bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of highly radiopure NaI(Tl) scintillator for PICOLON dark matter search project
Authors: Fushimi K , Kanemitsu Y , Hirata S , Chernyak D , Hazama R , Ikeda H , Imagawa K , Ishiura H , Ito H , Kisimoto T , Kozlov A , Takemoto Y , Yasuda K , Ejiri H , Hata K , Iida T , Inoue K , Koga M , Nakamura K , Orito R , Shima T , Umehara S , Yoshida S
Published: February 2021

Highly radiopure NaI(Tl) was developed to search for particle candidates of dark matter. Optimized methods were combined to reduce various radioactive impurities. $^{40}$K was effectively reduced by the recrystallization method. The progenies of the decay chains of uranium and thorium were reduced by appropriate resins. The concentration of natural potassium in NaI(Tl) crystal was reduced to 20 ppb. Concentrations of alpha-ray emitters were successfully reduced by appropriate resin selection. The present concentrations of the thorium series and $^{226}$Ra were $1.2\pm1.4$$\mu$Bq/kg and $13\pm4$$\mu$Bq/kg, respectively. No significant excess in the concentration of $^{210}$Pb was obtained, and the upper limit was 5.7 $\mu$Bq/kg at 90$\#$ CL. The achieved level of radiopurity of NaI(Tl) crystals makes the construction of a dark matter detector possible.
Gamow–Teller transitions of neutron-rich N = 82,81 nuclei by shell-model calculations
Authors: Shimizu Noritaka , Togashi Tomoaki , Utsuno Yutaka
Published: February 2021

$\beta$ -decay half-lives of neutron-rich nuclei around $N=82$ are key data to understand the $r$-process nucleosynthesis. We performed large-scale shell-model calculations in this region using a newly constructed shell-model Hamiltonian, and successfully described the low-lying spectra and half-lives of neutron-rich $N=82$ and $N=81$ isotones with $Z=42\text{--}49$ in a unified way. We found that their Gamow–Teller strength distributions have a peak in the low excitation energies, which significantly contributes to the half-lives. This peak, dominated by $\nu 0g_{7/2} \to \pi 0g_{9/2}$ transitions, is enhanced on the proton-deficient side because the Pauli-blocking effect caused by occupying the valence proton $0g_{9/2}$ orbit is weakened.
Effects of bacterial cultures, enzymes, and yeast-based feed additive combinations on ruminal fermentation in a dual-flow continuous culture system
Authors: Bennett S L , Arce-Cordero J A , Brandao V L N , Vinyard J R , Agustinho B C , Monteiro H F , Lobo R R , Tomaz L , Faciola A P
Published: February 2021

Bacterial cultures, enzymes, and yeast-derived feed additives are often included in commercial dairy rations due to their effects on ruminal fermentation. However, the effects of these additives when fed together are not well understood. The objective of this study was to evaluate the changes in ruminal fermentation when a dairy ration is supplemented with combinations of bacterial probiotics, enzymes and yeast. Our hypotheses were that ruminal fermentation would be altered, indicated through changes in volatile fatty acid profile and nutrient digestibility, with the inclusion of (1) an additive, (2) yeast, and (3) increasing additive doses. Treatments were randomly assigned to 8 fermenters in a replicated 4 × 4 Latin square with four 10 d experimental periods, consisting of 7 d for diet adaptation and 3 d for sample collection. Basal diets contained 52:48 forage:concentrate and fermenters were fed 106 g of dry matter per day divided equally between two feeding times. Treatments were: control (CTRL, without additives); bacterial culture/enzyme blend (EB, 1.7 mg/d); bacterial culture/enzyme blend with a blend of live yeast and yeast culture (EBY, 49.76 mg/d); and a double dose of the EBY treatment (2×, 99.53 mg/d). The bacterial culture/enzyme blend contained five strains of probiotics (Lactobacillus animalis, Propionibacterium freudenreichii, Bacillus lichenformis, Bacillus subtilis, and Enterococcus faecium) and three enzymes (amylase, hemicellulase, and xylanase). On d 8–10, samples were collected for pH, redox, volatile fatty acids, lactate, ammonia N, and digestibility measurements. Statistical analysis was performed using the GLIMMIX procedure of SAS. Repeated measures were used for pH, redox, VFA, NH3-N, and lactate kinetics data. Orthogonal contrasts were used to test the effect of (1) additives, ADD (CTRL vs. EB, EBY, and 2X); (2) yeast, YEAST (EB vs. EBY, and 2X); and (3) dose, DOSE (EBY vs. 2X). No effects (P > 0.05) were observed for pH, redox, NH3-N, acetate, isobutyrate, valerate, total VFA, acetate:propionate, nutrient digestibility or N utilization. Within the 24 h pool, the molar proportion of butyrate increased (P = 0.03) with the inclusion of additives when compared to the control while the molar proportion of propionate tended to decrease (P = 0.07). In conclusion, the inclusion of bacterial cultures, enzymes and yeast in the diet increased butyrate concentration; but did not result in major changes in ruminal fermentation.
Effect of feeding method on nutrient utilization and cow performance in limit-fed cow-calf systems
Authors: Baber J R , Sawyer J E , Trubenbach L A , Wickersham T A
Published: February 2021

