bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of the DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN subfamily in green plants
Authors: Han Jiapeng , Xie Xiaoxue , Zhang Yang , Yu Xiaofen , He Guangyuan , Li Yin , Yang Guangxiao
Published: June 2022

Adapting to unfavorable environments is a necessary step in plant terrestrialization and radiation. The dehydration-responsive element-binding (DREB) protein subfamily plays a pivotal role in plant abiotic stress regulation. However, relationships between the origin and expansion of the DREB subfamily and adaptive evolution of land plants are still being elucidated. Here, we constructed the evolutionary history of the DREB subfamily by compiling APETALA2/ethylene-responsive element-binding protein superfamily genes from 169 representative species of green plants. Through extensive phylogenetic analyses and comparative genomic analysis, our results revealed that the DREB subfamily diverged from the ethylene-responsive factor (ERF) subfamily in the common ancestor of Zygnemophyceae and Embryophyta during the colonization of land by plants, followed by expansions to form three different ancient archetypal genes in Zygnemophyceae species, designated as groups archetype-I, archetype-II/III, and archetype-IV. Four large-scale expansions paralleling the evolution of land plants led to the nine-subgroup divergence of group archetype-II/III in angiosperms, and five whole-genome duplications during Brassicaceae and Poaceae radiation shaped the diversity of subgroup IIb-1. We identified a Poaceae-specific gene in subgroup IIb-1, ERF014, remaining in a Poaceae-specific microsynteny block and co-evolving with a small heat shock protein cluster. Expression analyses demonstrated that heat acclimation may have driven the neofunctionalization of ERF014s in Pooideae by engaging in the conserved heat-responsive module in Poaceae. This study provides insights into lineage-specific expansion and neofunctionalization in the DREB subfamily, together with evolutionary information valuable for future functional studies of plant stress biology.
Increased incidence of pediatric narcolepsy following the 2009 H1N1 pandemic: a report from the pediatric working group of the sleep research network
Authors: Simakajornboon Narong , Mignot Emmanuel , Maski Kiran , Owens Judith , Rosen Carol , Ibrahim Sally , Hassan Fauziya , Chervin Ronald D , Perry Gayln , Brooks Lee , Kheirandish-Gozal Leila , Gozal David , Mason Thornton , Robinson Althea , Malow Beth , Naqvi Kamal , Chen Maida L , Jambhekar Supriya , Halbower Ann , Graw-Panzer Katharina , Dayyat Ehab , Lew Jenny , Melendres Cecilia , Kotagal Suresh , Jain Sejal , Super Elizabeth , Dye Thomas , Hossain Md Monir , Tadesse Dawit
Published: June 2022

This study was aimed to evaluate the yearly incidence of pediatric narcolepsy prior to and following the 2009 H1N1 pandemic and to evaluate seasonal patterns of narcolepsy onset and associations with H1N1 influenza infection in the United States. This was a multicenter retrospective study with prospective follow-up. Participants were recruited from members of the Pediatric Working Group of the Sleep Research Network including 22 sites across the United States. The main outcomes were monthly and yearly incident cases of childhood narcolepsy in the United States, and its relationship to historical H1N1 influenza data. A total of 950 participants were included in the analysis; 487 participants were male (51.3%). The mean age at onset of excessive daytime sleepiness (EDS) was 9.6  ±  3.9 years. Significant trend changes in pediatric narcolepsy incidence based on EDS onset (p  <  .0001) occurred over the 1998–2016 period, peaking in 2010, reflecting a 1.6-fold increase in narcolepsy incidence. In addition, there was significant seasonal variation in narcolepsy incident cases, with increased cases in spring (p  <  .05). Cross-correlation analysis demonstrated a significant correlation between monthly H1N1 infection and monthly narcolepsy incident cases (p  =  .397, p  <  .0001) with a lag time of 8 months. We conclude that there is a significant increase in pediatric narcolepsy incidence after the 2009 H1N1 pandemic in the United States. However, the magnitude of increase is lower than reported in European countries and in China. The temporal correlation between monthly H1N1 infection and monthly narcolepsy incidence, suggests that H1N1 infection may be a contributing factor to the increased pediatric narcolepsy incidence after the 2009 H1N1 pandemics.
The role of endogenous Smad7 in regulating macrophage phenotype following myocardial infarction
Authors: Li Jun , Li Ruoshui , Tuleta Izabela , Hernandez Silvia C. , Humeres Claudio , Hanna Anis , Chen Bijun , Frangogiannis Nikolaos G.
Published: June 2022

