bluuebunny/crossref_metadata_2025 huggingface dataset:
Musical Authenticity: Music Therapists’ Perceptions and Practices
Authors: Veblen Nora Bryant , Yinger Olivia Swedberg , Vasil Martina
Published: March 2021

Board-certified music therapists (MT-BCs) are expected to provide live music in numerous client-preferred genres, yet often face barriers that prevent them from recreating this music with musical authenticity, defined here as adhering to the expectations of the genre. The purpose of this survey was to investigate the perceptions and practices of MT-BCs (n = 904, 12%) regarding musical authenticity in their own practice. We collected quantitative and qualitative survey data on the importance of musical authenticity, barriers to and strategies for providing music authentically, and the use of electronic technology and the iPad. Descriptive and thematic analyses revealed that MT-BCs value musical authenticity but balance its importance with therapeutic needs and other types of authenticity that are deemed more important. Participants reported that they lacked knowledge of popular genres, functional musicianship, and electronic technology, which created major barriers to providing musical authenticity. Additionally, we found trends related to gender identity and the use of electronic technology in that significantly more male MT-BCs reported using electronic technology compared with female MT-BCs. Overall, however, less than half of the participants reported using either electronic technology or the iPad to increase musical authenticity. With these results in mind, and building on the results of Schippers and Fetterley, we created a model of recontextualization for music therapy practice. This practical tool is intended to guide music therapists to consider multiple issues of authenticity when learning music for clients.
Trends in SARS-CoV-2 detection during social relaxation measures over ten months of COVID-19 pandemic in the metropolitan area of Rio de Janeiro, Brazil
Authors: Alonso Fábio de O. M. , Sabino Bruno D. , de Oliveira Marcia Soraya C. , Knackfuss Fabiana B. , Varella Rafael B.
Published: March 2021

We analyzed the effects of sequential reopening events during COVID-19 pandemic, based on 76,419 SARS-CoV-2 molecular tests performed from April 2020 to January 2021 in Rio de Janeiro metropolitan area, Brazil, third largest in South America. Post-opening events provoked different impacts on cases and deaths, but showing limited temporary effect.
The UK experience of stereoelectroencephalography in children: An analysis of factors predicting the identification of a seizure onset zone and subsequent seizure freedom
Authors:   Children’s Epilepsy Surgery Service
Published: March 2021

Importance

Stereoelectroencephalography (SEEG) is more frequently being used in the pre-surgical evaluation of children with focal epilepsy. Many factors affect the rate of identification of a definable seizure onset zone (SOZ) and subsequent seizure freedom following SEEG-guided epilepsy surgery, which have not been systematically examined in multi-centre studies.

Objectives

Determine the rates and factors that predict (a) whether or not a definable putative SOZ was identified on SEEG and (b) subsequent seizure freedom following surgical intervention.

Design

Retrospective cohort study

Setting

Multicentre study involving 6 of 7 UK Children’s Epilepsy Surgery Service centres that perform paediatric SEEG in the UK.

Participants

All children undergoing SEEG from 2014 - March 2019 were included. Demographic, non-invasive evaluation, SEEG and operative factors were collected retrospectively from patient records.

Main Outcomes

The two main outcome measures were (a) whether or not a definable putative SOZ was identified on SEEG (binary yes/no outcome) and (b) subsequent seizure freedom following surgical intervention (Engel classification)

Findings

One hundred and thirty-five patients underwent 139 SEEG explorations using a total of 1767 electrodes. A definable SOZ was identified in 117 patients (85.7%); odds of successfully finding a SOZ were 6.4x greater for non-motor seizures compared to motor seizures (p=0.02) and 3.6x more if ≥ 4 seizures were recorded during SEEG (p=0.03). Of 100 patients undergoing surgical treatment, 47 (47.0%) had an Engel class I outcome at a median follow-up of 1.3 years; the only factor associated with outcome was indication for SEEG (p=0.03). SEEG was safe with one (0.7%) haematoma requiring surgical evacuation and no long-term neurological deficits as a result of the procedure.

Conclusions and Relevance

This large nationally representative cohort illustrates that, in these patients who may not have otherwise been offered resective surgery, SEEG-guided surgery can still achieve high rates of seizure freedom. Seizure semiology and the number of seizures recorded during SEEG are important factors in the identification of a definable SOZ and the indication for SEEG is an important factor in post-operative outcomes.
A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants
Authors: Banada Padmapriya , Green Raquel , Banik Sukalyani , Chopoorian Abby , Streck Deanna , Jones Robert , Chakravorty Soumitesh , Alland David
Published: March 2021

Background

The increased transmission of SARS-CoV-2 variants of concern (VOC) which originated in the United Kingdom (B.1.1.7), South Africa (B1.351), Brazil (P.1) and in United States (B.1.427/429) requires a vigorous public health response, including real time strain surveillance on a global scale. Although genome sequencing is the gold standard for identifying these VOCs, it is time consuming and expensive. Here, we describe a simple, rapid and high-throughput reverse-transcriptase PCR (RT-PCR) melting temperature (Tm) screening assay that identifies these three major VOCs.

