bluuebunny/crossref_metadata_2025 huggingface dataset:
3D-Strudel - a novel model-dependent map-feature validation method for high-resolution cryo-EM structures
Authors: Istrate Andrei , Wang Zhe , Murshudov Garib N , Patwardhan Ardan , Kleywegt Gerard J
Published: December 2021

Recent technological advances in electron cryo-microscopy (cryo-EM) have led to significant improvements in the resolution of many single-particle reconstructions and a sharp increase in the number of entries released in the Electron Microscopy Data Bank (EMDB) every year, which in turn has opened new possibilities for data mining. Here we present a resolution-dependent library of rotamer-specific amino-acid map motifs mined from entries in the EMDB archive with reported resolution between 2.0 and 4.0Å. We further describe 3D-Strudel, a method for map/model validation based on these libraries. 3D-Strudel calculates linear correlation coefficients between the map values of a map-motif from the library and the experimental map values around a target residue. We also present “Strudel Score”, a plug-in for ChimeraX, as a user-friendly tool for visualisation of 3D-Strudel validation results.
Galvanotaxis of ciliates: Spatiotemporal dynamics ofColeps hirtusunder electric fields
Authors: Daul Anna , Lemloh Marie-Louise , Hörning Marcel
Published: December 2021

Galvanotaxis describes the functional response of organisms to electric fields. In ciliates, the electric field influences the electrophysiology and thus the cilia beat dynamics. This leads to a change of the swimming direction towards the cathode. The dynamical response to electric fields ofColeps hirtushas not been studied since the observations of Verworn in 1890 (1). While galvanotaxis has been studied in other cilitates,C. hirtusexhibit properties not found elsewhere, such as biomineralization-processes of alveolar plates with impact on the intracellular calcium regulation and a bimodal resting membrane potential, which leads unique electrophysiological driven bimodal swimming dynamics. Here, we statistically analyze the galvanotactic dynamics ofC. hirtusby automated cell tracking routines. We found that the number of cells that show a galvanotactic response, increases with the increase of the applied electric field strength with a mean at about 2.1 V/cm. The spatiotemporal swimming dynamics change and lead to a statistical increase of linear elongated cell trajectories that point toward the cathode. Further, the increase of the electric fields decreases the mean velocity variance for electric fields larger than about 1.3 V/cm, while showing no significant change in the absolute velocity for any applied electric field. Fully functional galvanotactic responses were observed at a minimum extracellular calcium concentration of 20µM. The results add important insights to the current understanding of cellular dynamics of ciliates and suggest that the currently accepted model lags the inclusion of the swimming dynamics and the complex calcium regulatory system of the cell. The results of this study do not only extend the fundamental understanding ofC. hirtusdynamics, but also open possibilities for technical applications, such as biosensors or microrobots in the future.
Can Chemical Exchange Saturation Transfer (CEST MRI) be used as biomarker of disease progression in Prion Disease?
Authors: Demetriou Eleni , Tachrount Mohamed , Ellis Matthew , Linehan Jackeline , Brandner Sebastian , Collinge John , Mead Simon , Shmueli Karin , Farrow Mark , Golay Xavier
Published: December 2021

Human prion diseases are fatal neurodegenerative disorders that may have prolonged asymptomatic incubation periods. However, the underlying mechanism by which prions cause brain damage remains unclear. In turn, characterization of early pathological aspects would be of benefit for the diagnosis and potential treatment of these progressive neurodegenerative disorders. We investigated chemical exchange saturation transfer (CEST) MRI based on its exquisite sensitivity to cytosol protein content as a surrogate for prion disease pathology. Three groups of prion-infected mice at different stages of the disease underwent conventional magnetic resonance imaging and CEST MRI at 9.4T. For each mouse, chemical exchange contrasts were measured by applying five RF powers at various frequency offsets using magnetization transfer asymmetries. Relayed Nuclear Overhauser effects (NOE*) and amide proton transfer (APT*) were also assessed. For comparison, CEST MRI measurements were also made in healthy control mice brains. Here we show that alterations in CEST signal were detected before structural modifications or any clinical signs of prion disease. The detected CEST signal displayed different patterns at different stages of the disease indicating its potential for use as a longitudinal marker of disease progression. Highly significant correlations were found between CEST metrics and histopathological findings. A decline in NOE signal was positively correlated with abnormal prion protein deposition (R2 = 0.91) in the thalami of prion infected mice. Moreover, the NOE signal was negatively correlated with astrogliosis (R2 = 0.71) in the thalamus. No significant correlations were detected between NOE signals and spongiosis. MTR asymmetry at 3.5 ppm was also correlated with astrogliosis (R2 = 0.59), and prion protein deposition (R2 = 0.63) in thalamus. No significant changes were detected in APT* between prion-infected and control mice at all stages of the disease. Finally, MTR asymmetry between 2.8 and 3.2 ppm was correlated with prion protein deposition (R2 = 0.47) in the thalamus of prion -infected mice. To conclude, CEST MRI has potential utility as a biomarker of neurodegenerative processes in prion disease.
Sugar-rich larval diet promotes lower adult pathogen load and higher survival after infection in a polyphagous fly
Authors: Dinh Hue , Lundbäck Ida , Kumar Sheemal , Than Anh The , Morimoto Juliano , Ponton Fleur
Published: December 2021

