bluuebunny/crossref_metadata_2025 huggingface dataset:
Stem Cells: Importance of Elucidating a Stem Cell Laboratory
Authors: Thaller Seth R. , Elliot Sharon , Arroyo Ernesto J.
Published: August 2019

Stem cells, which were initially elucidated in the 1960s, are characterized by their ability to continuously renew themselves to differentiate into multiple cellular types. For this reason, they remain the subject of intensive research, for their potential to treat certain diseases. In craniofacial surgery, tissue engineering using stem cells can be employed in various techniques. These include 3D printing, which has the potential to regenerate dental, oral, and craniofacial structures, once lost to congenital anomalies, trauma and other diseases like cancer. With the growing battery of information about stem cells and their potential translation from research to clinical practice, it is important to outline what is the basic layout of a stem cell research facility.
Alopecia Risk and the Thickness, Number, and Frequency of Scalp Skin Harvests
Authors: Hwang Kun
Published: August 2019

The aim of this study was to elucidate the relationships between the thickness, number, and frequency of scalp skin harvests and alopecia risk.

In a PubMed search, the search terms (scalp AND graft AND alopecia) were used, resulting in 148 papers. Among 21 abstracts, 11 full papers were reviewed, and 3 papers were ultimately analyzed.

The donor-site alopecia rate was significantly higher in patients who experienced hair growth on their grafts than in those who did not (odds ratio = 10.875, 95% confidence interval, 2.677–44.178; P < 0.001). The depth of the infundibulum can be estimated to be 451.8 μm at 5 years of age, 528.8 μm at 10 years, 605.8 μm at 15 years, and 682.8 μm at 20 years. Therefore, the limits of safe thickness for graft harvesting from the scalp are <18/1000 inches for 5-year olds, 21/1000 inches for 10-year olds, 24/1000 inches for 15-year olds, and 27/1000 inches for 20-year olds. The safe number of harvests (intersection of the alopecia and nonalopecia groups) was 2.7, and the safer number of harvests (limits of 2 standard deviations of the alopecia group) was 1.0. The safe time interval between harvests was 14.0 days, and the safer time interval between harvests was 15.6 days. The safe single minimal interval (SMI) between harvests was 12.7 days, and the safer SMI was 13.7 days.

Since the safe thickness for graft harvesting from scalps exceeds the thickness in usual practice, following the safer SMI between harvests (13.7 days) is expected to be more important for minimizing alopecia risk.
Surgical Outcomes of Endoscopic Medial Orbital Wall Decompression
Authors: Kim Jong Woo , Kang Sung Mo
Published: August 2019

Study Design:

Retrospective chart review.

Purpose:

The aim of this study was to evaluate the surgical outcomes and complications after endoscopic medial orbital wall decompression.

Method:

From November 2016 to July 2017, we retrospectively reviewed 40 eyes of 20 patients who had undergone orbital decompression because of thyroid ophthalmopathy and other causes of proptosis.

The eyes were classified into 2 groups: orbits which received only endoscopic medial wall decompression, and orbits which received both endoscopic medial wall decompression and transconjunctival inferior wall decompression. Statistical analysis was performed for all data generated. The preoperative and 3-month postoperative follow-up examinations for all patients were assessed by Hertel ophthalmometry, interpalpebral fissure, marginal reflex distance 1, Goldmann applanation tonometry, diplopia test, and Grave ophthalmopathy specific quality of life survey.

Results:

Endoscopic medial wall decompression was performed in 17 of the total 40 eyes, and endoscopic medial wall decompression and transconjunctival inferior wall decompression was performed in the remaining 23 eyes. Proptosis improved from 20.4 ± 1.16 mm preoperatively to 16.8 ± 1.02 mm postoperatively in the endoscopic medial wall approach group, and from 20.8 ± 1.75 mm preoperatively to 14.8 ± 1.79 mm postoperatively in the endoscopic medial wall and transconjunctival inferior wall approach group. Postoperative complications occurred in 2 patients who displayed periphery diplopia, in the endoscopic medial wall and transconjunctival inferior wall approach group. A survey to assess the level of cosmetic satisfaction was significantly improved in both groups after surgery.

Conclusion:

Endoscopic medial wall decompression is an approach that achieves sufficient orbital decompression while minimizing complications.
HLA Class II Antibodies at the Time of Kidney Transplantation and Cardiovascular Outcome: A Retrospective Cohort Study
Authors: Malfait Thomas , Emonds Marie-Paule , Daniëls Liesbeth , Nagler Evi V. , Van Biesen Wim , Van Laecke Steven
Published: August 2019

Background.

The negative role of HLA class II donor-specific antibody on graft outcome is well recognized. However, the potentially negative cardiovascular effects of preformed HLA class II antibodies and donor HLA in kidney transplant recipients (KTRs) remain unestablished.

Methods.

We conducted a single-center, retrospective cohort study including 1115 KTRs (2003–2016) with up to 4449 person-years of follow-up after transplantation and a median follow-up time of 5.1 years (interquartile range, 2.7–7.6). We evaluated the unadjusted and multivariable-adjusted association between pretransplant HLA class I and II antibodies, as well as HLA-DR1 donor/recipient genotype and the primary (major adverse cardiac and cerebrovascular event [MACCE] or all-cause mortality) and secondary (MACCE or cardiovascular mortality) outcome.