Smad7 restrains TGF‐β responses, and has been suggested to exert both pro‐ and anti‐inflammatory actions that may involve effects on macrophages. Myocardial infarction triggers a macrophage‐driven inflammatory response that not only plays a central role in cardiac repair, but also contributes to adverse remodeling and fibrosis. We hypothesized that macrophage Smad7 expression may regulate inflammation and fibrosis in the infarcted heart through suppression of TGF‐β responses, or via TGF‐independent actions. In a mouse model of myocardial infarction, infiltration with Smad7+ macrophages peaked 7 days after coronary occlusion. Myeloid cell‐specific Smad7 loss in mice had no effects on homeostatic functions and did not affect baseline macrophage gene expression. RNA‐seq predicted that Smad7 may promote TREM1‐mediated inflammation in infarct macrophages. However, these alterations in the transcriptional profile of macrophages were associated with a modest and transient reduction in infarct myofibroblast infiltration, and did not affect dysfunction, chamber dilation, scar remodeling, collagen deposition, and macrophage recruitment. In vitro, RNA‐seq and PCR arrays showed that TGF‐β has profound effects on macrophage profile, attenuating pro‐inflammatory cytokine/chemokine expression, modulating synthesis of matrix remodeling genes, inducing genes associated with sphingosine‐1 phosphate activation and integrin signaling, and inhibiting cholesterol biosynthesis genes. However, Smad7 loss did not significantly affect TGF‐β‐mediated macrophage responses, modulating synthesis of only a small fraction of TGF‐β‐induced genes, including Itga5, Olfml3, and Fabp7. Our findings suggest a limited role for macrophage Smad7 in regulation of post‐infarction inflammation and repair, and demonstrate that the anti‐inflammatory effects of TGF‐β in macrophages are not restrained by endogenous Smad7 induction.
A non‐polar fraction of Saponaria officinalis L. acted as a TLR4/MD2 complex antagonist and inhibited TLR4/MyD88 signaling in vitro and in vivo
Authors: Yu Ga‐Ram , Lim Dong‐Woo , Karunarathne Wisurumuni Arachchilage Hasitha Maduranga , Kim Gi‐Young , Kim Hyuck , Kim Jai‐Eun , Park Won‐Hwan
Published: June 2022

Targeting Toll‐like receptor 4/myeloid differentiation factor 2 (TLR4/MD2) signaling is regarded as a potential strategy for treating inflammatory diseases. Saponaria officinalis L. is rich in saponin, which include quillaic acid, gypsogenin, saponarin, and hederagenin. We evaluated the pharmacological activity of a Saponaria officinalis extract in THP‐1 derived macrophages and RAW264.7 macrophages. TLR4/MyD88 complex formation and downstream signals were investigated by co‐immunoprecipitation (Co‐IP). In silico docking simulation was conducted to predict binding scores and perform 3D modeling of saponarin‐TLR4/MD2 complex. A hexane fraction of Saponaria officinalis (SH) and fr.1 (a sub‐fraction 1 of SH) inhibited mitogen‐activated protein kinase (MAPK) signaling, nuclear factor kappa b (NF‐κB) activity, cytokine production, and the expressions of marker genes specific for M1 polarization. The inhibitory effects of fr.1 and saponarin on TLR4/MyD88 complex formation were observed by western blotting TLR4 co‐immunoprecipitated proteins. Saponarin and fr.1 markedly attenuated LPS‐induced inflammatory cytokines, thus reducing mortality and morphological abnormality in zebrafish larvae. Finally, docking simulation revealed that saponarin can directly interact with TLR4/MD2 complex to inhibit downstream signalings. Our findings suggest that saponarin reduces downstream inflammatory response by disrupting TLR4/MD2 complex and blocking MyD88‐dependent inflammatory signaling.
Using the Parent Risk Screening Measure (PRISM) to Assess Pain-Related Risk Factors in Parents of Youth Seeking Treatment for Acute Musculoskeletal Pain
Authors: Holley Amy L. , Gaultney Wendy , Wilson Anna C.
Published: June 2022

Objectives:

The Parent Risk Screening Measure (PRISM) rapidly assesses parent distress, psychosocial function, and behaviors associated with child pain-related dysfunction in parents of youth with chronic pain. Recognizing the importance of parent pain-related cognitions and responses to pain during the acute pain period, the current study examined the utility of the PRISM in screening parents of youth with acute pain.

Methods:

Participants were 175 parent-youth dyads taking part in a larger study examining risk and resilience in youth with acute musculoskeletal pain. Parents completed the PRISM and a battery of measures reporting on their child’s pain-related disability and cognitions and behaviors in response to their child’s pain. Youth reported on their pain, pain-related disability, pain-related fear, catastrophizing, and pain self-efficacy.

Results:

PRISM total scores (M=2.55, SD=2.77) were correlated with many parent and child report measures (eg, protectiveness, catastrophizing, and pain-related fear), with higher scores associated with greater symptoms. Using published PRISM cutoffs, 86.9% of parents were classified as low and 13.13% as elevated risk. t tests revealed significant differences between elevated and low-risk groups on several measures. Moreover, youth of parents in the elevated risk group were more likely to meet clinical cutoffs on pain catastrophizing and fear avoidance measures.

