cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Patient age, diagnosis, hemoglobin level and sex in the optimal management of blood and blood products
Creators: name: Andoh, Cephas
Publisher: name: No Publisher Supplied
Year: 2021

description: Blood is a critically important human tissue, and for over a century, blood transfusions have saved the lives of countless patients. However, blood is often in short supply, and the cost of screening donated blood for immune compatibility and an ever-increasing number of blood-borne pathogens keeps rising. As healthcare systems search for ways to cut costs, it is appropriate to search for safe and effective ways to conserve blood and blood products.Aim: This study will examine the following questions:1. What is the relationship between the diagnosis and the amount of packed red blood cells (PRBC) used for patients with specific conditions? 2. What is the benefit of the transfusion for the patient in terms of the post transfusion hemoglobin and the clinical outcome?3. Is there an association between patient age, diagnosis and the amount PRBC used? 4. What common diagnoses usually result in patients being given transfusions, and what is the clinical benefit of those transfusions? The overall aim of this study is to identify conditions in which blood may be conserved, without affecting patient clinical outcomes.Methodology: All patient data were collected from the Meditech database of the Queen of Valley Medical Center (QVMC), with the permission of the Blood bank supervisor and Medical Laboratory Director.Results: Data was collected on 504 PRBC-transfused patients with various clinical conditions, who had critical pre-transfusion hemoglobin levels. Post-transfusion hemoglobin levels were examined at the time of patient discharge or patient death. A control cohort of twenty patients with the same conditions and critical hemoglobin levels but were not transfused due to religious or other reasons was also analyzed. Patients with acute kidney failure (AKF) and acute post-hemorrhagic anemia (APA) had better outcomes when they were transfused. The importance of any single transfusion to relapsed acute myeloid leukemia patients (AL) was difficult to assess as they are constantly being transfused. Patients with anemia of unknown causes (AU) and hemoglobin levels between 7-8g/dl did not require transfusion for survival.Conclusion: Low hemoglobin levels alone should not automatically trigger transfusions. Disease type, patient age, and other factors should be taken into consideration.
Current reversal in interacting colloids under time-periodic drive
Creators: name: Rana, Shubhashis
name: Goswami, Sanchari
name: Chatterjee, Sakuntala
name: Pradhan, Punyabrata
Publisher: name: arXiv
Year: 2018
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Using molecular dynamics simulations, we study particle-transport in a system of interacting colloidal particles on a ring, where the system is driven by a time-dependent external potential, moving along the ring. We consider two driving protocols: (i) the external potential barrier moves with a uniform velocity $v$ along the ring, and (ii) it moves in discrete jumps with jump-length $l$ and waiting time $τ$ with an effective velocity $v=l/τ$. The time-averaged (dc) particle current, which always remains positive in case (i), interestingly reverses its direction in case (ii) upon tuning the particle-number density $ρ_0$ and the effective barrier velocity $v$. We also find a scaling form for the current in terms of number density, barrier velocity, barrier height and temperature of the system.
description: 10 pages,13 figures
Gravitational waves from supermassive black hole binaries in ultra-luminous infrared galaxies
Creators: name: Inayoshi, Kohei
name: Ichikawa, Kohei
name: Haiman, Zoltan
Publisher: name: arXiv
Year: 2018
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Gravitational waves (GWs) in the nano-hertz band are great tools for understanding the cosmological evolution of supermassive black holes (SMBHs) in galactic nuclei. We consider SMBH binaries in high-$z$ ultra-luminous infrared galaxies (ULIRGs) as sources of a stochastic GW background (GWB). ULIRGs are likely associated with gas-rich galaxy mergers containing SMBHs that possibly occur at most once in the life of galaxies, unlike multiple dry mergers at low redshift. Adopting a well-established sample of ULIRGs, we study the properties of the GWB due to coalescing binary SMBHs in these galaxies. Since the ULIRG population peaks at $z>1.5$, the amplitude of the GWB is not affected even if BH mergers are delayed by as long as $\sim $ 10 Gyrs. Despite the rarity of the high-$z$ ULIRGs, we find a tension with the upper limits from Pulsar Timing Array (PTA) experiments. This result suggests that if a fraction $f_{\rm m,gal}$ of ULIRGs are associated with SMBH binaries, then no more than $20 f_{\rm m,gal}(λ_{\rm Edd}/0.3)^{5/3}(t_{\rm life}/30~{\rm Myr})~\%$ of the binary SMBHs in ULIRGs can merge within a Hubble time, for plausible values of the Eddington ratio of ULIRGs ($λ_{\rm Edd}$) and their lifetime ($t_{\rm life}$).
description: 7 pages, 4 figures, 1 table, Published in ApJL
Domain walls in a non-linear $\mathbb{S}^2$-sigma model with homogeneous quartic polynomial potential
Creators: name: Alonso-Izquierdo, A.
name: Sebastian, A. J. Balseyro
name: Leon, M. A. Gonzalez
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper the domain wall solutions of a Ginzburg-Landau non-linear $\mathbb{S}^2$-sigma hybrid model are exactly calculated. There exist two types of basic domain walls and two families of composite domain walls. The domain wall solutions have been identified by using a Bogomolny arrangement in a system of sphero-conical coordinates on the sphere $\mathbb{S}^2$. The stability of all the domain walls is also investigated.
description: 23 pages, 5 figures
Tissue specificity of MMP gene expression and secretion in tuberculosis
Creators: name: Dos Santos Brilha, Sara Sofia
Publisher: name: Imperial College London
Year: 2015

