bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep genetic structure of a ground-herb along contrasting environments of seasonally dry understories in Amazonia and Cerrado as revealed from targeted genomic sequencing
Authors: André Thiago , Sass Chodon , Yockteng Roxana , Wendt Tânia , Palma-Silva Clarisse , Specht Chelsea D
Published: September 2021

Central South America primarily comprises seasonally dry tropical domains, where a sharp rainy season defines phenological and yearly growth patterns. Here we examine if the genetic structure of the understorey ground-herb Chamaecostus subsessilis species complex, from South American seasonally dry forests, is defined by intrinsic contrasting environments of the Cerrado and southern Amazonia. We analysed a dataset of c. 20 kb of sequence data from targeted capture high-throughput sequencing using PCR-generated probes. We used an admixture model and population pairwise FST comparisons to interpret genetic structure. We also used a Bayesian coalescent approach with a relaxed clock to estimate divergence times between populations and haplotypes. Genetic structure reflects separate populations from Amazonia and from the Cerrado, whereas a haplotype-based phylogenetic tree provides further spatiotemporal evidence of this strong phylogeographical structure. Spatial arrangements among genetic lineages of the C. subsessilis species complex reveal that intraspecific evolution in Central South America seasonally dry understories is closely linked to environmental gradients.
Gynoecium and fruit histology, structure and development in corky-warted representatives of Livistoninae (Trachycarpeae: Coryphoideae: Arecaceae)
Authors: Bobrov Alexey V F C H , Romanov Mikhail S , Zdravchev Nikita S , Dransfield John
Published: September 2021

Representatives of three genera of Livistoninae (Johannesteijsmannia, Licuala and Pholidocarpus) develop corky-warted fruits in contrast to fruit with smooth surfaces in most other representatives of the ‘apocarpous clade’ of Arecaceae subfamily Coryphoideae. The present developmental study is focused on revealing the anatomical peculiarities of the fruit structure of corky-warted species of Livistoninae and tracing the development of their pericarp. Our study shows that the fruits of Johannesteijsmannia, Licuala bintulensis and Pholidocarpus macrocarpus are drupes of the Rhapis type and that the warts on their fruit surface originate soon after gynoecium pollination as the result of two or three developmental events: (1) suberinization of the exocarp cells; (2) progressive multiplication and growth of the outer zone of the mesocarp; and (3) cracking of the peripheral zone of the pericarp. The warts of taxa of Livistoninae develop at the mid stages of fruit organogenesis and are referred to as either alive, composed of parenchymatous cells and sclereids (species of Licuala and Pholidocarpus), or dead, consisting of cells with suberized walls and sclereids (Johannesteijsmannia). The nests of sclereids comprising the stone of Johannesteijsmannia spp. remain disunited during pericarp development until late developmental stages when the formation of a continuous sclerenchymatous layer occurs, which differs from other representatives of the ‘apocarpous clade’ of Coryphoideae with a continuous layer of sclereids persisting during fruit development (as in L. bintulensis). It is shown that the development of the stone within the drupes of the Rhapis type can be different even in closely related taxa. The recognition of the fruits of studied taxa of Livistoninae as drupes of the Rhapis type like the fruit of many other taxa of Trachycarpeae and the ‘apocarpous clade’ of Coryphoideae suggest this character as a synapomorphy for this tribe and the whole clade.
Primary hyperoxaluria type 1: urologic and therapeutic management
Authors: Kohli Harjivan , Kurtz Michael P
Published: September 2021

While the surgical approaches available in primary hyperoxaluria (PH) are common to all patients requiring intervention for urolithiasis, the indications for treatment and their corresponding toxicities are unique. Being a rare disease, we are guided by case series. This review summarizes the available literature highlighting the important disease-specific considerations. Shockwave lithotripsy (SWL) is of particular interest. It is generally the first-line treatment for stones in children, but here the stones produced will be relatively resistant to fragmentation. In addition, there are concerning reports in children of sudden unilateral decline in function in the treated kidney as measured by nuclear renography. Percutaneous nephrostolithotomy might intuitively seem favorable given the shortest drain duration and the ability to treat larger stones efficiently but, similar to SWL, rapid chronic kidney disease (CKD) progression has been seen postoperatively. Ureteroscopy is therefore generally the safest option, but considerations regarding stent encrustation, the growth of residual fragments and the large volume of stone often faced may limit this approach. The surgeon must balance the above with consideration of the patient's CKD status when considering a plan of monitoring and treating stones in PH.
Genome-wide simple sequence repeat markers in potato: abundance, distribution, composition, and polymorphism
Authors: Jian Yinqiao , Yan Wenyuan , Xu Jianfei , Duan Shaoguang , Li Guangcun , Jin Liping
Published: September 2021

