bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen
Authors: Wotton Janine M. , Peterson Emma , Flenniken Ann M. , Bains Rasneer S. , Veeraragavan Surabi , Bower Lynette R. , Bubier Jason A. , Parisien Marc , Bezginov Alexandr , Haselimashhadi Hamed , Mason Jeremy , Moore Michayla A. , Stewart Michelle E. , Clary Dave A. , Delbarre Daniel J. , Anderson Laura C. , D'Souza Abigail , Goodwin Leslie O. , Harrison Mark E. , Huang Ziyue , Mckay Matthew , Qu Dawei , Santos Luis , Srinivasan Subhiksha , Urban Rachel , Vukobradovic Igor , Ward Christopher S. , Willett Amelia M. ,   The International Mouse Phenotyping Consortium, Braun Robert E. , Brown Steve D.M. , Dickinson Mary E. , Heaney Jason D. , Kumar Vivek , Lloyd K.C. Kent , Mallon Ann-Marie , McKerlie Colin , Murray Stephen A. , Nutter Lauryl M.J. , Parkinson Helen , Seavitt John R. , Wells Sara , Samaco Rodney C. , Chesler Elissa J. , Smedley Damian , Diatchenko Luda , Baumbauer Kyle M. , Young Erin E. , Bonin Robert P. , Mandillo Silvia , White Jacqueline K.
Published: September 2021

Identifying the genetic determinants of pain is a scientific imperative given the magnitude of the global health burden that pain causes. Here, we report a genetic screen for nociception, performed under the auspices of the International Mouse Phenotyping Consortium. A biased set of 110 single-gene knockout mouse strains was screened for 1 or more nociception and hypersensitivity assays, including chemical nociception (formalin) and mechanical and thermal nociception (von Frey filaments and Hargreaves tests, respectively), with or without an inflammatory agent (complete Freund's adjuvant). We identified 13 single-gene knockout strains with altered nocifensive behavior in 1 or more assays. All these novel mouse models are openly available to the scientific community to study gene function. Two of the 13 genes (Gria1 and Htr3a) have been previously reported with nociception-related phenotypes in genetically engineered mouse strains and represent useful benchmarking standards. One of the 13 genes (Cnrip1) is known from human studies to play a role in pain modulation and the knockout mouse reported herein can be used to explore this function further. The remaining 10 genes (Abhd13, Alg6, BC048562, Cgnl1, Cp, Mmp16, Oxa1l, Tecpr2, Trim14, and Trim2) reveal novel pathways involved in nociception and may provide new knowledge to better understand genetic mechanisms of inflammatory pain and to serve as models for therapeutic target validation and drug development.
Use of pharmacological and nonpharmacological treatments for chronic noncancer pain among people using opioids: a longitudinal cohort study
Authors: Hopkins Ria E. , Campbell Gabrielle , Degenhardt Louisa , Nielsen Suzanne , Blyth Fiona , Cohen Milton , Gisev Natasa
Published: September 2021

Although multimodal management of chronic noncancer pain (CNCP) is recommended, long-term treatment utilization patterns among people using opioids are not well known. The Pain and Opioids IN Treatment study recruited Australian adults receiving opioids for CNCP for more than 6 weeks from community pharmacies. Pharmacological (opioid and nonopioid analgesics and psychotropic medicines) and nonpharmacological (physical, mental health, and specialized) treatments used in the previous 12 months and 30 days were collected annually over 4 years (2015-2018). Associations were explored between 30-day treatment use and sociodemographic characteristics and pain measures. Overall, 1334 participants completed at least one annual follow-up. The median pain severity (5.0, interquartile range [IQR] 3.8 to 6.3) and pain interference scores (5.7, IQR 3.9-7.3) indicated moderate pain throughout the study period, despite most participants reporting the use of nonopioid pharmacological (12 month: 97.6% and 30 day: 96.8%) and nonpharmacological treatments (12 month: 91.8% and 30 day: 66.1%). Some treatment use was inconsistent with guidelines: ongoing nonsteroidal anti-inflammatory drugs and sedative-hypnotic use were common, whereas fewer people engaged with pain management programs (12 month: 22.3%). Private health insurance was associated with using physical (adjusted odds ratio 1.61, 99.5% confidence intervals 1.15-2.24) and specialized nonpharmacological treatments (adjusted odds ratio 1.47, 99.5% confidence intervals 1.14-1.91). This study demonstrates that many Australians taking opioids long-term for CNCP also use nonopioid pharmacological and nonpharmacological treatments. The use of pharmacological treatments including nonsteroidal anti-inflammatory drugs, psychotropic medicines, and gabapentinoids, outside guidelines, warrants review. Furthermore, despite Australia's universal healthcare scheme subsidising some nonpharmacological treatments, overall use of these treatments was associated with having private health insurance, highlighting a need for more equitable service provision.
Perceptions of Work-Related Health and Cancer Risks Among Women Firefighters
Authors: Solle Natasha Schaefer , Santiago Katerina M. , Louzado Feliciano Paola , Calkins Miriam M. , Fent Kenny , Jahnke Sara , Parks Natasha , Buren Heather , Grant Casey , Burgess Jefferey L. , Caban-Martinez Alberto J.
Published: September 2021

Objectives:

We use a qualitative method to gain further insight into women firefighters’ experiences, perceptions of cancer, health, and safety risks in the fire service.

