bluuebunny/crossref_metadata_2025_split huggingface dataset:
Innovative solutions based on CAD of the protective barrier systems architecture for maritime disasters
Authors: Mihai C , Ene A G 
Published: January 2020

AbstractPollution of the waters of the planetary ocean is due both to the evacuation of waste water from industrial units along the sea, as well as to the operational or accidental losses that have occurred in the process of oil marine exploitation and the uncontrolled evacuation of the sentries of ships in traffic or stationary. Nowadays, in order to limit the effects of pollution, inflatable and non-inflatable systems based on composite structures are used in all riverside countries of the seas and oceans. The textile material covered with elastomeric mixture made up of special ingredients has proved to be a very successful material for marine environment applications. For establishing the design principles of a composite material, as part of a barrier protection system made of floating surface elements, used in dynamic conditions (for accidental pollution), in open water (offshore), a specialized software that enables the definition of the calculation parameters, accomplishment of the effective calculations, processing, visualization and the export of the numerical data was used.
A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae)
Authors: Wen Jun , Yu Yan , Xie Deng-Feng , Peng Chang , Liu Qing , Zhou Song-Dong , He Xing-Jin 
Published: January 2020

AbstractBackground and AimsA long-standing controversy in the subfamily Apioideae concerns relationships among the major lineages, which has prevented a comprehensive study of their fruits and evolutionary history. Here we use single copy genes (SCGs) generated from transcriptome datasets to generate a reliable species tree and explore the evolutionary history of Apioideae.MethodsIn total, 3351 SCGs were generated from 27 transcriptome datasets and one genome, and further used for phylogenetic analysis using coalescent-based methods. Fruit morphology and anatomy were studied in combination with the species tree. Eleven SCGs were screened out for dating analysis with two fossils selected for calibration.Key ResultsA well-supported species tree was generated with a topology [Chamaesieae, (Bupleureae, (Pleurospermeae, (Physospermopsis Clade, (Group C, (Group A, Group B)))))] that differed from previous trees. Daucinae and Torilidinae were not in the tribe Scandiceae and existed as sister groups to the Acronema Clade. Five branches (I–V) of the species tree showed low quartet support but strong local posterior probabilities. Dating analysis suggested that Apioideae originated around 56.64 Mya (95 % highest posterior density interval, 45.18–73.53 Mya).ConclusionsThis study resolves a controversial phylogenetic relationship in Apioideae based on 3351 SCGs and coalescent-based species tree estimation methods. Gene trees that contributed to the species tree may undergoing rapid evolutionary divergence and incomplete lineage sorting. Fruits of Apioideae might have evolved in two directions, anemochorous and hydrochorous, with epizoochorous as a derived mode. Molecular and morphological evidence suggests that Daucinae and Torilidinae should be restored to the tribe level. Our results provide new insights into the morphological evolution of this subfamily, which may contribute to a better understanding of species diversification in Apioideae. Molecular dating analysis suggests that uplift of the Qinghai–Tibetan Plateau (QTP) and climate changes probably drove rapid speciation and diversification of Apioideae in the QTP region.
Regression on imperfect class labels derived by unsupervised clustering
Authors: Brøndum Rasmus Froberg , Michaelsen Thomas Yssing , Bøgsted Martin 
Published: January 2020

Abstract
Outcome regressed on class labels identified by unsupervised clustering is custom in many applications. However, it is common to ignore the misclassification of class labels caused by the learning algorithm, which potentially leads to serious bias of the estimated effect parameters. Due to their generality we suggest to address the problem by use of regression calibration or the misclassification simulation and extrapolation method. Performance is illustrated by simulated data from Gaussian mixture models, documenting a reduced bias and improved coverage of confidence intervals when adjusting for misclassification with either method. Finally, we apply our method to data from a previous study, which regressed overall survival on class labels derived from unsupervised clustering of gene expression data from bone marrow samples of multiple myeloma patients.
Practical genotyping by single-nucleotide primer extension
Authors: Breyer Joan P , Smith Jeffrey R 
Published: January 2020

