bluuebunny/crossref_metadata_2025 huggingface dataset:
Paradoxical Case Fatality Rate dichotomy of Covid-19 among rich and poor nations points to the “hygiene hypothesis”
Authors: Chatterjee Bithika , Karandikar Rajeeva Laxman , Mande Shekhar C.
Published: August 2020

In the first six months of its deadly spread across the world, the Covid-19 incidence has exhibited interesting dichotomy between the rich and the poor countries. Surprisingly, the incidence and the Case Fatality Rate has been much higher in the richer countries compared with the poorer countries. However, the reasons behind this dichotomy have not been explained based on data or evidence, although some of the factors for the susceptibility of populations to SARS-CoV-2 infections have been proposed. We have taken into consideration all publicly available data and mined for the possible explanations in order to understand the reasons for this phenomenon. The data included many parameters including demography of nations, prevalence of communicable and non-communicable diseases, sanitation parameters etc. Results of our analyses suggest that demography, improved sanitation and hygiene, and higher incidence of autoimmune disorders as the most plausible factors to explain higher death rates in the richer countries Thus, the much debated “hygiene hypothesis” appears to lend credence to the Case Fatality Rate dichotomy between the rich and the poor countries.

Significance

The current COVID-19 epidemic has emerged as one of the deadliest of all infectious diseases in recent times and has affected all nations, especially the developed ones. In such times it is imperative to understand the most significant factor contributing towards higher mortality. Our analysis shows a higher association of demography, sanitation & autoimmunity to COVID-19 mortality as compared to the developmental parameters such as the GDP and the HDI globally. The dependence of sanitation parameters as well as autoimmunity upon the mortality gives direct evidences in support of the lower deaths in nations whose population do not confer to higher standards of hygiene practices and have lower prevalence of autoimmune diseases. This study calls attention to immune training and strengthening through various therapeutic interventions across populations.
Early clinical characteristics of Covid-19: scoping review
Authors: Manoharan Lakshmi , Cattrall Jonathan W S , Harris Carlyn , Newell Katherine , Thomson Blake , Pritchard Mark G , Bannister Peter G , Solomon Tom , Horby Peter W , Sigfrid Louise , Carson Gail , Olliaro Piero
Published: August 2020

Background

The Coronavirus disease 2019 (covid-19) pandemic has spread rapidly across the globe. Accurate clinical characterisation studies conducted early in the pandemic are essential to informing research, diagnosis and clinical management efforts. In this scoping review we identify the clinical characteristics of patients admitted to hospital in the early months of the pandemic, focusing on symptoms, laboratory and imaging findings, and clinical outcomes.

Methods

A scoping review. MEDLINE, EMBASE and Global Health databases were searched for studies published from January 1st2020 to April 28th2020. Studies which reported on at least 100 hospitalised patients with covid-19 of any age were included.

Results

Of 1,249 studies identified through the search 78 studies were eligible for inclusion; one randomized control trial and 77 observational studies presenting data on 77,443 patients admitted with covid-19. Most studies were conducted in China (82%), 9% in the US and 10% in Europe and two studies were set in more than one country. No studies included patients from low and middle income countries. Coagulopathy was underrecognised as a complication in the early months of the pandemic. Use of corticosteroids varied widely, and the use of anticoagulants was reported in only one study. Fever, cough and dyspnoea are less common in older adults; gastrointestinal symptoms, as the only presenting feature was underrecognised. The most common laboratory finding was lymphocytopenia. Inflammatory biomarkers were commonly elevated, including C-reactive protein and interleukin-6. Typical computed tomography findings include bilateral infiltrates however imaging may be normal in early disease. Data on clinical characteristics in children and vulnerable populations were limited.

Conclusions

Clinical characterisation studies from early in the pandemic indicated that covid-19 is a multisystem disease, with biomarkers indicating inflammation and coagulopathy. However, early data collection on symptoms and clinical outcomes did not consistently reflect this wide spectrum. Corticosteroid use varied widely, and anticoagulants were rarely used. Clinicians should remain vigilant to the possibility of covid-19 in patients presenting without fever, cough and dyspnoea, particularly in older adults. Further characterisation studies in different at-risk populations is needed.

Review registration

Available athttps://osf.io/r2ch9
High prevalence of food insecurity, the adverse impact of COVID-19 in Brazilian favela
Authors: Manfrinato Catarina Vezetiv , Marino Aluízio , Condé Vitória Ferreira , Pinho Franco Maria do Carmo , Stedefeldt Elke , Tomita Luciana Yuki
Published: August 2020

Objective

To investigate food insecurity prevalence in two favelas in Brazil in the early weeks from physical distancing policy, between March 27, 2020 to June 1, 2020.

Design

A cross-sectional study using online questionnaire to elicit information on socioeconomic and demographic characteristics, the types of stores visited to buy food and food insecurity screening. Experience of food insecurity was collected according to the Brazilian Food Insecurity Scale. Factors associated with moderate or severe food insecurity (EBIA≥3) were investigated using the logistic regression model.

Setting

São Paulo city, Brazil.

Participants

909 householders.

