bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of Transmissivity in Crystalline Rock Using Flow Logs Under Steady‐State Pumping: Impact of Multiscale Heterogeneity
Authors: Zou Liangchao , Cvetkovic Vladimir 
Published: August 2020

AbstractThe significance of fracture roughness for hydraulic characterization of sparsely fractured (crystalline) rock using flow logs under steady‐state pumping conditions is investigated by numerical simulations in three‐dimensional fracture networks. A new solver for simulating flow in three‐dimensional discrete fracture networks is implemented using a hybrid finite volume and finite element method. The analysis is focused on different scales of heterogeneity in three‐dimensions: the network scale heterogeneity, the fracture‐to‐fracture scale heterogeneity, and the individual fracture scale heterogeneity (fracture roughness). The results show that the individual fracture scale heterogeneity due to fracture roughness is potentially an additional source of uncertainty for hydraulic tests in fractured rocks using flow logs. Specifically, it enhances the variation in measured flowrates and inferred transmissivity in addition to the network scale heterogeneity and the fracture‐to‐fracture scale heterogeneity. However, the individual fracture scale heterogeneity has relatively small impact on the inferred transmissivity distributions compared to the fracture‐to‐fracture scale heterogeneity. Moreover, fracture roughness and fracture‐to‐fracture heterogeneity have limited influence on the median values of the inferred transmissivity such that the median transmissivity is mostly reliable when inferred from flow logs. Comparison between the inferred and underlying input transmissivity distributions shows that interpreting hydraulic tests in crystalline rock using flow logs and the Thiem equation may underestimate the variation range of the underlying transmissivity. The results are helpful for understanding the uncertainty in hydraulic characterization of sparsely fractured rocks using flow logs that are relevant for various geo‐engineering and water resources applications.
The tuatara genome reveals ancient features of amniote evolution
Authors: Gemmell Neil J. , Rutherford Kim , Prost Stefan , Tollis Marc , Winter David , Macey J. Robert , Adelson David L. , Suh Alexander , Bertozzi Terry , Grau José H. , Organ Chris , Gardner Paul P. , Muffato Matthieu , Patricio Mateus , Billis Konstantinos , Martin Fergal J. , Flicek Paul , Petersen Bent , Kang Lin , Michalak Pawel , Buckley Thomas R. , Wilson Melissa , Cheng Yuanyuan , Miller Hilary , Schott Ryan K. , Jordan Melissa D. , Newcomb Richard D. , Arroyo José Ignacio , Valenzuela Nicole , Hore Tim A. , Renart Jaime , Peona Valentina , Peart Claire R. , Warmuth Vera M. , Zeng Lu , Kortschak R. Daniel , Raison Joy M. , Zapata Valeria Velásquez , Wu Zhiqiang , Santesmasses Didac , Mariotti Marco , Guigó Roderic , Rupp Shawn M. , Twort Victoria G. , Dussex Nicolas , Taylor Helen , Abe Hideaki , Bond Donna M. , Paterson James M. , Mulcahy Daniel G. , Gonzalez Vanessa L. , Barbieri Charles G. , DeMeo Dustin P. , Pabinger Stephan , Van Stijn Tracey , Clarke Shannon , Ryder Oliver , Edwards Scott V. , Salzberg Steven L. , Anderson Lindsay , Nelson Nicola , Stone Clive ,   Ngatiwai Trust Board, Stone Clive , Smillie Jim , Edmonds Haydn 
Published: August 2020

AbstractThe tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
A global map of terrestrial habitat types
Authors: Jung Martin , Dahal Prabhat Raj , Butchart Stuart H. M. , Donald Paul F. , De Lamo Xavier , Lesiv Myroslava , Kapos Valerie , Rondinini Carlo , Visconti Piero 
Published: August 2020

