bluuebunny/crossref_metadata_2025 huggingface dataset:
Contactless analysis of heart rate variability during cold pressor test using radar interferometry and bidirectional LSTM networks
Authors: Shi Kilin , Steigleder Tobias , Schellenberger Sven , Michler Fabian , Malessa Anke , Lurz Fabian , Rohleder Nicolas , Ostgathe Christoph , Weigel Robert , Koelpin Alexander
Published: February 2021

Contactless measurement of heart rate variability (HRV), which reflects changes of the autonomic nervous system (ANS) and provides crucial information on the health status of a person, would provide great benefits for both patients and doctors during prevention and aftercare. However, gold standard devices to record the HRV, such as the electrocardiograph, have the common disadvantage that they need permanent skin contact with the patient. Being connected to a monitoring device by cable reduces the mobility, comfort, and compliance by patients. Here, we present a contactless approach using a 24 GHz Six-Port-based radar system and an LSTM network for radar heart sound segmentation. The best scores are obtained using a two-layer bidirectional LSTM architecture. To verify the performance of the proposed system not only in a static measurement scenario but also during a dynamic change of HRV parameters, a stimulation of the ANS through a cold pressor test is integrated in the study design. A total of 638 minutes of data is gathered from 25 test subjects and is analysed extensively. High F-scores of over 95% are achieved for heartbeat detection. HRV indices such as HF norm are extracted with relative errors around 5%. Our proposed approach is capable to perform contactless and convenient HRV monitoring and is therefore suitable for long-term recordings in clinical environments and home-care scenarios.
Association of HSS score and mechanical alignment after primary TKA of patients suffering from constitutional varus knee that caused by combined deformities: a retrospective study
Authors: Zhang Zhifeng , Chai Wei , Zhao Guanghui , Zhang Qida , Chen Zhenxian , Wang Xinyao , Wei Pingping , Zhang Yanwei , Jin Zhongmin , Qiu Yusheng
Published: February 2021

For pre-operative osteoarthritis (OA) patients with varus knee, previous studies showed inconsistent results. Therefore, we conducted this study to better identify the association of Hospital for Special Surgery (HSS) score and mechanical alignment. 44 patients (51 knees) with constitutional varus knee caused by combined deformities (LDFA (lateral distal femoral angle) > 90°and MPTA (medial proximal tibial angle) < 85°)) were selected and analyzed with a mean follow-up period of 14 months after total knee arthroplasty (TKA). From January 2015 to December 2016, patients were collected consecutively after primary TKA. After filtering, fifty-one knees (44patients) were analyzed with a mean follow-up period of 14 months. All patients were divided into two groups based on post-operative hip-knee-ankle (HKA) acute angle: varus mechanical alignment (VMA) group (HKA < − 3°) and neutral mechanical axis (NMA) group (− 3° ≤ HKA ≤ 3°). 30 knees were included in the NMA group, and 21 knees in the VMA group. Comparisons of HSS between NMA group and VMA group were performed. After adjusting for age and Body Mass Index (BMI) confounders, Compared with NMA group, the HSS score in VMA group decreased by 0.81 units (95% CI, − 3.37 to 1.75) p = 0.5370). For pre-operative constitutional varus knee caused by combined deformities in chinese populations, no significant association between post-operative lower limb mechanical alignment and HSS score was found.
Plasmodium oocysts respond with dormancy to crowding and nutritional stress
Authors: Habtewold Tibebu , Sharma Aayushi A. , Wyer Claudia A. S. , Masters Ellen K. G. , Windbichler Nikolai , Christophides George K.
Published: February 2021

Malaria parasites develop as oocysts in the mosquito for several days before they are able to infect a human host. During this time, mosquitoes take bloodmeals to replenish their nutrient and energy reserves needed for flight and reproduction. We hypothesized that these bloodmeals are critical for oocyst growth and that experimental infection protocols, typically involving a single bloodmeal at the time of infection, cause nutritional stress to the developing oocysts. Therefore, enumerating oocysts disregarding their growth and differentiation state may lead to erroneous conclusions about the efficacy of transmission blocking interventions. Here, we examine this hypothesis in Anopheles coluzzii mosquitoes infected with the human and rodent parasites Plasmodium falciparum and Plasmodium berghei, respectively. We show that oocyst growth and maturation rates decrease at late developmental stages as infection intensities increase; an effect exacerbated at very high infection intensities but fully restored with post infection bloodmeals. High infection intensities and starvation conditions reduce RNA Polymerase III activity in oocysts unless supplemental bloodmeals are provided. Our results suggest that oocysts respond to crowding and nutritional stress with a dormancy-like strategy, which urges the development of alternative methods to assess the efficacy of transmission blocking interventions.
The marker of alkyl DNA base damage, N7-methylguanine, is associated with semen quality in men
Authors: Altakroni B. , Nevin C. , Carroll M. , Murgatroyd C. , Horne G. , Brison D. R. , Povey A. C.
Published: February 2021

