gebhart/patrepeval huggingface dataset:
MicroRNA Polymorphisms and Risk of Colorectal (2014)

Background: miRNAs act as post-transcriptional regulators of geneexpression.GeneticvariationinmiRNA-encoding sequences or their corresponding binding sites may affect the fidelity of the miRNA–mRNA interaction and subsequently alter the risk of cancer development. Methods: This study expanded the search for miRNA-related polymorphisms contributing to the etiology of colorectal cancer acrossthegenomeusinganovelplatform,theAxiommiRNATarget SiteGenotypingArray(237,858markers).Afterqualitycontrol,the study included 596 cases and 429 controls from the Molecular Epidemiology of Colorectal Cancer study, a population-based case–control study of colorectal cancer in northern Israel. The association between each marker and colorectal cancer status was examined assuming a log-additive genetic model using logistic regression adjusted for sex, age, and two principal components. Results: Twenty-three markers had P values less than 5.0E� 04, and the most statistically significant association involved rs2985 (chr6:34845648; intronic of UHRF1BP1 ;O R ¼ 0.66; P ¼ 3.7E� 05). Furthermore, this study replicated a previously published risk locus, rs1051690, in the 3 0 -untranslated region of the insulin receptor gene INSR (OR ¼ 1.38; P ¼ 0.03), with strong evidence of differences in INSR gene expression by genotype. Conclusions: This study is the first to examine associations between genetic variation in miRNA target sites and colorectal cancer using a genome-wide approach. Functional studies to identify allele-specific effects on miRNA binding are needed to confirm the regulatory capacity of genetic variation to influence risk of colorectal cancer. Impact: This study demonstrates the potential for an miRNA-targeted genome-wide association study to identify candidate susceptibility loci and prioritize them for functional characterization. Cancer Epidemiol Biomarkers Prev; 24(1); 65–72. � 2014 AACR.
Infrared reflector based on liquid crystal polymers and its impact on thermal comfort conditions in buildings (2014)

There has been a huge increase in the global demand of energy over the last few years. One of the main contributors to energy consumption in buildings, cars, greenhouses and indoor spaces is the cooling devices needed to maintain the indoor temperature at comfortable levels. To reduce the energy used by cooling devices, we need improved light control in transparent building elements, such as windows. Infrared (IR) reflectors applied to the windows for rejection of infrared light would be very attractive, especially if they do not affect light in the visible region. A method to selectively and precisely control infrared transmission is via the use of cholesteric liquid crystal (Ch-LC) polymer reflectors. Ch-LCs, also known as chiral-nematic LCs, reflect circularly polarized light as a result of their self-organizing molecular helices. The pitch of the helix in these networks determines the wavelength of reflection. In contrast to existing alternatives, they are characterized by a very sharp cut-off between the transmissive and the reflective state enabling exact tailoring of the heat reflection. In this article we have focused on fabrication of infrared reflectors using Ch-LCs and a computational model was used to predict the energy savings of this IR-reflector in an office building in Abu Dhabi which indicated that 6 % energy savings can be realized.
Semantics and verification of information-based protocols (2012)

Information-Based Interaction-Oriented Programming, specifically as epitomized by the Blindingly Simple Protocol Language (BSPL), is a promising new approach for declaratively expressing multiagent protocols. BSPL eschews traditional control flow operators and instead emphasizes causality and integrity based solely on the information models of the messages exchanged. BSPL has been shown to support a rich variety of practical protocols and can be realized in a distributed asynchronous architecture wherein the agents participating in a protocol act based on local knowledge alone. The flexibility and generality of BSPL mean that it needs a strong formal semantics to ensure correctness as well as automated tools to help develop protocol specifications.We provide a formal semantics for BSPL and formulate important technical properties, namely, enactability, safety, and liveness. We further describe our declarative implementation of the BSPL semantics as well as of verifiers for the above properties using a temporal reasoner. We have validated our implementation by verifying the correctness of several protocols of practical interest.
Mechanically and Physiologically Optimizing Prosthetic Elevated Vacuum Systems in People with Transtibial Amputation: A Pilot Study (2021)

