bluuebunny/crossref_metadata_2025 huggingface dataset:
Alignment- and reference-free phylogenomics with colored de Bruijn graphs
Authors: Wittler Roland
Published: April 2020

Background

The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies—a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time.

Results

We present a new whole-genome based approach to infer phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits.

Conclusions

The introduced new methodology for large-scale phylogenomics shows high potential. Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency.
Influence of cement-augmented pedicle screw instrumentation in an osteoporotic lumbosacral spine over the adjacent segments: a 3D finite element study
Authors: Zhou Quan-kun , Zeng Fan-hui , Tu Jian-long , Dong Zhang-qing , Ding Zhi-Hui
Published: April 2020

Purpose

To compare the effect of conventional pedicle screw (CPS) and cement-augmented pedicle screw instrumentation (CAPSI) on adjacent segment degeneration (ASD).

Methods

A normal male volunteer without a history of spinal disease was selected, lumbar CT data was collected, an intact L3-S1 three-dimensional finite element model was created by software including Mimics, Geomagic, and SolidWorks, and the fixation methods were performed accordingly. A common pedicle screw model and a cement-augmented pedicle screw model of L4–L5 with fusion and internal fixation were constructed. With ANSYS Workbench 17.0, a 500 N load was applied to the upper surface of L3 to simulate the weight of a human body, and a 7.5 N m moment was applied at the neutral point to simulate flexion, extension, left/right bending, left/right rotation of the spine. The peak von Mises stress of intervertebral disc and the range of motion (ROM) on the adjacent segments (L3–4 and L5–S1) were compared.

Results

The validity of the intact model shows that the ROM of the model is similar to that of a cadaveric study. Compared with the intact model, CPS model and CAPSI model in all motion patterns increased the ROM of adjacent segments. The intervertebral disc stress and the ROM of adjacent segments were found to be higher in the CAPSI model than in the CPS model, especially in L3–4.

Conclusion

In general, the biomechanical analysis of an osteoporotic lumbar spine showed that both CPS and CAPSI can increase the ROM and disc stresses of osteoporotic lumbar models, and compared with CPS, CAPSI is more likely to increase the potential risk of adjacent segment degeneration.
Prevalence, indications, and outcomes of caesarean section deliveries in Ethiopia: a systematic review and meta-analysis
Authors: Gedefaw Getnet , Demis Asmamaw , Alemnew Birhan , Wondmieneh Adam , Getie Addisu , Waltengus Fikadu
Published: April 2020

Background

Caesarean section rates have increased worldwide in recent decades. Caesarean section is an essential maternal healthcare service. However, it has both maternal and neonatal adverse outcomes. Therefore this systematic review and meta-analysis aimed to estimate the prevalence, indication, and outcomes of caesarean section in Ethiopia.

Methods

Twenty three cross-sectional studies with a total population of 36,705 were included. Online databases (PubMed/Medline, Hinari, Web of Science, and Google Scholar) and online university repository was used. All the included papers were extracted and appraised using the standard extraction sheet format and Joanna Briggs Institute respectively. The pooled prevalence of the caesarean section, indications, and outcomes was calculated using the random-effect model.

Result

The overall pooled prevalence of Caesarean section was 29.55% (95% CI: 25.46–33.65). Caesarean section is associated with both maternal and neonatal complications. Cephalopelvic disproportion [18.13%(95%CI: 12.72–23.53] was the most common indication of Caesarean section followed by non-reassuring fetal heart rate pattern [19.57% (95%CI: 16.06–23.08]. The common neonatal complications following Caesarean section included low APGAR score, perinatal asphyxia, neonatal sepsis, meconium aspiration syndrome, early neonatal death, stillbirth, and prematurity whereas febrile morbidity, surgical site infection, maternal mortality, severe anemia, and postpartum hemorrhage were the most common maternal complications following Caesarean section.

Conclusion

In this systematic review and meta-analysis, the rate of Cesarean section was high. Cephalopelvic disproportion, low Apgar score, and febrile morbidity were the most common indication of Caesarean section, neonatal outcome and maternal morbidity following Caesarean section respectively. Increasing unjustified Caesarean section deliveries as a way to increase different neonatal and maternal complications, then several interventions needed to target both the education of professionals and the public.
Temporal expression profiling of DAMPs-related genes revealed the biphasic post-ischemic inflammation in the experimental stroke model
Authors: Yamaguchi Atsushi , Jitsuishi Tatsuya , Hozumi Takashi , Iwanami Jun , Kitajo Keiko , Yamaguchi Hiroo , Mori Yasutake , Mogi Masaki , Sawai Setsu
Published: April 2020

