bluuebunny/crossref_metadata_2025 huggingface dataset:
Brown dwarf census with the Dark Energy Survey year 3 data and the thin disc scale height of early L types
Authors: Carnero Rosell A , Santiago B , dal Ponte M , Burningham B , da Costa L N , James D J , Marshall J L , McMahon R G , Bechtol K , De Paris L , Li T , Pieres A , García-Bellido J , Abbott T M C , Annis J , Avila S , Bernstein G M , Brooks D , Burke D L , Carrasco Kind M , Carretero J , De Vicente J , Drlica-Wagner A , Fosalba P , Frieman J , Gaztanaga E , Gruendl R A , Gschwend J , Gutierrez G , Hollowood D L , Maia M A G , Menanteau F , Miquel R , Plazas A A , Roodman A , Sanchez E , Scarpine V , Schindler R , Serrano S , Sevilla-Noarbe I , Smith M , Sobreira F , Soares-Santos M , Suchyta E , Swanson M E C , Tarle G , Vikram V , Walker A R ,   (DES Collaboration)
Published: August 2019

In this paper we present a catalogue of 11 745 brown dwarfs with spectral types ranging from L0 to T9, photometrically classified using data from the Dark Energy Survey (DES) year 3 release matched to the Vista Hemisphere Survey (VHS) DR3 and Wide-field Infrared Survey Explorer (WISE) data, covering ≈2400 deg2 up to iAB = 22. The classification method follows the same phototype method previously applied to SDSS-UKIDSS-WISE data. The most significant difference comes from the use of DES data instead of SDSS, which allow us to classify almost an order of magnitude more brown dwarfs than any previous search and reaching distances beyond 400 pc for the earliest types. Next, we also present and validate the GalmodBD simulation, which produces brown dwarf number counts as a function of structural parameters with realistic photometric properties of a given survey. We use this simulation to estimate the completeness and purity of our photometric LT catalogue down to iAB = 22, as well as to compare to the observed number of LT types. We put constraints on the thin disc scale height for the early L (L0–L3) population to be around 450 pc, in agreement with previous findings. For completeness, we also publish in a separate table a catalogue of 20 863 M dwarfs that passed our colour cut with spectral types greater than M6. Both the LT and the late M catalogues are found at DES release page https://des.ncsa.illinois.edu/releases/other/y3-mlt.
Dust survival rates in clumps passing through the Cas A reverse shock – I. Results for a range of clump densities
Authors: Kirchschlager Florian , Schmidt Franziska D , Barlow M J , Fogerty Erica L , Bevan Antonia , Priestley Felix D
Published: August 2019

The reverse shock in the ejecta of core-collapse supernovae is potentially able to destroy newly formed dust material. In order to determine dust survival rates, we have performed a set of hydrodynamic simulations using the grid-based code astrobear in order to model a shock wave interacting with clumpy supernova ejecta. Dust motions and destruction rates were computed using our newly developed external, post-processing code paperboats, which includes gas drag, grain charging, sputtering, and grain–grain collisions. We have determined dust destruction rates for the oxygen-rich supernova remnant Cassiopeia A as a function of initial grain sizes and clump gas density. We found that up to $30\,\mathrm{{{\ \rm per\ cent}}}$ of the carbon dust mass is able to survive the passage of the reverse shock if the initial grain size distribution is narrow with radii around ∼10–50 nm for high gas densities, or with radii around $\sim 0.5\!-\!1.5\,\mathrm{\mu m}$ for low and medium gas densities. Silicate grains with initial radii around 10–30 nm show survival rates of up to $40\,\mathrm{{{\ \rm per\ cent}}}$ for medium- and high-density contrasts, while silicate material with micron-sized distributions is mostly destroyed. For both materials, the surviving dust mass is rearranged into a new size distribution that can be approximated by two components: a power-law distribution of small grains and a lognormal distribution of grains having the same size range as the initial distribution. Our results show that grain–grain collisions and sputtering are synergistic and that grain–grain collisions can play a crucial role in determining the surviving dust budget in supernova remnants.
The VMC survey – XXXIV. Morphology of stellar populations in the Magellanic Clouds
Authors: El Youssoufi Dalal , Cioni Maria-Rosa L , Bell Cameron P M , Rubele Stefano , Bekki Kenji , de Grijs Richard , Girardi Léo , Ivanov Valentin D , Matijevic Gal , Niederhofer Florian , Oliveira Joana M , Ripepi Vincenzo , Subramanian Smitha , van Loon Jacco Th
Published: August 2019

The Magellanic Clouds are nearby dwarf irregular galaxies whose morphologies show different properties when traced by different stellar populations, making them an important laboratory for studying galaxy morphologies. We study the morphology of the Magellanic Clouds using data from the Visible and Infrared Survey Telescope for Astronomy survey of the Magellanic Clouds system. We used about 10 and 2.5 million sources across an area of ∼105 and ∼42 deg2 towards the Large and Small Magellanic Cloud (LMC and SMC), respectively. We estimated median ages of stellar populations occupying different regions of the near-infrared (J − Ks, Ks) colour–magnitude diagram. Morphological maps were produced and detailed features in the central regions were characterized for the first time with bins corresponding to a spatial resolution of 0.13 kpc (LMC) and 0.16 kpc (SMC). In the LMC, we find that main-sequence stars show coherent structures that grow with age and trace the multiple spiral arms of the galaxy, star-forming regions become dimmer as we progress in age, while supergiant stars are centrally concentrated. Intermediate-age stars, despite tracing a regular and symmetrical morphology, show central clumps and hints of spiral arms. In the SMC, young main-sequence stars depict a broken bar. Intermediate-age populations show signatures of elongation towards the Magellanic Bridge that can be attributed to the LMC–SMC interaction ∼200 Myr ago. They also show irregular central features suggesting that the inner SMC has also been influenced by tidal interactions.
Predicting relationships between solar jet variables
Authors: Freeman Leonard A
Published: August 2019

