bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonutility of procalcitonin for diagnosing bacterial pneumonia in COVID-19
Authors: Cohen Avi J. , Glick Laura R. , Lee Seohyuk , Kunitomo Yukiko , Tsang Derek A. , Pitafi Sarah , Toro Patricia Valda , Zhang Ethan , Datta Rupak , Dela Cruz Charles S. , Gautam Samir
Published: April 2022

Patients hospitalized with COVID-19 are at significant risk for superimposed bacterial pneumonia. However, diagnosing superinfection is challenging due to its clinical resemblance to severe COVID-19. We therefore evaluated whether the immune biomarker, procalcitonin, could facilitate the diagnosis of bacterial superinfection. To do so, we identified 185 patients with severe COVID-19 who underwent lower respiratory culture; 85 had superinfection. Receiver operating characteristic curve analysis showed that procalcitonin at the time of culture was incapable of distinguishing patients with bacterial infection (AUC, 0.52). We conclude that static measurement of procalcitonin does not aid in the diagnosis of superinfection in severe COVID-19.
Cohort profile: The Pregnancy, Arsenic, and Immune Response (PAIR) Study, a longitudinal pregnancy and birth cohort in rural northern Bangladesh
Authors: Avolio Lindsay N. , Smith Tyler J. S. , Navas-Acien Ana , Kruczynski Kate , Pisanic Nora , Randad Pranay R. , Detrick Barbara , Fry Rebecca C. , van Geen Alexander , Goessler Walter , Karron Ruth A. , Klein Sabra L. , Ogburn Elizabeth L. , Wills-Karp Marsha , Alland Kelsey , Ayesha Kaniz , Dyer Brian , Islam Md. Tanvir , Oguntade Habibat A. , Rahman Md. Hafizur , Ali Hasmot , Haque Rezwanul , Shaikh Saijuddin , Schulze Kerry J. , Muraduzzaman A. K. M. , Alamgir A. S. M. , Flora Meerjady Sabrina , West Keith P. , Labrique Alain B. , Heaney Christopher D. ,   the JiVitA Maternal and Child Health and Nutrition Research Project
Published: April 2022

Purpose

Arsenic exposure and micronutrient deficiencies may alter immune reactivity to influenza vaccination in pregnant women, transplacental transfer of maternal antibodies to the fetus, and maternal and infant acute morbidity. The Pregnancy, Arsenic, and Immune Response (PAIR) Study is a longitudinal pregnancy and birth cohort designed to assess whether arsenic exposure and micronutrient deficiencies alter maternal or newborn immunity and acute morbidity following maternal seasonal influenza vaccination during pregnancy.

Participants

We enrolled 784 pregnant women in rural Gaibandha District in northern Bangladesh between October 2018 and March 2019. Women received a quadrivalent seasonal inactivated influenza vaccine at enrollment in the late first or early second trimester between 11 and 17 weeks of gestational age. Follow-up included up to 13 visits between enrollment and three months postpartum as well as weekly telephone surveillance to ascertain influenza-like illness and other acute morbidity symptoms in women and infants. Tube well drinking water and urine specimens were collected to assess arsenic exposure. Of 784 women who enrolled, 736 (93.9%) delivered live births and 551 (70.3%) completed follow-up visit to three months postpartum.

Findings to Date

Arsenic was ≥0.02 µg/L in 97.9% of water specimens collected from participants at enrollment. The medians (interquartile ranges) of water and urinary arsenic were 5.1 (0.5-25.1) µg/L and 33.1 (19.6-56.5) µg/L, respectively. Water and urinary arsenic were strongly correlated (Spearman’s ρ=0.72) among women with water arsenic ≥ median but weakly correlated (ρ=0.18) among women with water arsenic < median.

Future Plans

The PAIR Study is well positioned to examine the effects of low-moderate arsenic exposure and micronutrient deficiencies on immune outcomes in women and infants.

Registration

NCT03930017
Classification of Omicron BA.1, BA.1.1 and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data
Authors: Hirotsu Yosuke , Maejima Makoto , Shibusawa Masahiro , Natori Yume , Nagakubo Yuki , Hosaka Kazuhiro , Sueki Hitomi , Mochizuki Hitoshi , Tsutsui Toshiharu , Kakizaki Yumiko , Miyashita Yoshihiro , Omata Masao
Published: April 2022

Objective

Recently, the Omicron strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread and replaced the previously dominant Delta strain. Several Omicron sublineages (BA.1, BA.1.1 and BA.2) have been identified, with in vitro and preclinical reports showing that the pathogenicity and therapeutic efficacy differs between BA.1 and BA.2. We sought to develop a TaqMan assay to identify these subvariants.

Methods

A TaqMan assay was constructed for rapid identification and genotyping of Omicron sublineages. We analyzed three characteristic mutations of the spike gene, Δ69–70, G339D and Q493R, by TaqMan assay. The accuracy of the TaqMan assay was examined by comparing its results with the results of whole genome sequencing (WGS) analysis.

