cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The parity effect in Josephson junction arrays
Creators: name: Cole, Jared H.
name: Heimes, Andreas
name: Duty, Timothy
name: Marthaler, Michael
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study the parity effect and transport due to quasiparticles in circuits comprised of many superconducting islands. We develop a general approach and show that it is equivalent to previous methods for describing the parity effect in their more limited regimes of validity. As an example we study transport through linear arrays of Josephson junctions in the limit of negligible Josephson energy and observe the emergence of the parity effect with decreasing number of non-equilibrium quasiparticles. Due to the exponential increase in the number of relevant charge states with increasing length, in multi-junction arrays the parity effect manifests in qualitatively different ways to the two junction case. The role of charge disorder is also studied as this hides much of the parity physics which would otherwise be observed. Nonetheless, we see that the current through a multi-junction array at low bias is limited by the formation of meta-stable even-parity states.
description: 8 pages, 5 figures
Standardized versus research-based PAM50 intrinsic subtyping of breast cancer
Creators: name: Parker, J.S.
name: Prat, A.
Publisher: name: Springer
Year: 2020

description: To date, there is only one standardized assay for identification of the so-called intrinsic molecular subtypes of breast cancer (i.e., Luminal A, Luminal B, HER2-enriched, and Basal-like) described by Perou et al. This assay uses the nCounter technology, has been CE Marked, and is commercially available worldwide. Over the years, however, several research-based methods for subtype identification have been reported. However, none of them is standardized and, in most cases, proper controls or data to suggest that the method is accurate and precise compared to the standardized and clinically validated nCounter-based PAM50 assay are missing. This is worrisome, since important conclusions regarding the prognostic or predictive value of the PAM50 subtypes are being drawn from “homebrew” research-based PAM50 versions often run on different technologies.
Neoadjuvant pazopanib and molecular analysis of tissue response in renal cell carcinoma
Creators: name: Wallen, E.M.
name: Parker, J.S.
name: Moore, D.T.
name: Kim, W.Y.
name: Kimryn Rathmell, W.
name: Powles, T., Royal Free Hospital, London, United Kingdom
name: Beckermann, K.E.
name: Maygarden, S.J.
name: Vincent, B.G.
name: Bortone, D.S.
name: Wood, C.G.
name: Milowsky, M.I.
name: Whisenant, J.G.
name: Ferguson, J.E.
name: Davis, N.B.
name: Karam, J.A.
name: Haake, S.M.
Publisher: name: American Society for Clinical Investigation
Year: 2020

description: BACKGROUND. Surgery remains the frontline therapy for patients with localized clear cell renal cell carcinoma (ccRCC); however, 20%–40% recur. Angiogenesis inhibitors have improved survival in metastatic patients and may result in responses in the neoadjuvant setting. The impact of these agents on the tumor genetic heterogeneity or the immune milieu is largely unknown. This phase II study was designed to evaluate safety, response, and effect on tumor tissue of neoadjuvant pazopanib. METHODS. ccRCC patients with localized disease received pazopanib (800 mg daily; median 8 weeks), followed by nephrectomy. Five tumors were examined for mutations by whole exome sequencing from samples collected before therapy and at nephrectomy. These samples underwent RNA sequencing; 17 samples were available for posttreatment assessment. RESULTS. Twenty-one patients were enrolled. The overall response rate was 8 of 21 (38%). No patients with progressive disease. At 1-year, response-free survival and overall survival was 83% and 89%, respectively. The most frequent grade 3 toxicity was hypertension (33%, 7 of 21). Sequencing revealed strong concordance between pre- and posttreatment samples within individual tumors, suggesting tumors harbor stable core profiles. However, a reduction in private mutations followed treatment, suggesting a selective process favoring enrichment of driver mutations. CONCLUSION. Neoadjuvant pazopanib is safe and active in ccRCC. Future genomic analyses may enable the segregation of driver and passenger mutations. Furthermore, tumor infiltrating immune cells persist during therapy, suggesting that pazopanib can be combined with immune checkpoint inhibitors without dampening the immune response. FUNDING. Support was provided by Novartis and GlaxoSmithKline as part of an investigator-initiated study.
More Powerful Selective Inference for the Graph Fused Lasso
Creators: name: Chen, Yiqun
name: Jewell, Sean
name: Witten, Daniela
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
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: 110309 Infectious Diseases
subject: FOS: Health sciences