Methods:

We conducted six focus groups with U.S. women firefighters. Participants engaged in a 60 to 75-minute, semi-structured discussion and completed a sociodemographic questionnaire. A qualitative descriptive approach was used to inductively create themes. Data collection concluded when saturation was met.

Results:

Forty-nine women firefighters participated. Qualitative results indicated the main health concerns include: occupational cancer risks including, risks related to hazardous exposures, sleep disruption and stress; and women's health concerns including, cancer, pregnancy and breastfeeding, and lack of resources.

Conclusions:

Women firefighters are concerned about their risk for cancer due to their occupation and identify a lack of resources specific to health and safety needs of women firefighters.
Dermatologic simulations in nurse practitioner education: Improving skin cancer knowledge, confidence, and performance
Authors: Shue-McGuffin Katherine D. , Powers Kelly
Published: September 2021

Background:

The rising incidence of skin cancer continues to be a significant public health concern in the United States. Nurse practitioners (NPs) have a key role in early detection of skin cancer. However, NP students currently demonstrate low levels of knowledge related to skin cancer assessments and recognition of skin lesions.

Purpose:

The aim of this pilot study was to determine if simulations with standardized patients wearing three-dimensional (3D) prosthetic skin lesions improved NP students' knowledge, self-confidence, and observed simulation performance with regard to assessing, diagnosing, and managing patients with nonmalignant versus malignant skin lesions.

Methodology:

A quasi-experimental approach was used with a convenience sample of 39 NP students. Students participated in three consecutive simulations, each followed by a debriefing. Performance was assessed during the simulations using a rubric. Knowledge and self-confidence were measured immediately before and after the simulation.

Results:

Correct responses on knowledge items increased for 14 of the 18 items. Self-confidence significantly improved from pretest to posttest. There was a statistically significant improvement in performance from the first to third simulation encounter.

Conclusion:

Simulation with standardized patients wearing 3D lesions can enhance NP students' knowledge, self-confidence, and performance of skin cancer assessments.

Implications:

Nurse practitioner programs can consider using simulation to prepare students for dermatologic care and to help improve the probability of early detection of skin cancer in various health care settings.
Benefit of Higher Maximum Force Output in Bone Anchored Hearing Systems: A Crossover Study
Authors: Bergius Elin , Philipsson Marianne , Rosenbom Tove , Sadeghi André
Published: September 2021

Objective:

To investigate how higher maximum force output (MFO) in bone anchored hearing systems (BAHS) affects perceived benefit and the subjective experience of sound as well as hearing outcomes in subjects with mixed hearing loss.

Study Design:

Prospective single-center, randomized crossover design (A-B-A) with within-subject control design.

Patients:

The study included 19 experienced BAHS users with mixed hearing loss in the fitting range of a standard BAHS.

Interventions:

The study evaluated two sound processors with differing MFOs and sizes—Device A: standard sound processor with a lower MFO and Device B: superpower sound processor with a higher MFO.

Outcome Measures:

Speech recognition in noise at different signal to noise ratios, aided thresholds, and questionnaires.

Results:

Speech recognition test showed significant improvements using Device B compared with Device A at both 78 dB SPL (mean difference: 9%) and 75 dB SPL (mean difference: 12%) (p < 0.05). Moreover, speech, spatial and qualities of hearing scale (SSQ12-C) showed a significantly greater perceived benefit with Device B concerning spatial abilities (mean: 0.5–0.6) (p < 0.05). At the conclusion of the study, 58% of participants chose to keep Device A for further use. The main reasons for this were the size of the sound processor and a more comfortable sound experience.

Conclusions:

A BAHS sound processor with a higher MFO leads to improved speech-in-noise performance in loud/noisy listening situations and is perceived as significantly better to process spatial information in daily listening situations. However, the relation between cosmetics and performance is not straightforward, and several factors seem to affect the selection process of BAHS.
Deployment of the Water Drinking Test and iCare HOME Phasing for Intraocular Pressure Profiling in Glaucoma Evaluation
Authors: Phu Jack , Masselos Katherine , Kalloniatis Michael
Published: September 2021

SIGNIFICANCE

Intraocular pressure (IOP) profiling is an important component of the glaucoma examination. Two techniques for profiling are the water drinking test (WDT) and iCare HOME phasing, but the correlations between techniques and their ease of deployment have not been studied. These questions are important in determining suitability for clinical deployment.

PURPOSE

This study aimed to compare the IOP results of the WDT and iCare HOME phasing in patients with suspected or newly diagnosed glaucoma.

METHODS

Ninety-eight consecutive patients attending a glaucoma clinic underwent IOP profiling using both techniques. For the WDT, patients ingested 10 mL/kg body weight of water after a baseline applanation IOP measurement and then underwent serial IOP measurements approximately every 15 minutes, ceasing after 30 minutes of consecutive measurements within 3 mmHg of baseline. Patients successfully certified for self-administration of the iCare HOME were loaned the instrument for 1 week and instructed to take four measurements per day.

