gebhart/patrepeval huggingface dataset:
Cryomicroscopic analysis of freezing in liver of the freeze-tolerant wood frog (1992)

The technique of directional solidification coupled with low-temperature scanning electron microscopy was applied to analyze the freezing of liver slices from the freeze-tolerant frog Rana sylvatica. Micrographs of liver slices from 5 degrees C-acclimated frogs frozen on the directional stage to -7 degrees C showed continuous ice formed along an expanded vasculature with hepatocytes that were shrunken and virtually dehydrated. However, when frogs were given a survivable freezing exposure at -4 degrees C for 24 h, liver slices subsequently frozen in vitro at -7 degrees C were much less shrunken and the presence of intracellular ice crystals (formed when samples were plunged into liquid N2 before microscopy) demonstrated that ample free water remained in these hepatocytes at -7 degrees C. This reduced level of cell dehydration was correlated with the buildup of 280 +/- 61 mumol/g wet wt glucose as a cryoprotectant in liver during the -4 degrees C exposure in vivo. The study provides the first direct cytological analysis of the freezing process in an organ of a freeze-tolerant vertebrate and the first confirmation of the relationship between maintenance of a critical minimum cell volume and freezing survival by these animals.
Coupled-Cluster Studies of Extensive Green Fluorescent Protein Models Using the Reduced Virtual Space Approach (2015)

Accurate predictions of photoexcitation properties are a major challenge for modern methods of theoretical chemistry. We show here how approximate coupled-cluster singles and doubles (CC2) calculations in combination with the reduced virtual space (RVS) approach can be employed in studies of excited states of large biomolecular systems. The RVS-CC2 approach is used for accurately predicting optical properties of the p-hydroxybenzylidene-dihydroimidazolinone (p-HBDI) chromophore embedded in green fluorescent protein (GFP) models using quantum mechanical calculations in combination with large basis sets. We study the lowest excited states for the isolated and protein-embedded chromophore in two different protonation states, and show how omitting high-lying virtual orbitals in the RVS calculation of excitation energies renders large-scale CC2 studies computationally feasible. We also discuss how the error introduced by the RVS approach can be systematically estimated and controlled. The obtained CC2 excitation energies of 3.13-3.27 and 2.69-2.77 eV for the two protonation states of different protein models are in excellent agreement with the maxima of the experimental absorption spectra of 3.12-3.14 and 2.61-2.64 eV, respectively. Thus, the calculated energy splitting between the excited states of the two protonation states is 0.44-0.52 eV, which agrees very well with the experimental value of 0.48-0.51 eV. The calculations at the RVS-CC2 level on the protein models show the importance of using large QM regions in studies of biochromophores embedded in proteins.
Non-invasive Longitudinal Tracking of Human Amniotic Fluid Stem Cells in the Mouse Heart (2008)

Human stem cells from various sources have potential therapeutic applications. The clinical implementation of these therapies introduces the need for methods of noninvasive tracking of cells. The purpose of this study was to evaluate a high resolution magnetic resonance imaging (MRI) technique for in vivo detection and tracking of superparamagnetic micron sized iron oxide particle (MPIO)-labeled human amniotic fluid stem (hAFS) cells injected in the mouse heart. Because of the small subject size, MR signal and resolution of the in vivo MRI were increased using strong gradients, a 7.0 Tesla magnet, and an ECG and respiratory gated gradient echo sequence. MRI images of mouse heart were acquired during a 4 week course of this longitudinal study. At the end of the study, histological analysis was used to correlate cell localization with the MRI results. Introduction of MPIOs into hAFS had no significant effect upon cell proliferation and differentiation. Results of flow cytometry analysis indicated that hAFS cells remained labeled for up to 4 weeks. MRI of MPIO-labeled hAFS cells injected in agarose gels resulted in significant hypointense regions. Labeled hAFS cells injected into mouse hearts produced hypointense regions in the MR images that could be detected 24 hours and 7, 14, 21 and 28 days post injection. The co-localization of labeled cells within the hypointense regions was confirmed by histological analysis. These results indicate that high resolution MRI can be used successfully for noninvasive longitudinal tracking of hAFS cells injected in the mouse heart. The potential utility of this finding is that injected stem cells can be tracked in vivo and might serve to monitor cell survival, proliferation and integration into myocardial tissue.
Measuring changing spatial complexity in ventricular fibrillation using the Karhunen-Loeve decomposition of 506-channel epicardial data (2002)

