bluuebunny/crossref_metadata_2025 huggingface dataset:
The Transition from Acute to Chronic Pain: Dynamic Epigenetic Reprogramming of the Mouse Prefrontal Cortex up to One Year Following Nerve Injury
Authors: Topham Lucas , Gregoire Stephanie , Kang HyungMo , Salmon-Divon Mali , Lax Elad , Millecamps Magali , Szyf Moshe , Stone Laura
Published: February 2020

Chronic pain is associated with persistent structural and functional changes throughout the neuroaxis, including in the prefrontal cortex (PFC). The PFC is important in the integration of sensory, cognitive and emotional information and in conditioned pain modulation. We previously reported wide-spread epigenetic reprogramming in the PFC many months following nerve injury in rodents. Epigenetic modifications, including DNA methylation, can drive changes in gene expression without modifying DNA sequences. To date, little is known about epigenetic dysregulation at the onset of acute pain or how it progresses as pain transitions from acute to chronic. We hypothesize that acute pain following injury results in rapid and persistent epigenetic remodelling in the PFC that evolves as pain becomes chronic. We further propose that understanding epigenetic remodelling will provide insights into the mechanisms driving pain-related changes in the brain. Epigenome-wide analysis was performed in the mouse PFC 1 day, 2 weeks, 6 months, and 1 year following peripheral injury using the spared nerve injury (SNI) in mice. SNI resulted in rapid and persistent changes in DNA methylation, with robust differential methylation observed between SNI and sham-operated control mice at all time points. Hundreds of differentially methylated genes were identified, including many with known function in pain. Pathway analysis revealed enrichment in genes related to stimulus response at early time points, immune function at later time points and actin and cytoskeletal regulation throughout the time course. Increased attention to pain chronicity as a factor is recommended for both pain research and management.
Emergence of a novel interaction between brown bear and cicada due to anthropogenic habitat modification
Authors: Tomita Kanji , Hiura Tsutom
Published: February 2020

Novel species interactions have generally emerged in ecosystems that are highly modified by human activities. Anthropogenic habitat modification, such as afforestation, is one possible driver of novel species interactions; however, empirical evidence remains scarce. In this study, we show that a novel predator-prey interaction between the brown bear (Ursus arctos) and nymphs of a cicada species (Lyristes bihamatus) is generated by anthropogenic habitat modification. We evaluated the frequency of brown bear predation on cicada nymphs and the density of cicada nymphs between natural forests and plantations, which are a typical type of human-modified habitat. We found that brown bear predation on cicada nymphs occurred only in the plantations. The density of cicada nymphs in the plantations was significantly higher than in the natural forest. Our results indicate that the plantation leads to the emergence of the bear-cicada interaction due to increasing the density of cicada nymphs. The study draws attention to the overlooked effects of anthropogenic habitat modification on species interactions.
Current and potential contributions of the Gulf of Lion Fisheries Restricted Area to fisheries sustainability in the NW Mediterranean Sea
Authors: Vilas Daniel , Coll Marta , Corrales Xavier , Steenbeek Jeroen , Piroddi Chiara , Macias Diego , Ligas Alessandro , Sartor Paolo , Claudet Joachim
Published: February 2020

Many commercial species of the world are overexploited resulting in substantial reductions of biomass and ecological changes. Spatial-temporal restrictions of fishing activities are important measures used for the management of marine stocks. However, evidence of whether fishing bans benefit whole ecosystems is still scant. Here, we developed a food-web model approach using the Ecopath with Ecosim (EwE) model representing the Fisheries Restricted Area (FRA) of the Gulf of Lion ecosystem (CoSEGoL model) prior to the establishment of the fisheries restrictions (2006-2008) to characterize the structure and functioning of the ecosystem before and after its establishment. The constructed food-web model was, then, fitted to available time series of data from 2008 to 2016 to verify whether this FRA has contributed to recovery of target demersal species and the demersal community. The fitted model was used to explore alternative future management scenarios to explore feasible management options in order to ensure a full ecosystem recovery under climate change conditions. Both small positive and negative ecosystem changes occurred between prior and after the establishment of the FRA, potentially revealing a lack of protection efficiency and/or enforcement. Scenarios of management options under plausible climate futures revealed possible recovery of targeted species, especially European hake. The study highlighted the importance of considering trophic interactions between predators and prey to identify trade-offs and synergies in fisheries management outcomes and the need to consider both fishing and climate dynamics.
Mental health status and coping strategy of medical workers in China during The COVID-19 outbreak
Authors: Chen Siyu , Xia Min , Wen Weiping , Cui Liqian , Yang Weiqiang , Liu Shaokun , Fan Jiahua , Yue Huijun , Tang Shangqing , Tang Bingjie , Xiaoling Li , Chen Lin , Qin Zili , Lv Kexing , Guo Xueqin , Lin Yu , Wen Yihui , Gao Wenxiang , Zheng Ying , Xu Wei , Li Yun , Xu Yang , Ling Li , Lei Wenbin
Published: February 2020

The authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Drivers of grass endophyte communities in prairies of the Pacific Northwest, USA
Authors: Bailes Graham , Thomas Dan , Bridgham Scott D. , Roy Bitty A.
Published: February 2020

Prairies of the Pacific Northwest are highly threatened, with only ∼2% of historic land area remaining. The combined risk of global climate change and land use change make these prairies a high conservation priority. However, little attention has been paid to the microbiota of these systems, including the hyper diverse fungi that live asymptomatically in their leaves, the endophytes. Using culture-free, full-community DNA sequencing, we investigated the diversity, composition, and structure of full fungal foliar endophyte and ecological guild communities in two native, cool-season bunchgrasses along a climate gradient. We quantified the relative importance of host, host fitness, environment, and spatial structuring in microbial community structure. We found markedly different communities between the southern and central-northern sites, suggesting a potential dispersal limitation in the Klamath Mountains. We also found that each host species was home to distinct fungal communities. Climate was the strongest predictor of endophyte community, while fitness (e.g., plant size, reproductive status, density) was less important for community structure. For both host species, seasonality contributed strongly to the variation we observed. At the ecological guild level, saprotrophs tended to decline with latitude, whereas symbiotrophs and pathotrophs both tended to increase with latitude. Our results suggest that climate change will have large consequences for these diverse fungal communities.
Sequencing depth and genotype quality: Accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops
Authors: Gemenet Dorcus C , Lindqvist-Kreuze Hannele , Olukolu Bode A , Boeck Bert De , Pereira Guilherme da Silva , Mollinari Marcelo , Zeng Zhao-Bang , Yencho G Craig , Campos Hugo
Published: February 2020

The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: i) do polyploid crop breeders need to invest more for additional sequencing depth? ii) how many markers are required to make selection decisions? iii) does considering non-additive genetic effects improve predictive ability (PA)? iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction, hence it is possible to get this number at the current sequencing depth from most service providers. We also show that considering dosage information and additive-effects only models had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations.

Key message

Polypoid crop breeders do not need more investment for sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture.
Learning differentially reorganizes brain activity and connectivity
Authors: Bertolero Maxwell A. , Adebimpe Azeez , Khambhati Ankit N. , Mattar Marcelo G. , Romer Daniel , Thompson-Schill Sharon L. , Bassett Danielle S.
Published: February 2020

Human learning is a complex process in which future behavior is altered via the reorganization of brain activity and connectivity. It remains unknown whether activity and connectivity differentially reorganize during learning, and, if so, how that differential reorganization tracks stages of learning across distinct brain areas. Here, we address this gap in knowledge by measuring brain activity and functional connectivity in a longitudinal fMRI experiment in which healthy adult human participants learn the values of novel objects over the course of four days. An increasing similarity in activity or functional connectivity across subjects during learning reflects reorganization toward a common functional architecture. We assessed the presence of reorganization in activity and connectivity both during value learning and during the resting-state, allowing us to differentiate common elicited processes from intrinsic processes. We found a complex and dynamic reorganization of brain connectivity and activity—as a function of time, space, and performance—that occurs while subjects learn. Spatially localized brain activity reorganizes across the brain to a common functional architecture early in learning, and this reorganization tracks early learning performance. In contrast, spatially distributed connectivity reorganizes across the brain to a common functional architecture as training progresses, and this reorganization tracks later learning performance. Particularly good performance is associated with a sticky connectivity, that persists into the resting state. Broadly, our work uncovers distinct principles of reorganization in activity and connectivity at different phases of value learning, which inform the ongoing study of learning processes more generally.
Inferring transmission trees to guide targeting of interventions against visceral leishmaniasis and post-kala-azar dermal leishmaniasis
Authors: Chapman Lloyd A. C. , Spencer Simon E. F. , Pollington Timothy M. , Jewell Chris P. , Mondal Dinesh , Alvar Jorge , Hollingsworth T. Déirdre , Cameron Mary M. , Bern Caryn , Medley Graham F.
Published: February 2020

Understanding of spatiotemporal transmission of infectious diseases has improved significantly in recent years. Advances in Bayesian inference methods for individual-level geo-located epidemiological data have enabled reconstruction of transmission trees and quantification of disease spread in space and time, while accounting for uncertainty in missing data. However, these methods have rarely been applied to endemic diseases or ones in which asymptomatic infection plays a role, for which novel estimation methods are required. Here, we develop such methods to analyse longitudinal incidence data on visceral leishmaniasis (VL), and its sequela, post-kala-azar dermal leishmaniasis (PKDL), in a highly endemic community in Bangladesh. Incorporating recent data on infectiousness of VL and PKDL, we show that while VL cases drive transmission when incidence is high, the contribution of PKDL increases significantly as VL incidence declines (reaching 55% in this setting). Transmission is highly focal: >85% of mean distances from inferred infectors to their secondary VL cases were <300m, and estimated average times from infector onset to secondary case infection were <4 months for 90% of VL infectors, but up to 2.75yrs for PKDL infectors. Estimated numbers of secondary VL cases per VL and PKDL case varied from 0-6 and were strongly correlated with the infector’s duration of symptoms. Counterfactual simulations suggest that prevention of PKDL could have reduced VL incidence by up to a quarter. These results highlight the need for prompt detection and treatment of PKDL to achieve VL elimination in the Indian subcontinent and provide quantitative estimates to guide spatiotemporally-targeted interventions against VL.

