bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing damages of agricultural land due to flooding in a lagoon region based on remote sensing and GIS: case study of the Quang Dien district, Thua Thien Hue province, central Vietnam
Authors: NGUYEN Ngoc Bich , NGUYEN Ngu Huu , TRAN Duc Thanh , TRAN Phuong Thi , PHAM Tung Gia , NGUYEN Tri Minh
Published: February 2021

This study aims to create a flood extent map with Sentinel imagery and to evaluate impacts on agricultural land in the lagoon region of central Vietnam. In this study, remote sensing images, obtained from 2017 to 2019, were used to simultaneously map the land cover status of a flood in the Quang Dien district. This study highlights flooded areas from Sentinel-2 images by calculating some indicators such as the Land Surface Water Index (LSWI) and the Enhanced Vegetation Index (EVI). Comparisons between the floodplain samples (GPS point-based) and flood mapping results, with the ground-truth data, indicate that the overall accuracy and Kappa coefficients were 97.9% and 0.62 respectively for 2017; the values for 2019 were 95.7% and 0.77 for the same coefficients. Land use maps overlying the flood-affected maps show that approximately 11% of the agriculture land area was affected by floods in 2019 comparison to a 10% in 2017. Wet rice was the most affected crop with the flooded area accounting for more than 70% of the district under each flood event. The most affected communes are: Quang An, Quang Phuoc and Quang Thanh. This study provides valuable information for flood disaster planning, mitigation and recovery activities in Vietnam.

Mục tiêu của nghiên cứu là lập bản đồ phân bố ngập lụt với hình ảnh vệ tinh Sentinel và đánh giá ảnh hưởng ngập lụt đến sử dụng đất nông nghiệp ở vùng đầm phá miền Trung, Việt Nam. Trong nghiên cứu này, ảnh viễn thám thu nhận giai đoạn 2017- 2019 được sử dụng để xây dựng bản đồ hiện trạng sử dụng đất tại thời điểm bị ngập nước trên địa bàn huyện Quảng Điền. Nghiên cứu đã xác định được vùng ngập lụt ở huyện Quảng Điền bằng phương pháp phân loại chỉ số mặt nước (Land Surface Water Index – LSWI) và chỉ số khác biệt thực vật (Enhanced Vegetation Index-EVI) từ ảnh Sentinel-2. Xác định vùng nước lũ bị che khuất bởi mây bằng mô hình số hóa độ cao (DEM). Kết quả phân loại vùng ngập lụt được so sánh với giá trị tham chiếu mặt đất cho thấy độ chính xác tổng thể và hệ số Kappa đạt được trong năm 2017 là 97,9% và 0,62; trong khi năm 2019 đạt 95,7% và 0.77. Bản đồ sử dụng đất chồng lên bản đồ lũ lụt cho thấy khoảng 11% diện tích đất nông nghiệp bị ảnh hưởng bởi lũ lụt năm 2019 so với 10% năm 2017. Cây lúa nước là cây trồng bị ảnh hưởng nặng nề nhất, với diện tích bị ngập lụt chiếm hơn 70% diện tích lúa của huyện. Các xã bị ngập lớn là xã Quảng An, Quảng Phước và Quảng Thành. Nghiên cứu này cung cấp thông tin có giá trị cho các hoạt động lập kế hoạch, giảm nhẹ và phục hồi thiên tai lũ lụt ở Việt Nam.
Estudiantes de ciencias jurídicas y trabajos de investigación: análisis de los derechos de propiedad intelectual sobre el TFG, el TFM y la Tesis Doctoral
Authors: Llopis Nadal Patricia
Published: February 2021

El objetivo de este artículo es analizar los derechos de propiedad intelectual sobre los trabajos elaborados por quienes cursan estudios universitarios, con particular referencia a los TFG, TFM y tesis doctorales que se realizan en el ámbito de la ciencia jurídica. Para ello, en primer lugar, se examina la posibilidad de que el trabajo de investigación sea merecedor de la condición de obra; en segundo lugar, se clarifica la cuestión relativa a la titularidad de los derechos de autor sobre estos trabajos; y, en tercer lugar, se reflexiona en torno a la obligación de dejar las obras en repositorios institucionales de acceso abierto.
Docentes, discentes y trabajos académicos: Propiedad Intelectual en conflicto
Authors: Ramón Fernández Francisca , Giménez Chornet Vicent , Oltra Gutiérrez Juan Vicente
Published: February 2021

La participación del profesorado en la dirección de trabajos en el ámbito universitario plantea diversas cuestiones en relación con la protección de los derechos de autor. La orientación, líneas a seguir, así como la dedicación e implicación en la redacción del trabajo del alumnado no se contemplan como objeto protegido por la propiedad intelectual, ni en la legislación aplicable, ni en la normativa interna de la Universitat Politècnica de València. Proponemos en este trabajo una reflexión sobre la participación del profesorado, un replanteamiento de la definición de dirección, así como la redacción de un contrato entre alumnado y profesorado para delimitar la participación y protección de la obra.
Blurring the Boundaries: Reflections From Early Career Faculty During the COVID-19 Era
Authors: Rodriguez Geovanna , Monteleone Rebecca , Munandar Vidya D. , Bumble Jennifer L.
Published: February 2021