Sperm DNA contains a range of DNA base damage that can arise, in part, from exposure to methylating agents. However, the effects are not fully characterized and so the aim of this study was to investigate associations between semen quality and the levels of N7-methyldeoxyguanosine (N7-MedG), a marker of exposure to methylating agents, and other markers of DNA damage and DNA methylation. Sperm samples were collected from 105 men attending an assisted reproduction clinic as part of a couple undergoing treatment for infertility and semen quality assessed manually according to WHO guidelines. Semen levels of N7-MedG, quantified by immunoslotblot, were significantly higher in men with sperm concentration < 15 × 106/ml (p ≤ 0.01), semen volume < 1.5 ml (p ≤ 0.05) and also in men with any aspect of semen quality below WHO reference levels (p ≤ 0.001). Measures of neutral Comet DNA damage were correlated with semen quality in a univariate analysis but not after adjustment for N7-MedG levels. Sperm concentration was negatively associated with % methylation at the gene for DAZL but no other marker of global or gene-specific DNA methylation. Results support the hypothesis that the known toxic and DNA damaging properties of alkylating agent exposure may have direct deleterious consequences on semen quality.
Response differences of HepG2 and Primary Mouse Hepatocytes to morphological changes in electrospun PCL scaffolds
Authors: Bate Thomas S. R. , Gadd Victoria L. , Forbes Stuart J. , Callanan Anthony
Published: February 2021

Liver disease cases are rapidly expanding across the globe and the only effective cure for end-stage disease is a transplant. Transplant procedures are costly and current supply of donor livers does not satisfy demand. Potential drug treatments and regenerative therapies that are being developed to tackle these pressing issues require effective in-vitro culture platforms. Electrospun scaffolds provide bio-mimetic structures upon which cells are cultured to regulate function in-vitro. This study aims to shed light on the effects of electrospun PCL morphology on the culture of an immortalised hepatic cell line and mouse primary hepatocytes. Each cell type was cultured on large 4–5 µm fibres and small 1–2 µm fibres with random, aligned and highly porous cryogenically spun configurations. Cell attachment, proliferation, morphology and functional protein and gene expression was analysed. Results show that fibre morphology has a measurable influence on cellular morphology and function, with the alteration of key functional markers such as CYP1A2 expression.
Laying hen mortality in different indoor housing systems: a meta-analysis of data from commercial farms in 16 countries
Authors: Schuck-Paim Cynthia , Negro-Calduch Elsa , Alonso Wladimir J.
Published: February 2021

Societal concern with the welfare of egg laying hens housed in conventional cages is fostering a transition towards cage-free systems in many countries. However, although cage-free facilities enable hens to move freely and express natural behaviours, concerns have also been raised over the possibility that cage-free flocks experience higher mortality, potentially compromising some aspects of their welfare. To investigate this possibility, we conducted a large meta-analysis of laying hen mortality in conventional cages, furnished cages and cage-free aviaries using data from 6040 commercial flocks and 176 million hens from 16 countries. We show that except for conventional cages, mortality gradually drops as experience with each system builds up: since 2000, each year of experience with cage-free aviaries was associated with a 0.35–0.65% average drop in cumulative mortality, with no differences in mortality between caged and cage-free systems in more recent years. As management knowledge evolves and genetics are optimized, new producers transitioning to cage-free housing may experience even faster rates of decline. Our results speak against the notion that mortality is inherently higher in cage-free production and illustrate the importance of considering the degree of maturity of production systems in any investigations of farm animal health, behaviour and welfare.
The nuclear import of the transcription factor MyoD is reduced in mesenchymal stem cells grown in a 3D micro-engineered niche
Authors: Jacchetti Emanuela , Nasehi Ramin , Boeri Lucia , Parodi Valentina , Negro Alessandro , Albani Diego , Osellame Roberto , Cerullo Giulio , Matas Jose Felix Rodriguez , Raimondi Manuela Teresa
Published: February 2021

Smart biomaterials are increasingly being used to control stem cell fate in vitro by the recapitulation of the native niche microenvironment. By integrating experimental measurements with numerical models, we show that in mesenchymal stem cells grown inside a 3D synthetic niche both nuclear transport of a myogenic factor and the passive nuclear diffusion of a smaller inert protein are reduced. Our results also suggest that cell morphology modulates nuclear proteins import through a partition of the nuclear envelope surface, which is a thin but extremely permeable annular portion in cells cultured on 2D substrates. Therefore, our results support the hypothesis that in stem cell differentiation, the nuclear import of gene-regulating transcription factors is controlled by a strain-dependent nuclear envelope permeability, probably related to the reorganization of stretch-activated nuclear pore complexes.
Development, characterization, and applications of multi-material stereolithography bioprinting
Authors: Grigoryan Bagrat , Sazer Daniel W. , Avila Amanda , Albritton Jacob L. , Padhye Aparna , Ta Anderson H. , Greenfield Paul T. , Gibbons Don L. , Miller Jordan S.
Published: February 2021