Studies of spicules and similar solar jets reveal a strong correlation between some of the kinematic variables, particularly between the initial velocity V, and the subsequent deceleration, a. It has been proposed that there is a linear relationship between these two variables and that this offers proof for a shock wave mechanism acting on the spicules, although the linear equations found are all different. It is shown here that the relationship is better described by a non-linear form: V is proportional to the square root of a. This relationship between V and a also provides a simple physical interpretation for the results. The different linear equations are found to be simply tangents to this (a, V) curve. Another method used to investigate the (a, V) connection is to determine the correlation coefficients between the kinematic variables from their scatter plots. It is also shown how these correlations also can be predicted from the mean value of the acceleration and height and their standard deviations for the sample under consideration. The implications of these results and the possibility that spicule behaviour is partly due to magnetic fields are discussed.
Dust accretion in binary systems: implications for planets and transition discs
Authors: Chachan Yayaati , Booth Richard A , Triaud Amaury H M J , Clarke Cathie
Published: August 2019

The presence of planets in binary systems poses interesting problems for planet formation theories, both in cases where planets must have formed in very compact discs around the individual stars and where they are located near the edge of the stable circumbinary region, where in situ formation is challenging. Dust dynamics is expected to play an important role in such systems, since dust trapping at the inner edge of circumbinary discs could aid in situ formation, but would simultaneously starve the circumstellar discs of the solid material needed to form planets. Here we investigate the dynamics of dust in binary systems using Smooth Particle Hydrodynamics. We find that all our simulations tend towards dust trapping in the circumbinary disc, but the timescale on which trapping begins depends on binary mass ratio (q) and eccentricity as well as the angular momentum of the infalling material. For q ≳ 0.1, we find that dust can initially accrete onto the circumstellar discs, but as the circumbinary cavity grows in radius, dust eventually becomes trapped in the circumbinary disc. For q = 0.01, we find that increasing the binary eccentricity increases the time required for dust trapping to begin. However, even this longer timescale is likely to be shorter than the planet formation timescale in the inner disc and is insufficient to explain the observed pre-transitional discs. This indicates that increase in companion eccentricity alone is not enough to allow significant transfer of solids from the outer to the inner disc.
Galaxy properties as revealed by MaNGA – II. Differences in stellar populations of slow and fast rotator ellipticals and dependence on environment
Authors: Bernardi M , Domínguez Sánchez H , Brownstein J R , Drory N , Sheth R K
Published: August 2019

We present estimates of stellar population (SP) gradients from stacked spectra of slow rotator (SR) and fast rotator (SR) elliptical galaxies from the MaNGA-DR15 survey. We find that (1) FRs are ∼5 Gyr younger, more metal rich, less α-enhanced and smaller than SRs of the same luminosity Lr and central velocity dispersion σ0. This explains why when one combines SRs and FRs, objects which are small for their Lr and σ0 tend to be younger. Their SP gradients are also different. (2) Ignoring the FR/SR dichotomy leads one to conclude that compact galaxies are older than their larger counterparts of the same mass, even though almost the opposite is true for FRs and SRs individually. (3) SRs with σ0 ≤ 250 km s−1 are remarkably homogeneous within ∼Re: they are old, α-enhanced, and only slightly supersolar in metallicity. These SRs show no gradients in age and M*/Lr, negative gradients in metallicity, and slightly positive gradients in [α/Fe] (the latter are model dependent). SRs with σ0 ≥ 250 km s−1 are slightly younger and more metal rich, contradicting previous work suggesting that age increases with σ0. They also show larger M*/Lr gradients. (4) Self-consistently accounting for M*/L gradients yields Mdyn ≈ M* because gradients reduce Mdyn by ∼0.2 dex while only slightly increasing the M* inferred using a Kroupa (not Salpeter) initial mass function. (5) The SR population starts to dominate the counts above $M_*\ge 3\times 10^{11}\, \mathrm{M}_\odot$; this is the same scale at which the size–mass correlation and other scaling relations change. Our results support the finding that this is an important mass scale that correlates with the environment and above which mergers matter.
De novo design of programmable inducible promoters
Authors: Liu Xiangyang , Gupta Sanjan T P , Bhimsaria Devesh , Reed Jennifer L , Rodríguez-Martínez José A , Ansari Aseem Z , Raman Srivatsan
Published: August 2019

