bluuebunny/crossref_metadata_2025 huggingface dataset:
Hepatic Histology in Treatment‐naïve Children With Chronic Hepatitis B Infection Living in the United States and Canada
Authors: Rodriguez‐Baez Norberto , Murray Karen F. , Kleiner David E. , Ling Simon C. , Rosenthal Philip , Carlin Kristen , Cooper Kara , Schwarz Kathleen B. , Schwarzenberg Sarah J. , Teckman Jeffrey H. , Ghany Marc G. , Alawad Ahmad Samer
Published: April 2020

Objectives:

Chronic hepatitis B virus infection is a major cause of morbidity and mortality. The aim of the study is to describe the hepatic histology in children chronically infected with hepatitis B virus living in the United States and Canada.

Methods:

Liver biopsies of 134 treatment‐naïve children with chronic hepatitis B virus infection were scored for inflammation, fibrosis, and other histological features, and correlated with clinical and laboratory data.

Results:

Sixty percentage of subjects acquired the infection vertically, 51% were male, and 69% were hepatitis B e antigen‐positive at the time of the biopsy. Hepatitis B DNA levels were generally high (mean 7.70 log IU/mL), as was serum alanine aminotransferase (median 120 U/L). Using the Ishak‐modified histology activity index scoring system, interface hepatitis was mild in 31%, moderate in 61%, and severe in 6%. Lobular inflammation was mild in 54%, moderate in 29%, and marked in 7%. Portal inflammation was mild in 38% and moderate in 62% of subjects. Eighteen percentage had no fibrosis, 59% had portal expansion without bridging fibrosis, 19% had bridging fibrosis, and 4% had cirrhosis. Alanine aminotransferase positively correlated with inflammation and fibrosis. Neither age, duration of infection, nor Hepatitis B virus DNA levels correlated with fibrosis. Fibrosis‐4 index did not correlate with fibrosis but correlated with inflammation. Aspartate aminotransferase/platelet ratio index correlated with both inflammation and fibrosis.

Conclusions:

Chronic hepatitis B virus infection results in significant inflammation and fibrosis during childhood. Serum alanine aminotransferase is a strong indicator of the severity and extent of hepatic inflammation and fibrosis.
Coexistence of Conventional Leiomyoma, Fumarate Hydratase-deficient Atypical Leiomyoma, and Perivascular Epithelioid Cell Tumor in a Uterus: A Case Study
Authors: Liu Yuehua , DeLeon Essel Marie B. , Okour Salman , Vang Russell , Hung Chien-Fu , Wu Tzyy-Choou , Ronnett Brigitte M. , Xing Deyin
Published: April 2020

A 44-yr-old woman with menorrhagia and uterine fibroids underwent total laparoscopic hysterectomy, revealing several submucosal, intramural, and subserosal tan-white nodules in the uterus. Microscopic examination revealed tumors displaying 3 distinct morphologies: 1 tumor with features of conventional leiomyoma; 1 tumor with increased cellularity, staghorn/hemangiopericytoma-like vasculature, and occasional atypical cells with prominent red nucleoli and some perinucleolar halos suggesting a fumarate hydratase (FH)-deficient atypical leiomyoma; and 1 tumor with an admixture of epithelioid and spindled cells with the former arranged around blood vessels suggesting a perivascular epithelioid cell tumor (PEComa). Immunohistochemical studies confirmed these diagnoses by demonstrating loss of FH expression in the atypical leiomyoma and diffuse expression of HMB45 and cathepsin K in the tumor with epithelioid features. Sanger sequencing analysis revealed that the FH-deficient atypical leiomyoma harbored a c.181A>G (p.Lys61Glu) mutation in exon 2 of the FH gene. As this mutation was not present in either the other tumors or peripheral blood, the mutation is somatic and hereditary leiomyomatosis and renal cell cancer syndrome is excluded. This case highlights the importance of thorough examination of uterine mesenchymal tumors with atypical and epithelioid features so that tumors with some potential for recurrence (PEComas) and those that might indicate a hereditary cancer syndrome (FH-deficient atypical leiomyoma) are identified and can trigger appropriate clinical investigation and follow-up.
Early Progression and Immune Reconstitution Inflammatory Syndrome During Treatment of Mild-To-Moderate Kaposi Sarcoma in Sub-Saharan Africa and South America: Incidence, Long-Term Outcomes, and Effects of Early Chemotherapy
Authors: Nyirenda Mulinda , Ngongondo McNeil , Kang Minhee , Umbleja Triin , Krown Susan E. , Godfrey Catherine , Samaneka Wadzanai , Mngqibisa Rosie , Hoagland Brenda , Mwelase Noluthando , Caruso Stephanie , Martinez-Maza Oto , Dittmer Dirk P. , Borok Margaret , Hosseinipour Mina C. , Campbell Thomas B. ,   for the A5264/AMC-067 team
Published: April 2020

Background:

Early progression of AIDS-associated Kaposi sarcoma (KS-PD) and immune reconstitution inflammatory syndrome (KS-IRIS) sometimes occur after the initiation of antiretroviral therapy (ART).

