cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Pulmonary miRNA expression after polytrauma depends on the surgical invasiveness and displays an anti-inflammatory pattern by the combined inhibition of C5 and CD14
Creators: name: Zhou, Nan
name: Groven, Rald V. M.
name: Horst, Klemens
name: Mert, Ümit
name: Greven, Johannes
name: Mollnes, Tom Eirik
name: Huber-Lang, Markus
name: Van Griensven, Martijn
name: Hildebrand, Frank
name: Balmayor, Elizabeth R.
Publisher: name: Universität Ulm
Year: 2024
Subjects: subject: Respiratory failure
subject: Polytrauma
subject: MicroRNAs
subject: ARDS
subject: Early total care
subject: Damage control orthopedics
subject: DDC 610 / Medicine & health

description: Background Respiratory failure can be a severe complication after polytrauma. Extensive systemic inflammation due to surgical interventions, as well as exacerbated post-traumatic immune responses influence the occurrence and progression of respiratory failure. This study investigated the effect of different surgical treatment modalities as well as combined inhibition of the complement component C5 and the toll-like receptor molecule CD14 (C5/CD14 inhibition) on the pulmonary microRNA (miRNA) signature after polytrauma, using a translational porcine polytrauma model. Methods After induction of general anesthesia, animals were subjected to polytrauma, consisting of blunt chest trauma, bilateral femur fractures, hemorrhagic shock, and liver laceration. One sham group (n=6) and three treatment groups were defined; Early Total Care (ETC, n=8), Damage Control Orthopedics (DCO, n=8), and ETC + C5/CD14 inhibition (n=4). Animals were medically and operatively stabilized, and treated in an ICU setting for 72 h. Lung tissue was sampled, miRNAs were isolated, transcribed, and pooled for qPCR array analyses, followed by validation in the individual animal population. Lastly, mRNA target prediction was performed followed by functional enrichment analyses. Results The miRNA arrays identified six significantly deregulated miRNAs in lung tissue. In the DCO group, miR-129, miR-192, miR-194, miR-382, and miR-503 were significantly upregulated compared to the ETC group. The miRNA expression profiles in the ETC + C5/CD14 inhibition group approximated those of the DCO group. Bioinformatic analysis revealed mRNA targets and signaling pathways related to alveolar edema, pulmonary fibrosis, inflammation response, and leukocytes recruitment. Collectively, the DCO group, as well as the ETC + C5/CD14 inhibition group, revealed more anti-inflammatory and regenerative miRNA expression profiles. Conclusion This study showed that reduced surgical invasiveness and combining ETC with C5/CD14 inhibition can contribute to the reduction of pulmonary complications. © In Copyright http://rightsstatements.org/vocab/InC/1.0/
Improving the throughput of the AES algorithm with multicore processors
Creators: name: Barnes, A.
name: Fernando, R.
name: Mettananda, K.
name: Ragel, R. G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: AES, Advanced Encryption Standard, can be considered the most widely used modern symmetric key encryption standard. To encrypt/decrypt a file using the AES algorithm, the file must undergo a set of complex computational steps. Therefore a software implementation of AES algorithm would be slow and consume large amount of time to complete. The immense increase of both stored and transferred data in the recent years had made this problem even more daunting when the need to encrypt/decrypt such data arises. As a solution to this problem, in this paper, we present an extensive study of enhancing the throughput of AES encryption algorithm by utilizing the state of the art multicore architectures. We take a sequential program that implements the AES algorithm and convert the same to run on multicore architectures with minimum effort. We implement two different parallel programmes, one with the fork system call in Linux and the other with the pthreads, the POSIX standard for threads. Later, we ran both the versions of the parallel programs on different multicore architectures and compared and analysed the throughputs between the implementations and among different architectures. The pthreads implementation outperformed in all the experiments we conducted and the best throughput obtained is around 7Gbps on a 32-core processor (the largest number of cores we had) with the pthreads implementation.
Phenotype of HLA antibodies in patients with antibody mediated rejection
Creators: name: Gueret-Wardle, Alexander
Publisher: name: Imperial College London
Year: 2019

description: Renal transplantation is the treatment of choice for patients with end stage kidney disease. Not only is there a survival benefit but there is a significant improvement in quality of life when compared to patients that remain on dialysis. Although short term graft survival has improved in the last 60 years, late graft loss remains a problem. Antibody mediated rejection (AMR) is a major determinant of kidney allograft failure, with chronic AMR being the leading cause of late graft loss. Donor specific anti-HLA antibodies (DSA) have been reported to be strongly associated with an increased risk of rejection and allograft failure. Although the presence of anti-HLA DSAs is thought to be one of the most important biomarkers in predicting allograft failure there is no consensus on their pathogenicity and no standardised protocol on how to approach their clinical management. Whilst most DSAs are of immunoglobulin (Ig) G isotype Anti-HLA DSAs can also exist in IgM, IgE and IgA subtypes, although their roles are less well understood. The value of phenotyping these antibodies has not been fully established. The principal aim of this work is to determine whether more sophisticated assays help predict outcomes for those most at risk of allograft rejection. The underlying hypothesis of this work is that phenotyping of DSAs helps stratify the risk of poor outcomes according to the phenotype of rejection. Patients were recruited from Imperial College Renal and Transplant centre. The results are presented in several related studies. 1. IgG anti-HLA donor specific antibody subclass phenotyping in chronic antibody mediated rejection (cAMR) 2. C1q Binding anti-HLA donor specific antibodies in patients with cAMR 3. What is the role of IgM anti-HLA donor specific antibodies in renal transplantation 4. Anti-HLA IgE: good, bad or indifferent?
title: Фармакогностический анализ лекарственного растительного сырья топинамбура клубни
Creators: name: Орлова, Елизавета
Publisher: name: Новгородский государственный университет имени Ярослава Мудрого (НовГУ)
Year: 2020

