bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of the ctDNA LUNAR-2 Test In an Average Patient Screening Episode (ECLIPSE).
Authors: Raymond Victoria M. , Higashi Linda , Marino Enrique , Lang Kathryn
Published: January 2021

TPS142

Background: Population-wide colorectal cancer (CRC) screening has been recommended by the United States Preventive Task Force (USPSTF) since 2008. Despite multiple CRC screening options, screening compliance rates have plateaued well below the 80% compliance goal set by leading health organizations. Almost 1 in 3 Americans are non-compliant with screening recommendations, citing reasons that screening is time consuming, unpleasant, and in the case of colonoscopy, invasive. The potential exists for a blood-based CRC screening test with high sensitivity and specificity to improve uptake and adherence to CRC screening. Methods: ECLIPSE (Evaluation of the ctDNA LUNAR-2 Test In an Average Patient Screening Episode; NCT# 04136002) is a prospective, observational, multi-center study being conducted in the United States. The primary objective is performance of a proprietary blood-based circulating tumor DNA (ctDNA) test (LUNAR-2, Guardant Health, Redwood City, CA) developed to detect CRC in a screen-relevant, average risk population as compared to colonoscopy reference. ECLIPSE involves collection of whole blood prior to a standard of care screening colonoscopy and associated preparation from 10,000 subjects. Eligibility criteria include average risk adults age 45-84 without prior history of cancer, inflammatory bowel disease, or familial predisposition to CRC, and have not received recent CRC screening. Primary outcomes are sensitivity of CRC detection and specificity of advanced neoplasia (AN) detection. Health-related outcomes at one and two-years will be collected as secondary endpoints to investigate the possibility of incidental non-CRC cases and interval CRC cases that had not reached a clinical threshold for detection at time of colonoscopy. Additional secondary objectives are positive predictive value and negative predictive value for AN detection and sensitivity of advanced adenoma detection. Enrollment began in October 2019, continues at over 130 sites nationwide, and is on track for the 24-month enrollment goal. Study enrollment remained open despite the COVID-19 pandemic. Study features including mobile phlebotomy and remote site monitoring were implemented. This contributed to successful study execution during COVID-19, as demonstrated by the enrollment rebound observed as early as June 2020 which saw higher enrollment than prior months, even pre-COVID. Clinical trial information: NCT# 04136002.
A randomized controlled phase III trial of comparing local field with additional prophylactic irradiation in chemoradiotherapy for clinical-T1bN0M0 esophageal cancer:JCOG1904/ARMADILLO study.
Authors: Nomura Motoo , Sakanaka Katsuyuki , Kato Ken , Kadota Tomohiro , Ito Yoshinori , Machida Ryunosuke , Sasaki Keita , Kataoka Tomoko , Nishimura Yasumasa , Kitagawa Yuko
Published: January 2021

TPS257

Background:Parallel-group controlled trial of esophagectomy versus chemoradiotherapy (JCOG0502) showed chemoradiotherapy (CRT) is considered as a standard treatment option for clinical-T1bN0M0 esophageal squamous cell carcinoma (ESCC) with organ preservation. However, locoregional recurrence after CRT occurs in 20% of patients and requires salvage treatment including salvage surgery, chemo(radio)therapy, and endoscopic resection. Salvage treatments can cause complications and treatment-related death. CRT with elective nodal irradiation (ENI) have been reported to reduce the locoregional recurrence of esophageal cancer. We conduct the clinical trial to evaluate the efficacy of modified CRT with ENI compared with CRT without ENI for the patients with cTbN0M0 ESCC. The primary purpose of this study is to investigate whether modified CRT with ENI reduces the locoregional recurrence that cannot be completely resected by salvage endoscopic resection and preserve esophagus without compromising overall survival. Methods:Eligibility criteria include the followings; thoracic ESCC, adenosquamous, or basaloid cell carcinoma with clinical-T1bN0M0, age 20 or older, performance status 0 or 1, adequate organ function, and patient who do not have a preference to receive a surgical resection as an initial therapy. Patients are randomly assigned to following two arms using the minimization method with a random component to balance institution, tumor length (≤4cm versus > 4cm), and age (≤65 years old versus > 65 years old). Patients in arm A receive CRT consisted of CDDP (70 mg/m2/day, days 1 and 29) and 5-FU (700 mg/m2/day, days 1-4 and 29-32, civ) with concurrent radiotherapy (60 Gy/30 fr without ENI). Patients in arm B receive CRT consisted of CDDP (75 mg/m2/day, days 1 and 29) and 5-FU (1000 mg/m2/day, days 1-4 and 29-32, civ) with concurrent radiotherapy (50.4 Gy/ 28 fr with ENI of 41.4 Gy/23 fr). Primary endpoint is major progression-free survival (MPFS), defined as the time from randomization to the date of death or disease progression except achieving curative resection by salvage endoscopic resection. We assumed 5-year MPFS with arm A to be 70% and expected a 10% improvement for arm B. The planned sample size was calculated as a total of 280 patients (140 patients per arm) with a one-sided alpha of 5%, power of 70%, an accrual period of 4 years, and a follow-up period of 5 years. This trial was activated in July 2020. The study was also registered at the Japan Registry of Clinical Trials (jRCT) as study number jRCTs031200067. Clinical trial information: jRCTs031200067.
Phase II trial of the CDK4/6 inhibitor abemaciclib in patients (pts) with advanced and refractory well‐differentiated gastroenteropancreatic neuroendocrine tumors (GEP NETs).
Authors: Wong Kit Man , Askovich Bojana Irene , Ramachandran Harini , Hensel Jeniece , Ottermiller Susan , Alidina Annie , Hibbert Reina , Coveler Andrew L. , Thompson John A. , Chiorean Elena Gabriela
Published: January 2021

