bluuebunny/crossref_metadata_2025 huggingface dataset:
Intramedullary Subependymoma of the Cervical Spinal Cord: A Case Report and Review of the Literature
Authors: Chapa Eiralí , González Juana , Morquecho Mauricio , Martínez José , Flores Mariana , De León Ángel , Quintana Oralia , Márquez Rodolfo
Published: March 2019

Subependymoma is a rare tumor of the central nervous system, representing 0.2 to 0.7% of all intracranial tumors. They are usually found in the fourth ventricle or in the walls of the lateral ventricles, often remaining asymptomatic. Subependymomas occur rarely in the cervical or thoracic spinal cord. Since its first description in the spinal cord by Boykin et al in 1954, only 47 cases have been reported. A 49-year-old man presented with a 4-year-long-lasting neck pain, which radiated to the upper right extremity for 4 years. It was insidious at onset and revealed gradual progression, difficulty in performing fine hand movements, and hyperalgesia. Magnetic resonance imaging revealed irregular hyperintensity of T2 and dilatation of the spinal cord from C4 to T1 with associated edema and an intramedullary lesion with central location. During the surgical event, a transoperative biopsy was performed that revealed loose fibrillary networks and groups of nuclei showing mild pleomorphism and microcystic formations. Histologically, we observed groups of cells with mild nuclear pleomorphism embedded in a dense, thin, glial fibrillar fundus, and microcystic formations. Immunohistochemical staining revealed diffuse positivity for the glial fibrillary acidic protein, and negative for the epithelial membrane antigen. Subependymoma accounts for 8.3% of all ependymal tumors. There are few descriptions of the cytologic features of the subependymoma because this neoplasm is rare and most commonly found incidentally in autopsies.
The Uncommon Trapezium Fracture: A Case Series
Authors: Beekhuizen S. R. , Quispel C. R. , Jasper J. , Deijkers R. L. M.
Published: March 2019

Background Isolated trapezium fractures are rare and account for only 1 to 5% of all carpal fractures but are still the third most common carpal fracture. Trapezium fractures are hard to detect and easily missed on standard radiographs. Trapezium fractures can be treated conservatively, as well as operatively, the best treatment is still debatable. Damage of the joint surface between the trapezium and the base of the first metacarpal or scaphoid could cause pain and restriction of movements. Therefore, it is important to diagnose and treat the fracture at early stage, so that articular congruence is guaranteed.

Case description We present four cases of the uncommon trapezium fracture. All four cases are conservatively treated with good results, there was no need for operative treatment in all the cases.

Literature review The literature describes the possibility to use fixation techniques, only when it is not possible to reduce the displaced fracture or the residual articular step-off is too high a fixation technique should be used.

Clinical relevance Primarily, we would recommend navicular cast immobilization for 4 to 6 weeks as initial treatment.
Mild Persistent Isolated Hypermethioninemia Identified through Newborn Screening in Michigan
Authors: Sen Kuntal , Felice Michael , Bannick Allison , Colombo Roberto , Conway Robert
Published: March 2019

Methionine S-adenosyltransferase deficiency, due to mutations in MAT1A, is the most common cause of persistent isolated hypermethioninemia (PIH). While the recessive form may cause neurological consequences, the dominant form is typically benign. This condition may be found in asymptomatic infants through newborn screening programs. We describe 16 asymptomatic individuals with PIH. Our data reiterates the benign nature of PIH and reports two novel mutations in the gene. There were a disproportionate number of individuals with African descent in this cohort.
Multi-reference broadband laser ranging to increase the measuring range
Authors: Wang Jing , Liu Shouxian , Li Jianzhong , Tao ShiXing , Chen Guanghua , Deng Xiangyang , Peng Qixian
Published: March 2019

Broadband laser ranging (BLR) is an appropriate method to obtain absolute distance in dynamic experiments. In this article, we first analyze the performance limit for BLR and indicate that the measuring range can be hardly increased while keeping the distance or time resolution unchanged. Then, multi-reference BLR is proposed, which can break this limit and greatly increase the measuring range. Its validity is demonstrated by an experiment with an explosively driven aluminum surface flying over 100 mm. This method would improve the capability of BLR.
Hybrid ‘super-semi’ structures exhibit unprecedented Josephson junction quality
Authors: Johnson Sally Cole
Published: March 2019

Transparent superconductor-semiconductor Josephson junction forms a three-terminal device that can be tuned via gate voltages.
Green Synthesized Plasmonic Silver Systems for Potential Non-Linear Optical Applications: Optical Limiting and Dual Beam Mode Matched Thermal Lensing
Authors: Thomas Jeena , Perikaruppan Prakash , Thomas Vinoy , John Jancy , Mathew Raji Mary , Thomas Joice , Rejeena Ibrahimkutty , Mathew Sebastian , Mujeeb Abdulhassan
Published: March 2019

