bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using the Energy Distribution as a Benchmarking Among Models for Adiabatic Quantum Processing in the Protein Folding Problem
Authors: Anaya A , Delgado F 
Published: June 2020

Abstract
Determining the tertiary complexity of proteins using ab-initio algorithms is a hard problem. Adiabatic Quantum Computing allows to construct simple Ising-like Hamiltonians in order to elucidate the aminoacid interactions minimizing the conformation energy of the protein. Exploring the energy distribution of the Hamiltonian allows to compare the efficiency of different models there proposed. This article compare the efficiency of two algorithms through the conformation energy of a protein stating a benchmark through the energy distributions of the conformation states.
Multichannel fiber sensor for time delay and optical pulse form measuring
Authors: Arapov Y D , Turkin V N 
Published: June 2020

Abstract
This paper presents a description of engineering solutions and physical diagram of a device meant to measure spatially resolved time form of optical signals with detection accuracy up to 0.1 ns and a scalable number of monitoring points. It has been demonstrated that the number of simultaneously detected optical signals within the limit is up to one million. There are no moving mechanical units in the device design. A method for reducing the total length of the optical fiber based on the principle of the cascade optical delay is proposed for the multichannel sensor of diversification. The number of measured signals reaches a million. The capabilities and constraints of the described engineering solution for measuring the pulse form and monitoring the diversification of the multicomponent optical signals have been demonstrated. The principle of calculating a multichannel fiber device for recording optical pulses is presented and shown that the fiber length is up to 15 km for the detection system of 128 optical signals 100 ns long each. Generally, the number of measured signals may reach a million.
Tuneable liquid crystal asymmetric dual-core photonic crystal fiber mode converter
Authors: Montoya-Cardona J , Gomez-Cardona N , Gonzalez-Valencia E , Torres P , Reyes-Vera E 
Published: June 2020

Abstract
In this work, a novel and compact mode selective coupler based on an asymmetric dual core photonic crystal fiber with a thermo-responsive core is proposed and numerically studied. Simulation results show that high conversion efficiencies are achieved between LP01 and LP11 modes in the O-band with a wide bandwidth of 24.55 nm and a mode conversion efficiency over 60% when it has a total length of 3.15 mm and the operating wavelength is 1310 nm. In addition, the thermally tuneability was evaluated when this device was submitted to thermal changes from 15°C to 35°C. The results evidence that thermal effect allows to control the operating wavelength and the mode coupling efficiency of the mode converter when it is used to couple energy from the LP01 mode to the LP11 mode. Therefore, the proposed device could be useful in high-bandwidth mode division multiplexed communication systems.
Detection of effects of three different plant pests for chrysanthemum flowers by using image processing and spectral imaging
Authors: Sánchez-Ríos C A , Cardona A M , Echavarría A , Herrera-Ramírez J 
Published: June 2020

Abstract
Ornamental floriculture is one of the main economic activities in different regions of Colombia. Different flowers have a great success, but its industry faces some challenges on phytosanitary controls caused mainly by the dependence on human monitors and the expertise in the detection of diseases throughout the crop fields. This paper focuses on the detection of the affection patterns caused by tomato spotted wilt virus, puncture leaf miner, and leaf miner larvae on chrysanthemum flowers (Dendrathema grandiflorum). A spectral imaging system was with 11 spectral channels was implemented which were generated by the same number of light emitting diodes groups. By using these images, there were carried out different image processing techniques and the combination of different linear relations among the spectral images were tested to enhance, isolate and quantify the affected area on the leaves. The results show that our system has more selective spectral width than common artificial vision systems and the effects of the diseases can be effectively detected.
Mobility of localized beams in non-homogeneous photonic lattices
Authors: Sabogal M A , Parra I C , Bandera M , Gallardo J , Mejía-Cortés C 
Published: June 2020

