cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Adapting astronomical source detection software to help detect animals in thermal images obtained by unmanned aerial systems
Creators: name: Longmore, S. N.
name: Collins, R. P.
name: Pfeifer, S.
name: Fox, S. E.
name: Mulero-Pazmany, M.
name: Bezombes, F.
name: Goodwind, A.
name: Ovelar, M. de Juan
name: Knapen, J. H.
name: Wich, S. A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: In this paper we describe an unmanned aerial system equipped with a thermal-infrared camera and software pipeline that we have developed to monitor animal populations for conservation purposes. Taking a multi-disciplinary approach to tackle this problem, we use freely available astronomical source detection software and the associated expertise of astronomers, to efficiently and reliably detect humans and animals in aerial thermal-infrared footage. Combining this astronomical detection software with existing machine learning algorithms into a single, automated, end-to-end pipeline, we test the software using aerial video footage taken in a controlled, field-like environment. We demonstrate that the pipeline works reliably and describe how it can be used to estimate the completeness of different observational datasets to objects of a given type as a function of height, observing conditions etc. -- a crucial step in converting video footage to scientifically useful information such as the spatial distribution and density of different animal species. Finally, having demonstrated the potential utility of the system, we describe the steps we are taking to adapt the system for work in the field, in particular systematic monitoring of endangered species at National Parks around the world.
description: 16 pages, 6 figures, accepted to International Journal of Remote Sensing
Origin of Temperature Gradient in Nonequilibrium Steady States in Weakly Coupled Quantum Spin Systems
Creators: name: Ishida, Toyohiko
name: Sugita, Ayumu
Publisher: name: arXiv
Year: 2017
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study nonequilibrium steady states (NESSs) in quantum spin-1/2 chains in contact with two heat baths at different temperatures. We consider the weak-coupling limit both for spin-spin coupling in the system and for system-bath coupling. This setting allows us to treat NESSs with a nonzero temperature gradient analytically. We develop a perturbation theory for this weak-coupling situation and show a simple condition for the existence of nonzero temperature gradient. This condition is independent of the integrability of the system.
description: 26 pages, 6 figures
A review of the cost-effectiveness of genetic testing for germline variants in familial cancer
Creators: name: Teppala, Srinivas
name: Hodgkinson, Brent
name: Hayes, Sandi
name: Scuffham, Paul
name: Tuffaha, Haitham
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy

description: Background: Targeted germline testing is recommended for those with or at risk of breast, ovarian and colorectal cancer. The affordability of genetic sequencing has improved over the past decade, therefore the cost-effectiveness of testing for these cancers is worthy of reassessment. Objective: To systematically review economic evaluations on cost-effectiveness of germline testing in breast, ovarian or colorectal cancer. Methods: A search of PubMed and Embase databases for cost-effectiveness studies on germline testing in breast, ovarian or colorectal cancer, published between 1999 to May 2022. Synthesis of methodology, cost-effectiveness, and reporting (CHEERS checklist) was performed. Results: The incremental cost-effectiveness ratios (ICERs; in 2021-adjusted US$) for germline testing vs. the standard care option, in hereditary breast or ovarian cancer (HBOC) across target settings were as follows: 1) population-wide testing: 344-2.5 million/QALY 2) women with high-risk: dominant-78,118/QALY, 8,337-59,708/LYG 3) existing breast or ovarian cancer: 3,012-72,566/QALY, 39,835/LYG 4) metastatic breast cancer: 158,630/QALY. Likewise, ICERs of germline testing for colorectal cancer across settings were: 1) population-wide testing: 132,200/QALY, 1.1 million/LYG 2) people with high-risk: 32,322-76,750/QALY, dominant-353/LYG 3) patients with existing colorectal cancer: dominant – 54,122/QALY, 98,790-6.3 million/LYG. Key areas of underreporting were inclusion of a health economic analysis plan (100% of HBOC and colorectal studies), engagement of patients and stakeholders (95.4% of HBOC, 100% of colorectal studies) and measurement of outcomes (18.2% HBOC, 38.9% of colorectal studies). Conclusion: Germline testing for HBOC was likely to be cost-effective across most settings, except when used as a co-dependent technology with the PARP inhibitor, olaparib in metastatic breast cancer. In colorectal cancer studies, testing was cost-effective in those with high-risk, but inconclusive in other settings. Cost-effectiveness was sensitive to the prevalence of tested variants, cost of testing, uptake and benefits of prophylactic measures. Policy advice on germline testing should emphasize the importance of these factors in their recommendations.