AbstractWe provide a global, spatially explicit characterization of 47 terrestrial habitat types, as defined in the International Union for Conservation of Nature (IUCN) habitat classification scheme, which is widely used in ecological analyses, including for quantifying species’ Area of Habitat. We produced this novel habitat map for the year 2015 by creating a global decision tree that intersects the best currently available global data on land cover, climate and land use. We independently validated the map using occurrence data for 828 species of vertebrates (35152 point plus 8181 polygonal occurrences) and 6026 sampling sites. Across datasets and mapped classes we found on average a balanced accuracy of 0.77 ($$\bar{+}$$+¯0.14 SD) at Level 1 and 0.71 ($$\bar{+}$$+¯0.15 SD) at Level 2, while noting potential issues of using occurrence records for validation. The maps broaden our understanding of habitats globally, assist in constructing area of habitat refinements and are relevant for broad-scale ecological studies and future IUCN Red List assessments. Periodic updates are planned as better or more recent data becomes available.
Improvement of CRISPR/Cas9 system by transfecting Cas9-expressing Plasmodium berghei with linear donor template
Authors: Shinzawa Naoaki , Nishi Tsubasa , Hiyoshi Fumiya , Motooka Daisuke , Yuda Masao , Iwanaga Shiroh 
Published: August 2020

AbstractMalaria is caused by infection with Plasmodium parasites and is a major public health concern. The CRISPR/Cas9 system is a promising technology, but still has technical problems, such as low efficiency and unexpected recombination. Here, we solved these problems by transfecting Cas9-expressing parasites with linear donor templates. The use of a linear donor template prevented unexpected recombination; in addition, constitutive expression of Cas9 enabled immediate cleavage of the target locus after transfection, allowing efficient integration of the donor template. Furthermore, due to the absence of the cNHEJ pathway, there were no off-target mutations in the resultant parasites. In addition, this developed method could be applied for multiple genetic modifications on different chromosomes and for large-scale chromosomal deletion in the subtelomeric region. Because of its robustness, high efficiency, and versatile applicability, we hope this method will be standard in the post-genomic era of Plasmodium species.
PRMT5 promotes DNA repair through methylation of 53BP1 and is regulated by Src-mediated phosphorylation
Authors: Hwang Jee Won , Kim Su-Nam , Myung Nayeon , Song Doona , Han Gyoonhee , Bae Gyu-Un , Bedford Mark T. , Kim Yong Kee 
Published: August 2020

AbstractPRMT5 participates in various cellular processes, including transcription regulation, signal transduction, mRNA splicing, and DNA repair; however, its mechanism of regulation is poorly understood. Here, we demonstrate that PRMT5 is phosphorylated at residue Y324 by Src kinase, a negative regulator of its activity. Either phosphorylation or substitution of the Y324 residue suppresses PRMT5 activity by preventing its binding with the methyl donor S-adenosyl-L-methionine. Additionally, we show that PRMT5 activity is associated with non-homologous end joining (NHEJ) repair by methylating and stabilizing p53-binding protein 1 (53BP1), which promotes cellular survival after DNA damage. Src-mediated phosphorylation of PRMT5 and the subsequent inhibition of its activity during the DNA damage process blocks NHEJ repair, leading to apoptotic cell death. Altogether, our findings suggest that PRMT5 regulates DNA repair through Src-mediated Y324 phosphorylation in response to DNA damage.
Iron homeostasis disorder in piglet intestine
Authors: Ding Haoxuan , Yu Xiaonan , Feng Jie 
Published: August 2020

AbstractIron plays an essential role in preventing iron deficiency anemia and ensuring the healthy growth of animals. The special physiological condition of piglets is the main cause of iron deficiency. Iron metabolism in the intestine is the basis for understanding the effects of iron on the health of piglets. In order to scientifically evaluate dietary iron supplementation doses, it is necessary to recognize the effects of iron deficiency and iron overload on piglet intestinal health. Besides, iron as a cofactor is essential for the growth of microorganisms, and microorganisms compete with the host to absorb iron. Under the stress of iron deficiency and iron overload, various control schemes (such as precise nutrition, element balance, elimination of oxidation, etc.) are effective measures to eliminate adverse effects. In this review, we comprehensively review recent findings on the effects of iron deficiency and iron overload on intestinal health. This review will provide a rational design strategy to achieve a reasonable iron supplement, which will guide the use of iron in animal husbandry.
Optimal blood pressure for the minimum all-cause mortality in Chinese ESRD patients on maintenance hemodialysis
Authors: Wang Tao , Li Yang , Wu HaiBo , Chen Hua , Zhang Yan , Zhou HuiMin , Li Hang 
Published: August 2020