description: Использование лекарственного растительного сырья с целью создания высокоэффективных, малотоксичных и доступных препаратов является актуальной проблемой. Провели фармакогностический анализ клубней топинамбура. Определили количество экстрактивных веществ, аскорбиновой кислоты и антиокислительную
активность экстрактов. Установили количественное содержание суммы фруктозанов и фруктозидов в пересчете на инулин. Было выявлено большое содержание инулина в клубнях топинамбура.
ASReview Software Documentation
Creators: name: De Bruin, Jonathan
name: Ferdinands, Gerbrich
name: Harkema, Albert
name: De Boer, Jan
name: Van den Brand, Sofie
name: Ma, Yongchao
name: Van de Schoot, Rens
Publisher: name: Zenodo
Year: 2020
Subjects: systematic review
asreview
machine learning

description: This document contains detailed information for version 0.15 of the ASReview software. For more information, see https://github.com/asreview/asreview.
Multi-omics analysis reveals the host-microbe interactions in rhesus macaques at sexual maturity
Creators: name: 唐瑞祥(Ruixiang Tang)
Publisher: name: CNGB
Year: 2022
Subjects: Raw sequence reads
Metagenome
Transcriptome or Gene expression
Multiisolate
Model organism

description: Multi-omics analysis reveals the host-microbe interactions in rhesus macaques at sexual maturity
title: Острый респираторный дистресс-синдром при вирусных поражениях легких
Creators: name: Петрова, Екатерина
name: Парунов, Сергей
name: Смирнова, Марина
Publisher: name: Новгородский государственный университет имени Ярослава Мудрого (НовГУ)
Year: 2020

description: Острый респираторный дистресс-синдром (ОРДС) является жизнеугрожающим осложнением вирусных поражений легких. Несмотря на то, что активно изучаются механизмы развития данного состояния, разрабатываются новые
методы лечения, летальность по-прежнему остается очень высокой. Данный процесс практически не лечится на поздних стадиях, в связи с чем важной является ранняя диагностика и профилактика ОРДС. В статье приведены современные литературные данные и рассмотрен случай ОРДС у пациента с гриппом A(H1N1/2009).
On Conformal Powers of the Dirac Operator on Einstein Manifolds
Creators: name: Fischmann, Matthias
name: Krattenthaler, Christian
name: Somberg, Petr
Publisher: name: arXiv
Year: 2014
Subjects: subject: Differential Geometry (math.DG)
subject: Mathematical Physics (math-ph)
subject: Analysis of PDEs (math.AP)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 53C27, 34L40, 53A30, 33C20

description: We determine the structure of conformal powers of the Dirac operator on Einstein {\it Spin}-manifolds in terms of the product formula for shifted Dirac operators. The result is based on the techniques of higher variations for the Dirac operator on Einstein manifolds and spectral analysis of the Dirac operator on the associated Poincaré-Einstein metric, and relies on combinatorial recurrence identities related to the dual Hahn polynomials.
description: Conformal and semi-Riemannian {\it Spin}-geometry, conformal powers of the Dirac operator, Einstein manifolds, higher variations of the Dirac operator, Hahn polynomials
title: Host-preference and parasitic capacity of five Trichogramma species (Hym.: Trichogrammatidae) against some stored product moth pests
Creators: name: Hegazi, Esmat
name: Adler, Cornel
name: Khafagi, Wedad
name: Agamy, Essam
Publisher: name: Julius Kühn-Institut
Year: 2018

description: Julius-Kühn-Archiv, Nr. 463, Vol. 1 (2018): Proceedings of the 12th International Working Conference on Stored Product Protection (IWCSPP) in Berlin, Germany, October 7-11, 2018
STEREO-seq data of 8 mouse brain samples
Creators: name: 梁瀚(Lianghan)
Publisher: name: CNGB
Year: 2022
Subjects: Raw sequence reads
Multiisolate
Medical

description: 4 for young group and 4 for old group. Of each group, the genotype of half samples is wild-type while that of the rests is OVX.
ASReview Software Documentation
Creators: name: De Bruin, Jonathan
name: Ferdinands, Gerbrich
name: Harkema, Albert
name: De Boer, Jan
name: Van den Brand, Sofie
name: Ma, Yongchao
name: Van de Schoot, Rens
Publisher: name: Zenodo
Year: 2021
Subjects: systematic review
asreview
machine learning

description: This document contains detailed information for version 0.15 of the ASReview software. For more information, see https://github.com/asreview/asreview.
Impact of blood products on renal transplant allosensitisation
Creators: name: Hassan, Sevda
Publisher: name: Imperial College London
Year: 2019

