bluuebunny/crossref_metadata_2025 huggingface dataset:
Partial RdRp sequences offer a robust method for Coronavirus subgenus classification
Authors: Wilkinson David A , Joffrin Lea , Lebarbenchon Camille , Mavingui Patrick
Published: March 2020

The recent reclassification of theRiboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (familyCoronaviridae, subfamilyOrthocoronavirinae) represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardisation for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a partial region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with genome-scale analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses is sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, “MyCoV”, which provides a method for attributing subgenus and assessing the reliability of the attribution.

Importance Statement

The analysis of polymerase chain reaction amplicons derived from biological samples is the most common modern method for detection and classification of infecting viral agents, such as Coronaviruses. Recent updates to the official standard for taxonomic classification of Coronaviruses, however, may leave researchers unsure as to whether the viral sequences they obtain by these methods can be classified into specific viral taxa due to variations in the sequences when compared to type strains. Here, we present a plausible method for defining genetic dissimilarity cut-offs that will allow researchers to state which taxon their virus belongs to and with what level of certainty. To assist in this, we also provide the R package ‘MyCoV’ which classifies user generated sequences.
Transmission interval estimates suggest pre-symptomatic spread of COVID-19
Authors: Tindale Lauren C. , Coombe Michelle , Stockdale Jessica E. , Garlock Emma S. , Lau Wing Yin Venus , Saraswat Manu , Lee Yen-Hsiang Brian , Zhang Louxin , Chen Dongxuan , Wallinga Jacco , Colijn Caroline
Published: March 2020

Background

As the COVID-19 epidemic is spreading, incoming data allows us to quantify values of key variables that determine the transmission and the effort required to control the epidemic. We determine the incubation period and serial interval distribution for transmission clusters in Singapore and in Tianjin. We infer the basic reproduction number and identify the extent of pre-symptomatic transmission.

Methods

We collected outbreak information from Singapore and Tianjin, China, reported from Jan.19-Feb.26 and Jan.21-Feb.27, respectively. We estimated incubation periods and serial intervals in both populations.

Results

The mean incubation period was 7.1 (6.13, 8.25) days for Singapore and 9 (7.92, 10.2) days for Tianjin. Both datasets had shorter incubation periods for earlier-occurring cases. The mean serial interval was 4.56 (2.69, 6.42) days for Singapore and 4.22 (3.43, 5.01) for Tianjin. We inferred that early in the outbreaks, infection was transmitted on average 2.55 and 2.89 days before symptom onset (Singapore, Tianjin). The estimated basic reproduction number for Singapore was 1.97 (1.45, 2.48) secondary cases per infective; for Tianjin it was 1.87 (1.65, 2.09) secondary cases per infective.

Conclusions

Estimated serial intervals are shorter than incubation periods in both Singapore and Tianjin, suggesting that pre-symptomatic transmission is occurring. Shorter serial intervals lead to lower estimates of R0, which suggest that half of all secondary infections should be prevented to control spread.
Epidemiological and clinical features of 291 cases with coronavirus disease 2019 in areas adjacent to Hubei, China: a double-center observational study
Authors: Chen Xu , Zheng Fang , Qing Yanhua , Ding Shuizi , Yang Danhui , Lei Cheng , Yin Zhilan , Zhou Xianglin , Jiang Dixuan , Zuo Qi , He Jun , Lv Jianlei , Chen Ping , Chen Yan , Peng Hong , Li Honghui , Xie Yuanlin , Liu Jiyang , Zhou Zhiguo , Luo Hong
Published: March 2020

Background

The clinical outcomes of COVID-19 patients in Hubei and other areas are different. We aim to investigate the epidemiological and clinical characteristics of patient with COVID-19 in Hunan which is adjacent to Hubei.

Methods

In this double-center, observational study, we recruited all consecutive patients with laboratory confirmed COVID-19 from January 23 to February 14, 2020 in two designated hospitals in Hunan province, China. Epidemiological and clinical data from patients’ electronic medical records were collected and compared between mild, moderate and severe/critical group in detail. Clinical outcomes were followed up to February 20, 2020.

Findings

291 patients with COVID-19 were categorized into mild group (10.0%), moderate group (72.8%) and severe/critical group (17.2%). The median age of all patients was 46 years (49.8% were male). 86.6% patients had an indirect exposure history. The proportion of patients that had been to Wuhan in severe/critical group (48.0% vs 17.2%, p=0.006) and moderate group (43.4% vs 17.2%, p=0.007) were higher than mild group. Fever (68.7%), cough (60.5%), and fatigue (31.6%) were common symptoms especially for severe and critical patients. Typical lung imaging finding were bilateral and unilateral ground glass opacity or consolidation. Leukopenia, lymphopenia and eosinopenia occurred in 36.1%, 22.7% and 50.2% patients respectively. Increased fibrinogen was detected in 45 of 58 (77.6%) patients with available results. 29 of 44 (65.9%) or 22 of 40 (55.0%) patients were positive in Mycoplasma pneumonia or Chlamydia pneumonia antibody test respectively. Compared with mild or moderate group, severe/critical group had a relative higher level of neutrophil, Neutrophil-to-Lymphocyte Ratio, h-CRP, ESR, CK, CK–MB, LDH, D-dimer, and a lower level of lymphocyte, eosinophils, platelet, HDL and sodium (all p<0.01). Most patients received antiviral therapy and Chinese Medicine therapy. As of February 20, 2020, 159 (54.6%) patients were discharged and 2 (0.7%) patients died during hospitalization. The median length of hospital stay in discharged patients was 12 days (IQR: 10-15).

