bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of the PneumoGenius® and RealStar® Pneumocystis jirovecii PCR CE-IVD assays with a lab developed test for the detection of Pneumocystis jirovecii
Authors: Nijhuis Roel H T , Godschalk Peggy C R , Smink Jorike H I , van der Zee Cindy , van Hannen Erik J
Published: December 2021

Pneumocystis jirovecii (Pj) is a fungal pathogen that can cause severe and potential fatal pneumonia (Pneumocystis pneumonia, PCP) in immunocompromised patients. Microbiological diagnosis is necessary to confirm PCP, for which mainly real-time PCR assays are used by detecting Pj from bronchoalveolar lavage (BAL) specimens. In this study, we evaluate the performance of the CE-IVD PneumoGenius® assay and CE-IVD RealStar® Pneumocystis jirovecii PCR assay in comparison to the lab developed test (LDT) that is used in routine diagnostics. Comparison was done by including 100 BAL specimens: 25 retrospective specimens, selected based on results obtained with LDT (15 positive/10 negative), and 75 prospectively collected specimens. LDT (targeting MSG) was performed according to local procedures and the PneumoGenius® (targeting mtLSU and DHPS fas) and RealStar® assays (targeting mtLSU) according to the manufacturer's instructions. Combining results of retrospective and prospective analysis, sensitivity was 69.7, 100 and 100% for the LDT, PneumoGenius® and RealStar®, respectively. Specificity was 100% for LDT and Pneumogenius®, whereas RealStar® showed a specificity of 97%. Correlation of fungal loads found with the PneumoGenius® and RealStar® assays was high (R2: 0.98). The PneumoGenius® and RealStar® assays performed comparable, and both showed high sensitivity in comparison to the LDT. For optimal diagnosis of PCP, the LDT has to be replaced by another, more sensitive assay.

Lay summary

In this study, we evaluated the performance of two commercially available CE-IVD cleared real-time PCR assays to detect Pneumocystis jirovecii in comparison to the lab-developed test as used in routine diagnostics. Performance of the CE-IVD real-time PCR assay was superior to the lab-developed test.
Galaxy velocity bias in cosmological simulations: towards per cent-level calibration
Authors: Anbajagane Dhayaa , Aung Han , Evrard August E , Farahi Arya , Nagai Daisuke , Barnes David J , Cui Weiguang , Dolag Klaus , McCarthy Ian G , Rasia Elena , Yepes Gustavo
Published: December 2021

Galaxy cluster masses, rich with cosmological information, can be estimated from internal dark matter (DM) velocity dispersions, which in turn can be observationally inferred from satellite galaxy velocities. However, galaxies are biased tracers of the DM, and the bias can vary over host halo and galaxy properties as well as time. We precisely calibrate the velocity bias, bv – defined as the ratio of galaxy and DM velocity dispersions – as a function of redshift, host halo mass, and galaxy stellar mass threshold ($M_{\rm \star , sat}$), for massive haloes ($M_{\rm 200c}\gt 10^{13.5} \, {\rm M}_\odot$) from five cosmological simulations: IllustrisTNG, Magneticum, Bahamas + Macsis, The Three Hundred Project, and MultiDark Planck-2. We first compare scaling relations for galaxy and DM velocity dispersion across simulations; the former is estimated using a new ensemble velocity likelihood method that is unbiased for low galaxy counts per halo, while the latter uses a local linear regression. The simulations show consistent trends of bv increasing with M200c and decreasing with redshift and $M_{\rm \star , sat}$. The ensemble-estimated theoretical uncertainty in bv is 2–3 per cent, but becomes percent-level when considering only the three highest resolution simulations. We update the mass–richness normalization for an SDSS redMaPPer cluster sample, and find our improved bv estimates reduce the normalization uncertainty from 22 to 8 per cent, demonstrating that dynamical mass estimation is competitive with weak lensing mass estimation. We discuss necessary steps for further improving this precision. Our estimates for $b_v(M_{\rm 200c}, M_{\rm \star , sat}, z)$ are made publicly available.
Statistical similarity between soft gamma repeaters and repeating fast radio bursts
Authors: Sang Yu , Lin Hai-Nan
Published: December 2021

We study the statistical properties of the soft gamma repeater SGR 1935+2154. We find that the cumulative distributions of duration, waiting time, fluence, and flux can be well fitted by bent power law. In addition, the probability density functions of fluctuations of duration, waiting time, fluence, and flux well follow the Tsallis q-Gaussian distribution. The q values keep steady for different temporal scale intervals, indicating a scale-invariant structure of the bursts. Those features are very similar to the property of the repeating fast radio burst FRB 121102, indicating the underlying association between the origins of soft gamma repeaters and repeating fast radio bursts.
Grouped star formation: converting sink particles to stars in hydrodynamical simulations
Authors: Liow Kong You , Rieder Steven , Dobbs Clare L , Jaffa Sarah E
Published: December 2021