The last three issues of Intellectual and Developmental Disabilities (IDD) have featured perspectives from a diverse set of contributors on how the field of intellectual and developmental disabilities (IDD) is being impacted by COVID-19. As four newly appointed faculty members with diverse backgrounds, the editor of IDD invited us to share our experiences with beginning academic careers during this unique time. In making this request, he pointed out that approximately half the members of the American Association on Intellectual and Developmental Disabilities (AAIDD) are those who have some type of affiliation with an institution of higher education. While the perspectives outlined in this article do not represent those of all early career faculty, we hope our stories resonate with IDD readers who may be facing similar circumstances. This article includes a series of brief essays addressing how the pandemic has affected our academic job searches, research, teaching, and service. Although penned by different authors, each section encompasses our collective experiences, concerns, and hopes for the broader IDD community. We close with guiding questions that might support more socially responsive and integrated approaches to traditional academic roles as faculty continue to navigate the repercussions of COVID-19.
Probability of signal demodulation jump errors in the maximum-likelihood-estimation algorithm for a low SNR interference spectrum
Authors: Qi Yi , Zhang Peng , Chen Yuru , Lei Xiaohua , Feng Jianghua , Chen Weinin
Published: February 2021

When the signal-to-noise ratio (SNR) of an optical fiber sensor is lower than a specific value, jump errors will appear in the maximum-likelihood-estimation (MLE) algorithm. This research proposes a quantitative calculation method based on the MLE algorithm. This method can calculate the probability of jump errors by different SNRs. The SNR threshold can also be obtained in the MLE algorithm for the low-finesse interference spectrum. From the simulation, we find that when the SNR varies from 0 dB to 25 dB, the possibility of jump errors decreases exponentially. Subsequent experiments also verify the correctness of the simulation results.
Fabrication techniques and stability analysis of SMF-/MMF-based differently tapered optical fiber structures
Authors: Wang Zhi , Zhu Guo , Wang Yu , Li Muyang , Singh Ragini , Zhang Bingyuan , Kumar Santosh
Published: February 2021

In this work, fabrication techniques and optimization of single-mode fiber (SMF)- and multi-mode fiber (MMF)-based differently tapered optical fiber (TOF) structures are discussed. Further, taper characteristics such as diameter, transmitted intensity, and repeatability are analyzed. The results show that 25 µm TOF consists of lower transmitted intensity, meaning higher evanescent waves materialize at the tapered surface, which helps in suitable potential application of TOF as an optical fiber sensor.
Motion-compensated noninvasive periodontal health monitoring using handheld and motor-based photoacoustic-ultrasound imaging systems
Authors: Mozaffarzadeh Moein , Moore Colman , Golmoghani Erfan Barzegar , Mantri Yash , Hariri Ali , Jorns Alec , Fu Lei , Verweij Martin D. , Orooji Mahdi , de Jong Nico , Jokerst Jesse V.
Published: February 2021

Simultaneous visualization of the teeth and periodontium is of significant clinical interest for image-based monitoring of periodontal health. We recently reported the application of a dual-modality photoacoustic-ultrasound (PA-US) imaging system for resolving periodontal anatomy and periodontal pocket depths in humans. This work utilized a linear array transducer attached to a stepper motor to generate 3D images via maximum intensity projection. This prior work also used a medical head immobilizer to reduce artifacts during volume rendering caused by motion from the subject (e.g., breathing, minor head movements). However, this solution does not completely eliminate motion artifacts while also complicating the imaging procedure and causing patient discomfort. To address this issue, we report the implementation of an image registration technique to correctly align B-mode PA-US images and generate artifact-free 2D cross-sections. Application of the deshaking technique to PA phantoms revealed 80% similarity to the ground truth when shaking was intentionally applied during stepper motor scans. Images from handheld sweeps could also be deshaken using an LED PA-US scanner. In ex vivo porcine mandibles, pigmentation of the enamel was well-estimated within 0.1 mm error. The pocket depth measured in a healthy human subject was also in good agreement with our prior study. This report demonstrates that a modality-independent registration technique can be applied to clinically relevant PA-US scans of the periodontium to reduce operator burden of skill and subject discomfort while showing potential for handheld clinical periodontal imaging.
Dense stereo fish-eye images using a modified hemispherical ASW algorithm
Authors: Zhang Yakun , Li Haibin , Zhang Wenming , Xiao Cunjun
Published: February 2021

In this paper, we concentrate on dense estimation of disparities between fish-eye images without corrections. Because of the distortions, fish-eye images cannot be processed directly utilizing the classical adaptive support weight (ASW) method for perspective images. To address this problem, we propose a modified hemispherical ASW method in a hemispherical framework. First, 3D epipolar curves are calculated directly on a hemispherical model to deal with the problem that 2D epipolar curves cannot cover the whole image disc. Then, a modified ASW method with hemispherical support window and hemispherical geodesic distance is presented. Moreover, a three-dimensional epipolar distance transform (3DEDT) is proposed and fused into the matching cost to cope with the textureless region problem. The benefit of this approach is demonstrated by realizing the dense stereo matching for fish-eye images using a public fish-eye data set, for which both objectively evaluated as well as visually convincing results are provided.
Design optimization for bright electrically-driven quantum dot single-photon sources emitting in telecom O-band
Authors: Blokhin S. A. , Bobrov M. A. , Maleev N. A. , Donges J. N. , Bremer L. , Blokhin A. A. , Vasil’ev A. P. , Kuzmenkov A. G. , Kolodeznyi E. S. , Shchukin V. A. , Ledentsov N. N. , Reitzenstein S. , Ustinov V. M.
Published: February 2021

