cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
HGPEC: a Cytoscape app for prediction of novel disease-gene and disease-disease associations and evidence collection based on a random walk on heterogeneous network
Creators: name: Duc-Hau Le
Publisher: name: F1000Research
Year: 2017

description: Background: Finding gene-disease and disease-disease associations play important roles in the biomedical area and many prioritization methods have been proposed for this goal. Among them, approaches based on a heterogeneous network of genes and diseases are considered state-of-the-art ones, which achieve high prediction performance and can be used for diseases with/without known molecular basis.

Results: Here, we developed a Cytoscape app, namely HGPEC, based on a random walk with restart algorithm on a heterogeneous network of genes and diseases. This app can prioritize candidate genes and diseases by employing a heterogeneous network consisting of a network of genes/proteins and a phenotypic disease similarity network. Based on the rankings, novel disease-gene and disease-disease associations can be identified. These associations can be supported with network- and rank-based visualization as well as evidences and annotations from biomedical data. A case study on prediction of novel breast cancer-associated genes and diseases shows the abilities of HGPEC. In addition, we showed prominence in the performance of HGPEC compared to other tools for prioritization of candidate disease genes.

Conclusions: Taken together, our app is expected to effectively predict novel disease-gene and disease-disease associations and support network- and rank-based visualization as well as biomedical evidences for such the associations.
sj-docx-2-sgo-10.1177_21582440231209634 – Supplemental material for Ritual Performance as Gradual Recognition: Sere Bissu Maggiriq Dance of South Sulawesi Indonesia
Creators: name: Akhmar, Andi Muhammad
name: Muhammad, Harry Isra
name: Hasyim, Muhammad
name: Rahman, Fathu
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: Communication and Media Studies not elsewhere classified
subject: Criminology not elsewhere classified
subject: Education
subject: Psychology not elsewhere classified
subject: Sociology
subject: FOS: Sociology

description: Supplemental material, sj-docx-2-sgo-10.1177_21582440231209634 for Ritual Performance as Gradual Recognition: Sere Bissu Maggiriq Dance of South Sulawesi Indonesia by Andi Muhammad Akhmar, Harry Isra Muhammad, Muhammad Hasyim and Fathu Rahman in SAGE Open
title: Nine Stories, Minus One
Creators: name: Mazur, Claudia Anne
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 2011

description: This work consists of eight short works of fiction that reflect lessons on point of view, characterization, and voice, while demonstrating a voice and style particular to this author. The author's interest in setting and the characterization of personalities that are misfits in their environments is also reflected.
The Role of Geometry in Tailoring the Linear and Nonlinear Optical Properties of Semiconductor Quantum Dots
Creators: name: Mantashian, Grigor A.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The paper aims to reveal the relationship between the geometrical features and linear and nonlinear optical properties of InAs quantum dots (QDs). This problem is justified by the extreme variety offered by the recent advances in growth techniques tailored to the attainment of QDs and nanostructures with virtually any shape. To that end, the Finite Element Method in conjunction with the Effective Mass Approximation and Envelope Function Approximation was employed to solve the one-particle eigenproblems in domains with any complex geometries. The paper explores nanoplatelets, spherical QDs, nanocones, nanorods, nanotadpoles, and nanostars. It has been found that there is a clear correlation between the complexity and symmetry of the QDs and their linear and nonlinear absorption spectra for transitions between the electronic ground state and the first three excited states.
Identifiable Causal Representation Learning: Unsupervised, Multi-View, and Multi-Environment
Creators: name: von Kügelgen, Julius
Publisher: name: arXiv
Year: 2024
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Causal models provide rich descriptions of complex systems as sets of mechanisms by which each variable is influenced by its direct causes. They support reasoning about manipulating parts of the system and thus hold promise for addressing some of the open challenges of artificial intelligence (AI), such as planning, transferring knowledge in changing environments, or robustness to distribution shifts. However, a key obstacle to more widespread use of causal models in AI is the requirement that the relevant variables be specified a priori, which is typically not the case for the high-dimensional, unstructured data processed by modern AI systems. At the same time, machine learning (ML) has proven quite successful at automatically extracting useful and compact representations of such complex data. Causal representation learning (CRL) aims to combine the core strengths of ML and causality by learning representations in the form of latent variables endowed with causal model semantics.
 In this thesis, we study and present new results for different CRL settings. A central theme is the question of identifiability: Given infinite data, when are representations satisfying the same learning objective guaranteed to be equivalent? This is an important prerequisite for CRL, as it formally characterises if and when a learning task is, at least in principle, feasible. Since learning causal models, even without a representation learning component, is notoriously difficult, we require additional assumptions on the model class or rich data beyond the classical i.i.d. setting. By partially characterising identifiability for different settings, this thesis investigates what is possible for CRL without direct supervision, and thus contributes to its theoretical foundations. Ideally, the developed insights can help inform data collection practices or inspire the design of new practical estimation methods.
description: PhD Thesis; 190 pages, 33 figures, 6 tables
Additional file 3 of Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis
Creators: name: Kim, Seongryong
name: Leem, Galam
name: Choi, Junjeong
name: Koh, Yongjun
name: Lee, Suho
name: Nam, Sang-Hee
name: Kim, Jin Su
name: Park, Chan Hee
name: Hwang, Ho Kyoung
name: Min, Kyoung Il
name: Jo, Jung Hyun
name: Lee, Hee Seung
name: Chung, Moon Jae
name: Park, Jeong Youp
name: Park, Seung Woo
name: Song, Si Young
name: Shin, Eui-Cheol
name: Kang, Chang Moo
name: Bang, Seungmin
name: Park, Jong-Eun
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Virology

