bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a deep-learning semantic segmentation approach to fully automate MRI-based left-ventricular deformation analysis in cardiotoxicity
Authors: Karr Julia , Cohen Michael , McQuiston Samuel A , Poorsala Teja , Malozzi Christopher 
Published: February 2021

Objective:
Left-ventricular (LV) strain measurements with the Displacement Encoding with Stimulated Echoes (DENSE) MRI sequence provide accurate estimates of cardiotoxicity damage related to chemotherapy for breast cancer. This study investigated an automated and supervised deep convolutional neural network (DCNN) model for LV chamber quantification before strain analysis in DENSE images.

Methods:
The DeepLabV3 +DCNN with three versions of ResNet-50 backbone was designed to conduct chamber quantification on 42 female breast cancer data sets. The convolutional layers in the three ResNet-50 backbones were varied as non-atrous, atrous and modified, atrous with accuracy improvements like using Laplacian of Gaussian filters. Parameters such as LV end-diastolic diameter (LVEDD) and ejection fraction (LVEF) were quantified, and myocardial strains analyzed with the Radial Point Interpolation Method (RPIM). Myocardial classification was validated with the performance metrics of accuracy, Dice, average perpendicular distance (APD) and others. Repeated measures ANOVA and intraclass correlation (ICC) with Cronbach’s α (C-Alpha) tests were conducted between the three DCNNs and a vendor tool on chamber quantification and myocardial strain analysis.

Results:
Validation results in the same test-set for myocardial classification were accuracy = 97%, Dice = 0.92, APD = 1.2 mm with the modified ResNet-50, and accuracy = 95%, Dice = 0.90, APD = 1.7 mm with the atrous ResNet-50. The ICC results between the modified ResNet-50, atrous ResNet-50 and vendor-tool were C-Alpha = 0.97 for LVEF (55±7%, 54±7%, 54±7%, p = 0.6), and C-Alpha = 0.87 for LVEDD (4.6 ± 0.3 cm, 4.6 ± 0.3 cm, 4.6 ± 0.4 cm, p = 0.7).

Conclusion:
Similar performance metrics and equivalent parameters obtained from comparisons between the atrous networks and vendor tool show that segmentation with the modified, atrous DCNN is applicable for automated LV chamber quantification and subsequent strain analysis in cardiotoxicity.

Advances in knowledge:
A novel deep-learning technique for segmenting DENSE images was developed and validated for LV chamber quantification and strain analysis in cardiotoxicity detection.
Paediatric bone lesions: diagnostic accuracy of imaging correlation and CT-guided needle biopsy for differentiating benign from malignant lesions
Authors: Vidoni Alessandro , Pressney Ian , Saifuddin Asif 
Published: February 2021

Objective:
To determine the sensitivity, specificity and accuracy of CT-guided needle biopsy (CT-NB) for distinguishing benign and malignant lesions in children with suspected primary bone tumours, and to assess the correlation between imaging diagnosis and final diagnosis.

Methods:
Retrospective review of children who underwent CT-NB of a suspected primary bone tumour between October 2016 and October 2019. Data collected included anatomical location, imaging diagnosis, type of needle, type of biopsy sample, CT-NB diagnosis, final diagnosis and post-procedural complications. The final diagnosis was established based on surgical histology or clinical/imaging follow-up.

Results:
125 patients met the inclusion criteria (68M, 57F: mean age 11 years; range 10 months–18 years). Biopsy was performed using a 10 cm Jamshidi needle (10G n = 96; 13 G n = 8); 14G Tru-Cut needle (n = 18); 14G Temno needle (n = 3). The commonest anatomical locations were the femur (n = 40), tibia (n = 25) and humerus (n = 16), while the commonest diagnoses were osteosarcoma (n = 35), CRMO (n = 15) and LCH (n = 14). A benign tumour was correctly identified on imaging in 100% of cases, and a malignant tumour in 95.8%. Sensitivity, specificity and diagnostic accuracy of CT-NB for distinguishing malignant from benign lesions were 98%, 100 and 99%. Of 24 indeterminate biopsy results, all that had a non-aggressive radiological appearance were benign. No immediate complications were recorded.