Ligand-responsive allosteric transcription factors (aTF) play a vital role in genetic circuits and high-throughput screening because they transduce biochemical signals into gene expression changes. Programmable control of gene expression from aTF-regulated promoter is important because different downstream effector genes function optimally at different expression levels. However, tuning gene expression of native promoters is difficult due to complex layers of homeostatic regulation encoded within them. We engineered synthetic promoters de novo by embedding operator sites with varying affinities and radically reshaped binding preferences within a minimal, constitutive Escherichia coli promoter. Multiplexed cell-based screening of promoters for three TetR-like aTFs generated with this approach gave rich diversity of gene expression levels, dynamic ranges and ligand sensitivities and were 50- to 100-fold more active over their respective native promoters. Machine learning on our dataset revealed that relative position of the core motif and bases flanking the core motif play an important role in modulating induction response. Our generalized approach yields customizable and programmable aTF-regulated promoters for engineering cellular pathways and enables the discovery of new small molecule biosensors.
Assessment of kinship detection using RNA-seq data
Authors: Blay Natalia , Casas Eduard , Galván-Femenía Iván , Graffelman Jan , de Cid Rafael , Vavouri Tanya
Published: August 2019

Analysis of RNA sequencing (RNA-seq) data from related individuals is widely used in clinical and molecular genetics studies. Prediction of kinship from RNA-seq data would be useful for confirming the expected relationships in family based studies and for highlighting samples from related individuals in case-control or population based studies. Currently, reconstruction of pedigrees is largely based on SNPs or microsatellites, obtained from genotyping arrays, whole genome sequencing and whole exome sequencing. Potential problems with using RNA-seq data for kinship detection are the low proportion of the genome that it covers, the highly skewed coverage of exons of different genes depending on expression level and allele-specific expression. In this study we assess the use of RNA-seq data to detect kinship between individuals, through pairwise identity by descent (IBD) estimates. First, we obtained high quality SNPs after successive filters to minimize the effects due to allelic imbalance as well as errors in sequencing, mapping and genotyping. Then, we used these SNPs to calculate pairwise IBD estimates. By analysing both real and simulated RNA-seq data we show that it is possible to identify up to second degree relationships using RNA-seq data of even low to moderate sequencing depth.
LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro
Authors: Li Qian , Peng Xiaojun , Li Yuanqing , Tang Wenqin , Zhu Jia’an , Huang Jing , Qi Yifei , Zhang Zhuqing
Published: August 2019

Liquid-liquid phase separation (LLPS) leads to a conversion of homogeneous solution into a dense phase that often resembles liquid droplets, and a dilute phase. An increasing number of investigations have shown that biomolecular condensates formed by LLPS play important roles in both physiology and pathology. It has been suggested the phase behavior of proteins would be not only determined by sequences, but controlled by micro-environmental conditions. Here, we introduce LLPSDB (http://bio-comp.ucas.ac.cn/llpsdb or http://bio-comp.org.cn/llpsdb), a web-accessible database providing comprehensive, carefully curated collection of proteins involved in LLPS as well as corresponding experimental conditions in vitro from published literatures. The current release of LLPSDB incorporates 1182 entries with 273 independent proteins and 2394 specific conditions. The database provides a variety of data including biomolecular information (protein sequence, protein modification, nucleic acid, etc.), specific phase separation information (experimental conditions, phase behavior description, etc.) and comprehensive annotations. To our knowledge, LLPSDB is the first available database designed for LLPS related proteins specifically. It offers plenty of valuable resources for exploring the relationship between protein sequence and phase behavior, and will enhance the development of phase separation prediction methods, which may further provide more insights into a comprehensive understanding of LLPS in cellular function and related diseases.
Simultaneous targeting of DNA replication and homologous recombination in glioblastoma with a polyether ionophore
Authors: Lim Yi Chieh , Ensbey Kathleen S , Offenhäuser Carolin , D’souza Rochelle C J , Cullen Jason K , Stringer Brett W , Quek Hazel , Bruce Zara C , Kijas Amanda , Cianfanelli Valentina , Mahboubi Bijan , Smith Fiona , Jeffree Rosalind L , Wiesmüeller Lisa , Wiegmans Adrian P , Bain Amanda , Lombard Fanny J , Roberts Tara L , Khanna Kum Kum , Lavin Martin F , Kim Baek , Hamerlik Petra , Johns Terrance G , Coster Mark J , Boyd Andrew W , Day Bryan W
Published: August 2019

Background

Despite significant endeavor having been applied to identify effective therapies to treat glioblastoma (GBM), survival outcomes remain intractable. The greatest nonsurgical benefit arises from radiotherapy, though tumors typically recur due to robust DNA repair. Patients could therefore benefit from therapies with the potential to prevent DNA repair and synergize with radiotherapy. In this work, we investigated the potential of salinomycin to enhance radiotherapy and further uncover novel dual functions of this ionophore to induce DNA damage and prevent repair.

Methods

In vitro primary GBM models and ex vivo GBM patient explants were used to determine the mechanism of action of salinomycin by immunoblot, flow cytometry, immunofluorescence, immunohistochemistry, and mass spectrometry. In vivo efficacy studies were performed using orthotopic GBM animal xenograft models. Salinomycin derivatives were synthesized to increase drug efficacy and explore structure-activity relationships.

Results

Here we report novel dual functions of salinomycin. Salinomycin induces toxic DNA lesions and prevents subsequent recovery by targeting homologous recombination (HR) repair. Salinomycin appears to target the more radioresistant GBM stem cell–like population and synergizes with radiotherapy to significantly delay tumor formation in vivo. We further developed salinomycin derivatives which display greater efficacy in vivo while retaining the same beneficial mechanisms of action.