The neuroinflammation in the ischemic brain could occur as sterile inflammation in response to damage-associated molecular patterns (DAMPs). However, its long-term dynamic transcriptional changes remain poorly understood. It is also unknown whether this neuroinflammation contributes to the recovery or just deteriorates the outcome. The purpose of this study is to characterize the temporal transcriptional changes in the post-stroke brain focusing on DAMPs-related genes by RNA-sequencing during the period of 28 days. We conducted the RNA-sequencing on day 1, 3, 7, 14, 28 post-stroke in the mouse photothrombosis model. The gross morphological observation showed the ischemic lesion on the ipsilateral cortex turned into a scar with the clearance of cellular debris by day 28. The transcriptome analyses indicated that post-stroke period of 28 days was classified into four categories (I Baseline, II Acute, III Sub-acute-#1, IV Sub-acute-#2 phase). During this period, the well-known genes for DAMPs, receptors, downstream cascades, pro-inflammatory cytokines, and phagocytosis were transcriptionally increased. The gene ontology (GO) analysis of biological process indicated that differentially expressed genes (DEGs) are genetically programmed to achieve immune and inflammatory pathways. Interestingly, we found the biphasic induction of various genes, including DAMPs and pro-inflammatory factors, peaking at acute and sub-acute phases. At the sub-acute phase, we also observed the induction of genes for phagocytosis as well as regulatory and growth factors. Further, we found the activation of CREB (cAMP-response element binding protein), one of the key players for neuronal plasticity, in peri-ischemic neurons by immunohistochemistry at this phase. Taken together, these findings raise the possibility the recurrent inflammation occurs at the sub-acute phase in the post-stroke brain, which could be involved in the debris clearance as well as neural reorganization.
Sarilumab and adalimumab differential effects on bone remodelling and cardiovascular risk biomarkers, and predictions of treatment outcomes
Authors: Gabay Cem , Burmester Gerd R. , Strand Vibeke , Msihid Jérôme , Zilberstein Moshe , Kimura Toshio , van Hoogstraten Hubert , Boklage Susan H. , Sadeh Jonathan , Graham Neil M. H. , Boyapati Anita
Published: April 2020

Background

Interleukin-6 (IL-6) is a pleiotropic cytokine that plays a key role in the pathogenesis of rheumatoid arthritis. Sarilumab is a human monoclonal antibody that binds membrane-bound and soluble IL-6 receptor-α to inhibit IL-6 signalling. The aim of this study was to compare the effects of sarilumab and adalimumab (a tumour necrosis factor alpha inhibitor) monotherapy on levels of circulating biomarkers associated with the acute-phase response, bone remodelling, atherothrombosis, anaemia of chronic disease and markers purported to reflect synovial lymphoid and myeloid cell infiltrates, as well as the potential of these biomarkers to differentially predict clinical and patient-reported outcomes with sarilumab vs. adalimumab.

Methods

In this post hoc analysis, serum samples were analysed at baseline and prespecified post-treatment timepoints up to week 24 in adults with moderate-to-severe active rheumatoid arthritis intolerant of or inadequate responders to methotrexate from the MONARCH trial (NCT02332590).

Results

Greater reductions in C-reactive protein (CRP; − 94.0% vs. –24.0%), serum amyloid A (SAA; − 83.2% vs. –17.4%), total receptor activator of nuclear factor-κB ligand (RANKL; − 18.3% vs. 10.5%) and lipoprotein (a) (− 41.0% vs. –2.8%) were observed at week 24 with sarilumab vs. adalimumab, respectively (adjusted p < 0.0001). Greater increases in procollagen type 1 N-terminal propeptide (P1NP) were observed with sarilumab vs. adalimumab at week 24 (22.8% vs. 6.2%, p = 0.027). Patients with high baseline SAA, CRP and matrix metalloproteinase-3 (MMP-3) were more likely to achieve clinical efficacy, including American College of Rheumatology 20% improvement criteria and Disease Activity Score (28 joints)-CRP < 3.2, and report improvements in patient-reported outcomes, including Health Assessment Questionnaire-Disability Index and pain visual analogue scale, with sarilumab than adalimumab.

Conclusion

Sarilumab was associated with greater positive effects on bone remodelling and decreases in biomarkers of the acute-phase response, synovial inflammation and cardiovascular risk vs. adalimumab. High baseline concentrations of SAA, CRP and MMP-3 are predictive of clinical and patient-reported outcome responses to sarilumab treatment and prospective validation is warranted to confirm these results.

Trial registration

ClinicalTrials.gov, NCT02332590. Registered on 5 January 2015
Serum interleukin-16 significantly correlates with the Vasculitis Damage Index in antineutrophil cytoplasmic antibody-associated vasculitis
Authors: Yoon Taejun , Pyo Jung Yoon , Ahn Sung Soo , Song Jason Jungsik , Park Yong-Beom , Lee Sang-Won
Published: April 2020

Background

Interleukin (IL)-16 is a T cell chemoattractant produced by peripheral mononuclear cells. We investigated whether IL-16 plays a pro- or an anti-inflammatory role in antineutrophil cytoplasmic antibody-associated vasculitis (AAV). Furthermore, we investigated whether the level of IL-16 could predict the activity and extent of organ damage in AAV based on AAV-specific indices.

Methods

Seventy-eight patients with AAV from a prospective observational cohort were included in this analysis. Blood sampling and clinical assessments, including the Birmingham Vasculitis Activity Score (BVAS), Five-Factor Score (FFS), Short Form 36-item Health Survey (SF-36), and Vasculitis Damage Index (VDI), were performed, and laboratory data were collected. Serum IL-16 was measured from stored sera.

Results

The median age was 62.0 years, and 27 patients were male. The median serum IL-16 concentration was 84.1 pg/dL, and the median BVAS, FFS, VDI, and SF-36 scores were 7.0, 1.0, 3.0, and 48.0, respectively. Among the AAV-related indices, the serum IL-16 concentration was correlated with VDI (R2 = 0.306,P = 0.006), but not with BVAS (R2 = 0.024,P = 0.834), FFS (R2 = − 0.069,P = 0.550), or SF-36 (R2 = − 0.015,P = 0.898). The serum IL-16 concentration also did not correlate with either the erythrocyte sedimentation rate or the C-reactive protein concentration. Per our analysis based on organ involvement, only patients with ear, nose, and throat manifestations had higher serum IL-16 concentrations relative to those with other conditions (P = 0.030).