description: Patients with end stage renal disease (ESRD) who are sensitised with anti-human leucocyte antibodies (HLA) spend a longer time on the transplant wait list and have a greater risk of morbidity and mortality. Post-transplantation, sensitisation is significantly associated with inferior allograft outcomes, with chronic antibody medicated rejection (AMR), the leading cause of failure. Efforts to prevent sensitisation is key, as a unified approach to AMR management is lacking and desensitisation is not without risk. Blood transfusions, pregnancy and previous solid organ transplantation all increase the risk of sensitisation. Transfusions remain an important modifiable factor. Patients transplanted at Imperial College Renal and Transplant Centre were included. Healthy blood donors, who had historically donated, were recruited via NHS Blood and Transplant. The hypothesis, transfusions are a primary sensitising event associated with inferior allograft outcomes, is addressed in the following studies: 1. What are the factors and significance of de novo non-donor specific antibodies (NDSA)? 2. Are post-transplant blood transfusions (PTBT) associated with inferior allograft outcomes? 3. Does the blood donor HLA type increase the risk of de novo donor specific antibodies (DSA) in transplant recipients that have received a transfusion? 4. Do components carry the same sensitisation risk? 5. What is the understanding of transfusions within UK transplant centres and does this reflect practice? Outcome Summary: 1. De novo NDSA are seen in males and parous females with PTBT and associated with inferior allograft outcomes. 2. PTBTs are common and independently associated with allograft loss and de novo DSA. 3. Transplant recipients produce a primary alloimmune response against the blood donor. Multiple transfusions and HLA blood donor-recipient mismatch increase alloantibody formation. 4. Platelet-only transfusions are rare and not independently associated with inferior outcomes. 5. UK adult transplant units underestimate the number of transplant patients they transfuse. Post-transplant anaemia management lacks a unified approach.
Physical Origin of Elementary Particle Masses
Creators: name: Hansson, Johan
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Physics (physics.gen-ph)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In contemporary particle physics, the masses of fundamental particles are incalculable constants, being supplied by experimental values. Inspired by observation of the empirical particle mass spectrum, and their corresponding physical interaction couplings, we propose that the masses of elementary particles arise solely due to the self-interaction of the fields associated with the charges of a particle. A first application of this idea is seen to yield correct order of magnitude predictions for neutrinos, charged leptons and quarks. We then discuss more ambitious models, where also different generations may arise from \textit{e.g.} self-organizing bifurcations due to the underlying non-linear dynamics, with the coupling strength acting as "non-linearity" parameter. If the model is extended to include gauge bosons, the photon is automatically the only fundamental particle to remain massless as it has no charges. It results that gluons have an effective range $\sim 1$fm, physically explaining why QCD has finite reach.
description: 18 pages
Deep laser cooling and coherent control of molecules
Creators: name: Caldwell, Luke
Publisher: name: Imperial College London
Year: 2020

description: Ultracold molecules can be used for a diverse set of exciting applications including controlled quantum chemistry, probes of physics beyond the standard model, simulation of many-body quantum systems and quantum information processing. However their rich internal structure makes the required control of their motional and internal states difficult. In the last decade, the field has made rapid progress on developing techniques for producing, cooling and trapping molecules and, whilst challenges remain, many of these applications are now being realised. This thesis presents my work on laser cooling and coherent control of calcium monofluoride (CaF) molecules. We load molecules into a three-dimensional magneto-optical trap (MOT), the first such trap for CaF and the second for any molecule. The MOT contains around 2×10⁴ molecules with an initial temperature of 12 mK. Lowering the laser intensity brings the temperature of the MOT down to 960 μK. To further cool the molecules we load them into a blue-detuned optical molasses, cooling them to 5.4(7) μK. This temperature is ~40 times below the Doppler limit and corresponds to a typical molecule moving at only a few times the single-photon recoil velocity. We optically pump the molecules into a single Zeeman sub-level and coherently transfer them between rotational states using microwave radiation. We load the molecules into a magnetic trap where they remain confined for about 5 s, the lifetime being limited by vibrational excitation due to room-temperature blackbody radiation. We show how to prepare the trapped molecules in a coherent superposition of two rotational states, and how to maintain this coherence for long periods, up to 6.4(8) ms. Detailed simulations of the remaining decoherence mechanisms suggest that it is possible to extend this to more than a second by compressing the sample to a smaller size, and using a magnetic trap geometry where the direction of the field is nearly uniform across the trapping volume. Finally we explore theoretically how Raman sideband cooling can be applied to molecules in optical tweezer traps, potentially providing a route to full quantum control.
Upper Bound on Singlet Fraction of Two Qubit Mixed Entangled States
Creators: name: Adhikari, Satyabrata
name: Kumar, Atul
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Information Theory (cs.IT)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: We demonstrate the possibility of achieving the maximum possible singlet fraction using a entangled mixed two-qubit state as a resource. For this, we establish a tight upper bound on singlet fraction and show that the maximal singlet fraction obtained in \cite{Verstraete} does not attain the obtained upper bound on the singlet fraction. Interestingly, we found that the required upper bound can in fact be achieved using local filtering operations.
description: 4 pages, 1 figure
ASReview Software Documentation
Creators: name: De Bruin, Jonathan
name: Ferdinands, Gerbrich
name: Harkema, Albert
name: De Boer, Jan
name: Van den Brand, Sofie
name: Ma, Yongchao
name: Van de Schoot, Rens
Publisher: name: Zenodo
Year: 2021
Subjects: systematic review
asreview
machine learning
documentation
active learning