description: The graph fused lasso—which includes as a special case the one-dimensional fused lasso—is widely used to reconstruct signals that are piecewise constant on a graph, meaning that nodes connected by an edge tend to have identical values. We consider testing for a difference in the means of two connected components estimated using the graph fused lasso. A naive procedure such as a z-test for a difference in means will not control the selective Type I error, since the hypothesis that we are testing is itself a function of the data. In this work, we propose a new test for this task that controls the selective Type I error, and conditions on less information than existing approaches, leading to substantially higher power. We illustrate our approach in simulation and on datasets of drug overdose death rates and teenage birth rates in the contiguous United States. Our approach yields more discoveries on both datasets. Supplementary materials for this article are available online.
Electron acceleration from the interaction of three crossed parallel Alfvén waves
Creators: name: Daiffallah, Khalil
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Plasma Physics (physics.plasm-ph)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: We study the non-linear interaction of three parallel Alfvén wave packets (AWP) in an initially uniform plasma using 2.5D particle-in-a-cell (PIC) numerical simulations. We aim to help to explain the observation of suprathermal electrons by multiple Alfvén waves collision in regions where these waves are trapped like IAR (Ionospheric Alfvén Resonator), Earth radiation belts or coronal magnetic loops. In the context of APAWI process that have been described by Mottez (2012, 2015), the interaction of two parallel Alfvén waves (AW) generates longitudinal density modulations and parallel electric field at the APAWI crossing region that can accelerate particles effectively in the direction of the background magnetic field. Our simulations show that when a third parallel AWP of different initial position arrives at the APAWI crossing region, it gives rise to a strong parallel electron beams ($V \sim 5--7VTe$) at longitudinal cavity density gradients. We suggest that velocity drift from outgoing AW generates interface waves in the transverse direction, which allows propagating waves to develop parallel electric fields by phase mixing process when the transverse scale of the wavy density gradient (oblique gradient) is in the range of the electron inertial length.
description: 15 pages, 7 figures, Journal of Plasma Physics (2022) PLA2200012_R1
Recycling of Lithium-ion Batteries
Creators: name: Thompson, Dana Louise
Publisher: name: University of Leicester
Year: 2023
Subjects: Uncategorized

description: The electrification of transport is a major goal of the UK government to combat climate change. Consequently, the demand for lithium-ion batteries (LIBs) in electric vehicles has increased and is predicted to increase in the coming years. Currently, recycling is seen as an end-of-pipe process in which valuable materials are down-cycled and leave the supply chain. This necessitates a circular economy model whilst the scale of end-of-life (EoL) batteries is still manageable, to prevent a build-up of hazardous waste. Using retro-economic analysis, it was found that the cost of LIB recycling should be in the range of $2-6 /kg of battery to enable profit and allow processing without gate fees. A techno-economic assessment showed that this is possible with hydrometallurgical processing of EoL materials. Disassembly of the material prior to processing, rather than shredding, contributed to greater cost savings (40-80 %) in comparison to using virgin materials ( < 20 %). The main barrier to recycling was therefore identified as disassembly, in which lack of standardisation and safety issues renders the process slow and difficult. A process that enabled the rapid delamination (< 5 s) of electrode active material (AM) from metal foil current collectors was developed using high-powered ultrasound on electrodes that were uncycled or EoL. Particle size was determined to be the most crucial factor in AM adhesion to the current collector, in which it was easier to delaminate the larger anode particles than the smaller cathode particles. Increased PVDF crystallinity in the EoL anodes also increased the AM adhesive strength compared to the uncycled anodes, resulting in more force required for delamination. Finally, the recovery of the black mass from the cathode was investigated, producing a LIB precursor that could be reformulated into cathode active materials that are currently being used in industry. This was done using a deep eutectic solvent consisting of oxalic acid dihydrate and choline chloride, in which selectivity for manganese and cobalt over nickel was observed during dissolution. Cobalt and manganese oxalates were coprecipitated via the addition of water, in which nickel remained in the leachate and could be recovered by filtration.
title: Linguistic and Musical Information-Processing in Children with Autism
Creators: name: Järvinen, Anna-Maaria
Publisher: name: Goldsmiths, University of London
Year: 2005

description: This thesis focuses upon investigating the relationship between linguistic and musical information-processing in children with autism. The framework for the experiments presented herein derives from three main sources: first, studies highlighting enhanced musical pitch processing abilities in individuals with autism; second, findings from neurological and cognitive studies showing that social stimuli have substantially reduced salience for those with the disorder; and third, investigations reporting higher level language processing deficits in such individuals. Theories of autism that variously account for the featurally-biased information-processing style (weak central coherence hypothesis) (Frith, 1989a; Happe, 1999), atypical perceptual processing (theory of enhanced perceptual processing) (Mottron & Burack, 2001), as well as the social and communicative abnormalities in the disorder, are outlined and discussed within the context of the experimental findings. The experiments presented in this thesis examined the relationship between perceptual processing of pitch information in speech stimuli, and musical stimuli, and higher-level linguistic abilities, in children with autism. Additionally, a pilot study into rhythmic processing was conducted. The main findings showed that whilst children with autism exhibited enhanced perceptual processing of pitch in speech stimuli, marked deficits in the understanding of the linguistic function of prosodic cues were in evidence. Furthermore, children with autism failed to consistently outperform their controls in experimental conditions comprising non-social stimuli. These findings suggest that the enhanced perceptual processing in autism is a consequence of atypical social development. Evidence suggesting reduced neural specialisation in the speech domain was explained by an atypical modularisation hypothesis. Taken together, the findings suggest that many aspects of speech processing, as well as more general auditory processing, are down-stream effects of an early reduction in the salience of social information in autism. Consequently, these children develop finely-tuned appreciation of the physical features of stimuli, and show difficulties in interpreting socially relevant information meaningfully.
Broadband Impedance Calculations and Single Bunch Instabilities Estimations of the HLS-II storage ring
Creators: name: Zhang, Qingkun
name: Wang, Lin
name: Li, Weimin
name: Gao, Weiwei
Publisher: name: arXiv
Year: 2015
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: The upgrade project of Hefei Light Source storage ring is under way. In this paper, the broadband impedances of resistive wall and coated ceramic vacuum chamber were calculated using the analytic formula, the wake fields and impedances of other designed vacuum chambers have been simulated by the CST code, and then the broadband impedances model was obtained. Using the theoretical formula, longitudinal and transverse single bunch instabilities were discussed. With the carefully-designed vacuum chamber, we find that the thresholds of the beam instabilities are higher than the beam current goal.
description: 6 pages, 8 figures,2 tables. arXiv admin note: text overlap with arXiv:1405.4361
Counterexamples, covering systems, and zero-one laws for inhomogeneous approximation
Creators: name: Ramirez, Felipe A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics

