bluuebunny/crossref_metadata_2025_split huggingface dataset:
RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking
Authors: Wu Yue , Judge Michael T , Arnold Jonathan , Bhandarkar Suchendra M , Edison Arthur S 
Published: July 2020

AbstractMotivationTime-series nuclear magnetic resonance (NMR) has advanced our knowledge about metabolic dynamics. Before analyzing compounds through modeling or statistical methods, chemical features need to be tracked and quantified. However, because of peak overlap and peak shifting, the available protocols are time consuming at best or even impossible for some regions in NMR spectra.ResultsWe introduce Ridge Tracking-based Extract (RTExtract), a computer vision-based algorithm, to quantify time-series NMR spectra. The NMR spectra of multiple time points were formulated as a 3D surface. Candidate points were first filtered using local curvature and optima, then connected into ridges by a greedy algorithm. Interactive steps were implemented to refine results. Among 173 simulated ridges, 115 can be tracked (RMSD &lt; 0.001). For reproducing previous results, RTExtract took less than 2 h instead of ∼48 h, and two instead of seven parameters need tuning. Multiple regions with overlapping and changing chemical shifts are accurately tracked.Availability and implementationSource code is freely available within Metabolomics toolbox GitHub repository (https://github.com/artedison/Edison_Lab_Shared_Metabolomics_UGA/tree/master/metabolomics_toolbox/code/ridge_tracking) and is implemented in MATLAB and R.Supplementary informationSupplementary data are available at Bioinformatics online.
Too many species: morphometrics, molecular phylogenetics and genome structure of a Brazilian species complex inEpidendrum(Laeliinae; Orchidaceae) reveal fewer species than previously thought
Authors: Pessoa Edlley M , Cordeiro Joel M P , Felix Leonardo P , Almeida Erton M , Costa Lucas , Nepomuceno Álvaro , Souza Gustavo , Chase Mark W , Alves Marccus , van den Berg Cássio 
Published: July 2020

AbstractIn this study, we analyse a species complex in Epidendrum, a mega-diverse Neotropical orchid genus, that is formed by the 11 Brazilian species of the E. difforme group. Although this group (c. 100 taxa) exhibits relatively high levels of floral variation, the Brazilian species are similar, making delimitation problematic. Here we combine molecular (phylogenetics), morphological (geometric morphometrics), genome size and cytogenetic (chromosome counts and CMA/DAPI staining) data to investigate circumscription of these species. Our results were interpreted by looking for congruence of the results as a means to delimit species. The studied taxa appear to be monophyletic, and karyotypically all analysed accessions were 2n = 40. Their 1C values vary from 1.99 ± 07 pg to 2.84 ± 0.12 pg. We did not find evidence for recent polyploidy or dysploidy and, apparently, these phenomena have not been important in the evolution of this species complex. On the other hand, we found high levels of polymorphism for CMA/DAPI banding, and variation in genome size appears to be positively correlated with latitude. Geometric morphometrics indicate that E. sanchezii and E. anatipedium/E. amarajiense are distinct from the remaining species, and three groups of other species can be separated using canonical variables analysis (CVA). Variation in lip shape, genome size and heterochromatin patterns of the taxa are not fully congruent with the phylogenetic analysis, but our results allowed us to delimit with full confidence four species: E. amapense, E. anatipedium (including E. amarajiense), E. pseudodifforme (including E. campaccii and E. thiagoi) and E. sanchezii. Four others will be tentatively maintained but need further study. Our results indicate that it will be necessary to reassess many of the species complexes in the genus using a similar multidisciplinary perspective to evaluate the number of taxa that should be recognized.
Non-Malleable Zero-Knowledge Arguments with Lower Round Complexity
Authors: Yan Zhenbin , Deng Yi 
Published: July 2020