description: This document contains detailed information on the ASReview LAB software. The latest version of the documentation can also be found on the web page https://asreview.readthedocs.io/en/latest/index.html. For more information, see https://github.com/asreview/asreview or https://asreview.ai.
Metabolites in peanut root under nitrogen deficiency and soil compaction stress
Creators: name: 杨丽玉(Liyu Yang)
Publisher: name: CNGB
Year: 2022
Subjects: Metabolome
Multiisolate

description: The root metabolites of peanut growing under T1N0 (nitrogen deficiency, non-soil compaction), T1N1 (control), T2N0 (nitrogen deficiency and soil compaction stress) and T2N1(only soil compaction stress) conditions.
The development of optical projection tomography instrumentation and its application to in vivo three dimensional imaging of zebrafish
Creators: name: Davis, Samuel Pascal Xia
Publisher: name: Imperial College London
Year: 2019

description: OPT is a three dimensional (3D) imaging technique that can produce 3D reconstructions of transparent samples, requiring only a widefield imaging system and sample rotation. OPT can be readily applied to chemically cleared samples, or to live transparent organisms such as nematodes or zebrafish. For preclinical imaging, there is a trade-off between optical accessibility and biological relevance to humans. Adult Danio rerio (zebrafish) represent a promising compromise, with greater homology to humans than smaller animals, and superior optical accessibility than mice. However, their size and physiology present a number of imaging challenges including non-negligible absorption and optical scattering, and limited time for image data acquisition if the fish are to be recovered for longitudinal studies. A key goal of this PhD thesis research was to develop OPT to address these challenges and improve in vivo imaging capabilities for this model organism. This thesis builds on previous work at Imperial where angularly multiplexed OPT using compressed sensing was developed and applied to in vivo imaging of a cancer-burdened adult zebrafish, with a sufficiently short OPT data acquisition time to allow recovery of the fish after anaesthesia. The previous cross-sectional study of this work was extended to a longitudinal study of cancer progression that I undertook. The volume and quality of data acquired in the longitudinal study presented a number of data processing challenges, which I addressed with improved automation of the data processing pipeline and with the demonstration that convolutional neural networks (CNN) could replace the iterative compressed sensing algorithm previously used to suppress artifacts when reconstructing undersampled OPT data sets. To address the issue of high attenuation through the centre of an adult zebrafish, I developed conformal-high-dynamic-range (C-HDR) OPT and demonstrated that it could provide sufficient dynamic range for brightfield imaging of such optically thick samples, noting that transmitted light images can provide anatomical context for fluorescence image data. To reduce the impact of optical scattering in OPT, I developed a parallelised quasi-confocal version of OPT called slice-illuminated OPT (slice-OPT) to reject scattered photons and demonstrated this with live zebrafish. To enable 3D imaging with short wave infrared (SWIR) light, without the requirement of an expensive Ge or InGaAs camera, I implemented a single pixel camera and demonstrated single-pixel OPT (SP-OPT) for the first time.
title: Phytophthora σε Quercus ilex L. (αριά)
Creators: name: Cordobado Sánchez, Tamara
Publisher: name: Julius Kühn-Institut , Federal Research Centre for Cultivated Plants
Year: 2013

description: JKI Data Sheets Plant Pests and Diagnosis; 2013/70
description: Το είδος Quercus ilex L. (αριά) είναι κυρίαρχο είδος της λεκάνης της Μεσογείου και χρησιμοποιείται σαν βιοδείκτης των μεσογειακού τύπου οικοσυστημάτων (Plieninger et al., 2004. Για το χάρτη εξάπλωσης του είδους Q. ilex βλέπε στην ιστοσελίδα http://www.discoverlife.org). Το Q. ilex είναι αειθαλές δένδρο, αναπτύσσεται σε τέσσερις διαφορετικούς κλιματικούς τύπους (ημίξηρο, ύφυγρο, υγρό και υπέρυγρο) και σε διαφορετικούς τύπους εδαφών. Το ύψος του μπορεί να φθάσει τα 25 μέτρα και διαθέτει δερματώδη, χνουδωτά φύλλα με σχήμα που ποικίλει από στρογγυλό έως μακρόστενο, ενώ μπορεί να φέρουν ή όχι αγκάθια. Αποτελείται από δύο διαφορετικά υποείδη: το Q. ilex subsp. ilex και το Q. ilex subsp. ballota (συν. Q. rotundifolia). Στην Ιβηρική Χερσόνησο, η σημασία του είναι μεγάλη λόγω της παρουσίας του στα περισσότερα γεωργοδασοκομικά συστήματα. Αυτά τα οικοσυστήματα παίζουν πολύ σημαντικό ρόλο από οικολογικής, οικονομικής και κοινωνικής σκοπιάς. Χρησιμεύουν στην εκτροφή ζώων, στην παραγωγή βελανιδιών για ζωοτροφή, στην παραγωγή καύσιμης ύλης καθώς και για την καλλιέργεια δημητριακών.
Java application for the superposition T-matrix code to study the optical properties of cosmic dust aggregates
Creators: name: Halder, P.
name: Chakraborty, A.
name: Roy, P. Deb
name: Das, H. S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: In this paper, we report the development of a java application for the Superposition T-matrix code, JaSTA (Java Superposition T-matrix App), to study the light scattering properties of aggregate structures. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precession superposition codes for multi-sphere clusters in random orientation developed by Mackowski and Mischenko (1996). It consists of a graphical user interface (GUI) in the front hand and a database of related data in the back hand. Both the interactive GUI and database package directly enable a user to model by self-monitoring respective input parameters (namely, wavelength, complex refractive indices, grain size, etc.) to study the related optical properties of cosmic dust (namely, extinction, polarization, etc.) instantly, i.e., with zero computational time. This increases the efficiency of the user. The database of JaSTA is now created for a few sets of input parameters with a plan to create a large database in future. This application also has an option where users can compile and run the scattering code directly for aggregates in GUI environment. The JaSTA aims to provide convenient and quicker data analysis of the optical properties which can be used in different fields like planetary science, atmospheric science, nano science, etc. The current version of this software is developed for the Linux and Windows platform to study the light scattering properties of small aggregates which will be extended for larger aggregates using parallel codes in future.
description: 12 pages, 18 figures
Lacon insularis Fleutiaux 1926
Creators: name: Kotru, Akash
name: Chandran, Nithya
name: Dubey, Anil Kumar
name: Prosvirov, Alexander S.
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Elateridae
Lacon
Lacon insularis