Significance Statement

Although methods for analysing individual-level geo-located disease data have existed for some time, they have rarely been used to analyse endemic human diseases. Here we apply such methods to nearly a decade’s worth of uniquely detailed epidemiological data on incidence of the deadly vector-borne disease visceral leishmaniasis (VL) and its secondary condition, post-kala-azar dermal leishmaniasis (PKDL), to quantify the spread of infection around cases in space and time by inferring who infected whom, and estimate the relative contribution of different infection states to transmission. Our findings highlight the key role long diagnosis delays and PKDL play in maintaining VL transmission. This detailed characterisation of the spatiotemporal transmission of VL will help inform targeting of interventions around VL and PKDL cases.
Patient Perspectives on Home-Based Rehabilitation Exercise and General Physical Activity after Total Hip Arthroplasty: A qualitative study (PHETHAS-2)
Authors: Grøndahl Poulsen Anne , Gravesen Janni Dahlgaard , Nørgaard Madsen Merete , Mikkelsen Lone Ramer , Bandholm Thomas , Rossen Camilla Blach
Published: February 2020

Objectives

To investigate patient-perceived facilitators and barriers to home-based rehabilitation exercise and general physical activity after THA.

Design

Using a qualitative design, twenty-two semi-structured interviews were conducted and analyzed using an interpretive thematic analysis approach, with theoretical underpinning from the concept conduct of everyday life. The study is embedded within the PHETHAS-1 trial, quantitatively investigating recovery outcomes after a home-based rehabilitation exercise program.

Setting

A regional hospital in Denmark between January 2018 and May 2019.

Participants

Twenty-two patients who had undergone THA and performed home-based rehabilitation exercise.

Results

The main theme “Wishing to return to the well-known everyday life” and the subtheme “General physical activity versus rehabilitation exercise” were identified. Generally, the participants found the home-based rehabilitation exercise boring but were motivated by the goal of returning to their habitual conduct of everyday life and perform their usual general physical activities. Participants enrolled in the PHETHAS-1 study used the enrollment as part of their motivation for doing the exercises.

Both pain and no pain were identified as barriers for doing the home-based rehabilitation exercise. Pain could cause insecurity while no pain could cause the rehabilitation exercise to be perceived as pointless.

Conclusions

The overall goal for the THA patients was to return to their habitual everyday life. This goal served as a facilitator for undertaking home-based rehabilitation exercise. Being able to perform their usual activities paradoxically became a barrier for some of the participants, as they were more motivated towards general physical activity than the rehabilitation exercise.

Contribution of paper

Key messages

Patients undergoing total hip arthroplasty have goal of returning to their habitual everyday life doing their usual physical activities.

Home-based rehabilitation exercise can be perceived as boring and time-consuming and the goal of returning to their habitual everyday life serves as a facilitator to perform the rehabilitation exercise.

What this paper adds

Both pain and no pain can be a barrier to performing home-based rehabilitation exercise.

Pain can cause uncertainty as to whether performing an exercise could be harmful, while no pain can cause the rehabilitation exercise to be perceived as pointless.

Standard care patients tend to modify the rehabilitation program as they are gradually able to perform their usual general physical activities.

Enrolment in clinical studies and contact with health professionals can facilitate adherence to home-based rehabilitation exercise.

Trial identifier

NCT03109821
Pneumococcal colonization impairs nasal and lung mucosal immune responses to Live Attenuated Influenza Vaccination in adults
Authors: Carniel Beatriz F. , Marcon Fernando , Rylance Jamie , Zaidi Seher , Reine Jesus , Negera Edessa , Nikolaou Elissavet , Pojar Sherin , Solórzano Carla , Collins Andrea , Connor Victoria , Bogaert Debby , Gordon Stephen B. , Nakaya Helder , Ferreira Daniela M. , Jochems Simon P. , Mitsi Elena
Published: February 2020

