bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical and demographic correlates of accelerometer-measured physical activity in participants enrolled in the OPTIMISE HFpEF study
Authors: Lin Helen , Hartley Peter , Forsyth Faye , Pilling Mark , Hobbs F D Richard , Taylor Clare J , Schiff Rebekah , Deaton Christi 
Published: March 2021

AbstractAimsThis study aimed to measure physical activity (PA) in participants with suspected heart failure with preserved ejection fraction (HFpEF) and assess associations between PA and participant characteristics.Methods and resultsAdults with presumed HFpEF were recruited and received diagnostic evaluation and clinical assessment. Physical activity was objectively measured using accelerometers over 7 days. To examine predictors of PA, a best subset analysis was used, with the optimal model defined as that with the lowest Bayesian information criterion. One hundred and twenty-four participants with presumed HFpEF who had valid accelerometer data were included in this study. Seventy-six were confirmed by a cardiologist as meeting the European Society of Cardiology diagnosis criteria for HFpEF. The median age of all participants was 80.1 years, and 47.4% were female. Patients spent most of each 24-h period at low-intensity PA and few or no durations at high-intensity PA, with lower activity for those with HFpEF. Gait speed was the best univariate correlate of activity levels (adjusted R2 0.29). The optimal model using best subsets regression included six variables and improved adjusted R2 to 0.47. In the model, lower levels of PA were associated with slower gait speed, lower levels of anxiety, higher levels of depression, past smoking history, a confirmed HFpEF diagnosis, and higher body mass index.ConclusionParticipants demonstrated very low PA levels. The study has identified important patient characteristics associated with PA, which may help to identify those most in need of interventions. Notably, participants with confirmed HFpEF were more inactive than participants with other heart failure phenotypes.
Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition
Authors: Zhang Chuwen , Meckenstock Rainer U , Weng Shengze , Wei Guangshan , Hubert Casey R J , Wang Jiang-Hai , Dong Xiyang 
Published: March 2021

ABSTRACTMarine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.
Selection and characterization of twoBacillus thuringiensisstrains showing nematicidal activity againstCaenorhabditis elegansandMeloidogyne incognita
Authors: Verduzco-Rosas Luis A , García-Suárez Rosalina , López-Tlacomulco José J , Ibarra Jorge E 
Published: March 2021

AbstractBacillus thuringiensis has been widely used as a biological control agent against insect pests. Additionally, nematicidal strains have been under investigation. In this report, 310 native strains of B. thuringiensis against Caenorhabditis elegans were tested. Only the LBIT-596 and LBIT-107 strains showed significant mortality. LC50s of spore-crystal complexes were estimated at 37.18 and 31.89 μg/mL for LBIT-596 and LBIT-107 strains, respectively, while LC50s of partially purified crystals was estimated at 23.76 and 20.25 μg/mL for LBIT-596 and LBIT-107, respectively. The flagellin gene sequence and plasmid patterns indicated that LBIT-596 and LBIT-107 are not related to each other. Sequences from internal regions of a cry5B and a cyt1A genes were found in the LBIT-596 strain, while a cry21A, a cry14A and a cyt1A genes were found in the LBIT-107 strain. Genome sequence of the LBIT-107 strain showed new cry genes, along with other virulence factors, hence, total nematicidal activity of the LBIT-107 strain may be the result of a multifactorial effect. The highlight of this contribution is that translocation of spore-crystal suspensions of LBIT-107 into tomato plants inoculated at their rhizosphere decreased up to 90% the number of galls of Meloidogyne incognita, perhaps the most important nematode pest in the world.
X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters
Authors: Brekke Thomas D , Moore Emily C , Campbell-Staton Shane C , Callahan Colin M , Cheviron Zachary A , Good Jeffrey M 
Published: March 2021

AbstractEmbryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.
Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)
Authors: Wang Xuewen , Chen Shiyu , Ma Xiao , Yssel Anna E J , Chaluvadi Srinivasa R , Johnson Matthew S , Gangashetty Prakash , Hamidou Falalou , Sanogo Moussa D , Zwaenepoel Arthur , Wallace Jason , de Peer Yves , Bennetzen Jeffrey L , Van Deynze Allen 
Published: March 2021

Abstract

Background
Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement.

