bluuebunny/crossref_metadata_2025 huggingface dataset:
Robotic-assisted computed tomography-guided 18F-FDG PET/computed tomography-directed biopsy for diagnosis of intra thoracic lesions: An experience from a tertiary care centre in North India.
Authors: Nath Alok , Prashanth Arun , Lal Hira , Kumar Sheo , Barai Sukanta , Gambhir Sanjay
Published: January 2020

Objective

The aim of this study was to assess the diagnostic yield of robotic-assisted computed tomography (CT)-guided18F-FDG PET/CT-directed biopsy for the evaluation of intrathoracic space occupying lesions.

Methods

Twenty-four patients being evaluated for intrathoracic masses were included in the study. The indications were patients with unknown/likely primary detected from PET-CT, suspicious lesions identified from PET-CT in a known primary disease and fine needle aspiration cytology/CT-guided biopsy negative lesions with a high index of suspicion for malignancy. Biopsies were carried out with the help of automated radiology arm (ROBIO-EX) which is essentially a needle positioning and holding device. A two-day protocol was followed in which PET-CT scan was done on the first day, biopsy procedure was done on the next scheduled day. PET images were refused with the CT images done on the second day in the console by using manual alignment and then a biopsy was carried out with the help of a robotic arm. Primary outcome was histopathological yield from the obtained specimens.

Results

Tissue yield was 100% (n = 24) and histopathological diagnosis rate was 96% (n = 23). Out of the 24 lesions biopsied 30% (n = 8) were benign and 70% (n = 16) turned out to be malignant. The complication rates were pneumothorax 4% (n = 1) and haemothorax 4% (n = 1).

Conclusion

Robotic-assisted CT-guided18F-FDG PET/CT-directed biopsy is a useful and accurate technique for diagnostic evaluation of intrathoracic neoplasms with minimal complications rates as compared with conventional imaging techniques.
Direct comparisons of left ventricular volume and function by simultaneous cardiac magnetic resonance imaging and gated 13N-ammonia positron emission tomography
Authors: Kiko Takatoyo , Yoshihisa Akiomi , Yokokawa Tetsuro , Misaka Tomofumi , Yamada Shinya , Kaneshiro Takashi , Nakazato Kazuhiko , Takeishi Yasuchika
Published: January 2020

Objectives

Hybrid PET/MRI is useful for the simultaneous evaluation of both 13 N-ammonia PET and MRI data. The aim of the current study was to compare the accuracy of gated 13 N-ammonia PET with MRI for the measurement of left ventricular volumes and function in patients with coronary artery disease (CAD), using simultaneous acquisitions on a hybrid PET/MRI system.

Methods

Fifty-one consecutive patients with suspected CAD who underwent 13 N-ammonia PET/MRI were enrolled in this study. End-diastolic volume (EDV), end-systolic volume (ESV), and left ventricular ejection fraction (LVEF) were simultaneously evaluated using both gated 13 N-ammonia PET and cine MRI. Regional wall motion was visually scored on a 4-point scale using a 17-segment model for both methods.

Results

The correlations between each EDV (R = 0.99, P < 0.001), ESV (R = 0.98, P < 0.001), and LVEF (R = 0.99, P = 0.001) measured by gated 13 N-ammmonia and MRI were very high. These high correlations were also observed in postmyocardial infarction patients. Furthermore, the regional wall motion scores determined on gated 13 N-ammonia PET and MRI showed an agreement of 89.0% with a kappa value of 0.82 ± 0.02.

Conclusion

EDV, ESV, LVEF, and regional wall motion measured by gated 13 N-ammonia PET were highly correlated with those measured by MRI.
Complementary role of 18F-FDG PET/CT for sentinel lymph node algorithm in endometrial cancer with high-risk factors for lymphatic metastasis
Authors: Taşkin Salih , Varli Bulut , Ersöz Cevriye Cansiz , Altin Duygu , Soydal Çiğdem , Ortaç Firat
Published: January 2020

Objective

National Comprehensive Cancer Network (NCCN) sentinel lymph node (SLN) algorithm includes ‘mandatory steps’ for evaluating pelvic lymph nodes, but assessment of paraaortic area is left to surgeon’s discretion. In this study, we aimed to investigate the complementary role of preoperative 18F-FDG PET/computed tomography (CT) scan in detecting pelvic and especially paraaortic lymphatic metastasis in endometrial cancer patients with high-risk factor(s) according to Mayo Clinic Criteria and underwent SLN algorithm.

Methods

Patients who underwent preoperative 18F-FDG PET/CT scan, intraoperative SLN algorithm followed by systematic lymphadenectomy (LND) and had at least one high-risk criterion for lymphatic metastasis were included in this study. 18F-FDG PET/CT and SLN algorithm were compared with final histopathological results of systematic LND.

Results

Thirty-eight patients were eligible for the study. Lymphatic metastasis was seen in 10 patients (26.3%). Four cases had paraaortic lymphatic metastases which were together with pelvic (n:2) or isolated (n:2) metastases. SLN algorithm was able to detect all pelvic lymph node metastases. However, isolated paraaortic metastases were diagnosed only by 18F-FDG PET/CT. In 76 hemipelvises, sensitivity and negative predictive value of SLN algorithm for diagnosis of pelvic nodal metastasis were 100%, while sensitivity, specificity, positive predictive value and negative predictive value of 18F-FDG PET/CT were 45.4, 95.3, 62.5 and 91.1%, respectively.

