bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimates of regional infectivity of COVID-19 in the United Kingdom following imposition of social distancing measures
Authors: Challen Robert , Tsaneva-Atanasova Krasimira , Pitt Martin , Edwards Tom , Gompels Luke , Lacasa Lucas , Brooks-Pollock Ellen , Martin Chris , Griffith Gareth , Danon Leon
Published: April 2020

We describe regional variation in the reproduction number of SARS-CoV-2 infections observed using publicly reported data in the UK, with a view to understanding both if there are clear hot spots in viral spread in the country, or other spatial patterns. Based on case data up to the 9th April, we estimate that the viral replication number remains above 1 overall in the UK but that its trend is to decrease. This suggests the peak of the first wave of COVID-19 patients is imminent. We find that there is significant regional variation in the UK and that this is changing over time. Within England currently the reproductive ratio is lowest in the Midlands (1.11 95% CI 1.07; 1.14), and highest in the North East of England (1.38 95% CI 1.33-1.42). There are long and variable time delays between infection and detection of cases, and thus it remains unclear whether the reduction in the reproductive number is a result of social distancing measures. If we are to prevent further outbreaks, it is critical that we both reduce the time taken for detection and improve our ability to predict the regional spread of outbreaks.
Comparison of psychological distress and demand induced by COVID-19 during the lockdown period in patients undergoing peritoneal dialysis and hemodialysis: a cross-section study in a tertiary hospital
Authors: Xia Xiaoxiao , Wu Xiaofang , Zhou Xueli , Zang Zhiyun , Pu Li , Li Zi
Published: April 2020

Background

Since the outbreak of COVID-19 in December 2019, it has spread rapidly and widely, bringing great psychological pressure to the public. In order to prevent the epidemic, lockdown was required in many areas of China, which led to inconvenience of treatment for dialysis patients. To explore the psychological distress and the psychological demand induced by COVID-19 in the patients undergoing dialysis and compare the difference between hemodialysis (HD) and peritoneal (PD) patients during the lockdown period.

Methods

Questionnaires were given to the dialysis patients in West China Hospital of Sichuan University. The Impact of Event Scale (IES) was used to investigate the patients’ trauma-related distress in response to COVID-19.

Results

232 eligible respondents were enrolled in this cross-section study, consisting of 156 PD patients and 76 HD patients. The median IES score for all the enrolled patients was 8.00 (2.00-19.00), which belonged to the subclinical dimension of post-traumatic stress symptoms. HD patients had a significant higher IES score than PD patients (11.50 vs 8.00) (p<0.05). HD patients already got more psychological support from the medical staff. There was no significant difference on further demand of psychological support between the two groups. In the multivariate regression analysis, we found that dialysis vintage, the impact of COVID-19 on the severity of illness and daily life, and confidence in overcoming the disease contributed to IES score (p<0.05).

Conclusions

HD patients had more severe trauma-related stress symptoms than PD patients. When major public healthy events occurred, careful psychological estimate and sufficient psychological support should be provided to the dialysis patients, especially to the HD patients.
SimCOVID: Open-Source Simulation Programs for the COVID-19 Outbreak
Authors: Abdulrahman Ismael
Published: April 2020

This paper presents open-source computer simulation programs developed for simulating, tracking, and estimating the COVID-19 outbreak. The programs consist of two separate parts: one set of programs built in Simulink with a block diagram display, and another one coded in MATLAB as scripts. The mathematical model used in this package is the SIR, SEIR, and SEIRD models represented by a set of differential-algebraic equations. It can be easily modified to develop new models for the problem. A generalized method is adopted to simulate worldwide outbreaks in an efficient, fast, and simple way. To get a good tracking of the virus spread, a sum of sigmoid functions was proposed to capture any dynamic changes in the data. The parameters used for the input (infection and recovery rate functions) are computed using the parameter estimation tool in MATLAB. Several statistic methods were applied for the rate function including linear, mean, root-mean-square, and standard deviation. In addition, an adaptive neuro-fuzzy inference system is employed and proposed to train the model and predict its output. The programs can be used as a teaching tool and for research studies.
“Knowledge and practices towards COVID-19 during its outbreak: a multinational cross-sectional study”
Authors: Naser Abdallah Y , Dahmash Eman Zmaily , Alwafi Hassan , Alsairafi Zahra Khalil , Rajeh Ahmed M. Al , Alhartani Yosra J , Turkistani Fawaz Mohammad , Alyami Hamad S.
Published: April 2020

Background

The emergence of COVID-19 globally coupled with its unknown aetiology and its high transmission rate has created an unprecedented state of emergency worldwide. Public knowledge and awareness about COVID-19 are essential in suppressing its pandemic status.

Method

A cross-sectional study using an online survey was conducted between 19th of March and 6th of April 2020 in three Middle Eastern countries (Jordan, Saudi Arabia and Kuwait) to explore the knowledge and practices of Middle Eastern population towards COVID-19. A previously developed questionnaire was used. Multiple linear regression analysis was used to identify predictors of COVID-19 knowledge.

