gebhart/patrepeval huggingface dataset:
Novel long-wavelength emissive lysosome-targeting ratiometric fluorescent probes for imaging in live cells (2019)

Lysosomes are acidic organelles containing many hydrolytic enzymes responsible for degrading macromolecules. Aberrant lysosomal pH changes are known to associate with lysosomal dysfunctions linking to various diseases including cancer and neurodegenerative disorders. Thus, it is of paramount importance to monitor lysosomal pH changes in order to investigate the pathological conditions. We report herein two novel, highly sensitive and fast responsive carbazole-based ratiometric fluorescent probes with different emission wavelengths, namely MCDBI and MCDI for lysosomal pH detection and imaging. Importantly, the MCDBI and MCDI probes bearing indole and benzoindoles as acid-sensing sites exhibit pKa values of 4.26 and 4.51, respectively, which are ideal for the quantitative analysis of lysosomal pH changes in living cells. These probes exhibited a strong pH-dependent behavior and responded linearly and rapidly to minor pH fluctuations. Moreover, the two biocompatible probes are highly lysosomal targeting, sensitive towards H+ over metal ions and some bioactive molecules, and exhibit excellent photostability and good reversibility. These probes have excellent cell membrane permeability and are further applied successfully to monitor lysosomal pH fluctuations in the lysosomes of HepG2 cells.
IL-10 is involved in the protective effect of dibutyryl cyclic adenosine monophosphate on endotoxin-induced inflammatory liver injury (1995)

The effects of exogenous cAMP, dibutyryl cAMP (DBcAMP) on LPS-induced liver injury were examined in mice made hypersensitive to LPS by treatment with i.v. injection of Propionibacterium acnes. In vivo administration of DBcAMP significantly protected P. acnes-treated mice from LPS-induced liver injury, including apoptosis of hepatocytes. DBcAMP significantly increased circulating IL-10 level in correlation with suppression of the TNF-alpha level after LPS challenge in P. acnes-treated mice. Treatment with anti-IL-10 mAb abrogated the protective effect of DBcAMP on LPS-induced liver injury. Similar to in vivo findings, addition to DBcAMP to in vitro culture of liver adherent cells from P. acnes-treated mice enhanced IL-10 synthesis after LPS stimulation. These results suggest that the increment in IL-10 production by liver adherent cells is involved in the protective effect of DBcAMP on LPS-induced inflammatory liver injury.
Polariton spectroscopy of three-level atoms inside an optical cavity (2008)

Distinct peaks associated with atom-cavity polaritons are observed in the transmission spectrum of three-level rubidium atoms in an optically-dense vapor cell inside an optical ring cavity.
EphrinA4 mimetic peptide impairs fear conditioning memory reconsolidation in lateral amygdala (2022)