Abstract
Round complexity is one of the fundamental problems in zero-knowledge (ZK) proof systems. Non-malleable zero-knowledge (NMZK) protocols are ZK protocols that provide security even when man-in-the-middle adversaries interact with a prover and a verifier simultaneously. It is known that the first constant-round public-coin NMZK arguments for NP can be constructed by assuming the existence of collision-resistant hash functions (Pass, R. and Rosen, A. (2005) New and Improved Constructions of Non-Malleable Cryptographic Protocols. In Gabow, H.N. and Fagin, R. (eds) Proc. 37th Annual ACM Symposium on Theory of Computing, Baltimore, MD, USA, May 2224, 2005, pp. 533542. ACM) and has relatively high round complexity; the first four-round private-coin NMZK arguments for NP can be constructed in the plain model by assuming the existence of one-way functions (Goyal, V., Richelson, S., Rosen, A. and Vald, M. (2014) An Algebraic Approach to Non-Malleability. In 55th IEEE Annual Symposium on Foundations of Computer Science, FOCS 2014, Philadelphia, PA, USA, October 1821, 2014, pp. 4150. IEEE Computer Society and Ciampi, M., Ostrovsky, R., Siniscalchi, L. and Visconti, I. (2017) Delayed-Input Non-Malleable Zero Knowledge and Multi-Party Coin Tossing in Four Rounds. In Kalai, Y. and Reyzin, L. (eds) Theory of Cryptography15th Int. Conf., TCC 2017. Lecture Notes in Computer Science, Baltimore, MD, USA, November 1215, 2017, Part I, Vol. 10677, pp. 711742. Springer). In this paper, we present a six-round public-coin NMZK argument of knowledge system assuming the existence of collision-resistant hash functions and a three-round private-coin NMZK argument system from multi-collision resistance of hash functions assumption in the keyless setting.
Is obesity associated with poorer outcomes in patients undergoing minimally invasive mitral valve surgery?
Authors: Aljanadi Firas , Toolan Caroline , Theologou Thomas , Shaw Matthew , Palmer Kenneth , Modi Paul 
Published: July 2020

AbstractOBJECTIVESHigh body mass index (BMI) makes minimally invasive mitral valve surgery (MIMVS) more challenging with some surgeons considering this a contraindication. We sought to determine whether this is because the outcomes are genuinely worse than those of non-obese patients.METHODSThis is a retrospective cohort study of all patients undergoing MIMVS ± concomitant procedures over an 8-year period. Patients were stratified into 2 groups: BMI ≥ 30 kg/m2 and BMI ˂ 30 kg/m2, as per World Health Organization definitions. Baseline characteristics, operative and postoperative outcomes and 5-year survival were compared.RESULTSWe identified 296 patients (BMI ≥30, n = 41, median 35.3, range 30–43.6; BMI &lt;30, n = 255, median 26.2, range 17.6–29.9). The groups were well matched with regard to baseline characteristics. There was only 1 in-hospital mortality, and this was in the BMI &lt; 30 group. There was no difference in repair rate for degenerative disease (100% vs 96.3%, P &gt; 0.99 respectively) or operative durations [cross-clamp: 122 min interquartile range (IQR) 100–141) vs 125 min (IQR 105–146), P = 0.72, respectively]. There were only 6 conversions to sternotomy, all in non-obese patients. There was no significant difference in any other perioperative or post-operative outcomes. Using the Kaplan–Meier analysis, there was no significant difference in 5-year survival between the 2 groups (95.8% vs 95.5%, P = 0.83, respectively).CONCLUSIONSIn patients having MIMVS, there is insufficient evidence to suggest that obesity affects either short- or mid-term outcomes. Obesity should therefore not be considered as a contraindication to this technique for experienced teams.
Effects of Native Tree Planting on Soil Recovery in Tropical Montane Cloud Forests
Authors: Mendoza-Vega Jorge , Ku-Quej Victor M , Messing Ingmar , Pérez-Jiménez Juan Carlos 
Published: July 2020