Discussion:

Findings suggest the PRISM is useful in screening for parent distress and behaviors associated with elevated pain symptomatology in a pediatric acute musculoskeletal pain sample. The important next steps are to identify the ideal time for administering the PRISM and to examine the associations among PRISM scores and pain outcomes over time.
Lower serum copper concentrations are associated with higher prevalence of nonalcoholic steatohepatitis: a matched case–control study
Authors: Zhang Huai , Zheng Kenneth I. , Zhu Pei-Wu , Chen Sui-Dan , Li Gang , Ma Hong-Lei , Tang Liang-Jie , Huang Ou-Yang , Byrne Christopher D. , Targher Giovanni , Wang Xiao-Dong , Zheng Ming-Hua
Published: June 2022

Background and aim

Copper is an essential trace element involved in oxidative stress reactions and energy metabolism. While nonalcoholic fatty liver disease (NAFLD) is closely related to metabolic dysfunction, the role of copper in the development of simple steatosis (NAFL) and nonalcoholic steatohepatitis (NASH) is still unclear. We aimed to compare serum copper levels between patients with simple steatosis and those with NASH.

Methods and results

We studied 102 patients with biopsy-proven NASH (cases) and 102 NAFL controls, who were matched for age, sex, and residential city. Multivariable conditional logistic analysis was performed to explore associations between serum copper levels and the presence of NASH. Serum copper levels were significantly lower in patients with NASH than in those with matched NAFL controls (15.53 ± 2.41 μmol/l vs. 16.34 ± 3.23 μmol/l; P = 0.029). This intergroup difference in serum copper levels was more pronounced in men than in women. The per unit, per SD, and per doubling of serum copper levels were associated, respectively, with an approximately 20, 40, and 90% decrease in risk of having NASH, even after adjustment for potential confounding factors.

Conclusion

Lower serum copper concentrations are significantly associated with higher prevalence of NASH among biopsied-proven NAFLD patients, particularly in men.
Considerations for routinely testing for high Lp(a)
Authors: Nurmohamed Nick S. , Moriarty Patrick M. , Stroes Erik S.G.
Published: June 2022

Purpose of review

Lipoprotein(a) (Lp[a]) is a likely causal risk factor for atherosclerotic cardiovascular disease (ASCVD) and aortic valve disease, confirmed by Mendelian randomization. With reliable assays, it has been established that Lp(a) is linearly associated with ASCVD. Current low-density lipoprotein cholesterol (LDL-C) lowering therapies do not or minimally lower Lp(a). This review focuses on the clinical importance and therapeutic consequences of Lp(a) measurement.

Recent findings

Development of RNA-based Lp(a) lowering therapeutics has positioned Lp(a) as one of the principal residual risk factors to target in the battle against lipid-driven ASCVD risk. Pelacarsen, which is a liver-specific antisense oligonucleotide, has shown Lp(a) reductions up to 90% and its phase 3 trial is currently underway. Olpasiran is a small interfering RNA targeting LPA messenger RNA which is being investigated in phase 2 and has already shown dose-dependent Lp(a) reductions up to 90%.

Lp(a) should be measured in every patient at least once to identify patients with very high Lp(a) levels. These patients could benefit from Lp(a) lowering therapies when approved. In the meantime, therapy in high Lp(a) patients should focus on further reducing LDL-C and other ASCVD risk factors.
Postpyloric Feeding Access in Infants and Children: A State of the Art Review
Authors: Jazayeri Amir , McConnie Randolph M , Ross Albert M , Montijo-Barrios Ericka , Ballengee Menchini Cortney , Tulin-Silver Sheryl , Duron Vincent , Walsh Catharine M. , Lerner Diana G. , Mencin Ali
Published: June 2022

Achieving postpyloric feeding access is a clinical challenge faced by the pediatric gastroenterologist in everyday practice. Currently, there is limited literature published on the topic. This article provides a practical summary of the literature on the different methods utilized to achieve postpyloric feeding access including bedside, fluoroscopic, endoscopic and surgical options. Indications and complications of these methods are discussed as well as a general approach to infants and children that require intestinal feeding.
Identifying Barriers to Trainees Addressing Corporal Punishment and Effective Discipline Using Simulation and Semistructured Debriefing
Authors: Slingsby Brett , Moore Jessica , Wing Robyn , Garro Aris , Brown Linda
Published: June 2022

Objective

The objective of the current study was to examine (1) physician trainee interventions when confronted with a situation in which corporal punishment (CP) occurs in a simulated medical setting and (2) their knowledge, comfort, and experiences shared during a semistructured debriefing.

Methods

Themes were developed from simulation sessions from 2018 to 2019, where a convenience sample of training physicians was invited to participate. The simulation involved a medical visit where a caregiver becomes increasingly aggravated, eventually striking her child on the back of the head. There were a total of 7 simulations with one trainee participating while others observed. All trainees subsequently participated in a debriefing and educational session.

Results

A total of 37 physician trainees participated. Themes of not having the wording to address CP, not knowing the distinction between CP and physical abuse, previous negative experiences discussing discipline with families, and fear of offending families negatively impacted trainees' ability to intervene during the simulation. Trainees were interested in future education including simulated medical encounters to improve their responses to CP in the future.

Conclusions

Trainees felt uncomfortable with intervening when CP was observed and did not know how to provide appropriate guidance to families on discipline. Moreover, performance during the simulation and discussions during the debriefings revealed knowledge gaps regarding the difference between CP and physical abuse, how to word recommendations about CP to caregivers, and what resources should be provided. These data suggest the need for education on CP and discipline to be integrated into pediatric training.
Prehospital Epinephrine Use in Pediatric Anaphylaxis by Emergency Medical Services
Authors: Lowing Dena , Chung SunHee , Luk Jeffrey , Dingeldein Leslie
Published: June 2022

Objectives

Anaphylaxis requires prompt assessment and management with epinephrine to reduce its morbidity and mortality. This study examined the prehospital management of pediatric anaphylactic reactions in Northeast Ohio.