Bioactive compound functionalized plasmonic systems are evolving as a promising branch of nanotechnology. In this communication the synthesis of bioactive compound mimosine-based silver nanoparticles (AgNPs) and their non-linear optical and thermo-optic properties are presented. UV-Visible spectroscopy, optical bandgap measurement, fluorescence spectroscopy, and high-resolution transmission electron microscopy (HRTEM) techniques were used to characterize the synthesized AgNPs. An open aperture z-scan technique was used to determine the non-linear optical parameters. A very strong reverse saturable absorption (RSA) and low optical limiting threshold were observed for the present mimosine decorated AgNP system. The thermo-optic property of the present system was evaluated using a highly sensitive dual beam mode matched thermal lensing spectroscopic technique. A comparison of the low limiting threshold (242MWcm−2) and thermo-optic property (thermal diffusivity, D=1.13×10−7m2s−1) with similar systems proves its capability for non-linear optical and thermo-optic applications.
Corrigendum to: Spatial and seasonal variability of emergent aquatic insects and nearshore spiders in a subtropical estuary
Authors: Zapata Martha J. , Sullivan S. Mažeika P.
Published: March 2019

Variability in the density and distribution of adult aquatic insects is an important factor mediating aquatic-to-terrestrial nutritional subsidies in freshwater ecosystems, yet less is understood about insect-facilitated subsidy dynamics in estuaries. We surveyed emergent (i.e. adult) aquatic insects and nearshore orb-weaving spiders of the families Tetragnathidae and Araneidae in a subtropical estuary of Florida (USA). Emergent insect community composition varied seasonally and spatially; densities were lower at high- than low-salinity sites. At high-salinity sites, emergent insects exhibited lower dispersal ability and a higher prevalence of univoltinism than low- and mid-salinity assemblages. Orb-weaving spider density most strongly tracked emergent insect density rates at low- and mid-salinity sites. Tetragnatha body condition was 96% higher at high-salinity sites than at low-salinity sites. Our findings contribute to our understanding of aquatic insect communities in estuarine ecosystems and indicate that aquatic insects may provide important nutritional subsidies to riparian consumers despite their depressed abundance and diversity compared with freshwater ecosystems.
Synthesis of a burkholdine analogue containing β-hydroxytyrosine
Authors: Kato Seiya , Sasaki Mio , Yano Shigekazu , Konno Hiroyuki
Published: March 2019

Synthesis of a β-OHTyr-containing Bk analogue, a cyclic octalipopeptide with antifungal activities, is described. Since β-OHTyr-containing peptides generally are unstable in strong acidic conditions, synthesis of β-HOTyr-containing peptides by SPPS have rarely been reported. To overcome this problem, we found that using distilled TFA removed the protecting groups of side chains of β-OHTyr-containing Bk analogue, which was prepared by Fmoc-SPPS.

Abbreviations: β-OHTyr: β-hydroxytyrosine; β-OHAsn: β-hydroxyasparagine; Bk: burkholdine; FAA: fatty acyl amino acid; β-MeOTyr: β-methoxytyrosine; SPPS: solid phase peptide synthesis; MIC: minimun inhibitory concentration; DMF: dimethyl formamide; DIPEA: diisopropylethylamine; DIPC: diisopropylcarbodiimide; HOBt: 1-hydroxybenzotriazole; Fmoc: 9-fluorenylmethyloxycarbonyl; HFIP: 1,1,1,3,3,3-hexafluoropropan-2-ol; TFA: trifluoroacetic acid; LAP: N-lauryl −3-amino-4-carbamolypropanoic acid; HPLC: high performance liquid chromatography; ESI-TOFMS: electrospray ionization-time of flight mass spectrometry; Bn: benzyl; Boc: t-butyloxycatbonyl; 2-CTC: 2-chlorotritylchloride.
LncRNA CASC11 improves atherosclerosis by downregulating IL-9 and regulating vascular smooth muscle cell apoptosis and proliferation
Authors: Tao Kaiyu , Hu Zhanglong , Zhang Yigong , Jiang Daming , Cheng Haifeng
Published: March 2019

LncRNA CASC11 is an oncogene in several types of cancer, while its role in atherosclerosis is unknown. In the present study we found that CASC11 was downregulated, while IL-9 was upregulated in plasma of atherosclerosis patients compared with healthy controls. Altered plasma levels of CASC11 and IL-9 distinguished atherosclerosis patients from healthy controls. CASC11 and IL-9 were significantly and inversely correlated in atherosclerosis patients but not in healthy controls. Exogenous IL-9 treatment failed to significantly affect expression levels of CASC11 in vascular smooth muscle cells (VSMC), while CASC11 overexpression resulted in the downregulation of IL-9. CASC11 overexpression also resulted in the downregulation of proliferation and promoted apoptosis of VSMC. Therefore, CASC11 may improve atherosclerosis by downregulating IL-9 and regulating VSMC apoptosis and proliferation.
Validation of a scale to measure perceived residential environment quality in a Latin American setting / Validación de una escala para medir la percepción de la calidad del entorno residencial en un contexto latinoamericano
Authors: von-Breymann Helga , Montenegro-Montenegro Esteban
Published: March 2019