Results

A total of 1,208 participants were involved in this study from the three countries (Jordan = 389, Saudi Arabia = 433, and Kuwait = 386). The majority of participants (n = 810, 67.2%) were females and aged 30 to 49 years (n = 501, 41.5%). Participants had moderate overall COVID-19 knowledge with a mean score of 7.93 (±1.72) out of 12, 66.1%. Participants had better knowledge about disease prevention and control with 83.0%, whereas the lowest sub-scale scores were for questions about disease transmission routes (43.3%). High education level was an important predictor of greater COVID-19 knowledge scores (p<0.01).

Conclusion

Middle Eastern participants are of a relatively low level of knowledge about COVID-19, particularly regarding its transmission routes. Policymakers are recommended to develop informative COVID-19 related campaigns targeted specifically towards university students, unemployed individuals and those with lower levels of education.
Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries
Authors: Bryant Patrick , Elofsson Arne
Published: April 2020

Background

As governments across Europe have issued non-pharmaceutical interventions (NPIs) such as social distancing and school closing, the mobility patterns in these countries have changed. It is likely different countries and populations respond differently to the same NPIs and that these differences are reflected in the epidemic development.

Methods

We build a Bayesian model that estimates the number of deaths on a given day dependent on changes in the basic reproductive number, R0, due to changes in mobility patterns. We utilize mobility data from Google mobility reports using five different categories: retail and recreation, grocery and pharmacy, transit stations, workplace and residential. The importance of each mobility category for predicting changes in R0is estimated through the model.

Findings

The changes in mobility have a large overlap with the introduction of governmental NPIs, highlighting the importance of government action for population behavioural change. The grocery and pharmacy sector is estimated to account for 97 % of the reduction in R0(95% confidence interval [0·79,0·99]).

Interpretation

Our model predicts three-week epidemic forecasts, using real-time observations of changes in mobility patterns, which can provide governments with direct feedback on the effects of their NPIs. The model predicts the changes in a majority of the countries accurately but overestimates the impact of NPIs in Sweden and Denmark and underestimates them in France and Belgium.

Funding

Financial support: Swedish Research Council for Natural Science, grant No. VR-2016-06301 and Swedish E-science Research Center. Computational resources: Swedish National Infrastructure for Computing, grant No. SNIC-2019/3-319.
Severe underestimation of COVID-19 case numbers: effect of epidemic growth rate and test restrictions
Authors: Richterich Peter
Published: April 2020

To understand the scope and development of the COVID-19 pandemic, knowledge of the number of infected persons is essential. Often, the number of “confirmed cases”, which is based on positive RT-PCR test results, is regarded as a reasonable indicator. However, limited COVID-19 test capacities in many countries are restricting the amount of testing that can be done. This can lead to the implementation of testing policies that restrict access to COVID-19 tests, and to testing backlogs and delays. As a result, confirmed case numbers can be significantly lower than the actual number of infections, especially during rapid growth phases of the epidemic.

This study examines the quantitative relation between infections and reported confirmed case numbers for two different testing strategies, “limited” and “inclusive” testing, in relation to the growth rate of the epidemic. The results indicate that confirmed case numbers understate the actual number of infections substantially; during rapid growth phases where the daily growth rate can reach or exceed 30%, as has been seen in many countries, the confirmed case numbers under-report actual infections by up to 50 to 100-fold.
Estimating the number of SARS-CoV-2 infections in the United States
Authors: Thorpe Dayton G. , Lyberger Kelsey
Published: April 2020

We apply a model developed by The COVID-19 Response Team [S. Flaxman, S. Mishra, A. Gandy, et al., “Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in 11 European countries,” tech. rep., Imperial College London, 2020.] to estimate the total number of SARS-CoV-2 infections in the United States. Across the United States we estimate as of April 18, 2020 the fraction of the population infected was 4.6% [3.6%, 5.8%], 21 times the portion of the population with a positive test result. Excluding New York state, which we estimate accounts for over half of infections in the United States, we estimate an infection rate of 2.3% [2.1%, 2.8%].

We include the timing of each state’s implementation of interventions including encouraging social distancing, closing schools, banning public events, and a lockdown / stay-at-home order. We assume fatalities are reported correctly and infer the number and timing of infections based on the infection fatality rate measured in populations that were tested universally for SARS-CoV-2. Underreporting of deaths would drive our estimates to be too low. Reporting of deaths on the wrong day could drive errors in either direction. This model does not include effects of herd immunity; in states where the estimated infection rate is very high - namely, New York - our estimates may be too high.
Carbon Stock of Human-Disturbed Forest Areas in Bukidnon, Philippines
Authors: Medina Michael Arieh P. , Cabahug Vember C. , Zapico Gabriel Erico G.
Published: April 2020

A carbon stock assessment was done on two forest areas in Bukidnon, Philippines specifically in Mt. Kiamo in Kibalabag Village and Mt. Capistrano in Managok Village both in Malaybalay City, Bukidnon. Using a nested sampling design, tree diameter at breast height as well as tree height were measured. Allometric equations were then used to calculate for the above and below ground biomass density of trees. Destructive sampling was then employed to determine the biomass density of understory and litterfall, while composite sampling was done for soil analysis. Carbon content was then used to compute for the carbon stock of the different carbon pools in the studied ecosystems. The average biomass density of the two areas was found to be 247.80 Mg ha−1which are closely similar to other areas of the same forest type in Mindanao. Likewise the average carbon stock of the two areas is 143.14 MgC ha−1which is similar to tree plantations based on previous studies. Furthermore, the said carbon stock is approximately 40% lower than the country average for natural forests (250 MgC ha−1). The results demonstrate the extent of the diminishing carbon sequestration capability of forest areas due to human disturbance.
Pre operative fitness score accurately predicts uneventful post operative course in gastrointestinal and hepatobiliary surgery
Authors: Vasavada Bhavin , patel Hardik
Published: April 2020

Background

Aim of our study was to analyse if we can accurately predict uneventful post operative course pre operatively in gastrointestinal and HPB surgery patients.