Practitioners may use individual responses to optimize socket vacuum pressure settings, balancing mechanical and physiological effects of EV for improved clinical outcomes.
Grate aerodynamic : Model strategies for gas flow through a 2D iron ore pellet bed (2014)

Godkänd; 2014; 20140923 (andbra)
Bonding in clusters. Part 6. An evaluation of Stone's theory of bonding in closo-borane anions, through MNDO calculations (1983)

MNDO calculations on closo-borane anions are used to assess the accuracy of a recently reported theory of their electronic structure and bonding. The assumptions and results of the theory are found to be fully supported, and parameters are determined that allow molecular orbital energies and composition to be calculated in a manner similar to Hückel theory. The theory is found to be equally applicable to closo-carborane molecules, and parameters are determined for these, and also accounts for the exo-BH bonding orbitals. The implications of Stone's theory for the bonding of related metal clusters are considered.
Mapping the sequences of potential guanine quadruplex motifs (2011)

The knowledge that potential guanine quadruplex sequences (PQs) are non-randomly distributed in relation to genomic features is now well established. However, this is for a general potential quadruplex motif which is characterized by short runs of guanine separated by loop regions, regardless of the nature of the loop sequence. There have been no studies to date which map the distribution of PQs in terms of primary sequence or which categorize PQs. To this end, we have generated clusters of PQ sequence groups of various sizes and various degrees of similarity for the non-template strand of introns in the human genome. We started with 86 697 sequences, and successively merged them into groups based on sequence similarity, carrying out 66 clustering cycles before convergence. We have demonstrated here that by using complete linkage hierarchical agglomerative clustering such PQ sequence categorization can be achieved. Our results give an insight into sequence diversity and categories of PQ sequences which occur in human intronic regions. We also highlight a number of clusters for which interesting relationships among their members were immediately evident and other clusters whose members seem unrelated, illustrating, we believe, a distinct role for different sequence types.
Patterns in detection of recurrence among patients treated for breast cancer. (2020)

e14020 Background: Follow-up programs for breast cancer should according to ASCO and ESMO consist of regular visits including anamnestic screening for symptoms of recurrence and physical examination for ten years in addition to regular mammography. Recently, the Danish guideline for follow-up after early breast cancer was revised. Today most patients are offered open access to an outpatient clinic, but no scheduled visits following the first year after surgery. This strategy has been studied in regards to psychological and health related quality of life outcomes, but not in regards to detection of recurrence and survival. The aim of this study was to quantify the recurrences detected at scheduled outpatient visits in Denmark before the implementation of revised follow-up guidelines. Furthermore, we aimed to assess whether the duration of symptoms prior to recurrence detection differed depending on type of visit when recurrence was detected. Methods: We conducted a cross-sectional study among 310 patients with recurrent breast cancer. Through medical records, we retrieved information on type of visit when recurrence was detected, localization of recurrence, symptoms reported, and duration of symptoms. Tumor characteristics were obtained from the Danish Breast Cancer Group database. Results: Among the 310 breast cancer recurrences, more than half were distant (59%), 26% were loco-regional, and 15% loco-regional and distant. Among the 199 patients still in outpatient follow-up at time of recurrence, recurrence was detected at a scheduled outpatient visit (21%), at a patient-requested extra outpatient visit (15%), by the general practitioner or other specialist (47%), or on a scheduled mammography (11%). Among patients with recurrence detected at a scheduled outpatient visit, the majority (88%) reported symptoms related to the recurrence. Patients who waited for the scheduled outpatient visit despite symptoms had a markedly longer duration of symptoms (median 21 weeks) prior to detection of recurrence than patients who requested an extra visit (median 8 weeks). Conclusions: One-fifth of recurrences among patients attending outpatient follow-up were detected at scheduled outpatient visits. The majority was symptomatic, but the patients had not altered their scheduled appointment. Whether recurrences like these will be detected in follow-up without scheduled visits is unknown. Some recurrences may be detected earlier, if patients can be educated to react on relevant symptoms, but some recurrences may be detected with further delay. Thus, more research in this area is needed.
Supplementary Figure S4 from EGFR and RB1 as Dual Biomarkers in HPV-Negative Head and Neck Cancer (2023)