Conclusion:
CT-NB represents a safe and very effective tool for differentiating benign and malignant lesions in children presenting with a suspected primary bone tumour. Suspected radiological diagnosis plays a pivotal role in the management of indeterminate biopsy results.

Advances in knowledge:
Paediatric bone tumours pose a significant diagnostic and therapeutic challenge. The interpretation of the imaging findings is essential for the successful management of indeterminate histological results.
Low-dose CT urography using deep learning image reconstruction: a prospective study for comparison with conventional CT urography
Authors: Cheng Yannan , Han Yangyang , Li Jianying , Fan Ganglian , Cao Le , Li Junjun , Jia Xiaoqian , Yang Jian , Guo Jianxin 
Published: February 2021

Objectives:
To compare the image quality of low-dose CT urography (LD-CTU) using deep learning image reconstruction (DLIR) with conventional CTU (C-CTU) using adaptive statistical iterative reconstruction (ASIR-V).

Methods:
This was a prospective, single-institutional study using the excretory phase CTU images for analysis. Patients were assigned to the LD-DLIR group (100kV and automatic mA modulation for noise index (NI) of 23) and C-ASIR-V group (100kV and NI of 10) according to the scan protocols in the excretory phase. Two radiologists independently assessed the overall image quality, artifacts, noise and sharpness of urinary tracts. Additionally, the mean CT attenuation, signal-to-noise ratio (SNR) and contrast-to-noise (CNR) in the urinary tracts were evaluated.

Results:
26 patients each were included in the LD-DLIR group (10 males and 16 females; mean age: 57.23 years, range: 33–76 years) and C-ASIR-V group (14 males and 12 females; mean age: 60 years, range: 33–77 years). LD-DLIR group used a significantly lower effective radiation dose compared with the C-ASIR-V group (2.01 ± 0.44 mSv vs 6.9 ± 1.46 mSv, p &lt; 0.001). LD-DLIR group showed good overall image quality with average score &gt;4 and was similar to that of the C-ASIR-V group. Both groups had adequate and similar attenuation value, SNR and CNR in most segments of urinary tracts.

Conclusion:
It is feasibility to provide comparable image quality while reducing 71% radiation dose in low-dose CTU with a deep learning image reconstruction algorithm compared to the conventional CTU with ASIR-V.

Advances in knowledge:
(1) CT urography with deep learning reconstruction algorithm can reduce the radiation dose by 71% while still maintaining image quality.
Top health research funders’ guidance on selecting journals for funded research
Authors: Shamseer Larissa , Cobey Kelly D. , Page Matthew J. , Brehaut Jamie C. , Grimshaw Jeremy M. , Straus Sharon E. , Stewart Lesley A. , Moher David 
Published: February 2021

Background: Funded health research is being published in journals that many regard as “predatory”, deceptive, and non-credible. We do not currently know whether funders provide guidance on how to select a journal in which to publish funded health research. Methods: We identified the largest 46 philanthropic, public, development assistance, public-private partnership, and multilateral funders of health research by expenditure, globally as well as four public funders from lower-middle income countries, from the list at https://healthresearchfunders.org. One of us identified guidance on disseminating funded research from each funders’ website (August/September 2017), then extracted information about selecting journals, which was verified by another assessor. Discrepancies were resolved by discussion. Results were summarized descriptively. This research used publicly available information; we did not seek verification with funding bodies. Results: The majority (44/50) of sampled funders indicated funding health research. 38 (of 44, 86%) had publicly available information about disseminating funded research, typically called “policies” (29, 76%). Of these 38, 36 (95%) mentioned journal publication for dissemination of which 13 (36.11%) offer variable guidance on selecting a journal, all of which relate to the funder’s open access mandate. Six funders (17%) outlined publisher requirements or features by which to select a journal. One funder linked to a document providing features of journals to look for (e.g. listed in the Directory of Open Access Journals) and to be wary of (e.g., no journal scope statement, uses direct and unsolicited marketing). Conclusions: Few funders provided guidance on how to select a journal in which to publish funded research. Funders have a duty to ensure that the research they fund is discoverable by others. This research is a benchmark for funder guidance on journal selection prior to the January 2021 implementation of Plan S (a global, funder-led initiative to ensure immediate, open access to funded, published research).
Influence of polymorphisms in the vascular endothelial growth factor gene on allograft rejection after kidney transplantation: a meta-analysis
Authors: Eiamsitrakoon Thanee , Tharabenjasin Phuntila , Pabalan Noel , Jarjanazi Hamdi , Tasanarong Adis 
Published: February 2021