RESULTS

Twenty-seven patients (28%) successfully obtained four measurements per day using iCare HOME, and 96 patients (98%) were able to complete the WDT. Intraocular pressure profiles showed no difference between the time for peak IOP and across nearly all IOP parameters obtained from profiling except for the standard deviation of IOP measurements obtained using the iCare HOME (P = .005). There were moderate correlations between peak IOPs obtained using each technique (r = 0.67, P = .001, right eye; r = 0.66, P = .002, left eye) but no correlation between the daily range (iCare HOME) or peak-trough difference (WDT; r = 0.21, P = .28, right eye; r = 0.27, P = .02, left eye). Bland-Altman analysis returned similar results for peak and range.

CONCLUSIONS

Intraocular pressure profiling using both techniques can reveal the peak IOP, and these measurements are strongly correlated. Most patients were unable to complete the iCare HOME according to the manufacturer's recommendations. Clinicians should select the most appropriate technique for each patient.
Pulmonary Epithelioid Hemangioendothelioma: Imaging and Clinical Features
Authors: Liu Hui , Wang Jianhua , Lang Juntao , Zhang Xingwei
Published: September 2021

Objective

The aim of this study was to analyze the computed tomography (CT), fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT), and clinical findings of pulmonary epithelioid hemangioendothelioma.

Methods

Eighteen patients were included. We reviewed CT and PET/CT features and clinical information. Spearman correlation analysis was used to reveal the correlation between lesion size and maximum standardized uptake values (SUVmax).

Results

Eleven patients complained of different symptoms. The serum levels of tumor markers were elevated in 8 patients (44.4%). Multiple lesions were shown in 14 cases (77.8%). Eleven cases (61.1%) presented as bilateral multiple perivascular lesions. The size of the largest nodule was less than 20 mm in diameter in 11 cases (61.1%). Eleven cases underwent PET/CT examination, and 8 cases (72.7%) had increased FDG uptake. There was a positive correlation (Spearman correlation coefficient, 0.56; P = 0.009) between lesion size and SUVmax. Extrapulmonary involvement was shown in 7 cases, including the liver and bone.

Conclusions

Pulmonary epithelioid hemangioendothelioma on CT scan usually showed multiple bilateral perivascular lung nodules, generally measuring less than 20 mm in diameter. Lesions usually showed increased FDG uptake on PET/CT scans. There was a positive correlation between lesion size and SUVmax. The liver and bone were the most frequently involved extrapulmonary organs.
Monobloc Differential Distraction Osteogenesis
Authors: Polley John W. , Figueroa Alvaro A. , Girotto John A. , Dietze-Fiedler Megan L.
Published: September 2021

Midface advancement at the monobloc level can be the seminal life event for patients with craniofacial dysostosis. Monobloc reconstruction, when planned appropriately, can simultaneously and definitively address multiple functional and aesthetic deficiencies in these patients. The application of distraction has reduced the morbidity experienced with traditional monobloc surgery. The purpose of this study is to report on the outcomes, stability, and growth in younger patients after monobloc advancement in syndromic craniosynostosis patients. The authors report a consecutive series of thirty patients with craniofacial dysostosis treated through monobloc differential distraction osteogenesis. Detailed history, photographic, and long-term radiographic data are reviewed, including a subset of patients who were skeletally immature at the time of their treatment. Differential distraction allows control of midface pitch, roll, and yaw, optimizing functional and aesthetic outcomes. There were no infectious complications requiring reoperation. The average surgical age for all patients was 12.5 years. For the 7 patients age <7 years, average age was 6 years. For all patients, the mean horizontal movement was 12 mm at nasion and 10 mm at A-point. At mean follow-up (4.8 years entire group and 6.2 years age <7 years group) a positive horizontal advancement of 1.1 mm at nasion and 0.8 mm at A-point was observed. More pronounced positive horizontal changes were seen in the age <7 years group. Monobloc differential distraction osteogenesis affords safe and precise repositioning of the midface. The advancement is skeletally stable and young patients show moderate continued growth.
Epidemiological Characteristics of Children With Non-Cleft Lip/Palate Craniofacial Anomalies
Authors: Sawasdipanich Nantaga , Chaithat Bussara , Rojvachiranonda Nond , Dangsomboon Artiteeya
Published: September 2021

Non-cleft craniofacial anomalies are not as common as cleft lip and palate but resultant disability can be very severe. Although there are epidemiological studies of the clefts in the medical literature, the non-cleft group is still not well known. This study was to examine the epidemiological characteristics of the non-cleft craniofacial anomalies. Patients younger than 18 years old were included during a 1-year period. Patient information was retrieved from medical records and a questionnaire filled by primary caregivers.

There were 139 patients included in the study with an average age of 6 years and 7 months (4–194 months). Fifty-eight percent were male, 56% were first-born children, whereas 61.9% had siblings. Family history was positive in 6.5%. Almost all patients were in age-appropriate educational levels. Using Whitaker classification, Synostoses was the most common at 48.9%, followed by Unclassified, Clefts, Neoplasia-Hyperplasia, and Atrophy-Hypoplasia. Their anomalies were mostly detected at the regional hospitals. Outpatient visits throughout the course ranged from 1 to 100. Eighty-two percent of patients had at least 1 hospitalization, whereas 78% experienced at least 1 surgical treatment.