Results

88% of the households included young women working as cleaners or kitchen assistants and in sales services. One-fifth of the participants were recieving federal cash transfer programme, called Bolsa Família. There were 92% households with children. The most frequent experience reported was uncertainty about food acquisition or receiving more (89%), to eat less than one should (64%), not being able to eat healthy and nutritious food (46%), and skipping a meal (39%). 47% of the participants experienced moderate or severe food insecurity. Factors associated with moderate and severe food insecurity were low income, being Bolsa Família recipient, a low level of education, and households without children.

Conclusions

Half of the participants experienced moderate or severe food insecurity, and close to ten per cent was hungry. Our data suggest that families with children were at lower risk of moderate to severe food insecurity. It is possible that nationally established social programs like Bolsa Família were protecting those families.
Reconciling epidemiological models with misclassified case-counts for SARS-CoV-2 with seroprevalence surveys: A case study in Delhi, India
Authors: Bhattacharyya Rupam , Bhaduri Ritwik , Kundu Ritoban , Salvatore Maxwell , Mukherjee Bhramar
Published: August 2020

Underreporting of COVID-19 cases and deaths is a hindrance to correctly modeling and monitoring the pandemic. This is primarily due to limited testing, lack of reporting infrastructure and a large number of asymptomatic infections. In addition, diagnostic tests (RT-PCR tests for detecting current infection) and serological antibody tests for IgG (to assess past infections) are imperfect. In particular, the diagnostic tests have a high false negative rate. Epidemiologic models with a latent compartment for unascertained infections like the Susceptible-Exposed-Infected-Removed (SEIR) models can provide predictions for unreported cases and deaths under certain assumptions. Typically, the number of unascertained cases is unobserved and thus we cannot validate these estimates for a real study except for simulation studies. Population-based seroprevalence studies can provide a rough estimate of the total number of infections and help us check epidemiologic model projections. In this paper, we develop a method to account for high false negative rates in RT-PCR in an extension to the classic SEIR model. We apply this method to Delhi, the national capital region of India, with a population of 19.8 million and a COVID-19 hotspot of the country, obtaining estimates of underreporting factor for cases at 34-53 times and that for deaths at 8-13 times. Based on a recently released serological survey for Delhi with an estimated 22.86% seroprevalence, we compute adjusted estimates of the true number of infections reported by the survey (after accounting for misclassification of the antibody test results) which is largely consistent with the model outputs, yielding an underreporting factor for cases from 30-42. Together with the model and the serosurvey, this implies approximately 96-98% cases in Delhi remained unreported and whereas only 109,140 cases were reported on July 10, the true number of infections varied somewhere between 4.4-4.6 million across different estimates. While repeated serological monitoring is resource intensive, model-based adjustments, run with the most up to date data, can provide a viable option to keep track of the unreported cases and deaths and gauge the true extent of transmission of this insidious virus.
Sooner than you think: a very early affective reaction to the COVID-19 pandemic and quarantine in Argentina
Authors: Torrente F. , Yoris A. , Low D.M. , Lopez P. , Bekinschtein P. , Manes F. , Cetkovich M.
Published: August 2020

The unique circumstances created by the COVID-19 pandemic pose serious challenges to mood stability and emotional regulation at all ages. Although many people tend to react resiliently to stress, others appear to display emotional anxiety and depression-related symptoms. In this study, we carried out a survey (N = 10,053) during the first week of the general lockdown (quarantine) in Argentina to measure early affective reactions in Argentine adults. Respondents showed substantial anxious and depressive symptoms, with 33 % and 23% of participants reporting possible depressive and anxious syndromes, respectively, with the youngest group (18 to 25 y.o.) showing the highest prevalence of symptoms. Even if prior mental health problems predisposed or aggravated the reaction, participants without prior complaints showed signs of psychological impact. Using linear regression, the most important independent variables related to depressive symptoms was the feeling of loneliness followed by daily stress. In the case of anxious states, the strongest variables were negative repetitive thinking and feeling of loneliness. Other psychological, economic, and social factors are discussed.

This study is in line with previous literature that highlight the importance of the psychological impact of pandemics, but additionally demonstrates that these reactions are present at a large scale immediately after the start of quarantine with very low infectious rates as an early anticipatory adaptive reaction leading to potential negative outcomes from adjustment disorders to major disorders. In addition, the present results provide potentially relevant information about sudden environmental impacts on affective states and specific pathways for anxiety and depression to be expressed. We end by discussing implications for public policy based on considering the most vulnerable groups.

Key Findings

More than a third of the studied sample (n = 10,053) showed substantial depressive and anxious symptoms between 5 and 7 days after the start of the national quarantine.

33.7% of the sample scored above the PHQ-9 cutoff for possible diagnosis of a depressive disorder and 23.2% for an anxiety disorder.

28.6% of the participants showed moderate and severe levels of depressive symptoms and 23.2% showed moderate and severe levels of anxiety.

The youngest participants were affected the most by the situation.

The most important factor related to depressive symptoms was the feeling of loneliness followed by daily stress.

The most important factor related to anxious states was negative repetitive thinking followed by feeling of loneliness.

