bluuebunny/crossref_metadata_2025 huggingface dataset:
Vectors
Authors: Swartz Clifford E.
Published: September 2020

Vectors represent physical quantities that have both magnitude and direction, but not all such quantities can be represented by vectors. It is also necessary for these quantities to combine according to vector rules. Ordinary forces, for instance, have magnitude and direction, and do combine to produce net forces in the same way that the vector model predicts. Stresses, however, are usually more complicated. They have magnitude and direction, but must be described in terms of tensors. Vector properties, including an axial direction, can be assigned to angular velocity, and the rules of combination are satisfied. The same description does not work, however, for angular displacement. Mountains have magnitude and direction (up), but cannot be represented by vectors. On paper, vectors are usually pictured by drawing arrows, but as any Indian will testify, arrows cannot be decomposed into components like vectors. Whether or not a physical quantity has vector properties must usually be determined by experiment.
Complex Numbers
Authors: Swartz Clifford E.
Published: September 2020

Complex numbers, in close analogy with the negatives, rationals, and irrational numbers, are an extension of the whole number system. They make it possible to perform all the standard algebraic operations on all numbers—such as finding the square root of a negative number. Despite their forbidding name, they are not “complex” and they should not be relegated to second-class numbership. Very real physical phenomena, which would be difficult or impossible to describe using only real numbers, can be rendered in concise and particularly simple form using complex numbers.
Differential Operators
Authors: Swartz Clifford E.
Published: September 2020

Things change. We describe these changes mathematically in terms of derivatives. A change of a variable, Φ, with respect to time is simply dΦ/dt. If the variable is also a function of position, the change in the variable depends on the direction. ∂Φ/ ∂x may be different from ∂Φ/ ∂y.
FLUIDS
Authors: Frier G. D. , Anderson F. J.
Published: September 2020

Thistle tubes with rubber diaphrams are connected to manometers. One can show that the manometer reading depends only on the depth of the sensitive surface and not its orientation.
SOUND
Authors: Frier G. D. , Anderson F. J.
Published: September 2020

A slightly flexible support is made for three identical simple pendulums. When one is put into motion with the others initially at rest, the motion is slowly passed from one pendulum to the other in a cyclic manner.
MODERN PHYSICS
Authors: Frier G. D. , Anderson F. J.
Published: September 2020

A large clear plastic box has its bottom covered with set mousetraps, each holding a ping-pong ball. A ping-pong ball is dropped into the box through a hole in the top. A model nuclear explosion follows.
Physics Laboratory Activity #24a Ohm’s Law
Authors: Nelson Jim , Nelson Jane Bray
Published: September 2020

The purpose of this laboratory activity is to learn about Ohm’s law for resistors.
Physics Laboratory Activity #29a Milli-can Experiment
Authors: Nelson Jim , Nelson Jane Bray
Published: September 2020

On the table is a collection of 35 millimeter film cans (i.e., milli-cans). Inside each can are an unknown number of identical items. Your goal is to determine as much as possible about the objects inside the cans without opening the cans. You and your laboratory partner should take five of these cans and find the mass of each can including its contents.
Teaching about Lightwave Communications
Authors: Davids Mark , Rea R. Stephen , Zitzewitz Paul W.
Published: September 2020

This book features the historical and theoretical background information necessary to understand the mysteries of modern lightwave communications. Students receive hands-on learning through a series of laboratory activities beginning with experiments originally conducted by Alexander Graham Bell in the 1880s to moderen activities such as encoding analog signals in optical communications. The equipment used is as simple, rugged, and inexpensive as possible while still working reliably.
Introduction for Workshop Leaders
Authors: Davids Mark , Rea R. Stephen , Zitzewitz Paul W.
Published: September 2020

The study of lightwave communications is both interesting and relevant to high school students. Most students are interested in CD players, digital tapes, telephones, and other forms of modern communication. This unit is designed to provide students with both the historical and theoretical background information necessary to understand the fundamentals of lightwave communication (see student objectives, p. 2-1). The most important component of this unit is the set of student lab investigations. Starting with simple components, students will build a number of devices that will allow them to understand the mysteries of modern lightwave communications systems.
Teaching about Color and Color Vision
Authors: Franklin Bill
Published: September 2020

Energy is a fundamental concept in physics, playing an important role in every aspect of the world around us. The conversion of energy among its many forms has enabled both the sustenance of living organisms on Earth and our development of a society based on the manufacture of products for our own convenience. All of these aspects of energy are treated in this resource book, beginning with the relationship between the force and distance required to pull a roller coaster to the top of its first hill along inclines of different slope, and ending with energy choices we will need to make for our future.
HOMEWORK ASSIGNMENTS
Authors: Reiland Robert J.
Published: September 2020

A large number of qualitative, semi-qualitative and quantitative homework problems on introductory magnetism can be found in frequently used textbooks such as Conceptual Physics, by Paul Hewitt, the Project Physics Text, various editions of PSSC Physics, and the question sections of college and university texts such as those by Blatt, Halliday and Resnick, Giancoli, Serway and Tipler.
PHYSICS CONTEST EVENTS
Authors: Reiland Robert J.
Published: September 2020