description: Additional file 3. Supplementary materials and methods.
title: Hab ein gar kostbar Gut erfläht
Creators: name: Tschuden, Friedrich
Year: 2008

description: ABBILDUNGEN: nur in PRINTAUSGABE! -- Die Arbeit beschäftigt sich mit der Geschichte und der Entstehung großer und kleinerer Wallfahrtsorte im Waldviertel und nimmt Bezug auf die Geschichte des Wallfahrens ab dem späten Mittelalter in Niederösterreich.
Growth, proliferation, and the pursuit of fitness: How cell-scale forces shape competitive population dynamics
Creators: name: Carpenter, Logan
Publisher: name: Carnegie Mellon University
Year: 2025
Subjects: classificationCode: 320802
subject: Human biophysics

description: Cell competition is a fitness control mechanism in tissues, where less fit cells are eliminated to maintain tissue homeostasis. Two primary mechanisms of cell elimination have been identified in cell competition studies: contact-dependent cell death and mechanical compression-driven apoptosis. While both occur in tissues, their combined impact on population dynamics is unclear. Here we develop a cell-based computational model to study competition between two cell types with differing physical properties. We incorporate probabilistic rules governing cell growth, division, and elimination, while also taking into account their feedback with tissue mechanics. To both validate our model and acting as a necessary stepping stone to simulate cell competition, we first begin with a study of the mechanics of a growing tissue composed of a single cell type. In this effort we sought to predict how tissue confinement influences cell size and proliferation dynamics, and how single-cell physical properties influence the spatiotemporal patterns of tissue growth. We show that the cell size threshold at G1/S transition governs the homeostatic cell density and tissue turnover rate, while the mechanical state of the tissue governs the dynamics of tissue growth. Furthermore, by tuning cellular elasticity and contact inhibition of proliferation we can regulate the emergent patterns of cell proliferation, ranging from uniform growth at low contact inhibition to localized growth at higher contact inhibition. With this validation of our model for a single cell type, we move on to explore how differences in physical traits between cell types influence competitive interactions. Our findings show that differences in cell compressibility alone can drive mechanical competition, with stiffer cells out competing softer ones in otherwise identical populations. Surprisingly, mutations that reduce cell stiffness, combined with decreased contact inhibition of proliferation, can create a “soft” super-competitive mutant. We demonstrate that changes in apoptosis sensitivity, cell ad?hesion, and cell size significantly affect growth potential and susceptibility to apoptosis. Furthermore, mutant cell colonies require a critical colony size, dependent on cell compressibility, to overtake the surrounding wild-type tissue. For colonies below the critical size, the elimination process is stochastic, driven by a protrusive finger-like instability in the interface between two cells that promote invasion of the super-competitors.
High-throughput protein functional prediction by data science approach
Creators: name: Liu, Yi-Wei
name: Wen-Hung Liao
name: Chang, Jia-Ming
Publisher: name: F1000Research
Year: 2017

description: We proposed a new protein function prediction framework extended from PSLDoc and PSLDoc2, which have been used to predict protein subcellular localization with superior performance. We designed three different voting methods to solve multiple label predict problems. They perform better than the baseline models according to benchmark on CAFA2 and CAFA3 data sets. [team: NCCUCS @ CAFA3]
8 Sonates pour la guitarre avec un violon ... : Opera 2
Creators: name: Ritter, Georg Wenzel
Publisher: name: Sieber et Co.
Year: 1780

description: Gemäss dem Notentext offenbar für das als "Guitarre allemande" bekannte Cisterinstrument komponiert.
description: Digitalisierung=Digitization=Numérisation TIFF
CONFESS: Single-cell ordering by fluorescence signal estimation and modelling in R
Creators: name: Low, Diana HP
name: Motakis, Efthymios
Publisher: name: F1000Research
Year: 2017

description: We propose a novel statistical model whose multiple steps are integrated into the Cell OrderiNg (by) FluorEScence Signal (CONFESS) R package. CONFESS performs image analysis and fluorescence signal estimation for data coming from the Fluidigm C1. It collects extensive information on the cell morphology, location and signal that can be used for quality control and phenotype prediction. If applicable, it normalizes and uses the signals for unsupervised cell ordering (pseudotime estimation) and 2-dimensional clustering via scalar projection, change-point analysis and Data Driven Haar Fisz transformation for multivariate data. One could potentially use CONFESS to classify and sort fluorescent cells in various applications (cell cycle, cell differentiation, etc). Here we illustrate the use of CONFESS to trace Fucci-labeled Hela cells in their cell cycle progression. The output can be easily integrated with available single-cell RNA-seq (or other) expression profile packages for subsequent analysis.
Predicting protein functions from sequence and interactions using a neuro-symbolic deep learning model
Creators: name: Kulmanov, Maxat
name: Khan, Mohammed Asif
name: Hoehndorf, Robert
Publisher: name: F1000Research
Year: 2017

