bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects on nitrogen balance and metabolism of branched-chain amino acids by growing pigs of supplementing isoleucine and valine to diets with adequate or excess concentrations of dietary leucine
Authors: Kwon Woong B , Soto Jose A , Stein Hans H 
Published: October 2020

AbstractDiets based on high levels of corn protein have elevated concentrations of Leu, which may negatively affect N retention in pigs. An experiment was, therefore, conducted to test the hypothesis that Ile and Val supplementation may overcome the detrimental effects of excess dietary Leu on N balance and metabolism of branched-chain amino acids (BCAA) in growing pigs. A total of 144 barrows (initial body weight: 28.5 kg) were housed in metabolism crates and randomly assigned to 1 of 18 dietary treatments. The basal diet contained 0.98% standardized ileal digestible (SID) Lys and had SID Leu, Val, and Ile ratios to SID Lys of 100%, 60%, and 43%, respectively. Crystalline l-Leu (0% or 2.0%), l-Ile (0%, 0.1%, or 0.2%), and l-Val (0%, 0.1%, or 0.2%) were added to the basal diet resulting in a total of 18 dietary treatments that were arranged in a 2 × 3 × 3 factorial. Urine and fecal samples were collected for 5 d after 7 d of adaptation. Blood, skeletal muscle, and liver samples were collected at the conclusion of the experiment. There were no three-way interactions among the main effects. Excess Leu in diets reduced (P &lt; 0.05) N retention and biological value of protein and increased (P &lt; 0.001) plasma urea N (PUN), but PUN was reduced (P &lt; 0.05) as dietary Val increased. Concentrations of Leu in the liver were greater (P &lt; 0.001) in pigs fed excess Leu diets than in pigs fed adequate Leu diets, but concentrations of BCAA in muscle were greater (P &lt; 0.05) in pigs fed low-Leu diets. Increasing dietary Ile increased (P &lt; 0.001) plasma-free Ile and plasma concentration of the Ile metabolite, α-keto-β-methylvalerate, but the increase was greater in diets without excess Leu than in diets with excess Leu (interaction, P &lt; 0.001). Plasma concentrations of Val and the Val metabolite α-keto isovalerate increased (P &lt; 0.001) with increasing dietary Val in diets with adequate Leu, but not in diets with excess Leu (interaction, P &lt; 0.001). Increasing dietary Leu increased (P &lt; 0.001) plasma-free Leu and plasma concentration of the Leu metabolite, α-keto isocaproate (KIC). In contrast, increased dietary Val reduced (P &lt; 0.05) the plasma concentration of KIC. In conclusion, excess dietary Leu reduced N retention and increased PUN in growing pigs, but Val supplementation to excess Leu diets may increase the efficiency of amino acid utilization for protein synthesis as indicated by reduced PUN.
Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering
Authors: Wu Qiang , Shou Jia 
Published: October 2020

AbstractEver since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
Temporal Detection Limits of Remnant Larval Bloodmeals in Nymphal Ixodes scapularis (Say, Ixodida: Ixodidae) Using Two Next-Generation Sequencing DNA Barcoding Assays
Authors: Lumsden Genevieve A M , Zakharov Evgeny V , Dolynskyj Sarah , Weese J Scott , Lindsay L Robbin , Jardine Claire 
Published: October 2020