Nutrition is a central factor influencing immunity and resistance to infection, but the extent to which nutrition during development affects adult responses to infections is poorly understood. Our study investigated how the nutritional composition of the larval diet affects the survival, pathogen load, and food intake of adult fruit flies, Bactrocera tryoni, after bacterial septic infection. We found a sex-specific effect of larval diet composition on survival post-infection: survival rate was higher and bacterial load was lower for infected females fed sugar-rich larval diet compared with females fed protein-rich larval diet, an effect that was absent in males. Both males and females were heavier when fed a balanced larval diet compared to protein- or sugar-rich diet, while body lipid reserves were higher in the sugar-rich larval diet compared with other diets. Body protein reserve was lower for sugar-rich larval diets compared to other diets in males, but not females. Both females and males shifted their nutrient intake to ingest a sugar-rich diet when infected compared with sham-infected flies without any effect of the larval diet, suggesting that sugar-rich diets can be beneficial to fight off bacterial infection. Overall, our findings show that nutrition during early life can shape individual fitness in adulthood.

Summary statement

Developmental conditions influence adulthood. Here we showed that when the larval diet is rich in sugar, resistance to infection is increased in females at adulthood, in a polyphagous fly.
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks
Authors: Suter Polina , Kuipers Jack , Beerenwinkel Niko
Published: December 2021

Dynamic Bayesian networks (DBNs) can be used for the discovery of gene regulatory networks from time series gene expression data. Here, we suggest a strategy for learning DBNs from gene expression data by employing a Bayesian approach that is scalable to large networks and is targeted at learning models with high predictive accuracy. Our framework can be used to learn DBNs for multiple groups of samples and highlight differences and similarities in their gene regulatory networks. We learn these DBN models based on different structural and parametric assumptions and select the optimal model based on the cross-validated predictive accuracy. We show in simulation studies that our approach is better equipped to prevent overfitting than techniques used in previous studies. We applied the proposed DBN-based classification approach to two time series transcriptomic datasets from the Gene Expression Omnibus database, each comprising data from distinct phenotypic groups of the same tissue type. In the first case, we used DBNs to characterize responders and non-responders to anti-cancer therapy. In the second case, we compared normal to tumor cells of colorectal tissue. The classification accuracy reached by the DBN-based classifier for both datasets was higher than reported previously. For the colorectal cancer dataset, our analysis suggested that GRNs for cancer and normal tissues have a lot of differences, which are most pronounced in the neighborhoods of oncogenes and known cancer tissue markers. The identified differences in gene networks of cancer and normal cells may be used for the discovery of targeted therapies.
Diminished GAD67 Terminals and Ambient GABA Inhibition Associated with Reduced Motor Neuron Recruitment Threshold in the SOD1G93A ALS mouse
Authors: Venugopal Sharmila , Ghulam-Jhelani Zohal , Simmons Dwayne , Chandler Scott H
Published: December 2021

Pre-symptomatic studies in mouse models of the neurodegenerative motor neuron (MN) disease, Amyotrophic Lateral Sclerosis (ALS) highlight early alterations in intrinsic and synaptic excitability and have supported an excitotoxic theory of MN death. However, a role for synaptic inhibition in disease development is not sufficiently explored among other mechanisms. Since inhibition plays a role in both regulating motor output and in neuroprotection, we examined the age-dependent anatomical changes in inhibitory presynaptic terminals on MN cell bodies using fluorescent immunohistochemistry for GAD67 (GABA) and GlyT2 (glycine) presynaptic proteins comparing ALS-vulnerable trigeminal jaw closer (JC) motor pools with the ALS-resistant extraocular (EO) MNs in the SOD1G93A mouse model for ALS. Our results indicate differential patterns of temporal changes of these terminals in vulnerable versus resilient MNs and relative differences between SOD1G93A and wild-type (WT) MNs. Notably, we found pre-symptomatic up-regulation in inhibitory terminals in the EO MNs while the vulnerable JC MNs mostly showed a decrease in inhibitory terminals. Specifically, there was a statistically significant decrease in the GAD67 somatic abuttal in the SOD1G93A JC MNs compared to WT around P12. Using in vitro patch-clamp electrophysiology, we found a parallel decrease in the ambient GABA-dependent tonic inhibition in the SOD1G93A JC MNs. While it is unclear if the two mechanisms are directly related, pharmacological blockade of specific subtype of GABAA-α5 receptors suggests that tonic inhibition can control MN recruitment threshold. Furthermore, reduction in tonic GABA current as observed here in the mutant, identifies a putative molecular mechanism explaining our observations of hyperexcitable shifts in JC MN recruitment threshold in the SOD1G93A mouse. Lastly, we showcase non-parametric resampling-based bootstrap statistics for data analyses, and provide the Python code on GitHub for wider reuse.
Prediction of prophages and their host ranges in pathogenic and commensal Neisseria species
Authors: Orazi Giulia , Collins Alan J. , Whitaker Rachel J.
Published: December 2021

The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one other, primarily via transformation and homologous recombination, and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from other prophages and MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus.