With a given amount of wire, a few assorted objects such as nails scissors, sand paper, and a D cell each team will construct an electromagnet. The goal will be to get the electromagnet to hold as much weight as possible.
Size-dependent male mating tactics and their morphological correlates in Poecilia gillii
Authors: Furness Andrew I , Hagmayer Andres , Pollux Bart J A
Published: September 2020

Male alternative reproductive strategies are found in some species of most major animal taxa but are especially widespread in fishes. Mature males of the shortfin molly, Poecilia gillii, display extensive variation in size and morphology. We devised a field test of a priori hypotheses regarding the interrelationships between male size, coloration, morphology and mating tactics. Males did not occur in discrete size classes, but instead occurred in a size and morphological continuum. Large males exhibited darker and more orange-coloured dorsal and caudal fins, whereas small males exhibited lighter and more inconspicuous fin coloration. Furthermore, larger males had proportionately deeper bodies, larger dorsal and caudal fins and shorter gonopodia than smaller males. Our field study of male mating behaviour revealed a lack of courtship in this species, and similar levels of mating attempts (gonopodial thrusts) irrespective of male size. Instead, small males were significantly more likely to chase females than were large males. In contrast, large males exhibited higher rates of gonoporal nibbling (a likely means by which males determine, through chemical factors, whether a female is carrying fertilizable ova) and higher likelihood of chasing other males away. In total, we found evidence for the predicted associations between male size, coloration, morphology and mating behaviour. These associations appear likely to maximize mating success for males of a given body size and phenotype.
Functional trait coordination in the ancient and nutrient-impoverishedcampo rupestre: soil properties drive stem, leaf and architectural traits
Authors: Caminha-Paiva Dario , Negreiros Daniel , Barbosa Milton , Fernandes G Wilson
Published: September 2020

Old, climatically buffered and infertile landscapes (OCBILs) are remarkably species-diverse, but the assembly of their ecological communities is largely unknown. Our goal was to understand how edaphic filters drive the functional structure of plant communities in an ancient and nutrient-impoverished ecosystem. We carried out a functional screening across four types of campo rupestre habitats with different edaphic conditions. We investigated trait–soil relationships for ironstone and quartzitic substrate to obtain the optimal trait values of each condition. In addition, we built unipartite networks to explore trait–trait relationships to assess functional coordination among organs. Lower soil pH and less soil water retention potential increased the proportion of smaller leaves, tissue dry mass and tissue density, resulting in more resource-conservative plant species and communities. Trait functions were tightly correlated among organs at both the plot and the individual level, indicating a trend of phenotypic integration. Architectural traits were central to coordination, suggesting their key role in integrating sap transport, mechanical support and leaf display. We conclude that the trait adjustments in response to soil parameters are important for the coexistence of a large number of species in the campo rupestre ecosystem.
Total endovascular repair of a mycotic thoracic aortic aneurysm in a patient with an aberrant right subclavian artery
Authors: Nakamae Kosuke , Azuma Takashi , Yokoi Yoshihiko , Niinami Hiroshi
Published: September 2020

An aberrant right subclavian artery (ARSA) is a rare arterial anomaly. Although a few cases of total endovascular repair for the ARSA aneurysm have been previously reported, anatomical limitations and the possibility of endoleaks remained. In this case, we created 4 holes on the stent graft for each cervical branch, with reference to the preoperative computed tomography findings. This approach might enable us to repair all types of thoracic aortic aneurysms with ARSA with each anatomical feature.
Degradation of butachlor and propanil by Pseudomonas sp. strain But2 and Acinetobacter baumannii strain DT
Authors: Duc Ha Danh , Thuy Nguyen Thi Dieu , Truc Huynh Thi Thanh , Nhu Nguyen Thi Huynh , Oanh Nguyen Thi
Published: September 2020

Herbicides have been extensively used globally, resulting in severe environmental pollution. Novel butachlor-degrading Pseudomonas sp. strain But2 isolated from soil can degrade butachlor regardless of the concentration and grows without a lag phase. Specific degradation was increased at 0.01–0.1 mM, and did not change significantly at higher concentrations. During degradation, 2-chloro-N-(2,6-diethylphenyl) acetamide, 2,6-diethylaniline, and 1,3-diethylbenzene were formed, which indicated that deamination occurred. Moreover, Pseudomonas sp. strains could tolerate propanil at up to 0.8 mM. The mixed bacterial culture of Pseudomonas sp. But2 and Acinetobacter baumannii DT (a propanil-degrading bacterial strain) showed highly effective biodegradation of both butachlor and propanil in liquid media and soil. For example, under treatment with the mixed culture, the half-lives of propanil and butachlor were 1 and 5 days, respectively, whereas those for the control were 3 and 15 days. The adjuvants present in herbicides reduced degradation in liquid media, but did not influence herbicide removal from the soil. The results showed that the mixed bacteria culture is a good candidate for the removal of butachlor and propanil from contaminated soils.
The potential of video imagery from worldwide cabled observatory networks to provide information supporting fish-stock and biodiversity assessment
Authors: Aguzzi J , Chatzievangelou D , Company J B , Thomsen L , Marini S , Bonofiglio F , Juanes F , Rountree R , Berry A , Chumbinho R , Lordan C , Doyle J , del Rio J , Navarro J , De Leo F C , Bahamon N , García J A , Danovaro P R , Francescangeli M , Lopez-Vazquez V , Gaughan P
Published: September 2020

