bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation of the Allele Number in a Natural Population by the Method of Isofemale Lines
Authors: Capy P , Rouault J
Published: January 2021

The number of alleles present in a natural population of unknown structure is estimated using a sequential sampling procedure applied to isofemale lines. Two questions are raised: how many individuals per isofemale line must be assayed and how many isofemale lines must be sampled to get an adequate sample to estimate the number of alleles, at a given risk, of the natural population? On the one hand, we show that when wild females are inseminated once, only two individuals per line are required. On the other hand, the number of isofemale lines that must be sampled depends on the risk chosen of losing an allele, on the number of alleles present in the population and on their drawing probabilities. When the population structure is known, an accurate answer can be provided. For an unknown population structure, one general sequential sampling previously described by J. Rouault and P. Capy is proposed to estimate the number of alleles in the population from data on isofemale lines.
A genetic analysis of the rose-gespleten region (68C8-69B5) of Drosophila melanogaster.
Authors: Hoogwerf A M , Akam M , Roberts D
Published: January 2021

We describe a genetic analysis of the region 68C8-69B5 defined by Df(3L)vin-7. We have induced 35 new lethal mutations in this region, which together with 20 existing lethal mutations, visible mutations, genes identified by protein products and one gene deduced from complementation data fall into 37 complementation groups in this 35-band interval. Using existing and newly induced deficiencies we have assigned these to 11 intervals defined by deficiency breakpoints. Those mutations which fell in the same breakpoint interval as the Lsp-2 gene, which codes for the abundant larval serum protein 2, were the subject of detailed study. None was rescued by the active Lsp-2 gene transformed on to chromosome II and we conclude that, as yet, we have no lethal mutations of Lsp-2.
Transitory cis complementation: a method for providing transposition functions to defective transposons.
Authors: Hughes K T , Roth J R
Published: January 2021

A genetic complementation system is described in which the complementing components are close together in a single linear DNA fragment; the complementation situation is temporary. This system is useful for providing transposition functions to transposition-defective transposons, since transposition functions act preferentially in cis. The basic procedure involves placing a transposition-defective transposon near the gene(s) for its transposition functions on a single DNA fragment. This fragment is introduced, here by general transduction, into a new host. The transposase acts in cis to permit the defective element to transpose from the introduced fragment into the recipient chromosome. The helper genes do not transpose and are lost by degradation and segregation. The method yields single insertion mutants that lack transposase and are not subject to further transposition or chromosome rearrangement. The general procedure is applicable to other sorts of transposable elements and could be modified for use in other genetic systems.
The Mutator-Related Cy Transposable Element of Zea Mays L. Behaves as a near-Mendelian Factor.
Authors: Schnable P S , Peterson P A
Published: January 2021

The bz-rcy allele arose in a single gamete of the TEL (transposable-element laden) population, when the rcy receptor element inserted into the Bronze1 locus. This newly arisen receptor allele conditions a stable bronze kernel phenotype in the absence of the independently segregating regulatory element, Cy. In the presence of Cy, bz-rcy conditions fully colored spots on a bronze background. The spots represent clonal sectors arising from mutations of bz-rcy to Bz'. Although Cy exhibits genetic interactions with the Mutator system it differs from Mu-homologous elements in its near-Mendelian behavior which is in contrast to the non-Mendelian inheritance of Mutator and Mu-homologous elements. Evidence is presented which suggests that the timing and mode of Cy transposition differ from those of Mu1.
Surplus or surrender? Afterword to the Foreword by Neil Walker
Authors: Roughan Nicole
Published: January 2021

This Afterword argues that Neil Walker’s powerful and expansive “sovereignty frame” renders sovereignty with an air of inevitability that risks misrecognizing justifiable claims against sovereignty itself. The frame wraps sovereignty in constitutionalism in ways that gloss over critical attention to both sovereignty’s coercive element and its groundedness in physical space. I argue that the effect of an expansively constitutionalized sovereignty frame reduces, absorbs, or crowds out articulations of other ways to conceptualize relations among and between people in polities and the places in which they are grounded, most notably those examined in Indigenous legal and political theory. The framing of sovereignty may also serve to foreclose its claiming, so that an apparent surplus of sovereignty masks deep and justifiable incompatibilities, tensions, and genuine contestations that cannot be explained as an excess or surfeit.
Surgery for mediastinal neurogenic tumours: a 25-year single-centre retrospective study
Authors: Lacquet Mathieu , Moons Johnny , Ceulemans Laurens J , De Leyn Paul , Van Raemdonck Dirk
Published: January 2021

OBJECTIVES

Mediastinal neurogenic tumours are uncommon and often benign neoplasms mostly located in the posterior mediastinum and usually diagnosed incidentally. We reviewed our results after surgical resection. We compared patient characteristics and tumour nature between children and adults. Differences between thoracoscopic and open approach were analysed.

METHODS

Departmental thoracic surgical database was queried for primary mediastinal neurogenic tumours resected between 1992 and 2017. Data included demographics, pathology, tumour nature, symptoms, surgical approach and postoperative morbidity/mortality.