Results.

In a multivariate Cox proportional hazard model, HLA class II antibodies before transplantation were associated with increased adjusted hazard ratio (aHR) for MACCE or all-cause mortality (aHR, 1.71 [1.13–2.60];P= 0.012) even after adjustment for time-varying covariate graft loss (aHR, 1.68 [1.08–2.62];P= 0.022) and biopsy-proven acute rejection (aHR, 1.71 [1.13–2.60];P= 0.012). HLA class II antibodies were also associated with increased aHR for the secondary outcome, MACCE, or cardiovascular mortality (aHR, 1.92 [1.12–3.30];P= 0.018). We investigated the effect of donor and recipient HLA-DR1 on these outcome parameters and demonstrated that KTRs with HLA-DR1 positive donors had an increased aHR for MACCE with all-cause (aHR, 1.45 [1.09–1.94];P= 0.012) and cardiovascular mortality (aHR, 1.49 [1.00–2.22];P= 0.05).

Conclusions.

Prior sensitization against HLA class II antigens is associated with unfavorable long-term cardiovascular outcome in KTRs independent of graft loss or rejection. Recipients of an HLA-DR1 donor also have an impaired cardiovascular outcome.
Comparative functional survival and equivalent annual cost of three long lasting insecticidal net (LLIN) products in Tanzania
Authors: Lorenz Lena M , Bradley John , Yukich Joshua , Massue Dennis Joram , Mboma Zawadi Mageni , Pigeon Olivier , Moore Jason , Kilian Albert , Lines Jo , Kisinza William , Overgaard Hans J , Moore Sarah J
Published: August 2019

Almost 1.2 billion long-lasting insecticidal nets (LLINs) have been procured for malaria control. Institutional buyers often assume that World Health Organization (WHO) prequalified LLINs are functionally identical with a three-year lifespan. We measured the lifespans of three LLIN products, and calculated their cost-per-year of functional life, through a randomised double-blinded prospective evaluation among 3,420 study households in Tanzania using WHO-recommended methods. Primary outcome was LLIN functional survival (LLINs present in serviceable condition). Secondary outcomes were 1) bioefficacy and chemical content (residual insecticidal activity) and 2) protective efficacy for volunteers sleeping under LLINs (bite reduction and mosquitoes killed). LLIN median functional survival was significantly different: 2·0 years for Olyset, 2·5 years for PermaNet and 2·6 years for NetProtect. Functional survival was affected by accumulation of holes resulting in users discarding nets. Protective efficacy also significantly differed between products as they aged. The longer-lived nets were 20% cheaper than the shorter-lived product.
Mother-to-embryo vitellogenin transport in a viviparous teleostXenotoca eiseni
Authors: Iida Atsuo , Arai Hiroyuki , Someya Yumiko , Inokuchi Mayu , Onuma Takeshi A. , Yokoi Hayato , Suzuki Tohru , Sano Kaori
Published: August 2019

Vitellogenin (Vtg), a yolk nutrient protein that is synthesized in the livers of female animals, and subsequently carried into the ovary, contributes to vitellogenesis in oviparous animals. Thus, Vtg levels are elevated during oogenesis. In contrast, Vtg have been genetically lost in viviparous mammals, thus the yolk protein is not involved in their oogenesis and embryonic development. In this study, we identified Vtg protein in the livers of females during the gestation of the viviparous teleost,Xenotoca eiseni. Although vitellogenesis is arrested during gestation, biochemical assays revealed that Vtg protein was present in ovarian tissues and lumen fluid. The Vtg protein was also detected in the trophotaenia of the intraovarian embryo. Immunoelectron microscopy revealed that Vtg protein is absorbed into intracellular vesicles in the epithelial cells of the trophotaenia. Furthermore, extraneous Vtg protein injected into the abdominal cavity of a pregnant female was subsequently detected in the trophotaenia of the intraovarian embryo. Our data suggest that the yolk protein is one of the matrotrophic factors supplied from the mother to the intraovarian embryo during gestation inX. eiseni. To our knowledge, this is the first report of the experimental verification of mother-to-embryo substance transport in a viviparous teleost.
Improved Automatic Pharmacovigilance: An Enhancement to the MedWatcher Social System for Monitoring Adverse Events
Authors: Nguyen Andre T. , Lien Julia , Raff Edward , Mekaru Sumiko R.
Published: August 2019

Traditional pharmacovigilance systems rely on adverse event reports received by regulatory authorities such as the United States Food and Drug Administration (FDA). These traditional systems suffer from underreporting and are not timely due to their reliance on third-party sentinels. To address these issues, the MedWatcher Social system for monitoring adverse events through automated processing of digital social media data and crowdsourcing was launched in 2012 by Boston Children’s Hospital and the FDA. The system is rooted in the well-established FDA MedWatch system.

MedWatcher Social uses an indicator score approach to identify adverse events. This study evaluates the MedWatcher Social adverse event classifier’s performance on Twitter data and proposes an enhancement to the indicator score method that results in improved adverse event identification.

