bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon Neutral: The Failure of Dung Beetles (Coleoptera: Scarabaeidae) to Affect Dung-Generated Greenhouse Gases in the Pasture
Authors: Fowler Fallon , Denning Steve , Hu Shuijin , Watson Wes 
Published: July 2020

AbstractResearch suggests dung beetles can churn, aerate, and desiccate dung in ways that influence the dung and soil microbes producing greenhouse gases (GHGs). We examined the impacts of the tunneling beetle, Onthophagus taurus (Schreber), and the dwelling beetle, Labarrus pseudolividus (Balthasar), on the carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) emitted from pasture-laid bovine dung as well as their sum-total (CO2 + CH4 + N2O) effect on global warming, or their carbon dioxide equivalent (CO2e). Despite dung beetles potential effects on CH4 and N2O, the existing literature shows no ultimate CO2e reductions. We hypothesized that more dung beetles would degrade pats faster and reduce CO2e, and so we increased the average dung beetle biomass per dung volume 6.22× above previously published records, and visually documented any dung damage. However, the time effects were 2–5× greater for any GHG and CO2e (E = 0.27–0.77) than dung beetle effects alone (E = 0.09–0.24). This suggests that dung beetle communities cannot adequately reduce GHGs unless they can accelerate dung decomposition faster than time alone.
Risk of fracture in patients with non-valvular atrial fibrillation initiating direct oral anticoagulants vs. vitamin K antagonists
Authors: He Na , Dell'Aniello Sophie , Zhai Suodi , Suissa Samy , Renoux Christel 
Published: July 2020

Abstract

Aims
To determine the risk of fracture associated with direct oral anticoagulants (DOACs) compared with vitamin K antagonists (VKAs) in patients with non-valvular atrial fibrillation (NVAF), accounting for cumulative duration of use.

Methods and results
Using Quebec administrative healthcare databases, we formed a cohort of all patients aged 40 years or older newly diagnosed with NVAF, who filled a first prescription for DOACs or VKAs between 2011 and 2014. Exposure was modelled as a time-varying variable whereby patients were considered unexposed up to 180 days of cumulative duration of use (to account for a biologically meaningful exposure) and exposed thereafter. The final cohort included 10 306 new users of DOACs and 15 357 new users of VKAs. After propensity score-based fine stratification and weighting, use of DOACs for 180 days or greater was associated with a 35% decreased risk of fracture [crude incidence rates 7.5 vs. 15.3 per 1000 person-years; adjusted hazard ratio (HR) 0.65, 95% confidence interval (CI) 0.46–0.91] compared to VKA duration ≥180 days. Direct oral anticoagulants use was also associated with a lower risk of hip fracture (HR 0.51, 95% CI 0.31–0.86) compared with VKAs. There was no difference in the rate of fracture for shorter duration of use (HR 1.10; 95% CI 0.79–1.53). The risk was not modified by age, sex, chronic kidney disease, osteoporosis, history of fracture or falls.

Conclusion
Prolonged use of DOACs is associated with a lower risk of fracture compared with VKAs. These findings support the first-line recommendation for DOACs in patients with NVAF.
Water management and phenology influence the root-associated rice field microbiota
Authors: Chialva Matteo , Ghignone Stefano , Cozzi Paolo , Lazzari Barbara , Bonfante Paola , Abbruscato Pamela , Lumini Erica 
Published: July 2020

ABSTRACTMicrobial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.
Improved multichannel singular spectrum analysis for post-processing GRACE monthly gravity field models
Authors: Wang Fengwei , Shen Yunzhong , Chen Tianyi , Chen Qiujie , Li Weiwei 
Published: July 2020