Methods

This is a retrospective chart review using emergency medical service (EMS) run charts of patients 18 years and younger from February 2015 to April 2019. Patient charts with the diagnosis of “anaphylaxis” or “allergic reaction” were reviewed and confirmed that symptoms met anaphylaxis criteria. Information regarding epinephrine administration before EMS arrival and medications given by EMS providers was collected. Analysis was performed using descriptive statistics.

Results

From 646 allergic/anaphylactic reaction EMS run charts, 150 (23%) met the guideline criteria for anaphylaxis. The median patient age was 12 years. Only 57% (86/150) of these patients received intramuscular epinephrine, and the majority received it before EMS arrival. Epinephrine was administered by EMS to 32% (30/94; 95% confidence interval [CI], 22.7% to 42.3%) of patients who had not already received epinephrine. The odds of receiving prehospital epinephrine were significantly lower for patients 5 years and younger (risk difference [RD], −0.23; 95% CI, −0.43 to −0.04), those with no history of allergic reaction (RD, −0.20; 95% CI, −0.38 to −0.03), those who presented with lethargy (RD, −0.43; 95% CI, −0.79 to −0.06), and those whose trigger was a medication or environmental allergen (RD, −0.47; 95% CI, −0.72 to −0.23 for each).

Conclusions

Emergency medical service providers in this region demonstrated similar use of epinephrine as reported elsewhere. However, 43% (64/150) of pediatric patients meeting anaphylaxis criteria did not receive prehospital epinephrine, and 10% (15/150) received no treatment whatsoever. Efforts to improve EMS provider recognition and prompt epinephrine administration in pediatric cases of anaphylaxis seem necessary.
Standardized Scoring Tool and Weaning Guideline to Reduce Opioids in Critically Ill Neonates
Authors: Vyas Dipen , Quinones Cardona Vilmaris , Carroll Amanda , Markel Catherine , Young Megan , Fleishman Rachel
Published: June 2022

Introduction:

Pain impacts brain development for neonates, causing deleterious neurodevelopmental outcomes. Prescription opioids for analgesia or sedation are common; however, prolonged opioid exposure in neonates is associated with neurodevelopmental impairment. Balancing the impact of inadequate pain control against prolonged opioid exposure in neonates is a clinical paradox. Therefore, we sought to decrease the average days of opioids used for analgesia or sedation in critically ill neonates at a level IV Neonatal Intensive Care Unit by 10% within 1 year.

Methods:

A multidisciplinary quality improvement team used the model for improvement, beginning with a Pareto analysis, and identified a lack of consistent approach to weaning opioids as a primary driver for prolonged exposure. The team utilized 2 main interventions: (1) a standardized withdrawal assessment tool-1 and (2) a risk-stratified opioid weaning guideline.

Results:

We demonstrated a reduction in mean opioid duration from 34.3 to 14.1 days, an increase in nursing withdrawal assessment tool-1 documentation from 20% to 90%, and an increase in the documented rationale for daily opioid dose in provider notes from 20% to 70%. Benzodiazepine use did not change.

Conclusion:

Standardized withdrawal assessments combined with risk-stratified weaning guidelines can decrease opioid use in critically ill neonates.
Striking Size Reduction of Rapidly Growing Pancreatic Neuroendocrine Carcinoma Metastatic Nodal Conglomerate After Only 2 Cycles of 177Lu-DOTATATE
Authors: Somoza Eduardo A. , Duan Heying , Shaheen Shagufta , Fischer George A. , Aparici Carina Mari
Published: June 2022

Peptide receptor radionuclide therapy (PRRT) with 177Lu-DOTATATE has shown great treatment efficacy in patients with well-differentiated metastatic neuroendocrine tumors and a metastatic size reduction of ~20% for metastatic lesions <3 cm in size. We present a 66-year-old man with pancreatic neuroendocrine carcinoma, who had a rapidly growing metastatic nodal conglomerate, which measured close to 10 cm in size. After only 2 cycles of PRRT with 177Lu-DOTATATE, the nodal conglomerate had a striking size reduction greater than 75%. This case highlights the potential efficacy of PRRT with 177Lu-DOTATATE for treatment of aggressive neuroendocrine neoplasms.
Interventions Against Posttransplantation Diabetes: A Scientific Rationale for Treatment Hierarchy Based on Literature Review
Authors: Sharif Adnan
Published: June 2022

