cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels
Creators: name: Parker, J.S.
name: Löverli, E.
name: Lundberg, A.
name: Lindström, L.S.
name: Bergh, J.
name: Perou, C.M.
name: Tobin, N.P.
Publisher: name: Springer Nature
Year: 2020

description: Pan-cancer genomic analyses based on the magnitude of pathway activity are currently lacking. Focusing on the cell cycle, we examined the DNA mutations and chromosome arm-level aneuploidy within tumours with low, intermediate and high cell-cycle activity in 9515 pan-cancer patients with 32 different tumour types. Boxplots showed that cell-cycle activity varied broadly across and within all cancers. TP53 and PIK3CA mutations were common in all cell cycle score (CCS) tertiles but with increasing frequency as cell-cycle activity levels increased (P < 0.001). Mutations in BRAF and gains in 16p were less frequent in CCS High tumours (P < 0.001). In Kaplan–Meier analysis, patients whose tumours were CCS Low had a longer Progression Free Interval (PFI) relative to Intermediate or High (P < 0.001) and this significance remained in multivariable analysis (CCS Intermediate: HR = 1.37; 95% CI 1.17–1.60, CCS High: 1.54; 1.29–1.84, CCS Low = Ref). These results demonstrate that whilst similar DNA alterations can be found at all cell-cycle activity levels, some notable exceptions exist. Moreover, independent prognostic information can be derived on a pan-cancer level from a simple measure of cell-cycle activity.
Higher categorical aspects of Hall Algebras
Creators: name: Dyckerhoff, Tobias
Publisher: name: arXiv
Year: 2015
Subjects: subject: Category Theory (math.CT)
subject: Algebraic Topology (math.AT)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics

description: These are extended notes for a series of lectures on Hall algebras given at the CRM Barcelona in February 2015. The basic idea of the theory of Hall algebras is that the collection of flags in an exact category encodes an associative multiplication law. While introduced by Steinitz and Hall for the category of abelian p-groups, it has since become clear that the original construction can be applied in much greater generality and admits numerous useful variations. These notes focus on higher categorical aspects based on the relation between Hall algebras and Waldhausen's S-construction.
description: 60 pages, preliminary version, comments very welcome
Exploring the Expert Web Understanding Interactions Between Museums and Online Communities
Creators: name: Moskowitz, Blaire Melissa
Publisher: name: University of Leicester
Year: 2023
Subjects: Uncategorized

description: Museums have experienced and interacted with the ‘Expert Web’, a distinct niche of online communities full of knowledgeable and passionate people who spend time talking about the subjects they love most. The communities are eclectic, the participants are well-informed, and, most importantly, they know all about museums dedicated to their interests. The thesis first identifies the Expert Web: its value as an inherently social space, its distinct components (people, processes, and platforms), and its success with museums nearly three decades ago. Through a series of ‘episodes’ taken from a range of online communities, it evidences that some museums have recently recognised, acknowledged, and participated in these communities, but of these, only a few are confident in their interactions – and this confidence can wane depending on a variety of circumstances. The research illustrates how identities presented by the museum affect how online communities react and respond, platforms influence the type of person attracted to the conversation and resulting discourse, and that conversations can be categorised as exchanges of information or negotiations of control. The research demonstrates how the sector will benefit from a new awareness and literacy when interacting with such communities in order to stay relevant online and that entering the Expert Web demands a cultural shift for museums. Ultimately, the thesis recommends that museums: become aware of the range of communities discussing their topics and why participants are attracted to them; recognise their options in communication style and identify who is best positioned to understand the discourse; and with this knowledge, decide if and how it is appropriate to join. The research also proposes that perceiving these individuals as fans of a subject matter (as opposed to ‘audiences’) might prove a more pertinent way to describe community members, enabling museums to re-evaluate how they perceive both the notion of community and the wider online world.
Development and validation of a NanoString BASE47 bladder cancer gene classifier
Creators: name: Kardos, J.
name: Wobker, S.E.
name: Parker, J.S.
name: Moore, K.J.
name: Bivalaqua, T.J.
name: Manocha, U.
name: Damrauer, J.S.
name: Kates, M.
name: Rose, T.L.
name: Kim, W.Y.
Publisher: name: Public Library of Science
Year: 2020