SUMMARY
Multichannel singular spectrum analysis (MSSA) is a powerful tool to extract spatiotemporal signals and filter errors from the noisy time-series of monthly gravity field models from the satellite data of gravity recovery and climate experiment (GRACE). Since the GRACE monthly gravity models are missed about 17 months, we develop an improved MSSA approach, which can directly process the incomplete time-series without either data interpolation or iteration. The time-series of 14-yr (2002.04–2016.08) monthly gravity field models of CSR-RL06 up to degree and order 60 are analysed with improved MSSA compared to the MSSA with linear data interpolation and iteration MSSA. By using our improved MSSA approach, the first 11 principal components derived can capture 91.18 per cent of the total variance, higher than 85.80 and 86.44 per cent of the total variance, derived by linear interpolation MSSA and iteration MSSA, respectively. The ratios of the latitude weighted RMS over the land and ocean signals are used to evaluate the efficiency of eliminating noise by the MSSA approach. For improved MSSA, the mean RMS ratio of land and ocean signals of all available months is higher than linear interpolation and iteration MSSA, which indicates that improved MSSA can suppress noise more efficiently and extract more geophysical signals from real GRACE data. Furthermore, the 50 repeated experiments show that all the root mean squared errors and mean absolute errors derived by our improved MSSA are smaller than other MSSA approaches. Moreover, the improved MSSA performs still better than other MSSA based approaches for the cases of large data gaps.
Erbb4 regulates the oocyte microenvironment during folliculogenesis
Authors: Veikkolainen Ville , Ali Nsrein , Doroszko Milena , Kiviniemi Antti , Miinalainen Ilkka , Ohlsson Claes , Poutanen Matti , Rahman Nafis , Elenius Klaus , Vainio Seppo J , Naillat Florence 
Published: July 2020

AbstractPolycystic ovary syndrome (PCOS) is one of the most common endocrine disorders leading to infertility in women affecting reproductive, endocrine and metabolic systems. Recent genomewide association studies on PCOS cohorts revealed a single nucleotide polymorphism (SNP) in the ERBB4 receptor tyrosine kinase 4 gene, but its role in ovary development or during folliculogenesis remains poorly understood. Since no genetic animal models mimicking all PCOS reproductive features are available, we conditionally deleted Erbb4 in murine granulosa cells (GCs) under the control of Amh promoter. While we have demonstrated that Erbb4 deletion displayed aberrant ovarian function by affecting the reproductive function (asynchronous oestrous cycle leading to few ovulations and subfertility) and metabolic function (obesity), their ovaries also present severe structural and functional abnormalities (impaired oocyte development). Hormone analysis revealed an up-regulation of serum luteinizing hormone, hyperandrogenism, increased production of ovarian and circulating anti-Müllerian hormone. Our data implicate that Erbb4 deletion in GCs leads to defective intercellular junctions between the GCs and oocytes, causing changes in the expression of genes regulating the local microenvironment of the follicles. In vitro culture assays reducing the level of Erbb4 via shRNAs confirm that Erbb4 is essential for regulating Amh level. In conclusion, our results indicate a functional role for Erbb4 in the ovary, especially during folliculogenesis and its reduced expression plays an important role in reproductive pathophysiology, such as PCOS development.
Variation in behavioural responses of sub-tropical marine fishes to experimental longline capture
Authors: Talwar Brendan S , Bouyoucos Ian A , Brooks Edward J , Brownscombe Jacob W , Suski Cory D , Cooke Steven J , Grubbs R Dean , Mandelman John W 
Published: July 2020

AbstractFishes are often caught as bycatch on longlines and subsequently discarded. The behavioural response of fishes to longline capture is poorly understood, although it may be linked to the magnitude of the physiological stress response, and, ultimately, contribute to stress-induced mortality. We used accelerometers, video cameras, and hook timers to analyse the behavioural response of 13 subtropical teleost and elasmobranch species to experimental longline capture in The Bahamas. We found that, across all species and species groups, fight intensity during a capture event was best described by a negative linear and positive quadratic response. Nurse sharks and tiger sharks had lower fight intensity values and exhibited less steepness in their quadratic response during the first 10 min of capture than other species, particularly blacktip and Caribbean reef sharks. Nurse sharks also exhibited the most consistent fight intensity during the entire capture event compared to other shark species, particularly the blacknose shark. Generally, obligate ram ventilators and mixed ventilators exhibited higher steepness in fight intensity trajectories than buccal/spiracular pumpers, which had more consistent, lower fight intensity values. Behavioural responses to longline capture are species specific but may be linked to distinct evolutionary traits such as respiratory mode.
Late inflow or outflow obstruction requiring surgical intervention after HeartMate 3 left ventricular assist device insertion
Authors: Kaku Yuji , Naka Yoshifumi , Witer Lucas , Topkara Veli , Colombo Paolo , Sayer Gabriel , Uriel Nir , Takeda Koji 
Published: July 2020