AbstractGenome-wide association studies bring into focus specific genetic variants of particular interest for which validation is often sought in large numbers of study subjects. Practical alternative methods are limiting for the application of genotyping few variants in many samples. A common scenario is the need to genotype a study population at a specific high-value single nucleotide polymorphism (SNP) or insertion-deletion (indel). Not all such variants, however, will be amenable to assay by a given approach. We have adapted a single-nucleotide primer extension (SNuPE) method that may be tailored to genotype a required variant, and implemented it as a useful general laboratory protocol. We demonstrate reliable application for production-scale genotyping, successfully converting 87% of SNPs and indels for assay with an estimated error rate of 0.003. Our implementation of the SNuPE genotyping assay is a viable addition to existing alternative methods; it is readily customizable, scalable, and uses standard reagents and a laboratory plate reader.
Phylogenetic position and evolution of glandular structures of the unusual and narrowly distributed genus Rhytidanthera (Ochnaceae)
Authors: Reinales Sandra , Parra-O Carlos 
Published: January 2020

AbstractRhytidanthera is the only genus of Ochnaceae with compound leaves, and it forms sparse, small populations restricted to the primary forest of the Colombian and Venezuelan Andes and the sandstone hills of La Macarena and Chiribiquete. It has been suggested to be related to Godoya, Cespedesia and Krukoviella in taxonomic and phylogenetic studies. However, the relationships in this group remain poorly resolved, due to the lack of a wider molecular and taxonomic sampling. We present a phylogenetic study of tribe Sauvagesieae including three Rhytidanthera spp. and one species each of Godoya and Cespedesia, using sequences from one nuclear (ITS) and four plastid DNA regions (matK, ndhF, rbcL and trnL-F), in order to clarify the relationships among these four genera. We recover a new and well-supported phylogenetic hypothesis, with Rhytidanthera as sister to a clade comprising Godoya and the clade formed by Cespedesia and Krukoviella. This Neotropical clade was recovered as sister to the monotypic and African genus Fleurydora. The clade comprising Rhytidanthera, Godoya, Cespedesia and Krukoviella is supported by the presence of glandular structures (colleters) at the base of stipules and bracts. The colleters also evolved at the base of the sepals in this clade, with a secondary loss in Cespedesia and Krukoviella. We suggest that the combination of unequal-sized sepals enclosing the floral bud and the presence of colleters in members of this clade could have a role in the protection of leaves and flowers in the early stages of development, instead of acting in pollinator attraction.
Cardiac sympathetic denervation and synucleinopathy in Alzheimer’s disease with brain Lewy body disease
Authors: Serrano Geidy E , Shprecher David , Callan Michael , Cutler Brett , Glass Michael , Zhang Nan , Walker Jessica , Intorcia Anthony , Adler Charles H , Shill Holly A , Driver-Dunckley Erika , Mehta Shyamal H , Belden Christine M , Zamrini Edward , Sue Lucia I , Vargas Daisy , Beach Thomas G 
Published: January 2020