description: We develop the inhomogeneous counterpart to some key aspects of the story of the Duffin--Schaeffer Conjecture (1941). Specifically, we construct counterexamples to a number of candidates for a sans-monotonicity version of Szusz's inhomogeneous (1958) version of Khintchine's Theorem (1924). For example, given any real sequence {y_i}, we build a divergent series of non-negative reals psi(n) such that for any y in {y_i}, almost no real number is inhomogeneously psi-approximable with inhomogeneous parameter y. Furthermore, given any second sequence {z_i} not intersecting the rational span of {1,y_i}, and assuming a dynamical version of Erdos' Covering Systems Conjecture (1950), we can ensure that almost every real number is inhomogeneously psi-approximable with any inhomogeneous parameter z in {z_i}. Next, we prove a positive result that is near optimal in view of the limitations that our counterexamples impose. This leads to a discussion of natural analogues of the Duffin--Schaeffer Conjecture and Duffin--Schaeffer Theorem (1941) in the inhomogeneous setting. As a step toward these, we prove versions of Gallagher's Zero-One Law (1961) for inhomogeneous approximation by reduced fractions.
description: 19 pages; v2: changed Erd{\"o}s to Erd\H{o}s throughout; v3: made some expository changes suggested by referee; v4: updated a bilbliography entry and a footnote
More powerful selective inference for the graph fused lasso
Creators: name: Chen, Yiqun
name: Jewell, Sean
name: Witten, Daniela
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
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: 110309 Infectious Diseases
subject: FOS: Health sciences

description: The graph fused lasso — which includes as a special case the one-dimensional fused lasso — is widely used to reconstruct signals that are piecewise constant on a graph, meaning that nodes connected by an edge tend to have identical values. We consider testing for a difference in the means of two connected components estimated using the graph fused lasso. A naive procedure such as a z-test for a difference in means will not control the selective Type I error, since the hypothesis that we are testing is itself a function of the data. In this work, we propose a new test for this task that controls the selective Type I error, and conditions on less information than existing approaches, leading to substantially higher power. We illustrate our approach in simulation and on datasets of drug overdose death rates and teenage birth rates in the contiguous United States. Our approach yields more discoveries on both datasets.
A constructivist grounded theory exploring why UK paramedics are leaving ambulance services to work clinically elsewhere in the NHS
Creators: name: Hayes, Timothy
Publisher: name: Anglia Ruskin Research Online (ARRO)
Year: 2024

description: Background and AimsParamedic retention is a challenge for UK ambulance services, placing increasing strain on delivering safe levels of care. Increasingly leavers are taking up relatively new clinical roles in General Practice and hospitals. Research into UK paramedic turnover is limited. This PhD aimed to identify the relative importance of employee turnover factors to this paramedic population and perceptions of their employment move and subsequent professional identity.MethodsA constructivist grounded theory methodology was adopted, using semi-structured qualitative interviews. Paramedics who had left NHS ambulance services to work clinically in other areas of the NHS were recruited using snowball sampling followed by theoretical sampling. Nineteen paramedics were interviewed prior to theoretical saturation. Data analysis comprised initial, focused, and advanced coding leading to development of a framework explaining Ambulance Paramedic Turnover into the Wider NHS.ResultsTurnover is influenced by negative perceptions of ambulance service culture, in particular that the ambulance service does not value paramedics as individuals or care about their wellbeing. This exacerbates other leaving factors including poor mental health from the emotional impact of ambulance case work, coupled with a lack of informal and formal support mechanisms. Additionally, work-life conflict due to shift work and unpredictable late finishes leads to turnover. Some paramedics find that ambulance work lacks challenge. They seek clinical development and clinical career progression but are often unable to access these within ambulance services. This leads them to seek more challenging clinical work elsewhere in the NHS. Paramedics mostly retain a strong sense of paramedic identity and view their employment move as a change of job forming part of their paramedic career progression.ConclusionsThe combination of factors influencing UK paramedic turnover are unique to their context. The framework of Ambulance Paramedic Turnover into the Wider NHS explains paramedic turnover using their employment journey as its basis. Recommendations have been developed based on the findings across the identified turnover areas of ambulance culture, mental health, work-life conflict and lack of work challenge.
FGFR4 regulates tumor subtype differentiation in luminal breast cancer and metastatic disease
Creators: name: Johnson, G.L.
name: Rojo, F.
name: Garay, J.P.
name: Hollern, D.P.
name: Perou, C.M.
name: Brasó-Maristany, F.
name: Fan, C.
name: Thennavan, A.
name: Marron, D.
name: De Dueñas, E.M.
name: Selitsky, S.R.
name: Mott, K.R.
name: Albanell, J.
name: Prat, A.
name: Lluch, A.
name: Coffey, A.R.
name: Parker, J.S.
name: Carey, L.A.
name: Garcia-Recio, S.
name: He, X.
name: Rosen, J.M.
name: Cejalvo, J.M.
name: Galván, P.
name: East, M.P.
name: Burgués, O.
Publisher: name: American Society for Clinical Investigation
Year: 2020

