bluuebunny/crossref_metadata_2025_split huggingface dataset:
An arithmetic interpretation of intuitionistic verification
Authors: Protopopescu Tudor 
Published: January 2020

AbstractIntuitionistic epistemic logic introduces an epistemic operator to intuitionistic logic, which reflects the intended Brouwer–Heyting–Kolmogorov (BHK) semantics of intuitionism. The fundamental assumption concerning intuitionistic knowledge and belief is that it is the product of verification. The BHK interpretation of intuitionistic logic has a precise formulation in the logic of proofs and its arithmetical semantics. We show here that this interpretation can be extended to the notion of verification upon which intuitionistic knowledge is based, providing the systems of intuitionistic epistemic logic based on verification with an arithmetical semantics too. This confirms that the conception of verification incorporated in these systems reflects the BHK interpretation.
Military Health System Access to Care: Performance and Perceptions
Authors: Abiero Beatrice , Beamer Sharon , Roshwalb Alan , Sackett Amanda , Gliner Melissa , Marshall-Aiyelawo Kimberley , Ellison Janice , McDavid Terry , Bannick Richard , Muraida Daniel 
Published: January 2020

Abstract
Introduction: Access to care (ATC) is an important component of providing quality healthcare. Clinics need to be able to accurately measure access; however, patients’ reports of access may be different from performance-based data gathered using administrative measures. The purpose of this research is to examine the relationship between ATC administrative data and patient survey results. Materials and Methods: This is a retrospective study performed in military medical treatment facilities. Survey data were obtained from the Joint Outpatient Experience Survey (JOES), and administrative data were collected from the Military Health System Data Repository. The data period was from May 2016 through March 2017 for 135 parent Military Treatment Facilities. This study was approved under the Defense Health Agency Internal Review Board (IRB number: CDO-15-2025). The analyses compare JOES ATC measures to administrative ATC measures. Overall correlation analyses and multivariate regression analyses were performed in order to generate observable correlations between access and healthcare measures (both administrative measures and patient survey items). Results: Results show moderate correlations between the facilities’ ATC survey items and administrative measures. These correlations were affected by the composition of the facility patient mix. The patient-based ATC measures from the JOES survey are related to administrative ATC measures collected and monitored by the facilities. In each final regression model, the coefficients for the ATC administrative variables were significant and negative which indicates that as the wait time for an appointment increases, patients’ ratings of the time between scheduling and appointment dates declines and patients’ assessments of being able to see a provider declines as well. Conclusions: Measuring ATC is a vital step in ensuring the health of patients and the provision of high quality care. Both patient surveys and administrative data are widely used for measuring ATC. This study found statistically significant moderate associations between survey and administrative ATC measures, which remained significant even after controlling for patient characteristics of the facilities. These study results suggest that administrative data can provide an accurate assessment of access; however, survey items can be useful for diagnosing potential issues with access, such as call center scheduling and provider availability. Future studies should explore the gaps in research surrounding best practices at facilities which have high patient experience with access, and look at other survey measures related to access, such as telephone resources and web-based communication programs.
A spectroscopic survey of Abell 1703: is it a rare relaxed cluster hosting a radio halo or a usual merging system?
Authors: Boschin W , Girardi M , Gastaldello F 
Published: January 2020

ABSTRACT
We present the study of the internal dynamics of the intriguing galaxy cluster Abell 1703, a system hosting a probable giant radio halo whose dynamical status is still controversial. Our analysis is based on unpublished spectroscopic data acquired at the Italian Telescopio Nazionale Galileo and data publicly available in the literature. We also use photometric data from the Sloan Digital Sky Survey. We select 147 cluster members and compute the cluster redshift 〈z〉 ∼ 0.277 and the global line-of-sight velocity dispersion σv ∼ 1300 km s−1. We infer that Abell 1703 is a massive cluster: M200 ∼ 1–2 × 1015 M⊙. The results of our study disagree with the picture of an unimodal, relaxed cluster as suggested by previous studies based on the gravitational lensing analysis and support the view of a perturbed dynamics proposed by recent works based on Chandra X-ray data. The first strong evidence of a dynamically disturbed cluster comes from the peculiarity of the BCG velocity with respect to the first moment of the velocity distribution of member galaxies. Moreover, several statistical tests employed to study the cluster galaxies kinematics find significant evidence of substructure, being Abell 1703 composed by at least two or three subclumps probably caught after the core–core passage. In this observational scenario, the suspected existence of a radio halo in the centre of this cluster is not surprising and well agrees with the theoretical models describing diffuse radio sources in clusters.
KASHz: No evidence for ionised outflows instantaneously suppressing star formation in moderate luminosity AGN at z ∼ 1.4–2.6
Authors: Scholtz J , Harrison C M , Rosario D J , Alexander D M , Chen C-C , Kakkad D , Mainieri V , Tiley A L , Turner O , Cirasuolo M , Sharples R M , Stach S 
Published: January 2020