Interpretation

The epidemiological and clinical characteristics of COVID-19 patients in Hunan is different from patients in Wuhan. The proportion of patients that had been to Wuhan in severe/critical group and moderate group were higher than mild group. Laboratory and imaging examination can assist in the diagnosis and classification of COVID-19 patients.
Restoration of leukomonocyte counts is associated with viral clearance in COVID-19 hospitalized patients
Authors: Chen Xiaoping , Ling Jiaxin , Mo Pingzheng , Zhang Yongxi , Jiang Qunqun , Ma Zhiyong , Cao Qian , Hu Wenjia , Zou Shi , Chen Liangjun , Yao Lei , Luo Mingqi , Chen Tielong , Deng Liping , Liang Ke , Song Shihui , Yang Rongrong , Zheng Ruiying , Gao Shicheng , Gui Xien , Ke Hengning , Hou Wei , Lundkvist Åke , Xiong Yong
Published: March 2020

Background

Viral clearance is one important indicator for the recovery of SARS-CoV-2 infected patients. Previous studies have pointed out that suboptimal T and B cell responses can delay viral clearance in MERS-CoV and SARS-CoV infected patients. The role of leukomonocytes in viral clearance of COVID-19 patients is not yet well defined.

Methods

From January 26 to February 28, 2020, an observational study was launched at the Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China. We enrolled 25 laboratory-confirmed COVID-19 patients, whose throat-swab specimens were tested positive for SARS-CoV-2 infection by qRT-PCR. To investigate the factors that contribute to the viral clearance, we comprehensively analyzed clinical records, counts of lymphocyte subsets including CD3+, CD4+, CD8+ T cells, B cells and NK cells in the patients who successfully cleared SARS-CoV-2, and compared to those that failed to, after a standardized treatment of 8-14 days.

Findings

In 25 enrolled COVID-19 patients, lymphopenia was a common feature. After the treatment, 14 out of the 25 enrolled patients were tested negative for SARS-CoV-2. The patients that cleared the infection had restored the numbers of CD3+, CD4+, CD8+ T cells and B cells as compared to the still viral RNA positive patients, while the recovered patients had a higher count of leukomonocytes.

Conclusions

By comparison of leukomonocytes counts in COVID-19 patients at different stages of the disease, we found that CD3+, CD4+, CD8+ T cells and B cells appear to play important roles in viral clearance. The restoration of leukomonocytes counts from peripheral blood can be used as prognosis for the recovery of an COVID-19 infection. We propose that restoration of leukomonocytes counts can be added to the COVID-19 diagnostic guidance as a criterion for releasing and discharging patients.
Increased Expression of Colonic Mucosal Melatonin in Patients with Irritable Bowel Syndrome Correlated with Gut Dysbiosis
Authors: Wang Ben , Zhu Shiwei , Liu Zuojing , Wei Hui , Zhang Lu , Pei Fei , He Meibo , Zhang Jindong , Sun Qinghua , Duan Liping
Published: March 2020

Dysregulation of the gut microbiota/gut hormone axis contributes to the pathogenesis of irritable bowel syndrome (IBS). Melatonin plays a beneficial role in gut motility and immunity. However, altered expression of local mucosal melatonin in IBS and its relationship with the gut microbiota remain unclear. Therefore, we aimed to detect the colonic melatonin levels and microbiota profiles in patients with diarrhea-predominant IBS (IBS-D) and explore their relationship in germ-free (GF) rats and BON-1 cells. Thirty-two IBS-D patients and twenty-eight healthy controls (HC) were recruited. Fecal specimens from IBS-D patients and HCs were separately transplanted into GF rats by gavage. The levels of colon mucosal melatonin were assessed by immunohistochemical methods, and fecal microbiota communities were analyzed using 16S rDNA sequencing. The effect of butyrate on melatonin synthesis in BON-1 cells was evaluated by ELISA. Melatonin levels were significantly increased in IBS-D patients compared with HC and were significantly negatively correlated with visceral sensitivity in IBS-D patients. GF rats inoculated with fecal microbiota from IBS-D patients had high colonic melatonin levels. Butyrate-producing Clostridium cluster XIVa species, such as Roseburia species and Lachnospira species, were positively related to colonic mucosal melatonin expression. Butyrate significantly increased melatonin secretion in BON-1 cells. Increased melatonin expression may be an adaptive protective mechanism in the development of IBS-D. Moreover, some Clostridium cluster XIVa species could increase melatonin expression via butyrate production. Modulation of the gut hormone/gut microbiota axis offers a promising target of interest for IBS in the future.
Key Points of Clinical and CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV) Imported Pneumonia Based On 21 Cases Analysis
Authors: Xu Z.F. , Wu W.X. , Jin Y.B. , Pan A.Z.
Published: March 2020

Background and Objective

WHO Director-General declared that the 2019-nCoV outbreak constitutes a Public Health Emergency of International Concern,and the outbreak is still on-going.Chest CT had been a key component of the diagnostic workup for patients with suspected infection. In this retrospective study, we attempt to summarize and analyze the chest CT features of 2019-nCov infections, and to identify the typical features to improved the diagnostic accuracy of new coronavirus pneumonia (NCP).