description: Background Recent molecular characterization of urothelial cancer (UC) has suggested potential pathways in which to direct treatment, leading to a host of targeted therapies in development for UC. In parallel, gene expression profiling has demonstrated that high-grade UC is a heterogeneous disease. Prognostic basal-like and luminal-like subtypes have been identified and an accurate transcriptome BASE47 classifier has been developed. However, these phenotypes cannot be broadly investigated due to the lack of a clinically viable diagnostic assay. We sought to develop and evaluate a diagnostic classifier of UC subtype with the goal of accurate classification from clinically available specimens. Methods Tumor samples from 52 patients with high-grade UC were profiled for BASE47 genes concurrently by RNAseq as well as NanoString. After design and technical validation of a BASE47 NanoString probeset, results from the RNAseq and NanoString were used to translate diagnostic criteria to the Nanostring platform. Evaluation of repeatability and accuracy was performed to derive a final Nanostring based classifier. Diagnostic classification resulting from the NanoString BASE47 classifier was validated on an independent dataset (n = 30). The training and validation datasets accurately classified 87% and 93% of samples, respectively. Results Here we have derived a NanoString-platform BASE47 classifier that accurately predicts basal-like and luminal-like subtypes in high grade urothelial cancer. We have further validated our new NanoString BASE47 classifier on an independent dataset and confirmed high accuracy when compared with our original Transcriptome BASE47 classifier. Conclusions The NanoString BASE47 classifier provides a faster turnaround time, a lower cost per sample to process, and maintains the accuracy of the original subtype classifier for better clinical implementation.
DIMA-fr: a French adaptation and standardization of the Dutch Diagnostic Instrument for Mild Aphasia (DIMA-nl)
Creators: name: Clément, Aurélie
name: Perez, Anne
name: Mandonnet, Emmanuel
name: Satoer, Djaina
name: Visch-Brink, Evy
name: De Witte, Elke
name: Pierret, Héloïse
name: Barberis, Marion
name: Poisson, Isabelle
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: The Dutch Diagnostic Instrument for Mild Aphasia (DIMA-nl) is a standardized battery recently created for evaluating the language performance of patients during the perioperative period of glioma surgery. Our aim was to establish normative data for the DIMA-fr, a French version of the DIMA-nl. The DIMA-nl was first adapted to French. The 14 subtasks of the DIMA-fr were then administered to 391 participants recruited from the general French population. The effects of sex, age and level of education were determined by analysis of variance (ANOVA). Normative data were computed as means, medians, standard deviations and percentiles. Our results demonstrated that age and level of education had an effect on the performance of all subtests but not sex. We thus stratified the norms into four different groups: (i) 18–69 years-old with Baccalauréat (Bac, the French High School Diploma) (n = 246); (ii) 18–69 years-old without Bac (n = 70); (iii) >70 years-old with Bac (n = 48); (iv) >70 years-old without Bac (n = 27). The DIMA-fr is thus the first standardized French battery of tests to specifically assess language during the perioperative period of awake glioma surgery. However, to be used in the clinic, the DIMA-fr must now be validated in patients. The DIMA, which is currently standardized in several languages, could become a reference tool for international studies.
Unbiased constraints on the clumpiness of universe from standard candles
Creators: name: Li, Zhengxiang
name: Ding, Xuheng
name: Zhu, Zong-Hong
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We perform unbiased tests for the clumpiness of universe by confronting the Zel'dovich-Kantowski-Dyer-Roeder luminosity distance which describes the effect of local inhomogeneities on the propagation of light with the observational one estimated from measurements of standard candles, i.e., type Ia supernovae (SNe Ia) and gamma-ray bursts (GRBs). Methodologically, we first determine the light-curve fitting parameters which account for distance estimation in SNe Ia observations and luminosity/energy relations which are responsible for distance estimation of GRBs in the global fit to reconstruct the Hubble diagrams in the context of a clumpy universe. Subsequently, these Hubble diagrams allow us to achieve unbiased constraints on the matter density parameter $Ω_m$ as well as clumpiness parameter $η$ which quantifies the fraction of homogeneously distributed matter within a given light cone. At 1$σ$ confidence level, the constraints are $Ω_m=0.34\pm0.02$ and $η=1.00^{+0.00}_{-0.02}$ from the joint analysis. The results suggest that the universe full of Friedman-Lemaître-Robertson-Walker fluid is favored by observations of standard candles with very high statistical significance. On the other hand, they may also indicate that the Zel'dovich-Kantowski-Dyer-Roeder approximation is a sufficient accurate form to describe the effects of local homogeneity in the expanding universe.
description: 20 pages, 5 figures, and 2 tables. Accepted for publication in Phys. Rev. D
Genome-Wide RNAi Screen Identifies Regulators of Cardiomyocyte Necrosis
Creators: name: Opheim, Z.
name: Cheng, Z.
name: Zhu, Q.
name: Mack, C.P.
name: Combs, M.
name: Xia, P.
name: Taylor, J.M.
name: Parker, J.
Publisher: name: American Chemical Society
Year: 2019

description: Regulation of cellular death is central to nearly all physiological routines and is dysregulated in virtually all diseases. Cell death occurs by two major processes, necrosis which culminates in a pervasive inflammatory response and apoptosis which is largely immunologically inert. As necrosis has long been considered an accidental, unregulated form of cellular death that occurred in response to a harsh environmental stimulus, it was largely ignored as a clinical target. However, recent elegant studies suggest that certain forms of necrosis can be reprogrammed. However, scant little is known about the molecules and pathways that orchestrate calcium-overload-induced necrosis, a main mediator of ischemia/reperfusion (IR)-induced cardiomyocyte cell death. To rectify this critical gap in our knowledge, we performed a novel genome-wide siRNA screen to identify modulators of calcium-induced necrosis in human muscle cells. Our screen identified multiple molecular circuitries that either enhance or inhibit this process, including lysosomal calcium channel TPCN1, mitophagy mediatorTOMM7, Ran-binding protein RanBP9, Histone deacetylase HDAC2, chemokine CCL11, and the Arp2/3 complex regulator glia maturation factor-γ(GMFG). Notably, a number of druggable enzymes were identified, including the proteasome β5 subunit (encoded by PSMB5 gene), which controls the proteasomal chymotrypsin-like peptidase activity. Such findings open up the possibility for the discovery of pharmacological interventions that could provide therapeutic benefits to patients affected by myriad disorders characterized by excessive (or too little) necrotic cell loss, including but not limited to IR injury in the heart and kidney, chronic neurodegenerative disorders, muscular dystrophies, sepsis, and cancers.
RNA-Sequencing of Umbilical Cord Blood to Investigate Spontaneous Preterm Birth: A Pilot Study
Creators: name: Vora, N.L.
name: Fry, R.C.
name: Mieckowski, P.A.
name: Smeester, L.
name: Parker, J.S.
name: Boggess, K.A.
Publisher: name: Thieme Medical Publishers, Inc.
Year: 2019