description: In order to understand the molecular mechanisms of life it is necessary to know the functions of the proteins in an organism.
In this project, we are developing a tool for annotating proteins with Gene Ontology functions using sequence of the protein.
Since one protein can have multiple functions, our problem is to solve a multi-label classification task with a very large
number of classes. To tackle this problem we’ve built a deep neural network model with convolutional layers for learning
protein representation and hierarchical layers of fully connected neurons for classification. Our model matches state of the
art approaches and may outperform them.
SonicParanoid: extremely fast, easy and accurate orthology inference
Creators: name: Cosentino, Salvatore
name: Iwasaki, Wataru
Publisher: name: F1000Research
Year: 2017

description: Thanks to recent advancements in DNA sequencing technologies, the number of species for which genome sequences are available is growing at an accelerated pace. Accurate inference of orthologous genes encoded on multiple genomes is the key to various analyses based on those datasets. For example, elucidation of species-specific and/or evolutionarily shared genomic signatures at the sequence, structural, and/or functional levels (comparative genomics), transfer of genetic knowledge between genomes of model and non-model organisms, reconstruction of phylogenetic trees using genomic information (phylogenomics), and development of reference genome databases, all depend on reliable orthology inference. Despite its general importance, it is still time-consuming and difficult to conduct orthology inference on a specific set of genomes that often include in-house sequenced genomes. Here, we present SonicParanoid, which is orders of magnitude faster than, but comparably accurate to the existing tools, with a balanced precision-recall trade-off.
sj-docx-1-spp-10.1177_19485506221119357 – Supplemental material for Sensory Processing Sensitivity and Reactivity to Daily Events
Creators: name: Van Reyn, Chiara
name: Koval, Peter
name: Bastian, Brock
Publisher: name: SAGE Journals
Year: 2022
Subjects: subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology

description: Supplemental material, sj-docx-1-spp-10.1177_19485506221119357 for Sensory Processing Sensitivity and Reactivity to Daily Events by Chiara Van Reyn, Peter Koval and Brock Bastian in Social Psychological and Personality Science
Additional file 1 of Arginyltransferase 1 modulates p62-driven autophagy via mTORC1/AMPk signaling
Creators: name: Bonnet, Laura V.
name: Palandri, Anabela
name: Flores-Martin, Jesica B.
name: Hallak, Marta E.
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology

description: Additional file 1: Fig. S1. Ate1 isoform expression and subcellular distribution. Fig. S2. Solubility of Ate1 in aqueous and detergent phases. Fig. S3. Ate1 stability and colocalization with p62. Fig. S4. Rapamycin effect on p-mTORC1 levels.
Augocoris gomesii Burmeister (Scutellerinae 1835
Creators: name: Guzmán-Vásquez, Héctor M.
name: Martínez-Martínez, Laura
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Scutelleridae
Augocoris
Augocoris gomesii

description: Augocoris gomesii Burmeister, 1835
Figure 2a
Material examined: 2 specimens (♂) labeled: MEXICO, Oaxaca, Sta. María Chimalapas; Cerro Azul Reserve, Tropical montane cloud forest. 28-VIII-2022. UV light trap. Leg. Guzmán V, H. M. (1♂) // MEXICO, Oaxaca, Cuajinicuil. 20-X-2014. Leg. Ramírez, Y. G. (1♂). New state record.
Associated plants: No data
Remarks: Despite being a very colorful shield bug, there is little or no information on its distribution, biology, ecology, hosts and natural enemies. As for its habits, it is only known to be attracted to lights (Torre-Bueno 1914; Eger et al. 2015a; present study). In Mexico it has been recorded in the states of Chiapas, Nayarit and Veracruz (Rodríguez 1992). Here we record for the first time its presence in Oaxaca.
description: Published as part of Guzmán-Vásquez, Héctor M. & Martínez-Martínez, Laura, 2025, Checklist and bilingual key to the genera of Scutelleridae (Hemiptera: Heteroptera) from Mexico, with new distribution records for the state of Oaxaca, pp. 341-354 in Zootaxa 5594 (2) on pages 346-347, DOI: 10.11646/zootaxa.5594.2.6, http://zenodo.org/record/14954440
Particle models from special Jordan backgrounds and spectral triples
Creators: name: Besnard, Fabien
name: Farnsworth, Shane
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Rings and Algebras (math.RA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We put forward a definition for spectral triples and algebraic backgrounds based on Jordan coordinate algebras. We also propose natural and gauge-invariant bosonic configuration spaces of fluctuated Dirac operators and compute them for general, almost-associative, Jordan, coordinate algebras. We emphasize that the theory so obtained is not equivalent with usual associative noncommutative geometry, even when the coordinate algebra is the self-adjoint part of a $C^*$-algebra. In particular, in the Jordan case, the gauge fields are always unimodular, thus curing a long-standing problem in noncommutative geometry.
description: 37 pages
Single cell expression data reveal human genes that escape X-chromosome inactivation
Creators: name: Katsir, Kerem Wainer
name: Linial, Michal
Publisher: name: F1000Research
Year: 2017

description: Background: In mammals, sex chromosomes are a source of an inherent genetic difference between the sexes. A balance between the sexes is reached by random inactivation of one of the X-chromosomes, in each female somatic cell. Thus resulting in a tissue mosaic such that some of the cells express one of the X-chromosomes and some the other. While most genes from the inactivated X-chromosome are silenced, about 15-25% of them have been shown to escape inactivation (referred as escapees). These escapees have so far been identified using multiple indirect methods considering the mosaic nature of female tissues.