Sulla sociogenesi della sociologia
Creators: name: Elias, Norbert
name: Marasco, Vincenzo
Publisher: name: Cambio. Rivista sulle Trasformazioni Sociali
Year: 2019

description: Elias propose una prima versione del testo qui presentato al V World Congress of Sociology, nel Settembre 1962. Il titolo originale - La “rottura col tradizionalismo” e le origini della sociologia - riprendeva per l’appunto quello della sessione in cui era presentato: “La rottura col tradizionalismo”. Quasi venti anni dopo, nel 1984, il manoscritto fu rivisitato e pubblicato – col titolo attuale – sull’«Amsterdam Sociologisch Tijdschrift». La versione qui tradotta è quella contenuta in Collected Works, vol. 16, a cura di R. Kilminster e S. Mennell, 2009, pp. 43-69. ©2009 Norbert Elias Foundation, Amsterdam. Desideriamo ringraziare i colleghi del Norbert Elias Stitching per il permesso di tradurre e pubblicare questo scritto.
description: Cambio. Rivista sulle Trasformazioni Sociali, Vol 9 No 17 (2019): Political Solitude
Low-cost system for sunlight incidence angle measurement using Optical Fiber
Creators: name: Botero-Valencia, Juan
name: Rojas, Elizabeth
name: Mejia, Mateo
name: Montoya, Daniel
name: Flórez, Mariana
name: Ramos-Paja, Carlos
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Mechanical Engineering
subject: FOS: Mechanical engineering
subject: Power and Energy
subject: Energy Systems
subject: Environmental Engineering
subject: FOS: Environmental engineering
subject: Electrical and Computer Engineering
subject: Civil and Environmental Engineering
subject: Engineering

description: The system is based on an arrangement of 33 measurement points (optical fiber) spaced in arcs every 45 degrees in azimuth and every 22.5 degrees in elevation, which provides a wide range for analysis. The purpose is to estimate the angle of incidence of the Sun or other light source.
Cost-effectiveness analysis of bimekizumab for the treatment of active psoriatic arthritis in Sweden
Creators: name: Sigurdardottir, Valgerdur
name: Engstrom, Anna
name: Berling, Patric
name: Olofsson, Tor
name: Oldsberg, Linnea
name: Sadler, Susannah
name: Parra-Padilla, Devian
name: Melis, Lode
name: Willems, Damon
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy

description: To evaluate the cost-effectiveness of bimekizumab, an inhibitor of IL-17F and IL-17A, against biologic and targeted synthetic disease-modifying antirheumatic drugs (DMARD) for psoriatic arthritis (PsA) from the Swedish healthcare system perspective. A Markov model was developed to simulate the clinical pathway of biologic [b] DMARD-naïve or tumor necrosis factor inhibitor experienced [TNFi-exp] PsA patients over a lifetime horizon. Treatment response was incorporated as achievement of the American College of Rheumatology 50% (ACR50) and Psoriasis Area and Severity Index 75% (PASI75) response, and changes in the Health Assessment Questionnaire-Disability Index (HAQ-DI) score. The efficacy of bimekizumab was obtained from the BE OPTIMAL (bDMARD-naïve) and BE COMPLETE (TNFi-experienced) trials while a network meta-analysis (NMA) informed the efficacy of the comparators. Resource use and drug costs were obtained from published studies and databases of drug retail prices in Sweden. A willingness-to-pay threshold of €50,000 per quality-adjusted life year (QALY) was applied. In bDMARD-naïve patients, bimekizumab achieved greater QALYs (14.08) than with all comparators except infliximab (14.22), dominated guselkumab every 4 and 8 weeks, ixekizumab, secukinumab 300 mg, ustekinumab 45 mg and 90 mg, and was cost-effective against risankizumab, tofacitinib, upadacitinib and TNFis, except adalimumab biosimilar. In TNFi-experienced patients, bimekizumab led to greater QALYs (13.56) than all comparators except certolizumab pegol (13.84), and dominated ixekizumab and secukinumab 300 mg while being cost-effective against all other IL-17A-, IL-23- and JAK inhibitors. An NMA informed the comparative effectiveness estimates. Given gaps in evidence of disease management and indirect costs specific to HAQ-DI scores, and sequential clinical trial evidence in PsA, non-PsA cost data from similar joint conditions were used, and one line of active treatment followed by best supportive care was assumed. Bimekizumab was cost-effective against most available treatments for PsA in Sweden, irrespective of prior TNFi exposure
Understanding the effects of surface roughness and topology of zinc on biological cell function
Creators: name: Lapidge, Kieran
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: One significant research area in the rapidly advancing medical industry is the suitability of various materials for biodegradable bone implants. Amongst biodegradable solutions, zinc has seen an increased interest as it has displayed potential to be more suitable over common current materials such as magnesium. For this notion to progress, research must be done into how the surface conditions of zinc metal affects the biological cellular function in which it is to be applied. This project will see how changing the roughness and topology of zinc's surface can optimise its suitability for bone implants. The project yielded inconclusive results, showing that there is still much research to be done in this area in order to understand just how zinc may be applied to bone implantation.
