cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Geometry shapes evolution of early multicellularity
Creators: name: Libby, Eric
name: Ratcliff, William
name: Travisano, Michael
name: Kerr, Ben
Publisher: name: arXiv
Year: 2014
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences

description: Organisms have increased in complexity through a series of major evolutionary transitions, in which formerly autonomous entities become parts of a novel higher-level entity. One intriguing feature of the higher-level entity after some major transitions is a division of reproductive labor among its lower-level units. Although it can have clear benefits once established, it is unknown how such reproductive division of labor originates. We consider a recent evolution experiment on the yeast Saccharomyces cerevisiae as a unique platform to address the issue of reproductive differentiation during an evolutionary transition in individuality. In the experiment, independent yeast lineages evolved a multicellular "snowflake-like'' cluster form in response to gravity selection. Shortly after the evolution of clusters, the yeast evolved higher rates of cell death. While cell death enables clusters to split apart and form new groups, it also reduces their performance in the face of gravity selection. To understand the selective value of increased cell death, we create a mathematical model of the cellular arrangement within snowflake yeast clusters. The model reveals that the mechanism of cell death and the geometry of the snowflake interact in complex, evolutionarily important ways. We find that the organization of snowflake yeast imposes powerful limitations on the available space for new cell growth. By dying more frequently, cells in clusters avoid encountering space limitations, and, paradoxically, reach higher numbers. In addition, selection for particular group sizes can explain the increased rate of apoptosis both in terms of total cell number and total numbers of collectives. Thus, by considering the geometry of a primitive multicellular organism we can gain insight into the initial emergence of reproductive division of labor during an evolutionary transition in individuality.
description: 7 figures
Mendeley Dekstop: Import PDF, insert citation, bibiliography, and literatur search
Creators: name: Turista, Dora Dayu Rahma
Publisher: name: Zenodo
Year: 2020
Subjects: Mendeley, Citation, Bibiliography, Literatur, Literatur Search, Dekstop

description: Menjelaskan dasar-dasar Mendeley pada Mendeley Dekstop
An optical--near-IR study of a triplet of super star clusters in the starburst core of M82
Creators: name: Westmoquette, M. S.
name: Bastian, N.
name: Smith, L. J.
name: Seth, A. C.
name: Gallagher, J. S.
name: O'Connell, R. W.
name: Ryon, J. E.
name: Silich, S.
name: Mayya, Y. D.
name: Munoz-Tunon, C.
name: Gonzalez, D. Rosa
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present HST/STIS optical and Gemini/NIFS near-IR IFU spectroscopy, and archival HST imaging of the triplet of super star clusters (A1, A2 and A3) in the core of the M82 starburst. Using model fits to the STIS spectra, and the weakness of red supergiant CO absorption features (appearing at ~6 Myr) in the NIFS H-band spectra, the ages of A2 and A3 are $4.5\pm1.0$~Myr. A1 has strong CO bands, consistent with our previously determined age of $6.4\pm0.5$~Myr. The photometric masses of the three clusters are 4--$7\times10^5$~\Msol, and their sizes are $R_{\rm eff}=159$, 104, 59~mas ($\sim$2.8, 1.8, 1.0~pc) for A1,2 and 3. The STIS spectra yielded radial velocities of $320\pm2$, $330\pm6$, and $336\pm5$~\kms\ for A1,2, and 3, placing them at the eastern end of the $x_2$ orbits of M82's bar. Clusters A2 and A3 are in high density (800--1000~\cmt) environments, and like A1, are surrounded by compact H\two\ regions. We suggest the winds from A2 and A3 have stalled, as in A1, due to the high ISM ambient pressure. We propose that the 3 clusters were formed \textit{in-situ} on the outer $x_2$ orbits in regions of dense molecular gas subsequently ionized by the rapidly evolving starburst. The similar radial velocities of the 3 clusters and their small projected separation of $\sim 25$~pc suggest that they may merge in the near future unless this is prevented by velocity shearing.
description: 15 pages, 9 figures, ApJ in press
Gender-Neutral Integration Policies Fail Female Victims of Trafficking for Sexual Exploitation
Creators: name: Clerides, Elli
name: Kassinis, Elizabeth
Publisher: name: Zenodo
Year: 2022
Subjects: perceptions
narratives
migration
female victims
sexual exploitation

description: Migrant women victims of trafficking for sexual exploitation face a myriad of complex problems as they transition into European societies. Research—including by the COALESCE project—finds that, to be effective, integration efforts require a gender-specific lens and methodology and benefit from specialist knowledge and intersectional competence. Pulling from the COALESCE results in six countries, but especially Cyprus, this Policy Brief suggests ways to improve outcomes through gender-aware rather than gender-blind approaches.
CRISPR/Cas9-mediated TERT disruption in cancer cells
Creators: name: Wen, L
name: Zhao, C
name: Song, J
name: Ma, L
name: Ruan, J
name: Xia, X
name: Chen, YE
name: Zhang, J
name: Ma, PX
name: Xu, J
Publisher: name: MDPI
Year: 2020
Subjects: CRISPR/Cas9
TERT
cancer therapy
gene editing
telomerase
Animals
CRISPR-Cas Systems
Cell Line, Tumor
Cell Proliferation
Cell Survival
Female
Gene Knockout Techniques
Haploinsufficiency
HeLa Cells
Humans
INDEL Mutation
Mice
Mice, Nude
Neoplasm Transplantation
Telomerase
Uterine Cervical Neoplasms