Background: Reported associations of allograft rejection in kidney transplant patients with VEGF single nucleotide polymorphisms (SNPs) have been inconsistent between studies, which prompted a meta-analysis to obtain more precise estimates. Methods: Using the PICO elements, kidney transplant patients (P) were compared by genotype data between rejectors (I) and non-rejectors (C) in order to determine the risk of allograft rejection (O) attributed to the VEGF SNPs. Literature search of four databases yielded seven articles. To calculate risks for allograft rejection, four SNPs were examined. Using the allele-genotype model we compared the variant (var) with the wild-type (wt) and heterozygous (var-wt) alleles. Meta-analysis treatments included outlier and subgroup analyses, the latter was based on ethnicity (Indians/Caucasians) and rejection type (acute/chronic). Multiple comparisons were corrected with the Bonferroni test. Results: Five highly significant outcomes (Pa < 0.01) survived Bonferroni correction, one of which showed reduced risk for the var allele (OR 0.61, 95% CI 0.45-0.82). The remaining four indicated increased risk for the wt allele where the chronic rejection (OR 2.10, 95% CI 1.36-3.24) and Indian (OR 1.44, 95% CI 1.13-1.84) subgroups were accorded susceptibility status. Conclusions: Risk associations for renal allograft rejection were increased and reduced on account of the wt and var alleles, respectively. These findings could render the VEGF polymorphisms useful in the clinical genetics of kidney transplantation.
Cloning data with unchanged estimates of estimable non-linear functions of parameters
Authors: Hussain Sajid , Daniyal Muhammad , Ogundokun Roseline Oluwaseun , Shad Muhammad Yousaf , Iqbal Zafar , Ahmed Rashid 
Published: February 2021

Non-linear regression models occur in the fields of biology, banking, economics, and sociology, population and biological growth. The absolute growth, growth of humans, and most importantly, an economic variable is appropriately described by non-linear regression models. In this article, we present cloned datasets for bivariate and multivariate non-linear regression models with the same non-linear regression fit. The application of such cloned datasets is used for the confidentiality of sensitive data for publication purposes. In this article, we present cloned data sets which will yield the same fitted non-linear regression models.
Association between metabolic syndrome components and the risk of developing nephrolithiasis: A systematic review and bayesian meta-analysis
Authors: Rahman Ilham Akbar , Nusaly Ilham Fauzan , Syahrir Syakri , Nusaly Harry , Mansyur Makbul Aman 
Published: February 2021

Background: There is increasing evidence that nephrolithiasis is a systemic disease, as opposed to an isolated urinary metabolic problem, after considerable links were found between nephrolithiasis and systemic diseases such as hypertension, obesity, dyslipidemia, and insulin resistance. The interplay between these four factors defines metabolic syndrome (MetS). In this review we aim to clarify the associations of MetS and its components to kidney stone incident. Methods: Online databases of EMBASE, MEDLINE, and Google Scholar were searched from January 1998 up to October 2020 to identify observational studies examining the association between metabolic syndrome components and kidney stone incident. Bayesian random-effects meta-analysis and meta-regression were performed to observe the association. Linear dose-response analysis was conducted to shape the direction of the association. Data analysis was performed using STATA, and R statistics. Results: A total of 25 potentially relevant studies (n = 934,588 participants) were eventually identified. The pooled results suggested that metabolic syndrome was associated with an increased risk of nephrolithiasis with an odds ratio (OR) of 1.769 (95% CI: 1.386 – 2.309). The summary OR of hypertension and dyslipidemia for developing nephrolithiasis were 1.613 (95% CI: 1.213 – 2.169) and 1.586 (95% CI: 1.007 – 2.502) respectively. The presence of diabetes mellitus and obesity had an OR of 1.552 (95% CI: 1.027 – 2.344) and 1.531 (95% CI: 1.099 – 2.109) respectively. Our results revealed that the increasing number of MetS traits will increase the risk of developing nephrolithiasis, the higher the fasting plasma glucose, and body mass index, the higher the risk of kidney stones incident. Conclusions: Our results suggest that hypertension, diabetes, obesity and dyslipidemia are associated with increased risk of developing nephrolithiasis. Linear significant association between MetS components and nephrolithiasis were revealed in our study which reinforced the notion that should be considered a systemic disorder.
Exploring the critical points of teaching STEM subjects in the time of COVID 19: the experience of the course "Microscopy Techniques for Forensic Biology"
Authors: Brunelli Elvira , Macirella Rachele 
Published: February 2021