Material and Methods

We retrospectively evaluated patients who have undergone gastrointestinal and hepatobiliary surgery at our institute in last 3 years and analysed 90 days mortality and morbidity rates among these patients. We described any 90 day morbidity and mortality as an “event”. We performed univariate and multivariate analyses for factors predicting an “event”. Then based on pre operative factors that predicted an “event” we formulated a score. Statistical analysis was done using SPSS version 23.

Results

Total 264 patient operated for gastrointestinal and HPB surgeries between April 2016 to may 2019 were evaluated .Total 45 (17%) events occurred. On univariate analysis CDC grade, ASA score,Operative time,Blood products used, emergency surgeries and open surgeries predicted an event. We developed score based on pre operative factors like ASA score, CDC grade of surgery,open surgery and emergency surgeries included in the score. We proposed score grater than 2 was associated with 90 day event. This score had sensitivity of 77.78%, specificity of 81.65%. low positive predictive value of 46.67% but very high negative predictive value of 94.68%. AUROC showed AUROC of 0.797 (p < 0.0001, 95% confidence interval 0.721-0.874). Pre operative fitness score, Open Surgery and operative time independently predicted an “event” on multivariate analysis. (p =0.003 and 0.026 respectively.

Conclusions

Pre operative fitness score accurately predicts uneventful post operative course in gastrointestinal and hepatobiliary surgery.
Pre transplant malnutrition predicts post transplant respiratory complications in living donor liver transplantation for biliary atresia- single center retrospective analysis of 110 children
Authors: Vasavada BB
Published: April 2020

Back Ground

Biliary atresia is commonly associated with malnutrition and failure to thrive. Very few studies have been published on impact of preoperative malnutrition of post transplant outcome in these children.

Material and Methods

110 children underwent living donor liver transplantation between January 2003 to march 2013.Pre transplant malnutrition was defined according to z scores for weight for age and height for age as per who definition. Patients having both Z score of < −2 were compared with control group. Statistical analysis were done using SPSS version 21 (IBM).

Results

39 children out of 110 were having z score for weight for age < −2.There was no statistical difference between PELD score, graft weight, GRWR, intraoperative blood loss between to groups. 22 out of 39 patients in malnourished group developed clavein grade 3,garde 4 complications and 32 patients out of 71 in control group developed clavien grade 3 grade 4 complications. (p= 0.318). Over all mortality rate was 4.5% and mortality rates in malnourished vs control group was respectively 7.69% and 2.81% (p= 0.278). Total 14 patient developed postoperative pulmonary complications. Pulmonary complications were significantly high in malnourished group. p=0.003.

Conclusion

Preoperative malnutrition is associated with high postoperative pulmonary complication rate in liver transplantation for biliary atresia.
lncRNA DLEU2 acts as a miR-181a sponge regulated SEPP1 (may as a biomarker for sarcopenia) to inhibit skeletal muscle differentiation and regeneration
Authors: Wang Yao , Kang Xue-ran , Chen Yisheng
Published: April 2020

Background

Sarcopenia is a serious public health problem. The ceRNA network has been demonstrated vital in the development of skeletal muscle, but there is currently no effective method to assess the risk of sarcopenia. The purpose of this research is to create and authenticate a ceRNA pathway based on a predictive model of sarcopenia.

Methods

A clinical prediction model for sarcopenia was established using the RNAs (validated by clinical data) that are co-differentially expressed in the database, and a ceRNA network was constructed. The correlation analysis of each element in the ceRNA network was performed according to the clinical samples and the GTEX database, and the possible key ceRNA pathways were screened. C2C12 mouse myoblast Cells experiments were used to verify these ceRNA pathways.

Findings

Based on four molecular markers of SEPP1, SV2A, GOT1 and GFOD1, we developed a new model for predicting sarcopenia with well accuracy, and constructed a ceRNA network accordingly. Clinical sample showed that the expression levels of lncDLEU2, SEPP1, and miR-181a were closely related to the risk of sarcopenia. The C2C12 mouse myoblast cells were cultivated to verify that lncDLEU2 inhibits muscle proliferation and differentiation by acting as a miR-181a sponge regulated SEPP1.

