bluuebunny/crossref_metadata_2025 huggingface dataset:
Implant prominence and flexor tendon rupture in distal radial fractures using volar locking plate technology: a retrospective chart review
Authors: Ence Andrew K. , Leggett Andrew R. , Ashy Cody C. , Barfield William R. , Angermeier Eric W. , Kokko Kyle P.
Published: September 2020

Background:

Volar locking plate (VLP) fixation, an accepted treatment for distal radial fractures, has the known complication of flexor tendon rupture, theorized to be caused by implant positioning. Although implant position is a suspected risk factor, incidence of tendon rupture may be less than previously reported. This study investigated implant prominence and its relation to tendon rupture.

Methods:

Surgical records of 197 patients who underwent repair of distal radial fractures using VLP fixation between July 2014 and December 2017 were retrospectively reviewed. Pre- and postoperative radiographs were used to assign AO Foundation/Orthopaedic Trauma Association (AO/OTA) classification and implant prominence using the Soong classification. Chi square and Fisher’s Exact Tests compared Soong groups to fracture classification, hand function, and reoperation. A phone survey was used to determine finger function.

Results:

Eleven patients underwent reoperation, six for tendon irritation with no tendon ruptures. Fracture classification (P=0.601) and Soong grade (P=0.687) showed no difference when compared with reoperation. There was a difference (P=0.039) comparing fracture classification to Soong classification, with higher fracture classification associated with higher Soong classification. No difference (P>0.05) for finger function was found between either group.

Conclusions:

Flexor tendon rupture historically has been linked to VLP fixation in distal radial fractures. This study found tendon rupture was not associated with fracture classification or implant prominence and had a lower incidence than previously reported. Finger function had no relation to fracture classification or implant prominence. This study suggested implant prominence is more likely with increasing fracture complexity with little clinical significance.

Level of Evidence:

Level IV
BEVACIZUMAB FOR POST VITRECTOMY CYSTOID MACULAR EDEMA IN A SILICONE OIL–FILLED EYE
Authors: Lambat Sarang P. , Bajoria Sheetal L. , Nangia Vinay B. , Nangia Prabhat V. , Mishra Swati D. , Shah Neha H.
Published: September 2020

Purpose:

To report the safety and efficacy of intravitreal bevacizumab (IVB) in a case of cystoid macular edema (CME) in a silicone oil–filled eye.

Methods:

A man, aged 51 years, reported with poor visual improvement in the right eye (RE) after pars plana vitrectomy with oil injection performed 2 months back for a pseudophakic, macula-off rhegmatogenous retinal detachment. His best-corrected visual acuity in the RE was counting fingers 2 m. Fundus examination of the RE showed a silicone oil–filled eye with attached retina, and CME was confirmed on spectral-domain optical coherence tomography. He was advised to undergo IVB injection, which was given a few days later.

Results:

One week after IVB, the central macular thickness had decreased to 437 μm. Seven weeks later, the macular edema subsided completely with a final central macular thickness of 219 μm. His vision improved by seven lines to 6/24 and was stable for another 2 months. He underwent removal of silicone oil after 3 months, wherein his visual acuity improved further by one line to 6/18.

Discussion:

This case demonstrates the use IVB for CME in a silicone oil–filled eye. It was found that IVB was safe and effective in CME associated with a silicone oil–filled eye.
Leeia aquatica sp. nov., isolated from freshwater
Authors: Song Jaeho , Joung Yochan , Li Shan-Hui , Hwang Juchan , Cho Jang-Cheon
Published: September 2020

A Gram-stain-negative, rod-shaped, obligately aerobic, motile by a single polar flagellum, chemoheterotrophic bacterium, designated strain IMCC25680T, was isolated from surface water in Chungju Lake, Republic of Korea. 16S rRNA gene sequence analysis revealed that strain IMCC25680T was most closely related to

Leeia oryzae

HW7T with 95.5% sequence similarity and formed a robust clade with

L. oryzae

HW7T. Whole genome sequencing showed that strain IMCC25680T had a genome 3.6 Mbp long with 60.7 mol% DNA G+C content. Average nucleotide identity and digital DNA–DNA hybridization values between strain IMCC25680T and

L. oryzae

HW7T were 72.4% and 18.5%, respectively, indicating that the novel strain represents a novel species of the genus

Leeia

. The major cellular fatty acids of strain IMCC25680T were iso-C16:0 and summed feature 3 (comprising C16:1
ω6c and/or C16:1
ω7c). The respiratory quinone detected in the strain was ubiquinone-8. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified polar lipids. On the basis of the phylogenetic and phenotypic characterization, strain IMCC25680T was considered to represent a novel species within the genus

Leeia

, for which the name Leeia aquatica sp. nov. is proposed. The type strain is IMCC25680T (=KACC 19487T =NBRC 113132T).
A standalone approach to utilize telomere length measurement as a surveillance tool in oral leukoplakia
Authors: Pal Jagannath , Rajput Yogita , Shrivastava Shruti , Gahine Renuka , Mungutwar Varsha , Sahu Malti , barardiya Tripti , Chandrakar Ankur , R Pinaka Pani , Mishra Shovana S. , Banjara Hansa , Choudhary Vivek , Patra Pradeep K. , Shammas Masood A.
Published: September 2020

