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The 3-billion fossil question:How to automate classification of microfossils

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Artificial Intelligence in Geosciences 2024年第1期5卷 137-145页

作者： Iver Martinsen david Wade benjamin Ricaud Fred Godtliebsen UiT-The Arctic University of Norway TromsøNorway Equinor ASA StavangerNorway

Microfossil classification is an important discipline in subsurface exploration,for both oil&gas and Carbon Capture and Storage(CCS).The abundance and distribution of species found in sedimentary rocks provide valuable information about the age and depositional ***,the analysis is difficult and consuming,time-as it is based on manual work by human *** to automate this process face two key challenges:(1)the input data are very large-our dataset is projected to grow to 3 billion microfossils,and(2)there are not enough labeled data to use the standard procedure of training a deep learning *** propose an efficient pipeline for processing and grouping fossils by genus,or even species,from microscope slides using self-supervised *** we show how to efficiently extract crops from whole slide images by adapting previously trained object detection ***,we provide a comparison of a range of self-supervised learning methods to classify and identify microfossils from very few *** obtain excellent results with both convolutional neural networks and vision transformers fine-tuned by *** approach is fast and computationally light,providing a handy tool for geologists working with microfossils.

关键词： Self-supervised learning Palynology Deep learning Microfossils

A computational method to help identify and measure metallines in high resolution QSO spectra

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Research in Astronomy and Astrophysics 2011年第11期11卷 1279-1297页

作者： Xi-Heng Shi david Tytler Jin-Liang Hou david Kirkmant Jeffery Lee benjamin Ou Key Laboratory for Research in Galaxies and Cosmology Shanghai Astronomical ObservatoryChinese Academy of Sciences Shanghai 200030 China Center for Astrophysics and Space Sciences University of California San Diego La Jolla CA92093-0424 USA

A computational code is developed to help identify metal absorption lines in high resolution QSO spectra, especially in the Lyα forest. The input to the code includes a list of line central wavelengths, column densities and Doppler widths. The code then searches for candidate metal absorption systems and assesses the probability that each system could be real. The framework of the strategy we employ is described in detail and we discuss how to estimate the errors in line profile fitting that are essential to identification. A series of artificial spectra is constructed to calibrate the performance of the code. Due to the effects of blending and noise on Voigt profile fitting, the completeness of the identification depends on the column density of absorbers. For intermediate and strong artificial metal absorbers, more than 90% could be confirmed by the code. The results of applying the code to the real spectra of QSOs HS0757＋5218 and Q0100＋1300 are also presented.

关键词： methods data analysis-quasars absorption lines-quasars individual(HS0757+5218, Q0100+1300)

Dynamic conjugate F-SHARP microscopy

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Light(Science & Applications) 2020年第1期9卷 939-946页

作者： Ioannis N.Papadopoulos Jean-Sebastien Jouhanneau Naoya Takahashi david Kaplan Matthew Larkum James Poulet benjamin Judkewitz Charite-Universitatsmedizin Berlin Einstein Center for NeurosciencesNeuroCure Cluster of ExcellenceChariteplatz 110117 BerlinGermany Max Delbruck Center for Molecular Medicine Robert-Rossle-Str.1013092 BerlinGermany Institute for Biology Humboldt UniversityChariteplatz 110117 BerlinGermany

Optical microscopy is an indispensable tool in biomedical sciences,but its reach in deep tissues is limited due to aberrations and *** problem can be overcome by wavefront-shaping techniques,albeit at limited fields of view(FOVs).Inspired by astronomical imaging,conjugate wavefront shaping can lead to an increased field of view in microscopy,but this correction is limited to a set depth and cannot be dynamically ***,we present a conjugate wavefront-shaping scheme based on focus scanning holographic aberration probing(F-SHARP).We combine it with a compact implementation that can be readily adapted to a variety of commercial and home-built two-photon *** demonstrate the power of the method by imaging with high resolution over extended FOV(>80μm)deeper than 400μm inside a mouse brain through a thinned skull.