Results: We use single-cell RNA-seq to directly quantify the extent of escape from X-inactivation phenomenon. Analyzing data from single cells is preferable as in each cell only one of the X chromosomes is inactivated. Our method relies on allelic specific expression of genes with heterozygous SNPs, thus enabling us to discriminate between the expression of genes from the active X-chromosome (Xa) and from the inactive (Xi) one. We apply our method to datasets from (i) primary fibroblasts without genomic phasing (n=104), and (ii) clonal lymphoblasts cells with phased parental genomes (n=25). Applying our single-cell analysis we identify 27 and 34 escapees from fibroblasts and lymphoblasts, respectively. On the other hand, when analyzing a pool of lymphoblasts, only 14 escapees are discovered. Altogether, we report on 51 escapees, many of which are known escapees discovered by indirect methods (p=2.74e-06). We identify a few overlooked escapees, and propose to revise the annotations associated with some others.

Conclusions: Chromosome X-inactivation and escaping from it are robust phenomena detected at a single-cell resolution. These phenomena are apparent in isolated primary fibroblasts as well as in cell-lines. Genomic phasing substantially improves the detection of escapees. Cumulative data from individual cells increases the sensitivity of detecting escapees compared to data extracted from a pooled sample. Our results support the notion that different cell types express different escapees with only a handful of consistent escapees across cell types and experimental settings.
sj-docx-4-cre-10.1177_02692155221123544 - Supplemental material for Post-fracture rehabilitation pathways and association with mortality among adults with cerebral palsy
Creators: name: Whitney, Daniel G.
name: Xu, Tao
name: Ryan, Dayna
name: Whibley, Daniel
name: Caird, Michelle S.
name: Hurvitz, Edward A.
name: Haapala, Heidi
Publisher: name: SAGE Journals
Year: 2022
Subjects: subject: Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine
subject: Orthopaedics
subject: Sports Medicine

description: Supplemental material, sj-docx-4-cre-10.1177_02692155221123544 for Post-fracture rehabilitation pathways and association with mortality among adults with cerebral palsy by Daniel G. Whitney, Tao Xu, Dayna Ryan, Daniel Whibley, Michelle S. Caird and
Edward A. Hurvitz, Heidi Haapala in Clinical Rehabilitation
Camirus moestus
Creators: name: Guzmán-Vásquez, Héctor M.
name: Martínez-Martínez, Laura
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Scutelleridae
Camirus
Camirus moestus

description: Camirus moestus (Stål, 1862)
Figure 2b
Material examined: 1 specimen: MEXICO, Oaxaca, San Andrés Huayapam. 14-IX-2020. On flower of Dahlia pinnata Cav. (1791). Leg. Martínez M, L. (1♀). New state record and new plant association.
Associated plants: Ambrosia ambrosioides (Cav.) Payne (Asteraceae), Gossypium sp. (Malvaceae) (Rider 2015).
Remarks: Extremely little is known about the distribution, biology and ecology of this species. Here we report for the first time its association with Dahlia pinnata Cav and its occurrence in Oaxaca. In Mexico this species has previously been recorded in the states of Hidalgo, Puebla, and San Luis Potosi (supplementary material from Weiler et al. 2017).
description: Published as part of Guzmán-Vásquez, Héctor M. & Martínez-Martínez, Laura, 2025, Checklist and bilingual key to the genera of Scutelleridae (Hemiptera: Heteroptera) from Mexico, with new distribution records for the state of Oaxaca, pp. 341-354 in Zootaxa 5594 (2) on page 347, DOI: 10.11646/zootaxa.5594.2.6, http://zenodo.org/record/14954440
sj-pdf-1-jhs-10.1177_17531934221117429 - Supplemental material for Psychological sequelae of hand injuries: an integrative review
Creators: name: Maddison, Kay
name: Perry, Lin
name: Debono, Deborah
Publisher: name: SAGE Journals
Year: 2022
Subjects: subject: 110314 Orthopaedics
subject: FOS: Clinical medicine
subject: 110604 Sports Medicine
subject: FOS: Health sciences
subject: 110323 Surgery

description: Supplemental material, sj-pdf-1-jhs-10.1177_17531934221117429 for Psychological sequelae of hand injuries: an integrative review by Kay Maddison, Lin Perry and Deborah Debono in Journal of Hand Surgery (European Volume)
Additional file 2 of Arginyltransferase 1 modulates p62-driven autophagy via mTORC1/AMPk signaling
Creators: name: Bonnet, Laura V.
name: Palandri, Anabela
name: Flores-Martin, Jesica B.
name: Hallak, Marta E.
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology

description: Additional file 2: Fig. S5. Full-length original, uncropped blots in the study.
sj-pdf-3-jhs-10.1177_17531934221117429 - Supplemental material for Psychological sequelae of hand injuries: an integrative review
Creators: name: Maddison, Kay
name: Perry, Lin
name: Debono, Deborah
Publisher: name: SAGE Journals
Year: 2022
Subjects: subject: 110314 Orthopaedics
subject: FOS: Clinical medicine
subject: 110604 Sports Medicine
subject: FOS: Health sciences
subject: 110323 Surgery