Modelling star formation and resolving individual stars in numerical simulations of molecular clouds and galaxies is highly challenging. Simulations on very small scales can be sufficiently well resolved to consistently follow the formation of individual stars, whilst on larger scales sinks that have masses sufficient to fully sample the IMF can be converted into realistic stellar populations. However, as yet, these methods do not work for intermediate scale resolutions whereby sinks are more massive compared to individual stars but do not fully sample the IMF. In this paper, we introduce the grouped star formation prescription, whereby sinks are first grouped according to their positions, velocities, and ages, then stars are formed by sampling the IMF using the mass of the groups. We test our grouped star formation method in simulations of various physical scales, from sub-parsec to kilo-parsec, and from static isolated clouds to colliding clouds. With suitable grouping parameters, this star formation prescription can form stars that follow the IMF and approximately mimic the original stellar distribution and velocity dispersion. Each group has properties that are consistent with a star-forming region. We show that our grouped star formation prescription is robust and can be adapted in simulations with varying physical scales and resolution. Such methods are likely to become more important as galactic or even cosmological scale simulations begin to probe sub-parsec scales.
The dark matter haloes of HI selected galaxies
Authors: Dutta Saili , Khandai Nishikanta , Rana Sandeep
Published: December 2021

We present the neutral hydrogen mass (MHI) function (HIMF) and velocity width (w50) function (HIWF) based on a sample of 7857 galaxies from the 40 per cent data release of the ALFALFA survey (α.40). The low mass (velocity width) end of the HIMF (HIWF) is dominated by the blue population of galaxies whereas the red population dominates the HIMF (HIWF) at the high mass (velocity width) end. We use a deconvolution method to estimate the HI rotational velocity (Vrot) functions (HIVF) from the HIWF for the total, red, and blue samples. The HIWF and HIVF for the red and blue samples are well separated at the knee of the function compared to their HIMFs. We then use recent stacking results from the ALFALFA survey to constrain the halo mass (Mh) function of HI-selected galaxies. This allows us to obtain various scaling relations between MHI−w50−Vrot−Mh, which we present. The MHI−Mh relation has a steep slope ∼2.10 at small masses and flattens to ∼0.34 at masses larger than a transition halo mass, $\log _{10}(M_{\rm{ht}}h_{70}^2/M_{\odot })=10.62$. Our scaling relation is robust and consistent with a volume-limited sample of α.40. The MHI−Mh relation is qualitatively similar to the Mstar−Mh relation but the transition halo mass is smaller by ∼1.4 dex compared to that of the Mstar−Mh relation. Our results suggest that baryonic processes like heating and feedback in larger mass haloes suppress HI gas on a shorter time-scale compared to star formation.
Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors
Authors: Fiddaman Steven R , Vinkler Michal , Spiro Simon G , Levy Hila , Emerling Christopher A , Boyd Amy C , Dimopoulos Evangelos A , Vianna Juliana A , Cole Theresa L , Pan Hailin , Fang Miaoquan , Zhang Guojie , Hart Tom , Frantz Laurent A F , Smith Adrian L
Published: December 2021

Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.
Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa
Authors: Wang Shiyi , Sotcheff Stephanea L , Gallardo Christian M , Jaworski Elizabeth , Torbett Bruce E , Routh Andrew L
Published: December 2021

Adaptation of viruses to their environments occurs through the acquisition of both novel single-nucleotide variants (SNV) and recombination events including insertions, deletions, and duplications. The co-occurrence of SNVs in individual viral genomes during their evolution has been well-described. However, unlike covariation of SNVs, studying the correlation between recombination events with each other or with SNVs has been hampered by their inherent genetic complexity and a lack of bioinformatic tools. Here, we expanded our previously reported CoVaMa pipeline (v0.1) to measure linkage disequilibrium between recombination events and SNVs within both short-read and long-read sequencing datasets. We demonstrate this approach using long-read nanopore sequencing data acquired from Flock House virus (FHV) serially passaged in vitro. We found SNVs that were either correlated or anti-correlated with large genomic deletions generated by nonhomologous recombination that give rise to Defective-RNAs. We also analyzed NGS data from longitudinal HIV samples derived from a patient undergoing antiretroviral therapy who proceeded to virological failure. We found correlations between insertions in the p6Gag and mutations in Gag cleavage sites. This report confirms previous findings and provides insights on novel associations between SNVs and specific recombination events within the viral genome and their role in viral evolution.
Determinants of the temperature adaptation of mRNA degradation
Authors: Jaquet Vincent , Wallerich Sandrine , Voegeli Sylvia , Túrós Demeter , Viloria Eduardo C , Becskei Attila
Published: December 2021