description: Objective To analyze the transcriptomic gene expression of umbilical cord blood leukocytes using RNA-sequencing from preterm birth (PTB) and term birth (TB). Study Design Eight women with spontaneous PTB (sPTB) and eight women with unlabored TB were enrolled prospectively. The sPTB and TB cohorts were matched for maternal age, race, mode of delivery, and fetal sex. Cord blood RNA was extracted and a globin depletion protocol was applied, then sequenced on the Illumina HiSeq 4000. Raw read counts were analyzed with DESeq2 to test for gene expression differences between sPTB and TB. Results 148 genes had significant differential expression (q < 0.01). Cell cycle/metabolism gene expression was significantly higher and immune/inflammatory signaling gene expression significantly lower in the sPTB cohort compared with term. In African American (AA) infants, 18 genes specific to cell signaling, neutrophil activity, and major histocompatibility complex type 1 had lower expression in preterm compared with term cohort; the opposite pattern was seen in non-Hispanic Whites (NHWs). Conclusion Compared with term, preterm fetuses have higher cell cycle/metabolism gene expression, suggesting metabolic focus on growth and development. Immune function gene expression in this pilot study is lower in the sPTB group compared with term and differs in AA compared with NHW infants.
Improved indel detection in DNA and RNA via realignment with ABRA2
Creators: name: Parker, J.S.
name: Perou, C.M.
name: Mose, L.E.
Publisher: name: Oxford University Press
Year: 2019

description: Motivation: Genomic variant detection from next-generation sequencing has become established as an extremely important component of research and clinical diagnoses in both cancer and Mendelian disorders. Insertions and deletions (indels) are a common source of variation and can frequently impact functionality, thus making their detection vitally important. While substantial effort has gone into detecting indels from DNA, there is still opportunity for improvement. Further, detection of indels from RNA-Seq data has largely been an afterthought and offers another critical area for variant detection. Results: We present here ABRA2, a redesign of the original ABRA implementation that offers support for realignment of both RNA and DNA short reads. The process results in improved accuracy and scalability including support for human whole genomes. Results demonstrate substantial improvement in indel detection for a variety of data types, including those that were not previously supported by ABRA. Further, ABRA2 results in broad improvements to variant calling accuracy across a wide range of post-processing workflows including whole genomes, targeted exomes and transcriptome sequencing.
Embedding the Erdős-Rényi Hypergraph into the Random Regular Hypergraph and Hamiltonicity
Creators: name: Dudek, Andrzej
name: Frieze, Alan
name: Ruciński, Andrzej
name: Šileikis, Matas
Publisher: name: arXiv
Year: 2015
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C65, 05C80, 05C38

description: We establish an inclusion relation between two uniform models of random $k$-graphs (for constant $k \ge 2$) on $n$ labeled vertices: $\mathbb G^{(k)}(n,m)$, the random $k$-graph with $m$ edges, and $\mathbb R^{(k)}(n,d)$, the random $d$-regular $k$-graph. We show that if $n\log n\ll m\ll n^k$ we can choose $d = d(n) \sim {km}/n$ and couple $\mathbb G^{(k)}(n,m)$ and $\mathbb R^{(k)}(n,d)$ so that the latter contains the former with probability tending to one as $n\to\infty$. This extends an earlier result of Kim and Vu about "sandwiching random graphs". In view of known threshold theorems on the existence of different types of Hamilton cycles in $\mathbb G^{(k)}(n,m)$, our result allows us to find conditions under which $\mathbb R^{(k)}(n,d)$ is Hamiltonian. In particular, for $k\ge 3$ we conclude that if $n^{k-2} \ll d \ll n^{k-1}$, then a.a.s. $\mathbb R^{(k)}(n,d)$ contains a tight Hamilton cycle.
description: Published online in Journal of Combinatorial Theory, Series B on 16 Sep 2016
Technical report on environmental and socioeconomic impacts of the supported projects
Creators: name: Raffray, Morgan
name: Martin, Jean-Christophe
name: Anglada, Clémentine
name: Barry, David
name: Teillant, Boris
Publisher: name: Zenodo
Year: 2023