description: Supplemental material, sj-pdf-3-jhs-10.1177_17531934221117429 for Psychological sequelae of hand injuries: an integrative review by Kay Maddison, Lin Perry and Deborah Debono in Journal of Hand Surgery (European Volume)
sj-pdf-1-imr-10.1177_03000605221116757 - Supplemental material for Head rotation as an effective compensatory technique for dysphagia caused by unilateral cervical osteophytes
Creators: name: Seo, Minsu
name: Park, Jin-Woo
Publisher: name: SAGE Journals
Year: 2022
Subjects: subject: 111708 Health and Community Services
subject: FOS: Health sciences
subject: Cardiology
subject: 110599 Dentistry not elsewhere classified
subject: FOS: Clinical medicine
subject: 110305 Emergency Medicine
subject: 110306 Endocrinology
subject: 110308 Geriatrics and Gerontology
subject: 110904 Neurology and Neuromuscular Diseases
subject: 111099 Nursing not elsewhere classified
subject: 111199 Nutrition and Dietetics not elsewhere classified
subject: 111299 Oncology and Carcinogenesis not elsewhere classified
subject: 110314 Orthopaedics
subject: 110604 Sports Medicine
subject: 110315 Otorhinolaryngology
subject: 111702 Aged Health Care
subject: 111403 Paediatrics
subject: 111599 Pharmacology and Pharmaceutical Sciences not elsewhere classified
subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology
subject: 110319 Psychiatry (incl. Psychotherapy)
subject: 111799 Public Health and Health Services not elsewhere classified
subject: 110203 Respiratory Diseases
subject: 160807 Sociological Methodology and Research Methods
subject: FOS: Sociology
subject: 110323 Surgery

description: Supplemental material, sj-pdf-1-imr-10.1177_03000605221116757 for Head rotation as an effective compensatory technique for dysphagia caused by unilateral cervical osteophytes by Minsu Seo and Jin-Woo Park in Journal of International Medical Research
Orsilochides scurrilis
Creators: name: Guzmán-Vásquez, Héctor M.
name: Martínez-Martínez, Laura
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Scutelleridae
Orsilochides
Orsilochides scurrilis

description: Orsilochides scurrilis (Stål, 1855)
Figure 2c
Material examined: 6 specimens (4♂ and 2♀). MEXICO, Oaxaca, Villa de Zaachila; Native grassland. 20-IX-2021. On acahual Simsia amplexicaulis Pers. Leg. Guzmán V, H. M. (1♀). Same data except 22-VII-2016. (1♂) // MEXICO, Oaxaca, San Pedro Tapanatepec. 6-X-2004. On unidentified plant. Leg. Flores, A. S. (1♂, 1♀). Same data except 7-XII-2004. Leg. Coello C, M. M. (1♂) // MEXICO, Oaxaca, Cuilapam de Guerrero. 12-IX-2006. On Zea mays. Leg. López M, M. (1♂). New state record and new plant associations.
Associated plants: Ericameria laricifolia (A.Gray) Shinners (Asteraceae), Gossypium sp. (Malvaceae), Bougainvillea sp. (Nyctaginaceae), Saccharum sp. (Poaceae) (Meeds et al. 2021).
Remarks: Here we report for the first time the association of O. scurrilis with Simsia amplexicaulis (Cav.) Pers (Asteraceae) and Zea mays L. (Poaceae). Little is known about its geographic distribution, biology, life cycles, and immature stages. The data provided here represent the first records for Oaxaca. Brailovsky & Márquez (1974) recorded this species from Cuautla, Morelos and mentioned that records were known from Navojoa, Sonora and Tuxtla Gutiérrez, Chiapas. In addition to these records, in iNaturalist we found observations in the states of Baja California Sur, Colima, Estado de México, Guerrero, Guanajuato, Hidalgo, Jalisco, Michoacán, Nayarit, Quintana Roo, Sinaloa and San Luís Potosí.
description: Published as part of Guzmán-Vásquez, Héctor M. & Martínez-Martínez, Laura, 2025, Checklist and bilingual key to the genera of Scutelleridae (Hemiptera: Heteroptera) from Mexico, with new distribution records for the state of Oaxaca, pp. 341-354 in Zootaxa 5594 (2) on pages 347-348, DOI: 10.11646/zootaxa.5594.2.6, http://zenodo.org/record/14954440
Additional file 1 of Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle
Creators: name: Naji, Maulana Mughitz
name: Gualdrón Duarte, José Luis
name: Forneris, Natalia Soledad
name: Druet, Tom
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Summary statistics for linear classifications traits in Belgian Blue Beef cattle. Table S2. Correlations between individual proportions of the genome in different HBD classes (FHBD-c) estimated with AF from base population or with AF from the sample. Table S3. Correlation between estimators of the inbreeding coefficient estimated using sample allele frequencies or base population allele frequencies.
Convergence guarantees for forward gradient descent in the linear regression model
Creators: name: Bos, Thijs
name: Schmidt-Hieber, Johannes
Publisher: name: arXiv
Year: 2023
Subjects: subject: Statistics Theory (math.ST)
subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: Primary: 62L20, secondary: 62J05

description: Renewed interest in the relationship between artificial and biological neural networks motivates the study of gradient-free methods. Considering the linear regression model with random design, we theoretically analyze in this work the biologically motivated (weight-perturbed) forward gradient scheme that is based on random linear combination of the gradient. If d denotes the number of parameters and k the number of samples, we prove that the mean squared error of this method converges for $k\gtrsim d^2\log(d)$ with rate $d^2\log(d)/k.$ Compared to the dimension dependence d for stochastic gradient descent, an additional factor $d\log(d)$ occurs.
description: 17 pages
title: Räumliche Analyse von gravitativen Massenbewegungen mittels multivariater Statistik
Creators: name: Petschko, Helene
Year: 2008