The existence of previous mental health difficulties aggravated the reactions, but even people who had not sought out treatment previously showed signs of psychological impact.
Peritoneal macrophage phenotype correlates with pain scores in women with suspected endometriosis
Authors: Gibson Douglas A , Collins Frances , De Leo Bianca , Horne Andrew W , Saunders Philippa TK
Published: August 2020

Objective

To characterise peritoneal macrophage populations in women with suspected endometriosis and assess if they are correlated with severity of pelvic pain symptoms.

Design

Flow cytometry analysis of peritoneal fluid samples and clinical data.

Setting

University Research Institute.

Patients

Clinical questionnaires, surgical data and peritoneal fluid were collected with informed consent from women undergoing diagnostic laparoscopy for suspected endometriosis (n=54).

Intervention(s)

None

Main Outcome Measure(s)

Severity of pelvic pain symptoms was assessed by the EHP-30 questionnaire. Immune cells recovered from peritoneal fluid were analysed by flow cytometry.

Results

Pain scores (pain domain of EHP30) did not differ according to endometriosis diagnosis, stage of endometriosis or whether or not women were receiving hormone treatment. Analysis of immune cells in peritoneal fluid revealed two populations of peritoneal macrophages: CD14highand CD14lowwhich were not altered by menstrual cycle phase or hormone treatment. CD14highperitoneal macrophages were increased in women with endometriosis compared to those without but were not altered by coincident reproductive health issues such as infertility or heavy menstrual bleeding. Peritoneal macrophage phenotype correlated with pelvic pain symptoms in women with suspected endometriosis. Notably, CD14highperitoneal macrophages negatively correlated with pain scores whereas CD14lowperitoneal macrophages were positively correlated. This association was independent of endometriosis diagnosis.

Conclusion

Peritoneal macrophage phenotypes correlate with pelvic pain symptoms in women with suspected endometriosis and are altered by presence of disease. These results provide new insight into the association between endometriosis pathophysiology and pelvic pain symptoms.
A novel sodium signaling complex regulates uterine activity
Authors: Ferreira Juan J. , Amazu Chinwendu , Puga-Molina Lis C. , Ma Xiaofeng , England Sarah K. , Santi Celia M.
Published: August 2020

Depolarization of the myometrial smooth muscle cell (MSMC) resting membrane potential is necessary for the transition of the uterus from a quiescent state to a contractile state. The molecular mechanisms involved in this transition are not completely understood. Here, we report a novel coupled system between the Na+-activated K+channel (SLO2.1) and the non-selective Na+leak channel (NALCN) which determines the MSMC membrane potential. We show that SLO2.1 currents are activated by an inward Na+leak current carried by the NALCN channel leading to MSMC hyperpolarization. These results show an unanticipated role for the Na+leak currents in activating a negative feedback system countering the excitable effects of Na+currents. This is a novel role for the NALCN channel in which Na+acts as an intracellular signaling molecule. In fact, we report here that the net effect of Na+entry through NALCN channels is a hyperpolarization of the MSMCs plasma membrane because of the activation of SLO2.1 K channel. Importantly, we also report that a decrease in NALCN/SLO2.1 activity triggers both Ca2+entries through VDCCs, promoting myometrial contraction. Consistently, with a functional coupling, our data show that NALCN and SLO2.1 are in proximity to one another in human MSMCs. We propose that the spatial arrangement of SLO2.1 and NALCN permits these channels to functionally interact in order to regulate human MSMC membrane potential and cell excitability to modulate uterine contractile activity.
CSPα reduces aggregates and rescues striatal dopamine release in αsynuclein transgenic mice
Authors: Caló L , Hidari E , Wegrzynowicz M , Dalley JW , Schneider BL , Anichtchik O , Carlson E , Klenerman D , Spillantini MG
Published: August 2020

αSynuclein aggregation at the synapse is an early event in Parkinson’s disease and is associated with impaired striatal synaptic function and dopaminergic neuronal death. The cysteine string protein (CSPα) and αsynuclein have partially overlapping roles in maintaining synaptic function and mutations in each cause neurodegenerative diseases. CSPα is a member of the DNAJ/HSP40 family of co-chaperones and like αsynuclein, chaperones the SNARE complex assembly and neurotransmitter release. αSynuclein can rescue neurodegeneration in CSPαKO mice. However, whether αsynuclein aggregation alters CSPα expression and function is unknown. Here we show that αsynuclein aggregation at the synapse induces a decrease in synaptic CSPα and a reduction in the complexes that CSPα forms with HSC70 and STGa. We further show that viral delivery of CSPα rescuesin vitrothe impaired vesicle recycling in PC12 cells with αsynuclein aggregates andin vivoreduces synaptic αsynuclein aggregates restoring normal dopamine release in 1-120hαsyn mice. These novel findings reveal a mechanism by which αsynuclein aggregation alters CSPα at the synapse, and show that CSPα rescues αsynuclein aggregation-related phenotype in 1-120hαsyn mice similar to the effect of αsynuclein in CSPαKO mice. These results implicate CSPα as a potential therapeutic target for the treatment of early-stage PD.
Large frugivores matter more on an island: insights from island-mainland comparison of plant-frugivore communities
Authors: Naniwadekar Rohit , Gopal Abhishek , Page Navendu , Ghuman Sartaj , Ramachandran Vivek , Joshi Jahnavi
Published: August 2020