Seafloor multiparametric fibre-optic-cabled video observatories are emerging tools for standardized monitoring programmes, dedicated to the production of real-time fishery-independent stock assessment data. Here, we propose that a network of cabled cameras can be set up and optimized to ensure representative long-term monitoring of target commercial species and their surrounding habitats. We highlight the importance of adding the spatial dimension to fixed-point-cabled monitoring networks, and the need for close integration with Artificial Intelligence pipelines, that are necessary for fast and reliable biological data processing. We then describe two pilot studies, exemplary of using video imagery and environmental monitoring to derive robust data as a foundation for future ecosystem-based fish-stock and biodiversity management. The first example is from the NE Pacific Ocean where the deep-water sablefish (Anoplopoma fimbria) has been monitored since 2010 by the NEPTUNE cabled observatory operated by Ocean Networks Canada. The second example is from the NE Atlantic Ocean where the Norway lobster (Nephrops norvegicus) is being monitored using the SmartBay observatory developed for the European Multidisciplinary Seafloor and water column Observatories. Drawing from these two examples, we provide insights into the technological challenges and future steps required to develop full-scale fishery-independent stock assessments.
Regenerative medicine for radiation emergencies
Authors: Higashi Yukihito , Yusoff Farina Mohamad , Kishimoto Shinji , Maruhashi Tatsuya
Published: September 2020

Hiroshima University is a ‘medical institution for tertiary radiation emergencies’ and a ‘medical support organization as a part of the International Atomic Emergency Agency Emergency Preparedness Response–Response and Assistance Network (IAEA EPR-RANET)’. To establish a system of regenerative medicine for radiation emergencies with treatment by implantation of various types of cells derived from induced pluripotent stem (iPS) cells, it is necessary to establish methods of defense against and treatment for radiation-induced damage from nuclear power plant accidents and nuclear terrorism. It is also necessary to develop cell therapy, cellular repair technology and regenerative biotechnology as regenerative medicine for radiation emergencies. Such applications have not been established yet. To develop a regenerative medical system, by using the existing one, for radiation emergencies, we will attempt to manage the cell-processing center to establish a safe and secured iPS cell bank for radiation medicine. By using this iPS cell bank as the central leverage, we will develop an education program for radiation emergency medicine and construct a network of regenerative medicine for radiation emergency medicine.
An Efficient Bedside Measure Yields Prognostic Implications for Language Recovery in Acute Stroke Patients
Authors: Keator Lynsey M. , Faria Andreia V. , Kim Kevin T. , Saxena Sadhvi , Wright Amy E. , Sheppard Shannon M. , Breining Bonnie L. , Goldberg Emily , Tippett Donna C. , Meier Erin , Hillis Argye E.
Published: September 2020

Background:

It is estimated that ∼30% of stroke survivors have aphasia, a language disorder resulting from damage to left-hemisphere language networks. In acute care settings, efficient identification of aphasia is critical, but there is a paucity of efficient bedside assessments.

Objective:

To determine whether objective measures on a picture description task administered within 48 hours post stroke (a) predict language recovery, (b) estimate left-hemisphere lesion volume and location, and (c) correlate with other bedside language assessments.

Method:

Behavioral data were scored at acute and chronic time points. Neuroimaging data were used to determine associations between the picture description task, other language assessments, and lesion volume and location.

Results:

Acute content units, age, and total lesion volume predicted communication recovery; F
3,18 = 3.98, P = 0.024; r
2 = 0.40. Significant correlations were found between the picture description task and lesion volume and location. Picture description outcomes were also associated with other clinical language assessments.

Discussion:

This picture description task quickly predicted the language performance (communication recovery and outcome) for patients who suffered a left-hemisphere stroke. Picture description task measures correlated with damage in the left hemisphere and with other, more time-consuming and cumbersome language assessments that are typically administered acutely at bedside.

Conclusion:

The predictive value of this picture description task and correlations with existing language assessments substantiate the clinical importance of a reliable yet rapid bedside measure for acute stroke patients that can be administered by a variety of health care professionals.
Investigations of Memory Monitoring in Individuals With Subjective Cognitive Decline and Amnestic Mild Cognitive Impairment
Authors: Yu Hui , Wang Kai , Zhong Ping , Cheng Huai-Dong , Lv Xin-Yi , Yuan Li-Li
Published: September 2020

Background:

Subjective cognitive decline (SCD) has been called the prodromal stage of amnestic mild cognitive impairment (aMCI); however, further investigation is needed to confirm this observation.

Objective:

To define the relationship between SCD and aMCI.

Method:

In this case-control study, we used the feeling-of-knowing in episodic memory (FOK–EM) test to measure the memory-monitoring function of 40 adults with aMCI, 60 with SCD, and 55 healthy controls.