As a 3D bioprinting technique, hydrogel stereolithography has historically been limited in its ability to capture the spatial heterogeneity that permeates mammalian tissues and dictates structure–function relationships. This limitation stems directly from the difficulty of preventing unwanted material mixing when switching between different liquid bioinks. Accordingly, we present the development, characterization, and application of a multi-material stereolithography bioprinter that provides controlled material selection, yields precise regional feature alignment, and minimizes bioink mixing. Fluorescent tracers were first used to highlight the broad design freedoms afforded by this fabrication strategy, complemented by morphometric image analysis to validate architectural fidelity. To evaluate the bioactivity of printed gels, 344SQ lung adenocarcinoma cells were printed in a 3D core/shell architecture. These cells exhibited native phenotypic behavior as evidenced by apparent proliferation and formation of spherical multicellular aggregates. Cells were also printed as pre-formed multicellular aggregates, which appropriately developed invasive protrusions in response to hTGF-β1. Finally, we constructed a simplified model of intratumoral heterogeneity with two separate sub-populations of 344SQ cells, which together grew over 14 days to form a dense regional interface. Together, these studies highlight the potential of multi-material stereolithography to probe heterotypic interactions between distinct cell types in tissue-specific microenvironments.
Functional characterization of thermotolerant microbial consortium for lignocellulolytic enzymes with central role of Firmicutes in rice straw depolymerization
Authors: Gavande Parmeshwar V. , Basak Arijita , Sen Subhajit , Lepcha Khusboo , Murmu Nensina , Rai Vijeta , Mazumdar Deepika , Saha Shyama Prasad , Das Vaskar , Ghosh Shilpi
Published: February 2021

Rice (Oryza sativa L.) straw, an agricultural waste of high yield, is a sustainable source of fermentable sugars for biofuel and other chemicals. However, it shows recalcitrance to microbial catalysed depolymerization. We herein describe development of thermotolerant microbial consortium (RSV) from vermicompost with ability to degrade rice straw and analysis of its metagenome for bacterial diversity, and lignocellulolytic carbohydrate active enzymes (CAZymes) and their phylogenetic affiliations. RSV secretome exhibited cellulases and hemicellulases with higher activity at 60 °C. It catalysed depolymerization of chemical pretreated rice straw as revealed by scanning electron microscopy and saccharification yield of 460 mg g−1 rice straw. Microbial diversity of RSV was distinct from other compost habitats, with predominance of members of phyla Firmicutes, Proteobacteria and Bacteroidetes; and Pseudoclostridium, Thermoanaerobacterium, Chelatococcus and Algoriphagus being most abundant genera. RSV harboured 1389 CAZyme encoding ORFs of glycoside hydrolase, carbohydrate esterase, glycosyl transferase, carbohydrate binding module and auxiliary activity functions. Microorganisms of Firmicutes showed central role in lignocellulose deconstruction with importance in hemicellulose degradation; whereas representatives of Proteobacteria and Bacteroidetes contributed to cellulose and lignin degradation, respectively. RSV consortium could be a resource for mining thermotolerant cellulolytic bacteria or enzymes and studying their synergism in deconstruction of chemically pretreated rice straw.
The effect of multiple interventions to balance healthcare demand for controlling COVID-19 outbreaks: a modelling study
Authors: Yang Po , Yang Geng , Qi Jun , Sheng Bin , Yang Yun , Zhang Shuhao , Bi Gaoshan , Mao Xuxin
Published: February 2021

For controlling recent COVID-19 outbreaks around the world, many countries have implemented suppression and mitigation interventions. This work aims to conduct a feasibility study for accessing the effect of multiple interventions to control the COVID-19 breakouts in the UK and other European countries, accounting for balance of healthcare demand. The model is to infer the impact of mitigation, suppression and multiple rolling interventions for controlling COVID-19 outbreaks in the UK, with two features considered: direct link between exposed and recovered population, and practical healthcare demand by separation of infections. We combined the calibrated model with COVID-19 data in London and non-London regions in the UK during February and April 2020. Our finding suggests that rolling intervention is an optimal strategy to effectively control COVID-19 outbreaks in the UK for balancing healthcare demand and morality ratio. It is better to implement regional based interventions with varied intensities and maintenance periods. We suggest an intervention strategy named as “Besieged and rolling interventions” to the UK that take a consistent suppression in London for 100 days and 3 weeks rolling intervention in other regions. This strategy would reduce the overall infections and deaths of COVID-19 outbreaks, and balance healthcare demand in the UK.
Sensitive mass spectrometric determination of kinin-kallikrein system peptides in light of COVID-19
Authors: Gangnus Tanja , Burckhardt Bjoern B.
Published: February 2021