Additional file 2 of Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species
Creators: name: Huang, Yuying
name: Li, Jing
name: Yang, Zerui
name: An, Wenli
name: Xie, Chunzhu
name: Liu, Shanshan
name: Zheng, Xiasheng
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Table S1. Gene number and CDS nucleotide composition of the CP genomes in eleven Ficus species.
Unconventional magnetic order in the conical state of MnSi
Creators: name: de Reotier, P. Dalmas
name: Maisuradze, A.
name: Yaouanc, A.
name: Roessli, B.
name: Amato, A.
name: Andreica, D.
name: Lapertot, G.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: In the temperature-magnetic field phase diagram, the binary metallic compound MnSi exhibits three magnetic phases below Tc ~ 29 K. An unconventional helicoidal phase is observed in zero field. At moderate field intensity a conical phase sets in. Near Tc, in an intermediate field range, a skyrmion lattice phase appears. Here we show the magnetic structure in the conical phase to strongly depend on the field direction and to deviate substantially from a conventional conical structure.
description: 5 pages, 4 figures
Additional file 1: Appendix A. of Pregnancy outcomes in women taking probiotics or prebiotics: a systematic review and meta-analysis
Creators: name: Jarde, Alexander
name: Anne-Mary Lewis-Mikhael
name: Moayyedi, Paul
name: Stearns, Jennifer
name: Collins, Stephen
name: Beyene, Joseph
name: McDonald, Sarah
Publisher: name: figshare
Year: 2018
Subjects: subject: Biotechnology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Computational Biology

description: Complete search strategy. Complete search strategy; Search terms used in each of the databases used. (DOC 308 kb)
Categorification of integrable representations of quantum groups
Creators: name: Zheng, Hao
Publisher: name: arXiv
Year: 2008
Subjects: subject: Representation Theory (math.RT)
subject: Quantum Algebra (math.QA)
subject: FOS: Mathematics
subject: 17B37, 18F20

description: We categorify the highest weight integrable representations and their tensor products of a symmetric quantum Kac-Moody algebra. As byproducts, we obtain a geometric realization of Lusztig's canonical bases of these representations as well as a new positivity result. The main ingredient in the underlying geometric construction is a class of micro-local perverse sheaves on quiver varieties.
description: 35pages, v2: minor revisions, typo fixed
Cats and Captions vs. Creators and the Clock: Comparing Multimodal Content to Context in Predicting Relative Popularity
Creators: name: Hessel, Jack
name: Lee, Lillian
name: Mimno, David
Publisher: name: arXiv
Year: 2017
Subjects: subject: Social and Information Networks (cs.SI)
subject: Computation and Language (cs.CL)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: The content of today's social media is becoming more and more rich, increasingly mixing text, images, videos, and audio. It is an intriguing research question to model the interplay between these different modes in attracting user attention and engagement. But in order to pursue this study of multimodal content, we must also account for context: timing effects, community preferences, and social factors (e.g., which authors are already popular) also affect the amount of feedback and reaction that social-media posts receive. In this work, we separate out the influence of these non-content factors in several ways. First, we focus on ranking pairs of submissions posted to the same community in quick succession, e.g., within 30 seconds, this framing encourages models to focus on time-agnostic and community-specific content features. Within that setting, we determine the relative performance of author vs. content features. We find that victory usually belongs to "cats and captions," as visual and textual features together tend to outperform identity-based features. Moreover, our experiments show that when considered in isolation, simple unigram text features and deep neural network visual features yield the highest accuracy individually, and that the combination of the two modalities generally leads to the best accuracies overall.