description: Mammalian telomere lengths are primarily regulated by telomerase, a ribonucleoprotein consisting of a reverse transcriptase (TERT) and an RNA subunit (TERC). TERC is constitutively expressed in all cells, whereas TERT expression is temporally and spatially regulated, such that in most adult somatic cells, TERT is inactivated and telomerase activity is undetectable. Most tumor cells activate TERT as a mechanism for preventing progressive telomere attrition to achieve proliferative immortality. Therefore, inactivating TERT has been considered to be a promising means of cancer therapy. Here we applied the CRISPR/Cas9 gene editing system to target the TERT gene in cancer cells. We report that disruption of TERT severely compromises cancer cell survival in vitro and in vivo. Haploinsufficiency of TERT in tumor cells is sufficient to result in telomere attrition and growth retardation in vitro. In vivo, TERT haploinsufficient tumor cells failed to form xenograft after transplantation to nude mice. Our work demonstrates that gene editing-mediated TERT knockout is a potential therapeutic option for treating cancer.
The Panchromatic Hubble Andromeda Treasury V: Ages and Masses of the Year 1 Stellar Clusters
Creators: name: Fouesneau, Morgan
name: Johnson, L. Clifton
name: Weisz, Daniel R.
name: Dalcanton, Julianne J.
name: Bell, Eric F.
name: Bianchi, Luciana
name: Caldwell, Nelson
name: Gouliermis, Dimitrios A.
name: Guhathakurta, Puragra
name: Kalirai, Jason
name: Larsen, Søren S.
name: Rix, Hans-Walter
name: Seth, Anil C.
name: Skillman, Evan D.
name: Williams, Benjamin F.
name: collaboration, PHAT
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present ages and masses for 601 star clusters in M31 from the analysis of the six filter integrated light measurements from near ultraviolet to near infrared wavelengths, made as part of the Panchromatic Hubble Andromeda Treasury (PHAT). We derive the ages and masses using a probabilistic technique, which accounts for the effects of stochastic sampling of the stellar initial mass function. Tests on synthetic data show that this method, in conjunction with the exquisite sensitivity of the PHAT observations and their broad wavelength baseline, provides robust age and mass recovery for clusters ranging from $\sim 10^2 - 2 \times 10^6 M_\odot$. We find that the cluster age distribution is consistent with being uniform over the past $100$ Myr, which suggests a weak effect of cluster disruption within M31. The age distribution of older ($>100$ Myr) clusters fall towards old ages, consistent with a power-law decline of index $-1$, likely from a combination of fading and disruption of the clusters. We find that the mass distribution of the whole sample can be well-described by a single power-law with a spectral index of $-1.9 \pm 0.1$ over the range of $10^3-3 \times 10^5 M_\odot$. However, if we subdivide the sample by galactocentric radius, we find that the age distributions remain unchanged. However, the mass spectral index varies significantly, showing best fit values between $-2.2$ and $-1.8$, with the shallower slope in the highest star formation intensity regions. We explore the robustness of our study to potential systematics and conclude that the cluster mass function may vary with respect to environment.
description: 19 pages, 13 figures, catalog available as online material. Accepted for publication in ApJ
Thermal photon anisotropic flow serves as a quark-gluon plasma viscometer
Creators: name: Shen, Chun
name: Heinz, Ulrich
name: Paquet, Jean-Francois
name: Gale, Charles
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: Photons are a penetrating probe of the hot and dense medium created in heavy-ion collisions. We present state-of-the-art calculations of viscous photon emission from nuclear collisions at RHIC and LHC. Thermal photons anisotropic flow coefficients v_n are computed, both with and without accounting for viscous corrections to the standard thermal emission rates. These corrections are found to have a larger effect on the v_n coefficients than the viscous suppression of hydrodynamic flow anisotropies. For thermal photons, the ratio v_2{SP}/v_3{SP} shows stronger sensitivity to the quark-gluon plasma (QGP) shear viscosity than for hadrons, and it can thus serve as a sensitive QGP viscometer.
description: 4 pages, 6 figures, hard probes 2013 proceeding
Machine learning identifies weak prognostic signal in colorectal polyp’s transcriptome
Creators: name: Hung, Russell
name: Fisher, Simon
name: Andersen, Ditte
name: Lynch, Gerard
name: Maka, Noori
name: Hay, Jennifer
name: Jawny, Jakub
name: Sloan, William
name: McSorley, Stephen
name: Edwards, Joanne
name: Poole, Ian
Publisher: name: F1000 Research Limited
Year: 2022