Results:

The recognition rates of FOK–EM (53.53% ± 7.82%; 55.12% ± 6.08%) and judgment accuracy of the aMCI and SCD groups (γ values 0.21 ± 0.11; 0.30 ± 0.16) were significantly lower than those of the control group (72.32% ± 5.14%; 0.57 ± 0.16) (F = 116.24, P < 0.01; F = 128.57, P < 0.01; F = 73.33, P < 0.01). The scores for correct decision/correct recognition (RR; 27.2 ± 6.43; 29.36 ± 5.16) and correct decision/false recognition (RF; 30.41 ± 5.06; 27.26 ± 4.37) of the aMCI and SCD groups were also significantly lower than those of the control group (49.35 ± 7.13; 11.16 ± 4.35) (F
RR = 132.67, P < 0.01; F
RF = 131.8, P < 0.01).

Conclusion:

Mild clinical impairments in memory-monitoring function may precede clinically confirmed objective memory impairment in individuals with SCD.
The Unease When Using Anesthetics for Treatment-Refractory Status Epilepticus: Still Far Too Many Questions
Authors: Opić Petra , Sutter Raoul
Published: September 2020

Status epilepticus (SE), treatment-refractory status epilepticus (RSE), and super-treatment-refractory status epilepticus (SRSE) are associated with increased morbidity, mortality, and high socioeconomic burden and pose significant treatment challenges for intensivists and neurologists. To optimize and streamline emergency treatment, current practice guidelines recommend the use of continuously delivered intravenous anesthetic drugs such as midazolam, propofol, or barbiturates as the third-line therapy after first-line and second-line treatments have failed. Although the rationale for these third-line drugs seems intuitive at first glance, there is a clear paucity of evidence-based data on risks, benefits, and even on the choice of a third-line agent. Recent studies into safety and efficacy reveal disturbing results, such as a poor outcome and higher mortality associated with the use of intravenous anesthetic drugs, especially in patients with nonconvulsive SE without coma and in patients with out-of-hospital SE onset. Clinicians should deliberately weigh the advantages and disadvantages of intravenous anesthetic drug therapy in patients with different types of SE usually linked to a favorable outcome (i.e., simple partial, complex partial, or absence seizures). The lack of data to support evidence-based medicine prompts a careful balance of individual risks and benefits of intravenous anesthetic drug therapy in patients with SE, treatment-refractory SE, and super-RSE.
Drug Trials in Status Epilepticus: Current Evidence and Future Concepts
Authors: Mandge Vishal , Husain Aatif M.
Published: September 2020

Status epilepticus (SE) is a neurologic emergency with high morbidity and mortality. After many advances in the field, several unanswered questions remain for optimal treatment after the early stage of SE. This narrative review describes some of the important drug trials for SE treatment that have shaped the understanding of the treatment of SE. The authors also propose possible clinical trial designs for the later stages of SE that may allow assessment of currently available and new treatment options. Status epilepticus can be divided into four stages for treatment purposes: early, established, refractory, and superrefractory. Ongoing convulsive seizures for more than 5 minutes or nonconvulsive seizure activity for more than 10 to 30 minutes is considered early SE. Failure to control the seizure with first-line treatment (usually benzodiazepines) is defined as established SE. If SE continues despite treatment with an antiseizure medicine, it is considered refractory SE, which is usually treated with additional antiseizure medicines or intravenous anesthetic agents. Continued seizures for more than 24 hours despite use of intravenous anesthetic agents is termed superrefractory SE. Evidence-based treatment recommendations from high-quality clinical trials are available for only the early stages of SE. Among the challenges for designing a treatment trial for the later stages SE is the heterogeneity of semiology, etiology, age groups, and EEG correlates. In many instances, SE is nonconvulsive in later stages and diagnosis is possible only with EEG. EEG patterns can be challenging to interpret and only recently have consensus criteria for EEG diagnosis of SE emerged. Despite having these EEG criteria, interrater agreement in EEG interpretation can be challenging. Defining successful treatment can also be difficult. Finally, the ethics of randomizing treatment and possibly using a placebo in critically ill patients must also be considered. Despite these challenges, clinical trials can be designed that navigate these issues and provide useful answers for how best to treat SE at various stages.
Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively
Authors: Kang Heeyoung , Cha Inseong , Kim Haneul , Joh Kiseong
Published: September 2020

Two novel strains (HMF3257T and HMF4905T), isolated from freshwater and bark samples, were investigated to determine their relationships within and between species of the genus

Spirosoma

by using a polyphasic approach. They were aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria. The major fatty acids (>10%) in both strains were identified as summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and C16 : 1
ω5c, while strains HMF3257T and HMF4905T contained a moderately high amount of C16 : 0 and iso-C15 : 0, respectively. The predominant respiratory quinone was MK-7 for both strains. In addition to phosphatidylethanolamine and one unidentified glycolipid, the polar lipid profile of strain HMF3257T consisted of three unidentified aminophospholipids, one unidentified aminolipid and two unidentified polar lipids, and that of strain HMF4905T consisted of one unidentified aminophospholipid, two unidentified aminolipids and three unidentified polar lipids. The DNA G+C contents of strains HMF3257T and HMF4905T were 47.2 and 46.4 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains HMF3257T and HMF4905T are closely related to