Our research suggests that automatic pharmacovigilance systems using the original indicator score approach should be updated. Careful consideration of modeling assumptions is critical when designing algorithms for computational epidemiology, and algorithms should be regularly reevaluated to identify enhancements and to remedy concept drift.
Seasonal Variability and Shared Molecular Signatures of Inactivated Influenza Vaccination in Young and Older Adults
Authors: Avey Stefan , Mohanty Subhasis , Chawla Daniel G. , Meng Hailong , Bandaranayake Thilinie , Ueda Ikuyo , Zapata Heidi J. , Park Koonam , Blevins Tamara P. , Tsang Sui , Belshe Robert B. , Kaech Susan M. , Shaw Albert C. , Kleinstein Steven H.
Published: August 2019

The seasonal influenza vaccine is an important public health tool but is only effective in a subset of individuals. The identification of molecular signatures provides a mechanism to understand the drivers of vaccine-induced immunity. Most previously reported molecular signatures of influenza vaccination were derived from a single age group or season, ignoring the effects of immunosenescence or vaccine composition. Thus, it remains unclear how immune signatures of vaccine response change with age across multiple seasons. Here we profile the transcriptional landscape of young and older adults over five consecutive vaccination seasons to identify shared signatures of vaccine response as well as marked seasonal differences. Along with substantial variability in vaccine-induced signatures across seasons, we uncovered a common transcriptional signature 28 days post-vaccination in both young and older adults. However, gene expression patterns associated with vaccine-induced antibody responses were distinct in young and older adults; for example, increased expression of Killer Cell Lectin Like Receptor B1 (KLRB1;CD161) 28 days post-vaccination positively and negatively predicted vaccine-induced antibody responses in young and older adults, respectively. These findings contribute new insights for developing more effective influenza vaccines, particularly in older adults.
ProGeo-neo: a Customized Proteogenomic Workflow for Neoantigen Prediction and Selection
Authors: Li Yuyu , Wang Guangzhi , Tan Xiaoxiu , Ouyang Jian , Zhang Menghuan , Song Xiaofeng , Liu Qi , Leng Qibin , Chen Lanming , Xie Lu
Published: August 2019

Neoantigens can be differentially recognized by T cell receptor (TCR) as these sequences are derived from mutant proteins and are unique to the tumor. The discovery of neoantigens is the first key step for tumor-specific antigen (TSA) based immunotherapy. Based on high-throughput tumor genomic analysis, each missense mutation can potentially give rise to multiple neopeptides, resulting in a vast total number, but only a small percentage of these peptides may achieve immune-dominant status with a given major histocompatibility complex (MHC) class I allele. Specific identification of immunogenic candidate neoantigens is consequently a major challenge. Currently almost all neoantigen prediction tools are based on genomics data. Here we report the construction of proteogenomics prediction of neoantigen (ProGeo-neo) pipeline, which incorporates the following modules: mining tumor specific antigens from next-generation sequencing genomic and mRNA expression data, predicting the binding mutant peptides to class I MHC molecules by latest netMHCpan (v.4.0), verifying MHC-peptides by MaxQuant with mass spectrometry proteomics data searched against customized protein database, and checking potential immunogenicity of T-cell-recognization by additional screening methods. ProGeo-neo pipeline achieves proteogenomics strategy and the neopeptides identified were of much higher quality as compared to those identified using genomic data only. The pipeline was constructed based on the genomics and proteomics data of Jurkat leukemia cell line but is generally applicable to other solid cancer research. With massively parallel sequencing and proteomics profiling increasing, this proteogenomics workflow should be useful for neoantigen oriented research and immunotherapy.
Genetic factors underlie the association between anxiety, attitudes and performance in mathematics
Authors: Malanchini Margherita , Rimfeld Kaili , Wang Zhe , Petrill Stephen A. , Tucker-Dob Elliot M. , Plomin Robert , Kovas Yulia
Published: August 2019

Students struggling with mathematics anxiety (MA) tend to show lower levels of mathematics self-efficacy and interest as well as lower performance. The current study addresses: (1) how MA relates to different aspects of mathematics attitudes (self-efficacy and interest), ability (understanding numbers, problem-solving ability, and approximate number sense) and achievement (exam scores); (2) to what extent these observed relations are explained by overlapping genetic and environmental factors; and (3) the role of general anxiety in accounting for these associations. The sample comprised 3,410 twin pairs aged 16-21 years, from the Twins Early Development Study. Negative associations of comparable strength emerged between MA and the two measures of mathematics attitudes, phenotypically (∼ -.45) and genetically (∼ -.70). Moderate negative phenotypic (∼ -.35) and strong genetic (∼ -.70) associations were observed between MA and measures of mathematics performance. The only exception was approximate number sense whose phenotypic (-.10) and genetic (-.31) relation with MA was weaker. Multivariate quantitative genetic analyses indicated that all mathematics related measures combined accounted for ∼75% of the genetic variance in MA and ∼20% of its environmental variance. Genetic effects were largely shared across all measures of mathematics anxiety, attitudes, abilities and achievement, with the exception of approximate number sense. This genetic overlap was not accounted for by general anxiety. These results have important implications for future genetic research concerned with identifying the genetic underpinnings of individual variation in mathematics-related traits, as well as for developmental research into how children select and modify their mathematics-related experiences partly based on their genetic predispositions.
Novel mechanisms for phosphate acquisition in abundant rhizosphere-dwellingBacteroidetes
Authors: Lidbury Ian D.E.A. , Scanlan David J. , Murphy Andrew R. J. , Bottrill Andrew , Jones Alex , Tibbett Mark , Bending Gary , Hammond John P. , Wellington Elizabeth M. H.
Published: August 2019