Methods:

Early KS-PD and KS-IRIS were assessed in the A5264/AMC-067 trial in which participants with mild-to-moderate AIDS-KS were randomized to initiate ART with either immediate or as-needed oral etoposide. Early KS-PD was defined as tumor progression within 12 weeks of ART initiation. When investigators had concern that early KS-PD was KS-IRIS, additional evaluations were performed. Suspected KS-IRIS was defined as early KS-PD accompanied by a CD4+ count increase of ≥50 cells per cubic millimeter or plasma HIV-1 RNA decrease of ≥0.5 log10 copies/mL. Clinical outcome was a composite end point categorized as failure, stable, and response at 48 and 96 weeks compared with baseline.

Results:

Fifty of 190 participants had early KS-PD (27%): 28 had KS-IRIS and 22 were not evaluated for KS-IRIS. Early KS-PD and KS-IRIS incidences with immediate etoposide versus ART alone were 16% versus 39%, and 7% versus 21%, respectively. Week 48 clinical outcome was 45% failure, 18% stable, and 37% response for no early KS-PD; 82% failure, 2% stable, and 16% response for early KS-PD; and 88% failure, 0% stable, and 12% response for KS-IRIS. Cumulative incidence of KS tumor response by week 96 was 64% for no early KS-PD, 22% with early KS-PD, and 18% with KS-IRIS.

Conclusions:

Early KS-PD, including suspected KS-IRIS, was common after starting ART for AIDS-KS and was associated with worse long-term clinical outcomes. Starting ART concurrently with etoposide reduced the incidence of both early KS-PD and KS-IRIS compared with ART alone.
The Impact of Age on Perioperative Complications After Minimally Invasive Sacrocolpopexy
Authors: Edge Preston , Barletta Kathryn , Patnam Radhika , Geller Elizabeth J.
Published: April 2020

Objective

Our aim was to compare perioperative complications between older (≥65 years), middle-age (55–64 years), and younger (<55 years) women after minimally invasive sacrocolpopexy (SCP).

Methods

This retrospective cohort study included women undergoing SCP from 2006 to 2016 at a single academic center. Our primary outcome was the rate of perioperative complications (intraoperative and postoperative within 6 weeks of surgery), between groups. Secondary outcomes included readmission and reoperation rates.

Results

There were 440 consecutive participants: 159 (36.1%) older, 160 (36.4%) middle-age, and 121 (27.5%) younger women. The overall intraoperative complication rate from SCP was 9.1%, with the most common being cystotomy (5.0%) and vaginotomy (1.8%). There were no differences in intraoperative complications between groups. Urinary tract infection (10.9%) and port-site cellulitis (3.4%) were the most common postoperative complications. For our primary outcome, younger women had a higher rate of postoperative complications compared with middle-age and older women (P < 0.001). There was no difference in postoperative complications between older and middle-aged women. In a multivariate regression controlling for comorbidity, body mass index, diabetes, smoking status, concomitant hysterectomy, and/or sling, younger women retained a higher rate of postoperative complications (odds ratio, 1.7 [1.2,2.2]). Rates of readmission (3.2%) and reoperation (0.7%) were also similar between groups.

Conclusions

The rate of perioperative complications was low with no difference in intraoperative complications. Women under 55 had a higher rate of postoperative complications compared to women age 55 to 65 years and those older than 65 years. Our results suggest that it is reasonable to offer SCP to women older than 65 years.
Pilot Trial of Midstream Urine Collection Device Versus Transurethral Catheter in Women With Lower Urinary Tract Symptoms: Practicality of Use in a Clinical Setting, Patient Preferences, and Comparison of Laboratory Findings
Authors: High Rachel , Zhang Yu , Virani Shohaib , Eggleston Kimberly , Kuehl Thomas J. , Bird Erin T. , Danford Jill M.
Published: April 2020

Objectives

This study aimed to evaluate successful use of a midstream urine collection device in women with lower urinary tract symptoms and to assess specimen contamination.

Methods

Nonpregnant women 18 years or older without use of antibiotics in the last 4 weeks were recruited. After using the midstream urine collection device to obtain a specimen in a private restroom, a paired specimen was obtained by transurethral catheterization. Patients completed preference questionnaires. Culture organisms and microscopic urinalysis of paired specimens (device vs catheterized) were compared using the McNemar χ2 test. Bivariate analysis was performed.

Results

Successful use was demonstrated in 54 (77%) of 70. Reasons for failure included inadequate specimen volume and improper device use. Older median age (50 vs 72 years, P = 0.0003) and history of diabetes (7% vs 27%, P = 0.037) were associated with failed use. Organisms were discordant in 21 (41%) of 51 paired urine culture specimens. The device detected 7 (88%) of 8 uropathogens. There were no detectable differences in microscopic urinalysis.