Influenza virus infections affect millions of people annually. Current available vaccines provide varying rates of protection. There is a knowledge gap on how the nasal microbiota, particularly established pneumococcal colonization, shapes the response to influenza vaccination. In this study, we inoculated healthy adults with liveS. pneumoniaeand vaccinated them three days later with either TIV or LAIV. Vaccine-induced immune responses were assessed in nose, blood and lung. Nasal pneumococcal colonization had no impact upon TIV-induced antibody responses to influenza, which manifested in all compartments. However, pre-existing pneumococcal colonization dampened LAIV-mediated mucosal antibody responses, primarily IgA in the nose and IgG in the lung. Pulmonary influenza-specific cellular responses were more apparent in the LAIV group compared to either TIV or an unvaccinated group. These results indicate that TIV and LAIV elicit differential immunity to adults and that LAIV immunogenicity is diminished by the nasal presence ofS. pneumoniae. This important confounder should be considered when assessing LAIV efficacy.
Recovering Mandibular Morphology after Disease with Artificial Intelligence
Authors: Liang Ye , Huan JingJing , Li Jia-Da , Jiang CanHua , Fang ChangYun , Liu YongGang
Published: February 2020

Mandibular tumors and radical oral cancer surgery often cause bone dysmorphia and defects. Most patients present with noticeable mandibular deformations, and doctors often have difficulty determining their exact mandibular morphology. In this study, a deep convolutional generative adversarial network (DCGAN) called CTGAN is proposed to complete 3D mandibular cone beam computed tomography (CBCT) data from CT data. After extensive training CTGAN was tested on 6 mandibular tumor cases, resulting in 3D virtual mandibular completion. We found that CTGAN can generate mandibles with different levels and rich morphology, including positional and angular changes and local patterns. The completion results are shown as tomographic images combining generated and natural areas. The 3D generated mandibles have the anatomical morphology of the real mandibles and transition smoothly to the portions without disease, showing that CTGAN constructs mandibles with the expected patient characteristics and is suitable for mandibular morphological completion. The presented modeling principles can be applied to other areas for 3D morphological completion from medical images.

Clinical trial registration

This study is not a clinical trial. Patient data were only used for testing in a virtual environment. The use of digital data used in this study was ethically approved.
A high dimensional quantification of mouse defensive behaviours reveals enhanced diversity and stimulus specificity
Authors: Storchi Riccardo , Milosavljevic Nina , Allen Annette E. , Zippo Antonio G. , Agnihotri Aayushi , Cootes Timothy F. , Lucas Robert J.
Published: February 2020

Instinctive defensive behaviours, consisting of stereotyped sequences of movements and postures, are an essential component of the mouse behavioural repertoire. Since defensive behaviours can be reliably triggered by threatening sensory stimuli, the selection of the most appropriate action depends on the stimulus property. However, since the mouse has a wide repertoire of motor actions, it is not clear which set of movements and postures represent the relevant action. So far this has been empirically identified as a change in locomotion state. However, the extent to which locomotion alone captures the diversity of defensive behaviours and their sensory specificity is unknown.

To tackle this problem we developed a method to obtain a faithful 3D reconstruction of the mouse body that enabled to quantify a wide variety of motor actions. This higher dimensional description revealed that defensive behaviours are more stimulus-specific than indicated by locomotion data. Thus, responses to distinct stimuli that were equivalent in terms of locomotion (e.g. freezing induced by looming and sound) could be discriminated along other dimensions. The enhanced stimulus-specificity was explained by a surprising diversity. A clustering analysis revealed that distinct combinations of movements and postures, giving rise to at least 7 different behaviours, were required to account for stimulus-specificity. Moreover, each stimulus evoked more than one behaviour revealing a robust one-to-many mapping between sensations and behaviours that was not apparent from locomotion data. Our results indicate that diversity and sensory specificity of mouse defensive behaviours unfold in a higher dimensional space spanning multiple motor actions.
A Novel Index for Predicting Health Status Using Species-level Gut Microbiome Profiling
Authors: Gupta Vinod K. , Kim Minsuk , Bakshi Utpal , Cunningham Kevin Y. , Davis John M. , Lazaridis Konstantinos N. , Nelson Heidi , Chia Nicholas , Sung Jaeyun
Published: February 2020

The development of a biologically-interpretable and robust metric that provides clear insight into the general health status (i.e. healthy or non-healthy) of one’s gut microbiome remains an important target in human microbiome research. We introduce the Gut Microbiome Health Index (GMHI), a mathematical formula that determines the degree to which a gut microbiome profile reflects good or adverse health. GMHI was formulated based on microbial species specific to healthy gut ecosystems. These species were identified through a multi-study, integrative analysis on 4,347 human stool metagenomes from 34 published studies across healthy and 12 different disease or abnormal bodyweight conditions. When demonstrated on our population-scale meta-dataset, GMHI is the most robust and consistent predictor of general health compared to α-diversity indices commonly considered as markers for gut health. Validation of GMHI on 679 samples from 9 additional studies resulted in remarkable reproducibility in distinguishing healthy and non-healthy groups. Our findings suggest that gut taxonomic signatures can indeed serve as robust predictors of general health, and highlight the importance of how data sharing efforts can provide broadly-applicable novel discoveries.
PCV2 aggravated SS2 infection directly showed from differentially expressed proteome of PK15 cells
Authors: Jimin Tan , Qi Xiao , Xingguang Li , Hongjie Fan , Kongwang He
Published: February 2020