RESULTS

Fifty-one patients (8 children and 43 adults) underwent tumour resection. Pathology revealed nerve sheath tumour in 1 child (12.5%) versus 36 adults (83.7%; P < 0.001) and ganglion cell tumour in 7 (87.5%) versus 5 (11.6%; P < 0.001). Two adults had a paraganglioma. Malignancy was present in 2 children (25%) versus 2 adults (4.6%; P = 0.049). All malignant tumours caused symptoms while most patients with benign tumours (38/47) were asymptomatic (P < 0.001). Surgical approach included thoracotomy, thoracoscopy and cervicotomy (n = 19/31/1) of which 2 were combined neurosurgical approach. All malignant tumours were approached via thoracotomy while the majority of patients with benign tumours (31/47) underwent thoracoscopy (P = 0.007). No significant difference was noted in overall morbidity between thoracoscopic versus open approach (45.2% vs 42.1%; P = 0.83). Hospital stay was significantly shorter following thoracoscopy (7.4 ± 3.3 vs 13.1 ± 9.8 days; P = 0.001).

CONCLUSIONS

Children carry a higher incidence to present with a malignant tumour originating from ganglion cells while most tumours in adults are benign, originating from the nerve sheath. The majority of patients with mediastinal neurogenic tumours are asymptomatic. Most tumours are amenable for thoracoscopic resection.
Contribution of facility level factors to variation in antibiotic use in long-term care facilities: a national cohort study
Authors: Sluggett Janet K , Moldovan Max , Lang Catherine , Lynn David J , Papanicolas Lito E , Crotty Maria , Whitehead Craig , Rogers Geraint B , Wesselingh Steve L , Inacio Maria C
Published: January 2021

Objectives

To examine national variation in systemic antibiotic use in long-term care facilities (LTCFs) and identify facility characteristics associated with antibiotic utilization.

Methods

This retrospective cohort study included 312 375 residents of 2536 Australian LTCFs between 2011 and 2016. LTCFs were categorized as low, medium or high antibiotic use facilities according to tertiles of DDDs of systemic antibiotics dispensed per 1000 resident-days. Multivariable logistic regression estimated the associations between facility characteristics (ownership, size, location, medication quality indicator performance, prevalence of after-hours medical practitioner services) and antibiotic use (low versus high).

Results

LTCFs in the lowest and highest antibiotic use categories received a median of 54.3 (IQR 46.5–60.5) and 106.1 (IQR 95.9–122.3) DDDs/1000 resident-days, respectively. Compared with not-for-profit LTCFs in major cities, government-owned non-metropolitan LTCFs were less likely to experience high antibiotic use [adjusted OR (aOR) 0.47, 95% CI 0.24–0.91]. LTCFs with 69–99 residents were less likely to experience high antibiotic use (aOR 0.69, 95% CI 0.49–0.97) than those with 25–47 residents annually. Greater prevalence of medical practitioner services accessed after-hours was associated with high antibiotic use [aOR 1.10 (per 10% increase in after-hours services), 95% CI 1.01–1.21]. South Australian LTCFs (aOR 2.17, 95% CI 1.38–3.39) were more likely, while Queensland (0.43, 95% CI 0.30–0.62) and Western Australian (aOR 0.34, 95% CI 0.21–0.57) LTCFs were less likely to experience high antibiotic use than New South Wales LTCFs.

Conclusions

Considerable facility level variation in systemic antibiotic use was observed across Australian LTCFs. Identification of facility characteristics associated with antibiotic use provides a basis for targeted stewardship initiatives.
Trade-Offs Between Harms and Benefits of Different Breast Cancer Screening Intervals Among Low-Risk Women
Authors: van Ravesteyn Nicolien T , Schechter Clyde B , Hampton John M , Alagoz Oguzhan , van den Broek Jeroen J , Kerlikowske Karla , Mandelblatt Jeanne S , Miglioretti Diana L , Sprague Brian L , Stout Natasha K , de Koning Harry J , Trentham-Dietz Amy , Tosteson Anna N A ,   the Breast Cancer Surveillance Consortium and the Cancer Intervention and Surveillance Modeling Network
Published: January 2021

Background

A paucity of research addresses breast cancer screening strategies for women at lower-than-average breast cancer risk. The aim of this study was to examine screening harms and benefits among women aged 50-74 years at lower-than-average breast cancer risk by breast density.

Methods

Three well-established, validated Cancer Intervention and Surveillance Network models were used to estimate the lifetime benefits and harms of different screening scenarios, varying by screening interval (biennial, triennial). Breast cancer deaths averted, life-years and quality-adjusted life-years gained, false-positives, benign biopsies, and overdiagnosis were assessed by relative risk (RR) level (0.6, 0.7, 0.85, 1 [average risk]) and breast density category, for US women born in 1970.

Results

Screening benefits decreased proportionally with decreasing risk and with lower breast density. False-positives, unnecessary biopsies, and the percentage overdiagnosis also varied substantially by breast density category; false-positives and unnecessary biopsies were highest in the heterogeneously dense category. For women with fatty or scattered fibroglandular breast density and a relative risk of no more than 0.85, the additional deaths averted and life-years gained were small with biennial vs triennial screening. For these groups, undergoing 4 additional screens (screening biennially [13 screens] vs triennially [9 screens]) averted no more than 1 additional breast cancer death and gained no more than 16 life-years and no more than 10 quality-adjusted life-years per 1000 women but resulted in up to 232 more false-positives per 1000 women.