关键词： conjugate adapted overcome

Ultra-high suppression microwave photonic bandstop filters

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Chinese Science Bulletin 2014年第22期59卷 2684-2692页

作者： david Marpaung Blair Morrison Mattia Pagani Ravi Pant benjamin J.Eggleton Centre for Ultrahigh Bandwidth Devices for Optical Systems (CUDOS) the Institute of Photonics and Optical Sciences (IPOS) School of Physics University of Sydney Sydney NSW 2006 Australia

A bandstop radio frequency(RF)filter can enhance the capabilities of RF communication systems by removing unwanted signal components such as distortion,or *** modern cognitive radio systems,frequency agile filters are desired to block interferers with dynamically changing frequencies and *** filters should be tunable over a broad frequency range,and they should be capable of suppressing very strong signals with a high *** simultaneously meet these requirements with traditional RF filters are highly *** photonic(MWP),a technology that primary deals with the generation,distribution,and processing of high speed RF signals using photonic techniques and components,is promising for creating frequency agile RF ***,traditional MWP filters are lacking the high resolution and peak suppression exhibited by state-ofthe-art RF electrical *** recently introduced a new class of MWP notch filter which is free from this *** scheme allowed the creation of anomalously high suppression MWP notch filter from virtually any kind of optical resonance,irrespective of its type(gain or absorption),or its *** enabled,for the first time,simultaneous optimization of the MWP filter resolution,peak attenuation,and frequency tuning *** this paper,we present the analysis of notch filter response creation using the novel sideband processing *** thenshow the applicability of this technique to a wide range of optical *** compare simulated and experimental results of the notch filter response created using three types of optical filter commonly used in MWP signal processing,namely stimulated Brillouin scattering(SBS),an integrated optical ring resonator(ORR),and a phase-shifted fiber Bragg-grating(FBG).

关键词： RF滤波器微波光子陷波滤波器光学滤波器受激布里渊散射 RF信号光子技术频率捷变

Delayed diagnosis of alpha-1-antitrypsin deficiency following post-hepatectomy liver failure: A case report

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World Journal of Gastroenterology 2016年第11期22卷 3289-3295页

作者： benjamin Norton Jemimah Denson Christopher Briggs Matthew Bowles david Stell Somaiah Aroori Peninsula College of Medicine and Dentistry Tamar Science Park Department of Histopathology Plymouth Hospitals NHS Trust Peninsula HPB Unit Derriford Hospital

Post-hepatectomy liver failure(PHLF) is a leading cause of morbidity and mortality following major liver resection. The development of PHLF is dependent on the volume of the remaining liver tissue and hepatocyte function. Without effective pre-operative assessment, patients with undiagnosed liver disease could be at increased risk of PHLF. We report a case of a 60-year-old male patient with PHLF secondary to undiagnosed alpha-1-antitrypsin deficiency(AATD) following major liver resection. He initially presented with acute large bowel obstruction secondary to a colorectal adenocarcinoma, which had metastasized to the liver. There was no significant past medical history apart from mild chronic obstructive pulmonary disease. After colonic surgery and liver directed neo-adjuvant chemotherapy, he underwent a laparoscopic partially extended right hepatectomy and radio-frequency ablation. Post-operatively he developed PHLF. The cause of PHLF remained unknown, prompting reanalysis of the histology, which showed evidence of AATD. He subsequently developed progressive liver dysfunction, portal hypertension, and eventually an extensive parastomal bleed, which led to his death; this was ultimately due to a combination of AATD and chemotherapy. This case highlights that formal testing for AATD in all patients with a known history of chronic obstructive pulmonary disease, heavy smoking, or strong family history could help prevent the development of PHLF in patients undergoing major liver resection.

关键词： Post-hepatectomy liver failure Alpha-1-antitrypsin deficiency Hepatectomy Functional liver remnant Liver resection

Can DyeCycling break the photobleaching limit in single-molecule FRET?

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Nano Research 2022年第11期15卷 9818-9830页

作者： benjamin Vermeer Sonja Schmid NanoDynamicsLab Laboratory of BiophysicsWageningen UniversityStippeneng 46708WE WageningenThe Netherlands

Biomolecular systems,such as proteins,crucially rely on dynamic processes at the *** biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that controlbiomolecular ***-molecule fluorescence resonance energy transfer(smFRET)is a powerful technique to observe inreal-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural ***,this technique is fundamentally limited by irreversible photobleaching,causing the untimely end of the experiment andthus,a narrow temporal bandwidth of≤3 orders of ***,we introduce“DyeCycling”,a measurement scheme withwhich we aim to break the photobleaching limit in *** introduce the concept of spontaneous dye replacement bysimulations,and as an experimental proof-of-concept,we demonstrate the intermittent observation of a single biomolecule forone hour with a time resolution of ***,DyeCycling can provide>100-fold more information per singlemolecule than conventional *** discuss the experimental implementation of DyeCycling,its current and fundamentallimitations,and specific biological use *** its general simplicity and versatility,DyeCycling has the potential torevolutionize the field of time-resolved smFRET,where it may serve to unravel a wealth of biomolecular dynamics by bridgingfrom milliseconds to the hour range.