TPS376

Background: Despite advances in the treatment of advanced GEP NETs, long‐term disease control remains a challenge. Overexpression and altered regulation of cyclin-dependent kinases (CDK) 4 and 6 have been observed in multiple subtypes of GEP NETs. Preclinical studies have demonstrated that the CDK 4/6 inhibitor palbociclib reduces growth of pancreatic NET cell lines and levels of phosphorylated retinoblastoma protein in vitro. Moreover, the drug significantly inhibited tumor growth in vivo in pancreatic NET xenograft models. Abemaciclib is a selective small molecule CDK 4/6 inhibitor, approved for the treatment of HR+ HER2– metastatic breast cancer. Clinical activity and central nervous system penetration of the drug have been observed in several tumor types in clinical trials, including partial response in one pt with metastatic small intestinal NET. We have developed a Phase 2 trial of abemaciclib in GEP NETs to evaluate its efficacy and safety in these rare cancers. Methods: This is an investigator-initiated non-randomized phase 2 trial using a two-stage design. Eligible pts have metastatic or locally advanced unresectable well-differentiated grade 1-2 GEP NETs, ECOG PS 0-2, and must have progressed on at least one line of systemic therapy. Prior or concurrent treatment with somatostatin analogs is allowed,. Abemaciclib is administered at a dose of 200 mg orally every 12 hours continuously in 28-day cycles. Dose reductions for toxicities are allowed to level -1 (150 mg) and -2 (100 mg). Primary endpoint is objective response rate (ORR) by RECIST v1.1. Secondary endpoints include progression free survival (PFS), overall survival (OS), and toxicity. A two‐stage design with 88% power to detect an increase in ORR to 20% with abemaciclib at the 1‐sided 0.05 level would require a total of 37 patients. Stage 1 will include 20 patients, and if one response is seen among these patients, the study will continue to enroll another 17 patients. The trial was activated in January 2020, and 3 patients have been enrolled to date. Available archival tumor tissue and molecular profiling data are collected for future correlative studies including assessment of response biomarkers.
Long-Term Outcome and Treatment in Persistent and Transient Congenital Hyperinsulinism: A Finnish Population-Based Study
Authors: Männistö Jonna M E , Jääskeläinen Jarmo , Otonkoski Timo , Huopio Hanna
Published: January 2021

Context

The management of congenital hyperinsulinism (CHI) has improved.

Objective

To examine the treatment and long-term outcome of Finnish patients with persistent and transient CHI (P-CHI and T-CHI).

Design

A population-based retrospective study of CHI patients treated from 1972 to 2015.

Patients

106 patients with P-CHI and 132 patients with T-CHI (in total, 42 diagnosed before and 196 after year 2000) with median follow-up durations of 12.5 and 6.2 years, respectively.

Main Outcome Measures

Recovery, diabetes, pancreatic exocrine dysfunction, neurodevelopment.

Results

The overall incidence of CHI (n = 238) was 1:11 300 live births (1972-2015). From 2000 to 2015, the incidence of P-CHI (n = 69) was 1:13 500 and of T-CHI (n = 127) 1:7400 live births. In the 21st century P-CHI group, hyperinsulinemic medication was initiated and normoglycemia achieved faster relative to earlier. Of the 74 medically treated P-CHI patients, 68% had discontinued medication. Thirteen (12%) P-CHI patients had partial pancreatic resection and 19 (18%) underwent near-total pancreatectomy. Of these, 0% and 84% developed diabetes and 23% and 58% had clinical pancreatic exocrine dysfunction, respectively. Mild neurological difficulties (21% vs 16%, respectively) and intellectual disability (9% vs 5%, respectively) were as common in the P-CHI and T-CHI groups. However, the 21st century P-CHI patients had significantly more frequent normal neurodevelopment and significantly more infrequent diabetes and pancreatic exocrine dysfunction compared with those diagnosed earlier.

Conclusions

Our results demonstrated improved treatment and long-term outcome in the 21st century P-CHI patients relative to earlier.
Mammary Tumors Growing in the Absence of Growth Hormone Are More Sensitive to Doxorubicin Than Wild-Type Tumors
Authors: Lantvit Daniel D , Unterberger Christopher J , Lazar Michelle , Arneson Paige D , Longhurst Colin A , Swanson Steven M , Marker Paul C
Published: January 2021