Interpretation

Our research developed a highly accurate prediction tool for the risk of sarcopenia. These findings suggest that lncDLEU2-miR-181a-SEPP1 pathway inhibits muscle differentiation and regeneration. This pathway may uncover some new therapeutic targets for the treatment of sarcopenia caused by aging.
Clinically adaptable polymer enables simultaneous spatial analysis of colonic tissues and biofilms
Authors: Macedonia Mary C. , Drewes Julia L. , Markham Nicholas O. , Simmons Alan J. , Roland Joseph T. , Vega Paige N. , Scurrah Cherie’ R. , Coffey Robert J. , Shrubsole Martha J. , Sears Cynthia L. , Lau Ken S.
Published: April 2020

Microbial influences on host cells depend upon the identities of the microbes, their spatial localization, and the responses they invoke on specific host cell populations. Multi-modal analyses of both microbes and host cells in a spatially-resolved fashion would enable studies into these complex interactions in native tissue environments, potentially in clinical specimens. While techniques to preserve each of the microbial and host cell compartments have been used to examine tissues and microbes separately, we endeavored to develop approaches to simultaneously analyze both compartments. Herein, we established an original method for mucus preservation using Poloxamer 407 (also known as Pluronic F-127), a thermoreversible polymer with mucus-adhesive characteristics. We demonstrate that this approach can preserve spatially-defined compartments of the mucus bi-layer in the colon and the bacterial communities within, compared with their marked absence when tissues were processed with traditional formalin-fixed paraffin-embedded (FFPE) pipelines. Additionally, antigens for antibody staining of host cells were preserved and signal intensity for 16S rRNA fluorescencein situhybridization (FISH) was enhanced in Poloxamer-fixed samples. This in turn enabled us to integrate multi-modal analysis using a modified multiplex immunofluorescence (MxIF) protocol. Importantly, we have formulated Poloxamer 407 to polymerize and crosslink at room temperature for use in clinical workflows. These results suggest that the fixative formulation of Poloxamer 407 can be integrated into biospecimen collection pipelines for simultaneous analysis of microbes and host cells.
High content live profiling reveals concomitant gain and loss of function pathomechanisms in C9ORF72 amyotrophic lateral sclerosis
Authors: Pal Arun , Kretner Benedikt , Abo-Rady Masin , Glaß Hannes , Naumann Marcel , Japtok Julia , Kreiter Nicole , Böckers Tobias M. , Sterneckert Jared , Hermann Andreas
Published: April 2020

Intronic hexanucleotide repeat expansions (HREs) in C9ORF72 are the most frequent genetic cause of amyotrophic lateral sclerosis (ALS), a devastating, incurable motoneuron (MN) disease. The mechanism by which HREs trigger pathogenesis remains elusive. The discovery of repeat-associated non-ATG (RAN) translation of dipeptide repeat proteins (DPRs) from HREs along with reduced exonic C9ORF72 expression suggests gain of toxic functions (GOF) through DPRs versus loss of C9ORF72 functions (LOF). Through multiparametric HC live profiling in spinal MNs from induced pluripotent stem cells (iPSCs) and comparison to mutant FUS and TDP43, we show that HRE C9ORF72 caused a distinct, later spatiotemporal appearance of mainly proximal axonal organelle motility deficits concomitant to augmented DNA strand breaks (DSBs), DPRs and apoptosis. We show that both GOF and LOF were necessary to yield the overall C9ORF72 pathology. Finally, C9ORF72 LOF was sufficient – albeit to a smaller extent – to induce proximal axonal trafficking deficits and increased DSBs.

Single sentence summary

Pathogenesis in C9ORF72 ALS shows a distinct spatiotemporal axonal organelle trafficking impairment caused by gain and loss of function mechanisms.
Computational synthesis of cortical dendritic morphologies
Authors: Kanari Lida , Dictus Hugo , Chalimourda Athanassia , Van Geit Werner , Coste Benoit , Shillcock Julian , Hess Kathryn , Markram Henry
Published: April 2020

Neuronal morphologies provide the foundation for the electrical behavior of neurons, the connectomes they form, and the dynamical properties of the brain. Comprehensive neuron models are essential for defining cell types, discerning their functional roles and investigating structural alterations associated with diseased brain states. Recently, we introduced a topological descriptor that reliably categorizes dendritic morphologies. We apply this descriptor to digitally synthesize dendrites to address the challenge of insufficient biological reconstructions. The synthesized cortical dendrites are statistically indistinguishable from the corresponding reconstructed dendrites in terms of morpho-electrical properties and connectivity. This topology-guided synthesis enables the rapid digital reconstruction of entire brain regions from relatively few reference cells, thereby allowing the investigation of links between neuronal morphologies and brain function across different spatio-temporal scales. We synthesized cortical networks based on structural alterations of dendrites associated with medical conditions and revealed principles linking branching properties to the structure of large-scale networks.

