bluuebunny/crossref_metadata_2025 huggingface dataset:
Timely poacher detection and localization using sentinel animal movement
Authors: de Knegt Henrik J. , Eikelboom Jasper A. J. , van Langevelde Frank , Spruyt W. François , Prins Herbert H. T.
Published: February 2021

Wildlife crime is one of the most profitable illegal industries worldwide. Current actions to reduce it are far from effective and fail to prevent population declines of many endangered species, pressing the need for innovative anti-poaching solutions. Here, we propose and test a poacher early warning system that is based on the movement responses of non-targeted sentinel animals, which naturally respond to threats by fleeing and changing herd topology. We analyzed human-evasive movement patterns of 135 mammalian savanna herbivores of four different species, using an internet-of-things architecture with wearable sensors, wireless data transmission and machine learning algorithms. We show that the presence of human intruders can be accurately detected (86.1% accuracy) and localized (less than 500 m error in 54.2% of the experimentally staged intrusions) by algorithmically identifying characteristic changes in sentinel movement. These behavioral signatures include, among others, an increase in movement speed, energy expenditure, body acceleration, directional persistence and herd coherence, and a decrease in suitability of selected habitat. The key to successful identification of these signatures lies in identifying systematic deviations from normal behavior under similar conditions, such as season, time of day and habitat. We also show that the indirect costs of predation are not limited to vigilance, but also include (1) long, high-speed flights; (2) energetically costly flight paths; and (3) suboptimal habitat selection during flights. The combination of wireless biologging, predictive analytics and sentinel animal behavior can benefit wildlife conservation via early poacher detection, but also solve challenges related to surveillance, safety and health.
An NKX2-1GFP and TP63tdTomato dual fluorescent reporter for the investigation of human lung basal cell biology
Authors: Goh Kim Jee , Tan Ee Kim , Lu Hao , Roy Sudipto , Dunn N. Ray
Published: February 2021

Basal cells are multipotent stem cells responsible for the repair and regeneration of all the epithelial cell types present in the proximal lung. In mice, the elusive origins of basal cells and their contribution to lung development were recently revealed by high-resolution, lineage tracing studies. It however remains unclear if human basal cells originate and participate in lung development in a similar fashion, particularly with mounting evidence for significant species-specific differences in this process. To address this outstanding question, in the last several years differentiation protocols incorporating human pluripotent stem cells (hPSC) have been developed to produce human basal cells in vitro with varying efficiencies. To facilitate this endeavour, we introduced tdTomato into the human TP63 gene, whose expression specifically labels basal cells, in the background of a previously described hPSC line harbouring an NKX2-1GFP reporter allele. The functionality and specificity of the NKX2-1GFP;TP63tdTomato hPSC line was validated by directed differentiation into lung progenitors as well as more specialised lung epithelial subtypes using an organoid platform. This dual fluorescent reporter hPSC line will be useful for tracking, isolating and expanding basal cells from heterogenous differentiation cultures for further study.
High coercivity SmCo5 synthesized with assistance of colloidal SiO2
Authors: Tang Hao , Mamakhel Mohammad Aref Hasen , Christensen Mogens
Published: February 2021

SmCo5 is one of the most promising candidates for achieving a hard magnet with a high coercivity. Usually, composition, morphology, and size determine the coercivity of a magnet, however, it is challenging to synthesize phase pure SmCo5 with optimal size and high coercivity. In this paper, we report on the successful synthesis of phase pure SmCo5 with spherical/prolate spheroids shape. Size control is obtained by utilizing colloidal SiO2 as a template preventing aggregation and growth of the precursor. The amount of SiO2 nanoparticles (NPs) in the precursor tunes the average particle size (APS) of the synthesized SmCo5 with particle dimension from 740 to 504 nm. As-prepared pure SmCo5 fine powder obtained from using 2 ml SiO2 suspension possesses an APS of 625 nm and exhibits an excellent coercivity of 2986 kA m−1 (37.5 kOe) without alignment of the particles prior to magnetisation measurements. Comparing with a reference sample prepared without adding any SiO2 NPs, an enhancement of 35% of the coercivity was achieved. The improvement is due to phase purity, stable single-domain (SSD) size, and shape anisotropy originating from the prolate spheroid particles.
Pre-procedural proton pump inhibition is associated with fewer peri-oesophageal lesions after cryoballoon pulmonary vein isolation
Authors: Cordes F. , Ellermann C. , Dechering D. G. , Frommeyer G. , Kochhäuser S. , Lange P. S. , Pott C. , Lenze F. , Kabar I. , Schmidt H. , Ullerich H. , Eckardt L.
Published: February 2021

Pulmonary vein isolation (PVI) using cryoenergy is safe and efficient for treatment of atrial fibrillation (AF). Pre-existing upper gastrointestinal (GI) pathologies have been shown to increase the risk for AF. Therefore, this study aimed at assessing incidental pathologies of the upper GI tract in patients scheduled for PVI and to analyse the impact of patients’ characteristics on PVI safety outcome. In 71 AF patients, who participated in the MADE-PVI trial, oesophagogastroduodenoscopy and endosonography were prospectively performed directly before and the day after PVI to assess pre-existing upper GI pathologies and post-interventional occurrence of PVI-associated lesions. Subgroup analysis of the MADE-PVI trial identified clinically relevant incidental findings in 53 patients (74.6%) with age > 50 years being a significant risk factor. Pre-existing reflux oesophagitis increased risk for PVI-associated mediastinal oedema, while patients already treated with proton pump inhibitors (PPI) had significantly fewer mediastinal oedema. Our results suggest that AF patients with pre-existing reflux oesophagitis are at higher risk for PVI-associated mediastinal lesions, which is decreased in patients with constant PPI-treatment prior to PVI. Since PVI-associated mediastinal lesions are regarded as surrogate parameter for an increased risk of the fatal complication of an oesophago-atrial fistula, our findings hint at a beneficial effect of pre-interventional prophylactic PPI-treatment to reduce risk for PVI-associated complications.