description: In tuberculosis (TB), matrix metalloproteinases (MMPs) have a major role in tissue destruction and cavitation. The composition of each extracellular matrix (ECM) gives specificity to tissues and is important in control of local immune responses by acting as a “molecular postcode”. Hence, it is likely to have important implications in TB. During central nervous system (CNS) infection, the effect of TB on blood-brain barrier (BBB) function is unknown. I hypothesised that the ECM environment may determine the MMP response during innate immune activation in pulmonary and CNS TB. I aimed to investigate the effect of adhesion to the lung’s ECM in regulation of MMP expression and activity. I also aimed to develop a BBB cellular model and investigate the role of Mycobacterium tuberculosis (Mtb)-driven MMP secretion on BBB function. In a model of pulmonary TB, human bronchial epithelial cells (NHBEs) and monocytes were exposed to ECM components and stimulated with conditioned medium from Mtb-infected monocytes (CoMtb) or infected with Mtb. Type I collagen (Coll-I) matrix was shown to decrease MMP-1 mRNA accumulation by 48% and collagenolytic activity compared to NHBEs in the absence of matrix. MMP-1 co-localised with integrin α2β1 resulting in enhanced cell migration in wound healing assays. In contrast, soluble Coll-I led to integrin α2β1 occupancy without clustering and caused a 7-fold increase in collagenolytic activity but decreased migration. In Mtb-infected monocytes, adhesion to ECM components increased MMP-1 secretion by over 60%. Fibronectin and Coll-I also increased MMP-10 by 55% and 90% respectively. Surface expression of integrin αVβ3 was upregulated by Mtb-infection and adhesion to Coll-I. Activation of integrin αVβ3 mimicked the effect of Coll-I MMP secretion, while its inhibition impaired monocyte migration. CoMtb-stimulation of the BBB model decreased trans-endothelial electrical resistance from 154±1.2ohm.cm2 to 111.6±4.7ohm.cm2, while Papp increased 3-fold. Coll-IV and tight junction proteins (TJPs) degradation was also detected. MMP concentrations increased 125-fold for MMP-1 (0.35±2 to 43.8±5.1ng/mL) and 619-fold for MMP-9 (0.072±0.014 to 44.6±8.9ng/ml). Treatment with the MMP inhibitor Ro32-3555 prevented BBB disruption. Neutrophil and monocyte transmigration increased 60% and 80% respectively and returned to control levels with MMP blockade. MMP-9 was shown to be responsible for BBB disruption and its inhibition by antibodies prevented BBB disruption. The Hedgehog pathway was downregulated during infection, resulting in decrease TJPs gene expression, which contributes to BBB dysfunction. In summary, the ECM regulates both epithelial and monocyte expression of MMP-1 via integrins signalling. In the CNS, MMP-9 drives tissue destruction and BBB disruption which may be a potential reversible event in CNS TB immunopathology
The HST Quasar Absorption Line Key Project VII. Absorption Systems at $z_{\rm abs} \leq 1.3$
Creators: name: Bahcall, John N.
name: Bergeron, Jacqueline
name: Boksenberg, Alec
name: hartig, George F.
name: Jannuzi, Buell T.
name: Kirhakos, Sofia
name: Sargent, W. L. W.
name: Savage, Blair D.
name: Schneider, Donald P.
name: Turnshek, David A.
name: Weymann, Ray J.
name: Wolfe, Arthur M.
Publisher: name: arXiv
Year: 1995
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present evidence that clumps of \lya lines are physically associated with about half of the extensive metal-line systems (absorption systems with four or more observed metal-line species) found in this paper, demonstrate that all four \lylimit systems discussed here correspond to extensive metal-line absorption systems, and present an extraordinary pair of extensive metal-line absorption systems within 2000~km/s of each other at $z~=~0.95$ that are probably an early manifestation of large scale structure. These results are obtained using ultraviolet spectra, taken with the higher-resolution gratings of the Faint Object Spectrograph of the Hubble Space Telescope, for four quasars with emission-line redshifts between 1.0 and 1.3. We also determine the evolution of \lya absorption lines at redshifts less than 1.3 by combining the results for 13 smaller redshift quasars discussed in Paper I of this series with the 4 moderate redshift quasars analyzed in the present paper. For $z_{\rm abs}~\leq~1.3$, the density of \lya lines with equivalent widths greater than 0.24~Å is adequately fit by $\left(dN/dz\right) =\left(dN/dz\right)_0 \cdot(1 + z)^γ$ with $(dN/dz)_0 = 24.3 \pm 6.6$ \lya lines per unit redshift, and $γ= 0.58 \pm 0.50$ (1-$σ$ uncertainties). This rate of evolution at low redshifts is less than the evolutionary rate inferred from several different ground-based data samples that pertain to high redshifts. The observed gaseous structures at redshifts of $0.5$ to $1.0$ with velocity dispersions of $6 \times 10^2$ \kms to $1.4 \times 10^3$ \kms (or velocity spans of $1.2 \times 10^3$ \kms to $3 \times 10^3$ \kms) constitute a constraint on cosmological models of structure formation.
description: uuencoded compressed tar file. Figures and tables available by ftp to ftp://eku.ias.edu/pub/best/ (192.16.204.30) ; figures are kpfig1a.ps--kpfig1k.ps, kpfig2.ps, kpfig3.ps, kpfig4.ps; tables are kplandtabs.ps, kpporttabs.ps, submitted to The Astrophysical Journal
Emerging targets for analgesics to control inflammatory pain
Creators: name: Torres Perez, Jose Vicente
Publisher: name: Imperial College London
Year: 2017