Conclusions

Although SLN algorithm has an excellent diagnostic value for pelvic nodal metastasis, paraaortic metastasis might be underdiagnosed. 18F-FDG PET/CT may be a feasible tool to exclude paraaortic lymphatic metastasis in high-risk patients for lymphatic metastasis who will undergo SLN algorithm.
Gram‐negative Microbiota Blooms in Premature Twins Discordant for Parenteral Nutrition‐associated Cholestasis
Authors: Hourigan Suchitra K. , Moutinho Thomas J. , Berenz Andrew , Papin Jason , Guha Pallabi , Bangiolo Lois , Oliphant Sandra , Provenzano Marina , Baveja Raj , Baker Robin , Vilboux Thierry , Levy Shira , Deopujari Varsha , Nataro James P. , Niederhuber John E. , Moore Sean R.
Published: January 2020

Parenteral nutrition‐associated cholestasis (PNAC) causes serious morbidity in the neonatal intensive care unit. Infection with gut‐associated bacteria is associated with cholestasis, but the role of intestinal microbiota in PNAC is poorly understood. We examined the composition of stool microbiota from premature twins discordant for PNAC as a strategy to reduce confounding from variables associated with both microbiota and cholestasis. Eighty‐four serial stool samples were included from 4 twin sets discordant for PNAC. Random Forests was utilized to determine genera most discriminatory in classifying samples from infants with and without PNAC. In infants with PNAC, we detected a significant increase in the relative abundance of Klebsiella, Veillonella, Enterobacter, and Enterococcus (P < 0.05). Bray‐Curtis dissimilarities in infants with PNAC were significantly different (P < 0.05) from infants without PNAC. Our findings warrant further exploration in larger cohorts and experimental models of PNAC to determine if a microbiota signature predicts PNAC, as a basis for future interventions to mitigate liver injury.
Using a Quality Improvement Approach in the Prevention of Mother-to-Child HIV Transmission Program in Uganda Improves Key Outcomes and Is Sustainable in Demonstration Facilities: Partnership for HIV-Free Survival
Authors: Flax Valerie L. , Kasasa Simon , Ssendagire Steven , Lane Charlotte , Atuyambe Lynn , Lance Peter M. , Ssengooba Freddie , Draru Joyce , Bobrow Emily A.
Published: January 2020

Background:

The Partnership for HIV-Free Survival (PHFS) in Uganda used a quality improvement (QI) approach to integrate the prevention of mother-to-child transmission (MTCT) of HIV, maternal and child health, and nutrition services, with the goal of increasing the retention of mother–baby pairs in care and decreasing vertical transmission of HIV.

Methods:

This evaluation of PHFS used a retrospective longitudinal design to assess the program's association with 4 outcomes. Data were extracted from patient records from 2011 (before the program) to 2018 (after the program) at 18 demonstration, 18 scale-up, and 24 comparison facilities. Difference-in-differences analyses were conducted with significance set at P < 0.15 during and P > 0.15 or a significant continued improvement after PHFS.

Results:

PHFS was associated with an increase in exclusive breastfeeding (EBF) (P = 0.08), 12-month retention in care (P < 0.001), and completeness of child 18-month HIV test results (P = 0.13) at demonstration facilities during program implementation. MTCT at 18 months decreased, but did not differ between groups. Increases in EBF (P = 0.67) and retention in care (P = 0.16) were sustained, and data completeness (P = 0.10) continued to increase at demonstration facilities after the program. PHFS was associated with an increase in EBF (P < 0.001) at scale-up facilities, but there was no difference between groups for retention in care, MTCT, or data completeness. Gains in EBF were lost (P = 0.08) and retention in care declined (P < 0.001) at scale-up facilities after the program.

Conclusion:

PHFS′ quality improvement approach increased EBF, retention in care, and data completeness in demonstration facilities during the program and these benefits were sustained.
Interobserver Agreement of Magnetic Resonance Imaging of Liver Imaging Reporting and Data System Version 2018
Authors: Abdel Razek Ahmed Abdel Khalek , El-Serougy Lamiaa Galal , Saleh Gehad Ahmad , Abd el-wahab Rihame , Shabana Walaa
Published: January 2020

Aim

This study aimed to assess the interobserver agreement of magnetic resonance (MR) imaging of Liver Imaging Reporting and Data System version 2018 (LI-RADS v2018).

Subjects and Methods

Retrospective analysis was done for 119 consecutive patients (77 male and 42 female) at risk of hepatocellular carcinoma who underwent dynamic contrast MR imaging. Image analysis was done by 2 independent and blinded readers for arterial phase hyperenhancement, washout appearance, enhancing capsule appearance, and size. Hepatic lesions were classified into 7 groups according to LI-RADS v2018.

Results

There was excellent interobserver agreement of both reviewers for LR version 4 (κ = 0.887,P= 0.001) with 90.76% agreement. There was excellent interobserver agreement for nonrim arterial phase hyperenhancement(κ = 0.948; 95% confidence interval [CI], 0.89–0.99;P= 0.001), washout appearance (κ = 0.949; 95% CI, 0.89–1.0;P= 0.001); and enhancing capsule (κ = 0.848; 95% CI, 0.73–0.97;P= 0.001) and excellent reliability of size (interclass correlation, 0.99;P= 0.001). There was excellent interobserver agreement for LR-1 (κ = 1.00,P= 0.001), LR-2 (κ = 0.94,P= 0.001), LR-5 (κ = 0.839,P= 0.001), LR-M (κ = 1.00,P= 0.001), and LR-TIV (κ = 1.00; 95% CI, 1.0–1.0;P= 0.001), and good agreement for LR-3 (κ = 0.61,P= 0.001) and LR-4 (κ = 0.61,P= 0.001).