Delivery of limit-fed, complete rations requires significant capital investment, and creates logistical challenges for producers. Deconstruction and separate delivery of roughage and concentrate portions of diets may decrease feeding cost. Two experiments were conducted to evaluate the potential of separately limit-feeding roughage and concentrate. In Experiment 1, 4 ruminally cannulated steers (371 ± 12 kg bodyweight) were used in a 4 × 4 Latin square to evaluate the effects of time of concentrate delivery in deconstructed diets. Intake was restricted to 80% of predicted NEm requirements of a diet consisting of wheat straw (35%), cracked corn (29%), and distillers’ grains (27%) formulated to contain 1.58 Mcal NEm/kg. Treatments were: concentrate fed 2 h prior to wheat straw (–2S), concentrate and wheat straw fed as total mixed ration (TMR), concentrate fed 2 h after wheat straw (+2S), and concentrate fed 12 h after wheat straw (+12S). In Experiment 2, 95 mid- to late-gestation cows (503 ± 151 kg) were used in a 112-d trial to evaluate feeding system on cow performance. Cows were assigned to 1 of 12 pens. Treatments were limit-fed the complete diet from Experiment 1 (TMR), fed roughage and concentrate portions of the deconstructed TMR 12 h apart (SEP), and ad libitum bermudagrass hay (HAY). Bodyweight (BW), BCS, and back fat measures were collected every 28 d. In Experiment 1, treatment did not affect DM or OM digestion (P ≥ 0.88), rate of particulate passage (P ≥ 0.55), or ruminal DM fill (P ≥ 0.19). Fill averaged 3.8 kg DM. Nadir of ruminal pH occurred 4–8 h after concentrate was delivered, but mean ruminal pH was not different among treatments (P = 0.22) ranging from 6.4 to 6.6 for +2S and 12S, respectively. In Experiment 2, treatment did not affect final BW (518 kg; P = 0.72) or final BCS (5.6; P = 0.67), but limit-fed strategies tended (P = 0.06) to have greater final RE (137.1, 98.9, and –14.6 Mcal for TMR, SEP, and HAY, respectively). Delivering forage and concentrate separately did not change digestion, and timing of concentrate delivery had only minor effects on ruminal fermentation. Limit-feeding a TMR or separate delivery of roughage and concentrate sustained cow performance compared to ad libitum hay consumption.
Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Authors: Lucena Daercio A A , Almeida Eduardo A B
Published: February 2021

We integrated phylogenetic, biogeographic and palaeontological data to reconstruct the evolutionary history of the cuckoo wasps. We propose a phylogenetic hypothesis based on a comprehensive morphological study resulting in 300 characters coded for both living and extinct species. Phylogenetic relationships and divergence time estimation were simultaneously inferred in a Bayesian tip-dating framework, applying a relaxed morphological clock. Results unequivocally indicate Chrysididae to be monophyletic, as well as all traditionally recognized subfamilies and tribes. Within the Chrysidinae, Elampini was placed as the sister-group of the other three chrysidine tribes, with Parnopini as sister to the clade including Allocoeliini and Chrysidini. Dating analysis indicates that the major lineages started to differentiate around 130 Mya during the Early Cretaceous. The clades recognized as subfamilies started differentiating during the Palaeogene and the Neogene. Our results reveal an intricate process on the geographic evolution of chrysidid wasps and dispute previous ideas that Cretaceous-old splits in their early history could be associated with vicariant events related to the breakup between Africa and South America. The present-day southern disjunctions of some groups are interpreted as the outcome of more recent dispersals and extinctions of representatives from Nearctic and Palaearctic faunas during the Neogene, when northern continents became significantly colder.
Congenital Cutaneous Candidiasis With Systemic Dissemination in a Preterm Infant
Authors: Miras Isabel , Vierge Eva , García Macarena , Arruza Luis , Criado Enrique , Ramos José Tomás , Martínez-Orgado José
Published: February 2021

Congenital cutaneous candidiasis is an infrequent invasive fungal infection that usually appears in the first days of life. Extremely low birth weight infants are the most frequently affected. Classic presentation includes diffuse extensive erythematous rash with papules, plaques, pustules and vesicles, which later undergoes desquamation. Systemic dissemination is common in extremely low birth weight infants. Blood, urine and cerebrospinal fluid evaluation should be included in the initial assessment. Early and prolonged treatment has been associated with decreased mortality. We report the case of congenital cutaneous candidiasis in a preterm infant. Early skin lesion recognition allowed establishing adequate treatment in the first hours of life.
Oral Levodopa Formulation Does Not Affect Progression of Parkinson Disease
Authors: Sethi Ambica , Dilwali Sonam , McCreary Morgan , Dewey Richard B.
Published: February 2021

Objective

Motor fluctuations develop in most patients treated with carbidopa/levodopa for Parkinson disease. The continuous dopamine stimulation hypothesis suggests that longer-acting forms of levodopa might improve outcomes, but this has been inadequately tested in humans. We undertook to determine if there is any difference in symptom progression rate among patients taking immediate-release carbidopa/levodopa (IR), controlled-release carbidopa/levodopa (CR), or carbidopa/levodopa/entacapone (CLE) using standard outcome measures in a naturalistic study.