Conclusion

Triennial screening from age 50 to 74 years may be a reasonable screening strategy for women with lower-than-average breast cancer risk and fatty or scattered fibroglandular breast density.
CYP51A polymorphisms ofAspergillus fumigatusin lung transplant recipients: Prevalence, correlation with phenotype, and impact on outcomes
Authors: Henry Benoît , Guenette Alexis , Cheema Faiqa , Pérez-Cortés Armelle , McTaggart Lisa , Mazzulli Tony , Singer Lianne , Keshavjee Shaf , Kus Julianne V , Husain Shahid
Published: January 2021

Azole resistance in Aspergillus fumigatus is increasing worldwide and can affect prognosis. It is mostly mediated by cytochrome P51 (CYP51) mutations. In lung transplant recipients (LTR), little is known regarding the prevalence and clinical impact of CYP51 mutations. One hundred thirty-one consecutive A. fumigatus isolates from 103 patients were subjected to CYP51A genotyping through PCR and sequencing. Antifungal susceptibility testing was performed using the Sensititre YeastOne YO-9© broth microdilution technique. Correlations between genotype, phenotype, clinical manifestations of Aspergillus infection, and clinical outcomes were made. Thirty-four (26%) isolates harbored mutations of CYP51A; N248K (n = 14) and A9T (n = 12) were the most frequent. Three isolates displayed multiple point mutations. No significant influences of mutational status were identified regarding azole MICs, the clinical presentation of Aspergillus disease, 1-year all-cause mortality, and clinical outcomes of invasive forms. In the specific context of lung transplant recipients, non-hotspot CYP51A-mutated isolates are regularly encountered; this does not result in major clinical consequences or therapeutic challenges.

Lay Summary

In 131 isolates of Aspergillus fumigatus isolates originating from 103 lung transplant recipients, the CYP51A polymorphism rate was 26%, mostly represented by N248K and A9T mutations. These mutations, however, did not significantly impact azoles minimal inhibitory concentrations or clinical outcomes.
Impact of mass transfer schemes on mass–orbital period relation
Authors: Zhang Yangyang , Chen Hailiang , Chen Xuefei , Han Zhanwen
Published: January 2021

Binaries that evolved from red giant (RG) binaries through stable Roche lobe overflow follow the mass–orbital period relation if the donor’s core is degenerate. This relation is important for the studies of long orbital period blue stragglers, subdwarf B stars, and millisecond pulsars. To examine the influence of mass transfer schemes on this relation, we model the evolution of RG binaries at metallicity Z = 0.02 and Z = 0.001 with two different mass transfer schemes. In one of the scheme, it is assumed that mass transfer only occurs when the donor star’s radius is just larger than its Roche lobe radius (‘classical’ scheme). In another mass transfer scheme, the mass transfer can also occur when the donor’s radius is smaller than its Roche lobe radius as proposed by Ritter (1988) and further studied by Kolb & Ritter (1990; ‘Kolb’ scheme). We find that the mass transfer scheme has a significant influence on the evolution of RG binaries. In these RG binaries initiating mass transfer on the upper part of the RG branch, the final donor masses are smaller and orbital periods are larger in the models with the ‘Kolb’ scheme, compared with the models with the ‘classical’ scheme. The difference between orbital periods (donor masses) at the end of mass transfer under two different mass transfer schemes can be up to 500 d (0.04 M⊙) for the same donor mass (orbital period). The mass–orbital period relation from these models with the ‘Kolb’ scheme is above the relation from models with the ‘classical’ scheme. Additionally, similar to previous studies, we find that the final orbital period at metallicity Z = 0.02 is larger than that at metallicity Z = 0.001 for a given donor mass.
Evolutionary map of the Universe (EMU): Compact radio sources in the scorpio field towards the galactic plane
Authors: Riggi S , Umana G , Trigilio C , Cavallaro F , Ingallinera A , Leto P , Bufano F , Norris R P , Hopkins A M , Filipović M D , Andernach H , van Loon J Th , Michałowski M J , Bordiu C , An T , Buemi C , Carretti E , Collier J D , Joseph T , Koribalski B S , Kothes R , Loru S , McConnell D , Pommier M , Sciacca E , Schillirò F , Vitello F , Warhurst K , Whiting M
Published: January 2021

We present observations of a region of the Galactic plane taken during the Early Science Program of the Australian Square Kilometre Array Pathfinder (ASKAP). In this context, we observed the scorpio field at 912 MHz with an uncompleted array consisting of 15 commissioned antennas. The resulting map covers a square region of ∼40 deg2, centred on (l, b)  = (343.5°, 0.75°), with a synthesized beam of 24 × 21 arcsec2 and a background rms noise of 150–200 μJy beam−1, increasing to 500–600 μJy beam−1 close to the Galactic plane. A total of 3963 radio sources were detected and characterized in the field using the caesar source finder. We obtained differential source counts in agreement with previously published data after correction for source extraction and characterization uncertainties, estimated from simulated data. The ASKAP positional and flux density scale accuracy were also investigated through comparison with previous surveys (MGPS, NVSS) and additional observations of the scorpio field, carried out with ATCA at 2.1 GHz and 10 arcsec spatial resolution. These allowed us to obtain a measurement of the spectral index for a subset of the catalogued sources and an estimated fraction of (at least) 8 per cent of resolved sources in the reported catalogue. We cross-matched our catalogued sources with different astronomical data bases to search for possible counterparts, finding ∼150 associations to known Galactic objects. Finally, we explored a multiparametric approach for classifying previously unreported Galactic sources based on their radio-infrared colours.
Non-thermal neutrinos created by shock acceleration in successful and failed core-collapse supernova
Authors: Nagakura Hiroki , Hotokezaka Kenta
Published: January 2021