Methods

Chest CT scans and Clinical data of 21 patients confirmed NCP in our hospital were enrolled.These patients were divided into mild and sever group according to clinical manifestations described by the 6th clinical practice guideline of NCP in China. Main clinical and chest CT features were analyzed and identify.

Results

Fever (85.7%) and cough (80.9%) were the two main symptoms of NCP patients.More significantly higher incidence (85.7%) of shortness of breath in the severe cases. Multiple lesions in both lungs and with incidence of GGO(100%),vascular enlargement (76.5%) and cobblestone/reticular pattern(70.6%) were the major feature.The incidence of consolidation, mixed pattern and vascular enlargement features were up to 100% in the severe group, significantly higher than that of patients in mild group. In addition, the incidence of air-bronchogram, dilated bronchi with thickened wall and fibrosis in the severe group was significantly higher than that in the mild group.

Conclusions

Fever and cough are the typical clinical features of NCP patients, and chest CT mainly manifested as multiple lesions in both lungs, often accompanied by GGO, vascular enlargement and cobblestone/reticular pattern.Changes in these main CT features can indicate development of the disease

2019 novel Coronavirus (2019-nCov) had typical clinical manifestations (fever and cough), and presented with characteristic chest CT imaging features (multiple lesions in both lungs, often accompanied by GGO, vascular enlargement and cobblestone/reticular pattern), which are helpful to the radiologist in the early detection and diagnosis of this emerging global health emergency. In addition, changes in these main CT features can indicate development of the disease.

Highlights

Fever (85.7%) and cough (80.9%) were the two main symptoms of NCP patients.The incidence of shortness of breath was 85.7% in the severe cases, significantly higher than 21.4% in the mild cases.

Multiple lesions in both lungs and with incidence of GGO (100%), vascular enlargement (76.5%) and cobblestone/reticular pattern (70.6%) were the major features of NCP patients. 85.7% of cases in serve group displayed 4-5 lobes were involved simultaneously.

Changes in these main CT imaging features can indicate development of the disease. About 19.1% of patients (4 of 21) presented with a normal CT.
Psychological impact of the coronavirus disease 2019 (COVID-19) outbreak on healthcare workers in China
Authors: Dai Yuhong , Hu Guangyuan , Xiong Huihua , Qiu Hong , Yuan Xianglin
Published: March 2020

Introduction

Since the outbreak of coronavirus disease 2019 (COVID-19), more than 3000 (including clinical diagnosis) healthcare workers (HCWs) have been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China. This study is aimed to investigate the risk perception and immediate psychological state of HCWs in the early stage of the COVID-19 epidemic.

Methods

This study utilized a cross-sectional survey designed on a convenient sample of 4357 HCWs in China. Its data were collected using anonymous structured questionnaires distributed through social software. 6 questions were set to evaluate the participants’ risk perception of COVID-19, and a General Health Questionnaire was used to identify the participants’ immediate psychological status. Descriptive statistics were used for data analysis. Risk perception and psychological status were compared by demographic characteristics and COVID-19 exposure experiences.

Result

A total of 4,600 questionnaires were distributed, and 4,357 qualified ones (94.7%) were collected. The main concerns of HCWs are: infection of colleagues (72.5%), infection of family members (63.9%), protective measures (52.3%) and medical violence (48.5%). And 39.1% of the HCWs had psychological distress, especially working in Wuhan, participating in frontline treatments, having been isolated and having family members or colleagues infected.

Conclusions

The finding indicating that, faced with the COVID-19 epidemic, HCWs, especially in Wuhan, were worried about the risks of infection and protective measures, resulting in psychological distress, so further actions should be taken.
Influence of spatial structure on protein damage susceptibility – A bioinformatics approach
Authors: Fichtner Maximilian , Schuster Stefan , Stark Heiko
Published: March 2020

Aging research is a very popular field of research in which the gradual transformation of functional states into dysfunctional states are studied. Here we only consider the molecular level, which can also have effects on the macroscopic level. It is known that the proteinogenic amino acids differ in their modification susceptibilities and this can affect the function of proteins. For this it is important to know the distribution of amino acids between the protein surface/shell and the core. This was investigated in this study for all known structural data of peptides and proteins. As a result it is shown that the surface contains less susceptible amino acids than the core with the exception of thermophilic organisms. Furthermore, proteins could be classified according to their susceptibility. This can then be used in applications such as phylogeny, aging research, molecular medicine and synthetic biology.
A neural code for egocentric spatial maps in the human medial temporal lobe
Authors: Kunz Lukas , Brandt Armin , Reinacher Peter C. , Staresina Bernhard P. , Reifenstein Eric T. , Weidemann Christoph T. , Herweg Nora A. , Tsitsiklis Melina , Kempter Richard , Kahana Michael J. , Schulze-Bonhage Andreas , Jacobs Joshua
Published: March 2020