The outbreak of COVID-19 has raised interest in the kinin–kallikrein system. Viral blockade of the angiotensin-converting enzyme 2 impedes degradation of the active kinin des-Arg(9)-bradykinin, which thus increasingly activates bradykinin receptors known to promote inflammation, cough, and edema—symptoms that are commonly observed in COVID-19. However, lean and reliable investigation of the postulated alterations is currently hindered by non-specific peptide adsorption, lacking sensitivity, and cross-reactivity of applicable assays. Here, an LC–MS/MS method was established to determine the following kinins in respiratory lavage fluids: kallidin, bradykinin, des-Arg(10)-kallidin, des-Arg(9)-bradykinin, bradykinin 1-7, bradykinin 2-9 and bradykinin 1-5. This method was fully validated according to regulatory bioanalytical guidelines of the European Medicine Agency and the US Food and Drug Administration and has a broad calibration curve range (up to a factor of 103), encompassing low quantification limits of 4.4–22.8 pg/mL (depending on the individual kinin). The application of the developed LC–MS/MS method to nasal lavage fluid allowed for the rapid (~ 2 h), comprehensive and low-volume (100 µL) determination of kinins. Hence, this novel assay may support current efforts to investigate the pathophysiology of COVID-19, but can also be extended to other diseases.
The within-host fitness of HIV-1 increases with age in ART-naïve HIV-1 subtype C infected children
Authors: Nagaraja Pradeep , Gopalan Bindu P. , D’Souza Reena R. , Sarkar Debolina , Rajnala Niharika , Dixit Narendra M. , Shet Anita
Published: February 2021

As the immune system develops with age, children combat infections better. HIV-1, however, targets an activated immune system, potentially rendering children increasingly permissive to HIV-1 infection as they grow. How HIV-1 fitness changes with age in children is unknown. Here, we estimated the within-host basic reproductive ratio,R0, a marker of viral fitness, in HIV-1 subtype C-infected children in India, aged between 84 days and 17 years. We measured serial viral load and CD4 T cell counts in 171 children who initiated first-line ART. For 25 children, regular and frequent measurements provided adequate data points for analysis using a mathematical model of viral dynamics to estimateR0. For the rest, we used CD4 counts for approximate estimation ofR0. The viral load decline during therapy was biphasic. The mean lifespans of productively and long-lived infected cells were 1.4 and 27.8 days, respectively. The meanR0was 1.5 in children aged < 5 years, increased with age, and approached 6.0 at 18 years, close to 5.8 estimated previously for adults. The tolerogenic immune environment thus compromises HIV-1 fitness in young children. Early treatment initiation, when theR0is small, will likely improve viral control, in addition to suppressing the latent reservoir.
Mono-ubiquitination of Rabphilin 3A by UBE3A serves a non-degradative function
Authors: Avagliano Trezza Rossella , Punt A. Mattijs , Mientjes Edwin , van den Berg Marlene , Zampeta F. Isabella , de Graaf Ilona J. , van der Weegen Yana , Demmers Jeroen A. A. , Elgersma Ype , Distel Ben
Published: February 2021

Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by brain-specific loss of UBE3A, an E3 ubiquitin protein ligase. A substantial number of possible ubiquitination targets of UBE3A have been identified, although evidence of being direct UBE3A substrates is often lacking. Here we identified the synaptic protein Rabphilin-3a (RPH3A), an effector of the RAB3A small GTPase involved in axonal vesicle priming and docking, as a ubiquitination target of UBE3A. We found that the UBE3A and RAB3A binding sites on RPH3A partially overlap, and that RAB3A binding to RPH3A interferes with UBE3A binding. We confirmed previous observations that RPH3A levels are critically dependent on RAB3A binding but, rather surprisingly, we found that the reduced RPH3A levels in the absence of RAB3A are not mediated by UBE3A. Indeed, while we found that RPH3A is ubiquitinated in a UBE3A-dependent manner in mouse brain, UBE3A mono-ubiquitinates RPH3A and does not facilitate RPH3A degradation. Moreover, we found that an AS-linked UBE3A missense mutation in the UBE3A region that interacts with RPH3A, abrogates the interaction with RPH3A. In conclusion, our results identify RPH3A as a novel target of UBE3A and suggest that UBE3A-dependent ubiquitination of RPH3A serves a non-degradative function.
Sequence characterisation and novel insights into bovine mastitis-associated Streptococcus uberis in dairy herds
Authors: Vezina Ben , Al-harbi Hulayyil , Ramay Hena R. , Soust Martin , Moore Robert J. , Olchowy Timothy W. J. , Alawneh John I.
Published: February 2021

Streptococcus uberis is one of the most frequent mastitis-causing pathogens isolated from dairy cows. Further understanding of S. uberis genetics may help elucidate the disease pathogenesis. We compared the genomes of S. uberis isolates cultured from dairy cows located in distinctly different geographic regions of Australia. All isolates had novel multi locus sequence types (MLST) indicating a highly diverse population of S. uberis. Global clonal complexes (GCC) were more conserved. GCC ST86 and GCC ST143 represented 30% of the total isolates (n = 27) and were clustered within different geographic regions. Core genome phylogeny revealed low phylogenetic clustering by region, isolation source, and MLST. Identification of putative sortase (srtA) substrates and generation of a custom putative virulence factor database revealed genes which may explain the affinity of S. uberis for mammary tissue, evasion of antimicrobial efforts and disease pathogenesis. Of 27 isolates, four contained antibiotic resistance genes including an antimicrobial resistance cluster containing mel/mef(A), mrsE, vatD, lnuD, and transposon-mediated lnuC was also identified. These are novel genes for S. uberis, which suggests interspecies lateral gene transfer. The presence of resistance genes across the two geographic regions tested within one country supports the need for a careful, tailored, implementation and monitoring of antimicrobial stewardship.
Immediate and after effects of transcranial direct-current stimulation in the mouse primary somatosensory cortex
Authors: Sánchez-León Carlos A. , Cordones Isabel , Ammann Claudia , Ausín José M. , Gómez-Climent María A. , Carretero-Guillén Alejandro , Sánchez-Garrido Campos Guillermo , Gruart Agnès , Delgado-García José M. , Cheron Guy , Medina Javier F. , Márquez-Ruiz Javier
Published: February 2021