Global food production is reliant on the application of finite phosphorus (P) fertilisers. Numerous negative consequences associated with intensive P fertilisation have resulted in a high demand to find alternative sustainable methods that will enhance crop P uptake.Bacteroidetes, primarily from the genusFlavobacterium, have recently been shown to be abundant members of the plant microbiome, but their general ecological role and potential to mobilise P in the rhizosphere remains very poorly characterised. Here, we sought to determine the P mobilisation potential ofFlavobacteriumstrains isolated from the rhizosphere of oilseed rape (Brassica napusL.). We show that theseFlavobacteriumstrains possess novel mechanisms for P mobilisation and subsequent acquisition. These include the constitutive and inducible expression of completely novel and phylogenetically distinct phosphatases, the phosphate starvation inducible expression of uncharacterised and hypothetical genes and gene clusters and, for the first time, the involvement of outer membrane SusCD transport complexes (usually associated with carbohydrate transport) in P acquisition. The genes encoding these unusual phosphate starvation inducible proteins were enriched in plant-associatedFlavobacteriumstrains suggesting that this machinery represents niche-adaptive strategies for overcoming P scarcity in this genus. We propose that abundant rhizosphere-dwellingFlavobacteriumspp. have evolved unique mechanisms for coping with Pi-stress which may provide novel solutions for future sustainable agricultural practices.
A compartment size dependent selective threshold limits mutation accumulation in hierarchical tissues
Authors: Grajzel Daniel , Derenyi Imre , Szollosi Gergely J
Published: August 2019

Cancer is a genetic disease fueled by somatic evolution. Hierarchical tissue organization can slow somatic evolution by two qualitatively different mechanisms: by cell differentiation along the hierarchy "washing out" harmful mutations (Nowak et al. 2003, Werner et al. 2013) and by limiting the number of cell divisions required to maintain a tissue (Derenyi and Szollosi 2017). Here we explore the effects of compartment size on somatic evolution in hierarchical tissues by considering cell number regulation that acts on cell division rates such that the number of cells in the tissue has the tendency to return to its desired homeostatic value. Introducing mutants with a proliferative advantage we demonstrate the existence of a third fundamental mechanism by which hierarchically organized tissues are able to slow down somatic evolution. We show that tissue size regulation leads to the emergence of a threshold proliferative advantage, below which mutants cannot persist. We find that the most significant determinant of the threshold selective advantage is compartment size, with the threshold being higher the smaller the compartment. Our results demonstrate that in sufficiently small compartments even mutations that confer substantial proliferative advantage cannot persist, but are expelled from the tissue by differentiation along the hierarchy. The resulting selective barrier can significantly slow down somatic evolution and reduce the risk of cancer by limiting the accumulation of mutations that increase the proliferation of cells.
PIWIL3 forms a complex with TDRKH in mammalian oocytes
Authors: Tan Minjie , van Tol Helena T.A. , Rosenkranz David , Roovers Elke F. , Damen Mirjam J. , Stout Tom A.E. , Wu Wei , Roelen Bernard A.J.
Published: August 2019

PIWIs are crucial guardians of genome integrity, particularly in germ cells. While mammalian PIWIs have been primarily studied in mouse and rat, a homologue for the human PIWIL3 gene is absent in the Muridae family, and hence the unique function of PIWIL3 in germ cells cannot be effectively modeled by mouse knockouts. Herein, we investigated the expression, distribution and interaction of PIWIL3 in bovine oocytes. We localized PIWIL3 to mitochondria, and demonstrated that PIWIL3 expression is stringently controlled both spatially and temporally before and after fertilization. Moreover, we identified PIWIL3 in a mitochondrials-recruited three-membered complex with TDRKH and PNLDC1, and demonstrated by mutagenesis that PIWIL3 N-terminal arginine modifications are required for complex assembly. Finally we sequenced the piRNAs bound to PIWIL3-TDRKH-PNLDC1 and report here that about 50% of these piRNAs map to transposable elements, recapitulating the important role of PIWIL3 in maintaining genome integrity in mammalian oocytes.
Liquid biopsies for omics-based analysis in sentinel mussels
Authors: Caza France , de Boissel Philippine Granger Joly , Villemur Richard , Betoulle Stéphane , St-Pierre Yves
Published: August 2019

Liquid biopsy of plasma is a simple and non-invasive technology that holds great promise in biomedical research. It is based on the analysis of nucleic acid-based biomarkers with predictive potential. In the present work, we have combined this concept with the FTA technology for sentinel mussels. We found that hemocytes collected from liquid biopsies can be readily fixed on FTA cards and used for long-term transriptome analysis. We also showed that liquid biopsy is easily adaptable for metagenomic analysis of bacterial profiles of mussels. We finally provide evidence that liquid biopsies contained circulating cell-free DNA (ccfDNA) which can be used as an easily accessible genomic reservoir. Sampling of FTA-fixed circulating nucleic acids is stable at room temperature and does not necessitate a cold-chain protection. It showed comparable performance to frozen samples and is ideally adapted for sampling in remote areas, most notably in polar regions threatened by anthropogenic activities. From an ethical point of view, this minimally-invasive and non-lethal approach further reduces incidental mortality associated with conventional tissue sampling. This liquid biopsy-based approach should thus facilitate biobanking activities and development of omics-based biomarkers in sentinel mussels to assess the quality of marine ecosystems.
Medicago truncatula possesses a single Shaker outward K+ channel: functional characterization and roles in planta
Authors: Drain Alice , Thouin Julien , Wang Limin , Pauly Nicolas , Nieves-Cordones Manuel , Boeglin Martin , Gaillard Isabelle , Véry Anne-Aliénor , Sentenac Hervé
Published: August 2019