Previously, we reported that N-methyl-N-nitrosourea (MNU)-induced mammary tumors could be established in mutant spontaneous dwarf rats (SDRs), which lack endogenous growth hormone (GH) by supplementing with exogenous GH, and almost all such tumors regressed upon GH withdrawal. When the highly inbred SDR line was outcrossed to wild-type (WT) Sprague-Dawley rats, MNU-induced mammary tumors could still be established in resulting outbred SDRs by supplementing with exogenous GH. However, unlike tumors in inbred SDRs, 65% of mammary tumors established in outbred SDRs continued growth after GH withdrawal. We further tested whether these tumors were more sensitive to doxorubicin than their WT counterparts. To accomplish this, MNU-induced mammary tumors were established in WT rats and in SDRs supplemented with exogenous GH. Once mammary tumors reached 1 cm3 in size, exogenous GH was withdrawn from SDRs, and the subset that harbored tumors that continued or resumed growth in the absence of GH were selected for doxorubicin treatment. Doxorubicin was then administered in 6 injections over 2 weeks at 2.5 mg/kg or 1.25 mg/kg for both the WT and SDR groups. The SDR mammary tumors that had been growing in the absence of GH regressed at both doxorubicin doses while WT tumors continued to grow robustly. The regression of SDR mammary tumors treated with 1.25 mg/kg doxorubicin was accompanied by reduced proliferation and dramatically higher apoptosis relative to the WT mammary tumors treated with 1.25 mg/kg doxorubicin. These data suggest that downregulating GH signaling may decrease the doxorubicin dose necessary to effectively treat breast cancer.
EFA6A, an exchange factor for Arf6, regulates early steps in ciliogenesis
Authors: Partisani Mariagrazia , Baron Carole L. , Ghossoub Rania , Fayad Racha , Pagnotta Sophie , Abélanet Sophie , Macia Eric , Brau Frédéric , Lacas-Gervais Sandra , Benmerah Alexandre , Luton Frédéric , Franco Michel
Published: January 2021

Ciliogenesis is a coordinated process initiated by the recruitment and fusion of pre-ciliary vesicles at the distal appendages of the mother centriole through mechanisms that remain unclear. Here, we report that EFA6A (also known as PSD), an exchange factor for the small G protein Arf6, is involved in early stage of ciliogenesis by promoting the fusion of distal appendage vesicles forming the ciliary vesicle. EFA6A is present in the vicinity of the mother centriole before primary cilium assembly and prior to the arrival of Arl13B-containing vesicles. During ciliogenesis, EFA6A initially accumulates at the mother centriole and later colocalizes with Arl13B along the ciliary membrane. EFA6A depletion leads to the inhibition of ciliogenesis, the absence of centrosomal Rab8-positive structures and the accumulation of Arl13B-positive vesicles around the distal appendages. Our results uncover a novel fusion machinery, comprising EFA6A, Arf6 and Arl13B, that controls the coordinated fusion of ciliary vesicles docked at the distal appendages of the mother centriole.
Sexual organ-sparing with hydrogel spacer injections for rectal cancer radiotherapy: a feasibility pilot study
Authors: Achard Vérane , Ris Frederic , Rouzaud Michel , Puppa Giacomo , Buchs Nicolas C , De Perrot Thomas , Koessler Thibaud , Picardi Cristina , Zilli Thomas
Published: January 2021

Objectives:

The aim of this pilot study was to investigate in two rectal cancer patients undergoing neoadjuvant chemo-radiotherapy (nCRT) the implant feasibility and dosimetric benefit in sexual organ-sparing of an injectable, absorbable, radiopaque hydrogel spacer.

Methods:

Two rectal cancer patients (one male and one female) underwent hydrogel implant between rectum and vagina/prostate before nCRT and curative surgery. A CT scan was performed before and after injection and a comparative dosimetric study was performed testing a standard (45/50 Gy) and a dose escalated (46/55.2 Gy) schedule.

Results:

In both patients, the spacer implant in the recto-prostatic or recto-vaginal space was feasible and well tolerated. For the male, the dosimetric benefit with spacer was minimal for sexual organs. For the female however, doses delivered to the vagina were significantly reduced with spacer with a mean reduction of more than 5 Gy for both regimens.

Conclusions:

For organ preservation protocols and selected sexually active female patients, use of hydrogel spacers can be considered to spare sexual organs from the high radiotherapy dose levels.

Advances in knowledge:

For females with advanced rectal tumor, a spacer implant between the rectum and the vagina before nCRT is feasible and reduces doses delivered to the vagina.
The emerging structural complexity of G-quadruplex RNAs
Authors: Banco Michael T. , Ferré-D'Amaré Adrian R.
Published: January 2021

G-quadruplexes (G4s) are four-stranded nucleic acid structures that arise from the stacking of G-quartets, cyclic arrangements of four guanines engaged in Hoogsteen base-pairing. Until recently, most RNA G4 structures were thought to conform to a sequence pattern in which guanines stacking within the G4 would also be contiguous in sequence (e.g., four successive guanine trinucleotide tracts separated by loop nucleotides). Such a sequence restriction, and the stereochemical constraints inherent to RNA (arising, in particular, from the presence of the 2′-OH), dictate relatively simple RNA G4 structures. Recent crystallographic and solution NMR structure determinations of a number of in vitro selected RNA aptamers have revealed RNA G4 structures of unprecedented complexity. Structures of the Sc1 aptamer that binds an RGG peptide from the Fragile-X mental retardation protein, various fluorescence turn-on aptamers (Corn, Mango, and Spinach), and the spiegelmer that binds the complement protein C5a, in particular, reveal complexity hitherto unsuspected in RNA G4s, including nucleotides in syn conformation, locally inverted strand polarity, and nucleotide quartets that are not all-G. Common to these new structures, the sequences folding into G4s do not conform to the requirement that guanine stacks arise from consecutive (contiguous in sequence) nucleotides. This review highlights how emancipation from this constraint drastically expands the structural possibilities of RNA G-quadruplexes.
netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks
Authors: Pai Shraddha , Weber Philipp , Isserlin Ruth , Kaka Hussam , Hui Shirley , Shah Muhammad Ahmad , Giudice Luca , Giugno Rosalba , Nøhr Anne Krogh , Baumbach Jan , Bader Gary D.
Published: January 2021