Simple sequence repeats (SSRs) are important sources of genetic diversity and are widely used as markers in genetics and molecular breeding. In this study, we examined four potato genomes of DM1-3 516 R44 (DM) from Solanum phureja, RH89039-16 (RH) from Solanum tuberosum, M6 from Solanum chacoense and Solanum commersonii to determine SSR abundance and distribution and develop a larger list of polymorphic markers for a potentially wide range of uses for the potato community. A total of 1,734,619 SSRs were identified across the four genomes with an average of 433,655 SSRs per genome and 2.31kb per SSR. The most abundant repeat units for mono-, di-, tri-, and tetra-nucleotide SSRs were (A/T)n, (AT/AT)n, (AAT/ATT)n, and (ATAT/ATAT)n, respectively. The SSRs were most abundant (78.79%) in intergenic regions and least abundant (3.68%) in untranslated regions. On average, 168,069 SSRs with unique flanking sequences were identified in the four genomes. Further, we identified 16,245 polymorphic SSR markers among the four genomes. Experimental validation confirmed 99.69% of tested markers could generate target bands. The high-density potato SSR markers developed in this study will undoubtedly facilitate the application of SSR markers for genetic research and marker-pyramiding in potato breeding.
The time is ripe to investigate human centromeres by long-read sequencing
Authors: Suzuki Yuta , Morishita Shinichi
Published: September 2021

The complete sequencing of human centromeres, which are filled with highly repetitive elements, has long been challenging. In human centromeres, α-satellite monomers of about 171 bp in length are the basic repeating units, but α-satellite monomers constitute the higher-order repeat (HOR) units, and thousands of copies of highly homologous HOR units form large arrays, which have hampered sequence assembly of human centromeres. Because most HOR unit occurrences are covered by long reads of about 10 kb, the recent availability of much longer reads is expected to enable observation of individual HOR occurrences in terms of their single-nucleotide or structural variants. The time has come to examine the complete sequence of human centromeres.
Phenology of Lycorma delicatula (Hemiptera: Fulgoridae) in Virginia, USA
Authors: Dechaine Andrew C , Sutphin Mark , Leskey Tracy C , Salom Scott M , Kuhar Thomas P , Pfeiffer Douglas G
Published: September 2021

The spotted lanternfly, Lycorma delicatula (White), is an invasive planthopper that was first discovered in North America in Berks County, Pennsylvania in 2014. Currently, L. delicatula has spread to eight additional states and threatens agricultural, ornamental, and timber commodities throughout the United States. The timing of insect life events is very important in the development of pest management tools and strategies. In 2019 and 2020, L. delicatula phenology was successfully documented in Winchester, Virginia using weekly 5-min observational surveys at established monitoring plots. Each year, L. delicatula were active in the environment from May to November with initial detections of first, second, third, fourth, and adults occurring in May, May, June, June, and July, respectively. Cumulative average growing degree days were also calculated for the onset of each L. delicatula life stage using local weather data and a lower developmental threshold of 10°C. First-instar L. delicatula were initially observed at 135 and 111.5, adults at 835 and 887, and egg masses at 1673.5 and 1611.5 in 2019 and 2020, respectively. Combined, these data can be used by growers and land managers to facilitate timing of effective pest management strategies.
De novo and pre-existing atrial fibrillation in acute coronary syndromes: impact on prognosis and cardiovascular events in long-term follow-up
Authors: Buchta Piotr , Kalarus Zbigniew , Mizia-Stec Katarzyna , Myrda Krzysztof , Skrzypek Michał , Ga˛sior Mariusz
Published: September 2021

Aims

The aim of the study was to compare in-hospital and long-term prognosis in patients with acute coronary syndromes (ACS) and de novo vs. pre-existing atrial fibrillation (AF). Atrial fibrillation increases the risk of serious adverse events including death in patients with ACS. However, it is unclear whether de novo and pre-existing AF portend a different risk.

Methods and results

We analysed the incidence, clinical characteristics, and in-hospital and long-term outcomes in patients with AF and ACS based on combined data from Polish Registry of Acute Coronary Syndrome (PL-ACS) (n = 581 843) and SILICARD (n = 852 063) databases. Atrial fibrillation at admission was diagnosed in of 6.16% patients [de novo: 1129 (2.46%); pre-existing: 1691 (3.7%)]. Groups were compared (N = 1023 vs. 1023) after matching for relevant clinical factors. De novo and pre-existing AF differed in in-hospital diuretic (52% vs. 58%; P = 0.008) and aldosterone inhibitor (27.5% vs. 32.5%; P = 0.02) use, Thrombolysis In Myocardial Infarction (TIMI) flow before percutaneous coronary intervention (P = 0.016), and diuretic (52.1% vs. 58%; P = 0.008) and oral anticoagulant (27.5% vs. 32.5%; P = 0.018) use at discharge. In-hospital mortality in the de novo AF group was significantly higher (13.1% vs. 8.31%; P = 0.0005). Post-discharge 12-month survival was similar between groups (14.5% vs. 15.3%, P = 0.63). Long-term re-hospitalization due to heart failure (22.7% vs. 17.2%; P < 0.005) and medical contact due to AF (48.4% vs. 26.1%, P < 0.0001) rates were higher in the group with pre-existing AF, without the difference of stroke or myocardial infarction occurrence.

Conclusion

De novo AF accounts for 40% of all AF cases in ACS patients and is an unfavourable in-hospital prognostic factor. The occurrence of de novo AF during ACS should require special attention and caution in the treatment of these patients.
Characteristics and outcomes of patients with postoperative Candida versus bacterial mediastinitis: a case-matched comparative study
Authors: Moyon Quentin , Lebreton Guillaume , Huang Florent , Demondion Pierre , Desnos Cyrielle , Chommeloux Juliette , Hékimian Guillaume , Bréchot Nicolas , Nieszkowska Ania , Schmidt Matthieu , Leprince Pascal , Combes Alain , Luyt Charles-Edouard , Pineton de Chambrun Marc
Published: September 2021

OBJECTIVES

Postoperative mediastinitis, a feared complication after cardiac surgery, is associated with high mortality, especially of critically ill patients. Candida species infections are rare and severe, with poorly known outcomes. We conducted a case–control study to describe the characteristics, management and outcomes of patients with postoperative Candida mediastinitis.