description: Lacon insularis (Candèze, 1889)
Adelocera insularis Candèze, 1889: 70.
Lacon insularis (Candèze) Fleutiaux 1926: 93.
Type depository. Lectotype (RBINS).
Type locality. Andaman and Nicobar Islands (Andaman Islands).
Distribution. India: Andaman Islands (Chakraborty, Chakrabarti, 2000).
Literature. Candèze (1889: 70): original description; Fleutiaux (1926: 93): combination; Chakraborty and Chakrabarti (2000: 76): catalogue; Chandra et al. (2018: 275): faunistics.
description: Published as part of Kotru, Akash, Chandran, Nithya, Dubey, Anil Kumar & Prosvirov, Alexander S., 2025, A catalogue of Indian Agrypninae Candèze, 1857 (Coleoptera: Elateridae), pp. 1-66 in Zootaxa 5614 (1) on page 31, DOI: 10.11646/zootaxa.5614.1.1, http://zenodo.org/record/15217075
RANS Untersuchungen zur Strömungskontrolle in turbulenter Grenzschicht von Flügelprofilen
Creators: name: Fahland, Georg
name: Stroh, Alexander
name: Gatti, Davide
name: Frohnapfel, Bettina
Publisher: name: Karlsruhe
Year: 2020

description: Die vorgestellte Arbeit befasst sich mit homogenem Ausblasen und Einsaugen in turbulenter Grenzschicht. Im Zentrum der Arbeit steht die Frage, welche übergeordneten Effekte sich neben den lokalen für den Anwendungsfall von Flügelprofilen ergeben. Die mittels RANS durchgeführte Parameterstudie umfasst dabei Variationen von Anstellwinkel, Reynoldszahl, Kontrollintensität, Kontrollbereich, sowie Dicke und Wölbung der Profile anhand einer Reihe von NACA-Profilen.
Proportionate growth in patterns formed in the rotor-router model
Creators: name: Dandekar, Rahul
name: Dhar, Deepak
Publisher: name: arXiv
Year: 2013
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study the growing patterns in the rotor-router model formed by adding $N$ walkers at the center of a $L \times L$ two-dimensional square lattice, starting with a periodic background of arrows, and relaxing to a stable configuration. The pattern is made of large number of triangular regions, where in each region all arrows point in the same direction. The square circumscribing the region, where all the arrows have been rotated atleast one full circle, may be considered as made up of smaller squares of different sizes, all of which grow linearly with $N$, for $ 1 \ll N < 2 L$. We use the Brooks-Smith-Stone-Tutte theorem relating tilings of squares by smaller squares to resistor networks, to determine the exact relative sizes of the different elements of the asymptotic pattern. We also determine the scaling limit of the function describing the variation of number of visits to a site with its position in the pattern. We also present evidence that deviations of the sizes of different small squares from the linear growth for finite $N$ are bounded and quasiperiodic functions of $N$.
description: 16 pages, 17 figures
Caenorhabditis elegans as an animal host to study oomycete infection: Discovery of the chitinase-like gene family, resistance genes that are transcriptionally controlled by the antagonistic paralogs pals-22 and pals-25
Creators: name: Osman, Guled Ali
Publisher: name: Imperial College London
Year: 2019