Abstract
Comorbid Lewy body pathology is very common in Alzheimer’s disease and may confound clinical trial design, yet there is no in vivo test to identify patients with this. Tissue (and/or radioligand imaging) studies have shown cardiac sympathetic denervation in Parkinson’s disease and dementia with Lewy bodies, but this has not been explored in Alzheimer’s subjects with Lewy bodies not meeting dementia with Lewy bodies clinicopathological criteria. To determine if Alzheimer’s disease with Lewy bodies subjects show sympathetic cardiac denervation, we analysed epicardial and myocardial tissue from autopsy-confirmed cases using tyrosine hydroxylase and neurofilament immunostaining. Comparison of tyrosine hydroxylase fibre density in 19 subjects with Alzheimer’s disease/dementia with Lewy bodies, 20 Alzheimer’s disease with Lewy bodies, 12 Alzheimer’s disease subjects without Lewy body disease, 19 Parkinson’s disease, 30 incidental Lewy body disease and 22 cognitively normal without Alzheimer’s disease or Lewy body disease indicated a significant group difference (P &lt; 0.01; Kruskal–Wallis analysis of variance) and subsequent pair-wise Mann–Whitney U tests showed that Parkinson’s disease (P &lt; 0.05) and Alzheimer’s disease/dementia with Lewy bodies (P &lt; 0.01) subjects, but not Alzheimer’s disease with Lewy bodies subjects, had significantly reduced tyrosine hydroxylase fibre density as compared with cognitively normal. Both Parkinson’s disease and Alzheimer’s disease/dementia with Lewy bodies subjects also showed significant epicardial losses of neurofilament protein-immunoreactive nerve fibre densities within the fibre bundles as compared with cognitively normal subjects (P &lt; 0.01) and both groups showed high pathologic alpha-synuclein densities (P &lt; 0.0001). Cardiac alpha-synuclein densities correlated significantly with brain alpha-synuclein (P &lt; 0.001), while cardiac tyrosine hydroxylase and neurofilament immunoreactive nerve fibre densities were negatively correlated with the densities of both brain and cardiac alpha-synuclein, as well as Unified Parkinson’s Disease Rating Scale scores (P &lt; 0.05). The clear separation of Alzheimer’s disease/dementia with Lewy bodies subjects from Alzheimer’s disease and cognitively normal, based on cardiac tyrosine hydroxylase fibre density, is the first report of a statistically significant difference between these groups. Our data do not show significant sympathetic cardiac denervation in Alzheimer’s disease with Lewy bodies, but strongly confirm that cardiac nuclear imaging with a noradrenergic radioligand is worthy of further study as a potential means to separate Alzheimer’s disease from Alzheimer’s disease/dementia with Lewy bodies during life.
Disrupting nNOS–PSD95 Interaction Improves Neurological and Cognitive Recoveries after Traumatic Brain Injury
Authors: Qu Wenrui , Liu Nai-Kui , Wu Xiangbing , Wang Ying , Xia Yongzhi , Sun Yan , Lai Yvonne , Li Rui , Shekhar Anantha , Xu Xiao-Ming 
Published: January 2020

Abstract
Excessive activation of N-methyl-D-aspartate receptors (NMDARs) and the resulting neuronal nitric oxide synthase (nNOS) activation plays a crucial role in the pathogenesis of traumatic brain injury (TBI). However, directly inhibiting NMDARs or nNOS produces adverse side effects because they play key physiological roles in the normal brain. Since interaction of nNOS–PSD95 is a key step in NMDAR-mediated excitotoxicity, we investigated whether disrupting nNOS–PSD95 interaction with ZL006, an inhibitor of nNOS–PSD95 interaction, attenuates NMDAR-mediated excitotoxicity. In cortical neuronal cultures, ZL006 treatment significantly reduced glutamate-induced neuronal death. In a mouse model of controlled cortical impact (CCI), administration of ZL006 (10 mg/kg, i.p.) at 30 min postinjury significantly inhibited nNOS–PSD95 interaction, reduced TUNEL- and phospho-p38-positive neurons in the motor cortex. ZL006 treatment also significantly reduced CCI-induced cortical expression of apoptotic markers active caspase-3, PARP-1, ratio of Bcl-2/Bax, and phosphorylated p38 MAPK (p-p38). Functionally, ZL006 treatment significantly improved neuroscores and sensorimotor performance, reduced somatosensory and motor deficits, reversed CCI-induced memory deficits, and attenuated cognitive impairment. Histologically, ZL006 treatment significantly reduced the brain lesion volume. These findings collectively suggest that blocking nNOS–PSD95 interaction represents an attractive strategy for ameliorating consequences of TBI and that its action is mediated via inhibiting neuronal apoptosis and p38 MAPK signaling.
Sense of Agency Beyond Sensorimotor Process: Decoding Self-Other Action Attribution in the Human Brain
Authors: Ohata Ryu , Asai Tomohisa , Kadota Hiroshi , Shigemasu Hiroaki , Ogawa Kenji , Imamizu Hiroshi 
Published: January 2020