AbstractInflow or outflow obstruction is a rare, but critical complication after HeartMate 3 left ventricular assist device implantation. We retrospectively reviewed 166 patients who underwent primary HeartMate 3 implantation at our centre between November 2014 and July 2019. Three cases of inflow obstruction and 3 cases of outflow obstruction were identified. Presence of low flow alarm was the most common presenting sign and they were free from heart failure symptoms except in 1 case. They all underwent surgical correction and the median time from primary implantation to reintervention was 406.5 days. Computed tomography angiogram identified a problem in 5 out of 6 cases. Clinical symptoms and/or alarms resolved after surgery, but 1 case developed recurrent low flow alarm due to partial occlusion of inflow by fibrous tissue who eventually underwent heart transplant. All patients remain alive with median follow-up of 433.5 days. Prompt surgical intervention in late inflow and outflow obstruction after HeartMate 3 implantation resulted in favourable outcomes.
Pro- and Anti-Inflammatory Properties of Interleukin in Vitro: Relevance for Major Depression and Human Hippocampal Neurogenesis
Authors: Borsini Alessandra , Di Benedetto Maria Grazia , Giacobbe Juliette , Pariante Carmine M 
Published: July 2020

Abstract

Background
Although the pro-inflammatory cytokine interleukin (IL)6 has been generally regarded as “depressogenic,” recent research has started to question this assumption in light of the fact that this cytokine can also have anti-inflammatory properties. This bimodal action seems to be dependent on its concentration levels and on the concomitant presence of other pro-inflammatory cytokines.

Methods
We exposed a human hippocampal progenitor cell line, HPC0A07/03C, to cytokine levels described in depressed patients (IL6 5 pg/mL with IL1β 10 pg/mL or Macrophage Migration Inhibitory Factor (300 pg/mL) in healthy individuals (IL6 with IL1β, 1 pg/mL or Macrophage Migration Inhibitory Factor 10 pg/mL), as well as to the potentially anti-inflammatory, much higher concentrations of IL6 (50 000 pg/mL).

Results
Treatment with high concentrations of IL6 with IL1β or Macrophage Migration Inhibitory Factor (resembling depressed patients) decreases neurogenesis compared with low concentrations of the same cytokines (healthy individuals) and that this is mediated via production of, respectively, IL8 and IL1β in cell supernatant. Instead, treatment with very high, anti-inflammatory concentration of IL6 (50 000 pg/mL) together with high IL1β or Macrophage Migration Inhibitory Factor prevents decrease in neurogenesis and reduces both IL8 and IL1β. When high concentrations of both IL1β and Macrophage Migration Inhibitory Factor were used in co-treatment, as a model of treatment-resistant depression, we also demonstrated a reduction in neurogenesis and that this is mediated via a decrease in IL4; moreover, co-treatment with high IL1β and Macrophage Migration Inhibitory Factor and the very high concentration of IL6 prevented the reduction in neurogenesis and increased IL4.

Conclusions
Our results demonstrate that IL6 can exert both pro- and anti-inflammatory (potentially antidepressant) properties, depending on its concentrations and combinations with other inflammatory cytokines.
Functional Dysconnectivity of Frontal Cortex to Striatum Predicts Ketamine Infusion Response in Treatment-Resistant Depression
Authors: Chen Mu-Hong , Chang Wan-Chen , Lin Wei-Chen , Tu Pei-Chi , Li Cheng-Ta , Bai Ya-Mei , Tsai Shih-Jen , Huang Wen-Sheng , Su Tung-Ping 
Published: July 2020

Abstract

Background
Frontostriatal disconnectivity plays a crucial role in the pathophysiology of major depressive disorder. However, whether the baseline functional connectivity of the frontostriatal network could predict the treatment outcome of low-dose ketamine infusion remains unknown.

Methods
In total, 48 patients with treatment-resistant depression were randomly divided into 3 treatment groups (a single-dose 40-minute i.v. infusion) as follows: 0.5 mg/kg ketamine, 0.2 mg/kg ketamine, and saline placebo infusion. Patients were subsequently followed-up for 2 weeks. Resting-state functional magnetic resonance imaging was performed for each patient before infusion administration. In addition, the baseline frontostriatal functional connectivity of patients with treatment-resistant depression was also compared with that of healthy controls.