Endozoochory, a mutualistic interaction between plants and frugivores, is one of the key processes responsible for maintenance of tropical biodiversity. Islands, which have a smaller subset of plants and frugivores when compared with mainland communities, offer an interesting setting to understand the organization of plant-frugivore communities vis-a-vis the mainland sites. We examined the relative influence of functional traits and phylogenetic relationships on the plant-seed disperser interactions on an island and a mainland site. The island site allowed us to investigate the organization of the plant-seed disperser community in the natural absence of key frugivore groups (bulbuls and barbets) of Asian tropics. The endemic Narcondam Hornbill, was the most abundant frugivore on the island and played a central role in the community. Species strength, a measure of relevance of frugivores for plants, of frugivores was positively associated with their abundance. Among plants, figs had the highest species strength and played a central role in the community. Island-mainland comparison revealed that the island plant-seed disperser community was more asymmetric, connected and nested as compared to the mainland community. Neither phylogenetic relationships or functional traits (after controlling for phylogenetic relationships) were able to explain the patterns of interactions between plants and frugivores on the island or the mainland pointing towards the diffused nature of plant-frugivore interactions. The diffused nature is a likely consequence of plasticity in foraging behavior and trait convergence that contribute to governing the interactions between plants and frugivores.
Uncovering Transcriptional Dark Matter via Gene Annotation Independent Single-Cell RNA Sequencing Analysis
Authors: Wang Michael F.Z. , Mantri Madhav , Chou Shao-Pei , Scuderi Gaetano J. , McKellar David , Butcher Jonathan T. , Danko Charles G. , De Vlaminck Iwijn
Published: August 2020

Single-cell RNA sequencing (scRNA-seq) enables the study of cell biology with high resolution. scRNA-seq expression analyses rely on the availability of a high quality annotation of genes in the genome. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, gene annotations often fail to cover the full transcriptome of every cell type at every stage of development, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant information beyond the scope of the best available gene annotation. This is achieved by performing single-cell expression analysis on any region in the genome for which transcriptional products are detected. Our routine identifies transcriptionally active regions (TARs) using a hidden Markov model, generates a matrix of expression levels for all TARs across all cells in a dataset, performs single-cell TAR expression analysis to identify TARs that are biologically significant, and then annotates biologically significant TARs using gene homology analysis. This procedure leverages single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts in complex tissues and thereby uncovers biology to which scRNA-seq would otherwise be in the dark.
Memory for stimulus duration is not bound to spatial information
Authors: Kruijne Wouter , Olivers Christian N. L. , van Rijn Hedderik
Published: August 2020

Different theories have been proposed to explain how the human brain derives an accurate sense of time. One specific class of theories, intrinsic clock theories, postulate that temporal information of a stimulus is represented much like other features such as color and location, bound together to form a coherent percept. Here we explored to what extent this holds for temporal information after it has been perceived and is held in working memory for subsequent comparison. We recorded EEG of participants who were asked to time stimuli at lateral positions of the screen followed by comparison stimuli presented in the center. Using well-established markers of working memory maintenance, we investigated whether the usage of temporal information evoked neural signatures that were indicative of the location where the stimuli had been presented, both during maintenance and during comparison. Behavior and neural measures including the contralateral delay activity, lateralized alpha suppression and decoding analyses through time all supported the same conclusion: the representation of location was strongly involved during perception of temporal information, but when temporal information was to be used for comparison it no longer showed a relation to spatial information. These results support a model where the initial perception of a stimulus involves intrinsic computations, but that this information is subsequently translated to a stimulus-independent format to be used to further guide behavior.
Neural effects of placebo analgesia in fibromyalgia patients and healthy individuals
Authors: Frangos Eleni , Ceko Marta , Wang Binquan , Richards Emily A. , Gracely John L. , Colloca Luana , Schweinhardt Petra , Bushnell M. Catherine
Published: August 2020

Placebo analgesia is hypothesized to involve top-down engagement of prefrontal regions that access endogenous pain inhibiting opioid pathways. Fibromyalgia (FM) patients have neuroanatomical and neurochemical alterations in pathways relevant to placebo analgesia. Thus, it remains unclear whether placebo analgesic mechanisms would differ in FM patients compared to healthy controls (HCs). Here, using placebo-analgesia-inducing paradigms that included verbal suggestions and conditioning manipulations, we examined whether behavioral and neural placebo analgesic responses differed between 32 FM patients and 46 age- and sex-matched HCs. Participants underwent a manipulation scan, where noxious high and low heat were paired with the control and placebo cream, respectively, and a placebo experimental scan with equal noxious heat temperatures. Before the experimental scan, each participant received saline or naloxone, an opioid receptor antagonist. Across all participants, the placebo condition decreased pain intensity and unpleasantness ratings, decreased activity within the right insula and bilateral secondary somatosensory cortex, and modulated the Neurologic Pain Signature. There were no differences between HCs and FM patients in pain intensity ratings or neural responses during the placebo condition. Despite the perceptual and neural effects of the placebo manipulation, prefrontal circuitry was not activated during the expectation period and the placebo analgesia was unaltered by naloxone, suggesting placebo effects were driven more by conditioning than expectation. Together, these findings suggest that placebo analgesia can occur in both HCs and chronic pain FM patients, without the involvement of opiodergic prefrontal modulatory networks.
Evidence that non-pathogenic microorganisms drive sea star wasting disease through boundary layer oxygen diffusion limitation
Authors: Aquino Citlalli A. , Besemer Ryan M. , DeRito Christopher M. , Kocian Jan , Porter Ian R. , Raimondi Peter , Rede Jordan E. , Schiebelhut Lauren M. , Sparks Jed P. , Wares John P. , Hewson Ian
Published: August 2020