Background: The University was among the first structures to be hit by the health emergency, transferring all its teaching and research activities remotely. It was not easy for teachers and students to find themselves suddenly shifted into different teaching and socializing context. Results: This article describes and analyzes the online teaching experience carried out for the course of Microscopy Techniques for Forensic Biology offered as a part of the Master's degree program in Biology at the University of Calabria (Italy). A cross-sectional survey (pilot study) was designed to investigate the accessibility of distance learning along with an evaluation of adjustments needed for the conversion from offline to online instruction. Particular attention has been paid to learning material and lesson duration, with specific emphasis on practical activities. Conclusions: The author's intent is that of opening a comparison between the strengths and weaknesses that emerged in this experience, highlighting, in particular, how the educational relationship between teacher and student has changed.
Bias, Information, Noise: The BIN Model of Forecasting
Authors: Satopää Ville A. , Salikhov Marat , Tetlock Philip E. , Mellers Barbara 
Published: February 2021

A four-year series of subjective probability forecasting tournaments sponsored by the U.S. intelligence community revealed a host of replicable drivers of predictive accuracy, including experimental interventions such as training in probabilistic reasoning, anti‐groupthink teaming, and tracking of talent. Drawing on these data, we propose a Bayesian BIN model (Bias, Information, Noise) for disentangling the underlying processes that enable forecasters and forecasting methods to improve—either by tamping down bias and noise in judgment or by ramping up the efficient extraction of valid information from the environment. The BIN model reveals that noise reduction plays a surprisingly consistent role across all three methods of enhancing performance. We see the BIN method as useful in focusing managerial interventions on what works when and why in a wide range of domains. An R-package called BINtools implements our method and is available on the first author’s personal website. This paper was accepted by Manel Baucells, decision analysis.
Short Communication: A comparison of stand structure, species diversity and aboveground biomass between natural and planted mangroves in Sikka, East Nusa Tenggara, Indonesia
Authors: Matatula Jeriels , Afandi Ahmad Yusuf , Wirabuana Pandu 
Published: February 2021