Generally, non-cleft craniofacial anomalies were nonfamilial. We found a wide variety of anomalies. Patients were from all regions of the country. Their geographical location did not prevent access to receiving proper care and education. Having a child with an anomaly did not discourage the family from having more descendants. Among the available classifications, the Whitaker system is easier for clinical use.
Predictions of primate–parasite coextinction
Authors: Herrera James P. , Moody James , Nunn Charles L.
Published: September 2021

Future biodiversity loss threatens the integrity of complex ecological associations, including among hosts and parasites. Almost half of primate species are threatened with extinction, and the loss of threatened hosts could negatively impact parasite associations and ecosystem functions. If endangered hosts are highly connected in host–parasite networks, then future host extinctions will also drive parasite extinctions, destabilizing ecological networks. If threatened hosts are not highly connected, however, then network structure should not be greatly affected by the loss of threatened hosts. Networks with high connectance, modularity, nestedness and robustness are more resilient to perturbations such as the loss of interactions than sparse, nonmodular and non-nested networks. We analysed the interaction network involving 213 primates and 763 parasites and removed threatened primates (114 species) to simulate the effects of extinction. Our analyses revealed that connections to 23% of primate parasites (176 species) may be lost if threatened primates go extinct. In addition, measures of network structure were affected, but in varying ways because threatened hosts have fewer parasite interactions than non-threatened hosts. These results reveal that host extinctions will perturb the host–parasite network and potentially lead to secondary extinctions of parasites. The ecological consequences of these extinctions remain unclear.

This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
The future of zoonotic risk prediction
Authors: Carlson Colin J. , Farrell Maxwell J. , Grange Zoe , Han Barbara A. , Mollentze Nardus , Phelan Alexandra L. , Rasmussen Angela L. , Albery Gregory F. , Bett Bernard , Brett-Major David M. , Cohen Lily E. , Dallas Tad , Eskew Evan A. , Fagre Anna C. , Forbes Kristian M. , Gibb Rory , Halabi Sam , Hammer Charlotte C. , Katz Rebecca , Kindrachuk Jason , Muylaert Renata L. , Nutter Felicia B. , Ogola Joseph , Olival Kevin J. , Rourke Michelle , Ryan Sadie J. , Ross Noam , Seifert Stephanie N. , Sironen Tarja , Standley Claire J. , Taylor Kishana , Venter Marietjie , Webala Paul W.
Published: September 2021

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges?

This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
Land-use change and rodent-borne diseases: hazards on the shared socioeconomic pathways
Authors: García-Peña Gabriel E. , Rubio André V. , Mendoza Hugo , Fernández Miguel , Milholland Matthew T. , Aguirre A. Alonso , Suzán Gerardo , Zambrana-Torrelio Carlos
Published: September 2021

Land-use change has a direct impact on species survival and reproduction, altering their spatio-temporal distributions. It acts as a selective force that favours the abundance and diversity of reservoir hosts and affects host–pathogen dynamics and prevalence. This has led to land-use change being a significant driver of infectious diseases emergence. Here, we predict the presence of rodent taxa and map the zoonotic hazard (potential sources of harm) from rodent-borne diseases in the short and long term (2025 and 2050). The study considers three different land-use scenarios based on the shared socioeconomic pathways narratives (SSPs): sustainable (SSP1-Representative Concentration Pathway (RCP) 2.6), fossil-fuelled development (SSP5-RCP 8.5) and deepening inequality (SSP4-RCP 6.0). We found that cropland expansion into forest and pasture may increase zoonotic hazards in areas with high rodent-species diversity. Nevertheless, a future sustainable scenario may not always reduce hazards. All scenarios presented high heterogeneity in zoonotic hazard, with high-income countries having the lowest hazard range. The SSPs narratives suggest that opening borders and reducing cropland expansion are critical to mitigate current and future zoonotic hazards globally, particularly in middle- and low-income economies. Our study advances previous efforts to anticipate the emergence of zoonotic diseases by integrating past, present and future information to guide surveillance and mitigation of zoonotic hazards at the regional and local scale.

This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
Phanerozoic parasitism and marine metazoan diversity: dilution versus amplification
Authors: De Baets Kenneth , Huntley John Warren , Scarponi Daniele , Klompmaker Adiël A. , Skawina Aleksandra
Published: September 2021

Growing evidence suggests that biodiversity mediates parasite prevalence. We have compiled the first global database on occurrences and prevalence of marine parasitism throughout the Phanerozoic and assess the relationship with biodiversity to test if there is support for amplification or dilution of parasitism at the macroevolutionary scale. Median prevalence values by era are 5% for the Paleozoic, 4% for the Mesozoic, and a significant increase to 10% for the Cenozoic. We calculated period-level shareholder quorum sub-sampled (SQS) estimates of mean sampled diversity, three-timer (3T) origination rates, and 3T extinction rates for the most abundant host clades in the Paleobiology Database to compare to both occurrences of parasitism and the more informative parasite prevalence values. Generalized linear models (GLMs) of parasite occurrences and SQS diversity measures support both the amplification (all taxa pooled, crinoids and blastoids, and molluscs) and dilution hypotheses (arthropods, cnidarians, and bivalves). GLMs of prevalence and SQS diversity measures support the amplification hypothesis (all taxa pooled and molluscs). Though likely scale-dependent, parasitism has increased through the Phanerozoic and clear patterns primarily support the amplification of parasitism with biodiversity in the history of life.