description: 10 pages, data and models available at http://www.cs.cornell.edu/~jhessel/cats/cats.html, Proceedings of WWW 2017
Characterization and phylogenetic analysis of the chloroplast genome of Solanum pseudocapsicum (Solanaceae)
Creators: name: Liu, Yongle
name: Tang, Xuan
name: Deng, Aihua
name: Li, Huan
name: Xiao, Yulong
name: Zhao, Wenyan
name: Xiang, Lixuan
name: Liu, Yi
name: Yao, Zui
name: Zeng, Xingyu
name: Du, Zhitian
name: Huang, Rongjie
name: Yin, Hanbin
name: Huang, Kerui
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: Solanum pseudocapsicum Linnaeus 1753, a popular indoor potted plant known for its ornamental fruits, had its chloroplast genome sequenced in this study to determine its phylogenetic relationship with other related species and to construct a phylogenetic analysis tree. The research findings are as follows: 1. The chloroplast genome of S. pseudocapsicum comprises a large single-copy (LSC) region of 86,260 base pairs, a small single-copy (SSC) region of 18,325 base pairs, and two inverted repeat (IR) regions, each measuring 25,390 base pairs in length. 2. The G + C content of the entire chloroplast genome is 37.59%, with the highest G + C content found in the IR regions, reaching 43.03%; followed by the LSC region, which has a G + C content of 35.68%; and the lowest in the SSC region, with a G + C content of 31.53%. 3. The genome contains 127 genes, including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, with 18 genes duplicated in the IR regions. 4. Phylogenetic analysis revealed that S. pseudocapsicum, Solanum betaceum, Solanum laciniatum, and Solanum nitidum are genetically closely related and are located on the same branch of the phylogenetic tree, indicating a close relationship among them. This study provides a foundation for the identification, classification, and exploration of genetic diversity within the Solanum genus.
Cost-effectiveness analysis of HLA-B*13:01 screening for the prevention of co-trimoxazole-induced severe cutaneous adverse reactions among HIV-infected patients in Thailand
Creators: name: Kategeaw, Warittakorn
name: Nakkam, Nontaya
name: Kiertiburanakul, Sasisopin
name: Sukasem, Chonlaphat
name: Tassaneeyakul, Wichittra
name: Chaiyakunapruk, Nathorn
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Studies found a strong association between HLA-B*13:01 allele and co-trimoxazole-induced severe cutaneous adverse reactions (SCARs). Genetic screening before initiation of co-trimoxazole may decrease the incidence of co-trimoxazole-induced SCARs. This study aims to evaluate the cost-effectiveness of HLA-B*13:01 screening before co-trimoxazole initiation in HIV-infected patients in Thailand. A combination of a decision tree model and a Markov model was used to estimate lifetime costs and outcomes of two strategies including 1) HLA-B*13:01 screening before co-trimoxazole initiation and 2) usual practice from a societal perspective. Alternative drugs are not considered because dapsone (the second-line drug) also presents a genetic risk. Input parameters were obtained from literature, government documents, and part of the TREAT Asia HIV Observational Database (TAHOD). One-way sensitivity analyses and probabilistic analyses were performed to determine robustness of the findings. HLA-B*13:01 screening resulted in 0.0061 quality-adjusted life years (QALYs) loss with an additional cost of 370 THB ($11.84). At the cost-effectiveness threshold of 160,000 THB ($5,112.85), the probability of the genetic screening strategy being cost-effective is 9.54%. This analysis demonstrated that HLA-B*13:01 allele screening before initiation of co-trimoxazole among HIV-infected patients is unlikely to be cost-effective in Thailand. Our findings will help policymakers make an evidence-informed decision making.
Quantitative depth profiling of Si1-xGex structures by time-of-flight secondary ion mass spectrometry and secondary neutral mass spectrometry
Creators: name: Drozdov, M. N.
name: Drozdov, Y. N.
name: Csik, A.
name: Novikov, A. V.
name: Vad, K.
name: Yunin, P. A.
name: Yurasov, D. V.
name: Belykh, S. F.
name: Gololobov, G. P.
name: Suvorov, D. V.
name: Tolstogouzov, A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Quantification of Ge in Si1-xGex structures (0.0920.9997) of intensity ratios of GeCs2+/SiCs2+ and 74Ge-/30Si- secondary ions and post-ionized 70Ge+/28Si+ sputtered neutrals with Ge concentration was obtained. The calibration data were used for quantitative depth profiling of [10x(12.3 nm Si0.63Ge0.37/34 nm Si)] structures on Si. Satisfactory compliance of the quantified Ge concentration in SiGe layers with the data measured by high-resolution X-ray diffraction was obtained for both techniques. Both SIMS and SNMS experimental profiles were fitted using the Hofmann mixing-roughness-information depth (MRI) model. In case of TOF-SIMS the quality of the reconstruction was higher than for SNMS since not only the progressing roughening, but also crater effect and other processes unaccounted in the MRI simulation could have significant impact on plasma sputter depth profiling.