Conclusion

MR imaging of LI-RADS v2018 is a reliable imaging modality and reporting system that may be used for standard interpretation of hepatic focal lesions.
The Specific Magnetic Resonance Imaging Indicators in Predicting Clear-Cell Renal Cell Carcinoma Metastatic to the Sinonasal Region
Authors: Yang Bentao , Wang Ziyi , Dong Jiyong
Published: January 2020

Purpose

The aim of this study was to determine the valuable magnetic resonance imaging (MRI) features of sinonasal metastatic clear-cell renal cell carcinoma (cc-RCC), especially focusing on its dynamic-enhanced characteristics.

Methods

The conventional and dynamic-enhanced MRI findings of 8 patients with histopathologically confirmed sinonasal metastatic cc-RCC were reviewed by 2 radiologists. The control group of 8 patients with capillary hemangioma underwent the same MRI protocol.

Results

Metastatic cc-RCCs arose from the nasoethmoid region, maxillary sinus, posterior ethmoid and sphenoid sinus, and nasal cavity in 2 patients in each. These lesions were well circumscribed and the mean maximum dimension was 42 mm. The signal intensity of these lesions was isointense to brain stem on both MR T1- and T2-weighted images. All metastatic tumors showed vivid enhancement on enhanced T1-weighted image. Multiple flow voids within these metastatic lesions were identified in 6 patients. Peripheral cyst was detected around the metastatic tumor in 4 patients. Metastatic cc-RCCs exhibited a characteristic type 4 time intensity curve (TIC) similar to that of the internal carotid artery, whereas capillary hemangiomas showed a type 3 TIC on dynamic-enhanced MRI.

Conclusions

A hypervascular mass with the characteristic type 4 TIC in the sinonasal region is highly suggestive of a metastatic cc-RCC.
Normal Pressure Hydrocephalus: Clinical Symptoms, Cerebrospinal Fluid Flow Metrics and White Matter Changes
Authors: Atasoy Bahar , Aralasmak Ayse , Cetinkaya Ezra , Toprak Huseyin , Toprak Ali , Tokdemir Sevil , Babacan Gulsen , Alkan Alpay
Published: January 2020

Purpose

The aim of this study was to investigate correlations between clinical symptoms, cerebrospinal fluid flow metrics, hydrocephalus index, small-vessel disease, and white matter (WM) changes in normal pressure hydrocephalus (NPH).

Methods

Aquaductal stroke volumes (ASVs), Z Evans index, Fazekas grading (FG), and diffusion tensor imaging measurements from WM bundles of 37 patients with NPH were retrospectively evaluated. Mann-Whitney U test between clinical symptoms and other variables and Spearman ρ correlations for relationships between variables and Kruskal-Wallis to correlate FG with nonclinical variables were used.

Results

Patients with NPH had increased ASV (median 53 μL). No correlation was found between Z Evans index and ASV. Three groups of patients with dementia or ataxia or incontinence had increased ASV values than their counterparts without symptoms (55 vs 48.5 μL, 75 vs 47 μL, 64 vs 49.5 μL, respectively). Patients having 2 common symptoms of dementia and ataxia and patients having all 3 symptoms of dementia, ataxia, and incontinence were compared with ASV values of 63.5 versus 78 μL, respectively. Patients with FG 1 had median ASV values of 45 μL; FG 2, 82.5 μL; and FG 3, 59 μL. Patients with dementia had significantly higher apparent diffusion coefficient (ADC) values of corona radiata (CR) on both sides. There were no significant WM changes in patients with ataxia and incontinence. The Z Evans index was positively correlated with ADC values of CR on both sides and genu of corpus callosum. Fazekas grading was found positively correlated with ADC and negatively correlated with FA values of CR.

Conclusions

Patients with NPH, regardless of stages of the diseases, have increased ASV values and could benefit from shunting. Decreasing ASV values of patients with FG 3 comparing with those with FG 2 support the hypothesis of decreasing compliance of brain with aging and increasing severity of small-vessel disease.
The Diagnostic Accuracy of PET(CT) in Patients With Neuroblastoma: A Meta-Analysis and Systematic Review
Authors: Li Huai-Feng , Mao Hai-Jia , Zhao Li , Guo Dan-Ling , Chen Bo , Yang Jian-Feng
Published: January 2020

Objective

The objective of this study was to evaluate the overall diagnostic value of PET(CT) in patients with neuroblastoma (NB) based on qualified studies.

Methods

PubMed, Cochrane, and Embase database were searched by the index words to identify the qualified studies, and relevant literature sources were also searched. The latest research was performed in April 2019. Heterogeneity of the included studies was tested, which was used to select proper effect model to calculate pooled weighted sensitivity, specificity, and diagnostic odds ratio (DOR). Summary receiver operating characteristic (SROC) analyses were also performed.