Conclusions

This was the first study to elucidate the clinical implication of serum IL-16 in patients with AAV. We found that the serum IL-16 level may reflect the cross-sectional VDI scores among AAV-specific indices. Future studies with larger numbers of patients and serial measurements could provide more reliable data on the clinical implications of serum IL-16 in AAV.
Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons
Authors: Ruggiero Robert P. , Boissinot Stéphane
Published: April 2020

Background

Non-LTR retrotransposons often exhibit base composition that is markedly different from the nucleotide content of their host’s gene. For instance, the mammalian L1 element is AT-rich with a strong A bias on the positive strand, which results in a reduced transcription. It is plausible that the A-richness of mammalian L1 is a self-regulatory mechanism reflecting a trade-off between transposition efficiency and the deleterious effect of L1 on its host. We examined if the A-richness of L1 is a general feature of non-LTR retrotransposons or if different clades of elements have evolved different nucleotide content. We also investigated if elements belonging to the same clade evolved towards different base composition in different genomes or if elements from different clades evolved towards similar base composition in the same genome.

Results

We found that non-LTR retrotransposons differ in base composition among clades within the same host but also that elements belonging to the same clade differ in base composition among hosts. We showed that nucleotide content remains constant within the same host over extended period of evolutionary time, despite mutational patterns that should drive nucleotide content away from the observed base composition.

Conclusions

Our results suggest that base composition is evolving under selection and may be reflective of the long-term co-evolution between non-LTR retrotransposons and their host. Finally, the coexistence of elements with drastically different base composition suggests that these elements may be using different strategies to persist and multiply in the genome of their host.
Empagliflozin reduces vascular damage and cognitive impairment in a mixed murine model of Alzheimer’s disease and type 2 diabetes
Authors: Hierro-Bujalance Carmen , Infante-Garcia Carmen , del Marco Angel , Herrera Marta , Carranza-Naval Maria Jose , Suarez Javier , Alves-Martinez Pilar , Lubian-Lopez Simon , Garcia-Alloza Monica
Published: April 2020

Background

Both Alzheimer’s disease (AD) and type 2 diabetes (T2D) share common pathological features including inflammation, insulin signaling alterations, or vascular damage. AD has no successful treatment, and the close relationship between both diseases supports the study of antidiabetic drugs to limit or slow down brain pathology in AD. Empagliflozin (EMP) is a sodium-glucose co-transporter 2 inhibitor, the newest class of antidiabetic agents. EMP controls hyperglycemia and reduces cardiovascular comorbidities and deaths associated to T2D. Therefore, we have analyzed the role of EMP at the central level in a complex mouse model of AD-T2D.

Methods

We have treated AD-T2D mice (APP/PS1xdb/db mice) with EMP 10 mg/kg for 22 weeks. Glucose, insulin, and body weight were monthly assessed. We analyzed learning and memory in the Morris water maze and the new object discrimination test. Postmortem brain assessment was conducted to measure brain atrophy, senile plaques, and amyloid-β levels. Tau phosphorylation, hemorrhage burden, and microglia were also measured in the brain after EMP treatment.

Results

EMP treatment helped to maintain insulin levels in diabetic mice. At the central level, EMP limited cortical thinning and reduced neuronal loss in treated mice. Hemorrhage and microglia burdens were also reduced in EMP-treated mice. Senile plaque burden was lower, and these effects were accompanied by an amelioration of cognitive deficits in APP/PS1xdb/db mice.

Conclusions

Altogether, our data support a feasible role for EMP to reduce brain complications associated to AD and T2D, including classical pathological features and vascular disease, and supporting further assessment of EMP at the central level.
A simple and rapid protein purification method based on cell-surface display of SUMO-fused recombinant protein and Ulp1 protease
Authors: Zhou Xiao-Feng , Zhang Chen-Lu , Gao Xue-Ping , Wang Wei-Long , He Zheng-Fen , Jiang Feng-Ying , Pang Yi-Lin , Li Jiang-Hui , Ren Xiao-Jun , Zhou Huai-Bin , Tan Guo-Qiang , Lyu Jian-Xin , Wang Wu
Published: April 2020

The development of novel methods for highly efficient protein purification remains a research focus in the biotechnology field because conventional purification approaches, including affinity purification, gel filtration, and ion-exchange chromatography, require complex manipulation steps and are costly. Here, we describe a simple and rapid protein purification strategy in which the SUMO tag and Ulp1 protease are surface-displayed separately on Escherichia coli cells. After protein induction, the cells are harvested, resuspended in cleavage buffer, and incubated together for cleavage. In this approach, the surface-displayed Ulp1 cleaves the membrane-anchored SUMO fusion protein, resulting in the release of the target protein from the C-terminal of SUMO into the solution. The bacterial cells harboring SUMO and Ulp1 on their surfaces can be easily removed by centrifugation. To evaluate the purification method, we used red fluorescent protein (mCherry). Purified mCherry protein (7.72 ± 1.05 mg from 1 L of bacterial culture) was obtained after only 30 min of incubation. The protein purity was higher than 80%, and could be further improved (> 90%) by simple ultrafiltration. This study offers a promising and simple strategy for the purification of recombinant protein in its native form that requires only cleavage and centrifugation steps.
Finite-approximate controllability of fractional stochastic evolution equations with nonlocal conditions
Authors: Ding Yonghong , Li Yongxiang
Published: April 2020