METHODS

This French, monocentre, retrospective study included all patients with postoperative Candida mediastinitis (January 2003–February 2020) requiring intensive care unit admission. Candida mediastinitis patients (henceforth cases) were matched 1:1 with postoperative bacterial mediastinitis (henceforth control), based on 3 factors during mediastinitis management: age >40 years, cardiac transplantation and invasive circulatory device used. The primary end point was the probability of survival within 1 year after intensive care unit (ICU) admission.

RESULTS

Forty cases were matched to 40 controls. The global male/female ratio was 2.1, with mean age at admission 47.9 ± 13.8 years. Candida species were: 67.5% albicans, 17.5% glabrata, 15% parapsilosis, 5.0% tropicalis, 2.5% krusei and 2.5% lusitaniae. The median duration of mechanical ventilation was 23, 68.8% of patients received renal replacement therapy and 62.5% extracorporeal membrane oxygenation support. The probability of survival within the first year after ICU admission was 40 ± 5.5% and was significantly lower for cases than for controls (43 ± 8% vs 80 ± 6.3%, respectively; Log-rank test: P < 0.0001). The multivariable Cox proportional hazards model retained only renal replacement therapy [hazard ratio (HR) 3.7, 95% confidence interval (CI) 1.1–13.1; P = 0.04] and Candida mediastinitis (HR 2.4, 95% CI 1.1–5.6; P = 0.04) as independently associated with 1-year mortality.

CONCLUSIONS

Candida mediastinitis is a serious event after cardiac surgery and independently associated with 1-year mortality. Further studies are needed to determine whether deaths are directly attributable to Candida mediastinitis.
Predictors of safety and success in minimally invasive surgery for degenerative mitral disease
Authors: Bonaros Nikolaos , Hoefer Daniel , Oezpeker Cenk , Gollmann-Tepeköylü Can , Holfeld Johannes , Dumfarth Julia , Kilo Juliane , Ruttmann-Ulmer Elfriede , Hangler Herbert , Grimm Michael , Mueller Ludwig
Published: September 2021

OBJECTIVES

The aim of this study was to identify predictors of periprocedural success and safety in minimally invasive mitral valve surgery and to determine the impact of pathology localization and repair technique on reoperation-free survival.

METHODS

We isolated 686 patients (mean age 60.5, standard deviation 12.3 years, 69.4% male) who underwent surgery for mitral valve prolapse between 2002 and 2020 in a single institution. Patients with concomitant disease, redo or mitral pathology other than degenerative mitral disease were excluded from the analysis. Periprocedural safety was defined as: freedom from perioperative death, myocardial infarction, stroke, use of extracorporeal membrane oxygenation or reoperation for bleeding. Operative success was defined as: successful primary mitral repair without conversion to replacement or to larger thoracic incisions, without residual mitral regurgitation > mild at discharge or reoperation within 30 days. Predictors for perioperative success and safety were identified using univariable and multivariable analyses. The impact of prolapse localization and repair technique on reoperation-free survival was assessed by Cox regression.

RESULTS

The mitral repair rate and the need for concomitant tricuspid repair were 94.6% and 16.5%, respectively. Perioperative mortality occurred in 5 patients (0.7%). The criteria for perioperative safety and success were met in 646/686 (94.2%) and 648/686 (94.5%) patients, respectively. The absence of tricuspid disease requiring repair was the only independent predictor of safety in this cohort [hazard ratio (HR) 0.460 (0.225–0.941), P = 0.033]. The only independent predictor of operative success was the use of chordal replacement [0.27 (0.09–0.83), P = 0.022]. Reoperation-free survival was 98.5%, 94.5% and 86.9% at 1, 5 and 10 years, respectively. Posterior leaflet pathology demonstrated a higher reoperation-free survival as compared to other localizations (log-rank P = 0.002). The localization of leaflet pathology but not the repair method was an independent predictor for reoperation-free survival (HR 1.455, 95% confidence interval 1.098–1.930; P = 0.009).

CONCLUSIONS

In minimally invasive mitral surgery for degenerative disease, chordal replacement yields higher rates of periprocedural success than leaflet resection. Posterior leaflet pathology is an independent predictor of reoperation-free survival.
Optimal localisation of agricultural biofuel production facilities and feedstock: a Swedish case study
Authors: Nordin Ida , Elofsson Katarina , Jansson Torbjörn
Published: September 2021

Policies for investment in biofuel production facilities and feedstock may be necessary in order to meet climate and renewable energy targets. These policies entail a trade-off between high transportation costs of biomass and economies of scale of production facilities. We develop a spatial optimisation model and investigate the cost-effective localization of production facilities for ethanol from agricultural land in Sweden. Feedstock costs are found to be most important in determining the location, although high feedstock density motivates locating large facilities in areas with high feedstock costs. At higher production, feedstock from the whole country is preferred despite high transport costs.
Combinations of BMI and cardiorespiratory fitness categories: trends between 1995 and 2020 and associations with CVD incidence and mortality and all-cause mortality in 471 216 adults
Authors: Hemmingsson Erik , Väisänen Daniel , Andersson Gunnar , Wallin Peter , Ekblom-Bak Elin
Published: September 2021

Aims

To describe time trends in combinations of cardiorespiratory fitness (CRF) and body mass index (BMI) status, and to analyse their associations with cardiovascular disease (CVD) incidence and mortality and all-cause mortality.