The rate of chemical reactions increases proportionally with temperature, but the interplay of biochemical reactions permits deviations from this relation and adaptation. The degradation of individual mRNAs in yeast increased to varying degrees with temperature. We examined how these variations are influenced by the translation and codon composition of mRNAs. We developed a method that revealed the existence of a neutral half-life above which mRNAs are stabilized by translation but below which they are destabilized. The proportion of these two mRNA subpopulations remained relatively constant under different conditions, even with slow cell growth due to nutrient limitation, but heat shock reduced the proportion of translationally stabilized mRNAs. At the same time, the degradation of these mRNAs was partially temperature-compensated through Upf1, the mediator of nonsense-mediated decay. Compensation was also promoted by some asparagine and serine codons, whereas tyrosine codons promote temperature sensitization. These codons play an important role in the degradation of mRNAs encoding key cell membrane and cell wall proteins, which promote cell integrity.
Variegated Accountability: Devolved Public Accounts Committees in the UK
Authors: Foster Helen , Knox Colin
Published: December 2021

Devolution in the UK has now been in place for over 20 years. A key support mechanism for the devolved administrations in Scotland, Wales and Northern Ireland is the Public Account Committees (PACs). Aside from their formal role in ensuring financial regularity and probity, they aim to strengthen accountability at the regional level. This study examines the effectiveness of the PACs measured through the perception of key stakeholders (PAC members, witnesses, auditors and officials). Using Q methodology, it identifies four clusters of participants: Team Players, Peace Makers, Bureaucrats and Attention Seekers, and captures their perceptions of what makes the devolved PACs most effective.
Discursive Activists or Patriarchal Bargainers? Religion, Gender, and Neoliberal Governance in the “New” Turkey
Authors: Özdemir Şeyma
Published: December 2021

This article aims first to contribute to discussions on both the agency of religious women and feminist transversal politics, and second, to emphasize the need to build solidarity coalitions to resist interlocking oppressive structures. It examines the intellectual mobilization of religious women in Turkey (2010–2016), drawing on an ethnographic study of an Istanbul women’s organization. It explores the way religious women contextualized Turkey’s socio-political transformation and analyzed earlier initiatives, and analyses their struggle to challenge the perceptions of them as outsiders vis-a-vis the secularist Republican state patriarchy and Islamist neoliberal patriarchal state. The study concludes that national socio-political transformations curtailed their discursive activism and that broader solidarity networks, transversal politics, and feminist coalitions are necessary to resist such oppressive structures.
Original Research: Nurses' Experiences of Caring for Patients and Families During the COVID-19 Pandemic: Communication Challenges
Authors: Pariseault Christine A. , Copel Linda Carman , McKay Michelle A.
Published: December 2021

Objective:

The purpose of this study was to gain a better understanding of the perceptions and experiences of nurses caring for patients and families under the COVID-19 pandemic's socially restrictive practices and policies.

Background:

The COVID-19 global pandemic has affected the delivery of health care to patients and their families, with many aspects altered because of the need for social distancing, social isolation, and visitation restriction policies. These policies have created communication challenges for interdisciplinary health care teams, patients, and families. As frontline caregivers, nurses have felt strongly the impact of these challenges.

Methods:

A qualitative descriptive study was conducted among 17 RNs who were caring for patients during the COVID-19 pandemic and were recruited via social media posts on Facebook, Twitter, and LinkedIn. Watson's theory of human caring served as the conceptual framework for the study.

Results:

Several themes emerged regarding nurses' experiences of communication with patients and families. These include communication challenges and barriers, prioritization, integration of group communication, nurse self-reflection, and acceptance of gratitude.

Conclusions:

The study findings underscore the importance of nurses' communication with patients and families under the pandemic's restricted conditions. They demonstrate the value of nurses' ability to innovate in fostering all parties' participation in the plan of care, and highlight the comfort nurses provide to patients who are isolated from loved ones. Strategies that fostered communication were identified, as were areas for further research.
Genomic evolution during locoregional recurrence in colorectal cancer determined by whole-exome sequencing: a retrospective observational study
Authors: Lan Xiaoliang , Wu Xiaoxiao , Zhang Chao , Wei Genxia , Li Bingbing , Qiu Weihao , Li Danyi , Wu Huanwen , Ding Yanqing , Yuan Jie , Tai Zaixian , Yang Zuoquan , Liang Zhiyong , Su Dan , Liang Li
Published: December 2021

Objective:

The genomic landscapes of metastatic colorectal cancer (mCRC) have been extensively studied; however, the genetic mechanisms underlying the locoregional recurrence (LR) of CRC remain unclear. The objective of our study was to investigate genomic evolution during LR in CRC using high-throughput sequencing.

Methods:

Twenty-three CRC patients with matched primary and LR tissues were recruited from Nanfang Hospital and Zhejiang Cancer Hospital between January 2011 and December 2018. The last date of follow-up was March 2020. Tissue samples were analyzed by whole-exome sequencing and the genomic profiles were depicted by single nucleotide variation, mutational signature, copy number variation, clonal architecture, and other features. The evolutionary process was speculated with comparison of the genetic variations between primary and LR lesions. The disseminating clusters from primary to LR lesions were identified by variant allele frequency dynamics. Furthermore, the early-recurrent biomarker was explored by comparing the indel signature between early- and late-recurrent patients. The study was approved by the Institutional Review Board of Nanfang Hospital of Southern Medical University (approval No. 2020010) on September 11, 2020.