description: The work carried by Vertigo Lab is multifaceted as it undertook to connect entrepreneurial endeavors in new fields with regional socioeconomic impacts and global environmental impacts evaluation. The first part of the work was to connect the existing activity classification with the new Blue Economy fields defined by the European Union. These fields studied remain part of other industries and were difficult to truly identify. This was the case of biotechnologies and seabed mining. There are not yet developed enough to be fully integrated in the NACE classifications.
 Furthermore, the work conducted allowed the regionalization at the NUTS3 administrative scale in France and to expand the NACE 64 sectors to NACE 615 sectors in France. Other countries did not have sufficient open data to carry similar work. The sub sectorial granularity was only available for aquaculture practices, albeit only at the national level. Vertigo Lab used the development work and the database knowledge to estimate four companies across three countries in the Atlantic Area. Vertigo Lab worked with coaches to help them understand and transmit the results to the beneficiaries. The results were provided with the visuals developed for the project in addition to an explanatory note.
An Archival Search for Technosignatures During Planet-Planet Occultations
Creators: name: Sneed, Evan
Publisher: name: Zenodo
Year: 2022

description: Abstract: Over the past decade, new survey programs have greatly increased the analyzed fraction of the cosmic haystack, largely by observing new target systems for longer using different frequencies of light. However, these surveys rarely consider when one should search, instead assuming that technosignatures are persistent and detectable over long time frames. Here, we present a method to search for “spillover” radio signals by identifying when two or more exoplanets are collinear with Earth. This scenario, known as a planet-planet occultation, can be modeled using N-body gravitational simulations for well-defined planetary systems. This method provides both a time and place to search for technosignatures, and is sensitive to both deliberate transmission attempts and communications not intended for Earth. Here, we present the results of an archival search of Breakthrough Listen data and introduce plans for a future observational campaign.
Heavy quark mass expansion of vector and tensor currents and intrinsic charm in nucleon form factors
Creators: name: Polyakov, M. V.
name: Sieverding, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The framework of the expansion by subgraphs is used to compute asymptotic expansions for the vector and the tensor currents in the limit of large quark masses. We use the results to obtain an estimate for the influence of heavy quarks on the nucleon electromagnetic and tensor form factors.
description: 32 pages
Synthesis and fabrication of polyaniline/eggshell composite in ammonia detection
Creators: name: MAZLAN, Nurul Aqilla
Publisher: name: Metallurgy and Materials Science Research Institute Chulalongkorn University
Year: 2020
Subjects: Conducting polymers
Chemical sensor
Chicken eggshells
Ammonia sensor
Waste management

description: Journal of Metals Materials and Minerals, 30, 2, 50-57
Breast cancer PAM50 signature: Correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series
Creators: name: Ocaña, I.
name: Parker, J.S.
name: Ruiz Borrego, M.
name: López-Tarruella, S.
name: Gómez Moreno, H.
name: Martin, M.
name: Ballesteros, A.
name: Hoadley, K.
name: García Saenz, J.A.
name: Alvarez, E.
name: Del Monte-Millán, M.
name: Moreno, F.
name: Jerez, Y.
name: Perou, C.M.
name: Ramos-Medina, R.
name: Cebollero, M.
name: Echavarria, I.
name: Picornell, A.C.
name: Massarrah, T.
name: Gayarre, J.
Publisher: name: BioMed Central Ltd.
Year: 2019

description: Background: Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular. Results: The analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80. Conclusions: In our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method.
Cost-Benefit Analysis (CBA) for policy support: Evidence from Niger State
Creators: name: Sule, Balaraba
name: Coker, Alex
name: Sule, Balaraba
name: Coker, Alex
Publisher: name: Unknown
Year: 2022
Subjects: subject: Agricultural and Food Policy
subject: Nigeria
subject: Agriculture
subject: Economics
subject: Policy

description: The four-day training was held at the Niger State Ministry of Women Affairs and Social Development, from April 25th to April 28th, 2022. The training comprised eight modules, and covered all aspects of CBA, including risk analysis and the application of CBA to policy analysis.
Targeting DNA damage deficient mesotheliomas via synthetic lethal disruption of DNA double-strand repair
Creators: name: Bzura, Aleksandra
Publisher: name: University of Leicester
Year: 2023
Subjects: Uncategorized

description: Given that there is still lack of effective targeted therapy against relapsed malignant pleural mesothelioma (MPM), long latency of this disease and asbestos being used in several non-European countries, the MPM will remain heath issue for decades to come. Therefore, it is a pressing need establish strategies that can avail underlying vulnerabilities to optimise treatments against relapsed MPM and improve patient outcomes. Due to the loss of DNA repair components of Homologous recombination repair (HRR) mesotheliomas rely on Poly (ADP-ribose) polymerase (PARP)-related single-strand break repair pathway. Mesotheliomas tend to harbour HRR deficiency, and thus provide a therapeutic avenue to eliminate malignant cells selectively. Consequently, to test the hypothesis that disruption of homologous recombination DNA repair pathway in malignant pleural mesotheliomas can be therapeutically explored via PARP inhibition (rucaparib) to induce synthetic lethality, we used in vitro, ex vivo and in vivo models. BAP1 is an HRR-associated protein. Approximately 60% of MPMs harbour BAP1 alteration, therefore in the view of the prominence of this tumour suppressor gene, BAP1 could be a potential predictive therapeutic biomarker. Indeed, BAP1 loss of function has been found to be common in the current study. However, it did not render sensitivity to rucaparib in MPM cell lines, explants, nor patients. Nevertheless, FAAP20 loss consistently appeared to correlate with sensitivity to rucaparib in our MPMs models. Moreover, our findings also suggest that platinumbased therapy could be potentially used as a predictor for rucaparib response in MPM patients.
Separation of breast cancer and organ microenvironment transcriptomes in metastases
Creators: name: Turner, T.H.
name: Perou, C.M.
name: Bergh, J.
name: Sohal, S.S.
name: Harrell, J.C.
name: Hatschek, T.
name: Parker, J.S.
name: Dozmorov, M.G.
name: Recio, S.G.
name: Alzubi, M.A.
name: Olex, A.L.
name: Sartorius, C.A.
name: Tobin, N.P.
Publisher: name: BioMed Central Ltd.
Year: 2019