Oral Squamous Cell Carcinoma (OSCC) is often preceded by white patch, called oral leukoplakia (OL). Assessing relative telomere length (TL) in OL could be a predicting biomarker. Due to high variability and lack of universal reference, there has been a limited translational application of TL. Here, we describe an approach of evaluating TL using paired PBMC as internal reference and demonstrate its translational relevance. Oral brush biopsy and paired venous blood were collected from 50male OL patients and 44male healthy controls. Relative TL was measured by qPCR. TL of each OL sample was normalized to paired PBMC sample (TL ratio). Mean TL ratio in healthy controls with high risk oral habits, was shorter than those who did not have these habits (1.093±0.411 and 1.253±0.296, respectively; p=0.071). In OL patients, the mean TL ratio was not only significantly shorter in the patch but also in distal normal oral tissue (0.971± 0.317, p=0.0002 and0.896±0.284, p=0.00001, respectively), relative to healthy control without high risk oral habit. Based on the TL ratio, we proposed a classification of OL into four subgroups. Dysplastic pathology was frequently associated with a subgroup having normal TL ratio at patch while significantly shorter TL ratio at paired normal distal site. The approach of analyzing TL attrition of oral mucosa, eliminating requirement of external reference DNA, will enable the TL data universally comparable and provide a useful marker to define high risk OL group for follow-up program. Larger studies will further validate the approach and its broader application in other pre-malignant conditions.
Immediate post-operative PDE5i Therapy improves early Erectile Function Outcomes after Robot Assisted Radical Prostatectomy (RARP)
Authors: Nathan A. , Shukla S. , Sinha A. , Sivathasan S. , Rashid A. , Rassam J. , Smart S. , Patel K. , Shah N. , Lamb B.W.
Published: September 2020

Objectives

To assess whether the timing of post-operative Phosphodiesterase Inhibitor (PDE5i) therapy after Robot Assisted Radical Prostatectomy (RARP) is associated with a change in early erectile function outcomes. Additionally, to determine whether there are differences in continence or safety outcomes.

Subjects/patients and methods

Data was prospectively collected from a single surgeon in one tertiary centre and retrospectively evaluated. 158 patients were treated with PDE5i therapy post RARP over a two-year period. PDE5i therapy was started: immediately (day 1-2) post-op in 29%, early (day 3-14) post-op in 37% and late (after day 14) post-op in 34%. EPIC-26 Erectile Function (EF) scores were collected pre-op and post-op with a median follow-up time of 43 days.

Results

The median age was 64 and the median BMI was 27. 9% of the series had Charlson Co-Morbidities. There were no significant differences in pre-operative characteristics between the therapy groups.

Patients that had bilateral nerve sparing had a mean drop in Erectile Function (EF) score by 5.4 compared to 8.8 in the unilateral group. Additionally, 34.9% of bilateral nerve sparing patients returned to baseline compared to 12.1% of unilateral.

Drop in EF scores and percentage return to baseline for unilateral nerve sparing was respectively 9 and 11.1% of immediate therapy, 7 and 14.8% of early therapy and 9.7 and 9.5% of late therapy (p=0.9 and p=0.6). For bilateral nerve sparing this was respectively 3.5 and 42.9% immediate therapy, 5.5 and 35.5% early therapy and 7.3 and 25% late therapy (p=0.017 and p=0.045).

Pad free and social continence was achieved in 54% and 37% of those receiving immediate therapy, 60% and 33% for early therapy and 26% and 54% for late therapy. There were no differences in compliance, complication or readmission outcomes.

Conclusion

In patients with bilateral nerve sparing RARP, immediate post-operative PDE5i therapy may protect EF. Early onset (3-14 days) may also provide a benefit compared to initiating PDE5i therapy later (after 14 days). Expediting therapy for patients undergoing unilateral nerve sparing may also provide a benefit; however, the differences are less pronounced. Immediate or early PDE5i therapy also improved early continence outcomes for patients with bilateral nerve sparing, compared to late therapy. There were no differences in compliance, complication or readmission rates between the groups. Therefore, immediate PDE5i therapy should be considered in patients following nerve sparing RARP in order to maximise functional outcomes, especially in those undergoing bilateral nerve spare.
Improved Sensitivity, Safety, and Rapidity of COVID-19 Tests by Replacing Viral Storage Solution with Lysis Buffer
Authors: Erster Oran , Shkedi Omer , Benedek Gil , Zilber Eyal , Varkovitzky Itay , Shirazi Rachel , Shorka Dorit Oriya , Cohen Yuval , Bar Tzahi , Oikawa Michal Tepperberg , Venkert Dana , Linial Michal , Oiknine-Djian Esther , Mandelboim Michal , Livneh Zvi , Shenhav-Saltzman Gilat , Mendelson Ella , Wolf Dana , Szwarcwort-Cohen Moran , Mor Orna , Lewis Yair , Zeevi Danny
Published: September 2020

Conducting numerous, rapid, and reliable PCR tests for SARS-CoV-2 is essential for our ability to monitor and control the current COVID-19 pandemic.

Here, we tested the sensitivity and efficiency of SARS-CoV-2 detection in clinical samples collected directly into a mix of lysis buffer and RNA preservative, thus inactivating the virus immediately after sampling.

