cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Functional and genomic characterisation of a xenograft model system for the study of metastasis in triple-negative breast cancer
Creators: name: Johnstone, Cameron
name: Pattison, Andrew D
name: Gorringe, Kylie L
name: Harrison, Paul F
name: Powell, David R
name: Lock, Peter
name: Baloyan, David
name: Ernst, Matthias
name: Stewart, Alastair G
name: Beilharz, Traude H
name: Anderson, Robin
Publisher: name: La Trobe
Year: 2023
Subjects: classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences
classificationCode: 3105
subject: Genetics
classificationCode: 32
subject: Biomedical and clinical sciences
classificationCode: 3211
subject: Oncology and carcinogenesis

description: Triple-negative breast cancer (TNBC) represents 10-20% of all human ductal adenocarcinomas and has a poor prognosis relative to other subtypes. Hence, new molecular targets for therapeutic intervention are necessary. Analyses of panels of human or mouse cancer lines derived from the same individual that differ in their cellular phenotypes but not in genetic background have been instrumental in defining the molecular players that drive the various hallmarks of cancer. To determine the molecular regulators of metastasis in TNBC, we completed a rigorous in vitro and in vivo characterisation of four populations of the MDA-MB-231 human breast cancer line ranging in aggressiveness from non-metastatic to spontaneously metastatic to lung, liver, spleen and lymph node. Single nucleotide polymorphism (SNP) array analyses and genome-wide mRNA expression profiles of tumour cells isolated from orthotopic mammary xenografts were compared between the four lines to define both cell autonomous pathways and genes associated with metastatic proclivity. Gene set enrichment analysis (GSEA) demonstrated an unexpected association between both ribosome biogenesis and mRNA metabolism and metastatic capacity. Differentially expressed genes or families of related genes were allocated to one of four categories, associated with either metastatic initiation (e.g. CTSC, ENG, BMP2), metastatic virulence (e.g. ADAMTS1, TIE1), metastatic suppression (e.g. CST1, CST2, CST4, CST6, SCNNA1, BMP4) or metastatic avirulence (e.g. CD74). Collectively, this model system based on MDA-MB-231 cells should be useful for the assessment of gene function in the metastatic cascade and also for the testing of novel experimental therapeutics for the treatment of TNBC.
On electrical transport and thermoelectric performance in half-Heusler phase ScNiSb
Creators: name: Ciesielski, K. M.
name: Kaczorowski, D.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Half-Heusler phases are among the most extensively studied thermoelectic materials. Bipolar thermal conductivity analysis performed for their sub-group based on rare-earth (R) metals, RNiSb, indicated on high mobility ratio in favor of electrons. The suggestion found its experimental verification and led to significant improvement of thermoelectric properties in $n$-type doped series ScNiSb$_{1-x}$Te$_x$. Recently, an alternative interpretation of transport properties in ScNiSb was proposed, where multi-parameter fit lead to mobility ratio in favor of holes. In this work we discuss the details of electrical properties and thermoelectric performance of ScNiSb in context of structural disorder. The article considers also relevant assumptions regarding band degeneracy and scattering mechanisms for effective mass modeling in ScNiSb. Lastly, technical difficulties of the model proposed by the others are addressed. We believe, that the provided insight will be useful for understating electrical transport in half-Heusler compounds, which can contribute to further improvement of their thermoelectric performance.
Scorpiops (Euscorpiops) beccaloniae
Creators: name: Lourenço, Wilson R.
name: Ythier, Eric
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Scorpiops
Scorpiops beccaloniae