Southern Ocean sentinels: demographic insights into the declining population of Southern elephant seals at Macquarie Island
Creators: name: Desprez, Marine
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Some of the clearest expressions of climate change have been found in the Southern Ocean, one of the biggest marine ecosystems and a major component of the Earth's climate system. Top predators living in this ecosystem are considered to be one of the best indicators of these global changes as their population fluctuations reliably integrate and reflect prevailing environmental conditions. Southern elephant seals (Mirounga leonina) are pole-ward predators that feed throughout the Southern Ocean. In the past decades, their worldwide populations have been stable or increasing with the single exception of the Macquarie Island population that has been declining for unknown reasons over the past 50 years. This study, based on an 18-year capture-recapture dataset involving more than 6,000 individually marked females, aims to explore and understand the demographic mechanisms driving this decline and the potential impact of a changing environment on a key predator. Using models that deal with the issue of uncertainty in reproductive status, I showed that breeding is extremely costly in female elephant seals and results in a substantial decrease in survival of both first-time and experienced breeders. To offset this high reproductive cost to survival and maximize their reproductive success, female elephant seals tend to skip some reproductive events during their lifetime. Environmental conditions during the beginning of the post-moult foraging trip, which also corresponds to the beginning of females' pregnancy, play a critical role in this decision to skip reproduction or not. By incorporating this information into a matrix population model, I confirmed and reevaluated the decline of this population. Taken together, these results provide a detailed understanding of the southern elephant seals demography and give potential clues to the processes driving the decline of the Macquarie Island population. More broadly, my research contributes to a body of knowledge regarding the role of evolutionary and ecological processes in shaping life histories and population trajectories in long-lived species.
The complete mitochondrial genome of Chilean Jack Mackerel, Trachurus murphyi Nichols, 1920 (Teleostei, Carangidae)
Creators: name: Asorey, Cynthia M.
name: Larraín, María Angélica
name: Araneda, Cristian
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: The Chilean jack mackerel (Trachurus murphyi, Nichols, 1920) is a pelagic fish of high fishery interest, with a global capture of 828,358 mt in 2021. We report the complete mitochondrial genome of T. murphyi (Teleostei, Carangidae), collected in Bahia de Zapallar, Chile (32°33’02.59’’ S, 71°27’55.38’’ W). The size of the mitogenome is 16,561 bp (H-strand composition: 25.9% A, 16.7% C, 29.8% G, and 27.5% T). The mitogenome has the classic vertebrate gene content of 13 protein-coding, two rRNA, and 22 tRNA genes, as found in Carangidae and other Teleostei families. Phylogenetic analysis using mitochondrial genomes of 22 related species revealed that T. murphyi formed a well-supported monophyletic group with the other Trachurus species, being T. simmetricus its closest relative. Sequencing the mitochondrial genome from T. murphyi is the first step in developing traceability tools based on DNA analysis to enforce fishing quotas and trace the processed food and foodstuff containing Chilean jack mackerel following the objective of the South Pacific Regional Fisheries Management Organization (SPRFMO).
Hyper-Selective Plasmonic Color Filters
Creators: name: Fleischman, Dagny
name: Sweatlock, Luke
name: Murakami, Hirotaka
name: Atwater, Harry
Publisher: name: arXiv
Year: 2016
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The subwavelength mode volumes of plasmonic filters are well matched to the small size of state-of-the-art active pixels (~ 1 μm) in CMOS image sensor arrays used in portable electronic devices. Typical plasmonic filters exhibit broad (> 100 nm) transmission bandwidths. Dramatically reducing the peak width of filter transmission spectra would allow for the realization of CMOS hyperspectral imaging arrays, which demand the FWHM of transmission peaks to be less than 30 nm. We find that the design of 5 layer metal-insulator-metal-insulator-metal structures gives rise to multi-mode interference phenomena that suppresses spurious transmission features gives rise to a single narrow transmission band with FWHM as small as 17 nm. The transmission peaks of these multilayer slot-mode plasmonic filters (MSPFs) can be systematically varied throughout the visible and near infrared spectrum, so the same basic structure can serve as a filter over a large range of wavelengths.
description: 18 pages, 7 figures
Additional file 7: Figure S7. of Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing
Creators: name: MacConaill, Laura
name: Burns, Robert
name: Anwesha Nag
name: Coleman, Haley
name: Slevin, Michael
name: Giorda, Kristina
name: Light, Madelyn
name: Lai, Kevin
name: Jarosz, Mirna
name: McNeill, Matthew
name: Ducar, Matthew
name: Meyerson, Matthew
name: Thorner, Aaron
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Multiplex captures have comparable uniformity to individual captures. Uniform coverage enables accurate variant calling with minimal sequencing cost. (PDF 115 kb)
Boolean nested canalizing functions: a comprehensive analysis
Creators: name: Li, Yuan
name: Adeyeye, John O.
name: Murrugarra, David
name: Aguilar, Boris
name: Laubenbacher, Reinhard
Publisher: name: arXiv
Year: 2012
Subjects: subject: Dynamical Systems (math.DS)
subject: Molecular Networks (q-bio.MN)
subject: FOS: Mathematics
subject: FOS: Biological sciences

description: Boolean network models of molecular regulatory networks have been used successfully in computational systems biology. The Boolean functions that appear in published models tend to have special properties, in particular the property of being nested canalizing, a concept inspired by the concept of canalization in evolutionary biology. It has been shown that networks comprised of nested canalizing functions have dynamic properties that make them suitable for modeling molecular regulatory networks, namely a small number of (large) attractors, as well as relatively short limit cycles.