Results:

The results highlighted distinct origins of LR between patients with high microsatellite instability and microsatellite stability. LR lesions evolved independently in patients with high microsatellite instability, while LR lesions were highly clonally related to the primary lesions in patients with microsatellite stability. Late-acquired variations in LR lesions encompassed a wide range of driver genes involved in histone methylation, DNA replication, T cell activation,
PDCD1
gain, and
LMNA
loss. Furthermore, clonal analysis of the disseminating cells identified a dominant polyclonal seeding pattern during LR. The indel signature ID4 was associated with significantly shorter disease-free survival in patients with relapsed CRC according to a public dataset.

Conclusion:

These findings pose a challenge for the development of new approaches targeting the interactions of multiple clones in the establishment of LR and in terms of optimizing the clinical management of susceptible patients.
A Survey of Entry-Level Physical Therapy Education Content for Vestibular Rehabilitation
Authors: Galgon Anne K. , Roberts Holly J. , Littmann Andrew E. , Heusel-Gillig Lisa L. , Dransfield Lisa , Plishka Charles M. , Wrisley Diane M.
Published: December 2021

Introduction.

Vestibular rehabilitation (VR) represents an evolving area of physical therapy practice and is therefore pertinent to entry-level education. Currently, there is no consensus regarding the extent of content that should be covered in entry-level Doctor of Physical Therapy (DPT) programs. The first step in establishing standards of education in VR is to determine what content is currently taught and what is perceived to be important. The purpose of this study was to survey entry-level DPT programs as to what VR content is included in their curriculum and their perceptions of importance of VR examination and intervention techniques.

Methods.

Directors of 229 accredited physical therapy education programs in the United States were contacted to complete the survey. A task force of 3 clinicians and 4 faculty used a modified Delphi process to select survey items to examine content exposure, student assessment, and a rating for overall expected expertise. Modifications were made to the final survey for clarity and time requirements based on pilot survey data. Descriptive and correlational statistics were applied to the data.

Results.

Ninety-nine programs (43.23%) responded to the survey. More than 90% rated 7 vestibular conditions (unilateral vestibular hypofunction, posterior semicircular canal canalithiasis and cupulolithiasis, vestibular neuritis, labyrinthitis, bilateral vestibular hypofunction, and horizontal semicircular canal canalithiasis) as essential for entry-level practice. More than 90% of respondents rated all elements of clinical application and decision-making as essential for entry-level education except for billing/diagnosis codes. Most respondents expected students to perform at the intermediate or advanced beginner level in vestibular assessment and rehabilitation on graduation.

Discussion and Conclusion.

Disparities in VR content, expected level of performance, and the amount of time dedicated to VR exist. Vestibular rehabilitation education may not match current clinical practice. Future research should determine the level of education clinicians expect of entry-level DPT graduates.
Perfectionism, Stress, and the Entry-Level Doctor of Physical Therapy Student: A Cross-Sectional, Observational Study
Authors: Richardson Michael V. , Miller Haylie , Papa Evan , Santurri Laura
Published: December 2021

Introduction.

Perfectionism consists of high standards and hypercritical self-evaluation. Some doctor of physical therapy (DPT) students experience increased stress levels due to rigorous academic expectations. There is limited understanding of how successful these students are at managing increased stress, especially among perfectionists. The purpose was to examine perfectionism among entry-level DPT students and its relationship to perceived stress.

Review of Literature.

Researchers have studied perfectionism and stress in health professions programs, but not DPT programs. Being a Maladaptive Perfectionist (MP) was positively and strongly associated with stress among health professions students.

Subjects.

Convenience sample of first-year, second-year, and third-year DPT students (n = 163).

Methods.

This was a nonexperimental, single-site, cross-sectional study. Investigators used 3-way analysis of variance to compare student characteristics and binomial logistic regressions to determine whether characteristic and/or perceived stress was predictive of perfectionism subtype. They completed bivariate correlations to determine associations between perfectionism and stress.

Results.

Sample results demonstrated 41.10% Adaptive Perfectionists and 25.15% MPs. There was a moderate, direct association between perceived stress and the perfectionism discrepancy measure (r

s
= .51, P < .01). The perceived stress and perfectionism subtype logistic regression model was statistically significant, χ2(1) = 18.73, P < .01. Participants with increased perceived stress had 1.17 times higher odds of being categorized as an MP than those with lower stress levels.

Discussion and Conclusion.