This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
Flavobacterium tagetis sp. nov., a novel urea-hydrolysing bacterium isolated from the roots of Tagetes patula
Authors: Chhetri Geeta , Kim Inhyup , Kang Minchung , Kim Jiyoun , So Yoonseop , Seo Taegun
Published: September 2021

A Gram-stain-negative, rod-shaped, motile by gliding, non-sporulating and strictly aerobic bacterium, designated strain GN10T, was isolated from the roots of Tagetes patula, collected from the garden of Dongguk University, Goyang, Republic of Korea. The cells could grow at 10–42 °C and at pH 5.5–9.0. Strain GN10T was sensitive to NaCl and tolerated up to 4 % NaCl (w/v). Comparative analysis of 16S rRNA gene sequences revealed the highest similarities to

Flavobacterium tistrianum

GB 56.1T (98.9 %),

Flavobacterium sharifuzzamanii

A7.6T (98.6 %),

Flavobacterium zhairuonense

A5.7T (98.3 %) and

Flavobacterium anhuiense

D3T (98 %). Phylogenetic analysis showed that strain GN10T clustered within the genus

Flavobacterium

and formed a monophyletic cluster with its close relative members. The average nucleotide identity and digital DNA–DNA hybridization values between strain GN10T and related species belonging to the genus

Flavobacterium

were well below the standard threshold for prokaryotic species delineation. The DNA G+C content of strain GN10T was 33.6 mol%. The predominant cellular fatty acids (>10 %) were identified as iso-C15 : 0, C16 : 0 and summed feature 3 (C16  : 1
ω6c and/or C16  :  1
ω7c). Strain GN10T contained menaquinone 6 as the major respiratory quinone. The major polar lipids were phosphatidylethanolamine, three unidentified aminoglycolipids, two unidentified glycolipids, one unidentified phosphoglycolipid and five unidentified lipids. Urease is a nickel-containing enzyme found in archaea, bacteria, plants and unicellular eukaryotes. It serves as a virulence factor and is responsible for pathogenesis in humans and animals. Here, we describe a novel urease-hydrolysing bacterium, strain GN10T. The urease activity of this strain may serve as an indicator of pathogenic potential and drug resistance, which may facilitate the development of many diseases. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain GN10T from its closely related members and considered to represent novel species in the genus

Flavobacterium

, for which the name Flavobacterium tagetis (GN10T=KCTC 82695T=NBRC 114841T) is proposed.
Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula
Authors: Chhetri Geeta , Kim Inhyup , Kang Minchung , Kim Jiyoun , So Yoonseop , Seo Taegun
Published: September 2021

An aerobic, Gram-stain-positive, non-motile, dull-yellow, short rod-shaped actinomycete strain, designated G10T, was isolated from Tagetes patula (marigold) roots collected from Goyang in the Republic of Korea. The isolate showed best growth on Reasoner's 2A agar at 25 °C, pH 6.5.0 and with 0% NaCl (w/v). The strain was negative for oxidase activity and positive for catalase activity. On the basis of 16S RNA gene sequence similarity, strain G10T was affiliated to the genus

Nocardioides

and the closest species were

Nocardioides glacieisoli

HLT3-15T (98.8 %),

Nocardioides zhouii

HLT2-9T (98.8 %),

Nocardioides ganghwensis

JC2055T (98.7 %),

Nocardioides cavernae

YIM A1136T (98.6 %),

Nocardioides flavus

Y4T (98.5 %),

Nocardioides oleivorans

DSM 16090T (98.3 %),

Nocardioides alpinus

Cr7-14T (98.2 %),

Nocardioides exalbidus

DSM 22017T (98.1 %) and

Nocardioides hwasunensis

KCTC 19197T (98.1 %). Strain G10T formed a monophyletic cluster with

N. glacieisoli

HLT3-15T,

N. zhouii

HLT2-9T and

N. hwasunensis

KCTC 19197T in all phylogenetic trees. The cell-wall peptidoglycan of strain G10T contained ll-diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C16 : 0 and C17 : 1
 ω8c. MK-8(H4) was the major isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Average nucleotide identity and digital DNA–DNA hybridization values were 78.6–88.7 % and 21.5–36.2 %, respectively, with the type strains of related species of the genus

Nocardioides

, suggesting that strain G10T represents a novel species. The genome of strain G10T is 4 231 000 bp long with a DNA G+C content of 71.5 mol% and encodes 4071 predicted proteins, six rRNAs and 46 tRNAs. The genome of strain G10T comprises the biosynthetic gene cluster for T3PKS, terpene, NRPS-like fragment and RRE-containing element as secondary metabolites. The results of taxonomic, phylogenetic, biochemical, chemotaxonomic and genomic analysis clearly supported that strain G10T represent a novel species within the genus

Nocardioides

, for which the name Nocardioides baculatus sp. nov is proposed and the type strain is G10T (=KCTC 49626T=NBRC 114801T).
The aging lung mucosa: A proteomics study
Authors: Garcia-Vilanova Andreu , Olmo-Fontánez Angélica M. , Moliva Juan I. , Allué-Guardia Anna , Singh Harjinder , Merrit Robert E. , Caceres Diego M. , Peters Jay , Wang Yufeng , Schlesinger Larry S. , Turner Joanne , Weintraub Susan T. , Torrelles Jordi B.
Published: September 2021