Results

A total of 169 SARS-CoV-2 positive samples were analyzed by WGS and TaqMan assay. The 127 samples determined as BA.1/BA.1.1 by WGS were all positive for Δ69–70, G339D and Q493R by TaqMan assay. Forty-two samples determined as BA.2 by WGS were negative for Δ69–70 but positive for G339D and Q493R by TaqMan. The concordance rate between WGS and the TaqMan assay was 100% (169/169).

Conclusion

TaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages.
Automated Enhancement and Curation of Healthcare Data
Authors: Greer Melody , Zayas Cilia , Bhattacharyya Sudeepa
Published: April 2022

Social and behavioral aspects of our lives significantly impact our health, yet minimal social determinants of health (SDOH) data elements are collected in the healthcare system. In this study we developed a repeatable SDOH enrichment and integration process to incorporate dynamically evolving SDOH domain concepts from consumers into clinical data. This process included SDOH mapping, linking compiled consumer data, data quality analysis and preprocessing, storage, and visualization. Our preliminary analysis shows commercial consumer data can be a viable source of SDOH factor at an individual-level for clinical data thus providing a path for clinicians to improve patient treatment and care.
Effectiveness of a nation-wide COVID-19 vaccination program in Mexico
Authors: Bello-Chavolla Omar Yaxmehen , Antonio-Villa Neftali Eduardo , Valdés-Ferrer Sergio Iván , Fermín-Martínez Carlos A. , Fernández-Chirino Luisa , Ramírez-García Daniel , Mancilla-Galindo Javier , Kammar-García Ashuin , Ávila-Funes José Alberto , Zúñiga-Gil Clemente Humberto , García-Grimshaw Miguel , Ceballos-Liceaga Santa Elizabeth , Carbajal-Sandoval Guillermo , Montes-González José Antonio , Zaragoza-Jiménez Christian Arturo , García-Rodríguez Gabriel , Cortés-Alcalá Ricardo , Reyes-Terán Gustavo , López-Gatell Hugo , Gutiérrez-Robledo Luis Miguel
Published: April 2022

BACKGROUND

Vaccination has been effective in ameliorating the impact of COVID-19. However, estimation of vaccine effectiveness (VE) is still unavailable for some widely used vaccines and underrepresented groups. Here, we report on the effectiveness of a nation-wide COVID-19 vaccination program in Mexico.

METHODS

We used a test-negative design within a national COVID-19 surveillance system to assess VE of the BNT162b2, mRNA-12732, Gam-COVID-Vac, Ad5-nCoV, Ad26.COV2.S, ChAdOx1 and CoronaVac vaccines, against SARS-CoV-2 infection, COVID-19 related hospitalization and death for adults ≥18 years in Mexico. VE was estimated using Cox proportional hazard models considering time-varying vaccination status in partial and fully vaccinated individuals compared to unvaccinated adults, adjusted by age, sex, comorbidities and municipality. We also estimated VE for adults ≥60 years, for cases with diabetes and comparing periods with predominance of variants B.1.1.519 and B.1.617.2.

RESULTS

We assessed 793,487 vaccinated compared to 4,792,338 unvaccinated adults between December 24th, 2020, and September 27th, 2021. VE against SARS-CoV-2 infection was highest for fully vaccinated individuals with mRNA-12732 (91.5%, 95%CI 90.3-92.4) and Ad26.COV2.S (82.2%, 95%CI 81.4-82.9), whereas for COVID-19 related hospitalization were BNT162b2 (84.3%, 95%CI 83.6-84.9) and Gam-COVID-Vac (81.4% 95%CI 79.5-83.1) and for mortality BNT162b2 (89.8%, 95%CI 89.2-90.2) and mRNA-12732 (93.5%, 95%CI 86.0-97.0). VE for all evaluated vaccines was reduced for adults ≥60 years, people with diabetes, and in periods of Delta variant predominance.

CONCLUSIONS

All evaluated vaccines were effective against SARS-CoV-2 infection and COVID-19 related hospitalization and death. Mass vaccination campaigns with multiple vaccine products are feasible and effective to maximize vaccination coverage.
The network of SARS-CoV-2—cancer molecular interactions and pathways
Authors: Erola Pau , Martin Richard M. , Gaunt Tom R.
Published: April 2022

Background

Relatively little is known about the long-term impacts of SARS-CoV-2 biology, including whether it increases the risk of cancer. This study aims to identify the molecular interactions between COVID-19 infections and cancer processes.

Materials and Methods

We integrated recent data on SARS-CoV-2 – host protein interactions, risk factors for critical illness, known oncogenes, tumor suppressor genes and cancer drivers in EpiGraphDB, a database of disease biology and epidemiology. We used these data to reconstruct the network of molecular links between SARS-CoV-2 infections and cancer processes in various tissues expressing the angiotensin-converting enzyme 2 (ACE2) receptor. We applied community detection algorithms and Gene Set Enrichment Analysis (GSEA) to identify cancer-relevant pathways that may be perturbed by SARS-CoV-2 infection.

Results

In lung tissue, the results showed that 4 oncogenes are potentially targeted by SARS-CoV-2, and 92 oncogenes interact with other human genes targeted by SARS-CoV-2. We found evidence of potential SARS-CoV-2 interactions with Wnt and hippo signaling pathways, telomere maintenance, DNA replication, protein ubiquitination and mRNA splicing. Some of these pathways were potentially affected in multiple tissues.