The model legume Medicago truncatula possesses a single outward Shaker K+ channel, while Arabidopsis thaliana possesses two channels of this type, named SKOR and GORK, the former having been shown to play a major role in K+ secretion into the xylem sap in the root vasculature and the latter to mediate the efflux of K+ across the guard cell membrane upon stomatal closure. Here we show that the expression pattern of the single M. truncatula outward Shaker channel, which has been named MtGORK, includes the root vasculature, guard cells and root hairs. As shown by patch-clamp experiments on root hair protoplasts, besides the Shaker-type slowly-activating outwardly-rectifying K+ conductance encoded by MtGORK, a second K+-permeable conductance, displaying fast activation and weak rectification, can be expressed by M. truncatula. A KO mutation resulting in absence of MtGORK activity is shown to weakly reduce K+ translocation to shoots, and only in plants engaged in rhizobial symbiosis, but to strongly affect the control of stomatal aperture and transpitational water loss. In legumes, the early electrical signaling pathway triggered by Nod Factor perception is known to comprise a short transient depolarization of the root hair plasma membrane. In absence of MtGORK functional expression, while the rate of the membrane repolarization is shown to be decreased by about 3 times, this defect is without any consequence on infection thread development and nodule production, indicating that the plant capacity to engage rhizobial symbiosis does not require integrity of the early electrical signaling events.
Low-cost scalable discretization, prediction and feature selection for complex systems
Authors: Gerber S. , Pospisil L. , Navandar M. , Horenko I.
Published: August 2019

Finding reliable discrete approximations of complex systems is a key prerequisite when applying many of the most popular modeling tools. Common discretization approaches (for example, the very popular K-means clustering) are crucially limited in terms of quality and cost. We introduce a low-cost improved-quality Scalable Probabilistic Approximation (SPA) algorithm, allowing for simultaneous data-driven optimal discretization, feature selection and prediction. Cross-validated applications of SPA to a range of large realistic data classification and prediction problems reveal drastic cost and performance improvements. For example, SPA allows the unsupervised next-day surface temperature predictions for Europe with the mean crossvalidated one-day prediction error of 0.75°C on a common PC (being around 40% better in terms of errors and five to six orders-of-magnitude cheaper than the next-day surface temperature predictions calculated on supercomputers and provided by the weather services).

One Sentence Summary

Introduced computational tool allows obtaining drastic cost and quality gains for a broad range of science applications.
Human Inference in Changing Environments with Temporal Structure
Authors: Prat-Carrabin Arthur , Wilson Robert C. , Cohen Jonathan D. , da Silveira Rava Azeredo
Published: August 2019

To make informed decisions in natural environments that change over time, humans must update their beliefs as new observations are gathered. Studies exploring human inference as a dynamical process that unfolds in time have focused on situations in which the statistics of observations are history-independent. Yet temporal structure is everywhere in nature, and yields history-dependent observations. Do humans modify their inference processes depending on the latent temporal statistics of their observations? We investigate this question experimentally and theoretically using a change-point inference task. We show that humans adapt their inference process to fine aspects of the temporal structure in the statistics of stimuli. As such, humans behave qualitatively in a Bayesian fashion, but, quantitatively, deviate away from optimality. Perhaps more importantly, humans behave suboptimally in that their responses are not deterministic, but variable. We show that this variability itself is modulated by the temporal statistics of stimuli. To elucidate the cognitive algorithm that yields this behavior, we investigate a broad array of existing and new models that characterize different sources of suboptimal deviations away from Bayesian inference. While models with ‘output noise’ that corrupts the response-selection process are natural candidates, human behavior is best described by sampling-based inference models, in which the main ingredient is a compressed approximation of the posterior, represented through a modest set of random samples and updated over time. This result comes to complement a growing literature on sample-based representation and learning in humans.
Theranostic cranial implant for hyperspectral light delivery and microcirculation imaging without scalp removal
Authors: Davoodzadeh Nami , Cano-Velázquez Mildred S. , Jonak Carrie R. , Halaney David L. , Binder Devin K. , Hernández-Cordero Juan A. , Aguilar Guillermo
Published: August 2019