Methods

We evaluated Parkinson disease subjects prospectively followed for up to 48 months in the Parkinson's Disease Biomarker Project. Bayesian linear or generalized linear mixed-effects models were developed to determine if oral levodopa formulation influenced the rate of symptom progression as measured by 8 outcome measures.

Results

At baseline, the IR, CR, and CLE groups were similar except that the CR group had milder disease and was represented at only 1 site, and the CLE group had a longer disease duration. In the primary analysis, there was no difference in rate of symptom progression as measured by the Movement Disorder Society–Sponsored Revision of the Unified Parkinson’s Disease Rating Scale Part II, Part IV, or total score. In the secondary exploratory analysis, there was no difference in progression rate as measured by change in levodopa equivalent daily dose, Montreal Cognitive Assessment, Parkinson's Disease Questionnaire mobility subscore, Schwab and England Activities of Daily Living Scale, or a global composite outcome.

Conclusions

We found no difference in symptom progression rate in patients taking IR, CR, or CLE. This clinical observation supports pharmacokinetic studies demonstrating that none of these oral levodopa formulations achieve continuous dopamine stimulation.
Hypercapnia in the critically ill: insights from the bench to the bedside
Authors: Masterson Claire , Horie Shahd , McCarthy Sean D. , Gonzalez Hector , Byrnes Declan , Brady Jack , Fandiño Juan , Laffey John G. , O'Toole Daniel
Published: February 2021

Carbon dioxide (CO2) has long been considered, at best, a waste by-product of metabolism, and at worst, a toxic molecule with serious health consequences if physiological concentration is dysregulated. However, clinical observations have revealed that ‘permissive’ hypercapnia, the deliberate allowance of respiratory produced CO2to remain in the patient, can have anti-inflammatory effects that may be beneficial in certain circumstances. In parallel, studies at the cell level have demonstrated the profound effect of CO2on multiple diverse signalling pathways, be it the effect from CO2itself specifically or from the associated acidosis it generates. At the whole organism level, it now appears likely that there are many biological sensing systems designed to respond to CO2concentration and tailor respiratory and other responses to atmospheric or local levels. Animal models have been widely employed to study the changes in CO2levels in various disease states and also to what extent permissive or even directly delivered CO2can affect patient outcome. These findings have been advanced to the bedside at the same time that further clinical observations have been elucidated at the cell and animal level. Here we present a synopsis of the current understanding of how CO2affects mammalian biological systems, with a particular emphasis on inflammatory pathways and diseases such as lung specific or systemic sepsis. We also explore some future directions and possibilities, such as direct control of blood CO2levels, that could lead to improved clinical care in the future.
Carbon dioxide-dependent signal transduction in mammalian systems
Authors: Phelan D. E. , Mota C. , Lai C. , Kierans S. J. , Cummins E. P.
Published: February 2021

Carbon dioxide (CO2) is a fundamental physiological gas known to profoundly influence the behaviour and health of millions of species within the plant and animal kingdoms in particular. A recent Royal Society meeting on the topic of ‘Carbon dioxide detection in biological systems' was extremely revealing in terms of the multitude of roles that different levels of CO2play in influencing plants and animals alike. While outstanding research has been performed by leading researchers in the area of plant biology, neuronal sensing, cell signalling, gas transport, inflammation, lung function and clinical medicine, there is still much to be learned about CO2-dependent sensing and signalling. Notably, while several key signal transduction pathways and nodes of activity have been identified in plants and animals respectively, the precise wiring and sensitivity of these pathways to CO2remains to be fully elucidated. In this article, we will give an overview of the literature relating to CO2-dependent signal transduction in mammalian systems. We will highlight the main signal transduction hubs through which CO2-dependent signalling is elicited with a view to better understanding the complex physiological response to CO2in mammalian systems. The main topics of discussion in this article relate to how changes in CO2influence cellular function through modulation of signal transduction networks influenced by pH, mitochondrial function, adenylate cyclase, calcium, transcriptional regulators, the adenosine monophosphate-activated protein kinase pathway and direct CO2-dependent protein modifications. While each of these topics will be discussed independently, there is evidence of significant cross-talk between these signal transduction pathways as they respond to changes in CO2. In considering these core hubs of CO2-dependent signal transduction, we hope to delineate common elements and identify areas in which future research could be best directed.
Hypercapnia selectively modulates LPS-induced changes in innate immune and DNA replication-related gene transcription in the macrophage
Authors: Casalino-Matsuda S. Marina , Berdnikovs Sergejs , Wang Naizhen , Nair Aisha , Gates Khalilah L. , Beitel Greg J. , Sporn Peter H. S.
Published: February 2021