We tested 79 COVID-19 patients and 20 healthy controls. We collected two samples (nasopharyngeal swabs) from each participant: one swab was inserted into a test tube with Viral Transport Medium (VTM), following the standard guideline used as the recommended method for sample collection; the other swab was inserted into a lysis buffer supplemented with nucleic acid stabilization mix (coined NSLB).

We found that RT-qPCR tests of patients were significantly more sensitive with NSLB sampling, reaching detection threshold 2.1±0.6 (Mean±SE) PCR cycles earlier then VTM samples from the same patient. We show that this improvement is most likely since NSLB samples are not diluted in lysis buffer before RNA extraction. Re-extracting RNA from NSLB samples after 72 hours at room temperature did not affect the sensitivity of detection, demonstrating that NSLB allows for long periods of sample preservation without special cooling equipment. We also show that swirling the swab in NSLB and discarding it did not reduce sensitivity compared to retaining the swab in the tube, thus allowing improved automation of COVID-19 tests. Overall, we show that using NSLB instead of VTM can improve the sensitivity, safety, and rapidity of COVID-19 tests at a time most needed.
Telomere length andTERTexpression are associated with age in almond (Prunus dulcis[Mill.] D.A.Webb)
Authors: D’Amico-Willman Katherine M. , Anderson Elizabeth , Gradziel Thomas M. , Fresnedo-Ramírez Jonathan
Published: September 2020

While it is well known that all organisms age, our understanding of how aging occurs varies dramatically among species. The aging process in perennial plants is not well defined, yet can have implications on production and yield of valuable fruit and nut crops. Almond, a relevant nut crop, exhibits an age-related disorder known as non-infectious bud failure (BF) that affects vegetative bud development, indirectly affecting kernel-yield. This species and disorder present an opportunity to address aging in a commercially-relevant and vegetatively-propagated, perennial crop threatened by an aging-related disorder. In this study, we tested the hypothesis that telomere length and/orTERTexpression can serve as biomarkers of aging in almond using both whole-genome sequencing data and leaf samples collected from distinct age cohorts over a two-year period. To measure telomere lengths, we employed bothin silicoand molecular approaches. We also measured expression ofTERT, a subunit of the enzyme telomerase, which is responsible for maintaining telomere lengths. Results from this work show a marginal but significant association between both telomere length measured by monochrome multiplex quantitative PCR andTERTexpression, and age of almond seedlings. These results suggest that as almonds age,TERTexpression decreases and telomeres shorten. This work provides valuable information on potential biomarkers of perennial plant aging, contributing to our limited knowledge of this process. In addition, translation of this information will provide opportunities to address BF in almond breeding and nursery propagation.
Topological Features of Electroencephalography are Reference-Invariant
Authors: Billings Jacob , Tivadar Ruxandra , Murray Micah M. , Franceschiello Benedetta , Petri Giovanni
Published: September 2020

Electroencephalography (EEG) is among the most widely diffused, inexpensive, and applied neuroimaging techniques. Nonetheless, EEG requires measurements against a reference site(s), which is typically chosen by the experimenter, and specific pre-processing steps precede analysis. It is therefore valuable to obtain quantities that are reference-independent and minimally affected by pre-processing choices. Here, we show that the topological structure of embedding spaces, constructed either from multi-channel EEG timeseries or from their temporal structure, are subject-specific and robust to re-referencing and pre-processing pipelines. By contrast, the shape of correlation spaces, that is, discrete spaces where each point represents an electrode and the distance between them that is in turn related to the correlation between the respective timeseries, were neither significantly subject-specific nor robust to changes of reference. Our results suggest that the shape of spaces describing the observed configurations of EEG signals holds information about the individual specificity of the underlying individual’s brain dynamics, and that temporal correlations constrain to a large degree the set of possible dynamics. In turn, these encode the differences between subjects’ space of resting state EEG signals. Finally, our results and proposed methodology provide tools to explore the individual topographical landscapes and how they are explored dynamically. We propose therefore to augment conventional topographic analyses with an additional – topological – level of analysis, and to consider them jointly. More generally, these results provide a roadmap for the incorporation of topological analyses within EEG pipelines.
Tracking Closely Related Enteric Bacteria at High Resolution in Fecal Samples of Premature Infants Using a Novel rRNA Amplicon
Authors: Graf J. , Ledala N. , Caimano M. J. , Jackson E. , Gratalo D. , Fasulo D. , Driscoll M. D. , Coleman S. , Matson A.
Published: September 2020

Identifying and tracking microbial strains as microbiomes evolve is a major challenge in the field of microbiome research. Longitudinal microbiome samples of co-admitted twins from two different neonatal intensive care units (NICUs) were analyzed using a ∼2,500 base amplicon that spans the 16S and 23S rRNA genes, and mapped to a new 16S-23S rRNA database. Amplicon Sequence Variants inferred using DADA2 provided sufficient resolution for differentiation of rRNA variants from closely related, but not previously sequenced Klebsiella, E. coli, and Enterobacter, among the first bacteria colonizing the gut of these infants after admission to the NICU. Distinct ASV groups (fingerprints) were followed between co-admitted twins over time, demonstrating the potential to track the source and spread of both commensals and pathogens.The high-resolution taxonomy obtained from long amplicon sequencing enable tracking of strains temporally and spatially as microbiomes are established in infants in the hospital environment.
Evolution of COVID-19 cases in selected low- and middle-income countries: past the herd immunity peak?
Authors: Lexmond Axel S. , Nouwen Carlijn J.A. , Callan J. Paul
Published: September 2020