description: Background: The seed and soil hypothesis was proposed over a century ago to describe why cancer cells (seeds) grow in certain organs (soil). Since then, the genetic properties that define the cancer cells have been heavily investigated; however, genomic mediators within the organ microenvironment that mediate successful metastatic growth are less understood. These studies sought to identify cancer- and organ-specific genomic programs that mediate metastasis. Methods: In these studies, a set of 14 human breast cancer patient-derived xenograft (PDX) metastasis models was developed and then tested for metastatic tropism with two approaches: spontaneous metastases from mammary tumors and intravenous injection of PDX cells. The transcriptomes of the cancer cells when growing as tumors or metastases were separated from the transcriptomes of the microenvironment via species-specific separation of the genomes. Drug treatment of PDX spheroids was performed to determine if genes activated in metastases may identify targetable mediators of viability. Results: The experimental approaches that generated metastases in PDX models were identified. RNA sequencing of 134 tumors, metastases, and normal non-metastatic organs identified cancer- and organ-specific genomic properties that mediated metastasis. A common genomic response of the liver microenvironment was found to occur in reaction to the invading PDX cells. Genes within the cancer cells were found to be either transiently regulated by the microenvironment or permanently altered due to clonal selection of metastatic sublines. Gene Set Enrichment Analyses identified more than 400 gene signatures that were commonly activated in metastases across basal-like PDXs. A Src signaling signature was found to be extensively upregulated in metastases, and Src inhibitors were found to be cytotoxic to PDX spheroids. Conclusions: These studies identified that during the growth of breast cancer metastases, there were genomic changes that occurred within both the cancer cells and the organ microenvironment. We hypothesize that pathways upregulated in metastases are mediators of viability and that simultaneously targeting changes within different cancer cell pathways and/or different tissue compartments may be needed for inhibition of disease progression.
Coherent optical control of polarization with a critical metasurface
Creators: name: Kang, Ming
name: Chong, Y. D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We describe the mechanism by which a metamaterial surface can act as an ideal phase-controlled rotatable linear polarizer. With equal-power linearly polarized beams incident on each side of the surface, varying the relative phase rotates the polarization angles of the output beams, while keeping the polarization exactly linear. The explanation is based on coupled-mode theory and the idea of coherent perfect absorption into auxiliary polarization channels. The polarization-rotating behavior occurs at a critical point of the coupled-mode theory, which can be associated with the exceptional point of a parity-time (PT) symmetric effective Hamiltonian.
A functional role for the cancer disparity-linked genes, CRYβB2 and CRYβB2P1, in the promotion of breast cancer
Creators: name: Parker, J.S.
name: Coffey, A.
name: Fleming, J.M.
name: Reaves, D.K.
name: Martin, M.E.
name: Barrow, M.A.
name: Troester, M.A.
name: Andrews, P.L.
name: Jones, G.S.
Publisher: name: BioMed Central Ltd.
Year: 2019