Methods and results

Prospective cohort study with data from occupational health screenings in Swedish employees, including n = 471 216 (aged 18–74 years) between 1995 and 2020, and n = 169 989 in risk analyses. Cardiorespiratory fitness was estimated from a submaximal cycle test. High CRF was defined as top quartile, and low CRF as bottom quartile. Body mass index was used to define normal weight (18.5–24.9 kg/m2), overweight (25.0–29.9 kg/m2), and obesity (≥30 kg/m2). Outcome data (CVD incidence and mortality, all-cause mortality) were obtained from national registers. From 1995 to 2020, the combination of obesity + low CRF increased from 2.1% to 5.3% (relative increase 154%) whereas the combination of normal weight + high CRF decreased from 13.2% to 9.3% (−30%) (both P < 0.001). Negative changes were more pronounced in men, younger ages, and non-university educated. At the end of the period, prevalence of obesity + low CRF were higher in men vs. women (3.1% vs. 2.2%), older vs. younger (3.7% vs. 1.7%), and in non-university vs. university educated (5.0% vs. 0.3%), all P-value <0.001. Having a high CRF attenuated the risk of all three outcomes in all BMI categories, especially in individuals with obesity (hazard ratio 3.90 vs. 6.67 for CVD mortality). Both a low BMI and a high CRF prolonged age of onset for all three outcomes.

Conclusions

The combination of obesity with low CRF has increased markedly since the mid-90s, with clear implications for increased CVD morbidity and mortality, and all-cause mortality.
Trajectories of working hours in later careers and their association with social and health-related factors: a follow-up study
Authors: Suur-Uski Johanna , Pietiläinen Olli , Rahkonen Ossi , Lallukka Tea
Published: September 2021

Background

The aim was to identify working hours’ trajectories in later work careers over a follow-up of 15–17 years and to examine their association with social factors and health.

Methods

A subsample from the Helsinki Health Study was extracted comprising employees of the City of Helsinki, Finland. Growth mixture modelling was used to identify different working hour trajectories. Age, gender, occupational class, marital status, health behaviour, physical and mental functioning and current pain were associated with trajectory membership. Relative risks (RRs) and their 95% confidence intervals (CIs) were estimated.

Results

A two-trajectory model was selected: ‘Stable regular working hours’ (90%) and ‘Shorter and varying working hours’ (10%). Women (RR 1.40, 95% CI 1.09–1.78), the oldest employees (RR 2.71, 95% CI 2.06–3.57), managers and professionals (RR 1.56, 95% CI 1.20–2.02), those reporting non-drinker (RR 1.66, 95% CI 1.32–2.10), those reporting sleeping more than 8 h per night (RR 1.74 95% CI 1.25–2.42) and those reporting poor mental functioning (RR 1.39 95% CI 1.15–1.68) had higher likelihood of belonging to the trajectory ‘Shorter and varying working hours’. There were no differences between the trajectories in marital status, smoking, body mass index, current pain or physical functioning. However, routine non-manual workers (RR 0.74, 95% CI 0.55–0.98), and semi-professionals (RR 0.70, 95% CI 0.50–0.96) had lower likelihood of belonging to this trajectory.

Conclusions

Trajectories of working hours in later work career differ by age, gender and occupational class but also by health behaviours and mental health functioning.
Electronic cigarette use among adolescents in 17 European study sites: findings from the Global Youth Tobacco Survey
Authors: Tarasenko Yelena , Ciobanu Angela , Fayokun Ranti , Lebedeva Elizaveta , Commar Alison , Mauer-Stender Kristina
Published: September 2021

Background

As new findings on public health implications of electronic cigarette (e-cigarette) use emerge, its surveillance remains of utmost importance. This study examined the latest state of e-cigarette use in youth in 17 European study sites (i.e. 16 countries and the Federation of Bosnia and Herzegovina) using the Global Youth Tobacco Survey (GYTS).

Methods

This was an observational study. Cross-sectional data on students aged 11–17 years from the latest available GYTS round completed in 17 study sites were used to estimate crude and adjusted prevalence of e-cigarette use by sex and pocket money. Panel GYTS data from five countries were used for the trend analyses. All analyses were weighted to account for the survey design and non-response.

Results

Compared to 2014, the age-adjusted prevalence of e-cigarette use more than doubled in Georgia and Italy, and nearly doubled in Latvia. Significantly more male than female students aged 11–17 years reported use of e-cigarettes, with little to no confounding by age, grade and pocket money across countries. Youth with medium or higher amount of pocket money was 20–200% more likely to use e-cigarettes than those with fewer to no pocket money in 14 study sites.