Patient classification based on clinical and genomic data will further the goal of precision medicine. Interpretability is of particular relevance for models based on genomic data, where sample sizes are relatively small (in the hundreds), increasing overfitting risk netDx is a machine learning method to integrate multi-modal patient data and build a patient classifier. Patient data are converted into networks of patient similarity, which is intuitive to clinicians who also use patient similarity for medical diagnosis. Features passing selection are integrated, and new patients are assigned to the class with the greatest profile similarity. netDx has excellent performance, outperforming most machine-learning methods in binary cancer survival prediction. It handles missing data – a common problem in real-world data – without requiring imputation. netDx also has excellent interpretability, with native support to group genes into pathways for mechanistic insight into predictive features.

The netDx Bioconductor package provides multiple workflows for users to build custom patient classifiers. It provides turnkey functions for one-step predictor generation from multi-modal data, including feature selection over multiple train/test data splits. Workflows offer versatility with custom feature design, choice of similarity metric; speed is improved by parallel execution. Built-in functions and examples allow users to compute model performance metrics such as AUROC, AUPR, and accuracy. netDx uses RCy3 to visualize top-scoring pathways and the final integrated patient network in Cytoscape. Advanced users can build more complex predictor designs with functional building blocks used in the default design. Finally, the netDx Bioconductor package provides a novel workflow for pathway-based patient classification from sparse genetic data.
IMPORTANCE trial: a provisional study-design of a single-center, phase II, double-blinded, placebo-controlled, randomized, 4-week study to compare the efficacy and safety of intranasal esketamine in chronic opioid refractory pain
Authors: Fernandes Mauricio , Schelotto Magdalena , Doldi Philipp Maximilian , Milani Giovanna , Ariza Manzano Abul Andrés , Perera Valdivia Doriam , Winter Matos Alexandra Marie , Hamdy Abdelrahim Yasmin , Hamad Bek Shaza Ahmed , Benitez Benito K. , Romanelli Tavares Vanessa Luiza , Basendwah Abdulrahim M. , Albuquerque Sousa Luis Henrique , Xavier Naiara Faria , Zertuche Maldonado Tania , Toyomi de Oliveira Sarah , Chaker Melisa , Menon Miyake Michelle , Uygur Kucukseymen Elif , Waqar Kinza , Alkhozondar Ola M.J. , Bernardo da Silva Ricardo , Droppelmann Guilhermo , Vaz de Macedo Antonio , Nakamura Rui , Fregni Felipe
Published: January 2021

Background:  Cancer is the second leading cause of death globally. Up to 86% of advanced cancer patients experience significant pain, while 10-20% live in chronic pain. Besides, increasing prescription of opioids resulted in 33,000 deaths in the US in 2015. Both reduce patients’ functional status and quality of life. While cancer survival rates are increasing, therapeutic options for chronic opioid refractory pain are still limited. Esketamine is the s-enantiomer of ketamine, with superior analgesic effect and less psychotomimetic side effects. Intranasal esketamine was approved by the FDA for treatment-resistant depression. However, its use in chronic cancer pain has never been tested. Therefore, we propose a phase II, randomized, placebo-controlled trial to evaluate the efficacy and safety of intranasal esketamine in chronic opioid refractory cancer pain.

Methods and analysis: We will recruit 120 subjects with chronic opioid refractory pain, defined as pain lasting more than 3 months despite optimal therapy with high dose opioids (>60 mg morphine equivalent dose/day) and optimal adjuvant therapy. Subjects will be randomized into two groups: intranasal esketamine (56mg) and placebo. Treatment will be administered twice a week for four consecutive weeks. The primary outcome is defined as reduction in the Numeric Pain Rating Scale (NPRS) after first application. Secondary outcomes include NPRS reduction after four weeks, the number of daily morphine rescue doses, functional status and satisfaction, and depression.

Conclusion: This study may extend therapeutic options in patients with chronic pain, thus improving their quality of life and reducing opioid use.

Trial registration: Clinical Trials.gov, NCT04666623. Registered on 14 December 2020
6th European Student Council Symposium (ESCS): overcoming obstacles to enhance virtuality, connectivity, inclusivity and community engagement
Authors: Olguín-Orellana Gabriel J. , Papadimitriou Sofia , Langtry Yáñez Alberto , Eranti Pradeep , Flores-Vallejo Rosario del Carmen , Castillo-Orozco Ana I. , Mayoral-Peña Kalaumari , Parra R. Gonzalo
Published: January 2021

This editorial summarises the organisation, activities, and scientific content of the 6th European Student Council Symposium (ESCS) organised by the International Society for Computational Biology Student Council (ISCB-SC). The event was held on September 6, 2020, as a satellite event preceding the ISCB’s  19th European Conference in Computational Biology. Both events were first planned to be held in-person in Sitges, Spain, but moved virtually as a strategy to face the SARS-CoV2 sanitary crisis. This completely unforeseen situation has posed several challenges that have been successfully addressed thanks to the robust ISCB Student Council community structure and the strong commitment of the organisers. Despite all the obstacles and challenges, we have found that virtuality has several advantages that can continue to be kept to improve in-person meetings in the future and make conferences more inclusive allowing a larger audience to participate.
Selfishness Need Not Be Bad
Authors: Wu Zijun , Möhring Rolf H. , Chen Yanyan , Xu Dachuan
Published: January 2021