&lt;p&gt;(A) Kaplan-Meier survival curves stratified by the expression of the indicated marker (patients treated with surgery only and patients treated with surgery and radiation therapy were included) and multivariate analysis for each marker. Kaplan-Meier survival curves for T1/2 and T3/4 tumors stratified by the expression of (B) NSDHL, (C) PTEN, and (D) BCAR1. Based on AQUA-expression scores.&lt;/p&gt;
Bidirectional induction of the cognate receptor-ligand α4/VCAM-1 pair defines a novel mechanism of tumor intravasation (2000)

Engagement of cell surface adhesion receptors with extracellular constituents and with cellular counter-receptors is crucial for the extravasation of blood-borne neoplastic cells and their seeding at distant sites; however, the early events of tumor dissemination-ie, the intravasation step(s)-have been largely neglected. A role for the alpha4beta7 integrin was hypothesized to explain the high leukemogenicity exhibited by one (NQ22) among several T-cell lymphomas studied. To clarify the mechanisms of early aggressivity, the behavior of highly and poorly leukemogenic cell lines were compared in vitro. Cocultivation of physically separated leukemic cells with resting endothelial cells resulted in the up-regulation of VCAM-1 expression. NQ22 cells expressed mRNA of different cytokines that up-regulate VCAM-1 and at higher levels than cells of a nonaggressive lymphoma, and they migrated more efficiently through an activated endothelial cell layer. With the use of neutralizing antibodies against interferon-gamma, granulocyte macrophage colony-stimulating factor, and tumor necrosis factor (TNF)-alpha, it was determined that TNF-alpha is one of the soluble factors released by NQ22 cells involved in the up-regulation of VCAM-1. The finding that vascular cells within the early local growth were strongly positive for VCAM-1 indicated that NQ22 cells could activate endothelial cells also in vivo. Finally, cocultivation of preleukemic alpha4(-)NQ22 cells with TNF-alpha-activated endothelial cells induced the expression of alpha4 integrins on the former cells. Reciprocal up-regulation and engagement of alpha4/VCAM-1 pairs determined the sequential transmigration and intravasation steps, and similar mechanisms might affect the aggressivity of human T lymphoblastic lymphomas.
Assessment of Imaging Modalities Against Liver Biopsy in Nonalcoholic Fatty Liver Disease: The Amsterdam NAFLD‐NASH Cohort (2021)

2 TECHNICAL EFFICACY: 2.
The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells (2023)

Telomeres are the nucleoprotein structures at the ends of linear chromosomes. Telomeres are transcribed into long non-coding Telomeric Repeat-Containing RNA (TERRA), whose functions rely on its ability to associate with telomeric chromatin. The conserved THO complex (THOC) was previously identified at human telomeres. It links transcription with RNA processing, decreasing the accumulation of co-transcriptional DNA:RNA hybrids throughout the genome. Here, we explore the role of THOC at human telomeres, as a regulator of TERRA localization to chromosome ends. We show that THOC counteracts TERRA association with telomeres via R-loops formed co-transcriptionally and also post-transcriptionally, in trans. We demonstrate that THOC binds nucleoplasmic TERRA, and that RNaseH1 loss, which increases telomeric R-loops, promotes THOC occupancy at telomeres. Additionally, we show that THOC counteracts lagging and mainly leading strand telomere fragility, suggesting that TERRA R-loops can interfere with replication fork progression. Finally, we observed that THOC suppresses telomeric sister-chromatid exchange and C-circle accumulation in ALT cancer cells, which maintain telomeres by recombination. Altogether, our findings reveal crucial roles of THOC in telomeric homeostasis through the co- and post-transcriptional regulation of TERRA R-loops.
Preliminary Results Suggest Tranexamic Acid is Safe and Effective in Arthroplasty Patients with Severe Comorbidities (2013)