description: Mechanisms driving tumor progression from less aggressive subtypes to more aggressive states represent key targets for therapy. We identified a subset of luminal A primary breast tumors that give rise to HER2-enriched (HER2E) subtype metastases, but remain clinically HER2 negative (cHER2-). By testing the unique genetic and transcriptomic features of these cases, we developed the hypothesis that FGFR4 likely participates in this subtype switching. To evaluate this, we developed 2 FGFR4 genomic signatures using a patient-derived xenograft (PDX) model treated with an FGFR4 inhibitor, which inhibited PDX growth in vivo. Bulk tumor gene expression analysis and single-cell RNA sequencing demonstrated that the inhibition of FGFR4 signaling caused molecular switching. In the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) breast cancer cohort, FGFR4-induced and FGFR4-repressed signatures each predicted overall survival. Additionally, the FGFR4-induced signature was an independent prognostic factor beyond subtype and stage. Supervised analysis of 77 primary tumors with paired metastases revealed that the FGFR4-induced signature was significantly higher in luminal/ER+ tumor metastases compared with their primaries. Finally, multivariate analysis demonstrated that the FGFR4- induced signature also predicted site-specific metastasis for lung, liver, and brain, but not for bone or lymph nodes. These data identify a link between FGFR4-regulated genes and metastasis, suggesting treatment options for FGFR4-positive patients, whose high expression is not caused by mutation or amplification.
Integrated broadband bowtie antenna on transparent substrate
Creators: name: Zhang, Xingyu
name: Wang, Shiyi
name: Subbaraman, Harish
name: Zhan, Qiwen
name: Pan, Zeyu
name: Chung, Chi-jui
name: Yan, Hai
name: Chen, Ray T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The bowtie antenna is a topic of growing interest in recent years. In this paper, we design, fabricate, and characterize a modified gold bowtie antenna integrated on a transparent glass substrate. We numerically investigate the antenna characteristics, specifically its resonant frequency and enhancement factor. We simulate the dependence of resonance frequency on bowtie geometry, and verify the simulation results through experimental investigation, by fabricating different sets of bowtie antennas on glass substrates utilizing CMOS compatible processes and measuring their resonance frequencies. Our designed bowtie antenna provides a strong broadband electric field enhancement in its feed gap. The far-field radiation pattern of the bowtie antenna is measured, and it shows dipole-like characteristics with large beam width. Such a broadband antenna will be useful for a myriad of applications, ranging from wireless communications to electromagnetic wave detection.
description: 8 pages, 7 figures, SPIE Photonics West Conference
The Ethos of the Church of Ireland Primary School: The Student Voice
Creators: name: Wilkinson, Jacqueline
Publisher: name: University of Leicester
Year: 2023
Subjects: Uncategorized

description: This study aimed to investigate the explicit ethos of the Church of Ireland (Anglican) primary school in the Republic of Ireland, and to gain insight into ethos as a lived experience among the students. The explicit ethos of the school was explored, as presented through the voices of the State, the Church of Ireland, and the school patrons. After considering the ethos of Anglican primary schools in England, a model of prescribed ethos for Church of Ireland primary schools was proposed. The model says the individual school has certainty about its Christian identity, it promotes inclusion, encourages parish-school links, values school assembly and religious education, and regards core Christian values as important to the school community. The empirical research was conducted through pupil surveys in October 2019; it investigated the lived experience of the ethos of the Church of Ireland primary school as voiced by its students, and explored a number of factors that affected student attitudes. The research employed three key instruments: adapted Lankshear Student Voice Scales (Lankshear, 2017), The Francis Scale of Attitude toward Christianity (Francis, 1978a; 1978b), and the Stirling Children’s Well-being Scale (Liddle & Carter, 2010). Each research instrument was found to be reliable and valid in this new context. It was concluded that students had positive attitudes towards the ethos of their schools, demonstrated positive levels of psychological wellbeing, and had positive attitudes toward Christianity; implying the Church of Ireland primary schools were working well in terms of student experiences of ethos and wellbeing, and were Christian in ethos. The study demonstrated the potential for listening to the student voice in relation to school ethos, and their voice being included in articulated school ethos statements. It has also added a new study to the international field of research into Anglican primary school ethos.
Survival, pathologic response, and genomics in CALGB 40601 (Alliance), a neoadjuvant Phase III trial of paclitaxel-trastuzumab with or without lapatinib in HER2-positive breast cancer
Creators: name: Polley, M.-Y.
name: Fernandez-Martinez, A.
name: Krop, I.E.
name: Hudis, C.
name: Berry, D.
name: Harris, L.
name: Shepherd, J.
name: Hillman, D.W.
name: Dang, C.
name: Partridge, A.
name: Huebner, L.
name: Perou, C.M.
name: Hoadley, K.A.
name: Parker, J.S.
name: Tolaney, S.
name: Lynn Henry, N.
name: Carey, L.A.
name: Winer, E.
name: Hahn, O.
Publisher: name: American Society of Clinical Oncology
Year: 2020