Hypercapnia, the elevation of CO
2
in blood and tissues, commonly occurs in severe acute and chronic respiratory diseases and is associated with increased risk of death. Recent studies have shown that hypercapnia inhibits expression of select innate immune genes and suppresses host defence against bacterial and viral pneumonia in mice. In the current study, we evaluated the effect of culture under conditions of hypercapnia (20% CO
2
) versus normocapnia (5% CO
2
), both with normoxia, on global gene transcription in human THP-1 and mouse RAW 264.7 macrophages stimulated with lipopolysaccharide (LPS). We found that hypercapnia selectively downregulated transcription of LPS-induced genes associated with innate immunity, antiviral response, type I interferon signalling, cytokine signalling and other inflammatory pathways in both human and mouse macrophages. Simultaneously, hypercapnia increased expression of LPS-downregulated genes associated with mitosis, DNA replication and DNA repair. These CO
2
-induced changes in macrophage gene expression help explain hypercapnic suppression of antibacterial and antiviral host defence in mice and reveal a mechanism that may underlie, at least in part, the high mortality of patients with severe lung disease and hypercapnia.
Prolonged activation of carbon dioxide-sensitive neurons in mosquitoes
Authors: Chen Stephanie Turner , Kowalewski Joel , Ray Anandasankar
Published: February 2021

Many insects can detect carbon dioxide (CO
2
) plumes using a conserved receptor made up of members of the gustatory receptor (Gr) family Gr1, Gr2 and Gr3. Mosquitoes are attracted to host animals for blood meals using plumes of CO
2
in the exhaled breath using the receptor expressed in the A neuron of the capitate peg sensilla type on the maxillary palps. The receptor is known to also detect several other classes of odorants, including ones emitted from human skin. Here, we discover that a common skin odorant, butyric acid, can cause a phasic activation followed by an unusually prolonged tonic activity after the stimulus is over in the CO
2
neurons of mosquitoes. The effect is conserved in both
Aedes aegypti
and
Anopheles gambiae
mosquitoes. This raises a question about its role in a mosquito's preference for the skin odour of different individuals. Butyric acid belongs to a small number of odorants known to cause the prolonged activation of the CO
2
receptor. A chemical informatic analysis identifies a specific set of physico-chemical features that can be used in a machine learning predictive model for the prolonged activators. Interestingly, this set is different from physico-chemical features selected for activators or inhibitors, indicating that each has a distinct structural basis. The structural understanding opens up an opportunity to find novel ligands to manipulate the CO
2
receptor and mosquito behaviour.
Hospitalizations, resource use and outcomes of acute pulmonary embolism in Germany during the Covid-19 pandemic Emergence of different phenotypes of thrombotic disease?
Authors: Husser Daniela , Hohenstein Sven , Pellissier Vincent , König Sebastian , Ueberham Laura , Hindricks Gerhard , Meier-Hellmann Andreas , Kuhlen Ralf , Bollmann Andreas
Published: February 2021

Background

There is discussion evolving around the emergence of different phenotypes of Covid-19-associated thromboembolic disease, i.e. acute pulmonary embolism vs pulmonary thrombosis and different phenotypes of in situ thrombosis. With this study, we wish to provide hospitalization, treatment and in-hospital outcome data for pulmonary embolism during the 2020 Covid-19 pandemic and a corresponding 2016 – 2019 control period.

Methods

We performed a retrospective analysis of claims data of Helios hospitals in Germany. Consecutive cases with a hospital admission between January 1 and December 15, 2020 and pulmonary embolism as primary discharge diagnosis were analyzed and compared to a corresponding period covering the same weeks in 2016 – 2019.

Results

As previously reported for other emergent medical conditions, there was a hospitalization deficit coinciding with the 1st pandemic wave. Beginning with the 12-week interval May 6 – July 28, there was a stable surplus of hospital admissions in 2020. During this surplus period (May 6 – December 15, 2020), there were 2,449 hospitalizations including 45 PCR-confirmed Covid-19 cases (1.8%) as opposed to 8,717 in 2016 – 2019 (IRR 1.12, 95% CI 1.07 – 1.18, P<0.01). When excluding Covid-19 cases IRR was 1.10 (95% CI 1.05 – 1.15, P<0.01). While overall comorbidities expressed as weighted AHRQ Elixhauser Comorbidity Index (14.1 ± 10.1 vs. 13.9 ±10.3, P=0.28), the presence of thrombosis (46.1 vs 45.4%, P=0.55) and surgery (3.8 vs. 4.3%, P=0.33) were comparable, coagulopathy (3.3 vs 4.5%, P=0.01) and metastatic cancer (3.0 vs 4.0%, P=0.03) as contributing factors were less frequently observed during the 2020 surplus. Interventional treatments (thrombolytic therapy, thrombectomy or inferior vena cava filter placement) were less frequently used (4.7 vs 6.6%, OR 0.72, 95% CI 0.58 − 0.89, P< 0.01). Similarly, intensive care (35.1 vs 38.8%, OR 0.83, 95% CI 0.75 − 0.92, P< 0.01) and mechanical ventilation utilization (7.2 vs 8.1%, OR 0.88, 95% CI 0.74 – 1.04, P=0.14) as well as in-hospital-mortality rates (7.8 vs 9.8%, OR 0.76, 95% CI 0.64 − 0.90, P< 0.01) were lower in 2020 compared with 2016 – 2019. This was associated with a shorter length of hospital stay (6.4 ±5.4 vs. 7.2 ±5.7 days, P< 0.01) during the 2020 surplus period.