Findings
We sequenced the fonio genome with long-read SMRT-cell technology, yielding a ∼761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of &gt;99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by ∼4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence ∼3.1 million years ago. The repeat content (&gt;49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (∼6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains.

Conclusions
We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.
Bulk modulus for fluid-saturated rocks at intermediate frequencies: modification of squirt flow model proposed by Gurevich et al.
Authors: Zhao Liming , Chen Tongjun , Tang Genyang 
Published: March 2021

SUMMARY
Squirt flow is an essential cause of wave dispersion and attenuation in saturated rocks. The squirt flow model, proposed by Gurevich et al., has been widely applied to explain the wave dispersion and associated attenuation for saturated rocks at sonic and seismic frequency bands. In this model, the saturated bulk modulus is obtained by taking the partially relaxed frame bulk modulus as the dry frame modulus into Gassmann's formula with the mineral bulk modulus as the matrix bulk modulus. However, because of the weakening effect of soft pores on rock matrix bulk modulus, the model cannot accurately predict the saturated bulk modulus when the soft-pore fraction (the ratio of the soft porosity to total porosity) becomes large. We modified this model following Gurevich et al. by setting a different boundary condition. The modified squirt flow model can obtain correct saturated bulk modulus for large soft-pore fractions in the full range of frequencies, showing excellent consistency with the predictions of Gassmann, Mavko & Jizba (modified) at both low- and high-frequency limits, respectively. Modelling results show that the saturated bulk moduli and their dispersions calculated by the original and modified models exhibit little difference when the soft-pore fraction is small. Under this condition, the original model is as effective and accurate as the modified one. When the soft-pore fraction becomes larger, the differences in the bulk moduli and their dispersions become substantial, suggesting the original model is not applicable any longer. Furthermore, the differences calculated for the intermediate frequency range is even more obvious than other ranges, suggesting that the modified model should be used to calculate the bulk modulus and the dispersion in this frequency range. In summary, the modified squirt flow model can extend the original model's applicable range in terms of soft-pore fraction and has a potential application in rocks having a relatively large amount of soft-pore fraction such as basalts.
Imaging of a magma system beneath the Merapi Volcano complex, Indonesia, using ambient seismic noise tomography
Authors: Yudistira T , Metaxian J-P , Putriastuti M , Widiyantoro S , Rawlinson N , Beauducel F , Zulfakriza Z , Nugraha A D , Laurin A , Fahmi A A , Budi-Santoso A 
Published: March 2021

SUMMARYMt Merapi, which lies just north of the city of Yogyakarta in Java, Indonesia, is one of the most active and dangerous volcanoes in the world. Thanks to its subduction zone setting, Mt Merapi is a stratovolcano, and rises to an elevation of 2968 m above sea level. It stands at the intersection of two volcanic lineaments, Ungaran–Telomoyo–Merbabu–Merapi (UTMM) and Lawu–Merapi–Sumbing–Sindoro–Slamet, which are oriented north–south and west–east, respectively. Although it has been the subject of many geophysical studies, Mt Merapi's underlying magmatic plumbing system is still not well understood. Here, we present the results of an ambient seismic noise tomography study, which comprise of a series of Rayleigh wave group velocity maps and a 3-D shear wave velocity model of the Merapi–Merbabu complex. A total of 10 months of continuous data (October 2013–July 2014) recorded by a network of 46 broad-band seismometers were used. We computed and stacked daily cross-correlations from every pair of simultaneously recording stations to obtain the corresponding inter-station empirical Green's functions. Surface wave dispersion information was extracted from the cross-correlations using the multiple filtering technique, which provided us with an estimate of Rayleigh wave group velocity as a function of period. The group velocity maps for periods 3–12 s were then inverted to obtain shear wave velocity structure using the neighbourhood algorithm. From these results, we observe a dominant high velocity anomaly underlying Mt Merapi and Mt Merbabu with a strike of 152°N, which we suggest is evidence of old lava dating from the UTMM double-chain volcanic arc which formed Merbabu and Old Merapi. We also identify a low velocity anomaly on the southwest flank of Merapi which we interpret to be an active magmatic intrusion.
Mevolectin specificity toward high-mannose structures with terminal αMan(1,2)αMan residues and its implication to inhibition of the entry ofMycobacterium tuberculosisinto macrophages
Authors: Sivaji Nukathoti , Harish Nikitha , Singh Samsher , Singh Amit , Vijayan Mamannamana , Surolia Avadhesha 
Published: March 2021