We present a comprehensive study of neutrino shock acceleration in core-collapse supernova (CCSN). The leading players are heavy leptonic neutrinos, νμ and ντ; the former and latter potentially gain the energy up to ∼100 and ∼200 MeV, respectively, through the shock acceleration. Demonstrating the neutrino shock acceleration by Monte Carlo neutrino transport, we make a statement that it commonly occurs in the early post-bounce phase (≲50 ms after bounce) for all massive stellar collapse experiencing nuclear bounce and would reoccur in the late phase (≳100 ms) for failed CCSNe. This opens up a new possibility to detect high energy neutrinos by terrestrial detectors from Galactic CCSNe; hence, we estimate the event counts for Hyper(Super)-Kamiokande, DUNE, and JUNO. We find that the event count with the energy of ≳80 MeV is a few orders of magnitude higher than that of the thermal neutrinos regardless of the detectors, and muon production may also happen in these detectors by νμ with the energy of ≳100 MeV. The neutrino signals provide a precious information on deciphering the inner dynamics of CCSN and placing a constraint on the physics of neutrino oscillation; indeed, the detection of the high energy neutrinos through charged current reaction channels will be a smoking gun evidence of neutrino flavour conversion.
Functional Diversification, Redundancy, and Epistasis among Paralogs of the Drosophila melanogaster Obp50a–d Gene Cluster
Authors: Johnstun Joel A , Shankar Vijay , Mokashi Sneha S , Sunkara Lakshmi T , Ihearahu Ugonna E , Lyman Roberta L , Mackay Trudy F C , Anholt Robert R H
Published: January 2021

Large multigene families, such as the insect odorant-binding proteins (OBPs), are thought to arise through functional diversification after repeated gene duplications. Whereas many OBPs function in chemoreception, members of this family are also expressed in tissues outside chemosensory organs. Paralogs of the Obp50 gene cluster are expressed in metabolic and male reproductive tissues, but their functions and interrelationships remain unknown. Here, we report the genetic dissection of four members of the Obp50 cluster, which are in close physical proximity without intervening genes. We used CRISPR technology to excise the entire cluster while introducing a PhiC31 reintegration site to reinsert constructs in which different combinations of the constituent Obp genes were either intact or rendered inactive. We performed whole transcriptome sequencing and assessed sexually dimorphic changes in transcript abundances (transcriptional niches) associated with each gene-edited genotype. Using this approach, we were able to estimate redundancy, additivity, diversification, and epistasis among Obp50 paralogs. We analyzed the effects of gene editing of this cluster on organismal phenotypes and found a significant skewing of sex ratios attributable to Obp50a, and sex-specific effects on starvation stress resistance attributable to Obp50d. Thus, there is functional diversification within the Obp50 cluster with Obp50a contributing to development and Obp50d to stress resistance. The deletion–reinsertion approach we applied to the Obp50 cluster provides a general paradigm for the genetic dissection of paralogs of multigene families.
A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol
Authors: Anastasakis Dimitrios G , Jacob Alexis , Konstantinidou Parthena , Meguro Kazuyuki , Claypool Duncan , Cekan Pavol , Haase Astrid D , Hafner Markus
Published: January 2021

Crosslinking and immunoprecipitation (CLIP) methods are powerful techniques to interrogate direct protein-RNA interactions and dissect posttranscriptional gene regulatory networks. One widely used CLIP variant is photoactivatable ribonucleoside enhanced CLIP (PAR-CLIP) that involves in vivo labeling of nascent RNAs with the photoreactive nucleosides 4-thiouridine (4SU) or 6-thioguanosine (6SG), which can efficiently crosslink to interacting proteins using UVA and UVB light. Crosslinking of 4SU or 6SG to interacting amino acids changes their base-pairing properties and results in characteristic mutations in cDNA libraries prepared for high-throughput sequencing, which can be computationally exploited to remove abundant background from non-crosslinked sequences and help pinpoint RNA binding protein binding sites at nucleotide resolution on a transcriptome-wide scale. Here we present a streamlined protocol for fluorescence-based PAR-CLIP (fPAR-CLIP) that eliminates the need to use radioactivity. It is based on direct ligation of a fluorescently labeled adapter to the 3′end of crosslinked RNA on immobilized ribonucleoproteins, followed by isolation of the adapter-ligated RNA and efficient conversion into cDNA without the previously needed size fractionation on denaturing polyacrylamide gels. These improvements cut the experimentation by half to 2 days and increases sensitivity by 10–100-fold.
Using datasets to ascertain the generalizability of clinical cohorts: the example of the European QUALity study on the treatment of advanced chronic kidney disease
Authors: Rao Anirudh , MacNeill Stephanie J , van de Luijtgaarden Moniek W M , Chesnaye Nicholas C , Drechsler Christiane , Wanner Chistoph , Torino Claudia , Postorino Maurizio , Szymczak Maciej , Evans Marie , Dekker Friedo W , Jager Kitty J , Ben-Shlomo Yoav , Caskey Fergus J
Published: January 2021

Background

Cohort studies are among the most robust of observational studies but have issues with external validity. This study assesses threats to external validity (generalizability) in the European QUALity (EQUAL) study, a cohort study of people >65 years of age with Stage 4/5 chronic kidney disease.

Methods

Patients meeting the EQUAL inclusion criteria were identified in The Health Improvement Network database and stratified into those attending renal units, a secondary care cohort (SCC) and a not primary care cohort (PCC). Survival, progression to renal replacement therapy (RRT) and hospitalization were compared.