ABSTRACT
As part of our KMOS AGN Survey at High-redshift (KASHz), we present spatially resolved VLT/KMOS and VLT/SINFONI spectroscopic data and ALMA 870 μm continuum imaging of eight z = 1.4–2.6 moderate AGN ($L_{\rm 2-10 \, \rm kev}$ = 1042–1045 ergs s−1). We map [O iii], H α and rest-frame FIR emission to search for any spatial anticorrelation between ionised outflows (traced by the [O  iii] line) and star formation (SF; traced by H α and FIR), that has previously been claimed for some high-z AGN and used as evidence for negative and/or positive AGN feedback. First, we conclude that H α is unreliable to map SF inside our AGN host galaxies based on: (i) SF rates inferred from attenuation-corrected H α can lie below those inferred from FIR; (ii) the FIR continuum is more compact than the H α emission by a factor of ∼2 on average; (iii) in half of our sample, we observe significant spatial offsets between the FIR and H α emission, with an average offset of 1.4 ± 0.6 kpc. Secondly, for the five targets with outflows we find no evidence for a spatial anticorrelation between outflows and SF using either H α or FIR as a tracer. This holds for our re-analysis of a famous z = 1.6 X-ray AGN (‘XID 2028’) where positive and negative feedback has been previously claimed. Based on our results, any impact on SF by ionised outflows must be subtle, either occurring on scales below our resolution, or on long time-scales.
Fructose consumption during pregnancy and lactation causes DNA damage and biochemical changes in female mice
Authors: Magenis Marina Lummertz , Damiani Adriani Paganini , de Marcos Pamela Souza , de Pieri Ellen , de Souza Emanuel , Vilela Thais Ceresér , de Andrade Vanessa Moraes 
Published: January 2020

AbstractThe consumption of fructose during pregnancy can cause hyperglycaemia and may stimulate production of reactive oxygen species; however, there are only a few studies reporting whether fructose consumption during pregnancy causes DNA damage. Therefore, the aim of this study was to evaluate the effects of fructose consumption on genetic and biochemical parameters in Swiss mice treated during pregnancy and lactation. For this, 15 couples of 60-day-old Swiss mice were divided into three groups of five couples: negative control (water) and two fructose groups (fructose dose of 10%/l and 20%/l). During this period, we evaluated food consumption, energy efficiency and body weight. Samples of blood were collected from the females before copulation, after the 15th day of conception and on the 21st day after the lactation period, for the glycaemic and lipid profiles as well as comet assay and micronucleus (MN) test. Comet assay and MN test evaluate DNA damage and clastogenicity, respectively. In the gestation and lactation period, the two fructose doses tested showed DNA damage as observed in the comet assay, which is associated with an increase in dietary intake, body weight, lipid profile and fasting glycaemia in females. Thus, it can be suggested that the high consumption of fructose during these periods is harmful for pregnancy and lactation.
The internal loops in the lower stem of primary microRNA transcripts facilitate single cleavage of human Microprocessor
Authors: Nguyen Thuy Linh , Nguyen Trung Duc , Bao Sheng , Li Shaohua , Nguyen Tuan Anh 
Published: January 2020