This paper deals with the finite-approximate controllability for a class of fractional stochastic evolution equations with nonlocal initial conditions in a Hilbert space. We establish sufficient conditions for the finite-approximate controllability of the control system when the compactness conditions or Lipschitz conditions for the nonlocal term and uniform boundedness conditions for the nonlinear term are not required. The discussion is based on the fixed point theorem, approximation techniques and diagonal argument. In the end, an example is presented to illustrate the abstract theory. Our result improves and extends some relevant results in this area.
A filter method for inverse nonlinear sideways heat equation
Authors: Anh Triet Nguyen , O’Regan Donal , Baleanu Dumitru , Hoang Luc Nguyen , Can Nguyen
Published: April 2020

In this paper, we study a sideways heat equation with a nonlinear source in a bounded domain, in which the Cauchy data at $x = \mathcal {X}$x=X are given and the solution in $0 \le x < \mathcal {X}$0≤x<X is sought. The problem is severely ill-posed in the sense of Hadamard. Based on the fundamental solution to the sideways heat equation, we propose to solve this problem by the filter method of degree α, which generates a well-posed integral equation. Moreover, we show that its solution converges to the exact solution uniformly and strongly in $\mathscr {L}^{p}(\omega,\mathcal {X};\mathscr {L}^{2}(\mathbb {R}))$Lp(ω,X;L2(R)), $\omega\in [0,\mathcal {X})$ω∈[0,X) under a priori assumptions on the exact solution. The proposed regularized method is illustrated by numerical results in the final section.
Porosity–permeability relationship derived from Upper Jurassic carbonate rock cores to assess the regional hydraulic matrix properties of the Malm reservoir in the South German Molasse Basin
Authors: Bohnsack D. , Potten M. , Pfrang D. , Wolpert P. , Zosseder K.
Published: April 2020

For the successful realization and productivity prediction of new hydrothermal projects in the South German Molasse Basin, the hydraulic matrix properties of the Upper Jurassic Malm reservoir have to be determined as accurately as possible. To obtain specific information on the distribution of the petrophysical parameters (e.g., rock density, porosity, and permeability) 363 samples of rare drilling cores from the reservoir northeast of Munich (wells Moosburg SC4 and Dingolfing FB) were investigated using different experimental methods. Additionally, porosity was calculated by a downhole resistivity log of a nearby borehole close to Munich for comparison and the attempt of transferability of the data set to other locations within the Central Molasse Basin. Core data were divided into groups of different stratigraphic and petrographic units to cover the heterogeneity of the carbonate aquifer and provide data ranges to improve reservoir and prediction models. Data for effective porosity show a high variance from 0.3 to 19.2% throughout this heterogeneous aquifer. Permeability measured on core samples is scattered over several orders of magnitude (10−4–102 mD). Permeability models based on the porosity–permeability relationship were used to estimate permeability for the whole aquifer section and identify possible flow zones. A newly developed empirical model based on distinct lithofacies types allows a permeability estimation with a deviation < 10 mD. However, fractured, karstified, and vuggy zones occurring in this typically karstified, fractured, and porous reservoir cannot yet be taken into account by the model and result in an underestimation of permeability on reservoir scale. Overall, the dominant permeability trends can be mapped well using this model. For the regional transfer and the correlation of the results, a core-related porosity/permeability log for the reservoir was compiled for a well close to Munich showing similarities to the core investigations. The validation of the regional transferability of the parameter set to other locations in the Molasse Basin was carried out by correlation with the interpreted log data of a well near Munich.
Japan ECMOnet for COVID-19: telephone consultations for cases with severe respiratory failure caused by COVID-19
Authors:   Japan ECMOnet for COVID-19
Published: April 2020

Recently, the novel coronavirus disease 2019 (COVID-19) started spreading in Japan. Therefore, the number of patients with severe COVID-19 requiring extracorporeal membranous oxygenation (ECMO) is expected to increase. A working group has been formed to provide telephone consultation services for cases with severe respiratory failure caused by COVID-19 in Japan. During the first 13 days of the service, there were 12 consultations. For each consultation, we advised the patient on the initiation of ECMO and arranged transportation for patients with ECMO. Based on experience from the H1N1 influenza pandemic, transporting patients to experienced facilities is essential to obtain better outcomes.
A framework for estimating spherical vector fields using localized basis functions and its application to SuperDARN data processing
Authors: Nakano S. , Hori T. , Seki K. , Nishitani N.
Published: April 2020

A technique for estimating a plasma drift velocity distribution in the ionosphere is presented. This technique is based on a framework for representing a global vector field on a sphere by using a set of localized basis functions which is newly derived as a variant of the spherical elementary current system (SECS). A vector field on a sphere can be divided into its divergence-free (DF) component and curl-free (CF) component. The DF and CF components can then be represented by weighted sums of the DF and CF vector-valued basis functions, respectively. While the SECS basis functions have a singular point, the new basis functions do not diverge over a sphere. This property of the new basis function allows us to achieve robust prediction of the drift velocity at any point in the ionosphere. Assuming that the ionospheric plasma drift velocity has no divergence, its distribution can be represented by a weighted sum of the DF basis functions. The proposed technique estimates the ionospheric plasma drift velocity distribution from the SuperDARN data by using the DF basis functions. Since there are some wide gaps in the spatial coverage of the SuperDARN, an empirical convection model is combined with the framework based on the new basis functions. It is demonstrated that the proposed technique is useful for the estimation and modeling of the ionospheric plasma velocity distribution.
A novel ophthalmic viscosurgical device-free phakic intraocular lens implantation makes myopic surgery safer
Authors: Pan An-Peng , Wen Li-Jin , Shao Xu , Zhou Kai-Jing , Wang Qin-Mei , Qu Jia , Yu A-Yong
Published: April 2020

Purpose

To assess the efficacy and safety of a novel ophthalmic viscosurgical device-free (OVD-free) method for posterior chamber phakic intraocular lens (PIOL) implantation in myopic eyes.