This article presents the findings of a research project that aimed to validate, in a Latin American setting, a scale to measure perceived residential environment quality (PREQ), developed principally on the basis of several studies conducted in different Italian cities in the 1990s. The instrument, a questionnaire comprising 19 sub-scales, was completed by 394 residents of Flores, in the canton of Heredia, Costa Rica. The scales were validated using Confirmatory Factor Analysis (CFA). The results confirm reliability and validity for the majority of the 12 factors examined, in spite of geographical, morphological and socio-cultural dissimilarities between the different urban contexts where the studies were conducted. The scales for which a favourable result was not obtained were reconfigured and yielded good fit indices, also managing to reduce the number of factors to 11 ((1) Architecture and Urban Space; (2) Mobility, Transport and Connectivity; (3) Green Areas; (4) Socio-Relational Features; (5) Social Care; (6) Recreational Services; (7) Commercial Services; (8) Pace of Life; (9) Environmental Health; (10) Upkeep; (11) Place Attachment) along with the total number of items included on the instrument.
Codifference can detect ergodicity breaking and non-Gaussianity
Authors: Ślęzak Jakub , Metzler Ralf , Magdziarz Marcin
Published: March 2019

We show that the codifference is a useful tool in studying the ergodicity breaking and non-Gaussianity properties of stochastic time series. While the codifference is a measure of dependence that was previously studied mainly in the context of stable processes, we here extend its range of applicability to random-parameter and diffusing-diffusivity models which are important in contemporary physics, biology and financial engineering. We prove that the codifference detects forms of dependence and ergodicity breaking which are not visible from analysing the covariance and correlation functions. We also discuss a related measure of dispersion, which is a nonlinear analogue of the mean squared displacement.
The NOMAD laboratory: from data sharing to artificial intelligence
Authors: Draxl Claudia , Scheffler Matthias
Published: March 2019

The Novel Materials Discovery (NOMAD) Laboratory is a user-driven platform for sharing and exploiting computational materials science data. It accounts for the various aspects of data being a crucial raw material and most relevant to accelerate materials research and engineering. NOMAD, with the NOMAD Repository, and its code-independent and normalized form, the NOMAD Archive, comprises the worldwide largest data collection of this field. Based on its findable accessible, interoperable, reusable data infrastructure, various services are offered, comprising advanced visualization, the NOMAD Encyclopedia, and artificial-intelligence tools. The latter are realized in the NOMAD Analytics Toolkit. Prerequisite for all this is the NOMAD metadata, a unique and thorough description of the data, that are produced by all important computer codes of the community. Uploaded data are tagged by a persistent identifier, and users can also request a digital object identifier to make data citable. Developments and advancements of parsers and metadata are organized jointly with users and code developers. In this work, we review the NOMAD concept and implementation, highlight its orthogonality to and synergistic interplay with other data collections, and provide an outlook regarding ongoing and future developments.
rMTA: robust metabolic transformation analysis
Authors: Valcárcel Luis V , Torrano Verónica , Tobalina Luis , Carracedo Arkaitz , Planes Francisco J
Published: March 2019

Motivation

The development of computational tools exploiting -omics data and high-quality genome-scale metabolic networks for the identification of novel drug targets is a relevant topic in Systems Medicine. Metabolic Transformation Algorithm (MTA) is one of these tools, which aims to identify targets that transform a disease metabolic state back into a healthy state, with potential application in any disease where a clear metabolic alteration is observed.

Results

Here, we present a robust extension to MTA (rMTA), which additionally incorporates a worst-case scenario analysis and minimization of metabolic adjustment to evaluate the beneficial effect of gene knockouts. We show that rMTA complements MTA in the different datasets analyzed (gene knockout perturbations in different organisms, Alzheimer’s disease and prostate cancer), bringing a more accurate tool for predicting therapeutic targets.

Availability and implementation

rMTA is freely available on The Cobra Toolbox: https://opencobra.github.io/cobratoolbox/latest/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Shouji: a fast and efficient pre-alignment filter for sequence alignment
Authors: Alser Mohammed , Hassan Hasan , Kumar Akash , Mutlu Onur , Alkan Can
Published: March 2019

Motivation

The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes. We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator that adopts modern field-programmable gate array (FPGA) architectures to further boost the performance of our algorithm.

Results

Shouji significantly improves the accuracy of pre-alignment filtering by up to two orders of magnitude compared to the state-of-the-art pre-alignment filters, GateKeeper and SHD. Our FPGA-based accelerator is up to three orders of magnitude faster than the equivalent CPU implementation of Shouji. Using a single FPGA chip, we benchmark the benefits of integrating Shouji with five state-of-the-art sequence aligners, designed for different computing platforms. The addition of Shouji as a pre-alignment step reduces the execution time of the five state-of-the-art sequence aligners by up to 18.8×. Shouji can be adapted for any bioinformatics pipeline that performs sequence alignment for verification. Unlike most existing methods that aim to accelerate sequence alignment, Shouji does not sacrifice any of the aligner capabilities, as it does not modify or replace the alignment step.

Availability and implementation

https://github.com/CMU-SAFARI/Shouji.