The elderly population is at increased risk of acute and chronic respiratory infections and other pulmonary diseases, and it is estimated that this population will double in the next 30 years. Biochemical changes in the lung alveolar mucosa and lung cells alter local immune response as we age, creating opportunities for invading pathogens to establish successful infections. Indeed, the lungs of the elderly are a pro-inflammatory, pro-oxidative, dysregulated environment but this environment has remained understudied. We performed a comprehensive, quantitative proteomic profile of the lung mucosa in the elderly, developing insight into the molecular fingerprints, pathways, and regulatory networks that characterize the lung in old age. We identified neutrophils in the lungs of elderly individuals as possible contributors to dysregulated lung tissue environment. This study establishes a baseline for future investigations to develop strategies to mitigate susceptibility to respiratory infections in the elderly.
Biomechanical interactions of Schistosoma mansoni eggs with vascular endothelial cells facilitate egg extravasation
Authors: Yeh Yi-Ting , Skinner Danielle E. , Criado-Hidalgo Ernesto , Chen Natalie Shee , Garcia-De Herreros Antoni , El-Sakary Nelly , Liu Lawrence , Zhang Shun , Chien Shu , Lasheras Juan C. , del Álamo Juan C. , Caffrey Conor R.
Published: September 2021

The eggs of the parasitic blood fluke, Schistosoma, are the main drivers of the chronic pathologies associated with schistosomiasis, a disease of poverty afflicting approximately 220 million people worldwide. Eggs laid by Schistosoma mansoni in the bloodstream of the host are encapsulated by vascular endothelial cells (VECs), the first step in the migration of the egg from the blood stream into the lumen of the gut and eventual exit from the body. The biomechanics associated with encapsulation and extravasation of the egg are poorly understood. We demonstrate that S. mansoni eggs induce VECs to form two types of membrane extensions during encapsulation; filopodia that probe eggshell surfaces and intercellular nanotubes that presumably facilitate VEC communication. Encapsulation efficiency, the number of filopodia and intercellular nanotubes, and the length of these structures depend on the egg’s vitality and, to a lesser degree, its maturation state. During encapsulation, live eggs induce VEC contractility and membranous structures formation, in a Rho/ROCK pathway-dependent manner. Using elastic hydrogels embedded with fluorescent microbeads as substrates to culture VECs, live eggs induce VECs to exert significantly greater contractile forces during encapsulation than dead eggs, which leads to 3D deformations on both the VEC monolayer and the flexible substrate underneath. These significant mechanical deformations cause the VEC monolayer tension to fluctuate with eventual rupture of VEC junctions, thus facilitating egg transit out of the blood vessel. Overall, our data on the mechanical interplay between host VECs and the schistosome egg improve our understanding of how this parasite manipulates its immediate environment to maintain disease transmission.
SEQUENCE SLIDER: integration of structural and genetic data to characterize isoforms from natural source
Authors: Borges Rafael J. , Salvador Guilherme H. M. , Pimenta Daniel C. , dos Santos Lucilene D. , Fontes Marcos R. M. , Usón Isabel
Published: September 2021

Proteins isolated from natural source can be composed of a mixture of isoforms with similar physicochemical properties that coexists in final steps of purification, toxins being prominent examples. Sequence composition is enforced throughout structural studies even when unsubstantiated. Herein, we propose a novel perspective to address the usually neglected heterogeneity of natural products by integrating biophysical, genetic and structural data in our program SEQUENCE SLIDER.

The aim is to assess the evidence supporting chemical composition in structure determination. Locally, we interrogate the experimental map to establish which side chains are supported by the structural data and the genetic information relating sequence conservation is integrated in this statistic. Hence, we build a constrained peptide database, containing most probable sequences to interpret mass spectrometry data (MS). In parallel, we perform MSde novosequencing with genomic-based algorithms that foresee point mutations.

We calibrated SLIDER withGallus galluslysozyme, for which sequence is unequivocally established and numerous natural isoforms are reported. We used SLIDER to characterise a metalloproteinase and a phospholipase A2-like protein from the venom ofBothrops moojeniand a crotoxin fromCrotalus durissus collilineatus. This integrated approach offers a more realistic structural descriptor to characterize macromolecules isolated from natural source.

Key points

The method SEQUENCE SLIDER integrates biophysical, genetic and structural data to assign sequence.

It joins crystallography, mass spectrometry and phylogenetic data to characterize isoforms.