IMPORTANCE

Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus, and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) have been identified and characterized in Neisseria species. In this study, we identified a large number of candidate phages integrated within the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.
Enhancer RNA-based modeling of adverse events and objective responses of immunotherapy
Authors: Guo Mengbiao , Lu Zhiya , Xiong Yuanyan
Published: December 2021

Immune checkpoint inhibitors (ICI) targeting PD-1/PD-L1 or CTLA-4 are emerging and effective immunotherapy strategies. However, ICI treated patients present heterogeneous responses and adverse events, thus demanding effective ways to assess benefit over risk before treatment. Here, by integrating pan-cancer clinical and molecular data, we tried to predict immune-related adverse events (irAEs, risk) and objective response rates (ORRs, benefit) based on enhancer RNAs (eRNAs) expression among patients receiving anti-PD-1/PD-L1 therapy. We built two effective regression models, explaining 71% variance (R=0.84) of irAEs with three eRNAs and 79% (R=0.89) of ORRs with five eRNAs. Interestingly, target genes of irAE-related enhancers, including upstream regulators of MYC, were involved in metabolism, inflammation, and immune activation, while ORR-related enhancers target PAK2 and DLG1 which directly participate in T cell activation. Our study provides references for the identification of immunotherapy-related biomarkers and potential therapeutic targets during immunotherapy.
Optimal spatial allocation of enzymes as an investment problem
Authors: Giunta Giovanni , Tostevin Filipe , Tănase-Nicola Sorin , Gerland Ulrich
Published: December 2021

Given a limited number of molecular components, cells face various allocation problems demanding decisions on how to distribute their resources. For instance, cells decide which enzymes to produce at what quantity, but also where to position them. Here we focus on the spatial allocation problem of how to distribute enzymes such as to maximize the total reaction flux produced by them in a system with given geometry and boundary conditions. So far, such distributions have been studied by computational optimization, but a deeper theoretical understanding was lacking. We derive an optimal allocation principle, which demands that the available enzymes are distributed such that the marginal flux returns at each occupied position are equal. This ‘homogeneous marginal returns criterion’ (HMR criterion) corresponds to a portfolio optimization criterion in a scenario where each investment globally feeds back onto all payoffs. The HMR criterion allows us to analytically understand and characterize a localization-delocalization transition in the optimal enzyme distribution that was previously observed numerically. In particular, our analysis reveals the generality of the transition, and produces a practical test for the optimality of enzyme localization by comparing the reaction flux to the influx of substrate. Based on these results, we devise an additive construction algorithm, which builds up optimal enzyme arrangements systematically rather than by trial and error. Taken together, our results reveal a common principle in allocation problems from biology and economics, which can also serve as a design principle for synthetic biomolecular systems.
Assessment and Comparative Study of Biofilm Formation with frequency of Multi Drug Resistance in strains of Staphylococcus aureus
Authors: Fatima Kiran , Ali Kashif
Published: December 2021

Background

The study was conducted to identify the role of biofilms in the antibiotic susceptibility in the strains of Staphylococcus aureus. A total of 19 non repeated pus/wound swab samples from different anatomic locations and 17 samples that were previously identified as S. aureus and preserved in the labs were included in the study. The Staphylococcus aureus was identified on the basis of colony morphology, Gram’s stain, biochemical tests (catalase and coagulase tests) and molecular identification through PCR amplification.

Methodology

A total of 26 samples were recovered out of the 31 samples. Kirby-Bauer disk diffusion susceptibility test was used to determine the sensitivity or resistance of S. aureus to methicillin. Out of the 26 strains, 4 were highly resistant, 10 were moderately resistant and 12 strains were sensitive. Three different protocols (Tube Method, Congo Red Agar Method and Tissue Culture plate method) were used for the detection of biofilm formation for both resistant and sensitive strains.

Result

Comparative analysis of the antibiotic susceptibility and biofilm formation by different protocols showed that 70% strains that are resistant to antibiotic methicillin produced moderate-strong biofilms. 50% have produced the moderate-strong biofilms in all 3 protocols. In case of sensitive, 50% strains had produced none-weak biofilms in all 3 protocols.