Results

Eleven studies with 580 patients were involved in the meta-analysis to explore the diagnostic accuracy of PET(CT) for NB. PET(CT) has high diagnostic accuracy of NB: the global sensitivity was 91% (95% confidence interval [CI], 86%–94%), the global specificity was 78% (95% CI, 66%–86%), the global positive likelihood ratio was 4.07 (95% CI, 2.54–6.50), the global negative likelihood ratio was 0.12 (95% CI, 0.08–0.18), the global DOR was 27.43 (95% CI, 14.45–52.07), and the area under the SROC was high (area under the curve, 0.93; 95% CI, 0.90–0.95). Besides this, PET(CT) has high diagnostic accuracy of primary NB: the global sensitivity was 86% (95% CI, 73%–93%), the global specificity was 82% (95% CI, 57%–94%), the global positive likelihood ratio was 4.90 (95% CI, 1.63–14.72), the global negative likelihood ratio was 0.17 (95% CI, 0.07–0.40), the global DOR was 25.427 (95% CI, 3.988–162.098), and the area under the SROC was high (area under the curve, 0.91; 95% CI, 0.88–0.93). However, there has no significant accuracy of PET(CT) in NB with bone marrow.

Conclusions

This study provides a systematic review and meta-analysis of diagnostic accuracy studies of PET(CT) for NB. The results indicated that PET(CT) is a highly accurate diagnostic tool for NB.
From one pattern into another: analysis of Turing patterns in heterogeneous domains via WKBJ
Authors: Krause Andrew L. , Klika Václav , Woolley Thomas E. , Gaffney Eamonn A.
Published: January 2020

Pattern formation from homogeneity is well studied, but less is known concerning symmetry-breaking instabilities in heterogeneous media. It is non-trivial to separate observed spatial patterning due to inherent spatial heterogeneity from emergent patterning due to nonlinear instability. We employ WKBJ asymptotics to investigate Turing instabilities for a spatially heterogeneous reaction–diffusion system, and derive conditions for instability which are local versions of the classical Turing conditions. We find that the structure of unstable modes differs substantially from the typical trigonometric functions seen in the spatially homogeneous setting. Modes of different growth rates are localized to different spatial regions. This localization helps explain common amplitude modulations observed in simulations of Turing systems in heterogeneous settings. We numerically demonstrate this theory, giving an illustrative example of the emergent instabilities and the striking complexity arising from spatially heterogeneous reaction–diffusion systems. Our results give insight both into systems driven by exogenous heterogeneity, as well as successive pattern forming processes, noting that most scenarios in biology do not involve symmetry breaking from homogeneity, but instead consist of sequential evolutions of heterogeneous states. The instability mechanism reported here precisely captures such evolution, and extends Turing’s original thesis to a far wider and more realistic class of systems.
Multi-scale characterization of bamboo bonding interfaces with phenol-formaldehyde resin of different molecular weight to study the bonding mechanism
Authors: Huang Yuxiang , Lin Qiuqin , Yang Chan , Bian Guomin , Zhang Yahui , Yu Wenji
Published: January 2020

Understanding the bonding mechanism of the interfacial region between bamboo and adhesives is essential for accelerating the development of improved adhesives for advanced bamboo-based materials. In this study, Br-labelled phenol-formaldehyde (PF) resins with four different molecular weights (MWs) were used to make bamboo–adhesive interfaces for tracing the adhesives in bamboo. Ultra-depth-of-field microscopy and scanning electron microscopy in conjunction with energy dispersion spectrometry were used to access the distribution and penetration of resin in the bamboo polymer. Fourier transform infrared images and solid-state cross-polarization/magic angle spinning nuclear magnetic resonance spectra were used to access the molecular-scale interactions between PF resins and bamboo cell walls. The results showed that the PF resins with high MW infiltrated into the lumina of damaged bamboo cells near the bondline to form glue nails, while those with low MW penetrated into the bamboo cell wall to form nanomechanical interlocking. Chemical bonds and secondary forces such as polar forces and hydrogen bonds were generated between bamboo and PF resin. Finally, the twice-adhesive dispensing method combining low-MW resins with high-MW resins was used to improve the bonding strength of the interface.
Automated detection of lameness in sheep using machine learning approaches: novel insights into behavioural differences among lame and non-lame sheep
Authors: Kaler Jasmeet , Mitsch Jurgen , Vázquez-Diosdado Jorge A. , Bollard Nicola , Dottorini Tania , Ellis Keith A.
Published: January 2020

Lameness in sheep is the biggest cause of concern regarding poor health and welfare among sheep-producing countries. Best practice for lameness relies on rapid treatment, yet there are no objective measures of lameness detection. Accelerometers and gyroscopes have been widely used in human activity studies and their use is becoming increasingly common in livestock. In this study, we used 23 datasets (10 non-lame and 13 lame sheep) from an accelerometer- and gyroscope-based ear sensor with a sampling frequency of 16 Hz to develop and compare algorithms that can differentiate lameness within three different activities (walking, standing and lying). We show for the first time that features extracted from accelerometer and gyroscope signals can differentiate between lame and non-lame sheep while standing, walking and lying. The random forest algorithm performed best for classifying lameness with an accuracy of 84.91% within lying, 81.15% within standing and 76.83% within walking and overall correctly classified over 80% sheep within activities. Both accelerometer- and gyroscope-based features ranked among the top 10 features for classification. Our results suggest that novel behavioural differences between lame and non-lame sheep across all three activities could be used to develop an automated system for lameness detection.
Sexual frequency is associated with age of natural menopause: results from the Study of Women's Health Across the Nation
Authors: Arnot Megan , Mace Ruth
Published: January 2020