German Clinical Trials Register (DRKS00016006; date of registration: 17/12/2018).
Protocol for preparation of heterogeneous biological samples for 3D electron microscopy: a case study for insects
Authors: Polilov Alexey A. , Makarova Anastasia A. , Pang Song , Shan Xu C. , Hess Harald
Published: February 2021

Modern morphological and structural studies are coming to a new level by incorporating the latest methods of three-dimensional electron microscopy (3D-EM). One of the key problems for the wide usage of these methods is posed by difficulties with sample preparation, since the methods work poorly with heterogeneous (consisting of tissues different in structure and in chemical composition) samples and require expensive equipment and usually much time. We have developed a simple protocol allows preparing heterogeneous biological samples suitable for 3D-EM in a laboratory that has a standard supply of equipment and reagents for electron microscopy. This protocol, combined with focused ion-beam scanning electron microscopy, makes it possible to study 3D ultrastructure of complex biological samples, e.g., whole insect heads, over their entire volume at the cellular and subcellular levels. The protocol provides new opportunities for many areas of study, including connectomics.
Airspace Dimension Assessment (AiDA) by inhaled nanoparticles: benchmarking with hyperpolarised 129Xe diffusion-weighted lung MRI
Authors: Petersson-Sjögren Madeleine , Chan Ho-Fung , Collier Guilhem J. , Norquay Graham , Olsson Lars E. , Wollmer Per , Löndahl Jakob , Wild Jim M.
Published: February 2021

Enlargements of distal airspaces can indicate pathological changes in the lung, but accessible and precise techniques able to measure these regions are lacking. Airspace Dimension Assessment with inhaled nanoparticles (AiDA) is a new method developed for in vivo measurement of distal airspace dimensions. The aim of this study was to benchmark the AiDA method against quantitative measurements of distal airspaces from hyperpolarised 129Xe diffusion-weighted (DW)-lung magnetic resonance imaging (MRI). AiDA and 129Xe DW-MRI measurements were performed in 23 healthy volunteers who spanned an age range of 23–70 years. The relationship between the 129Xe DW-MRI and AiDA metrics was tested using Spearman’s rank correlation coefficient. Significant correlations were observed between AiDA distal airspace radius (rAiDA) and mean 129Xe apparent diffusion coefficient (ADC) (p < 0.005), distributed diffusivity coefficient (DDC) (p < 0.001) and distal airspace dimension (LmD) (p < 0.001). A mean bias of − 1.2 µm towards rAiDA was observed between 129Xe LmD and rAiDA, indicating that rAiDA is a measure of distal airspace dimension. The AiDA R0 intercept correlated with MRI 129Xe α (p = 0.02), a marker of distal airspace heterogeneity. This study demonstrates that AiDA has potential to characterize the distal airspace microstructures and may serve as an alternative method for clinical examination of the lungs.
Time-for-space substitution in N-mixture models for estimating population trends: a simulation-based evaluation
Authors: Costa Andrea , Salvidio Sebastiano , Penner Johannes , Basile Marco
Published: February 2021

N-mixture models usually rely on a meta-population design, in which repeated counts of individuals in multiple sampling locations are obtained over time. The time-for-space substitution (TSS) in N-mixture models allows to estimate population abundance and trend of a single population, without spatial replication. This application could be of great interest in ecological studies and conservation programs; however, its reliability has only been evaluated on a single case study. Here we perform a simulation-based evaluation of this particular application of N-mixture modelling. We generated count data, under 144 simulated scenarios, from a single population surveyed several times per year and subject to different dynamics. We compared simulated abundance and trend values with TSS estimates. TSS estimates are overall in good agreement with real abundance. Trend and abundance estimation is mainly affected by detection probability and population size. After evaluating the reliability of TSS, both against real world data, and simulations, we suggest that this particular application of N-mixture model could be reliable for monitoring abundance in single populations of rare or difficult to study species, in particular in cases of species with very narrow geographic ranges, or known only for few localities.
Asthma and asthma symptom control in relation to incidence of lung cancer in the HUNT study
Authors: Jiang Lin , Sun Yi-Qian , Langhammer Arnulf , Brumpton Ben Michael , Chen Yue , Nilsen Tom IL , Leivseth Linda , Wahl Sissel Gyrid Freim , Mai Xiao-Mei
Published: February 2021

Large prospective studies on asthma, especially asthma symptom control, as a potential risk factor for lung cancer are limited. We followed up 62,791 cancer-free Norwegian adults from 1995–1997 to 2017. Self-reported doctor-diagnosed asthma was categorized into active and non-active asthma. Levels of asthma symptom control were classified into controlled and partially controlled (including partly controlled and uncontrolled) according to the Global Initiative for Asthma guidelines. Incident lung cancer cases were ascertained from the Cancer Registry of Norway. Cox regression models were used to estimate hazard ratios (HRs) with 95% confidence intervals (CIs) for possible associations. Totally, 984 participants developed lung cancer during a median follow-up of 21.1 years. After adjustment for smoking and other potential confounders, an increased incidence of lung cancer was found for adults with partially controlled asthma (HR 1.39, 95% CI 1.00–1.92) compared with those without asthma at baseline. Adults with active asthma had a tendency of increased lung cancer incidence (HR 1.29, 95% CI 0.95–1.75). Sensitivity analyses indicated that the observed associations were less likely resulted from reverse causation or residual confounding by smoking. Our findings suggested that proper control of asthma symptoms might contribute to a reduced incidence of lung cancer.
Experimental demonstration of negative refraction with 3D locally resonant acoustic metafluids
Authors: Tallon Benoit , Kovalenko Artem , Poncelet Olivier , Aristégui Christophe , Mondain-Monval Olivier , Brunet Thomas
Published: February 2021