description: The nematode Caenorhabditis elegans is used as a model system to study eukaryotic molecular responses to pathogens. These investigations have contributed to revealing key C. elegans innate immune defense mechanisms, such as the expression of inducible pathogen specific resistance genes. In general, researchers have mainly utilised pathogens not shown to naturally interact with C. elegans, or natural pathogens largely restricted to species of fungi and microsporidia. Towards the goal of expanding this field, we have identified the oomycete Myzocytiopsis humicola, as a new natural pathogen of C. elegans. Due in part to the absence of robust and genetically tractable experimental systems, animal pathogenic oomycetes encompass a diverse range of under-studied organisms. Thus, our discovery has provided us the opportunity to establish a novel and experimentally tractable pathosystem to examine animal oomycete infections. In this thesis, we will present this new experimental system, the pathogen infection strategy and how C. elegans responds transcriptionally to an oomycete infection. Additionally, we will describe the discovery of the chitinase-like (chil) genes, a novel family of uncharacterised C. elegans resistance genes, and discuss their functional role to antagonise M. humicola infection. Intriguingly, we show, chil gene expression is induced in response to pathogen detection, an ability previously not attributed to C. elegans. Finally, we will also describe our efforts to find transcriptional regulators of chil gene expression, and the discovery of the pals-22/pals-25 genes, C. elegans specific antagonistic paralogs involved in a novel mechanism that balances development against immunity. In summary, the work presented here, expands our knowledge of natural pathogens of C. elegans, introduces a new genetically tractable pathosystem to examine how animals respond to an oomycete infection, reveals a novel family of C. elegans pathogen resistance genes and a new C. elegans specific mechanism that regulates development and immunity.
A functional data analysis approach for genetic association studies
Creators: name: Reimherr, Matthew
name: Nicolae, Dan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: We present a new method based on Functional Data Analysis (FDA) for detecting associations between one or more scalar covariates and a longitudinal response, while correcting for other variables. Our methods exploit the temporal structure of longitudinal data in ways that are otherwise difficult with a multivariate approach. Our procedure, from an FDA perspective, is a departure from more established methods in two key aspects. First, the raw longitudinal phenotypes are assembled into functional trajectories prior to analysis. Second, we explore an association test that is not directly based on principal components. We instead focus on quantifying the reduction in $L^2$ variability as a means of detecting associations. Our procedure is motivated by longitudinal genome wide association studies and, in particular, the childhood asthma management program (CAMP) which explores the long term effects of daily asthma treatments. We conduct a simulation study to better understand the advantages (and/or disadvantages) of an FDA approach compared to a traditional multivariate one. We then apply our methodology to data coming from CAMP. We find a potentially new association with a SNP negatively affecting lung function. Furthermore, this SNP seems to have an interaction effect with one of the treatments.
description: Published in at http://dx.doi.org/10.1214/13-AOAS692 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Developing a framework for the optimal deployment of negative emissions technologies
Creators: name: Fajardy, Mathilde Clemence
Publisher: name: Imperial College London
Year: 2019

description: In delivering on the world’s climate goals, removing carbon dioxide from the atmosphere is required in addition to deep mitigation efforts. As no carbon dioxide removal method stands out as an obvious winner, which, how, and how much of these technologies should be deployed to guarantee efficient, sustainable and permanent carbon dioxide removal remains a fundamental research challenge. One potential option, bioenergy with carbon capture and storage (BECCS) is likely to play an important role. BECCS’s ability to sustainably remove carbon dioxide from the atmosphere is, however, controversial. Given the range of potential outcomes, it is crucial to understand how, if at all, this technology can be deployed in a way which minimises its cost and impact on natural resources and ecosystems, while maximising both carbon removal and energy production. In this dissertation, we explore the regional drivers of BECCS sustainability and cost, and provide insights into the where, when, and extent of environmentally sustainable and economically viable BECCS deployment. We conclude that the total quantity of atmospheric carbon dioxide removal and energy production over the lifetime of a BECCS project, and the time required to start removing carbon dioxide from the atmosphere will likely vary from project to project. This has profound implications for the policy frameworks required to incentivise and regulate the widespread deployment of BECCS technology. When optimising regional biomass supply chains, we find that a myopic focus on energy generation and carbon dioxide removal can result in negative consequences for the broader environment, which warrants consideration for all impacts when assessing the performance of a BECCS project. Finally, when exploring least-cost BECCS deployment pathways to meet global carbon dioxide removal targets, an important finding is that inter-regional cooperation and collaboration are central to sustainably and affordably meeting these targets, with important value creation opportunities for key providers of carbon dioxide removal.
Signatures of selection in recently domesticated macadamia
Creators: name: 林继山(Lin Jishan)
Publisher: name: CNGB
Year: 2022
Subjects: Genome sequencing and assembly
Raw sequence reads
Genome sequencing
Assembly
Transcriptome or Gene expression
Multispecies
Agricultural

description: Macadamia is a high value nut crop that is a recently domesticated crop, ideal for testing the effect of artificial selection. The genome of Hawaiian cultivar ‘KAU’ was sequenced and assembled intochromosome level. To further investigate the genetic mechanisms underlying high oil accumulation in macadamia seed, we performed a serial transcriptomes during kernel development. In order to acquired insights into the genetic mechanisms bringing about the exceptional strength of macadamia seed coats, we performed a serial transcriptomes during shell development. To explore the introduction history and genetic diversity within macadamia, we resequenced 112 macadamia accessions.
Tile optimization for area in FPGA based hardware acceleration of peptide identification
Creators: name: Vidanagamachchi, S. M.
name: Dewasurendra, S. D.
name: Ragel, R. G.
name: Niranjan, M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computational Engineering, Finance, and Science (cs.CE)
subject: FOS: Computer and information sciences