Conclusions

The long-term implications of SARS-CoV-2 infection are still unknown, but our results point to the potential impact of infection on pathways relevant to cancer affecting cell proliferation, development and survival, favoring DNA degradation, preventing the repair of damaging events and impeding the translation of RNA into working proteins. This highlights the need for further research to investigate whether such effects are transient or longer lasting. Our results are openly available in the EpiGraphDB platform at https://epigraphdb.org/covid-cancer and the repository https://github.com/MRCIEU/covid-cancer (https://doi.org/10.5281/zenodo.6391588).
The theta paradox: 4-8 Hz EEG oscillations reflect both local sleep and cognitive control
Authors: Snipes Sophia , Krugliakova Elena , Meier Elias , Huber Reto
Published: April 2022

Human brain activity generates electroencephalographic (EEG) oscillations that characterize specific behavioral and vigilance states. The frequency of these oscillations is typically sufficient to distinguish a given state, however theta oscillations (4-8 Hz) have instead been found in near-opposite conditions of drowsiness during sleep deprivation and alert cognitive control. While the latter has been extensively studied and is often referred to as “frontal midline theta”, the former has been investigated far less but is considered to be a marker for local sleep during wake. In this study we investigated to what extent theta oscillations differed during cognitive tasks and sleep deprivation. We measured high-density EEG in 18 young healthy adults performing 6 tasks under 3 levels of sleep deprivation. We found both cognitive load and sleep deprivation increased theta power in medial prefrontal cortical areas, however sleep deprivation caused additional increases in theta in many other, predominantly frontal, areas. The sources of sleep deprivation theta were task-dependent, with a visual-spatial task and short-term memory task showing the most widespread effects. Notably, theta was highest in supplementary motor areas during passive music listening, and highest in the inferior temporal cortex during a spatial game. This suggests that theta caused by sleep deprivation may preferentially occur in cortical areas not involved in ongoing behavior. While our results find differences in topography from frontal midline theta, they raise the possibility that a common mechanism may underly both theta oscillations during cognition and during sleep deprivation.
Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids
Authors: Li Qin , Lin Chao , Li Haitao , Li Xueming , Sun Qianwen
Published: April 2022

The three-stranded chromatin structure R-loop is commonly found in the genomes of different species, and functions as the double-edged sword in gene expression and genome stability. The monoclonal antibody S9.6 specifically recognizes RNA:DNA hybrids, and has been widely used as a powerful tool to detect R-loops genome-widely. However, the structure basis and the molecular recognition mechanism of S9.6 to the nucleic acid substrates is still limited. Here, applying cryo-electron microscopy, we have determined a 4.9 Å structure of S9.6 antigen-binding fragment (Fab) complexed with RNA:DNA hybrids. We found that the native Fab cleaved from S9.6 antibody has much higher affinity to RNA:DNA hybrids than to the double-strand RNAs, and the minimum length of the hybrids should be more than 8 base-pair. The structure of Fab binding to the hybrids suggested one loop of S9.6 heavy chain inserts into the minor groove in the RNA:DNA hybrids, and the other three loops flank to the hybrids. The top of four loop all enrich with aromatic or positive charge residues which are potentially responsible for nucleic acids binding specificity. Our results revealed the recognition mechanism of S9.6 on R-loops, which directs the future engineering of S9.6, and thus could further promote R-loop biology studies.
Low-dose IL-2 reduces IL-21+T cells and induces a long-lived anti-inflammatory gene expression signature inversely modulated in COVID-19 patients
Authors: Zhang Jia-Yuan , Hamey Fiona , Trzupek Dominik , Mickunas Marius , Lee Mercede , Godfrey Leila , Yang Jennie H.M. , Pekalski Marcin L , Kennet Jane , Waldron-Lynch Frank , Evans Mark L. , Tree Timothy I. M. , Wicker Linda S. , Todd John A. , Ferreira Ricardo C.
Published: April 2022

Despite early clinical successes, the mechanisms of action of low-dose interleukin-2 (LD-IL-2) immunotherapy remain only partly understood. Here, we examined the effects of interval administration of low-dose recombinant IL-2 (iLD-IL-2) using high-resolution, single-cell multiomics and flow cytometry. We confirmed that iLD-IL-2 selectively expands thymic-derived FOXP3+HELIOS+Tregs and CD56brNK cells, and showed that treatment reduced the frequency of IL-21-producing CD4+T cells and of two subsets of innate-like CD8+T cells, mucosal-associated invariant T cells and Vγ9Vδ2T cells. The cellular changes induced by LD-IL-2 were associated with an anti-inflammatory gene expression signature, which remains detectable in all T and NK cell subsets analysed one month after treatment. The anti-inflammatory nature of this gene expression signature was supported by the observation that the same genes were also modulated in COVID-19 patients, but in the opposite direction. These findings warrant continued investigations of the potential clinical benefits of iLD-IL-2 in immunotherapy and further understanding of the development of long-term sequelae in convalescent COVID-19 patients.
Diabetes Management Beliefs among Adults Diagnosed with Type 2 Diabetes in Iran: A Theory Informed Approach from a Theory of Planned Behavior Framework
Authors: Ghaffari Mohammad Payam , White Katherine M. , Djafarian Kourosh , Cartledge Susie , Keshavarz Seyed Ali , Daryabeygi-Khotbehsara Reza , Shariful Islam Sheikh Mohammad
Published: April 2022

Objective

The current study was informed by the belief basis of Ajzen’s (1991) Theory of Planned Behavior (TPB) to identify the important behavioral (advantages and disadvantages), normative (important referents) and control (barriers and facilitators) beliefs associated with the key recommended prevention and management behaviors for adults in Iran diagnosed with Type 2 diabetes (T2D).