Transcranial direct-current stimulation (tDCS) is a non-invasive brain stimulation technique consisting in the application of weak electric currents on the scalp. Although previous studies have demonstrated the clinical value of tDCS for modulating sensory, motor, and cognitive functions, there are still huge gaps in the knowledge of the underlying physiological mechanisms. To define the immediate impact as well as the after effects of tDCS on sensory processing, we first performed electrophysiological recordings in primary somatosensory cortex (S1) of alert mice during and after administration of S1-tDCS, and followed up with immunohistochemical analysis of the stimulated brain regions. During the application of cathodal and anodal transcranial currents we observed polarity-specific bidirectional changes in the N1 component of the sensory-evoked potentials (SEPs) and associated gamma oscillations. On the other hand, 20 min of cathodal stimulation produced significant after-effects including a decreased SEP amplitude for up to 30 min, a power reduction in the 20–80 Hz range and a decrease in gamma event related synchronization (ERS). In contrast, no significant changes in SEP amplitude or power analysis were observed after anodal stimulation except for a significant increase in gamma ERS after tDCS cessation. The polarity-specific differences of these after effects were corroborated by immunohistochemical analysis, which revealed an unbalance of GAD 65–67 immunoreactivity between the stimulated versus non-stimulated S1 region only after cathodal tDCS. These results highlight the differences between immediate and after effects of tDCS, as well as the asymmetric after effects induced by anodal and cathodal stimulation.
Cytoplasmic vacuolation with endoplasmic reticulum stress directs sorafenib induced non-apoptotic cell death in hepatic stellate cells
Authors: Sharma Sachin , Ghufran Shaikh Maryam , Ghose Sampa , Biswas Subhrajit
Published: February 2021

The activated hepatic stellate cells (HSCs) are the major cells that secrete the ECM proteins and drive the pathogenesis of fibrosis in chronic liver disease. Targeting of HSCs by modulating their activation and proliferation has emerged as a promising approach in the development of anti-fibrotic therapy. Sorafenib, a multi-kinase inhibitor has shown anti-fibrotic properties by inhibiting the survival and proliferation of HSCs. In present study we investigated sorafenib induced cytoplasmic vacuolation mediated decreased cell viability of HSCs in dose and time dependent manner. In this circumstance, sorafenib induces ROS and ER stress in HSCs without involvement of autophagic signals. The protein synthesis inhibitor cycloheximide treatment significantly decreased the sorafenib-induced cytoplasmic vacuolation with increasing cell viability. Antioxidant human serum albumin influences the viability of HSCs by reducing sorafenib induced vacuolation and cell death. However, neither caspase inhibitor Z-VAD-FMK nor autophagy inhibitor chloroquine could rescue the HSCs from sorafenib-induced cytoplasmic vacuolation and cell death. Using TEM and ER organelle tracker, we conclude that the cytoplasmic vacuoles are due to ER dilation. Sorafenib treatment induces calreticulin and GPR78, and activates IRE1α-XBP1s axis of UPR pathway, which eventually trigger the non-apoptotic cell death in HSCs. This study provides a notable mechanistic insight into the ER stress directed non-apoptotic cell death with future directions for the development of efficient anti-fibrotic therapeutic strategies.
Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies
Authors: Sucháčková Bartoňová Alena , Konvička Martin , Marešová Jana , Wiemers Martin , Ignatev Nikolai , Wahlberg Niklas , Schmitt Thomas , Faltýnek Fric Zdeněk
Published: February 2021

The bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host’s mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.
A recombinase polymerase amplification assay for rapid detection of rabies virus
Authors: Faye Martin , Abd El Wahed Ahmed , Faye Oumar , Kissenkötter Jonas , Hoffmann Bernd , Sall Amadou Alpha , Faye Ousmane
Published: February 2021