Decisions

The strains that had zone of inhibition of close to resistance produced weak-strong biofilms but they all produced weak biofilms in CRA method. It can be concluded that the strains of S. aureus that have the ability to produce biofilms become methicillin resistant.
Reconstitution of T cell immunity against EBV in the immunocompromised host by adoptive transfer of peptide-stimulated T cells after allogeneic stem cell transplantation
Authors: Lammoglia Cobo María Fernanda , Ritter Julia , Gary Regina , Seitz Volkhard , Mautner Josef , Aigner Michael , Völkl Simon , Schaffer Stefanie , Moi Stephanie , Seegebarth Anke , Bruns Heiko , Rösler Wolf , Amann Kerstin , Büttner-Herold Maike , Hennig Steffen , Mackensen Andreas , Hummel Michael , Moosmann Andreas , Gerbitz Armin
Published: December 2021

Reconstitution of T cell repertoire after allogeneic stem cell transplantation is a long and often incomplete process. As a result, reactivation of Epstein-Barr virus (EBV) is a frequent complication that may be treated by adoptive transfer of donor-derived EBV-specific T cells. We generated donor-derived EBV-specific T cells by peptide stimulation and adoptively transferred them to a patient with angioimmunoblastic T-cell lymphoma (AITL), who had developed persisting high titers of EBV concomitant to relapse after transplantation. T cell receptor beta (TCRβ) deep sequencing showed that the T cell repertoire of the patient early after transplantation (day 60) was strongly reduced and only very low numbers of EBV-specific T cells were detectable. Manufacturing andin vitroexpansion of donor-derived EBV-specific T cells resulted in enrichment of EBV epitope-specific, HLA-restricted T cells. Monitoring after adoptive transfer revealed that the dominant TCR sequences from peptide-stimulated T cells persisted long-term and established an EBV-specific TCR clonotype repertoire in the host, with many of the EBV-specific TCRs present in the donor. This reconstituted repertoire was associated with immunological control of EBV and with lack of further AITL relapse.

Author summary

A characteristic feature of all herpesviruses is their persistence in the host’s body after primary infection. Hence, the host’s immune system is confronted with the problem to control these viruses life-long. Well-known representative of the herpesvirus group are the classic Herpes-Simplex Virus (HSV-1) and Varicella Zoster Virus (VZV, causing chicken pox); a less known representative is Epstein Barr Virus (EBV, causing mononucleosis). When the immune system is severely compromised, for example after stem cell transplantation from a foreign (allogeneic) donor, these viruses can reappear, as they are already in the host’s body. Especially EBV cause life-threatening complications after stem cell transplantation and only reinforcement of the host’s immune system can reestablish viral control. Here we show thatex vivomanufactured EBV-specific T cells can reestablish long-term control of EBV and that these cells persist in the host’s body over months. These results give us a better understanding of viral immune reconstitution post-transplant and of clinically-relevant T cell populations against EBV.
p166 links membrane and intramitochondrial modules of the trypanosomal tripartite attachment complex
Authors: Schimanski Bernd , Aeschlimann Salome , Käser Sandro , Gala Maria Gomez-Fabra , Vögtle Nora , Schneider André
Published: December 2021

The protist parasiteTrypanosomabrucei has a single mitochondrion with a single unit genome termed kinetoplast DNA (kDNA). Faithfull segregation of replicated kDNA is ensured by a complicated structure termed tripartite attachment complex (TAC). The TAC physically links the basal body of the flagellum with the kDNA spanning the two mitochondrial membranes. Here, we characterized p166 as the only TAC subunit that is anchored in the inner membrane. Its C-terminal transmembrane domain separates the protein into a large N-terminal region that interacts with the kDNA-localized TAC102 and a 34 aa C-tail that binds to the intermembrane space-exposed loop of the integral outer membrane protein TAC60. Thus, in contrast to the outer membrane TAC region which requires four essential subunits for proper function a single inner membrane TAC subunit is sufficient to bridge the distance from the OM to the kDNA. Surprisingly, non-functional p166 lacking the C-terminal 34 aa still localizes to the TAC region. This suggests the existence of non-essential TAC-associated proteins in the OM. These proteins can loosely bind to non-functional p166 lacking the C-terminal 34 aa and keep it at the TAC but their binding would not be strong enough to withstand the mechanical force upon kDNA segregation.

AUTHOR SUMMARY

Mitochondria evolved from a single endosymbiotic event and are a hallmark of eukaryotes. The large majority of genes for mitochondrial proteins are nuclear encoded now and only a small number are found in the mitochondrial genome. The protistTrypanosoma bruceiis an extreme eukaryote in many aspects. For instance, trypanosomes have a single mitochondrion and its genome – called kinetoplast DNA (kDNA) – locates as a single unit inside the mitochondrion close to the basal body of the flagellum. The tripartite attachment complex (TAC) forms a connection between the basal body and the kDNA ensuring faithful segregation of kDNA among the daughter cells upon cytokinesis. Recently, several TAC subunits of the cytoplasm, the outer mitochondrial membrane (OM) and the mitochondrial matrix have been characterized. Here, we identify p166 as the first TAC subunit of the inner mitochondrial membrane. It is anchored with a single transmembrane domain separating the protein into a N-terminal moiety located in the matrix and a short C-tail. The latter reaches into the intermembrane space and binds the OM subunit TAC60 whereas the N-terminus interacts with the matrix subunit TAC102. Thus, with p166 we identified the missing link required to connect different modules of the TAC.
Presentation, characteristics, treatments and outcomes of mechanically ventilated patients with COVID-19 in Bulgaria
Authors: Bakalova Neda , Natsev Ivats , Damov Hristo , Yatsenko Irina , Jovinska Stefanija , Enev Rostislav , Cholakov Mihail , Abedinov Filip , Kalendjieva Denitza
Published: December 2021