Sea star wasting disease describes a condition affecting asteroids that resulted in significant Northeastern Pacific population decline following a mass mortality event in 2013. The etiology of sea star wasting is unresolved. We hypothesized that asteroid wasting is a sequela of microbial organic matter remineralization near respiratory surfaces which leads to boundary layer oxygen diffusion limitation (BLODL). Wasting lesions were induced inPisaster ochraceusby enrichment with a variety of organic matter (OM) sources and by experimentally reduced oxygen conditions. Microbial assemblages inhabiting tissues and at the asteroid-water interface bore signatures of copiotroph proliferation before wasting onset, followed by the proliferation of putatively facultative and strictly anaerobic taxa. These results together illustrate that suboxic conditions at the animal-water interface may be established by heterotrophic bacterial activity in response to organic matter loading. Wasting susceptibility was significantly and positively correlated with rugosity, a key determinant of boundary layer thickness. At a semi-continuously monitored field site (Langley Harbor), wasting predictably occurred at annual peak or decline in phytoplankton biomass over 5 years, suggesting that primary production-derived OM may contribute to BLODL. Finally, wasting individuals from 2013 – 2014 bore stable isotopic signatures reflecting anaerobic processes which suggests that this phenomenon may have affected asteroids during mass mortality. The impacts of BLODL may be more pronounced under higher temperatures due to lower O2solubility, in more rugose asteroid species due to restricted hydrodynamic flow, and in larger specimens due to their lower surface area to volume ratios which affects diffusive respiratory potential. Moreover, our results demonstrate that marine invertebrate disease may result from heterotrophic microbial activity that occurs adjacent to respiratory tissues, which raises important questions about the etiology of marine diseases in other benthic taxa.
Cardiac Cell-Derived Matrices Impart Age-Specific Functional Properties to Human Cardiomyocytes
Authors: Kauss M. A. , Rockwood S. J. , Silva A. C. , Joy D. A. , Mendoza-Camacho N. , Whittaker M. N. , Stevenson Erica , Krogan N. J. , Swaney D. L. , McDevitt T. C.
Published: August 2020

Cell-derived matrices (CDMs) isolated from cultured cells provide complex and tissue-specific biochemical and physical cues derived from the extracellular matrix (ECM) that are lacking in typical tissue culture environments. However, current methods enhance ECM adhesion and thickness via introduction and promotion of singular matrix proteins, skewing the matrix composition, and confounding comparisons between CDMs. Here we developed a protocol that enhances CDM stability and deposition, respectively, by combining an L-polydopamine surface coating with Ficoll macromolecular crowing prior to hypotonic decellularization. This methodology was applied to the study of age-dependent phenotypic and functional changes observed in cardiac ECM by comparing the morphologic, electrophysiological and metabolic response of cardiomyocytes in response to CDMs produced by fetal and adult cardiac fibroblasts. Furthermore, mass spectrometry proteomics identified the enrichment of collagen VI in fetal CDMs, which we determined via siRNA-mediated silencing during CDM production to be necessary for maximal oxidative respiration in cardiomyocytes.
GridFree: A Python Package of Image Analysis for Interactive Grain Counting and Measuring
Authors: Hu Yang , Zhang Zhiwu
Published: August 2020

Grain characteristics, including kernel length, kernel width, and thousand kernel weight, are critical component traits for grain yield. Manual measurements and counting are expensive, forming the bottleneck for dissecting the genetic architecture of these traits toward ultimate yield improvement. High-throughput phenotyping methods have been developed by analyzing images of kernels. However, segmenting kernels from the image background and noise artifacts or from other kernels positioned in close proximity remain challenges. In this study, we developed a software package, named GridFree, to overcome these challenges. GridFree uses an unsupervised machine learning approach, K-Means, to segment kernels from the background by using principal component analysis on both raw image channels and their color indices. GridFree incorporates users’ experiences as a dynamic criterion to set thresholds for a divide-and-combine strategy that effectively segments adjacent kernels. When adjacent multiple kernels are incorrectly segmented as a single object, they form an outlier on the distribution plot of kernel area, length, and width. GridFree uses the dynamic threshold settings for splitting and merging. In addition to counting, GridFree measures kernel length, width, and area with the option of scaling with a reference object. Evaluations against existing software programs demonstrated that GridFree had the smallest error on counting seeds for multiple crops, including alfalfa, canola, lentil, wheat, chickpea, and soybean. GridFree was implemented in Python with a friendly graphical user interface to allow users to easily visualize the outcomes and make decisions, which ultimately eliminates time-consuming and repetitive manual labor. GridFree is freely available at the GridFree website (https://zzlab.net/GridFree).
The association between COVID-19-imposed lockdowns and online searches for toothache using Google Trends
Authors: Sofi-Mahmudi Ahmad , Shamsoddin Erfan , Ghasemi Peyman , Nasser Mona , Mesgarpour Bita
Published: August 2020

Objective

To assess the association between the lockdowns due to COVID-19 and global online searches for toothache using Google Trends (GT).