Rabies is a generally fatal encephalitis caused by a negative-sense single-stranded RNA lyssavirus transmitted to humans mainly from dog bite. Despite the recommendation by WHO and OIE to use the direct immunofluorescence test as standard method, molecular diagnostic assays like reverse transcription quantitative polymerase chain reaction (RT-qPCR) are increasing as a confirmatory method. However, both technologies are inaccessible in resource-limited settings. Moreover, the available point-of-need molecular assay is of poor detection limit for African strains. Herein, we developed a reverse transcription recombinase polymerase amplification (RT-RPA) assay as potential point-of-need diagnostic tool for rapid detection of various strains of rabies virus including locally isolated African strains. The sensitivity and specificity of the method was evaluated using a molecular RNA standard and different Rabies-related viruses belonging to theRhabdovirideafamily, respectively. The RABV-RPA performances were evaluated on isolates representative of the existing diversity and viral dilutions spiked in non-neural clinical specimen. The results were compared with RT-qPCR as a gold standard. The RABV-RPA detected down to 4 RNA molecules per reaction in 95% of the cases in less than 10 min. The RABV-RPA assay is highly specific as various RABV isolates were identified, but no amplification was observed for other member of theRhabdoviridea family. The sample background did not affect the performance of the RABV-RPA as down to 11 RNA molecules were identified, which is similar to the RT-qPCR results. Our developed assay is suitable for use in low-resource settings as a promising alternative tool forante-mortemrabies diagnosis in humans for facilitating timely control decisions.
Identification of a solo acylhomoserine lactone synthase from the myxobacterium Archangium gephyra
Authors: Albataineh Hanan , Duke Maya , Misra Sandeep K. , Sharp Joshua S. , Stevens D. Cole
Published: February 2021

Considered a key taxon in soil and marine microbial communities, myxobacteria exist as coordinated swarms that utilize a combination of lytic enzymes and specialized metabolites to facilitate predation of microbes. This capacity to produce specialized metabolites and the associated abundance of biosynthetic pathways contained within their genomes have motivated continued drug discovery efforts from myxobacteria. Of all myxobacterial biosynthetic gene clusters deposited in the antiSMASH database, only one putative acylhomoserine lactone (AHL) synthase, agpI, was observed, in genome data from Archangium gephyra. Without an AHL receptor also apparent in the genome of A. gephyra, we sought to determine if AgpI was an uncommon example of an orphaned AHL synthase. Herein we report the bioinformatic assessment of AgpI and discovery of a second AHL synthase from Vitiosangium sp. During axenic cultivation conditions, no detectible AHL metabolites were observed in A. gephyra extracts. However, heterologous expression of each synthase in Escherichia coli provided detectible quantities of 3 AHL signals including 2 known AHLs, C8-AHL and C9-AHL. These results suggest that A. gephyra AHL production is dormant during axenic cultivation. The functional, orphaned AHL synthase, AgpI, is unique to A. gephyra, and its utility to the predatory myxobacterium remains unknown.
Multicenter evaluation of Verigene Enteric Pathogens Nucleic Acid Test for detection of gastrointestinal pathogens
Authors: Kosai Kosuke , Suzuki Hiromichi , Tamai Kiyoko , Okada Yuya , Akamatsu Norihiko , Ueda Atsuo , Notake Shigeyuki , Yaguchi Yuji , Yanagihara Katsunori
Published: February 2021

We investigated the efficiency of the Verigene Enteric Pathogens Nucleic Acid Test (Verigene EP test), which is an automated microarray-based assay system that enables rapid and simultaneous genetic detection of gastrointestinal pathogens and toxins, including those in the Campylobacter Group, Salmonella species, Shigella species, the Vibrio Group, Yersinia enterocolitica, Shiga toxin 1 and 2, norovirus GI/GII, and rotavirus A. Three clinical laboratories evaluated the Verigene EP test, using 268 stool samples for bacterial and toxin genes and 167 samples for viral genes. Culture-based reference methods were used for the detection of bacteria and toxins, while a different molecular assay was used for viral detection. The overall concordance rate between the Verigene EP test and the reference methods for the 1940 assays was 99.0%. The overall sensitivity and specificity of the Verigene EP test were 97.0% and 99.3%, respectively. Of the 19 samples with discordant results, 13 samples were false positives and six were false negatives. The Verigene EP test simultaneously detected two targets in 11 samples; overall, the test demonstrated high efficiency in detecting crucial diarrheagenic pathogens, indicating its suitability for clinical practice.
Cerebellar rTMS and PAS effectively induce cerebellar plasticity
Authors: Pauly Martje G. , Steinmeier Annika , Bolte Christina , Hamami Feline , Tzvi Elinor , Münchau Alexander , Bäumer Tobias , Weissbach Anne
Published: February 2021

Non-invasive brain stimulation techniques including repetitive transcranial magnetic stimulation (rTMS), continuous theta-burst stimulation (cTBS), paired associative stimulation (PAS), and transcranial direct current stimulation (tDCS) have been applied over the cerebellum to induce plasticity and gain insights into the interaction of the cerebellum with neo-cortical structures including the motor cortex. We compared the effects of 1 Hz rTMS, cTBS, PAS and tDCS given over the cerebellum on motor cortical excitability and interactions between the cerebellum and dorsal premotor cortex / primary motor cortex in two within subject designs in healthy controls. In experiment 1, rTMS, cTBS, PAS, and tDCS were applied over the cerebellum in 20 healthy subjects. In experiment 2, rTMS and PAS were compared to sham conditions in another group of 20 healthy subjects. In experiment 1, PAS reduced cortical excitability determined by motor evoked potentials (MEP) amplitudes, whereas rTMS increased motor thresholds and facilitated dorsal premotor-motor and cerebellum-motor cortex interactions. TDCS and cTBS had no significant effects. In experiment 2, MEP amplitudes increased after rTMS and motor thresholds following PAS. Analysis of all participants who received rTMS and PAS showed that MEP amplitudes were reduced after PAS and increased following rTMS. rTMS also caused facilitation of dorsal premotor-motor cortex and cerebellum-motor cortex interactions. In summary, cerebellar 1 Hz rTMS and PAS can effectively induce plasticity in cerebello-(premotor)-motor pathways provided larger samples are studied.
Low cost and long-focal-depth metallic axicon for terahertz frequencies based on parallel-plate-waveguides
Authors: Hernandez-Serrano A. I. , Pickwell-MacPherson Emma
Published: February 2021