description: Burn injury is followed by one of the most severe inflammatory conditions and associated with one of the most excruciating persistent pain. Current therapeutics for burn injury-associated pain are limited and produce undesired side effects. The development and particularly the maintenance of persistent pain depend on plastic changes in neurons involved in the processing of noxious stimulation-evoked (nociceptive) information including nociceptive primary sensory neurons and spinal dorsal horn neurons. Those plastic changes include changes in gene expression that are regulated largely by epigenetic mechanisms including post-translational modification of histones. Here, I show inflammatory conditions including that following burn injury significantly and specifically up-regulates, both in a group of primary sensory neurons and spinal dorsal horn neurons, the expression of phosphorylated serine 10 in histone H3 (pS10H3), a transcriptionally permissive histone mark. This up-regulation is associated, in superficial spinal cord neurons, with up-regulation in the expression of cFos a known marker for nociceptive processing. In superficial spinal cord neurons, these up-regulations depend on the activation of the N-methyl-D aspartate receptor, extracellular signal-regulated kinase 1 and 2 and mitogen and stress-activated kinase 1 and 2 (MSK1/2). Importantly, deletion of MSK1/2 blocks the development of inflammatory heat hyperalgesia. Further, blocking the voltage-gated sodium channel type 1.7 significantly reduces pS10H3 up-regulation both in primary sensory neurons and superficial spinal dorsal horn neurons. I conclude that pS10H3 represents a novel marker for nociceptive processing both in primary sensory and superficial spinal dorsal horn neurons, and transcriptional changes downstream of S10H3 phosphorylation are pivotal in the development of inflammatory heat hyperalgesia. I further conclude that Nav1.7 is a promising target for the control of heat hyperalgesia in burn injury.
Machine perfusion for assessing and optimizing kidney and pancreas allografts
Creators: name: Hamaoui, Karim
Publisher: name: Imperial College London
Year: 2014

description: Introduction: The predominate issue in transplantation today is the inadequate supply of suitable organs for an increasing number of patients on the transplant waiting lists. In efforts to address this demand there has been an increasing use of expanded-criteria and donation-after-cardiac death donor kidneys and pancreases, however these organs are at higher risk for reperfusion injury. Advances in organ preservation thus need to focus on techniques to assess and optimise organ viability prior to transplantation. Methods: This research focuses on organ viability assessment during preservation using rapid sampling micro-dialysis (rsMD); preconditioning organs with novel endothelial localising anticoagulants to prevent micro-vascular thrombotic complications; development of both novel hypothermic machine perfusion (HMP) solutions to minimise reperfusion injury, and HMP strategies that offer superior preservation of organ integrity compared to static cold storage (SCS). Using HMP and normothermic-reperfusion models of porcine and human kidney and pancreatic grafts, this project has investigated strategies addressing these themes. Results: rsMD can successfully provide detailed real-time information on tissue and organ viability during both SCS and HMP. Pre-conditioning grafts with novel localising anticoagulant proteins has been successful in ameliorating disturbances in macro and micro-vascular perfusion and graft microcvascular thrombosis, processes which play key roles in reperfusion injury and organ dysfunction. Separately the application of a novel adenosine/lidocaine based preservation solution in renal HMP preservation can potentially ameliorate reperfusion injury seen using conventional solutions. Post-ischaemic HMP reconditioning has been investigated in the context of recovering organs with an extreme period of SCS which may be a potential option to expand donor organ pools. Finally models of pancreatic HMP have been successfully established, opening the potential for organ viability assessment and optimization. Conclusion: This research has been successful in its overall objective to develop novel translational strategies that have high potential for clinical implementation. In doing so the goal would be to enable an expansion of the pool of acceptable donor organs by improving the methods used to determine and optimise their viability, specifically more effective preservation techniques and by addressing specific post-operative complications through graft preconditioning.
Simia cephus Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Primates
Atelidae
Simia
Simia cephus