Graphical abstract

A topological model of neuronal shapes is used to investigate the link between the branching patterns of dendritic morphologies and the connectivity of the neuronal networks they form. Starting from reconstructed cells (in black) of cortical dendrites, we extract the topological barcode that is used to create a statistically similar synthesized pyramidal cell (in red), and respectively a group of pyramidal cells of the same morphological type. From reconstructed cells examples of all layers and morphological types we generate synthesized dendrites and build a synthesized cortical column (colors corresponds to cortical layers). The synthesized dedrites are statistically similar to the reconstructed dendrites in terms of morpho-electrical properties and the connectome of the synthesized column (colored connectome) is almost indistinguishable from the connectome of the reconstructed column (greyscale).
Classifying protein structures into folds by convolutional neural networks, distance maps, and persistent homology
Authors: Hong Yechan , Deng Yongyu , Cui Haofan , Segert Jan , Cheng Jianlin
Published: April 2020

The fold classification of a protein reveals valuable information about its shape and function. It is important to find a mapping between protein structures and their folds. There are numerous machine learning techniques to predict protein folds from 1-dimensional (1D) protein sequences, but there are few machine learning methods to directly class protein 3D (tertiary) structures into predefined folds (e.g. folds defined in the SCOP database). We develop a 2D-convolutional neural network to classify any protein structure into one of 1232 folds. We extract two classes of input features for each protein: residue-residue distance matrix and persistent homology images derived from 3D protein structures. Due to restrictions in computing resources, we sample every other point in the carbon alpha chain to generate a reduced distance map representation. We find that it does not lead to significant loss in accuracy. Using the distance matrix, we achieve an accuracy of 95.2% on the SCOP dataset. With persistence homology images of 100 × 100 resolution, we achieve an accuracy of 56% on SCOPe 2.07 dataset. Combining the two kinds of features further improves classification accuracy. The source code of our method (PRO3DCNN) is available athttps://github.com/jianlin-cheng/PRO3DCNN.
Deep Learning Improves Macromolecule Identification in 3D Cellular Cryo-Electron Tomograms
Authors: Moebel E. , Martinez-Sanchez A. , Lamm L. , Righetto R. , Wietrzynski W. , Albert S. , Larivière D. , Fourmentin E. , Pfeffer S. , Ortiz J. , Baumeister W. , Peng T. , Engel B.D. , Kervrann C.
Published: April 2020

Cryo-electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. While this label-free cryogenic imaging technology produces data containing rich structural information, automated identification of macromolecules inside cellular tomograms is challenged by noise and reconstruction artifacts, as well as the presence of many molecular species in the crowded volumes. Here, we present a computational procedure that uses artificial neural networks to simultaneously localize with a multi-class strategy several macromolecular species in cellular cryo-electron tomograms. Once trained, the inference stage of DeepFinder is significantly faster than template matching, and performs better than other competitive deep learning methods at identifying macromolecules of various sizes in both synthetic and experimental datasets. On cellular cryo-ET data, DeepFinder localized membrane-bound and cytosolic ribosomes (~3.2 MDa), Rubisco (~540 kDa soluble complex), and photosystem II (~550 kDa membrane complex) with comparable accuracy to expert-supervised ground truth annotations. Furthermore, we show that DeepFinder is flexible and can be combined with template matching to localize the missing macromolecules not found by one or the other method. The DeepFinder algorithm is therefore very promising for the semi-automated analysis of a wide range of molecular targets in cellular tomograms, including macromolecules with weights of 500-600 kDa and membrane proteins.
Uneven distribution of Purkinje cell injury in the cerebellar vermis of term neonates with hypoxic-ischemic encephalopathy
Authors: Annink K.V. , van Leeuwen I.C.E. , van der Aa N.E. , Alderliesten T. , Groenendaal F. , Jellema R.K. , Nijboer C.H.A. , Nikkels P.G.J. , Lammens M. , Benders M.J.N.L. , Hoebeek F.E. , Dudink J.
Published: April 2020

Introduction

In term neonates with hypoxic-ischemic encephalopathy (HIE), cerebellar injury is becoming more and more acknowledged. Animal studies demonstrated that Purkinje cells (PCs) are especially vulnerable for hypoxic-ischemic injury. In neonates, however, the extent and pattern of PC injury has not been investigated. The aim of this study was to determine the distribution of PC injury in the cerebellar vermis of term born neonates with HIE.

Methods

Term born neonates with HIE that underwent post-mortem autopsy of the cerebellar vermis were included. Haematoxylin & Eosin (H&E) stained sections of the vermis were used to determine total PC count and morphology (normal, abnormal or non-classified) at the bases and crown of the folia and of the lobules in both the anterior and posterior lobes. Differences in PC count and PC morphology between the anterior and posterior lobe and between the bases and crown were calculated using the paired samples T-test or Wilcoxon-signed rank test.

Results

The total number of PCs were significantly higher at the crown compared to the bases (p<0.001) irrespective of the precise location. Besides, PCs at the bases more often had an abnormal morphology. No significant difference between the total number of PCs in the anterior and posterior lobe was observed.