Light based techniques for imaging, diagnosing and treating the brain have become widespread clinical tools, but application of these techniques is limited by optical attenuation in the scalp and skull. This optical attenuation reduces the achievable spatial resolution, precluding the visualization of small features such as brain microvessels. The goal of this study was to assess a strategy for providing ongoing optical access to the brain without the need for repeated craniectomy or retraction of the scalp. This strategy involves the use of a transparent cranial implant and skin optical clearing agents, and was tested in mice to assess improvements in optical access which could be achieved for laser speckle imaging of cerebral microvasculature. Combined transmittance of the optically cleared scalp overlying the transparent cranial implant was as high as 89% in the NIR range, 50% in red range, 24% in green range, and 20% in blue range.In vivolaser speckle imaging experiments of mouse cerebral blood vessels showed that the proposed optical access increased signal-to-noise ratio and image resolution, allowing for visualization of microvessels through the transparent implant, which was not possible through the uncleared scalp and intact skull.
Taking the next-gen step: comprehensive antimicrobial resistance detection from Burkholderia pseudomallei genomes
Authors: Madden Danielle E. , Webb Jessica R. , Steinig Eike J. , Currie Bart J. , Price Erin P. , Sarovich Derek S.
Published: August 2019

Background

Antimicrobial resistance (AMR) poses a major threat to human health. Whole-genome sequencing holds great potential for AMR identification; however, there remain major gaps in comprehensively detecting AMR across the spectrum of AMR-conferring determinants and pathogens.

Methods

Using 16 wild-type Burkholderia pseudomallei and 25 with acquired AMR, we first assessed the performance of existing AMR software (ARIBA and CARD) for detecting clinically relevant AMR in this pathogen. B. pseudomallei was chosen due to limited treatment options, high fatality rate, and AMR caused exclusively by chromosomal mutation (i.e. single-nucleotide polymorphisms [SNPs], insertions-deletions [indels], copy-number variations [CNVs], and functional gene loss). Due to poor performance with existing tools, we developed ARDaP (Antimicrobial Resistance Detection and Prediction) to identify the spectrum of AMR-conferring determinants in B. pseudomallei.

Results

CARD failed to identify any clinically-relevant AMR in B. pseudomallei, ARIBA cannot differentiate AMR determinants from natural genetic variation, and neither CARD or ARIBA can identify CNV or gene loss determinants. In contrast, ARDaP accurately detected all SNP, indel, CNV, and gene loss AMR determinants described in B. pseudomallei (n≈50). Additionally, ARDaP accurately predicted three previously undescribed determinants. In mixed strain data, ARDaP identified AMR to as low as ~5% allelic frequency.

Conclusions

We demonstrate that existing AMR software are inadequate for comprehensive AMR detection; ARDaP overcomes the shortcomings of existing tools. Further, ARDaP enables AMR prediction from mixed sequence data down to 5% allelic frequency. ARDaP databases can be constructed for any microbial species of interest for comprehensive AMR detection.
Minimum Error Calibration and Normalization for Genomic Copy Number Analysis
Authors: Gao Bo , Baudis Michael
Published: August 2019

Copy number variations (CNV) are regional deviations from the normal autosomal bi-allelic DNA content. While germline CNVs are a major contributor to genomic syndromes and inherited diseases, the majority of cancers accumulate extensive “somatic” CNV (sCNV or CNA) during the process of oncogenetic transformation and progression. While specific sCNV have closely been associated with tumorigenesis, intriguingly many neoplasias exhibit recurrent sCNV patterns beyond the involvement of a few cancer driver genes.

Currently, CNV profiles of tumor samples are generated using genomic micro-arrays or high-throughput DNA sequencing. Regardless of the underlying technology, genomic copy number data is derived from the relative assessment and integration of multiple signals, with the data generation process being prone to contamination from several sources. Estimated copy number values have no absolute and linear correlation to their corresponding DNA levels, and the extent of deviation differs between sample profiles which poses a great challenge for data integration and comparison in large scale genome analysis.

In this study, we present a novel method named Minimum Error Calibration and Normalization of Copy Numbers Analysis (Mecan4CNA). For each sCNV profile,Mecan4CNAreduces the noise level, calculates values representing the normal DNA copies (baseline) and the change of one copy (level distance), and finally normalizes all values. Experiments ofMecan4CNAon simulated data showed an overall accuracy of 93% and 91% in determining the baseline and level distance, respectively. Comparison of baseline and level distance estimation with existing methods and karyotyping data on the NCI-60 tumor cell line produced coherent results. To estimate the method’s impact on downstream analyses we performed GISTIC analyses on original andMecan4CNAdata from the Cancer Genome Atlas (TCGA) where the normalized data showed prominent improvements of both sensitivity and specificity in detecting focal regions.

In general,Mecan4CNAprovides an advanced method for CNA data normalization especially in research involving data of high volume and heterogeneous quality. but with its informative output and visualization can also facilitate analysis of individual CNA profiles.Mecan4CNAis freely available as a Python package and through Github.
Phenomenological models of NaV1.5. A side by side, procedural, hands-on comparison between Hodgkin-Huxley and kinetic formalisms
Authors: Andreozzi Emilio , Carannante Ilaria , D’Addio Giovanni , Cesarelli Mario , Balbi Pietro
Published: August 2019

Background

Computational models of ionic channels represent the building blocks of conductance-based, biologically inspired models of neurons and neural networks. Ionic channels are still widely modelled by means of the formalism developed by the seminal work of Hodgkin and Huxley, although the electrophysiological features of the channels are currently known to be better fitted by means of kinetic (Markov-type) models.

Objective

The present study is aimed at showing why kinetic, simplified models are better suited to model ionic channels compared to Hodgkin and Huxley models, and how the manual optimization process is rationally carried out in practice for these two kinds of models.