We have studied the evolution of COVID-19 in 12 low- and middle-income countries in which reported cases have peaked and declined rapidly in the past 2-3 months. In most of these countries the declines happened while control measures were consistent or even relaxing, and without signs of significant increases in cases that might indicate second waves. For the 12 countries we studied, the hypothesis that these countries have reached herd immunity warrants serious consideration. The Reed-Frost model, perhaps the simplest description for the evolution of cases in an epidemic, with only a few constant parameters, fits the observed case data remarkably well, and yields parameter values that are reasonable. The best-fitting curves suggest that the effective basic reproduction numberin these countries ranged between 1.5 and 2.0, indicating that the curve was “flattened “in some countries but not “suppressed “by pushing the reproduction number below 1. The results suggest that between 51 and 80% of the population in these countries have been infected, and that between 0.05% and 2.50% of cases have been detected – values which are consistent with findings from serological and T-cell immunity studies. The infection rates, combined with data and estimates for deaths from COVID-19, allow us to estimate overall infection fatality rates for three of the countries. The values are lower than expected from reported infection fatality rates by age, based on data from several high-income countries, and the countries ‘ populations by age. COVID-19 may have a lower mortality risk in these three countries (to differing degrees in each country) than in high-income countries, due to differences in immune-response, prior exposure to coronaviruses, disease characteristics or other factors. We find that the herd immunity hypothesis would not have fit the evolution of reported cases in several European countries, even just after the initial peaks – and subsequent resurgences of cases obviously prove that those countries have infection rates well below herd immunity levels. Our hypothesis that the 12 countries we studied have reached herd immunity should now be tested further, through serological and T-cell-immunity studies.
A Multi-center Study of COVID-19 with Multivariate Prognostic Analysis
Authors: Zeng Wen , Feng Xin , Huang Jie , Du Chuan , Qu Dongming , Zhang Xiang , Zhang Jianquan
Published: September 2020

Purpose

Coronavirus disease (COVID-19) pandemic is now a global health concern. However, there is no detailed analysis of the factors related to patients’ improvement.

Patients and methods

We compared the clinical characteristics, laboratory findings, CT images, and treatment of COVID-19 patients from two different cities in China. One hundred and sixty-nine patients were recruited from January 27 to March 17, 2020 at five hospitals in Hubei and Guangxi. They were divided into four groups according to age and into two groups according to presence of comorbidities. Multivariate statistical analyses were performed for the prognosis of the disease.

Results

Fifty-two patients (30.8%) had comorbidities, and the percentage of critical COVID-19was higher in the comorbidities group (11.6%vs.0.9%, p<0.05). Older patients had higher proportion of severe or critical disease. The results showed that lymphocyte count was significantly associated with the number of days from positive COVID-19 nucleic acid test to negative test; number of days from onset of symptoms to confirmation of diagnosis was significantly associated with the time it took for symptoms to improve; and number of days from onset of symptoms to confirmation of diagnosis and disease severity were significantly associated with chest computed tomography improvement.

Conclusions

Age, comorbidities, lymphocyte count, and SpO2 may predict the risk of severity of COVID-19. Early isolation, early diagnosis, and early initiation of management can slow down the progression and spread of COVID-19.

Key Points

Age and comorbidities can predict the risk of severity of COVID-19, Lymphocyte count and SpO2 may predict the risk of severity of COVID-19. Early isolation, Early diagnosis can slow down the progression of COVID-19
Urbanization alters ecological and evolutionary interactions between Darwin’s finches andTribulus cistoideson the Galápagos Islands
Authors: Rivkin L. Ruth , Johnson Reagan A. , Chaves Jaime A. , Johnson Marc T.J.
Published: September 2020

Emerging evidence suggests that urbanization shapes the ecology and evolution of species interactions. Islands are particularly susceptible to urbanization due to the fragility of their ecosystems; however, few studies have examined the effects of urbanization on species interactions on islands. To address this gap, we studied the effects of urbanization on interactions between Darwin’s finches and its key food resource,Tribulus cistoides, in three towns on the Galápagos Islands. We assessed the effects of urbanization on seed and mericarp removal, mericarp morphology, and finch community composition using natural population surveys, experimental manipulations, and finch observations. We found that both seed and fruit removal rates were higher in urban compared to non-urban populations in the natural and experimental populations, and that urbanization modified selection on mericarp size and defense. Urban environments supported smaller and less diverse finch communities than non-urban environments. Together, our results suggest that urbanization can dramatically alter ecological interactions between Darwin’s finches andT. cistoides, leading to modified selection onT. cistoidespopulations. Our study demonstrates that urban development on islands can have profound effects on the ecology and evolution of trophic interactions.
Enhanced retinoid response by a combination of the vitamin A ester retinyl propionate with niacinamide and a flavonoid containingCeratonia siliquaextract in retinoid responsivein vitromodels
Authors: Lam Eric C.S. , Li Rui , Rodrigues MyriamRubecca , Vires Laura , Adams Rachel L. , Sherrill Joseph D. , Oblong John E.
Published: September 2020

OBJECTIVES

Retinoids have been used for decades as efficacious topical agents to treat photoaged skin. The purpose of our present research is to evaluate whether the activity of the Vitamin A ester retinyl propionate (RP) can be enhanced by niacinamide (Nam) and a flavonoid containingCeratonia siliqua(CS) fruit extract in retinoid responsivein vitromodels.