Methods

RT-PCR primers and four sloppy molecular beacon (SMB) probes were designed to amplify and detect the SARS-CoV-2 N501Y (A23063T) and E484K (G23012A) mutations and their corresponding wild type sequences. After RT-PCR, the VOCs were identified by a characteristic Tm of each SMB. Assay optimization and testing was performed with RNA from SARS-CoV-2 USA WA1/2020 (WT), a B.1.17 and a B.1.351 variant strains. The assay was then validated using clinical samples.

Results

The limit of detection (LOD) for both the WT and variants was 4 and 10 genomic copies/reaction for the 501 and 484 codon assays, respectively. The assay was 100% sensitive and 100% specific for identifying the N501Y and E484K mutations in cultured virus and in clinical samples as confirmed by Sanger sequencing.

Conclusion

We have developed an RT-PCR melt screening test for the three major VOCs which can be used to rapidly screen large numbers of patient samples providing an early warning for the emergence of these variants and a simple way to track their spread.
SARS-CoV-2 spike protein S1 induces fibrin(ogen) resistant to fibrinolysis: Implications for microclot formation in COVID-19
Authors: Grobbelaar Lize M. , Venter Chantelle , Vlok Mare , Ngoepe Malebogo , Laubscher Gert Jacobus , Lourens Petrus Johannes , Steenkamp Janami , Kell Douglas B. , Pretorius Etheresia
Published: March 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2)-induced infection, the cause of coronavirus disease 2019 (COVID-19), is characterized by unprecedented clinical pathologies. One of the most important pathologies, is hypercoagulation and microclots in the lungs of patients. Here we study the effect of isolated SARS-CoV-2 spike protein S1 subunit as potential inflammagensui generis. Using scanning electron and fluorescence microscopy as well as mass spectrometry, we investigate the potential of this inflammagen to interact with platelets and fibrin(ogen) directly to cause blood hypercoagulation. Using platelet poor plasma (PPP), we show that spike protein may interfere with blood flow. Mass spectrometry also showed that when spike protein S1 is added to healthy PPP, it results in structural changes to β and γ fibrin(ogen), complement 3, and prothrombin. These proteins were substantially resistant to trypsinization, in the presence of spike protein S1. Here we suggest that, in part, the presence of spike protein in circulation may contribute to the hypercoagulation in COVID-19 positive patients and may cause substantial impairment of fibrinolysis. Such lytic impairment may result in the persistent large microclots we have noted here and previously in plasma samples of COVID-19 patients. This observation may have important clinical relevance in the treatment of hypercoagulability in COVID-19 patients.
Nonuniform UV-C dose across N95 facepieces can cause 2.9-log variation in SARS-CoV-2 inactivation
Authors: Geldert Alisha , Su Alison , Roberts Allison W. , Golovkine Guillaume , Grist Samantha M. , Stanley Sarah A. , Herr Amy E.
Published: March 2021

During public health crises like the COVID-19 pandemic, ultraviolet-C (UV-C) decontamination of N95 respirators for emergency reuse has been implemented to mitigate shortages. However, decontamination efficacy across N95s is poorly understood, due to the dependence on received UV-C dose, which varies across the complex three-dimensional N95 shape. Robust quantification of UV-C dose across N95 facepieces presents challenges, as few UV-C measurement tools have sufficient 1) small, flexible form factor, and 2) angular response. To address this gap, we combine optical modeling and quantitative photochromic indicator (PCI) dosimetry with viral inactivation assays to generate high-resolution maps of “on-N95” UV-C dose and concomitant SARS-CoV-2 viral inactivation across N95 facepieces within a commercial decontamination chamber. Using modeling to rapidly identify on-N95 locations of interest, in-situ measurements report a 17.4 ± 5.0-fold dose difference across N95 facepieces in the chamber, yielding 2.9 ± 0.2-log variation in SARS-CoV-2 inactivation. UV-C dose at several on-N95 locations was lower than the lowest-dose locations on the chamber floor, highlighting the importance of on-N95 dose validation. Overall, we couple optical simulation with in-situ PCI dosimetry to relate UV-C dose and viral inactivation at specific on-N95 locations, informing the design of safe and effective decontamination protocols.
Combined landscape of single-nucleotide variants and copy-number alterations in clonal hematopoiesis
Authors: Saiki Ryunosuke , Momozawa Yukihide , Nannya Yasuhito , Nakagawa Masahiro M , Ochi Yotaro , Yoshizato Tetsuichi , Terao Chikashi , Kuroda Yutaka , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Niida Atsushi , Imoto Seiya , Matsuda Koichi , Morisaki Takayuki , Murakami Yoshinori , Kamatani Yoichiro , Matsuda Shuichi , Kubo Michiaki , Miyano Satoru , Makishima Hideki , Ogawa Seishi
Published: March 2021