Background

The first surge of coronavirus disease 2019 (COVID-19) cases in Bulgaria occurred in the fall of 2020. Here we describe the clinical presentation, patient characteristics, treatments and outcomes of mechanically ventilated COVID-19 patients in a newly formed COVID-19 ICU at a tertiary cardiac center in Sofia, Bulgaria.

Methods

This is a retrospective observational study of mechanically ventilated COVID-19 patients admitted to Sveta Ekaterina University Hospital in Sofia, Bulgaria, between November 4th, 2020 and January 6th, 2021. Data were collected from electronic and written patient records and charts.

Results

We identified 38 critical care patients admitted with respiratory failure and treated with mechanical ventilation at our COVID-19 ICU during this period. The median age was 66 (IQR 57-76, range 27-89) and 74% were male. Most patients, 36 (95%), had at least one comorbidity. The most common comorbidities were hypertension, valvular heart disease, ischemic heart disease and diabetes mellitus. Overall, 27 (71%) patients had a concomitant cardiac disease other than hypertension and 24% were recent cardiac surgical patients. Inotropic support was required in 29 (76%) patients, renal replacement therapy in 12 (32%) patients and prone positioning and ECMO were used in 5 (13%) and 2 (5%) patients respectively. The median duration of mechanical ventilation was 7.5 (IQR 5-14) days overall and 9 (IQR 6-13) days for survivors. At 30-days 28 (74%) of patients had died. Overall, 32 (84%) patients died in hospital and only 6 (16%) patients were discharged home.

Conclusions

During the first major surge of COVID-19 cases in Bulgaria, despite the wave arriving later than in other countries, the healthcare system was largely unprepared. In our setting, mortality in mechanically ventilated patients was very high at 84%. Several factors might have contributed to these results, namely the predominance of cardiovascular comorbidities in our patient population, the strained ICU capacity and the lack of medical personnel.
Dopaminergic modulation of local non-oscillatory activity and global-network properties in Parkinson’s disease: an EEG study
Authors: Zhang Juanli , Villringer Arno , Nikulin Vadim V.
Published: December 2021

Dopaminergic medication for Parkinson’s disease (PD) modulates neuronal oscillations and functional connectivity across the basal ganglia-thalamic-cortical circuit. However, the non-oscillatory component of the neuronal activity, potentially indicating a state of excitation/inhibition balance, has not yet been investigated and previous studies have shown inconsistent changes of cortico-cortical connectivity as a response to dopaminergic medication. To further elucidate changes of regional non-oscillatory component of the neuronal power spectra, functional connectivity, and to determine which aspects of network organization obtained with graph theory respond to dopaminergic medication, we analyzed a resting-state EEG (Electroencephalogram) dataset including 15 PD patients during OFF and ON medication conditions. We found that the spectral slope, typically used to quantify the broadband non-oscillatory component of power spectra, steepened particularly in the left central region in the ON compared to OFF condition. In addition, using lagged coherence as a functional connectivity measure, we found that the functional connectivity in the beta frequency range between centro-parietal and frontal regions was enhanced in the ON compared to the OFF condition. After applying graph theory analysis, we observed that at the lower level of topology the node degree was increased, particularly in the centro-parietal area. Yet, results showed no significant difference in global topological organization between the two conditions: either in global efficiency or clustering coefficient for measuring global and local integration, respectively. Interestingly, we found a close association between local/global spectral slope and functional network global efficiency in the OFF condition, suggesting a crucial role of local non-oscillatory dynamics in forming the functional global integration which characterizes PD. These results provide further evidence and a more complete picture for the engagement of multiple cortical regions at various levels in response to dopaminergic medication in PD.
Predictive value of isolated symptoms for diagnosis of SARS-CoV-2 infection in children tested during peak circulation of the delta variant
Authors: Westbrook Adrianna L. , Benedit Laura C. , Frediani Jennifer K , Griffiths Mark A. , Khan Nabeel Y. , Levy Joshua M. , Morris Claudia R. , Rostad Christina A. , Stone Cheryl L. , Sullivan Julie , Vos Miriam B. , Welsh Jean , Wood Anna , Martin Greg S. , Lam Wilbur , Pollock Nira R.
Published: December 2021

Background

COVID-19 testing policies for symptomatic children attending U.S. schools or daycare vary, and whether isolated symptoms should prompt testing is unclear. We evaluated children presenting for SARS-CoV-2 testing to determine if the likelihood of having a positive SARS-CoV-2 test differed between participants with one versus ≥2 symptoms, and to examine the predictive capability of isolated symptoms.