description: Im August 2005 sind nach intensiven Regenfällen in der Region Gasen und Haslau in der Oststeiermark, mehr als 500 gravitative Massenbewegungen (auf 60km²) aufgetreten, die hohe ökonomische Schäden verursachten und auch 2 Todesopfer forderten. Das Ziel der vorliegenden Analyse war, eine Gefahrenhinweiskarte für die Region Gasen und Haslau zu erstellen und eine unabhängige Validierung der Ergebnisse durchzuführen. Dazu wurden die in Österreich vorhanden Geodaten in Rasterdatensätze mit 10m x 10m und 50m x 50m Rasterweite konvertiert, um auch den Effekt von unterschiedlichen Auflösungen auf die resultierende Gefahrenhinweiskarte aufzuzeigen. Für die Analyse wurde das statistische Likelihood Quotienten Modell von Chung und Fabbri (1993, 2005) angewendet. Die Ergebnisse zeigen zufriedenstellende statistische Gütemaße darunter hohe Vorhersageraten aus der unabhängige Validierung der Gefahrenhinweiskarten.
In-silico read normalization using Set Multi-Cover optimization
Creators: name: Durai, Dilip A
name: Schulz, Marcel H
Publisher: name: F1000Research
Year: 2017

description: De Bruijn graph is a common assembly data structure. But, with the advances in deep sequencing technologies, assembling high coverage datasets has become a computational challenge. Read normalization, a lossy read filtering approach, is widely applied to reduce resource requirements. Current normalization algorithms, though efficient, provide no guarantee to preserve important k-mers having low abundance. Here normalization is phrased as a Set Multi Cover problem on n reads and a heuristic algorithm is proposed, named ORNA. ORNA normalizes to the minimum number of reads required to retain all k-mers and its relative abundance information. Hence, no connection information from the original graph is lost. ORNA was compared against two other normalization algorithms and was found to be performing better in many cases. Though this work is based on RNA-seq data, ORNA can also be applied for other non-uniform datasets
Experimental and Predicted Behavior of FRP Beam-Columns Including Retrofitting
Creators: name: Al-Huazy, Ali
Publisher: name: Old Dominion University Libraries
Year: 2015

description: This thesis presents the outcome of a theoretical and experimental study of Fiber Reinforce Polymer (FRP) beam-columns with uniaxial bending and including retrofitting. The research involved the design and fabrication of a testing apparatus which was then used for a series of beam-column tests. Three different types of beam-column cross sections were used, namely, channel section, I-section, and square tube section. Six non-retrofitted beam-columns were tested in addition to two retrofitted ones. The members were subjected to an eccentric vertical load applied through a lever arm generating gradually increasing axial load and uniaxial bending moment up to the maximum load. To predict the load-deflection relations up to the peak axial load and bending moment, a system of three coupled differential equations of flexural and torsional equilibrium were solved using finite-difference method. The effect of initial geometric imperfections were embedded in the governing differential equations. The predicted behavior and strength was in good agreement for the load-deflection relations and in excellent agreement for the maximum loads. The ASCE-LRFD Pre-Standard beam-column design expression was found to be unconservative for the non-retrofitted beam-columns except for that with the I-section with minor axis loading. It was also found that retrofitting the channel section beam-column with steel plates in the vicinity of maximum bending moment results in a dramatic increase in strength.
EFO-3 "YOUR" Experimental Factor Ontology
Creators: name: Sirarat Sarntivijai
name: Jupp, Simon
name: Welter, Danielle
name: Parkinson, Helen
Publisher: name: F1000Research
Year: 2017

description: The Experimental Factor Ontology (EFO) is an open-source ontology established in 2009 to aid the annotation of data at the EBI Expression Atlas. EFO has grown from ~2,600 classes to 19,799 classes (as of March 15th 2017). The growing number of classes in EFO reflects the expanding user-base from multiple databases and serves a wider set of use-cases. EFO now covers various life science domains, both animal and plant in many projects i.e., Open Targets, GWAS Catalog, EXCELERATE, and Genomics England. EFO also facilitates knowledge sharing in multi-organisation collaborative work such as ENCODE Consortium, NASA GeneLab, and GSK (Sarntivijai et al., 2016). The growing user-base has necessitated the development of a new operational pipeline for EFO that presents a more generalised approach to application ontology building.
http://www.ebi.ac.uk/efo/
sj-docx-1-dli-10.1177_23969415221121089 - Supplemental material for Coordinated social communication in toddlers with and without autism spectrum disorder during a home observation
Creators: name: Delehanty, Abigail
name: Wetherby, Amy M.
Publisher: name: SAGE Journals
Year: 2022
Subjects: subject: 110904 Neurology and Neuromuscular Diseases
subject: FOS: Clinical medicine
subject: 200399 Language Studies not elsewhere classified
subject: FOS: Languages and literature
subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology
subject: 130312 Special Education and Disability
subject: FOS: Educational sciences