Methods

A cross-sectional study was conducted. A total of 115 adults diagnosed with T2D completed a questionnaire examining behavioral, normative and control beliefs and intention in relation to the three diabetes management behaviors including low fat food consumption, carbohydrate counting and physical activity. For each behavior, intention was considered as dependent variable; beliefs were independent variables. Analyses involved three multivariate one-way analysis of variance (MANOVAs).

Results

The findings for carbohydrate counting and physical activity suggested behavioral and control beliefs as differentiating high from low intenders to perform the behavior. For carbohydrate counting, behavioral beliefs such as weight control, improving one’s health, feeling good and controlling diabetic complications differed significantly between low and high intenders. For physical activity, feeling good, controlling blood sugar and tiredness were among behavioral beliefs differentiating low and high intenders. Medical advice from professionals and greater knowledge were identified as facilitators of carbohydrate counting. High costs were identified as a key barrier preventing individuals from engaging in physical activity. Spouse was the single significant referent influencing carbohydrate counting.

Conclusions & Implications

Identifying the underlying beliefs of key diabetes management behaviors can assist in the design of tailored educational interventions for individuals with T2D.
Canonical Strigolactones Are Not the Tillering-Inhibitory Hormone but Rhizospheric Signals in Rice
Authors: Ito Shinsaku , Braguy Justine , Wang Jian You , Yoda Akiyoshi , Fiorilli Valentina , Takahashi Ikuo , Jamil Muhammad , Felemban Abrar , Miyazaki Sho , Mazzarella Teresa , Shinozawa Akihisa , Balakrishna Aparna , Berqdar Lamis , Rajan Chakravarty , Ali Shawkat , Haider Imran , Sasaki Yasuyuki , Yajima Shunsuke , Akiyama Kohki , Lanfranco Luisa , Zurbriggen Matias , Nomura Takahito , Asami Tadao , Al-Babili Salim
Published: April 2022

The plant hormones strigolactones (SLs) regulate shoot branching and mediate the communication with symbiotic mycorrhizal fungi, but also with noxious root parasitic weeds, such as Striga spp. SLs derive from carlactone (CL) and are divided structurally into canonical and non-canonical SLs. However, the questions about particular biological functions of the two groups and the identification of the SL that inhibits shoot branching are still unanswered, hampering targeted modification of SL pattern towards improving plant architecture and resistance against Striga. Here, we reported that 4-deoxyorobanchol (4DO) and orobanchol, the two canonical SLs in rice, do not have major role in determining rice shoot architecture. CRISPR/Cas9 mediated Osmax1-900 mutants, lacking these two SLs, do not show the high tillering and dwarf phenotype typical for SL-deficient plants. However, the absence of 4DO and orobanchol in root exudates significantly decreased their capability in inducing Striga seed germination, while caused only a delay in root colonization by mycorrhizal fungi. To confirm the genetic evidence, we used the SL-biosynthesis inhibitor TIS108. Our results showed that TIS108 is a MAX1-specific inhibitor that lowers 4DO and orobanchol synthesis, conferring a resistance to Striga without a severe impact on rice architecture. Hence, our work uncovers the specific function of canonical SLs as rhizospheric signals and paves the way for establishing chemical and genetic based approaches for combating the root parasitic weeds, by targeted depletion of their release.
Single-cell transcriptomics to definePlasmodium falciparumstage-transition in the mosquito midgut
Authors: Mohammed Mubasher , Dziedziech Alexis , Sekar Vaishnovi , Ernest Medard , Alves E Silva Thiago Luiz , Balan Balu , Emami S. Noushin , Biryukova Inna , Friedländer Marc R. , Jex Aaron , Lorena Marcelo Jacobs , Henriksson Johan , Rodriguez Joel Vega , Ankarklev Johan
Published: April 2022

Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory vector mosquito provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzedPlasmodium falciparumdevelopment in the mosquito gut, from unfertilized female gametes through the first 20 hours post blood feeding, including the zygote and ookinete stages. This study revealed the transcriptional trajectories of the ApiAP2 family of transcription factors, and of parasite stress genes in response to the harsh environment of the mosquito midgut. Further, employing structure-based functional predictions we found several upregulated genes predicted to encode intrinsically disordered proteins (IDPs), a category of proteins known for their importance in regulation of transcription, translation and protein-protein interactions. IDPs are known for their antigenic properties and may serve as suitable targets for antibody or peptide-based transmission suppression strategies.
Direct evidence for pinning of single, ice-bound antifreeze proteins by subzero nanoscopy
Authors: Tas Roderick P. , Hendrix Marco M. R. M. , Voets Ilja K.
Published: April 2022