Conclusion

Our findings highlight the potential of salinomycin to induce DNA lesions and inhibit HR to greatly enhance the effect of radiotherapy. Importantly, first-generation salinomycin derivatives display greater efficacy and may pave the way for clinical testing of these agents.
The Presence and Persistence of Unrealistic Expectations in Patients Undergoing Nerve Surgery
Authors: Kirsch Michael , Brown Shawn , Smith Brandon W , Chang Kate W C , Koduri Sravanthi , Yang Lynda J S
Published: August 2019

BACKGROUND

Unrealistic expectations of the outcomes of peripheral nerve surgery reduce patient satisfaction. Most clinicians can recall patients with unrealistic expectations despite verbal preoperative education.

OBJECTIVE

To assess patients’ baseline level of understanding regarding nerve surgery and appropriate expectations. Additionally, we tested the effect of a written, preoperative educational handout on the patients’ retention of knowledge.

METHODS

This cross-sectional survey recruited patients scheduled to undergo peripheral nerve surgery at a single institution in 2016 to 2017. During the preoperative visit, a specialized nurse practitioner reviewed perioperative protocols, risks and benefits of the surgery, and postoperative care. Patients immediately completed a survey to assess their preoperative understanding of the verbally reviewed information. During the same visit, an additional written handout was given to patients in a randomized fashion. At their first postoperative visit, all patients completed the survey again.

RESULTS

A total of 60 patients (mean age 52 yr) were enrolled of which 62% were male. Immediately following verbal instruction, 31% of patients had erroneous (unrealistic) expectations regarding pain, 30% had erroneous expectations regarding postoperative motor outcome, and 41% had erroneous expectations regarding the timing of postoperative recovery. There was no significant difference between patients who received the written handout vs those who did not, on retesting in the postoperative period.

CONCLUSION

Patients undergoing peripheral nerve procedures demonstrated a high baseline level of unrealistic expectations despite standard in-person verbal counseling by specialty providers. A written handout did not have clear benefit in the retention of preoperative surgical teaching. Further investigation into more effective preoperative patient counseling is needed.
The Safety and Feasibility of Mechanical Thrombectomy for Mild Acute Ischemic Stroke With Large Vessel Occlusion
Authors: Toth Gabor , Ortega-Gutierrez Santiago , Tsai Jenny P , Cerejo Russell , Al Kasab Sami , Uchino Ken , Hussain M Shazam , Bain Mark , Bullen Jennifer , Samaniego Edgar A
Published: August 2019

BACKGROUND

Prospective evidence to support mechanical thrombectomy (MT) for mild ischemic stroke with large vessel occlusion (LVO) is lacking. There is uncertainty about using an invasive procedure in patients with mild symptoms.

OBJECTIVE

To evaluate the safety and feasibility of MT in patients with mild symptoms and LVO.

METHODS

Our single-arm prospective pilot study recruited patients with LVO and initial National Institute of Health Stroke Scale (NIHSS) <6, who underwent standard MT. Primary safety endpoints were symptomatic intracerebral hemorrhage (sICH), and/or worsening NIHSS by ≥4 points. Secondary endpoints included angiographic recanalization, NIHSS change, final infarct volume, and modified Rankin score (mRS).

RESULTS

We enrolled 20 patients (mean age 65.6 ± 12.3 yr; 45% females). Thrombolysis in Cerebral Ischemia 2B/3 thrombectomy was achieved in 95%. No patients suffered sICH. One patient (5%) had neurologic worsening within 24 h because of underlying intracranial stenosis. No other complications or safety concerns were identified. Median NIHSS was significantly better at discharge (0.5, P = .007) and at last follow-up (0, P < .001) than before treatment (3). Mean post vs preintervention infarct volumes were small without significant difference (1.2 ml, P = .434). Most patients (85%) were discharged directly home. Excellent clinical outcome (mRS 0-1) at last follow-up was seen in 95% of patients.

CONCLUSION

This is one of the first specifically designed prospective studies showing that MT is safe and feasible in patients with low NIHSS and LVO. Chronic underlying vasculopathy may be a challenging dilemma. We observed excellent clinical and radiographic outcomes, but randomized controlled trials are needed to demonstrate the efficacy of MT in this unique cohort.
Marketing Influences on Perceptions of Reduced Nicotine Content Cigarettes
Authors: Johnson Andrea C , Mays Darren , Villanti Andrea C , Niaura Raymond S , Rehberg Kathryn , Phan Lilianna , Mercincavage Melissa , Luta George , Strasser Andrew A
Published: August 2019

Introduction

The Food and Drug Administration announced intent to reduce the nicotine content in cigarettes. There is limited evidence on how reduced nicotine content cigarette (RNC) marketing affects product beliefs and use, and research on this is needed to inform regulations.

Methods

In an online experiment, 426 young adult cigarette smokers (aged 18–30 years) were randomized in a 2 (implicit: red package vs. blue package) × 2 (explicit: corrective message vs. no corrective message) design to view an advertisement for previously commercially available RNCs. Outcomes were advertisement content recall, product beliefs, and use intentions. Participants’ responses to open-ended assessment of their beliefs about the stimuli were coded to identify prevailing themes.