A combination of advanced light engineering concepts enables a substantial improvement in photon extraction efficiency of micro–cavity–based single–photon sources in the telecom O–band at ∼1.3 µm. We employ a broadband bottom distributed Bragg reflector (DBR) and a top DBR formed in a dielectric micropillar with an additional circular Bragg grating in the lateral plane. This device design includes a doped layer in pin–configuration to allow for electric carrier injection. It provides broadband (∼8–10 nm) emission enhancement with an overall photon–extraction efficiency of ∼83% into the upper hemisphere and photon–extraction efficiency of ∼79% within numerical aperture NA=0.7. The efficiency of photon coupling to a single–mode fiber reaches 11% for SMF28 fiber (with NA=0.12), exceeds 22% for 980HP fiber (with NA=0.2) and reaches ∼40% for HNA fiber (with NA=0.42) as demonstrated by 3D finite–difference time–domain modeling.
Fast automatic frequency calibration assisted phase-locked highly stable optoelectronic oscillator
Authors: Peng Huanfa , Liu Naijin , Xie Xiaopeng , Chen Zhangyuan
Published: February 2021

Highly stable, low phase noise microwave oscillators are essential for various applications. An optoelectronic oscillator (OEO) can overcome the short-term phase noise limitation of pure electronic oscillators at high oscillation frequency. Nonetheless, the long-term frequency stability should be addressed. To stabilize the frequency of OEO, a phase-locked loop (PLL) is widely used to synchronize the OEO to a stable reference. However, due to the narrow free-spectral-range (FSR) of the oscillation cavity of the OEO, the pull-in range of the PLL is limited. It is challenging to acquire phase-locking at startup and phase-relocking when mode-hopping of OEO occurs. Here, by using an automatic frequency calibration (AFC) assisted PLL, we attain a highly stable 10 GHz phase-locked OEO with robust phase-locking at startup and phase-relocking when mode-hopping of OEO occurs, for the first time. With the use of a fast digitally-controlled frequency shifter and a real-time frequency error detection unit in the AFC loop, the phase-locking and phase-relocking time are below 120 ms. Furthermore, it shows the phase noise of −135 dBc/Hz at 10 kHz offset, side-mode suppression ratio (SMSR) of 128 dBc, and Allan deviation of 4.8×10−11 at 5000 s for the phase-locked OEO. We thoroughly investigate the dynamics of the automatic frequency calibration, the phase-locking process, the phase-relocking after OEO mode-hopping, the system under vibration, and the frequency switching. Our approach is promising to generate a highly stable, low phase noise, and determinate frequency microwave signal, which can be used as a low phase noise reference for a microwave frequency synthesizer and high performance sampling clock for a data conversion system.
Spectral control of terahertz radiation from inhomogeneous plasma filaments by tailoring two-color laser beams
Authors: Sheng Wang , Tang Fu , Zhang Zhelin , Chen Yanping , Peng Xiao-Yu , Sheng Zheng-Ming
Published: February 2021

Terahertz (THz) radiation from an inhomogeneous plasma filament generated by focusing two-color femtosecond laser pulses into argon gas filled in a chamber is investigated experimentally by tailoring the Gaussian pump laser beams with an iris, where broadband THz emission over 10 THz is produced. It is found that the collected far-field THz radiation includes not only coherent but also partial-coherent components of the THz waves, which are emitted from the different parts of the inhomogeneous plasma filament with different plasma densities, contributing correspondingly to the different frequencies of the THz spectrum. Our results suggest that the THz spectrum can be manipulated by controlling the plasma density distribution of the filaments.
Characterizing and correcting camera noise in back-illuminated sCMOS cameras
Authors: Zhang Zhaoning , Wang Yujie , Piestun Rafael , Huang Zhen-li
Published: February 2021

With promising properties of fast imaging speed, large field-of-view, relative low cost and many others, back-illuminated sCMOS cameras have been receiving intensive attention for low light level imaging in the past several years. However, due to the pixel-to-pixel difference of camera noise (called noise non-uniformity) in sCMOS cameras, researchers may hesitate to use them in some application fields, and sometimes wonder whether they should optimize the noise non-uniformity of their sCMOS cameras before using them in a specific application scenario. In this paper, we systematically characterize the impact of different types of sCMOS noise on image quality and perform corrections to these types of sCMOS noise using three representative algorithms (PURE, NCS and MLEsCMOS). We verify that it is possible to use appropriate correction methods to push the non-uniformity of major types of camera noise, including readout noise, offset, and photon response, to a satisfactory level for conventional microscopy and single molecule localization microscopy. We further find out that, after these corrections, global read noise becomes a major concern that limits the imaging performance of back-illuminated sCMOS cameras. We believe this study provides new insights into the understanding of camera noise in back-illuminated sCMOS cameras, and also provides useful information for future development of this promising camera technology.
Multispectral compressive fluorescence lifetime imaging microscopy with a SPAD array detector
Authors: Ghezzi Alberto , Farina Andrea , Bassi Andrea , Valentini Gianluca , Labanca Ivan , Acconcia Giulia , Rech Ivan , D’Andrea Cosimo
Published: February 2021