Results

The analysis included 250, 633 and 2464 patients in EQUAL, PCC and SCC. EQUAL had a higher proportion of men compared with PCC and SCC (60.0% versus 34.8% versus 51.4%). Increasing age ≥85 years {odds ratio [OR] 0.25 [95% confidence interval (CI) 0.15–0.40]} and comorbidity [Charlson Comorbidity Index ≥4, OR 0.69 (95% CI 0.52–0.91)] were associated with non-participation in EQUAL. EQUAL had a higher proportion of patients starting RRT at 1 year compared with SCC (8.1% versus 2.1%; P < 0.001). Patients in the PCC and SCC had increased risk of hospitalization [incidence rate ratio 1.76 (95% CI 1.27–2.47) and 2.13 (95% CI 1.59–2.86)] and mortality at 1 year [hazard ratio 3.48 (95% CI 2.1–5.7) and 1.7 (95% CI 1.1–2.7)] compared with EQUAL.

Conclusions

This study provides evidence of how participants in a cohort study can differ from the broader population of patients, which is essential when considering external validity and application to local practice.
The Shifting Life Course Patterns of Wage Inequality
Authors: Cheng Siwei
Published: January 2021

Prior inequality literature has mainly focused on the period trends of inequality. This paper advances this literature by adopting a cohort approach to examine the age and cohort patterns of wage inequality. Employing a trajectory-based analytic framework to analyze almost 50 years of longitudinal data from the Panel Study of Income Dynamics, I found that the life course patterns of inequality among American men have shifted across cohorts on both aggregate level and microlevel. The cumulative wage advantage associated with higher educational attainment has become more important across cohorts. Wage volatility has increased from earlier to later cohorts and the trend varies by age. The increase in volatility occurred first among mid-career workers and then among early-career workers. Additional analysis suggests that these cohort shifts differ by educational and occupational groups. The findings highlight the value of a cohort and life course approach for studying the process of social stratification.
The Value of Obtaining Colonic Mucosal Biopsies of Grossly Normal Tissue in Pediatric Patients
Authors: Glass Joshua , Alcalá Héctor E. , Tobin Michelle
Published: January 2021

Objectives:

Current practice during pediatric colonoscopy is to obtain random colonic biopsies, even from normal appearing tissue. The majority of literature published on colonic biopsy practice analyzes adults; however, limited data examines the pediatric population. The lack of standardization regarding tissue sampling during pediatric colonoscopy reinforces the necessity to study this question objectively. The aim of the present study was to assess the value of obtaining mucosal biopsies from grossly normal colonic tissue.

Methods:

A retrospective study was performed to examine the utility of obtaining colonic biopsies from normal appearing tissue. Subjects included patients who underwent colonoscopy during a 2-year period. Descriptive analyses and logistic regression models were used to determine endoscopic and histologic agreement and to characterize predictors of agreement.

Results:

The predictive value of agreement between normal appearing colonoscopies (n = 237) and histopathology was 81%. Excluding patients with inflammatory bowel disease (IBD) increased the predictive value to 85%. Two and a half percent of grossly normal colonoscopies had histological findings consistent with newly diagnosed IBD. Predictors of normal histology included abdominal pain (odds ratio [OR] 3.68, 95% CI 1.84–7.37), whereas a known diagnosis of IBD was predictive of abnormal histology (OR 0.22, 95% CI 0.08–0.67). Among the full sample, elevated inflammatory markers (OR 2.02, 95% CI 1.06–3.86) or fatigue (OR 2.60, 95% CI 1.13–5.94) were predictive of abnormal histology.

Conclusions:

Results suggest that colonic biopsies may not need to be routinely obtained from all pediatric colonoscopies, particularly in those patients with complaints of abdominal pain. Biopsies should continue to be obtained from patients with a known diagnosis of IBD, elevated inflammatory markers, or fatigue. Further studies are needed to standardize protocols for biopsy practice in pediatric colonoscopy.
Cupidesulfovibrio liaohensis gen. nov., sp. nov., a novel sulphate-reducing bacterium isolated from an oil reservoir and reclassification of Desulfovibrio oxamicus and Desulfovibrio termitidis as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov.
Authors: Wan Yun Yang , Luo Na , Liu Xiao-Li , Lai Qi-Liang , Goodfellow Michael
Published: January 2021

A novel sulphate-reducing, Gram-stain-negative, anaerobic strain, isolate XJ01T, recovered from production fluid at the LiaoHe oilfield, PR China, was the subject of a polyphasic study. The isolate together with

Desulfovibrio oxamicus

NCIMB 9442T and

Desulfovibrio termitidis

DSM 5308T formed a distinct, well-supported clade in the

Desulfovibrionaceae

16S rRNA gene tree. The taxonomic status of the clade was underscored by complementary phenotypic data. The three isolates comprising the clade formed distinct phyletic branches and were distinguished using a combination of physiological features and by low average nucleotide identity and digital DNA–DNA hybridization values. Consequently, it is proposed that isolate XJ01T represents a novel genus and species for which the name Cupidesulfovibrio liaohensis gen. nov., sp. nov. is proposed with the type strain XJ01T (=CGMCC 1.5227T=DSM 107637T). It is also proposed that

D. oxamicus

and

D. termitidis

be reclassified as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov., respectively.
Relatedness of type IV pilin PilA amongst geographically diverse Moraxella bovoculi isolated from cattle with infectious bovine keratoconjunctivitis
Authors: Angelos John A. , Clothier Kristin A. , Agulto Regina L. , Mandzyuk Boguslav , Tryland Morten
Published: January 2021

Introduction.Moraxella bovoculiis frequently isolated from the eyes of cattle with infectious bovine keratoconjunctivitis (IBK; pinkeye). As withM. bovis,which has been causally linked to IBK,M. bovoculiexpresses an RTX (repeats in the structural toxin) cytotoxin that is related toM. boviscytotoxin. Pilin, another pathogenic factor inM. bovis, is required for corneal attachment. Seven antigenically distinct pilin serogroups have been described inM. bovis.