Ice-binding by antifreeze proteins (AFPs) reduces freezing temperatures and arrests ice-crystal ripening, making AFPs essential for survival in ice-laden environments and attractive as biocompatible antifreezes. Whilst their activity was identified over 50 years ago, the physical mechanisms are still debated because experimental insights at the molecular scale remain elusive. Here we introduce optical nanoscopy to resolve the ice/water interfacial dynamics of single AFPs. Using this method, we demonstrate pinning of individual proteins. Surprisingly, this quasi-permanent pinning is lost when freezing point depression activity is inhibited by a single mutation in the ice-binding site. These findings provide direct experimental evidence for the adsorption-inhibition paradigm, pivotal to all theoretical descriptions of activity and offer new insights in the molecular mechanisms by which these biological antifreezes function.
A cryptic plastid and a novel mitochondrial plasmid inLeucomyxa plasmidiferagen. and sp. nov. (Ochrophyta) push the frontiers of organellar biology
Authors: Barcytė Dovilė , Jaške Karin , Pánek Tomáš , Yurchenko Tatiana , Ševčíková Tereza , Eliášová Anežka , Eliáš Marek
Published: April 2022

Complete plastid loss seems to be very rare among secondarily non-photosynthetic eukaryotes.Leukarachnionsp. PRA-24, an amoeboid colourless protist related to the photosynthetic algal class Synchromophyceae (Ochrophyta), is a candidate for such a case based on a previous investigation by transmission electron microscopy. Here we characterise this organism in further detail and describe it asLeucomyxa plasmidifera, gen. et sp. nov., additionally demonstrating it is the first known representative of a broader clade of non- photosynthetic ochrophytes. We recovered its complete plastid genome, exhibiting a reduced gene set similar to plastomes of other non-photosynthetic ochrophytes yet being even more extreme in sequence divergence. Identification of components of the plastid protein import machinery in theLeuc. plasmidiferatranscriptome assembly corroborated the organism possesses a cryptic plastid organelle. According to our bioinformatic reconstruction the plastid contains a unique combination of biosynthetic pathways producing haem, a folate precursor, and tocotrienols. As another twist to its organellar biology,Leuc. plasmidiferaturned out to contain an unusual long insertion in its mitogenome related to a newly discovered mitochondrial plasmid exhibiting unprecedented features in terms of its size and coding capacity. Combined, our work uncovered further striking outcomes of the evolutionary course of semiautonomous organelles in protists.
Parental histone distribution at nascent strands controls homologous recombination during DNA damage tolerance
Authors: González-Garrido Cristina , Prado Félix
Published: April 2022

The advance and stability of replication forks rely on a tight co-regulation of the processes of DNA synthesis and nucleosome assembly. We have addressed the relevance of parental histone recycling in the mechanisms of DNA damage tolerance (DDT) – homologous recombination (HR) and translesion synthesis (TLS) – that assist replication forks under conditions that block their advance. We show that mutants affected in the deposition of parental histones are impaired in the recombinational repair of the single-strand DNA gaps generated during DDT, with the defects being more severe in mutants impaired in the lagging strand-specific deposition pathway. These recombinational defects are not due to a deficit of parental histones at the nascent strands but to an excess of parental nucleosomes at the invaded strand that destabilizes the sister chromatid junction formed after strand invasion. In conclusion, parental histone distribution at stressed forks regulates HR and provides a potential mechanism for the choice between HR and TLS that would depend on whether DNA synthesis is blocked at the lagging or the leading strand.
Comparative genomics of Minnesotan barley-infecting Xanthomonas translucens shows overall genomic similarity but virulence factor diversity
Authors: Heiden Nathaniel , Roman-Reyna Verónica , Curland Rebecca , Dill-Macky Ruth , Jacobs Jonathan M.
Published: April 2022

Xanthomonas translucens pv. translucens (Xtt) is a global barley pathogen and a concern for resistance breeding and regulation. Long-read whole genome sequences allow in-depth understanding of pathogen diversity. We have completed long-read PacBio sequencing of two Minnesotan Xtt strains and an in-depth analysis of available Xtt genomes. We found that average nucleotide identity(ANI)-based approaches organize Xtt strains differently than the previously standard MLSA approach. According to ANI, Xtt forms a separate clade from Xanthomonas translucens pv. undulosa and consists of three main groups which are represented on multiple continents. The global distribution of Xtt groups suggests that regulation of seed is not important for prevention of Xtt spread. Some virulence factors, such as 17 Type III-secreted effectors, are highly conserved and offer potential targets for the elicitation of broad resistance. However, there is a high degree of variation in virulence factors meaning that germplasm should be screened for resistance with a diverse panel of Xtt.
Effects of experiencing CS-US pairings on instructed fear reversal
Authors: Wisniewski David , Braem Senne , González-García Carlos , De Houwer Jan , Brass Marcel
Published: April 2022