Multispectral/hyperspectral fluorescence lifetime imaging microscopy (

λ

FLIM) is a promising tool for studying functional and structural biological processes. The rich information content provided by a multidimensional dataset is often in contrast with the acquisition speed. In this work, we develop and experimentally demonstrate a wide-field

λ

FLIM setup, based on a novel time-resolved

18
×
1

single-photon avalanche diode array detector working in a single-pixel camera scheme, which parallelizes the spectral detection, reducing measurement time. The proposed system, which implements a single-pixel camera with a compressive sensing scheme, represents an optimal microscopy framework towards the design of

λ

FLIM setups.
In-vivo sub-diffraction adaptive optics imaging of photoreceptors in the human eye with annular pupil illumination and sub-Airy detection
Authors: Lu Rongwen , Aguilera Nancy , Liu Tao , Liu Jianfei , Giannini John P. , Li Joanne , Bower Andrew J. , Dubra Alfredo , Tam Johnny
Published: February 2021

Adaptive optics scanning light ophthalmoscopy (AOSLO) allows non-invasive visualization of the living human eye at the microscopic scale; but even with correction of the ocular wavefront aberrations over a large pupil, the smallest cells in the photoreceptor mosaic cannot always be resolved. Here, we synergistically combine annular pupil illumination with sub-Airy disk confocal detection to demonstrate a 33% improvement in transverse resolution (from 2.36 to 1.58 µm) and a 13% axial resolution enhancement (from 37 to 32 µm), an important step towards the study of the complete photoreceptor mosaic in heath and disease. Interestingly, annular pupil illumination also enhanced the visualization of the photoreceptor mosaic in non-confocal detection schemes such as split detection AOSLO, providing a strategy for enhanced multimodal imaging of the cone and rod photoreceptor mosaic.
Transitions intensities and cross-sections of Tb3+ ions in YAl3(BO3)4 crystal
Authors: Demesh Maxim , Gorbachenya Konstantin , Kisel Viktor , Volkova Elena , Maltsev Viktor , Koporulina Elizaveta , Dunina Elena , Kornienko Alexey , Fomicheva Ludmila , Kuleshov Nikolay
Published: February 2021

A Tb3+:YAB crystal was grown using a high-temperature solution growth on dipped seeds technique. Polarized ground state absorption and fluorescence spectra from the 5D4 level, as well as a fluorescence decay curves of 5D4 and 5D3 levels, were recorded at room temperature. Radiative properties such as emission probabilities, branching ratios, and radiative lifetime were investigated within the theory of 4f-4f transition intensity in the case of the intermediate configuration interaction.
Intelligent coding metasurface holograms by physics-assisted unsupervised generative adversarial network
Authors: Liu Che , Yu Wen Ming , Ma Qian , Li Lianlin , Cui Tie Jun
Published: February 2021

Intelligent coding metasurface is a kind of information-carrying metasurface that can manipulate electromagnetic waves and associate digital information simultaneously in a smart way. One of its widely explored applications is to develop advanced schemes of dynamic holographic imaging. By now, the controlling coding sequences of the metasurface are usually designed by performing iterative approaches, including the Gerchberg–Saxton (GS) algorithm and stochastic optimization algorithm, which set a large barrier on the deployment of the intelligent coding metasurface in many practical scenarios with strong demands on high efficiency and capability. Here, we propose an efficient non-iterative algorithm for designing intelligent coding metasurface holograms in the context of unsupervised conditional generative adversarial networks (cGANs), which is referred to as physics-driven variational auto-encoder (VAE) cGAN (VAE-cGAN). Sharply different from the conventional cGAN with a harsh requirement on a large amount of manual-marked training data, the proposed VAE-cGAN behaves in a physics-driving way and thus can fundamentally remove the difficulties in the conventional cGAN. Specifically, the physical operation mechanism between the electric-field distribution and metasurface is introduced to model the VAE decoding module of the developed VAE-cGAN. Selected simulation and experimental results have been provided to demonstrate the state-of-the-art reliability and high efficiency of our VAE-cGAN. It could be faithfully expected that smart holograms could be developed by deploying our VAE-cGAN on neural network chips, finding more valuable applications in communication, microscopy, and so on.
Tailoring spatial structure of Brillouin spectra via spiral phase precoding
Authors: Li Hongwei , Zhao Bo , Ni Jipeng , Gao Wei
Published: February 2021

Brillouin spectroscopy is an important topic and powerful tool in modern optics, as the acquisitions of acoustic velocities and elastic moduli are one of the keys to investigate and analyze the contents of material science and condensed matter physics. Although stimulated Brillouin spectroscopy based on the pump-probe technique has striking advantages that include higher spectral resolution and signal-to-noise ratio, it is challenging to accomplish high-speed acquisition in the presence of pump background noise. In this paper, we propose a method for signal–noise separation through spiral phase precoding of the Brillouin spectrum signal. We achieve on-demand tailoring spatial distribution of the signal, and hence the signal can be separated from the background noise. Furthermore, this approach has little energy loss due to phase-only modulation, and retains the advantages of high efficiency and high gain in Brillouin interaction. The proof-of-principle demonstration provides a practical way to reshape the spatial structure of Brillouin spectra, and shows the potential in quasi-noise-free nonlinear interactions.
80  GHz germanium waveguide photodiode enabled by parasitic parameter engineering
Authors: Shi Yang , Zhou De , Yu Yu , Zhang Xinliang
Published: February 2021