Abstract
Using next-generation sequencing DNA barcoding, we aimed to determine: 1) if the larval bloodmeal can be detected in Ixodes scapularis nymphs and 2) the post-moult temporal window for detection of the larval bloodmeal. Subsets of 30 nymphs fed on a domestic rabbit (Oryctolagus cuniculus Linnaeus, Lagomorphia: Leporidae) as larvae were reared and frozen at 11 time points post-moult, up to 150 d. Vertebrate DNA was amplified using novel universal (UP) and species-specific primers (SSP) and sequenced for comparison against cytochrome c oxidase subunit I barcodes to infer host identification. Detectable bloodmeals decreased as time since moult increased for both assays. For the SSP assay, detection of bloodmeals decreased from 96.7% (n = 29/30) in day 0 nymphs to 3.3% (n = 1/30) and 6.7% (n = 2/30) at 4- and 5-mo post-moult, respectively. A shorter temporal detection period was achieved with the UP assay, declining from 16.7% (n = 5/30) in day 0 nymphs to 0/30 in 3-d-old nymphs. Bloodmeal detection was nonexistent for the remaining cohorts, with the exception of 1/30 nymphs at 2-mo post-moult. Host detection was significantly more likely using the SSP assay compared to the UP assay in the first three time cohorts (day 0: χ 2 = 39.1, P &lt; 0.005; day 2: χ 2 = 19.2, P &lt; 0.005; day 3: χ 2 = 23.3, P &lt; 0.005). Regardless of the primer set used, the next-generation sequencing DNA barcoding assay was able to detect host DNA from a larval bloodmeal in the nymphal life stage; however, a short window with a high proportion of detection post-moult was achieved.
Personal Data Portability In The Platform Economy: Economic Implications And Policy Recommendations
Authors: Krämer Jan 
Published: October 2020

Abstract
Article 20 of the General Data Protection Regulation (GDPR) gave consumers in the European Union the right to port their personal data between digital service providers. We critically assess the economic implications of this new right in the light of the extant economic literature and with a focus on competition and innovation in the digital platform economy. In particular, we conclude that observed user behaviour data should clearly fall under the scope of data portability and that, above and beyond the regulations set out under GDPR, a right to port personal data continuously and in real-time would be necessary to truly empower consumers in the context of the digital platform economy. We also discuss the economics of Personal Information Management Systems (PIMSs), which many policymakers see as an essential tool for consumers in an economy where data portability becomes more widespread. However, we are sceptical that PIMS will be self-sustainable and instead advocate to facilitate the development of open-source projects, which have made little progress so far due to a lack of interfaces (which would come about with a right to continuous data portability) and due to a lack of common standards.
Configuration of the Martian dust rings: shapes, densities, and size distributions from direct integrations of particle trajectories
Authors: Liu Xiaodong , Schmidt Jürgen 
Published: October 2020

ABSTRACTIt is expected since the early 1970s that tenuous dust rings are formed by grains ejected from the Martian moons Phobos and Deimos by impacts of hypervelocity interplanetary projectiles. In this paper, we perform direct numerical integrations of a large number of dust particles originating from Phobos and Deimos. In the numerical simulations, the most relevant forces acting on the dust are included: Martian gravity with spherical harmonics up to fifth degree and fifth order, gravitational perturbations from the Sun, Phobos, and Deimos, solar radiation pressure, as well as the Poynting–Robertson drag. In order to obtain the ring configuration, simulation results of various grain sizes ranging from submicrometres to 100 μm are averaged over a specified initial mass distribution of ejecta. We find that for the Phobos ring grains smaller than about 2 μm are dominant; while the Deimos ring is dominated by dust in the size range of about 5–20 μm. The asymmetries, number densities, and geometric optical depths of the rings are quantified from simulations. The results are compared with the upper limits of the optical depth inferred from Hubble observations. We compare to previous work and discuss the uncertainties of the models.
On the delay times of merging double neutron stars
Authors: Greggio Laura , Simonetti Paolo , Matteucci Francesca 
Published: October 2020