description: Colorectal polyps are growths that can appear on the lining of the colon or rectum and represent possible
 premalignant lesions to colorectal cancers (CRC). As most polyps are asymptomatic, in the UK surveillance of
 polyps is monitored through colonoscopies, which is an expensive and unpleasant procedure.
 Patients with metachronous polyps may need multiple colonoscopies throughout their lifetime. Understanding
 the risk factors associated with development of metachronous polyps can result in better risks stratification and
 management of screening program resources. In this study, we are particularly concerned with identifying
 distinct patterns in the transcriptome of index polyps related to metachronous risks. We aim to use machine
 learning and deep learning techniques to:
 1. Model occurrence of metachronous polyps based on the index polyp transcriptome
 2. Compare binary classification and time-to-event approach in modelling polyp recurrence
 This research is part of the Integrated Technologies for Improved Polyp Surveillance1 (INCISE) project that aims
 to improve on current bowel cancer screening program in the UK. The INCISE project is a retrospective study
 that seeks to develop a comprehensive risk stratification tool for metachronous polyps prediction.
Investigating the transcriptome of adenomatous colorectal polyps in the context of metachronous recurrence
Creators: name: Fisher, Simon
name: Hung, Russell
name: Andersen, Ditte
name: Lynch, Gerard
name: Maka, Noori
name: Hay, Jennifer
name: Jawny, Jakub
name: Sloan, William
name: McSorely, Stephen
name: Edwards, Joanne
name: Poole, Ian
Publisher: name: F1000 Research Limited
Year: 2022

description: Adenomatous polyps are aberrant gland-like growths of the colon or rectum. These growths can potentially progress to cancer, thus understanding the prognostic risk markers of index polyps and how they may correlate with downstream recurrence is likely to have significant patient benefits.
 In this study, we obtained TempOSeq transcriptomic count data of index polyps, alongside clinical information including metachronous polyp incidence, as part of the Integrated Technologies for Improved Polyp Surveillance (INCISE) project (n=1826, total). We performed differential expression analysis with DESeq2 for participants stratified by metachronous occurrence. Furthermore, we performed unsupervised weighted-gene-co-expression-analysis (WGCNA) and correlated gene modules with clinical traits, including metachronous occurrence and time-to-event. Finally, we analysed enriched hub genes for their ability to predict disease free survival (DFS) by Kaplan Meier analysis.
 A total of 241 differentially expressed genes (DEGs) were detected, 100 downregulated and 141 upregulated, in individuals with metachronous polyps versus healthy controls (PAdj < 0.05). A total of 11 modules were detected by WGCNA, one of which correlated with metachronous polyps. Gene set enrichment analysis for both DEGs and this module identified enrichment toward extracellular matrix invasion and immune regulation. Six overlapping hub genes between both methods, HMOX, COL1A1, CD163, CTSL, FN1 and LOX, were found. By median split, none of these genes had significant prognostic potential in predicting metachronous events (p < 0.05).
 Index polyps of individuals who develop metachronous events may have greater infiltrative and immunoregulatory capacity, but the prognostic signal of identified drivers is poor.
CRISPR/Cas9 Ribonucleoprotein-mediated Precise Gene Editing by Tube Electroporation.
Creators: name: Ma, L
name: Jang, L
name: Chen, J
name: Song, J
name: Yang, D
name: Zhang, J
name: Chen, YE
name: Xu, J
Publisher: name: MyJove Corporation
Year: 2019
Subjects: Animals
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Electroporation
Endonucleases
Gene Editing
Humans
Rabbits
Ribonucleoproteins
Transfection