Implicated in the development of hematological malignancies (HM) and cardiovascular mortality, clonal hematopoiesis (CH) in apparently healthy individuals has been investigated by detecting either single-nucleotide variants and indels (SNVs/indels) or copy number alterations (CNAs), but not both. Here by combining targeted sequencing of 23 CH-related genes and array-based CNA detection of blood-derived DNA, we have delineated the landscape of CH-related SNVs/indels and CNAs in a general population of 11,234 individuals, including 672 with subsequent HM development. Both CH-related lesions significantly co-occurred, which combined, affected blood count, hypertension, and the mortality from HM and cardiovascular diseases depending on the total number of both lesions, highlighting the importance of detecting both lesions in the evaluation of CH.
Genomic prediction in an outcrossing and autotetraploid fruit crop: lessons from blueberry breeding
Authors: Ferrão Luís Felipe V. , Amadeu Rodrigo R. , Benevenuto Juliana , de Bem Oliveira Ivone , Munoz Patricio R.
Published: March 2021

Blueberry (Vaccinium corymbosumand hybrids) is a specialty crop, with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to the expansion of production areas by developing low-chilling cultivars better adapted to subtropical and Mediterranean climates of the globe. The breeding program has historically focused on phenotypic recurrent selection. As an autopolyploid, outcrossing, perennial, long juvenile phase crop, blueberry’s breeding cycles are costly and time-consuming, which results in low genetic gains per unit of time. Motivated by the application of molecular markers for a more accurate selection in early stages of breeding, we performed pioneering genomic prediction studies and optimization for implementation in the blueberry breeding program. We have also addressed some complexities of sequence-based geno- typing and model parametrization for an autopolyploid crop, providing empirical contributions that can be extended to other polyploid species. We herein revisited some of our previous genomic prediction studies and described the current achievements in the crop. In this paper, our contribution for genomic prediction in an autotetraploid crop is three-fold: i) summarize previous results on the relevance of model parametrizations, such as diploid or polyploid methods, and inclusion of dominance effects; ii) assess the importance of sequence depth of coverage and genotype dosage calling steps; iii) demonstrate the real impact of genomic selection on leveraging breeding decisions by using an independent validation set. Altogether, we propose a strategy for the use of genomic selection in blueberry, with potential to be applied to other polyploid species of a similar background.
Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets
Authors: Shainer Inbal , Stemmer Manuel
Published: March 2021

Background

Single-cell RNA sequencing (scRNA-seq) has quickly become one of the most dominant techniques in modern transcriptome assessment. In particular, 10X Genomics’ Chromium system, with its high throughput approach, turn key and thorough user guide made this cutting-edge technique accessible to many laboratories using diverse animal models. However, standard pre-processing, including the alignment and cell filtering pipelines might not be ideal for every organism or tissue. Here we applied an alternative strategy, based on the pseudoaligner kallisto, on twenty-two publicly available single cell sequencing datasets from a wide range of tissues of eight organisms and compared the results with the standard 10X Genomics’ Cell Ranger pipeline.

Results

In most of the tested samples, kallisto produced higher sequencing read alignment rates and total gene detection rates in comparison to Cell Ranger. Although datasets processed with Cell Ranger had higher cell counts, outside of human and mouse datasets, these additional cells were routinely of low quality, containing low gene detection rates. Thorough downstream analysis of one kallisto processed dataset, obtained from the zebrafish pineal gland, revealed clearer clustering, allowing the identification of an additional photoreceptor cell type that previously went undetected. The finding of the new cluster suggests that the photoreceptive pineal gland is essentially a bi-chromatic tissue containing both green and red cone-like photoreceptors and implies that the alignment and pre-processing pipeline can affect the discovery of biologically-relevant cell types.

Conclusion

While Cell Ranger favors higher cell numbers, using kallisto results in datasets with higher median gene detection per cell. We could demonstrate that cell type identification was not hampered by the lower cell count, but in fact improved as a result of the high gene detection rate and the more stringent filtering. Depending on the acquired dataset, it can be beneficial to favor high quality cells and accept a lower cell count, leading to an improved classification of cell types.
Hepatic Leukemia Factor supports the propagation of leukemia and hematopoietic stem cell function during stress-induced regeneration
Authors: Baudet Aurélie , Komorowska Karolina , Hultmark Simon , Chapellier Marion , Miharada Kenichi , Larsson Jonas , Bryder David , Järås Marcus , Juliusson Gunnar , Magnusson Mattias
Published: March 2021

The processes regulating hematopoietic stem cells (HSC) during aging are not fully understood1, but it is clear that the incidence of hematological malignancies increases with age, highlighting the importance of unravelling the cellular and molecular networks involved. Recently, we identified Hepatic Leukemia Factor (HLF) as an essential transcription factor in maintaining the HSC pool during regeneration2and showed that failure to downregulate HLF leads to disrupted differentiation3.

Here, we found that HLF is dispensable for hematopoiesis during systemic aging, but needed during stress-induced hematopoietic recovery of aged HSC after transplantation. Additionally, HLF was dispensable for leukemic initiation but required for disease propagation. Taken together, our findings demonstrate the existence of a HLF-dependent mechanism that uncouples stress-induced regeneration from hematopoietic homeostasis during aging, that can be used by malignant cells to gain stem cell properties to propagate the disease.