Supplementary information

Supplementary data are available at Bioinformatics online.
Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies
Authors: Zemeckis Douglas R , Dean Micah J , DeAngelis Annamaria I , Van Parijs Sofie M , Hoffman William S , Baumgartner Mark F , Hatch Leila T , Cadrin Steven X , McGuire Christopher H
Published: March 2019

Effective fishery management measures to protect fish spawning aggregations require reliable information on the spatio-temporal distribution of spawning. Spawning closures have been part of a suite of fishery management actions to rebuild the Gulf of Maine stock of Atlantic cod (Gadus morhua), but difficulties remain with managing rebuilding. The objective of this study was to identify the spatial and temporal distribution of cod spawning during winter in Massachusetts Bay to improve our understanding of cod spawning dynamics and inform fisheries management. Spawning was investigated in collaboration with commercial fishermen during three winter spawning seasons (October 2013–March 2016) using acoustic telemetry and passive acoustic monitoring equipment deployed in fixed-station arrays and mounted on mobile autonomous gliders. Tagged cod exhibited spawning site fidelity and spawning primarily occurred from early November through January with a mid-December peak and some inter-annual variability. The spatial distribution of spawning was generally consistent among years with multiple hotspots in areas >50 m depth. Current closures encompass most of spawning, but important areas are recommended for potential modifications. Utilizing multiple complementary technologies and deployment strategies in collaboration with commercial fishermen enabled a comprehensive description of spawning and provides a valuable model for future studies.
Antibacterial effect of imipenem/relebactam on aerobic Gram-negative bacilli: in vitro simulations of 7 or 14 day human exposures
Authors: Noel Alan R , Bowker Karen E , Attwood Marie , MacGowan Alasdair P
Published: March 2019

Objectives

We assessed the antibacterial effect of human simulations of dosing with imipenem/relebactam (with or without amikacin) on Enterobacteriaceae or Pseudomonas aeruginosa over 7 or 14 day antibiotic exposures.

Methods

An in vitro pharmacokinetic model was used to assess changes in bacterial load and population profiles.

Results

Imipenem/relebactam produced an initial >4 log drop in viable counts followed by suppression for 7 days for Enterobacteriaceae whether the strain was WT, produced KPC enzymes or produced an AmpC enzyme with porin loss. Similarly, with the P. aeruginosa strains, there was an initial >4 log clearance over the first 24 h irrespective of whether the strain was WT, hyperexpressed AmpC or had OprD mutation with porin loss. However, with three of four strains there was modest regrowth over the 7 days. There were no changes in imipenem/relebactam MICs over the 7 days. Addition of amikacin in 7 day simulations resulted in more suppression of pseudomonal growth. In 14 day simulations with P. aeruginosa there was regrowth to 8 log10 by 14 days with imipenem/relebactam alone and associated increases in MICs. Addition of amikacin resulted in clearance from the model and prevented changes in population profiles.

Conclusions

Imipenem/relebactam was highly effective at reducing the bacterial load of Enterobacteriaceae and there was no emergence of resistance. Against P. aeruginosa, the initial bacterial burden was also rapidly reduced, but there was subsequent regrowth, especially after 7 days of exposure. Addition of amikacin increased the clearance of P. aeruginosa and prevented emergence of resistance.
Improvements in Gulf War Illness Symptoms After Near-Infrared Transcranial and Intranasal Photobiomodulation: Two Case Reports
Authors: Chao Linda L
Published: March 2019

At least one-fourth of US veterans who served in the 1990–1991 Gulf War (GW) are affected by the chronic symptomatic illness known as Gulf War illness (GWI). This condition typically includes some combination of fatigue, headaches, cognitive dysfunction, musculoskeletal pain, and respiratory, gastrointestinal and dermatologic complaints. To date, effective treatments for GWI have been elusive. Photobiomodulation (PBM) describes the non-pharmacological, non-thermal use of light to stimulate, heal, and protect tissue that has either been injured, is degenerating, or else is at risk of dying. Significant benefits have been reported following application of transcranial PBM to humans with acute stoke, traumatic brain injury (TBI), and dementia. This report describes the first documentation of improved GWI symptoms in two GW veterans following 12 weeks of PBM treatments.
The time delay between star formation quenching and morphological transformation of galaxies in clusters: a phase–space view of EDisCS
Authors: Kelkar Kshitija , Gray Meghan E , Aragón-Salamanca Alfonso , Rudnick Gregory , Jaffé Yara L , Jablonka Pascale , Moustakas John , Milvang-Jensen Bo
Published: March 2019