Discussion

As e-cigarette use is becoming widespread throughout the world, there is variation in use among and between countries. Expanded and consistent surveillance of e-cigarette use by all World Health Organization member states is essential to generate data on the extent and correlates of youth e-cigarette use for evidence-based planning and evaluation of the electronic nicotine delivery systems and electronic non-nicotine delivery systems national and global control programmes.
Virophages: association with human diseases and their predicted role as virus killers
Authors: Dutta Debrupa , Ravichandiran Velayutham , Sukla Soumi
Published: September 2021

The fascinating discovery of the first giant virus, Acanthamoeba polyphaga mimivirus (APMV), belonging to the family Mimiviridae in 2008, and its associated virophage, Sputnik, have left the world of microbiology awestruck. To date, about 18 virophages have been isolated from different environmental sources. With their unique feature of resisting host cell infection and lysis by giant viruses, analogous to bacteriophage, they have been assigned under the family Lavidaviridae. Genome of T-27, icosahedral-shaped, non-enveloped virophages, consist of dsDNA encoding four proteins, namely, major capsid protein, minor capsid protein, ATPase and cysteine protease, which are essential in the formation and assembly of new virophage particles during replication. A few virophage genomes have been observed to contain additional sequences like PolB, ZnR and S3H. Another interesting characteristic of virophage is that Mimivirus lineage A is immune to infection by the Zamilon virophage through a phenomenon termed MIMIVIRE, resembling the CRISPR-Cas mechanism in bacteria. Based on the fact that giant viruses have been found in clinical samples of hospital-acquired pneumonia and rheumatoid arthritis patients, virophages have opened a novel era in the search for cures of various diseases. This article aims to study the prospective role of virophages in the future of human therapeutics.
Reflectance spectroscopy to characterize the response of Corymbia calophylla to Phytophthora root rot and waterlogging stress
Authors: Croeser Louise , Admiraal Ryan , Barber Paul , Burgess Treena I , Hardy Giles E St J
Published: September 2021

The health of Corymbia calophylla (marri), a keystone tree species in the native forests of southwest Western Australia, has been in decline for the past few decades. Phytophthora root disease and waterlogging have often been cited as contributing to this decline. Traditional methods (i.e., field surveys and sampling) of mapping Phytophthora root infection in the field are time-consuming and expensive; thus, the potential of reflectance spectroscopy to characterize marri response to Phytophthora and waterlogging stress was investigated. Twelve-month old marri plants were infected with either P. cinnamomi or P. multivora in two glasshouse trials and waterlogged for 24 h each fortnight. Spectral measurements with a portable high-resolution spectroradiometer were taken weekly. Plant biophysical measurements were taken at harvest time. Normalized difference spectral index (NDSI) was calculated for every combination of reflectance values between 400 and 2500 nm for all time points, correlated with the treatment effects and displayed as heat maps. Narrowband vegetation indices (VIs), utilizing different wavelengths of the electromagnetic spectrum, were also calculated from the spectral data. The Phytophthora treatments did not cause significant differences with the biophysical measurements in both trials. In the second trial, the waterlogging treatment significantly lowered plant top dry weight (P = 0.016) and diameter (P = 0.044). Reflectance values plotted against wavelength displayed differences between treatments as well as a seasonal trend. The NDSI heat maps indicated that the Phytophthora and waterlogging treatment effects were strongest correlated with bandwidths in the visible and near-infrared portions of the electromagnetic spectrum (538–558 nm and 701–709 nm). Six of the VIs (normalized difference nitrogen index 2, anthocyanin reflectance index 1, photochemical reflectance index, Carter index 1, Vogelman index 3 and water band index) were able to track the biochemical changes in the leaves over the 10 weeks, confirming the seasonal trend. The interaction effect between P. cinnamomi, waterlogging and elapsed time in the first trial was significant for water band index (P = 0.010). This study demonstrates that reflectance spectroscopy holds promise for characterizing marri response but more work needs to be done to identify the optimum wavelengths for identifying Phytophthora and waterlogging stress with marri.
Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage
Authors: Benites Luis Felipe , Bucchini François , Sanchez-Brosseau Sophie , Grimsley Nigel , Vandepoele Klaas , Piganeau Gwenaël
Published: September 2021

Although sex is now accepted as a ubiquitous and ancestral feature of eukaryotes, direct observation of sex is still lacking in most unicellular eukaryotic lineages. Evidence of sex is frequently indirect and inferred from the identification of genes involved in meiosis from whole genome data and/or the detection of recombination signatures from genetic diversity in natural populations. In haploid unicellular eukaryotes, sex-related chromosomes are named mating-type (MTs) chromosomes and generally carry large genomic regions where recombination is suppressed. These regions have been characterized in Fungi and Chlorophyta and determine gamete compatibility and fusion. Two candidate MT+ and MT− alleles, spanning 450–650 kb, have recently been described in Ostreococcus tauri, a marine phytoplanktonic alga from the Mamiellophyceae class, an early diverging branch in the green lineage. Here, we investigate the architecture and evolution of these candidate MT+ and MT− alleles. We analyzed the phylogenetic profile and GC content of MT gene families in eight different genomes whose divergence has been previously estimated at up to 640 Myr, and found evidence that the divergence of the two MT alleles predates speciation in the Ostreococcus genus. Phylogenetic profiles of MT trans-specific polymorphisms in gametologs disclosed candidate MTs in two additional species, and possibly a third. These Mamiellales MT candidates are likely to be the oldest mating-type loci described to date, which makes them fascinating models to investigate the evolutionary mechanisms of haploid sex determination in eukaryotes.
Anticoagulation in syncardia total artificial heart recipients: anti-factor Xa or activated partial thromboplastin time?
Authors: Monteagudo-Vela María , Bowles Christopher , Raj Binu , Robinson Derek , Simon Andre
Published: September 2021