Hypothesis/Gap Statement.Multiple different serogroups exist amongst type IV pilin encoded byM. bovis, however, it is not known whetherM. bovoculiexhibits a similar degree of diversity in type IV pilin that it encodes.

Aim.This study was done to characterize a structural pilin (PilA) encoded byM. bovoculiisolated from cases of IBK to determine if diversity exists amongst PilA sequences.

Methodology.Ninety-four isolates ofM. bovoculicollected between 2002 and 2017 from 23 counties throughout California and from five counties in four other Western states were evaluated.

Results.DNA sequencing and determination of deduced amino acid sequences revealed ten (designated groups A through J) unique PilA sequences that were ~96.1–99.3 % identical. Pilin groups A and C matched previously reported putative PilA sequences fromM. bovoculiisolated from IBK-affected cattle in the USA (Virginia, Nebraska, and Kansas) and Asia (Kazakhstan). The ten pilin sequences identified were only ~74–76 % identical to deduced amino acid sequences of putative pilin proteins identified from the previously reported whole-genome sequences ofM. bovoculiderived from deep nasopharyngeal swabs of IBK-asymptomatic cattle.

Conclusions.Compared to the diversity reported between structural pilin proteins amongst different serogroups ofM. bovis,M. bovoculiPilA from geographically diverse isolates derived from IBK-affected cattle are more conserved.
Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations
Authors: Koçhan Necla , Eskier Doğa , Suner Aslı , Karakülah Gökhan , Oktay Yavuz
Published: January 2021

SARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic that has affected millions of people worldwide, with no dedicated treatment or vaccine currently available. As pharmaceutical research against and the most frequently used tests for SARS-CoV-2 infection both depend on the genomic and peptide sequences of the virus for their efficacy, understanding the mutation rates and content of the virus is critical. Two key proteins for SARS-CoV-2 infection and replication are the S protein, responsible for viral entry into the cells, and RdRp, the RNA polymerase responsible for replicating the viral genome. Due to their roles in the viral cycle, these proteins are crucial for the fitness and infectiousness of the virus. Our previous findings had shown that the two most frequently observed mutations in the SARS-CoV-2 genome, 14408C>T in the RdRp coding region, and 23403A>G in the S gene, are correlated with higher mutation density over time. In this study, we further detail the selection dynamics and the mutation rates of SARS-CoV-2 genes, comparing them between isolates carrying both mutations, and isolates carrying neither. We find that the S gene and the RdRp coding region show the highest variance between the genotypes, and their selection dynamics contrast each other over time. The S gene displays higher positive selection in mutant isolates early on, and undergoes increasing negative selection over time, whereas the RdRp region in the mutant isolates shows strong negative selection throughout the pandemic.
State-level COVID-19 Trend Forecasting Using Mobility and Policy Data
Authors: Wang Yifei , Peng Hao (Michael) , Sha Long , Liu Zheyuan , Hong Pengyu
Published: January 2021

Abstract

The importance of pandemic forecast cannot be overemphasized. We propose an interpretable machine learning approach for forecasting pandemic transmission rates by utilizing local mobility statistics and government policies. A calibration step is introduced to deal with time-varying relationships between transmission rates and predictors. Experimental results demonstrate that our approach is able to make accurate two-week ahead predictions of the state-level COVID-19 infection trends in the US. Moreover, the models trained by our approach offer insights into the spread of COVID-19, such as the association between the baseline transmission rate and the state-level demographics, the effectiveness of local policies in reducing COVID-19 infections, and so on. This work provides a good understanding of COVID-19 evolution with respect to state-level characteristics and can potentially inform local policymakers in devising customized response strategies.
Prevalence and Factors associated with Mental health impact of COVID-19 Pandemic in Bangladesh: A survey based cross sectional study
Authors: Abir Tanvir , Kalimullah Nazmul Ahsan , Osuagwu Uchechukwu L , Nur –A Yazdani Dewan Muhammad , Husain Taha , Goson Piwuna Christopher , Basak Palash , Rahman Md Adnan , Mamun Abdullah Al , Permarupan P. Yukthamarani , Khan Md Yusuf Hossein , Agho Kingsley
Published: January 2021

Background

Feelings of isolation, insecurity, and instability triggered by COVID-19 could have a long-term impact on the mental health status of individuals. This study examined the prevalence and factors associated with the mental health symptoms of anxiety, depression, and stress during the COVID-19 pandemic in Bangladesh.

Methods

From 1st– 30thApril 2020, we used a validated self-administered questionnaire to conduct a cross-sectional study on 10,609 participants through an online survey platform. We assessed mental health status using the Depression, Anxiety, and Stress Scale (DASS-21). The total depression, anxiety, and stress subscale scores were divided into normal, mild, moderate, severe, and multinomial logistic regression was used to examine associated factors.