Maladaptive Perfectionist students may be at greater risk for stress-related issues. Perfectionism and stress measures may assist educators in identifying at-risk students, monitor student response to stress management interventions, and consider curricular changes to lower stress. Students who effectively manage stress may ultimately have overall greater well-being.
Effects of regular breakfast habits on metabolic and cardiovascular diseases
Authors: Li Zhi-hui , Xu Lei , Dai Rao , Li Li-jie , Wang Hao-jie
Published: December 2021

Background:

Breakfast, which is considered as an important meal of the day, is being ignored by an increasing number of people as the pace of modern life accelerates. Although a large number of previous studies have reported the relationship between skipping breakfast and type 2 diabetes mellitus, most of them were cross-sectional studies. It remains unclear how skipping breakfast affects such specific cardio-metabolic diseases as hypertension, strokes and hypercholesterolemia.

Methods:

The protocols and reports of this meta-analysis are based on a meta-analysis of observational studies in epidemiological guidelines (MOOSE). Relevant studies were systematically retrieved from PubMed, Embase, Web of Science and the Cochrane Library, and were restricted to English from the inception to May 10, 2019. All the results were obtained by RRs, and outcomes of interests should include the occurrence of cardiovascular and metabolic diseases.

Results:

Fourteen cohort studies in total were eventually included. Compared with people having breakfast frequency

≦3times/week

, those with a frequency

>3 times/week

have reduced the risk of type 2 diabetes mellitus, obesity, Metabolic Syndrome, Low high-density lipoprotein cholesterolemia, Cardiovascular Diseases, cardiovascular Mortality, hypertension and strokes, with (RR = 0.8 [95% CI: 0.7–0.91], P = .142, I
2 = 37.6%), (RR = 0.74 [95% CI: 0.59–0.94], P < .001, I
2 = 89%), (RR = 0.86 [95% CI:0.75–0.99], P = .512, I
2 = 0%), (RR = 0.75 [95% CI:0.61–0.93], P = .643, I
2 = 0%), (RR = 0.87 [95% CI:0.81–0.93], P = .479, I
2 = 0%), (RR = 0.63 [95% CI:0.51–0.78], P = .396, I
2 = 0%), (RR = 0.92 [95% CI:0.86–0.98], P = .419, I
2 = 0.7%), and (RR = 0.89 [95% CI:0.79–0.99], P = .238, I
2 = 29%), respectively.

Conclusions:

A regular daily breakfast habit benefits the cardio-metabolism to a great extent, reducing the risk of Cardiovascular Diseases, type 2 diabetes mellitus, obesity, hypertension, strokes, Metabolic Syndrome, cardiovascular Mortality, Low high-density lipoprotein cholesterolemia, and Abdominal obesity, while it is not significantly related to hypercholesterolemia and coronary heart disease regardless of gender. Nevertheless, skipping breakfast once a week may greatly reduce the benefits of cardio-metabolism. Therefore, public institutions should promote and encourage citizens to cultivate regular daily breakfast habits.
Sneathia amnii bacteraemia and chorioamnionitis leading to second trimester abortion: a case report
Authors: Gruwier Lien , Sprenkels Aaron , Hulsbosch Sofie , Vankeerberghen Anne , Cartuyvels Reinoud
Published: December 2021

Background.

Sneathia amnii

(formerly designated as

Leptotrichia amnionii

) was first described in 2002 in the USA. Members of the genus

Sneathia

can be part of the normal flora of the genitourinary tract, but have been implicated in invasive (mostly gynaecological) infections.

Case presentation. To the best of our knowledge, here we present the first case of

S. amnii

infection in Belgium, in a young woman presenting with fever leading to second trimester septic abortion.

Conclusions. Despite its pathogenicity,

S. amnii

remains an underrated cause of infections due to inherent difficulties with conventional laboratory methods. By extracting the bacterial DNA directly from the blood culture broth and performing a 16S ribosomal RNA gene sequence analysis we succeeded in identifying

S. amnii

as the most probable cause of the septic abortion in our patient.
Clinical Evaluation of a Combo Rapid Antigen Test QuickNavi-Flu+COVID19 Ag for Simultaneous Detection of SARS-CoV-2 and Influenza Viruses
Authors: Takeuchi Yuto , Akashi Yusaku , Kiyasu Yoshihiko , Terada Norihiko , Kurihara Yoko , Kato Daisuke , Miyazawa Takashi , Muramatsu Shino , Shinohara Yuki , Ueda Atsuo , Notake Shigeyuki , Nakamura Koji , Suzuki Hiromichi
Published: December 2021

Introduction

Since respiratory sample collection is an uncomfortable experience, simultaneous detection of pathogens with a single swab is preferable. We prospectively evaluated the clinical performance of a newly developed antigen test QuickNavi-Flu+COVID19 Ag (Denka Co., Ltd., Tokyo, Japan) which can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses at the same time with a single testing device.