Sequence heterogeneity of four proteins purified directly from snake venom was established.
Synchronous spiking of cerebellar Purkinje cells during control of movements
Authors: Sedaghat-Nejad Ehsan , Pi Jay S. , Hage Paul , Fakharian Mohammad Amin , Shadmehr Reza
Published: September 2021

The information that the brain transmits from one region to another is often viewed through the lens of firing rates. However, if the output neurons could vary the timing of their spikes with respect to each other, then through synchronization they could highlight information that may be critical for control of behavior. In the cerebellum, the computations that are performed by the cerebellar cortex are conveyed to the nuclei via inhibition. Yet, synchronous activity entrains nucleus neurons, making them fire. Does the cerebellar cortex rely on spike synchrony within populations of Purkinje cells (P-cells) to convey information to the nucleus? We recorded from multiple P-cells while marmosets performed saccadic eye movements and organized them into populations that shared a complex spike response to error. Before movement onset, P-cells transmitted information via a rate code: the simple spike firing rates predicted the direction and velocity of the impending saccade. However, during the saccade, the spikes became temporally aligned within the population, signaling when to stop the movement. Thus, the cerebellar cortex relies on spike synchronization within a population of P-cells, not individual firing rates, to convey to the nucleus when to stop a movement.
Cognitive processing of a common stimulus synchronizes brains, hearts, and eyes
Authors: Madsen Jens , Parra Lucas C.
Published: September 2021

Neural, physiological and behavioral signals synchronize between human subjects in a variety of settings. Multiple hypotheses have been proposed to explain this interpersonal synchrony, but there is no clarity under which conditions it arises, for which signals, or whether there is a common underlying mechanism. We hypothesized that similar cognitive processing of a shared stimulus is the source of synchrony between subjects, measured here as inter-subject correlation. To test this we presented informative videos to participants in an attentive and distracted condition and subsequently measured information recall. Inter-subject correlation was observed for electro-encephalography, gaze position, pupil size and heart rate, but not respiration and head movements. The strength of correlation was co-modulated in the different signals, changed with attentional state, and predicted subsequent recall of information presented in the videos. There was robust within-subject coupling between brain, heart and eyes, but not respiration or head movements. The results suggest that inter-subject correlation is the result of similar cognitive processing and thus emerges only for those signals that exhibit a robust brain-body connection. While physiological and behavioral fluctuations may be driven by multiple features of the stimulus, correlation with other individuals is co-modulated by the level of attentional engagement with the stimulus.
SMAP: A pipeline for sample matching in proteogenomics
Authors: Li Ling , Niu Mingming , Erickson Alyssa , Luo Jie , Rowbotham Kincaid , Huang He , Li Yuxin , Jiang Yi , Liu Chunyu , Peng Junmin , Wang Xusheng
Published: September 2021

Integration of genomics and proteomics (proteogenomics) offers unprecedented promise for in-depth understanding of human diseases. However, sample mix-up is a pervasive, recurring problem, due to complex sample processing in proteogenomics. Here we present a pipeline for Sample Matching in Proteogenomics (SMAP) for verifying sample identity to ensure data integrity. SMAP infers sample-dependent protein-coding variants from quantitative mass spectrometry (MS), and aligns the MS-based proteomic samples with genomic samples by two discriminant scores. Theoretical analysis with simulation data indicates that SMAP is capable of uniquely match proteomic and genomic samples, when ≥20% genotypes of individual samples are available. When SMAP was applied to a large-scale proteomics dataset from 288 biological samples generated by the PsychENCODE BrainGVEX project, we identified and corrected 18.8% (54/288) mismatched samples. The correction was further confirmed by ribosome profiling and assay for transposase-accessible chromatin sequencing data from the same set of samples. Thus our results demonstrate that SMAP is an effective tool for sample verification in a large-scale MS-based proteogenomics study. The source code, manual, and sample data of the SMAP are publicly available at https://github.com/UND-Wanglab/SMAP, and a web-based SMAP can be accessed at https://smap.shinyapps.io/smap/.
Moderate DNA methylation changes associated with nitrogen remobilization and leaf senescence in Arabidopsis
Authors: Vatov Emil , Zentgraf Ulrike , Ludewig Uwe
Published: September 2021

The lifespan of plants and tissues is restricted by environmental and genetic components. Following the transition to reproductive growth, leaf senescence ceases cellular life in monocarpic plants to remobilize nutrients to storage organs.

We observed altered leaf to seed ratios, faster senescence progression and enhanced nitrogen remobilization from the leaves in two methylation mutants (ros1 and the triple dmr1/2 cmt3 knockout).

DNA methylation in wild type Col-0 leaves initially moderately declined with progressing leaf senescence, predominantly in the CG context, while the ultimate phase of leaf discoloration was associated with moderate de novo methylation of cytosines, primarily in the CHH context.

Relatively few differentially methylated regions, including one in the ROS1 promoter linked to the down-regulation of ROS1, were present, but these were unrelated to known senescence-associated genes.

Differential methylation patterns were identified in transcription factor binding sites, such as the W-boxes that are targeted by WRKYs, which impaired transcription factor binding when methylated in vitro.

Mutants that are defective in DNA methylation showed distinct nitrogen remobilization, which was associated with altered patterns of leaf senescence progression. But moderate methylome changes during leaf senescence were not specifically associated with up-regulated genes during senescence.
APPRIS principal isoforms and MANE Select transcripts in clinical variant interpretation
Authors: Pozo Fernando , Rodriguez Jose Manuel , Vazquez Jesus , Tress Michael L.
Published: September 2021

Most coding genes are able to generate multiple alternatively spliced transcripts. Determining which of these transcript variants produces the main protein isoform, and which of a gene’s multiple splice variants are functionally important, is crucial in comparative genomics and essential for clinical variant interpretation.