PCV2 and SS2 were clinically two major pathogens in pigs and they were zoonotic pathogens. There was extensive cellular tropism for both PCV2 and SS2, as well as, PK15 cells was PCV2 infection mainly cell model. It was found that when PCV2 infected PK15 cells before at the MOI=0.1, SS2 could cause more damage to PK15 cells. ITRAQ labeling proteomic technology was used to explore the differentially expressed proteome of PCV2 and SS2 single infection and co-infection in PK15 cells. The results showed that there were total 4736 proteins distinct changed in this infection models for PK15 cells. PCV2 aggravated SS2 infection were showed directly in the big amount of differentially expressed proteins like AGO3, OSBPL1A, ALB, RIC8A, UBL4A, INTS5 and so on. For the KEGG pathway analysis, it indicated that PCV2 mainly induced the proteins lessen though a series of disease pathway like metabolic pathways, huntington’s disease, insulin signaling pathways, long-term depression, etc. to make cell at a state of compensation. PCV2 before infection made the cells was on the chopping block. Contemporary, SS2 induced the proteins of PK15 rapidly changing, including pathways like spliceosome, endoplasmic reticulum, tight junction, actin cytoskeleton and some involved in parasitic infections pathways like ECM-receptor interaction, Leishmaniasis, Toxoplasmosis and so on. Simultaneously, PCV2 and SS2 existed common ground that they influence PK15 cell by some virulence factor interacted with cytomembrane, influenced the function of ribosome and tRNA. The role of SS2 in the co-infection like a cook chopper.
Ecdysone steroid hormone remote controls intestinal stem cell fate decisions via thePPARγ-homologEip75BinDrosophila
Authors: Zipper Lisa , Jassmann Denise , Burgmer Sofie , Görlich Bastian , Reiff Tobias
Published: February 2020

Developmental studies revealed fundamental principles on how organ size and function is achieved, but less is known about organ adaptation to new physiological demands. In fruit flies, juvenile hormone (JH) induces intestinal stem cell (ISC) driven absorptive epithelial expansion balancing energy uptake with increased energy demands of pregnancy. Here, we show 20-Hydroxy-Ecdysone (20HE)-signaling controlling organ homeostasis with physiological and pathological implications. Upon mating, 20HE titer in ovaries and hemolymph are increased and act on nearby midgut progenitors inducingEcdysone-induced-protein-75B (Eip75B). Strikingly, thePPARγ-homologueEip75Bdrives ISC daughter cells towards absorptive enterocyte lineage ensuring epithelial growth. To our knowledge, this is the first time a systemic hormone is shown to direct local stem cell fate decisions. Given the protective, but mechanistically unclear role of steroid hormones in female colorectal cancer patients, our findings suggest a tumor-suppressive role for steroidal signaling by promoting postmitotic fate when local signaling is deteriorated.
Transparent and flexible ECoG electrode arrays based on silver nanowire networks for neural recordings
Authors: Neto Joana P. , Costa Adriana , Vaz Pinto Joana , Marques–Smith André , Costa Júlio , Martins Rodrigo , Fortunato Elvira , Kampff Adam R. , Barquinha Pedro
Published: February 2020

This work explored hybrid films of silver nanowires (AgNWs) with indium-zinc oxide (IZO) for developing high-performance and low-cost electrocorticography (ECoG) electrodes. The transparent hybrid films achieved a sheet resistance of 6 Ω/sq enabling electrodes with 500 μm diameter to reach an impedance of 20 kΩ at 1 kHz and a charge storage capacity of 3.2 mC/cm2, an improvement in properties over IZO electrodes, whose performance is on par with the classical tin doped indium oxide (ITO). Characterization of light-induced artifacts was performed showing that light intensities <14 mW/mm2elicit minimal electrical potential variation, which falls within the magnitude of baseline noise. The validation of electrodes in vivo was achieved by recording electrical neural activity from the surface of rat cortex under anaesthesia. Moreover, the presence of the hybrid films did not cause distortion of light during fluorescence microscopy. This study highlighted the capabilities of the hybrid structure of AgNWs with IZO, that can be fabricated with industrially-established processes at low cost, to be used for transparent ECoG electrodes, offering a new way to record neural electrical activity on a large and fast scale with direct visualization of neurons.
A streamlined workflow for automated cryo focused ion beam milling
Authors: Tacke Sebastian , Erdmann Philipp , Wang Zhexin , Klumpe Sven , Grange Michael , Plitzko Jürgen M. , Raunser Stefan
Published: February 2020