Methods

Included were those who were suspected of contracting coronavirus disease 2019 (COVID-19) and referred to a PCR center at Ibaraki prefecture in Japan, between August 2, 2021 to September 13, 2021, when the L452R mutant strains of SARS-CoV-2 were prevalent. Additional nasopharyngeal samples and anterior nasal samples were obtained for the antigen test and were compared with a reference reverse transcription PCR (RT-PCR) using nasopharyngeal samples.

Results

In total, 1510 nasopharyngeal samples and 862 anterior nasal samples were evaluated. For SARS-CoV-2 detection in nasopharyngeal samples, the sensitivity and specificity of the antigen test were 80.9% and 99.8%, respectively. The sensitivity and specificity using anterior nasal samples were 67.8% and 100%, respectively. In symptomatic cases, the sensitivities increased to 88.3% with nasopharyngeal samples and 73.7% with anterior nasal samples. There were three cases of discrepant results between the antigen test and the real-time RT-PCR. All of them were positive with the antigen test but negative with the real-time RT-PCR in SARS-CoV-2 detection. During the study period, influenza viruses were not detected.

Conclusion

A combo kit, QuickNavi-Flu+COVID19 Ag, showed an acceptable sensitivity and sufficient specificity for SARS-CoV-2 detection, especially using nasopharyngeal sample collected from symptomatic patients.
De novo missense variants in SLC32A1 cause a neurodevelopmental disorder with epilepsy due to impaired GABAergic neurotransmission
Authors: Platzer Konrad , Sticht Heinrich , Bupp Caleb , Ganapathi Mythily , Pereira Elaine M. , Le Guyader Gwenaël , Bilan Frederic , Henderson Lindsay B. , Taschenberger Holger , Brose Nils , Jamra Rami Abou , Wojcik Sonja M.
Published: December 2021

We describe four patients with a neurodevelopmental disorder and de novo missense variants in SLC32A1, the gene that encodes the vesicular GABA transporter (VGAT). The main phenotype comprises moderate to severe intellectual disability, early onset epilepsy within the first 18 months of life and a choreatic, dystonic or dyskinetic movement disorder. In silico modeling and functional analyses in cultured neurons reveal that three of these variants, which are located in helices that line the putative GABA transport pathway, result in reduced quantal size, consistent with impaired filling of synaptic vesicles with GABA. The fourth variant, located in the VGAT N-terminus, does not affect quantal size, but increases presynaptic release probability, leading to more severe synaptic depression during high frequency stimulation. Thus, variants in VGAT can impair GABAergic neurotransmission via at least two mechanisms, by affecting synaptic vesicle filling and by altering synaptic short-term plasticity. This work establishes de novo missense variants in SLC32A1 as a novel cause for a neurodevelopmental disorder with epilepsy.
Consequence of adjustments for demographic or clinical covariates and a recommended solution in genome-wide association studies
Authors: Sun Xiaoru , Li Hongkai , Yu Yuanyuan , Yuan Zhongshang , Jin Chuandi , Hou Lei , Liu Xinhui , Wang Qing , Xue Fuzhong
Published: December 2021

Genome-wide association study (GWAS) is fundamentally designed to detect disease-causing genes. To reduce spurious associations or improve statistical power, about 80% of GWASs arbitrarily adjusted for demographic or clinical covariates. However, adjustment strategies in GWASs have not achieved consistent conclusions. Given the initial aim of GWAS that is to identify the causal association between a specific causal single-nucleotide polymorphism (SNP) and disease trait, we summarized all complex relationships of the target SNP, covariate and disease trait into 15 causal diagrams according to various roles of the covariate. Following each causal diagram, we conducted a series of theoretical justifications and statistical simulations. Our results demonstrate that it is unadvisable to adjust for any demographic or clinical covariates. We illustrate our point by applying GWASs for body mass index (BMI) and breast cancer, including adjusting and non-adjusting for age and smoking status. Genetic effects and P values might vary across different strategies. Instead, adjustments for SNPs (G′) should be strongly recommended when G′ are in linkage disequilibrium with the target SNP, and correlated with disease trait conditional on the target SNP. Specifically, adjustment for such G′ can block all the confounding paths between the target SNP and disease trait, and avoid over-adjusting for colliders or intermediaries.
SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection
Authors: Cele Sandile , Jackson Laurelle , Khoury David S. , Khan Khadija , Moyo-Gwete Thandeka , Tegally Houriiyah , San James Emmanuel , Cromer Deborah , Scheepers Cathrine , Amoako Daniel , Karim Farina , Bernstein Mallory , Lustig Gila , Archary Derseree , Smith Muneerah , Ganga Yashica , Jule Zesuliwe , Reedoy Kajal , Hwa Shi-Hsia , Giandhari Jennifer , Blackburn Jonathan M. , Gosnell Bernadett I. , Karim Salim S. Abdool , Hanekom Willem ,   NGS-SA,   COMMIT-KZN Team, von Gottberg Anne , Bhiman Jinal , Lessells Richard J. , Moosa Mahomed-Yunus S. , Davenport Miles P. , de Oliveira Tulio , Moore Penny L. , Sigal Alex
Published: December 2021