Abstract
Blood pressure (BP) is a known prognostic marker for mortality in patients on maintenance hemodialysis (MHD). However, definition of the BP and its optimal values vary essentially among different MHD populations. Our purpose was to clarify these important clinical parameters in a Chinese MHD cohort. Accordingly, we reviewed the available records of patients on regular MHD during the past 10 years and made a comparison between the deceased (n=81) and survival ones (n=131). Multiple logistic regression and Kaplan–Meier survival analysis were used to examine the effect of BP on mortality and long-term survival, respectively. The all-cause mortality in our patients was 38.2%, in which 49.4% was from cardio-cerebrovascular deaths. Using the multiple logistic regression, we found that the sitting (the same definition hereafter) pre-dialysis systolic BP (SBP) was significantly associated with both the all-cause mortality and cardio-cerebrovascular deaths exclusively in patients of 60–80 years. Moreover, a pre-dialysis SBP of 140–160 mmHg in these patients had the minimum all-cause mortality (23.5%) against that conferred by either a lower (42.1%) or higher SBP value (61.5%). This observation was further confirmed by the Kaplan–Meier survival analysis. As fresh gain to the practice of hemodialysis, our report revealed that BP worked in a time-dependent way among a Chinese MHD cohort and highlighted a U-shaped association between the pre-dialysis SBP and all-cause mortality. These findings may hence help to obtain optimal BP control for better survival and lend some prognostic insight into mortality in these MHD patients.
Communication Limitations in Patients With Progressive Apraxia of Speech and Aphasia
Authors: Utianski Rene L. , Clark Heather M. , Duffy Joseph R. , Botha Hugo , Whitwell Jennifer L. , Josephs Keith A. 
Published: August 2020

Purpose
Individuals with primary progressive apraxia of speech (AOS) have AOS in which disruptions in articulation and prosody predominate the speech pattern. Many develop aphasia and/or dysarthria later in the disease course. The aim of this study was to describe the communication limitations in these patients, as measured by (a) the patient via the Communicative Participation Item Bank (CPIB) and (b) the speech-language pathologist via the American Speech-Language-Hearing Association's (ASHA) Functional Communication Measures (FCMs) and an adapted motor speech disorder (MSD) severity rating.

Method

Speech and language evaluations were completed for 24 patients with progressive AOS (
n
= 7 with isolated AOS;
n
= 17 with a combination of AOS and aphasia). Descriptive comparisons were utilized to evaluate differences in communication measures among patients with various combinations of MSDs and aphasia. Differences associated with phonetic predominant or prosodic predominant AOS were also examined. Across the entire cohort, correlations were calculated between the participation ratings and other clinical assessment measures.

Results

The CPIB reflected greater limitations for those with aphasia and AOS compared to isolated AOS, but was not notably different when dysarthria occurred with AOS (
n
= 9/24). Across the cohort, there were statistically significant correlations between the CPIB and ASHA FCM–Motor Speech and Language Expression ratings and the MSD severity rating. The CPIB did not correlate with the ASHA FCM–Language Comprehension or other speech-language measures.

Conclusions
Patients with neurodegenerative AOS experience reduced participation in communication that is further exacerbated by co-occurring language deficits. The study suggests measures of severity cannot be assumed to correlate with measures of participation restrictions and offers a foundation for further research examining the day-to-day sequela of progressive speech and language disorders.

Supplemental Material

https://doi.org/10.23641/asha.12743252
Mechanisms of Impaired Swallowing on Thin Liquids Following Radiation Treatment for Oropharyngeal Cancer
Authors: Barbon Carly E. A. , Chepeha Douglas B. , Hope Andrew J. , Peladeau-Pigeon Melanie , Waito Ashley A. , Steele Catriona M. 
Published: August 2020