Conclusions

The midstream urine collection device could increase comfort, and many patients prefer it to transurethral catheterization. With proper patient selection and instructions for use, this device could increase satisfaction. Further studies are needed to assess contamination rates with this device.
Effect of myofibre architecture on ventricular pump function by using a neonatal porcine heart model: from DT-MRI to rule-based methods
Authors: Guan Debao , Yao Jiang , Luo Xiaoyu , Gao Hao
Published: April 2020

Myofibre architecture is one of the essential components when constructing personalized cardiac models. In this study, we develop a neonatal porcine bi-ventricle model with three different myofibre architectures for the left ventricle (LV). The most realistic one is derived from
ex vivo
diffusion tensor magnetic resonance imaging, and other two simplifications are based on rule-based methods (RBM): one is regionally dependent by dividing the LV into 17 segments, each with different myofibre angles, and the other is more simplified by assigning a set of myofibre angles across the whole ventricle. Results from different myofibre architectures are compared in terms of cardiac pump function. We show that the model with the most realistic myofibre architecture can produce larger cardiac output, higher ejection fraction and larger apical twist compared with those of the rule-based models under the same pre/after-loads. Our results also reveal that when the cross-fibre contraction is included, the active stress seems to play a dual role: its sheet-normal component enhances the ventricular contraction while its sheet component does the opposite. We further show that by including non-symmetric fibre dispersion using a general structural tensor, even the most simplified rule-based myofibre model can achieve similar pump function as the most realistic one, and cross-fibre contraction components can be determined from this non-symmetric dispersion approach. Thus, our study highlights the importance of including myofibre dispersion in cardiac modelling if RBM are used, especially in personalized models.
The smallest known Devonian tetrapod shows unexpectedly derived features
Authors: Ahlberg Per E. , Clack Jennifer A.
Published: April 2020

A new genus and species of Devonian tetrapod,Brittagnathus minutusgen. et sp. nov., is described from a single complete right lower jaw ramus recovered from theAcanthostegamass-death deposit in the upper part of the Britta Dal Formation (upper Famennian) of Stensiö Bjerg, Gauss Peninsula, East Greenland. Visualization by propagation phase contrast synchrotron microtomography allows a complete digital dissection of the specimen. With a total jaw ramus length of 44.8 mm,Brittagnathusis by far the smallest Devonian tetrapod described to date. It differs from all previously known Devonian tetrapods in having only a fang pair without a tooth row on the anterior coronoid and a large posterior process on the posterior coronoid. The presence of an incipient surangular crest and a concave prearticular margin to the adductor fossa together cause the fossa to face somewhat mesially, reminiscent of the condition in Carboniferous tetrapods. A phylogenetic analysis placesBrittagnathuscrownward to other Devonian tetrapods, adjacent to the Tournaisian genusPederpes. Together with other recent discoveries, it suggests that diversification of ‘Carboniferous-grade’ tetrapods had already begun before the end of the Devonian and that the group was not greatly affected by the end-Devonian mass extinction.
Modulating yaw with an unstable rigid body and a course-stabilizing or steering caudal fin in the yellow boxfish (Ostracion cubicus)
Authors: Boute Pim G. , Van Wassenbergh Sam , Stamhuis Eize J.
Published: April 2020

Despite that boxfishes have a rigid carapace that restricts body undulation, they are highly manoeuvrable and manage to swim with remarkably dynamic stability. Recent research has indicated that the rigid body shape of boxfishes shows an inherently unstable response in its rotations caused by course-disturbing flows. Hence, any net stabilizing effect should come from the fishes' fins. The aim of the current study was to determine the effect of the surface area and orientation of the caudal fin on the yaw torque exerted on the yellow boxfish,Ostracion cubicus, a square cross-sectional shaped species of boxfish. Yaw torques quantified in a flow tank using a physical model with an attachable closed or open caudal fin at different body and tail angles and at different water flow speeds showed that the caudal fin is crucial for controlling yaw. These flow tank results were confirmed by computational fluid dynamics simulations. The caudal fin acts as both a course-stabilizer and rudder for the naturally unstable rigid body with regard to yaw. Boxfishes seem to use the interaction of the unstable body and active changes in the shape and orientation of the caudal fin to modulate manoeuvrability and stability.
Stability of women's facial shape throughout the menstrual cycle
Authors: Marcinkowska U. M. , Holzleitner I. J.
Published: April 2020