Results

Red packaging and corrective messaging were independently associated with greater advertisement content recall (p = .01 and p = .04, respectively). There were no significant main or interaction effects on product beliefs or use intentions. Controlling for condition, advertisement content recall was significantly associated with less favorable product beliefs (p < .001) and favorable product beliefs were associated with intent to use the product (p < .001). Open-ended responses converged on the finding that respondents were interested in RNCs, but expressed skepticism about effectiveness and value.

Conclusions

Brief exposure to an RNC advertisement with red packaging and corrective messaging were each independently associated with greater advertisement content recall. The results indicate: (1) interest and confusion among young adult smokers regarding RNCs, (2) beliefs about RNCs are influenced by marketing, and (3) beliefs are associated with intention to use RNCs.

Implications

Findings from this study demonstrate the importance of advertising effects on beliefs about RNC products and support the need to regulate advertising and labeling alongside product regulation. More detailed study of advertisement features that affect consumers’ beliefs about RNCs and how they impact their processing of explicit messaging about product risks will be important to guide regulatory decision-making.
Predicting Improved Daily Use of the More Affected Arm Poststroke Following Constraint-Induced Movement Therapy
Authors: Rafiei Mohammad H , Kelly Kristina M , Borstad Alexandra L , Adeli Hojjat , Gauthier Lynne V
Published: August 2019

Background

Constraint-induced movement therapy (CI therapy) produces, on average, large and clinically meaningful improvements in the daily use of a more affected upper extremity in individuals with hemiparesis. However, individual responses vary widely.

Objective

The study objective was to investigate the extent to which individual characteristics before treatment predict improved use of the more affected arm following CI therapy.

Design

This study was a retrospective analysis of 47 people who had chronic (> 6 months) mild to moderate upper extremity hemiparesis and were consecutively enrolled in 2 CI therapy randomized controlled trials.

Methods

An enhanced probabilistic neural network model predicted whether individuals showed a low, medium, or high response to CI therapy, as measured with the Motor Activity Log, on the basis of the following baseline assessments: Wolf Motor Function Test, Semmes-Weinstein Monofilament Test of touch threshold, Motor Activity Log, and Montreal Cognitive Assessment. Then, a neural dynamic classification algorithm was applied to improve prognostic accuracy using the most accurate combination obtained in the previous step.

Results

Motor ability and tactile sense predicted improvement in arm use for daily activities following intensive upper extremity rehabilitation with an accuracy of nearly 100%. Complex patterns of interaction among these predictors were observed.

Limitations

The fact that this study was a retrospective analysis with a moderate sample size was a limitation.

Conclusions

Advanced machine learning/classification algorithms produce more accurate personalized predictions of rehabilitation outcomes than commonly used general linear models.
Improving the feasibility of MRI in clinically suspect arthralgia for prediction of rheumatoid arthritis by omitting scanning of the feet
Authors: Boer Aleid C , Wouters Fenne , Dakkak Yousra J , Niemantsverdriet Ellis , van der Helm-van Mil Annette H M
Published: August 2019

Objectives

The use of MR-imaging is recommended for the early detection of RA. Next to the small joints of the hands, foot-joints are often involved. Therefore, imaging inflammation of the feet in addition to hands may be informative, but prolongs scan-time and leads to additional costs. We studied the value of MRI of the feet alone and complementary to MRI of the hands in patients with clinically suspect arthralgia (CSA).

Methods

357 consecutively included CSA patients underwent contrast-enhanced 1.5 T-MRI of hand (MCP2-5 and wrist) and foot (MTP1-5) joints at baseline. Scans were scored for synovitis, osteitis and tenosynovitis. After ⩾1 year follow-up, the development of clinically apparent inflammatory arthritis (IA) was studied. Cox regression was performed and test characteristics were evaluated. Sensitivity analyses were performed for the outcome RA-development (2010-criteria).

Results

MRI-detected tenosynovitis of the feet was associated with IA-development, independently from synovitis and osteitis hazard ratio (HR) (95%CI) 4.75 (2.38; 9.49), and independently from ACPA and CRP, HR 3.13 (1.48; 6.64). From all CSA patients, 11% had inflammation in hands and feet, 29% only in hands and 3% only in feet. In line with this finding, the addition of MRI-feet to MRI-hands did not increase the predictive accuracy; the sensitivity remained 77%, while the specificity decreased from 66% to 62%. Sensitivity analyses with RA development as outcome showed similar results.

Conclusion

Tenosynovitis at the forefeet in CSA predicted IA and RA development. Addition of foot MRI to hand MRI did not increase the accuracy. Foot MRI can be omitted to reduce scan time and costs and increase the feasibility.
Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning
Authors: Suvorov Anton , Hochuli Joshua , Schrider Daniel R
Published: August 2019

Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies have identified several “zones” of parameter space where accuracy of some methods can plummet, even for four-taxon trees. Further, some methods can have undesirable statistical properties such as statistical inconsistency and/or the tendency to be positively misleading (i.e. assert strong support for the incorrect tree topology). Recently, deep learning techniques have made inroads on a number of both new and longstanding problems in biological research. In this study, we designed a deep convolutional neural network (CNN) to infer quartet topologies from multiple sequence alignments. This CNN can readily be trained to make inferences using both gapped and ungapped data. We show that our approach is highly accurate on simulated data, often outperforming traditional methods, and is remarkably robust to bias-inducing regions of parameter space such as the Felsenstein zone and the Farris zone. We also demonstrate that the confidence scores produced by our CNN can more accurately assess support for the chosen topology than bootstrap and posterior probability scores from traditional methods. Although numerous practical challenges remain, these findings suggest that the deep learning approaches such as ours have the potential to produce more accurate phylogenetic inferences.
Tracking the route of atmospheric nitrogen to diazotrophs colonizing buried mangrove roots
Authors: Inoue Tomomi , Kohzu Ayato , Shimono Ayako
Published: August 2019

Nitrogen-fixing activity has been observed in the rhizosphere of mangrove ecosystems, suggesting a close mangrove–diazotroph relationship. In regularly flooded soil, however, the pathway by which atmospheric nitrogen reaches the diazotrophs in the rhizosphere is unknown. This study provides evidence that mangrove aerial roots serve as pathways that supply nitrogen gas to the diazotrophs colonizing buried roots. A plastic chamber was attached on the exposed part of a Rhizophora stylosa Griff prop root, and 15N2 tracer gas was injected into it. The entire root, including the below-ground part, was collected for analysis of 15N labelling and nitrogenase activity. We detected 15N labelling in buried root materials 2 h after gas injection. Compared with the δ15N contents in root material from an untreated tree, the increment was >10‰ in lateral roots. The nitrogenase activity measured on the other R. stylosa roots was highest in lateral roots, matching well with the results of 15N labelling. Our results indicate that atmospheric nitrogen is taken into aerial mangrove roots through lenticels, diffuses into the buried root system and is fixed by diazotrophs. The unusual appearance of mangrove aerial roots, which has intrigued researchers for many years, could be a key to the high productivity of mangrove ecosystems.
Genetic differentiation in functional traits among European sessile oak populations
Authors: Torres-Ruiz José M , Kremer Antoine , Carins Murphy Madeline R , Brodribb Tim , Lamarque Laurent J , Truffaut Laura , Bonne Fabrice , Ducousso Alexis , Delzon Sylvain
Published: August 2019

The vulnerability of forest species and tree populations to climate change is related to the exposure of the ecosystem to extreme climatic conditions and to the adaptive capacity of the population to cope with those conditions. Adaptive capacity is a relatively under-researched topic within the forest science community, and there is an urgent need to understand to what extent particular combinations of traits have been shaped by natural selection under climatic gradients, potentially resulting in adaptive multi-trait associations. Thus, our aim was to quantify genetic variation in several leaf and woody traits that may contribute to multi-trait associations in which intra-specific variation could represent a source for species adaptation to climate change. A multi-trait approach was performed using nine Quercus petraea provenances originating from different locations that cover most of the species’ distribution range over Europe and that were grown in a common garden. Multiple adaptive differences were observed between oak provenances but also some evolutionary stasis. In addition, our results revealed higher genetic differentiation in traits related to phenology and growth than in those related to xylem anatomy, physiology and hydraulics, for which no genetic differentiation was observed. The multiple associations between those traits and climate variables resulting from multivariate and path analyses suggest a multi-trait association largely involving phenological and growth traits for Q. petraea.
Embolism resistance of different aged stems of a California oak species (Quercus douglasii): optical and microCT methods differ from the benchtop-dehydration standard
Authors: Pratt R Brandon , Castro Viridiana , Fickle Jaycie C , Jacobsen Anna L
Published: August 2019

Vulnerability of xylem to embolism is an important trait related to drought resistance of plants. Methods continue to be developed and debated for measuring embolism. We tested three methods (benchtop dehydration/hydraulic, micro-computed tomography (microCT) and optical) for assessing the vulnerability to embolism of a native California oak species (Quercus douglasii Hook. & Arn.), including an analysis of three different stem ages. All three methods were found to significantly differ in their estimates, with a greater resistance to embolism as follows: microCT > optical > hydraulic. Careful testing was conducted for the hydraulic method to evaluate multiple known potential artifacts, and none was found. One-year-old stems were more resistant than older stems using microCT and optical methods, but not hydraulic methods. Divergence between the microCT and optical methods from the standard hydraulic method was consistent with predictions based on known errors when estimating theoretical losses in hydraulic function in both microCT and optical methods. When the goal of a study is to describe or predict losses in hydraulic conductivity, neither the microCT nor optical methods are reliable for accurately constructing vulnerability curves of stems; nevertheless, these methods may be useful if the goal of a study is to identify embolism events irrespective of hydraulic conductivity or hydraulic function.
Effects of elevated carbon dioxide and elevated temperature on morphological, physiological and anatomical responses of Eucalyptus tereticornis along a soil phosphorus gradient
Authors: Duan Honglang , Ontedhu Josephine , Milham Paul , Lewis James D , Tissue David T
Published: August 2019