Spirosoma migulaei

15J9-8T (97.0 % sequence similarity), while sharing 97.4 % sequence similarity with each other. The average nucleotide identity value between strains HMF3257T and HMF4905T was 81.1 %, and the digital DNA–DNA hybridization value between these two strains was 24.4 %. Based on the above data, strains HMF3257T and HMF4905T represent two novel members within the genus

Spirosoma

, for which the names Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. are proposed, respectively. The type strain of S. telluris is HMF3257T (=KCTC 62463T=NBRC 112670T) and type strain of S. arboris is HMF4905T (=KCTC 72779T=NBRC 114270T).
Mendelian pathway analysis of laboratory traits reveals distinct roles for ciliary subcompartments in common disease pathogenesis
Authors: Drivas Theodore George , Lucas Anastasia , Zhang Xinyuan , Ritchie Marylyn DeRiggi
Published: September 2020

Rare monogenic disorders of the primary cilium, termed ciliopathies, are characterized by extreme presentations of otherwise-common diseases, such as diabetes, hepatic fibrosis, and kidney failure. However, despite a revolution in our understanding of the cilium’s role in rare disease pathogenesis, the organelle’s contribution to common disease remains largely unknown. We hypothesized that common genetic variants affecting Mendelian ciliopathy genes might also contribute to common complex diseases pathogenesis more generally. To address this question, we performed association studies of 16,875 common genetic variants across 122 well-characterized ciliary genes with 12 quantitative laboratory traits characteristic of ciliopathy syndromes in 378,213 European-ancestry individuals in the UK BioBank. We incorporated tissue-specific gene expression analysis, expression quantitative trait loci (eQTL) and Mendelian disease information into our analysis, and replicated findings in meta-analysis to increase our confidence in observed associations between ciliary genes and human phenotypes. 73 statistically-significant gene-trait associations were identified across 34 of the 122 ciliary genes that we examined (including 8 novel, replicating associations). With few exceptions, these ciliary genes were found to be widely expressed in human tissues relevant to the phenotypes being studied, and our eQTL analysis revealed strong evidence for correlation between ciliary gene expression levels and patient phenotypes. Perhaps most interestingly our analysis identified different ciliary subcompartments as being specifically associated with distinct sets of patient phenotypes, offering a number of testable hypotheses regarding the cilium’s role in common complex disease. Taken together, our data demonstrate the utility of a Mendelian pathway-based approach to genomic association studies, and challenge the widely-held belief that the cilium is an organelle important mainly in development and in rare syndromic disease pathogenesis. The continued application of techniques similar to those described here to other phenotypes/Mendelian diseases is likely to yield many additional fascinating associations that will begin to integrate the fields of common and rare disease genetics, and provide insight into the pathophysiology of human diseases of immense public health burden.

Contact

theodore.drivas@gmail.com
Clinical evaluation of BD Veritor™SARS-CoV-2 point-of-care test performance compared to PCR-based testing and versus the Sofia®2 SARS Antigen point-of-care test
Authors: Young Stephen , Taylor Stephanie N. , Cammarata Catherine L. , Roger-Dalbert Celine , Montano Amanda , Griego-Fullbright Christen , Burgard Cameron , Fernandez Catherine , Eckert Karen , Andrews Jeffrey C. , Ren Huimiao , Allen Joseph , Ackerman Ronald , Cooper Charles K.
Published: September 2020

Objectives

The clinical performance of the BD Veritor™ System for Rapid Detection of SARS-CoV-2 antigen (Veritor), a chromatographic immunoassay that detects the SARS-CoV-2 nucleocapsid antigen as a point-of-care test, was evaluated on nasal specimens from individuals with COVID-19 symptoms.

Methods and Materials

Two studies were completed to determine clinical performance. In the first study, nasal specimens and either nasopharyngeal or oropharyngeal specimens from 251 participants with COVID-19 symptoms (≤7 days from symptom onset [DSO]), ≥18 years of age, were utilized to compare Veritor with the Lyra®SARS-CoV-2 PCR Assay (Lyra). In the second study, nasal specimens from 361 participants with COVID-19 symptoms (≤5 DSO), ≥18 years of age, were utilized to compare performance of Veritor to that of the Sofia®2 SARS Antigen FIA test (Sofia 2). Positive, negative, and overall percent agreement (PPA, NPA, and OPA, respectively) were the primary outcomes.

Results

In study 1, PPA for Veritor, compared to Lyra, ranged from 81.8%-87.5% for 0-1 through 0-6 DSO ranges. In study 2, Veritor had a PPA, NPA, and OPA of 97.4%, 98.1%, and 98.1%, respectively, with Sofia 2. Discordant analysis showed one Lyra positive missed by Veritor and five Lyra positives missed by Sofia 2; one Veritor positive result was negative by Lyra.

Conclusions

Veritor met FDA-EUA acceptance criteria for SARS-CoV-2 antigen testing (≥80% PPA point estimate) for the 0-5 and 0-6 DSO ranges. Veritor and Sofia 2 showed a high degree of agreement for SARS-CoV-2 detection. The Veritor test should facilitate rapid and reliable results for COVID-19 diagnosis utilizing easy-to-collect nasal swabs.