description: Simia cephus [spec. nov.]
S. caudata, buccis barbatis, vertice flavescente, pedibus nigris, cauda apice ferruginea.
Cercopithecus bar batus alius guineensis. Marcgr. bras. 228. Raj. quadr. 156.
Habitat in America.
Corpus subfuscum, subtus subcaerulescens; Os caerulescens: barba flavescens.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 27, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Quantum fluctuations and Gross-Pitaevskii theory
Creators: name: Stringari, Sandro
Publisher: name: arXiv
Year: 2018
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: Using the linearized version of the time dependent Gross-Pitaevskii equation we calculate the dynamic response of a Bose-Einstein condensed gas to periodic density and particle perturbations. The zero temperature limit of the fluctuation-dissipation theorem is used to evaluate the corresponding quantum fluctuations induced by the elementary excitations in the ground state. In uniform conditions the predictions of Bogoliubov theory, including the infrared divergency of the particle distribution function and the quantum depletion of the condensate, are exactly reproduced by Gross-Pitaevskii theory. Results are also given for the crossed particle-density response function and the extension of the formalism to non uniform systems is discussed. The generalization of the Gross-Pitaevskii equation to include beyond mean field effects is finally considered and an explicit result for the chemical potential is found, in agreement with the prediction of Lee-Huang-Yang theory.
description: 6 pages. To appear in the Journal of the Experimental and Theoretical Physics (JETP) dedicated to the 85th anniversary of L.P. Pitaevskiy
Discovery of the compact X-ray source inside the Cygnus Loop
Creators: name: Miyata, E.
name: Tsunemi, H.
name: Torii, K.
name: Hashimotodani, K.
name: Tsuru, T. G.
name: Koyama, K.
name: Ayani, K.
name: Ohta, K.
name: Yoshida, M.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We detected an X-ray compact source inside the Cygnus Loop during the observation project of the whole Cygnus Loop with the ASCA GIS. The source intensity is 0.11 c s$^{-1}$ for GIS and 0.15 c s$^{-1}$ for SIS, which is the strongest in the ASCA band. The X-ray spectra are well fitted by a power law spectrum of a photon index of \error{-2.1}{0.1} with neutral H column of (\error{3.1}{0.6})${\rm \times 10^{21} cm^{-2}}$. Taking into account the interstellar absorption feature, this source is X-ray bright mainly above 1 keV suggesting either an AGN or a rotating neutron star. So far, we did not detect intensity variation nor coherent pulsation mainly due to the limited observation time. There are several optical bright stellar objects within the error region of the X-ray image. We carried out the optical spectroscopy for the brightest source (V=+12.6) and found it to be a G star. The follow up deep observation both in optical and in X-ray wavelengths are strongly required.
description: Accepted for Publications of the Astronomical Society of Japan 17 pages, 3 figure
Diagnosis of bone loss at the distal femur and proximal tibia in persons with spinal cord injury
Creators: name: Cirnigliaro, Christopher
Publisher: name: No Publisher Supplied
Year: 2021

description: Objectives: Persons with traumatic spinal cord injury (SCI) have severe bone loss below the level of lesion with the distal femur (DF) and proximal tibia (PT) being the skeletal regions appreciated to have the highest risk of fracture. While a reference areal bone mineral density (aBMD) database is available at the total hip (TH) using the combined National Health and Nutrition Examination Survey (NHANES) III study and General Electric (GE) combined (GE/NHANES) to calculate T-score (T-scoreGE/NHANES), no such reference database exists for aBMD of the DF and PT. The primary objectives of this study were (1) to create a reference dataset of young-healthy able-bodied (YHAB) persons to calculate T-score (T-scoreYHAB) values at the DF and PT, (2) to explore the impact of time since injury (TSI) on relative bone loss in the DF and PT regions using the two computation models to determine T-score values, 3 and (3) to determine agreement between T-score values for a cohort of persons with SCI using the T-scoreYHAB and T-scoreGE/NHANES reference datasets. Participants: A normative reference aBMD database at the DF and PT was collected in 32 male and 32 female Caucasian YHAB participants (n=64) and then applied to calculate T-score values at the DF and PT in 105 SCI participants from a historical cohort. The SCI participants were then grouped based on TSI epochs (E-I: TSI < 1y, E-II: TSI 1-5y, E-III: TSI 6-10y, E-IV: TSI 11-20y, E-V: TSI > 20y). Main Outcome Measures: The knee and hip aBMD values were obtained by dual energy X-ray absorptiometry (GE Lunar iDXA). Results: There were no significant differences in mean aBMD values across the four YHAB age subgroups at the TH, DF, and PT, and mean aBMD values were higher in men compared to the women at all skeletal regions of interest. Using the mean YHAB aBMD values to calculate T-score values at each TSI epoch for persons with SCI, T-score values decreased as a function of TSI and continued to decline for 11-20 years (E-IV epoch). Moderate kappa agreement was noted between the YHAB and the World Health Organization (WHO) reference datasets for the T-score cutoff criteria accepted to diagnose osteoporosis (e.g., SD
Evaluation of drug resistance markers in breast cancers: roles in stemness and epithelial-to-mesenchymal transitions
Creators: name: Asaduzzaman, Muhammad
Publisher: name: Imperial College London
Year: 2016