description: Background: In the USA, the breast cancer mortality rate is 41% higher for African-American women than non-Hispanic White women. While numerous gene expression studies have classified biological features that vary by race and may contribute to poorer outcomes, few studies have experimentally tested these associations. CRYβB2 gene expression has drawn particular interest because of its association with overall survival and African-American ethnicity in multiple cancers. Several reports indicate that overexpression of the CRYβB2 pseudogene, CRYβB2P1, and not CRYβB2 is linked with race and poor outcome. It remains unclear whether either or both genes are linked to breast cancer outcomes. This study investigates CRYβB2 and CRYβB2P1 expression in human breast cancers and breast cancer cell line models, with the goal of elucidating the mechanistic contribution of CRYβB2 and CRYβB2P1 to racial disparities. Methods: Custom scripts for CRYβB2 or CRYβB2P1 were generated and used to identify reads that uniquely aligned to either gene. Gene expression according to race and tumor subtype were assessed using all available TCGA breast cancer RNA sequencing alignment samples (n = 1221). In addition, triple-negative breast cancer models engineered to have each gene overexpressed or knocked out were developed and evaluated by in vitro, biochemical, and in vivo assays to identify biological functions. Results: We provide evidence that CRYβB2P1 is expressed at higher levels in breast tumors compared to CRYβB2, but only CRYβB2P1 is significantly increased in African-American tumors relative to White American tumors. We show that independent of CRYβB2, CRYβB2P1 enhances tumorigenesis in vivo via promoting cell proliferation. Our data also reveal that CRYβB2P1 may function as a non-coding RNA to regulate CRYβB2 expression. A key observation is that the combined overexpression of both genes was found to suppress cell growth. CRYβB2 overexpression in triple-negative breast cancers increases invasive cellular behaviors, tumor growth, IL6 production, immune cell chemoattraction, and the expression of metastasis-associated genes. These data underscore that both CRYβB2 and CRYβB2P1 promote tumor growth, but their mechanisms for tumor promotion are likely distinct. Conclusions: Our findings provide novel data emphasizing the need to distinguish and study the biological effects of both CRYβB2 and CRYβB2P1 as both genes independently promote tumor progression. Our data demonstrate novel molecular mechanisms of two understudied, disparity-linked molecules.
Entanglement Distillation using the Exchange Interaction
Creators: name: Auer, Adrian
name: Schwonnek, René
name: Schoder, Christian
name: Dammeier, Lars
name: Werner, Reinhard F.
name: Burkard, Guido
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A key ingredient of quantum repeaters is entanglement distillation, i.e., the generation of high-fidelity entangled qubits from a larger set of pairs with lower fidelity. Here, we present entanglement distillation protocols based on qubit couplings that originate from exchange interaction. First, we make use of asymmetric bilateral two-qubit operations generated from anisotropic exchange interaction and show how to distill entanglement using two input pairs. We furthermore consider the case of three input pairs coupled through isotropic exchange. Here, we characterize a set of protocols which are optimizing the tradeoff between the fidelity increase and the probability of a successful run.
description: 8 pages, 5 figures, v2: corrected typo in Eq. (7)
Male breast cancer: a disease distinct from female breast cancer
Creators: name: Eisner, J.R.
name: Parker, J.S.
name: Gucalp, A.
name: Park, B.H.
name: Cardoso, F.
name: Traina, T.A.
name: Baskin-Bey, E.S.
name: Elias, A.D.
name: Selitsky, S.R.
Publisher: name: Springer New York LLC
Year: 2019

description: Purpose: Male breast cancer (BC) is rare, representing approximately 1% of cancers that occur in men and approximately 1% of all BCs worldwide. Because male BC is rare, not much is known about the disease, and treatment recommendations are typically extrapolated from data available from clinical trials enrolling female BC patients. Methods: We review the epidemiology, risk factors, prognosis, and the varied molecular and clinicopathologic features that characterize male BC. In addition, we summarize the available data for the use of systemic therapy in the treatment of male BC and explore the ongoing development of targeted therapeutic agents for the treatment of this subgroup of BCs. Results: There are important biological differences between male and female BC. Male BC is almost exclusively hormone receptor positive (+), including the androgen receptor (AR), and is associated with an increased prevalence of BRCA2 germline mutations, especially in men with increased risk for developing high-risk BC. Additional research is warranted to better characterize male BC. To accomplish this, a multi-national consortium approach, such as the International Male Breast Cancer Program, is needed in response to the scarcity of patients. This approach allows the pooling of information from a large number of men with BC and the creation of registries for future therapeutic-focused clinical trials. Conclusions: Given the unique biology of BC in men, promising new therapeutic targets are currently under investigation, including the use of poly-ADP-ribose polymerase inhibitors or AR-targeted agents either as monotherapy or in combination with other agents.
Experimental prospects for C, P, T, CP, and CPT tests
Creators: name: Bevan, Adrian
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Discrete symmetry violation in the weak interaction is central to the Standard Model of particle physics, however the origin of these violations is not well understood. Nor are we able to provide a satisfactory explanation of the Universal dominance of matter over antimatter, an issue related to CP violation. As a result study of discrete symmetry violation remains a topic of broad interest. These proceedings discuss experimental prospects of studying C, P, T, CP and CPT symmetries in a number of contexts, including the use of triple product asymmetries and entangled neutral meson systems.
description: 9 pages, Contribution to Discrete 2014
Broadband energy-efficient optical modulation by hybrid integration of silicon nanophotonics and organic electro-optic polymer
Creators: name: Zhang, Xingyu
name: Hosseini, Amir
name: Subbaraman, Harish
name: Luo, Jingdong
name: Jen, Alex K. -Y
name: Chung, Chi-jui
name: Yan, Hai
name: Pan, Zeyu
name: Nelson, Robert L.
name: Chen, Ray T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Silicon-organic hybrid integrated devices have emerging applications ranging from high-speed optical interconnects to photonic electromagnetic-field sensors. Silicon slot photonic crystal waveguides (PCWs) filled with electro-optic (EO) polymers combine the slow-light effect in PCWs with the high polarizability of EO polymers, which promises the realization of high-performance optical modulators. In this paper, a broadband, power-efficient, low-dispersion, and compact optical modulator based on an EO polymer filled silicon slot PCW is presented. A small voltage-length product of Vπ*L=0.282Vmm is achieved, corresponding to an unprecedented record-high effective in-device EO coefficient (r33) of 1230pm/V. Assisted by a backside gate voltage, the modulation response up to 50GHz is observed, with a 3-dB bandwidth of 15GHz, and the estimated energy consumption is 94.4fJ/bit at 10Gbit/s. Furthermore, lattice-shifted PCWs are utilized to enhance the optical bandwidth by a factor of ~10X over other modulators based on non-band-engineered PCWs and ring-resonators.
description: 12 pages, 4 figures, SPIE Photonics West Conference 2015
Educator attitudes to English as a lingua franca in the international university: A Q-sort intervention study
Creators: name: Kavanagh, Paul
Publisher: name: University of Leicester
Year: 2023
Subjects: Uncategorized