Although the activated partial thromboplastin time (aPTT) has historically been the method of choice for anticoagulation monitoring in patients undergoing mechanical circulatory support with intravenous unfractionated heparin, it is being progressively superseded by the anti-factor Xa (anti-Xa) method. A retrospective single-arm, single-centre analysis of 20 patients who underwent total artificial heart implantation entailed simultaneous determinations of aPTT and anti-Xa. Agreement between these parameters was assessed using the Bland–Altman method. Despite a positive correlation between aPTT and anti-Xa, normal target ranges were poorly aligned: from 5th to 30th postoperative day, for anti-Xa values of 0.2 and 0.4 U/ml corresponding aPTT values were 52.1 and 65.2 s, 7.9 and 14.8 lower than predicted values, respectively. This was not associated with thromboembolic sequalae. It was not possible to demonstrate a significant relationship between the predictor variables (postoperative day; white blood cell count; C-reactive protein concentration; alanine transaminase and alkaline phosphatase level; bilirubin; haemoglobin; albumin and total protein concentration) and the agreement between aPTT and anti-Xa levels. In summary, when anti-Xa levels were used to guide anticoagulation therapy, corresponding aPTT levels were low with respect to target range. Methodology applied in this study is generalizable to other forms of mechanical circulatory support.
The Human Rights Approach to ‘Persecution’ and Its Child Rights Discontents
Authors: Smyth Ciara
Published: September 2021

The longstanding debate in refugee law about the meaning of persecution has been largely resolved in favour of the human rights approach – the idea that basic human rights serve as an objective yardstick for evaluating whether a particular act might constitute persecution. However, the human rights approach produces several dilemmas, not least the question of which human rights are ‘basic’ human rights, and how to ascertain whether a given human rights violation reaches the threshold for persecution. These dilemmas have spawned various, sometimes competing, theories within refugee law scholarship. Meanwhile, a distinctive strain of child rights scholarship has emerged within refugee law, concerned with how to adapt the status determination procedure and refugee definition to children. Building upon that work, this article systematically examines the implications of the general human rights approach to persecution, and its various dilemmas, for the development of a child rights approach. The central thesis is that the human rights approach to persecution erects hidden barriers to the acceptance that violations of child rights (also) constitute persecution. Part 2 makes some preliminary observations on children’s rights that serve as a backdrop to exploring and critiquing, in part 3, the key features of the human rights approach to persecution and its implications for the rights of the child. Part 4 is a case study, based on the text of the European Union Qualification Directive and the case law of the Court of Justice of the European Union, of how the child rights implications identified in part 3 play out ‘in the real world’. It is found that when the human rights approach, based on lex generalis, is superimposed on the lex specialis that is the rights of the child, the results are disappointing. Nonetheless, the article identifies how the human rights approach to persecution can be adjusted so as to accommodate the rights of the child.
Research-Relevant Clinical Pathology Resources: Emphasis on Mice, Rats, Rabbits, Dogs, Minipigs, and Non-Human Primates
Authors: Bau-Gaudreault Liza , Arndt Tara , Provencher Anne , Brayton Cory F
Published: September 2021

Clinical pathology testing for investigative or biomedical research and for preclinical toxicity and safety assessment in laboratory animals is a distinct specialty requiring an understanding of species specific and other influential variables on results and interpretation. This review of clinical pathology principles and testing recommendations in laboratory animal species aims to provide a useful resource for researchers, veterinary specialists, toxicologists, and clinical or anatomic pathologists.
Does SLOPE outperform bridge regression?
Authors: Wang Shuaiwen , Weng Haolei , Maleki Arian
Published: September 2021

A recently proposed SLOPE estimator [6] has been shown to adaptively achieve the minimax $\ell _2$ estimation rate under high-dimensional sparse linear regression models [25]. Such minimax optimality holds in the regime where the sparsity level $k$, sample size $n$ and dimension $p$ satisfy $k/p\rightarrow 0, k\log p/n\rightarrow 0$. In this paper, we characterize the estimation error of SLOPE under the complementary regime where both $k$ and $n$ scale linearly with $p$, and provide new insights into the performance of SLOPE estimators. We first derive a concentration inequality for the finite sample mean square error (MSE) of SLOPE. The quantity that MSE concentrates around takes a complicated and implicit form. With delicate analysis of the quantity, we prove that among all SLOPE estimators, LASSO is optimal for estimating $k$-sparse parameter vectors that do not have tied nonzero components in the low noise scenario. On the other hand, in the large noise scenario, the family of SLOPE estimators are sub-optimal compared with bridge regression such as the Ridge estimator.
Middle power hedging in the era of security/economic disconnect: Australia, Japan, and the ‘Special Strategic Partnership’
Authors: Wilkins Thomas
Published: September 2021