A high-speed germanium (Ge) waveguide photodiode (PD) is one of the key components of an integrated silicon photonics platform for large-capacity data communication applications, but the parasitic parameters limit the increase of its bandwidth. Several studies have been reported to reduce parasitic parameters, at the cost of compromising other performances. Here, we propose and investigate a bandwidth-boosting technique by comprehensively engineering the parasitic parameters. Experimentally, a bandwidth up to 80 GHz is realized for vertical positive-intrinsic-negative (PIN) Ge PDs without decreasing the responsivity and dark current, indicating that parasitic parameter engineering is a promising method to promote high-speed performance of Ge PDs.
Stimulated emission at 1.54  μm from erbium/oxygen-doped silicon-based light-emitting diodes
Authors: Hong Jin , Wen Huimin , He Jiajing , Liu Jingquan , Dan Yaping , Tomm Jens W. , Yue Fangyu , Chu Junhao , Duan Chungang
Published: February 2021

Silicon-based light sources, including light-emitting diodes (LEDs) and laser diodes (LDs) for information transmission, are urgently needed for developing monolithic integrated silicon photonics. Silicon with erbium ions (

Er

3
+

) doped by ion implantation is considered a promising approach, but it suffers from an extremely low quantum efficiency. Here we report an electrically pumped superlinear emission at 1.54 μm from Er/O-doped silicon planar LEDs, which are produced by applying a new deep cooling process. Stimulated emission at room temperature is realized with a low threshold current of

∼
6
  
mA

(

∼
0.8
  
A
/

cm

2

). Time-resolved photoluminescence and photocurrent results have revealed the complex carrier transfer dynamics by relaxing electrons from the Si conduction band to the

Er

3
+

ion. This picture differs from the frequently assumed energy transfer via electron–hole pair recombination of the silicon host. Moreover, the amplified emission from the LEDs is likely due to a quasi-continuous Er/O-related donor band created by the deep cooling technique. This work paves the way for fabricating superluminescent diodes or efficient LEDs at communication wavelengths based on rare-earth-doped silicon.
Developmental outcomes in children exposed to Zika virus in utero from a Brazilian urban slum cohort study
Authors: Aguilar Ticona Juan P. , Nery Nivison , Ladines-Lim Joseph B. , Gambrah Claudia , Sacramento Gielson , de Paula Freitas Bruno , Bouzon Joseane , Oliveira-Filho Jamary , Borja Ana , Adhikarla Haritha , Montoya Magelda , Chin Athena , Wunder Elsio A. , Ballalai Verena , Vieira Carina , Belfort Rubens , P. Almeida Antonio R. , Reis Mitermayer G. , Harris Eva , Ko Albert I. , Costa Federico
Published: February 2021

Background

The prevalence of developmental alterations associated with in-utero Zika virus (ZIKV) exposure in children is not well understood. Furthermore, estimation of the Population Attributable Fraction (PAF) of developmental alterations attributed to ZIKV has not been performed due to lack of population-based cohorts with data on symptomatic and asymptomatic ZIKV exposures and an appropriate control group. The aim of this study was to characterize neurodevelopmental outcomes of children at 11 to 32 months of age with intrauterine ZIKV exposure and estimate the PAF of alterations secondary to ZIKV exposure.

Methodology/Principal findings

We performed a cohort of biannual community-based prospective serosurveys in a slum community in Salvador, Brazil. We recruited women participating in our cohort, with a documented pregnancy from January 2015 to December 2016 and children born to those mothers. Children were classified as ZIKV exposed in utero (born from women with ZIKV seroconversion during pregnancy) or unexposed (born from women without ZIKV seroconversion or that seroconverted before/after pregnancy) by using an IgG monoclonal antibody blockade-of-binding (BoB). We interviewed mothers and performed anthropometric, audiometric, ophthalmological, neurologic, and neurodevelopmental evaluations of their children at 11 to 32 months of age. Among the 655 women participating in the cohort, 66 (10%) were pregnant during the study period. 46 (70%) of them completed follow-up, of whom ZIKV seroconversion occurred before, during, and after pregnancy in 25 (54%), 13 (28%), and 1 (2%), respectively. The rest of women, 7 (21.2%), did not present ZIKV seroconversion. At 11 to 32 months of life, the 13 ZIKV-exposed children had increased risk of mild cognitive delay (RR 5.1; 95%CI 1.1–24.4) compared with the 33 children unexposed, with a PAF of 53.5%. Exposed children also had increased risk of altered auditory behavior (RR 6.0; 95%CI 1.3–26.9), with a PAF of 59.5%.