Methods

We investigated GT online searches for the search terms “toothache” and “tooth pain”, within the past five years. The time frame for data gathering was considered as the initiation and end dates of national/regional lockdowns in each country. Relative search volumes (RSVs) for online Google Search queries in 2019 was considered as the control. We analysed data after normalising based on the Internet penetration rate. We used one-way ANOVA to identify statistical difference for RSVs between 2020 and 2016-2019 for each country. A linear regression model was used to assess whether there is a correlation between RSVs in 2020 and gross domestic production, COVID-19 deaths, dentists’ density, YLDs of oral conditions, Internet access, lockdown duration, Education Index, and dental expenditure per capita.

Results

The results of worldwide RSVs for toothache and tooth pain also showed significantly higher values in 2020 compared to the previous four years. Of 23 included countries in our study, 16 showed significantly increased RSVs during the lockdown period compared to the same periods in the past four years. There was a statistically significant relationship between difference of RSVs means in 2020 and in 2016-2019 combined with percent of urban residency (B=-1.82; 95% CI: (-3.38, −0.26); p=0.026) and dental expenditure per capita (B=-0.42; 95% CI: (-0.80, −0.05); p=0.031) (R2=0.66).

Conclusion

Generally, the interest in toothache and tooth pain has significantly increased in 2020 compared to the last four years. This could implicitly reinforce the importance of dental care, as urgent medical care worldwide. Governments’ expenditure on oral healthcare and the rate of urban residency, could be mentioned as important factors to direct general populations’ online care-seeking behaviour with regard to dental pain.
A Study on Survival Scenario of COVID-19 patients in India: An Application of Survival Analysis on patient demographics
Authors: Kundu Sampurna , Kirti  , Mandal Debarghya
Published: August 2020

The study of transmission dynamics of COVID-19, have depicted the rate, patterns and predictions of the pandemic cases. In order to combat the disease transmission in India, the Government had declared lockdown on the 25th of March. Even after a strict lockdown nationwide, the cases are increasing and have crossed 4.5 lakh positive cases. A positive point to be noted amongst all that the recovered cases are slowly exceeding the active cases. The survival of the patients, taking death as the event that varies over age groups and gender wise is noteworthy. This study aims in carrying out a survival analysis to establish the variability in survivorship among age groups and sex, at different levels, that is, national, state and district level. The open database of COVID-19 tracker (covid19india.org) of India has been utilized to fulfill the objectives of the study. The study period has been taken from the beginning of the first case which was on 30th Jan 2020 till 30th June. Due to the amount of under-reporting of data and dropping missing columns a total of 26,815 sample patients were considered. The entry point of each patient is different and event of interest is death in the study. Kaplan Meier survival estimation, Cox proportional hazard model and multilevel survival model has been used to perform survival analysis. Kaplan Meier survival function, shows that the probability of survival has been declining during the study period of five months. A significant variability has been observed in the age groups, as evident from all the survival estimates, with increasing age the risk of dying from COVID-19 increases. When Western and Central India show ever decreasing survival rate in the framed time period then Eastern, North Eastern and Southern India shows a slightly better picture in terms of survival. Maharashtra, Gujarat, Delhi, Rajasthan and West bengal showed alrmingly poor survival as well. This study has depicted a grave scenario of gradation of ever decreasing survival rates in various regions and shows the variability by age and gender.
Characteristics of 24,516 Patients Diagnosed with COVID-19 Illness in a National Clinical Research Network: Results from PCORnet®
Authors: Block Jason P. , Marsolo Keith A. , Nagavedu Kshema , Bailey L. Charles , Cruz Henry , Forrest Christopher B. , Haynes Kevin , Hernandez Adrian F. , Kaushal Rainu , Kho Abel , McTigue Kathleen M. , Nair Vinit P. , Platt Richard , Puro Jon , Rothman Russell L. , Shenkman Elizabeth , Waitman Lemuel Russell , Weiner Mark G. , Williams Neely , Carton Thomas W. ,   Network Partners
Published: August 2020

Background

National data from diverse institutions across the United States are critical for guiding policymakers as well as clinical and public health leaders. This study characterized a large national cohort of patients diagnosed with COVID-19 in the U.S., compared to patients diagnosed with viral pneumonia and influenza.

Methods and Findings

We captured cross-sectional information from 36 large healthcare systems in 29 U.S. states, participating in PCORnet®, the National Patient-Centered Clinical Research Network. Patients included were those diagnosed with COVID-19, viral pneumonia and influenza in any care setting, starting from January 1, 2020. Using distributed queries executed at each participating institution, we acquired information for patients on care setting (any, ambulatory, inpatient or emergency department, mechanical ventilator), age, sex, race, state, comorbidities (assessed with diagnostic codes), and medications used for treatment of COVID-19 (hydroxychloroquine with or without azithromycin; corticosteroids, anti-interleukin-6 agents).