PurposeDysphagia is one of the most debilitating chronic symptoms experienced by patients who undergo radiation treatment for head and neck cancer. Despite the high prevalence of dysphagia in patients with head and neck cancer, we lack understanding of the specific changes in swallowing physiology that arise in the short-term following radiation therapy and how these changes impact the key functions of swallowing safety and efficiency. This study sought to identify pathophysiological mechanisms underlying impairments in swallowing safety and efficiency on thin liquids following (chemo)radiation for oropharyngeal cancer.MethodVideofluoroscopic swallowing studies were completed in 12 male patients within 6 months following completion of (chemo)radiation and in 12 healthy male controls. To compare swallowing function and physiology between groups, we analyzed three discrete sips of 20% w/v thin liquid barium per participant. The videofluoroscopic swallowing study recordings were rated for swallowing safety, efficiency, timing parameters, and pixel-based measures of structural area or movement.ResultsThe oropharyngeal cancer cohort displayed significantly higher frequencies of penetration–aspiration, incomplete laryngeal vestibule closure, prolonged time-to-laryngeal vestibule closure, and poor pharyngeal constriction. Incomplete or delayed laryngeal vestibule closure was associated with airway invasion, while poor pharyngeal constriction was associated with pharyngeal residue.ConclusionsThis study highlights the primary mechanisms behind impaired safety and efficiency of the swallow in patients following (chemo)radiation for oropharyngeal cancer.
Mineral cloud and hydrocarbon haze particles in the atmosphere of the hot Jupiter JWST target WASP-43b
Authors: Helling Ch. , Kawashima Y. , Graham V. , Samra D. , Chubb K. L. , Min M. , Waters L. B. F. M. , Parmentier V. 
Published: August 2020

Context. Having a short orbital period and being tidally locked makes WASP-43b an ideal candidate for the James Webb Space Telescope (JWST) phase curve measurements. Phase curve observations of an entire orbit will enable the mapping of the atmospheric structure across the planet, with different wavelengths of observation allowing different atmospheric depths to be seen.
Aims. We provide insight into the details of the clouds that may form on WASP-43b and their impact on the remaining gas phase, in order to prepare the forthcoming interpretation of the JWST and follow-up data.
Methods. We follow a hierarchical modelling strategy. We utilise 3D GCM results as input for a kinetic, non-equilibrium model for mineral cloud particles and for a kinetic model to study a photochemically-driven hydrocarbon haze component.
Results. Mineral condensation seeds form throughout the atmosphere of WASP-43b. This is in stark contrast to the ultra-hot Jupiters, such as WASP-18b and HAT-P-7b. The dayside is not cloud free but it is loaded with few yet large mineral cloud particles in addition to hydrocarbon haze particles of a comparable abundance. Photochemically driven hydrocarbon haze appears on the dayside, but it does not contribute to the cloud formation on the nightside. The geometrical cloud extension differs across the globe due to the changing thermodynamic conditions. Day and night differ by 6000 km in pressure scale height. As reported for other planets, the C/O is not constant throughout the atmosphere and varies between 0.74 and 0.3. The mean molecular weight is approximately constant in a H2-dominated WASP-43b atmosphere because of the moderate day/night-temperature differences compared to the super-hot Jupiters.
Conclusions. WASP-43b is expected to be fully covered in clouds which are not homogeneously distributed throughout the atmosphere. The dayside and the terminator clouds are a combination of mineral particles of locally varying size and composition as well as of hydrocarbon hazes. The optical depth of hydrocarbon hazes is considerably lower than that of mineral cloud particles such that a wavelength-dependent radius measurement of WASP-43b would be determined by the mineral cloud particles but not by hazes.
OB stars and YSO populations in the region of NGC 6334–NGC 6357 as seen withGaiaDR2
Authors: Russeil D. , Zavagno A. , Nguyen A. , Figueira M. , Adami C. , Bouret J. C. 
Published: August 2020

Aims.Our goal is to better understand the origin and the star-formation history of regions NGC 6334 and NGC 6357. We focus our study on the kinematics of young stars (young stellar objects and OB stars) in both regions mainly on the basis of theGaiaDR2 data.Methods.For both regions, we compiled catalogs of OB stars and young stellar objects from the literature and complemented them using VPHAS+ DR2 andSpitzerIRAC/GLIMPSE photometry catalogues. We applied a cross-match with theGaiaDR2 catalog to obtain information on the parallax and transverse motion.Results.We confirm that NGC 6334 and NGC 6357 are in the far side of the Saggitarius-Carina arm at a distance of 1.76 kpc. For NGC 6357, OB stars show strong clustering and ordered star motion with Vlon ∼–10.7 km s−1and Vlat ∼3.7 km s−1, whereas for NGC 6334, no significant systemic motion was observed. The OB stars motions and distribution in NGC 6334 suggest that it should be classified as an association. Ten runaway candidates may be related to NGC 6357 and two to NGC 6334, respectively. The spatial distributions of the runaway candidates in and around NGC 6357 favor a dynamical (and early) ejection during the cluster(s) formation. Because such stars are likely to be ejected during a cluster’s formation, the fact that not as many such stars are observed towards NGC 6334 suggests different formation conditions than have been assumed for NGC 6357.
The halo of M 105 and its group environment as traced by planetary nebula populations
Authors: Hartke J. , Arnaboldi M. , Gerhard O. , Coccato L. , Pulsoni C. , Freeman K. C. , Merrifield M. , Cortesi A. , Kuijken K. 
Published: August 2020