Conclusions

Only a minority of cases were associated with PCR-confirmed Covid-19 but this does not rule out preceding or undetected SARS-CoV-2 infection. Although there is a shift towards milder disease course, the increased incidence of hospitalizations for pulmonary embolism requires immediate attention, close surveillance and further studies.
Combinatorial analysis of phenotypic and clinical risk factors associated with hospitalized COVID-19 patients
Authors: Das Sayoni , Pearson Matthew , Taylor Krystyna , Bouchet Veronique , Møller Gert Lykke , Hall Taryn O. , Strivens Mark , Tzeng Kathy T. H. , Gardner Steve
Published: February 2021

1

Characterization of the risk factors associated with variability in the clinical outcomes of COVID-19 is important. Our previous study using genomic data identified a potential role of calcium and lipid homeostasis in severe COVID-19. This study aimed to identify similar combinations of features (disease signatures) associated with severe disease in a separate patient population with purely clinical and phenotypic data.

The PrecisionLife combinatorial analytics platform was used to analyze features derived from de-identified health records in the UnitedHealth Group COVID-19 Data Suite. The platform identified and analyzed 836 disease signatures in two cohorts associated with increased risk of COVID-19 hospitalization. Cohort 1 was formed of cases hospitalized with COVID-19 and a set of controls who developed mild symptoms. Cohort 2 included Cohort 1 individuals for whom additional laboratory test data was available.

We found several disease signatures where lower levels of lipids were found co-occurring with lower levels of serum calcium and leukocytes. Many of the low lipid signatures were independent of statin use and 50% of cases with hypocalcemia signatures were reported with vitamin D deficiency. These signatures may be attributed to similar mechanisms linking calcium and lipid signaling where changes in cellular lipid levels during inflammation and infection affect calcium signaling in host cells.

This study and our previous genomics analysis demonstrate that combinatorial analysis can identify disease signatures associated with the risk of developing severe COVID-19 separately from genomic or clinical data in different populations. Both studies suggest associations between calcium and lipid signalling in severe COVID-19.
Pooling of samples for SARS-CoV-2 surveillance using a rapid antigen test
Authors: Salcedo Nol , Harmon Alexander , Herrera Bobby Brooke
Published: February 2021

While molecular assays, such as RT-PCR, have been widely used throughout the COVID-19 pandemic, the technique is costly and resource intensive. As a means to reduce costs and increase diagnostic efficiency, pooled testing for RT-PCR has been implemented. However, pooling samples for antigen testing has not been evaluated. We propose a pooling strategy for antigen testing that would significantly expand SARS-CoV-2 surveillance, especially for low-to-middle income countries, schools, and workplaces. Our data demonstrate that combining of up to 20 nasal swab specimens per pool can expand surveillance with antigen tests, even if a pool contains only one positive sample.
Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay
Authors: Kováčová Viera , Boršová Kristína , Paul Evan D , Radvánszka Monika , Hajdu Roman , Čabanová Viktória , Sláviková Monika , Ličková Martina , Lukáčiková Ľubomíra , Belák Andrej , Roussier Lucia , Kostičová Michaela , Líšková Anna , Maďarová Lucia , Štefkovičová Mária , Reizigová Lenka , Nováková Elena , Sabaka Peter , Koščálová Alena , Brejová Broňa , Staroňová Edita , Mišík Matej , Vinař Tomáš , Nosek Jozef , Čekan Pavol , Klempa Boris
Published: February 2021

Background

The emergence of a novel SARS-CoV-2 variant of concern called B.1.1.7 lineage sparked global alarm due to evidence of increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating efforts to detect and track the variant. Current approaches to detect lineage B.1.1.7 include sequencing and RT-qPCR tests containing a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant.

Aim

Since many countries lack robust genomic surveillance programs and failed assays detect multiple unrelated variants containing similar mutations as B.1.1.7, we sought to develop an RT-qPCR test that can accurately and rapidly differentiate the B.1.1.7 variant from other SARS-CoV-2 variants.

Methods

We used bioinformatics, allele-specific PCR, and judicious placement of LNA-modified nucleotides to develop a test that differentiates B.1.1.7 from other SARS-CoV-2 variants. We validated the test on 106 clinical samples with lineage status confirmed by sequencing and conducted a surveillance study of B.1.1.7 lineage prevalence in Slovakia.

Results

Our multiplexed RT-qPCR test showed 97% clinical sensitivity at detecting lineage B.1.1.7. The assay was used in a country-wide surveillance of B.1.1.7 lineage spread in Slovakia. Retesting nearly 7,000 SARS-CoV-2 positive samples obtained during three campaigns performed within a one month period, revealed pervasive spread of B.1.1.7 with an average prevalence of 82%.