description: - S. (Euscorpiops) beccaloniae (Kovarík, 2005)
Myanmar
description: Published as part of Lourenço, Wilson R. & Ythier, Eric, 2022, A new species of the genus Scorpiops Peters, 1861, subgenus Euscorpiops Vachon, 1980 from Laos (Scorpiones: Scorpiopidae), pp. 1-9 in Faunitaxys 10 (27) on page 3, DOI: 10.57800/faunitaxys-10(27), http://zenodo.org/record/15352467
An improved Tully-Fisher estimate of $H_0$
Creators: name: Boubel, Paula
name: Colless, Matthew
name: Said, Khaled
name: Staveley-Smith, Lister
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We propose an improved comprehensive method for determining the Hubble constant ($H_0$) using the Tully-Fisher relation. By fitting a peculiar velocity model in conjunction with the Tully-Fisher relation, all available data can be used to derive self-consistent Tully-Fisher parameters. In comparison to previous approaches, our method offers several improvements: it can be readily generalised to different forms of the Tully-Fisher relation and its intrinsic scatter; it uses a peculiar velocity model to predict distances more accurately; it can account for all selection effects; it uses the entire dataset to fit the Tully-Fisher relation; and it is fully self-consistent. The Tully-Fisher relation zero-point is calibrated using the subset of galaxies with distances from absolute distance indicators. We demonstrate this method on the Cosmicflows-4 catalogue $i$-band and $W1$-band Tully-Fisher samples and show that the uncertainties from fitting the Tully-Fisher relation amount to only 0.2 km s$^{-1}$Mpc$^{-1}$. Using all available absolute distance calibrators, we obtain $H_0=73.3$ $\pm$ 2.1 (stat) $\pm$ 3.5 (sys) km s$^{-1}$Mpc$^{-1}$, where the statistical uncertainty is dominated by the small number of galaxies with absolute distance estimates. The substantial systematic uncertainty reflects inconsistencies between various zero-point calibrations of the Cepheid period-luminosity relation, the tip of the red giant branch standard candle, and the Type Ia supernova standard candle. However, given a reliable set of absolute distance calibrators, our method promises enhanced precision in $H_0$ measurements from large new Tully-Fisher samples such as the WALLABY survey.
Zinc finger nuclease-mediated precision genome editing of an endogenous gene in hexaploid bread wheat (Triticum aestivum) using a DNA repair template
Creators: name: Ran, Y
name: Patron, N
name: Kay, Pippa
name: Wong, Debbie
name: Buchanan, M
name: Cao, YY
name: Sawbridge, Tim
name: Davies, JP
name: Mason, John
name: Webb, SR
name: Spangenberg, German
name: Ainley, WM
name: Walsh, TA
name: Hayden, Matthew
Publisher: name: La Trobe
Year: 2023
Subjects: classificationCode: 3001
subject: Agricultural biotechnology
subject: FOS: Agricultural biotechnology
classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences
classificationCode: 3102
subject: Bioinformatics and computational biology
classificationCode: 3108
subject: Plant biology

description: Sequence-specific nucleases have been used to engineer targeted genome modifications in various plants. While targeted gene knockouts resulting in loss of function have been reported with relatively high rates of success, targeted gene editing using an exogenously supplied DNA repair template and site-specific transgene integration has been more challenging. Here, we report the first application of zinc finger nuclease (ZFN)-mediated, nonhomologous end-joining (NHEJ)-directed editing of a native gene in allohexaploid bread wheat to introduce, via a supplied DNA repair template, a specific single amino acid change into the coding sequence of acetohydroxyacid synthase (AHAS) to confer resistance to imidazolinone herbicides. We recovered edited wheat plants having the targeted amino acid modification in one or more AHAS homoalleles via direct selection for resistance to imazamox, an AHAS-inhibiting imidazolinone herbicide. Using a cotransformation strategy based on chemical selection for an exogenous marker, we achieved a 1.2% recovery rate of edited plants having the desired amino acid change and a 2.9% recovery of plants with targeted mutations at the AHAS locus resulting in a loss-of-function gene knockout. The latter results demonstrate a broadly applicable approach to introduce targeted modifications into native genes for nonselectable traits. All ZFN-mediated changes were faithfully transmitted to the next generation.
Additional file 1 of Physical and mental health outcomes of an integrated cognitive behavioural and weight management therapy for people with an eating disorder characterized by binge eating and a high body mass index: a randomized controlled trial
Creators: name: Hay, Phillipa
name: Palavras, Marly Amorim
name: da Luz, Felipe Quinto
name: dos Anjos Garnes, Sérgio
name: Sainsbury, Amanda
name: Touyz, Stephen
name: Appolinario, José Carlos
name: Claudino, Angélica Medeiros
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Supplementary File 1. Changes from the published protocol paper (Palavras et al., Trials 2015 16:578) and as reported in the Trial registration of the present paper.
Report On Policies And Procedures For Sensitive Human Data Management  - D7.2
Creators: name: Ebbels Tim
name: Robert, Glen
name: Namrata, Kale
name: Kenneth, Haug
Publisher: name: Zenodo
Year: 2016
Subjects: Privacy
Ethics

description: This deliverable summarises the process by which the project has come to an ethical framework which will ensure the infrastructure supports proper use of sensitive human data.
Bioschemas: structured data for life science using schema.org
Creators: name: Beard, Niall
name: Cook, Martin
name: Nenadic, Aleksandra
name: Jimenez, Rafael
name: Attwood, Teresa
name: Morrison, Norman
name: Gelder, Celia Van
name: Coppens, Frederik
name: Leskosek, Brane
name: Ison, Jon
name: McQuilton, Peter
name: Gonzalez-Beltran, Alejandra
name: Susanna-Assunta Sansone
name: Bo, Christof De
name: Botzki, Alexander
name: Horn, John Darrell Van
name: Jose-Luis Ambite
name: Lerman, Kristina
name: Tractenberg, Rochelle
name: Horro, Carlos
name: Preste, Roberto
name: Janko, Christa
name: Johnson, Claire
name: Dallakian, Pavel
name: Pergl, Robert
Publisher: name: F1000Research
Year: 2016