Conclusions

A significant proportion of children exposed in utero to ZIKV developed mild cognitive delay and auditory behavioral abnormalities even in the absence of gross birth defects such as microcephaly and other neurodevelopmental domains. Furthermore, our findings suggest that over half of these abnormalities could be attributed to intrauterine ZIKV exposure.
Mathematical modelling of oxygen gradients in stem cell-derived liver tissue
Authors: Leedale Joseph A. , Lucendo-Villarin Baltasar , Meseguer-Ripolles Jose , Kasarinaite Alvile , Webb Steven D. , Hay David C.
Published: February 2021

A major bottleneck in the study of human liver physiology is the provision of stable liver tissue in sufficient quantity. As a result, current approaches to modelling human drug efficacy and toxicity rely heavily on immortalized human and animal cell lines. These models are informative but do possess significant drawbacks. To address the issues presented by those models, researchers have turned to pluripotent stem cells (PSCs). PSCs can be generated from defined genetic backgrounds, are scalable, and capable of differentiation to all the cell types found in the human body, representing an attractive source of somatic cells for in vitro and in vivo endeavours. Although unlimited numbers of somatic cell types can be generated in vitro, their maturation still remains problematic. In order to develop high fidelity PSC-derived liver tissue, it is necessary to better understand the cell microenvironment in vitro including key elements of liver physiology. In vivo a major driver of zonated liver function is the oxygen gradient that exists from periportal to pericentral regions. In this paper, we demonstrate how cell culture conditions for PSC-derived liver sphere systems can be optimised to recapitulate physiologically relevant oxygen gradients by using mathematical modelling. The mathematical model incorporates some often-understated features and mechanisms of traditional spheroid systems such as cell-specific oxygen uptake, media volume, spheroid size, and well dimensions that can lead to a spatially heterogeneous distribution of oxygen. This mathematical modelling approach allows for the calibration and identification of culture conditions required to generate physiologically realistic function within the microtissue through recapitulation of the in vivo microenvironment.
Voting-based integration algorithm improves causal network learning from interventional and observational data: An application to cell signaling network inference
Authors: Sinha Meghamala , Tadepalli Prasad , Ramsey Stephen A.
Published: February 2021

In order to increase statistical power for learning a causal network, data are often pooled from multiple observational and interventional experiments. However, if the direct effects of interventions are uncertain, multi-experiment data pooling can result in false causal discoveries. We present a new method, “Learn and Vote,” for inferring causal interactions from multi-experiment datasets. In our method, experiment-specific networks are learned from the data and then combined by weighted averaging to construct a consensus network. Through empirical studies on synthetic and real-world datasets, we found that for most of the larger-sized network datasets that we analyzed, our method is more accurate than state-of-the-art network inference approaches.
Guideline adherence in the management of attention deficit hyperactivity disorder in children: An audit of selected medical records in three Australian states
Authors: Ellis Louise A. , Blakely Brette , Hazell Philip , Woolfenden Sue , Hiscock Harriet , Sarkozy Vanessa , Gould Bronwyn , Hibbert Peter D. , Arnolda Gaston , Ting Hsuen P. , Wiles Louise K. , Molloy Charlotte J. , Churruca Kate , Warwick Meagan , Braithwaite Jeffrey ,   on behalf of the CareTrack Kids Investigative Team
Published: February 2021

Objective

To assess General Practitioner (GP) and pediatrician adherence to clinical practice guidelines (CPGs) for diagnosis, treatment and management of attention deficit hyperactivity disorder (ADHD).

Method

Medical records for 306 children aged ≤15 years from 46 GP clinics and 20 pediatric practices in Australia were reviewed against 34 indicators derived from CPG recommendations. At indicator level, adherence was estimated as the percentage of indicators with ‘Yes’ or ‘No’ responses for adherence, which were scored ‘Yes’. This was done separately for GPs, pediatricians and overall; and weighted to adjust for sampling processes.

Results

Adherence with guidelines was high at 83.6% (95% CI: 77.7–88.5) with pediatricians (90.1%; 95% CI: 73.0–98.1) higher than GPs (68.3%; 95% CI: 46.0–85.8; p = 0.02). Appropriate assessment for children presenting with signs or symptoms of ADHD was undertaken with 95.2% adherence (95% CI: 76.6–99.9), however ongoing reviews for children with ADHD prescribed stimulant medication was markedly lower for both pediatricians (51.1%; 95% CI: 9.6–91.4) and GPs (18.7%; 95% CI: 4.1–45.5).

Conclusion

Adherence to CPGs for ADHD by pediatricians was generally high. Adherence by GPs was lower across most domains; timely recognition of medication side effects is a particular area for improvement.
Postpartum infection, pain and experiences with care among women treated for postpartum hemorrhage in three African countries: A cohort study of women managed with and without condom-catheter uterine balloon tamponade
Authors: Anger Holly A. , Durocher Jill , Dabash Rasha , Hassanein Nevine , Ononge Sam , Burkhardt Gillian , Frye Laura J. , Diop Ayisha , Beye Diop Seynabou Bop Moctar , Darwish Emad , Ramadan Mohamed Cherine , Kayaga Juliana , Charles Dyanna , Gaye Alioune , Eckardt Melody , Winikoff Beverly
Published: February 2021

Objective

We aimed to determine the risk of postpartum infection and increased pain associated with use of condom-catheter uterine balloon tamponade (UBT) among women diagnosed with postpartum hemorrhage (PPH) in three low- and middle-income countries (LMICs). We also sought women’s opinions on their overall experience of PPH care.

Methods

This prospective cohort study compared women diagnosed with PPH who received and did not receive UBT (UBT group and no-UBT group, respectively) at 18 secondary level hospitals in Uganda, Egypt, and Senegal that participated in a stepped wedge, cluster-randomized trial assessing UBT introduction. Key outcomes were reported pain (on a scale 0–10) in the immediate postpartum period and receipt of antibiotics within four weeks postpartum (a proxy for postpartum infection). Outcomes related to satisfaction with care and aspects women liked most and least about PPH care were also reported.