description: Gene editing nucleases, represented by CRISPR-associated protein 9 (Cas9), are becoming mainstream tools in biomedical research. Successful delivery of CRISPR/Cas9 elements into the target cells by transfection is a prerequisite for efficient gene editing. This protocol demonstrates that tube electroporation (TE) machine-mediated delivery of CRISPR/Cas9 ribonucleoprotein (RNP), along with single-stranded oligodeoxynucleotide (ssODN) donor templates to different types of mammalian cells, leads to robust precise gene editing events. First, TE was applied to deliver CRISPR/Cas9 RNP and ssODNs to induce disease-causing mutations in the interleukin 2 receptor subunit gamma (IL2RG) gene and sepiapterin reductase (SPR) gene in rabbit fibroblast cells. Precise mutation rates of 3.57%-20% were achieved as determined by bacterial TA cloning sequencing. The same strategy was then used in human iPSCs on several clinically relevant genes including epidermal growth factor receptor (EGFR), myosin binding protein C, cardiac (Mybpc3), and hemoglobin subunit beta (HBB). Consistently, highly precise mutation rates were achieved (11.65%-37.92%) as determined by deep sequencing (DeepSeq). The present work demonstrates that tube electroporation of CRISPR/Cas9 RNP represents an efficient transfection protocol for gene editing in mammalian cells.
Nucleon-to-pion transition distribution amplitudes: a challenge for PANDA
Creators: name: Pire, B.
name: Semenov-Tian-Shansky, K.
name: Szymanowski, L.
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Baryon-to-meson Transition Distribution Amplitudes (TDAs) appear as building blocks in the collinear factorized description of amplitudes for a class of hard exclusive reactions, prominent examples being hard exclusive pion electroproduction off a nucleon in the backward region and baryon-antibaryon annihilation into a pion and a lepton pair or a charmonium. Baryon-to-meson TDAs extend both the concepts of generalized parton distributions (GPDs) and baryon distribution amplitudes (DAs) encoding valuable complementary information on the hadronic structure. We review the basic properties of baryon-to-meson TDAs and discuss the perspectives for the experimental access with the PANDA detector.
description: 6 pages, 4 figures. Contribution presented at the Lightcone 2013+ Conference, Skiathos, Greece, 20-24 May, 2013. To be published in Few Body Systems
CUDA programs for GPU computing of Swendsen-Wang multi-cluster spin flip algorithm: 2D and 3D Ising, Potts, and XY models
Creators: name: Komura, Yukihiro
name: Okabe, Yutaka
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We present sample CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm. We deal with the classical spin models; the Ising model, the $q$-state Potts model, and the classical XY model. As for the lattice, both the 2D (square) lattice and the 3D (simple cubic) lattice are treated. We already reported the idea of the GPU implementation for 2D models [Comput. Phys. Commun. 183 (2012) 1155-1161]. We here explain the details of sample programs, and discuss the performance of the present GPU implementation for the 3D Ising and XY models. We also show the calculated results of the moment ratio for these models, and discuss phase transitions.
description: arXiv admin note: text overlap with arXiv:1202.0635
“As the World Fell, Each of Us in Our Own Way was Broken”: Infrastructure in Post-Apocalyptic Cinema
Creators: name: Lazarus, Reuben
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: This thesis applies infrastructural theory to recent science fiction cinema that explores the post-apocalyptic subgenre. Mad Max: Fury Road (George Miller, 2015), Snowpiercer (Bong Joon-ho, 2013), and Dredd (Pete Travis, 2012) each provide a unique set of apocalyptic circumstances leading to the creation of their new world and the subsequent infrastructures that fill them. By applying infrastructural theories such as the flows of society from Brian Larkin (2013) and the infrastructural inversion from various sources such as Nicole Starosielski (2015), it is seen how these cinematic worlds function and operate. This approach is undertaken by examining the types of infrastructures that are created and maintained within these new worlds and how through their interactions, they enable the flows of goods, people and ideas to circulate within a society. My thesis expands on this infrastructural understanding further by examining how infrastructure, once understood within the context of their cinematic narrative, can create and reinforce social relations and a new ruling-class. This thesis’ perspective will also show the prevalence of dystopias within each narrative world, which, as a result of the infrastructurally created power-relations, enable these films to be reflective of modern circumstances to be critical of their socio-political trends by showing a possible outcome.
Persistence of transition state structure in chemical reactions driven by fields oscillating in time
Creators: name: Craven, Galen T.
name: Bartsch, Thomas
name: Hernandez, Rigoberto
Publisher: name: arXiv
Year: 2014
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: Chemical reactions subjected to time-varying external forces cannot generally be described through a fixed bottleneck near the transition state barrier or dividing surface. A naive dividing surface attached to the instantaneous, but moving, barrier top also fails to be recrossing-free. We construct a moving dividing surface in phase space over a transition state trajectory. This surface is recrossing-free for both Hamiltonian and dissipative dynamics. This is confirmed even for strongly anharmonic barriers using simulation. The power of transition state theory is thereby applicable to chemical reactions and other activated processes even when the bottlenecks are time-dependent and move across space.
Structural determination and electronic properties of 4d perovskite SrPdO3
Creators: name: He, Jiangang
name: Franchini, Cesare
Publisher: name: arXiv
Year: 2013
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The structure and ground state electronic structure of the recently synthesized SrPdO$_3$ perovskite [A. Galal {\em et al.}, J. Power Sources, {\bf 195}, 3806 (2010)] have been studied by means of screened hybrid functional and the GW approximation with the inclusion of electron-hole interaction within the test-charge/test-charge scheme. By conducting a structural search based on lattice dynamics and group theoretical method we identify the orthorhombic phase with $P_{nma}$ space group as the most stable crystal structure. The phase transition from the ideal cubic perovskite structure to the $P_{nma}$ one is explained in terms of the simultaneous stabilization of the antiferrodistortive phonon modes $R_4^+$ and $M_3^+$. Our results indicate that SrPdO$_3$ exhibits an insulating ground state, substantiated by a GW$_0$ gap of about 1.1 eV. Spin polarized calculations suggests that SrPdO$_3$ adopts a low spin state ($t_{2g}^{\uparrow\downarrow\uparrow\downarrow\uparrow\downarrow}e_g^0$), and is expected to exhibit spin excitations and spin state crossovers at finite temperature, analogous to the case of 3$d$ isoelectronic LaCoO$_3$. This would provide a new playground for the study of spin state transitions in 4$d$ oxides and new opportunity to design multifunctional materials based on 4$d$ $P_{nma}$ building block.
title: Talking about Chinese Society and Talking to Chinese Society
Creators: name: Rocca, Jean-Louis Laurent
Publisher: name: DWARC Policy Brief
Year: 2023
Subjects: classificationCode: 5.6
subject: FOS: Political science