Although TXA seemed safe and effective in this database review of patients with severe medical comorbidities, a larger prospective trial is warranted to confirm these results.
Protein arginine methyltransferase 1 regulates B cell fate after positive selection in the germinal center in mice (2023)

Positively selected germinal center B cells (GCBC) can either resume proliferation and somatic hypermutation or differentiate. The mechanisms dictating these alternative cell fates are incompletely understood. We show that the protein arginine methyltransferase 1 (Prmt1) is upregulated in murine GCBC by Myc and mTORC-dependent signaling after positive selection. Deleting Prmt1 in activated B cells compromises antibody affinity maturation by hampering proliferation and GCBC light zone to dark zone cycling. Prmt1 deficiency also results in enhanced memory B cell generation and plasma cell differentiation, albeit the quality of these cells is compromised by the GCBC defects. We further demonstrate that Prmt1 intrinsically limits plasma cell differentiation, a function co-opted by B cell lymphoma (BCL) cells. Consistently, PRMT1 expression in BCL correlates with poor disease outcome, depends on MYC and mTORC1 activity, is required for cell proliferation, and prevents differentiation. Collectively, these data identify PRMT1 as a determinant of normal and cancerous mature B cell proliferation and differentiation balance.
Dynamic coherent backscattering of ultrasound in three-dimensional strongly-scattering media (2017)

We present measurements of the diffusion coefficient of ultrasound in strongly scattering three-dimensional (3D) disordered media using the dynamic coherent backscattering (CBS) effect. Our experiments measure the CBS of ultrasonic waves using a transducer array placed in the far-field of a 3D slab sample of brazed aluminum beads surrounded by vacuum. We extend to 3D media the general microscopic theory of CBS that was developed initially for acoustic waves in 2D. This theory is valid in the strong scattering, but still diffuse, regime that is realized in our sample, and is evaluated in the diffuse far field limit encountered in our experiments. By comparing our theory with the experimental data, we obtain an accurate measurement of the Boltzmann diffusion coefficient of ultrasound in our sample. We find that the value of D B is quite small, 0.74 ± 0.03 mm2/μs, and comment on the implications of this slow transport for the energy velocity.
Rational Design of Potent and Selective VLA-4 Inhibitors and their Utility in the Treatment of Asthma (2004)

Asthma, a chronic inflammatory disease of the airways, is a significant burden on our healthcare system. There is high unmet need for treatments directed towards the underlying causes of the disease. The cell surface integrin VLA-4 (very late antigen-4; alpha4beta1; CD49d/CD29) plays an important role in the trafficking of white blood cells to sites of inflammation and represents an exciting target for the development of novel anti-inflammatory drugs for the treatment of asthma. Here, we review our efforts to use rational design to identify potent, selective inhibitors of VLA-4. We describe the discovery of a series of potent VLA-4 inhibitors through the addition of a novel N-terminal organic cap to a tetrapeptide VLA-4 binding motif 4-((N'-2-methylphenyl)uriedo)phenylacetyl-Leu-Asp-Val-Pro ; Kd = 70 pM), and rationalize their structure-activity relationships using 3D-QSAR. Also, we show our rational peptidomimetic design strategy using "template hopping" from the gpIIb/IIIa integrin antagonist field, and also a novel virtual screening strategy. Two series have been developed, one that has high selectivity for the activated over the non-activated state of the receptor, and the other which is non-selective inhibiting both activated and non-activated VLA-4. Both series are highly selective for VLA-4 versus against other integrin family members. These inhibitors show promise in the treatment of asthma, based upon efficacy in a sheep model of asthma, where they inhibit both the early and late-phase responses to asthma and also block hypersensitivity.
List decoding of burst errors (2008)