description: PURPOSE CALGB 40601 assessed whether dual versus single human epidermal growth factor receptor 2 (HER2) -targeting drugs added to neoadjuvant chemotherapy increased pathologic complete response (pCR). Here, we report relapse-free survival (RFS), overall survival (OS), and gene expression signatures that predict pCR and survival. PATIENTS AND METHODS Three hundred five women with untreated stage II and III HER2-positive breast cancer were randomly assigned to receive weekly paclitaxel combined with trastuzumab plus lapatinib (THL), trastuzumab (TH), or lapatinib (TL). The primary end point was pCR, and secondary end points included RFS, OS, and gene expression analyses. mRNA sequencing was performed on 264 pretreatment samples. RESULTS One hundred eighteen patients were randomly allocated to THL, 120 to TH, and 67 to TL. At more than 7 years of follow-up, THL had significantly better RFS and OS than did TH (RFS hazard ratio, 0.32; 95% CI, 0.14 to 0.71; P 5.005; OS hazard ratio, 0.34; 95% CI, 0.12 to 0.94; P 5.037), with no difference between TH and TL. Of 688 previously described gene expression signatures, significant associations were found in 215 with pCR, 45 with RFS, and only 22 with both pCR and RFS (3.2%). Specifically, eight immune signatures were significantly correlated with a higher pCR rate and better RFS. Among patients with residual disease, the immunoglobulin G signature was an independent, good prognostic factor, whereas the HER2-enriched signature, which was associated with a higher pCR rate, showed a significantly shorter RFS. CONCLUSION In CALGB 40601, dual HER2-targeting resulted in significant RFS and OS benefits. Integration of intrinsic subtype and immune signatures allowed for the prediction of pCR and RFS, both overall and within the residual disease group. These approaches may provide means for rational escalation and de-escalation treatment strategies in HER2-positive breast cancer.
Generate Uniform Transverse Distributed Electron Beam along a Beam Line
Creators: name: Jiao, Y.
name: Cui, X.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: It has been reported that transverse distribution shaping can help to further enhance the energy extraction efficiency in a terawatt, tapered X-ray free-electron laser. Thus, methods of creating and keeping almost uniform transverse distributed (UTD) beam within undulators are required. This study shows that a UTD electron beam can be generated within evenly distributed drift sections where undulators can be placed, by means of octupoles and particular optics. A concrete design is presented, and numerical simulations are done to verify the proposed method.
description: 7 pages, 3 figures, submitted to Chinese Physics C
Mutually Exciting Point Process Graphs for Modeling Dynamic Networks
Creators: name: Passino, Francesco Sanna
name: Heard, Nicholas A.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: A new class of models for dynamic networks is proposed, called mutually exciting point process graphs (MEG). MEG is a scalable network-wide statistical model for point processes with dyadic marks, which can be used for anomaly detection when assessing the significance of future events, including previously unobserved connections between nodes. The model combines mutually exciting point processes to estimate dependencies between events and latent space models to infer relationships between the nodes. The intensity functions for each network edge are characterized exclusively by node-specific parameters, which allows information to be shared across the network. This construction enables estimation of intensities even for unobserved edges, which is particularly important in real world applications, such as computer networks arising in cyber-security. A recursive form of the log-likelihood function for MEG is obtained, which is used to derive fast inferential procedures via modern gradient ascent algorithms. An alternative EM algorithm is also derived. The model and algorithms are tested on simulated graphs and real world datasets, demonstrating excellent performance. Supplementary materials for this article are available online.
An improvement in complex Langevin dynamics from a view point of Lefschetz thimbles
Creators: name: Tsutsui, Shoichiro
name: Doi, Takahiro M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We develop a way of improving complex Langevin dynamics motivated by the Lefschetz-thimble decomposition of integrals. In our method, arbitrary observables of an original model with multiple Lefschetz thimbles are computed by a modified model with a single thimble. We apply our modification method to a one dimensional integral in which the naive implementation of the complex Langevin dynamics fails to reproduce the exact results due to the severe sign problem. We show that the toy model can be modified so that the new model consists of a single Lefschetz thimble. We find that correct results can be obtained by the improved complex Langevin dynamics.
description: 7 pages, 7 figures
In search for near-room-temperature superconducting critical temperature of metal superhydrides under high pressure - A review
Creators: name: Udomsilp PINSOOK
Publisher: name: Metallurgy and Materials Science Research Institute Chulalongkorn University
Year: 2020
Subjects: Superconductors
Metal superhydrides
Near-room-temperature
Critical temperature
High pressure