The emergence of SARS-CoV-2 Omicron, first identified in Botswana and South Africa, may compromise vaccine effectiveness and the ability of antibodies triggered by previous infection to protect against re-infection (1). Here we investigated whether Omicron escapes antibody neutralization in South Africans, either previously SARS-CoV-2 infected or uninfected, who were vaccinated with Pfizer BNT162b2. We also investigated if Omicron requires the ACE2 receptor to infect cells. We isolated and sequence confirmed live Omicron virus from an infected person in South Africa and compared plasma neutralization of this virus relative to an ancestral SARS-CoV-2 strain with the D614G mutation, observing that Omicron still required ACE2 to infect. For neutralization, blood samples were taken soon after vaccination, so that vaccine elicited neutralization was close to peak. Neutralization capacity of the D614G virus was much higher in infected and vaccinated versus vaccinated only participants but both groups had 22-fold Omicron escape from vaccine elicited neutralization. Previously infected and vaccinated individuals had residual neutralization predicted to confer 73% protection from symptomatic Omicron infection, while those without previous infection were predicted to retain only about 35%. Both groups were predicted to have substantial protection from severe disease. These data support the notion that high neutralization capacity elicited by a combination of infection and vaccination, and possibly boosting, could maintain reasonable effectiveness against Omicron. A waning neutralization response is likely to decrease vaccine effectiveness below these estimates. However, since protection from severe disease requires lower neutralization levels and involves T cell immunity, such protection may be maintained.
Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography
Authors: Ravikumar Ashraya , Gopnarayan Mrugsen Nagsen , Subramaniam Sriram , Srinivasan Narayanaswamy
Published: December 2021

An evaluation of systematic differences in local structure and conformation in the interior of protein tertiary structures determined by crystallography and by cryo-electron microscopy (cryo-EM) is reported. The expectation is that any consistent differences between the derived atomic models could provide insights into variations in side-chain packing that result from differences in specimens prepared for analysis between these two methods. By computing an atomic packing score, which provides a quantitative measure of clustering of side-chain atoms in the core of the tertiary structures, it is found that, in general, for structures determined by cryo-EM, side chains are more dispersed than in structures determined by X-ray crystallography over a similar resolution range. This trend is also observed in the packing comparison at subunit interfaces. Similar trends were observed in the packing comparison at the core of tertiary structures of the same proteins determined by both X-ray and cryo-EM methods. It is proposed here that the reduced dispersion of side chains in protein crystals could be due to some level of dehydration in 3D crystals prepared for X-ray crystallography and also because the higher rate of freezing of protein samples for cryo-EM may enable preservation of a more native conformation.
Institutional entrepreneurship: collaborative change in a complex Canadian organization
Authors: Opara Michael , Okafor Oliver Nnamdi , Ufodike Akolisa , Kalu Kenneth
Published: December 2021

Purpose

This study adopts an institutional entrepreneurship perspective in the context of public–private partnerships (P3s) to highlight the role of social actors in enacting institutional change in a complex organizational setting. By studying the actions of two prominent social actors, the authors argue that successful institutional change is the result of dynamic managerial activity supported by political clout, organizational authority and the social positioning of actors.

Design/methodology/approach

The authors conducted a field-based case study in a complex institutional and organizational setting in Alberta, Canada. The authors employed an institutional entrepreneurship perspective to identify and analyze the activities of two allied actors motivated to transform the institutional environment for public infrastructure delivery.

Findings

The empirical study suggests that the implementation of institutional change is both individualistic and collaborative. Moreover, it is grounded in everyday organizational practices and activities and involves a coalition of allies invested in enacting lasting change in organizational practice(s), even when maintaining the status quo seems advantageous.

Originality/value

The authors critique the structural explanations that dominate the literature on public–private partnership implementation, which downplays the role of agency and minimizes its interplay with institutional logics in effecting institutional change. Rather, the authors demonstrate that, given the observed impact of social actors, public–private partnership adoption and implementation can be theorized as a social phenomenon.
Understanding salesperson intention to use AI feedback and its influence on business-to-business sales outcomes
Authors: Hall Kelly R. , Harrison Dana E. , Ajjan Haya , Marshall Greg W.
Published: December 2021

Purpose

Artificial intelligence (AI) is a rapidly growing frontier. One promising area for AI is its potential to assist sales managers in providing salesperson feedback. Despite this promise, little work has been done within the business-to-business (B2B) sales domain to investigate the potential impact of AI feedback on critical sales outcomes. The purpose of this research is to explore these issues and respond to calls in the literature to determine how AI can enhance salesperson adaptability and performance.

Design/methodology/approach

Survey data from a sample of 246 B2B salespeople was used to test the conceptual model and research hypotheses. The data were analyzed using partial least squares structural equation modeling (PLS-SEM).