Deeping superpower rivalry between the United States and China has created acute strategic dilemmas for secondary powers in the Indo-Pacific such as Australia and Japan. This predicament is exacerbated by their divergent security and economic interests which cut across the superpower divide; a condition dubbed a ‘security/economic disconnect’. These two intimately related dynamics preclude clear-cut implementation of conventional balancing/bandwagoning alignment choices and have led to mixed hedging strategies to cope with this situation. To address these issues, the article presents a refinement of the hedging concept in International Relations (IR) that emphasizes its multi-dimensional nature, within a broader interpretation of alignment itself. It applies this to the case of the Australia and Japan with reference to their Strategic Partnership, which is both emblematic of hedging responses to systemic uncertainty, and an institutional mechanism through which to operationalize joint hedging policies. This provides insights into how middle power strategic partnerships are managing strategic risks across the security, economic, and other, domains.
Spanish adaptation and validation of the User Version of the Mobile Application Rating Scale (uMARS)
Authors: Martin-Payo Ruben , Carrasco-Santos Sergio , Cuesta Marcelino , Stoyan Stoyan , Gonzalez-Mendez Xana , Fernandez-Alvarez María del Mar
Published: September 2021

Objective

While the professional version of the Mobile App Rating Scale (MARS) has already been translated, and validated into the Spanish language, its user-centered counterpart has not yet been adapted. Furthermore, no other similar tools exist in the Spanish language. The aim of this paper is to adapt and validate User Version of the MARS (uMARS) into the Spanish language.

Materials and Methods

Cross-cultural adaptation, translation, and metric evaluation. The internal consistency and test-retest reliability of the Spanish version of the uMARS were evaluated using the RadarCovid app. Two hundred and sixteen participants rated the app using the translated scale. The app was then rated again 2 weeks later by 21 of these participants to measure test-retest reliability.

Results

No major differences were observed between the uMARS original and the Spanish version. Discrimination indices (item-scale correlation) obtained appropriate results for both raters. The Spanish uMARS presented with excellent internal consistency, α = .89 and .67 for objective and subjective quality, respectively, and temporal stability (r > 0.82 for all items and subscales).

Discussion

The Spanish uMARS is a useful tool for health professionals to recommend high-quality mobile apps to their patients based on the user’s perspective and for researchers and app developers to use end-user feedback and evaluation, to help them identify highly appraised and valued components, as well as areas for further development, to continue ensuring the increasing quality and prominence of the area of mHealth.

Conclusion

uMARS Spanish version is an instrument with adequate metric properties to assess the quality of health apps from the user perspective.
Establishment of a Chemiluminescence Immunoassay Combined with Immunomagnetic Beads for Rapid Analysis of Ochratoxin A
Authors: Zhang Bo , Liu Wenting , Liu Zhenjiang , Fu Xiaoling , Du Daolin
Published: September 2021

Background

Ochratoxin A (OTA) is a harmful mycotoxin and secondary metabolite produced by several species of Aspergillus and Penicillium. It is of vital importance to establish a sensitive method to detect OTA in various grains.

Objective

A novel, highly sensitive chemiluminescence immunoassay was developed to determine OTA in wheat, corn, and poultry feed.

Methods

The immunomagnetic beads were used as solid phase carriers and separators in the competitive chemiluminescence method. Anti-OTA monoclonal antibodies coated on the magnetic beads were applied as the capturing antibodies, in which OTA would compete with OTA-alkaline phosphatase in binding with OTA antibodies.

Results

The proposed method exhibited good linearity (R2 ≥ 0.999), adequate OTA recovery rate (83.60–102.50%), and good repeatability. The sensitivity of the proposed method was 2.05 pg/mL. In addition, the method was highly selective and showed no cross-reactions with other mycotoxins (e.g., AFB1, DON, ZEN). The developed method was applied in the analysis of wheat, corn, and two animal feeds successfully. The results obtained by the chemiluminescence method showed a high correlation with those obtained by the HPLC method (correlation coefficient 0.9958).

Conclusion

This strategy shows great potential for other toxic and harmful mycotoxin detection.

Highlights

A novel highly rapid and sensitive chemiluminescence immunoassay was established for quantitation of OTA.
Validation of Modifications to the Soleris®E. coli Method for Detection and Threshold Determination of Escherichia coli in Select Foods: Level 3 Modification to AOAC Performance Tested MethodSM 101101
Authors: Beck Nancy , Le Quynh-Nhi , Mozola Mark , Roman Brooke , Montei Carolyn , Zhang Lei , Biswas Preetha , Donofrio Robert
Published: September 2021

Background

Soleris®E. coli is an automated, growth-based method for detection and semi-quantitative determination of Escherichia coli in foods. The method can be used in dilute-to-specification (threshold) or presence/absence modes.

Objective

The objective of the study was to validate four modifications to the method: (1) a change in the vial detection window plug composition from agar to agarose to improve plug consistency and robustness, (2) a change in pre-enrichment incubation time for presence/absence testing from 6 h to 18–24 h, (3) a change in vial incubation temperature from 44.5 to 43.5°C, and (4) incorporation of a simple direct-from-vial confirmation test as an alternative to traditional procedures.

Methods

Elements of the study included inclusivity/exclusivity testing, matrix testing in comparison to the ISO 7251:2005 reference method, reagent stability/lot-to-lot consistency testing, and an independent laboratory study.

Results

In inclusivity testing, all 55 Escherichia coli strains tested produced positive results. In exclusivity testing, 30 of 31 strains of other bacterial species produced negative results, the sole exception being a strain of Enterobacter cloacae. In internal and independent laboratory matrix testing of mozzarella cheese, condensed milk, pasteurized liquid egg, and frozen green beans, results showed no significant differences in performance of the Soleris and reference methods with two exceptions, one in which the Soleris method produced more positive results, and one in which the reference method produced more positive results.