Facial characteristics can serve as a cue for judgements of multiple human traits, from maternal tendencies, overall fertility to sexual openness. In this study, we tested previously found fluctuations in facial shape throughout the menstrual cycle. With methods more robust than those formerly used (larger sample size and detailed hormonal assessments determining the timing of the ovulation), we did not find significant changes in either of the three facial measurements conducted: symmetry, averageness and sexual dimorphism (all
F
≤ 0.78, all partial
η
2
≤ 0.01, all
p
≥ 0.542). After narrowing the sample to cycles that had a higher probability of being ovulatory (based on daily measurements of luteinizing hormone and oestradiol), the results remained non-significant (all
F
≤ 1.20, all partial
η
2
≤ 0.03, all
p
≥ 0.315). Our results (i) suggest that the previously found increased facial attractiveness of women in the most fertile phase of the menstrual cycle is not driven by changes in facial shape, but might instead stem from other changes in facial appearance, such as a more attractive skin tone; and (ii) underline the importance of replication of studies with new methods.
Anthropogenic noise impairs foraging for cryptic prey via cross-sensory interference
Authors: Halfwerk Wouter , van Oers Kees
Published: April 2020

Anthropogenic noise levels are globally rising with profound impacts on ecosystems and the species that live in them. Masking or distraction by noise can interfere with relevant sounds and thereby impact ecological interactions between individuals of the same or different species. Predator–prey dynamics are particularly likely to be influenced by rising noise levels, with important population- and community-level consequences, as species may differentially adapt to noise disturbance. Acoustic noise can, however, also impair the use of visual information by animals through the process of cross-sensory interference, possibly impacting species interactions that have so far been largely ignored by noise impact studies. Here, we assessed how noise affected the performance of great tit (
Parus major
) foraging on cryptic prey. Birds trained individually to search for paper moths differing in the level of camouflage with the test background were tested in the presence and absence of noise. We found that noise significantly increased approach and attack latencies, but that the effect depended on the level of crypsis. Noise increased latencies for cryptic prey targets, but not for conspicuous and colour-matched prey targets. Our results show that noise can interfere with the processing of visual information, particularly in difficult tasks such as separating objects from a similar looking background. These results have important ecological and evolutionary implications as they demonstrate how globally rising anthropogenic noise levels can influence the arms race between predators and prey across sensory domains.
Vasoactive intestinal peptide as a mediator of the effects of a supergene on social behaviour
Authors: Horton Brent M. , Michael Christina M. , Prichard Mackenzie R. , Maney Donna L.
Published: April 2020

Supergenes, or linked groups of alleles that are inherited together, present excellent opportunities to understand gene–behaviour relationships. In white-throated sparrows (Zonotrichia albicollis), a supergene on the second chromosome associates with a more aggressive and less parental phenotype. This supergene includes the gene for vasoactive intestinal peptide (VIP), a neuropeptide known to play a causal role in both aggression and parental behaviour. Here, using a free-living population, we compared the levels of VIP mRNA between birds with and without the supergene. We focused on the anterior hypothalamus and infundibular region, two brain regions containing VIP neurons known to play a causal role in aggression and parental behaviour, respectively. First, we show that the supergene enhances VIP expression in the anterior hypothalamus and that expression positively predicts vocal aggression independently of genotype in both sexes. Next, we show that the supergene reduces VIP expression in the infundibular region, which suggests reduced secretion of prolactin, a pro-parental hormone. Thus, the patterns of VIP expression in these two regions are consistent with the enhanced aggression and reduced parental behaviour of birds with the supergene allele. Our results illustrate mechanisms by which elements of genomic architecture, such as supergenes, can contribute to the evolution of alternative behavioural phenotypes.
The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases
Authors: Close Roger A. , Benson Roger B. J. , Alroy John , Carrano Matthew T. , Cleary Terri J. , Dunne Emma M. , Mannion Philip D. , Uhen Mark D. , Butler Richard J.
Published: April 2020

There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 60 859 fossil occurrences, we show that the spatial extent of the worldwide terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic. Changes in spatial sampling explain up to 67% of the change in known fossil species counts, and these changes are decoupled from variation in habitable land area that existed through time. Spatial sampling therefore represents a real and profound sampling bias that cannot be explained as redundancy. To address this bias, we estimate terrestrial tetrapod diversity for palaeogeographical regions of approximately equal size. We find that regional-scale diversity was constrained over timespans of tens to hundreds of millions of years, and similar patterns are recovered for major subgroups, such as dinosaurs, mammals and squamates. Although the Cretaceous/Palaeogene mass extinction catalysed an abrupt two- to three-fold increase in regional diversity 66 million years ago, no further increases occurred, and recent levels of regional diversity do not exceed those of the Palaeogene. These results parallel those recovered in analyses of local community-level richness. Taken together, our findings strongly contradict past studies that suggested unbounded diversity increases at local and regional scales over the last 100 million years.
Effectiveness of active learning for ecology teaching: the perspective of students vs their grades
Authors: Sperber Carlos Frankl , Szinwelski Neucir , Ferreira Frederico Fernandes , Paiva Lucas Ferreira , Prasniewski Victor Mateus , de Paula Teixeira Ana Flávia , Costa Bruno Cabral , Campos Renata Bernardes Faria , Vaz de Mello Rita Márcia Andrade , Wiggins Benjamin
Published: April 2020