description: Journal of Metals Materials and Minerals, 30, 2, 31-41
HER2-Enriched Subtype and ERBB2 Expression in HER2-Positive Breast Cancer Treated with Dual HER2 Blockade
Creators: name: Forero, A.
name: Vidal, M.
name: Galván, P.
name: Llombart-Cussac, A.
name: Morales, S.
name: Izquierdo, M.
name: Oliveira, M.
name: Wang, T.
name: Paré, L.
name: Nuciforo, P.
name: Rimawi, M.F.
name: Pavlick, A.C.
name: Adamo, B.
name: Gutierrez, C.
name: Veeraraghavan, J.
name: Brasó-Maristany, F.
name: Prat, A.
name: Griguolo, G.
name: Wolff, A.C.
name: Pascual, T.
name: Guarneri, V.
name: Parker, J.S.
name: DIeci, M.V.
name: Hilsenbeck, S.G.
name: Cortés, J.
name: Reis-Filho, J.S.
name: Rodrik-Outmezguine, V.
name: Schiff, R.
name: Osborne, C.K.
name: Krop, I.
name: Bermejo, B.
name: De Angelis, C.
name: Conte, P.
name: Fasani, R.
name: Rexer, B.
Publisher: name: Oxford University Press
Year: 2020

description: Background: Identification of HER2-positive breast cancers with high anti-HER2 sensitivity could help de-escalate chemotherapy. Here, we tested a clinically applicable RNA-based assay that combines ERBB2 and the HER2-enriched (HER2-E) intrinsic subtype in HER2-positive disease treated with dual HER2-blockade without chemotherapy. Methods: A research-based PAM50 assay was applied in 422 HER2-positive tumors from five II-III clinical trials (SOLTI-PAMELA, TBCRC023, TBCRC006, PER-ELISA, EGF104090). In SOLTI-PAMELA, TBCRC023, TBCRC006, and PER-ELISA, all patients had early disease and were treated with neoadjuvant lapatinib or pertuzumab plus trastuzumab for 12-24 weeks. Primary outcome was pathological complete response (pCR). In EGF104900, 296 women with advanced disease were randomized to receive either lapatinib alone or lapatinib plus trastuzumab. Progression-free survival (PFS), overall response rate (ORR), and overall survival (OS) were evaluated. Results: A total of 305 patients with early and 117 patients with advanced HER2-positive disease were analyzed. In early disease, HER2-E represented 83.8% and 44.7% of ERBB2-high and ERBB2-low tumors, respectively. Following lapatinib and trastuzumab, the HER2-E and ERBB2 (HER2-E/ERBB2)-high group showed a higher pCR rate compared to the rest (44.5%, 95% confidence interval [CI] = 35.4% to 53.9% vs 11.6%, 95% CI = 6.9% to 18.0%; adjusted odds ratio [OR] = 6.05, 95% CI = 3.10 to 11.80, P <. 001). Similar findings were observed with neoadjuvant trastuzumab and pertuzumab (pCR rate of 66.7% in HER2-E/ERBB2-high, 95% CI = 22.3% to 95.7% vs 14.7% in others, 95% CI = 4.9% to 31.1%; adjusted OR = 11.60, 95% CI = 1.66 to 81.10, P =. 01). In the advanced setting, the HER2-E/ERBB2-high group was independently associated with longer PFS (hazard ratio [HR] = 0.52, 95% CI = 0.35 to 0.79, P <. 001); higher ORR (16.3%, 95% CI = 8.9% to 26.2% vs 3.7%, 95% CI = 0.8% to 10.3%, P =. 02); and longer OS (HR = 0.66, 95% CI = 0.44 to 0.97, P =. 01). Conclusions: Combining HER2-E subtype and ERBB2 mRNA into a single assay identifies tumors with high responsiveness to HER2-targeted therapy. This biomarker could help de-escalate chemotherapy in approximately 40% of patients with HER2-positive breast cancer.
IMPACT OF PREHOSPITAL NOTIFICATION AND HOSPITAL PREPAREDNESS ON OUTCOMES FOR TIME-SENSITIVE EMERGENCIES: A LITERATURE REVIEW
Creators: name: Saeed Abdulkhaliq Saeed Alghamdi, Rayan Ahmed Alqarni, Saeed Abdullah Al Zahrani, Othman Ali Othman Alshehri, Fouzan Fouad Nezlawi, Bassam Mohammed Aljuaid, Abdullah Atteah Alzahrani, Raed Ibrahim Sanky, Naif Nasser Alqhtani, Fahad Mohammed Ali Aladwani
Publisher: name: Zenodo
Year: 2024

description: This literature review investigates the critical roles of prehospital notification and hospital preparedness in influencing patient outcomes during time-sensitive emergencies, including cardiac arrests, strokes, and trauma incidents. Effective prehospital communication is essential for ensuring that hospitals are adequately prepared to receive critically ill patients, which can significantly impact survival rates and recovery. The review synthesizes findings from a diverse range of studies, demonstrating that timely prehospital notifications lead to improved emergency department response times and enhanced patient management upon arrival. Despite the established benefits, the review reveals significant gaps in the literature, particularly concerning the effects of prehospital notification on trauma care and the need for standardized protocols across different healthcare systems. Furthermore, many regions lack organized prehospital care frameworks, which exacerbates delays in treatment and compromises patient safety. This study emphasizes the urgent need for research addressing these gaps, advocating for the development of more effective prehospital care systems and hospital preparedness protocols. By identifying best practices and areas for improvement, the research aims to inform policymakers and healthcare administrators, ultimately enhancing emergency response strategies and improving outcomes for patients facing critical health crises.