Eucalypts are likely to play a critical role in the response of Australian forests to rising atmospheric CO2 concentration ([CO2]) and temperature. Although eucalypts are frequently phosphorus (P) limited in native soils, few studies have examined the main and interactive effects of P availability, [CO2] and temperature on eucalypt morphology, physiology and anatomy. To address this issue, we grew seedlings of Eucalyptus tereticornis Smith across its P-responsive range (6–500 mg kg−1) for 120 days under two [CO2] (ambient: 400 μmol mol−1 (Ca) and elevated: 640 μmol mol−1 (Ce)) and two temperature (ambient: 24/16 °C (Ta) and elevated: 28/20 °C (Te) day/night) treatments in a sunlit glasshouse. Seedlings were well-watered and supplied with otherwise non-limiting macro- and micro-nutrients. Increasing soil P supply increased growth responses to Ce and Te. At the highest P supplies, Ce increased total dry mass, leaf number and total leaf area by ~50%, and Te increased leaf number by ~40%. By contrast, Ce and Te had limited effects on seedling growth at the lowest P supply. Soil P supply did not consistently modify photosynthetic responses to Ce or Te. Overall, effects of Ce and Te on growth, physiological and anatomical responses of E. tereticornis seedlings were generally neutral or negative at low soil P supply, suggesting that native tree responses to future climates may be relatively small in native low-P soils in Australian forests.
Identifying borrowed sources in secured transactions law reform
Authors: Wood Roderick J
Published: August 2019

The enactment of Article 9 of the Uniform Commercial Code in the USA has had a profound influence on the reform of secured transactions law in other countries. The operational principles that animate Article 9 were first transplanted into Canada and later into New Zealand. In the last two decades, at least 25 countries have passed personal property security legislation (PPSA) based on these principles. On one level, one could claim that Article 9 has been transplanted into each of these 25 countries. However, on another level this story is far too simplistic. If one examines the various statutes, it becomes clear that a more complex process has been at work in which there has been innovation as well as borrowing. These innovations, in turn, influence the borrowings of other countries that enact a PPSA. In this highly dynamic environment the source of borrowing can be difficult to identify. This article examines the nature and extent of the borrowings that occur in connection with the reform of secured transactions in countries that have enacted a PPSA. It will identify three major templates that are available—namely, the most recent version of Article 9, the Canadian/New Zealand model, and the UNCITRAL Model Law. These templates will be reviewed in order to find markers that are present only in that template and not in the other two. These markers will be used to ‘fingerprint’ the PPSA legislation in other countries in order to measure the extent to which the jurisdiction has borrowed from each of the three templates. The article will conclude with a number of observations about the path of secured transactions law reform on an international level.
Assessing Rate-Reducing Foliar Resistance to Anthracnose Crown Rot and Fruit Rot in Strawberry
Authors: Jacobs Raymond L. , Adhikari Tika B. , Pattison Jeremy , Yencho G. Craig , Fernandez Gina E. , Louws Frank J.
Published: August 2019

Anthracnose fruit rot and anthracnose crown rot (ACR) caused by two species complexes of the fungus referred to as Colletotrichum acutatum and Colletotrichum gloeosporioides, respectively, are major pathogens of strawberry in North Carolina. Anthracnose epidemics are common when susceptible cultivars and asymptomatic planting stocks carrying quiescent Colletotrichum infection or hemibiotrophic infection (HBI) are planted. The main objective of this study was to assess resistance to HBI and ACR in strawberry. Strawberry cultivars and breeding lines were spray inoculated with isolates of C. acutatum or C. gloeosporioides. Four epidemiological parameters providing estimates of rate-reducing resistance to HBI and ACR in strawberry cultivars and lines were evaluated in repeated experiments in controlled environments in a greenhouse. HBI severity, measured as the percentage of total leaf area covered by acervuli, was estimated visually and by image analysis. ACR severity was rated weekly for wilt symptoms, and relative area under disease progress curve scores were calculated for comparing strawberry cultivars and lines. Significant differences (P ≤ 0.005) in HBI severity were found among strawberry genotypes; however, the correlations were not remarkable between Colletotrichum species (r = 0.4251). Although significant variation in resistance was observed for ACR, this was also weakly correlated (r = 0.2430) with resistance to C. gloeosporioides HBI. Overall, rate-reducing resistance to HBI and ACR in strawberry identified in this study could be utilized in breeding programs to develop durable resistance to anthracnose in North Carolina.
Enteric dysbiosis is associated with sepsis in patients
Authors: Liu Zhanguo , Li Na , Fang Heng , Chen Xiaojiao , Guo Yuexun , Gong Shenhai , Niu Mengwei , Zhou Hongwei , Jiang Yong , Chang Ping , Chen Peng
Published: August 2019

Sepsis is defined as a life‐threatening organ dysfunction caused by a dysregulated host response to microbial infection. For decades, the potential role of gut microbiota in sepsis pathogenesis has been revealed. However, the systemic and functional link between gut microbiota and sepsis has remained unexplored. To address this gap in knowledge, we carried out systematic analyses on clinical stool samples from patients with sepsis, including 16S rDNA sequencing, metabolomics, and metaproteomics analyses. In addition, we performed fecal microbiota transplantation from human to mice to validate the roles of gut microbiota on sepsis progression. We found that the composition of gut microbiota was significantly disrupted in patients with sepsis compared with healthy individuals. Besides, the microbial functions were significantly altered in septic feces as identified by metabolomics and metaproteomics analyses. Interestingly, mice that received septic feces exhibited more severe hepatic inflammation and injury than mice that received healthy feces after cecal ligation and puncture. Finally, several strains of intestinal microbiota and microbial metabolites were corelated with serum total bilirubin levels in patients with sepsis. Taken together, our data indicated that sepsis development is associated with the disruption of gut microbiota at both compositional and functional levels, and such enteric dysbiosis could promote organ inflammation and injury during sepsis.—Liu, Z., Li, N., Fang H., Chen, X., Guo, Y., Gong, S., Niu, M., Zhou, H., Jiang, Y., Chang, P., Chen, P. Enteric dysbiosis is associated with sepsis in patients. FASEB J. 33, 12299‐12310 (2019). www.fasebj.org
Growth of the capitellar ossification center and its relationship within the lateral condyle of the distal humerus in skeletally immature elbows: a study using MR images
Authors: Lee Jaehyung , Cha Yunsik , Kang Michael Seungcheol , Park Soo-Sung
Published: August 2019