The BD Veritor SARS-CoV-2 antigen test met FDA-EUA acceptance criteria for SARS-CoV-2 antigen testing for subjects with COVID-19 symptoms (0-5 days post-onset). BD Veritor and Quidel Sofia 2 antigen tests had good agreement for SARS-CoV-2 detection; discordant analysis favored Veritor.
The impact of hypertension and use of calcium channel blockers on tuberculosis treatment outcomes
Authors: Chidambaram Vignesh , Gupte Akshay , Wang Jann-Yuan , Golub Jonathan E. , Karakousis Petros C.
Published: September 2020

Background

Hypertension induces systemic inflammation, but its impact on the outcome of infectious diseases like tuberculosis (TB) is unknown. Calcium channel blockers (CCB) improve TB treatment outcomes in pre-clinical models, but their effect in patients with TB remain unclear.

Methods

This retrospective cohort study, including all patients > 18 years receiving treatment for culture-confirmed, drug-sensitive TB from 2000 to 2016 at the National Taiwan University Hospital, assessed the association of hypertension and CCB use with all-cause and infection-related mortality during the first 9 months of TB treatment, as well as sputum-smear microscopy and sputum-culture positivity at 2 and 6 months.

Results

1052 of the 2894 patients (36.4%) had hypertension. Multivariable analysis revealed that hypertension was associated with increased mortality due to all causes (HR 1.57, 95% confidence interval[CI], 1.23-1.99) and infections (HR 1.87, 95%CI, 1.34-2.6), but there was no statistical difference in microbiological outcomes when stratified based on hypertensive group. Dihydropyridine-CCB (DHP-CCB) use was associated with reduced all-cause mortality (HR 0.67, 95%CI: 0.45-0.98) only by univariate Cox regression. There was no association between DHP-CCB use and infection-related mortality (HR 0.78, 95%CI: 0.46-1.34) or microbiological outcomes in univariate or multivariate regression analyses.

Conclusions

Patients with hypertension have increased all-cause mortality and infection-related mortality during the 9 months following TB treatment initiation. DHP-CCB use may lower all-cause mortality in TB patients with hypertension. The presence of hypertension or the use of CCB did not result in a significant change in microbiological outcomes.
Fine-scale spatial patterns of wildlife disease are common and understudied
Authors: Albery Gregory F , Sweeny Amy R , Becker Daniel J , Bansal Shweta
Published: September 2020

All parasites are heterogeneous in space, yet little is known about the prevalence and scale of this spatial variation, particularly in wild animal systems. To address this question, we sought to identify and examine spatial dependence of wildlife disease across a wide range of systems.

Conducting a broad literature search, we collated 31 such datasets featuring 89 replicates and 71 unique host-parasite combinations, only 51% of which had previously been used to test spatial hypotheses. We analysed these datasets for spatial dependence within a standardised modelling framework using Bayesian linear models, and we then meta-analysed the results to identify generalised determinants of the scale and magnitude of spatial autocorrelation.

We detected spatial autocorrelation in 48/89 model replicates (54%) across 21/31 datasets (68%), spread across parasites of all groups. Even some very small study areas (under 0.01km2) exhibited substantial spatial variation.

Despite the common manifestation of spatial variation, our meta-analysis was unable to identify host-, parasite-, or sampling-level determinants of this heterogeneity across systems. Parasites of all transmission modes had easily detectable spatial patterns, implying that structured contact networks and susceptibility effects are potentially as important in spatially structuring disease as are environmental drivers of transmission efficiency.

Our findings demonstrate that fine-scale spatial patterns of infection manifest frequently and across a range of wild animal systems, and many studies are able to investigate them whether or not the original aim of the study was to examine spatially varying processes. Given the widespread nature of these findings, studies should more frequently record and analyse spatial data, facilitating development and testing of spatial hypotheses in disease ecology. Ultimately, this may pave the way for ana prioripredictive framework for spatial variation in novel host-parasite systems.
Accurate transcription start sites enable mining for the cis-regulatory determinants of tissue specific gene expression
Authors: Ansariola Mitra , Fraser Valerie N. , Filichkin Sergei A. , Ivanchenko Maria G. , Bright Zachary A. , Gould Russell A. , Ozguc Olivia R. , O’Neil Shawn T. , Megraw Molly
Published: September 2020

Across tissues, gene expression is regulated by a combination of determinants, including the binding of transcription factors (TFs), along with other aspects of cellular state. Recent studies emphasize the importance of both genetic and epigenetic states – TF binding sites and binding site chromatin accessibility have emerged as potentially causal determinants of tissue specificity. To investigate the relative contributions of these determinants, we constructed three genome-scale datasets for both root and shoot tissues of the sameArabidopsis thalianaplants: TSS-seq data to identify Transcription Start Sites, OC-seq data to identify regions of Open Chromatin, and RNA-seq data to assess gene expression levels. For genes that are differentially expressed between root and shoot, we constructed a machine learning model predicting tissue of expression from chromatin accessibility and TF binding information upstream of TSS locations. The resulting model was highly accurate (over 90% auROC and auPRC), and our analysis of model contributions (feature weights) strongly suggests that patterns of TF binding sites within ∼500 nt TSS-proximal regions are predominant explainers of tissue of expression in most cases. Thus, in plants, cis-regulatory control of tissue-specific gene expression appears to be primarily determined by TSS-proximal sequences, and rarely by distal enhancer-like accessible chromatin regions. This study highlights the exciting future possibility of a native TF site-based design process for the tissue-specific targeting of plant gene promoters.
Amyloid particles facilitate surface-catalyzed cross-seeding by acting as promiscuous nanoparticles
Authors: Koloteva-Levine Nadejda , Marchante Ricardo , Purton Tracey J. , Hiscock Jennifer R. , Tuite Mick F. , Xue Wei-Feng
Published: September 2020