description: ELIXIR explicitly supports the FAIR Principles – Findable, Accessible, Interoperable, Reusable – for its data, software, tools, events and training resources. “Finding” has the significant challenge of effective discovery and indexing of web-based resources across all ELIXIR information providers – this is an issue because there has been no agreement within ELIXIR about how to expose such resources in order to make them discoverable. One solution to this problem is to adopt Schema.org mark-up. Schema.org is a community initiative supported by four major search-engine providers: Google, Bing, Yahoo and Yandex. It provides a simple way to publish data in a standard format. If websites publishing life-science training materials, data, tools, profiles etc. were to use Schema.org mark-up, then their websites could be crawled, and the data could be indexed and exposed in searchable portals. However, this approach has challenges. Bioschemas is a newly formed community group in the life sciences to address these challenges, aiming to make the adoption of Schema.org part of a powerful way to discover and collect life-science information. It produces specifications, one for each information type (‘Training Course’, ‘Event’, 'Sample Data', 'Ontology Term', 'Tool', etc.). Each specification lists the Schema.org minimum properties expected, and the constraints for each property: for example, the ‘Events’ specification that the property ‘topic’ should be an EDAM ontology topic. The specifications are developed openly and are available on GitHub, with the support of existing communities of domain experts. Bioschemas also identifies the types or properties that are needed in the life sciences but not present in Schema.org, and works with the community to encourage the adoption of these types and properties into Schema.org.
title: Primakov Redux? Putin's Pursuit of "Multipolarism" in Asia
Creators: name: Katz, Mark N.
Publisher: name: Heldref Publications
Year: 2006
Subjects: subject: Putin
subject: Asia
subject: International relations
subject: Russian foreign policy

description: http://www.heldref.org/
description: This article explores why Putin has revived Primakov's efforts to build a "multipolar" alliance challenging American "hegemony" and "unipolarity," examines why he is pursuing it primarily in Asia, and assesses how effective this policy has been and can be.
Chainsaw-Carved Cavities Better Mimic the Thermal Properties of Natural Tree Hollows than Nest Boxes and Log Hollows
Creators: name: Griffiths, Stephen
name: Lentini, Pia
name: Semmens, Kristin
name: Watson, Simon
name: Lumsden, Linda
name: Robert, Kylie
Publisher: name: La Trobe
Year: 2023
Subjects: classificationCode: 30
subject: Agricultural, veterinary and food sciences
classificationCode: 3007
subject: Forestry sciences
classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences
classificationCode: 3103
subject: Ecology

description: The creation of supplementary habitats that effectively mimic the physical and thermal characteristics of natural tree hollows should be a key priority for landscape restoration and biodiversity offset programs. Here, we compare the thermal profiles of natural tree hollows with three types of artificial hollows designed for small marsupial gliders and tree-roosting insectivorous bats: (1) 'chainsaw hollows' carved directly into the trunks and branches of live trees, (2) 'log hollows', and (3) plywood nest boxes. Chainsaw hollows had thermal profiles that were similar to natural tree hollows: they were consistently warmer than ambient conditions at night, while remaining cooler than ambient during the day. In contrast, glider and bat boxes had the opposite pattern of heating and cooling, being slightly cooler than ambient at night and substantially hotter during the day. Glider log hollows had greater variation in internal temperatures compared to natural hollows and chainsaw hollows, but fluctuated less than glider boxes. Our results provide the first empirical evidence that artificial hollows carved directly into live trees can produce thermally stable supplementary habitats that could potentially buffer hollow-dependent fauna from weather extremes; whereas, poorly insulated plywood nest boxes produce lower-quality thermal environments. Together these findings provide positive impetus for stakeholders involved in conservation management and biodiversity offset programs to consider trialing chainsaw hollows in situations where target fauna require well-insulated supplementary habitats.
Additional file 3 of Physical and mental health outcomes of an integrated cognitive behavioural and weight management therapy for people with an eating disorder characterized by binge eating and a high body mass index: a randomized controlled trial
Creators: name: Hay, Phillipa
name: Palavras, Marly Amorim
name: da Luz, Felipe Quinto
name: dos Anjos Garnes, Sérgio
name: Sainsbury, Amanda
name: Touyz, Stephen
name: Appolinario, José Carlos
name: Claudino, Angélica Medeiros
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 3: Supplementary File 3. Summary of similarities and differences between HAPIFED and Cognitive Behaviour Therapy–Enhanced therapies as implemented in the present study.
Dimensionality reduction of rule-based simulation results using intrinsic dimensionality analysis
Creators: name: Wysocka, Emilia M.
name: Page, Matthew
name: Snowden, James
name: T. Ian Simpson
Publisher: name: F1000Research
Year: 2016