Methods

Participants ≤ 18 years presenting for clinical SARS-CoV-2 molecular testing in six sites in urban/suburban/rural Georgia (July-October, 2021; delta variant predominant) were queried about individual symptoms. Participants were classified into three groups: asymptomatic, one symptom only, or ≥2 symptoms. SARS-CoV-2 test results and clinical characteristics of the three groups were compared. Sensitivity, specificity, and positive/negative predictive values (PPV/NPV) for isolated symptoms were calculated by fitting a saturated Poisson model.

Results

Of 602 participants, 21.8% tested positive and 48.7% had a known or suspected close contact. Children reporting one symptom (n=82; OR=6.00, 95% CI: 2.70-13.33) and children reporting ≥2 symptoms (n=365; OR=5.25: 2.66-10.38) were significantly more likely to have a positive COVID-19 test than asymptomatic children (n=155), but they were not significantly different from each other (OR=0.88: 0.52-1.49). Sensitivity/PPV were highest for isolated fever (33%/57%), cough (25%/32%), and sore throat (21%/45%); headache had low sensitivity (8%) but higher PPV (33%). Sensitivity/PPV of isolated congestion/rhinorrhea were 8%/9%.

Conclusions

With high delta variant prevalence, children with isolated symptoms were as likely as those with multiple symptoms to test positive for COVID-19. Isolated fever, cough, sore throat, or headache, but not congestion/rhinorrhea, offered highest predictive value.

Key points

In an area with high community prevalence of the delta variant, children presenting with one symptom were as likely as those with two or more symptoms to test positive for SARS-CoV-2 infection. Isolated symptoms should be considered in testing decisions.
Perceptions and Attitudes Towards COVID-19 Vaccination Amongst Pregnant and Postpartum Individuals
Authors: Siegel Molly R. , Lumbreras-Marquez Mario I. , James Kaitlyn , McBay Brandon R. , Gray Kathryn J. , Schantz-Dunn Julianna , Diouf Khady , Goldfarb Ilona T.
Published: December 2021

Introduction

This study aims to characterize attitudes towards COVID-19 vaccination and to evaluate factors associated with vaccine uptake amongst pregnant individuals.

Methods

An anonymous survey was distributed to a convenience sample of pregnant individuals receiving prenatal care at two large urban academic hospitals in a single healthcare network in Massachusetts. Individual demographic variables were included in the survey along with questions assessing attitudes towards COVID-19 and vaccination in pregnancy.

Results

Of 477 respondents, 233 (49.3%) had received or were scheduled to receive a COVID-19 vaccine. Age, White race, non-Hispanic/LatinX ethnicity, working from home, and typical receipt of the influenza vaccine were associated with COVID-19 vaccination. 276 respondents (58.4%) reported that their provider recommended the COVID-19 vaccine in pregnancy; these participants were more likely to have received a vaccine (OR 5.82, 95% confidence interval [CI] 3.68-9.26). Vaccinated individuals were less likely to be worried about the effects of the vaccine on themselves (OR 0.18, 95% CI 0.12-0.27) or their developing babies (OR 0.17, 95% CI 0.11-0.26). Unvaccinated individuals were less likely to report that it is easy to schedule a COVID-19 vaccine (OR 0.56, 95% CI 0.34-0.93), to travel to receive a vaccine (OR 0.19, 95% CI 0.10-0.36), and to miss work to receive a vaccine (OR 0.30, 95% CI 0.18-0.48).

Conclusions

Strategies are needed to improve patient education regarding vaccine side effects and safety in pregnancy and to change policy to make it feasible for pregnant patients to schedule and miss work without loss of pay to get vaccinated.

Key Points

There were racial and ethnic disparities in COVID-19 vaccination.

Unvaccinated respondents were more likely to be concerned about vaccine effects for themselves or their growing babies.

Unvaccinated respondents cited work and scheduling-related barriers to vaccination, indicating areas for advocacy
Provider Confidence in Counseling Preconception, Pregnant, and Postpartum Patients Regarding COVID-19 Vaccination
Authors: Siegel Molly R. , James Kaitlyn E. , Jaffe Elana , L’Heureux Michelle M. , Kaimal Anjali J. , Goldfarb Ilona T.
Published: December 2021

Objective

To assess knowledge and confidence in COVID-19 vaccine counseling among practitioners who provide care to pregnant persons and to describe factors associated with confidence in counseling.

Study Design

A web-based anonymous survey was distributed via email to a cross-sectional convenience sample of OB/GYN, Primary Care, and Internal Medicine faculty at three hospitals in a single healthcare network in Massachusetts. Individual demographics and institution-specific variables were included in the survey along with questions assessing both attitudes toward COVID-19 illness in pregnancy as well as confidence in counseling regarding the use of the vaccine for pregnant patients.