Conclusion

Labs can easily implement this test to rapidly scale B.1.1.7 surveillance efforts and it is particularly useful in countries with high prevalence of variants possessing only the ΔH69/ΔV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.
Rapid Rise of S-Gene Target Failure and the UK variant B.1.1.7 among COVID-19 isolates in the Greater Toronto Area, Canada
Authors: Brown Kevin Antoine , Gubbay Jonathan , Hopkins Jessica , Patel Samir , Buchan Sarah A , Daneman Nick , Goneau Lee
Published: February 2021

A novel variant of SARS-CoV-2, B.1.1.7, originally discovered in the United Kingdom (UK), is rapidly overtaking other strains around the globe. In certain assays, absence of detection of the S-gene target, also known as S-gene target failure (SGTF) can be a sensitive surrogate of B.1.1.7. We analyzed daily counts of SGTF among samples from Dynacare Laboratory Ontario (which draws samples from the Greater Toronto Area) and resulted between December 16, 2020 and February 3, 2021. We identified 11,485 positive COVID-19 tests, of which 448 had SGTF (3.9%). The estimated prevalence of SGTF rose from 2.0% on December 16 to 15.2% on February 3 (1.8-fold weekly increase, 95%CI: 1.5, 2.2). The estimated reproduction number for SGTF cases was 1.17 (95%CI: 0.94 to 1.46), while the reproduction number for non-SGTF cases was 0.82 (95%CI: 0.65 to 1.01); the relative reproduction number was 1.44 (95%CI: 1.03, 1.99). 59 samples were sent for confirmatory testing, of which 53 (90%) were identified as B.1.1.7 using whole genome sequencing or found to have the N501Y mutation. In order to pre-emptively plan and implement public health measures to control COVID-19 now and through the spring, accurate and up-to-date early warning systems for new variants, including B.1.1.7, are essential across North America and the globe.
Demographic and Hygienic Factors as Predictors of Face Mask Wearing During Covid-19 Pandemic in Malaysia
Authors: Looi Kim Hoe , Zhang Stephen X. , Li Nicolas
Published: February 2021

Wearing a face mask has been recognised as an effective way of slowing down the spread of the Covid-19 pandemic. However, there is scarce evidence on predictors of face mask wearing during a pandemic. This research aims to investigate which demographic and hygienic factors could predict the compliance for face mask wearing in Malaysia. We employed a structured online survey of 708 Malaysian adult respondents. Among the factors examined, we found gender, hand washing and wearing of personal protective equipment significantly predicted face mask wearing.
A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
Authors: Rajczewski Andrew T. , Mehta Subina , Nguyen Dinh Duy An , Grüning Björn A. , Johnson James E. , McGowan Thomas , Griffin Timothy J. , Jagtap Pratik D.
Published: February 2021

The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world’s population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 639 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Applying stringent statistical scoring thresholds, combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.
Performing arts as a health resource? An umbrella review of the health impacts of music and dance participation
Authors: McCrary J. Matt , Redding Emma , Altenmüller Eckart
Published: February 2021

An increasing body of evidence notes the health benefits of arts engagement and participation. However, specific health effects and optimal modes and ‘doses’ of arts participation remain unclear, limiting evidence-based recommendations and prescriptions. The performing arts are the most popular form of arts participation, presenting substantial scope for established interest to be leveraged into positive health outcomes. Results of a three-component umbrella review (PROSPERO ID #: CRD42020191991) of relevant systematic reviews (33), epidemiologic studies (9) and descriptive studies (87) demonstrate that performing arts participation is broadly health promoting activity. Beneficial effects of performing arts participation were reported in healthy (non-clinical) children, adolescents, adults, and older adults across 17 health domains (9 supported by moderate-high quality evidence (GRADE criteria)). Positive health effects were associated with as little as 30 (acute effects) to 60 minutes (sustained weekly participation) of performing arts participation, with drumming and both expressive (ballroom, social) and exercise-based (aerobic dance, Zumba) modes of dance linked to the broadest health benefits. Links between specific health effects and performing arts modes/doses remain unclear and specific conclusions are limited by a still young and disparate evidence base. Further research is necessary, with this umbrella review providing a critical knowledge foundation.
Evaluation of Facial Protection Against Close-Contact Droplet Transmission
Authors: Stephenson Thomas B. , Cumberland Courtney , Kibble Geoff , Church Christopher , Nogueira-Prewitt Sheila , MacNamara Sebastian , Harnish Delbert A. , Heimbuch Brian K.
Published: February 2021

Background

Face shields are used as an alternative to facemasks, but their effectiveness in mitigating the spread of SARS-CoV-2 is unclear. The goal of this study is to compare the performance of face shields, surgical facemasks, and cloth facemasks for mitigation of droplet transmission during close contact conditions.

Methods

A novel test system was developed to simulate droplet transmission during close contact conditions using two breathing headforms (transmitter and receiver) placed 4 feet apart with one producing droplets containing a DNA marker. Sampling coupons were placed throughout the test setup and subsequently analyzed for presence of DNA marker using quantitative PCR.

Results

All PPE donned on the transmitter headform provided a significant reduction in transmission of DNA marker to the receiver headform: cloth facemask (78.5%), surgical facemask (89.4%), and face shield (96.1%). All PPE resulted in increased contamination of the eye region of the transmitter headform (9,525.4% average for facemasks and 765.8% for the face shield). Only the face shield increased contamination of the neck region (207.4%), with the cloth facemask and surgical facemask resulting in reductions of 85.9% and 90.2%, respectively.