description: Rule-based (RB) languages such as Kappa and BioNetGen embody a new approach to dynamical modelling in Biology. One of their key advantages is that they can efficiently encode the combinatorial complexity of molecular events commonly found in biological systems. Static and causal analysis of RB model simulation data are usually undertaken using visualisation tools, but more detailed analysis often requires use of bespoke sets of heuristic tests in order to unravel the complex behaviour of molecular species in the simulation. Further, relatively small models can generate very large numbers of molecular species during simulation; identifying which of these dynamic features to focus on in downstream analyses is critical to the refinement and practical use of the model. Problematically, the theoretical development and implementation of model reduction methods has lagged behind the ability to build realistic models and to simulate them at scale. This has greatly hindered principled approaches to the quantitative analysis of dynamical models. We present a potential solution to this problem using a dimensionality reduction technique based on multivariate mutual information (Correlation Explanation, CorEx) that searches for a set of latent variables to best explain correlations within time-series data. We demonstrate the first use of this approach to evaluate our novel Kappa model of DARPP-32 (dopamine and cAMP-regulated phosphoprotein of 32 KDa) phosphorylation; a dynamically regulated process in the integration of neurotransmitter and neuromodulator activity in GABAergic spiny neurons, in response to dopamine and glutamate.
Toward broadband, dynamic structuring of a complex plasmonic field
Creators: name: Wei, Shibiao
name: Si, Guangyuan
name: Malek, Michael
name: Earl, Stuart K
name: Du, Luping
name: Kou, Shanshan
name: Yuan, Xiaocong
name: Lin, Jiao
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 51
subject: Physical sciences
subject: FOS: Physical sciences
classificationCode: 5108
subject: Quantum physics

description: The ability to tailor a coherent surface plasmon polariton (SPP) field is an important step toward many new opportunities for a broad range of nanophotonic applications. Previously, both scanning a converging SPP spot and designing SPP profiles using an ensemble of spots have been demonstrated. SPPs, however, are normally excited by intense, coherent light sources, that is, lasers. Hence, interference between adjacent spots is inevitable and will affect the overall SPP field distributions. We report a reconfigurable and wavelength-independent platform for generating a tailored two-dimensional (2D) SPP field distribution by considering the coherent field as a whole rather than as individual spots. With this new approach, the inherent constraints in a 2D coherent field distribution are revealed. Our design approach works not only for SPP waves but also for other 2D wave systems such as surface acoustic waves.
title: Enhancing Forensic Science Education for Law Enforcement Personnel
Creators: name: Anderson, Sydney
Publisher: name: George Mason University
Year: 2022
Subjects: subject: Law Enforcement
subject: Training
subject: Forensic Science

description: As crime escalates throughout the United States, it is important that law enforcement personnel are aware of, and educated, in the vast array of forensic science disciplines that can, in many cases, aid in the identification of suspects. This research project aims to identify and examine the needs of the law enforcement community regarding forensic science education, with the goal of constructing easily accessible training programs and information repositories. Questionnaires to assess current knowledge and training, and to identify areas of need and improvement, were recently formulated and disseminated to law enforcement agencies across the United States. Forty-eight responses were received from officers/agents in 20 states. Thirty-eight respondents were invited to participate in focus groups, with 8 opting to participate in a final survey instead. An additional 23 individuals were excluded due to missing response fields or incorrect self-identification as a member of the law enforcement community. The survey focused on assessing the needs for future trainings as identified and articulated by Law Enforcement Personnel. Focus groups were conducted following the initial survey to learn in greater detail what training topics are the most valuable. Five focus group sessions were held with 2-4 attendants per session; each session lasted approximately one hour long. Exploratory methodology was employed in the focus groups conduct and design to gather information regarding the favored method of training, desired tools, and information dissemination techniques. Following the focus groups a final survey was distributed to the law enforcement community. 161 responses were received from officers/agents nationwide. 85 respondents answered all survey questions provided, 17 respondents answered some survey questions provided and 59 respondents answered zero questions. Training programs are planned in the near future with the goal of creating accessible educational training online, and/or in person, to all individuals involved in law enforcement.
Toward broadband, dynamic structuring of a complex plasmonic field
Creators: name: Wei, Shibiao
name: Si, Guangyuan
name: Malek, Michael
name: Earl, Stuart K
name: Du, Luping
name: Kou, Shan Shan
name: Yuan, Xiaocong
name: Lin, Jiao
Publisher: name: La Trobe
Year: 2023

description: The ability to tailor a coherent surface plasmon polariton (SPP) field is an important step toward many new opportunities for a broad range of nanophotonic applications. Previously, both scanning a converging SPP spot and designing SPP profiles using an ensemble of spots have been demonstrated. SPPs, however, are normally excited by intense, coherent light sources, that is, lasers. Hence, interference between adjacent spots is inevitable and will affect the overall SPP field distributions. We report a reconfigurable and wavelength-independent platform for generating a tailored two-dimensional (2D) SPP field distribution by considering the coherent field as a whole rather than as individual spots. With this new approach, the inherent constraints in a 2D coherent field distribution are revealed. Our design approach works not only for SPP waves but also for other 2D wave systems such as surface acoustic waves.
Additional file 2 of Physical and mental health outcomes of an integrated cognitive behavioural and weight management therapy for people with an eating disorder characterized by binge eating and a high body mass index: a randomized controlled trial
Creators: name: Hay, Phillipa
name: Palavras, Marly Amorim
name: da Luz, Felipe Quinto
name: dos Anjos Garnes, Sérgio
name: Sainsbury, Amanda
name: Touyz, Stephen
name: Appolinario, José Carlos
name: Claudino, Angélica Medeiros
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 2: Supplementary File 2. Description of the topics of each session for the HAPIFED and CBT-E as implemented in the present study.
Scorpiops (Euscorpiops) novaki
Creators: name: Lourenço, Wilson R.
name: Ythier, Eric
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Scorpiops
Scorpiops novaki