Methods

In this retrospective cohort study, the medical records of myopic eyes that underwent PIOL (Implantable Collamer Lens, ICL) implantation for myopia correction at the Eye Hospital of Wenzhou Medical University between May 2015 and March 2017 were reviewed. A total of 49 eyes with complete data that met follow up requirements (2 h, 1 day, 1 week, 3 months postoperatively) were recruited. Based on the surgical techniques used, the eyes were divided into the OVD-free method group and the standard method group. The clinical data, including intraocular pressure (IOP), corrected distance visual acuity (CDVA) and spherical equivalent (SE), at each follow-up were collected for comparison. Endothelial cell loss and complications were also investigated.

Results

Twenty-one eyes received the standard method, and 28 eyes received the OVD-free method. A rise in IOP > 22 mmHg at 2 h was noted in 14 eyes (66.7%) in the standard group and none (0%) in the OVD-free group (p < 0.001). The rise in IOP from baseline was significantly higher at 2 h in the standard group (10.5 ± 5.2 mmHg vs. 2.2 ± 3.3 mmHg, difference: 8.3, 95% CI 5.8 to 10.8; p < 0.001). There was a significant difference in the time course of LogMAR CDVA changes between the two groups (p = 0.047). The LogMAR CDVA was significantly better in the OVD-free method group compared to the standard group at 1 day (− 0.076, 95% CI − 0.134 to − 0.018; p = 0.012), 1 week (− 0.071, 95% CI − 0.135 to − 0.007; p = 0.03), but not at 3 months (− 0.046, 95% CI − 0.107 to 0.015; p = 0.134). There was no significant difference in the time course of SE changes between the two groups (p = 0.471; p = 0.705). In the OVD-free group, mean endothelial cell loss was 4.6% at 3 months (2522 ± 281 vs. 2407 ± 226 cells/mm2, difference: -115, 95% CI − 295 to 65; p = 0.187). No complications were reported in both groups except for the early IOP elevation in the standard group during the observation period.

Conclusions

The OVD-free method is safe and efficient for ICL implantation. It can be a safer method of ICL implantation compared to the standard method in that it completely eliminates ophthalmic viscoelastic devices-related complications without causing additional complications.
Benefits of past inventory data as prior information for the current inventory
Authors: Kangas Annika , Gobakken Terje , Næsset Erik
Published: April 2020

Background

When auxiliary information in the form of airborne laser scanning (ALS) is used to assist in estimating the population parameters of interest, the benefits of prior information from previous inventories are not self-evident. In a simulation study, we compared three different approaches: 1) using only current data, 2) using non-updated old data and current data in a composite estimator and 3) using updated old data and current data with a Kalman filter. We also tested three different estimators, namely i) Horwitz-Thompson for a case of no auxiliary information, ii) model-assisted estimation and iii) model-based estimation. We compared these methods in terms of bias, precision and accuracy, as estimators utilizing prior information are not guaranteed to be unbiased.

Results

The largest standard errors were obtained when neither prior information nor auxiliary information were used. If a growth model was not applied to update the old data, the resulting composite estimators were biased. Largest RMSEs were obtained using non-updated prior information in a composite estimator. Using the ALS data as auxiliary information produced smaller RMSE than using prior information from the old inventory. The smallest RMSEs were obtained when both the auxiliary data and updated old data were used. With growth updating the bias can be substantially reduced, although design-unbiasedness of the estimator cannot be guaranteed.

Conclusions

Prior information from old inventory data can be useful also when combined with highly accurate auxiliary information, when both data sources are efficiently used. The benefits obtained from using the old data will increase if the past harvests can be detected without errors from changes in the auxiliary data instead of being predicted with models.
Growing a circular economy with fungal biotechnology: a white paper
Authors: Meyer Vera , Basenko Evelina Y. , Benz J. Philipp , Braus Gerhard H. , Caddick Mark X. , Csukai Michael , de Vries Ronald P. , Endy Drew , Frisvad Jens C. , Gunde-Cimerman Nina , Haarmann Thomas , Hadar Yitzhak , Hansen Kim , Johnson Robert I. , Keller Nancy P. , Kraševec Nada , Mortensen Uffe H. , Perez Rolando , Ram Arthur F. J. , Record Eric , Ross Phil , Shapaval Volha , Steiniger Charlotte , van den Brink Hans , van Munster Jolanda , Yarden Oded , Wösten Han A. B.
Published: April 2020

Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition from our petroleum-based economy into a bio-based circular economy and has the ability to sustainably produce resilient sources of food, feed, chemicals, fuels, textiles, and materials for construction, automotive and transportation industries, for furniture and beyond. Fungal biotechnology offers solutions for securing, stabilizing and enhancing the food supply for a growing human population, while simultaneously lowering greenhouse gas emissions. Fungal biotechnology has, thus, the potential to make a significant contribution to climate change mitigation and meeting the United Nation’s sustainable development goals through the rational improvement of new and established fungal cell factories. The White Paper presented here is the result of the 2nd Think Tank meeting held by the EUROFUNG consortium in Berlin in October 2019. This paper highlights discussions on current opportunities and research challenges in fungal biotechnology and aims to inform scientists, educators, the general public, industrial stakeholders and policymakers about the current fungal biotech revolution.
No association between three polymorphisms (rs1800629, rs361525 and rs1799724) in the tumor necrosis factor-α gene and susceptibility to prostate cancer: a comprehensive meta-analysis
Authors: Yin Lei , Yue Chuang , Jing Hongwei , Yu Hongyuan , Zuo Li , Liu Tao
Published: April 2020

Background

Inflammation is one of the factors associated with prostate cancer. The cytokine tumor necrosis factor-alpha (TNF-α) plays an important role in inflammation. Several studies have focused on the association between TNF-α polymorphisms and prostate cancer development. Our meta-analysis aimed to estimate the association between TNF-α rs1800629 (− 308 G/A), rs361525 (− 238 G/A) and rs1799724 polymorphisms and prostate cancer risk.

Methods

Eligible studies were identified from electronic databases (PubMed, Embase, Wanfang and CNKI) using keywords: TNF-α, polymorphism, prostate cancer, until Nov 15, 2019. Odds ratios (ORs) with 95% confidence intervals (CIs) were applied to determine the association from a quantitative point-of-view. Publication bias and sensitivity analysis were also applied to evaluate the power of current study. All statistical analyses were done with Stata 11.0 software.

Results

Twenty-two different articles were included (22 studies about rs1800629; 8 studies for rs361525 and 5 studies related to rs1799724). Overall, no significant association was found between rs1800629 and rs1799724 polymorphisms and the risk of prostate cancer in the whole (such as: OR = 1.03, 95% CI = 0.92–1.16, P = 0.580 in the allele for rs1800629; OR = 0.95, 95% CI = 0.84–1.07, P = 0.381 in the allele for rs1799724). The rs361525 polymorphism also had no association with prostate cancer in the cases (OR = 0.93, 95% CI = 0.66–1.32, P = 0.684 in the allele) and ethnicity subgroup. The stratified subgroup of genotype method, however, revealed that the rs361525 variant significantly decreased the risk of prostate cancer in the Others (OR = 0.65, 95% CI = 0.47–0.89, P = 0.008, A-allele vs G-allele) and PCR-RFLP (OR = 2.68, 95% CI = 1.00–7.20, P = 0.050, AG vs GG or AA+AG vs GG) methods.

Conclusions

In summary, the findings of the current meta-analysis indicate that the TNF-α rs1800629, rs361525 and rs1799724 polymorphisms are not correlated with prostate cancer development, although there were some pooled positive results. Further well-designed studies are necessary to form more precise conclusions.
Prevalence of class 1 integron in Escherichia coli isolated from animal sources in Iran: a systematic review and meta-analysis
Authors: Karimi Dehkordi Maryam , Halaji Mehrdad , Nouri Samereh
Published: April 2020

Background

Among the genetic elements, integrons may contribute to the widespread incidence and spreading of antibiotic resistance among Escherichia coli isolates. Accordingly, this review aims to investigate the prevalence of class 1 integron in E. coli isolated from animal sources in Iran.

Methods

This systematic literature search was performed from January 1, 2000 to the end of May 1, 2019.

Then, publications that met our inclusion criteria were selected for data extraction and analysis. Also, the quality of included studies was independently assessed by two researchers based on the Joanna Briggs Institute. Meta-analysis was performed by the Comprehensive Meta-Analysis (CMA) software using the random effects model, Cochran’s Q, and I2 tests. Publication bias was estimated by funnel plot and Egger’s linear regression test.

Results

Based on inclusion criteria, five studies were included to meta-analysis. From those studies, the pooled prevalence of integrons was 33% (95% CI, 23.8–43.7%) ranging from 23.8 to 52.4%. There was a significant heterogeneity among the 5 studies (χ2 = 11.73; p < 0.019; I2 = 65.91%). Additionally, Begg’s and Egger’s tests were performed to quantitatively evaluate the publication biases. According to the results of Begg’s test (z = 1.22, p = 0.22) and Egger’s test (t = 3.03, p = 0.056), a significant publication bias was not observed.

Conclusions

Our finding revealed the relatively high prevalence of class 1 integrons among E. coli isolates. Moreover, there was a significant heterogeneity among studies and subgroup analysis also showed that there was no difference about prevalence of class 1 integrons among different sample source.
Theoretical framework for predicting solute concentrations and solute-induced stresses in finite volumes with arbitrary elastic fields
Authors: Gu Yejun , El-Awady Jaafar A.
Published: April 2020