Abstract
The tropical montane cloud forest is one of the most biodiverse ecosystems on Earth and is one of the areas most threatened by anthropogenic disturbance. This study assessed the temporal impact on soil properties (organic carbon, total nitrogen, cation exchange capacity, bulk density) following establishment of native tree species in two degraded tropical montane cloud forest areas with different soil types and land-use intensities in south-east Mexico. In Pueblo Nuevo, Chiapas, Pinus chiapensis and Alnus spp. were established at two sites with humic Nitisols with low and moderate disturbance levels, respectively. In Xalapa, Veracruz, plum pine (Podocarpus matudae), American hornbeam (Carpinus caroliniana), Oaxaca walnut (Juglans pyriformis Liebm.), and sweetgum (Liquidambar styraciflua) were established on a grassland-covered humic Andosol with a high level of disturbance. After 16 years, soil properties had generally improved, although in the initial years after planting, the values declined, indicating a possible negative impact because of disturbance during tree establishment. Land-use intensity prior to tree establishment influenced the level of recovery in soil properties. The Pueblo Nuevo sites, with low to moderate disturbance levels, regained soil quality faster than the highly disturbed Xalapa site, despite better initial soil quality in the latter.
Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock
Authors: Burskaia Valentina , Naumenko Sergey , Schelkunov Mikhail , Bedulina Daria , Neretina Tatyana , Kondrashov Alexey , Yampolsky Lev , Bazykin Georgii A 
Published: July 2020

Abstract
Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.
Ion-exchange purification and structural characterization of five sulfated fucoidans from brown algae
Authors: Sichert Andreas , Le Gall Sophie , Klau Leesa Jane , Laillet Brigitte , Rogniaux Hélène , Aachmann Finn Lillelund , Hehemann Jan-Hendrik 
Published: July 2020

Abstract
Fucoidans are a diverse class of sulfated polysaccharides integral to the cell wall of brown algae, and due to their various bioactivities, they are potential drugs. Standardized work with fucoidans is required for structure–function studies, but remains challenging since available fucoidan preparations are often contaminated with other algal compounds. Additionally, fucoidans are structurally diverse depending on species and season, urging the need for standardized purification protocols. Here, we use ion-exchange chromatography to purify different fucoidans and found a high structural diversity between fucoidans. Ion-exchange chromatography efficiently removes the polysaccharides alginate and laminarin and other contaminants such as proteins and phlorotannins across a broad range of fucoidans from major brown algal orders including Ectocarpales, Laminariales and Fucales. By monomer composition, linkage analysis and NMR characterization, we identified galacturonic acid, glucuronic acid and O-acetylation as new structural features of certain fucoidans and provided a novel structure of fucoidan from Durvillaea potatorum with α-1,3-linked fucose backbone and β-1,6 and β-1,3 galactose branches. This study emphasizes the use of standardized ion-exchange chromatography to obtain defined fucoidans for subsequent molecular studies.
Organic matter assimilation by hard substrate fauna in an offshore wind farm area: a pulse-chase study
Authors: Mavraki Ninon , Degraer Steven , Vanaverbeke Jan , Braeckman Ulrike 
Published: July 2020

AbstractThe installation of offshore wind farms (OWFs) adds artificial hard substrates into naturally soft-bottom areas, changing the local biodiversity. The turbine foundations are rapidly colonized by colonizing organisms, mainly consisting of suspension feeders that can potentially reduce the local primary producer standing stock. In this study, we estimated the amount of organic matter processed by colonizing assemblages of OWFs. We conducted a laboratory pulse-chase experiment, by offering 13C-labelled fragmented microalgae to PVC panels colonized by OWF colonizing fauna. The blue mussel Mytilus edulis showed the highest biomass-specific carbon assimilation, while the high densities of the amphipod Jassa herdmani resulted in the highest total carbon assimilation. By upscaling our results to the total number of the installed offshore wind turbines in the Belgian part of the North Sea, we estimate that these species can reduce the local primary producer standing stock in the area by ca. 1.3%. Mytilus edulis and J. herdmani communities colonizing offshore wind turbine foundations significantly increase carbon assimilation compared to natural soft sediment macrofauna inhabiting the same surface area (i.e. footprint of the turbines).
Ostrea edulis beds in the central North Sea: delineation, ecology, and restoration
Authors: Bennema Floris P , Engelhard Georg H , Lindeboom Han 
Published: July 2020