Results

Almost all providers (151, 98.1%) reported already receiving or being scheduled to receive a COVID-19 vaccine, and a majority of providers (111, 72.1%) reported that they believe the benefits of the mRNA COVID-19 vaccine in pregnancy outweigh the risks. Forty-one (26.6%) reported feeling very confident in counseling patients who primarily speak English about the evidence for mRNA vaccination in pregnancy, and 36 (23%) reported feeling very confident in counseling patients who are not primarily English-speaking. Forty-three providers (28.1%) expressed strong confidence in their comfort talking to individuals with vaccine hesitancy based on historic and continued racism and systemic injustices. The sources that survey respondents most commonly used to find information regarding COVID-19 vaccination in pregnancy were the CDC (112, 74.2%), hospital-specific resources (94, 62.3%) and ACOG (82, 54.3%).

Conclusion

While providers reported high personal uptake of COVID-19 vaccination and felt that the benefits of vaccination outweigh the risks in pregnancy, less than one-third felt very confident in counseling pregnant patients about available evidence for mRNA vaccine safety in pregnancy. Ensuring that providers feel comfortable bridging the gap between their belief that the vaccine is beneficial for pregnant patients and their comfort with holding conversations with patients regarding vaccination is paramount in order to ensure equitable access to vaccines for pregnant patients.
OPEN leaf: an open-source cloud-based phenotyping system for tracking dynamic changes at leaf-specific resolution in Arabidopsis
Authors: Swartz Landon G. , Liu Suxing , Dahlquist Drew , Kramer Skyler , Walter Emily S. , McInturf Sam , Bucksch Alexander , Mendoza-Cozatl David G.
Published: December 2021

The first draft of the Arabidopsis genome was released more than 20 years ago and despite intensive molecular research, more than 30% of Arabidopsis genes remained uncharacterized or without an assigned function. This is in part due to gene redundancy within gene families or the essential nature of genes, where their deletion results in lethality (i.e., the dark genome).

High-throughput plant phenotyping (HTPP) offers an automated and unbiased approach to characterize subtle or transient phenotypes resulting from gene redundancy or inducible gene silencing; however, commercial HTPP platforms remain unaffordable. Here we describe the design and implementation of OPEN leaf, an open-source HTPP system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing.

OPEN leaf, coupled with the SMART imaging processing package was able to consistently document and quantify dynamic morphological changes over time at the whole rosette level and also at leaf-specific resolution when plants experienced changes in nutrient availability.

The modular design of OPEN leaf allows for additional sensor integration. Notably, our data demonstrate that VIS sensors remain underutilized and can be used in high-throughput screens to identify characterize previously unidentified phenotypes in a leaf-specific manner.

Significance Statement

Many bottlenecks exist in high-throughput phenotyping involving computing power for processing and a lack of focus on abiotic stresses that has prevented an advancement in phenotyping on par with genotyping. Therefore, we create an automated HTP system that performs nutrient studies on Arabidopsis thaliana with cloud-based image processing that quantifies plant traits at a whole and leaf-level.
Integrative small and long RNA-omics analysis of human healing and non-healing wounds discovers cooperating microRNAs as therapeutic targets
Authors: Liu Zhuang , Zhang Letian , Toma Maria A. , Li Dongqing , Bian Xiaowei , Pastar Irena , Tomic-Canic Marjana , Sommar Pehr , Landén Ning Xu
Published: December 2021

MicroRNAs (miR) are important posttranscriptional regulators and exhibit a high potential to be utilized in diagnosis and therapy. However, our insufficient knowledge of the miR-mediated gene regulation in human skin wound healing severely hinders the identification of clinically relevant miRs. Here, we performed paired small RNA and long RNA sequencing in human tissue samples, including matched skin and acute wounds collected at each healing stage and chronic non-healing venous ulcers (VU). With integrative small and long RNA-omics analysis, we developed a compendium (https://www.xulandenlab.com/humanwounds-mirna-mrna), which will be an open, comprehensive resource to broadly aid wound healing research. With this first clinical, wound-centric resource of miRs and mRNAs, we identified 17 pathologically relevant miRs that exhibited abnormal VU expression and displayed their targets enriched explicitly in the VU gene signature. Intermeshing regulatory networks controlled by these miRs revealed their high cooperativity in contributing to chronic wound pathology characterized by persistent inflammation and proliferative phase initiation failure. Furthermore, we demonstrated that miR-34a, miR-424, and miR-516, upregulated in VU, cooperatively suppressed keratinocyte growth while promoting inflammatory response. Collectively, our study opens the possibility of developing innovative wound treatment that targets pathologically relevant cooperating miRs to attain higher therapeutic efficacy and specificity.
Inferring community assembly processes from functional seed trait variation along temperature gradient
Authors: Sergey Rosbakh , Loïc Chalmandrier , Shyam Phartyal , Peter Poschlod
Published: December 2021

Assembly of plant communities has long been scrutinized through the lens of trait-based ecology. Studies generally analyze functional traits related to the vegetative growth, survival and resource acquisition and thus ignore how ecological processes may affect plants at other stages of their lifecycle, particularly when seeds disperse, persist in soil and germinate.