Results
Compared with the healthy controls, patients with treatment-resistant depression had a decreased functional connectivity in the frontostriatal circuits, especially between the right superior frontal cortex and executive region of the striatum and between the right paracingulate cortex and rostral-motor region of the striatum. The baseline hypoconnectivity of the bilateral superior frontal cortex to the executive region of the striatum was associated with a greater reduction of depression symptoms after a single 0.2-mg/kg ketamine infusion.

Conclusion
Reduced connectivity of the superior frontal cortex to the striatum predicted the response to ketamine infusion among patients with treatment-resistant depression.
Exponential convergence of mixed hp-DGFEM for the incompressible Navier–Stokes equations in ℝ2
Authors: Schötzau Dominik , Marcati Carlo , Schwab Christoph 
Published: July 2020

Abstract
In a polygon $\varOmega \subset \mathbb{R}^2$ we consider mixed $hp$-discontinuous Galerkin approximations of the stationary, incompressible Navier–Stokes equations, subject to no-slip boundary conditions. We use geometrically corner-refined meshes and $hp$ spaces with linearly increasing polynomial degrees. Based on recent results on analytic regularity of velocity field and pressure of Leray solutions in $\varOmega$, we prove exponential rates of convergence of the mixed $hp$-discontinuous Galerkin finite element method, with respect to the number of degrees of freedom, for small data which is piecewise analytic.
Brownian Motions and Heat Kernel Lower Bounds on Kähler and Quaternion Kähler Manifolds
Authors: Baudoin Fabrice , Yang Guang 
Published: July 2020

Abstract
We study the radial parts of the Brownian motions on Kähler and quaternion Kähler manifolds. Thanks to sharp Laplacian comparison theorems, we deduce as a consequence a sharp Cheeger–Yau-type lower bound for the heat kernels of such manifolds and also sharp Cheng’s type estimates for the Dirichlet eigenvalues of metric balls.
Regularity of Weak Solution of Variational Problems Modeling the Cosserat Micropolar Elasticity
Authors: Li Yimei , Wang Changyou 
Published: July 2020

Abstract
In this paper, we consider weak solutions of the Euler–Lagrange equation to a variational energy functional modeling the geometrically nonlinear Cosserat micropolar elasticity of continua in dimension three, which is a system coupling between the Poisson equation and the equation of $p$-harmonic maps ($2\le p\le 3$). We show that if a weak solution is stationary, then its singular set is discrete for $2&lt;p&lt;3$ and has zero one-dimensional Hausdorff measure for $p=2$. If, in addition, it is a stable-stationary weak solution, then it is regular everywhere when $p\in [2, \frac{32}{15}]$.
Evaluation of the Aptima HCV Quant Dx Assay for Hepatitis C Virus RNA Detection from Fingerstick Capillary Dried Blood Spot and Venepuncture-Collected Samples
Authors: Catlett Beth , Bajis Sahar , Starr Mitchell , Dore Gregory J , Hajarizadeh Behzad , Cunningham Philip H , Applegate Tanya L , Grebely Jason 
Published: July 2020

Abstract

Background
Simplified diagnostic strategies are needed increase hepatitis C virus (HCV) testing to determine active infection and link people into treatment. Collection methods such as dried blood spots (DBS) have advantages over standard phlebotomy, especially within marginalized populations.

Methods
We evaluated the diagnostic performance of the Aptima HCV Quant assay for the quantification and detection of HCV RNA from paired DBS and venepuncture samples. Specimens were collected from participants enrolled in an Australian observational study. We compared HCV RNA detection from DBS against venepuncture samples (gold standard).

Results
One hundred sixty-four participants had paired samples and HCV RNA was detected in 45 (27% [95% confidence interval, 21%–35%]) by the Aptima assay in venepuncture samples. Sensitivity of the Aptima assay for HCV RNA quantification from DBS (≥10 IU/mL in plasma) was 100% and specificity was 100%. Sensitivity for HCV RNA detection from DBS was 95.6% and specificity was 94.1%. A small bias in plasma over DBS was observed with good agreement (R2 = 0.96).