AbstractThe human Microprocessor complex cleaves primary microRNA (miRNA) transcripts (pri-miRNAs) to initiate miRNA synthesis. Microprocessor consists of DROSHA (an RNase III enzyme), and DGCR8. DROSHA contains two RNase III domains, RIIIDa and RIIIDb, which simultaneously cleave the 3p- and 5p-strands of pri-miRNAs, respectively. In this study, we show that the internal loop located in the lower stem of numerous pri-miRNAs selectively inhibits the cleavage of Microprocessor on their 3p-strand, thereby, facilitating the single cleavage on their 5p-strand. This single cleavage does not lead to the production of miRNA but instead, it downregulates miRNA expression. We also demonstrate that by manipulating the size of the internal loop in the lower stem of pri-miRNAs, we can alter the ratio of single-cut to double-cut products resulted from the catalysis of Microprocessor, thus changing miRNA production in the in vitro pri-miRNA processing assays and in human cells. Therefore, the oscillating level of the single cleavage suggests another way of regulation of miRNA expression and offers an alternative approach to miRNA knockdown.
Prevalence and architecture of posttranscriptionally impaired synonymous mutations in 8,320 genomes across 22 cancer types
Authors: Teng Huajing , Wei Wenqing , Li Qinglan , Xue Meiying , Shi Xiaohui , Li Xianfeng , Mao Fengbiao , Sun Zhongsheng 
Published: January 2020

Abstract
Somatic synonymous mutations are one of the most frequent genetic variants occurring in the coding region of cancer genomes, while their contributions to cancer development remain largely unknown. To assess whether synonymous mutations involved in post-transcriptional regulation contribute to the genetic etiology of cancers, we collected whole exome data from 8,320 patients across 22 cancer types. By employing our developed algorithm, PIVar, we identified a total of 22,948 posttranscriptionally impaired synonymous SNVs (pisSNVs) spanning 2,042 genes. In addition, 35 RNA binding proteins impacted by these identified pisSNVs were significantly enriched. Remarkably, we discovered markedly elevated ratio of somatic pisSNVs across all 22 cancer types, and a high pisSNV ratio was associated with worse patient survival in five cancer types. Intriguing, several well-established cancer genes, including PTEN, RB1 and PIK3CA, appeared to contribute to tumorigenesis at both protein function and posttranscriptional regulation levels, whereas some pisSNV-hosted genes, including UBR4, EP400 and INTS1, exerted their function during carcinogenesis mainly via posttranscriptional mechanisms. Moreover, we predicted three drugs associated with two pisSNVs, and numerous compounds associated with expression signature of pisSNV-hosted genes. Our study reveals the prevalence and clinical relevance of pisSNVs in cancers, and emphasizes the importance of considering posttranscriptional impaired synonymous mutations in cancer biology.
Pure Apraxia of Speech After Resection Based in the Posterior Middle Frontal Gyrus
Authors: Chang Edward F , Kurteff Garret , Andrews John P , Briggs Robert G , Conner Andrew K , Battiste James D , Sughrue Michael E 
Published: January 2020

Abstract

BACKGROUND AND IMPORTANCE
Apraxia of speech is a disorder of articulatory coordination and planning in speech sound production. Its diagnosis is based on deficits in articulation, prosody, and fluency. It is often described concurrent with aphasia or dysarthria, while pure apraxia of speech is a rare entity.

CLINICAL PRESENTATION
A right-handed man underwent focal surgical resection of a recurrent grade III astrocytoma in the left hemisphere dorsal premotor cortex located in the posterior middle frontal gyrus. After the procedure, he experienced significant long-term speech production difficulties. A battery of standard and custom language and articulatory assessments were administered, revealing intact comprehension and naming abilities, and preserved strength in orofacial articulators, but considerable deficits in articulatory coordination, fluency, and prosody—consistent with diagnosis of pure apraxia of speech. Tractography and resection volumes compared with publicly available imaging data from the Human Connectome Project suggest possible overlap with area 55b, an under-recognized language area in the dorsal premotor cortex and has white matter connectivity with the superior longitudinal fasciculus.