Findings

The findings provide broad support for the model. An AI-feedback rich environment and salesperson feedback orientation predicted perceived accuracy of AI feedback which, in turn, strengthened intentions to use AI feedback. These favorable reactions to AI feedback positively related to adaptive selling behaviors, and adaptive selling behaviors mediated the relationships between intentions to use AI feedback and organizational commitment, as well as sales performance. Contrary to expectations, it did not mediate the relationship between intentions to use AI feedback and job satisfaction.

Practical implications

The managerial implications of this study lie in explaining practical considerations for the implementation and use of AI feedback in the sales context.

Originality/value

This study extends literature on technology adoption, performance feedback and the use of AI in the B2B sales domain. It offers practical insight for sales managers and those responsible for implementing AI solutions in sales.
Constraints to the development of MSMEs in Assam, India: do owner-managers’ background characteristics and firm-specific characteristics matter?
Authors: Sanu Md Sahnewaz , Anjum Shabana
Published: December 2021

Purpose

The purpose of the research is to identify the major constraints to the growth of micro, small and medium enterprises (MSMEs) in a less-developed region of an emerging economy and how these constraints are affected by owner/manager's attributes and firm-specific characteristics.

Design/methodology/approach

To fulfill the objectives, a structured questionnaire is used to gather data from 200 randomly selected MSMEs located in Cachar district of Assam, India. The study applies factor analysis to categorize various perceived constraints into resolute sets of problem variables or factors. Then, the summated scales are regressed on the predictors related to owner-manager's attributes and firm characteristics to validate the hypotheses.

Findings

The results demonstrate that the broad factors constraining the development of MSMEs in Cachar district are as follows: (1) financial issues, (2) infrastructure problems, (3) labor and management issues, (4) market problems and (5) input problems. Furthermore, the findings confirm that firm growth, size, age, sector, location, innovation activity, owner-manager's gender, age and level of education significantly affect the identified constraints.

Research limitations/implications

Although the research is limited to the Cachar district of India, the findings are relevant for other similar districts of India and less-developed regions of emerging economies. However, the study needs to be replicated in other regions of India as well as in other emerging economies for cross-validation and to determine the generalizability of the results.

Originality/value

To the authors' knowledge, no studies linking the constraints faced by MSMEs to owner/manager's attributes and firm-specific characteristics are carried out in the north-eastern region of India. The study also extends the limited researches on the influence of owner-manager's attributes and firm characteristics on the constraints to the growth of MSMEs by incorporating additional predictors.
Digital image correlation for sensing kinematic fields in manufacturing processes: a review
Authors: Zhu Pingan , Zhang Chao , Zou Jun
Published: December 2021

Purpose

The purpose of the work is to provide a comprehensive review of the digital image correlation (DIC) technique for those who are interested in performing the DIC technique in the area of manufacturing.

Design/methodology/approach

No methodology was used because the paper is a review article.

Findings

no fundings.

Originality/value

Herein, the historical development, main strengths and measurement setup of DIC are introduced. Subsequently, the basic principles of the DIC technique are outlined in detail. The analysis of measurement accuracy associated with experimental factors and correlation algorithms is discussed and some useful recommendations for reducing measurement errors are also offered. Then, the utilization of DIC in different manufacturing fields (e.g. cutting, welding, forming and additive manufacturing) is summarized. Finally, the current challenges and prospects of DIC in intelligent manufacturing are discussed.
Risks of expressing your authentic self in sport: the influence of stigma covering on perceived job fit and hiring recommendations
Authors: MacCharles Jeffrey D. , Melton E. Nicole
Published: December 2021

Purpose

The purpose of this study was to examine how identity covering techniques can influence raters' perceptions of job candidates who have a socially stigmatized identity. Specifically, the authors explore how raters respond to two types of candidates: one who does not mention his gay identity during the interview process, and one who openly discusses their gay identity during the interview process. The authors also investigate whether job type (sport operations vs business operations) and the rater's views toward social equality influence perceptions of job fit and subsequent hiring recommendations.

Design/methodology/approach

The authors conducted an experiment to examine whether an applicant's level of stigma covering, type of job posting and rater's views toward social equality influenced perceptions of job fit. The authors then tested whether perceptions of job fit mediated hiring recommendations. Adults in the USA (n = 237) who were employed and had served on a hiring committees participated in the survey.

Findings

When applying for sport operations jobs, as opposed to business operations jobs, gay male applicants are viewed more favorably if they engage in high levels of identity covering. Further, the applicant's level of stigma covering influenced raters who reported high or moderate social dominance orientation but did not impact raters with low social dominance orientation. Overall, the findings reveal that identity covering techniques do have relevance for studying the dynamics of hiring gay men who apply for jobs in the sport industry.

Originality/value

The study advances the understanding of identity management techniques by examining the nuances of how applicants can choose to disclose their stigmatized identity, and how those decision influence the hiring process.