 This paper contains a detailed analysis of this class of functions, based on a novel normal form as polynomial functions over the Boolean field. The concept of layer is introduced that stratifies variables into different classes depending on their level of dominance. Using this layer concept a closed form formula is derived for the number of nested canalizing functions with a given number of variables. Additional metrics considered include Hamming weight, the activity number of any variable, and the average sensitivity of the function. It is also shown that the average sensitivity of any nested canalizing function is between 0 and 2. This provides a rationale for why nested canalizing functions are stable, since a random Boolean function in n variables has average sensitivity n/2. The paper also contains experimental evidence that the layer number is an important factor in network stability.
description: 21 pages, 1 figure. arXiv admin note: substantial text overlap with arXiv:1111.7217
Transient flows in active porous media
Creators: name: Kosmidis, Lefteris I.
name: Jensen, Kaare H.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Stimuli-responsive materials that modify their shape in response to changes in environmental conditions -- such as solute concentration, temperature, pH, and stress -- are widespread in nature and technology. Applications include micro- and nanoporous materials used in filtration and flow control. The physiochemical mechanisms that induce internal volume modifications have been widely studies. The coupling between induced volume changes and solute transport through porous materials, however, is not well understood. Here, we consider advective and diffusive transport through a small channel linking two large reservoirs. A section of stimulus-responsive material regulates the channel permeability, which is a function of the local solute concentration. We derive an exact solution to the coupled transport problem and demonstrate the existence of a flow regime in which the steady state is reached via a damped oscillation around the equilibrium concentration value. Finally, the feasibility of an experimental observation of the phenomena is discussed. Please note that this version of the paper has not been formally peer reviewed, revised or accepted by a journal.
Molecular Network Control Through Boolean Canalization
Creators: name: Murrugarra, David
name: Dimitrova, Elena S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Molecular Networks (q-bio.MN)
subject: FOS: Biological sciences

description: Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of network modeling where each layer of canalization adds a degree of stability in the dynamics of the network. Recently, dynamic network control approaches have been used for the design of new therapeutic interventions and for other applications such as stem cell reprogramming. This work studies the role of canalization in the control of Boolean molecular networks. It provides a method for identifying the potential edges to control in the wiring diagram of a network for avoiding undesirable state transitions. The method is based on identifying appropriate input-output combinations on undesirable transitions that can be modified using the edges in the wiring diagram of the network. Moreover, a method for estimating the number of changed transitions in the state space of the system as a result of an edge deletion in the wiring diagram is presented. The control methods of this paper were applied to a mutated cell-cycle model and to a p53-mdm2 model to identify potential control targets.
Additional file 1: of Physiciansâ knowledge and practice on death certification in the North West Bank, Palestine: across sectional study
Creators: name: Qaddumi, Jamal
name: Nazzal, Zaher
name: Allam Yacoub
name: Mansour, Mahmoud
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 60506 Virology

description: Case scenario and its model answer. (DOCX 196 kb)
Frequency and clinicoeconomic impact of delays to definitive diagnosis of obstructive hypertrophic cardiomyopathy in the United States
Creators: name: Naidu, Srihari S.
name: Sutton, Megan B.
name: Gao, Wei
name: Fine, Jennifer T.
name: Xie, Jipan
name: Desai, Nihar R.
name: Owens, Anjali T.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Medicine
Cell Biology
Biotechnology
Biological Sciences not elsewhere classified
Cancer
Science Policy
Mental Health

description: The diagnostic history in the years leading up to the definitive diagnosis of patients with obstructive hypertrophic cardiomyopathy (HCM) has not been studied. Patients with a delay in the definitive diagnosis of obstructive HCM from January 2009 to March 2019 were identified in the US IBM MarketScan Commercial and Medicare Supplemental Databases if they had an alternative diagnosis indicating a misdiagnosis during the 24 months before the definitive obstructive HCM diagnosis. Resource use and costs associated with the delay were estimated during the same period. Of 3,888 eligible patients with obstructive HCM, 59.5% had a delay in definitive diagnosis. Patients received a mean of 4.0 misdiagnoses before the definitive obstructive HCM diagnosis, most of which were other cardiovascular conditions. Consequently, 15.7% of patients may have received inappropriate treatment. Approximately 78.4% of patients visited a cardiologist (mean 4.7 visits) before the definitive obstructive HCM diagnosis. Additionally, 26.8% and 32.1% of patients had an inpatient and emergency room visit, respectively. Annualized healthcare costs associated with the delay were $4,379 per patient. The current study used administrative claims data for a commercially insured population. Therefore, the results may not be generalizable to other populations (e.g. those insured by Medicare or Medicaid and the uninsured). Like other database studies, the current study may have suffered from miscoding or undercoding, which may have caused misclassification of patients. Owing to insufficient data, the study could not evaluate all potential consequences of a delay in definitive diagnosis. Most patients with obstructive HCM had a delay of ≤ 2 years before receiving the definitive diagnosis. The diagnostic journey involved multiple potential misdiagnoses, predominantly cardiovascular, as well as a substantial clinical and economic burden on patients and the healthcare system.