description: - S. (Euscorpiops) novaki (Kovarík, 2005)
China
description: Published as part of Lourenço, Wilson R. & Ythier, Eric, 2022, A new species of the genus Scorpiops Peters, 1861, subgenus Euscorpiops Vachon, 1980 from Laos (Scorpiones: Scorpiopidae), pp. 1-9 in Faunitaxys 10 (27) on page 3, DOI: 10.57800/faunitaxys-10(27), http://zenodo.org/record/15352467
Mapping-based horizontal gene transfer detection from sequencing data – enhancing metagenomic approaches for pathogen identification
Creators: name: Trappe, Kathrin
name: Seiler, Enrico
name: Marschall, Tobias
name: Renard, Bernhard Y.
Publisher: name: F1000Research
Year: 2016

description: Horizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material between distant species. This way, for instance, bacteria can acquire antibiotic resistance genes or pathogenic toxins with possible severe consequences for public health. Current bioinformatics approaches focus on the detection of past HGT events by exploring phylogenetic tree or genome composition inconsistencies. To the best of our knowledge, so far, no approach uses next-generation sequencing (NGS) data or methods. A mapping-based approach offers the chance of detecting HGT events in the sequenced HGT organism early in analyses, even when the HGT organism has not been sequenced before. We propose the tools Daisy and Donald, novel mapping-based pipelines for HGT detection from NGS data. Donald leverages metagenomic profiling tools to identify candidate references for the acceptor genome reference (the parent genome of the HGT organism acquiring the HGT sequence) and the donor genome reference (the parent donating the HGT sequence). Subsequently, Daisy determines specific HGT regions relying on established methods from structural variant detection approved for human NGS data. Preliminary results of simulated and real data show that Donald successfully identifies acceptor and donor candidates as such and is able to distinguish non-HGT samples as true negatives. Daisy detects HGT regions with base pair resolution, and outperforms alternative approaches using a genome assembly of the reads. We see our approach as a powerful complement for comprehensive analysis of bacterial genomes in the context of NGS data.
title: Using an Improved Coupling Drought Index to Predict the Persistence of Meteorological Drought over West Central India
Creators: name: Guha, Shreya
Publisher: name: George Mason University
Year: 2021
Subjects: subject: Improved coupling drought index
subject: Anderson-Darling test
subject: Meteorological drought
subject: West central India

description: The objective of this study is to investigate the role of the atmospheric boundary layer (ABL) and hence, roles of evaporation and convection in the process of intensification or persistence of meteorological droughts in west central India. The reason of choice of this region is that it is seen to be statistically significant in terms of spatial extent of droughts from 1951-2010. Although local geographic factors influence rainfall in this region, the main source of precipitation is the Southwest monsoons during the months of June, July, August and September (JJAS); which are affected by the tropical sea surface anomalies; and hence by El Nino/Southern Oscillation (ENSO), Indian Ocean Dipole (IOD) and other synoptic systems (like monsoon depressions) which are due to the dynamical instabilities of the mean circulation. These affect the slowly changing variable soil moisture; the soil moisture anomalies then affect the summer rainfall. However, most of the land-atmosphere coupling studies conducted earlier over India ignore the role of the ABL which controls the major thermodynamics and dynamical circulations. Hence, here we try to apply the concept of coupling drought index (CDI) during the periods of monsoon onset (March, April, and May [MAM]) over the entire spatial extent over the time-period of 1979-2010; when the atmosphere represents somewhat transitional coupling conditions, to identify regions of dry and wet coupling regions. Here, however, while testing the normality of the soil moisture anomaly curves, we have replaced the Kolmogorov-Smirnov Test with the Anderson-Darling test to build an improved CDI to gain more accuracy and sensitivity. Thereby, it is expected to predict whether drought will persist, intensify, or recover over the study region. The results from the developed index indicated that the drought conditions would neither intensify nor recover over the study region for the year 2011 and would continue to persist as it was for the past three decades. The observations validate this result. Keywords: Improved coupling drought index, meteorological drought, west central India, Anderson-Darling Test
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries
Creators: name: Trappe, Kathrin
name: Marschall, Tobias
name: Renard, Bernhard
Publisher: name: F1000Research
Year: 2016