description: In Europe, the mainstream discourse on China reduces Chinese society to its political system. Chinese society is presented as being backward, rigid, fragmented, and incapable of challenging political power. European values are systematically opposed to supposed Chinese values. In this polarized framework, the Chinese are generally considered to be devoid of opinions, or at least unable to express them. The first problem of this narrative is that many Chinese, including those who are most critical of the current regime, consider it as “anti-Chinese”. The second is that it does not correspond to reality. As a consequence, if we want to talk about China and to China, we have to change our vision of Chinese society. Chinese society is different from the mainstream image of a totalitarian society populated by submissive individuals who are dominated by an omnipotent power. First, the Chinese population is not submissive. Social conflict arises in a very broad range of situations. Second, new opinion movements question the new model of society which has emerged in the 1990s. Third, Chinese people, and more particularly the middle class, enjoy a large scope of freedom in matter of lifestyle and personal choices. Finally, despite censorship, social networks have become a genuine forum for exchanging information and view. All these changes oblige the Party to take into account new norms and values which are not so different from those expressed in European societies. The political authorities know that they are judged by the people, and the people know that they can put pressure on the authorities. Chinese society therefore maintains a critical distance from the authorities. It is less influenced by ideological currents than by “interests.” From this point of view, the Chinese population shares a lot of opinions and expectations with the European population. Moreover, the supposed “Chinese values” are in fact found all over the world and that there is nothing inherently “Chinese” about them. What they all have in common is that they stem from European political theories or ideologies that developed precisely in reaction to the emergence of the Enlightenment and democracy. Today in Europe, xenophobic, homophobic, and ultra-nationalist ideologies, illiberal parties, and even some national governments defend the idea that values are not universal. And these ideas can be leveraged to obtain good electoral results. The fact that liberal European values are being challenged in Europe itself should encourage us to take account of the doubts being expressed in Chinese society.
QCAD Simulation and Optimization of Semiconductor Quantum Dots
Creators: name: Gao, Xujiao
name: Nielsen, Erik
name: Muller, Richard P.
name: Young, Ralph W.
name: Salinger, Andrew G.
name: Bishop, Nathan C.
name: Lilly, Michael P.
name: Carroll, Malcolm S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present the Quantum Computer Aided Design (QCAD) simulator that targets modeling multi-dimensional quantum devices, particularly silicon multi-quantum dots (QDs) developed for quantum bits (qubits). This finite-element simulator has three differentiating features: (i) its core contains nonlinear Poisson, effective mass Schrodinger, and Configuration Interaction solvers that have massively parallel capability for high simulation throughput, and can be run individually or combined self-consistently for 1D/2D/3D quantum devices; (ii) the core solvers show superior convergence even at near-zero-Kelvin temperatures, which is critical for modeling quantum computing devices; and (iii) it interfaces directly with the full-featured optimization engine Dakota. In this work, we describe the capabilities and implementation of the QCAD simulation tool, and show how it can be used to both analyze existing experimental QD devices through capacitance calculations, and aid in the design of few-electron multi-QDs. In particular, we observe that computed capacitances are in rough agreement with experiment, and that quantum confinement increases capacitance when the number of electrons is fixed in a quantum dot. Coupling of QCAD with the optimizer Dakota allows for rapid identification and improvement of device layouts that are likely to exhibit few-electron quantum dot characteristics.
E-SNPs&GO: Embedding of protein sequence and function improves the prediction of human pathogenic variants
Creators: name: Manfredi, Matteo
name: Castrense Savojardo
name: Martelli, Pier Luigi
name: Casadio, Rita
Publisher: name: F1000 Research Limited
Year: 2022

description: Massive DNA sequencing technologies produce an ever-increasing number of human single-
 nucleotide polymorphisms occurring in protein-coding regions and possibly changing protein

 sequences. Discriminating harmful protein variations from neutral ones is one of the crucial
 challenges in precision medicine. Computational tools based on artificial intelligence provide
 models for protein sequence encoding, bypassing database searches for evolutionary
 information. We leverage the new encoding schemes for efficient annotation of protein variants.
 We develop E-SNPs&GO, a novel method that, given an input protein sequence and a single
 residue variation, can predict whether the variation is related to diseases or not. The proposed
 method adopts an input encoding completely based on protein language models and embedding
 techniques, specifically devised to encode protein sequences and GO functional annotations.
 The model is trained on a dataset of 101,146 human protein single residue variants in 13,661
 proteins, derived from public resources. When tested on a blind set comprising 10,266 variants,
 our method well compares with recent approaches released in literature for the same task,

 reaching an MCC score of 0.72. We propose E-SNPs&GO as a suitable, efficient and accurate large-
 scale annotator of protein variant datasets.