Fear memory may undergo a process after memory reactivation called reconsolidation. To examine the roles of ephrinA4 in fear memory reconsolidation an inhibitory ephrinA4 mimetic peptide (pep-ephrinA4), that targets the EphA binding site and inhibits EphA activation, was used. Pep-ephrinA4 was microinjected into the lateral amygdala (LA) of fear-conditioned rats 24 h after training and 30 min before tone CS memory retrieval. Memory retrieval was unaffected by pep-ephrinA4. However, the animals were impaired in fear memory tested 1 h or 24 h afterward when compared to controls. Fear-conditioned animals injected with pep-ephrinA4 into LA immediately after long-term memory retrieval were unaffected when tested 24 h afterward. Microinjection into LA of a peptide originated from an ephrinA4 site that does not interact with EphA did not affect fear memory reconsolidation. Rats that were administrated with pep-ephrinA4 systemically 24 h after fear conditioning and 30 min before CS memory retrieval were impaired in long-term fear conditioning memory tested 24 h afterward when compared to the control peptide. These results show that ephrinA4 binding sites are needed for long-term fear memory reconsolidation in LA and may serve as a target for the treatment of fear-related disorders by blocking reconsolidation.
Data from KIF5B-ALK, a Novel Fusion Oncokinase Identified by an Immunohistochemistry-based Diagnostic System for ALK-positive Lung Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; EML4-ALK is a transforming fusion tyrosine kinase, several isoforms of which have been identified in lung cancer. Immunohistochemical detection of EML4-ALK has proved difficult, however, likely as a result of low transcriptional activity conferred by the promoter-enhancer region of &lt;i&gt;EML4&lt;/i&gt;. The sensitivity of EML4-ALK detection by immunohistochemistry should be increased adequately.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We developed an intercalated antibody-enhanced polymer (iAEP) method that incorporates an intercalating antibody between the primary antibody to ALK and the dextran polymer-based detection reagents.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Our iAEP method discriminated between tumors positive or negative for &lt;i&gt;EML4-ALK&lt;/i&gt; in a test set of specimens. Four tumors were also found to be positive for ALK in an archive of lung adenocarcinoma (&lt;i&gt;n&lt;/i&gt; = 130) and another 4 among fresh cases analyzed in a diagnostic laboratory. These 8 tumors were found to include 1 with &lt;i&gt;EML4-ALK&lt;/i&gt; variant 1, 1 with variant 2, 3 with variant 3, and 2 with previously unidentified variants (designated variants 6 and 7). Inverse reverse transcription-PCR analysis revealed that the remaining tumor harbored a novel fusion in which intron 24 of &lt;i&gt;KIF5B&lt;/i&gt; was ligated to intron 19 of &lt;i&gt;ALK&lt;/i&gt;. Multiplex reverse transcription-PCR analysis of additional archival tumor specimens identified another case of lung adenocarcinoma positive for &lt;i&gt;KIF5B-ALK&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; The iAEP method should prove suitable for immunohistochemical screening of tumors positive for ALK or ALK fusion proteins among pathologic archives. Coupling of PCR-based detection to the iAEP method should further facilitate the rapid identification of novel ALK fusion genes such as &lt;i&gt;KIF5B-ALK&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Final Results of the Sunbelt Melanoma Trial: A Multi-Institutional Prospective Randomized Phase III Study Evaluating the Role of Adjuvant High-Dose Interferon Alfa-2b and Completion Lymph Node Dissection for Patients Staged by Sentinel Lymph Node Biopsy (2016)

No survival benefit for adjuvant HDI in patients with a single positive SLN was found. Among patients with tumor-negative SLN by conventional pathology but with melanoma detected in the SLN by RT-PCR, there was no OS benefit for CLND or CLND+HDI.
On-chip quantum teleportation (2013)

Integrated quantum optics provides great promise for enabling photonic experiments to reach new regimes of complexity. Chip-based fabrication enables sophisticated networks involving multiple interfering pathways in a compact and stable physical architecture. In a recent work we demonstrated an advance in the complexity of these integrated devices by showing the first quantum interference of three separate input photons. Such complexity allows the demonstration of three qubit protocols never before realised on-chip. Here, we report the first results showing quantum teleportation on an integrated photonic circuit. Quantum teleportation provides the mechanism for quantum relay schemes and is an important constituent in linear optical quantum computing. Whilst demonstrations to date have relied upon complex and fragile bulk optical systems, being able to teleport quantum states on a compact and stable integrated architecture will be a critical step towards scalable realisations of these schemes.
Latest Research Trends in Agrochemical Fungicides: Any Learnings for Pharmaceutical Antifungals? (2022)

For a long time, fungal pathogens have been a threat to the health and diet of humans. Consequently, antimycotic agents have been developed, which are called fungicides in agriculture and antifungals in medicine. Because fungi constantly develop resistance to established modes of action and because of the need for reducing the required use rates/doses, immense research efforts are still being undertaken to discover novel antimycotics. The research-based agrochemical industry has proven that these requirements can be fulfilled by a constant flow of novel fungicidal modes of action, the expansion of agronomical scope and applicability of existing fungicidal mode of action classes, and the design of resistance-breaking active ingredients in an established fungicidal mode of action class, if the molecular structure of the mutated fungal strain is known. Such strategies could be also useful for the discovery of novel antifungals.
Mild, Redox-Neutral Alkylation of Imines Enabled by an Organic Photocatalyst (2017)