Key points

HLF is dispensable for HSC function and hematopoietic homeostasis during physiological aging, but crucial during stress induced regeneration.

HLF supports the propagation of leukemia-initiating cells
Transcriptional census of epithelial-mesenchymal plasticity in cancer
Authors: Cook David P. , Vanderhyden Barbara C.
Published: March 2021

Epithelial-mesenchymal plasticity (EMP) contributes to tumour progression, promoting therapy resistance and immune cell evasion. Definitive molecular features of this plasticity have largely remained elusive due to the limited scale of most studies. Leveraging scRNA-seq data from 160 tumours spanning 8 different cancer types, we identify expression patterns associated with intratumoural EMP. Integrative analysis of these programs confirmed a high degree of diversity among tumours. These diverse programs are associated with combinations of various common regulatory mechanisms initiated from cues within the tumour microenvironment. We highlight that inferring regulatory features can inform effective therapeutics to restrict EMP.
More than the eye can see – shedding new light on SARS-CoV-2 Lateral Flow Device-based immunoassays
Authors: Koller Garrit , Morrell Alexander P , Galão Rui Pedro , Pickering Suzanne , MacMahon Eithne , Johnson Joanna , Ignatyev Konstantin , Neil Stuart JD , Elsharkawy Sherif , Fleck Roland , Pereira Machado Pedro Miguel , Addison Owen
Published: March 2021

Containing the global SARS-CoV-2 pandemic has been an unprecedented challenge due to high horizontal transmissivity and asymptomatic carriage rates. Lateral Flow Device (LFD) immunoassays were introduced in late 2020 to detect SARS-CoV-2 infection in asymptomatic or pre-symptomatic individuals rapidly. Whilst LFD technologies have been used for over 60 years, their widespread use as a public health tool during a pandemic is unprecedented. By the end of 2020, data from studies into the efficacy of the LFDs emerged and showed these point-of-care devices to have very high specificity (ability to identify true negatives) but inadequate sensitivity with high false-negative rates. The low sensitivity (<50%) shown in several studies is a critical public health concern, as asymptomatic or pre-symptomatic carriers may wrongly be assumed to be non-infectious, posing a significant risk of further spread in the community. Here we show that the direct visual readout of SARS-CoV-2 LFDs is an inadequate approach to discriminate a potentially infective viral concentration in a bio-sample. We quantified significant immobilized antigen-antibody-label conjugate complexes within the LFDs visually scored as negative using high-sensitivity synchrotron X-ray fluorescence imaging. Correlating quantitative X-ray fluorescence measurements and qRT-PCR determined numbers of viral copies, we identified that negatively scored samples could contain up to 100 PFU (equivalent here to ∼10,000 RNA copies/test). The study demonstrates where the shortcomings arise in many of the current direct-readout SARS-CoV-2 LFDs, namely being a deficiency in the readout as opposed to the potential level of detection of the test, which is orders of magnitude higher. The present findings are of importance, both to public health monitoring during the COVID-19 pandemic and to the rapid refinement of these tools for immediate and future applications.
An Automated Radio-Telemetry System (ARTS) for Monitoring Small Mammals
Authors: Wallace Gerard , Elden (née Gorinshteyn) Marija , Boucher (née Sheely) Rachel , Phelps Steven
Published: March 2021

Point 1: The study of animals in nature is essential for developing an ecologically valid understanding of behavior. Small mammals, however, are often fossorial and exceedingly difficult to monitor in the wild. This limits both the taxonomic scope of field observation, and excludes species that are powerful models for the study of behavioral mechanisms.

Point 2: Here, we implement an automated radio telemetry system (ARTS) designed to track small fossorial mammals. Our ARTS uses an isotropic antenna array coupled with broadband receivers. We characterized transmission at our study site and tested the ARTS’ ability to track 48 prairie voles.

Point 3: We compared position estimates from nonlinear least squares, nonparameteric, and Bayesian trilateration methods and found Bayesian trilateration to have the smallest error. To examine the ability of the system to track biologically significant behavior we used ARTS data to investigate circadian rhythms of freely behaving prairie voles. We used Lomb-Scargle analysis to estimate periodic patterns from irregularly sampled time series of speed. Prairie voles demonstrated ultradian movement at periods of approximately 45 and 90 min, observations on a time scale not possible using data from traditional methods.

Point 4: This ARTS offers a new tool to observe rodent field behavior at time scales and in environments which have not been previously possible, such as investigating social and spatial behaviors on the scale of minutes, hours, and days in natural environments.
COVID-19 vaccine hesitancy in care home staff: a survey of Liverpool care homes
Authors: Tulloch John S P , Lawrenson Karen , Gordon Adam L , Ghebrehewet Sam , Ashton Matthew , Peddie Steve , Parvulescu Paula
Published: March 2021

Background

COVID-19 has caused high morbidity and mortality in UK care homes. Vaccinating staff members and residents will protect care homes from severe clinical cases. Uptake of COVID-19 vaccine first doses in care homes has been higher among residents compared to staff members.