Fear learning allows us to identify and anticipate aversive events, and adapt our behavior accordingly. This is often thought to rely on associative learning mechanisms where an initially neutral conditioned stimulus (CS) is repeatedly paired with an aversive unconditioned stimulus (US), eventually leading to the CS also being perceived as aversive and threatening. Importantly, however, humans also show verbal fear learning. Namely, they have the ability to change their responses to stimuli rapidly through verbal instructions about CS-US pairings. Past research on the link between experience-based and verbal fear learning indicated that verbal instructions about a reversal of CS-US pairings can fully override the effects of previously experienced CS-US pairings, as measured through fear ratings, skin conductance, and fear-potentiated startle. However, it remains an open question whether such instructions can also annul memory traces in the brain. Here, we used a fear reversal paradigm in conjunction with representational similarity analysis of fMRI data to test whether verbal instructions fully override the effects of experienced CS-US pairings in fear-related brain regions or not. Previous research suggests that only the right amygdala should show lingering representations of previously experienced threat (a so-called “Pavlovian trace”). Unexpectedly, we found evidence for the residual effect of prior CS-US experience to be much more widespread than anticipated, in the amygdala but also cortical regions like the dorsal anterior cingulate or dorso-lateral prefrontal cortex. This finding shines a new light on the interaction of different fear learning mechanisms, at times with unexpected consequences.
Blood oxygenation-level dependent cerebrovascular reactivity imaging as strategy to monitor CSF-hemoglobin toxicity
Authors: Thomson Bart R. , Richter Henning , Akeret Kevin , Buzzi Raphael M. , Anagnostakou Vania , van Niftrik Christiaan H. B. , Schwendinger Nina , Kulcsar Zsolt , Kronen Peter W. , Regli Luca , Fierstra Jorn , Schaer Dominik J. , Hugelshofer Michael
Published: April 2022

Purpose

Cell-free hemoglobin in the cerebrospinal fluid (CSF-Hb) may be one of the main drivers of secondary brain injury after aneurysmal subarachnoid hemorrhage. Haptoglobin scavenging of CSF-Hb has been shown to mitigate cerebrovascular disruption. Using digital subtraction angiography (DSA) and blood oxygenation-level dependent cerebrovascular reactivity imaging (BOLD-CVR) the aim was to assess the acute toxic effect of CSF-Hb on cerebral blood flow and autoregulation, as well as to test the protective effects of haptoglobin.

Methods

DSA imaging was performed in eight anesthetized and ventilated sheep (mean weight: 80.4 kg) at baseline, 15, 30, 45 and 60 minutes after infusion of hemoglobin (Hb) or co-infusion with haptoglobin (Hb:Haptoglobin) into the left lateral ventricle. Additionally, 10 ventilated sheep (mean weight: 79.8 kg) underwent BOLD-CVR imaging to assess the cerebrovascular reserve capacity.

Results

DSA imaging did not show a difference in mean transit time or cerebral blood flow. Wholebrain BOLD-CVR compared to baseline decreased more in the Hb group after 15 minutes (Hb vs Hb:Haptoglobin: −0.03 ±0.01 vs −0.01 ±0.02) and remained diminished compared to Hb:Haptoglobin group after 30 minutes (Hb vs Hb:Haptoglobin: −0.03 ±0.01 vs 0.0 ±0.01), 45 minutes (Hb vs Hb:Haptoglobin: −0.03 ±0.01 vs 0.01 ±0.02) and 60 minutes (Hb vs Hb:Haptoglobin: −0.03 ±0.02 vs 0.01 ±0.01).

Conclusion

It is demonstrated that CSF-Hb toxicity leads to rapid cerebrovascular reactivity impairment, which is blunted by haptoglobin co-infusion. BOLD-CVR may therefore be further evaluated as a monitoring strategy for CSF-Hb toxicity after aSAH.
How to select the best model from AlphaFold2 structures?
Authors: Takei Yuma , Ishida Takashi
Published: April 2022

Among the methods for protein structure prediction, which is important in biological research, AlphaFold2 has demonstrated astonishing accuracy in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14). The accuracy is close to the level of experimental structure determination. Furthermore, AlphaFold2 predicts three-dimensional structures and estimates the accuracy of the predicted structures. AlphaFold2 outputs two model accuracy estimation scores, pLDDT, and pTM, enabling the user to judge the reliability of the predicted structures. Original research of AlphaFold2 showed that those scores had good correlations to actual prediction accuracy. However, it was unclear whether we could select a structure close to the native structure when multiple structures are predicted for a single protein. In this study, we generated several hundred structures with different combinations of parameters for 500 proteins and verified the performance of the accuracy estimation scores of AlphaFold2. In addition, we compared those scores with existing accuracy estimation methods. As a result, pLDDT and pTM showed better performance than the existing accuracy estimation methods for AlphaFold2 structures. However, the estimation performance of relative accuracy of the scores was still insufficient, and the improvement would be needed for further utilization of AlphaFold2.
Does pre-infection stress increase the risk of long COVID? Longitudinal associations between adversity worries and experiences in the month prior to COVID-19 infection and the development of long COVID and specific long COVID symptoms
Authors: Paul Elise , Fancourt Daisy
Published: April 2022

Background

Long COVID is increasingly recognised as public health burden. Demographic and infection-related characteristics have been identified as risk factors, but less research has focused on psychosocial predictors such as stress immediately preceding the index infection. Research on whether stressors predict the development of specific long COVID symptoms is also lacking.