Negative refraction of acoustic waves is demonstrated through underwater experiments conducted at ultrasonic frequencies on a 3D locally resonant acoustic metafluid made of soft porous silicone-rubber micro-beads suspended in a yield-stress fluid. By measuring the refracted angle of the acoustic beam transmitted through this metafluid shaped as a prism, we determine the acoustic index to water according to Snell’s law. These experimental data are then compared with an excellent agreement to calculations performed in the framework of Multiple Scattering Theory showing that the emergence of negative refraction depends on the volume fraction $$\Phi$$
Φ
of the resonant micro-beads. For diluted metafluid ($$\Phi =3\%$$

Φ
=
3
%

), only positive refraction occurs whereas negative refraction is demonstrated over a broad frequency band with concentrated metafluid ($$\Phi =17\%$$

Φ
=
17
%

).
The dominance model for heterosis explains culm length genetics in a hybrid sorghum variety
Authors: Hashimoto Shumpei , Wake Tatsuro , Nakamura Haruki , Minamiyama Masaki , Araki-Nakamura Satoko , Ohmae-Shinohara Kozue , Koketsu Eriko , Okamura Shinnosuke , Miura Kotaro , Kawaguchi Hideo , Kasuga Shigemitsu , Sazuka Takashi
Published: February 2021

Heterosis helps increase the biomass of many crops; however, while models for its mechanisms have been proposed, it is not yet fully understood. Here, we use a QTL analysis of the progeny of a high-biomass sorghum F1 hybrid to examine heterosis. Five QTLs were identified for culm length and were explained using the dominance model. Five resultant homozygous dominant alleles were used to develop pyramided lines, which produced biomasses like the original F1 line. Cloning of one of the uncharacterised genes (Dw7a) revealed that it encoded a MYB transcription factor, that was not yet proactively used in modern breeding, suggesting that combining classic dw1or dw3, and new (dw7a) genes is an important breeding strategy. In conclusion, heterosis is explained in this situation by the dominance model and a combination of genes that balance the shortness and early flowering of the parents, to produce F1 seed yields.
Role of sex in the association between childhood socioeconomic position and cognitive ageing in later life
Authors: Wolfova Katrin , Csajbok Zsofia , Kagstrom Anna , Kåreholt Ingemar , Cermakova Pavla
Published: February 2021

We aimed to explore sex differences in the association of childhood socioeconomic position (SEP) with the level of cognitive performance and the rate of cognitive decline. We studied 84,059 individuals (55% women; mean age 64 years) from the Survey on Health, Ageing and Retirement in Europe. Sex differences in the association of childhood SEP (household characteristics at age 10) with the level of cognitive performance (verbal fluency, immediate recall, delayed recall) were analysed using multilevel linear regression. Structural equation modelling tested education, depressive symptoms and physical state as mediators. The relationship between childhood socioeconomic advantage and disadvantage and the rate of cognitive decline was assessed using linear mixed-effects models. Higher childhood SEP was associated with a higher level of cognitive performance to a greater extent in women (B = 0.122; 95% CI 0.092–0.151) than in men (B = 0.109; 95% CI 0.084–0.135). The strongest mediator was education. Childhood socioeconomic disadvantage was related to a higher rate of decline in delayed recall in both sexes, with a greater association in women. Strategies to prevent impaired late-life cognitive functioning, such as reducing childhood socioeconomic disadvantages and improving education, might have a greater benefit for women.
Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring
Authors: Wüllems Karsten , Zurowietz Annika , Zurowietz Martin , Schneider Roland , Bednarz Hanna , Niehaus Karsten , Nattkemper Tim W.
Published: February 2021

Mass Spectrometry Imaging (MSI) is an established and still evolving technique for the spatial analysis of molecular co-location in biological samples. Nowadays, MSI is expanding into new domains such as clinical pathology. In order to increase the value of MSI data, software for visual analysis is required that is intuitive and technique independent. Here, we present QUIMBI (QUIck exploration tool for Multivariate BioImages) a new tool for the visual analysis of MSI data. QUIMBI is an interactive visual exploration tool that provides the user with a convenient and straightforward visual exploration of morphological and spectral features of MSI data. To improve the overall quality of MSI data by reducing non-tissue specific signals and to ensure optimal compatibility with QUIMBI, the tool is combined with the new pre-processing tool ProViM (Processing for Visualization and multivariate analysis of MSI Data), presented in this work. The features of the proposed visual analysis approach for MSI data analysis are demonstrated with two use cases. The results show that the use of ProViM and QUIMBI not only provides a new fast and intuitive visual analysis, but also allows the detection of new co-location patterns in MSI data that are difficult to find with other methods.
CircSLC8A1 and circNFIX can be used as auxiliary diagnostic markers for sudden cardiac death caused by acute ischemic heart disease
Authors: Tian Meihui , Xue Jiajia , Dai Cuiyun , Jiang Enzhu , Zhu Baoli , Pang Hao
Published: February 2021