Cryo-electron tomography is an emerging technique to study the cellular architecture and the structure of proteins at high resolutionin situ. Most biological specimens are too thick to be directly investigated and are therefore thinned by milling with a focused ion beam under cryogenic conditions. This procedure is prone to frost and amorphous ice depositions which makes it a tedious process, leading to suboptimal results especially when larger batches are milled. Here, we present new hardware that overcomes the current limitations. We developed a new glove box and a high vacuum cryo transfer system and installed a stage heater, a cryo-shield and a cryo-shutter in the FIB milling microscope. This tremendously reduces the ice depositions during transfer and milling, and simplifies the handling of the sample. In addition, we tested a new software application that automates the key milling steps. Together, these improvements allow for high-quality, high-throughput cryo-FIB milling.
Neutral auditory words immediately followed by painful electric shock show reduced next-day recollection
Authors: Norton Caroline M. , Ibinson James W. , Pcola Samantha J. , Popov Vencislav , Tremel Joshua J. , Reder Lynne M. , Fiez Julie A. , Vogt Keith M.
Published: February 2020

In this study, we investigated the effect of experimentally delivered acute pain on explicit and implicit memory. Twenty-five subjects participated in experimental sessions on consecutive days. The first session involved a categorization task intended to induce incidental memory encoding. There were two conditions, presented in randomized order, in which subjects listened to a series of words, which was repeated three times. In one condition, one-third of the word items were immediately followed by a painful electrical shock and these pain-paired items were presented unpredictably. In the other condition, all word items were not associated with pain. Response times over these repeated presentations were assessed for differences. Explicit memory was tested the following day, employing a Remember-Know assessment of word recognition, with no shocks employed. Recollection was significantly reduced for pain-paired words, as the proportion of correct Remember responses (out of total correct responses) was significantly lower. There were no significant reductions in memory for non-pain items that followed painful stimulation after a period of several seconds. Consistent with the experience of pain consuming working memory resources, we theorize that painful shocks interrupt memory encoding for the immediately preceding experimental items, due to a shift in attention away from the word item.
Normalizing and denoising protein expression data from droplet-based single cell profiling
Authors: Mulè Matthew P. , Martins Andrew J. , Tsang John S.
Published: February 2020

Multimodal single-cell protein and transcriptomic profiling (e.g. CITE-seq) holds promise for comprehensive dissection of cellular heterogeneity, yet protein counts measured by oligo-conjugated-antibody can have substantial noise that masks biological variations. Here we integrated experiments and computational analysis to reveal two major noise sources: protein-specific noise from unbound antibodies and cell-specific noise captured by the shared variance of isotype controls and background protein counts. We provide an open source R package (dsb) to denoise and normalize CITE-seq data based on these findings. (https://cran.r-project.org/web/packages/dsb/index.html).
Whole Slide Preview Image Segmentation and Setup for Digital Pathology Scanners
Authors: Hosseini Mahdi S. , Lee Dohyoung , Gershanik Daniel , Lee Dongwoon , Damaskinos Savvas , Plataniotis Konstantinos N.
Published: February 2020

The problem of tissue finding is of special interest in automating WSI scanners where it decomposes the preview image of tissue glass slides into a simplified and abstract level of localization and identification to setup WSI scanner for high-resolution scan. Prior to such scanning, a preview image is captured to calibrate the scanner’s parameters. Scan parameters such as focus depth and scan region are determined using a tissue finding software package. This paper introduces a series of pipelines (e.g. binary mask segmentation, tissue/artifact classification, region-of-interest allocation) to automate tissue preview segmentation in both brightfield and darkfield microscopy.
Knockdown of CSNK2β suppresses MDA-MB231 cells growth, induces apoptosis, inhibits migration and invasion
Authors: Lal Karna Shibendra Kumar , Lone Bilal Ahmad , Ahmad Faiz , Shahi Nerina , Pokharel Yuba Raj
Published: February 2020

Breast cancer is most common cancer among women worldwide and among different types of breast cancer treatment of triple-negative breast cancer is major challenge, thus identification of specific drivers is required for targeted therapies of this malignancy. The aim of the present study is to elucidate the effects of silencing of CSNK2β gene by small interfering RNA (siRNA) on proliferation, cell cycle and apoptosis in breast carcinoma MDA MB-231 cells. Silencing of CSNK2β in MDA-MB-231(a triple negative cell line) cells resulted in decreased cell viability and colony formation. Cell cycle analysis showed that silencing of CSNK2β arrested MDA MB-231 cells in G2/M phase. We demonstrated that silencing of CSNK2β promoted nuclear condensation and augmented intracellular ROS production. Furthermore, Silencing of CSNK2β in MDA-MB 231 cells modulated the apoptotic machinery- BAX, Bcl-xL and caspase 3; autophagy machinary-Beclin-1 and LC3-1; and inhibited the vital markers (p-ERK, c-Myc, NF-κB, E2F1, PCNA, p38-α) associated with cell proliferation and DNA replication pathways. In addition, Knocking down of CSNK2 β also affected the migration potential of MDA-MB231 as observed in the wound healing and transwell migration assays. Together, our study suggests that CSNK2β silencing may offer future therapeutic target in triple negative breast cancer.
Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing
Authors: Silvestre-Ryan Jordi , Holmes Ian
Published: February 2020