CONCLUSION
The case reported here details a rare clinical entity, pure apraxia of speech resulting from resection of posterior middle frontal gyrus. While not a classical language area, emerging literature supports the role of this area in the production of fluent speech, and has implications for surgical planning and the general neurobiology of language.
Carbon allocation to the root system of tropical tree Ceiba pentandra using 13C pulse labelling in an aeroponic facility
Authors: Mannerheim Neringa , Blessing Carola H , Oren Israel , Grünzweig José M , Bachofen Christoph , Buchmann Nina 
Published: January 2020

AbstractDespite the important role of tropical forest ecosystems in the uptake and storage of atmospheric carbon dioxide (CO2), the carbon (C) dynamics of tropical tree species remains poorly understood, especially regarding belowground roots. This study assessed the allocation of newly assimilated C in the fast-growing pioneer tropical tree species Ceiba pentandra (L.), with a special focus on different root categories. During a 5-day pulse-labelling experiment, 9-month-old (~3.5-m-tall) saplings were labelled with 13CO2 in a large-scale aeroponic facility, which allowed tracing the label in bulk biomass and in non-structural carbohydrates (sugars and starch) as well as respiratory CO2 from the canopy to the root system, including both woody and non-woody roots. A combined logistic and exponential model was used to evaluate 13C mean transfer time and mean residence time (MRT) to the root systems. We found 13C in the root phloem as early as 2 h after the labelling, indicating a mean C transfer velocity of 2.4 ± 0.1 m h−1. Five days after pulse labelling, 27% of the tracers taken up by the trees were found in the leaves and 13% were recovered in the woody tissue of the trunk, 6% in the bark and 2% in the root systems, while 52% were lost, most likely by respiration and exudation. Larger amounts of 13C were found in root sugars than in starch, the former also demonstrating shorter MRT than starch. Of all investigated root categories, non-woody white roots (NRW) showed the largest 13C enrichment and peaked in the deepest NRW (2–3.5 m) as early as 24 ± 2 h after labelling. In contrast to coarse woody brown roots, the sink strength of NRW increased with root depth. The findings of this study improve the understanding of C allocation in young tropical trees and provide unique insights into the changing contributions of woody and non-woody roots to C sink strengths with depth.
In vivomolecular signatures of cerebellar pathology in spinocerebellar ataxia type 3
Authors: Costa Maria do Carmo , Radzwion Maria , McLoughlin Hayley S. , Ashraf Naila S. , Fischer Svetlana , Shakkottai Vikram G. , Maciel Patrícia , Paulson Henry L. , Öz Gülin 
Published: January 2020

AbstractBackgroundNo treatment exists for the most common dominantly inherited ataxia Machado-Joseph disease, or spinocerebellar ataxia type 3 (SCA3). Successful evaluation of candidate therapeutics will be facilitated by validated noninvasive biomarkers of aspects of disease pathology recapitulated by animal models.ObjectiveWe sought to identify shared neurochemical signatures in two mouse models of SCA3 that reflect aspects of the human disease pathology.MethodsCerebellar neurochemical concentrations in homozygous YACMJD84.2 (Q84/Q84) and hemizygous CMVMJD135 (Q135) mice were measured by magnetic resonance spectroscopy at 9.4 tesla. Motivated by the shared neurochemical abnormalities in the two models, we determined the levels of neurofilament medium (NFL, indicator of neuroaxonal integrity) and myelin basic protein (MBP, indicator of myelination) in cerebellar lysates from a subset of mice and from patients with SCA3. Finally, NFL and MBP levels were measured in cerebellar extracts of Q84/Q84 mice upon sustained silencing of the mutantATXN3gene from 6-8 weeks-of-age until death.ResultsBoth Q84/Q84 and Q135 mice displayed lowerN-acetylaspartate than wild-type littermates, indicating neuroaxonal loss/dysfunction, and lowermyo-inositol and total choline, indicating disturbances in phospholipid membrane metabolism and demyelination. Cerebellar NFL and MBP levels were accordingly lower in both models as well as in the cerebellar cortex of patients with SCA3 than controls. Furthermore, long-term sustained RNAi-mediated reduction of ATXN3 levels increased NFL and MBP in Q84/Q84 cerebella.ConclusionsN-acetylaspartate,myo-inositol and total choline levels in the cerebellum are candidate biomarkers of neuroaxonal and oligodendrocyte pathology in SCA3, which are reversible by reduction of mutantATXN3levels.
Improved multi-type birth-death phylodynamic inference in BEAST 2
Authors: Scire Jérémie , Barido-Sottani Joëlle , Kühnert Denise , Vaughan Timothy G. , Stadler Tanja 
Published: January 2020