Results

Among women diagnosed with PPH, 58 were in the UBT group and 2188 in the no-UBT group. Self-reported, post-discharge antibiotic use within four weeks postpartum was similar in the UBT (3/58, 5.6%) and no-UBT groups (100/2188, 4.6%, risk ratio = 1.22, 95% confidence interval [CI]: 0.45–3.35). A high postpartum pain score of 8–10 was more common among women in the UBT group (17/46, 37.0%) than in the no-UBT group (360/1805, 19.9%, relative risk ratio = 3.64, 95% CI:1.30–10.16). Most women were satisfied with their care (1935/2325, 83.2%). When asked what they liked least about care, the most common responses were that medications (580/1511, 38.4%) and medical supplies (503/1511, 33.3%) were unavailable.

Conclusion

UBT did not increase the risk of postpartum infection among this population. Women who receive UBT may experience higher degrees of pain compared to women who do not receive UBT. Women’s satisfaction with their care and stockouts of medications and other supplies deserve greater attention when introducing new technologies like UBT.
Development and validation of a multigene variant profiling assay to guide targeted and immuno therapy selection in solid tumors
Authors: Akolkar Dadasaheb , Patil Darshana , Srivastava Navin , Patil Revati , Datta Vineet , Apurwa Sachin , Yashwante Nitin , Dhasarathan Raja , Gosavi Rahul , John Jinumary , Khan Shabishta , Jadhav Ninad , Mene Priti , Ahire Dhanashri , Pawar Sushant , Bodke Harshal , Sahoo Subhraline , Nile Arun , Saindane Dinesh , Darokar Harshal , Devhare Pradip , Srinivasan Ajay , Datar Rajan
Published: February 2021

We present data on analytical validation of the multigene variant profiling assay (CellDx) to provide actionable indications for selection of targeted and immune checkpoint inhibitor (ICI) therapy in solid tumors. CellDx includes Next Generation Sequencing (NGS) profiling of gene variants in a targeted 452-gene panel as well as status of total Tumor Mutation Burden (TMB), Microsatellite instability (MSI), Mismatch Repair (MMR) and Programmed Cell Death—Ligand 1 (PD-L1) respectively. Validation parameters included accuracy, sensitivity, specificity and reproducibility for detection of Single Nucleotide Alterations (SNAs), Copy Number Alterations (CNAs), Insertions and Deletions (Indels), Gene fusions, MSI and PDL1. Cumulative analytical sensitivity and specificity of the assay were 99.03 (95% CI: 96.54–99.88) and 99.23% (95% CI: 98.54% - 99.65%) respectively with 99.20% overall Accuracy (95% CI: 98.57% - 99.60%) and 99.7% Precision based on evaluation of 116 reference samples. The clinical performance of CellDx was evaluated in a subsequent analysis of 299 clinical samples where 861 unique mutations were detected of which 791 were oncogenic and 47 were actionable. Indications in MMR, MSI and TMB for selection of ICI therapies were also detected in the clinical samples. The high specificity, sensitivity, accuracy and reproducibility of the CellDx assay is suitable for clinical application for guiding selection of targeted and immunotherapy agents in patients with solid organ tumors.
The composition of the founding population of Iceland: A new perspective from 3D analyses of basicranial shape
Authors: Plomp Kimberly A. , Gestsdóttir Hildur , Dobney Keith , Price Neil , Collard Mark
Published: February 2021

The settlement of Iceland in the Viking Age has been the focus of much research, but the composition of the founding population remains the subject of debate. Some lines of evidence suggest that almost all the founding population were Scandinavian, while others indicate a mix of Scandinavians and people of Scottish and Irish ancestry. To explore this issue further, we used three-dimensional techniques to compare the basicrania of skeletons from archaeological sites in Iceland, Scandinavia, and the British Isles. Our analyses yielded two main results. One was that the founding population likely consisted of roughly equal numbers of Scandinavians and people from the British Isles. The other was that the immigrants who originated from the British Isles included individuals of southern British ancestry as well as individuals of Scottish and Irish ancestry. The first of these findings is consistent with the results of recent analyses of modern and ancient DNA, while the second is novel. Our study, therefore, strengthens the idea that the founding population was a mix of Scandinavians and people from the British Isles, but also raises a new possibility regarding the regions from which the settlers originated.
Use of artificial intelligence on Electroencephalogram (EEG) waveforms to predict failure in early school grades in children from a rural cohort in Pakistan
Authors: Rasheed Muneera A. , Chand Prem , Ahmed Saad , Sharif Hamza , Hoodbhoy Zahra , Siddiqui Ayat , Hasan Babar S.
Published: February 2021