Conclusion

The abnormal PC count and morphology in term neonates with HIE resembles supratentorial ulegyria.
Genetic variation reveals individual-level climate tracking across the annual cycle of a migratory bird
Authors: Bay Rachael A. , Karp Daniel S. , Saracco James F. , Anderegg William R.L. , Frishkoff Luke O. , Wiedenfeld David , Smith Thomas B. , Ruegg Kristen
Published: April 2020

For migratory species, seasonal movements complicate local climate adaptation, as it is unclear whether individuals track climate niches across the annual cycle. In the migratory songbird yellow warbler (Setophaga petechia), we find a correlation between individual-level wintering and breeding precipitation but not temperature. Birds wintering in the driest regions of the Neotropics breed in the driest regions of North America. Individuals from drier regions also possess distinct morphologies and population responses to varying rainfall. We find a positive association between bill size and breeding season precipitation which, given documented climate-associated genomic variation, might reflect adaptation to local precipitation regimes. Relative abundance in the breeding range is linked to interannual fluctuations in precipitation, but the directionality of this response varies across geography. Together, our results suggest that variation in climate optima may exist across the breeding range of yellow warblers and provide a mechanism for selection across the annual cycle.
Incremental language comprehension difficulty predicts activity in the language network but not the multiple demand network
Authors: Wehbe Leila , Blank Idan Asher , Shain Cory , Futrell Richard , Levy Roger , von der Malsburg Titus , Smith Nathaniel , Gibson Edward , Fedorenko Evelina
Published: April 2020

What role do domain-general executive functions play in human language comprehension? To address this question, we examine the relationship between behavioral measures of comprehension and neural activity in the domain-general “multiple demand” (MD) network, which has been linked to constructs like attention, working memory, inhibitory control, and selection, and implicated in diverse goal-directed behaviors. Specifically, fMRI data collected during naturalistic story listening are compared to theory-neutral measures of online comprehension difficulty and incremental processing load (reading times and eye-fixation durations). Critically, to ensure that variance in these measures is driven by features of the linguistic stimulus rather than reflecting participant-or trial-level variability, the neuroimaging and behavioral datasets were collected in non-overlapping samples. We find no behavioral-neural link in functionally localized MD regions; instead, this link is found in the domain-specific, fronto-temporal “core language network”, in both left hemispheric areas and their right hemispheric homologues. These results argue against strong involvement of domain-general executive circuits in language comprehension.
Evaluating rehabilitation progress using motion features identified by machine learning
Authors: Lu Lei , Tan Ying , Klaic Marlena , Galea Mary P. , Khan Fary , Oliver Annie , Mareels Iven , Oetomo Denny , Zhao Erying
Published: April 2020

Evaluating progress throughout a patient’s rehabilitation episode is critical for determining effectiveness of the selected treatments and contributing to the evidence-based practice. The evaluation process is complex due to the inherent large human variations in motor recovery and the limitations of commonly used clinical measurement tools. Information recorded during a robot-assisted rehabilitation process can provide an effective means to continuously quantitatively assess movement performance and rehabilitation progress. However, selecting appropriate motion features for rehabilitation evaluation has always been challenging. This paper exploits unsupervised feature learning techniques to reduce the complexity of building the evaluation model of patients’ progress. A new feature learning technique is developed to select the most significant features from a large amount of kinematic features measured from robotics, providing clinically useful information to health practitioners with reduction of modeling complexity. A novel indicator that can reflect monotonicity and trendability is proposed to evaluate the suitability of kinematic features, which are derived from the collected data of a population of stroke patients participating in robot-aided rehabilitation. The selected kinematic features allow for human variations across a population of patients as well as over the sequence of rehabilitation sessions. The study is based on data records pertaining to 41 stroke patients using three different robot assisted exercises for upper limb rehabilitation. Consistent with the literature, the results indicate that features based on movement smoothness are the best measures among 17 kinematic features used to evaluate rehabilitation progress.
Toward a single dose cure for Buruli ulcer
Authors: Thomas Sangeeta S , Kalia Nitin Pal , Ruf Marie-Thérèse , Pluschke Gerd , Pethe Kevin
Published: April 2020

A single dose of TELACEBEC (Q203), a phase 2 clinical candidate for tuberculosis, eradicatesMycobacterium ulceransin a mouse model of Buruli ulcer infection without relapse up to 19 weeks post treatment. Clinical use of Q203 could dramatically simplify the clinical management of Buruli ulcer, a neglected mycobacterial disease.
Stability ofβ-lactam antibiotics in bacterial growth media
Authors: Brouwers Rebecca , Vass Hugh , Dawson Angela , Squires Tracey , Tavaddod Sharareh , Allen Rosalind J.
Published: April 2020

Laboratory assays such as MIC tests assume that antibiotic molecules are stable in the chosen growth medium - but rapid degradation has been observed for antibiotics includingβ-lactams under some conditions in aqueous solution. Degradation rates in bacterial growth medium are less well known. Here, we develop a ‘delay time bioassay’ that provides a simple way to estimate antibiotic stability in bacterial growth media. We use the bioassay to measure degradation half-lives of theβ-lactam antibiotics mecillinam, aztreonam and cefotaxime in widely-used bacterial growth media based on MOPS and Luria-Bertani (LB) broth. We find that mecillinam degradation can occur rapidly, with a half-life as short as 2 hours in MOPS medium at 37°C and pH 7.4, and 4-5 hours in LB, but that adjusting the pH and temperature can increase its stability to a half-life around 6 hours without excessively perturbing growth. Aztreonam and cefotaxime were found to have half-lives longer than 6 hours in MOPS medium at 37°C and pH 7.4, but still shorter than the timescale of a typical minimum inhibitory concentration (MIC) assay. Taken together, our results suggest that care is needed in interpreting MIC tests and other laboratory growth assays forβ-lactam antibiotics, since there may be significant degradation of the antibiotic during the assay.
RAPID SEROLOGICAL TESTS HAVE A ROLE IN ASYMPTOMATIC HEALTH WORKERS COVID-19 SCREENING
Authors: Paradiso Angelo Virgilio , Summa SimonaDe , Silvestris Nicola , Tommasi Stefania , Tufaro Antonio , De Palma Giuseppe , Larocca Angela Maria Vittoria , Chironna Maria , D’Addabbo Vincenzo , Raffaele Donata , Cafagna Vito , Garrisi Vito
Published: April 2020