Methods

We aimed to identify causes of lower COVID-19 vaccine uptake amongst care home staff members within the Liverpool City Council region. An anonymised online survey was distributed to all care home managers between the 21st and the 29th of January 2021. Descriptive analysis was performed on responses.

Results

46/87 (53%) of Liverpool care homes responded. The mean staff vaccination rate per home was 51.4% (95% CI 43.9-58.8%). The most common reasons for staff not receiving the vaccine were: concerns about lack of vaccine research (37.0%), staff being off-site during vaccination sessions (36.5%), pregnancy and fertility concerns (5.6%), and concerns about allergic reactions (3.2%). Care home managers reported the necessity to combat vaccine hesitancy through meetings and conversations with health professionals, and provision of supporting evidence to dispel vaccine misinformation.

Conclusions

Vaccine hesitancy was the main cause for reduced vaccine uptake among care home staff members. These concerns could be addressed by targeted evidence-based training, and a public health communication campaign to build vaccine confidence and increase acceptance of COVID-19 vaccines. The speed of vaccination roll-out has also led to unexpected logistical issues that lowered vaccine uptake rates. Addressing both these challenges could increase uptake by more than 40%.

Key Points

COVID-19 vaccine uptake rates are lower in staff than residents

Three main causes of reduced uptake have been identified: vaccine hesitancy, logistical issues, and medical concerns.

The main reasons for vaccine hesitancy were concerns about limited research into vaccine safety, and concerns about long-term impact on pregnancy and fertility.

Addressing care home staff vaccination concerns should be given priority in these settings.
Temperature-dependent Self assembly of biofilaments during red blood cell sickling
Authors: Behera Arabinda , Sharma Oshin , Paul Debjani , Sain Anirban
Published: March 2021

Molecular self-assembly plays vital role in various biological functions. However, when aberrant molecules self-assemble to form large aggregates, it can give rise to various diseases. For example, the sickle cell disease and Alzheimer’s disease are caused by self-assembled hemoglobin fibers and amyloid plaques, respectively. Here we study the assembly kinetics of such fibers using kinetic Monte-Carlo simulation. We focus on the initial lag time of these highly stochastic processes, during which self-assembly is very slow. The lag time distributions turn out to be similar for two very different regimes of polymerization, namely, a) when polymerization is slow and depolymerization is fast, and b) the opposite case, when polymerization is fast and depolymerization is slow. Using temperature dependent on- and off-rates for hemoglobin fiber growth, reported in recent in-vitro experiments, we show that the mean lag time can exhibit non-monotonic behaviour with respect to change of temperature.
Label free sensing with Terahertz multiple ring resonators
Authors: Bai Xaing , Zhe Lujun
Published: March 2021

Apart from their relevance for spectroscopy and imaging, terahertz signals have attracted a lot of interest for sensing. In this paper, a label free terahertz sensor is proposed, which can be employed to detect the presence of molecules in the environment. The proposed sensor consists of an array of ring resonators, resonating at the frequency off=1.2 THz. By providing full-wave numerical simulations, it is shown that the proposed sensor is able to sense the variation of the refractive index in the environment. The proposed structure is found to show larger sensitivity compared to previous reports. Our findings provide a novel platform to realize label free terahertz sensors with extremely large sensitivity.
Increased disease burden in Interleukin-3 deficient mice afterMycobacterium tuberculosisand herpes simplex virus infections
Authors: Kunnath-Velayudhan Shajo , Ng Tony W. , Saini Neeraj K. , Goldberg Michael F. , Arora Pooja , Xu Jiayong , Kim John , Herold Betsy C. , Chan John , Jacobs William R. , Porcelli Steven A.
Published: March 2021

Interleukin-3 (IL-3) is produced during infections caused by parasites, bacteria and viruses, but its contribution to immunity in this context remains largely unknown. In mouse models of parasitic infections, in which the effects of IL-3 have been most extensively studied, IL-3 has been variously reported as protective, detrimental or inconsequential. Similarly, mixed results have been reported in viral and bacterial infection models. Here, we investigated the effects of IL-3 in mouse models ofMycobacterium tuberculosisand herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) infections by assessing the pathogen burden, disease manifestations and survival following infection. After infection withM. tuberculosis,IL-3 deficient mice showed higher bacillary burden, increased lung pathology and reduced survival compared to wild type mice. After infection with HSV-1 through cutaneous route and HSV-2 through vaginal route, IL-3 deficient mice showed higher viral burden, increased disease manifestations and reduced survival compared to wild type mice. Our results show that IL-3 makes a subtle but significant contribution to protective immunity in these mouse models of bacterial and viral infections.
Revision and annotation of DNA barcode records for marine invertebrates: report of the 8thiBOL conference hackathon
Authors: Radulovici Adriana E. , Vieira Pedro E. , Duarte Sofia , Teixeira Marcos A. L. , Borges Luisa M. S. , Deagle Bruce , Majaneva Sanna , Redmond Niamh , Schultz Jessica A. , Costa Filipe O.
Published: March 2021