Conclusions
The Aptima HCV Quant assay detects active infection from DBS samples with acceptable diagnostic performance and is clinically comparable to plasma. These data will strengthen the case for the registration of a DBS kit insert claim, enabling future clinical utility.
Analysis of Treponema pallidum Strains From China Using Improved Methods for Whole-Genome Sequencing From Primary Syphilis Chancres
Authors: Chen Wentao , Šmajs David , Hu Yongfei , Ke Wujian , Pospíšilová Petra , Hawley Kelly L , Caimano Melissa J , Radolf Justin D , Sena Arlene , Tucker Joseph D , Yang Bin , Juliano Jonathan J , Zheng Heping , Parr Jonathan B 
Published: July 2020

Abstract

Background
Whole-genome sequencing (WGS) of Treponema pallidum subspecies pallidum (TPA) has been constrained by the lack of in vitro cultivation methods for isolating spirochetes from patient samples.

Methods
We built upon recently developed enrichment methods to sequence TPA directly from primary syphilis chancre swabs collected in Guangzhou, China.

Results
By combining parallel, pooled whole-genome amplification with hybrid selection, we generated high-quality genomes from 4 of 8 chancre-swab samples and 2 of 2 rabbit-passaged isolates, all subjected to challenging storage conditions.

Conclusions
This approach enabled the first WGS of Chinese samples without rabbit passage and provided insights into TPA genetic diversity in China.
Reliability of Self-Sampling for Accurate Assessment of Respiratory Virus Viral and Immunologic Kinetics
Authors: Waghmare Alpana , Krantz Elizabeth M , Baral Subhasish , Vasquez Emma , Loeffelholz Tillie , Chung E Lisa , Pandey Urvashi , Kuypers Jane , Duke Elizabeth R , Jerome Keith R , Greninger Alexander L , Reeves Daniel B , Hladik Florian , Cardozo-Ojeda E Fabian , Boeckh Michael , Schiffer Joshua T 
Published: July 2020

Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrates the need for accurate and convenient approaches to diagnose and therapeutically monitor respiratory viral infections. We demonstrated that self-sampling with mid-nasal foam swabs is well-tolerated and provides quantitative viral output concordant with flocked swabs. Using longitudinal home-based self-sampling, we demonstrate that nasal cytokine levels correlate and cluster according to immune cell of origin. Periods of stable viral loads are followed by rapid elimination, which could be coupled with cytokine expansion and contraction. Nasal foam swab self-sampling at home provides a precise, mechanistic readout of respiratory virus shedding and local immune responses.
Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals
Authors: Chimukangara Benjamin , Giandhari Jennifer , Lessells Richard , Yende-Zuma Nonhlanhla , Sartorius Benn , Samuel Reshmi , Khanyile Khulekani S , Stray-Pedersen Babill , Moodley Pravi , Metzner Karin J , Padayatchi Nesri , Naidoo Kogieleum , De Oliveira Tulio 
Published: July 2020

Abstract

Objectives
To determine the impact of pretreatment low-abundance HIV-1 drug-resistant variants (LA-DRVs) on virological failure (VF) among HIV-1/TB-co-infected individuals treated with NNRTI first-line ART.

Methods
We conducted a case–control study of 170 adults with HIV-1/TB co-infection. Cases had at least one viral load (VL) ≥1000 RNA copies/mL after ≥6 months on NNRTI-based ART, and controls had sustained VLs &lt;1000 copies/mL. We sequenced plasma viruses by Sanger and MiSeq next-generation sequencing (NGS). We assessed drug resistance mutations (DRMs) using the Stanford drug resistance database, and analysed NGS data for DRMs at ≥20%, 10%, 5% and 2% thresholds. We assessed the effect of pretreatment drug resistance (PDR) on VF.

Results
We analysed sequences from 45 cases and 125 controls. Overall prevalence of PDR detected at a ≥20% threshold was 4.7% (8/170) and was higher in cases than in controls (8.9% versus 3.2%), P = 0.210. Participants with PDR at ≥20% had almost 4-fold higher odds of VF (adjusted OR 3.7, 95% CI 0.8–18.3) compared with those without, P = 0.104. PDR prevalence increased to 18.2% (31/170) when LA-DRVs at ≥2% were included. Participants with pretreatment LA-DRVs only had 1.6-fold higher odds of VF (adjusted OR 1.6, 95% CI 0.6–4.3) compared with those without, P = 0.398.

Conclusions
Pretreatment DRMs and LA-DRVs increased the odds of developing VF on NNRTI-based ART, although without statistical significance. NGS increased detection of DRMs but provided no additional benefit in identifying participants at risk of VF at lower thresholds. More studies assessing mutation thresholds predictive of VF are required to inform use of NGS in treatment decisions.