description: There is an urgent need to identify markers of diagnostic and prognostic significance that can help in the development of novel cancer therapeutics. The principal aim of the present study was to evaluate nicastrin and EP300 as potential markers associated with breast cancer drug resistance. Nicastrin is a component of γ-secretase, an intermembrane complex of four proteins with roles in proliferation, cell adhesion and tamoxifen resistance. EP300 is a histone acetyltransferase and a transcriptional activator of E-cadherin which has been shown to regulate epidermal-to-mesenchymal transition and doxorubicin resistance via escape from drug-induced senescence. Using breast cancer cellular models in which nicastrin had been modulated or γ-secretase activity impaired with an inhibitor, we have found an insignificant role of nicastrin in altering chemosensitivity to doxorubicin and paclitaxel. Similarly, we have used stably transfected breast cancer cell models in which EP300 was either over-expressed or down-regulated and a knocked-out EP300 colon carcinoma cell model. We have confirmed EP300 role in regulating E-cadherin levels in vitro, to alter paclitaxel sensitivity and the generation of drug resistance. Furthermore, EP300 silencing was associated with increased in vitro tumourigenicity and cancer stem cell-like properties, while its ectopic expression in mesenchymal breast cancer cells rescued the epithelial, differentiated, paclitaxel sensitive phenotype. Gene expression profiling identified down-stream EP300 targets associated with drug resistance, epithelial-to-mesenchymal transition and cancer stem cells including ABCG2, BCL2, TNFRSF11B and TGFB2. Finally, immunohistochemical analysis of patient samples revealed a strong correlation between co-expression of EP300 and E-cadherin, particularly in metaplastic breast cancer, a rare aggressive form of invasive breast cancer with histological evidence of epithelial-to-mesenchymal transition which has a poor clinical outcome. Taken together, this study highlights the role of EP300 in mediating paclitaxel resistance by apoptosis evasion, probably via up-regulation of Bcl-2, and its link to regulation of epithelial-to-mesenchymal transition and stemness.
The Physical State of the Intergalactic Medium or Can We Measure Y?
Creators: name: Bartlett, J. G.
name: Barbosa, D.
name: Blanchard, A.
Publisher: name: arXiv
Year: 1995
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present an argument for a {\it lower limit} to the Compton-$y$ parameter describing spectral distortions of the cosmic microwave background (CMB). The absence of a detectable Gunn-Peterson signal in the spectra of high redshift quasars demands a high ionization state of the intergalactic medium (IGM). Given an ionizing flux at the lower end of the range indicated by the proximity effect, an IGM representing a significant fraction of the nucleosynthesis-predicted baryon density must be heated by sources other than the photon flux to a temperature $\go {\rm few} \times 10^5\, K$. Such a gas at the redshift of the highest observed quasars, $z\sim 5$, will produce a $y\go 10^{-6}$. This lower limit on $y$ rises if the Universe is open, if there is a cosmological constant, or if one adopts an IGM with a density larger than the prediction of standard Big Bang nucleosynthesis.
description: Proceedings of `Unveiling the Cosmic Infrared Background', April 23-25, 1995, Maryland. Self-unpacking uuencoded, compressed tar file with two figures included
MOESM7 of Stacking of a low-lignin trait with an increased guaiacyl and 5-hydroxyguaiacyl unit trait leads to additive and synergistic effects on saccharification efficiency in Arabidopsis thaliana
Creators: name: Vries, Lisanne De
name: Vanholme, Ruben
name: Acker, Rebecca Van
name: Meester, Barbara De
name: Sundin, Lisa
name: Boerjan, Wout
Publisher: name: figshare
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: Ecology
subject: Developmental Biology
subject: Science Policy
subject: Plant Biology

description: Additional file 7. Inflorescence stem pieces after saccharification. Inflorescence stem pieces of A) tra2 comt-1, B) c4h-3 comt-4, and C) 4cl1-1 comt-4 and their respective control lines after the plateau of saccharification was reached, without, with acid and with alkaline pretreatment. Bar 1Â mm.
Spectral signatures of fractionalization in the frustrated Heisenberg model on the square lattice
Creators: name: Ferrari, Francesco
name: Becca, Federico
Publisher: name: arXiv
Year: 2018
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We employ a variational Monte Carlo approach to efficiently obtain the dynamical structure factor for the spin-1/2 $J_1-J_2$ Heisenberg model on the square lattice. Upon increasing the frustrating ratio $J_2/J_1$, the ground state undergoes a continuous transition from a Néel antiferromagnet to a $\mathbb{Z}_{2}$ gapless spin liquid. We identify the characteristic spectral features in both phases and highlight the existence of a broad continuum of excitations in the proximity of the spin-liquid phase. The magnon branch, which dominates the spectrum of the unfrustrated Heisenberg model, gradually loses its spectral weight, thus releasing nearly-deconfined spinons, whose signatures are visible even in the magnetically ordered state. Our results show how free spinons emerge across a quantum critical point, providing evidence for the fractionalization of magnons into deconfined spinons.
description: 5 pages, 3 figures + supplemental materials
Intraoperative vision-based instrument tracking and localisation for endovascular procedures
Creators: name: Vandini, Alessandro
Publisher: name: Imperial College London
Year: 2016