Results

The prevalence of depressive symptoms was 15%, 34%, and 15% for mild, moderate, and severe depressive symptoms, respectively. The prevalence of anxiety symptoms was 59% for severe anxiety symptoms, 14% for moderate anxiety symptoms, and 14% for mild anxiety symptoms while, the prevalence for stress levels were 16% for severe stress level, 22% for moderate stress level and 13% for mild stress level. Multivariate analyses revealed that the most consistent factors associated with mild, moderate, and severe of the three mental health subscales (depression, anxiety, and stress) were respondents who lived in Dhaka and Rangpur division, females, those who self-quarantine in the previous 7 days before the survey and those respondents who experienced chills, breathing difficulty, dizziness, and sore throat.

Conclusion

Our results showed that about 64%, 87%, and 61% experienced depressive symptoms, anxiety symptoms, and levels of stress, respectively. In Bangladesh, there is a need for better mental health support for females especially those that lived in Dhaka and Rangpur division and experienced chills, breathing difficulty, dizziness, and sore throat during COVID-19 and other future pandemics.
Codon composition in human oocytes reveals age-associated defects in mRNA decay
Authors: Alvarez Nehemiah S. , Brachova Pavla , Christenson Lane K.
Published: January 2021

Oocytes from women of advanced reproductive age have lower developmental potential, yet the underlying mechanisms of this phenomena are incompletely understood. Oocyte maturation is dependent upon translational control of stored maternal mRNA that were synthesized during oocyte growth. We observed that GC content of mRNA was negatively associated with half-life in oocytes from reproductively young women (< 30 years), contrastingly directly with oocytes from reproductively aged women (≥ 40 years) where mRNA half-lives were positively associated with GC nucleotide content. Additionally, we observed that mRNA half-lives were negatively associated with protein abundance in young oocytes, while GC content was positively associated with protein abundance in aged oocytes. Examination of codon composition during the GV-to-MII transition revealed that codons that facilitate rapid translation promoted mRNA stability and are considered optimal, while codons that slow translation destabilized mRNA, and are considered non-optimal. GC-containing codons were more optimal in reproductive aging, and also correlated positively with protein abundance. This study indicates that reproductive aging coincides with the stabilization of a subset of mRNA that have the potential to be over-translated during oocyte maturation, this is likely to lead to observed decreases in oocyte quality in older women. Because oocyte mRNA decay is translationally linked, this suggests that maternal aging causes defects in translation, which results in reduced translational efficiency and the retention of maternal mRNA that are normally degraded in oocytes from young women. In the case of oocytes, defects in translation can alter the RNA decay pathways and result in incorrect maternal mRNA dosage, which may negatively impact embryonic development.
The association between hidradenitis suppurativa and male and female infertility: A population‐based study
Authors: Tzur Bitan Dana , Kridin Khalaf , Hodak Emmilia , Cohen Arnon , Sherman Shany
Published: January 2021

Background

Endocrine and metabolic associations have been recently reported in patients with hidradenitis suppurativa (HS); however, fertility was only rarely investigated in women and not at all in men.

Objective

To evaluate the association of HS with male and female infertility.

Methods

A cross‐sectional, matched controlled, population‐based study was designed. The association between HS and male and female infertility was evaluated in patients with HS (n = 4191) and age‐ and gender‐matched controls (n = 20 941), while utilising the Clalit Health Services databases, the largest community‐based health maintenance organisation in Israel.

Results

Hidradenitis suppurativa was associated with infertility in males and females over all reproductive‐age groups, especially among individuals aged 36–45 years (OR 4.50, 95%CI 2.55–7.93, P < 0.001), and in female patients (OR 3.10, 95%CI 2.57–3.74, P < 0.001). After adjustment for demographic and clinical factors, the association remained significant only in females (OR 1.26 95%CI 1.04–1.55, P < 0.05).

Conclusion

Patients with HS are at increased risk of infertility, particularly females and patients in the 36‐ to 45‐year age group. Physicians should take the additional physiological and psychological burden of infertility among HS patients into account, primarily among female patients at procreative age.
Chemical composition and in vitro ruminal digestibility of Ludwigia grandiflora
Authors: Oku Misaki , Inoue Chiho , Hieda Shinya , Noma Naohiko , Nakagawa Toshinori
Published: January 2021

Ludwigia grandiflora is an amphibious plant that has been designated as a specific alien plant in Japan. Due to the risk of regeneration on land, plants are burned after eradication. Since L. grandiflora is fertile and rich in biomass, this study investigated the use of L. grandiflora as a feed for ruminants. We measured general components, detergent fiber components, and in vitro dry matter digestibility (IVDMD) using rumen microbes for three forms (terrestrial form, emergent form, and floating‐leaved form) of L. grandiflora. In addition, concentrations of hazardous metallic elements were also measured from the viewpoint of feed safety. Crude protein, neutral detergent fiber, acid detergent fiber, and acid detergent lignin were contained 10.31–14.62, 27.83–42.28, 20.54–36.05, and 6.94–18.90 (%DM), respectively. IVDMD was 50.75%–68.24%. Toxic elements such as Pb, Cd, and Hg were not detected in all forms. These results suggest that L. grandiflora could be partially used as alternative roughage for ruminants.
Adaptation and evolution of institutions and governance in community‐based conservation
Authors: Salerno Jonathan , Romulo Chelsie , Galvin Kathleen A , Brooks Jeremy , Mupeta‐Muyamwa Patricia , Glew Louise
Published: January 2021