Methods

Previously published experimental data on macroscopic currents of an illustrative ionic channel (NaV1.5) are exploited to develop a step by step optimization of the two models in close comparison. The proposed kinetic model is a simplified one, consisting of five states and ten transitions.

Results

A conflicting practical limitation is recognized for the Hodgkin and Huxley model, which only supplies one parameter to model two distinct electrophysiological behaviours (namely the steady-state availability and the recovery from inactivation). In addition, a step by step procedure is provided to correctly optimize the kinetic model.

Conclusion

Simplified kinetic models are at the moment the best option to closely approximate the known complexity of the ionic channel macroscopic currents. Their optimization is achievable by means of a rationally guided procedure, and it results in models with computational burdens comparable with those from Hodgkin and Huxley models.
A high-throughput segregation analysis identifies the sex chromosomes ofCannabis sativa
Authors: Prentout Djivan , Razumova Olga , Rhoné Bénédicte , Badouin Hélène , Henri Hélène , Feng Cong , Käfer Jos , Karlov Gennady , Marais Gabriel AB
Published: August 2019

Cannabis sativa-derived tetrahydrocannabinol (THC) production is increasing very fast worldwide.C. sativais a dioecious plant with XY chromosomes, and only females (XX) are useful for THC production. TheC. sativasex chromosomes sequence would improve early sexing and better management of this crop; however, theC. sativagenome projects failed to identify the sex chromosomes so far. Moreover, dioecy in the Cannabaceae family is ancestral,C. sativasex chromosomes are potentially old and thus very interesting to study as little is known about the last steps of sex chromosome evolution in plants. Here we RNA-sequenced aC. sativafamily (2 parents and 10 male and female offspring) and performed a segregation analysis for allC. sativagenes using the probabilistic method SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to aC. sativagenome assembly identified a single chromosome pair with a large non-recombining region. Further analysis of the >500 sex-linked genes revealed thatC. sativahas a strongly degenerated Y chromosome and represents the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large non-recombining regions and be very differentiated and still be of similar size (homomorphic).
mDia2 formin selectively interacts with catenins and not E-cadherin to regulate Adherens Junction formation
Authors: Zhang Yuqi , Pettee Krista M. , Becker Kathryn N. , Eisenmann Kathryn M.
Published: August 2019

Background

Epithelial ovarian cancer (EOC) cells disseminate within the peritoneal cavity, in part, via the peritoneal fluid as single cells, clusters, or spheroids. Initial single cell egress from a tumor can involve disruption of cell-cell adhesions as cells are shed from the primary tumor into the peritoneum. In epithelial cells, Adherens Junctions (AJs) are characterized by homotypic linkage of E-cadherins on the plasma membranes of adjacent cells. AJs are anchored to the intracellular actin cytoskeletal network through a complex involving E-cadherin, p120 catenin, β-catenin, and αE-catenin. However, the specific players involved in the interaction between the junctional E-cadherin complex and the underlying F-actin network remains unclear. Recent evidence indicates that mammalian Diaphanous-related (mDia) formins plays a key role in epithelial cell AJ formation and maintenance through generation of linear actin filaments. Binding of αE-catenin to linear F-actin inhibits association of the branched-actin nucleator Arp2/3, while favoring linear F-actin bundling. We previously demonstrated that loss of mDia2 was associated with invasive single cell egress from EOC spheroids through disruption of junctional F-actin.

Results

In the current study, we now show that mDia2 has a role at adherens junctions (AJs) in EOC OVCA429 cells and human embryonic kidney (HEK) 293 cells through its association with αE-catenin and β-catenin. mDia2 depletion in EOC cells leads to reduction in actin polymerization and disruption of cell-cell junctions with decreased interaction between β-catenin and E-cadherin.

Conclusions

Our results support a necessary role for mDia2 in AJ stability in EOC cell monolayers and indicate a critical role for mDia formins in regulating EOC AJs during invasive transitions.
jULIEs: extracellular probes for recordings and stimulation in the structurally and functionally intact mouse brain
Authors: Racz Romeo , Kollo Mihaly , Racz Gabriella , Bulz Ciprian , Ackels Tobias , Warner Tom , Wray William , Kiskin Nikolai , Chen Chi , Ye Zhiwen , de Hoz Livia , Rancz Ede , Schaefer Andreas
Published: August 2019

High signal-to-noise, scalable and minimally invasive recording and stimulation of the nervous system in intact animals is of fundamental importance to advance the understanding of brain function. Extracellular electrodes are among the most powerful tools capable of interfacing with large neuronal populations1-3. Neuronal tissue damage remains a major limiting factor in scaling electrode arrays, and has been found to correlate with electrode diameter across different electrode materials, such as microfabricated Michigan and Utah-style arrays4, MEMS and microsystems5, soft polymer or tungsten electrodes6 and Parylene C probes7. Small diameter ultramicroelectrodes (UMEs), while highly desirable, pose significant technical challenges such as reaching sufficient electrolyte-electrode coupling and limiting stray signal loss. To overcome these challenges, we have designed juxtacellular Ultra-Low Impedance Electrodes (jULIEs), a scalable technique for achieving high signal-to-noise electrical recordings as well as stimulation with UMEs. jULIEs are metal-glass composite UMEs thermally drawn to outer diameters (OD) of <25 µm, with metal core diameters (ID) of as little as 1 µm. We introduce a two-step electrochemical modification strategy that reduces UME coupling impedances by two orders of magnitude. Modifications enabled high signal-to-noise neural recordings in vivo through wires with micrometer scale core diameters. Histological and imaging experiments indicated that local vascular damage is minimal. Spikes reached amplitudes over 1 mV in vivo, indicating that recordings are possible in close proximity to intact neurons. Recording sites can be arranged in arbitrary patterns tailored to various neuroanatomical target structures and allowing parallel penetrations. jULIEs thus represent a versatile platform that allows for reliable recording and manipulation of neural activity in any areas of the functionally intact mammalian brain.
Small circRNAs with self-cleaving ribozymes are frequently expressed in metazoan transcriptomes
Authors: Cervera Amelia , De la Pena Marcos
Published: August 2019