Conclusions

This study demonstrates face shields can provide similar levels of protection against direct droplet exposure compared to surgical and cloth masks. However, all PPE tested resulted in release of particles that contaminated surfaces. Contamination caused by deflection of the user’s exhalation prompts concerns for contact transmission via surfaces in exhalation flow path (e.g., face, eyeglasses, etc.).
SEED: Symptom Extraction from English Social Media Posts using Deep Learning and Transfer Learning
Authors: Magge Arjun , Weissenbacher Davy , O’Connor Karen , Scotch Matthew , Gonzalez-Hernandez Graciela
Published: February 2021

Abstract

The increase of social media usage across the globe has fueled efforts in digital epidemiology for mining valuable information such as medication use, adverse drug effects and reports of viral infections that directly and indirectly affect population health. Such specific information can, however, be scarce, hard to find, and mostly expressed in very colloquial language. In this work, we focus on a fundamental problem that enables social media mining for disease monitoring. We present and make available SEED, a natural language processing approach to detect symptom and disease mentions from social media data obtained from platforms such as Twitter and DailyStrength and to normalize them into UMLS terminology. Using multi-corpus training and deep learning models, the tool achieves an overall F1 score of 0.86 and 0.72 on DailyStrength and balanced Twitter datasets, significantly improving over previous approaches on the same datasets. We apply the tool on Twitter posts that report COVID19 symptoms, particularly to quantify whether the SEED system can extract symptoms absent in the training data. The study results also draw attention to the potential of multi-corpus training for performance improvements and the need for continuous training on newly obtained data for consistent performance amidst the ever-changing nature of the social media vocabulary.
The Milano Sforza Registers of the Dead: Health Policies in Italian Renaissance
Authors: Biganzoli Elia , Luconi Ester , Boracchi Patrizia , Nodari Riccardo , Comandatore Francesco , Ferrara Alfio , Castaldi Silvana , Vaglienti Folco , Panella Cristiana , Galli Massimo
Published: February 2021

The institution of theLiber Mortuorumin Milan greatly anticipates death registrations in Europe. Introduced in 1450 by Duke Francesco Sforza for the early containment of plague it was daily compiled until 1801, reporting demographical data and causes of death, leaving a corpus of 366 volumes, an outstanding source for interdisciplinary research. Addressed to ascertain individual causes of death, it represents an unprecedented early example of disease monitoring and prevention. The paper discusses Sforza’s health policy in Milan, describes the Mortuorum registres features at the end of the 15thcentury, and analyzes the distribution of the city deaths in 1480, a year without epidemic events. These data constituted the first entry of a database of theLiber Mortuorum.
‘Leading from the front’ implementation strategies increase the success of influenza vaccination drives among healthcare workers: A reanalysis of Systematic Review evidence using Intervention Component Analysis (ICA) and Qualitative Comparative Analysis (QCA)
Authors: Sutcliffe Katy , Kneale Dylan , Thomas James
Published: February 2021

Background

Seasonal influenza vaccination of healthcare workers (HCW) is widely recommended to protect staff and patients. A previous systematic review examined interventions to encourage uptake finding that hard mandates, such as loss of employment for non-vaccination, were more effective than soft mandates, such as signing a declination form, or other interventions such as incentives. Despite these overarching patterns the authors of the review concluded that ‘substantial heterogeneity’ remained requiring further analysis. This paper reanalyses the evidence using Intervention Component Analysis (ICA) and Qualitative Comparative Analysis (QCA) to examine whether the strategies used to implement interventions explain the residual heterogeneity.

Methods

We used ICA to extract implementation features and trialist’s reflections on what underpinned the success of the intervention they evaluated. The ICA findings then informed and structured two QCA analyses to systematically analyse associations between implementation features and intervention outcomes. Analysis 1 examined hard mandate studies. Analysis 2 examined soft mandates and other interventions.

Results

In Analysis 1 ICA revealed the significance of ‘leading from the front’ rather than ‘top-down’ implementation of hard mandates. Four key features underpinned this: providing education prior to implementation; two-way engagement so HCW can voice concerns prior to implementation; previous use of other strategies so that institutions ‘don’t-go-in-cold’ with hard-mandates; and support from institutional leadership. QCA revealed that either of two configurations were associated with greater success of hard mandates. The first involves two-way engagement, leadership support and a ‘don’t-go-in-cold’ approach. The second involves leadership support, education and a ‘don’t-go-in-cold’ approach. Reapplying the ‘leading from the front’ theory in Analysis 2 revealed similar patterns.