Context. M 105 (NGC 3379) is an early-type galaxy in the Leo I group. The Leo I group is the nearest group that contains all main galaxy types and can thus be used as a benchmark to study the properties of the intra-group light (IGL) in low-mass groups.
Aims. We present a photometric survey of planetary nebulae (PNe) in the extended halo of the galaxy to characterise its PN populations and investigate the presence of an extended PN population associated with the intra-group light.
Methods. We use PNe as discrete stellar tracers of the diffuse light around M 105. These PNe were identified on the basis of their bright [O III]5007 Å emission and the absence of a broad-band continuum using automated detection techniques. We compare the PN number density profile with the galaxy surface-brightness profile decomposed into metallicity components using published photometry of the Hubble Space Telescope in two halo fields.
Results. We identify 226 PNe candidates within a limiting magnitude of m5007, lim = 28.1 from our Subaru-SuprimeCam imaging, covering 67.6 kpc (23 effective radii) along the major axis of M 105 and the halos of NGC 3384 and NGC 3398. We find an excess of PNe at large radii compared to the stellar surface brightness profile from broad-band surveys. This excess is related to a variation in the luminosity-specific PN number α with radius. The α-parameter value of the extended halo is more than seven times higher than that of the inner halo. We also measure an increase in the slope of the PN luminosity function at fainter magnitudes with radius.
Conclusions. We infer that the radial variation of the PN population properties is due to a diffuse population of metal-poor stars ([M/H] < −1.0) following an exponential profile, in addition to the M 105 halo. The spatial coincidence between the number density profile of these metal-poor stars and the increase in the α-parameter value with radius establishes the missing link between metallicity and the post-asymptotic giant branch phases of stellar evolution. We estimate that the total bolometric luminosity associated with the exponential IGL population is 2.04 × 109 L⊙ as a lower limit. The lower limit on the IGL fraction is thus 3.8%. This work sets the stage for kinematic studies of the IGL in low-mass groups.
Automatic detection of different types of small-bowel lesions on capsule endoscopy images using a newly developed deep convolutional neural network
Authors: Otani Keita , Nakada Ayako , Kurose Yusuke , Niikura Ryota , Yamada Atsuo , Aoki Tomonori , Nakanishi Hiroyoshi , Doyama Hisashi , Hasatani Kenkei , Sumiyoshi Tetsuya , Kitsuregawa Masaru , Harada Tatsuya , Koike Kazuhiko 
Published: August 2020

Abstract
Background Previous computer-aided detection systems for diagnosing lesions in images from wireless capsule endoscopy (WCE) have been limited to a single type of small-bowel lesion. We developed a new artificial intelligence (AI) system able to diagnose multiple types of lesions, including erosions and ulcers, vascular lesions, and tumors.
Methods We trained the deep neural network system RetinaNet on a data set of 167 patients, which consisted of images of 398 erosions and ulcers, 538 vascular lesions, 4590 tumors, and 34 437 normal tissues. We calculated the mean area under the receiver operating characteristic curve (AUC) for each lesion type using five-fold stratified cross-validation.
Results The mean age of the patients was 63.6 years; 92 were men. The mean AUCs of the AI system were 0.996 (95 %CI 0.992 – 0.999) for erosions and ulcers, 0.950 (95 %CI 0.923 – 0.978) for vascular lesions, and 0.950 (95 %CI 0.913 – 0.988) for tumors.
Conclusion We developed and validated a new computer-aided diagnosis system for multiclass diagnosis of small-bowel lesions in WCE images.