Nanopore technology allows for direct sequencing of individual DNA duplexes. However, its higher error rate compared to other sequencing methods has limited its application in situations where deep coverage is unavailable, such as detection of rare variants or characterization of highly polymorphic samples. In principle, 2X coverage is available even for single duplexes, using Oxford Nanopore Technologies’ 1D2protocol or related methods which sequence both strands of the duplex consecutively. Using both strands should improve accuracy; however, most neural network basecaller architectures are designed to operate on single strands. We have developed a general approach for improving accuracy of 1D2and related protocols by finding the consensus of two neural network basecallers, by combining a constrained profile-profile alignment with a heuristic variant of beam search. When run on a basecalling neural network we trained, our consensus algorithm improves median basecall accuracy from 86.2% (for single-read decoding) to 92.1% (for pair decoding). Our software can readily be adapted to work with the output of other basecallers, such as the recently released Bonito basecaller. Although Bonito operates only on individual strands and was not designed to leverage the 1D2protocol, our method lifts its median accuracy from 93.3% to 97.7%, more than halving the median error rate. This surpasses the maximum accuracy achievable with Guppy, an alternate basecaller which was designed to include pair decoding of 1D2reads. Our software PoreOver, including both our neural network basecaller and our consensus pair decoder (which can be separably applied to improve other basecallers), is implemented in Python 3 and C++11 and is freely available athttps://github.com/jordisr/poreover.
Using Major Depression Polygenic Risk Scores to Explore the Depressive Symptom Continuum
Authors: Jermy Bradley S , Hagenaars Saskia P , Glanville Kylie P , Coleman Jonathan RI , Howard David M , Breen Gerome , Vassos Evangelos , Lewis Cathryn M
Published: February 2020

Background

It is not clear whether major depression (MD) is a categorical disorder or if depressive symptoms exist on a continuum based on severity. Observational studies comparing sub-threshold and clinical depression suggest MD is continuous, but many do not explore the full continuum and are yet to consider genetics as a risk factor. This study sought to understand if polygenic risk for MD could provide insight into the continuous nature of MD.

Methods

Factor analysis on symptom-level data from the UK Biobank (N=148,957) was used to derive continuous depression phenotypes which were tested for association with polygenic risk scores for a categorical definition of MD (N=119,692).

Results

Confirmatory factor analysis showed a five-factor hierarchical model, incorporating 15 of the original 18 items, produced good fit to the observed covariance matrix (CFI = 0.992, TLI = 0.99, RMSEA = 0.038, SRMR = 0.031). MD PRS associated with each factor score (standardised ß range: 0.057 – 0.064) and the association remained when the sample was stratified into case- and control-only subsets. The case-only subset had an increased association compared to controls for all factors, shown via a significant interaction between lifetime MD diagnosis and MD PRS (p-value range: 2.28×10−3- 4.56×10−7).

Conclusions

An association between MD PRS and a continuous phenotype of depressive symptoms in case- and control-only subsets provides support against a purely categorical phenotype; indicating further insights into MD can be obtained when this within-group variation is considered. The stronger association within cases suggests this variation may be of particular importance.
X-ray and solution structures of human beta-2 glycoprotein I reveal a new mechanism of autoantibody recognition
Authors: Ruben Eliza , Planer William , Chinnaraj Mathivanan , Chen Zhiwei , Zuo Xiaobing , Pengo Vittorio , Filippis Vincenzo De , Alluri Ravi K. , McCrae Keith R. , Macor Paolo , Tedesco Francesco , Pozzi Nicola
Published: February 2020

Venous and arterial thromboses in patients suffering from the autoimmune disorder Antiphospholipid Syndrome (APS) are caused by the presence of antiphospholipid antibodies (aPL). Emerging evidence indicates that autoantibodies targeting the epitope R39-R43 in the N-terminal domain, Domain I (DI), of β2-glycoprotein I (β2GPI) are among the most pathogenic aPL in patients with APS. How such autoantibodies engage β2GPI at the molecular level remains incompletely understood. Here, we have used X-ray crystallography, single-molecule FRET, and small-angle X-ray scattering to demonstrate that, in the free form, under physiological pH and salt concentrations, human recombinant β2GPI adopts an elongated, flexible conformation in which DI is exposed to the solvent, thus available for autoantibody recognition. Consistent with this structural model, binding and mutagenesis studies revealed that the elongated form interacts with a pathogenic anti-DI antibody in solution, without the need of phospholipids. Furthermore, complex formation was affected neither by the neighboring domains, nor by the presence of the linkers, nor by the glycosylations. Since the pathogenic autoantibody requires residues R39 and R43 for optimal binding, these findings challenge longstanding postulates in the field envisioning β2GPI adopting immunologic inert conformations featuring inaccessibility of the epitope R39-R43 in DI and support an alternative model whereby the preferential binding of anti-DI antibodies towards phospholipid-bound β2GPI arises from the ability of the pre-existing elongated form to bind to the membranes and then oligomerize, processes that are likely to be supported by protein conformational changes. Interfering with these steps may limit the pathogenic effects of anti-DI antibodies in APS patients.