Here, we analyzed an extensive data set of 16 traits for 167 species measured in-situ in 36 grasslands located along an elevational gradient and compared the impact of abiotic filtering, biotic interactions and dispersal on traits reflecting different trait categories: plant vegetative growth, germination, dispersal, and seed morphology. For each community, we quantified community weighted mean (CWM) and functional diversity (FD) for all traits and established their relationships to mean annual temperature.

The seed traits were weakly correlated to vegetative traits and thus constituted independent axes of plant phenotypical variation that were affected differently by the ecological processes considered. Abiotic filtering impacted mostly the vegetative traits and to a lesser extent on seed germination and morphological traits. Increasing low-temperature stress towards colder sites selected for short-stature, slow-growing and frost-tolerant species that produce small quantity of smaller seeds with higher degree of dormancy, high temperature requirements for germination and comparatively low germination speed.

Biotic interactions, specifically competition in the lowlands and facilitation in uplands, also filtered certain functional traits in the study communities. The benign climate in lowlands promoted plant with competitive strategies including fast growth and resource acquisition (vegetative growth traits) and early and fast germination (germination traits), whereas the effects of facilitation on the vegetative and germination traits were cancelled out by the strong abiotic filtering.

The changes in the main dispersal vector from zoochory to anemochory along the gradient strongly affected the dispersal and the seed morphological trait structure of the communities. Specifically, stronger vertical turbulence and moderate warm-upwinds combined with low grazing intensity selected for light and non-round shaped seeds with lower terminal velocity and endozoochorous potential.

Synthesis. We clearly demonstrate that, in addition to vegetation traits, seed traits can substantially contribute to functional structuring of plant communities along environmental gradients. Thus, the, hard’ seed traits related to germination and dispersal are critical to detect multiple, complex community assembly rules. Consequently, such traits should be included in core lists of plant traits and, when applicable, be incorporated into analysis of community assembly.
Population coding and oscillatory subspace synchronization integrate context into actions
Authors: Weber Jan , Solbakk Anne-Kristin , Blenkmann Alejandro O. , Llorens Anais , Funderud Ingrid , Leske Sabine , Larsson Pål Gunnar , Ivanovic Jugoslav , Knight Robert T. , Endestad Tor , Helfrich Randolph F.
Published: December 2021

Contextual cues and prior evidence guide human goal-directed behavior. To date, the neurophysiological mechanisms that implement contextual priors to guide subsequent actions remain unclear. Here we demonstrate that increasing behavioral uncertainty introduces a shift from an oscillatory to a continuous processing mode in human prefrontal cortex. At the population level, we found that oscillatory and continuous dynamics reflect dissociable signatures that support distinct aspects of encoding, transmission and execution of context-dependent action plans. We show that prefrontal population activity encodes predictive context and action plans in serially unfolding orthogonal subspaces, while prefrontal-motor theta oscillations synchronize action-encoding population subspaces to mediate the hand-off of action plans. Collectively, our results reveal how two key features of large-scale population activity, namely continuous population trajectories and oscillatory synchrony, operate in concert to guide context-dependent human behavior.
Use of standard U-bottom and V-bottom well plates to generate neuroepithelial embryoid bodies
Authors: Buentello David Choy , Koch Lena Sophie , Santiago Grissel Trujillo-de , Alvarez Mario Moisés , Broersen Kerensa
Published: December 2021

The use of organoids has become increasingly popular recently due to their self-organizing abilities, which facilitate developmental and disease modeling. Various methods have been described to create embryoid bodies (EBs) generated from embryonic or pluripotent stem cells but with varying levels of differentiation success and producing organoids of variable size. Commercial ultra-low attachment (ULA) V-bottom well plates are frequently used to generate EBs. These plates are relatively expensive and not as widely available as standard concave well plates. Here, we describe a cost-effective and low labor-intensive method that creates homogeneous EBs at high yield in standard V- and U-bottom well plates by applying an antiadherence solution to reduce surface attachment, followed by centrifugation to enhance cellular aggregation. We also explore the effect of different seeding densities, in the range of 1 to 11 ×103 cells per well, for the fabrication of neuroepithelial EBs. Our results show that the use of V-bottom well plates briefly treated with anti-adherent solution (for 5 min at room temperature) consistently yields functional neural EBs in the range of seeding densities from 5 to 11×103 cells per well. A brief post-seeding centrifugation step further enhances EB establishment. EBs fabricated using centrifugation exhibited lower variability in their final size than their noncentrifuged counterparts, and centrifugation also improved EB yield. The span of conditions for reliable EB production is narrower in U-bottom wells than in V-bottom wells (i.e., seeding densities between 7×103 and 11×103 and using a centrifugation step). We show that EBs generated by the protocols introduced here successfully developed into neural organoids and expressed the relevant markers associated with their lineages.

We anticipate that the cost-effective and easily implemented protocols presented here will greatly facilitate the generation of EBs, thereby further democratizing the worldwide ability to conduct organoid-based research.