description: Advances in life sciences over the last few decades have lead to the generation of a huge amount of biological data. Computing research has become a vital part in driving biological discovery where analysis and categorization of biological data are involved. String matching algorithms can be applied for protein/gene sequence matching and with the phenomenal increase in the size of string databases to be analyzed, software implementations of these algorithms seems to have hit a hard limit and hardware acceleration is increasingly being sought. Several hardware platforms such as Field Programmable Gate Arrays (FPGA), Graphics Processing Units (GPU) and Chip Multi Processors (CMP) are being explored as hardware platforms. In this paper, we give a comprehensive overview of the literature on hardware acceleration of string matching algorithms, we take an FPGA hardware exploration and expedite the design time by a design automation technique. Further, our design automation is also optimized for better hardware utilization through optimizing the number of peptides that can be represented in an FPGA tile. The results indicate significant improvements in design time and hardware utilization which are reported in this paper.
Gut Microbiota of Preterm Infants and Full-term Infants at Early Life
Creators: name: Ju-Sheng Zheng
Publisher: name: CNGB
Year: 2022
Subjects: Raw sequence reads
Multispecies

description: Premature birth is a global clinical problem. Early colonization and development of the neonatal gut microbiome is critically important with a profound impact on the host lifelong health. The aim of this study is to obtain a longitudinal view of the gut microbial establishment of a cohort of 51 preterm (PT) infants compared to 51 full-term (FT) infants from birth to 5 years of age, and to identify key clinical factors that affect the establishment of neonatal microbiome.
Modeling, shape analysis and computation of the equilibrium pore shape near a PEM-PEM intersection
Creators: name: Berg, Peter
name: Kimmerle, Sven-Joachim
name: Novruzi, Arian
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics
subject: 49K20, 49K10, 74Pxx, 65NXX

description: In this paper we study the equilibrium shape of an interface that represents the lateral boundary of a pore channel embedded in an elastomer. The model consists of a system of PDEs, comprising a linear elasticity equation for displacements within the elastomer and a nonlinear Poisson equation for the electric potential within the channel (filled with protons and water). To determine the equilibrium interface, a variational approach is employed. We analyze: i) the existence and uniqueness of the electrical potential, ii) the shape derivatives of state variables and iii) the shape differentiability of the corresponding energy and the corresponding Euler-Lagrange equation. The latter leads to a modified Young-Laplace equation on the interface. This modified equation is compared with the classical Young-Laplace equation by computing several equilibrium shapes, using a fixed point algorithm.
description: 24 pages, 8 figures
Phenomenological modelling of molten salt reactors with coupled point nuclear reactor kinetics and thermal hydraulic feedback models
Creators: name: Morgan, Gareth
Publisher: name: Imperial College London
Year: 2018

description: The Molten Salt Reactor Experiment (MSRE) was a small circulating fuel reactor operated at Oak Ridge National Laboratory (ORNL) between 1965 and 1969. To do date it remains the only molten salt reactor (MSR) that has been operated for extended periods, on diverse nuclear fuels. Reactor physics in MSRs differs from conventional solid-fuelled reactors due to the circulation of hot fuel and delayed neutron precursors (DNPs) in the primary circuit. This alters the steady state and time-dependent behaviours of the system. A coupled point kinetic-thermal hydraulic feedback model of an MSRE-like system was constructed in order to investigate the effect of uncertainties in the values of key physical parameters on the model’s response to step and ramp reactivity insertions. This information was used to determine the parameters that affected the steady state condition and transient behaviours. The model was also used to investigate features identified in the frequency response, in particular a feature corresponding to fuel recirculation. Greater than expected mixing in the primary circuit has been previously proposed as an explanation for the lack of observation of this feature. A velocity-dependent turbulent dispersion term is proposed to increase dispersion of the fuel temperature field in order to suppress the recirculation feature in the frequency response. An additional semi-analytical model was constructed as a part verification of the mixing hypothesis - this model was also used to examine the stability of an MSRE-like design. Finally the validated coupled system model was used to establish the just-safe combination of intrinsic source and ramp rate that does not exceed an estimated maximum permissible vessel temperature. The CALLISTO-SPK stochastic point kinetics code is used to demonstrate that the intrinsic source in an MSRE-like design is sufficient to reduce the probability of a rogue startup transient to an acceptably small value from the point of view of regulatory safety analysis. Such analyses may be used to support the case for extrinsic source deletion in future MSR designs.
Hallmarks of plasma eccDNAs in type II diabetes mellitus patients with short-term intensive insulin therapy
Creators: name: 陈晨
Publisher: name: CNGB
Year: 2022
Subjects: Raw sequence reads
Other
Human plasma extrachromosomal circular DNA

description: Circulating extrachromosomal circular DNA (eccDNA) has evolved as a novel biomarker for cellular homeostasis in the body. Here we investigated circulating eccDNAs in type 2 diabetes mellitus (T2DM) patients with short-term intensive insulin therapy (SIIT), which induces long-term glycemic remission in newly diagnosed T2DM patients.
ASReview Software Documentation
Creators: name: De Bruin, Jonathan
name: Ferdinands, Gerbrich
name: Harkema, Albert
name: De Boer, Jan
name: Van den Brand, Sofie
name: Ma, Yongchao
name: Van de Schoot, Rens
Publisher: name: Zenodo
Year: 2021
Subjects: systematic review
asreview
machine learning
documentation
active learning