 Availability: The method is available as a web server at https://esnpsandgo.biocomp.unibo.it.
 Datasets and predictions are available at https://esnpsandgo.biocomp.unibo.it/datasets.
Improved NSGA-II algorithms for multi-objective biomarker discovery
Creators: name: Cattelani, Luca
name: Fortino, Vittorio
Publisher: name: F1000 Research Limited
Year: 2022

description: We propose two improved NSGA2 algorithms for finding subsets of biomarkers exhibiting different trade-offs between accuracy and feature number. The performances are investigated on gene expression data of breast cancer patients. The results are compared with NSGA2 and LASSO. The benchmarking dataset includes internal and external validation sets. The results show that the proposed algorithms generate a better approximation of the optimal trade-offs between accuracy and set size. Moreover, validation and test accuracies are better than those provided by NSGA2 and LASSO. Remarkably, the GA-based methods provide biomarkers that achieve a very high prediction accuracy (>80%) with a small number of features (<10), representing a valid alternative to known biomarker models, such as Pam50 and MammaPrint.
Maximally Natural Supersymmetry
Creators: name: Dimopoulos, Savas
name: Howe, Kiel
name: March-Russell, John
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider 4D weak scale theories arising from 5D supersymmetric (SUSY) theories with maximal Scherk-Schwarz breaking at a Kaluza-Klein (KK) scale of several TeV. Many of the problems of conventional SUSY are avoided. Apart from 3rd family sfermions the SUSY spectrum is heavy, with only ~50% tuning at a gluino mass of ~2TeV and a stop mass of ~650 GeV. A single Higgs doublet acquires a vacuum expectation value, so the physical Higgs is automatically Standard-Model-like. A new U(1)' interaction raises the Higgs mass to 126 GeV. For minimal tuning the associated Z', as well as the 3rd family sfermions, must be accessible to LHC13. A gravitational wave signal consistent with BICEP2 is possible if inflation occurs when the extra dimensions are small.
description: 5 pages, 4 figures
Matemáticas, tecnología y formación STEM
Creators: name: Acevedo-Rincón J., P.
name: Flórez-Pabón C., E.
Publisher: name: Zenodo
Year: 2020
Subjects: MATEMÁTICAS
TECNOLOGÍA
FORMACIÓN STEM

description: Esta propuesta pretende identificar indicadores de conocimiento especializado del profesor de Matemáticas bajo una propuesta STEM, del inglés, ciencias, tecnología, ingeniería y matemáticas. Esta investigación es cualitativa. Los resultados iniciales muestran algunos elementos teóricos frente a una propuesta de formación inicial de profesores de matemáticas, bajo una perspectiva interdisciplinar.
A name entity recognition pipeline for custom anonymisation of clinical free-text notes
Creators: name: Rogerio, Andreia
name: Boustred, Chris
name: Broad, Nicholas
name: Rogge, Niels
name: Gbelidji, Florent
name: Need, Anna
name: Azuaje, Francisco
Publisher: name: F1000 Research Limited
Year: 2022

description: Sharing clinical data leads to faster collaboration in medical research and ultimately contributes to disease prevention and improved treatments. At Genomics England, data sharing is crucial to research and to enable the infinity loop that allows continuous improvement of cancer and rare disease diagnosis.
 Unfortunately, ensuring personal identifiable data (PID) is anonymized and compliant with the relevant governance is still challenging, especially in unstructured data. In the Clinical Variant Ark (CVA) Portal, clinical scientist share their interpretations of genomic variants in free text boxes. This is highly valuable information but can only be shared with researchers if completely anonymised.
 Here we propose a prof of concept solution to identify and redact all personal names in the CVA database, while still maintaining the relevant medical content. We show that with NLP techniques the anonymisation can reach values of 100% of recall and 80% of precision.
Validating Predictions of Unobserved Quantities
Creators: name: Oliver, Todd A.
name: Terejanu, Gabriel
name: Simmons, Christopher S.
name: Moser, Robert D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Methodology (stat.ME)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: The ultimate purpose of most computational models is to make predictions, commonly in support of some decision-making process (e.g., for design or operation of some system). The quantities that need to be predicted (the quantities of interest or QoIs) are generally not experimentally observable before the prediction, since otherwise no prediction would be needed. Assessing the validity of such extrapolative predictions, which is critical to informed decision-making, is challenging. In classical approaches to validation, model outputs for observed quantities are compared to observations to determine if they are consistent. By itself, this consistency only ensures that the model can predict the observed quantities under the conditions of the observations. This limitation dramatically reduces the utility of the validation effort for decision making because it implies nothing about predictions of unobserved QoIs or for scenarios outside of the range of observations. However, there is no agreement in the scientific community today regarding best practices for validation of extrapolative predictions made using computational models. The purpose of this paper is to propose and explore a validation and predictive assessment process that supports extrapolative predictions for models with known sources of error. The process includes stochastic modeling, calibration, validation, and predictive assessment phases where representations of known sources of uncertainty and error are built, informed, and tested. The proposed methodology is applied to an illustrative extrapolation problem involving a misspecified nonlinear oscillator.
Supplementary material-Elastin Morphometry Protocol.pdf
Creators: name: Ramamurthi, Anand
name: Dahal, Shataakshi
name: Damaser, Margot
name: Kuang, Mei
name: Riestch, Anna
name: Butler, Robert
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 400399
subject: Biomedical engineering not elsewhere classified

description: This is a protocol for quantifying morphological characteristics of elastin in histological samples using Image-Pro software.
Effective synchronization of a class of Chua's chaotic systems using an exponential feedback coupling
Creators: name: Louodop, Patrick
name: Fotsin, Hilaire
name: Ngouonkadi, Elie B. Megam
name: Bowong, Samuel
name: Cerdeira, Hilda A.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: In this work a robust exponential function based controller is designed to synchronize effectively a given class of Chua's chaotic systems. The stability of the drive-response systems framework is proved through the Lyapunov stability theory. Computer simulations are given to illustrate and verify the method.
description: 12 pages, 18 figures
The Geometry of the Minimal Resultant Locus
Creators: name: Rumely, Robert
Publisher: name: arXiv
Year: 2014
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 37P50, 11S82, 37P05, 11Y40, 11U05