During this time period, 24,516 patients were diagnosed with COVID-19, with 42% in an emergency department or inpatient hospital setting; 79,639 were diagnosed with viral pneumonia (53% inpatient/ED) and 163,984 with influenza (41% inpatient/ED). Among COVID-19 patients, 68% were 20 to <65 years of age, with more of the hospitalized/ED patients in older age ranges (23% 65+ years vs. 12% for COVID-19 patients in the ambulatory setting). Patients with viral pneumonia were of a similar age, and patients with influenza were much younger. Comorbidities were common, especially for patients with COVID-19 and viral pneumonia, with hypertension (32% for COVID-19 and 46% for viral pneumonia), arrhythmias (20% and 35%), and pulmonary disease (19% and 40%) the most common. Hydroxychloroquine was used in treatment for 33% and tocilizumab for 11% of COVID-19 patients on mechanical ventilators (25% received azithromycin as well).

Conclusion and Relevance

PCORnet leverages existing data to capture information on one of the largest U.S. cohorts to date of patients diagnosed with COVID-19 compared to patients diagnosed with viral pneumonia and influenza.
Comparison of media and standards for SARS-CoV-2 RT-qPCR without prior RNA preparation
Authors: Ragan Katherine B. , Bhadra Sanchita , Choi Joon H. , Towers Dalton , Sullivan Christopher S. , Ellington Andrew D.
Published: August 2020

Since the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there have been demands on the testing infrastructure that have strained testing capacity. As a simplification of method, we confirm the efficacy of RNA extraction-free RT-qPCR and saline as an alternative patient sample storage buffer. In addition, amongst potential reagent shortages, it has sometimes been difficult to obtain inactivated viral particles. We have therefore also characterized armored SARS-CoV-2 RNA from Asuragen as an alternative diagnostic standard to ATCC genomic SARS-CoV-2 RNA and heat inactivated virions and provide guidelines for its use in RT-qPCR.
On the temporal spreading of the SARS-CoV-2
Authors: Bertacchini Francesca , Bilotta Eleonora , Pantano Pietro S.
Published: August 2020

The behaviour of SARS-CoV-2 virus is certainly one of the most challenging in contemporary world. Although the mathematical modelling of the virus has made relevant contributions, the unpredictable behaviour of the virus is still not fully understood. To identify some aspects of the virus elusive behaviour, we focused on the temporal characteristics of its course. We have analysed the latency trends the virus has realized worldwide, the outbreak of the hot spots, and the decreasing trends of the pandemic. We found that the spatio-temporal pandemic dynamics shows a power law distribution. As with physical systems, these changes in the pandemic’s course, which we have calledtransitional stages of contagion, highlight shared characteristics in many countries. The main results of this work is that the pandemic progression rhythms have been clearly identified for each country, providing the processes and the stages at which the virus develops, thus giving important information on the activation of containment and control measures.

Highlights

Temporal spreading of the novel SARS-CoV-2 is analysed all over the world, and the distribution of infected people follows a power law.

Latency, hot spots ignition, decreasing of the virus course all over the world are detected.

As in physical systems, the virus behaviour showstransitional stagesin its evolution.

Temporal rhythms of the virus behaviour have key biological significance from the theoretical point of view, disclosing the steps of the virus evolution.

Predictions on the contagion dynamics, for each country, for all countries may be embodied into applications, for allowing forecasting about the contagion risk.
Limited Utility of Cardiovascular Risk Scores for People Living with HIV in Malawi
Authors: Goh Chia Y , Mwandumba Henry , Rapala Alicja , Tinago Willard , Sheha Irene , Chammudzi Mishek , Mallon Patrick , Klein Nigel , Khoo Saye , Kelly C
Published: August 2020

HIV is associated with increased cardiovascular disease (CVD) risk. Despite the high prevalence of HIV in low income sub-Saharan Africa, there are few data on the assessment of CVD risk in the region. In this study, we aimed to compare the utility of existing CVD risk scores in a cohort of Malawian adults, and assess to what extent they correlate with established markers of endothelial damage: carotid intima-media thickness (IMT) and pulse wave velocity (PWV).

WHO/ISH, SCORE, FRS, ASCVD, QRISK2 and D:A:D scores were calculated for 279 Malawian adults presenting with HIV and low CD4. Correlation of the calculated 10-year CVD risk score with IMT and PWV was assessed using Spearman’s rho.

The median (IQR) age of patients was 37 (31 – 43) years and 122 (44%) were female. Median (IQR) blood pressure was 120/73mmHg (108/68 – 128/80) and 88 (32%) study participants had a new diagnosis of hypertension. The FRS and QRISK2 scores included the largest number of participants in this cohort (96% and 100% respectively). D:A:D, a risk score specific for people living with HIV, identified more patients in moderate and high-risk groups. Although all scores correlated well with physiological markers of endothelial damage, FRS and QRISK2 correlated most closely with both IMT [r2 0.51, p<0.0001 and r2 0.47, p<0.0001 respectively] and PWV [r2 0.47, p<0.0001 and r2 0.5, p<0.0001 respectively].