It is often observed that married women have a later age of natural menopause (ANM) than unmarried women; however, the reason for this association is unknown. We test an original hypothesis that sexual frequency acts as a bio-behavioural mediator between marital status and ANM. We hypothesize that there is a trade-off between continued ovulation and menopause based on the woman's chances of becoming pregnant. If a woman is sexually inactive, then pregnancy is impossible, and continued investment in ovulation would not be adaptive. In addition, we test an existing hypothesis that the observed relationship is because of the exposure to male pheromones. Data from 2936 women were drawn from 11 waves of the Study of Women's Health Across the Nation, which is a longitudinal study conducted in the United States. Using time-varying Cox regression, we found no evidence for the pheromone hypothesis. However, we did observe that women who reported to have sex weekly during the study period were 28% less likely to experience menopause than women who had sex less than monthly. This is an indication that ANM may be somewhat facultative in response to the likelihood of pregnancy.
Extinction debt in local habitats: quantifying the roles of random drift, immigration and emigration
Authors: Wu Yongbin , Chen Youhua , Chang Shui-Ching , Chen You-Fang , Shen Tsung-Jen
Published: January 2020

We developed a time-dependent stochastic neutral model for predicting diverse temporal trajectories of biodiversity change in response to ecological disturbance (i.e. habitat destruction) and dispersal dynamic (i.e. emigration and immigration). The model is general and predicts how transition behaviours of extinction may accumulate according to a different combination of random drift, immigration rate, emigration rate and the degree of habitat destruction. We show that immigration, emigration, the areal size of the destroyed habitat and initial species abundance distribution (SAD) can impact the total biodiversity loss in an intact local area. Among these, the SAD plays the most deterministic role, as it directly determines the initial species richness in the local target area. By contrast, immigration was found to slow down total biodiversity loss and can drive the emergence of species credits (i.e. a gain of species) over time. However, the emigration process would increase the extinction risk of species and accelerate biodiversity loss. Finally but notably, we found that a shift in the emigration rate after a habitat destruction event may be a new mechanism to generate species credits.
Dealing with uncertainty in agent-based models for short-term predictions
Authors: Kieu Le-Minh , Malleson Nicolas , Heppenstall Alison
Published: January 2020

Agent-based models (ABMs) are gaining traction as one of the most powerful modelling tools within the social sciences. They are particularly suited to simulating complex systems. Despite many methodological advances within ABM, one of the major drawbacks is their inability to incorporate real-time data to make accurate short-term predictions. This paper presents an approach that allows ABMs to be dynamically optimized. Through a combination of parameter calibration and data assimilation (DA), the accuracy of model-based predictions using ABM in real time is increased. We use the exemplar of a bus route system to explore these methods. The bus route ABMs developed in this research are examples of ABMs that can be dynamically optimized by a combination of parameter calibration and DA. The proposed model and framework is a novel and transferable approach that can be used in any passenger information system, or in an intelligent transport systems to provide forecasts of bus locations and arrival times.
The effect of bed roughness uncertainty on tidal stream power estimates for the Pentland Firth
Authors: Kreitmair M. J. , Adcock T. A. A. , Borthwick A. G. L. , Draper S. , van den Bremer T. S.
Published: January 2020

Uncertainty affects estimates of the power potential of tidal currents, resulting in large ranges in values reported for sites such as the Pentland Firth, UK. Kreitmair
et al.
(2019,
R. Soc. open sci.
6
, 180941. (
doi:10.1098/rsos.191127
)) have examined the effect of uncertainty in bottom friction on tidal power estimates by considering idealized theoretical models. The present paper considers the role of bottom friction uncertainty in a realistic numerical model of the Pentland Firth spanned by different fence configurations. We find that uncertainty in removable power estimates resulting from bed roughness uncertainty depends on the case considered, with relative uncertainty between 2% (for a fully spanned channel with small values of mean roughness and input uncertainty) and 44% (for an asymmetrically confined channel with high values of bed roughness and input uncertainty). Relative uncertainty in power estimates is generally smaller than (input) relative uncertainty in bottom friction by a factor of between 0.2 and 0.7, except for low turbine deployments and very high mean values of friction. This paper makes a start at quantifying uncertainty in tidal stream power estimates, and motivates further work for proper characterization of the resource, accounting for uncertainty inherent in resource modelling.
Liquid cell transmission electron microscopy and its applications
Authors: Pu Shengda , Gong Chen , Robertson Alex W.
Published: January 2020

Transmission electron microscopy (TEM) has long been an essential tool for understanding the structure of materials. Over the past couple of decades, this venerable technique has undergone a number of revolutions, such as the development of aberration correction for atomic level imaging, the realization of cryogenic TEM for imaging biological specimens, and new instrumentation permitting the observation of dynamic systems
in situ
. Research in the latter has rapidly accelerated in recent years, based on a silicon-chip architecture that permits a versatile array of experiments to be performed under the high vacuum of the TEM. Of particular interest is using these silicon chips to enclose fluids safely inside the TEM, allowing us to observe liquid dynamics at the nanoscale.
In situ
imaging of liquid phase reactions under TEM can greatly enhance our understanding of fundamental processes in fields from electrochemistry to cell biology. Here, we review how
in situ
TEM experiments of liquids can be performed, with a particular focus on microchip-encapsulated liquid cell TEM. We will cover the basics of the technique, and its strengths and weaknesses with respect to related
in situ
TEM methods for characterizing liquid systems. We will show how this technique has provided unique insights into nanomaterial synthesis and manipulation, battery science and biological cells. A discussion on the main challenges of the technique, and potential means to mitigate and overcome them, will also be presented.
Prediction of polyproline II secondary structure propensity in proteins
Authors: O’Brien Kevin T. , Mooney Catherine , Lopez Cyril , Pollastri Gianluca , Shields Denis C.
Published: January 2020