Enhanced physicochemical and biological properties of ion-implanted Titanium using Electron Cyclotron Resonance ion sources
Creators: name: Hegedűs, Csaba
name: Ho, Chia-Che
name: Csik, Attila
name: Biri, Sándor
name: Ding, Shinn-Jyh
Publisher: name: arXiv
Year: 2017
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The surface properties of metallic implants play an important role in their clinical success. Improving upon the inherent shortcomings of Ti implants, such as poor bioactivity, is imperative for achieving clinical use. In this study, we have developed a Ti implant modified with Ca or dual Ca + Si ions on the surface using an electron cyclotron resonance ion source (ECRIS). The physicochemical and biological properties of ion-implanted Ti surfaces were analyzed using various analytical techniques, such as surface analyses, potentiodynamic polarization and cell culture. Experimental results indicated that a rough morphology was observed on the Ti substrate surface modified by ECRIS plasma ions. The in vitro electrochemical measurement results also indicated that the Ca + Si ion-implanted surface had a more beneficial and desired behavior than the pristine Ti substrate. Compared to the pristine Ti substrate, all ion-implanted samples had a lower hemolysis ratio. MG63 cells cultured on the high Ca and dual Ca + Si ion-implanted surfaces revealed significantly greater cell viability in comparison to the pristine Ti substrate. In conclusion, surface modification by electron cyclotron resonance Ca and Si ion sources could be an effective method for Ti implants.
On the skein polynomial for links
Creators: name: Jiang, Boju
name: Wang, Jiajun
name: Zheng, Hao
Publisher: name: arXiv
Year: 2016
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: Primary 57M25, Secondary 20F36

description: We give characterizations of the skein polynomial for links (as well as Jones and Alexander-Conway polynomials derivable from it), avoiding the usual "smoothing of a crossing" move. As by-products we have characterizations of these polynomials for knots, and for links with any given number of components.
Postfeminism and the representation of acquaintance rape in young adult fiction
Creators: name: Altrows, Aiyana
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Anti-rape discourse was key to the success of the Women's Liberation Movement, which insisted on bringing rape into public focus. Western popular culture is now inundated with rape stories, and yet the feminism has largely disappeared from these narratives. This shift can be ascribed to postfeminism, which appears feminist through a use of feminist vocabulary but instead promotes anti-feminist neoliberal meaning. The last fifteen years have seen an increasing number of young adult novels about rape. My first chapter asserts that while authorial intention is doubtlessly to empower teenage girls, as evidenced in paratextual direct addresses to the reader, implicit anti-feminist neoliberal ideologies in the texts undermine that goal. Chapter Two examines how novels naturalise rape and condone surveillance frameworks through restrictive discourses on clothing and food, presenting female bodies as rape spaces. Chapter Three shifts focus to the affective regulation of mental states, arguing that the predominant 'silent victim' script stigmatises feminist anger, and makes the victim's traumatised psyche the 'problem' of the 'problem novel.' My fourth chapter shifts focus to boyhood, particularly the New Age Boyfriend type, whose construction in contrast to the essentially evil and undeveloped off-page rapist not only exonerates 'good guy' types from a potential to rape, but identifies rape as an inhuman, and therefore uninterrogable act. My final chapter argues that novels which reject dominant schemas of victims as isolated within hostile communities are better able to demonstrate feminist models of collectivity and interrogate rape culture. The success of the #MeToo movement signals a return to the second-wave tactic of reclaiming rape narratives as a means of empowerment. This thesis participates in this reclamation by examining how young adult fiction displaces feminism in its anti-rape discourse, and how it might be restored to promote an empowering vision of girlhood.
