automatically organizing personal web history were developed and evaluated, and compared to the Internet Explorer history. One method grouped visited web pages based on similarity of root URL and time co-occurrence. The second method started with the similarity ratings and further associated or dissociated web pages using an associative learning rule. In a preliminary experiment, participants reported that both methods organized their web history significantly more like their own mental organization of their web history than did IE history. Participants were also faster to revisit web pages using both organizations than when using IE history.
Oligomeric Aβ-induced synaptic dysfunction in Alzheimer’s disease (2014)

Alzheimer's disease (AD) is a devastating disease characterized by synaptic and neuronal loss in the elderly. Compelling evidence suggests that soluble amyloid-β peptide (Aβ) oligomers induce synaptic loss in AD. Aβ-induced synaptic dysfunction is dependent on overstimulation of N-methyl-D-aspartate receptors (NMDARs) resulting in aberrant activation of redox-mediated events as well as elevation of cytoplasmic Ca2+, which in turn triggers downstream pathways involving phospho-tau (p-tau), caspases, Cdk5/dynamin-related protein 1 (Drp1), calcineurin/PP2B, PP2A, Gsk-3β, Fyn, cofilin, and CaMKII and causes endocytosis of AMPA receptors (AMPARs) as well as NMDARs. Dysfunction in these pathways leads to mitochondrial dysfunction, bioenergetic compromise and consequent synaptic dysfunction and loss, impaired long-term potentiation (LTP), and cognitive decline. Evidence also suggests that Aβ may, at least in part, mediate these events by causing an aberrant rise in extrasynaptic glutamate levels by inhibiting glutamate uptake or triggering glutamate release from glial cells. Consequent extrasynaptic NMDAR (eNMDAR) overstimulation then results in synaptic dysfunction via the aforementioned pathways. Consistent with this model of Aβ-induced synaptic loss, Aβ synaptic toxicity can be partially ameliorated by the NMDAR antagonists (such as memantine and NitroMemantine). PSD-95, an important scaffolding protein that regulates synaptic distribution and activity of both NMDA and AMPA receptors, is also functionally disrupted by Aβ. PSD-95 dysregulation is likely an important intermediate step in the pathological cascade of events caused by Aβ. In summary, Aβ-induced synaptic dysfunction is a complicated process involving multiple pathways, components and biological events, and their underlying mechanisms, albeit as yet incompletely understood, may offer hope for new therapeutic avenues.
Inhibition of Epidermal Growth Factor-Mediated ERK1/2 Activation by in Situ Electroporation of Nonpermeant [(alkylamino)methyl]Acrylophenone Derivatives (1998)

The interruption of signaling cascades in intact cells through the introduction of nonpermeant compounds inferred by in vitro studies to specifically inhibit epidermal growth factor (EGF) receptor (EGF-R) function is described. Two nonpermeant [(alkylamino)methyl]acrylophenone derivatives, [(dimethylamino)methyl] acrylo-para-[(benzoylsulfonyl)-oxy]phenone and [(dimethylamino)-methyl]acrylo-para-[(hydroxy-benzoylsulfonyl++ +)-oxy]phenone, were introduced by in situ electroporation into mouse or rat fibroblasts growing on indium-tin oxide-coated glass. Cells were subsequently stimulated with growth factors and assessed for activation of a downstream target, the extracellular signal-regulated kinase (ERK1/2), by probing with specific antibodies. Electrodes and slides were configured to provide non-electroporated control cells side by side with the electroporated ones, both growing on the same type of indium-tin oxide-coated glass surface. Using this set-up, these compounds could inhibit EGF- but not platelet-derived growth factor (PDGF)-mediated ERK1/2 activation in vivo. These results demonstrate the potential of the in situ electroporation approach for the study of tyrosine kinase action using selective but nonpermeant inhibitors that would otherwise be ineffective in intact cells.
Posttranscriptional control of human homeobox gene expression in induced NTERA‐2 embryonal carcinoma cells (1989)

We have studied the expression of four human homeobox genes representative of four different clusters (i.e., HOX-1, HOX-2, HOX-3 and HOX-5) in the embryonal carcinoma (EC) cell line NT2/D1. Following treatment with retinoic acid (RA), these cells differentiate into several cell types, including neurons, and steadily accumulate polyadenylated transcripts derived from the genes in a period ranging from 18 hr to 14 days of RA treatment. The sizes of major transcripts in differentiated EC cells coincide with those previously detected by the same probes in human embryos. Nuclear run-on transcriptional analysis showed no difference in the transcription rate of the four homeobox genes in differentiated vs. undifferentiated EC cells. Inhibition of protein synthesis by 5-18 hr of treatment of undifferentiated cells with cycloeximide causes accumulation of some homeobox transcripts at levels comparable to those observed after 18 hr of RA induction, although it does not cause superinduction in fully differentiated cells. These data suggest that the activation of homeobox gene expression in RA-induced EC cells is controlled, at least in part, by posttranscriptional mechanisms.
Optical Linewidth and RF Phase Noise Reduction of a Chip-scale CPM Laser Using COEO Multi-tone Injection Locking (2017)