Amyloid seeds are nanometre-sized protein particles that accelerate amyloid assembly, as well as propagate and transmit the amyloid protein conformation associated with a wide range of protein misfolding diseases. However, seeded amyloid growth through templated elongation at fibril ends cannot explain the full range of molecular behaviours observed during cross-seeded formation of amyloid by heterologous seeds. Here, we demonstrate that amyloid seeds can accelerate amyloid formation via a surface catalysis mechanism without propagating the specific amyloid conformation associated with the seeds. This type of seeding mechanism is demonstrated through quantitative characterisation of the cross-seeded assembly reactions involving two non-homologous and unrelated proteins: the human Aβ42 peptide and the yeast prion-forming protein Sup35NM. Our results suggest experimental approaches to differentiate seeding by templated elongation from non-templated amyloid seeding, and rationalise the molecular mechanism of the cross-seeding phenomenon as a manifestation of the aberrant surface activities presented by amyloid seeds as nanoparticles.
Response to Kozlovet al.: Inaccurate estimation of biases in herbarium specimen data
Authors: Meineke Emily K. , Davis Charles C. , Jonathan Davies T.
Published: September 2020

Kozlov and colleagues1call into question the application of herbarium specimens to quantify historical patterns of herbivory2–5. It is already widely appreciated that collectors of herbarium specimens may tend to avoid insect damage, thus making herbivory estimates from herbarium specimens potentially down-biased2. However, Kozlovet al.additionally suggest that variation in sampling selectivity among collectors and curators may lead herbarium specimens to misrepresent patterns of herbivory in nature. The authors sought to quantify these biases by collecting and contrasting insect herbivory data across 17 plant species from herbarium versus standard field ecological sampling procedures, and then assessed the selection of these specimens by curators. They concluded that herbivory estimates from herbarium specimens are highly variable, rendering them an inaccurate representation of herbivory in nature. Our re-analysis of Kozlovet al.’s data suggests that, in contrast with their results, herbarium specimens indeed provide a useful record of herbivory as long as sample sizes are appropriate. In addition, we assert that by arguing that herbarium specimens are “distorting mirrors”, Kozlovet al.’s conclusions fundamentally overstep their data, which narrowly assesses biases across species. Kozlovet al.argue that herbarium specimens are inaccurate data sources, but fail to characterize the specific circumstances under which assumed biases would apply. Thus, Kozlovet al.’s data do not support their main premise, and the authors extrapolate beyond the specific biases investigated in their study; we believe their contribution does a disservice to researchers interested in exploring the potential value of herbarium specimens for studying herbivory through time.
Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility
Authors: Plante Jessica A. , Liu Yang , Liu Jianying , Xia Hongjie , Johnson Bryan A. , Lokugamage Kumari G. , Zhang Xianwen , Muruato Antonio E. , Zou Jing , Fontes-Garfias Camila R. , Mirchandani Divya , Scharton Dionna , Bilello John P. , Ku Zhiqiang , An Zhiqiang , Kalveram Birte , Freiberg Alexander N. , Menachery Vineet D. , Xie Xuping , Plante Kenneth S. , Weaver Scott C. , Shi Pei-Yong
Published: September 2020

A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to be defined. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an “up” conformation for binding to ACE2 receptor. Hamsters infected with D614 or G614 variants developed similar levels of weight loss. However, the G614 virus produced higher infectious titers in the nasal washes and trachea, but not lungs, than the D614 virus. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. For antibody neutralization, sera from D614 virus-infected hamsters consistently exhibit higher neutralization titers against G614 virus than those against D614 virus, indicating that (i) the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19 and (ii) therapeutic antibodies should be tested against the circulating G614 virus before clinical development.

Importance

Understanding the evolution of SARS-CoV-2 during the COVID-19 pandemic is essential for disease control and prevention. A spike protein mutation D614G emerged and became dominant soon after the pandemic started. By engineering the D614G mutation into an authentic wild-type SARS-CoV-2 strain, we demonstrate the importance of this mutation to (i) enhanced viral replication on human lung epithelial cells and primary human airway tissues, (ii) improved viral fitness in the upper airway of infected hamsters, and (iii) increased susceptibility to neutralization. Together with clinical findings, our work underscores the importance of this mutation in viral spread, vaccine efficacy, and antibody therapy.
Potential universal PCR method to detect decapod hepanhamaparvovirus (DHPV) in crustaceans
Authors: Srisala Jiraporn , Thaiue Dararat , Sanguanrut Piyachat , Aldama-Cano Diva January , Flegel Timothy W. , Sritunyalucksana Kallaya
Published: September 2020