description: Let K be a complete, algebraically closed, nonarchimedean valued field, and let f(z) be a rational function in K(z) of degree d at least 2. We show there is a natural way to assign non-negative integer weights w_f(P) to points of the Berkovich projective line over K, in such a way that the sum over all points is d-1. When f(z) has bad reduction, the set of points with nonzero weight forms a distributed analogue of the single point which occurs when f(z) has potential good reduction. Using this, we characterize the Minimal Resultant Locus of f(z) in dynamical and moduli-theoretic terms: dynamically, it is the barycenter of the weight-measure attached to f(z); moduli-theoretically, it is the closure of the set of type II points where f(z) has semi-stable reduction in the sense of Geometric Invariant Theory.
description: 53 pages
Focusing and imaging with increased numerical apertures through multimode fibers with micro-fabricated optics
Creators: name: Bianchi, S.
name: Rajamanickam, V. P.
name: Ferrara, L.
name: Di Fabrizio, E.
name: Liberale, C.
name: Di Leonardo, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The use of individual multimode optical fibers in endoscopy applications has the potential to provide highly miniaturized and noninvasive probes for microscopy and optical micromanipulation. A few different strategies have been proposed recently, but they all suffer from intrinsically low resolution related to the low numerical aperture of multimode fibers. Here, we show that two-photon polymerization allows for direct fabrication of micro-optics components on the fiber end, resulting in an increase of the numerical aperture to a value that is close to 1. Coupling light into the fiber through a spatial light modulator, we were able to optically scan a submicrometer spot (300 nm FWHM) over an extended region, facing the opposite fiber end. Fluorescence imaging with improved resolution is also demonstrated.
description: 5 pages, 3 figures
34 Briefe an Johan[n] Caspar Lavater
Brief an Lavater ...
Creators: name: Hartmann, Johann Leonhart
name: Hartmann, ...
Publisher: name: [s.n.]
Year: 1771

description: von Gebrüder Johan[n] Leonhart Hartmann, Hartmann
description: Davon 4 Briefe nur von Johann Leonhart Hartmann (Nr. 144, 149, 151, 177), 1 Brief an Anna Lavater (Nr. 172)
description: Davon 1 Brief mit Auszug aus einem Brief von Caspar Fels (Nr. 152), 1 Brief mit Auszügen von Sardi (Nr. 167)
description: Davon 1 Brief mit Beischrift von anderer Hand (wohl Bruder von Johann Leonhart)
17 Briefe an [Johann Caspar] Lavater
Brief an Lavater ...
Creators: name: Haschka, Lorenz Leopold
Publisher: name: [s.n.]
Year: 1782

description: von Lorenz Leopold Haschka
description: Davon 1 Brief mit Beischrift von Charlotte von Greiner (Nr. 179)
description: Davon 2 Briefe von Charlotte von Greiner mit Beischrift von Haschka (Nr. 180 und 186)
Electron transport signature of H$_2$ dissociation on atomic gold wires
Creators: name: Zanchet, Alexandre
name: Dorta-Urra, Anaís
name: Roncero, Octavio
name: Aguado, Alfredo
name: Martínez, José Ignacio
name: Flores, Fernando
name: Lorente, Nicolás
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Non-equilibrium Green's functions calculations based on density functional theory show a direct link between the initial stages of H$_2$ dissociation on a gold atomic wire and the electronic current supported by the gold wire. The simulations reveal that for biases below the stability threshold of the wire, the minimum-energy path for H$_2$ dissociation is not affected. However, the electronic current presents a dramatic drop when the molecule initiates its dissociation. This current drop is traced back to quantum interference between electron paths when the molecule starts interacting with the gold wire.
[Johannes Itten]: Grundlegende Bemerkungen zu unserer Arbeit an der höheren Fachschule für textile Flächenkunst in Krefeld
Creators: name: Itten, Johannes
Publisher: name: [s.n.]
Year: 1930

description: 3 Sätze von Durchschlägen eines Typoskripts von 4 Seiten, mit handschriftlichen Korrekturen
Boris Kleint an Johannes Itten
Creators: name: Kleint, Boris
Publisher: name: [s.n.]
Year: 1945