description: Horizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material between distant species. This way, bacteria can acquire new traits such as antibiotic resistance or pathogenic toxins. Current bioinformatics approaches focus on the detection of past HGT events by exploring phylogenetic trees or genome composition inconsistencies. However, these techniques normally require the availability of finished and fully annotated genomes and of sufficiently large deviations that allow detection and are thus not widely applicable. Especially in outbreak scenarios with HGT-mediated emergence of new pathogens, like the enterohemorrhagic Escherichia coli outbreak in Germany 2011, there is need for fast and precise HGT detection. Next-generation sequencing (NGS) technologies facilitate rapid analysis of unknown pathogens but, to the best of our knowledge, so far no approach detects HGTs directly from NGS reads.
We present Daisy, a novel mapping-based tool for HGT detection. Daisy determines HGT boundaries with split-read mapping and evaluates candidate regions relying on read pair and coverage information. Daisy successfully detects HGT regions with base pair resolution in both simulated and real data, and outperforms alternative approaches using a genome assembly of the reads. We see our approach as a powerful complement for a comprehensive analysis of HGT in the context of NGS data.
Color spectrographic respiratory monitoring from the external ear canal
Creators: name: Doyle, Daniel John
Publisher: name: F1000Research
Year: 2016

description: Background & Objectives: The need for a simple and reliable means of respiratory monitoring has become stronger in recent years with the widespread use of opioids such as morphine for acute pain management.  In this preliminary report we describe the use of color spectrographic analysis of breath sounds recorded from the external ear canal as a candidate technology to meet this important clinical need.

Materials & Methods: A miniature electret microphone was modified with the addition of an adapter to allow it to be placed comfortably in the external ear canal. The amplified signal was then connected to a real-time color spectrogram program (spectrogram16.exe) running on a Personal Computer.

Results: The image on the  right shows a spectrogram obtained for 30 seconds of nasal breathing; note that inspiration is more evident than expiration. The range of frequencies displayed is 500 Hz to 2000 Hz. The highest frequency components of the signal are at the top, with the lowest at the bottom. Red areas indicate strongest signal levels, blue areas the weakest nonzero levels: BLACK < BLUE < GREEN < YELLOW < RED.

Conclusion: Although the results presented here are preliminary, it is hoped that the real-time display of color spectrogram breathing patterns locally or at a central monitoring station may turn out to be a useful means of respiratory monitoring in patients at increased risk of respiratory depression.  Limitations of the present study include the fact that it is a single subject investigation (the author as the experimental subject), that the contributions of sounds from outside the ear canal are not known, and that the contribution of oto-acoustic emissions to the color spectrogram have not been considered.
Assessing the Efficacy of Cell Transplantation for Parkinson’s Disease: A Patient-Centered Approach
Creators: name: Polgar, Stephen
name: Karimi, Leila
name: Buultjens, Melissa
name: Morris, Meg
name: Busse, Monica
Publisher: name: La Trobe
Year: 2022
Subjects: classificationCode: 32
subject: Biomedical and clinical sciences
classificationCode: 3206
subject: Medical biotechnology
subject: FOS: Medical biotechnology
classificationCode: 3209
subject: Neurosciences
subject: FOS: Clinical medicine

description: Background: Evidence from a growing number of preclinical studies indicate that recently discovered stem cell lines may be translated into viable cellular therapies for people with Parkinson's disease. Objectives: In a brief but critical review, we examine the use of primary and secondary outcome measures currently used to evaluate the efficacy of cellular therapies. Methods: The current practice of relying on a single primary outcome measure does not appear to provide the evidence required for demonstrating the robust, life-changing recovery anticipated with the successful implementation of cellular therapies. Results: We propose a 360-degree assessment protocol, which includes co-primary and composite outcome measures to provide accurate and comprehensive evidence of treatment efficacy, from the perspectives of both the researchers and the patients.
Separation of mixed source RNA-Seq reads by comparative genomic processing
Creators: name: Heron, Samuel
name: Dando, Owen
name: Hardingham, Giles
name: T. Ian Simpson
Publisher: name: F1000Research
Year: 2016

description: Knowledge of the cell-autonomous and non-autonomous mechanisms operating within biological systems is essential to reveal the underlying molecular processes at work and is particularly important in functional studies of neurological diseases and cancers. These studies commonly measure gene expression levels in different cell types, but are often confounded by invasive sample processing. Indeed physical separation techniques for cell mixtures have been shown to trigger stress and apoptosis related genes, obscuring the identification of genes of interest and introducing bias. We present a novel approach that alleviates this issue for gene expression quantification using RNA-seq by conducting in silico sequence separation between different sources. Our method takes sequences from mixed species RNA-seq samples (for example two cell types each belonging to closely related species, or different strains of the same species) and differentially maps them between the two genomes. The mappings for each read are then assessed by alignment quality factors and assigned to one source genome or the other
according to tuneable selection criteria. Separated read sets can then be examined using standard quantification and differential expression methods for RNA-seq data. Using simulated and real data for rat and mouse we demonstrate here that reads from closely related species can be successfully separated in this manner.
D5.6 Proceedings of the TIMEPAC-21 workshop in Ljubljana
Creators: name: Sucic, Boris
name: Alexandre-Klein, Sabine
Publisher: name: Zenodo
Year: 2022
Subjects: TIMEPAC-21
Enhancement of EPCs

description: This is a report of the TIMEPAC-21 workshop “Dynamic EPC as enabler of Smart Energy Services – Energy Efficiency, Integration of RES in Buildings and Demand Response” organized by the Jožef Stefan Institute (JSI) that took place online on December 14th and 15th 2021.