Sudden cardiac death (SCD) caused by acute ischemic heart disease (IHD) is a major cause of sudden death worldwide. Circular RNAs (circRNAs) are abundant in the heart and play important roles in cardiovascular diseases, but the role of circRNAs as biomarkers in the forensic diagnosis of SCD caused by acute IHD remains poorly characterized. To investigate the potential of two heart-enriched circRNAs, circNFIX and circSLC8A1, we explored the expression of these two circRNAs in different kinds of commonly used IHD models, and further verified their expressions in forensic autopsy cases. The results from both the IHD rat and H9c2 cell models revealed that circSlc8a1 level was upregulated, while the circNfix level was elevated in the early stage of ischemia and subsequently downregulated. The time-dependent expression patterns of the two circRNAs suggested their potential as SCD biomarkers. In autopsy cases, the results showed that the expression of these two circRNAs in the myocardium with acute IHD-related SCDs corresponded to the observations in the ischemic models. Further analysis related to myocardial ischemia indicated that circSLC8A1 showed high sensitivity and specificity for myocardial infarction and was positively correlated with creatine kinase MB in pericardial fluid. Downregulated circNFIX level could indicate the ischemic myocardial damage, and it was negatively correlated with the coronary artery stenosis grade. The combination of circSLC8A1 and circNFIX had better performance to discriminate IHD-related SCDs. The results suggested that circSLC8A1 and circNFIX may be used as auxiliary diagnostic markers for SCD caused by acute IHD in forensic medicine.
Adipose-derived mesenchymal stem cells differentiate into heterogeneous cancer-associated fibroblasts in a stroma-rich xenograft model
Authors: Miyazaki Yoshihiro , Oda Tatsuya , Inagaki Yuki , Kushige Hiroko , Saito Yutaka , Mori Nobuhito , Takayama Yuzo , Kumagai Yutaro , Mitsuyama Toutai , Kida Yasuyuki S.
Published: February 2021

Cancer-associated fibroblasts (CAFs) are the key components of the densely proliferated stroma in pancreatic ductal adenocarcinoma (PDAC) and contribute to tumor progression and drug resistance. CAFs comprise heterogeneous subpopulations playing unique and vital roles. However, the commonly used mouse models have not been able to fully reproduce the histological and functional characteristics of clinical human CAF. Here, we generated a human cell-derived stroma-rich CDX (Sr-CDX) model, to reproduce the clinical tumor microenvironment. By co-transplanting human adipose-derived mesenchymal stem cells (AD-MSCs) and a human PDAC cell line (Capan-1) into mice, the Sr-CDX model recapitulated the characteristics of clinical pancreatic cancer, such as accelerated tumor growth, abundant stromal proliferation, chemoresistance, and dense stroma formed from the heterogeneous CAFs. Global RNA sequencing, single-cell based RNA sequencing, and histological analysis of CAFs in the Sr-CDX model revealed that the CAFs of the Sr-CDX mice were derived from the transplanted AD-MSCs and composed of heterogeneous subpopulations of CAF, including known and unknown subtypes. These lines of evidences suggest that our new tumor-bearing mouse model has the potential to address an open question in CAF research, that is the mechanism of CAF differentiation.
The effect of deformation of absorbing scatterers on Mie-type signatures in infrared microspectroscopy
Authors: Brandsrud Maren Anna , Blümel Reinhold , Solheim Johanne Heitmann , Kohler Achim
Published: February 2021

Mie-type scattering features such as ripples (i.e., sharp shape-resonance peaks) and wiggles (i.e., broad oscillations), are frequently-observed scattering phenomena in infrared microspectroscopy of cells and tissues. They appear in general when the wavelength of electromagnetic radiation is of the same order as the size of the scatterer. By use of approximations to the Mie solutions for spheres, iterative algorithms have been developed to retrieve pure absorbance spectra. However, the question remains to what extent the Mie solutions, and approximations thereof, describe the extinction efficiency in practical situations where the shapes of scatterers deviate considerably from spheres. The aim of the current study is to investigate how deviations from a spherical scatterer can change the extinction properties of the scatterer in the context of chaos in wave systems. For this purpose, we investigate a chaotic scatterer and compare it with an elliptically shaped scatterer, which exhibits only regular scattering. We find that chaotic scattering has an accelerating effect on the disappearance of Mie ripples. We further show that the presence of absorption and the high numerical aperture of infrared microscopes does not explain the absence of ripples in most measurements of biological samples.
The influence of human genetic variation on Epstein–Barr virus sequence diversity
Authors: Rüeger Sina , Hammer Christian , Loetscher Alexis , McLaren Paul J. , Lawless Dylan , Naret Olivier , Khanna Nina , Bernasconi Enos , Cavassini Matthias , Günthard Huldrych F. , Kahlert Christian R. , Rauch Andri , Depledge Daniel P. , Morfopoulou Sofia , Breuer Judith , Zdobnov Evgeny , Fellay Jacques ,   the Swiss HIV Cohort Study, Aebi-Popp Karoline , Anagnostopoulos Alexia , Battegay Manuel , Bernasconi Enos , Böni Jürg , Braun Dominique , Bucher Heiner , Calmy Alexandra , Cavassini Matthias , Ciuffi Angela , Dollenmaier Guenter , Egger Matthias , Elzi Luigia , Fehr Jan , Fellay Jacques , Furrer Hansjakob , Fux Christoph , Günthard Huldrych F. , Haerry David , Hasse Barbara , Hirsch Hans , Hoffmann Matthias , Hösli Irene , Huber Michael , Kahlert Christian R. , Kaiser Laurent , Keiser Olivia , Klimkait Thomas , Kottanattu Lisa , Kouyos Roger , Kovari Helen , Ledergerber Bruno , Martinetti Gladys , de Tejada Begoña Martinez , Marzolini Catia , Metzner Karin , Müller Nicolas , Nicca Dunja , Paioni Paolo , Pantaleo Giuseppe , Perreau Matthieu , Rauch Andri , Rudin Christoph , Scherrer Alexandra , Schmid Patrick , Speck Roberto , Stöckle Marcel , Tarr Philip , Trkola Alexandra , Vernazza Pietro , Wagner Noémie , Wandeler Gilles , Weber Rainer , Yerly Sabine
Published: February 2021