Abstract
The sense of agency is defined as the subjective experience that “I” am the one who is causing the action. Theoretical studies postulate that this subjective experience is developed through multistep processes extending from the sensorimotor to the cognitive level. However, it remains unclear how the brain processes such different levels of information and constitutes the neural substrates for the sense of agency. To answer this question, we combined two strategies: an experimental paradigm, in which self-agency gradually evolves according to sensorimotor experience, and a multivoxel pattern analysis. The combined strategies revealed that the sensorimotor, posterior parietal, anterior insula, and higher visual cortices contained information on self-other attribution during movement. In addition, we investigated whether the found regions showed a preference for self-other attribution or for sensorimotor information. As a result, the right supramarginal gyrus, a portion of the inferior parietal lobe (IPL), was found to be the most sensitive to self-other attribution among the found regions, while the bilateral precentral gyri and left IPL dominantly reflected sensorimotor information. Our results demonstrate that multiple brain regions are involved in the development of the sense of agency and that these show specific preferences for different levels of information.
Searching and Finding the Hidden Treasure: A Retrospective Analysis of Rickettsial Disease Among Dutch International Travelers
Authors: de Vries Sophia G , van Eekeren Louise E , van der Linden Hans , Visser Benjamin J , Grobusch Martin P , Wagenaar Jiri F P , Goris Marga G A , Goorhuis Abraham 
Published: January 2020

Abstract

Background
Rickettsial disease (RD) is a prevalent and underestimated cause of febrile illness worldwide, especially in the absence of an inoculation eschar. We attempted to quantify this underestimation at our clinic, by investigating past cases of febrile illness in travelers who had tested negative for leptospirosis, a disease that can initially present similarly to non-eschar RD, and which we routinely consider when other important causes of unspecified febrile illness have tested negative.

Methods
We performed a retrospective analysis in febrile returned travelers from Asia, Africa, or the Americas between 2010 and 2017, who had tested negative for leptospirosis. Serologic immunofluorescence assays were performed for Orientia tsutsugamushi (scrub typhus), typhus group, and spotted fever group RD. We performed a medical records review of all patients who tested positive. In case of a fitting medical history, cases were deemed either confirmed (based on convalescent serology) or suspected (based on single serology).

Results
Among 97 patients, convalescent serology was available in 16 (16.5%) patients, and a single serology in 81 (83.5%) patients. RD was the likely diagnosis in 8 of 16 (50.0%) patients with convalescent serology, and in 8 of 81 (9.9%) with single serology. Of the 16 confirmed/suspected cases, 11 (69%) had been missed and 7 (44%) had not received adequate empiric antibiotic therapy.

Conclusions
This study shows that non-eschar RD is an important and poorly recognized cause of illness in travelers, even in a specialized travel clinic. A lower threshold to test and treat for RD is warranted in returning travelers with febrile illness.
Shadow constitutional review: The dark side of pre-enactment political review in Ireland and Japan
Authors: Kenny David , Casey Conor 
Published: January 2020

Abstract
Political constitutionalism is a major area of inquiry in contemporary constitutional discourse. A significant and increasingly central aspect of political constitutionalism is pre-enactment political review: laws being reviewed for constitutionality or rights compliance by parliament or the executive. This institution is said to be a good augmentation of, or even replacement for, the institution of judicial review, and it is said to bring with it a host of normative benefits. In this article, we wish to highlight an under-explored dark side to pre-enactment review. By undertaking a comparative analysis of functional pre-enactment review in several similar jurisdictions—Canada, New Zealand, and the UK—we contrast these systems, and the ordinary failings they display, with the much deeper problems of pre-enactment review in Ireland and Japan. These latter jurisdictions, we argue, not only fail to instantiate the benefits of pre-enactment review but in fact show that, in the right circumstances, pre-enactment review can have negative effects that are antithetical to the goals and values of political constitutionalism. We call this phenomenon “shadow constitutional review,” and suggest that it adds a layer of complexity and nuance to contemporary discussions of political constitutionalism.
Thoracic endovascular aortic repair for acute type B aortic dissection complicated by total occlusion of the abdominal aorta
Authors: Shikata Daichi , Omura Atsushi , Matsuo Jiro , Matsuda Hitoshi 
Published: January 2020