Abstract
Until the late 19th century, extensive beds of flat oyster Ostrea edulis populated the Central North Sea, which have vanished after intensive fisheries. At present, various initiatives are being carried out to investigate the potential to restore this former key species in the area. This historical ecological study contributes by delineating the former oyster bed area and through an assessment of its limits against known gradients in the North Sea. Extensive data from historical maps, texts, and ship-based surveys were used to synthesize our knowledge on the former beds. It was revealed that the area with oyster beds covered ∼6.2% of the total North Sea bottom, with a delineation that could partly be explained by hydrodynamic and temperature gradients. The position and extent of the area are notably different from the area that is used in recent feasibility studies on the restoration of North Sea oyster beds. The offshore oysters lived on muddy sand in relatively cold conditions, and there are several indications that their reproductive rate was low. The apparent disappearance of cold water adapted flat oysters will challenge restoration projects. This study provides indispensable information for the future restoration of flat oyster beds in the North Sea.
Qualitative exploration of factors associated with shared decision-making in diabetes management: a health care provider’s perspective
Authors: Baig Amena Moazzam , Humayaun Ayesha , Mehmood Sara , Akram Muhammed Waqar , Raza Syed Abbass , Shakoori Tania 
Published: July 2020

Abstract

Objective
Internationally, patient–doctor interaction has shifted from the paternalist model to the shared decision-making (SDM) model, which is an essential part of effective management of chronic illnesses, especially diabetes. It is a relatively new concept in Pakistan, and data about healthcare providers’ perspectives are lacking. The aim was to explore significant facilitators and barriers to effective SDM as perceived by endocrinologists.

Design
A qualitative research using in-depth interviews based on grounded theory was done. It was written in line with the Consolidated Criteria for Reporting Qualitative Research checklist.

Setting
The interviews were conducted at the workplace of the endocrinologist between April and July 2019.

Participants
Prominent endocrinologists of Pakistan residing in Lahore were approached for in-depth interviews. The transcripts were analyzed simultaneously, and theme saturation was achieved in 11 interviews.

Main outcome measures
Thematic analysis of data done using grounded theory.

Results
Four major and two minor themes were identified. The most cited barriers to effective SDM from the doctors’ side were the shortage of time during consultations and the absence of formal training of clinicians in communication skills. However, the patients’ hesitation in questioning the doctor, perceiving him as a paternalist ‘messiah’ in society and lack of education limits their ability to understand and comprehend treatment options.

Conclusion
There are many barriers perceived by providers as well as clients/patients by effectively using SDM. Local cultural context is influencing a lot.
Methods for Distinguishing Aspen Seedlings from Suckers in the Field
Authors: Kreider Mark R , Mock Karen E , Yocom Larissa L 
Published: July 2020