The Karhunen-Loeve (K-L) decomposition was used to describe quantitatively changes in spatial organization during extended episodes of ventricular fibrillation (VF). VF was induced by premature stimulation in 5 pigs. Unipolar epicardial electrograms were simultaneously recorded with a 22/spl times/23 array of electrodes spaced 1.12 mm apart. Data consisting of epicardial potentials during VF, as well as during sinus rhythm, were decomposed into orthogonal spatial modes using the K-L method. In sinus rhythm, 3-4 K-L modes were required to account for 90% of the total variance, compared to 5-28 during VF. As VF progressed from 1 to 3 seconds the number of modes, M*, required to reach the 90% threshold increased in, every animal. From 5 seconds to 60 seconds M* always decreased. These differences were significant with p<0.05, suggesting that electrically induced VF in pigs increases in organization during the first minute after initiation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mitochondria‐targeted disruptors and inhibitors of cytochrome c/cardiolipin peroxidase complexes: A new strategy in anti‐apoptotic drug discovery (2008)

The critical role of mitochondria in programmed cell death leads to the design of mitochondriotropic agents as a strategy in regulating apoptosis. For anticancer therapy, stimulation of proapoptotic mitochondrial events in tumor cells and their suppression in surrounding normal cells represents a promising paradigm for new therapies. Different approaches targeting regulation of components of mitochondrial antioxidant system such as Mn-SOD demonstrated significant antitumor efficiency, particularly in combination therapy. This review is focused on a newly discovered early stage of mitochondria-dependent apoptosis - oxidative lipid signaling involving a mitochondria-specific phospholipid cardiolipin (CL). Cytochrome c (cyt c) acts as a CL-specific peroxidase very early in apoptosis. At this stage, the hostile events are still secluded within the mitochondria and do not reach the cytosolic targets. CL oxidation process is required for the release of pro-apoptotic factors into the cytosol. Manipulation of cyt c interactions with CL, inhibition of peroxidase activity, and prevention of CL peroxidation are prime targets for the discovery of anti-apoptotic drugs acting before the "point-of-no-return" in the fulfillment of the cell death program. Therefore, mitochondria-targeted disruptors and inhibitors of cyt c/CL peroxidase complexes and suppression of CL peroxidation represent new strategies in anti-apoptotic drug discovery.
Marine Natural Products. XXXVI. Biologically Active Polyacetylenes, Adociacetylenes A, B, C, and D, from an Okinawan Marine Sponge of Adocia sp. (1996)

Adociacetylenes A (1), B (2), C (3), and D (4) were isolated as new polyacetylenes from an Okinawan marine sponge of Adocia sp. Their chemical structures have been elucidated on the bases of their chemical and physicochemical properties. Adociacetylenes A (1), C (3), and D (4) exhibited inhibitory activity in the in vitro endothelial cell-neutrophil leukocyte adhesion assay.
(Pyridinylmethylidene)dithioles: synthesis, structure, and reactivity (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT(Pyridinylmethylidene)dithioles: synthesis, structure, and reactivityKevin T. Potts, Susan A. Nye, and Kennith A. SmithCite this: J. Org. Chem. 1992, 57, 14, 3895–3901Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/jo00040a032https://doi.org/10.1021/jo00040a032research-articleACS PublicationsRequest reuse permissionsArticle Views565Altmetric-Citations19LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Promoter methylation of MCAM, ERα and ERβ in serum of early stage prostate cancer patients (2017)

Promoter methylation of MCAM, ERα and ERβ have a potential to be utilized as biomarker for the early detection of prostate PC as their sensitivity and specificity seem to be better than serum PSA in our cohort of samples. After robust validation in a larger prospective cohort, our findings may reduce the numbers of unwarranted prostate biopsies.
Intricacies for Posttranslational Tumor-Targeted Cytokine Gene Therapy (2013)