Within conservation science and practice, community‐based conservation (CBC) includes policy and management interventions incorporating engagement or participation of local communities and resource users. Evidence across scales points to the importance of supporting local actors and management institutions for better social and ecological outcomes of CBC interventions. However, the institutional and governance processes underlying CBC outcomes remain poorly understood, specifically how institutions respond to opportunities and constraints posed by CBC. In response, this special issue ofConservation Science & Practicesolicited contributions investigating adaptation and evolution of institutions and governance in CBC. In this paper, we introduce the special issue and its 13 contributions, representing cases from Africa, Asia, and the Americas across organizational scales and resource systems. We assess the state of knowledge of CBC, identify common themes and lessons learned, and suggest future priorities for research and practice.
Extreme Wages, Performance, and Superstars in a Market for Footballers
Authors: Scarfe Rachel , Singleton Carl , Telemo Paul
Published: January 2021

We study the determinants of superstar wage effects, asking whether productivity or popularity‐based explanations are more appropriate. We use longitudinal wage and performance data for workers (players) and firms (teams) from a particular market for sports talent: Major League Soccer (MLS) in the United States. We find evidence that the top earners, whose annual salaries are mostly not accounted for by their past MLS performances, when compared to other footballers, are paid more because they attract significantly higher stadium attendances and thus revenues. There is no evidence that higher residual salary spending by the teams affects their relative performance in football terms, or that the amounts the teams spend on actual talent affect attendances. Taken together, these results suggest that a popularity‐based explanation of superstar wage effects is appropriate among the top earners in this labor market.
Skeletal deformities and meristic trait variations are common in the intertidal fish Bathygobiuscocosensis (Perciformes‐Gobiidae)
Authors: Malard Lucie , Riginos Cynthia , McGuigan Katrina
Published: January 2021

Extreme environmental conditions, such as temperature, can lead to meristic trait variation and skeletal deformities, which may have major impacts on individual fitness. As intertidal ecosystems experience rapid temperature and physicochemical fluctuations, intertidal fish living and reproducing in these environmental conditions may have phenotypes influenced by such variable environments. The impact of intertidal variability on fish development, however, has not been previously investigated. Skeletal deformities and meristic traits were assessed for Bathygobius cocosensis, a common intertidal fish living across the Indo‐Pacific region, using a clearing and staining method on 72 individuals. Over 87% of individuals presented meristic variation and over 70% exhibited at least one type of skeletal deformity, mostly recorded in the caudal fin area. The unexpected prevalence of skeletal deformities among this intertidal fish population suggests that such deformities may be suitable markers to evaluate an individual's stress exposure during development and the subsequent fitness effects.
Associations Between Trauma, Sleep, and Cognitive Impairment Among Latino and Asian Older Adults
Authors: Saadi Altaf , Cruz‐Gonzalez Mario , Hwang Andrew , Cohen Lauren , Alegria Margarita
Published: January 2021

BACKGROUND/OBJECTIVES

Trauma survivors with chronic post‐traumatic stress disorder (PTSD) have been found to have cognitive impairment. But little is known about these outcomes among Latino and Asians who comprise more than 80% of the U.S. immigrant population. They also experience disparities in PTSD and dementia care albeit increased exposure to trauma. This study aimed to (1) examine the association between trauma exposures and PTSD with cognitive impairment in a sample of Latino and Asian older adults; and (2) assess whether sleep quality attenuated the PTSD‐cognitive impairment association.

DESIGN

Cross‐sectional secondary analysis of baseline data from the Positive Minds‐Strong Bodies randomized controlled trial on disability prevention.

SETTING

Community‐based organizations serving minority or immigrant older adults in Massachusetts, New York, Florida, or Puerto Rico.

PARTICIPANTS

Hispanic/Latino and Asian/Pacific Islander adults aged 60 or older eligible per randomized controlled trial screening for elevated mood symptoms and minor‐to‐moderate physical dysfunction (n = 134 and n = 86, respectively).

MEASUREMENTS

Neuropsychiatric measures were cognitive impairment (Mini Montreal Cognitive Assessment (MoCA)), PTSD (Posttraumatic Stress Disorder Checklist for Diagnostic and Statistical Manual‐5), trauma exposure (Brief Trauma Questionnaire), depression (Patient Health Questionnaire‐9), generalized anxiety (Generalized Anxiety Disorder Scale‐7), and daytime sleepiness (Epworth Sleepiness Scale).

RESULTS

Mean age was 72.8 years and 77.5 years for the Latino and Asian groups, respectively. The Asian group was 100% immigrant, whereas 70.2% (n = 92) of the Latino group was foreign‐born. In unadjusted models, higher Posttraumatic Stress Disorder Checklist for Diagnostic and Statistical Manual‐5 scores were associated with decreased odds of normal cognitive functioning (MoCA ≥25) in the Asian group (odds ratio (95% confidence interval) = .93 (.87, .99)), but not the Latino group (odds ratio (95% confidence interval) = .99 (.95, 1.05)). This association remained significant after adjusting for covariates. Daytime sleepiness did not moderate the association between PTSD and cognitive functioning in the Asian group.

CONCLUSION

Higher PTSD symptoms were associated with cognitive impairment in Asian, but not Latino, older adults. Clinicians serving older Asians should integrate trauma and cognitive screening to ensure this growing, underserved population receives appropriate evidence‐based treatments.