A novel method of regenerative mode-locking using multi-tone optical injection locking of a chip-scale CPM laser is demonstrated. This technique achieves simultaneous reduction in RF phase noise (8x) and narrows the longitudinal mode by 4,000x.
Anion‐exchange HPLC separation of five major rabbit lipoproteins using a nonporous diethylaminoethyl‐ligated gel with a perchlorate‐containing eluent (2011)

Rabbits are often used as experimental animals in studies of atherosclerosis and hyperlipidemia. Although rabbit lipoproteins can be quantitated by sequential ultracentrifugation, a simpler and more reproducible method is desirable for detailed analyses. The current study describes a method to analyze rabbit lipoproteins in plasma by anion-exchange high-performance liquid chromatography using a column filled with nonporous, diethylaminoethyl-ligated polymers. A solution of NaClO₄ was used to adjust the ionic strength of the eluent. The method required only 15 μL of plasma and analysis was completed in 23 min. Five lipoprotein fractions (high-density lipoprotein, low-density lipoprotein, intermediate-density lipoprotein, very-low-density lipoprotein and chylomicrons) were eluted with step-wise increases in a concentration of NaClO₄. The post-column eluate was reacted with an enzymatic reagent to determine total cholesterol, and the lipoprotein-cholesterol fraction was calculated according to relative peak areas in the chromatogram. The within-day and between-day assay coefficients of variation for lipoprotein cholesterol levels ranged between 0.436 and 7.143% and between 2.905 and 10.526%, respectively. Administering a high-fat diet increased lipoprotein-cholesterol concentrations by 6- to 77-fold. The method described here was nevertheless able to quantitate levels of lipoprotein-cholesterol in plasma samples from these rabbits. These results indicate that this method may be applied to lipoprotein studies using hyperlipidemic rabbit models.
Gene Co-expression Connectivity Predicts Gene Targets Underlying High Ionic Liquid Tolerance in Yarrowia lipolytica (2022)

ABSTRACT Microbial tolerance to organic solvents such as ionic liquids (ILs) is a robust phenotype beneficial for novel biotransformation. While most microbes become inhibited in 1%-5% (v/v) IL (e.g., 1-ethyl-3-methylimidazolium acetate), we engineered a robust Yarrowia lipolytica (YlCW001) that tolerates a record high of 18% (v/v) IL via adaptive laboratory evolution. Yet, genotypes conferring high IL tolerance in YlCW001 remain to be discovered. Using dynamic RNA-Seq data, we shed light on the underlying cellular processes that Y. lipolytica responds to IL. We introduced Gene Co-expression Connectivity (GeCCo) to discover genotypes conferring desirable phenotypes that might not be found by the conventional differential expression (DE) approaches. GeCCo selects genes based on their number of co-expressed genes in a sub-network of upregulated genes by the target phenotype. We experimentally validated GeCCo by reversely engineering high IL-tolerant phenotype in wildtype Y. lipolytica . We found that gene targets selected by both DE and GeCCo exhibited the best statistical chance at increasing IL tolerance when individually overexpressed. Remarkably, the best combination of dual-overexpressed genes were genes selected by GeCCo alone. This non-intuitive combination of genes, BRN1 and OYE2, are involved in guiding/regulating mitotic cell division, chromatin segregation/condensation, microtubule and cytoskeletal organization, and Golgi vesicle transport.
Urban Planning and Corona Spaces – Scales, Walls and COVID-19 Coincidences (2020)

This study focuses on the role and responsibility of urban planning in mitigating the COVID-19 pandemic ́s impact. The far-reaching social and economic consequences of this threat are counteracted by organisational and constructional measures to prevent lockdowns and finally illnesses and deaths. Corona spaces and voids are introduced as a consistent multi scale approach concerning the pandemics spatial implications and respective measures. These terms are operationalised for urban planning and can be used as an overarching concept to be communicated within cross-sectoral planning tasks. A comparison of Taiwan's and the USA's responses to the outbreak suggests that the coincidence at the beginning of a pandemic can be controlled by institutional precautions. On an urban scale, organisational measures (e.g. contact tracing, quarantine, and lockdown) can be supported by constructional ones concerning e.g. transport, public spaces, urban agriculture, and offices aimed at crowding reduction. If appropriate measures are applied, urban density does not seem to increase spreading the virus, whereby a regression analysis based on data of districts in Germany shows no relationship between population density and COVID-19 deaths. Lockdown prevention should be a planning goal and multifunctional approaches that integrate aspects of virus resilience should be favoured over the monothematic urban development approach (Leitbild) of a virus resilient city. Urban planning can contribute to the mitigation of future outbreaks by including pandemic preparedness in planning frameworks.
python-pillow/Pillow: (2021)