Epstein–Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imprint of host genomic variation on the EBV sequence, we jointly analyzed paired viral and human genomic data from 268 HIV-coinfected individuals with CD4 + T cell count < 200/mm3and elevated EBV viremia. We hypothesized that the reactivated virus circulating in these patients could carry sequence variants acquired during primary EBV infection, thereby providing a snapshot of early adaptation to the pressure exerted on EBV by the individual immune response. We searched for associations between host and pathogen genetic variants, taking into account human and EBV population structure. Our analyses revealed significant associations between human and EBV sequence variation. Three polymorphic regions in the human genome were found to be associated with EBV variation: one at the amino acid level (BRLF1:p.Lys316Glu); and two at the gene level (burden testing of rare variants in BALF5 and BBRF1). Our findings confirm that jointly analyzing host and pathogen genomes can identify sites of genomic interactions, which could help dissect pathogenic mechanisms and suggest new therapeutic avenues.
Molecular imaging of orthotopic prostate cancer with nanobubble ultrasound contrast agents targeted to PSMA
Authors: Wang Yu , De Leon Al Christopher , Perera Reshani , Abenojar Eric , Gopalakrishnan Ramamurthy , Basilion James P. , Wang Xinning , Exner Agata A.
Published: February 2021

Ultrasound imaging is routinely used to guide prostate biopsies, yet delineation of tumors within the prostate gland is extremely challenging, even with microbubble (MB) contrast. A more effective ultrasound protocol is needed that can effectively localize malignancies for targeted biopsy or aid in patient selection and treatment planning for organ-sparing focal therapy. This study focused on evaluating the application of a novel nanobubble ultrasound contrast agent targeted to the prostate specific membrane antigen (PSMA-targeted NBs) in ultrasound imaging of prostate cancer (PCa) in vivo using a clinically relevant orthotopic tumor model in nude mice. Our results demonstrated that PSMA-targeted NBs had increased extravasation and retention in PSMA-expressing orthotopic mouse tumors. These processes are reflected in significantly different time intensity curve (TIC) and several kinetic parameters for targeted versus non-targeted NBs or LUMASON MBs. These, may in turn, lead to improved image-based detection and diagnosis of PCa in the future.
A glycoside analog of mammalian oligomannose formulated with a TLR4-stimulating adjuvant elicits HIV-1 cross-reactive antibodies
Authors: Bruxelle Jean-François , Kirilenko Tess , Trattnig Nino , Yang Yiqiu , Cattin Matteo , Kosma Paul , Pantophlet Ralph
Published: February 2021

The occurrence of oligomannose-specific broadly neutralizing antibodies (bnAbs) has spurred efforts to develop immunogens that can elicit similar antibodies. Here, we report on the antigenicity and immunogenicity of a CRM197-conjugate of a previously reported oligomannose mimetic. Oligomannose-specific bnAbs that are less dependent on interactions with the HIV envelope protein sequence showed strong binding to the glycoconjugates, with affinities approximating those reported for their cognate epitope. The glycoconjugate is also recognized by inferred germline precursors of oligomannose-specific bnAbs, albeit with the expected low avidity, supporting its potential as an immunogen. Immunization of human-antibody transgenic mice revealed that only a TLR4-stimulating adjuvant formulation resulted in antibodies able to bind a panel of recombinant HIV trimers. These antibodies bound at relatively modest levels, possibly explaining their inability to neutralize HIV infectivity. Nevertheless, these findings contribute further to understanding conditions for eliciting HIV-cross-reactive oligomannose-specific antibodies and inform on next steps for improving on the elicited response.
Tuberculosis case notifications in Malawi have strong seasonal and weather-related trends
Authors: Kirolos Amir , Thindwa Deus , Khundi McEwen , Burke Rachael M. , Henrion Marc Y. R. , Nakamura Itaru , Divala Titus H. , Nliwasa Marriott , Corbett Elizabeth L. , MacPherson Peter
Published: February 2021