Estimating Propensity Parameters using Google PageRank and Genetic Algorithms
Creators: name: Murrugarra, David
name: Miller, Jacob
name: Mueller, Alex
Publisher: name: arXiv
Year: 2016
Subjects: subject: Molecular Networks (q-bio.MN)
subject: FOS: Biological sciences

description: Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS) is a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html.
description: 20 pages, 4 figures, 2 tables
Hamiltonian and Lagrangian formalisms of mutations in cluster algebras and application to dilogarithm identities
Creators: name: Gekhtman, Michael
name: Nakanishi, Tomoki
name: Rupel, Dylan
Publisher: name: arXiv
Year: 2016
Subjects: subject: Rings and Algebras (math.RA)
subject: Quantum Algebra (math.QA)
subject: FOS: Mathematics
subject: 13F60 (Primary), 33E20 (Secondary)

description: We introduce and study a Hamiltonian formalism of mutations in cluster algebras using canonical variables, where the Hamiltonian is given by the Euler dilogarithm. The corresponding Lagrangian, restricted to a certain subspace of the phase space, coincides with the Rogers dilogarithm. As an application, we show how the dilogarithm identity associated with a period of mutations in a cluster algebra arises from the Hamiltonian/Lagrangian point of view.
description: ver1: 28 pages; ver2: 30 pages, Sec.5.4.3 revised + minor changes; ver3: 30 pages, Remark 6.9 replaced with Theorem 6.9 + minor changes; ver4:31 pages, Sec.5.2, 5.3 revised + minor changes; ver5: 31 pages, minor changes, final version to appear in J. Integrable Syst
1.3 mm ALMA Observations of the Fomalhaut Debris System
Creators: name: White, J. A.
name: Boley, A. C.
name: Dent, W. R. F.
name: Ford, E. B.
name: Corder, S.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present ALMA Band 6 observations (1.3 mm/233 GHz) of Fomalhaut and its debris disc. The observations achieve a sensitivity of 17 $μ$Jy and a resolution of 0.28 arcsec (2.1 au at a distance of 7.66 pc), which are the highest resolution observations to date of the millimetre grains in Fomalhaut's main debris ring. The ring is tightly constrained to $139^{+2}_{-3}$ au with a FWHM of $13\pm3$ au, following a Gaussian profile. The millimetre spectral index is constrained to $α_{mm} = -2.62\pm0.12$. We explore fitting debris disc models in the image plane, as well as fitting models using visibility data directly. The results are compared and the potential advantages/disadvantages of each approach are discussed. The detected central emission is indistinguishable from a point source, with a most probable flux of $0.90\pm 0.12$ mJy (including calibration uncertainties). This implies that any inner debris structure, as was inferred from far-Infrared observations, must contribute little to the total central emission. Moreover, the stellar flux is less than 70\% of that predicted by extrapolating a black body from the constrained stellar photosphere temperature. This result emphasizes that unresolved inner debris components cannot be fully characterized until the behaviour of the host star's intrinsic stellar emission at millimetre wavelengths is properly understood.
description: 10 pages, 7 figures, Submitted to MNRAS after addressing referee's comments
A multi-Frey approach to Fermat equations of signature $(r,r,p)$
Creators: name: Billerey, Nicolas
name: Chen, Imin
name: Dieulefait, Luis
name: Freitas, Nuno
Publisher: name: arXiv
Year: 2017
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11D41, 11F80, 11G05

description: In this paper, we give a resolution of the generalized Fermat equations $$x^5 + y^5 = 3 z^n \text{ and } x^{13} + y^{13} = 3 z^n,$$ for all integers $n \ge 2$, and all integers $n \ge 2$ which are not a multiple of $7$, respectively, using the modular method with Frey elliptic curves over totally real fields. The results require a refined application of the multi-Frey technique, which we show to be effective in new ways to reduce the bounds on the exponents $n$.
 We also give a number of results for the equations $x^5 + y^5 = d z^n$, where $d = 1, 2$, under additional local conditions on the solutions. This includes a result which is reminiscent of the second case of Fermat's Last Theorem, and which uses a new application of level raising at $p$ modulo $p$.
description: Post-publication revised version. No modifications in the numbering compared to the published version (Trans. Amer. Math. Soc. 371 (2019), no. 12, 8651--8677). Fixed some typos. Expanded proofs of Proposition 6, Theorem 7, and Lemma 10. Updated bibliography. Fixed some mistake (coming from the code) in the proof of Theorem 2
An application of Brascamp-Lieb's inequality
Creators: name: Weber, Michel
Publisher: name: arXiv
Year: 2018
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: We use Brascamp-Lieb's inequality to obtain new decoupling inequalities for general Gaussian vectors, and for stationary cyclic Gaussian processes. In the second case, we use a version by Bump and Diaconis of the strong Szego limit theorem. This extends results of Klein, Landau and Shucker.
description: 12 pagess