https://pillow.readthedocs.io/en/stable/releasenotes/8.1.2.html
ChemInform Abstract: SYNTHESIS OF A PROTECTED PHOSPHOAMINO ACID, Nα‐TERT‐BUTYLOXYCARBONYL‐O‐DIETHYLPHOSPHORO‐L‐SERINE (1983)

Abstract Zum Aufbau phosphorylierter Peptide wird das geschützte, phosphorylierte Serin (V) benötigt, das auf dem skizzierten Wege ausgehend von N‐tert.‐Boc‐Serin (I) in guten Ausbeuten zugänglich ist.
Molecular and immunochemical analyses ofRB1 and cyclin D1 in human ductal pancreatic carcinomas and cell lines (1996)

Somatic mutations in the retinoblastoma-1 gene (RB1) and loss of RB1 protein function have been implicated in a number of human malignancies, but the role of RB1 gene and protein abnormalities in ductal pancreatic cancer (DPCA) is virtually unknown. We therefore analyzed expression of the RB1 protein immunohistochemically and/or by western blotting in a total of 54 sporadic and eight familial cases of archival and frozen DPCA and in 18 pancreatic carcinoma cell lines by using the antibodies RB-WL-1, 84-B3-1, and PMG3-245. Mutations in the RB1 promotor region and exons 13-21 of the RB1 gene were likewise examined by single-strand conformation polymorphism (SSCP) analyses and DNA sequencing of genomic DNA from 30 microdissected primary pancreatic tumors and the pancreatic carcinoma cell lines. Moreover, amplification and expression of a major regulatory component of RB1 function, cyclin D1, were assessed by southern and immunohistochemical analyses, respectively. The DPCAs were heterogeneous in both the intensity of RB1 nuclear staining and the percentage of immunoreactive cells. The tumors often had areas where RB1 staining was weak or absent adjacent to normal pancreatic tissue; however, only two of 32 archival cases and one of 30 frozen cases of DPCA completely lacked RB1 nuclear staining. Immunohistochemical and western blot analyses of 18 pancreatic carcinoma cell lines demonstrated the absence of RB1 expression in only two cell lines, Capan-1 and QGP-1. Analyses of the RB1 gene and promotor region by SSCP and DNA sequencing largely confirmed the immunochemical findings. Three of 30 primary carcinomas had abnormalities revealed by SSCP analyses. In one case a single base-pair deletion was confirmed in exon 18 and resulted in premature termination and the absence of detectable RB1 protein. A second case had TAC-->TTC missense mutation in exon 13. The third primary carcinoma could not be reliably sequenced because it had a low percentage of epithelial cells. The cyclin D1 gene was not amplified in any of the primary pancreatic tumors or cell lines examined. These immunochemical and molecular analyses of the RB1 tumor suppressor gene and cyclin D1 proto-oncogene in a large series of human pancreatic cancers and cell lines indicate that RB1 and cyclin D1 alterations occur during the development of some human DPCAs. Nevertheless, it is probable that alterations in cell-cycle regulation in DPCAs more frequently involve pathways other than those involving RB1 and cyclin D1.
Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution (2012)

There is a particularly high interest to derive carotenoids such as β-carotene and lutein from higher plants and algae for the global market. It is well known that β-carotene can be overproduced in the green microalga Dunaliella salina in response to stressful light conditions. However, little is known about the effects of light quality on carotenoid metabolism, e.g., narrow spectrum red light. In this study, we present UPLC-UV-MS data from D. salina consistent with the pathway proposed for carotenoid metabolism in the green microalga Chlamydomonas reinhardtii. We have studied the effect of red light-emitting diode (LED) lighting on growth rate and biomass yield and identified the optimal photon flux for D. salina growth. We found that the major carotenoids changed in parallel to the chlorophyll b content and that red light photon stress alone at high level was not capable of upregulating carotenoid accumulation presumably due to serious photodamage. We have found that combining red LED (75 %) with blue LED (25 %) allowed growth at a higher total photon flux. Additional blue light instead of red light led to increased β-carotene and lutein accumulation, and the application of long-term iterative stress (adaptive laboratory evolution) yielded strains of D. salina with increased accumulation of carotenoids under combined blue and red light.