description: Supplemental material, sj-docx-1-dli-10.1177_23969415221121089 for Coordinated social communication in toddlers with and without autism spectrum disorder during a home observation by Abigail Delehanty and Amy M. Wetherby in Autism & Developmental Language Impairments
Additional file 2 of Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle
Creators: name: Naji, Maulana Mughitz
name: Gualdrón Duarte, José Luis
name: Forneris, Natalia Soledad
name: Druet, Tom
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Annual trend for the average inbreeding levels by birth years (a) estimated with sample AF; (b) estimated with base population AF. Figure S2. Inbreeding depression associated with different HBD classes estimated for length, pelvis length and pelvis width (with 50K genotyping array). Figure S3. Inbreeding depression associated with different HBD classes estimated for length, pelvis length and pelvis width (with high-density genotyping array). Figure S4. Inbreeding effects and associated significance levels in 100 simulations. Figure S5. Recent evolution of past effective population size (Ne) estimated in Belgian Blue cattle with GONE.
title: "John Palmers ökonomisch-commerzielle Reise durch Nordamerika" im mährischen Nachdruck
Creators: name: Weinberger-Zauner, Barbara Christine
Year: 2008

description: Die von mir verfasste Diplomarbeit trägt den Titel „John Palmers ökonomisch-commerzielle Reise durch Nordamerika im mährischen Nachdruck. Vom Emigrations-Ratgeber zum Reisebericht.“ Sie befasst sich in erster Linie mit der Präsentation der Palmerschen Reisebeschreibung in der Ausgabe des Traßler-Verlages, die am Ende einer Entwicklung mit Verlagerung des thematischen Schwerpunktes steht. Dieser Themenschwerpunkt liegt im englischsprachigen Original auf der Informationsvermittlung für zukünftige Emigranten. In der deutschen Übersetzung und Bearbeitung, sowie der Veröffentlichung in der Zeitschrift Ethnographisches Archiv durch den Verlag der Bran´schen Buchhandlung in Jena, verschiebt sich die thematische Ausrichtung nur geringfügig. Der Brünner Traßler-Verlag benutzte diese Jenaer Publikation als Vorlage für einen Nachdruck und dessen Veröffentlichung in der verlagseigenen Zeitschrift Neueste Gallerie der auserlesensten Reisebeschreibungen. Da der Text in seiner ursprünglichen Form aber nicht der Zeitschriftenintention entsprach, wurden umfangreiche thematische Änderungen durchgeführt, die sich folgendermaßen klassifizieren lassen. Der Text wurde, um dem Bildungsanspruch der Neuesten Gallerie gerecht zu werden, um eine allgemeine Beschreibung der USA eines bekannten Geographen erweitert, die ebenfalls in Ausschnitten nachgedruckt wurde. Die Auswanderungsthematik wurde zugunsten dieser Abhandlung gestrichen. Aus dem Auswanderungsratgeber, der vom Autor als solcher konzipiert worden war, blieb allein der unterhaltsame Bericht seiner Reise übrig. Um die Aktualität des Emigrationsthemas zu verdeutlichen, und die nötigen Hintergrundinformationen zu liefern wurden dem Vergleich der Ausgaben einige Kapitel vorangestellt, die sich mit der historischen Situation der USA, der Informationslage im deutschsprachigen Raum zum Entwicklungsstand der USA, der Situation der Auswanderer, sowie der Auswanderungs-bestimmungen im deutschsprachigen Raum befassen. Im Abschnitt Textgeschichte werden die einzelnen Ausgaben dargestellt. Danach zeige ich anhand einiger ausgewählter Textstellen die Abweichungen und Veränderungen im Textvergleich. Das Ergebnis stellt die oben genannte Schwerpunktveränderung dar.
Additional file 1 of RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci
Creators: name: Fazal, Sarah
name: Danzi, Matt C.
name: Xu, Isaac
name: Kobren, Shilpa Nadimpalli
name: Sunyaev, Shamil
name: Reuter, Chloe
name: Marwaha, Shruti
name: Wheeler, Matthew
name: Dolzhenko, Egor
name: Lucas, Francesca
name: Wuchty, Stefan
name: Tekin, Mustafa
name: Züchner, Stephan
name: Aguiar-Pulido, Vanessa
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Additional file 1: Supplementary results. Further details on features, age of onset analysis, and outcome metrics from randomly splitting the dataset into training and testing datasets multiple times [38, 39]. Fig. S1. GERP scores for TRs in the training dataset. Fig. S2. Age of onset for known repeat expansion disorders and the maximum RExPRT pathogenicity score predicted for the associated TR locus. Table S1. Features tested for significant association with pathogenic TRs. Table S2. Quantitative and multivalued features tested in machine learning models. Table S3. Summary metrics for randomly generated training and testing datasets.
Supplemental Material - Evaluation of pharmacists’ Preferences and Barriers to Access Continuing Education: A Cross-Sectional Study in Lebanon
Creators: name: Hatem, Georges
name: Ismaiil, Lina
name: Awada, Sanaa
name: Ghanem, Diana
name: Assi, Roula Bou
name: Goossens, Mathijs
Publisher: name: SAGE Journals
Year: 2022
Subjects: subject: 111708 Health and Community Services
subject: FOS: Health sciences
subject: 111099 Nursing not elsewhere classified
subject: 111799 Public Health and Health Services not elsewhere classified
subject: 160807 Sociological Methodology and Research Methods
subject: FOS: Sociology