We explore the possible effect of cluster environments on the structure and star formation histories of galaxies by analysing the projected phase–space (PPS) of intermediate-redshift clusters (0.4 ≤ z ≤ 0.8). HST I−band imaging data from the ESO Distant Cluster Survey (EDisCS) allow us to measure deviations of the galaxies’ light distributions from symmetric and smooth profiles using two parameters, Ares (‘asymmetry’) and RFF (residual flux fraction or ‘roughness’). Combining these structural parameters with age-sensitive spectral indicators ($H_{\delta \rm {A}}$, $H_{\gamma \rm {A}}$, and Dn4000), we establish that in all environments younger star-forming galaxies of all morphologies are ‘rougher’ and more asymmetric than older, more quiescent ones. Combining a subset of the EDisCS clusters, we construct a stacked PPS diagram and find a significant correlation between the position of the galaxies on the PPS and their stellar ages, irrespective of their morphology. We also observe an increasing fraction of galaxies with older stellar populations towards the cluster core, while the galaxies’ structural parameters (Ares and RFF) do not seem to segregate strongly with PPS. These results may imply that, under the possible influence of their immediate cluster environment, galaxies have their star formation suppressed earlier, while their structural transformation happens on a longer time-scale as they accumulate and age in the cluster cores.
Association of changes in bone mineral parameters with mortality in haemodialysis patients: insights from the ARO cohort
Authors: Lamina Claudia , Kronenberg Florian , Stenvinkel Peter , Froissart Marc , Forer Lukas , Schönherr Sebastian , Wheeler David C , Eckardt Kai-Uwe , Floege Jürgen
Published: March 2019

Background

There is little information in haemodialysis (HD) patients on whether temporal changes in serum calcium, phosphate or intact parathyroid hormone (iPTH) are associated with mortality.

Methods

We analysed associations of phosphate, total calcium and iPTH with all-cause and cardiovascular mortality in 8817 incident HD patients from the European second Analyzing Data, Recognizing Excellence and Optimizing Outcomes (AROii) cohort enrolled in 2007–09, which were prospectively followed for a median of 3 years, using time-dependent Cox proportional hazards models. We evaluated changes in risk over time depending on changes in phosphate, calcium or iPTH.

Results

The association of phosphate and iPTH with all-cause mortality was U-shaped, with the lowest risk ranges between 1.20 and 1.89 mmol/L for phosphate and between 239 and 710 ng/L for iPTH. For total calcium, the associations were J-shaped, with an increased risk for all-cause mortality at levels >2.36 mmol/L. Lowest risk ranges for cardiovascular mortality did not change markedly for all three parameters. If iPTH was below the lowest risk range at baseline (iPTH <239 ng/L), a subsequent increase in levels was associated with improved survival. For phosphate, an increase or decrease out of the lowest risk range was associated with increased mortality risk. For calcium, this was only the case when the values increased above the lowest risk range.

Conclusion

In the AROii cohort, the ranges of bone mineral biomarkers associated with the lowest mortality ranges were largely consistent with the current Kidney Disease: Improving Global Outcomes chronic kidney disease–mineral and bone disorder guideline recommendations. Allowing a suppressed iPTH to increase was associated with a lower mortality, whereas shifts of phosphate or calcium outside the lowest risk range increased mortality.
Integrating morphological and molecular taxonomy with the revised concept of Stelligeridae (Porifera: Demospongiae)
Authors: Morrow Christine , Cárdenas Paco , Boury-Esnault Nicole , Picton Bernard , McCormack Grace , Van Soest Rob , Collins Allen , Redmond Niamh , Maggs Christine , Sigwart Julia , Allcock Louise A
Published: March 2019

This study reinforces and extends the findings of previous molecular studies showing that there is a close relationship between species assigned to the sponge genera Halicnemia, Higginsia, Paratimea and Stelligera and that the family Heteroxyidae is polyphyletic. The present study has led to the description of one new species of Halicnemia and six new species of Paratimea, the resurrection of Halicnemia gallica and a better understanding of the characters uniting Stelligeridae. A new species of Heteroxya is also described. We demonstrate that many of the taxa assigned to Heteroxyidae are more closely related to other families, and we propose several changes to the classification of Heteroscleromorpha. Desmoxyidae is resurrected from synonymy and transferred to Poecilosclerida; Higginsia anfractuosa is transferred to Hymedesmiidae, and a new genus, Hooperia, is erected for its reception; Higginsia durissima is returned to Bubaris (Bubaridae); Higginsia fragilis is transferred to Spanioplon (Hymedesmiidae); Hemiasterella camelus is transferred to Paratimea; and Raspailia (Parasyringella) australiensis and Ceratopsion axiferum are transferred to Adreus (Hemiasterellidae).
Cross Pathogenicity Studies Show South Dakota Isolates of Fusarium acuminatum, F. equiseti, F. graminearum, F. oxysporum, F. proliferatum, F. solani, and F. subglutinans from Either Soybean or Corn are Pathogenic to Both Crops
Authors: Okello Paul N. , Mathew Febina M.
Published: March 2019

In South Dakota, despite that integrated pest management options are available, Fusarium root rot is an emerging disease on soybean (Glycine max L.) and corn (Zea mays L.). Surveys were conducted across South Dakota on soybean and corn fields in 2014 and 2015, respectively, to assess the prevalence of species of Fusarium causing root rot. Fusarium acuminatum, F. equiseti, F. graminearum, F. oxysporum, F. proliferatum, F. solani, and F. subglutinans were identified common to soybean and corn. A total of 21 isolates, representing these seven species, were evaluated for their pathogenicity on soybean (‘Williams 82’) and corn (‘B73’) using the inoculum layer inoculation method in the greenhouse. At 14 days postinoculation, the seedlings were evaluated for root rot severity (1-to-5 rating scale), and relative treatment effects (RTEs) were estimated. A significant effect of the treatments was observed on RTE for soybean (P = 1.1 × 10−7) and corn (P = 3.0 × 10−14). Two F. proliferatum isolates and one F. graminearum isolate from corn caused significantly greater RTE than the other treatments (including the noninoculated control) on soybean and corn. Results indicate that soybean and corn can serve as inoculum sources of the seven species of Fusarium that are pathogenic to both crops.
Vagus Nerve Stimulation Attenuates Multiple Organ Dysfunction in Resuscitated Porcine Progressive Sepsis
Authors: Kohoutova Michaela , Horak Jan , Jarkovska Dagmar , Martinkova Vendula , Tegl Vaclav , Nalos Lukas , Vistejnova Lucie , Benes Jan , Sviglerova Jitka , Kuncova Jitka , Matejovic Martin , Stengl Milan
Published: March 2019