The accuracy of the identification of unknown specimens using DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. A rampant growth in barcode data led to a stringent need for data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data deposited in the Barcode of Life Data Systems (BOLD) has been undertaken during the 8thInternational Barcode of Life Conference (Trondheim, Norway, 2019). For practical reasons, only major taxonomic groups were reviewed and annotated (crustaceans, echinoderms, molluscs, and polychaetes). The congruence of Linnean names with Barcode Index Numbers (BINs) was investigated, and the records deemed uncertain were annotated with four tags: a) MIS-ID (misidentified, mislabeled or contaminated records), b) AMBIG (ambiguous records unresolved with the current data), c) COMPLEX (species occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. This high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross -contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is crucial for barcode applications, such manual efforts of reviewing large datasets are not sustainable and the implementation of automated solutions to the furthest possible extent is hi ghly desirable.
Clustering-based time series analysis on insulin response in the blood-brain barrier
Authors: Kalari Krishna R. , Wang Zengtao , Tang Xiaojia , Swaminathan Suresh K. , Kandimalla Karunya K.
Published: March 2021

Background

Critical functions of the blood-brain barrier (BBB), including cerebral blood flow and vascular response, are regulated by insulin signaling pathways. Therefore, endothelial insulin resistance could lead to vascular dysfunction, which is associated with neurodegenerative diseases such as Alzheimer’s disease (AD).

Objective

The objective of the current study is to map the dynamics of insulin-responsive pathways in polarized human cerebral microvascular endothelial cells (hCMEC/D3) cell monolayers, a widely used BBB cell culture model, to identify molecular mechanisms underlying BBB dysfunction in AD.

Methods

RNA-Sequencing (RNA-Seq) was performed on hCMEC/D3 cell monolayers with and without insulin treatment at various time points. The Short Time-series Expression Miner (STEM) method was used to identify clusters of genes with distinct and representative patterns. Functional annotation and pathway analysis of the genes from top clusters were conducted using the Webgestalt and Ingenuity Pathway Analysis (IPA) software, respectively.

Results

Quantitative expression differences of 19,971 genes between the insulin-treated and control monolayers at five-time points were determined. STEM software identified 11 clusters with 3061 genes across that displayed various temporal patterns. Gene ontology enrichment analysis performed using the top 5 clusters demonstrated that these genes were enriched in various biological processes associated with AD pathophysiology. The IPA analyses revealed that signaling pathways exacerbating AD pathology such as inflammation were downregulated after insulin treatment (clusters 1 to 3). In contrast, pathways attenuating AD pathology were upregulated, including synaptogenesis and BBB repairment (clusters 4 and 5).

Conclusions

These findings unravel the dynamics of insulin action on the BBB endothelium and inform about downstream signaling cascades that potentially regulate neurovascular unit (NVU) functions that are disrupted in AD.
Fluidics System for Resolving Concentration-Dependent Effects of Dissolved Gases on Tissue Metabolism
Authors: Kamat Varun , Robbings Brian M. , Jung Seung-Ryoung , Kelly John , Hurley James B. , Bube Kenneth P. , Sweet Ian R.
Published: March 2021

Oxygen (O2) and other dissolved gases such as the gasotransmitters H2S, CO and NO affect cell metabolism and function. To evaluate effects of dissolved gases on processes in tissue, we developed a fluidics system that controls dissolved gases while simultaneously measuring parameters of electron transport, metabolism and secretory function. We use pancreatic islets, retina and liver to highlight its ability to assess effects of O2and H2S. Protocols aimed at emulating hypoxia-reperfusion conditions resolved a previously unrecognized transient spike in O2consumption rate (OCR) following replenishment of O2, and tissue-specific recovery of OCR following hypoxia. The system revealed both inhibitory and stimulatory effects of H2S on insulin secretion rate from isolated islets. The unique ability of this new system to quantify metabolic state and cell function in response to precise changes in dissolved gases provides a powerful platform for cell physiologists to study a wide range of disease states.
Development of an ensemble machine learning prognostic model to predict 60-day risk of major adverse cardiac events in adults with chest pain
Authors: Kennedy Chris J. , Mark Dustin G. , Huang Jie , van der Laan Mark J. , Hubbard Alan E. , Reed Mary E.
Published: March 2021