We evaluated the effectiveness of active learning for ecology teaching by comparing the perspective of students to their grades in exams. We estimated the perspective of the students through anonymous survey; we used students’ exam grades to estimate their ecology learning, and their effort and performance in the active learning tasks through their grades and proportion of intermediate steps for each active learning task. Active learning involved teachers’ stimuli for students’ active involvement, extra-class group task, individual online writing assessments, redoing exam in pairs, and classroom writing group assessments. We also evaluated the impact, unto the effectiveness of active learning, of several student characteristics, such as sex, age, individual study effort, and previous basic knowledge. We found that self-evaluated learning increased linearly with teachers’ attempts to stimulate students’ active involvement (P= 0.0003), extra-class group task (P= 0.0003), and previous basic knowledge (P= 0.02), while students’ grades increased asymptotically with extra-class group task (P <2−16), and increased linearly with online writing assessments (P= 9.3−8) and classroom-based writing group assessments (P= 0.03). Our results showed that students perceive most part of the effectiveness of active-learning tasks and of teachers’ efforts. We showed that active learning tasks are complementary, so we recommend that teachers in both college and high school should implement simultaneous active-learning tasks, that include extra-class work in group, individual and group writing assessments, and should stimulate students’ engagement through respectful and non-authoritarian behavior of the teacher. Our results also showed that previous basic knowledge also plays a central role in driving effective learning, evidencing the importance of students instruction outside college. The applied teaching methodology is cheap and feasible for large classes. In these times of rising intolerance, prejudice, dismiss of environmental issues and disregard of science itself, we need an effective, pluralistic, respectful, and student-centred education, that fosters critical thinking, tolerance and respect for differing points of view.
Corona Epidemic in Indian context: Predictive Mathematical Modelling
Authors: Bhola Jyoti , Venkateswaran Vandana Revathi , Koul Monika
Published: April 2020

The novel Coronavirus pathogen Covid-19 is a cause of concern across the world as the human-to-human infection caused by it is spreading at a fast pace. The virus that first manifested in Wuhan, China has travelled across continents. The increase in number of deaths in Italy, Iran, USA, and other countries has alarmed both the developed and developing countries. Scientists are working hard to develop a vaccine against the virus, but until now no breakthrough has been achieved. India, the second most populated country in the world, is working hard in all dimensions to stop the spread of community infection. Health care facilities are being updated; medical and paramedical staffs are getting trained, and many agencies are raising awareness on the issues related to this virus and its transmission. The administration is leaving no stone unturned to prepare the country to mitigate the adverse effects. However, as the number of infected patients, and those getting cured is changing differently in different states everyday it is difficult to predict the spread of the virus and its fate in Indian context. Different states have adopted measures to stop the community spread. Considering the vast size of the country, the population size and other socio-economic conditions of the states, a single uniform policy may not work to contain the disease. In this paper, we discuss a predictive mathematical model that can give us some idea of the fate of the virus, an indicative data and future projections to understand the further course this pandemic can take. The data can be used by the health care agencies, the Government Organizations and the Planning Commission to make suitable arrangements to fight the pandemic. Though the model is preliminary, it can be used at regional level to manage the health care system in the present scenario. The recommendations can be made, and advisories prepared based on the predictive results that can be implemented at regional levels.
Analysis of electronic health records reveals medication-related interference on point-of-care urine drug screening assays
Authors: Ayala-Lopez Nadia , Colby Jennifer M. , Hughey Jacob J.
Published: April 2020

Background

Point-of-care (POC) urine drug screening (UDS) assays provide immediate information for patient management. However, POC UDS assays can produce false positive results, which may not be recognized until confirmatory testing is completed several days later. To minimize the potential for patient harm, it is critical to identify sources of interference. Here we applied an approach based on statistical analysis of electronic health record (EHR) data to identify medications that may cause false positives on POC UDS assays.

Methods

From our institution’s EHR data, we extracted 120,670 POC UDS and confirmation results, covering 12 classes of target drugs, along with each individual’s prior medication exposures. For a given assay and medication ingredient, we quantified potential interference as an odds ratio from logistic regression. We evaluated interference experimentally by spiking compounds into drug-free urine and testing the spiked samples on the POC device (Integrated E-Z Split Key Cup II, Alere).

Results

Our dataset included 446 false positive UDS results (presumptive positive screen followed by negative confirmation). We quantified potential interference for 528 assay-ingredient pairs. Of the six assay-ingredient pairs we evaluated experimentally, two showed interference capable of producing a presumptive positive: labetalol on the MDMA assay (at 200 μg/mL) and ranitidine on the methamphetamine assay (at 50 μg/mL). Ranitidine also produced a presumptive positive for opiates at 1600 μg/mL and for propoxyphene at 800 μg/mL.