Abstract
Waveguide arrays offer enormous potential to design circuit elements essential to fabricate optical devices capable to processing information codified by light. In this work we study the existence and stability of localized beams in one dimensional photonic lattices composed by a Kerr type waveguide array. We analyzed the case where discrete translation symmetry is broken in as much as one of the waveguides lacks a nonlinear response. Specifically, we determined the space of parameters where a coherent and robust mobility across the lattice is achieved. Moreover, we calculate the reflection and transmission coefficients when localized beams interact directly with the impurity, finding that it behaves as a variable filter depending of system parameters. Our results would shed light on develop solutions to keep unaltered information during its transmission within future optical devices.
Recombination effects in the ionization chambers dose delivery monitor of the TOP-IMPLART proton beam
Authors: Ampollini A. , Basile E. , Bazzano G. , Cisbani E. , De Angelis C. , Della Monaca S. , Ghio F. , Giuliani F. , Lucentini M. , Nenzi P. , Placido C. , Picardi L. , Ronsivalle C. , Santavenere F. , Spurio A. , Surrenti V. , Vadrucci M. 
Published: June 2020

Abstract
The Intensity Modulated Proton Linear Accelerator for Cancer Therapy (TOP-IMPLART) is under development and construction by ENEA in collaboration with the Italian Institute of Health (ISS) and the Oncological Hospital Regina Elena-IFO with financial support of Regione Lazio.
Its peculiar time structure (few microseconds pulse width) and very high peak intensity (≍ 109 proton/pulse) demand for ad hoc dose delivery monitors (DDM). The TOP-IMPLART DDM is based on ionization gas chambers. One segmented chamber prototype uses Micro Pattern Gaseous Detector technology for the 2-dimensional simultaneous x/y readout; the charge collected from each active segment (strips with pad-like shape) is readout by a dedicated gain-adaptable electronics. Two small, highly sensitive, integral ionization chambers, using the same electronics, complement the 2D chamber for the monitor of the single pulse beam charge, down to 1 pC/pulse.
While under development and deployment of its accelerating modular cavities, the linear TOP-IMPLART beam is improved thanks also to the continuous monitoring and characterization by these devices, whose responses are periodically compared to calibrated dosimetric detectors such as real-time active microDiamond sensor, passive Alanine pellets, intrinsically stable integral Faraday Cup.
Different calibration campaigns have been recently conducted to measure the recombination and dose-rate effects on the above ionization chambers. The outcome of these measurements shows clear electron-ion recombination in the chamber active volume, largely related to the high beam intensity and its small transverse cross section. Those effects can be taken into account and used to correct the actual measurement of the DDM.
In this paper, the TOP-IMPLART project and the DDM devices are shortly presented and details of the above experimental studies are discussed.
An overview of OSCAR: a new hodoscope of silicon detectors for low energy charged particles
Authors: Dell’Aquila D. 
Published: June 2020

Abstract
Modern nuclear physics experiments demand for new high-resolution and high-versatility detectors for the reconstruction of collision events. In this framework, we have developed a new hodoscope of silicon detectors for charged particles called OSCAR. This new device consists of individual modules with partially embedded electronics capable to identify low energy particles down to about 1 MeV/u. OSCAR is a particularly suitable detector to be used as a standalone detector or as ancillary system for large acceptance devices. This paper presents an overview of the layout and capabilities of the detector.
Energy response and identification efficiency of CsI(Tl) crystals irradiated with energetic protons
Authors: Frosin C , Barlini S , Poggi G , Casini G , Bini M , Stefanini A A , Valdré S , Gruyer D , Ciemala M , Maj A , Ziebliński M , Sowicki B , Mazurek K , Cieplicka-Oryńczak N , Matejska-Minda M , Bonnet E , Borderie B , Bougault R , Bruno M , Buccola A , Camaiani A , Chibhi A , Cinausero M , Cicerchia M , Dueñs J , Fabris D , Frankland J , Gramegna F , Henri M , Kordyasz A , Le Neindre N , Lombardo I , Lopez O , Mantovani G , Marchi T , Olmi A , Ottanelli P , Parlog M , Piantelli S , Pasquali G , Upadhyahya S , Verde G , Vient E 
Published: June 2020