description: While consideration of language issues arising out of ongoing internationalisation has long been a feature of higher education in non-native-English-speaking (NNES) contexts, discussion within universities who receive NNES students from abroad is less developed. As English on these campuses increasingly becomes a lingua franca, this research examines the dynamics of attitude formation and their potential practical effects. The overall research design is based around a comparison of the attitudes of a group of novice English language teachers completing the CELTA qualification to those of an equal cohort of established university lecturers. Employing the techniques of Q-methodology, four distinct patterns of belief (or ‘mindsets’) were identified, corresponding to orientations attested in Communication Accommodation Theory research: Convergent, Divergent, Maintaining and Over-Accommodating. A two-stage approach to data-gathering was employed to investigate the stability of these attitudes and the effects of training. Data gathered showed that adherence to each of the four mindsets identified did not divide along professional lines, with each being exemplified by educators from both academic and CELTA trainee groups. However, by the end of their training period, while academic lecturers held firm on their mindsets, the CELTA group showed a marked shift from a Divergent to a Convergent mindset, a development accompanied by new perspectives on the role of the instructor, the realities of English as a lingua franca, and the linguistic experience of the NNES student within the international university. The practical implications of these mindsets were then investigated by looking at educators’ perceptions of the level of difficulty in instructional language, as they would be experienced by NNES students. The research generated casts some light on practical issues of communication in the modern university, by considering the effect of attitudes, experience, context and training on the ability of educators to co-construct meaning in the lingua franca environment.
LifeComp for the Employability of young NEETs. State of the Art and Best practices (Spain)
Creators: name: Gonzalez Costas, Almudena
Publisher: name: Zenodo
Year: 2022
Subjects: NEETs, LifeComp, Spain

description: This first project result aims at analyzing the existing status and the successful practices in the application of the LifeComp Framework in education and training programs for young people and NEETs. The report consists of the analysis of at least 20 semi-structured interviews and a collection of best practices on the implementation of the LifeComp Framework in curricula and courses in formal and non-formal education and the conclusions of the focus groups from each participant country.
Οι επιδράσεις της ηλιακής ακτινοβολίας στο δέρμα
Creators: name: Καρακελίδης, Αντώνιος Θεόδωρου
Publisher: name: Aristotle University of Thessaloniki
Year: 2024
Subjects: Ηλιακή ακτινοβολία
Δερματολογικές επιπτώσεις
Προστασία δέρματος
Solar radiation
Dermatological effects
Skin protection

description: Η διπλωματική εργασία μελετάει την επίδραση της ηλιακής ακτινοβολίας στο δέρμα, εστιάζοντας τόσο στις θετικές όσο και στις αρνητικές επιδράσεις της. Η μεθοδολογία που ακολουθήθηκε περιλαμβάνει βιβλιογραφική ανασκόπηση και ανάλυση επιστημονικών δεδομένων σχετικά με τις δερματολογικές και ψυχολογικές επιπτώσεις της έκθεσης στον ήλιο. Τα αποτελέσματα δείχνουν ότι η ηλιακή ακτινοβολία συμβάλλει στην παραγωγή βιταμίνης D και βελτιώνει τη ψυχική υγεία, αλλά παράλληλα προκαλεί φωτογήρανση, ακτινική υπερκεράτωση, φωτοδερματοπάθειες και αυξάνει τον κίνδυνο εμφάνισης καρκίνου του δέρματος. Τα συμπεράσματα υπογραμμίζουν την αναγκαιότητα ισορροπημένης έκθεσης στον ήλιο και την αποτελεσματική χρήση αντηλιακών για την προστασία του δέρματος .
description: This thesis examines the effects of solar radiation on the skin, focusing on both its positive and negative impacts. The methodology includes a literature review and analysis of scientific data concerning the dermatological and psychological effects of sun exposure. The results show that solar radiation contributes to vitamin D production and improves mental health, but it also causes photoaging, actinic keratosis, photodermatoses, and increases the risk of skin cancer. The conclusions highlight the necessity of balanced sun exposure and the effective use of sunscreens to protect the skin.
description: Τμήμα Ιατρικής, Συνεργαζόμενα Τμήματα Γεωλογίας, Ιατρικής (Δημοκρίτειο Πανεπιστήμιο Θράκης), Μηχανικών Περιβάλλοντος (Διεθνές Πανεπιστήμιο Ελλάδας)
Correlation-enhanced odd-parity inter-orbital singlet pairing in the iron-pnictide superconductor LiFeAs
Creators: name: Nourafkan, R.
name: Kotliar, G.
name: Tremblay, A. -M. S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The rich variety of iron-based superconductors and their complex electronic structure lead to a wide range of possibilities for gap symmetry and pairing components. Here we solve in the 2-Fe Brillouin zone the full frequency-dependent linearized Eliashberg equations for LiFeAs with spin-fluctuation mediated pairing interactions. The magnetic excitations are calculated with the random phase approximation on a correlated electronic structure obtained with density functional theory and dynamical mean field theory. Correlations induce long-lived local moments with orbital-dependent dynamics. The interaction between electrons through Hund's coupling promotes inter-orbital magnetic susceptibility. As a consequence, the leading pairing channel, conventional $s^{+-}$, acquires sizeable inter-orbital $d_{xy}-d_{xz(yz)}$ singlet pairing with odd parity under glide-plane symmetry. These components reduce the superconducting gap magnitude induced by the intra-orbital components of the gap function at the electron pockets intersection where the Fe-d $t_{2g}$ orbitals strongly mix. This in turn makes the results consistent with available experiments on the angular dependence of the gaps observed on the different Fermi surfaces.
PAM50 molecular intrinsic subtypes in the nurses' health Study cohorts
Creators: name: Baker, G.M.
name: Hoadley, K.A.
name: Rubadue, C.A.
name: Stancu, A.L.
name: Eliassen, A.H.
name: Pyle, M.E.
name: Parker, J.S.
name: Heng, Y.J
name: Zhang, X.
name: Wang, J.
name: Hunter, D.J.
name: Hankinson, S.E.
name: Tamimi, R.M.
name: Sankar, V.N.
name: Kensler, K.H.
name: Collins, L.C.
Publisher: name: American Association for Cancer Research Inc.
Year: 2019