Here we show that the principal isoforms chosen by APPRIS and the MANE Select variants provide the best approximations of the main cellular protein isoforms. Principal isoforms are predicted from conservation and from protein features, and MANE transcripts are chosen from the consensus between teams of expert manual curators. APPRIS principal isoforms coincide in over 94% of coding genes with MANE Select transcripts and the two methods are particularly discriminating when they agree on the main splice variant. Where the two methods agree, the splice variants coincide with the main isoform detected in proteomics experiments in 98.2% of genes with multiple protein isoforms.

We also find that almost all ClinVar pathogenic mutations map to MANE Select or APPRIS principal isoforms. Where APPRIS and MANE agree on the main isoform, 99.93% of validated pathogenic variants map to principal rather than alternative exons. MANE Plus Clinical transcripts cover most validated pathogenic mutations in alternative coding exons. TRIFID functional importance scores are particularly useful for distinguishing clinically important alternative isoforms: the highest scoring TRIFID isoforms are more than 300 times more likely to have validated pathogenic mutations.

We find that APPRIS, MANE and TRIFID are important for determining the biological relevance of splice isoforms and should be an essential part of clinical variant interpretation.
Volumetric ultrasound localization microscopy of the whole brain microvasculature
Authors: Heiles Baptiste , Chavignon Arthur , Bergel Antoine , Hingot Vincent , Serroune Hicham , Maresca David , Pezet Sophie , Pernot Mathieu , Tanter Mickael , Couture Olivier
Published: September 2021

Technologies to visualize whole organs across scalesin vivoare essential for our understanding of biology in health and disease. To date, onlypost-mortemtechniques such as perfused computed tomography scanning or optical microscopy of cleared tissues achieve cellular resolution across entire organs and imaging methods with equal performance in living mammalian organs have yet to be developed. Recently, 2D ultrasound localization microscopy has successfully mapped the fine-scale vasculature of various organs down to a 10μmprecision. However, reprojection issues and out-of-plane motion prevent complex blood flow quantification and fast volumetric imaging of whole organs. Here, we demonstrate for the first timein vivovolumetric ultrasound localization microscopy mapping of the rodent brain vasculature. We developed a complete methodological pipeline that includes specific surgery, a dedicated 3D ultrasound acquisition sequence, localization and tracking algorithms, motion correction and realignment, as well as the post-processing quantification of cerebral blood flow. We illustrate the power of this approach, by mapping the whole rat brain vasculature at a resolution of 12μm, revealing mesoscopic to macroscopic vascular architectures and cerebral blood flows ranging from 1 to 100mm/s. Our results pave the way to the investigation ofin vivovascular processes across the mammalian brain in health and disease, in a wide range of contexts and models.
Herbivorous fish of Sinai marine protected areas (Gulf of Aqaba): Structure baseline for potential thermal stress impact management
Authors: El-Haddad Khaled M. , Ali Abdel-Hamid A. M. , Abdel-Rahman Mohammed S. , Mohammed Saad Z. , Abdel-Gawad Fagr Kh. , Guerriero Giulia , Temraz Tarek A.
Published: September 2021

Herbivorous reef fishes are critically important for maintaining the health and resilience of coral reefs. In the Egyptian Gulf of Aqaba (GoA), many of these herbivores are important fishery targets, however, little is known about their biomass and size structure patterns. Here, we conduct a large-scale (∼250 km of coastline) assessment of the status of herbivorous fish populations on 30 reef sites from eight coastal regions in the GoA. These regions are subjected to three levels of fishing and protection, ranging from almost no fishing (No-take, NT), and moderately fished (via Gear-restriction, GR) to heavily fished (Open-access, OA). We found that the NT fishery reserve was the most effective in maintaining herbivorous fish richness, body-size, and biomass across all functional groups, though numerical density was not. Total herbivore biomass was 4.3 and 2.8 times higher on NT reefs and GR reefs respectively than on OA reefs. Among GoA regions, only Ras Mohammed and Sharm El-Sheikh (unfished), and Nabq (moderately fished) met the global mean herbivore biomass target of ∼30 kg/500 m2. Our work also highlights three important results regarding the impacts of fishing and fisheries management on herbivorous fish populations: (i) size structure was heavily skewed toward smaller individuals, with fishes less than (20 cm) accounting for 81.1% of the population in heavily fished OA reefs vs. 52.8% at unfished NT reefs, (ii) biomass of larger herbivore individuals (>35 cm) accounted for less than 1% of the total biomass in OA reefs vs. 37% at NT reefs, and (iii) large-bodied target species, Cetoscarus bicolor, Naso unicorn, and Kyphosus spp., accounting for 15.9% of the total biomass at NT reefs on average, while they were virtually absent from OA reefs. Collectively, these findings suggest that many principal fishery species in the central-northern regions of the GoA have been overexploited, which in turn can lead to reef degradation. Therefore, there is an urgent need to develop a participatory management approach and enforce restrictions on destructive fishing gear in order to promote recovery of herbivore biomass.

Highlights

Large-scale assessment of the status of herbivorous fishes in the northern Red Sea.

Comparison of herbivorous fish assemblages across three levels of fishing pressure.

Large-bodied herbivore species were either rare or absent at heavily fished reefs.

Loss of these key herbivores may boost algal dominance, thus diminish reef functionality.

Promoting local community participation in the fishery management process.