The safest and most effective cytokine therapies require the favorable accumulation of the cytokine in the tumor environment. While direct treatment into the neoplasm is ideal, systemic tumor-targeted therapies will be more feasible. Electroporation-mediated transfection of cytokine plasmid DNA including a tumor-targeting peptide-encoding sequence is one method for obtaining a tumor-targeted cytokine produced by the tumor-bearing patient's tissues. Here, the impact on efficacy of the location of targeting peptide, choice of targeting peptide, tumor histotype, and cytokine utilization are studied in multiple syngeneic murine tumor models. Within the same tumor model, the location of the targeting peptide could either improve or reduce the antitumor effect of interleukin (IL)12 gene treatments, yet in other tumor models the tumor-targeted IL12 plasmid DNAs were equally effective regardless of the peptide location. Similarly, the same targeting peptide that enhances IL12 therapies in one model fails to improve the effect of either IL15 or PF4 for inhibiting tumor growth in the same model. These interesting and sometimes contrasting results highlight both the efficacy and personalization of tumor-targeted cytokine gene therapies while exposing important aspects of these same therapies which must be considered before progressing into approved treatment options.
Scaling of the sampling period in nonlinear system identification (2005)

The paper presents a scaling algorithm for system identification, based on a nonlinear black box differential equation model. The model is discretized by an Euler forward numerical integration scheme. A scale factor is applied to the explicitly appearing sampling period, when iterating the discrete time state space model and the corresponding gradient recursion. The result is an exponential scaling of the state components of the model, and a scaling of the estimated parameter vector. The original parameter vector can be explicitly calculated from the scaled parameter vector using a diagonal matrix that is a function only of the scale factor. A new analysis of the effect of scaling on the Hessian, shows how the same diagonal matrix affects its eigenvalue distribution. A simulation study illustrates the beneficial effects on e.g. the condition number that can be obtained with the algorithm.
Development and Validation of the Actionable Bladder Symptom Screening Tool for Multiple Sclerosis Patients (2013)

Bladder symptoms such as urinary urgency, frequency, and incontinence are common in people with multiple sclerosis (MS). These symptoms, which often result from neurogenic detrusor overactivity (NDO), can have a major impact on patients' day-to-day lives. However, in many cases they are over-looked in the clinical management of MS. The objective of this study was to develop and validate a reliable, sensitive, and specific screening tool for patients with bladder problems related to MS. We performed a literature review and then conducted a content validation study followed by a multisite observational study of a new screening tool, the Actionable Bladder Symptom Screening Tool (ABSST). All ABSST domains as well as the total score met the threshold for good internal consistency (Cronbach α ≥ 0.70), with a Cronbach α value of 0.95 for the total score and values ranging from 0.85 to 0.90 for the three domains. The validity of the ABSST was demonstrated by high correlation of the domains and total score with the Overactive Bladder Questionnaire Short Form (OAB-q SF) Symptom Severity and Total Health-Related Quality of Life (HRQOL) scores (Spearman correlation coefficient ≥ 0.782). The predictive validity of the ABSST total score to identify patients who might receive a recommendation to see a urologist was strong. This new instrument, which was developed with input from clinicians as well as MS patients, meets the current content validity and psychometric testing thresholds established by the US Food and Drug Administration, with high sensitivity and specificity.
Relating requirements to implementation via topic analysis: Do topics extracted from requirements make sense to managers and developers? (2012)