METHODS

RP was tested alone and in combination with Nam andCSin an RARα reporter cell line for promoter activation and compared totrans-retinoic acid (tRA) activation. These treatments were also tested in keratinocytes for gene expression profiling by qPCR using a panel of 40 retinoid responsive genes.

RESULTS

tRA or RP elicited RARα reporter activation in a dose dependent manner. The combination of 0.5 μM or 2 μM RP with 10 mM Nam had a 56% and 95% signal increase compared to RP, respectively. The addition of 1%CSto 0.5 μM or 2 μM RP with 10 mM Nam elicited a further increase of 114% and 156%, respectively, over RP and Nam combinations. All retinoids elicited an increase in expression of 40 retinoid sensitive genes over control levels. Of the 40 genes 27 were enhanced by either 0.5 μM RP or 2 μM RP with 10 mM Nam and 1%CS. Nam orCShad very modest activity in both models.

CONCLUSION

The combination of RP with Nam andCSshowed a higher retinoid response than RP in two separate retinoid responsivein vitromodels. We hypothesize Nam andCSenhances RP activity by modulating metabolism to tRA via increasing NAD+pools and inhibiting reduction of retinal (RAL) back to retinol, respectively. The findings provide evidence that this combination may have enhanced efficacy for treating the appearance of photoaged skin.
Cytokines (IL-17, IL-23 and IL-33) in Systemic lupus erythematosus in Trinidad and Tobago
Authors: Vaillant Angel Justiz , Akpaka Patrick E
Published: September 2020

Systemic lupus erythematosus (SLE) is the most common autoimmune disease. It is characterized by the presence of hundreds of autoantibodies against many organs and tissues, including the presence of a large number of autoantibodies, which are specific to self-antigens mainly of nuclear origin such as Smith antigen, double-stranded DNA (dsDNA), anti-Sjögren’s syndrome-related antigen A and B (SSA/Ro and SSB/La, respectively) and ribonucleoproteins, which are the hallmarks of the disease. Type I and II interferons, interleukin-6 (IL-6), IL-1, tumor necrosis factor-alpha (TNF-α), and immunomodulatory cytokines such as IL-10 and TGF-β are essential players in SLE. Additionally, T-cell-derived cytokines such as IL-17, IL-21, and IL-2 are dysregulated in SLE. In this study among cohorts of 60 individuals attending the hospital clinics in Trinidad and Tobago, blood samples were analyzed and the levels of the essential cytokines were measured using SLE Disease Activity Index (SLEDAI) 2000 score. The results confirmed that serum IL-17 and IL-23 levels were positively correlated with the SLE Disease Activity Index (SLEDAI) 2000 score in these patients. These findings have diagnostic and therapeutic implications. However, more work must be done targeting other cytokines relevant to autoimmunity and SLE in particular. Interleulin-33 is not an SLE marker, as has been noted in other populations.
Transposon- and genome dynamics in the fungal genusNeurospora: insights from nearly gapless genome assemblies
Authors: Nguyen Diem , Peona Valentina , Unneberg Per , Suh Alexander , Jern Patric , Johannesson Hanna
Published: September 2020

Background

A large portion of nuclear DNA is composed of transposable element (TE) sequences, whose transposition is controlled by diverse host defense strategies in order to maintain genomic integrity. One such strategy is the fungal-specific Repeat-Induced Point (RIP) mutation that hyper-mutates repetitive DNA sequences. While RIP is found across Fungi, it has been shown to vary in efficiency. To date, detailed information on the TE landscapes and associated RIP patterns exist only in a few species belonging to highly divergent lineages.

Result

We investigated 18 nearly gapless genome assemblies of tenNeurosporaspecies, which diverged from a common ancestor about 7 MYA, to determine genome-wide TE distribution and their associated RIP patterns. We showed that the TE contents between 8.7-18.9% covary with genome sizes that range between 37.8-43.9 Mb. Degraded copies of Long Terminal Repeat (LTR) retrotransposons were abundant among the identified TEs, and these are distributed across the genome at varying frequencies. In all investigated genomes, TE sequences had signs of numerous C-to-T substitutions, suggesting that RIP occurred in all species. RIP signatures in all genomes correlated with TE-dense regions.

Conclusions

Essentially gapless genome assemblies allowed us to identify TEs inNeurosporagenomes, and reveal that TEs contribute to genome size variation in this group. Our study suggests that TEs and RIP are highly correlated inNeurospora, and hence, the pattern of interaction is conserved over the investigated evolutionary timescale. We show that RIP signatures can be used to facilitate the identification of TE-rich region in the genome.
Control of helical navigation by three-dimensional flagellar beating
Authors: Cortese Dario , Wan Kirsty Y.
Published: September 2020