Background:
The polyproline II helix (PPIIH) is an extended protein left-handed secondary structure that usually but not necessarily involves prolines. Short PPIIHs are frequently, but not exclusively, found in disordered protein regions, where they may interact with peptide-binding domains. However, no readily usable software is available to predict this state.
Results:
We developed PPIIPRED to predict polyproline II helix secondary structure from protein sequences, using bidirectional recurrent neural networks trained on known three-dimensional structures with dihedral angle filtering. The performance of the method was evaluated in an external validation set. In addition to proline, PPIIPRED favours amino acids whose side chains extend from the backbone (Leu, Met, Lys, Arg, Glu, Gln), as well as Ala and Val. Utility for individual residue predictions is restricted by the rarity of the PPIIH feature compared to structurally common features.
Conclusion:
The software, available at
http://bioware.ucd.ie/PPIIPRED
, is useful in large-scale studies, such as evolutionary analyses of PPIIH, or computationally reducing large datasets of candidate binding peptides for further experimental validation.
New theropod remains and implications for megaraptorid diversity in the Winton Formation (lower Upper Cretaceous), Queensland, Australia
Authors: White Matt A. , Bell Phil R. , Poropat Stephen F. , Pentland Adele H. , Rigby Samantha L. , Cook Alex G. , Sloan Trish , Elliott David A.
Published: January 2020

The holotype specimen of the megaraptorid
Australovenator wintonensis
, from the Upper Cretaceous Winton Formation (Rolling Downs Group, Eromanga Basin) of central Queensland, is the most complete non-avian theropod found in Australia to date. In fact, the holotype of
A. wintonensis
and isolated megaraptorid teeth (possibly referable to
Australovenator
) constitute the only theropod body fossils reported from the Winton Formation. Herein, we describe a new fragmentary megaraptorid specimen from the Winton Formation, found near the type locality of
A. wintonensis
. The new specimen comprises parts of two vertebrae, two metatarsals, a pedal phalanx and multiple unidentifiable bone fragments. Although the new megaraptorid specimen is poorly preserved, it includes the only megaraptorid vertebrae known from Queensland. The presence of pleurocoels and highly pneumatic caudal centra with camerate and camellate internal structures permit the assignment of these remains to Megaraptora gen. et sp. indet. A morphological comparison revealed that the distal end of metatarsal II and the partial pedal phalanx II-1 of the new specimen are morphologically divergent from
Australovenator
. This might indicate the presence of a second megaraptorid taxon in the Winton Formation, or possibly intraspecific variation.
Spectroscopic and molecular docking studies reveal binding characteristics of nazartinib (EGF816) to human serum albumin
Authors: Almehizia Abdulrahman A. , AlRabiah Haitham , Bakheit Ahmed H. , Hassan Eman S. G. , Herqash Rashed N. , Abdelhameed Ali Saber
Published: January 2020

The interactions of novel anti-cancer therapeutic agents with the different plasma and tissue components, specifically serum albumins, have lately gained considerable attention due to the significant influence of such interactions on the pharmacokinetics and/or -dynamics of this important class of therapeutics. Nazartinib (EGF 816; NAZ) is a new anti-cancer candidate proposed as a third-generation epidermal growth factor receptor tyrosine kinase inhibitor that is being developed and clinically tested for the management of non-small cell lung cancer. The current study aimed to characterize the interaction between NAZ and human serum albumin (HSA) using experimental and theoretical approaches. Experimental results of fluorescence quenching of HSA induced by NAZ revealed the development of a statically formed complex between NAZ and HSA. Interpretation of the observed fluorescence data using Stern–Volmer, Lineweaver–Burk and double-log formulae resulted in binding constants for HSA-NAZ complex in the range of (2.34–2.81) × 104M–1over the studied temperatures. These computed values were further used to elucidate thermodynamic attributes of the interaction, which showed that NAZ spontaneously binds to HSA with a postulated electrostatic force-driven interaction. This was further verified by theoretical examination of the NAZ docking on the HSA surface that revealed an HSA-NAZ complex where NAZ is bound to HSA Sudlow site I driven by hydrogen bonding in addition to electrostatic forces in the form of pi-H bond. The HSA binding pocket for NAZ was shown to encompass ARG 257, ARG 222, LYS 199 and GLU 292 with a total binding energy of −25.59 kJ mol–1.
Swimming exercise enhances brain plasticity in fish
Authors: Mes Daan , Palstra Arjan P. , Henkel Christiaan V. , Mayer Ian , Vindas Marco A.
Published: January 2020