An operationally simple, mild, redox-neutral method for the photoredox alkylation of imines is reported. Utilizing an inexpensive organic photoredox catalyst, alkyl radicals are readily generated from the single-electron oxidation of ammonium alkyl bis(catecholato)silicates and are subsequently engaged in a C-C bond-forming reaction with imines. The process is highly selective, metal-free, and does not require a large excess of the alkylating reagent or the use of acidic additives.
Detecting Information Literacy: Choose Your Own Adventure Video Series (2020)

Abstract Finding interesting approaches to teach the concepts of information literacy is a problem that many face in library instruction. The Lichtenberger Engineering Library at the University of Iowa has been working to create a fun and engaging way through an online video series that walks students through different parts of information literacy while allowing the students to choose their own path. Using the concept of the Choose Your Own Adventure books published by Bantam Books and the They Made Me Do Research series by the University of Northern Colorado, the Lichtenberger Engineering Library has set out to create a video series that will help students explore various topics of information literacy. Each series of videos, called a module, teaches one topic of information literacy. The first module – which has been completed – focuses on evaluating information using the CRAAP Test. The second module, which is under development, will focus on setting up search strategies. A module will consist of 18 to 20 videos, each less than 2 minutes in length. Each video will end with a question and require the viewer to choose from several video options. Each option takes the storyline in a different direction. The video series is no longer passive learning – by requiring the viewer to evaluate each scene and the potential outcomes, it becomes active engagement and learning. These videos will be embedded in various seminars and classes throughout the College of Engineering. They are created to help in both classroom instruction and as stand-alone learning tools. Completion of a module will award the student a digital badge that can be linked directly to an online course management system, allowing instructors to see who has completed the assignment. By completing a video series, or module, the student will have created their own adventure while learning different aspects of information literacy in a fun and engaging way.
The value of public-private collaborative real-world evidence platforms to monitor vaccine performance post authorization: DRIVE - a European initiative (2022)

The DRIVE partners propose that a debate on the benefits of Public-Private-Partnership-generated real-world evidence for vaccine effectiveness monitoring should be pursued to clarify roles and responsibilities, set up expectations, and decide the future environment for vaccine monitoring in Europe. In parallel, the driving factors behind PPP hesitancy should be studied.
Food chemistry and nutritional biochemistry (1985)

This comprehensive text on food chemistry and metabolism surveys molecular genetics. It is a narrative survey of basic food chemistry, basic nutritional research, food composition, food resource biochemistry and certain health implications of food constituents involved in both normal and abnormal nutritional conditions.
Letter to the editor – HPV vaccine and autoimmunity Incidence of new‐onset autoimmune disease in girls and women with pre‐existing autoimmune disease after quadrivalent human papillomavirus vaccination: a cohort study (2016)

Click here to view the Letter to the Editor by Dr. O. Grönlund et al .
Influence of step-like portions on the surface of ZnO/glass SAW filters on their frequency characteristics (1997)

The frequency amplitudes of surface acoustic wave (SAW) filters mass produced of zinc oxide (ZnO) films on glass were found to be different among the filters even when their center frequencies are the same. We attempted various experiments In order to reduce the deviation of amplitudes. We accidentally found that the frequency characteristics and the amplitude deviation could be improved by mirror-polishing the ZnO film surface. In a SAW filter with a ZnO/interdigital transducer (IDT)/glass substrate structure, periodic step-like portions due to the thickness of the finger electrode of IDT and fine roughness were present on the ZnO film surface. As a result of investigating the effect of surface structure on amplitude deviation, the step-like portions did not affect the electromechanical coupling factors but reduced the SAW phase velocities, experimentally and theoretically. In addition, it was clarified that the step-like portions due to the finger electrodes and fine roughness on the ZnO surface caused deviations in the SAW velocities and their reflections, causing the deviation in the amplitude characteristics.
Molecular diagnosis and novel genes and phenotypes in a pediatric thoracic insufficiency cohort (2023)