Helical swimming is a ubiquitous strategy for motile cells to generate self-gradients for environmental sensing. The model biflagellateChlamydomonas reinhardtiirotates at a constant 1 – 2 Hz as it swims, but the mechanism is unclear. Here, we show unequivocally that the rolling motion derives from a persistent, non-planar flagellar beat pattern. This is revealed by high-speed imaging and micromanipulation of live cells. We construct a fully-3D model to relate flagellar beating directly to the free-swimming trajectories. For realistic geometries, the model reproduces both the sense and magnitude of the axial rotation of live cells. We show that helical swimming requires further symmetry-breaking between the two flagella. These functional differences underlie all tactic responses, particularly phototaxis. We propose a control strategy by which cells steer towards or away from light by modulating the sign of biflagellar dominance.
CARMIL3 is important for cell migration and morphogenesis during early development in zebrafish
Authors: Stark Benjamin C. , Gao Yuanyuan , Belk Lakyn , Culver Matthew A. , Hu Bo , Sepich Diane S. , Mekel Marlene , Solnica-Krezel Lilianna , Lin Fang , Cooper John A.
Published: September 2020

Cell migration is important during early animal embryogenesis. Cell migration and cell shape are controlled by actin assembly and dynamics, which depend on capping proteins, including the barbed-end heterodimeric actin capping protein (CP). CP activity can be regulated by capping-protein-interacting (CPI) motif proteins, including CARMIL (capping protein Arp2/3 myosin-I linker) family proteins. Previous studies of CARMIL3, one of the three highly conserved CARMIL genes in vertebrates, have largely been limited to cells in culture. Towards understanding CARMIL function during embryogenesisin vivo, we analyzed zebrafish lines carrying mutations ofcarmil3. Maternal-zygotic mutants show impaired endodermal migration during gastrulation, along with defects in dorsal forerunner cell (DFC) cluster formation, affecting the morphogenesis of Kupffer’s vesicle (KV). Mutant KVs are smaller and display decreased numbers of cilia, leading to defects in left/right (L/R) patterning with variable penetrance and expressivity. The penetrance and expressivity of the KV phenotype incarmil3mutants correlated well with the L/R heart positioning defect at the end of embryogenesis. This firstin vivoanimal study of CARMIL3 reveals its new role for CARMIL3 during morphogenesis of the vertebrate embryo. This role involves migration of endodermal cells and DFCs, along with subsequent morphogenesis of the KV and L/R asymmetry.
Isoform-specific characterization implicates alternative splicing inAPOBEC3Bas a mechanism restricting APOBEC-mediated mutagenesis
Authors: Banday A. Rouf , Onabajo Olusegun O. , Lin Seraph Han-Yin , Obajemu Adeola , Vargas Joselin M. , Delviks-Frankenberry Krista A. , Lamy Philippe , Bayanjargal Ariunaa , Zettelmeyer Clara , Florez-Vargas Oscar , Pathak Vinay K. , Dyrskjøt Lars , Prokunina-Olsson Ludmila
Published: September 2020

APOBEC3A (A3A) and APOBEC3B (A3B) enzymes drive APOBEC-mediated mutagenesis, but the understanding of the regulation of their mutagenic activity remains limited. Here, we showed that mutagenic and non-mutagenic A3A and A3B enzymes are produced by canonical and alternatively splicedA3AandA3Bisoforms, respectively. Notably, increased expression of the canonicalA3Bisoform, which encodes the mutagenic A3B enzyme, predicted shorter progression-free survival of bladder cancer patients. Expression of the mutagenicA3Bisoform was reduced by exon 5 skipping, generating a non-mutagenicA3Bisoform. The exon 5 skipping, which was dependent on the interaction between SF3B1 splicing factor and weak branch point sites in intron 4, could be enhanced by an SF3B1 inhibitor, decreasing the production of the mutagenic A3B enzyme. Thus, our results underscore the role of A3B, especially in bladder cancer, and implicate alternative splicing ofA3Bas a mechanism and therapeutic target to restrict APOBEC-mediated mutagenesis.
Individual variation in Achilles tendon morphology and geometry changes susceptibility to injury
Authors: Yin Nai-Hao , Fromme Paul , McCarthy Ian , Birch Helen
Published: September 2020

The unique structure of the Achilles tendon, combining three smaller sub-tendons, enhances movement efficiency by allowing individual control from connected muscles. This requires compliant interfaces between sub-tendons, but compliance decreases with age and may account for increased injury frequency. Current understanding of sub-tendon sliding and its role in the whole Achilles tendon function is limited. Here we show changing the degree of sliding greatly affects the tendon mechanical behaviour. Ourin vitrotesting discovered distinct sub-tendon mechanical properties in keeping with their mechanical demands.In silicostudy based on measured properties, subject-specific tendon geometry, and modified sliding capacity demonstrated age-related displacement reduction similar to ourin vivoultrasonography measurements. Peak stress magnitude and distribution within the whole Achilles tendon is affected by individual tendon geometries, the sliding capacity between sub-tendons, and different muscle loading conditions. These results suggest clinical possibilities to identify patients at risk and design personalised rehabilitation protocols.
Ets2frame-shift mutant models express in-frame mRNA by exon skipping that complements Ets2 function in the skin
Authors: Kishimoto Yuki , Nishiura Iori , Yuri Shunsuke , Yamamoto Nami , Ikawa Masahito , Isotani Ayako
Published: September 2020

The Ets2 transcription factor has been implicated in various biological processes. AnEts2mutant model, which lacks the DNA-binding domain (ETS domain), was previously reported to exhibit embryonic lethality caused by a trophoblast abnormality. This phenotype could be rescued by tetraploid complementation, resulting in pups with wavy hair.