Objectives:

To investigate the potential benefits of vagus nerve stimulation in a clinically-relevant large animal model of progressive sepsis.

Design:

Prospective, controlled, randomized trial.

Setting:

University animal research laboratory.

Subjects:

Twenty-five domestic pigs were divided into three groups: 1) sepsis group (eight pigs), 2) sepsis + vagus nerve stimulation group (nine pigs), and 3) control sham group (eight pigs).

Interventions:

Sepsis was induced by cultivated autologous feces inoculation in anesthetized, mechanically ventilated, and surgically instrumented pigs and followed for 24 hours. Electrical stimulation of the cervical vagus nerve was initiated 6 hours after the induction of peritonitis and maintained throughout the experiment.

Measurements and Main Results:

Measurements of hemodynamics, electrocardiography, biochemistry, blood gases, cytokines, and blood cells were collected at baseline (just before peritonitis induction) and at the end of the in vivo experiment (24 hr after peritonitis induction). Subsequent in vitro analyses addressed cardiac contractility and calcium handling in isolated tissues and myocytes and analyzed mitochondrial function by ultrasensitive oxygraphy. Vagus nerve stimulation partially or completely prevented the development of hyperlactatemia, hyperdynamic circulation, cellular myocardial depression, shift in sympathovagal balance toward sympathetic dominance, and cardiac mitochondrial dysfunction, and reduced the number of activated monocytes. Sequential Organ Failure Assessment scores and vasopressor requirements significantly decreased after vagus nerve stimulation.

Conclusions:

In a clinically-relevant large animal model of progressive sepsis, vagus nerve stimulation was associated with a number of beneficial effects that resulted in significantly attenuated multiple organ dysfunction and reduced vasopressor and fluid resuscitation requirements. This suggests that vagus nerve stimulation might provide a significant therapeutic potential that warrants further thorough investigation.
Cellular parabiosis and the latency of age-related diseases
Authors: Radman Miroslav
Published: March 2019

Cellular parabiosis is tissue-based phenotypic suppression of cellular dysfunction by intercellular molecular traffic keeping initiated age-related diseases and conditions in long latency. Interruption of cellular parabiosis (e.g. by chronic inflammation) promotes the onset of initiated pathologies.

The stability of initiated latent cancers and other age-related diseases (ARD) hints to phenotypically silent genome alterations. I propose that latency in the onset of ageing and ARD is largely due to phenotypic suppression of cellular dysfunctions via molecular traffic among neighbouring cells. Intercellular trafficking ranges from the transfer of ions and metabolites (via gap junctions) to entire organelles (via tunnelling nanotubes). Any mechanism of cell-to-cell communication resulting in functional cross-complementation among the cells is called
cellular parabiosis
. Such ‘cellular solidarity’ creates tissue homeostasis by buffering defects and averaging cellular functions within the tissues. Chronic inflammation is known to (i) interrupt cellular parabiosis by the activity of extracellular proteases, (ii) activate dormant pathologies and (iii) shorten disease latency, as in tumour promotion and inflammaging. Variation in cellular parabiosis and protein oxidation can account for interspecies correlations between body mass, ARD latency and longevity. Now, prevention of ARD onset by phenotypic suppression, and healing by phenotypic reversion, become conceivable.
Sleep restriction caused impaired emotional regulation without detectable brain activation changes—a functional magnetic resonance imaging study
Authors: Tamm Sandra , Nilsonne Gustav , Schwarz Johanna , Golkar Armita , Kecklund Göran , Petrovic Predrag , Fischer Håkan , Åkerstedt Torbjörn , Lekander Mats
Published: March 2019