description: Supplemental Material for Evaluation of pharmacists’ Preferences and Barriers to Access Continuing Education: A Cross-Sectional Study in Lebanon by Georges Hatem, Lina Ismaiil, Sanaa Awada, Diana Ghanem, Roula Bou Assi, Mathijs Goossens in Evaluation & the Health Professions
Additional file 2 of RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci
Creators: name: Fazal, Sarah
name: Danzi, Matt C.
name: Xu, Isaac
name: Kobren, Shilpa Nadimpalli
name: Sunyaev, Shamil
name: Reuter, Chloe
name: Marwaha, Shruti
name: Wheeler, Matthew
name: Dolzhenko, Egor
name: Lucas, Francesca
name: Wuchty, Stefan
name: Tekin, Mustafa
name: Züchner, Stephan
name: Aguiar-Pulido, Vanessa
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Additional file 2. Review history.
Comparison of open source (Galaxy based) and commercial pipelines for RNA-Seq data analysis
Creators: name: Trajanoski, Slave
name: Djurdjevic, Marija
name: Groselj-Strele, Andrea
Publisher: name: F1000Research
Year: 2017

description: From the first RNA-Seq projects until today software for data analysis was constantly developed and improved. Nowadays we’re finding a plethora of different solutions of tools for either single parts of RNA-Seq data analysis as well as complete pipelines that deliver gene expression results. In our work, we present a comparison of one commercial software from the company Partek as two implementations: Partek Flow and Partekâ Genomics Suiteâ and open source tools implemented as pipeline in a very popular web-based framework Galaxy1 .
By using test dataset from the NCBI Sequence Read Archive (SRA) we could run performance and usability tests of the two different approaches. We come to the conclusion that:

	Results from both solutions are comparable, but one should be very careful about parameters used in each step since they can lead to different results;
	Usability is on the side of the commercial solution, even though Galaxy developers are making good progress in this direction;
	For the sake of easy and fast analysis a lot of parameters are hidden from the user in the commercial software, which leads to lower flexibility in comparison with the open source pipelines;
	Less management effort when using commercial software, which on the other hand is connected with license costs.

1. Afgan E, et al. The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016;44(W1):W3.
sj-docx-1-cho-10.1177_18632521221124632 – Supplemental material for Management of iatrogenic ulnar nerve palsies after cross pinning of pediatric supracondylar humerus fractures: A systematic review
Creators: name: Graff, Christy
name: Dounas, George Dennis
name: Sung, Jonghoo
name: Kumawat, Medhir
name: Huang, Yue
name: Todd, Maya
Publisher: name: SAGE Journals
Year: 2022
Subjects: Orthopaedics
Sports Medicine

description: Supplemental material, sj-docx-1-cho-10.1177_18632521221124632 for Management of iatrogenic ulnar nerve palsies after cross pinning of pediatric supracondylar humerus fractures: A systematic review by Christy Graff, George Dennis Dounas, Jonghoo Sung, Medhir Kumawat, Yue Huang and Maya Todd in Journal of Children’s Orthopaedics
Stethaulax marmorata
Creators: name: Guzmán-Vásquez, Héctor M.
name: Martínez-Martínez, Laura
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Scutelleridae
Stethaulax
Stethaulax marmorata

description: Stethaulax marmorata (Say, 1831)
Figure 2f
Material examined: 1 specimen labeled: MEXICO, Oaxaca, Santa Cruz Xoxocotlán; CIIDIR. 14-X-2024. Leg. Martínez M, L. (1♂). New state and national record.
Associated plants: Rhus aromatica Aiton, R. copallinum L., R. glabra L. (Anacardiaceae); Chamaecyparis sp. (Cupressaceae) (Tecic & McPherson 2004; Rider 2015)
Remarks: Little is known about the habits and hosts of this species. Walt & Mcpherson (1973) described the immature stages and provided some notes on their life cycle. In a paper still in progress and not yet published, Eger (pers. comm.) provides a concise summary of plants associated with S. marmorata in the United States.
description: Published as part of Guzmán-Vásquez, Héctor M. & Martínez-Martínez, Laura, 2025, Checklist and bilingual key to the genera of Scutelleridae (Hemiptera: Heteroptera) from Mexico, with new distribution records for the state of Oaxaca, pp. 341-354 in Zootaxa 5594 (2) on page 349, DOI: 10.11646/zootaxa.5594.2.6, http://zenodo.org/record/14954440
Additional file 1 of Outpatient hysteroscopy impact on subsequent assisted reproductive technology: a systematic review and meta-analysis in patients with normal transvaginal sonography or hysterosalpingography images
Creators: name: Hou, Jung-Hsiu
name: Lu, Buo-Jia
name: Huang, Ya-Li
name: Chen, Chih-Heng
name: Chen, Chi-Huang
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy

description: Supplementary Material: Supplementary Table S1. Characteristics of the infertility condition and artificial reproductive treatment of the included RCTs
title: Die Entwicklung der filmischen Beleuchtung anhand des expressionistischen Films und Film noir
Creators: name: Lang, Mario
Year: 2008

description: Die vorliegende Diplomarbeit beschäftigt sich mit der Licht- und Schattendramaturgie im Film. Zentrale Zielsetzung ist es, die filmische Beleuchtung mit deren Funktionen und Wirkungsweisen darzustellen und die daraus entstandenen Möglichkeiten und Entwicklungen anhand des expressionistischen Films und des Film noir zu thematisieren. Vor diesem Hintergrund war es vor allem von elementarer Bedeutung für den Forschungsprozess den allmählichen Übergang vom Sonnenlicht bis hin zur künstlichen Beleuchtung nachvollziehbar zu machen bzw. die mit diesem Prozess ebenso einhergehenden Komplikationen aufzuzeigen. Im Kern beschränkt sich die Arbeit überwiegend auf die Filmarbeit in Deutschland und Amerika.