Parvoviruses that infect the hepatopancreas (HP) of the penaeid shrimpPenaeus chinensis,P. monodon, andP. merquiensiswere previously called hepatopancreatic parvoviruses (HPV). They are now classified in the familyParvoviridae, sub-familyHamaparvovirinaeas members of the same genus calledHepanhamaparvovirusand referred to as decapod hepanhamaparvovirus, designated here as DHPV. However, a virus that causes similar lesions in the HP of the giant river prawnMacrobrachium rosenbergiiresembles hepanhamaparvoviruses by microscopy and histochemistry. Unfortunately, no genome information is yet available and PCR detection methods that work for DHPV inP. monodondo not work withM. rosenbergii. For hatchery samples ofM. rosenbergiiin Thailand with DHPV-like lesions, we hypothesized it might be possible to design primer pairs from 8 full DHPV genome sequences at GenBank for use in PCR detection of DHPV inM. rosenbergii. Using this strategy, we successfully designed a new set of primers and a PCR protocol called the DHPV-U method that gave an amplicon with DNA extracts from larvae of M. rosenberigii samples that showed DHPV-like lesions, while extracts from normal larvae gave none. DNA extracts fromP. monodoninfected with DHPV also gave amplicons. At the same time, the normal PCR method for DHPV inP. monodongave no amplicon with theM. rosenbergiiDNA extracts. The DHPV-U amplicons fromP. monodonandM. rosenbergiishared 99% sequence identity, andin situhybridization (ISH) assays using the DIG-labeled amplicon gave positive histochemical results in the HP tissue of bothP. monodonandM. rosenbergii. The DHPV-U method is now being used in Thailand for detection of DHPV in bothP. monodonandM. rosenbergii. Overall, the results support the proposal that the HP virus inM. rosenbergiiis also ahepanhamaparvovirus. Based on 100% sequence identity of the target region in the currently published DHPV sequences at GenBank, the DHPV-U method may also work for detection of other DHPV isolates.
“SARS-CoV-2 antibody seroprevalence and stability in a tertiary care hospital-setting”
Authors: Siddiqui Samreen , Naushin Salwa , Pradhan Shalini , Misra Archa , Tyagi Akansha , Loomba Menka , Waghdhare Swati , Pandey Rajesh , Sengupta Shantanu , Jha Sujeet
Published: September 2020

Background

SARS-CoV-2 infection has caused 64,469 deaths in India, with 7, 81, 975 active cases till 30th August 2020, lifting it to 3rd rank globally. To estimate the burden of the disease with time it is important to undertake a longitudinal seroprevalence study which will also help to understand the stability of anti SARS-CoV-2 antibodies. Various studies have been conducted worldwide to assess the antibody stability. However, there is very limited data available from India. Healthcare workers (HCW) are the frontline workforce and more exposed to the COVID-19 infection (SARS-CoV-2) compared to the community. This study was conceptualized with an aim to estimate the seroprevalence in hospital and general population and determine the stability of anti SARS-CoV-2 antibodies in HCW.

Methods

Staff of a tertiary care hospital in Delhi and individuals visiting that hospital were recruited between April to August 2020. Venous blood sample, demographic, clinical, COVID-19 symptoms, and RT-PCR data was collected from all participants. Serological testing was performed using the electro-chemiluminescence based assay developed by Roche Diagnostics, in Cobas Elecsys 411. Seropositive participants were followed- upto 83 days to check for the presence of antibodies.

Results

A total of 780 participants were included in this study, which comprised 448 HCW and 332 individuals from the general population. Among the HCW, seroprevalence rates increased from 2.3% in April to 50.6% in July. The cumulative prevalence was 16.5% in HCW and 23.5% (78/332) in the general population with a large number of asymptomatic individuals. Out of 74 seropositive HCWs, 51 were followed-up for the duration of this study. We observed that in all seropositive cases the antibodies were sustained even up to 83 days.

Conclusion

The cumulative prevalence of seropositivity was lower in HCWs than the general population. There were a large number of asymptomatic cases and the antibodies developed persisted through the duration of the study. More such longitudinal serology studies are needed to better understand the antibody response kinetics.
An epidemic model for economical impact predicting and spatiotemporal spreading of COVID-19
Authors: Cámara Mateo , Miravete Mario , Navarro Eduardo
Published: September 2020

Since the emergence of a new strain of coronavirus known as SARS-CoV-2, many countries around the world have reported cases of COVID-19 disease caused by this virus. Numerous people’s lives have been affected both from a health and an economic point of view. The long tradition of using mathematical models to generate insights about the transmission of a disease, as well as new computer techniques such as Artificial Intelligence, have opened the door to diverse investigations providing relevant information about the evolution of COVID-19. In this research, we seek to advance the existing epidemiological models based on microscopic Markov chains to predict the impact of the pandemic at medical and economic levels. For this purpose, we have made use of the Spanish population movements based on mobile-phone geographically-located information to determine its economic activity using Artificial Intelligence techniques and have developed a novel advanced epidemiological model that combines this information with medical data. With this tool, scenarios can be released with which to determine which restriction policies are optimal and when they have to be applied both to limit the destruction of the economy and to avoid the feared possible upsurge of the disease.