Spatial navigation relies on neural systems that encode information about places, distances, and directions in relation to the external world or relative to the navigating organism. Since the proposal of cognitive maps, the neuroscience of navigation has focused on allocentric (world-referenced) neural representations including place, grid, and head-direction cells. Here, using single-neuron recordings during virtual navigation, we identify “anchor cells” in the human brain as a neural code for egocentric (self-centered) spatial maps: Anchor cells represent egocentric directions towards “anchor points” located in the environmental center or periphery. Anchor cells were abundant in parahippocampal cortex, supported full vectorial representations of egocentric space, and were integrated into a neural memory network. Neurons encoding allocentric direction complemented anchor-cell activity, potentially assisting anchor cells in transforming percepts into allocentric representations. Anchor cells may facilitate egocentric navigation strategies, may support route planning from egocentric viewpoints, and may underlie the first-person perspective in episodic memories.
Ex-VivoEquine Cartilage Explant Osteoarthritis Model - A Metabolomics and Proteomics Study
Authors: Anderson James R , Phelan Marie M , Foddy Laura , Clegg Peter D , Peffers Mandy J
Published: March 2020

Osteoarthritis (OA) is an age-related degenerative musculoskeletal disease characterised by loss of articular cartilage, synovitis, abnormal bone proliferation and subchondral bone sclerosis. Underlying OA pathogenesis is yet to be fully elucidated with no OA specific biomarkers in clinical use.Ex-vivoequine cartilage explants (n=5) were incubated in TNF-α/IL-1β supplemented culture media for 8 days, with media removed and replaced at 2, 5 and 8 days. Acetonitrile metabolite extractions of 8 day cartilage explants and media samples at all time points underwent 1D1H nuclear magnetic resonance metabolomic analysis with media samples also undergoing mass spectrometry proteomic analysis. Within the cartilage, metabolites glucose and lysine were elevated following TNF-α/IL-1β treatment whilst adenosine, alanine, betaine, creatine, myo-inositol and uridine levels decreased. Within the culture media, four, four and six differentially abundant metabolites and 154, 138 and 72 differentially abundant proteins, with > 2 fold change, were identified for 1-2 day, 3-5 day and 6-8 day time points respectively. Nine potential novel OA neopeptides were elevated in treated media. Our innovative study has identified differentially abundant metabolites, proteins and extracellular matrix derived neopeptides, providing insightful information on OA pathogenesis, enabling potential translation for clinical markers and possible new therapeutic targets.
Deletion of Autophagy geneATG1and Glyoxylate cycle Regulator encoding geneUCC1together leads to Synthetic Growth Defects and Sensitivity to Genotoxic agents inSaccharomyces cerevisiae
Authors: Pandita Monika , Sharma Vishali , Sharma Meenu , Shoket Heena , Parvez Sadia , Kumar Prabhat , Bairwa Narendra K
Published: March 2020

Atg1 ofS. cerevisiaeis a key component of autophagy encoded byATG1gene, involved in the process of degradation of cytosolic components through autophagy.UCC1, an F-box encoding gene is involved in the negative regulation of glyoxylate pathway via degradation of Cit2 enzyme by ubiquitin proteasome system. We investigated the genetic interaction betweenATG1andUCC1using the gene deletion approach. Theatg1Δucc1Δcells showed the synthetic growth defects with abnormal budding and sensitivity to genotoxic and oxidative stress agents. Based on the observations, we report thatATG1andUCC1interact genetically to regulate the cell growth fitness and function in parallel pathway in cellular response to the genotoxic stress agents. The present investigation also revealed the cross talks among autophagy, ubiquitin proteasome system, and glyoxylate pathways.
Identification of an Aggregation Pheromone from the Small Hive Beetle (Coleoptera: Nitidulidae)
Authors: Stuhl Charles J. , Teal Peter E. A.
Published: March 2020

Newly emerged adult small hive beetleAethina tumida(Coleoptera: Nitidulidae) emerge from the soil and seek refuge in honey bee hives. Observations of wild and colony reared populations indicate that the beetles form aggregations of many individuals of both sexes. Volatile collections performed on males and females have identified a male produced aggregation pheromone comprised of 6-methyl-5-hepten-2-one, nonanal and decanal. Synergistic effects of the pheromone and a blend of fruit volatiles provide for an effective attractant for both sexes of the small hive beetle. Laboratory assays were performed with the pheromone blend and kairomone blend tested individually combined. This was done using a synthetic aggregation blend along with a fruit-based attractant containing ethanol, ethyl butyrate, acetic acid, ethyl acetate and acetaldehyde. Our results showed that the synthetic aggregation blend along with a fruit-based attractant captured significantly more beetles than the control. The key to a good trapping system is and effective attractant. Our pheromone/kairomone based attractant shows promise to be used as an effective outside the hive control measure for small hive beetle. The identification of the aggregation pheromone is an important step in the search to provide effective control and monitoring of the small hive beetle.
Analysis of structural brain asymmetries in Attention-Deficit/Hyperactivity Disorder in 39 datasets
Authors: Postema Merel C. , Hoogman Martine ,   ENIGMA ADHD Working Group, Glahn David C. , Jahanshad Neda , Medland Sarah E. , Thompson Paul M. , Fisher Simon E. , Franke Barbara , Francks Clyde
Published: March 2020