AbstractMannose-binding lectins can specifically recognize and bind complex glycan structures on pathogens and have potential as antiviral and antibacterial agents. We previously reported the structure of a lectin from an archaeal species, Mevo lectin, which has specificity toward terminal α1,2 linked manno-oligosaccharides. Mycobacterium tuberculosis expresses mannosylated structures including lipoarabinomannan (ManLAM) on its surface and exploits C-type lectins to gain entry into the host cells. ManLAM structure has mannose capping with terminal αMan(1,2)αMan residues and is important for recognition by innate immune cells. Here, we aim to address the specificity of Mevo lectin toward high-mannose type glycans with terminal αMan(1,2)αMan residues and its effect on M. tuberculosis internalization by macrophages. Isothermal titration calorimetry studies demonstrated that Mevo lectin shows preferential binding toward manno-oligosaccharides with terminal αMan(1,2)αMan structures and showed a strong affinity for ManLAM, whereas it binds weakly to Mycobacterium smegmatis lipoarabinomannan, which displays relatively fewer and shorter mannosyl caps. Crystal structure of Mevo lectin complexed with a Man7D1 revealed the multivalent cross-linking interaction, which explains avidity-based high-affinity for these ligands when compared to previously studied manno-oligosaccharides lacking the specific termini. Functional studies suggest that M. tuberculosis internalization by the macrophage was impaired by binding of Mevo lectin to ManLAM present on the surface of M. tuberculosis. Selectivity shown by Mevo lectin toward glycans with terminal αMan(1,2)αMan structures, and its ability to compromise the internalization of M. tuberculosis in vitro, underscore the potential utility of Mevo lectin as a research tool to study host-pathogen interactions.
Voluntary fishing restrictions alone do not promote growth of bryozoan-dominated biogenic habitat on the Otago shelf, southeastern New Zealand
Authors: Mello H Lee , Smith Abigail M , Wood Anna C L 
Published: March 2021

AbstractOn the continental shelf, New Zealand bryozoans dominate ecologically-important three-dimensional benthic habitat providing structural complexity which hosts a wide variety of fauna, including economically valuable species (e.g. oysters and blue cod). The association between these species and bryozoan-dominated biogenic habitat commonly results in trawling damage to the benthos; eliminating pressure from destructive fishing practices could support bryozoan regrowth. In 2002, a voluntary fishing restriction was designated over part of one such bryozoan-dominated biogenic habitat, but the efficacy of this ban has not been assessed. Statutory marine protected areas have been proposed in the same area; they aim to achieve bryozoan protection and recovery. A comparison of the bryozoan fauna using benthic images from 2003 and 2019 from the Otago shelf, South Island, New Zealand/Te Waipounamu, Aotearoa shows that a 17-year voluntary fishing ban has been ineffective at increasing the cover and richness of bryozoan-dominated biogenic habitat on the Otago shelf. This study provides a baseline for future monitoring and develops useful metrics for recovery, while calling for further research on the biology and ecology of habitat-forming bryozoans.
Quantifying the contribution of modifiable risk factors to socio-economic inequities in cancer morbidity and mortality: a nationally representative population-based cohort study
Authors: Nejatinamini Sara , Godley Jenny , Minaker Leia M , Sajobi Tolulope T , McCormack Gavin R , Cooke Martin J , Nykiforuk Candace I J , Koning Lawrence de , Olstad Dana Lee 
Published: March 2021

Abstract

Background
Compared with those with a higher socio-economic position (SEP), individuals with a lower SEP have higher cancer morbidity and mortality. However, the contribution of modifiable risk factors to these inequities is not known. This study aimed to quantify the mediating effects of modifiable risk factors to associations between SEP and cancer morbidity and mortality.