Abstract
A 72-year-old man presenting with lower body malperfusion and complete paralysis was transferred for emergency treatment of a complicated acute type B aortic dissection. Enhanced computed tomography showed occlusion of the true lumen inside the abdominal aorta due to compression of the false lumen, accompanied by a Crawford extension type IV thoraco-abdominal aortic aneurysm. The primary entry tear was located at the level of the tenth thoracic vertebra above the aneurysm. Emergency thoracic endovascular aortic repair was performed to cover the entry tear and to regain perfusion of the lower body. Efforts to perform retrograde insertion of a guidewire from the femoral arteries to pass the occluded abdominal aorta were unsuccessful. A through-and-through guidewire technique between the left brachial artery and the right femoral artery was performed to deliver a Zenith TX-2 stent graft from the right femoral artery. After closure of the primary entry tear, complete recovery from the occlusion of the abdominal aorta was obtained 6 h after the onset. His paralysis recovered completely, and the postoperative course was uneventful without reperfusion injury.
Representation Homology of Topological Spaces
Authors: Berest Yuri , Ramadoss Ajay C , Yeung Wai-Kit 
Published: January 2020

AbstractIn this paper, we introduce and study representation homology of topological spaces, which is a natural homological extension of representation varieties of fundamental groups. We give an elementary construction of representation homology parallel to the Loday–Pirashvili construction of higher Hochschild homology; in fact, we establish a direct geometric relation between the two theories by proving that the representation homology of the suspension of a (pointed connected) space is isomorphic to its higher Hochschild homology. We also construct some natural maps and spectral sequences relating representation homology to other homology theories associated with spaces (such as Pontryagin algebras, ${{\mathbb {S}}}^1$-equivariant homology of the free loop space, and stable homology of automorphism groups of f.g. free groups). We compute representation homology explicitly (in terms of known invariants) in a number of interesting cases, including spheres, suspensions, complex projective spaces, Riemann surfaces, and some 3-dimensional manifolds, such as link complements in ${\mathbb {R}}^3$ and the lens spaces $ L(p,q) $. In the case of link complements, we identify the representation homology in terms of ordinary Hochschild homology, which gives a new algebraic invariant of links in ${\mathbb {R}}^3$.
Impact of genotypic diversity on selection of subtype-specific drug resistance profiles during raltegravir-based therapy in individuals infected with B and BF recombinant HIV-1 strains
Authors: Sánchez Daniela , Arazi Caillaud Solange , Zapiola Ines , Fernandez Giuliano Silvina , Bologna Rosa , Mangano Andrea , Aulicino Paula C 
Published: January 2020

AbstractBackgroundCurrent knowledge on HIV-1 resistance to integrase inhibitors (INIs) is based mostly on subtype B strains. This contrasts with the increasing use of INIs in low- and middle-income countries, where non-B subtypes predominate.Materials and methodsHIV-1 drug resistance genotyping was performed in 30 HIV-1-infected individuals undergoing virological failure to raltegravir. Drug resistance mutations (DRMs) and HIV-1 subtype were characterized using Stanford HIVdb and phylogenetic analyses.ResultsOf the 30 integrase (IN) sequences, 14 were characterized as subtype F (47%), 8 as subtype B (27%), 7 as BF recombinants (23%) and 1 as a putative CRF05_DF (3%). In 25 cases (83%), protease and reverse transcriptase (PR-RT) sequences from the same individuals confirmed the presence of different BF recombinants. Stanford HIVdb genotyping was concordant with phylogenetic inference in 70% of IN and 60% of PR-RT sequences. INI DRMs differed between B and F IN subtypes, with Q148K/R/H, G140S and E138K/A being more prevalent in subtype B (63% versus 0%, P = 0.0021; 50% versus 0%, P = 0.0096; and 50% versus 0%, P = 0.0096, respectively). These differences were independent of the time on raltegravir therapy or viral load at the time of genotyping. INI DRMs in subtype F IN genomes predicted a lower level of resistance to raltegravir and no cross-resistance to second-generation INIs.ConclusionsAlternative resistance pathways to raltegravir develop in subtypes B and F IN genomes, with implications for clinical practice. Evaluating the role of HIV-1 subtype in development and persistence of mutations that confer resistance to INIs will be important to improve algorithms for resistance testing and optimize the use of INIs.