The price of anarchy (PoA) is a standard measure for the inefficiency of selfish routing in the static Wardrop traffic model. Empirical studies and a recent analysis reveal a surprising property that the PoA tends to one when the total demand T gets large. These results are extended by a new framework for the limit analysis of the PoA in arbitrary nonatomic congestion games that apply to arbitrary growth patterns of T and all regularly varying cost functions. For routing games with Bureau of Public Road (BPR) cost functions, the convergence follows a power law determined by the degree of the BPR functions, and a related conjecture need not hold. These findings are confirmed by an empirical analysis of traffic in Beijing.
Dielectric Properties of Switchgrass and Corn Stover in the Radio Frequency Range
Authors: Souza Augusto M. , Birrell Stuart J. , Steward Brian L.
Published: January 2021

Highlights

Dielectric permittivities of switchgrass and corn stover in the radio frequency range were calculated.

Prediction models achieved R2 > 0.9, except for the switchgrass loss factor for the material in motion.

The loss factors were different when static and in motion, but the dielectric constants were similar.

Abstract. The dielectric properties of biological materials are relevant when developing moisture content sensors. However, little is known about the permittivities of switchgrass and corn stover in a wider frequency range. The goal of this research was to determine their dielectric constants and loss factors at different moisture contents across a frequency range of 5 Hz to 13 MHz and with the material static and in motion inside a sample container. The permittivity of these materials was calculated by measuring their admittance in a test fixture using an impedance analyzer at three different moisture levels (9.0% to 30.5%). Overall, the materials’ dielectric properties increased with moisture but decreased with frequency. Prediction models were developed using the data in a frequency range of 10 kHz to 5 MHz. Model coefficients of determination were higher than 0.90 in general, except for the model measuring the loss factor of switchgrass in motion. Additionally, the dielectric constant was not different with the materials static or in motion, but the loss factor values were distinct. This work can be used for the development of electrical moisture content sensors for switchgrass and corn stover. Keywords: Corn stover, Dielectric constant, Loss factor, Moisture content, Permittivity, Switchgrass.
When evidence alone is not enough: the problem, policy and politics of water fluoridation in England
Authors: Lowery Gary , Flinders Matthew , Gibson Barry J.
Published: January 2021

Background:

Tooth extractions are the most common cause of hospital admissions for children in England. Water fluoridation has the potential to reduce this number by 60%, is backed by the scientific and public health communities, and yet is currently consumed by only 10% of the population.

Aims and objectives:

This ‘evidence-policy gap’ is explored through Kingdon’s ‘multi-streams approach’ which provides insights into the circumstances under which water fluoridation has made it onto the political agenda, the rationale underpinning opponent and advocate policy positions, and the role of the political arena in fostering or hindering policy action.

Methods:

Over 100 primary documents were reviewed to develop an understanding of the scientific and ethical arguments for and against water fluoridation, as well as to identify how they have all historically sought to mobilise their policy preferences. Eleven consultations were also conducted with stakeholders as part of the knowledge exchange process.

Findings:

The key finding of this research is that evidence is only likely to trigger policy change if it emerges into a receptive sociopolitical context. In substantiating this claim we identify evidence not of an ‘evidence-policy gap’ but of a more complex and multidimensional ‘evidence-policy-politics gap’.

Discussion and conclusions:

The findings contribute to a range of debates in relation to: (1) the apparent irreconcilability of background ideas about what ought to form the basis of public health policymaking; (2) the presence of differing evidential standards that create an uneven playing field; and (3) the central underpinning role of politics in public health policymaking.
On-line three-dimensional coordinate measurement of dynamic binocular stereo vision based on rotating camera in large FOV
Authors: Wang Yue , Wang Xiangjun
Published: January 2021

A dynamic binocular stereo vision (DBSV) based on a non-zoom rotating camera in a large field of view (FOV) is established herein. A novel two-point method is proposed to estimate the initial parameters of the camera quickly. The intrinsic parameters and roll angle of each camera remains constant, and the pitch and yaw angles after the camera rotates are directly estimated from output of high-precision two-axes platform, which makes it possible that three-dimensional (3D) coordinate can be measured online after rotation. Moreover, a target matching algorithm based on moving DLT is proposed to achieve automatic alignment of the camera. The accuracy of 3D coordinate measurement is evaluated on various synthetic and real data, and the DBSV is suitable for occasions where extremely high accuracy is not required in large FOV.
Multiplexing-oriented plasmon-MoS2 hybrid metasurfaces driven by nonlinear quasi bound states in the continuum
Authors: Ren Qun , Feng Feng , Yao Xiang , Xu Quan , Xin Ming , Lan Zhihao , You Jianwei , Xiao Xiaofei , Sha Wei E. I.
Published: January 2021