Conclusions

These findings support the generalizability of our approach to use EHR data to identify medications that interfere with clinical immunoassays.
Search for trends of Covid-19 infection in India, China, Denmark, Brazil, France. Germany and the USA on the basis of power law scaling
Authors: Bhattacharya Srijit , De Alokkumar , Islam Md Moinul
Published: April 2020

The corona virus (SARS-CoV-2) or Covid-19 pandemic is growing alarmingly throughout the whole world. Using the power law scaling we analyze the data of different countries and three states of India up to 1st April, 2020 and explain in terms of power law exponent. We find significant reduction in growth of infections in China and Denmark (γ reduced from approximately 2.18 to 0.05 and 11.41 to 6.95, respectively). Very slow reduction is also seen in Brazil and Germany (γ reduced from approximately 6 to 4 and 11 to 7, respectively). Infection in India is growing (γ=9.23) though lesser in number than that in the USA (highest γ of 16 approximately, studied so far), Italy and a few other countries. Among three Indian states the growth in West Bengal (γ=0.64) is much slower than other states like Maharashtra and Kerala (γ=3.23 and 3.32, respectively). Some future predictions, though not rigid, has also been incorporated in our analysis. The earlier lock-down and stricter measures from the Governments concerned are being thought to be the only possible solutions, in the present situation, to fight against this virus.
Fast spread of COVID-19 in Europe and the US suggests the necessity of early, strong and comprehensive interventions
Authors: Ke Ruian , Sanche Steven , Romero-Severson Ethan , Hengartner Nick
Published: April 2020

Abstrat

The COVID-19 pandemic caused more than 800,000 infections and 40,000 deaths by the end of March 2020. However, some of the basic epidemiological parameters, such as the exponential epidemic growth rate andR0are debated. We developed an inference approach to control for confounding factors in data collection, such as underreporting and changes in surveillance intensities, and fitted a mathematical model to infection and death count data collected from eight European countries and the US. In all countries, the early epidemic grew exponentially at rates between 0.19-0.29/day (epidemic doubling times between 2.4-3.7 days). This suggests a highly infectious virus with anR0likely between 4.0 and 7.1. We show that similar levels of intervention efforts are needed, no matter the goal is mitigation or containment. Early, strong and comprehensive intervention efforts to achieve greater than 74-86% reduction in transmission are necessary.

One-sentence Summary

We estimated that COVID-19 spreads rapidly in 8 European countries and the US, suggesting that early, strong and comprehensive interventions are necessary.
EARLY DETECTION OF COVID-19
Authors: Sattar Hashmi Hafiz Abdul , Asif Hafiz Muhammad
Published: April 2020

Since SARS-Cov-2 epidemic appeared in Wuhan China, it became challenge for health authorities to counter Covid-19 epidemic. Early evaluation of suspects, screening for Covid-19 and management posed challenge to health authorities especially in developing countries which were not ready to cope with it. Early mild symptoms appeared during course of disease provide a chance to early detect Covid-19. We use retrospective methodology to collect available data on early sign and symptoms of Covid-19 through accessing World Health Organization (WHO) webpages, New England Journal of Medicine (NEJM), Nature Journal, Journal of American Medical Association (JAMA) network, British Medical Journal (BJM), Lancet and other world renowned journal publications to establish a relationship of early symptoms for detection of Covid-19. Data of 2707 Covid-19 laboratory confirmed cases was collected and analyzed for early signs. Available data was categorized into physical and blood biomarkers. This categorized data was assessed for scoring early detection of Covid-19 by scoring Hashmi-Asif Covid-19 formula. Each characteristic was given a score in Hashmi-Asif Covid-19 chart with maximum score of 28. Scoring 16 on chart means Covid-19 will fully develop in near future. Correlation of each sign and symptoms with development of Covid-19 in formula showed significant correlation assessed by Pearson correlation and Spearman Correlation coefficient (rho) showed significant correlation of development of Covid-19 with fever 64.11% (P=0.001), cough 65% and dry mucus 19.67% equally sensitive (P=0.000), leukopenia 19.06% (P=0.006), lymphopenia 52.93% (P=0.005), thrombopenia 19.1% (P=0.013), elevated Aspartate aminotransferase 12.79% (P=0.007) and elevated Alanine aminotransferase 11.34% (P=0.006). Chart can sense Covid-19 progression 72-96 hours earlier compared to usual course of disease and detection by standard method. Chart for early detection provides early quarantine decision to reduce disease spread and give ample time for intervening disease progression to reduce morbidity time due to Covid-19.
Association of COVID-19 Infections in San Francisco in Early March 2020 with Travel to New York and Europe
Authors: Gu Wei , Reyes Kevin , Hsu Elaine , Miller Steve , Chiu Charles
Published: April 2020

Real-time dissemination of epidemiological survey data from positive COVID-19 cases is critical to support efforts to contain or reduce spread of viral infection in the community. Here we detected a significant association between domestic travel or travel to Europe and the identification of new cases in San Francisco, California, USA. These findings suggest that domestic and European travelers may need to be prioritized for evaluation of acute infection from COVID-19 in the setting of limited testing capacity.
Development of the reproduction number from coronavirus SARS-CoV-2 case data in Germany and implications for political measures
Authors: Khailaie Sahamoddin , Mitra Tanmay , Bandyophadhyay Arnab , Schips Marta , Mascheroni Pietro , Vanella Patrizio , Lange Berit , Binder Sebastian C. , Meyer-Hermann Michael
Published: April 2020