Universal primary education is critical for individual academic growth and overall adult productivity of nations. Estimates indicate that 25% of 59 million primary age out of school children drop out and early grade failure is one of the factors. An objective and feasible screening measure to identify at-risk children in the early grades can help to design appropriate interventions. The objective of this study was to use a Machine Learning algorithm to evaluate the power of Electroencephalogram (EEG) data collected at age 4 in predicting academic achievement at age 8 among rural children in Pakistan. Demographic and EEG data from 96 children of a cohort along with their academic achievement in grade 1–2 measured using an academic achievement test of Math and language at the age of 7–8 years was used to develop the machine learning algorithm. K- Nearest Neighbor (KNN) classifier was used on different model combinations of EEG, sociodemographic and home environment variables. KNN model was evaluated using 5 Stratified Folds based on the sensitivity and specificity. In the current dataset, 55% and 74% failed in the mathematics and language test respectively. On testing data across each fold, the mean sensitivity and specificity was calculated. Sensitivity was similar when EEG variables were combined with sociodemographic, and home environment (Math = 58.7%, Language = 66.3%) variables but specificity improved (Math = 43.4% to 50.6% and Language = 32% to 60%). The model requires further validation for EEG to be used as a screening measure with adequate sensitivity and specificity to identify children in their preschool age who may be at high risk of failure in early grades.
Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis
Authors: Revilla Lluís , Mayorgas Aida , Corraliza Ana M. , Masamunt Maria C. , Metwaly Amira , Haller Dirk , Tristán Eva , Carrasco Anna , Esteve Maria , Panés Julian , Ricart Elena , Lozano Juan J. , Salas Azucena
Published: February 2021

Background

Personalized medicine requires finding relationships between variables that influence a patient’s phenotype and predicting an outcome. Sparse generalized canonical correlation analysis identifies relationships between different groups of variables. This method requires establishing a model of the expected interaction between those variables. Describing these interactions is challenging when the relationship is unknown or when there is no pre-established hypothesis. Thus, our aim was to develop a method to find the relationships between microbiome and host transcriptome data and the relevant clinical variables in a complex disease, such as Crohn’s disease.

Results

We present here a method to identify interactions based on canonical correlation analysis. We show that the model is the most important factor to identify relationships between blocks using a dataset of Crohn’s disease patients with longitudinal sampling. First the analysis was tested in two previously published datasets: a glioma and a Crohn’s disease and ulcerative colitis dataset where we describe how to select the optimum parameters. Using such parameters, we analyzed our Crohn’s disease data set. We selected the model with the highest inner average variance explained to identify relationships between transcriptome, gut microbiome and clinically relevant variables. Adding the clinically relevant variables improved the average variance explained by the model compared to multiple co-inertia analysis.

Conclusions

The methodology described herein provides a general framework for identifying interactions between sets of omic data and clinically relevant variables. Following this method, we found genes and microorganisms that were related to each other independently of the model, while others were specific to the model used. Thus, model selection proved crucial to finding the existing relationships in multi-omics datasets.
Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches
Authors: Chu Shirley , Skidmore Zachary L. , Kunisaki Jason , Walker Jason R. , Griffith Malachi , Griffith Obi L. , Bryan Jeffrey N.
Published: February 2021

Osteosarcoma is a rare disease in children but is one of the most common cancers in adult large breed dogs. The mutational landscape of both the primary and pulmonary metastatic tumor in two dogs with appendicular osteosarcoma (OSA) was comprehensively evaluated using an automated whole genome sequencing, exome and RNA-seq pipeline that was adapted for this study for use in dogs. Chromosomal lesions were the most common type of mutation. The mutational landscape varied substantially between dogs but the lesions within the same patient were similar. Copy number neutral loss of heterozygosity in mutantTP53was the most significant driver mutation and involved a large region in the middle of chromosome 5. Canine and human OSA is characterized by loss of cell cycle checkpoint integrity and DNA damage response pathways. Mutational profiling of individual patients with canine OSA would be recommended prior to targeted therapy, given the heterogeneity seen in our study and previous studies.
Exposure and risk factors for COVID-19 and the impact of staying home on Michigan residents
Authors: Wu Kuan-Han H. , Hornsby Whitney E. , Klunder Bethany , Krause Amelia , Driscoll Anisa , Kulka John , Bickett-Hickok Ryan , Fellows Austin , Graham Sarah , Kaleba Erin O. , Hayek Salim S. , Shi Xu , Sutton Nadia R. , Douville Nicholas , Mukherjee Bhramar , Jamerson Kenneth , Brummett Chad M. , Willer Cristen J.
Published: February 2021

COVID-19 has had a substantial impact on clinical care and lifestyles globally. The State of Michigan reports over 80,000 positive COVID-19 tests between March 1, 2020 and July 29, 2020. We surveyed 8,041 Michigan Medicine biorepository participants in late June 2020. We found that 55% of COVID-19 cases reported no known exposure to family members or to someone outside the house diagnosed with COVID-19. A significantly higher rate of COVID-19 cases were employed as essential workers (45% vs 19%, p = 9x10-12). COVID-19 cases reporting a fever were more likely to require hospitalization (categorized as severe; OR = 4.4 [95% CI: 1.6–12.5, p = 0.005]) whereas respondents reporting rhinorrhea was less likely to require hospitalization (categorized as mild-to-moderate; OR = 0.16 [95% CI: 0.04–0.73, p = 0.018]). African-Americans reported higher rates of being diagnosed with COVID-19 (OR = 4.0 [95% CI: 2.2–7.2, p = 5x10-6]), as well as higher rates of exposure to family or someone outside the household diagnosed with COVID-19, an annual household income < $40,000, living in rental housing, and chronic diseases. During the Executive Order in Michigan, African Americans, women, and the lowest income group reported worsening health behaviors and higher overall concern for the potential detrimental effects of the pandemic. The higher risk of contracting COVID-19 observed among African Americans may be due to the increased rates of working as essential employees, lower socioeconomic status, and exposure to known positive cases. Continued efforts should focus on COVID-19 prevention and mitigation strategies, as well as address the inequality gaps that result in higher risks for both short-term and long-term health outcomes.