Posttransplant diabetes (PTD) is a common medical complication after solid organ transplantation. Because of adverse outcomes associated with its development and detrimental impact on long-term survival, strategies to prevent or manage PTD are critically important but remain underresearched. Treatment hierarchies of antidiabetic therapies in the general population are currently being revolutionized based on cardiovascular outcome trials, providing evidence-based rationale for optimization of medical management. However, opportunities for improving medical management of PTD are challenged by 2 important considerations: (1) translating clinical evidence data from the general population to underresearched solid organ transplant cohorts and (2) targeting treatment based on primary underlying PTD pathophysiology. In this article, the aim is to provide an overview of PTD treatment options from a new angle. Rationalized by a consideration of underlying PTD pathophysiological defects, which are heterogeneous among diverse transplant patient cohorts, a critical appraisal of the published literature and summary of current research in progress will be reviewed. The aim is to update transplant professionals regarding medical management of PTD from a new perspective tailored therapeutic intervention based on individualized characteristics. As the gap in clinical evidence between management of PTD versus type 2 diabetes widens, it is imperative for the transplant community to bridge this gap with targeted clinical trials to ensure we optimize outcomes for solid organ transplant recipients who are at risk or develop PTD. This necessary clinical research should help efforts to improve long-term outcomes for solid transplant patients from both a patient and graft survival perspective.
Is mirtazapine augmentation effective for patients with obsessive-compulsive disorder who failed to respond to sertraline monotherapy? A placebo-controlled, double-blind, clinical trial
Authors: Mowla Arash , Baniasadipour Haniyeh
Published: June 2022

Mirtazapine upsurges serotonergic activity by a mechanism different from reuptake inhibition. Our aim is to assess the efficacy of mirtazapine augmentation for patients with obsessive-compulsive disorder (OCD) who did not respond to sertraline monotherapy. Sixty-one patients suffering from OCD who were resistant to sertraline monotherapy were randomly allocated to receive mirtazapine (mean dosage = 39.56 mg/day) or placebo plus their current anti-OCD treatment (sertraline: average dose = 251.37 mg/day and 255.10 mg/day in the mirtazapine and placebo groups, respectively; P = 0.871). The primary outcome was OCD symptom severity as measured by Yale-Brown Obsessive-Compulsive Scale (YBOCS). Forty-five patients (22 in the mirtazapine group and 23 in the placebo group) completed the trial. Average YBOCS score decreased in the mirtazapine group from 27.14 ± 8.05 at baseline to 11.13 ± 4.27 at week 12. In the placebo group, average YBOCS score declined from 28.15 ± 3.27 at baseline to 18.94 ± 3.88 at week 12. Nine patients (40.90%) in the mirtazapine group and only one patient (4.34%) in the placebo group revealed at least a 35% decrease in YBOCS (P < 0.000). We found that mirtazapine adds to the effect of sertraline in improving obsessive and compulsive symptoms in OCD patients.
Genomic architecture and functional unit of mimicry supergene in female limited Batesian mimicPapiliobutterflies
Authors: Komata Shinya , Kajitani Rei , Itoh Takehiko , Fujiwara Haruhiko
Published: June 2022

It has long been suggested that dimorphic female-limited Batesian mimicry of two closely relatedPapiliobutterflies,Papilio memnonandPapilio polytes,is controlled by supergenes. Whole-genome sequencing, genome-wide association studies and functional analyses have recently identified mimicry supergenes, including thedoublesex (dsx)gene. Although supergenes of both the species are composed of highly divergent regions between mimetic and non-mimetic alleles and are located at the same chromosomal locus, they show critical differences in genomic architecture, particularly with or without an inversion:P.polyteshas an inversion, butP.memnondoes not. This review introduces and compares the detailed genomic structure of mimicry supergenes in twoPapiliospecies, including gene composition, repetitive sequence composition, breakpoint/boundary site structure, chromosomal inversion and linkage disequilibrium. Expression patterns and functional analyses of the respective genes within or flanking the supergene suggest thatdsxand other genes are involved in mimetic traits. In addition, structural comparison of the corresponding region for the mimicry supergene among furtherPapiliospecies suggests three scenarios for the evolution of the mimicry supergene between the twoPapiliospecies. The structural features revealed in thePapiliomimicry supergene provide insight into the formation, maintenance and evolution of supergenes.

This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
Inversions and parallel evolution
Authors: Westram Anja M. , Faria Rui , Johannesson Kerstin , Butlin Roger , Barton Nick
Published: June 2022

Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.

This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
A case of atypical vivax malaria with a global review of reports on myriads of morpho-variations in parasitized red blood cells.
Authors: Biswal Debasish , Mirdha Bijay Ranjan
Published: June 2022

Plasmodium vivax ( P.vivax ), one of the major species of human malaria continues to be a major public health problem in many parts of the world. Numerous studies related to vivax malaria have described the quantitative haematological findings (level of haemoglobin, thrombocytopenia, haematocrit values), however, diverse morphological changes of parasite forms within infected red blood cells (iRBCs) have been mentioned only in few studies. Here we report a case of 13-year–old boy presented with fever, significant low platelet counts, hypovolemia and created diagnostic dilemma. Detection of microgametocytes by microscopic examinations, further confirmed by multiplex nested polymerase chain reaction (PCR) assay besides response to anti-malarials helped to make the diagnosis. We present an atypical case of vivax malaria with review of morpho-variations of iRBCs and have summarized the characteristics that aid in creating increased awareness among laboratory health professionals and public health workers.
Fourteen new Polynucleobacter species: P. brandtiae sp. nov., P. kasalickyi sp. nov., P. antarcticus sp. nov., P. arcticus sp. nov., P. tropicus sp. nov., P. bastaniensis sp. nov., P. corsicus sp. nov., P. finlandensis sp. nov., P. ibericus sp. nov., P. hallstattensis sp. nov., P. alcilacus sp. nov., P. nymphae sp. nov., P. paludilacus sp. nov. and P. parvulilacunae sp. nov.
Authors: Hahn Martin W. , Pitt Alexandra , Schmidt Johanna , Camacho Antonio
Published: June 2022