Large organizations like Microsoft tend to rely on formal requirements documentation in order to specify and design the software products that they develop. These documents are meant to be tightly coupled with the actual implementation of the features they describe. In this paper we evaluate the value of high-level topic-based requirements traceability in the version control system, using Latent Dirichlet Allocation (LDA). We evaluate LDA topics on practitioners and check if the topics and trends extracted matches the perception that Program Managers and Developers have about the effort put into addressing certain topics. We found that effort extracted from version control that was relevant to a topic often matched the perception of the managers and developers of what occurred at the time. Furthermore we found evidence that many of the identified topics made sense to practitioners and matched their perception of what occurred. But for some topics, we found that practitioners had difficulty interpreting and labelling them. In summary, we investigate the high-level traceability of requirements topics to version control commits via topic analysis and validate with the actual stakeholders the relevance of these topics extracted from requirements.
A non-canonical role for the EDC4 decapping factor in regulating MARF1-mediated mRNA decay (2020)

EDC4 is a core component of processing (P)-bodies that binds the DCP2 decapping enzyme and stimulates mRNA decay. EDC4 also interacts with mammalian MARF1, a recently identified endoribonuclease that promotes oogenesis and contains a number of RNA binding domains, including two RRMs and multiple LOTUS domains. How EDC4 regulates MARF1 action and the identity of MARF1 target mRNAs is not known. Our transcriptome-wide analysis identifies bona fide MARF1 target mRNAs and indicates that MARF1 predominantly binds their 3' UTRs via its LOTUS domains to promote their decay. We also show that a MARF1 RRM plays an essential role in enhancing its endonuclease activity. Importantly, we establish that EDC4 impairs MARF1 activity by preventing its LOTUS domains from binding target mRNAs. Thus, EDC4 not only serves as an enhancer of mRNA turnover that binds DCP2, but also as a repressor that binds MARF1 to prevent the decay of MARF1 target mRNAs.
Extent of branching from linear viscoelasticity of long‐chain‐branched polymers (2004)

Abstract We present new results and examine literature data concerning the linear viscoelastic behavior of polyethylene with sparse to intermediate levels of long‐chain branching (LCB). These branched polymers displayed a common rheological signature, namely, a region of frequency‐independent loss tangent along with the corequisite scaling of the storage and loss moduli to the same frequency exponent. This apparent power‐law response occurred within a finite frequency window and bore resemblance to the behavior of physical gels. The appearance of this region, however, was the consequence of the presence of two distinct, yet partially overlapping, terminal relaxation processes. After considering the analogous relaxation behavior of wholly linear polymers with bimodal molecular weight distributions, we considered the polymers with LCB as blends of linear and branched species to develop a simple method of quantifying the extent of LCB. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 1671–1684, 2004
09201 Abstracts Collection – Self-Healing and Self-Adaptive Systems (2009)

From May 10th 2009 to May 15th 2009 the Dagstuhl Seminar 09201 ``Self-Healing and Self-Adaptive Systems'' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar are put together in this paper. Links to extended abstracts or full papers are provided, if available. A description of the seminar topics, goals and results in general can be found in a separate document ``Executive Summary''.
Biosynthesis of Commodity Chemicals From Oil Palm Empty Fruit Bunch Lignin (2021)

Lignin is one of the most abundant natural resources that can be exploited for the bioproduction of value-added commodity chemicals. Oil palm empty fruit bunches (OPEFBs), byproducts of palm oil production, are abundant lignocellulosic biomass but largely used for energy and regarded as waste. Pretreatment of OPEFB lignin can yield a mixture of aromatic compounds that can potentially serve as substrates to produce commercially important chemicals. However, separation of the mixture into desired individual substrates is required, which involves expensive steps that undermine the utility of OPEFB lignin. Here, we report successful engineering of microbial hosts that can directly utilize heterogeneous mixtures derived from OPEFB lignin to produce commodity chemicals, adipic acid and levulinic acid. Furthermore, the corresponding bioconversion pathway was placed under a genetic controller to autonomously activate the conversion process as the cells are fed with a depolymerized OPEFB lignin mixture. This study demonstrates a simple, one-pot biosynthesis approach that directly utilizes derivatives of agricultural waste to produce commodity chemicals.
Hochsensitive mtDNA Sequenzierung in Plattenepithelkarzinomen des Hals-/Kopf-Bereiches als Marker der Tumorheterogenität und Lymphknotenmetastasierung (2018)