Methods

Data from 1,966 UK adults who had previously been infected with COVID-19 and who took part in the UCL COVID-19 Social Study were analysed. The number of adversity experiences (e.g., job loss) and the number of worries about adversity experiences within the month prior to COVID-19 infection were used to predict the development of self-reported long COVID and the presence of three specific long COVID symptoms (difficulty with mobility, cognition, and self-care). The interaction between a three-level index of socio-economic position (SEP; with higher values indicating lower SEP) and the exposure variables in relation to long COVID status was also examined. Analyses controlled for a range of COVID-19 infection characteristics, socio-demographics, and health-related factors.

Findings

Odds of self-reported long COVID increased by 1.25 (95% confidence interval [CI]: 1.04 to 1.51) for each additional worry about adversity in the month prior to COVID-19 infection. Although there was no evidence for an interaction between SEP and either exposure variable, individuals in the lowest SEP group were nearly twice as likely to have developed long COVID as those in the highest SEP group (OR: 1.95; 95% CI: 1.19 to 3.19) and worries about adversity experiences remained a predictor of long COVID (OR: 1.43; 95% CI: 1.04 to 1.98). The number of worries about adversity experiences also corresponded with increased odds of certain long COVID symptoms such as difficulty with cognition (e.g., difficulty remembering or concentrating) by 1.46 (95% CI: 1.02 to 2.09) but not with mobility (e.g., walking or climbing steps) or self-care (e.g., washing all over or dressing).

Interpretation

Results suggest a key role of stress in the time preceding the acute COVID-19 infection for the development of long COVID and for difficulty with cognition specifically. These findings point to the importance of mitigating worries and experiences of adversities during pandemics both to reduce their psychological impact but also help reduce the societal burden of longer-term illness.

Funding

The Nuffield Foundation [WEL/FR-000022583], the MARCH Mental Health Network funded by the Cross-Disciplinary Mental Health Network Plus initiative supported by UK Research and Innovation [ES/S002588/1], and the Wellcome Trust [221400/Z/20/Z and 205407/Z/16/Z].
Earnings quality determinants in pre-corona crisis: another insight from bank core capital categories
Authors: Valdiansyah Riyan Harbi , Murwaningsari Etty
Published: April 2022

Purpose

Discretionary accruals are earnings quality proxies that illustrate that the greater the value of discretionary accruals, the greater the practice of earnings management and vice versa. High-quality financial reports (especially earnings quality) are expected to help investors and potential investors to make decisions. This study analyses the factors that affect earnings quality, such as pre-managed earnings, liquidity and efficiency. Furthermore, the authors identify the moderating effect of the governance mechanisms proxied by the proportion of independent commissioners in conventional commercial banks listed on the Indonesia Stock Exchange.

Design/methodology/approach

This study uses 226 banking data in the pre-corona crisis period 2013 until 2019. The data were analyzed using EViews 10 for hypothesis and MS Excel for a differential test.

Findings

The results show that pre-managed earnings, liquidity and efficiency affect earnings quality. The governance mechanisms can moderate liquidity and efficiency on earnings quality, while pre-managed earnings cannot be moderated. The different bank categories (BUKU) of earnings management mechanisms are shown for each BUKU (BUKU 1, 3 and 4 perform earnings management by increasing earnings, BUKU 2 lowering earnings). Another thing is information on the earnings quality between BUKU 2 with BUKU 3 and BUKU 4 because of differences in capital and bank operating coverage regulations.

Research limitations/implications

Further research expects to analyze the factors affecting banking earnings quality concerning applying IFRS 9 (PSAK 71) in Indonesia. Future researchers expect to apply mixed methods to verify the financial statement data and provide comprehensive discussion and genuine insight from their study. Future research requires more samples from companies or an international scale (cross country) to obtain maximum results and be generally accepted.

Practical implications

This study implies that managers should have more control over pre-managed earnings and bank liquidity as manager's incentive to do earnings smoothing. Managers should also pay attention to cost-efficiency and effective implementation of governance mechanisms to maximize earnings quality. This study also implies that policymakers can encourage commercial banks to apply more prudential principles in terms of a reserve for failed loans to minimize earnings management in banking.

Originality/value

The significance of this study revealed in the discussion of the difference test between bank core capital categories (BUKU) and its relation to earnings quality.
College of Business Administration: change and growth
Authors: Enkuzena Signe , Supe Janis , Roze Jana
Published: April 2022

Learning outcomes

Learning outcomes are as follows: Students will understand the main characteristics of Agile leader and importance of these characteristics in successful change management. Students will understand how Agile leader works to manage changes in organizations and what steps the leader must take to make successful changes in the organization. Students will know in details the Kotter change management model, will recognize and will be able to apply this model in real-life situations.

Case overview/synopsis

The case study is about the College of Business Administration (CBA). The CBA is a private higher education institution located in Riga, Latvia, Eastern Europe. The CBA provides professional higher education programs. The case study tells the story how Susan was at first hired as free-lancer for specific tasks at the College in 2017. After successful competition of these tasks, Susan was hired as the new director in 2018. The management at the College was almost non-existent at that moment, and Susan had to face the question how to develop the CBA and make it profitable. Susan had to build her management team, had to review and describe all processes and had to build the internal culture of the organization. Susan implemented change management plan, and in four years, the number of students and lecturers at the College had doubled, and the turnover of the CBA had reached more than one million euros. The case study shows Agile leader characteristics and change management process in details.