The workshop was divided into three sessions:

Session 1 - Legislative context and requirements for deep renovation of EU building stock. This session analysed the legislative context and requirements for the deep renovation of the EU building stock that has been included in National Energy and Climate Plans and National Long-Term Renovation Strategies.

Session 2 - Enhancement of EPCs with the integration of other data sources. This session dealt with the enhancement of EPCs with the integration of other data sources (BIM, sensors, smart meters, energy management, etc.).

Session 3 - Management of active buildings and the use of innovative technologies in order to enable smart energy services. The third session was dedicated to the management of active buildings and the use of innovative technologies in order to enable smart energy service

The workshop was carried out as a hybrid event with participants online while representatives of the Jožef Stefan Institute and the Ministry of Infrastructure of Slovenia were present in Ljubljana. The fact that the TIMEPAC-21 received twenty abstracts was quite remarkable. The programme attracted 68 participants; 50 and 60 of whom constantly attended all the workshop session. In order to attract more attendees, the access to the workshop was free of charge.

This document contains the programme of the workshop, the agenda of the interventions and the abstracts of the presentations, which can be found on the project's web page. It ends with some concluding remarks on the results and on future prospects, which will be taken into account in the next workshop.
Scorpiops (Euscorpiops) shidian
Creators: name: Lourenço, Wilson R.
name: Ythier, Eric
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Scorpiops
Scorpiops shidian

description: - S. (Euscorpiops) shidian (Qi, Zhu & Lourenço, 2005)
China
description: Published as part of Lourenço, Wilson R. & Ythier, Eric, 2022, A new species of the genus Scorpiops Peters, 1861, subgenus Euscorpiops Vachon, 1980 from Laos (Scorpiones: Scorpiopidae), pp. 1-9 in Faunitaxys 10 (27) on page 3, DOI: 10.57800/faunitaxys-10(27), http://zenodo.org/record/15352467
title: Chinese-Indonesian Religious-Institutional Protectionism in Post-1998 Society
Creators: name: Mahuna, Joshua M
Publisher: name: George Mason University
Year: 2019
Subjects: subject: Chinese-Indonesian
subject: Religion
subject: Tionghoa
subject: Communitarianism
subject: Security

description: Chinese-Indonesian communities are experiencing identity crises from socio-normative anti-Chinese sentiment and discrimination. Since the conclusion of the Suharto administration, Chinese-Indonesian populations are publicly victimized for the degradation of the state—labeled as ‘suspicious’ ‘foreign orientals’—and have experienced devastating violence. Basing this sentiment and discrimination on centuries of compounded social, colonial, and nationalistic perceptions, Chinese-Indonesians experience structural violence that continues to impede their observation of cultural-religious affinities and security in lieu of Indonesian societal-exceptionalism. In response to this environment, Chinese-Indonesian communities have erected communal security apparatuses founded within religious institutions in attempt to solidify the components of Chinese-Indonesian-ness to mitigate continued violence. This thesis analyzes these apparatuses to identity the dilemma and status of Chinese-Indonesian cultural identity.
Additional file 1 of What methods are used to study the association between medication adherence trajectories, estimated with the group-based trajectory modeling (GBTM) method, and health-related outcomes?—a protocol for a systematic review
Creators: name: Memoli, Victoria
name: Ekanmian, Giraud
name: Lunghi, Carlotta
name: Bouhnik, Anne-Déborah
name: Lauzier, Sophie
name: Guénette, Line
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Science Policy
subject: Sociology
subject: FOS: Sociology

description: Additional file 1. PRISMA-P 2015 Checklist.
title: Flyer: Guillotine the Gators Free T-Shirt Offer, ca. 2006
Creators: name: University, George Mason
Publisher: name: George Mason University
Year: 2006
Subjects: subject: George Mason University
subject: Basketball
subject: National Collegiate Athletic Association (NCAA)
subject: Florida Gators

description: Flyer: color, 4" x 9.5" (10.16 cm x 24.13 cm)
description: Flyer advertising an offer to get a free "Guillotine the Gators" t-shirt at the George Mason University campus store. 2005-06 Men's Basketball Season and Tournament Run Collection 2.03
Additional file 2 of What methods are used to study the association between medication adherence trajectories, estimated with the group-based trajectory modeling (GBTM) method, and health-related outcomes?—a protocol for a systematic review
Creators: name: Memoli, Victoria
name: Ekanmian, Giraud
name: Lunghi, Carlotta
name: Bouhnik, Anne-Déborah
name: Lauzier, Sophie
name: Guénette, Line
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Science Policy
subject: Sociology
subject: FOS: Sociology