Keywords: prehospital notification, hospital preparedness, emergency care, patient outcomes, time-sensitive emergencies.
PIK3CA mutation in HPV-associated OPSCC patients receiving deintensified chemoradiation
Creators: name: Shen, C.J.
name: Hackman, T.G.
name: Parker, J.S.
name: Weck, K.E.
name: Blumberg, J.M.
name: Grilley-Olson, J.
name: Yarbrough, W.G.
name: Sheets, N.C.
name: Thorp, B.
name: Weissler, M.C.
name: Tan, X.
name: Patel, S.N.
name: Dagan, R.
name: Chera, B.S.
name: Ramkissoon, L.A.
name: Weiss, J.
name: Mendenhall, W.M.
name: Beaty, B.T.
name: Hayes, D.N.
name: Zanation, A.
name: Gupta, G.P.
name: Patel, S.
name: Amdur, R.J.
name: Moon, D.H.
Publisher: name: Oxford University Press
Year: 2020

description: PIK3CA is the most frequently mutated gene in human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC). Prognostic implications of such mutations remain unknown. We sought to elucidate the clinical significance of PIK3CA mutations in HPV-associated OPSCC patients treated with definitive chemoradiation (CRT). Seventyseven patients with HPV-associated OPSCC were enrolled on two phase II clinical trials of deintensified CRT (60 Gy intensitymodulated radiotherapy with concurrent weekly cisplatin). Targeted next-generation sequencing was performed. Of the 77 patients, nine had disease recurrence (two regional, four distant, three regional and distant). Thirty-four patients had mutation( s) identified; 16 had PIK3CA mutations. Patients with wild-type-PIK3CA had statistically significantly higher 3-year disease-free survival than PIK3CA-mutant patients (93.4%, 95% confidence interval [CI] = 85.0% to 99.9% vs 68.8%, 95% CI = 26.7% to 89.8%; P=.004). On multivariate analysis, PIK3CA mutation was the only variable statistically significantly associated with disease recurrence (hazard ratio = 5.71, 95% CI = 1.53 to 21.3; P=.01). PIK3CA mutation is associated with worse diseasefree survival in a prospective cohort of newly diagnosed HPV-associated OPSCC patients treated with deintensified CRT.
Preparation of alginate/2-hydroxyethyl methacrylate composite beads: Role of fillers and characteristics of bead formation
Creators: name: Somkiet URUSETTHANON
Publisher: name: Metallurgy and Materials Science Research Institute Chulalongkorn University
Year: 2020
Subjects: Alginate bead
2-Hydroxyethyl methacrylate
Cotton dust
Sawdust
Viscosity

description: Journal of Metals Materials and Minerals, 30, 2, 42-49
Technosignatures as a Path Towards Identifying Life Outside the Solar System
Creators: name: Beatty, Thomas
Publisher: name: Zenodo
Year: 2022

description: Abstract: The search for biosignatures on potentially habitable exoplanets has driven much of the recent planning in the exoplanet community for the next generation of space telescopes, and as our ability to characterize exoplanets improves, we also move closer to the direct detection of technosignatures on exoplanets. Though likely less common than biosignature signals, in many cases the clearly artificial nature of certain technosignatures would make their detection clearly indicative of life outside the Solar System. In the last few years serious thought has been given to the types of technosignatures one could reasonably expect to detect using current and next-generation observatories, giving a firm astrophysical foundation to this sub-field. I will summarize the immediate prospects for technosignature detection using JWST, and using a LUVOIR- or HabEx-like next generation space telescope. I will particularly focus on the possibilities of detecting industrial pollutants in exoplanet atmospheres, the emission from nightside city lights on exoplanets, and the spectroscopic signatures of advanced spaceflight. All three of these possible technosignatures now have detailed and physically-based expectations for their observability, and I will also discuss how non-detections can place meaningful upper limits on the frequency of technological life in the Solar Neighborhood.
Identifying transcriptional profiles and evaluating prognostic biomarkers of HIV-associated diffuse large B-cell lymphoma from Malawi
Creators: name: Gopal, S.
name: Kendall, S.M.
name: Fedoriw, Y.
name: Richards, K.L.
name: Du, W.
name: Parker, J.S.
name: Selitsky, S.
name: Tomoka, T.
name: Montgomery, N.D.
name: Dave, S.S.
name: Mulenga, M.
Publisher: name: Springer Nature
Year: 2020