Fourteen strains, all isolated from the surface of freshwater habitats, were genomically, phylogenetically and phenotypically characterized. The strains were obtained from geographically and climatically broadly scattered sites. This included two lakes in Antarctica, one arctic pond located on the Svalbard archipelago (Norway), a tropical habitat located in Uganda, some lakes in Southern Europe (Spain and France), lakes, ponds and a puddle in Central Europe (Austria, Czech Republic and Germany), and lakes in Northern Europe (Finland). Most of the investigated strains were characterized by rather small cell sizes and rather slow growth on media such as nutrient broth–soyotone–yeast extract (NSY) medium. Phylogenomic analyses indicated that all fourteen strains are affiliated with the genus

Polynucleobacter

(

Burkholderiaceae

,

Pseudomonadota

). Thirteen of the strains were found to be affiliated with subcluster PnecC of the genus. All these strains were characterized by genome sizes in the range of 1.7–2.3 Mbp and G+C values of 44.9–46.5 mol%. Furthermore, all PnecC-affiliated strains shared 16S rRNA gene sequence similarities >99 %. Only one strain characterized by a larger genome size of 2.9 Mbp and a lower G+C value of 41.0 mol% was found to be affiliated with subcluster PnecA. Whole genome sequence comparisons revealed that all 14 strains shared among each other, as well as with the type strains of the previously described 17

Polynucleobacter

species, whole-genome average nucleotide identities values <95 %. This suggested that the 14 investigated strains represent 14 different new species. We propose the establishment of 14 new

Polynucleobacter

species represented by the following type strains: UB-Domo-W1T (=DSM 103491T=CIP 111598T=JCM 32562T), VK13T (=DSM 103488T=JCM 32564T), LimPoW16T (=DSM 24085T=CIP 111098T), UK-Long2-W17T (=DSM 103489T=CIP 111328T=JCM 32563T), UK-Pondora-W15T (=DSM 103423T=JCM 32939T), MWH-Mekk-B1T (=DSM 106779T=JCM 32556T), MWH-Mekk-C3T (=DSM 103415T=JCM 32557T), Ross1-W9T (=DSM 103416T=JCM 32561T), MWH-Hall10T (=DSM 107042T=JCM 32938T), AP-Basta-1000A-D1T (=DSM 107039T=JCM 32933T), AP-Melu-1000-A1T (=DSM 107036T=JCM 32935T), es-MAR-2T (=DSM 103424T=JCM 32554T), AP-Mumm-500A-B3T (=DSM 107037T=JCM 32936T), MWH-UH21BT (=DSM 23884T=LMG 29707T).
Flavobacterium taihuense sp. nov., a bacterium isolated from lake sediment
Authors: Yang Bang-Bang , Ma Bo-wen , Zhou Jia , Ma Wen-wen , Luo Yu , Qu Jian-Hang
Published: June 2022

A novel bacterium, designated NAS39T, was isolated from the interfacial sediment of Taihu Lake in PR China and its taxonomic position was investigated by using a polyphasic approach. Cells of the isolate were Gram-stain-negative, aerobic, non-motile, catalase-positive, yellow and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences supported that strain NAS39T formed a cluster within the genus

Flavobacterium

, and was most closely related to

Flavobacterium laiguense

LB2P30T (98.4 %), followed by

Flavobacterium tiangeerense

0563T (97.4 %). The average nucleotide identity values between strain NAS39T and

F. laiguense

LB2P30T and

F. tiangeerense

0563T were 82.5 and 75.3 %, respectively. The digital DNA–DNA hybridization values between strain NAS39T and

F. laiguense

LB2P30T and

F. tiangeerense

0563T were 40.9 and 18.6 %, respectively. The genomic DNA G+C content was 34.1 mol%. The major respiratory quinone was menaquinone-6. The dominant cellular fatty acids were iso-C15 : 0 and summed feature 3 comprising C16 : 1 ω7c/C16 : 1 ω6c. The polar lipids comprised phosphatidyl ethanolamine, two amino lipids, three amino phospholipids and two unidentified lipids. Based on the phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, strain NAS39T (=MCCC 1K06094T=KACC 22328T) represents a novel species of the genus

Flavobacterium

, for which the name Flavobacterium taihuense sp. nov. is proposed.
Genomic analyses provide new insights into the evolutionary history and reproduction of the Paleogene relictual Kingdonia (Circaeasteraceae, Ranunculales)
Authors: Sun Yanxia , Zhang Xu , Zhang Aidi , Landis Jacob B. , Zhang Huajie , Sun Hang , Xiang Qiu-Yun (Jenny) , Wang Hengchang
Published: June 2022