In this work we demonstrate a triangular surface lens (axicon) operating at frequencies between 350 and 450 GHz using parallel-plate-waveguide technology. The proposed axicon offers longer focal depth characteristics compared to conventional plastic lenses, surpassing common TPX lenses by one order of magnitude. Additionally, due to the triangular surface of the axicon, this device is able to focus THz radiation onto smaller areas than TPX lenses, enhancing the resolution characteristics of THz imaging systems. The frequency range of operation of the proposed axicon can be easily tuned by changing the space between plates, making this approach a very attractive candidate for low-cost, robust and easy to assemble solutions for the next generation of active THz devices.
The Souss lagerstätte of the Anti-Atlas, Morocco: discovery of the first Cambrian fossil lagerstätte from Africa
Authors: Geyer Gerd , Landing Ed
Published: February 2021

Episodic low oxygenated conditions on the sea-floor are likely responsible for exceptional preservation of animal remains in the upper Amouslek Formation (lower Cambrian, Stage 3) on the northern slope of the western Anti-Atlas, Morocco. This stratigraphic interval has yielded trilobite, brachiopod, and hyolith fossils with preserved soft parts, including some of the oldest known trilobite guts. The “Souss fossil lagerstätte” (newly proposed designation) represents the first Cambrian fossil lagerstätte in Cambrian strata known from Africa and is one of the oldest trilobite-bearing fossil lagerstätten on Earth. Inter-regional correlation of the Souss fossil lagerstätte in West Gondwana suggests its development during an interval of high eustatic levels recorded by dark shales that occur in informal upper Cambrian Series 2 in Siberia, South China, and East Gondwana.
An evaluation of approaches for rare variant association analyses of binary traits in related samples
Authors: Chen Ming-Huei , Pitsillides Achilleas , Yang Qiong
Published: February 2021

Recognizing that family data provide unique advantage of identifying rare risk variants in genetic association studies, many cohorts with related samples have gone through whole genome sequencing in large initiatives such as the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. Analyzing rare variants poses challenges for binary traits in that some genotype categories may have few or no observed events, causing bias and inflation in commonly used methods. Several methods have recently been proposed to better handle rare variants while accounting for family relationship, but their performances have not been thoroughly evaluated together. Here we compare several existing approaches including SAIGE but not limited to related samples using simulations based on the Framingham Heart Study samples and genotype data from Illumina HumanExome BeadChip where rare variants are the majority. We found that logistic regression with likelihood ratio test applied to related samples was the only approach that did not have inflated type I error rates in both single variant test (SVT) and gene-based tests, followed by Firth logistic regression that had inflation in its direction insensitive gene-based test at prevalence 0.01 only, applied to either related or unrelated samples, though theoretically logistic regression and Firth logistic regression do not account for relatedness in samples. SAIGE had inflation in SVT at prevalence 0.1 or lower and the inflation was eliminated with a minor allele count filter of 5. As for power, there was no approach that outperformed others consistently among all single variant tests and gene-based tests.
Tactile sensing biohybrid soft E-skin based on bioimpedance using aloe vera pulp tissues
Authors: Mousa Mostafa A. , Soliman MennaAllah , Saleh Mahmood A. , Radwan Ahmed G.
Published: February 2021

Soft and flexible E-skin advances are a subset of soft robotics field where the soft morphology of human skin is mimicked. The number of prototypes that conformed the use of biological tissues within the structure of soft robots—to develop “Biohybrid Soft Robots”—has increased in the last decade. However, no research was conducted to realize Biohybrid E-skin. In this paper, a novel biohybrid E-skin that provides tactile sensing is developed. The biohybrid E-skin highly mimics the human skin softness and morphology and can sense forces as low as 0.01 newton . The tactile sensing feature is augmented through the use of Aloe Vera pulp, embedded in underlying channel, where the change in its bioimpedance is related to the amount of force exerted on the E-skin surface. The biohybrid E-skin employs high biomimicry as the sensorial output is an oscillating signal similar to signals sent from the human sensing neurons to the brain. After investigating different channel geometries, types of filling tissues, and usage of two silicone materials, their frequency-force behaviour is modelled mathematically. Finally, a functional multichannel prototype “ImpEdded Skin” is developed. This prototype could efficiently detect the position of a tactile touch. This work employs the development of discrete sensing system that exhibits morphological computation that consequently enhances performance.
Cecr2 mutant mice as a model for human cat eye syndrome
Authors: Dicipulo Renée , Norton Kacie A. , Fairbridge Nicholas A. , Kibalnyk Yana , Fox Sabrina C. , Hornberger Lisa K. , McDermid Heather E.
Published: February 2021