To more accurately interpret the anterior humeral and radiocapitellar lines on simple radiographs of pediatric elbow, we investigated age-related changes of the capitellar ossific nucleus (CON) by using MRIs. Elbow MRIs from 79 children aged 1–16 years and free from demonstrable lesions in the distal humerus were retrospectively reviewed. On coronal images, the distal cartilaginous vertex of the capitellum, which articulates with the center of the radial head, was situated about 15%p laterally from the center of CON regardless of age. On sagittal images, the anterior humeral line passed the center of CON in older children (>6 years), but passed anteriorly in children with an age ≤6 years. Also on sagittal images, the anterior cartilaginous vertex of the capitellum was positioned within 10% of the level of the center of CON in all age groups. Recognition of the capitellar ossification pattern within the lateral condyle would aid in more accurate assessment of pediatric elbows on simple radiographs. Based on the results of the present MRI study, the following points were identified for the interpretation of simple radiographs: (1) The radiocapitellar line on anteroposterior views intersects the CON by about 15%p laterally regardless of age; (2) The anterior humeral line on lateral views intersects the center of the CON in older children, but passes anteriorly in younger (≤6 years) children; and (3) The radiocapitellar line on lateral radiographs invariably passes the center of CON regardless of the age.
Neck and Cervical Spine Injuries in National College Athletic Association Athletes
Authors: Deckey David G. , Makovicka Justin L. , Chung Andrew S. , Hassebrock Jeffrey D. , Patel Karan A. , Tummala Sailesh V. , Pena Austin , Asprey Walker , Chhabra Anikar
Published: August 2019

Study Design.

Descriptive epidemiology study.

Objective.

The purpose of this study was to describe the epidemiology of neck and cervical spine injuries in collegiate athletes over a 5-year period.

Summary of Background Data.

The incidence and etiology of neck and cervical spine injuries in National Collegiate Athletic Association (NCAA) athletes has not been well defined in recent years.

Methods.

The incidence and characteristics of neck and cervical spine injuries were identified utilizing the NCAA Injury Surveillance Program database. Rates of injury were calculated as the number of injuries divided by the total number of athlete-exposures (AEs). AEs were defined as any student participation in one NCAA-sanctioned practice or competition.

Results.

Nationally, there were an estimated 11,510 neck and cervical spine injuries over the 5-year period. These occurred at a rate of 7.05 per 100,000 athlete-exposures (AEs). The rate of neck and cervical spine injuries in men was 2.66 per 100,000 AEs, while women suffered injuries at a rate of 1.95 per 100,000 AEs. In sex-comparable sports, men were 1.36 times more likely to suffer a neck or cervical spine injury compared with women. Men's football (29.09 per 100,000 AEs) and women's field hockey (11.51 per 100,000 AEs) were the sports with the highest rates of injuries. These injuries were 3.94 times more likely to occur during competition compared with practice. In-season injury rates were the highest, at 8.18 per 100,000 AEs.

Conclusion.

The vast majority of neck and cervical spine injuries in NCAA athletes are minor and uncommon. Across all sports in both sexes, the majority of injuries were new, and occurred during in-season competitions. Most athletes returned to play within 24 hours of injury. These data can inform players, parents, coaches, athletic trainers, and physicians regarding the prevalence and rates of these injuries and potentially inform decision-making regarding injury prevention, treatment, and rehabilitation.

Level of Evidence: 4
Consensus on Risk Factors and Prevention in SSI in Spine Surgery
Authors: Galetta Matthew S. , Kepler Christopher K. , Divi Srikanth N. , Boody Barrett S. , Bronson Wesley H. , Segar Anand H. , Russo Glenn S. , Mujica Victor , Yayac Michael , Goyal Dhruv K.C. , Fang Taolin , Schroeder Gregory D. , Vaccaro Alexander R.
Published: August 2019

In July of 2018, the Second International Consensus Meeting (ICM) on Musculoskeletal Infection convened in Philadelphia, PA to discuss issues regarding infection in orthopedic patients and to provide consensus recommendations on these issues to practicing orthopedic surgeons. During this meeting, attending delegates divided into subspecialty groups to discuss topics specifics to their respective fields, which included the spine. At the spine subspecialty group meeting, delegates discussed and voted upon the recommendations for 63 questions regarding the prevention, diagnosis, and treatment of infection in spinal surgery. Of the 63 questions, 11 focused on risk factors and prevention questions in spine surgery, for which this article provides the recommendations, voting results, and rationales.