description: Background: Modified median and subgroup-specific gene subtypes by PAM50 and IHC surrogates improved to fair centering are two essential preprocessing methods to assign when Luminal subtypes were grouped together. Using the breast cancer molecular subtypes by PAM50. We evaluated the modified median method, our study consisted of 46% PAM50 subtypes derived from both methods in a subset of Luminal A, 18% Luminal B, 14% HER2-enriched, 15% Nurses' Health Study (NHS) and NHSII participants; correlat-Basal-like, and 8% Normal-like subtypes; 53% of tumor-ed tumor subtypes by PAM50 with IHC surrogates; and adjacent tissues were Normal-like. Women with the Basal-characterized the PAM50 subtype distribution, proliferation like subtype had a higher rate of relapse within 5 years. scores, and risk of relapse with proliferation and tumor size HER2-enriched subtypes had poorer outcomes prior to weighted (ROR-PT) scores in the NHS/NHSII. 1999. Methods: PAM50 subtypes, proliferation scores, and Conclusions: Either preprocessing method may be uti-ROR-PT scores were calculated for 882 invasive breast tumors lized to derive PAM50 subtypes for future studies. The and 695 histologically normal tumor-adjacent tissues. Cox majority of NHS/NHSII tumor and tumor-adjacent tissues proportional hazards models evaluated the relationship were classified as Luminal A and Normal-like, respectively. between PAM50 subtypes or ROR-PT scores/groups with Impact: Preprocessing methods are important for the recurrence-free survival (RFS) or distant RFS. accurate assignment of PAM50 subtypes. These data provide Results: PAM50 subtypes were highly comparable evidence that either preprocessing method can be used in between the two methods. The agreement between tumor epidemiologic studies.
Observation of the Monoceros Loop SNR with the HEGRA system of Cherenkov Telescopes
Creators: name: Lucarelli, Fabrizio
Publisher: name: Zenodo
Year: 2003
Subjects: gamma-rays
Imaging atmospheric Cherenkov Telescopes
supernova remnants

description: The HEGRA collaboration has built one of the most powerful instrument to detect
 very high energy (VHE) photons (E>500 GeV) from astrophysical sources. In this PhD thesis, we reviewed the possibility of the HEGRA system of Cherenkov telescopes in observation of extended gamma-ray emission from supernova remnants (SNRs) (Chapter 6). By means of very detailed Monte Carlo simulation, we showed that the detector is still very efficient for gamma-ray-induced cascades with axes inclined with respect to the telescope axes, as could be the case of those ones emitted by extended SNRs. As practical study, we observed a very extended shell-type SNRs, the Monoceros Loop SNR, which appears to interact with a very dense nearby molecular cloud, the Rosette Nebula. The analysis of more than 100 hours taken towards the direction of the remnant (Chapter 7), in which very sophisticated techniques of background estimation were applied, showed hints of gamma-ray extended emission. A brief review of gamma-ray astronomy and the sources of VHE photons are given in the first Chapter. The technique to detect VHE
 photons by ground-based telescopes and the physical processes involved are given in Chapter 2 and 3. Chapter 4 is explicitly dedicated to the description of the system of five imaging atmospheric Cherenkov telescopes, which was deployed at La Palma of Canary Islands (Spain) and was shutdown on Sept. 2002. As one of the main goal of the next generation of Cherenkov telescopes is to lower the energy threshold down to the sub-TeV energy range, we also implemented a technique to lower the energy threshold of the HEGRA system (Chapter 5). This technique made use of an advanced topological trigger and permitted to lower the energy threshold by a factor 1.4 without any hardware changes.