A generalization of the Reiger bound is presented for the list decoding of burst errors. It is then shown that Reed-Solomon codes attain this bound.
Feeds and Feed Additives, Ruminant Feeds (2000)

Abstract This article discusses feedstuffs and feed additives that are incorporated into ruminant diets based on various physiological states of the animal. The ruminant animal is unique because it can utilize highly fibrous feedstuffs unsuitable for consumption by monogastrics. Primary feedstuffs include forages/roughages, high energy feeds, supplements, feed additives, and young animal feeds. Forages/roughages (fibrous feeds) are the predominant feedstuffs consumed by ruminants throughout their lifetimes. Ruminants consume fibrous feeds either by grazing or by being fed preharvested forage. High energy feeds are those that are more energy‐dense than forages/roughages. These consist primarily of readily fermentable carbohydrates (grains) and lipids (animal or plant origin). Several supplemental sources of protein, energy, macrominerals, microminerals, and vitamins are discussed. Primary classes of feed additives include ionophores, ion‐exchange compounds, direct‐fed microbials, bloat preventatives, ruminal buffers, defaunation agents, hormones, antibiotics, and miscellaneous compounds. Situations in which young ruminants consume feed other than mother's milk are discussed. Various feed sources for these young animals are identified. Because of the extreme diversity in ruminant production systems, the sources of ruminant feedstuffs are extremely diverse.
The Benzil Dicyanohydrin Rearrangement Analogy with the Benzil-Cyanide Reaction (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleThe Benzil Dicyanohydrin Rearrangement Analogy with the Benzil-Cyanide ReactionAngelo Clerici and Ombretta PortaCite this: J. Org. Chem. 1994, 59, 6, 1591–1592Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/jo00085a057https://doi.org/10.1021/jo00085a057research-articleACS PublicationsRequest reuse permissionsArticle Views117Altmetric-Citations3LEARN 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
In search of the lost tradition: towards a history of Church paintings in the 1840s — first half of the 1850s (2023)

The last decade of the reign of Nicholas I (1845 - 1855) was the time when the projects of renewal of church paintings in Russia appeared. Public discussion of the problems of the tradition of the Russian art started with the publication in 1845 of a brochure "On Icon-paintings" by the Ostrog bishop Anatoly, who wasn't, however, a zealous adherent to the traditional icon-paintings, his "theory" of icon-paintings tending towards neoclassicism. In difference from the Right Reverend Anatoly's approach in his brochure, the Rev'd Grigoriy Debolsky argued for the inseparable connection between the national spirit (narodnost') of the church paintings and the tradition of icon-painting in an article published in the same year. Russian Academic school did not respond to the new attitudes in society: propelled by the Emperor, this school acknowledged the tradition in symbolic terms only - in the Byzantinine golden impressions in the paintings in St Isaac's Cathedral. On the whole, the ensemble of these paintings promised to become a brilliant legacy of Bologna academism. 1848, the year of a wave of revolutions in Europe that were perceived as a direct threat to the Empire, opened a period of Nicholas's reign marked, on the other hand, by the intensification of censorship, and, on the other hand, by the two projects of renewal of national church art: those by Duke G.G. Gagarin and by I.P. Sakharov, an archaeologist. The first project, which had at its base the idea, taken from French artists, of christianising ancient art, was an attempt to adapt the Byzantine tradition to the framework of the academic artistic paradigm. Sakharov's project, on the contrary, presupposed complete rejection of this academic paradigm and going back to the icon-paintings that were not yet "spoiled" by Western influences. On the eve of the Crimean war the government made an attempt to expand the national tradition by including in it the ancient paintings from the Mount Athos, in particular, the wall-paintings by Panselinos, which, as A.N. Mouravyov claimed, "are on a par with the works by Rafael and Michelangelo in colouration and modest comportment of the figures". In the new era, marked by the Great Reform of Alexander II, the attempts at a renewal of church paintings that flourished in Nicholas's times, become, for the most part, a thing of the past.