Methods
This study used a prospective observational cohort design. We combined eight cycles of the Canadian Community Health Survey (2000/2001–2011) as baseline data to identify a cohort of adults (≥35 years) without cancer at the time of survey administration (n = 309 800). The cohort was linked to the Discharge Abstract Database and the Canadian Mortality Database for cancer morbidity and mortality ascertainment. Individuals were followed from the date they completed the Canadian Community Health Survey until 31 March 2013. Dates of individual first hospitalizations for cancer and deaths due to cancer were captured during this time period. SEP was operationalized using a latent variable combining measures of education and household income. Self-reported modifiable risk factors, including smoking, excess alcohol consumption, low fruit-and-vegetable intake, physical inactivity and obesity, were considered as potential mediators. Generalized structural equation modelling was used to estimate the mediating effects of modifiable risk factors in associations between low SEP and cancer morbidity and mortality in the total population and stratified by sex.

Results
Modifiable risk factors together explained 45.6% of associations between low SEP and overall cancer morbidity and mortality. Smoking was the most important mediator in the total population and for males, accounting for 15.5% and 40.2% of the total effect, respectively. For females, obesity was the most important mediator.

Conclusions
Modifiable risk factors are important mediators of socio-economic inequities in cancer morbidity and mortality. Nevertheless, more than half of the variance in these associations remained unexplained. Midstream interventions that target modifiable risk factors may help to alleviate inequities in cancer risk in the short term. However, ultimately, upstream interventions that target structural determinants of health are needed to reduce overall socio-economic inequities in cancer morbidity and mortality.
IL-6: from arthritis to CAR-T-cell therapy and COVID-19
Authors: Kishimoto Tadamitsu 
Published: March 2021

AbstractBlockade of IL-6 function by an anti-IL-6 receptor (IL-6R) antibody (tocilizumab, trade name Actemra) has been shown to be effective for the treatment of chronic autoimmune inflammatory diseases including rheumatoid arthritis. Interestingly, treatment with tocilizumab has also been found to alleviate the cytokine storm induced by chimeric antigen receptor (CAR)-T-cell therapy. Patients with serious cases of coronavirus disease 2019 (COVID-19) exhibit cytokine release syndrome (CRS), which suggested that tocilizumab might be an effective therapeutic for serious cases of COVID-19. In the first part of this short review, the therapeutic effect of tocilizumab for the disease induced by IL-6 overproduction is described. CRS induced by CAR-T-cell therapy and COVID-19 is then discussed.
Systematics of the rodent genusNeacomysThomas (Cricetidae: Sigmodontinae): two new species and a discussion on carotid patterns
Authors: Caccavo Aldo , Weksler Marcelo 
Published: March 2021

AbstractThe taxonomy of the oryzomyine genus Neacomys currently is in a state of flux: systematic studies in the last 20 years increased its diversity from four to 16 species, with an additional several undescribed phylogenetic lineages. Despite this progress, morphological variation and species limits remain poorly known for several species groups and complexes within the genus, such as N. tenuipes, N. musseri, and N. dubosti. Here we analyze the variation of morphological characters and morphometric patterns of two new candidate species of Neacomys for northern Venezuela and Pará state, Brazil, that are characterized by the presence of derived carotid circulation, a rare character state for the genus. Analyzed material included holotypes, type series, and/or topotypes of almost all described species of Neacomys, including type series of N. musseri, the holotype of N. tenuipes, and sequenced specimens of N. xingu. Qualitative comparison showed that 25 characters are informative for the distinction of the two new forms, and morphometric analyses corroborated the morphological separation of the new species. Results also point that N. tenuipes might represent a species complex. The new forms are sympatric with other species, including N. tenuipes and N. xingu, and can be identified by a suite of morphological characters, including the presence of a derived carotid pattern and, for the Pará form, by a unique morphology of the first upper molar. We review the occurrence of carotid circulation patterns within Sigmodontinae and discuss its use for the systematics of the subfamily. Further studies involving the new Neacomys species will contribute to understanding the biogeographic patterns and evolutionary trends within this distinct and diverse genus.