Significance

In the autoimmune disorder called Antiphospholipid Syndrome (APS), the presence of autoantibodies targeting the plasma glycoprotein beta-2 glycoprotein I (β2GPI) is associated with arterial and venous thrombosis as well as pregnancy complications. Understanding how β2GPI becomes immunogenic and how autoantibodies in complex with β2GPI cause the blood to clot remains a top priority in the field. By elucidating the structural architecture of β2GPI free in solution, our studies challenge longstanding postulates in the field and shed new light on the pathogenic mechanisms of APS that may help the development of new diagnostics and therapeutic approaches.
Purple bacteria as added-value protein ingredient in shrimp feed:Litopenaeus vannameigrowth performance, and tolerance againstVibrioand ammonia stress
Authors: Alloul Abbas , Wille Mathieu , Lucenti Piergiorgio , Bossier Peter , Van Stappen Gilbert , Vlaeminck Siegfried E.
Published: February 2020

Purple non-sulfur bacteria (PNSB) biomass is an emerging alternative protein source, yet research of PNSB as added-value protein ingredient is limited. This research aimed to study the use of PNSB as protein source for shrimp and investigate the shrimp’s tolerance againstVibrioand ammonia stress. A 28-day shrimp feeding trial was performed withRhodopseudomonas palustris, Rhodobacter capsulatusand a mixed PNSB culture. PNSB contained in feed (5-10% protein substitution) resulted in 5-26% higher individual weights, better feed conversions ratios (1.2-1.7) compared to commercial feed (1.7) and tolerance against ammonia. In parallel, the effect of PNSB on the growth ofVibriopathogens was testedin vitro.The speciesRps. palustris, Rb. capsulatus, Rb. sphaeroides, Rhodospirillum rubrumandAfifella marinasuppressed the growth ofVibrio parahaemolyticusTW01 andV. campbelliiLMG 21363. Overall, this study demonstrated the potential of PNSB as nutritious feed ingredient for shrimp. This can contribute to circular economy, as PNSB enable resource recovery from wastewater.

Abstract Figure

Graphical abstract

Highlights

Purple non-sulfur bacteria (PNSB) enhance the growth performance of shrimp

PNSB-fed shrimp has better feed conversion ratio, growth rate and weight gain

Shrimp fed withRhodopseudomonasare more resistance against ammonia stress

Freeze-dried and live PNSB inhibitVibriopathogensin vitro
Three-dimensional synaptic organization of the human hippocampal CA1 field
Authors: Montero-Crespo Marta , Domínguez-Álvaro Marta , Rondón-Carrillo Patricia , Alonso-Nanclares Lidia , DeFelipe Javier , Blázquez-Llorca Lidia
Published: February 2020

The hippocampal CA1 field integrates a wide variety of subcortical and cortical inputs, but its synaptic organization in humans is still unknown due to the difficulties involved studying the human brain via electron microscope techniques. However, we have shown that the 3D reconstruction method using Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) can be applied to study in detail the synaptic organization of the human brain obtained from autopsies, yielding excellent results. Using this technology, 24,752 synapses were fully reconstructed in CA1, revealing that most of them were excitatory, targeting dendritic spines and displaying a macular shape, regardless of the layer examined. However, remarkable differences were observed between layers. These data constitute the first extensive description of the synaptic organization of the neuropil of the human CA1 region.
The occurrence of tarsal injuries in male mice of C57BL/6N substrains in multiple international mouse facilities
Authors: Herbert Eleanor , Stewart Michelle , Hutchison Marie , Flenniken Ann M. , Qu Dawei , Nutter Lauryl M. J. , McKerlie Colin , Hobson Liane , Kick Brenda , Lyons Bonnie , Wiegand Jean-Paul , Doty Rosalinda , Aguilar-Pimentel Juan Antonio , Hrabe de Angelis Martin , Dickinson Mary , Seavitt John , White Jacqueline K. , Scudamore Cheryl L , Wells Sara
Published: February 2020

Dislocation in hindlimb tarsals are being observed at a low, but persistent frequency in adult male mice from C57BL/6N substrains. Clinical signs included a sudden onset of mild to severe unilateral or bilateral tarsal abduction, swelling, abnormal hindlimb morphology and lameness. Contraction of digits and gait abnormalities were noted in multiple cases. Radiographical and histological examination revealed caudal dislocation of the calcaneus and partial dislocation of the calcaneoquartal (calcaneous-tarsal bone IV) joint. The detection, frequency, and cause of this pathology in five large mouse production and phenotyping centres (MRC Harwell, UK; The Jackson Laboratory, USA; The Centre for Phenogenomics, Canada; German Mouse Clinic, Germany; Baylor College of Medicine, USA) are discussed.