Cat eye syndrome (CES), a human genetic disorder caused by the inverted duplication of a region on chromosome 22, has been known since the late 1890s. Despite the significant impact this disorder has on affected individuals, models for CES have not been produced due to the difficulty of effectively duplicating the corresponding chromosome region in an animal model. However, the study of phenotypes associated with individual genes in this region such as CECR2 may shed light on the etiology of CES. In this study we have shown that deleterious loss of function mutations in mouse Cecr2 effectively demonstrate many of the abnormal features present in human patients with CES, including coloboma and specific skeletal, kidney and heart defects. Beyond phenotypic analyses we have demonstrated the importance of utilizing multiple genetic backgrounds to study disease models, as we see major differences in penetrance of Cecr2-related abnormal phenotype between mouse strains, reminiscent of the variability in the human syndrome. These findings suggest that Cecr2 is involved in the abnormal features of CES and that Cecr2 mice can be used as a model system to study the wide range of phenotypes present in CES.
The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
Authors: Kim Jung-Hyun , Noskov Vladimir N. , Ogurtsov Aleksey Y. , Nagaraja Ramaiah , Petrov Nikolai , Liskovykh Mikhail , Walenz Brian P. , Lee Hee-Sheung , Kouprina Natalay , Phillippy Adam M. , Shabalina Svetlana A. , Schlessinger David , Larionov Vladimir
Published: February 2021

The rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.
Demographic effects of interacting species: exploring stable coexistence under increased climatic variability in a semiarid shrub community
Authors: García-Cervigón Ana I. , Quintana-Ascencio Pedro F. , Escudero Adrián , Ferrer-Cervantes Merari E. , Sánchez Ana M. , Iriondo José M. , Olano José Miguel
Published: February 2021

Population persistence is strongly determined by climatic variability. Changes in the patterns of climatic events linked to global warming may alter population dynamics, but their effects may be strongly modulated by biotic interactions. Plant populations interact with each other in such a way that responses to climate of a single population may impact the dynamics of the whole community. In this study, we assess how climate variability affects persistence and coexistence of two dominant plant species in a semiarid shrub community on gypsum soils. We use 9 years of demographic data to parameterize demographic models and to simulate population dynamics under different climatic and ecological scenarios. We observe that populations of both coexisting species may respond to common climatic fluctuations both similarly and in idiosyncratic ways, depending on the yearly combination of climatic factors. Biotic interactions (both within and among species) modulate some of their vital rates, but their effects on population dynamics highly depend on climatic fluctuations. Our results indicate that increased levels of climatic variability may alter interspecific relationships. These alterations might potentially affect species coexistence, disrupting competitive hierarchies and ultimately leading to abrupt changes in community composition.
Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees
Authors: Kapheim Karen M. , Johnson Makenna M. , Jolley Maggi
Published: February 2021

Increasing evidence suggests the microbiome plays an important role in bee ecology and health. However, the relationship between bees and their bacterial symbionts has only been explored in a handful of species. We characterized the microbiome across the life cycle of solitary, ground-nesting alkali bees (Nomia melanderi). We find that feeding status is a major determinant of microbiome composition. The microbiome of feeding larvae was similar to that of pollen provisions, but the microbiome of post-feeding larvae (pre-pupae) was similar to that of the brood cell walls and newly-emerged females. Feeding larvae and pollen provisions had the lowest beta diversity, suggesting the composition of larval diet is highly uniform. Comparisons between lab-reared, newly-emerged, and nesting adult females suggest that the hindgut bacterial community is largely shaped by the external environment. However, we also identified taxa that are likely acquired in the nest or which increase or decrease in relative abundance with age. Although Lactobacillus micheneri was highly prevalent in pollen provisions, it was only detected in one lab-reared female, suggesting it is primarily acquired from environmental sources. These results provide the foundation for future research on metagenomic function and development of probiotics for these native pollinators.
A shape-adjusted ellipse approach corrects for varied axonal dispersion angles and myelination in primate nerve roots
Authors: Bartmeyer Petra M. , Biscola Natalia P. , Havton Leif A.
Published: February 2021

Segmentation of axons in light and electron micrographs allows for quantitative high-resolution analysis of nervous tissues, but varied axonal dispersion angles result in over-estimates of fiber sizes. To overcome this technical challenge, we developed a novel shape-adjusted ellipse (SAE) determination of axonal size and myelination as an all-inclusive and non-biased tool to correct for oblique nerve fiber presentations. Our new resource was validated by light and electron microscopy against traditional methods of determining nerve fiber size and myelination in rhesus macaques as a model system. We performed detailed segmental mapping and characterized the morphological signatures of autonomic and motor fibers in primate lumbosacral ventral roots (VRs). An en bloc inter-subject variability for the preganglionic parasympathetic fibers within the L7-S2 VRs was determined. The SAE approach allows for morphological ground truth data collection and assignment of individual axons to functional phenotypes with direct implications for fiber mapping and neuromodulation studies.