AbstractThe multi-type birth-death model with sampling is a phylodynamic model which enables quantification of past population dynamics in structured populations, based on phylogenetic trees. The BEAST 2 packagebdmmimplements an algorithm for numerically computing the probability density of a phylogenetic tree given the population dynamic parameters under this model. In the initial release ofbdmm, analyses were limited to trees consisting of up to approximately 250 genetic samples for numerical reasons. We implemented important algorithmic changes tobdmmwhich dramatically increase the number of genetic samples that can be analyzed, and improve the numerical robustness and efficiency of the calculations. Being able to use bigger datasets leads to improved precision of parameter estimates. Furthermore, we report on several model extensions tobdmm, inspired by properties common to empirical datasets. We apply this improved algorithm to two partly overlapping datasets of Influenza A virus HA sequences sampled around the world, one with 500 samples, the other with only 175, for comparison. We report and compare the global migration patterns and seasonal dynamics inferred from each dataset.AvailabilityThe latest release with our updates,bdmm0.3.5, is freely available as an open access package of BEAST 2. The source code can be accessed athttps://github.com/denisekuehnert/bdmm.
PEDF-Rpsa-Itga6 signaling regulates cortical neuronal morphogenesis
Authors: Blazejewski Sara M. , Bennison Sarah A. , Ha Ngoc T. , Liu Xiaonan , Smith Trevor H. , Dougherty Kimberly J. , Toyo-oka Kazuhito 
Published: January 2020

AbstractNeuromorphological defects underlie neurodevelopmental disorders and functional defects. We identified a function for ribosomal protein SA (Rpsa) in regulating neuromorphogenesis usingin uteroelectroporation to knockdown Rpsa, which results in apical dendrite misorientation, fewer/shorter extensions with decreased arborization, and decreased spine density with altered spine morphology. We investigated Rpsa’s ligand, pigment epithelium-derived factor (PEDF), and interacting partner on the plasma membrane, Integrin subunit α6 (Itga6). Rpsa, PEDF, and Itga6 knockdown cause similar phenotypes, with Rpsa and Itga6 overexpression rescuing morphological defects in PEDF deficient neuronsin vivo. Additionally, Itga6 overexpression increases and stabilizes Rpsa expression on the plasma membrane by preventing ubiquitination of Rpsa. GCaMP6s was used to functionally analyze Rpsa knockdown viaex vivocalcium imaging. Rpsa deficient neurons showed less fluctuation in fluorescence intensity, suggesting defective sub-threshold calcium signaling. Our study identifies a role for PEDF-Rpsa-Itga6 signaling in neuromorphogenesis, thus implicating these molecules in the etiology of neurodevelopmental disorders and identifying them as potential therapeutic candidates.
Phylogenomics unravels speciation patterns in temperate-montane plant species: a case study on the recently radiatingRanunculus auricomusspecies complex
Authors: Tomasello Salvatore , Karbstein Kevin , Hodač Ladislav , Paetzold Claudia , Hörandl Elvira 
Published: January 2020

ABSTRACTThe time frame and geographical patterns of diversification processes in European temperate-montane herbs are still not well understood. We used the sexual species of theRanunculus auricomuscomplex as a model system to understand how vicariance vs. dispersal processes in the context of Pleistocene climatic fluctuations have triggered speciation in temperate-montane plant species. We employed Target Enrichment sequence data from about 600 nuclear genes and coalescent-based species tree inference methods to resolve phylogenetic relationships among the sexual taxa of the complex. We estimated absolute divergence times and, using ancestral range reconstruction, we tested if speciation was rather enhanced by vicariance or dispersal processes.Phylogenetic relationships among taxa were fully resolved. Incongruence among species trees mainly concerned the intraspecific relationships inR. notabiliss.l.,R. cassubicifoliuss.l., and the position of the tetraploidR. marsicus. Speciation events took place in a very short time at the end of the Mid-Pleistocene Transition (830-580 ka). A second wave of intraspecific geographical differentiation within and around the European mountain systems happened between 200-100 ka. Ancestral range reconstruction supports the existence of a widespread European ancestor of theR. auricomuscomplex. Vicariance processes have triggered allopatric speciation in temperate-montane plant species during the climatic deterioration occurred in the last phase of the Mid-Pleistocene Transition. Vegetation restructuring from forest into tundra could have confined these forest species into isolated glacial refugia. During subsequent warming periods, range expansions of these locally distributed species could have been hampered by congeneric competitors in the same habitat.