Health workers are at high risk for SARS-CoV-2 infection and, if asymptomatic, for transmitting the virus on to fragile cancer patients. We screened 525 health workers of our Cancer Institute with rapid serological test Viva-Diag analyzingCOVID-19 associated-IgG/IgM. Six subjects (1,1%) resulted with Viva-Diag test not-negative for IgM. All 6 cases had RT-PCR SARS-CoV-2 test negative; repeating analysis ofIgG/IgM expression by CLIA assay also, 2 cases resulted IgM positive and 1 case IgG/IgM positive. This latter subject reported a contact with an infected SARS-CoV-2 person, a month earlier.In conclusion our study seems to suggest: a) a different analytical sensitivity inIgG/IgM evaluation for Viva-Diag and CLIA assays needing to be further determined; b) the ability of Viva-Diagrapid COVID-19 test to evidence health workers positive for Immunoglobulins expression. Discordant results of rapid serological tests with respect to RT-PCR stress the different clinical meaning the two assays can have, question clearly referring to further studies to optimize the utilization of rapid serological test in asymptomatic subjects at high risk for infection.
Association between ABO blood groups and clinical outcome of coronavirus disease 2019: Evidence from two cohorts
Authors: Zeng Xianfei , Fan Hongyan , Lu Dongxue , Huang Fang , Meng Xi , Li Zhuo , Tang Mei , Zhang Jing , Liu Nannan , Liu Zhixin , Zhao Jingya , Yin Wen , An Qunxing , Zhang Xijing , Hu Xingbin
Published: April 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become the third most common coronavirus that causes large-scale infections worldwide. The correlations between pathogen susceptibility and blood type distribution have attracted attention decades ago. The current retrospective study aimed to examine the correlation between blood type distribution and SARS-CoV-2 infection, progression, and prognosis in patients with coronavirus disease 2019 (COVID-19). With 265 patients from multiple medical centers and two established cohorts, we found that the blood type A population was more sensitive to SARS-CoV-2. Moreover, the blood type distribution was not relevant to acute respiratory distress syndrome (ARDS), acute kidney injury (AKI), and mortality in COVID-19 patients. These findings are indicative of coping with the great threat since it probed the relationship between blood types and ARDS, AKI, and mortality, in addition to susceptibility in COVID-19 patients.
The microbes found in the honey of New York City beehives
Authors: Weiss Tallisker , Mayle Allison , Nash Bruce
Published: April 2020

Bees are incredibly important to the Earth’s ecosystem and provide humans with a variety of fruits and vegetables; however, due to Colony Collapse Disorder, hives are dying at an alarming rate. Colony Collapse Disorder is caused by a number of factors such as pesticides and bacteria that kill the bees. With the increase of urban beekeeping created in an effort to replenish the bee population, little is known about the microbes the bees are interacting with in New York City. This research looked at what microbes the bees came in contact with to use as a resource in identifying the differences between the neighborhoods. Two methods were used to extract the DNA, one looking at gram-positive and gram-negative bacteria and the other looking at only gram-positive. The samples were taken from around New York City, Westchester County and Pennsylvania. The Pennsylvania sample was collected from a container of honey bought from Trader Joe’s. The reason both urban and rural samples were used was to see if there is an obvious difference in the microbes found between them.
Genetic signatures of evolution of the pluripotency gene regulating network across mammals
Authors: Endo Yoshinori , Kamei Ken-ichiro , Inoue-Murayama Miho
Published: April 2020

Mammalian pluripotent stem cells (PSCs) have distinct molecular and biological characteristics, but we lack a comprehensive understanding of regulatory network evolution in mammals. Here, we applied a comparative genetic analysis of 134 genes constituting the pluripotency gene regulatory network across 48 mammalian species covering all the major taxonomic groups. We found evolutionary conservation in JAK-STAT and PI3K-Akt signaling pathways, suggesting equivalent capabilities in self-renewal and proliferation of mammalian PSCs. On the other hand, we discovered rapid evolution of the downstream targets of the core regulatory circuit, providing insights into variations of characteristics. Our data indicate that the variations in the PSCs characteristics may be due to positive selections in the downstream targets of the core regulatory circuit. We further reveal that positively selected genes can be associated with species unique adaptation that is not dedicated to regulation of PSCs. These results provide important insight into the evolution of the pluripotency gene regulatory network underlying variations in characteristics of mammalian PSCs.
Plasma-derived exosome-like vesicles are enriched in lyso-phospholipids and pass the blood-brain barrier
Authors: Jakubec Martin , Maple-Grødem Jodi , Akbari Saleha , Nesse Susanne , Halskau Øyvind , Mork-Jansson Astrid
Published: April 2020