Larger cohort studies are required to adapt and validate risk prediction scores in this region, so that limited healthcare resources can be effectively targeted.
Characteristics of COVID-19 fatality cases in East Kalimantan, Indonesia
Authors: Paramita Swandari , Isnuwardana Ronny , Duma Krispinus , Bakhtiar Rahmat , Nuryanto Muhammad Khairul , Pramulia Yudia Riries Choiru , Fitriany Evi , Aminyoto Meiliati
Published: August 2020

Introduction

Coronavirus Disease (COVID-19) is caused by SARS-CoV-2 infection. On March 2, 2020, Indonesia announced the first confirmed cases of COVID-19 infection. East Kalimantan will play an important role as the new capital of Indonesia. There is attention to the preparedness of East Kalimantan to respond to COVID-19. We report the characteristics of COVID-19 fatality cases in here.

Methods

We retrospectively analyzed the fatality cases of COVID-19 patients from the East Kalimantan Health Office information system. All patients were confirmed COVID-19 by RT-PCR examination.

Results

By July 31, 2020, 31 fatality cases of patients had been identified as having confirmed COVID-19 in East Kalimantan. The mean age of the patients was 55.1 ± 9.2 years. Most of the patients were men (22 [71.0%]) with age more than 60 years old (14 [45.2%]). Balikpapan has the highest number of COVID-19 fatality cases from all regencies. Hypertension was the most comorbidities in the fatality cases of COVID-19 patients in East Kalimantan.

Discussion

Older age and comorbidities still contributed to the fatality cases of COVID-19 patients in East Kalimantan, Indonesia. Hypertension, diabetes, cardiovascular disease, and cerebrovascular disease were underlying conditions for increasing the risk of COVID-19 getting into a serious condition.

Conclusion

Active surveillance for people older than 60 years old and having underlying diseases is needed for reducing the case fatality rate of COVID-19 in East Kalimantan.
Acute cognitive deficits after traumatic brain injury predict Alzheimer’s disease-like degradation of the human default mode network
Authors: Irimia Andrei , Maher Alexander S. , Chaudhari Nikhil N. , Chowdhury Nahian F. , Jacobs Elliot B. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: August 2020

Traumatic brain injury (TBI) and Alzheimer’s disease (AD) are prominent neurological conditions whose neural and cognitive commonalities are poorly understood. The extent of TBI-related neurophysiological abnormalities has been hypothesized to reflect AD-like neurodegeneration because TBI can increase vulnerability to AD. However, it remains challenging to prognosticate AD risk partly because the functional relationship between acute post-traumatic sequelae and chronic AD-like degradation remains elusive. Here, functional magnetic resonance imaging (fMRI), network theory and machine learning (ML) are leveraged to study the extent to which geriatric mild TBI (mTBI) can lead to AD-like alteration of resting-state activity in the default mode network (DMN). This network is found to contain modules whose extent of AD-like, post-traumatic degradation can be accurately prognosticated based on the acute cognitive deficits of geriatric mTBI patients with cerebral microbleeds. Aside from establishing a predictive physiological association between geriatric mTBI, cognitive impairment and AD-like functional degradation, these findings advance the goal of acutely forecasting mTBI patients’ chronic deviations from normality along AD-like functional trajectories. The association of geriatric mTBI with AD-like changes in functional brain connectivity as early as ∼6 months post-injury carries substantial implications for public health because TBI has relatively high prevalence in the elderly.
Peripheral innate and adaptive immune cells during COVID-19: Functional neutrophils, pro-inflammatory monocytes and half-dead lymphocytes
Authors: Ekşioğlu-Demiralp Emel , Alan Servet , Sili Uluhan , Bakan Dilek , Ocak İlhan , Yürekli Rayfe , Alpay Nadir , Görçin Serpil , Yıldız Alaattin
Published: August 2020

A better understanding of the innate and adaptive cells in the COVID-19 disease caused by the SARS-CoV-2 coronavirus is a necessity for the development of effective treatment methods and vaccines. We studied phenotypic features of innate and adaptive immune cells, oxidative burst, phagocytosis and apoptosis. One hundred and three patients with COVID-19 grouped according to their clinical features as mild (35%), moderate (40.8%), and severe (24.3%) were included in the study. Monocytes from all COVID-19 patients were CD16+ pro-inflammatory monocytes. Neutrophils were mature and functional. No defect has been found in ROS production of monocytes and neutrophils as well as no defect in their apoptosis. As bridging cells of the innate and adaptive immune system; the percentage of NK cells was in normal range whereas the percentages of CD3-CD8+CD56+ innate lymphoid and CD3+CD56+ NK like T cells were found to be high in the severe cases of COVID-19. Although absolute numbers of all lymphocyte subsets were low and showed a tendency for a gradual decrease in accord with the disease progression, in all COVID-19 patients, the lymphocyte subset with the most decreased absolute number was B lymphocytes, followed by CD4 + T cells in the severe cases. The percentages of suppressive, CD3+CD4-CD8-; HLA-DR+CD3+ and CD28-CD8+ cells were found to be significantly increased. Importantly, we demonstrated spontaneous caspase-3 activation and increased lymphocyte apoptosis. Altogether our data suggest that SARS-CoV-2 primarily affects lymphocytes not innate cells. So that, it may interrupt the cross-talk between adaptive and innate immune systems.