description: Lymphoma incidence in sub-Saharan Africa (SSA) is increasing due to HIV and population aging. Diffuse Large B-cell lymphoma (DLBCL), the most common lymphoma in SSA and worldwide, is highly associated with HIV, but molecular studies of HIV-associated DLBCL are scarce globally. We describe profiling of DLBCL from Malawi, aiming to elucidate tumor biology and identify clinically meaningful biomarkers specifically for SSA. Between June 1, 2013 and June 1, 2016, 59 cases of DLBCL (32 HIV+/27 HIV−) enrolled in the Kamuzu Central Hospital Lymphoma Study were characterized, of which 54 (92%) were negative for Epstein–Barr virus. Gene expression profiling (GEP) by whole transcriptome sequencing was performed on the first 36 cases (22 HIV+/14 HIV−). Immunohistochemistry (IHC) and GEP results were compared with published data and correlated to clinical outcome and pathologic features. Unsupervised clustering strongly segregated DLBCL by HIV status (p = 0.0003, Chi-squared test), indicating a marked contribution of HIV to expression phenotype. Pathway analysis identified that HIV-associated tumors were enriched in hypoxia, oxidative stress, and metabolism related gene expression patterns. Cell-of-origin subtype, determined by sequencing and IHC, did not associate with differences in overall survival (OS), while Ki-67 proliferation index ≥80% was associated with inferior OS in HIV+ DLBCL only (p = 0.03) and cMYC/BCL2 co-expression by IHC was negatively prognostic across the entire cohort (p = 0.01). This study provides among the first molecular characterizations of DLBCL from SSA, demonstrates marked gene expression differences by HIV status, and identifies genomic and immunophenotypic characteristics that can inform future basic and clinical investigations.
Multitip scanning gate microscopy for ballistic transport studies in systems with two-dimensional electron gas
Creators: name: Kolasiński, K.
name: Szafran, B.
name: Hackens, B.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We consider conductance mapping of systems based on the two-dimensional electron gas with scanning gate microscopy using two and more tips of the atomic force microscope. The paper contains results of numerical simulations for a model tip potential with a proposal of a few procedures for extraction and manipulation the ballistic transport properties. In particular, we demonstrate that the multi-tip techniques can be used for readout of the Fermi wavelength, detection of potential defects, filtering specific transverse modes, tuning the system into resonant conditions under which a stable map of a local density of states can be extracted from conductance maps using a third tip.
description: 9 pages, 12 figures
Tesis_Msc_GEOREC_Fluorita.pdf
Creators: name: Solano Acosta, Juan David
name: Domínguez, Rafael Navarro
name: Ruano, Salvador Morales
Publisher: name: figshare
Year: 2023
Subjects: Mineralogy and crystallography
Geology not elsewhere classified

description: Samples of fluorite and carbonates from the F-Pb-(Zn) deposit of Sierra de Lujar (Órgiva, Granada, Spain) have been analysed to create a geochemical inventory - with special attention to rare earth elements - that can contribute to the understanding of the genesis of the mineralising fluids. For this purpose, the composition of 29 fluorite samples (classified according to their colour and texture in 10 categories) and 9 carbonate samples (dolomites and limestones) were analysed by XRF and ICP-MS. This study has recognised three different stages of fluorite mineralisationy. Group I fluorite (fine-grained, light green shades) is the oldest, and is associated with higher concentrations of rare earths -especially light ones-. In contrast, the more recent fluorites of groups II (with light shades) and III (purple or black shades) have higher concentrations of trace elements and are accompanied by SiO2 and Al2O3. The Tb/Ca and Y/Ho ratios suggest a hydrothermal origin for the Sierra de Lujar fluorites, while the Yb /Ca vs. Yb/La and Y/Ho vs. La/Ho ratios show that the early fluorites (group I) could be the result of replacement of the carbonate bedrock, and the late fluorites (groups II and III) could be the result of remobilization and recrystallization. Tb/Yb, La/Yb, La/Sm ratios and chondrite-normalised patterns reveal that the early fluorites are highly enriched in light rare earths, while the heavy rare earth contents are similar in the three fluorite groups. Considering the negative Ce/Ce* anomalies in the late fluorites, it can be assumed that the mineralisation of the early fluorites in this deposit occurred under relatively reducing conditions and switched to relatively oxidising conditions in the later fluorites (groups II and III). From the negative Eu/Eu* anomaly in all fluorites from Sierra de Lujar, it can be observed that the fluorites were formed below 250◦C
Tn-Seq Analysis Identifies Genes Important for Yersinia pestis Adherence during Primary Pneumonic Plague
Creators: name: Mieczkowski, P.A.
name: Selitsky, S.R.
name: Goldmana, W.E.
name: Eichelberger, K.R.
name: Parker, J.S.
name: Sepúlveda, V.E.
name: Ford, J.
name: Parker, J.S.
name: Ford, J.
name: Selitsky, S.R.
Publisher: name: American Society for Microbiology
Year: 2020

description: Following inhalation, Yersinia pestis rapidly colonizes the lung to establish infection during primary pneumonic plague. Although several adhesins have been identified in Yersinia spp., the factors mediating early Y. pestis adherence in the lung remain unknown. To identify genes important for Y. pestis adherence during primary pneumonic plague, we used transposon insertion sequencing (Tn-seq). Wild-type and capsule mutant (Δcaf1) Y. pestis transposon mutant libraries were serially passaged in vivo to enrich for nonadherent mutants in the lung using a mouse model of primary pneumonic plague. Sequencing of the passaged libraries revealed six mutants that were significantly enriched in both the wild-type and Δcaf1 Y. pestis backgrounds. The enriched mutants had insertions in genes that encode transcriptional regulators, chaperones, an endoribonuclease, and YPO3903, a hypothetical protein. Using single-strain infections and a transcriptional analysis, we identified a significant role for YPO3903 in Y. pestis adherence in the lung and showed that YPO3903 regulated transcript levels of psaA, which encodes a fimbria previously implicated in Y. pestis adherence in vitro. Deletion of psaA had a minor effect on Y. pes-tis adherence in the lung, suggesting that YPO3903 regulates other adhesins in addition to psaA. By enriching for mutations in genes that regulate the expression or assembly of multiple genes or proteins, we obtained screen results indicating that there may be not just one dominant adhesin but rather several factors that contribute to early Y. pestis adherence during primary pneumonic plague.