It is well-established that sustained exercise training can enhance brain plasticity and boost cognitive performance in mammals, but this phenomenon has not received much attention in fish. The aim of this study was to determine whether sustained swimming exercise can enhance brain plasticity in juvenile Atlantic salmon. Brain plasticity was assessed by both mapping the whole telencephalon transcriptome and conducting telencephalic region-specific microdissections on target genes. We found that 1772 transcripts were differentially expressed between the exercise and control groups. Gene ontology (GO) analysis identified 195 and 272 GO categories with a significant overrepresentation of up- or downregulated transcripts, respectively. A multitude of these GO categories was associated with neuronal excitability, neuronal signalling, cell proliferation and neurite outgrowth (i.e. cognition-related neuronal markers). Additionally, we found an increase inproliferating cell nuclear antigen(pcna) after both three and eight weeks of exercise in the equivalent to the hippocampus in fish. Furthermore, the expression of the neural plasticity markerssynaptotagmin(syt) andbrain-derived neurotrophic factor(bdnf) were also increased due to exercise in the equivalent to the lateral septum in fish. In conclusion, this is the first time that swimming exercise has been directly linked to increased telencephalic neurogenesis and neural plasticity in a teleost, and our results pave the way for future studies on exercise-induced neuroplasticity in fish.
Antioxidant supplementation slows telomere shortening in free-living white stork chicks
Authors: Pineda-Pampliega Javier , Herrera-Dueñas Amparo , Mulder Ellis , Aguirre José I. , Höfle Ursula , Verhulst Simon
Published: January 2020

Telomere length (TL) and shortening is increasingly shown to predict variation in survival and lifespan, raising the question of what causes variation in these traits. Oxidative stress is well known to accelerate telomere attrition
in vitro
, but its importance
in vivo
is largely hypothetical. We tested this hypothesis experimentally by supplementing white stork (
Ciconia ciconia
) chicks with antioxidants. Individuals received either a control treatment, or a supply of tocopherol (vitamin E) and selenium, which both have antioxidant properties. The antioxidant treatment increased the concentration of tocopherol for up to two weeks after treatment but did not affect growth. Using the telomere restriction fragment technique, we evaluated erythrocyte TL and its dynamics. Telomeres shortened significantly over the 21 days between the baseline and final sample, independent of sex, mass, size and hatching order. The antioxidant treatment significantly mitigated shortening rate of average TL (−31% in shorter telomeres; percentiles 10th, 20th and 30th). Thus, our results support the hypothesis that oxidative stress shortens telomeres
in vivo
.
Overcoming the detectability costs of symmetrical coloration
Authors: Wainwright J. Benito , Scott-Samuel Nicholas E. , Cuthill Innes C.
Published: January 2020

For camouflaged prey, enhanced conspicuousness due to bilaterally symmetrical coloration increases predation risk. The ubiquity of symmetrical body patterns in nature is therefore paradoxical, perhaps explicable through tight developmental constraints. Placing patterns that would be salient when symmetrical (e.g. high contrast markings) away from the axis of symmetry is one possible strategy to reduce the predation cost of symmetrical coloration. Artificial camouflaged prey with symmetrical patterns placed at different distances from the axis were used in both visual search tasks with humans and survival experiments with wild avian predators. Targets were less conspicuous when symmetrical patterning was placed outside a ‘critical zone’ near the midline. To assess whether real animals have evolved as predicted from these experiments, the saliency of features at different distances from the midline was measured in the cryptically coloured forewings of 36 lepidopteran species. Salience, both in absolute terms and relative to wing area, was greatest away from the axis of symmetry. Our work, therefore, demonstrates that prey morphologies may have evolved to exploit a loophole in the ability of mammalian and avian visual systems to spot symmetrical patterns.
In-SilicoInvestigation of Luminol, Its Analogues and Improved Mechanism of Chemiluminescence for Blood Identification Beyond Forensics
Authors: Fatoki Toluwase Hezekiah
Published: January 2020

This study aimed to discover chemiluminescent analogues of luminol, understand their molecular binding to hemoglobin of bloodstains in the household crime, and the mechanism of chemiluminescence. Similarity and clustering analyses of luminol analogues were conducted, and molecular docking was carried out on hemoglobin fromHomo sapiensand other four domestic organism namelyGallus gallus, Drosophila melanogaster, Rattus norvegicus,andCanis familiaris. The results show that the order of overall binding score isD. melanogaster > H. sapiens > C. familiaris > R. norvegicus > G. gallus. Seven compounds namely ZINC16958228, ZINC17023010, ZINC19915427, ZINC34928954, ZINC19915369, ZINC19915444, and ZINC82294978, were found to be consistently stable in binding to diverse hemoglobin and possibly have chemiluminescence than luminol. The amino acid residues involved in the interaction of human hemoglobin with the 30 test compounds, show that His45, Lys61, Asn68, Val73, Met76, Pro77, Ala79, Ala82, Leu83, Pro95, Phe98, Lys99, Ser102, Ser133, Ala134, and Thr134 are significant in the mechanism of action of presumptive test compounds. The improved mechanism of chemiluminescent identification of blood hypothesized that nitrite interact with the Fe(II) heme, with the cleavage of a hydroxide ion and the formation of the nitrosonium cation in peroxidase reaction. It was proposed that degradation of rhombic heme complex to fluorescent products is possibly inhibited by nitric oxide from the test compound luminol. This study provides novel insight on the luminol and its actual mechanism for broader possible applications of luminol with careful development of new methodologies.
Ribo-ODDR: Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs in Ribo-seq
Authors: Alkan Ferhat , Silva Joana , Barberà Eric Pintó , Faller William J.
Published: January 2020