Complexity academic level

Undergraduate studies.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 7: Management Science
Defining critical aspects in interaction: examples from a learning study on welding based on CAVTA
Authors: Kilbrink Nina , Axelsson Jan , Asplund Stig-Börje
Published: April 2022

Purpose

The purpose of this study is to explore how critical aspects can be defined in a learning study on welding without conducting any pre-tests.

Design/methodology/approach

In this study, the authors focus on empirical examples from a learning study on welding conducted in six iterative cycles, with conversation analysis and variation theory approach (CAVTA) as a theoretical basis. The welding lessons have been video-recorded, and in the study, the authors analyze examples where the teachers try to identify critical aspects of a vocational practical object of learning in interaction. CAVTA permeates the complete process, where the analysis has been part of the iterative cycles and further developed when the six cycles were completed.

Findings

The results show how critical aspects can be made visible in the interaction between teacher(s) and student(s) in the enacted learning situation. In the process, the authors work with the three concepts expected critical aspects, displayed critical aspects and targeted critical features in relation to a vocational practical object of learning where conducting a pre-test to define critical aspects is not educationally possible.

Originality/value

Teaching vocational practical objects of learning could be seen as something different from teaching other kinds of objects of learning and the use of the traditional pre-tests in learning studies may be problematic. From that follows, that other ways of finding the critical aspects for the students regarding a vocational practical object of learning might be needed. In this study, such a way is presented.
COVID-19 and mandatory teleworking from home in Japan: taking stock to improve satisfaction and job performance
Authors: Magnier-Watanabe Remy , Benton Caroline , Orsini Philippe , Uchida Toru , Magnier-Watanabe Kaoruko
Published: April 2022

Purpose

This exploratory paper aims to examine attitudes and practices with regard to the COVID-19 pandemic, as well as the effects of mandatory teleworking from home in the wake of the first state of emergency orders in Japan in 2020.

Design/methodology/approach

An online survey of married employees retrospectively assessed changes in work style, subjective well-being, work–family conflict and job performance before and during forced teleworking from home in Tokyo and three of the surrounding prefectures.

Findings

Regular employees reported high levels of anxiety and to have thoroughly implemented government-recommended hygiene and safety practices. A majority of respondents were satisfied with mandatory telework from home and desired to continue partial telework after the end of the pandemic. The strongest predictor of satisfaction with mandatory telework from home turned out to be adequate workspace at home for both men and women. However, the antecedents of the desire to continue working from home differed by gender.

Practical implications

These findings can help individuals, firms and governments better understand the effects of mandatory teleworking from home and devise countermeasures to maximize employee well-being and job performance. This is all the more crucial, as Japan has had successive waves of the virus and has declared numerous states of emergency since the beginning of the pandemic, forcing office workers to continue social distancing and remote working for the time being.

Originality/value

To the best of the authors’ knowledge, this research is one of the first to provide insights on how imposed teleworking from home in the context of COVID-19 in Japan affected regular employees’ personal and professional lives and to identify predictors of satisfaction with teleworking and the desire to continue doing so.
Research on recognition method of wear debris based on YOLO V5S network
Authors: Shi Xinfa , Cui Ce , He Shizhong , Xie Xiaopeng , Sun Yuhang , Qin Chudong
Published: April 2022

Purpose

The purpose of this paper is to identify smaller wear particles and improve the calculation speed, identify more abrasive particles and promote industrial applications.

Design/methodology/approach

This paper studies a new intelligent recognition method for equipment wear debris based on the YOLO V5S model released in June 2020. Nearly 800 ferrography pictures, 23 types of wear debris, about 5,000 wear debris were used to train and test the model. The new lightweight approach of wear debris recognition can be implemented in rapidly and automatically and also provide for the recognition of wear debris in the field of online wear monitoring.

Findings

An intelligent recognition method of wear debris in ferrography image based on the YOLO V5S model was designed. After the training, the GIoU values of the model converged steadily at about 0.02. The overall precision rate and recall rate reached 0.4 and 0.5, respectively. The overall MAP value of each type of wear debris was 40.5, which was close to the official recognition level of YOLO V5S in the MS COCO competition. The practicality of the model was approved. The intelligent recognition method of wear debris based on the YOLO V5S model can effectively reduce the sensitivity of wear debris size. It also has a good recognition effect on wear debris in different sizes and different scales. Compared with YOLOV. YOLOV, Mask R-CNN and other algorithms%2C, the intelligent recognition method based on the YOLO V5S model, have shown their own advantages in terms of the recognition effect of wear debris%2C the operation speed and the size of weight files. It also provides a new function for implementing accurate recognition of wear debris images collected by online and independent ferrography analysis devices.

Originality/value

To the best of the authors’ knowledge, the intelligent identification of wear debris based on the YOLO V5S network is proposed for the first time, and a large number of wear debris images are verified and applied.