Thoracic insufficiency syndromes are a genetically and phenotypically heterogeneous group of disorders characterized by congenital abnormalities or progressive deformation of the chest wall and/or vertebrae that result in restrictive lung disease and compromised respiratory capacity. We performed whole exome sequencing on a cohort of 42 children with thoracic insufficiency to elucidate the underlying molecular etiologies of syndromic and non-syndromic thoracic insufficiency and predict extra-skeletal manifestations and disease progression. Molecular diagnosis was established in 24/42 probands (57%), with 18/24 (75%) probands having definitive diagnoses as defined by laboratory and clinical criteria and 6/24 (25%) probands having strong candidate genes. Gene identified in cohort patients most commonly encoded components of the primary cilium, connective tissue, and extracellular matrix. A novel association between KIF7 and USP9X variants and thoracic insufficiency was identified. We report and expand the genetic and phenotypic spectrum of a cohort of children with thoracic insufficiency, reinforce the prevalence of extra-skeletal manifestations in thoracic insufficiency syndromes, and expand the phenotype of KIF7 and USP9X-related disease to include thoracic insufficiency.
[Molecular cloning of MuLV proviruses integrated into the genome of mouse erythroleukemia cells. I. Characteristics of endogenous proviruses]. (1985)

The library of genes was obtained from erythroleukemic AKR cells (C-1), that were maintained as suspension culture. Thirty four clones that had homology with 60-70S RNA of Rauscher Leukemia virus (RLV) were separated from this library. The restriction mapping was carried out with 14 clones, that contained most extensive proviral sequences. One clone (107) contains proviral sequences that are derived from one of the components of the RLV complex. The other 13 clones contain sequences of endogenous xenotropic viruses. The endogenous retroviral sequences obtained differ in restrictive maps from proviruses of ecotropic and xenotropic infectious endogenous MuLV and, apparently, might be attributed as non-inducible infectious xenotropic MuLV of class III. Some of the cloned retroviral sequences had symmetrical structure, that is typical for integrated proviruses, i. e. these sequences were separated from flanking cellular ones by long terminal repeats. All investigated retroviral sequences are deletion mutants of MuLV proviruses. It was shown that the inner regions of proviruses diverged more than the long terminal repeats. The expression of the main inner MuLV polypeptide (p30) was detected in NIH 3T3 cells, transfected with DNA of some clones.
ChemInform Abstract: α‐SUBSTITUTED PHOSPHONATES. 37. DERIVATIVES OF α‐PYRROLOMETHYLPHOSPHONIC ACID AND N‐VINYLPYRROLES (1982)

Abstract Das α‐Aminomethanphosphonat (Ia) und seine α‐Aryl‐Derivate (Ib,c) reagieren mit dem THF (II) zu dem α‐Pyrrolomethanphosphonat (IIIa) und den α‐Aryl‐ Derivaten (IIIb,c).
Estimation of 3D shape and reflectance using multiple moiré images and shading model (2003)

We consider a method of determining the shape of object and the reflectance of its surface simultaneously using the Moiré technique and shape from shading. If the object surface has multiple reflectance, it must be classified to different reflectance. This classification is formulated as a simple clustering problem. By applying expectation-maximization(EM) algorithm, shape and reflectance can be estimated, and classification can be performed. However, as the relationship between the position of the light source and the gradient of the object surface gives rise to ambiguities in the reflectance, classification may fail. To solve this problem, we capture multiple Moiré images and propose a method of estimation using these images. The usefulness of the proposed method is confirmed by results obtained from simulation and real image experiments.
Whole-heart non-rigid motion corrected coronary MRA with autofocus virtual 3D iNAV (2022)