Objective

Some studies have suggested alterations of structural brain asymmetry in attention-deficit/hyperactivity disorder (ADHD), but findings have been contradictory and based on small samples. Here we performed the largest-ever analysis of brain left-right asymmetry in ADHD, using 39 datasets of the ENIGMA consortium.

Methods

We analyzed asymmetry of subcortical and cerebral cortical structures in up to 1,978 people with ADHD and unaffected 1,917 controls. Asymmetry Indexes (AIs) were calculated per participant for each bilaterally paired measure, and linear mixed effects modelling was applied separately in children, adolescents, adults, and the total sample, to test exhaustively for potential associations of ADHD with structural brain asymmetries.

Results

There was no evidence for altered caudate nucleus asymmetry in ADHD, in contrast to prior literature. In children, there was less rightward asymmetry of the total hemispheric surface area compared to controls (t=2.4,P=0.019). Lower rightward asymmetry of medial orbitofrontal cortex surface area in ADHD (t=2.4,P=0.007) was similar to a recent finding for autism spectrum disorder. There were also some differences in cortical thickness asymmetry across age groups. In adults with ADHD, globus pallidus asymmetry was altered compared to those without ADHD. However, all effects were small (Cohen’sdfrom −0.18 to 0.18) and would not survive study-wide correction for multiple testing.

Conclusion

Prior studies of altered structural brain asymmetry in ADHD were likely underpowered to detect the small effects reported here. Altered structural asymmetry is unlikely to provide a useful biomarker for ADHD, but may provide neurobiological insights into the trait.
Variance in within-pair reproductive success influences the opportunity for selection annually and over the lifetimes of males in a multi-brooded songbird
Authors: Germain Ryan R. , Hallworth Michael T. , Kaiser Sara A. , Sillett T. Scott , Webster Michael S.
Published: March 2020

In socially monogamous species, male reproductive success consists of ‘within-pair’ offspring produced with their socially-paired mate(s), and ‘extra-pair’ offspring produced with additional females throughout the population. Both reproductive pathways offer distinct opportunities for selection in wild populations, as each is composed of separate components of mate attraction, female fecundity, and paternity allocation. Identifying key sources of variance and covariance among these components is a crucial step towards understanding the reproductive strategies that males use to maximize fitness both annually and over their lifetimes. We use 16 years of complete reproductive data from a population of black-throated blue warblers (Setophaga caerulescens) to partition variance in male annual and lifetime reproductive success, and thereby identify if the opportunity for selection varies over the lifetimes of individual males and what reproductive strategies likely favor maximum lifetime fitness. The majority of variance in male reproduction was attributable to within-pair success, but the specific effects of individual components of variance differed between total annual and total lifetime reproductive success. Positive overall lifetime covariance between within-pair and extra-pair components indicates that males able to maximize within-pair success, particularly with double-brooding females, likely achieve higher overall lifetime fitness via both within-pair and extra-pair reproductive pathways.
A lineage-tracing tool to map the fate of hypoxic tumour cells
Authors: Vermeer Jenny A.F. , Ient Jonathan , Markelc Bostjan , Kaeppler Jakob , Barbeau Lydie M.O. , Groot Arjan J. , Muschel Ruth J. , Vooijs Marc A.
Published: March 2020

Intratumoural hypoxia is a common characteristic of malignant treatment-resistant cancers. However, hypoxia-modification strategies for the clinic remain elusive. To date little is known on the behaviour of individual hypoxic tumour cells in their microenvironment. To explore this issue in a spatial and temporally-controlled manner we developed a genetically encoded sensor by fusing the O2-labile Hypoxia-Inducible Factor 1α to eGFP and a tamoxifen-regulated Cre recombinase. Under normoxic conditions HIF-1α is degraded but under hypoxia, the HIF-1α-GFP-Cre-ERT2fusion protein is stabilised and in the presence of tamoxifen activates a tdTomato reporter gene that is constitutively expressed in hypoxic progeny. We visualise the random distribution of hypoxic tumour cells from hypoxic or necrotic regions and vascularised areas using immunofluorescence and intravital microscopy. Once tdTomato expression is induced, it is stable for at least 4 weeks. Using this system, we could show that the post-hypoxic cells were more proliferativein vivothan non-labelled cells. Our results demonstrate that single-cell lineage tracing of hypoxic tumour cells can allow visualisation of their behaviour in living tumours using intravital microscopy. This tool should prove valuable for the study of dissemination and treatment response of post-hypoxic tumour cellsin vivoat single-cell resolution.