Conclusions

Regardless of intervention type a ‘leading from the front’ approach to implementation will likely enhance intervention success. While the results pertain to flu vaccination among HCWs, the components identified here may be relevant to public health campaigns regarding COVID-19 vaccination.
Impact of a Chlorhexidine Decolonization on the Nasal and Dermal Microbiome of Therapy Dogs Participating in Hospital Animal-Assisted Intervention Programs: A Pilot Study
Authors: Dalton Kathryn R. , Ruble Kathy , Carroll Karen C. , Redding Laurel E. , Chen Allen R. , Grice Elizabeth A. , Morris Daniel O. , Davis Meghan F.
Published: February 2021

Therapy animals in hospital animal-assisted intervention programs are an invaluable part of holistic patient care. However, therapy dogs may be exposed to hospital-associated pathogens through these activities. This pilot study sought to examine the effect of topical chlorhexidine application, used as an infection control measure, on the microbial composition of the skin and mucous membranes of therapy dogs. We found that the chlorhexidine decolonization intervention altered microbial alpha diversity and shifted microbial structures in these therapy dogs, and particularly influenced more phylogenetically rare taxa. Specifically, the intervention reduced the abundance of Staphylococcus pseudintermedius, the archetypal canine commensal and a frequent cause of opportunistic infections. However, it did not reduce levels of S. aureus, which is a common hospital-associated pathogen of people. These preliminary findings highlight the importance of considering holistic microbial communities when undertaking infection control strategies, and stress the need for further research to understand the unintended consequences of antiseptic use on therapy dogs.
SARS-CoV-2 genome surveillance in Mainz, Germany, reveals convergent origin of the N501Y spike mutation in a hospital setting
Authors: Lemmermann NA , Lieb B , Laufs T , Renzaho A , Runkel S , Kohnen W , Linke M , Gerber S , Schweiger S , Michel A , Bikar S-E , Plachter B , Hankeln T
Published: February 2021

While establishing a regional SARS-Cov-2 variant surveillance by genome sequencing, we have identified three infected individuals in a clinical setting (two long-term hospitalized patients and a nurse) that shared the spike N501Y mutation within a genotype background distinct from the current viral variants of concern. We suggest that the adaptive N501Y mutation, known to increase SARS-CoV-2 transmissibility, arose by convergent evolution around December in Mainz, Germany. Hospitalized patients with a compromised immune system may be a potential source of novel viral variants, which calls for monitoring viral evolution by genome sequencing in clinical settings.
Prevalence of dementia in elderly age population of Barangay Bangkal, City
Authors: Jaiswal Vikash , Lourdes Pormento Maria Kezia , Hange Namrata , Ngaba Neguemadji Ngardig , Somagutta Manoj Kumar , Apostol Dy Inna Celina , Savani Saloni , Javed Sana , Nagpal Shavy , Bhatnagar Arushee , Mohit  , Singh Annie , Mukherjee Dattatreya , Paladiya Ruchir , Malanyaon Freda
Published: February 2021

Background

Dementia, a significant cause of disability and dependency among older adults. The growing population of the elderly in the Philippines is expected to increase the prevalence of dementia in the country.

Purpose

This study aims to determine the prevalence of dementia in the elderly population of Barangay Bangkal, Makati City.

Methods

Descriptive cross-sectional community-based study was conducted to determine the prevalence of dementia in the elderly population of Barangay Bangkal, Makati City, aged 60 years and above over one month from mid-October to mid-November 2019. Data was collected with help of Mini-Mental State Examination – Philippines version (MMSE-P) to determine the cognitive status and diagnose dementia in elderly population.

Results

A total of 266 elderly adults participated in the study. Representatives of the study population were male (59.0%), married (68.0%), with an income of less than 5,000 peso (51.1%), working (64.3%), and with high school education (42.1%). The average age of the study population was 68.02 (+ 6.76) years. The average MMSE score of the participants was 27.05 (+ 3.94). The prevalence of dementia in the sample was 18.8%. Age, income, and level of education were associated with the MMSE score (r□ = - 0.26, n = 266, p < 0.001, r□ = 0.23, n = 266, p < 0.001, and rs = 0.19, n = 266, p = 0.002, respectively). The findings for statistical significance do resonate with clinical significance as evident during administration of MMSE score.

Conclusion

Advancing age increases the risk for cognitive decline while higher income and education level prevent or delays the onset of dementia. Collaborative management between the medical education faculty & students, researchers, and local state health officials might address dementia in the region.
Long stability of SARS-CoV-2 RNA in dry and saliva swab samples stored for diagnostics, Denmark
Authors: Alfaro-Núñez Alonzo , Crone Stephanie , Mortensen Shila , Worsøe Rosenstierne Maiken , Fomsgaard Anders , Marving Ellinor , Nielsen Sofie Holdflod , Jørgensen Michelle Grace Pinto , Cohen Arieh S. , Nielsen Claus
Published: February 2021

During the current COVID-19 pandemic, Danish authorities demand that clinical swab samples must be analysed within 72 hours. This time constraint was adopted to guarantee a quick and efficient response. As today, analysis results are given within 20 hours average fulfilling this demand. However, it is unclear for how long and under which conditions swab specimens can be stored without clinically affecting SARS-CoV-2 RNA stability. This study demonstrates that swabs specimens can be stored at −20°C and +4°C for up to 26 days without affecting RT-qPCR results. However, early detection of asymptomatic cases is important to reduce spreading COVID-19 may be the final consequence not only in Denmark but worldwide.