关键词： biomolecular dynamics single-molecule fluorescence resonance energy transfer(smFRET) photobleaching conformational changes single-molecule kinetics

Current and future pharmacological therapies for managing cirrhosis and its complications

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World Journal of Gastroenterology 2019年第8期25卷 888-908页

作者： david Kockerling Rooshi Nathwani Roberta Forlano Pinelopi Manousou benjamin H Mullish Ameet Dhar Liver Unit/Division of Integrative Systems Medicine and Digestive Disease Imperial College London

Due to the restrictions of liver transplantation,complication-guided pharmacological therapy has become the mainstay of long-term management of *** article aims to provide a complete overview of pharmacotherapy options that may be commenced in the outpatient setting which are available for managing cirrhosis and its complications,together with discussion of current controversies and potential future ***/Medline/Cochrane Library were electronically searched up to December 2018 to identify studies evaluating safety,efficacy and therapeutic mechanisms of pharmacological agents in cirrhotic adults and animal models of ***-selective betablockers effectively reduce variceal re-bleeding risk in cirrhotic patients with moderate/large varices,but appear ineffective for primary prevention of variceal development and may compromise renal function and haemodynamic stability in advanced *** observational studies suggest protective,haemodynamically-independent effects of beta-blockers relating to reduced bacterial *** gut-selective antibiotic rifaximin is effective for secondary prophylaxis of hepatic encephalopathy;recent small trials also indicate its potential superiority to norfloxacin for secondary prevention of spontaneous bacterial *** remain the mainstay of uncomplicated ascites treatment,and early trials suggest alpha-adrenergic receptor agonists may improve diuretic response in refractory *** have not demonstrated clinical effectiveness in treating refractory ascites and may cause detrimental *** initial hepatotoxicity concerns,safety of statin administration has been demonstrated in compensated ***,statins are suggested to have protective effects upon fibrosis progression,decompensation and *** as to whether proton pump inhibitors cause gut-liver-brain axis dysfunction is *** evidence indicates that anticoa

关键词： Cirrhosis Beta-blockers Rifaximin Diuretics Statins Proton pump inhibitors Pharmacology

Testing a hypothesis arising from the epidemiology of schizophrenia in New Zealand

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General Psychiatry 2019年第2期32卷 57-58页

作者： Graham Mellsop Rees lapsell david benjamin Menkes Department of Psychological Medicine University of Auckland Waikato Clinical School Hamilton New Zealand

A 2011 publication in World Psychiatry thoughtfully, but somewhat pessimistically, addressed the question of how schizophrenia might be prevented.1 A review of causal evidence2 a decade later offers little further hope. We hypothesise that an emergent increase in syndromal schizophrenia in New Zealand, particularly in Maori (descendants of the indigenous Polynesian population), may present opportunities for prevention.

关键词： New Zealand schizophrenia epidemiology

Modelling of photovoltaic production and electrochemical storage in an autonomous solar drone

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eScience 2022年第2期2卷 235-241页

作者： Mickael Cosson benjamin david Ludovic Arzel Philippe Poizot Ahmed Rhallabi Nantes Universite CNRSInstitut des Materiaux de Nantes Jean Rouxel2 rue de la Houssiniere44322NantesFrance XSun 1 Route de la Croix Moriau44350GuerandeFrance

A simple,efficient simulator has been developed to predict the generation of photovoltaic energy and its storage in Li-ion batteries,for an autonomous drone with four wings covered by solar panels based on thin-film gallium arsenide photovoltaic cells(III–V).This simulator allows prediction of the effective photovoltaic power produced by the solar panels as well as the battery pack voltage when the drone is *** parameters such as irra-diance,sun inclination angles,and drone Euler angles are considered as input *** measured photovoltaic power and battery pack voltage are in good agreement with the simulated values,making practical use by the XSun company *** parametric study shows the effects of climatic and geographic conditions on drone *** optimal weather conditions on a sunny day,drone flight can last 12 h.

关键词： Unmanned aerial vehicle Drone flight simulator Simulation Energy storage Photovoltaic energy