Summary Statement

Here we developed and characterised a novel HIF-1α-Cre fusion gene to trace the progeny of hypoxic tumour cells in a temporal and spatially resolved manner using intravital microscopy.
Phenotypic and microsite plant individual variation determine the pollination network structure and its functional consequences
Authors: Arroyo-Correa Blanca , Bartomeus Ignasi , Jordano Pedro
Published: March 2020

The biotic and abiotic context of individual plants in animal-pollinated plant populations may influence pollinator foraging behaviour and therefore how the pollen flow occurs. Thus, this variation among conspecifics within a given plant population can ultimately influence the plant reproductive success. Here we used a fine-scale, well characterized population ofHalimium halimifoliumin combination with exponential random graph models (ERGMs) to assess how the intrapopulation variation in intrinsic (i.e. phenotype and phenology) and extrinsic (i.e. microsite) plant attributes configures individual plant-pollinator networks and its functional consequences. We found that pollinator visitation patterns and the emerging network configuration were associated with both intrinsic and extrinsic plant attributes, such as the number of flowers, the flowering synchrony and the cover of intraspecific and interspecific neighbours. Both intrinsic and extrinsic plant attributes also affected the plant female reproductive success directly and indirectly - through its effects on the probability of conspecifics plants to share pollinators. Our study opens up new approaches to assess and predict the functional consequences of context-dependency in plant-pollinator interactions, especially under global change scenarios, where the ecological context of individual plants is likely to change.
CRISPR-mediated Multiplexed Live Cell Imaging of Nonrepetitive Genomic Loci
Authors: Clow Patricia A. , Du Menghan , Jillette Nathaniel , Taghbalout Aziz , Zhu Jacqueline J. , Cheng Albert W.
Published: March 2020

Three-dimensional (3D) structures of the genome are dynamic, heterogeneous and functionally important. Live cell imaging has become the leading method for chromatin dynamics tracking. However, existing CRISPR- and TALE-based genomic labeling techniques have been hampered by laborious protocols and are ineffective in labeling non-repetitive sequences. Here, we report a versatile CRISPR/Casilio-based imaging method that allows for a nonrepetitive genomic locus to be labeled using one guide RNA. We construct Casilio dual-color probes to visualize the dynamic interactions of DNA elements in single live cells in the presence or absence of the cohesin subunit RAD21. Using a three-color palette, we track the dynamic 3D locations of multiple reference points along a chromatin loop. Casilio imaging reveals intercellular heterogeneity and interallelic asynchrony in chromatin interaction dynamics, underscoring the importance of studying genome structures in 4D.
Differential impacts of repeated sampling on odor representations by genetically-defined mitral and tufted cell subpopulations in the mouse olfactory bulb
Authors: Eiting Thomas P. , Wachowiak Matt
Published: March 2020

Sniffing—the active control of breathing beyond passive respiration—is used by mammals to modulate olfactory sampling. Sniffing allows animals to make odor-guided decisions within ~200 ms, but animals routinely engage in bouts of high-frequency sniffing spanning several seconds; the impact of such repeated odorant sampling on odor representations remains unclear. We investigated this question in the mouse olfactory bulb, where mitral and tufted cells (MTCs) form parallel output streams of odor information processing. To test the impact of repeated odorant sampling on MTC responses, we used two-photon imaging in anesthetized male and female mice to record activation of MTCs while precisely varying inhalation frequency. A combination of genetic targeting and viral expression of GCaMP6 reporters allowed us to access mitral (MC) and superficial tufted cell (sTC) subpopulations separately. We found that repeated odorant sampling differentially affected responses in MCs and sTCs, with MCs showing more diversity than sTCs over the same time period. Impacts of repeated sampling among MCs included both increases and decreases in excitation, as well as changes in response polarity. Response patterns across ensembles of simultaneously-imaged MCs reformatted over time, with representations of different odorants becoming more distinct. MCs also responded differentially to changes in inhalation frequency, whereas sTC responses were more uniform over time and across frequency. Our results support the idea that MCs and TCs comprise functionally distinct pathways for odor information processing, and suggest that the reformatting of MC odor representations by high-frequency sniffing may serve to enhance the discrimination of similar odors.
AIDeveloper: deep learning image classification in life science and beyond
Authors: Kräter Martin , Abuhattum Shada , Soteriou Despina , Jacobi Angela , Krüger Thomas , Guck Jochen , Herbig Maik
Published: March 2020

Publications on artificial intelligence (AI)-based image analysis have increased drastically in recent years. However, all applications use individual solutions highly specialized for a particular task. Here, we present an easy-to-use, adaptable, open source software, called AIDeveloper (AID) to train neural nets (NN) for image classification without the need for programming. The software provides a variety of NN-architectures that can be simply selected for training. AID allows the user to apply trained models on new data, obtain metrics for classification performance, and export final models to different formats. The working principles of AID are first illustrated by training a convolutional neural net (CNN) on a large dataset consisting of images of different objects (CIFAR-10). We further explore the potential of AID by training a model to distinguish areas of differentiated and non-differentiated mesenchymal stem cells (MSCs) in culture. Additionally, we compare a conventional clinical whole blood cell count with a whole blood cell count performed by an NN-trained, using a dataset of more than 1.2 million images obtained by real-time deformability cytometry, delivering comparable results. Finally, we demonstrate how AID can be used for label-free classification of B- and T-cells derived from human blood, which currently requires costly and time-consuming sample preparation. Thus, AID can empower anyone to develop, train, and apply NNs for image classification. Moreover, models can be generated by non-programmers, exported, and used on different devices, which allows for an interdisciplinary use.
A Comprehensive Analysis of the Phylogenetic Signal in Ramp Sequences in 211 Vertebrates
Authors: McKinnon Lauren M. , Miller Justin B. , Whiting Michael F. , Kauwe John S.K. , Ridge Perry G.
Published: March 2020

Background

Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented.