The novel Coronavirus SARS-CoV-2 (COVID-19) has induced a world-wide pandemic and subsequent non-pharmaceutical interventions (NPI) in order to control the spreading of the virus. NPIs are considered to be critical in order to at least delay the peak number of infected individuals and to prevent the health care system becoming overwhelmed by the number of patients to treat in hospitals or in intensive care units (ICUs). However, there is also increasing concern that the NPIs in place would increase mortality because of other diseases, increase the frequency of suicide and increase the risk of an economic recession with unforeseeable implications. It is therefore instrumental to evaluate the necessity of NPIs and to monitor the progress of containment of virus spreading.

We used a data-driven estimation of the evolution of the reproduction number for viral spreading in Germany as well as in all its federal states. Based on an extended infection-epidemic model, parameterized with data from the Robert Koch Institute and, alternatively, with parameters stemming from a fit to the initial phase of COVID-19 spreading in different regions of Italy, we found that the reproduction number was decreased to a range below 1 in all federal states. The development in Germany suggests that NPIs can be partially released based on an established new culture of social distancing, face masks and mutual care within the population. However, any release of measures delays reaching low incidence numbers. The strategy to reduce daily new cases to a sufficiently low level to be controlled by contact tracing and testing turned out to work in Germany. This requires a responsible behaviour of the population, optimised contact tracing techniques and extended testing capacities in contact clusters.

Author summary

As of mid-June Germany was able to control the pandemic to an extent that the health care system was not overwhelmed and the daily new reported infections appear under control. We analysed the evolution of the reproduction number during the epidemic in Germany and the efficiency of non-pharmaceutical interventions (NPIs) in containing viral spread. The results suggest that the cultural change induced by NPIs in interpersonal interactions and distancing allows for a partial release of political measures. However, this requires a functional case isolation and contact tracing of new cases by local health departments, early identification of contact clusters and consequent isolation of those clusters.
Little Risk of the COVID-19 Resurgence on Students in China (outside Hubei) Caused by School Reopening
Authors: Long Cheng , Zeng Tieyong , Fu Xinmiao
Published: April 2020

Objective

School reopening has not yet started in China where the COVID-19 outbreak has reached ending stage, largely due to a great concern about COVID-19 infections on students. We attempted to quantitatively evaluate the risk of COVID-19 infections on students caused by school reopening.

Study design

We collected the data of the numbers of teachers, population size and newly confirmed COVID-19 cases in the past 14 days in typical provinces/cities of China, and then analyzed the risk of COVID-19 infections in schools with respect to each province/city.

Methods

A step-by-step procedure was explored to calculate the probability of COVID-19 infections on students as transmitted from infected teachers. Two critical assumptions for analysis were proposed: (i) only locally generated cases were counted while imported cases were omitted; (ii) the secondary attack rate of the COVID-19 virus in schools is similar to that in households in China, ranging from 3-10%.

Results

The probability of COVID-19 resurgence within one week on students of primary, middle and high schools in China (outside Hubei) is extremely low (<0.2%) in each province/city, and such probability can be updated daily and weekly based on the newly confirmed cases in the past 14 days. In some areas without newly confirmed cases in the past 14 days, the risk is zero.

Conclusions

Our work provides guidance for local governments to make risk level-based policies for school reopening. Currently, the risk of COVID-19 infections on students is extremely low in China (outside Hubei) and therefore school reopening can be initiated without the endanger of infections on students.
A protocol for adding knowledge to Wikidata, a case report
Authors: Waagmeester Andra , Willighagen Egon L. , Su Andrew I , Kutmon Martina , Labra Gayo Jose Emilio , Fernández-Álvarez Daniel , Groom Quentin , Schaap Peter J. , Verhagen Lisa M. , Koehorst Jasper J.
Published: April 2020

Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a “commons”. Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modelled with entity schemas represented by Shape Expressions. As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable, is demonstrated by integrating data from NCBI Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, Human Coronavirus NL63, Human coronavirus 229E, Human coronavirus HKU1, Human coronavirus OC4).
The phenotypic changes of γδ T cells in COVID-19 patients
Authors: Lei Lei , Qian Hongbo , Yang Xiaofang , Zhou Xiaobo , Zhang Xingzhe , Zhang Dan , Dai Tongxin , Guo Rui , Shi Lin , Cheng Yanbin , Zhang Baojun , Hu Jinsong , Guo Yaling
Published: April 2020