Sleep restriction has been proposed to cause impaired emotional processing and emotional regulation by inhibiting top-down control from prefrontal cortex to amygdala. Intentional emotional regulation after sleep restriction has, however, never been studied using brain imaging. We aimed here to investigate the effect of partial sleep restriction on emotional regulation through cognitive reappraisal. Forty-seven young (age 20–30) and 33 older (age 65–75) participants (38/23 with complete data and successful sleep intervention) performed a cognitive reappraisal task during fMRI after a night of normal sleep and after restricted sleep (3 h). Emotional downregulation was associated with significantly increased activity in the dorsolateral prefrontal cortex (
p
FWE
< 0.05) and lateral orbital cortex (
p
FWE
< 0.05) in young, but not in older subjects. Sleep restriction was associated with a decrease in self-reported regulation success to negative stimuli (
p
< 0.01) and a trend towards perceiving all stimuli as less negative (
p
= 0.07) in young participants. No effects of sleep restriction on brain activity nor connectivity were found in either age group. In conclusion, our data do not support the idea of a prefrontal-amygdala disconnect after sleep restriction, and neural mechanisms underlying behavioural effects on emotional regulation after insufficient sleep require further investigation.
A simple micropump based on a freeze-dried superabsorbent polymer for multiplex solution processing in disposable devices
Authors: Biswas Gokul Chandra , Rana Md. Mohosin , Kazuhiro Takekoshi , Suzuki Hiroaki
Published: March 2019

We describe a simple micropump for disposable microfluidic devices. The pump is constructed using a freeze-dried disc of a superabsorbent polymer (SAP). The disc absorbs a solution in a flow channel and swells upward in a pumping chamber. Despite the simple structure of this device, the rate of absorption remains constant and can be adjusted by changing the composition of the SAP, its size, the dimensions of the flow channel and the medium to be absorbed. The pumping action can be initiated by applying an electrical signal using a switchable hydrophobic valve. The integrated approach of the SAP pump and switchable valve could facilitate the automatic processing of many solutions required for bioassay.
Shifts in cranial integration associated with ecological specialization in pinnipeds (Mammalia, Carnivora)
Authors: Randau Marcela , Sanfelice Daniela , Goswami Anjali
Published: March 2019

Patterns of trait integration reflect the underlying genetic and developmental architecture of morphology and significantly influence the direction of evolution. Nevertheless, the relationship between integration and disparity is complex and unlikely to be uniform across large phylogenetic and ecological scales. To date, there are little data comparing patterns of integration across major ecological transitions, limiting understanding of the processes driving changes in trait integration and their consequences. Here, we investigated patterns of cranial integration and disparity across pinnipeds, three closely related carnivoran families that have undergone a secondary adaptation to the aquatic niche with varying levels of ecological differentiation. With a three-dimensional geometric morphometric dataset of 677 specimens spanning 15 species, we compared five models of trait integration, and examined the effects of sexual dimorphism and allometry on model support. Pinnipeds varied greatly in patterns of cranial integration compared to terrestrial carnivorans. Interestingly, this variation is concentrated in phocids, which may reflect the broader range of ecological and life-history specializations across phocid species, and greater independence from the terrestrial habitat observed in that group, relative to otariids. Overall, these results indicate that major ecological transitions, and presumably large changes in selection pressures, may drive changes in phenotypic trait integration.
Flexible identification procedure for thermodynamic constitutive models for magnetostrictive materials
Authors: Rasilo Paavo , Singh Deepak , Jeronen Juha , Aydin Ugur , Martin Floran , Belahcen Anouar , Daniel Laurent , Kouhia Reijo
Published: March 2019

We present a novel approach for identifying a multiaxial thermodynamic magneto-mechanical constitutive law by direct bi- or trivariate spline interpolation from available magnetization and magnetostriction data. Reference data are first produced with a multiscale model in the case of a magnetic field and uniaxial and shear stresses. The thermodynamic model fits well to the results of the multiscale model, after which the models are compared under complex multiaxial loadings. A surprisingly good agreement between the two models is found, but some differences in the magnetostrictive behaviour are also pointed out. Finally, the model is fitted to measurement results from an electrical steel sheet. The spline-based constitutive law overcomes several drawbacks of analytical approaches used earlier. The presented models and measurement results are openly available.
The evolution of life-history theory: a bibliometric analysis of an interdisciplinary research area
Authors: Nettle Daniel , Frankenhuis Willem E.
Published: March 2019

The term ‘life-history theory’ is a familiar label in several disciplines. Life-history theory has its roots in evolutionary models of the fitness consequences of allocating energy to reproduction, growth and self-maintenance across the life course. Increasingly, the term is also used in the conceptual framing of psychological and social-science studies. As a scientific paradigm expands its range, its parts can become conceptually isolated from one another, even to the point that it is no longer held together by a common core of shared ideas. Here, we investigate the literature invoking the term ‘life-history theory’ using quantitative bibliometric methods based on patterns of shared citation. Results show that the literature up to and including 2010 was relatively coherent: it drew on a shared body of core references and had only weak cluster divisions running along taxonomic lines. The post-2010 literature is more fragmented: it has more marked cluster boundaries, both between the human and non-human literatures, and within the human literature. In particular, two clusters of human research based on the idea of a fast–slow continuum of individual differences are bibliometrically isolated from the rest. We also find some evidence suggesting a decline over time in the incidence of formal modelling. We point out that the human fast–slow continuum literature is conceptually closer to the non-human ‘pace-of-life’ literature than it is to the formal life-history framework in ecology and evolution.
Darwin review: angiosperm phylogeny and evolutionary radiations
Authors: Soltis Pamela S. , Folk Ryan A. , Soltis Douglas E.
Published: March 2019