description: Additional file 2. Inclusion Criteria: Table S1: Inclusion criteria. Search strategy: Table S2: Search strategy. Data extraction grid: Table S3: Data extraction grid.
Supplementary document for Direct-write laser-assisted patterning of form birefringence in waveplates fabricated by glancing-angle deposition - 6410541.pdf
Creators: name: Ramirez, Marcela Mireles
name: Hoffman, Brittany
name: MacNally, Sara
name: Smith, Chris
name: Lakshmanan, Sanjay Nana
name: Lambropoulos, John
name: Rigatti, Amy
name: Demos, Stavros
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Uncategorized

description: Supp document Mireles et al
title: Presentation: Klaus Scheelhaase, October 6-14, 1980
Creators: name: Scheelhaase, Klaus
Publisher: name: George Mason University
Year: 2006
Subjects: subject: International New Towns Association (INTA)
subject: City centers
subject: Traffic
subject: Transportation
subject: Public transportation
subject: Pedestrians

description: Presentation: photocopied, 11" x 8.5" (29.7 cm x 21.6 cm)
description: The Impact of Energy Availability on City Traffic and Development, prepared by Klaus Scheelhaase, presented at the 4th Annual Conference of the International New Towns Association (INTA), October 6-14, 1980. This paper traces the historical development of the city center as the intellectual, economic, and cultural center of a region and its relationship to its citizens as traffic patterns change over time. The sections include Analysis of defects; Possible Solutions; Analysis of energy economics of transportation systems; Areas of operation of the transportation system; and summary. Many of the solutions offered advocate public transportation and greater pedestrian access. Three graphics accompany the report as visual aides. Planned Community Archives Collection, 421.04.
Scorpiops (Euscorpiops) vachoni
Creators: name: Lourenço, Wilson R.
name: Ythier, Eric
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Scorpiops
Scorpiops vachoni

description: - S. (Euscorpiops) vachoni (Qi, Zhu & Lourenço, 2005)
China
description: Published as part of Lourenço, Wilson R. & Ythier, Eric, 2022, A new species of the genus Scorpiops Peters, 1861, subgenus Euscorpiops Vachon, 1980 from Laos (Scorpiones: Scorpiopidae), pp. 1-9 in Faunitaxys 10 (27) on page 3, DOI: 10.57800/faunitaxys-10(27), http://zenodo.org/record/15352467
title: Trompe l’Oeil and Vik Muniz’s Verso Series: The Back of the Canvas as an Original Copy
Creators: name: Suiter, Greta Kuriger
Publisher: name: George Mason University
Year: 2014
Subjects: subject: Trompe l'oeil
subject: Copies
subject: Sculpture
subject: Painting
subject: Dutch art

description: In much of his work Vik Muniz recreates well known images in sculptural form using unexpected materials such as diamonds, sugar, and garbage. He then photographs the pieces and presents the photograph as his final work. Over the course of six years, from 2002 to 2008, Muniz created Verso, a sculpture series that reverses his usual artistic process. With Verso, Muniz recreated the backs of iconic works of art instead of the widely circulated images found on the front. He took the project a step further by not just photographing the back of a work of art but by hiring artisans to meticulously recreate the backs in three dimensions. This thesis argues that the sculptural imitation of a photograph complicates and updates the tradition of trompe l’oeil. This theme is explored through an investigation of the history of the back of the canvas in trompe l’oeil painting and its relationship to contemporary art as evidenced in the Verso series.
MicroRNA–mRNA interactions underlying colorectal cancer molecular subtypes
Creators: name: Cantini, Laura
Publisher: name: F1000Research
Year: 2016

description: Colorectal cancer (CRC) transcriptional subtypes have been recently identified by gene expression profiling. Here we describe an analytical pipeline, microRNA master regulator analysis (MMRA), developed to search for microRNAs potentially driving CRC subtypes. Starting from a microRNA–mRNA tumour expression data set, MMRA identifies candidate regulator microRNAs by assessing their subtype-specific expression, target enrichment in subtype mRNA signatures and network analysis-based contribution to subtype gene expression. When applied to a CRC data set of 450 samples, assigned to subtypes by 3 different transcriptional classifiers, MMRA identifies 24 candidate microRNAs, in most cases downregulated in the stem/serrated/mesenchymal (SSM) poor prognosis subtype. Functional validation in CRC cell lines confirms downregulation of the SSM subtype by miR-194, miR-200b, miR-203 and miR-429, which share target genes and pathways mediating this effect. These results show that, by combining statistical tests, target prediction and network analysis, MMRA effectively identifies microRNAs functionally associated to cancer subtypes.