Methods

Ramp sequences were compared from 211 vertebrates (110 Mammalian and 101 non-mammalian). The presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life taxonomy to determine the number of parallelisms and reversals that occurred, and these results were compared to what would be expected due to random chance. Lastly, aligned nucleotides in ramp sequences were compared to the rest of the sequence in order to examine possible differences in phylogenetic signal between these regions of the gene.

Results

Parsimony and maximum likelihood analyses of the presence/absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, the retention index of ramp sequences is significantly higher than would be expected due to random chance (p-value = 0). A chi-square analysis of completely orthologous ramp sequences resulted in a p-value of approximately zero as compared to random chance.

Discussion

Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches.
GmVTL1 is an iron transporter on the symbiosome membrane of soybean with an important role in nitrogen fixation
Authors: Brear Ella M. , Bedon Frank , Gavrin Aleksandr , Kryvoruchko Igor S. , Torres-Jerez Ivone , Udvardi Michael K. , Day David A. , Smith Penelope M.C.
Published: March 2020

Legumes establish symbiotic relationships with soil bacteria (rhizobia), housed in nodules on plant roots. The plant supplies carbon substrates and other nutrients to the bacteria in exchange for fixed nitrogen. The exchange occurs across a plant-derived symbiosome membrane (SM), which encloses rhizobia to form a symbiosome. Iron supplied by the plant is crucial for the rhizobial enzyme nitrogenase that catalyses N2fixation, but the SM iron transporter has not been identified.

We use complementation of yeast and plant mutants, real-time PCR, hairy root transformation, microscopy and proteomics to demonstrate the role of soybean GmVTL1 and 2.

Both are members of the vacuolar iron transporter family and homologous toLotus japonicusSEN1 (LjSEN1), previously shown to be essential for N2fixation.GmVTL1expression is enhanced in nodule infected cells and both proteins are localised to the SM.

GmVTL1 and 2 transport iron in yeast and GmVTL1 restores N2fixation when expressed in theLjsen1mutant.

Three GmVTL1 amino acid substitutions that reduce iron transport in yeast also block N2fixation inLjsen1plants.

We conclude GmVTL1 is responsible for transport of iron across the SM to bacteroids and plays a crucial role in the N2-fixing symbiosis.
Clinical Features of Patients Infected with the 2019 Novel Coronavirus (COVID-19) in Shanghai, China
Authors: Cao Min , Zhang Dandan , Wang Youhua , Lu Yunfei , Zhu Xiangdong , Li Ying , Xue Honghao , Lin Yunxiao , Zhang Min , Sun Yiguo , Yang Zongguo , Shi Jia , Wang Yi , Zhou Chang , Dong Yidan , Peng Longping , Liu Ping , Dudek Steven M. , Xiao Zhen , Lu Hongzhou
Published: March 2020

Background

Since mid-December 2019, a cluster of pneumonia-like diseases caused by a novel coronavirus, now designated COVID-19 by the WHO, emerged in Wuhan city and rapidly spread throughout China. Here we identify the clinical characteristics of COVID-19 in a cohort of patients in Shanghai.

Methods

Cases were confirmed by real-time RT-PCR and were analysed for demographic, clinical, laboratory and radiological features.

Results

Of 198 patients, the median duration from disease onset to hospital admission was 4 days. The mean age of the patients was 50.1 years, and 51.0% patients were male. The most common symptom was fever. Less than half of the patients presented with respiratory systems including cough, sputum production, itchy or sore throat, shortness of breath, and chest congestion. 5.6% patients had diarrhoea. On admission, T lymphocytes were decreased in 45.8% patients. Ground glass opacity was the most common radiological finding on chest computed tomography. 9.6% were admitted to the ICU because of the development of organ dysfunction. Compared with patients not treated in ICU, patients treated in the ICU were older, had longer waiting time to admission, fever over 38.5° C, dyspnoea, reduced T lymphocytes, elevated neutrophils and organ failure.