description: Endovascular procedures are increasingly performed with the benefits of minimal invasiveness, short recovery time and hospital stay, as well as improved patient safety. In addition, several robotic platforms have been recently introduced to overcome the challenges of manually performed endovascular procedures, by improving the tool stability and precision, as well as minimising radiation exposure for the physician and patient. Despite these advances, endovascular procedures are usually performed under 2D image guidance provided by X-ray fluoroscopic images which lack depth perception and soft tissue information. These limitations make challenging and potentially dangerous the navigation of interventional tools through complex anatomies. This research aims to improve the physician's perception during surgery by tracking and localising interventional tools using vision-based approaches. For this purpose, an algorithm that tracks interventional tools in fluoroscopic video sequences is proposed. The algorithm is based on robust features termed SEGlets for segment-like features and their organisation in tracking hypotheses. Furthermore, shape reconstruction of a medical continuum robot is achieved by fusing information extracted from intraoperative images with the kinematics model of the robotic tool. In addition, a 3D vision-based catheter shape reconstruction and localisation algorithm is proposed. The technique does not rely on kinematics modelling of the robot but employs the robot's shape prior and optimal positioning of the imaging system. Finally, an algorithm that addresses simultaneously tracking and shape estimation of a medical continuum robot using a Markov random field framework is proposed. These two steps are usually treated independently in the literature, despite their coupled relationship. Our joint framework, however, proved to be more robust than independently achieving the tracking and shape reconstruction of the robot. Extensive evaluations of the proposed techniques in phantom and surgical data have been performed for demonstrating their potential clinical value towards safe navigation of interventional tools during endovascular procedures.
Modelling and parametrization of the convective flow over leads in sea ice and comparison with airborne observations
Creators: name: Michaelis, Janosch
name: Lüpkes, Christof
name: Schmitt, Amelie U.
name: Hartmann, Jörg
Publisher: name: John Wiley & Sons, Ltd
Year: 2021

description: A non‐eddy‐resolving microscale model is applied to simulate convection over three different leads (elongated channels in sea ice), which were observed by aircraft over the Arctic Marginal Ice Zone in 2013. The study aims to evaluate the quality of a local and a non‐local turbulence parametrization. The latter represents a lead‐width‐dependent approach for the turbulent fluxes designed for idealised conditions of a lead‐perpendicular, near‐neutral inflow in an atmospheric boundary layer (ABL) capped by a strong inversion at around 250 to 350 m height. The observed cases considered here are also characterised by an almost lead‐perpendicular flow but, in comparison to the idealised conditions, our analysis covers effects in stable inflow conditions and a much shallower ABL. The model simulations are initialised with observed surface parameters and upwind profiles, and the results are compared with measurements obtained above and downwind of the leads. The basic observed features related to the lead‐generated convection can be reproduced with both closures, but the observed plume inclination and vertical entrainment near the inversion layer by the penetrating plume are underestimated. The advantage of the non‐local closure becomes obvious by the more realistic representation of regions with observed vertical entrainment or where the observations hint at counter‐gradient transport. It is shown by comparison with the observations that results obtained with the non‐local closure can be further improved by including the determination of a fetch‐dependent inversion height and by specifying a parameter determining the plume inclination as a function of the upwind ABL stratification. Both effects improve the representation of fluxes, boundary‐layer warming, and vertical entrainment. The model is also able to reproduce the observed vanishing of a weak low‐level jet over the lead, but its downwind regeneration and related momentum transport are not always well captured, irrespective of the closure used.
description: In typical springtime conditions of a cold atmospheric flow over the warm surfaces of leads, which are open‐water channels in sea ice, strong convective plumes are generated which have a large impact on atmospheric boundary‐layer characteristics. Here, a small‐scale model is applied to simulate such situations and model results obtained with different turbulence parametrizations are evaluated using airborne measurements. Based on the observations, a non‐local parametrization developed for the small‐scale modelling of the inhomogeneous convection over leads is further improved.
description: Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via the Transregional Collaborative Research Center ArctiC Amplification (AC)3 (project number 268020496 TRR 172) and via the priority program SPP 1158 (grant LU 818/5‐1)
Minimally Invasive Concepts in Treating Synchronous Liver Metastases Rectal Cancer Patients: Six Cases Report
Creators: name: Zhang, Hao
name: Jin, Yinghu
name: Huang, Rui
name: Wang, Guiyu
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Rectal cancer patients with synchronous liver metastases (SLM) is common in clinical practice. However, the application of conventional natural orifice specimen extraction surgery (NOSES) and NOSES with specimen extraction via stoma/hepatectomy incision in the special population is rarely explored. Six SLM rectal cancer patients were treated with simultaneous surgical resection and the specimens were extracted via anal/stoma/hepatectomy incision. Respectively, intraoperative and postoperative data, anal function 3 months after surgery and long-term prognosis were reviewed. Intraoperative and postoperative data and anal function were reliable for the six cases. Only one patient died of brain and bone metastases at 84 months after surgery and the other five patients were alive at their last follow-up. Simultaneous surgical resection with the concept of conventional NOSES and NOSES with specimen extraction via stoma/hepatectomy incision is safety for SLM rectal patients.
MOESM7 of Integrative analysis of the cancer genome atlas and cancer cell lines encyclopedia large-scale genomic databases: MUC4/MUC16/MUC20 signature is associated with poor survival in human carcinomas
Creators: name: Jonckheere, Nicolas
name: Seuningen, Isabelle Van
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Plant Biology
subject: Computational Biology