description: This document contains detailed information for version 0.17 of the ASReview software. For more information, see https://github.com/asreview/asreview.
Chemical looping water splitting for hydrogen production, decarbonised steel production and energy storage/generation in-situ with CO2 capture
Creators: name: Bahzad, Husain
Publisher: name: Imperial College London
Year: 2020

description: In the research described in this thesis, a novel hydrogen production process via integrated chemical looping water splitting technology (ICLWS) was developed. In addition, a state-of-the-art process for production of decarbonised iron through a four-stage chemical looping water splitting technology (CLWSFe) was proposed. Both processes were simulated using the Aspen Plus simulator. Heat integration analysis was applied to the two processes, utilising pinch-point analysis in order to minimise utility usage and optimise their thermodynamic performance. Furthermore, sensitivity analysis was performed for the ICLWS process to detect the optimum operating conditions. Both processes were thermodynamically and economically assessed to determine their viability by comparing them with benchmark processes, i.e. the steam methane reforming process (SMR) that was developed earlier in this work and other competitive chemical looping processes described in the literature. The thermodynamic results showed that the ICLWS and the CLWSFe processes exhibited improved effective efficiency by 12.3% and 20.8% compared with the SMR process. Regarding the efficiency of hydrogen production, the ICLWS process exhibited 11.7% higher efficiency than the SMR process; however, the efficiency of hydrogen production by the CLWSFe process was 1.6% lower than that of the SMR process. For the economic assessment, CAPEX, OPEX and the hydrogen production cost were evaluated for both processes. Results indicated that the hydrogen production cost through the ICLWS process with MgAl2O4 as support material was 17.5% lower than that through the SMR process, and was 26.3% lower through use of the CLWSFe process than through use of the SMR when iron as a saleable product was considered. In addition, a one-dimensional steady-state model was developed to obtain the conversion and temperature profiles for all the reactors involved in the ICLWS and CLWSFe processes. Consequently, the size of each reactor was determined. Furthermore, a system of integrated pumped heat-energy storage (IPHES) was developed by integrating pumped-energy storage with the ICLWS process. Then, an open-cycle gas turbine was merged with this system to form another novel energy-storage system called OIPHES. The transient behaviour of the temperature of the solid inside the storage tanks and the daily energy generation for a selected days in the year in both systems were investigated. Based on that, both systems were assessed thermodynamically and economically. Also, an economic sensitivity analysis was performed for the OIPHES process and a feasibility equation was derived showing the conditions required to enhance the feasibility of the OIPHES system. As a case study, the influence of the hydrogen fuel feed rate on the system’s daily profits was studied. Therefore, the optimum hydrogen fuel feed rate to maximise the daily profits of the OIPHES system was selected.
NeoPLANET
Creators: name: 唐兆庆(TANG ZHAOQING)
Publisher: name: CNGB
Year: 2022
Subjects: Raw sequence reads
Exome
Multiisolate
Medical

description: 本研究为一项开放式，单臂，单中心，前瞻性II期临床研究，旨在评价局部晚期(cT3~4aN+M0)的近端胃腺癌患者中，进行以PD-1抗体SHR-1210联合放化疗的新辅助治疗继以根治术的疗效与安全性。
Positronium hyperfine splitting at order $m α^7$: light-by-light scattering in the two-photon-exchange channel
Creators: name: Adkins, Gregory S.
name: Fell, Richard N.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We have calculated the contribution to the positronium hyperfine splitting at order $m α^7$ of the light-by-light scattering process in the exchange of two photons between the electron and positron. Our result is $ΔE = -0.235355(8) m α^4 \left ( \fracαπ \right )^3 = -1.034 kHz$. As a check of our approach we confirm earlier evaluations of the analogous correction for a bound system (such as muonium) with unequal masses.
description: 10 pages, 2 figures
title: Phytophthora em Quercus ilex L. (azinheira)
Creators: name: Cordobado Sánchez, Tamara
Publisher: name: Julius Kühn-Institut , Federal Research Centre for Cultivated Plants
Year: 2013

description: JKI Data Sheets Plant Pests and Diagnosis; 2013/32
description: Quercus ilex L. (azinheira) é uma árvore dominante na Bacia do Mediterrâneo sendo usada como bioindicador dos ecossistemas-tipo Mediterrâneo (Plieninger et al., 2004; ver mapa de distribução de Q. ilex http://www.discoverlife.org). Q. ilex é uma árvore de folha não caduca que pode desenvolver-se em quatro bioclimas (semiárido, subhúmido, húmido e perhúmido), encontrandose presente em diferentes tipos de solo. Pode atingir 25 m de altura, apresentando folhas coriáceas e tomentosas cuja forma pode ser elítica ou oblongo-lanceolada com margem inteira ou dentadoespinhosa. Esta espécie compreende duas subespécies: Q. ilex subsp. ilex e Q. ilex subsp. ballota* (syn. Q. rotundifolia). Na Península Ibérica, a sua importância está relacionada com a sua presença no sistema agroflorestal de maior interesse na Europa conhecido como Montado (Dehesa). Os montados de azinho apresentam um papel muito importante do ponto de vista ecológico, económico e social. Neste sistema a azinheira é caracterizada como produtora de bolota para a alimentação do porco de montanheira e fonte de carvão e de lenha. As pastagens e as culturas agrícolas ocupam também um papel de relevo neste tipo de sistema.  *mais comum em Portugal