Abstract
Proton energy calibration and identification efficiency of few Thallium activated Cesium Iodide (CsI(Tl)) crystals of the FAZIA detection system, have been studied in the range 59-180 MeV by using the proton beam delivered by the cyclotron of the CCB (Cyclotron Center Bronowice) facility. We observe that the light output versus energy is linear in the lower investigated energy range while showing a deviation from linearity above 140 MeV. The effects of proton induced nuclear reactions and multiple scattering causing incomplete energy deposition (IED) events have been identified and estimated via Pulse Shape Analysis in CsI(Tl) crystals. The measured experimental efficiency for proton identification in the examined energy range is then compared with GEANT4 simulations. For a centered collimated irradiation on the crystal, and at the highest measured energy, the resulting experimental efficiency value is about 70%.
3D Detectors on Hydrogenated Amorphous Silicon for particle tracking in high radiation environment
Authors: Menichelli M , Boscardin M , Crivellari M , Davis J , Dunand S , Fanò L , Moscatelli F , Movileanu-Ionica M , Petasecca M , Piccini M , Rossi A , Scorzoni A , Verzellesi G , Wyrsch N 
Published: June 2020

Abstract
The vertex detectors for the future hadronic colliders will operate under proton fluencies above 1016 p/cm2. Crystalline Silicon detector technology, up to now, has kept the pace of the increasing fluencies in the LHC era and it is still the prevalent vertex detector material for the present and for the immediate future. Looking ahead in time, an alternative solution for such a detector has to be found because for the future there is no guarantee that Crystalline Silicon will hold this challenge. For this reason the development of hydrogenated amorphous silicon vertex detectors based on 3D-technology have been proposed and the technological solutions in order to build these detectors are described in this paper.
On the Causal Interpretation of Rate-Change Methods: The Prior Event Rate Ratio and Rate Difference
Authors: van Aalst Robertus , Thommes Edward , Postma Maarten , Chit Ayman , Dahabreh Issa J 
Published: June 2020

Abstract
A growing number of studies use data before and after treatment initiation in groups exposed to different treatment strategies to estimate “causal effects” using a ratio measure called the prior event rate ratio (PERR). Here, we offer a causal interpretation for PERR and its additive scale analog, the prior event rate difference (PERD). We show that causal interpretation of these measures requires untestable rate-change assumptions about the relationship between 1) the change of the counterfactual rate before and after treatment initiation in the treated group under hypothetical intervention to implement the control strategy; and 2) the change of the factual rate before and after treatment initiation in the control group. The rate-change assumption is on the multiplicative scale for PERR but on the additive scale for PERD; the 2 assumptions hold simultaneously under testable, but unlikely, conditions. Even if investigators can pick the most appropriate scale, the relevant rate-change assumption might not hold exactly, so we describe sensitivity analysis methods to examine how assumption violations of different magnitudes would affect study results. We illustrate the methods using data from a published study of proton pump inhibitors and pneumonia.
Optogenetic Activation of Type III Taste Cells Modulates Taste Responses
Authors: Vandenbeuch Aurelie , Wilson Courtney E , Kinnamon Sue C 
Published: June 2020

Abstract
Studies have suggested that communication between taste cells shapes the gustatory signal before transmission to the brain. To further explore the possibility of intragemmal signal modulation, we adopted an optogenetic approach to stimulate sour-sensitive (Type III) taste cells using mice expressing Cre recombinase under a specific Type III cell promoter, Pkd2l1 (polycystic kidney disease-2-like 1), crossed with mice expressing Cre-dependent channelrhodopsin (ChR2). The application of blue light onto the tongue allowed for the specific stimulation of Type III cells and circumvented the nonspecific effects of chemical stimulation. To understand whether taste modality information is preprocessed in the taste bud before transmission to the sensory nerves, we recorded chorda tympani nerve activity during light and/or chemical tastant application to the tongue. To assess intragemmal modulation, we compared nerve responses to various tastants with or without concurrent light-induced activation of the Type III cells. Our results show that light significantly decreased taste responses to sweet, bitter, salty, and acidic stimuli. On the contrary, the light response was not consistently affected by sweet or bitter stimuli, suggesting that activation of Type II cells does not affect nerve responses to stimuli that activate Type III cells.
Initiation of Antiretroviral Therapy in the Hospital Is Associated With Linkage to Human Immunodeficiency Virus (HIV) Care for Persons Living With HIV and Substance Use Disorder
Authors: Jacobs Petra , Feaster Daniel J , Pan Yue , Gooden Lauren K , Daar Eric S , Lucas Gregory M , Jain Mamta K , Marsh Eliza L , Armstrong Wendy S , Rodriguez Allan , del Rio Carlos , Metsch Lisa R 
Published: June 2020