Ribosome profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution. Yet, several technical limitations restrict the sequencing depth of such experiments, the most common of which is the overabundance of ribosomal RNA (rRNA) fragments, which frequently make up more than 90% of sequencing reads if not depleted. Various strategies can be employed to tackle this issue, including the use of commercial rRNA depletion kits. However, as they are designed for more standardized RNAseq experiments, such kits may perform suboptimally in Ribo-seq. There is therefore potential to significantly increase the information that can be gleaned from Ribo-seq experiments. Here we show that a major confounding issue is that the rRNA fragments generated via Ribo-seq vary significantly with differing experimental conditions, suggesting that a “one-size-fits-all” approach may result in inefficient rRNA depletion. In order to overcome this, it is possible to use custom-designed biotinylated oligos complementary to the most abundant rRNA fragments, however currently no computational framework exists to aid the design of optimal oligos. We have developed Ribo-ODDR, an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oligos. We show that Ribo-ODDR designed oligos lead to a significant increase in rRNA depletion, and increased sequencing depth as a result, providing substantial information that would otherwise have been lost. Ribo-ODDR is freely accessible at https://github.com/fallerlab/Ribo-ODDR
Windows out of Africa: A 300,000-year chronology of climatically plausible human contact with Eurasia
Authors: Beyer Robert M. , Krapp Mario , Eriksson Anders , Manica Andrea
Published: January 2020

Whilst an African origin for Anatomically Modern Humans is well established1, the timings of their expansions into Eurasia are the subject to heated debate, due to the scarcity of fossils and the lack of suitably old ancient DNA2. Here, we estimate potential timings and routes out of Africa by deriving anthropologically and ecologically plausible precipitation requirements for human existence, and applying them to high-resolution palaeoclimate reconstructions for the past 300k years. We find that exit routes and timings previously suggested based on archaeological and genetic evidence coincide precisely with the presence of sufficiently wet corridors into Eurasia, while the gaps between the proposed exit timings co-occur with periods of insufficient rainfall. This demonstrates the key role that palaeoclimatic conditions played for out-of-Africa expansions. The challenging environmental conditions outside of Africa that occurred between windows of potential contact, coupled with the lack of a demographic rescue effect from migration and possible competition with other hominins, likely explain the demise of early colonists prior to the large-scale colonisation of the world beginning from ∼65kya.
The Nigro-Thalamic Projection contributes to the Control of Action Initiation Timing
Authors: Catanese Julien , Jaeger Dieter
Published: January 2020

The nigro-thalamic pathway is one of the main outputs from the basal ganglia, known to be involved in action selection, learning motor skills, and/or control the vigor of actions. However, the specific function of the nigral input to the motor thalamus remains unclear. Using a combination of in vivo electrophysiological recordings from motor thalamic neurons and optogenetic activation of nigral inputs in behaving head-fixed mice, we determined that this pathway is primarily involved in the proper timing of the release of goal directed actions. At the behavioral level, we were able to reduce the amount of impulsive licking by activating thalamic terminals. We describe changes in thalamic neuronal activity explaining this effect and propose a parsimonious model to account for our observations. These results provide new insight in the circuitry for timing control, a critical part of motor planning, and reveal a potential new target to modulate impulsivity.
Dissociation of connectivity for syntactic irregularity and perceptual ambiguity in musical chord stimuli
Authors: Kim Chan Hee , Jin Seung-Hyun , Kim June Sic , Kim Youn , Yi Suk Won , Chung Chun Kee
Published: January 2020

Previously syntactic irregularity has been most studied with chord sequences. However, the same chord may be interpreted as having different harmonic functions, implying perceptual ambiguity. Hence, syntactic irregularity and perceptual ambiguity may be processed simultaneously. We devised 3 different 5-chord sequences in which the ending chord differed with the tonic (T), submediant (SM), and supertonic (ST). In terms of syntactic regularity, T is most regular, ST is most irregular. However, in terms of perceptual ambiguity, the most irregular ST had the salient highest voice. Therefore, the SM was the most ambiguous condition. We investigated how the human brain separates syntactic irregularity and perceptual ambiguity in terms of effective connectivity in bilateral inferior frontal gyri (IFGs) and superior temporal gyri (STGs) with magnetoencephalography in 19 subjects. Correct rate was lower for the most ambiguous chord (SM) (P= 0.020) as expected. Connectivity from the right to the left IFG was enhanced for the most irregular chord (ST) (P= 0.024, false discovery rate (FDR) corrected), whereas connectivity from the right to the left STG was enhanced for the most ambiguous chord (SM) (P< 0.001, FDR corrected). The correct rate was negatively correlated with connectivity in the STG, further reflecting perceptual ambiguity (P= 0.026). We found that syntactic irregularity and perceptual ambiguity in music are dissociated in connectivity between bilateral IFGs and STGs, respectively.

Significance Statement

We provide the first neurophysiological evidence of the processing of perceptual ambiguity, other than syntactic irregularity, implied in musical chords. We found that the notion of “perceptually ambiguity” is applicable to musical chord stimuli different in syntactic irregularity, and that perceptual ambiguity is separate from syntactic irregularity. Our data demonstrate that the brain interprets the three conditions of musical chords as both “from regular to irregular” and “from ambiguous to unambiguous” conditions simultaneously. This study is the first to unveil dissociation of connectivity by syntactic irregularity and perceptual ambiguity involved in musical chord stimuli.