Here, we generated newEts2mutant models with deletions in exon 8 and with frame-shift mutations using the CRISPR/Cas9 method. Homozygous mutants could not be obtained by natural mating as previously reported. After rescuing with tetraploid complementation, homozygous mutant mice were generated, but these mice did not exhibit wavy hair phenotype. Our newly generated mice exhibited exon 8 skipping, which led to in-frame mutant mRNA expression in the skin and thymus but not in E7.5 embryos. As this in-frame mutation contained the ETS domain, the exon 8-skippedEts2mRNA was likely translated into protein in the skin that complemented the Ets2 function. Thus, theseEts2mutant models, depending on the cell types, exhibited novel phenotypes due to exon skipping and are expected to be useful in several fields of research.

Summary statement

New Ets2 mutant models showed embryonic lethal phenotype by a placental abnormality but did not exhibit a wavy hair phenotype as a previous model.
Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy
Authors: Shabalin Ivan G. , Czub Mateusz P. , Majorek Karolina A. , Brzezinski Dariusz , Grabowski Marek , Cooper David R. , Panasiuk Mateusz , Chruszcz Maksymilian , Minor Wladek
Published: September 2020

Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Here, the first structure of serum albumin in complex with dexamethasone is reported. Dexamethasone binds to drug site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with an analysis of publicly available clinical data from Wuhan and suggests that an adjustment of the dexamethasone regimen should be further investigated as a strategy for patients affected by two major COVID-19 risk factors: low albumin levels and diabetes.
The use of the Montreal Cognitive Assessment (MoCA) to assess cognitive impairment in Prader-Willi syndrome
Authors: Chevalère Johann , Laurier Virginie , Tauber Maite , Camblats Anna-Malika , Thuilleaux Denise , Postal Virginie
Published: September 2020

Purpose

When a comprehensive neuropsychological assessment cannot be carried out, a quick and discriminant tool of good psychometric properties can be useful to practitioners. The purpose of this paper is to examine the use of the Montreal Cognitive Assessment (MoCA) in patients with Prader–Willi syndrome (PWS) and to test its reliability for cognitive assessment in a population with intellectual disabilities.

Design/methodology/approach

Thirty-seven adults with PWS took the MoCA. Reliability of the battery was tested using Cronbach’s alphas. The performance of PWS adults in each subtest was then compared to that of a normative population of healthy adults.

Findings

The MoCA was found to be unreliable in PWS. The subtests analyses indicated that the PWS sample underperformed the normative population of healthy adults on most subtests of the MoCA. A sub-sample aged between 17and 29 years showed normal performance on Naming and Memory, and a sub-sample aged from 30 to 39 years showed similar performance on Language, Memory and Orientation relative to age-matched normative healthy adults.

Research limitations/implications

Results showed that the current version of the MoCA, if taken as a whole test for cognitive assessment, does not present with adequate psychometric properties, which the authors interpret as reflecting the heterogeneity in PWS cognitive profiles. If used in PWS, the MoCA may however be useful in examining cognitive functions separately using subtest-based comparisons to normative data.

Originality/value

This research contributes to a better assessment of cognitive profile in PWS and people with learning disabilities by arguing that the use of psychometric tests should depend more on the specificity of the population under evaluation.
The concept of competitive productivity (CP): a linguistic investigation
Authors: Hoadley Susan
Published: September 2020

Purpose

The paper presents an investigation into the validity and robustness of the concept of competitive productivity (CP) using linguistic analysis and theory to explore the foundational CP concepts and the relationships between them.

Design/methodology/approach

The aim of this paper is to make a theoretical contribution to the conceptualisation of CP in order to inform its understanding, measurement and application.

Findings

The investigation indicates the relevance of three dimensions (instantiation, stratification and system) to understand CP as a complex, multidimensional system. Instantiation both clarifies CP as a multilevel system and highlights the need for an additional dimension(s) to understand the relationship between national, firm and individual CP (NCP, FCP and ICP). In combination, the two dimensions of stratification and system model CP as a series of nested strata (theory/models, concepts, constructs, variables and measures) through which marketing and management theory and knowledge is created and demonstrate how the options at each level can be articulated as system networks.

Research limitations/implications

Managing the complexity of CP by mapping different aspects along different dimensions and, in doing so, better understanding the nature of and relationships between different phenomena within the domain can potentially inform future qualitative and quantitative research in business studies and beyond.

Originality/value

The paper uses a novel, interdisciplinary approach to demonstrate the existence of CP as a complex, multidimensional system, where such dimensions inform the understanding, measurement and application of CP, and so is of value to marketing and management researchers and practitioners.
Challenges on contemporary architectural technology on durability of reinforced concrete structures
Authors: Charalambidi Barbara , Markou Panagiotis , Drakakaki Argyro , Oungrinis Konstantinos-Alketas
Published: September 2020

Purpose

This study aims to discuss the causes of short-lived structuring of contemporary buildings. The life expectancy of structures may be theoretically predefined during the state of the design. This time period, known as the service life of structures, is determined by the load or the deformation level at which irreversible failures of the bearing structure may occur. On the other hand, planned obsolescence and perceived obsolescence, observed in the western world since the first half of 20th century, are currently setting an economic reality and are part of an expanded framework that, apart from architectural structures, extends to all design fields. The effects of short-lived structuring on environmental and energy terms are presented and theoretical and experimental recommendations from the literature are cited, as well as recommendations that have already been successfully applied in some countries.