Asexual lineages are perceived to be short-lived on evolutionary timescales due to accumulation of deleterious mutations. Hence reports for exceptional cases of putative ‘ancient asexual’ species usually raise doubts about whether such species are recently derived or engage in some undocumented sexual reproduction. However, there have been few studies to solve the mystery. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having closely related congeneric sexual species, seeming to have persisted under strict asexuality for long periods of time. In this study, we use population genomic analyses to test for reproduction mode and infer the evolutionary process and mechanisms facilitating the survival of the species. Our results indicate the presence of three differentiating genetic lineages within the species and support that asexual reproduction in K. uniflora indicated by high allelic heterozygosity had occurred prior to the lineage differentiation (∼0.5 mya). We also detected DNA recombination events in some populations, in line with occurrence of unseen and unevenly distributed sexual reproduction among populations. However the observation of high linkage disequilibrium, relatively high ratio of πN/πS (nonsynonymous versus synonymous nucleotide diversity), together with high allelic heterozygosity suggest the sexual reproduction is infrequent. Furthermore, we found that genes containing SNPs with elevated Fst values are significantly enriched in functions associated with seed development, suggesting differentiation in genes regulating seed development is likely to be the key reason of the uneven distribution of sexual reproduction in K. uniflora. Evidence from our study supports predominate asexual reproduction in K. uniflora, but unseen sexual reproduction must have played a key role to ensure the long-term survival of the lineage in general. Uneven distribution of sexual reproduction in the species may be a key factor underlying the observed genetic differentiation between populations. This study provides novel insights into the reproduction and evolution of Kingdonia, a relict lineage evolved in the Paleogene and known for asexual reproduction, and demonstrate the power of data from population genome sequencing in resolving long-standing evolutionary questions.
GWAS identifies candidate regulators of in planta regeneration in Populus trichocarpa
Authors: Nagle Michael F. , Yuan Jialin , Kaur Damanpreet , Ma Cathleen , Peremyslova Ekaterina , Jiang Yuan , de Rivera Alexa Niño , Jawdy Sara , Chen Jin-Gui , Feng Kai , Yates Timothy B. , Tuskan Gerald A. , Muchero Wellington , Fuxin Li , Strauss Steven H.
Published: June 2022

Plant regeneration is an important dimension of plant propagation, and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. While association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait variation in plants, the power of these methods relies on the accuracy and scale of phenotypic data used. To enable a largescale GWAS ofin plantaregeneration in model treePopulus, we implemented a workflow involving semantic segmentation to quantify regenerating plant tissues (callus and shoot) over time. We found the resulting statistics are of highly non-normal distributions, which necessitated transformations or permutations to avoid violating assumptions of linear models used in GWAS. While transformations can lead to a loss of statistical power, we demonstrate that this can be mitigated by the application of the Augmented Rank Truncation method, or avoided altogether using the Multi-Threaded Monte Carlo SNP-set (Sequence) Kernel Association Test to compute empiricalp-values in GWAS. We report over 200 statistically supported candidate genes, with top candidates including regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. We demonstrate that sensitive genetic discovery for complex developmental traits can be enabled by a workflow based on computer vision and adaptation of several statistical approaches necessitated by to the complexity of regeneration trait expression and distribution.
Markonv: a novel convolutional layer with inter-positional correlations modeled
Authors: Li Jing-Yi , Tan Yuhao , Wen Zheng-Yang , Kang Yu-Jian , Ding Yang , Gao Ge
Published: June 2022

Deep neural networks equipped with convolutional neural layers have been widely used in omics data analysis. Though highly efficient in data-oriented feature detection, the classical convolutional layer is designed with inter-positional independent filters, hardly modeling inter-positional correlations in various biological data. Here, we proposed Markonv layer (Markov convolutional neural layer), a novel convolutional neural layer with Markov transition matrices as its filters, to model the intrinsic dependence in inputs as Markov processes. Extensive evaluations based on both synthetic and real-world data showed that Markonv-based networks could not only identify functional motifs with inter-positional correlations in large-scale omics sequence data effectively, but also decode complex electrical signals generated by Oxford Nanopore sequencing efficiently. Designed as a drop-in replacement of the classical convolutional layer, Markonv layers enable an effective and efficient identification for inter-positional correlations from various biological data of different modalities. All source codes of a PyTorch-based implementation are publicly available on GitHub for academic usage.
Single cell transcriptomics reveals functionally specialized vascular endothelium in brain
Authors: Jeong Hyun-Woo , Diéguez-Hurtado Rodrigo , Arf Hendrik , Song Jian , Park Hongryeol , Kruse Kai , Sorokin Lydia , Adams Ralf H.
Published: June 2022

The blood-brain barrier (BBB) limits the entry of leukocytes and potentially harmful substances from the circulation into the central nervous system (CNS). While BBB defects are a hallmark of many neurological disorders, the cellular heterogeneity at the neurovascular interface and the mechanisms governing neuroinflammation are not fully understood. Through single cell RNA sequencing of non-neuronal cell populations of the murine cerebral cortex during development, adulthood, ageing and neuroinflammation, we identify reactive endothelial venules (REVs), a compartment of specialised post-capillary endothelial cells (ECs) that are characterized by consistent expression of cell adhesion molecules, preferential leukocyte transmigration, association with perivascular macrophage populations, and endothelial activation initiating CNS immune responses. Our results provide novel insights into the heterogeneity of the cerebral vasculature and a useful resource for the molecular alterations associated with neuroinflammation and ageing.
Decarbonization strategy of businesses, stock return performance and investment styles: a systematic review
Authors: Ghosh Namrata , Gupta Dipti
Published: June 2022

Purpose

This paper aims to provide a systematic review of the research focusing on the decarbonization strategy of businesses, stock return performance, and investment styles.