Conclusions

In this single centre cohort of COVID-19 patients, the most common symptom was fever, and the most common laboratory abnormality was decreased blood T cell counts. Older age, male, fever over 38.5°C, symptoms of dyspnoea, and underlying comorbidity, were the risk factors most associated with severity of disease.
Utility of circulating tumor DNA for detection and monitoring of endometrial cancer recurrence and progression
Authors: Moss Esther L. , Gorsia Diviya N. , Collins Anna , Sandhu Pavandeep , Foreman Nalini , Gore Anu , Wood Joey , Kent Christopher , Silcock Lee , Guttery David S.
Published: March 2020

Despite the increasing incidence of endometrial cancer (EC) worldwide and the poor overall survival of patients who recur, no reliable biomarker exists for detecting and monitoring EC recurrence and progression during routine follow-up. Circulating tumor DNA (ctDNA) is a sensitive method for monitoring cancer activity and stratifying patients that are likely to respond to therapy. As a pilot study, we investigated the utility of ctDNA for detecting and monitoring EC recurrence and progression in 13 patients using targeted next-generation sequencing (tNGS) and personalized ctDNA assays. Using tNGS, at least 1 somatic mutation at a variant allele frequency (VAF) >20% was detected in 69% (9/13) of patient tumors. The four patients with no detectable tumor mutations at >20% VAF were whole exome sequenced, with all four harboring mutations in genes not analyzed by tNGS. Analysis of matched and longitudinal plasma DNA revealed earlier detection of EC recurrence and progression and dynamic kinetics of ctDNA levels reflecting treatment response. We also detected acquired high microsatellite instability (MSI-H) in ctDNA from one patient whose primary tumor was MSI stable. Our study suggests that ctDNA analysis, and in particular MSI analysis in ctDNA could become a useful biomarker for early detection and monitoring of EC recurrence and progression.
Study of the mental health status of medical personnel dealing with new coronavirus pneumonia
Authors: Xing Jun , Sun Ning , Xu Jun , Geng Shuling , Li Yuqian
Published: March 2020

Objective

This paper studied the relationship between personality traits and mental health conditions of medical personnel to provide a basis and reference for the implementation of targeted education on mental health.

Methods

A self-report inventory, the Symptom Checklist-90 (SCL-90), was used to investigate the mental health status of 548 medical personnel dealing with the new coronavirus pneumonia in eight provinces and cities of China.

Results

The overall mean SCL-90 score and mean values of factors (somatization, obsessive-compulsive, anxiety, phobic anxiety, and psychoticism) of the medical personnel were significantly higher than in the norm group (p < 0.05), while their average interpersonal sensitivity score was significantly lower (p < 0.01). In addition, personal factors affecting the mental health status of medical personnel were identified. ( all p < 0.05).

Conclusion

The overall mental health status of medical personnel responding to new coronavirus pneumonia is generally higher than that of the norm group in China. The results of this study should contribute to measures to alleviate the psychological pressures on medical personnel dealing with the new coronavirus epidemic in China.
Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period
Authors: Kissler Stephen M. , Tedijanto Christine , Goldstein Edward M. , Grad Yonatan H. , Lipsitch Marc
Published: March 2020

There is an urgent need to project how transmission of the novel betacoronavirus SARS-CoV-2 will unfold in coming years. These dynamics will depend on seasonality, the duration of immunity, and the strength of cross-immunity to/from the other human coronaviruses. Using data from the United States, we measured how these factors affect transmission of human betacoronaviruses HCoV-OC43 and HCoV-HKU1. We then built a mathematical model to simulate transmission of SARS-CoV-2 through the year 2025. We project that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after an initial pandemic wave. We summarize the full range of plausible transmission scenarios and identify key data still needed to distinguish between them, most importantly longitudinal serological studies to determine the duration of immunity to SARS-CoV-2.
The impact of social distancing and epicenter lockdown on the COVID-19 epidemic in mainland China: A data-driven SEIQR model study
Authors: Zhang Yuzhen , Jiang Bin , Yuan Jiamin , Tao Yanyun
Published: March 2020

The outbreak of coronavirus disease 2019 (COVID-19) which originated in Wuhan, China, constitutes a public health emergency of international concern with a very high risk of spread and impact at the global level. We developed data-driven susceptible-exposed-infectious-quarantine-recovered (SEIQR) models to simulate the epidemic with the interventions of social distancing and epicenter lockdown. Population migration data combined with officially reported data were used to estimate model parameters, and then calculated the daily exported infected individuals by estimating the daily infected ratio and daily susceptible population size. As of Jan 01, 2020, the estimated initial number of latently infected individuals was 380.1 (95%-CI: 379.8∼381.0). With 30 days of substantial social distancing, the reproductive number in Wuhan and Hubei was reduced from 2.2 (95%-CI: 1.4∼3.9) to 1.58 (95%-CI: 1.34∼2.07), and in other provinces from 2.56 (95%-CI: 2.43∼2.63) to 1.65 (95%-CI: 1.56∼1.76). We found that earlier intervention of social distancing could significantly limit the epidemic in mainland China. The number of infections could be reduced up to 98.9%, and the number of deaths could be reduced by up to 99.3% as of Feb 23, 2020. However, earlier epicenter lockdown would partially neutralize this favorable effect. Because it would cause in situ deteriorating, which overwhelms the improvement out of the epicenter. To minimize the epidemic size and death, stepwise implementation of social distancing in the epicenter city first, then in the province, and later the whole nation without the epicenter lockdown would be practical and cost-effective.