Background: Chest pain is the second leading reason for emergency department (ED) visits and is commonly identified as a leading driver of low-value health care. Accurate identification of patients at low risk of major adverse cardiac events (MACE) is important to improve resource allocation and reduce over-treatment. Objectives: We assessed machine learning (ML) methods and electronic health record (EHR) covariate collection for MACE prediction. We aimed to maximize the pool of low-risk patients that were accurately predicted to have less than 0.5% MACE risk and could be eligible for reduced testing ("rule-out" strategy). Population Studied: 116,764 adult patients presenting with chest pain in the ED between 2013 and 2015 and evaluated for potential acute coronary syndrome (ACS). 60-day MACE rate was 2%. Setting: Data analysis was performed May 2018 to August 2021. Methods: We evaluated ML algorithms (lasso, splines, random forest, extreme gradient boosting, Bayesian additive regression trees) and SuperLearner stacked ensembling. We tuned ML hyperparameters through nested ensembling, and imputed missing values with generalized low-rank models (GLRM). Performance was benchmarked against individual biomarkers, validated clinical risk scores, decision trees, and logistic regression. We assessed clinical utility through net benefit analysis and explained the models through variable importance ranking and accumulated local effect visualization Results: The SuperLearner ensemble provided the best cross-validated discrimination with areas under the curve of 0.15 for precision-recall (PR-AUC) and 0.87 for receiver operating characteristic (ROC-AUC), and the best accuracy with an index of prediction accuracy of 0.07. The ensemble's risk estimates were miscalibrated by 0.2 percentage points on average, and dominated the net benefit analysis at all examined thresholds. At a 0.5% threshold the ensemble model yielded 32 benefit-adjusted workups avoided per 100 patients, compared to 25 for logistic regression and 2-14 for clinical risk scores. The most important predictors were age, troponin, clinical risk scores, and electrocardiogram. GLRM achieved a 90% average reduction in reconstruction error compared to median-mode imputation. Conclusion: Combining ML algorithms with a broad set of EHR covariates improved MACE risk prediction and would reduce over-treatment compared to simpler alternatives, while providing calibrated predictions and interpretability. Patients should receive targeted benefit in their care from thorough detection of nuanced health patterns via ML.
Retention Time Prediction Using Neural Networks Increases Identifications in Crosslinking Mass Spectrometry
Authors: Giese Sven H. , Sinn Ludwig R. , Wegner Fritz , Rappsilber Juri
Published: March 2021

Crosslinking mass spectrometry (Crosslinking MS) has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the spectra limits the numbers of protein-protein interactions (PPIs) that can be confidently identified. Here, we successfully leveraged chromatographic retention time (RT) information to aid the identification of crosslinked peptides from spectra. Our Siamese machine learning model xiRT achieved highly accurate RT predictions of crosslinked peptides in a multi-dimensional separation of crosslinkedE. colilysate. We combined strong cation exchange (SCX), hydrophilic strong anion exchange (hSAX) and reversed-phase (RP) chromatography and reachedR20.94 in RP and a margin of error of 1 fraction for hSAX in 94%, and SCX in 85% of the predictions. Importantly, supplementing the search engine score with retention time features led to a 1.4-fold increase in PPIs at a 1% false discovery rate. We also demonstrate the value of this approach for the more routine analysis of a crosslinked multiprotein complexes. An increase of 1.7-fold in heteromeric crosslinked residue-pairs was achieved at 1% residue-pair FDR for Fanconi anaemia monoubiquitin ligase complex, solely using reversed-phase RT. Retention times are a powerful complement to mass spectrometric information to increase the sensitivity of Crosslinking MS analyses.
Understanding learners' completion intention of massive open online courses (MOOCs): role of personality traits and personal innovativeness
Authors: Gupta Kriti Priya
Published: March 2021

Purpose

The present study investigates the influence of five personality traits based on the Big Five model, i.e. extraversion, neuroticism, conscientiousness, agreeableness and openness to experience and personal innovativeness on learners' intention to complete MOOCs.

Design/methodology/approach

The proposed model was empirically tested using cross-sectional design. The primary data were gathered through a survey of 515 students at five higher educational institutions in the National Capital Region of Delhi, India. Structural equation modelling was used to test the hypothesized relationships in the proposed model.

Findings

The study has found significant associations between the personality traits, personal innovativeness and MOOC completion intention. The findings indicate that extraversion, conscientiousness, agreeableness, openness to experience and personal innovativeness have significant positive effects whereas neuroticism has no significant effect on MOOCs continuance intention. Personal innovativeness has been found to mediate the relationships between all the personality traits and MOOCs completion intention of learners.

Practical implications

Our findings can potentially address the issue of drop-out rates of MOOCs in developing countries such as India. The findings of the study are helpful for MOOCs providers and other stakeholders. The MOOC developers should develop courses with wide scope so as to accommodate learners with different personality profiles. Additionally, during the enrolment process, MOOC providers can identify the students' attributes through personality tests. This will help in customizing the study material and teaching pedagogy as per the needs of the students.

Originality/value

The study contributes to the growing area of research in MOOCs usage by exploring the influence of personality traits on learners' behaviour towards completing MOOCs. Since the learners' intention to complete MOOCs is a major concern for MOOC developers, hence the present study makes a worthwhile contribution as it is a relatively under-researched area.
The management of talent: Optimal contracting for selection and incentives
Authors: Foarta Dana , Sugaya Takuo
Published: March 2021

Optimally reallocating human capital to tasks is key for an organization to successfully navigate a transition. We study how to design employment contracts to allocate employees to different valuable projects within an organization given two simultaneous challenges: The employees have private information about their cost of effort, and they exert unobservable effort. The optimal contract menu pairs a higher probability of assignment to a valuable project with a lower bonus in case of success. In limited cases, a fixed salary may be offered to employees with high effort cost. We link our results to job design features encountered in practice.
Persons with pre‐dementia have no Kantian duty to die
Authors: Huang Yuanyuan , Cong Yali
Published: March 2021