Ribozymes are catalytic RNAs present in modern genomes but considered as remnants of a prebiotic RNA world. The paradigmatic hammerhead ribozyme (HHR) is a small self-cleaving motif widespread from bacterial to human genomes. Here, we report that most of the classical type I HHRs frequently found in the genomes of diverse animals are contained within a novel family of non-autonomous non-LTR retrotransposons. These retroelements are expressed as abundant linear and circular RNAs of ~170-400 nt in different animal tissues. In vitro analyses confirm an efficient self-cleavage of the HHRs harboured in invertebrate retrozymes, whereas those in retrozymes of vertebrates, such as the axolotl, require to act as dimeric motifs to reach higher self-cleavage rates. Ligation assays of retrozyme RNAs with a protein ligase versus HHR self-ligation indicate that, most likely, tRNA ligases and not the ribozymes are involved in the step of RNA circularization. Altogether, these results confirm the existence of a new and conserved pathway in animals and, likely, in eukaryotes in general, for the efficient biosynthesis of RNA circles through small ribozymes, which will allow the development of biotechnological tools in the emerging field of circRNAs.
Measuring Robustness of Brain Networks in Autism Spectrum Disorder with Ricci Curvature
Authors: Simhal Anish K. , Carpenter Kimberly L.H. , Nadeem Saad , Kurtzberg Joanne , Song Allen , Tannenbaum Allen , Sapiro Guillermo , Dawson Geraldine
Published: August 2019

Ricci curvature is a method for measuring the robustness of networks. In this work, we use Ricci curvature to measure robustness of brain networks affected by autism spectrum disorder (ASD). Subjects with ASD are given a stem cell infusion and are imaged with diffusion MRI before and after the infusion. By using Ricci curvature to measure changes in robustness, we quantify both local and global changes in the brain networks correlated with the infusion. Our results find changes in regions associated with ASD that were not detected via traditional brain network analysis.
Structural variation of the malaria-associated human glycophorin A-B-E region
Authors: Louzada Sandra , Algady Walid , Weyell Eleanor , Zuccherato Luciana W. , Brajer Paulina , Almalki Faisal , Scliar Marilia O , Naslavsky Michel S , Yamamoto Guilherme L , Duarte Yeda A O , Passos-Bueno Maria Rita , Zatz Mayana , Yang Fengtang , Hollox Edward J
Published: August 2019

Approximately 5% of the human genome consists of structural variants, which are enriched for genes involved in the immune response and cell-cell interactions. A well-established region of extensive structural variation is the glycophorin gene cluster, comprising three tandemly-repeated regions about 120kb in length, carrying the highly homologous genesGYPA,GYPBandGYPE. Glycophorin A and glycophorin B are glycoproteins present at high levels on the surface of erythrocytes, and they have been suggested to act as decoy receptors for viral pathogens. They act as receptors for invasion of a causative agent of malaria,Plasmodium falciparum. A particular complex structural variant (DUP4) that creates aGYPB/GYPAfusion gene is known to confer resistance to malaria. Many other structural variants exist, and remain poorly characterised. Here, we analyse sequences from 6466 genomes from across the world for structural variation at the glycophorin locus, confirming 15 variants in the 1000 Genomes project cohort, discovering 9 new variants, and characterising a selection using fibre-FISH and breakpoint mapping. We identify variants predicted to create novel fusion genes and a common inversion duplication variant at appreciable frequencies in West Africans. We show that almost all variants can be explained by unequal cross over events (non-allelic homologous recombination, NAHR) and. by comparing the structural variant breakpoints with recombination hotspot maps, show the importance of a particular meiotic recombination hotspot on structural variant formation in this region.
Round A/Round B Amplification of DNA for Microarrays
Authors: Rando Oliver
Published: August 2019

The goal of this procedure is to randomly amplify a sample of DNA to achieve the best possible sequence representation for hybridization to microarrays. This protocol has been used successfully to amplify genomic representations starting with <10 ng of DNA. The protocol consists of three sets of enzymatic reactions. In Round A, Sequenase is used to extend randomly annealed primers to generate templates for subsequent PCR. During Round B, a specific primer is used to amplify the previously generated templates. Amplified material can be labeled by adding fluorescent moieties to the nucleic acids. Alternatively, Round C in this protocol can be used to incorporate either aminoallyl-dUTP or Cy-dye-coupled nucleotides during additional PCR cycles. This protocol may be unsuitable for amplifying material smaller than 250 bp because such material will not be amplified uniformly.