description: Additional file 7: Table S3. Hazard-ratio and survival analysis of top genes associated with MUC4 expression in TCGA tumor databases. Hazard ratio and p-value were determined using SurvExpress tool ( http://bioinformatica.mty.itesm.mx/SurvExpress ). Risk groups were defined using the optimization algorithm (maximize) from the ordered prognostic. Selected genes (ADGRF1, LCN2, MUC20, C1ORF116, SCEL, STEAP4) harbored Pearson’s correlation with MUC4 > 0.5.
Supplementary information: A two-step site and mRNA-level model for predicting microRNA targets
Creators: name: Saito, Takaya
Publisher: name: figshare
Year: 2021
Subjects: subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 60405 Gene Expression (incl. Microarray and other genome-wide approaches)
subject: FOS: Biological sciences
subject: 170203 Knowledge Representation and Machine Learning
subject: FOS: Psychology
subject: 60408 Genomics
subject: Computational Biology
subject: Cell Biology
subject: Developmental Biology

description: Supplementary information of "A two-step site and mRNA-level model for predicting microRNA targets".
The file contains five sections of supplementary information, and the sections are: Supplementary Methods (3 subsections), Supplementary Results (6 subsections), Supplementary Tables (15 tables), Supplementary Figures (22 figures), and the Reference.
Statistical analysis of articulation points in configuration model networks
Creators: name: Tishby, Ido
name: Biham, Ofer
name: Kühn, Reimer
name: Katzav, Eytan
Publisher: name: arXiv
Year: 2018
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: An articulation point (AP) in a network is a node whose deletion would split the network component on which it resides into two or more components. APs are vulnerable spots that play an important role in network collapse processes, which may result from node failures, attacks or epidemics. Therefore, the abundance and properties of APs affect the resilience of the network to these collapse scenarios. We present analytical results for the statistical properties of APs in configuration model networks. In order to quantify their abundance, we calculate the probability $P(i \in {\rm AP})$, that a random node, i, in a configuration model network with P(K=k), is an AP. We also obtain the conditional probability $P(i \in {\rm AP}|k)$ that a random node of degree k is an AP, and find that high degree nodes are more likely to be APs than low degree nodes. Using Bayes' theorem, we obtain the conditional degree distribution, $P(K=k|{\rm AP})$, over the set of APs and compare it to P(K=k). We propose a new centrality measure based on APs: each node can be characterized by its articulation rank, r, which is the number of components that would be added to the network upon deletion of that node. For nodes which are not APs the articulation rank is $r=0$, while for APs $r \ge 1$. We obtain a closed form expression for the distribution of articulation ranks, P(R=r). Configuration model networks often exhibit a coexistence between a giant component and finite components. To examine the distinct properties of APs on the giant and on the finite components, we calculate the probabilities presented above separately for the giant and the finite components. We apply these results to ensembles of configuration model networks with a Poisson, exponential and power-law degree distributions. The implications of these results are discussed in the context of common attack scenarios and network dismantling processes.
description: 53 pages, 16 figures. arXiv admin note: text overlap with arXiv:1804.03336
Tolerance of vascularised composite allografts: the effect of major histocompatibility matching
Creators: name: Shanmugarajah, Kumaran
Publisher: name: Imperial College London
Year: 2016