Design/methodology/approach

The paper utilizes bibliometric methods and content analysis to present a broad overview of the research on the association between decarbonization strategies in businesses and financial performance in the last few decades. The final dataset contains 272 records published between 2001 and early 2021, available in the Web of Science (WoS) database.

Findings

The authors find a relatively small number of publications before 2010 and the research focus increases only after 2016. There exists limited knowledge on the links between climate change strategies and firm performance till date. The top management journals have also failed to respond to the importance of decarbonization strategies in firms and their relationship with stock returns and investment styles. Furthermore, there is a limited indication of publications from ecology and the environmental sciences, in general, being included or cited by the business and management research studies, thus highlighting weak network linkages between the two fields.

Research limitations/implications

The study contributes to the literature on decarbonization strategies of businesses, and the strategies' relation with firm performance by consolidating the extant research and thus finding the research gaps and research areas that require further investigation.

Practical implications

For the industry professionals, this research provides a comprehensive repository of articles on incorporating decarbonization strategies in industry professionals' decisions on improving firm performance.

Originality/value

This paper examines the history and development of themes, related to firms' emission mitigation strategies, firm performance and investment styles, across the journal articles in the WoS database published from 2001 to early 2021. In addition, the authors highlight research directions and the need for research on sustainable strategies in businesses, stock return, and investment styles.
Inventory management practices at a big-box retailer: a case study
Authors: Esrar Haya , Zolfaghariania Hossein , Yu Hong
Published: June 2022

Purpose

Managing inventory continues to be a growing area of concern for many retailers due to the multitude of issues that arise from either an excess or shortage of inventory. This study aims to understand how a large-scale retail chain can improve its handling of excess seasonal inventory using three common strategies: information sharing, visibility, and collaboration.

Design/methodology/approach

This study has been designed utilizing a case study method focusing on one retail chain at three key levels: strategic (head office), warehouses, and retail stores. The data have been collected by conducting semi-structured interviews with senior-level employees at each of the three levels and employing a thematic analysis to examine the major themes.

Findings

The results show how three common strategies are being practiced by this retailer and how utilizing these strategies aids the retailer in improving its performance in regard to seasonal inventory. Among our research findings, some challenges were discovered in implementing the strategies, most notably: human errors, advanced forecasting deficiencies, and the handling of return merchandise authorizations.

Originality/value

This research takes a case study approach and focuses on one big-box retailer. The authors chose to study three levels (head office, warehouses, and retail stores) to gain a deeper understanding of the functions and processes of each level, and to understand the working relationships between them. Through the collection of primary data in a Canadian context, this study contributes to the literature by investigating supply chain strategies for managing inventory. The Canadian context is especially interesting due to the multi-cultural demographics of the country.
Investigating building information modeling acceptance in the Chinese AECO industry
Authors: Xue Xiaolong , Sun Xiliang , Xue Weirui , Wang Yaxin , Liao Longhui
Published: June 2022

Purpose

Conscious of the benefits building information modeling (BIM) has brought about to the architecture, engineering, construction and operations (AECO) industry, the Chinese government has been driving BIM adoption. Nonetheless, its acceptance and proliferation in China remain stagnant. Most relevant literature focuses on BIM diffusion at the industry and organizational levels, but the impact of non-managerial practitioners executing BIM or the traditional drafting approach in day-to-day work tends to be disregarded. This study aims to extend theoretical models pertaining to technology acceptance to understand non-managerial practitioners’ perceptions toward working with BIM in China.

Design/methodology/approach

A new BIM acceptance model was proposed based on previous technology acceptance theories. After a pilot study, a survey was conducted with 153 non-managerial practitioners in the Chinese AECO industry.

Findings

Among factors impacting non-managerial practitioners’ BIM acceptance in China, performance expectancy and task-technology fit significantly and positively influence behavioral intention to accept BIM, while the impacts from effort expectancy, social influence and facilitating conditions are not essential.

Research limitations/implications

Management strategies, such as improving non-managerial staff’s benefits and sense of BIM usefulness, selecting suitable tools to match with the staff’s tasks and promoting a middle-out approach in parallel with top-down interventions, are proposed for Chinese AECO organizations to enhance BIM acceptance.

Originality/value

Few studies have explored BIM acceptance from the perspective of non-managerial users in the Chinese AECO industry, especially using the theories related to technology acceptance. The BIM acceptance model developed in this study is different from those used in previous global studies in terms of influencing factors.