Seasonal trends in tuberculosis (TB) notifications have been observed in several countries but are poorly understood. Explanatory factors may include weather, indoor crowding, seasonal respiratory infections and migration. Using enhanced citywide TB surveillance data collected over nine years in Blantyre, Malawi, we set out to investigate how weather and seasonality affect temporal trends in TB case notification rates (CNRs) across different demographic groups. We used data from prospective enhanced surveillance between April 2011 and December 2018, which systematically collected age, HIV status, sex and case notification dates for all registering TB cases in Blantyre. We retrieved temperature and rainfall data from the Global Surface Summary of the Day weather station database. We calculated weekly trends in TB CNRs, rainfall and temperature, and calculated 10-week moving averages. To investigate the associations between rainfall, temperature and TB CNRs, we fitted generalized linear models using a distributed lag nonlinear framework. The estimated Blantyre population increased from 1,068,151 in April 2011 to 1,264,304 in December 2018, with 15,908 TB cases recorded. Overall annual TB CNRs declined from 222 to 145 per 100,000 between 2012 and 2018, with the largest declines seen in HIV-positive people and adults aged over 20 years old. TB CNRs peaks occurred with increasing temperature in September and October before the onset of increased rainfall, and later in the rainy season during January-March, after sustained rainfall. When lag between a change in weather and TB case notifications was accounted for, higher average rainfall was associated with an equivalent six weeks of relatively lower TB notification rates, whereas there were no changes in TB CNR associated with change in average temperatures. TB CNRs in Blantyre have a seasonal pattern of two cyclical peaks per year, coinciding with the start and end of the rainy season. These trends may be explained by increased transmission at certain times of the year, by limited healthcare access, by patterns of seasonal respiratory infections precipitating cough and care-seeking, or by migratory patterns related to planting and harvesting during the rainy season.
Exploring the genetic architecture of feed efficiency traits in chickens
Authors: Marchesi Jorge Augusto Petroli , Ono Rafael Keith , Cantão Maurício Egídio , Ibelli Adriana Mércia Guaratini , Peixoto Jane de Oliveira , Moreira Gabriel Costa Monteiro , Godoy Thaís Fernanda , Coutinho Luiz Lehmann , Munari Danísio Prado , Ledur Mônica Corrêa
Published: February 2021

Chicken feed efficiency (FE) traits are the most important economic traits in broiler production. Several studies evaluating genetic factors affecting food consumption in chickens are available. However, most of these studies identified genomic regions containing putative quantitative trait loci for each trait separately. It is still a challenge to find common gene networks related to these traits. Therefore, here, a genome-wide association study (GWAS) was conducted to explore candidate genomic regions responsible for Feed Intake (FI), Body Weight Gain (BWG) and Feed Conversion Ratio (FCR) traits and their gene networks. A total of 1430 broilers from an experimental population was genotyped with the high density Affymetrix 600K SNP array. A total of 119 associated SNPs located in 20 chromosomes were identified, where some of them were common in more than one FE trait. In addition, novel genomic regions were prospected considering the SNPs dominance effects and sex interaction, identifying putative candidate genes only when these effects were fit in the model. Relevant candidate genes such as ATRNL1, PIK3C2A, PTPRN2, SORCS3 and gga-mir-1759 were highlighted in this study helping to elucidate the genomic architecture of feed efficiency traits. These results provide new insights on the mechanisms underlying the consumption and utilization of food in chickens.
Comparison of E. coli based self-inducible expression systems containing different human heat shock proteins
Authors: Shariati Fatemeh Sadat , Keramati Malihe , Valizadeh Vahideh , Cohan Reza Ahangari , Norouzian Dariush
Published: February 2021

IPTG-inducible promoter is popularly used for the expression of recombinant proteins. However, it is not suitable at the industrial scale due to the high cost and toxicity on the producing cells. Recently, a Self-Inducible Expression (SILEX) system has developed to bypass such problems using Hsp70 as an autoinducer. Herein, the effect of other heat shock proteins on the autoinduction of green fluorescent protein (EGFP), romiplostim, and interleukin-2 was investigated. For quantitative measurements, EGFP expression was monitored after double-transformation of pET28a-EGFP and pET21a-(Hsp27/Hsp40/Hsp70) plasmids into E.coli using fluorimetry. Moreover, the expression level, bacterial growth curve, and plasmid and expression stability were compared to an IPTG- inducible system using EGFP. Statistical analysis revealed a significant difference in EGFP expression between autoinducible and IPTG-inducible systems. The expression level was higher in Hsp27 system than Hsp70/Hsp40 systems. However, the highest amount of expression was observed for the inducible system. IPTG-inducible and Hsp70 systems showed more lag-time in the bacterial growth curve than Hsp27/Hsp40 systems. A relatively stable EGFP expression was observed in SILEX systems after several freeze–thaw cycles within 90 days, while, IPTG-inducible system showed a decreasing trend compared to the newly transformed bacteria. Moreover, the inducible system showed more variation in the EGFP expression among different clones than clones obtained by SILEX systems. All designed SILEX systems successfully self-induced the expression of protein models. In conclusion, Hsp27 system could be considered as a suitable autoinducible system for protein expression due to less metabolic burden, lower variation in the expression level, suitable plasmid and expression stability, and a higher expression level.
Circulating cell free DNA response to exhaustive exercise in average trained men with type I diabetes mellitus
Authors: Walczak Konrad , Stawski Robert , Perdas Ewelina , Brzezinska Olga , Kosielski Piotr , Galczynski Szymon , Budlewski Tomasz , Padula Gianluca , Nowak Dariusz
Published: February 2021