Darwin's dual interests in evolution and plants formed the basis of evolutionary botany, a field that developed following his publications on both topics. Here, we review his many contributions to plant biology—from the evolutionary origins of angiosperms to plant reproduction, carnivory, and movement—and note that he expected one day there would be a ‘true’ genealogical tree for plants. This view fuelled the field of plant phylogenetics. With perhaps nearly 400 000 species, the angiosperms have diversified rapidly since their origin in the Early Cretaceous, often through what appear to be rapid radiations. We describe these evolutionary patterns, evaluate possible drivers of radiations, consider how new approaches to studies of diversification can contribute to our understanding of angiosperm diversity, and suggest new directions for further insight into plant evolution.
Drivers of geographical patterns of North American language diversity
Authors: Pacheco Coelho Marco Túlio , Pereira Elisa Barreto , Haynie Hannah J. , Rangel Thiago F. , Kavanagh Patrick , Kirby Kathryn R. , Greenhill Simon J. , Bowern Claire , Gray Russell D. , Colwell Robert K. , Evans Nicholas , Gavin Michael C.
Published: March 2019

Although many hypotheses have been proposed to explain why humans speak so many languages and why languages are unevenly distributed across the globe, the factors that shape geographical patterns of cultural and linguistic diversity remain poorly understood. Prior research has tended to focus on identifying universal predictors of language diversity, without accounting for how local factors and multiple predictors interact. Here, we use a unique combination of path analysis, mechanistic simulation modelling, and geographically weighted regression to investigate the broadly described, but poorly understood, spatial pattern of language diversity in North America. We show that the ecological drivers of language diversity are not universal or entirely direct. The strongest associations imply a role for previously developed hypothesized drivers such as population density, resource diversity, and carrying capacity with group size limits. The predictive power of this web of factors varies over space from regions where our model predicts approximately 86% of the variation in diversity, to areas where less than 40% is explained.
Two accessory proteins govern MmpL3 mycolic acid transport in mycobacteria
Authors: Fay Allison , Czudnochowski Nadine , Rock Jeremy , Johnson Jeffrey R. , Krogan Nevan J. , Rosenberg Oren , Glickman Michael S.
Published: March 2019

Mycolic acids are the signature lipid of mycobacteria and constitute an important physical component of the cell wall, a target of mycobacterial specific antibiotics, and a mediator of M. tuberculosis pathogenesis. Mycolic acids are synthesized in the cytoplasm and are thought to be transported to the cell wall as a trehalose ester by the MmpL3 transporter, an antibiotic target for M. tuberculosis. However, the mechanism by which mycolate synthesis is coupled to transport, and the full MmpL3 transport machinery, is unknown. Here we identify two new components of the MmpL3 transport machinery in mycobacteria. The protein encoded by MSMEG_0736/Rv0383c is essential for growth of M. smegmatis and M. tuberculosis, is anchored to the cytoplasmic membrane, physically interacts with and colocalizes with MmpL3 in growing cells, and is required for trehalose monomycolate transport to the cell wall. In light of these findings we propose Msmeg_0736/Rv0383c be named “TMM transport factor A”, TtfA. The protein encoded by MSMEG_5308 also interacts with the MmpL3 complex, but is nonessential for growth or TMM transport. However, MSMEG_5308 accumulates with inhibition of MmpL3 mediated TMM transport and stabilizes the MmpL3/TtfA complex, indicating that it stabilizes the transport system during stress. These studies identify two new components of the mycobacterial mycolate transport machinery, an emerging antibiotic target in M. tuberculosis.
The C-terminal domains SnRK2-box and ABA-box have a role in sugarcane SnRK2s auto-activation and activity
Authors: Righetto Germanna , Sriranganadane Dev , Halabelian Levon , Chiodi Carla G. , Elkins Jonathan M. , Massirer Katlin B. , Gileadi Opher , Menossi Marcelo , Couñago Rafael M.
Published: March 2019

Resistance to drought stress is fundamental to plant survival and development. Abscisic acid (ABA) is one of the major hormones involved in different types of abiotic and biotic stress responses. ABA intracellular signaling has been extensively explored in Arabidopsis thaliana and occurs via a phosphorylation cascade mediated by three related protein kinases, denominated SnRK2s (SNF1-related protein kinases). However, the role of ABA signaling and the biochemistry of SnRK2 in crop plants remains underexplored. Considering the importance of the ABA hormone in abiotic stress tolerance, here we investigated the regulatory mechanism of sugarcane SnRK2s - known as SAPKs (Stress/ABA-activated Protein Kinases). The crystal structure of ScSAPK10 revealed the characteristic SnRK2 family architecture, in which the regulatory SnRK2-box interacts with the kinase domain αC helix. To study sugarcane SnRK2 regulation, we produced a series of mutants for the protein regulatory domains SnRK2-box and ABA-box. Surprisingly, mutations in the SnRK2-box did not drastically affect sugarcane SnRK2 activity, in contrast to previous observations for the homologous proteins in Arabidopsis. Also, we found that the ABA-box might have a role in SnRK2 activation in the absence of PP2C phosphatase. Taken together, our results demonstrate that both C-terminal domains of sugarcane SnRK2 proteins play a fundamental role in protein activation and activity.