The proposed virtual 3D iNAV NRMC reconstruction further improved NRMC CMRA image quality by reducing artefacts arising from residual AP motion, however the level of improvement was subject-dependent.
Culturable bacterial populations associated with ectomycorrhizae of Norway spruce stands with different degrees of decline in the Czech Republic (2010)

The aim of this study was to determine which species of culturable bacteria are associated with ectomycorrhizae (ECM) of Norway spruce (Picea abies (L.) Karst) in the Sudety Mountains, exposed for years to atmospheric pollutants, acid rain, and climatic stress, and to identify particular species that have adapted to those conditions. Biolog identification was performed on bacterial species from ECM of adult spruce trees and seedlings of stands with low, intermediate, and high forest decline. Bacterial diversity in ECM associated with adult spruce trees, seedlings, and seedlings grown on monoliths was calculated; although the expected values appeared to vary widely, no significant differences among sites were observed. Dendrograms based on the identified bacterial species showed that stands with low forest decline clustered separately from the others. Principal component analysis of the normalized data for ECM-associated species showed a clear separation between stands with high forest decline and stands with low forest decline for seedlings and a less evident separation for adult spruce trees. In conclusion, shifts in ECM-associated culturable bacterial populations seem to be associated with forest decline in Norway spruce stands. Some bacterial species were preferentially associated with mycorrhizal roots depending on the degree of forest decline; this was more evident in seedlings where the species Burkholderia cepacia and Pseudomonas fluorescens were associated with, respectively, ECM of the most damaged stands and those with low forest decline.
Structure and organization of genes for sporozoite surface antigens (1984)

The major surface antigen (circumsporozoite-protein) of the sporozoite stage of Plasmodium knowlesi has been cloned and characterized. The gene is notable for the presence of a 36 base pair unit repeated in tandem 12 times. These repeats may function at the DNA level in regulating gene expression and at the protein level in providing multiple copies of a single epitope (repitope) as part of a protein designed to evade and decoy the immune system.
Birefringence control and dispersion characteristics of silicon oxynitride optical waveguides (1991)

The design, fabrication and characterisation of birefringent silicon oxynitride planar optical waveguides are described for applications at the wavelength of 1.54 μm. Form birefringence is attained by interposing a thin silicon nitride film in the waveguide stack, and can be controlled by adjusting the nitride layer thickness. Dispersion characteristics of the oxynitride waveguides have been measured and compared with theory.
Generation of high frequency gravitational waves (2001)

An electric charge shaken in an homogeneous stationary magnetic field produces both electromagnetic and gravitational waves (Gertsenshtein waves). We first study this process in a homogeneous medium with a refractive index n, expressing the gravitational wave as a simple functional of the electromagnetic field. Then, an inhomogeneous dielectric is considered: under certain conditions, the diffraction of a plane electromagnetic wave by a small dielectric sphere produces a promising gravitational energy flux.
<title>Optical and digital processing of radiographs for the early detection of osteoporosis</title> (1995)

The diagnosis of osteoporosis has traditionally been made by observing bone radiographs and analyzing the optical density. More advanced methods measure the mineral content or the quantity of bone tissue, but do not determine bone quality, which depends on the bone tissue architecture. The structure and organization of bone tissue is a vital factor for assessing bone strength, as minute changes in the structure strongly affect bone strength. This study describes a novel method, based on optical and digital image processing of conventional radiographs for a quantitative evaluation of bone tissue architecture. The trabecular pattern appearing on the femoral neck radiograph was analyzed based on the power spectrum of this pattern, which was obtained by optical Fourier transform. The two-dimensional optical power spectrum was captured to the computer by a CCD device and after filtering and noise reduction, it was characterized using spatial frequencies in different directions. Software was developed for the analysis of the power spectrum of the trabecular pattern to yield a bone index. The effect of the image optical density on the calculated bone index was not significant. On the other hand, the bone index, based on the trabecular structure, was found to differ significantly between normal and osteoporotic bones. Thus, the power spectrum analysis could differentiate normal from osteoporotic bones much better than the amount of radiation absorbed by the bone.