Abstract

Background
Studies have demonstrated benefits of antiretroviral therapy (ART) initiation on the day of human immunodeficiency virus (HIV) testing or at first clinical visit. The hospital setting is understudied for immediate ART initiation.

Methods
CTN0049, a linkage-to-care randomized clinical trial, enrolled 801 persons living with HIV (PLWH) and substance use disorder (SUD) from 11 hospitals across the United States. This secondary analysis examined factors related to initiating (including reinitiating) ART in the hospital and its association with linkage to HIV care, frequency of outpatient care visits, retention, and viral suppression.

Results
Of 801 participants, 124 (15%) initiated ART in the hospital, with more than two-thirds of these participants (80/124) initiating ART for the first time. Time to first HIV care visit among those who initiated ART in the hospital and those who did not was 29 and 54 days, respectively (P = .0145). Hospital initiation of ART was associated with increased frequency of HIV outpatient care visits at 6 and 12 months. There was no association with ART initiation in the hospital and retention and viral suppression over a 12-month period. Participants recruited in Southern hospitals were less likely to initiate ART in the hospital (P &lt; .001).

Conclusions
Previous research demonstrated benefits of immediate ART initiation, yet this approach is not widely implemented. Research findings suggest that starting ART in the hospital is beneficial for increasing linkage to HIV care and frequency of visits for PLWH and SUD. Implementation research should address barriers to early ART initiation in the hospital.
Prospective Validation of PREDICT and Its Impact on the Transesophageal Echocardiography Use in Management of Staphylococcus aureus Bacteremia
Authors: Abu Saleh Omar , Fida Madiha , Asbury Kara , Narichania Aalap , Sotello David , Bosch Wendelyn , Vikram Holenarasipur R , Palraj Raj , Lahr Brian , Baddour Larry M , Sohail M Rizwan 
Published: June 2020

Abstract

Background
Infective endocarditis (IE) is the most feared complication of Staphylococcus aureus bacteremia (SAB). Transesophageal echocardiogram (TEE) is generally recommended for all patients with SAB; however, supporting data for this are limited. We previously developed a scoring system, “PREDICT,” that quantifies the risk of IE and identifies patients who would most benefit most from undergoing TEE. The current prospective investigation aims to validate this score.

Methods
We prospectively screened all consecutive adults (≥18 years) hospitalized with SAB at 3 Mayo Clinic sites between January 2015 and March 2017.

Results
Of 220 patients screened, 199 with SAB met study criteria and were included in the investigation. Of them, 23 (11.6%) patients were diagnosed with definite IE within 12 weeks of initial presentation based on modified Duke’s criteria. Using the previously derived PREDICT model, the day 1 score of ≥4 had a sensitivity of 30.4% and a specificity of 93.8%, whereas a day 5 score of ≤2 had a sensitivity and negative-predictive value of 100%. Additional factors including surgery or invasive procedure in the past 30 days, prosthetic heart valve, and higher number of positive blood culture bottles in the first set of cultures were associated with increased risk of IE independent of the day 5 risk score.