Rapid progress in nonlinear plasmonic metasurfaces enabled many novel optical characteristics for metasurfaces, with potential applications in frequency metrology [Zimmermann et al. Opt. Lett. 29:310 (2004)], timing characterization [Singh et al. Laser Photonics Rev. 14:1 (2020)] and quantum information [Kues et al. Nature. 546:622 (2017)]. However, the spectrum of nonlinear optical response was typically determined from the linear optical resonance. In this work, a wavelength-multiplexed nonlinear plasmon-MoS2 hybrid metasurface with suppression phenomenon was proposed, where multiple nonlinear signals could to be simultaneously processed and optionally tuned. A clear physical picture to depict the nonlinear plasmonic bound states in the continuum (BICs) was presented, from the perspective of both classical and quantum approaches. Particularly, beyond the ordinary plasmon-polariton effect, we numerically demonstrated a giant BIC-inspired second-order nonlinear susceptibility 10−5 m/V of MoS2 in the infrared band. The novelty in our study lies in the presence of a quantum oscillator that can be adopted to both suppress and enhance the nonlinear quasi BICs. This selectable nonlinear BIC-based suppression and enhancement effect can optionally block undesired modes, resulting in narrower linewidth as well as smaller quantum decay rates, which is also promising in slow-light-associated technologies.
Macroscopic wave-optical simulation of dielectric metasurfaces
Authors: Linss Sebastian , Michaelis Dirk , Zeitner Uwe D.
Published: January 2021

We propose a novel method for the wave-optical simulation of diffractive optical elements (DOEs) like metasurfaces or computer-generated holograms (CGHs). Existing techniques mostly rely on the assumption of local periodicity to predict the performance of elements. The utilization of a specially adapted finite-difference beam propagation method (BPM) allows the semi-rigorous simulation of entire DOEs within a reasonable runtime due to linear scaling with the number of grid points. Its applicability is demonstrated by the simulation of a metalens and a polarization-dependent beamsplitter, both based on effective-medium metasurfaces. A comparison shows high conformity to rigorous simulations.
Investigation of spatiotemporal output beam profile instabilities from differentially pumped capillaries
Authors: Gebhardt Martin , Amuah Emmanuel B. , Klas Robert , Stark Henning , Buldt Joachim , Steinkopff Albrecht , Limpert Jens
Published: January 2021

Differentially pumped capillaries, i.e., capillaries operated in a pressure gradient environment, are widely used for nonlinear pulse compression. In this work, we show that strong pressure gradients and high gas throughputs can cause spatiotemporal instabilities of the output beam profile. The instabilities occur with a sudden onset as the flow evolves from laminar to turbulent. Based on the experimental and numerical results, we derive guidelines to predict the onset of those instabilities and discuss possible applications in the context of nonlinear flow dynamics.
Broadband achromatic metasurfaces for sub-diffraction focusing in the visible
Authors: Lu Xinjian , Guo Yinghui , Pu Mingbo , Zhang Yaxin , Li Zhu , Li Xiong , Ma Xiaoliang , Luo Xiangang
Published: January 2021

Conventional achromatic optical systems are matured to achieve effective chromatic aberration correction and diffraction-limited resolution by the multiple bulky lenses. The emergence of the super-oscillation phenomenon provides an effective method for non-invasive far-field super-resolution imaging. Nevertheless, most super-oscillatory lenses are significantly restricted by the chromatic aberration due to the reliance on delicate interference; on the other hand, most achromatic lenses cannot break the diffraction limit. In this article, a single-layer broadband achromatic metasurface comprising sub-wavelength anisotropic nanostructures has been proposed to achieve sub-diffraction focusing with a focal length of f=60 µm and a diameter of 20 µm in the visible ranging from 400 nm to 700 nm, which are capable of generating sub-diffraction focal spots under the left-handed circularly polarized incident light with arbitrary wavelength in the working bandwidth at the same focal plane. This method may find promising potentials in various applications such as super-resolution color imaging, light field cameras, and machine vision.
Tight focusing properties and focal field tailoring of cylindrical vector beams generated from a linearly polarized coherent beam array
Authors: Zhang Yuqiu , Hou Tianyue , Chang Hongxiang , Yu Tao , Chang Qi , Jiang Man , Ma Pengfei , Su Rongtao , Zhou Pu
Published: January 2021

We investigate the focusing properties of cylindrical vector beams (CVBs) generated from the combination of an array of beams, each with sub-apertures and controllable polarization. The analytical expression of the tight focusing field of the combined CVBs has been derived based on the Richard-Wolf vector diffraction integral. To obtain a desired focal spot size which includes efficient sidelobe suppression, the required parameters, such as the exit sub-aperture, numerical aperture and truncation parameter, have been studied in detail. The result shows that the combined CVB distribution has a good match with the theoretical ideal CVB distribution. However, compared with the ideal CVBs, the focal spot width produced by the combined radially polarized beams is smaller. With the increase of initial polarization rotation of sub-aperture, the focal spot width increases, and the focal shape shifts from Gaussian-like to a flat-topped distribution and then to an annular distribution. Furthermore, flexible focal field tailoring can also be realized by adjusting the initial polarization rotation of each sub-aperture. These results might provide a valuable reference for material processing, microlithography and multi-particle manipulation.
Discrete Ordinate Adding Method (DOAM), a new solver for Advanced Radiative transfer Modeling System (ARMS)
Authors: Shi Yi-Ning , Yang Jun , Weng Fuzhong
Published: January 2021