Cooley's argument that persons with pre‐dementia have a Kantian duty to die has led to much debate. Cooley gives two reasons for his claim, the first being that a person with pre‐dementia should end his/her life when he/she will inevitably and irreversibly lose rationality and be unable to live morally as a result. This paper argues that this reason derives from an unsubstantiated premise and general confusion regarding the condition for a Kantian duty to die. Rather, a close reading of Kant reveals that such a condition occurs when a person confronts an external handicap that does not undermine his/her rational ability but deprives him/her of the possibility of living the way a person should. People do not confront this experience with progressive dementia. The other reason Cooley proposes is that a person should not allow their continued existence to become a burden to others. This claim partly stems from a radical interpretation of a case discussed by Kant and is partly based on a misuse of Kant's formulation of humanity. Based on a prudent inference from Kantian ethics, this article argues against Cooley that persons with pre‐dementia have no Kantian duty to die.
Estimating counterfactuals for evaluation of ecological and conservation impact: an introduction to matching methods
Authors: Ribas Luiz G. S. , Pressey Robert L. , Bini Luis M.
Published: March 2021

Matching methods encompass non‐parametric approaches to estimating counterfactual states through a rigorous selection of control units with similar characteristics to units submitted to an intervention. These methods enable comparisons between treated and control units in a way that facilitates understanding of causal relationships between interventions and outcomes. Matching methods have been used only recently in ecology and conservation biology, where such applications changed the way the field investigates causal questions, for example, in impact‐evaluation studies. However, the strengths and limitations of matching methods are not well understood by most ecologists and environmental scientists. Herein, we review state‐of‐the‐art matching methods aiming to help fill this gap in understanding. First, we present relevant theoretical concepts related to matching methods and related subjects such as counterfactual states and causation. Next, we propose guidelines and strategies for the application of matching methods in ecology and conservation biology. Finally, we discuss the possibilities for future applications of matching methods in the environmental sciences.
The Intertwined Past, Present, and Future of Local Natural History Museum and Amateur Naturalism in Tampere, Finland
Authors: Santaoja Minna
Published: March 2021

The history of natural history museums (NHMs) is closely tied with amateur naturalism, now often discussed as citizen science. This paper discusses the relations between a local NHM and amateur naturalists in Tampere, Finland, in three temporalities: the past, the present, and the future. The analysis highlights the contingencies and materialities of the relations between the museum and naturalists, showing them to be at times close, at other times distant. Local NHMs are facing the same expectations and challenges as larger museums, such as the tension between their research and education functions, and making their collections digitally available. NHMs are expected to participate in creating sustainable futures, looking far ahead. The case proposes the strength of local NHMs may be their embeddedness in local networks and their agility to react to ecosocial changes.
Recollections of Who We Were: Nostalgic Retrospective Perceptions of Japanese Society Following a Visit to a Shōwa‐era Museum
Authors: Anderson David , Shimizu Hiroyuki , Iwasaki Shota
Published: March 2021

Understanding visitors' retrospective perceptions in museums as they connect objects with their personal identities and life stories, as well as their collective social identities, is of considerable interest to the museum field. This study employed a multiple case narrative methodology to understand the common perceptual themes of post‐World War II Japanese society between 1955 and 1970 (Shōwa 30–45) held by older Japanese adults following their visit to a Shōwa‐era social history museum. From an inductive analysis ofn = 29 face‐to‐face interviews, five sustaining characteristic themes emerged which were later interpreted through the historical backdrop of the period together with Carstensen's socioemotional selectivity theory (SST) to provide deeper interpretation of the themes. Through their museum experiences, the visitors recalled a society characterized by; (1) close human relationships; (2) strong values and morals; (3) freedom, openness, and peace; (4) struggles and poverty, which could be overcome with patient effort; and, (5) hopes and dreams. These themes were key to the visitors' own identity and values – both personal and collective. This study contributes to a broader understanding of the power of museum experiences to evoke strong nostalgic recollections by Japanese citizens of their unique personal and collective identities, and the characteristics their retrospective memories from the perspective of the present day vantage point. It speaks to the power of the museum, not as a learning or knowledge acquisition experience, but rather in its power to affirm both personal and collective identity and the values that were retrospectively important for these visitors looking back.
Facilitated Making in Museum‐Based Educational Makerspaces
Authors: White Annie M. , Akiva Thomas , Wardrip Peter S. , Brahms Lisa
Published: March 2021

The Maker Movement is on the rise and research shows that the ways educators facilitate making activities is a key element of supporting children’s learning and development in this setting. As a field, we need to better understand how educators and children interact in makerspaces and the context that surrounds facilitation. In this study, we describe a research‐practice partnership between 11 museum educators and 4 researchers. Over two years, participants met to reflect on videos of educator‐child interactions and engage in dialog, reflective activities, and interviews around the topic of facilitation. Our collaboration resulted in a Model of Facilitated Making that categorizes types of facilitation moves, describes environmental influences on facilitation, and offers a process for considering techniques educators may use to facilitate. This model offers a framework for reflecting on facilitation in makerspaces, which has implications for practice and future research.