A novel pneumonia-associated respiratory syndrome named coronavirus disease-2019 (COVID-19), which caused by SARS-CoV-2 and broken in Wuhan, China in the end of 2019. Unfortunately, there is no specific antiviral agent or vaccine available to treat SARS-CoV-2 infections. Also, information regarding the immunological characteristics in COVID-19 patients remains limited. Here we collected the blood samples from 18 healthy donors (HD) and 38 COVID-19 patients to analyze changes in γδ T cells. In comparison to HD, the γδ T cells percentage was decreased. γδ T cells are able to immediately respond to SARS-CoV-2 infection and upregulate the activation marker CD25. In addition, the increased expression of CD4 in γδ T cells may serve as a biomarker for the assessment of SARS-CoV-2 infection.
Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR
Authors: Wikramaratna Paul , Paton Robert S , Ghafari Mahan , Lourenço José
Published: April 2020

Reverse transcription-polymerase chain reaction (RT-PCR) assays are used to test patients and key workers for infection with the causative SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives can occur if the sample contains insufficient quantities of the virus to be successfully amplified and detected. The amount of virus in a swab is likely to vary between patients, sample location (nasal, throat or sputum) and through time as infection progresses. Here, we analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once. We identify that the probability of a positive test decreases with time after symptom onset, with throat samples less likely to yield a positive result relative to nasal samples. Empirically derived distributions of the time between symptom onset and hospitalisation allowed us to comment on the likely false negative rates in cohorts of patients who present for testing at different clinical stages. We further estimate the expected numbers of false negative tests in a group of tested individuals and show how this is affected by the timing of the tests. Finally, we assessed the robustness of these estimates of false negative rates to the probability of false positive tests. This work has implications both for the identification of infected patients and for the discharge of convalescing patients who are potentially still infectious.
Mandated Bacillus Calmette-Guérin (BCG) vaccination predicts flattened curves for the spread of COVID-19
Authors: Berg Martha K. , Yu Qinggang , Salvador Cristina E. , Melani Irene , Kitayama Shinobu
Published: April 2020

BCG vaccination may reduce the risk of a range of infectious diseases, and, if so, could serve as a protective factor against COVID-19. Here, we compared countries that mandated BCG vaccination at least until 2000 with to countries that did not (140 countries in total). To minimize any systematic effects of reporting biases, we analyzed the rate of the day-by-day increase in both confirmed cases and deaths in the first 30-day period of country-wise outbreaks. The 30-day window was adjusted to begin at the country-wise onset of the pandemic. Linear mixed models revealed a significant effect of mandated BCG policies on the growth rate of both cases and deaths after controlling for median age, gross domestic product per capita, population density, population size, net migration rate, and various cultural dimensions (e.g., individualism and the tightness vs. looseness of social norms). Our analysis suggests that mandated BCG vaccination can be effective in the fight against COVID-19.

Teaser

National policies for universal BCG vaccination are associated with flattened growth of country-wise COVID-19 cases and deaths.
Efficient sample pooling strategies for COVID-19 data gathering
Authors: Szapudi Istvan
Published: April 2020

Sample pooling of CoViD-19 PCR tests has been recently proposed as a low cost alternative to individual tests. We show that sample pooling is efficient as long as the fraction of the population infected is relatively small. Fisher information theory suggests a rule of thumb that for low infection rates p, pooling 2/p samples is close to optimal. We present a simple strategy for survey design when not even a ballpark estimate of the infection rate is available.
Using single-plant -omics in the field to link maize genes to functions and phenotypes
Authors: Felipe Cruz Daniel , De Meyer Sam , Ampe Joke , Sprenger Heike , Herman Dorota , Van Hautegem Tom , De Block Jolien , Inzé Dirk , Nelissen Hilde , Maere Steven
Published: April 2020

Most of our current knowledge on plant molecular biology is based on experiments in controlled lab environments. Over the years, lab experiments have generated substantial insights in the molecular wiring of plant developmental processes, stress responses and phenotypes. However, translating these insights from the lab to the field is often not straightforward, in part because field growth conditions are very different from lab conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field, and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional lab-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict at least some individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.
Neural signatures of performance feedback in the paced auditory serial addition task (PASAT): an ERP study
Authors: Sommer Anja , Ziegler Lukas , Plewnia Christian
Published: April 2020

Due to its importance for successful human behavior, research into cognitive control functioning has gained increasing interest. The paced auditory serial addition task (PASAT) has been used to test and train this fundamental function. It is a challenging task, requiring a high cognitive load in a stressful and frustrating environment. Its underlying neural mechanisms, however, are still unclear. To explore the neural signatures of the PASAT and their link to ongoing cognitive processing, feedback locked event-related potentials were derived from healthy participants during an adaptive 2-back version of the PASAT. Larger neural activation after negative feedback was found for feedback related negativity (FRN), P300 and late positive potential (LPP). In early stages of feedback processing (FRN), a larger difference between positive and negative feedback responses was associated with poorer overall performance, whereas this association was inverted for the later stages (P300 and LPP). This indicates stage-dependent associations of neural activation after negative information and cognitive functioning. Conceivably, increased early responses to negative feedback signify distraction whereas higher activity at later stages reflect cognitive control processes to preserve ongoing performance.