Satellite data assimilation requires a computationally fast and accurate radiative transfer model. Currently, three fast models are commonly used in the Numerical Weather Prediction models (NWP) for satellite data assimilation, including Radiative Transfer for TIROS Operational Vertical Sounder (RTTOV), Community Radiative Transfer Model (CRTM), and Advanced Radiative transfer Modeling System (ARMS). ARMS was initiated in 2018 and is now becoming the third pillar supporting many users in NWP and remote sensing fields. Its radiative transfer solvers (e.g. Doubling Adding method) is inherited from CRTM. In this study, we propose a Discrete Ordinate Adding Method (DOAM) to solve the radiative transfer equation including both solar and thermal source terms. In order to accelerate the DOAM computation, the single scattering approximation is used in the layer with an optical depth less than 10−8 or a single scattering albedo less than 10−10. From principles of invariance, the adding method is then applied to link the radiances between the layers. The accuracy of DOAM is evaluated through four benchmark cases. It is shown that the difference between DOAM and DIScrete Ordinate Radiative Transfer (DISORT) decreases with an increase of stream number. The relative bias of the 4-stream DOAM ranges from -5.03 % to 5.92 % in the triple layers of a visible wavelength case, while the maximum bias of the 8-stream DOAM is only about 1 %. The biases can be significantly reduced by the single scattering correction. Comparing to the visible case, the accuracy of the 4-stream DOAM is much higher in the thermal case with a maximum bias -1.69 %. Similar results are also shown in two multiple-layer cases. In the MacBook Pro (15-inch, 2018) laptop, the 2-stream DOAM only takes 1.68 seconds for calculating azimuthally independent radiance of 3000 profiles in the hyper-spectral oxygen A-band (wavelength ranges from 0.757 µm to 0.775 µm), while the 4-stream DOAM takes 4.06 seconds and the 16-stream DOAM takes 45.93 seconds. The time of the 2-, 4- and 16- stream DOAM are 0.86 seconds, 1.09 seconds and 4.34 seconds for calculating azimuthally averaged radiance. DISORT with 16 streams takes 1521.56 seconds and 127.64 seconds under the same condition. As a new solver, DOAM has been integrated into ARMS and is used to simulate the brightness temperatures at MicroWave Humidity Sounder (MWHS) as well as MicroWave Radiation Imager (MWRI) frequencies. The simulations by DOAM are compared to those by Doubling Adding method and accuracy of both solvers shows a general agreement. All the results show that the DOAM is accurate and computational efficient for applications in NWP data assimilation and satellite remote sensing.
Bidirectional band-switchable nano-film absorber from narrowband to broadband
Authors: Wang Fei , Gao Huixuan , Peng Wei , Li Rui , Chu Shuwen , Yu Li , Wang Qiao
Published: January 2021

We propose a switchable perfect absorber with broadband and narrowband absorption based on alternating dielectric and metal nano-film structures in this paper. The lithography-free pattern is equipped with polarization insensitivity, good ductility and manufacturability, which has great significance in practical device development and applications. The quasi-complete selective absorption of incident light can be originated from asymmetric Fabry-Perot resonance, which combines the destructive interference in dielectric layers with inherent absorption in metal layers. When the light incidents on the surface covered with ultra-thin metal film of this structure, it acts as a narrowband absorber with over 99.90% absorption at 771 nm wavelength and a full wave at half maximum of 20 nm. When the light incidents on other surfaces covered with anti-reflective dielectric film, it achieves broadband perfect absorption with an average absorption exceeding 96.02% in a 500-1450 nm wavelength range. The absorption spectrum of oblique incidence shows that the broadband absorption behaves big angle range tolerance while the narrowband absorption exhibits angular dependence. The band-switchable performance of this absorber makes it valuable for energy harvesting/re-radiation applications in solar thermal photovoltaic systems.
Mitigating photorefractive effect in thin-film lithium niobate microring resonators
Authors: Xu Yuntao , Shen Mohan , Lu Juanjuan , Surya Joshua B. , Sayem Ayed Al , Tang Hong X.
Published: January 2021

Thin-film lithium niobate is an attractive integrated photonics platform due to its low optical loss and favorable optical nonlinear and electro-optic properties. However, in applications such as second harmonic generation, frequency comb generation, and microwave-to-optics conversion, the device performance is strongly impeded by the photorefractive effect inherent in thin-film lithium niobate. In this paper, we show that the dielectric cladding on a lithium niobate microring resonator has a significant influence on the photorefractive effect. By removing the dielectric cladding layer, the photorefractive effect in lithium niobate ring resonators can be effectively mitigated. Our work presents a reliable approach to control the photorefractive effect on thin-film lithium niobate and will further advance the performance of integrated classical and quantum photonic devices based on thin-film lithium niobate.
Towards smart optical focusing: deep learning-empowered dynamic wavefront shaping through nonstationary scattering media
Authors: Luo Yunqi , Yan Suxia , Li Huanhao , Lai Puxiang , Zheng Yuanjin
Published: January 2021