AbstractQuaking aspen is a common component of postdisturbance landscapes, in part because of its ability to regenerate via asexual suckers. Previously viewed as exceedingly rare in the western United States, sexual seedling establishment is increasingly seen as another important natural regeneration pathway for aspen, because sexual regeneration increases genetic diversity and facilitates long-distance dispersal. However, aspen seedling research is hampered by difficulties in visually distinguishing seedlings from suckers in the field, and few resources exist to guide managers and researchers. We present methods for distinguishing aspen seedlings from aspen suckers, suitable for use in field studies. Using these methods, we achieved 99 percent predictive accuracy in a recently burned area in southern Utah, although accuracy decreased to 90 percent following one summer’s growth, as seedlings and suckers became more similar in appearance.Study Implication: Sexual regeneration may play an important role in aspen’s response to climate change, as it increases genetic diversity and adaptive capacity, and allows aspen populations and their ecological associates to better track changing climate through increased dispersal distances. The methods we present allow managers and researchers to accurately identify aspen seedling populations, which can then be protected and monitored through time to better understand aspen demography and the factors limiting establishment and survival of new clones. Aspen seedling ecology is an area with many knowledge gaps currently, and these methods remove a barrier that has hindered research in the past.
Outcomes after reirradiation of spinal metastasis with stereotactic body radiation therapy (SBRT): a retrospective single institutional study
Authors: Sasamura Kazuma , Suzuki Ryoko , Kozuka Takuyo , Yoshimura Ryoichi , Yoshioka Yasuo , Oguchi Masahiko 
Published: July 2020

ABSTRACT
This study was aimed at assessing the feasibility and toxicity of using stereotactic body radiation therapy (SBRT) for reirradiation of spinal metastatic tumors. We conducted a retrospective review, from our institutional database, of the data of patients who received reirradiation, with overlap of some prescribed isodose lines to the vertebra from the initial radiation therapy, between 2007 and 2019. We identified 40 patients with spinal metastatic tumors, of whom 2 had 2 metastatic vertebral lesions each, totaling up to 42 target lesions. The median dose to spinal cord at the initial radiation therapy was 30 Gy. SBRT based on the intensity-modulated radiation therapy (IMRT) technique was used for reirradiation to spare the spinal cord. All patients received a prescription dose of 25 Gy in 5 fractions to the planning target volume (PTV). Among the 40 cases who had pain, pain relief was obtained in 24 (60%) after reirradiation. Neurologic improvement was obtained in 8 of 15 cases (53%). The adverse events were evaluated using the Common Terminology Criteria for Adverse Events Version 5.0. Reirradiation was well-tolerated, with only 2 patients experiencing adverse events ≥grade 2 in severity, including 1 patient with grade 3 pain, and another patient with grade 3 spinal fracture. None of the patients developed radiation myelopathy. Our data demonstrated that reirradiation of spinal metastasis using SBRT provided effective pain relief and neurologic improvement, with minimal toxicity.
Capsicum annum Hsp26.5 promotes defense responses against RNA viruses via ATAF2 but is hijacked as a chaperone for tobamovirus movement protein
Authors: Foong Siew-Liang , Paek Kyung-Hee 
Published: July 2020

Abstract
The expression of Capsicum annuum HEAT SHOCK PROTEIN 26.5 (CaHsp26.5) was triggered by the inoculation of Tobacco mosaic virus pathotype P0 (TMV-P0) but its function in the defense response of plants is unknown. We used gene silencing and overexpression approaches to investigate the effect of CaHsp26.5 expression on different plant RNA viruses. Moreover, we performed protein–protein and protein–RNA interaction assays to study the mechanism of CaHsp26.5 function. CaHsp26.5 binding to a short poly-cytosine motif in the 3'-untranslated region of the genome of some viruses triggers the expression of several defense-related genes such as PATHOGENESIS-RELATED GENE 1 with the help of a transcription factor, NAC DOMAIN-CONTAINING PROTEIN 81 (ATAF2). Thus, an elevated CaHsp26.5 level was accompanied by increased plant resistance against plant viruses such as Cucumber mosaic virus strain Korea. However, the movement proteins of Pepper mild mottle virus pathotype P1,2,3 and TMV-P0 were shown to be able to interact with CaHsp26.5 to maintain the integrity of their proteins. Our work shows CaHsp26.5 as a positive player in the plant defense response against several plant RNA viruses. However, some tobamoviruses can hijack CaHsp26.5’s chaperone activity for their own benefit.