Exosomes are vesicles involved in intercellular communication. Their membrane structure and core content is largely dependent on the cell of origin. Exosomes have been investigated both for their biological roles and their possible use as disease biomarkers and drug carriers. These potential technological applications require the rigorous characterization of exosomal blood brain barrier permeability and a description of their lipid bilayer composition. To achieve these goals, we have established a 3D static blood brain barrier system based on existing systems for liposomes and a complementary LC-MS/MS and31P nuclear magnetic resonance methodology for the analysis of purified human plasma-derived exosome-like vesicles. Results show that the isolated vesicles pass the blood brain barrier and are taken up in endothelial cells. The compositional analysis revealed that the isolated vesicles are enriched in lyso phospholipids and do not contain phosphatidylserine. These findings deviate significantly from the composition of exosomes originating from cell culture, and may reflect active removal by macrophages that respond to exposed phosphahtidylserine.
Gut Mycobiome Dysbiosis is Linked to Hypertriglyceridemia Among Home Dwelling Elderly Danes
Authors: Ahmad Hajar Fauzan , Castro Mejia Josue Leonardo , Krych Lukasz , Khakimov Bekzod , Kot Witold , Bechshøft Rasmus Leidesdorff , Reitelseder Søren , Højfeldt Grith Westergaard , Engelsen Søren Balling , Holm Lars , Nielsen Dennis Sandris
Published: April 2020

Gut microbial dysbiosis have been linked to frailty in elderly, yet the presence of fungal communities and their possible association with host health are little understood. This study attempts to identify gut microbial fungal associations with the progression of atherogenic dyslipidemia in a population of older adults by investigating the interplay between dietary intake, gut mycobiome composition, plasma and fecal metabolome and anthropometric/body-composition measurements of 99 Danes aged 65 to 81 (69.57 ± 3.64) years. The gut mycobiome composition were determined by high-throughput sequencing of internal transcribed spacer (ITS2) gene amplicons, while the plasma and fecal metabolome was determined by GC-MS. The gut microbiome of the subjects investigated is home to three main eukaryotic phyla, namely Ascomyco-ta, Basidiomycota and Zygomycota, with generaPenicillium, Candida, andAspergillusbeing particularly common. Hypertriglyceridemia was associated with fewer observed fungal species, and Bray-Curtis dissimilarity matrix-based analysis showed significant (p< 0.05) clustering according to fasting levels of circulating plasma triglycerides (Tg) and very low-density lipoprotein (VLDL) cholesterol fasting levels, respectively. Higher levels of Tg and VLDL cholesterol significantly associates with increased relative abundance of genusPenicillium, andSaccha:ramyceslikely mediated by a higher dietary fatty acids intake (p< 0.05), andSac-charomyces, Debaryomyces, Candida, AgaricusandStarmerellawere moderately associated with SCF As groups. Collectively, these findings suggest that gut mycobiome dysbiosis on older adults is associated with hypertriglyceridemia, a known risk factor for development of cardiovascular disease.
Tuning of crystallization method and ligand conformation to give a mononuclear compound or two-dimensional SCO coordination polymer based on a new semi-rigid V-shaped bis-pyridyl bis-amide ligand
Authors: Hao Xiaoyun , Dou Yong , Cao Tong , Qin Lan , Yang Lu , Liu Hui , Li Dacheng , Liu Qingyun , Zhang Daopeng , Zhou Zhen
Published: April 2020

With the new semi-rigid V-shaped bidentate pyridyl amide compound 5-methyl-N,N′-bis(pyridin-4-yl)benzene-1,3-dicarboxamide (L) as an auxiliary ligand and the FeII ion as the metal centre, one mononuclear complex, bis(methanol-κO)bis[5-methyl-N,N′-bis(pyridin-4-yl)benzene-1,3-dicarboxamide-κN]bis(thiocyanato-κN)iron(II), [Fe(SCN)2(C19H16N4O2)2(CH3OH)2] (1), and one two-dimensional coordination polymer, catena-poly[[[bis(thiocyanato-κN)iron(II)]-bis[μ-5-methyl-N,N′-bis(pyridin-4-yl)benzene-1,3-dicarboxamide-κ2
N:N′]] methanol disolvate dihydrate], {[Fe(SCN)2(C19H16N4O2)2]·2CH3OH·2H2O}
n
(2), were prepared by slow evaporation and H-tube diffusion methods, respectively, indicating the effect of the method of crystallization on the structure type of the target product. Both complexes have been structurally characterized by elemental analysis, IR spectroscopy and single-crystal X-ray crystallography. The single-crystal X-ray diffraction analysis shows that L functions as a monodentate ligand in mononuclear 1, while it coordinates in a bidentate manner to two independent Fe(SCN)2 units in complex 2, with a different conformation from that in 1 and the ligands point in two almost orthogonal directions, therefore leading to a two-dimensional grid-like network. Investigation of the magnetic properties reveals the always high-spin state of the FeII centre over the whole temperature range in 1 and a gradual thermally-induced incomplete spin crossover (SCO) behaviour below 150 K in 2, demonstrating the influence of the different coordination fields on the spin properties of the metal ions. The current results provide useful information for the rational design of functional complexes with different structure dimensionalities by employing different conformations of the ligand and different crystallization methods.