Design/methodology/approach

This study aims to discuss the issues associated with short-lived structuring, durability and obsolescence of contemporary structures. For this purpose, theoretical and experimental recommendations from the literature are cited, via an extensive state of the art research.

Findings

Short-lived structuring has been a field of research during recent years. Terms such as durability are being introduced into Design Codes, while trends like perceived obsolescence and environmental impact raise issues for research. Moreover, the results of short-lived structuring are becoming more and more apparent, indicating an unsustainable reality. Issues like maintenance of structures, sustainability in design, corrosion effects, repair techniques and building waste management are an important field of research among the engineering community. In this study, the parameters affecting the lifespan of contemporary structures have been discussed.

Originality/value

The effects of short-lived structuring on environmental and energy terms are presented and theoretical and experimental recommendations from the literature are cited. The parameters studied herein concern material properties and design approach but also environmental and energy-related ones.
Unifying spatial and social network analysis in disease ecology
Authors: Albery Gregory F. , Kirkpatrick Lucinda , Firth Josh A. , Bansal Shweta
Published: September 2020

Social network analysis has achieved remarkable popularity in disease ecology, and is sometimes carried out without investigating spatial heterogeneity. Many investigations into sociality and disease may nevertheless be subject to cryptic spatial variation, so ignoring spatial processes can limit inference regarding disease dynamics.

Disease analyses can gain breadth, power and reliability from incorporating both spatial and social behavioural data. However, the tools for collecting and analysing these data simultaneously can be complex and unintuitive, and it is often unclear when spatial variation must be accounted for. These difficulties contribute to the scarcity of simultaneous spatial‐social network analyses in disease ecology thus far.

Here, we detail scenarios in disease ecology that benefit from spatial‐social analysis. We describe procedures for simultaneous collection of both spatial and social data, and we outline statistical approaches that can control for and estimate spatial‐social covariance in disease ecology analyses.

We hope disease researchers will expand social network analyses to more often include spatial components and questions. These measures will increase the scope of such analyses, allowing more accurate model estimates, better inference of transmission modes, susceptibility effects and contact scaling patterns, and ultimately more effective disease interventions.
Micro‐scale geography of synchrony in a serpentine plant community
Authors: Walter Jonathan A. , Hallett Lauren M. , Sheppard Lawrence W. , Anderson Thomas L. , Zhao Lei , Hobbs Richard J. , Suding Katharine N. , Reuman Daniel C.
Published: September 2020

Fluctuations in population abundances are often correlated through time across multiple locations, a phenomenon known as spatial synchrony. Spatial synchrony can exhibit complex spatial structures, termed ‘geographies of synchrony’, that can reveal mechanisms underlying population fluctuations. However, most studies have focused on spatial extents of 10s to 100s of kilometres, making it unclear how synchrony concepts and approaches should apply to dynamics at finer spatial scales.

We used network analyses, multiple regression on similarity matrices, and wavelet coherence analyses to examine micro‐scale synchrony and geographies of synchrony, over distances up to 30 m, in a serpentine grassland plant community.

We found that species' populations exhibited a geography of synchrony even over such short distances. Often, well‐synchronized populations were geographically separate, a spatial structure that was shaped mainly by gopher disturbance and dispersal limitation, and to a lesser extent by relationships with other plant species. Precipitation was a significant driver of site‐ and community‐wide temporal dynamics. Gopher disturbance appeared to drive synchrony on 2‐ to 6‐year timescales, and we detected coherent fluctuations among pairs of focal plant taxa.

Synthesis. Micro‐geographies of synchrony are an intriguing phenomenon that may also help us better understand community dynamics. Additionally, the related geographies of synchrony and coherent temporal dynamics among some species pairs indicate that incorporating interspecific interactions can improve understanding of population spatial synchrony.
Variation at the common polysaccharide antigen locus drives lipopolysaccharide diversity within the Pseudomonas syringae species complex
Authors: Jayaraman Jay , Jones William T. , Harvey Dawn , Hemara Lauren M. , McCann Honour C. , Yoon Minsoo , Warring Suzanne L. , Fineran Peter C. , Mesarich Carl H. , Templeton Matthew D.
Published: September 2020

The common polysaccharide antigen (CPA) of the lipopolysaccharide (LPS) from Pseudomonas syringae is highly variable, but the genetic basis for this is poorly understood. We have characterized the CPA locus from P. syringae pv. actinidiae (Psa). This locus has genes for l‐ and d‐rhamnose biosynthesis and an operon coding for ABC transporter subunits, a bifunctional glycosyltransferase and an o‐methyltransferase. This operon is predicted to have a role in the transport, elongation and termination of the CPA oligosaccharide and is referred to as the TET operon. Two alleles of the TET operon were present in different biovars (BV) of Psa and lineages of the closely related pathovar P. syringae pv. actinidifoliorum. This allelic variation was reflected in the electrophoretic properties of purified LPS from the different isolates. Gene knockout of the TET operon allele from BV1 and replacement with that from BV3, demonstrated the link between the genetic locus and the biochemical properties of the LPS molecules in Psa. Sequence analysis of the TET operon from a range of P. syringae and P. viridiflava isolates displayed a phylogenetic history incongruent with core gene phylogeny but correlates with previously reported tailocin sensitivity, suggesting a functional relationship between LPS structure and tailocin susceptibility.