A theoretical model for computing the interstitial solute concentration and the interstitial solute-induced stress field in a three-dimensional finite medium with any arbitrary elastic fields was developed. This model can be directly incorporated into two-dimensional or three-dimensional discrete dislocation dynamics simulations, continuum dislocation dynamics simulations, or crystal plasticity simulations. Using this model, it is shown that a nano-hydride can form in the tensile region below a dissociated edge dislocation at hydrogen concentration as low as χ0=5×10−5, and its formation induces a localized hydrogen elastic shielding effect that leads to a lower stacking fault width for the edge dislocation. Additionally, the model also predicts the segregation of hydrogen at Σ109(13 7 0)/33.4∘ symmetric tilt grain boundary dislocations. This segregation strongly alters the magnitude of the shear stresses at the grain boundary, which can subsequently alter dislocation-grain boundary interactions and dislocation slip transmissions across the grain boundary. Moreover, the model also predicts that the hydrogen concentration at a mode-I central crack tip increases with increasing external loading, higher intrinsic hydrogen concentration, and/or larger crack lengths. Finally, linearized approximate closed-form solutions for the solute concentration and the interstitial solute-induced stress field were also developed. These approximate solutions can effectively reduce the computation cost to assess the concentration and stress field in the presence of solutes. These approximate solutions are also shown to be a good approximation when the positions of interest are several nanometers away (i.e. long-ranged elastic interactions) from stress singularities (e.g. dislocation core and crack tip), for low solute concentrations, and/or at high temperatures.
Skin manifestations of malnutrition in HIV-positive meningitis patients
Authors: Amalakanti Sridhar
Published: April 2020

Background

HIV infection and meningitis are diseases which are known to precipitate malnutrition. Skin manifestations of malnutrition are easy to identify. We tried to describe the skin manifestations of malnutrition in HIV-positive patients with meningitis.

Setting

Patients included in the study were from a tertiary referral hospital in South India.

Methods

In a cross-sectional observational design, we studied 56 adult [> 14 years] HIV-seropositive patients with meningitis by clinical assessment of skin manifestations of malnutrition.

Results

Skin wasting (31.5%), hyperpigmentation of skin (22.2%) and skin ulceration (16.4%) were the chief skin manifestations of malnutrition in HIV-positive patients with meningitis.

Conclusions

Our study shows that certain cutaneous features of malnutrition like skin ulcers, skin wasting and hypo pigmentation are common in HIV patients with meningitis.
Endoscopic assisted microvascular decompression versus new antiepileptics and BOTOX in treatment of hemifacial spasm: a clinical trial
Authors: Morsy Moamen Mohamed , Foaud Wael Ahmed , Abu-Elenain Hisham Adel , Aly Mohammed Abbas
Published: April 2020

Introduction

Hemifacial spasm (HFS) is a chronic movement disorder characterized by twitching of muscles of facial expression which is innervated by the facial nerve. The condition is unilaterally, beginning in the orbicularis occuli, and later on progress to involve the perioral, platysma, and other muscles of facial expression. Endoscopic assisted microvascular decompression is considered the state of the art in hemi-facial spasm surgery. New antiepileptic have emerged with a new hope for good control with few side effects. Botulinum toxin is still a good option for some patients.

Methods

This study is a prospective study that was conducted on 30 patients with primary hemifacial spasm. Bilateral and secondary cases where excluded. All patients were subjected to proper pre-treatment assessment including; proper history taking, clinical examination, and proper radiological investigations (MRI, FISTA) when needed. They were divided into three groups according to treatment modality: group A where patient's general condition was unfit for surgical intervention, received oral medications (gabapentin or levetiracetam); group B included those patients unfit for surgical intervention and did not respond to oral therapy, received Botox injection; and group C underwent endoscopic assisted microvascular decompression. Follow-up period ranged from 6 to 24 months. Outcome of different treatment modalities were compared among different groups.

Results

Among group A patients, one patient showed excellent response to treatment (Gabapentin 1200 mg), three patients had good response, four patients had fair response, and three patients had poor response to treatment (one used levetiracetam, two used gabapentin). Overall success rate is 72.7%. Among group B patients, four patients enjoyed excellent response. Another four patients had good response, while three patients had fair response. Only one patient had poor response. Overall success rate was 83.3%. Among group C patients, five cases had excellent outcome and two cases had good outcome. Overall success rate is 100%.

Conclusion

Endoscopic assisted microvascular decompression offers the best chance to permanent cure with low complication rate. New antiepileptics (levetiracetam, gabapentin) provide a safe therapy for patients refusing surgical intervention. Botox is an attractive local therapy with reversible complications but with non-sustainable effect. From our results, we conclude that endoscopic assisted microvascular decompression is superior to either BOTOX or antiepiletics for the permanent cure of hemifacial spasm.
Asia–Gondwana connections indicated by Devonian fishes from Australia: palaeogeographic considerations
Authors: Young Gavin Charles , Lu Jing
Published: April 2020

Middle Palaeozoic vertebrate fossil occurrences are summarised for Australia, with reference to faunal connections between Asia and East Gondwana, as first indicated by fish distributions of Lower Devonian fossil sites. Major endemic groups discussed are pituriaspid (Australian) and galeaspid (Asian) agnathans, wuttagoonaspids (Australian) and antarctaspid (Antarctic, Australian, Asian) arthrodires, yunnanolepid and sinolepid antiarchs (South China, Indochina terrane, Australia), and early tetrapodomorphs (South China, Australia). More widespread groups that lived in shallow marine environments (lungfishes, buchanosteid arthrodires, antiarchBothriolepis) also show species groups shared between South China and East Gondwana. Exchange of continental facies fishes (e.g. tristichopterid tetrapodomorphs) may have been interrupted by marine transgression in the Frasnian, but were restored in the late Famennian with the appearance ofGrenfellaspisin eastern Australia, the only sinolepid antiarch known from outside Asia. The hypothesis of Gondwana dispersion and Asian accretion, to explain the collage of geological terranes forming modern east and southeast Asia, implies increasing dissimilarity with increasing age, but the Siluro-Devonian early vertebrate evidence is inconsistent with this. Previous cladistic analysis of Asian terranes predicted galeaspid agnathans on the Indochina terrane, and their subsequent discovery at Ly Hoa, Vietnam, confirms that Indochina and South China had come together across the Song Ma suture by Middle Devonian time.
Frequency of de novo atrial fibrillation in patients presenting with acute ischemic cerebrovascular stroke
Authors: Abdelnabi Mahmoud , Almaghraby Abdallah , Saleh Yehia , Özden Tok Özge , Kemaloğlu Öz Tuğba , Abdelkarim Ola , Badran Haitham
Published: April 2020