Die Prognose und Wahl der Behandlungsmodalität bei Plattenepithelkarzinomen des Hals-/Kopf-Bereiches hängt mit dem Vorhandensein von Lymphknoten (LK) Metastasen zusammen. Aktuelle Tests für die Detektion von Mikrometastasen in LK, sind möglicherweise zu wenig sensitiv. Hier bieten moderne Techniken auf Basis der NGS neue Chancen zur Verbesserung der Risikobeurteilung und Therapiewahl. Aufgrund ihrer Klonalität, höherer Mutationsrate und Anzahl pro Zelle, könnte sich die Analyse von tumorspezifischen Mutationen der mitochondrialen DNA (mtDNA) in histologisch tumorfreien LK zu einem sensitiven Werkzeug entwickeln. Zusätzlich ist die mtDNA wegen ihrer zirkulären Konfiguration stabiler als genomische DNA und könnte deshalb auch in Formalin fixiertem in Paraffin eingebettetem Material untersucht werden, einer extrem wertvollen Ressource in der klinischen Forschung. Für die Tiefensequenzierung der gesamten mtDNA, speziell auch für fraktionierte DNA haben wir einen Amplicon basierten Ansatz entwickelt. Mit diesem haben wir 28 Plattenepithelkarzinome (multiregionale Sequenzierung für Tumorheterogenität) und multiple zugehörige LK-Metastasen sowie tumorfreie LK sequenziert. Soweit vorhanden wurden auch Speichel, Serum und Plasma geprüft. Es wurde eine Abdeckung der mtDNA von 97% erreicht und eine mittlere Sequenzierungstiefe von 4179X. In 8 von 16 multiregional untersuchten Tumoren fanden sich klonale Mutationen, nebst einer ausgeprägten intratumoralen Heterogenität. Interessanterweise hatten 6 Patienten in zum Teil multiplen histologisch tumorfreien LK mtDNA Mutationen.
Preliminary Result of Percutaneous Screw Fixation for Bone Bruise of the Tibial Plateau (2015)

This study reports the preliminary results of surgical treatment of bone bruise of the tibial plateau. Twelve patients underwent percutaneous screw fixation with a mean follow-up of 15 months. The mean duration of surgery was 15 minutes. Preoperatively, 1 week postoperatively, 1 month postoperatively, 6 months postoperatively, and 12 months postoperatively, the mean visual analog scale scores were 7.3, 2.6, 1.2, 0.6, and 0.5, respectively. The mean Hospital for Special Surgery scores were 56, 78, 89, 95, and 98, respectively. In selective patients with bone bruise, the percutaneous screw fixation is feasible to resolve pain and prevent compression of the articular surface.
Rearrangement of (±)-Flavipucine and Its Diastereoisomer. Chemistry of the Transformation Product (1977)

Flavipucine rearranges under a variety of conditions via bond reorganization involving C-C bond cleavage of the epoxide function to yield the isobutylglyoxal acetal of 3,4-dihydroxy-6-methyl-2-pyridone.Transformations of this product are presented in support of its structure.In view of a recent article by Findlay 3 , l .l concerned with the rearrangement of (-)-flavipucine, we are prompted to report our findings which differ from those of the aforementioned authors in significant respects.Recently we published the total synthesis of (f)-flavipucine and its diastereoisomer.2It had been observed at that time that both of these substances on silica gel produce a minor amount of the same entity, more polar than flavipucine.The substance in question may be prepared by a variety of techniques including warming in benzene at 50' with DABCO, treatment in benzene with BF etherate at ambient temperatures, by melting,la or best by refluxing in 3 xylene.By the latter technique an 80% yield of rearrangement product can be realized after 10 hr.M.p. 163-64°;1b ir (CHC13) 2. 20-4.40,5.78, 5.98 and 6.17~; hMeoH 304 (E, 6290), 250 (2100) and 216 nm (20550); nmr (CDC13) 66.02 (s, 7 4 , max + 5.95 (broad s, 5-H), 2.37 (s, 6-CH3 and 0.93 (d, J 6 Hz CHMe2); M 237; Calcd for C H 0 N: C, 60.