Conclusions
We validated the previously developed PREDICT scoring tools for stratifying risk of IE, and the need for undergoing a TEE, among cases of SAB. We also identified other factors with predictive potential, although larger prospective studies are needed to further evaluate possible enhancements to the current scoring system.
Estimation of SARS-CoV-2 Infection Fatality Rate by Real-time Antibody Screening of Blood Donors
Authors: Erikstrup Christian , Hother Christoffer Egeberg , Pedersen Ole Birger Vestager , Mølbak Kåre , Skov Robert Leo , Holm Dorte Kinggaard , Sækmose Susanne Gjørup , Nilsson Anna Christine , Brooks Patrick Terrence , Boldsen Jens Kjærgaard , Mikkelsen Christina , Gybel-Brask Mikkel , Sørensen Erik , Dinh Khoa Manh , Mikkelsen Susan , Møller Bjarne Kuno , Haunstrup Thure , Harritshøj Lene , Jensen Bitten Aagaard , Hjalgrim Henrik , Lillevang Søren Thue , Ullum Henrik 
Published: June 2020

AbstractBackgroundThe pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has tremendous consequences for our societies. Knowledge of the seroprevalence of SARS-CoV-2 is needed to accurately monitor the spread of the epidemic and to calculate the infection fatality rate (IFR). These measures may help the authorities make informed decisions and adjust the current societal interventions. The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population-based IFR.MethodsDanish blood donors aged 17–69 years giving blood 6 April to 3 May were tested for SARS-CoV-2 immunoglobulin M and G antibodies using a commercial lateral flow test. Antibody status was compared between geographical areas, and an estimate of the IFR was calculated. Seroprevalence was adjusted for assay sensitivity and specificity taking the uncertainties of the test validation into account when reporting the 95% confidence intervals (CIs).ResultsThe first 20 640 blood donors were tested, and a combined adjusted seroprevalence of 1.9% (95% CI, .8–2.3) was calculated. The seroprevalence differed across areas. Using available data on fatalities and population numbers, a combined IFR in patients &lt;70 years is estimated at 89 per 100 000 (95% CI, 72–211) infections.ConclusionsThe IFR was estimated to be slightly lower than previously reported from other countries not using seroprevalence data. The IFR is likely severalfold lower than the current estimate. We have initiated real-time nationwide anti–SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic.
Asymptomatic Transmission and the Infection Fatality Risk for COVID-19: Implications for School Reopening
Authors: Vermund Sten H , Pitzer Virginia E 
Published: June 2020

AbstractAsymptomatic infection occurs for numerous respiratory viral diseases, including influenza and coronavirus disease 2019 (COVID-19). We seek to clarify confusion in 3 areas: age-specific risks of transmission and/or disease; various definitions for the COVID-19 “mortality rate,” each useful for specific purposes; and implications for student return strategies from preschool through university settings.
Managing Coronavirus Disease 2019 Spread With Voluntary Public Health Measures: Sweden as a Case Study for Pandemic Control
Authors: Kamerlin Shina C L , Kasson Peter M 
Published: June 2020

Abstract

Background
The coronavirus disease 19 (COVID-19) pandemic has spread globally, causing extensive illness and mortality. In advance of effective antiviral therapies, countries have applied different public health strategies to control spread and manage healthcare need. Sweden has taken a unique approach of not implementing strict closures, instead urging personal responsibility. We analyze the results of this and other potential strategies for pandemic control in Sweden.

Methods
We implemented individual-based modeling of COVID-19 spread in Sweden using population, employment, and household data. Epidemiological parameters for COVID-19 were validated on a limited date range; where substantial uncertainties remained, multiple parameters were tested. The effects of different public health strategies were tested over a 160-day period, analyzed for their effects on intensive care unit (ICU) demand and death rate, and compared with Swedish data for April 2020.

Results
Swedish mortality rates are intermediate between rates for European countries that quickly imposed stringent public health controls and those for countries that acted later. Models most closely reproducing reported mortality data suggest that large portions of the population voluntarily self-isolate. Swedish ICU use rates remained lower than predicted, but a large fraction of deaths occurred in non-ICU patients. This suggests that patient prognosis was considered in ICU admission, reducing healthcare load at a cost of decreased survival in patients not admitted.

Conclusions
The Swedish COVID-19 strategy has thus far yielded a striking result: mild mandates overlaid with voluntary measures can achieve results highly similar to late-onset stringent mandates. However, this policy causes more healthcare demand and more deaths than early stringent control and depends on continued public will.