Background

Atrial fibrillation (AF) affects millions of people worldwide and can remain undiagnosed for years. It is a major cause of cerebrovascular stroke (CVS); hence, early detection is extremely important in order to decrease the risk of CVS. We conducted a retrospective observational study looking into the prevalence of silent AF in 3299 patients admitted from January 2014 to December 2017 in a tertiary care stroke specialized center. Ischemic CVS was confirmed either by using multislice computed tomography (MSCT) or magnetic resonance imaging (MRI) of the brain. AF was diagnosed by electrocardiography (ECG) at the time of admission or during the hospital stay. Patients with a history of AF were excluded from the study.

Results

Of the 3299 patients admitted by acute ischemic CVS, 707 (21.43%) had a history of AF and thus were excluded from the study. Of the remaining 2592 patients eligible for the study, 1666 (64.27%) were males with a mean age of 56.06 years (± 16.01). A total of 2313 (89.24%) patients remained in sinus rhythm throughout the hospital stay, 211 (8.14%) patients were in AF on admission, and 68 (2.62 %) patients developed AF during their hospital stay. The total number of newly diagnosed patients with AF was 279 (10.76%).

Conclusion

The prevalence of de novo atrial fibrillation in patients presented with acute cerebrovascular stroke is high. The implementation of good screening programs can significantly reduce the risk of disabilities and morbidities.
Kinesin-1-mediated axonal transport of CB1 receptors is required for cannabinoid-dependent axonal growth and guidance
Authors: Saez Trinidad M. M. , Fernandez Bessone Iván , Rodriguez María S. , Alloatti Matías , Otero María G. , Cromberg Lucas E. , Pozo Devoto Victorio M. , Oubiña Gonzalo , Sosa Lucas , Buffone Mariano G. , Gelman Diego M. , Falzone Tomás L.
Published: April 2020

Endocannabinoids (eCB) modulate growth cone dynamics and axonal pathfinding through the stimulation of cannabinoid type-1 receptors (CB1R), the function of which depends on their delivery and precise presentation at the growth cone surface. However, the mechanism involved in the axonal transport of CB1R and its transport role in eCB signaling remains elusive. As mutations in the kinesin-1 molecular motor have been identified in patients with abnormal cortical development and impaired white matter integrity, we studied the defects in axonal pathfinding and fasciculation in mice lacking the kinesin light chain 1 (Klc1−/−) subunit of kinesin-1. Reduced levels of CB1R were found in corticofugal projections and axonal growth cones in Klc1−/− mice. By live-cell imaging of CB1R-eGFP we characterized the axonal transport of CB1R vesicles and described the defects in transport that arise after KLC1 deletion. Cofilin activation, which is necessary for actin dynamics during growth cone remodeling, is impaired in the Klc1−/− cerebral cortex. In addition, Klc1−/− neurons showed expanded growth cones that were unresponsive to CB1R-induced axonal elongation. Together, our data reveal the relevance of kinesin-1 in CB1R axonal transport and in eCB signaling during brain wiring.
Mitochondrial–nuclear heme trafficking in budding yeast is regulated by GTPases that control mitochondrial dynamics and ER contact sites
Authors: Martinez-Guzman Osiris , Willoughby Mathilda M. , Saini Arushi , Dietz Jonathan V. , Bohovych Iryna , Medlock Amy E. , Khalimonchuk Oleh , Reddi Amit R.
Published: April 2020

Heme is a cofactor and signaling molecule that is essential for much of aerobic life. All heme-dependent processes in eukaryotes require that heme is trafficked from its site of synthesis in the mitochondria to hemoproteins located throughout the cell. However, the mechanisms governing the mobilization of heme out of the mitochondria, and the spatio-temporal dynamics of these processes, are poorly understood. Here, using genetically encoded fluorescent heme sensors, we developed a live-cell assay to monitor heme distribution dynamics between the mitochondrial inner membrane, where heme is synthesized, and the mitochondrial matrix, cytosol and nucleus. Surprisingly, heme trafficking to the nucleus is ∼25% faster than to the cytosol or mitochondrial matrix, which have nearly identical heme trafficking dynamics, potentially supporting a role for heme as a mitochondrial–nuclear retrograde signal. Moreover, we discovered that the heme synthetic enzyme 5-aminolevulinic acid synthase (ALAS, also known as Hem1 in yeast), and GTPases in control of the mitochondrial dynamics machinery (Mgm1 and Dnm1) and ER contact sites (Gem1), regulate the flow of heme between the mitochondria and nucleus. Overall, our results indicate that there are parallel pathways for the distribution of bioavailable heme.

This article has an associated First Person interview with the first author of the paper.