It is believed that neutrophils extracellular traps (NETs) formation is responsible for the increase in cf DNA after exercise. Since T1DM is accompanied by enhanced NETs generation, we compared exercise-induced increase in cf DNA in 14 men with T1DM and 11 healthy controls and analyzed its association with exercise load. Subjects performed a treadmill run to exhaustion at speed corresponding to 70% of their personal VO2max. Blood was collected before and just after exercise for determination of plasma cf nuclear and mitochondrial DNA (cf n-DNA, cf mt-DNA) by real-time PCR, blood cell count and metabolic markers. Exercise resulted in the increase in median cf n-DNA from 3.9 ng/mL to 21.0 ng/mL in T1DM group and from 3.3 ng/mL to 28.9 ng/mL in controls. Median exercise-induced increment (∆) in cf n-DNA did not differ significantly in both groups (17.8 ng/mL vs. 22.1 ng/mL, p = 0.23), but this variable correlated with run distance (r = 0.66), Δ neutrophils (r = 0.86), Δ creatinine (r = 0.65) and Δ creatine kinase (r = 0.77) only in controls. Pre- and post-exercise cf mt-DNA were not significantly different within and between groups. These suggest low usefulness of Δ cf n-DNA as a marker of exercise intensity in T1DM men.
Aptamer-targeting of Aleutian mink disease virus (AMDV) can be an effective strategy to inhibit virus replication
Authors: Lu Taofeng , Zhang Hui , Zhou Jie , Ma Qin , Yan Wenzhuo , Zhao Lili , Wu Shuguang , Chen Hongyan
Published: February 2021

Aleutian mink disease (AMD), which is caused by Aleutian mink disease virus (AMDV), is an important contagious disease for which no effective vaccine is yet available. AMD causes major economic losses for mink farmers globally and threatens some carnivores such as skunks, genets, foxes and raccoons. Aptamers have exciting potential for the diagnosis and/or treatment of infectious viral diseases, including AMD. Using a magnetic beads-based systemic evolution of ligands by exponential enrichment (SELEX) approach, we have developed aptamers with activity against AMDV after 10 rounds of selection. After incubation with the ADVa012 aptamer (4 μM) for 48 h, the concentration of AMDV in the supernatant of infected cells was 47% lower than in the supernatant of untreated cells, whereas a random library of aptamers has no effect. The half-life of ADVa012 was ~ 32 h, which is significantly longer than that of other aptamers. Sequences and three dimensions structural modeling of selected aptamers indicated that they fold into similar stem-loop structures, which may be a preferred structure for binding to the target protein. The ADVa012 aptamer was shown to have an effective and long-lasting inhibitory effect on viral production in vitro.
Isotopic discrimination in helminths infecting coral reef fishes depends on parasite group, habitat within host, and host stable isotope value
Authors: Riekenberg Philip M. , Briand Marine J. , Moléana Thibaud , Sasal Pierre , van der Meer Marcel T. J. , Thieltges David W. , Letourneur Yves
Published: February 2021

Stable isotopes of carbon and nitrogen characterize trophic relationships in predator–prey relationships, with clear differences between consumer and diet (discrimination factor Δ13C and Δ15N). However, parasite–host isotopic relationships remain unclear, with Δ13C and Δ15N remaining incompletely characterized, especially for helminths. In this study, we used stable isotopes to determine discrimination factors for 13 parasite–host pairings of helminths in coral reef fish. Differences in Δ15N values grouped according to parasite groups and habitat within the host with positive Δ15N values observed for trematodes and nematodes from the digestive tract and variable Δ15N values observed for cestodes and nematodes from the general cavity. Furthermore, Δ13C values showed more complex patterns with no effect of parasite group or habitat within host. A negative relationship was observed between Δ15N and host δ15N values among different host-parasite pairings as well as within 7 out of the 13 pairings, indicating that host metabolic processing affects host-parasite discrimination values. In contrast, no relationships were observed for Δ13C values. Our results indicate that parasite group, habitat within host, and host stable isotope value drive Δ15N of helminths in coral reef fish while their effect on Δ13C is more idiosyncratic. These results call for use of taxon- or species-specific and scaled framework for bulk stable isotopes in the trophic ecology of parasites.
Chemical methods for protein site-specific ubiquitination
Authors: Gui Weijun , Davidson Gregory A. , Zhuang Zhihao
Published: February 2021

Chemical methods for protein site-specific ubiquitination are important for the understanding of Ub signaling.
Differential hysteresis scanning of non-templated monomodal amorphous aerogels
Authors: Taheri Poroshat , Lang John C. , Kenvin Jeffrey , Kroll Peter
Published: February 2021

We perform Differential Hysteresis Scanning (DHS) Porosimetry of amorphous silicon oxycarbide aerogels to quantify hierarchical connectivity in these porous materials.
Ideal strength and strain engineering of the Rashba effect in two-dimensional BiTeBr
Authors: Yang Wei , Guan Zhizi , Wang Hailong , Li Junwen
Published: February 2021

Strain engineering can lead to enhanced charge transfer and therefore, can effectively tune Rashba effect.
Magnetism manipulated by ferroelectric polarization and epitaxial strain in a La0.75Sr0.25MnO3/BaTiO3system
Authors: Chen Dong , Wang Chun-Lei
Published: February 2021

The magnetism and electronic structure of the La0.75Sr0.25MnO3/BaTiO3superlattice have been manipulated by introducing epitaxial strain and ferroelectric polarization. The underlying mechanism of magnetic properties is also revealed.
Visible light promoted photoredox C(sp3)–H bond functionalization of tetrahydroisoquinolines in flow
Authors: Filipović Ana , Džambaski Zdravko , Vasiljević-Radović Dana , Bondžić Bojan P.
Published: February 2021

Visible light promoted C(sp3)–H functionalization ofN-aryl-protected tetrahydroisoquinolines under microflow conditions with various coupling partners in excellent yields and efficiencies.
Predicting OH stretching fundamental wavenumbers of alcohols for conformational assignment: different correction patterns for density functional and wave-function-based methods
Authors: Medel Robert , Suhm Martin A.
Published: February 2021