description: Textincipit: "Lieber Herr Itten, / ich [sic] war sehr erfreut, nach so langer Zeit wieder etwas / von Ihnen zu hören! [...]"
Dem Brief wurde ein Foto von Boris Kleint beigelegt.
Inertial particle trapping in an open vortical flow
Creators: name: Angilella, Jean-Regis
name: Vilela, Rafael D.
name: Motter, Adilson E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: Recent numerical results on advection dynamics have shown that particles denser than the fluid can remain trapped indefinitely in a bounded region of an open fluid flow. Here, we investigate this counterintuitive phenomenon both numerically and analytically to establish the conditions under which the underlying particle-trapping attractors can form. We focus on a two-dimensional open flow composed of a pair of vortices and its specular image, which is a system we represent as a vortex pair plus a wall along the symmetry line. Considering particles that are much denser than the fluid, we show that two point attractors form in the neighborhood of the vortex pair provided that the particle Stokes number is smaller than a critical value of order unity. In the absence of the wall, the boundaries of the basins of the attracting points are smooth. When the wall is present, the point attractors describe counter-rotating ellipses in this frame, with a period equal to half the period of one isolated vortex pair. However, their boundaries are shown to become fractal if the distance to the wall is smaller than a critical distance that scales with the inverse square root of the Stokes number. This transformation is related to the breakdown of a separatrix that gives rise to a heteroclinic tangle close to the vortices, which we describe using a Melnikov function. For an even smaller distance to the wall, we demonstrate that a second separatrix breaks down and a new heteroclinic tangle forms farther away from the vortices. Particles released in the open part of the flow can approach the attractors and be trapped permanently provided that they cross the two separatrices. Furthermore, the trapping of heavy particles from the open flow is shown to be robust to the presence of gravity, viscosity, and noise.
Investigating the dynamics of hand and lips in French Cued Speech using attention mechanisms and CTC-based decoding
Creators: name: Sankar, Sanjana
name: Beautemps, Denis
name: Elisei, Frédéric
name: Perrotin, Olivier
name: Hueber, Thomas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Hard of hearing or profoundly deaf people make use of cued speech (CS) as a communication tool to understand spoken language. By delivering cues that are relevant to the phonetic information, CS offers a way to enhance lipreading. In literature, there have been several studies on the dynamics between the hand and the lips in the context of human production. This article proposes a way to investigate how a neural network learns this relation for a single speaker while performing a recognition task using attention mechanisms. Further, an analysis of the learnt dynamics is utilized to establish the relationship between the two modalities and extract automatic segments. For the purpose of this study, a new dataset has been recorded for French CS. Along with the release of this dataset, a benchmark will be reported for word-level recognition, a novelty in the automatic recognition of French CS.
Origin of atmospheric aerosols at the Pierre Auger Observatory using studies of air mass trajectories in South America
Creators: name: Pierre Auger Collaboration
name: Curci, Gabriele
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: FOS: Physical sciences

description: The Pierre Auger Observatory is making significant contributions towards understanding the nature and origin of ultra-high energy cosmic rays. One of its main challenges is the monitoring of the atmosphere, both in terms of its state variables and its optical properties. The aim of this work is to analyze aerosol optical depth $τ_{\rm a}(z)$ values measured from 2004 to 2012 at the observatory, which is located in a remote and relatively unstudied area of the Pampa Amarilla, Argentina. The aerosol optical depth is in average quite low - annual mean $τ_{\rm a}(3.5~{\rm km})\sim 0.04$ - and shows a seasonal trend with a winter minimum - $τ_{\rm a}(3.5~{\rm km})\sim 0.03$ -, and a summer maximum - $τ_{\rm a}(3.5~{\rm km})\sim 0.06$ -, and an unexpected increase from August to September - $τ_{\rm a}(3.5~{\rm km})\sim 0.055$). We computed backward trajectories for the years 2005 to 2012 to interpret the air mass origin. Winter nights with low aerosol concentrations show air masses originating from the Pacific Ocean. Average concentrations are affected by continental sources (wind-blown dust and urban pollution), while the peak observed in September and October could be linked to biomass burning in the northern part of Argentina or air pollution coming from surrounding urban areas.
description: 16 pages, 9 figures, accepted in Atmospheric Research journal
Link Quality and MAC-Overhead aware Predictive Preemptive Routing Protocol for Mobile Ad hoc Network
Creators: name: Moussa, Ali Cherif
name: Kamel, Faraoun Mohamed
Publisher: name: arXiv
Year: 2013
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences
subject: 68

description: In Ad Hoc networks, route failure may occur due to less received power, mobility, congestion and node failures. Many approaches have been proposed in literature to solve this problem, where a node predicts pre-emptively the route failure that occurs with the less received power. However, this approach encounters some difficulties, especially in scenario without mobility where route failures may arise. In this paper, we propose an improvement of AODV protocol called LO-PPAODV (Link Quality and MAC-Overhead aware Predictive Preemptive AODV). This protocol is based on new metric combine more routing metrics (Link Quality, MAC Overhead) between each node and one hop neighbor. Also we propose a cross-layer networking mechanism to distinguish between both situations, failures due to congestion or mobility, and consequently avoiding unnecessary route repair process. The LO-PPAODV was implemented using NS-2. The simulation results show that our approach improves the overall performance of the network. It reduces the average end to end delay, the routing overhead, MAC errors and route errors, and increases the packet delivery fraction of the network.
description: 10 pages, 19 figures. arXiv admin note: text overlap with arXiv:0907.5441 by other authors
Fotografie von Johannes Itten und Absolventen der Universität Bern mit Sekundarlehrer-Diplom
Creators: name: [s.n.]
Publisher: name: [s.n.]
Year: 1912
Subjects: Itten, JohannesJohannItten1888-11-11dpcAbgebildet

description: Auf Karton aufgeklebter Fotoabzug