description: Background: Vascularised composite allografts (VCAs), such as face, hand and abdominal wall transplants, have resulted in excellent functional and quality-of-life outcomes. The development of VCA tolerance protocols would obviate the need for immunosuppression and allow widespread use of this reconstructive modality. But tolerance of VCA skin has been particularly difficult to achieve. I hypothesised that sharing of MHC class I and/or class II between donor and recipient influences VCA tolerance. Methods: Two large animal experimental models were used. In model 1, MGH miniature swine recipients (n=8) underwent non-myeloablative conditioning and haematopoietic stem cell transplantation (HSCT), generating mixed chimeras across either a class I (n=4) or class II (n=4) MHC mismatch. VCAs were transplanted at the time of HSCT. In model 2, VCAs were transplanted onto animals already tolerant of heart and kidney transplants across haploidentical and full MHC barriers through regulatory pathways (n=4). Serial biopsies of VCAs were performed to assess rejection and cellular infiltrate. Flow cytometry was used to assess chimerism in the peripheral blood and tissues. Immune responsiveness was assessed using mixed lymphocyte reaction, cell-mediated lymphocytotoxicity and alloantibody assays. Results: In model 1, animals displayed stable mixed chimerism in lymphoid, myeloid and granulocyte lineages. MHC class II-mismatched chimeras remained tolerant of VCAs (>500 days). In contrast, MHC class I-mismatched chimeras experienced rejection of VCA skin, characterised by infiltration of recipient-type CD8+ T lymphocytes. All animals demonstrated systemic donor-specific non-responsiveness in vitro, including after rejection episodes. In model 2, animals rejected all components of VCAs placed across haploidentical and full MHC-mismatched barriers. VCA rejection correlated with re-establishment of in vitro donor responsiveness. Despite VCA rejection, tolerance of heart and kidney allografts persisted. Conclusions: MHC matching of donor and recipient has not been considered in clinical VCAs to date. This study shows that in a mixed chimerism model, MHC class I antigen mismatching mediates VCA skin rejection whereas robust VCA tolerance can be induced across MHC class II barriers. In addition, we found that local regulation of immune tolerance is critical in long-term acceptance of VCAs. Based on the tolerance of VCAs and non-vascularised skin grafts in MHC class II-mismatched chimeras, we hypothesised that establishing tolerance of allogeneic MHC class II antigens would facilitate more robust tolerance, via induction of regulatory pathways. However, tolerance of VCAs was not seen in a large animal model in which regulatory tolerance of solid organs was established across MHC class II barriers. Taken together, our results identify mechanisms underlying VCA skin tolerance, with important implications for future clinical strategies.
Transient Events from Neutron Star Mergers
Creators: name: Li, Li-Xin
name: Paczyński, Bohdan
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Mergers of neutron stars (NS+NS) or neutron stars and stellar mass black holes (NS+BS) eject a small fraction of matter with a sub-relativistic velocity. Upon rapid decompression nuclear density medium condenses into neutron rich nuclei, most of them radioactive. Radioactivity provides a long term heat source for the expanding envelope. A brief transient has the peak luminosity in the supernova range, and the bulk of radiation in the UV -- Optical domain. We present a very crude model of the phenomenon, and simple analytical formulae which may be used to estimate the parameters of a transient as a function of poorly known input parameters. The mergers may be detected with high redshift supernova searches as rapid transients, many of them far away from the parent galaxies. It is possible that the mysterious optical transients detected by Schmidt et al. (1998) are related to neutron star mergers as they typically have no visible host galaxy.
description: 13 pages, 4 figures, AAS LaTex file. An abbreviated version of this paper has been accepted for publication in ApJ Letters
Versatile parametrization of the perturbation growth rate on the phantom brane
Creators: name: Viznyuk, Alexander
name: Bag, Satadru
name: Shtanov, Yuri
name: Sahni, Varun
Publisher: name: arXiv
Year: 2018
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We derive an analytical expression for the growth rate of matter density perturbations on the phantom brane (which is the normal branch of the Dvali-Gabadadze-Porrati model). This model is characterized by a phantomlike effective equation of state for dark energy at the present epoch. It agrees very well with observations. We demonstrate that the traditional parametrization $f=Ω_m^γ$ with a quasiconstant growth index $γ$ is not successful in this case. Based on a power series expansion at large redshifts, we propose a different parametrization for this model: $f=Ω_m^γ\left(1+\frac{b}{\ell H}\right)^β$, where $β$ and $b$ are constants. Our numerical simulations demonstrate that this new parametrization describes the growth rate with great accuracy - the maximum error being $\leq 0.1\%$ for parameter values consistent with observations.
description: 21 pages, 5 figures, published version
Propagation of inflammation in burn injury and the role of microvesicles
Creators: name: Katbeh, Umar
Publisher: name: Imperial College London
Year: 2016

description: Burn injuries are the fourth most common type of major trauma and responsible for approximately 300,000 deaths worldwide. Most of these deaths are ascribed to the systemic inflammation and multiple organ failure that commonly manifests following burn injury. The ideology that systemic inflammatory response syndrome develops secondary to the action of systemic cytokines has led to clinical trials aimed at intercepting these blood-borne inflammatory mediators before reaching their target sites, these efforts were however in vain. Microvesicles (MVs) are cell-derived signalling particles emerging as important mediators of local and systemic inflammation. Our objective was to investigate the role of microvesicles in the propagation of inflammation following burn injury, focussing on their induction in skin by extracellular ATP signalling. In vitro models of cell injury demonstrated that high temperature causes the release and stabilisation of ATP, in contrast to ATP degradation following mechanically-induced cell lysis. Treatment of skin explants ex vivo with ATP resulted in microvesicle release, which were macrophage-derived, capable of stimulating inflammatory responses in vitro and packaged with pro-IL-1β. Burn injury to skin explants via scalding (steam or immersion) also resulted in the release of microvesicles that were pro-inflammatory in vitro and following intravenous injection into mice, induced leukocyte activation and margination in the vascular beds of the lung and liver. Using a partial-width contact burn injury in skin explants, we were able to demonstrate ATP-purinergic receptor mediated microvesicle release. In conclusion, the results here demonstrate that burn injury can elicit a significant release of microvesicles from skin tissue and that ATP release from injured cells could play a central role in this process. The stabilisation of extracellular ATP by burn injury would produce a unique pathophysiological environment for microvesicle production, which, if released systemically, could play an important and disproportionate role in promoting systemic inflammation following severe burn injury as compared to other SIRS aetiologies.
Additional file 2: of Occurrence, Risk Factors, Prognosis and Prevention of Swimming-Induced Pulmonary Oedema: a Systematic Review
Creators: name: Spencer, Sarah
name: Dickinson, John
name: Forbes, Lindsay
Publisher: name: figshare
Year: 2018
Subjects: subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy
subject: Computational Biology

description: Inclusion criteria. (DOCX 14 kb)