Affordable predictions for absolute OH stretching fundamental wavenumbers of alcohols with conformational accuracy are possible when the different deficiencies of quantum chemical methods are empirically corrected.
Recent progress in oxychalcogenides as IR nonlinear optical materials
Authors: Shi Yang-Fang , Wei Wen-Bo , Wu Xin-Tao , Lin Hua , Zhu Qi-Long
Published: February 2021

This Frontiers article discusses the recent progress and challenges of non-centrosymmetric oxychalcogenides in the IR nonlinear optical field.
Exploring the effects of approach velocity on depletion force and coalescence in oil-in-water emulsions
Authors: Aarøen Ola , Riccardi Enrico , Sletmoen Marit
Published: February 2021

Presented here are ways of producing unstable emulsions and use these in optical tweezers studies to determine the effects of system parameters on droplet depletion force and coalescence time.
17O NMR spectroscopy of crystalline microporous materials
Authors: Ashbrook Sharon E. , Davis Zachary H. , Morris Russell E. , Rice Cameron M.
Published: February 2021

Cost-effective and atom-efficient isotopic enrichment enables 17O NMR spectroscopy of microporous materials to be used to probe local structure and disorder and to explore chemical reactivity.
Core–shell Cu2S:NiS2@C hybrid nanostructure derived from a metal–organic framework with graphene oxide for photocatalytic synthesis of N-substituted derivatives
Authors: Yusuf Mohammad , Hira Shamim Ahmed , Lim Hyeonhan , Song Sehwan , Park Sungkyun , Park Kang Hyun
Published: February 2021

A series of MOF modified with GO was fabricated by a facile method and the Cu:Ni sulfide encapsulated on porous C with reduced GO (Cu2S:NiS2@C/rGO) showed superior photocatalytic activity for three kinds of C–N oxidative coupling reactions.
The Association Between Brain Reserve, Cognitive Reserve, and Neuropsychological and Functional Outcomes in Males With Chronic Moderate-to-Severe Traumatic Brain Injury
Authors: Pettemeridou Eva , Constantinidou Fofi
Published: February 2021

Purpose

Moderate-to-severe traumatic brain injury (TBI) leads to significant neural and cognitive impairment, affecting functional outcome. This study investigated the chronic effects of moderate-to-severe TBI on brain reserve (BR), cognitive reserve (CR), and neuropsychological and functional outcome.

Method

The group with TBI consisted of 41 male participants with a primary diagnosis of moderate-to-severe closed head injury (time since injury [TSI],
M
= 6.12 years, range: 1–23,
SD
= 5.99,
Mdn
= 4). TBI survivors were compared to 24 neurotypical male participants, matched on age and education. Magnetic resonance imaging T1 anatomical images were used to calculate gray and white matter and cerebrospinal fluid volume. BR was calculated using the ventricle-to-brain ratio. CR was assessed using two hold measures: the Peabody Picture Vocabulary Test and the Pseudowords task. Functional outcome was measured using the Glasgow Outcome Scale–Extended.

Results

Neuropsychological performance of TBI survivors was significantly lower than their neurotypical controls, as measured by theoretically driven composites of verbal and visual memory, executive functions, attention, and CR. They presented greater ventricle-to-brain ratio volume, compared to noninjured controls, with higher scores indicating lower BR levels. Both BR and TSI were significantly associated with CR. Also, a median-split analysis revealed a TSI effect on CR. Significant associations were evident between the Glasgow Outcome Scale–Extended and the BR and CR measures.

Conclusions

Lingering neuropsychological deficits in chronic TBI support the role of BR and CR in functional outcome. Furthermore, TSI interferes with CR supporting the notion that TBI sets off a chronic neurodegenerative and progressive course that interferes with semantic knowledge.

Supplemental Material

https://doi.org/10.23641/asha.14049923
Combined Memory Training: An Approach for Episodic Memory Deficits in Traumatic Brain Injury
Authors: D'Angelo Elisabeth Cochran , Ober Beth A. , Shenaut Gregory K.
Published: February 2021

Purpose

The study aimed to test a combination of semantic memory and traditional episodic memory therapies on episodic memory deficits in adults with traumatic brain injury.

Method

Twenty-five participants who had been diagnosed with traumatic brain injury and had episodic memory deficits were randomly assigned either to a combined memory treatment group (
n
= 16) or to a wait-list control group (
n
= 9). Before and after treatment, they completed standardized neuropsychological testing for episodic memory and related cognitive domains, including the California Verbal Learning Test–Second Edition, the Controlled Oral Word Association Test, the University of Southern California Repeatable Episodic Memory Test, the Wechsler Abbreviated Scale of Intelligence–Second Edition Matrices, the Test of Everyday Attention, the Memory Assessment Clinics Self-Rating Scale, the Expressive Vocabulary Test–Second Edition, and the Story Recall subtest from the Rivermead Behavioural Memory Test. In addition to a traditional episodic memory therapy, the treatment group received a novel semantic memory–focused therapy, which involved participants finding meaningful connections between diverse concepts represented by sets of two or three words.

Results

The treatment group demonstrated statistically significant improvement in memory for list learning tasks, and there was a significant difference from pretest to posttest between the treatment group and the wait-list control group. Clinical significance was demonstrated for the treatment group using minimally important difference calculations.

Conclusion

Combined memory therapy resulted in significant improvements in episodic memory, semantic memory, and attention, in comparison to no treatment.

Supplemental Material

https://doi.org/10.23641/asha.14049968