Conclusion

Performance characteristics of the modified Soleris E. coli method are consistent with those of the original validated method.

Highlights

The Soleris E. coli method offers improvements in ease of use and reagent robustness.
Qualitative LC–Q-TOF Analysis of Umbilical Cord Tissue via Data-Dependent Acquisition as an Indicator of In Utero Exposure to Toxic Adulterating Substances
Authors: Nelson Brandon N , Strathmann Frederick G , Browne Thom , Cervantes Abigail , Logan Barry K
Published: September 2021

Toxic adulterants are drug or chemical agents used to add bulk volume to traditional drugs of abuse such as cocaine and heroin. These cutting agents include levamisole, metamizole, noxiptillin, phenacetin and xylazine as well as common legal drugs such as acetaminophen, caffeine, diphenhydramine, lidocaine, quinine, quetiapine and tramadol. Because they possess pharmacological activity they result in exposure of the user, but also in the case of pregnant women, the developing fetus, to potential drug toxicity. We describe the development, validation and implementation of a rapid (48 second sample-to-sample) test based on a qualitative data-dependent liquid chromatography–quadrupole time of flight mass spectrometry method for the analysis of toxic adulterating substances in umbilical cord tissue (UCT) samples. The method provides a means of studying potential in utero exposure to these agents. Library spectra comparison at three different collision energies was used in conjunction with retention time and accurate mass to identify these substances in UCT. Analytically based reporting limits were established to determine positivity rates of adulterants in UCT utilizing a standard addition approach. The method was applied to authentic cocaine and opioid positive UCT to screen for toxic adulterants. There were a total of 82 potential adulterant positives found in a 30-sample cohort of authentic UCT samples, with an average of 2.7 substances per case. Lidocaine was the predominant finding followed by caffeine, and diphenhydramine all of which could result from non-illicit drug exposure, however, there were positives for levamisole, phenacetin, noxiptillin and xylazine none of which are approved in the United States for human therapeutic use. This initial set of data established a preliminary positivity rate of potentially toxic adulterants in UCT samples positive for cocaine or opioid use.
Streptomyces clavuligerus: The Omics Era
Authors: Liras Paloma , Martín Juan F
Published: September 2021

The Streptomyces clavuligerus genome consists in a linear chromosome of about 6.7 Mb and four plasmids (pSCL1 to pSCL4), the latter one of 1.8 Mb. Deletion of pSCL4, results in viable mutants with high instability in the chromosome arms, which may lead to chromosome circularisation. Transcriptomic and proteomic studies comparing different mutants with the wild-type strain improved our knowledge on the biosynthesis and regulation of clavulanic acid, cephamycin C and holomycin. Additional knowledge has been obtained on the SARP-type CcaR activator and the network of connections with other regulators (Brp, AreB, AdpA, BldG, RelA) controlling ccaR expression. The transcriptional pattern of the cephamycin and clavulanic acid clusters is supported by the binding of CcaR to different promoters and confirmed that ClaR is a CcaR-dependent activator that controls the late steps of clavulanic biosynthesis. Metabolomic studies allowed the detection of new metabolites produced by S. clavuligerus such as naringenin, desferroxamines, several N-acyl tunicamycins, the terpenes carveol and cuminyl alcohol or bafilomycin J. Heterologous expression of S. clavuligerus terpene synthases resulted in the formation of no less than 15 different terpenes, although none of them was detected in S. clavuligerus culture broth. In summary, application of the Omic tools results in a better understanding of the molecular biology of S. clavuligerus, that allows the use of this strain as an industrial actinobacterial platform and helps to improve CA production.
Multi-generational Effects of Different Resistant Wheat Varieties on Fitness of Sitobion avenae (Hemiptera: Aphididae)
Authors: Hu Xiang-Shun , Luo Chen , Li Guang-Kuo , Zhang Zhan-Feng , Wang Chun-Ping , Hu Zu-Qing , Zhao Hui-Yan , Liu Tong-Xian
Published: September 2021

Crop resistance plays a role in preventing aphid damage, benefiting food production industries, but its effects are limited due to aphid adaptation and phenotypic plasticity. Therefore, furthering understanding of aphid–crop interactions will improve our ability to protect crops from aphids. To determine how aphids adapt to resistant varieties of wheat, Triticum aestivum L. over time, we performed a laboratory experiment to assess the multi-generational effects of three wheat varieties, Batis, Ww2730, and Xiaoyan22, with different resistance levels on the fitness of Sitobion avenae (Fab.) (Hemiptera: Aphididae). The results showed that Ww2730 and Xiaoyan22 were more resistant than Batis to S. avenae, regardless of whether the aphids were newly introduced or had been acclimated before being introduced to the three wheat varieties. However, the effect of resistance on aphid life-history traits was time dependent. Aphid weigh gain increased and they development faster of the acclimated generation compared to the newly introduced generation on all three varieties. And the fecundity on the three varieties and net reproduction rates on Batis and Xiaoyan22 significantly decreased. Aphid fitness in terms of individual life-history parameters improved, whereas aphid fitness in terms of reproductive decreased, and a convergence effect, the difference gaps and standard errors of all life-history traits among the three acclimated populations had narrowed and were less than those in the three first-generation populations, was observed during the 3-mo experimental period. We suggested that S. avenae could rapidly respond to wheat resistance through life-history plasticity.