Abstract. Matatula J, Afandi AY, Wirabuana PYAP. 2021. Short Communication: A comparison of stand structure, species diversity and aboveground biomass between natural and planted mangroves in Sikka, East Nusa Tenggara, Indonesia. Biodiversitas 22: 1098-1103. The effectiveness of mangroves reforestation can be evaluated by comparing the stand dynamics of planted mangroves with natural mangroves in similar site conditions. This study investigated stand structure, species diversity and aboveground biomass between natural and planted mangroves in Sikka, East Nusa Tenggara. A field survey was conducted using quadrat transect method for vegetation measurement, especially related to species composition and its size distribution. Several parameters were recorded in field observation, including number of species, diameter, height, volume, and aboveground biomass. The stand structure of both mangroves was demonstrated by the distribution of diameter class while the species diversity was described using three parameters, i.e., richness, heterogeneity, and evenness. Moreover, the IVI of each species recorded was also calculated to understand the contribution of species in the mangrove ecosystems. The comparison of stand characteristics between natural and planted mangroves was examined by Mann-Whitney test and Spearman Correlation was also applied to understand the relationship between IVI and aboveground biomass. The results showed that the diameter and height between the natural and planted mangroves significantly differed (P<0.05). In contrast, there was no significant difference in tree density, volume, and aboveground biomass (P<0.05). The stand structure of both mangrove stands followed the pattern of J-inverse in which the frequency of trees decreased with the increase in diameter class. Species diversity in both stands was statistically equal in richness, heterogeneity, and evenness (P>0.05) even though there were some specific species which only observed in the natural or planted mangroves. The most superior species in the planted mangroves was Rhizophora mucronata (IVI = 96.99) while the most important plant in the natural mangroves was Sonneratia alba (IVI = 82.49). Our study found there was a significant correlation between IVI and aboveground biomass in which species with higher IVI indicated greater aboveground biomass. Based on these findings, restoration efforts of degraded mangroves in Sikka have been effective. The restoration, which has been conducted for almost three decades, has not only brought back its vegetation cover but also the functional traits of the mangrove stand to mimic with natural mangroves in the area.
Raman/EDFA hybrid bidirectional amplifier for fiber-optic time and frequency synchronization
Authors: Mu Kuanlin , Zhao Zhuoze , Wang Zhengkang , Shang Jianmin , Yu Song , Qiao Yaojun 
Published: February 2021

Herein, we verify that a Raman/EDFA hybrid amplifier can improve the stability of fiber-optic time and frequency synchronization systems compared to the Er3+-doped fiber amplifier (EDFA), owing to its higher gain and lower noise figure (NF) performance. We studied the variation law of Raman gain efficiency for a fiber Raman amplifier (FRA) as a function of pump power and input signal power, designed a bidirectional Raman/EDFA hybrid amplifier, and proved that equivalent NF below 0 dB can be obtained. Finally, hybrid amplifiers were compared to EDFAs in a free-running frequency synchronization system. The transfer stabilities reached 1.9678 × 10−13/1sand 2.0248 × 10−13/1swhen FRA + EDFA and EDFA + FRA configurations were used, respectively, both exhibiting better performance than the stability of 3.0905 × 10−13/1 sobtained by EDFA.
Hybrid electro-optic modulator combining silicon photonic slot waveguides with high-k radio-frequency slotlines
Authors: Ummethala Sandeep , Kemal Juned N. , Alam Ahmed S. , Lauermann Matthias , Kuzmin Artem , Kutuvantavida Yasar , Nandam Sree H. , Hahn Lothar , Elder Delwin L. , Dalton Larry R. , Zwick Thomas , Randel Sebastian , Freude Wolfgang , Koos Christian 
Published: February 2021

Electro-optic (EO) modulators rely on the interaction of optical and electrical signals with second-order nonlinear media. For the optical signal, this interaction can be strongly enhanced using dielectric slot–waveguide structures that exploit a field discontinuity at the interface between a high-index waveguide core and the low-index EO cladding. In contrast to this, the electrical signal is usually applied through conductive regions in the direct vicinity of the optical waveguide. To avoid excessive optical loss, the conductivity of these regions is maintained at a moderate level, thus leading to inherentRClimitations of the modulation bandwidth. In this paper, we show that these limitations can be overcome by extending the slot–waveguide concept to the modulating radio-frequency (RF) signal. Our device combines an RF slotline that relies onBaTiO3as a high-k dielectric material with a conventional silicon photonic slot waveguide and a highly efficient organic EO cladding material. In a proof-of-concept experiment, we demonstrate a 1 mm long Mach–Zehnder modulator that offers a 3 dB bandwidth of 76 GHz and a 6 dB bandwidth of 110 GHz along with a smallπvoltage of 1.3 V (UπL=1.3Vmm). We further demonstrate the viability of the device in a data-transmission experiment using four-state pulse-amplitude modulation (PAM4) at line rates up to 200 Gbit/s. Our first-generation devices leave vast room for further improvement and may open an attractive route towards highly efficient silicon photonic modulators that combine sub-1 mm device lengths with sub-1 V drive voltages and modulation bandwidths of more than 100 GHz.