Optical focusing through scattering media is of great significance yet challenging in lots of scenarios, including biomedical imaging, optical communication, cybersecurity, three-dimensional displays, etc. Wavefront shaping is a promising approach to solve this problem, but most implementations thus far have only dealt with static media, which, however, deviates from realistic applications. Herein, we put forward a deep learning-empowered adaptive framework, which is specifically implemented by a proposed Timely-Focusing-Optical-Transformation-Net (TFOTNet), and it effectively tackles the grand challenge of real-time light focusing and refocusing through time-variant media without complicated computation. The introduction of recursive fine-tuning allows timely focusing recovery, and the adaptive adjustment of hyperparameters of TFOTNet on the basis of medium changing speed efficiently handles the spatiotemporal non-stationarity of the medium. Simulation and experimental results demonstrate that the adaptive recursive algorithm with the proposed network significantly improves light focusing and tracking performance over traditional methods, permitting rapid recovery of an optical focus from degradation. It is believed that the proposed deep learning-empowered framework delivers a promising platform towards smart optical focusing implementations requiring dynamic wavefront control.
Seipin traps triacylglycerols to facilitate their nanoscale clustering in the endoplasmic reticulum membrane
Authors: Prasanna Xavier , Salo Veijo T. , Li Shiqian , Ven Katharina , Vihinen Helena , Jokitalo Eija , Vattulainen Ilpo , Ikonen Elina
Published: January 2021

Seipin is a disk-like oligomeric endoplasmic reticulum (ER) protein important for lipid droplet (LD) biogenesis and triacylglycerol (TAG) delivery to growing LDs. Here we show through biomolecular simulations bridged to experiments that seipin can trap TAGs in the ER bilayer via the luminal hydrophobic helices of the protomers delineating the inner opening of the seipin disk. This promotes the nanoscale sequestration of TAGs at a concentration that by itself is insufficient to induce TAG clustering in a lipid membrane. We identify Ser166 in the α3 helix as a favored TAG occupancy site and show that mutating it compromises the ability of seipin complexes to sequester TAG in silico and to promote TAG transfer to LDs in cells. While the S166D-seipin mutant colocalizes poorly with promethin, the association of nascent wild-type seipin complexes with promethin is promoted by TAGs. Together, these results suggest that seipin traps TAGs via its luminal hydrophobic helices, serving as a catalyst for seeding the TAG cluster from dissolved monomers inside the seipin ring, thereby generating a favorable promethin binding interface.
DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
Authors: Tesei Giulio , Martins João M. , Kunze Micha B. A. , Wang Yong , Crehuet Ramon , Lindorff-Larsen Kresten
Published: January 2021

Owing to their plasticity, intrinsically disordered and multidomain proteins require descriptions based on multiple conformations, thus calling for techniques and analysis tools that are capable of dealing with conformational ensembles rather than a single protein structure. Here, we introduce DEER-PREdict, a software program to predict Double Electron-Electron Resonance distance distributions as well as Paramagnetic Relaxation Enhancement rates from ensembles of protein conformations. DEER-PREdict uses an established rotamer library approach to describe the paramagnetic probes which are bound covalently to the protein.DEER-PREdict has been designed to operate efficiently on large conformational ensembles, such as those generated by molecular dynamics simulation, to facilitate the validation or refinement of molecular models as well as the interpretation of experimental data. The performance and accuracy of the software is demonstrated with experimentally characterized protein systems: HIV-1 protease, T4 Lysozyme and Acyl-CoA-binding protein. DEER-PREdict is open source (GPLv3) and available at github.com/KULL-Centre/DEERpredict and as a Python PyPI package pypi.org/project/DEERPREdict.
Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies
Authors: Keeling Matt J. , Hill Edward M. , Gorsich Erin E. , Penman Bridget , Guyver-Fletcher Glen , Holmes Alex , Leng Trystan , McKimm Hector , Tamborrino Massimiliano , Dyson Louise , Tildesley Michael J.
Published: January 2021

Efforts to suppress transmission of SARS-CoV-2 in the UK have seen non-pharmaceutical interventions being invoked. The most severe measures to date include all restaurants, pubs and cafes being ordered to close on 20th March, followed by a “stay at home” order on the 23rd March and the closure of all non-essential retail outlets for an indefinite period. Government agencies are presently analysing how best to develop an exit strategy from these measures and to determine how the epidemic may progress once measures are lifted. Mathematical models are currently providing short and long term forecasts regarding the future course of the COVID-19 outbreak in the UK to support evidence-based policymaking. We present a deterministic, age-structured transmission model that uses real-time data on confirmed cases requiring hospital care and mortality to provide up-to-date predictions on epidemic spread in ten regions of the UK. The model captures a range of age-dependent heterogeneities, reduced transmission from asymptomatic infections and produces a good fit to the key epidemic features over time. We simulated a suite of scenarios to assess the impact of differing approaches to relaxing social distancing measures from 7th May 2020 on the estimated number of patients requiring inpatient and critical care treatment, and deaths. With regard to future epidemic outcomes, we investigated the impact of reducing compliance, ongoing shielding of elder age groups, reapplying stringent social distancing measures using region based triggers and the role of asymptomatic transmission. We find that significant relaxation of social distancing measures from 7th May onwards can lead to a rapid resurgence of COVID-19 disease and the health system being quickly overwhelmed by a sizeable, second epidemic wave. In all considered age-shielding based strategies, we projected serious demand on critical care resources during the course of the pandemic. The reintroduction and release of strict measures on a regional basis, based on ICU bed occupancy, results in a long epidemic tail, until the second half of 2021, but ensures that the health service is protected by reintroducing social distancing measures for all individuals in a region when required. Our work confirms the effectiveness of stringent non-pharmaceutical measures in March 2020 to suppress the epidemic. It also provides strong evidence to support the need for a cautious, measured approach to relaxation of lockdown measures, to protect the most vulnerable members of society and support the health service through subduing demand on hospital beds, in particular bed occupancy in intensive care units.