ABSTRACT
The merging rate of double neutron stars (DNS) has a great impact on many astrophysical issues, including the interpretation of gravitational waves signals, of the short gamma-ray bursts (GRBs), and of the chemical properties of stars in galaxies. Such rate depends on the distribution of the delay times (DDT) of the merging events. In this paper, we derive a theoretical DDT of merging DNS following from the characteristics of the clock controlling their evolution. We show that the shape of the DDT is governed by a few key parameters, primarily the lower limit and the slope of the distribution of the separation of the DNS systems at birth. With a parametric approach, we investigate on the observational constraints on the DDT from the cosmic rate of short GRBs and the europium-to-iron ratio in Milky Way stars, taken as tracer of the products of the explosion. We find that the local rate of DNS merging requires that $\sim \! 1 {{\ \rm per\ cent}}$ of neutron stars progenitors live in binary systems which end their evolution as merging DNS within a Hubble time. The redshift distribution of short GRBs does not yet provide a strong constraint on the shape of the DDT, although the best-fitting models have a shallow DDT. The chemical pattern in Milky Way stars requires an additional source of europium besides the products from merging DNS, which weakens the related requirement on the DDT. At present both constraints can be matched with the same DDT for merging DNS.
Surface roughness of asteroid (162173) Ryugu and comet 67P/Churyumov–Gerasimenko inferred fromin situobservations
Authors: Otto K A , Matz K-D , Schröder S E , Parekh R , Krohn K , Honda R , Kameda S , Jaumann R , Schmitz N , Stephan K , Sugita S , Tatsumi E , Ho T-M , Koncz A , Trauthan F , Cho Y , Hayakawa M , Honda C , Kouyama T , Matsuoka M , Morota T , Mottola S , Ogawa K , Preusker F , Sakatani N , Sawada H , Scholten F , Suzuki H , Yamada M , Yokota Y , Yoshioka K 
Published: October 2020

ABSTRACTAlteration processes on asteroid and comet surfaces, such as thermal fracturing, (micrometeorite) impacts or volatile outgassing, are complex mechanisms that form diverse surface morphologies and roughness on various scales. These mechanisms and their interaction may differ on the surfaces of different bodies. Asteroid Ryugu and comet 67P/Churyumov–Gerasimenko, both, have been visited by landers that imaged the surfaces in high spatial resolution. We investigate the surface morphology and roughness of Ryugu and 67P/Churyumov–Gerasimenko based on high-resolution in situ images of 0.2 and 0.8 mm pixel resolution over an approximately 25 and 80 cm wide scene, respectively. To maintain comparability and reproducibility, we introduce a method to extract surface roughness descriptors (fractal dimension, Hurst exponent, joint roughness coefficient, root-mean-square slope, hemispherical crater density, small-scale roughness parameter, and Hapke mean slope angle) from in situ planetary images illuminated by LEDs. We validate our method and choose adequate parameters for an analysis of the roughness of the surfaces. We also derive the roughness descriptors from 3D shape models of Ryugu and orbiter camera images and show that the higher spatially resolved images result in a higher roughness. We find that 67P/Churyumov–Gerasimenko is up to 6 per cent rougher than Ryugu depending on the descriptor used and attribute this difference to the different intrinsic properties of the materials imaged and the erosive processes altering them. On 67P/Churyumov–Gerasimenko sublimation appears to be the main cause for roughness, while on Ryugu micrometeoroid bombardment as well as thermal fatigue and solar weathering may play a significant role in shaping the surface.
An environmental dependence of the physical and structural properties in the Hydra cluster galaxies
Authors: Lima-Dias Ciria , Monachesi Antonela , Torres-Flores Sergio , Cortesi Arianna , Hernández-Lang Daniel , Barbosa Carlos Eduardo , Mendes de Oliveira Claudia , Olave-Rojas Daniela , Pallero Diego , Sampedro Laura , Molino Alberto , Herpich Fabio R , Jaffé Yara L , Amorín Ricardo , Chies-Santos Ana L , Dimauro Paola , Telles Eduardo , Lopes Paulo A A , Alvarez-Candal Alvaro , Ferrari Fabricio , Kanaan Antonio , Ribeiro Tiago , Schoenell William 
Published: October 2020

ABSTRACT
The nearby Hydra cluster (∼50 Mpc) is an ideal laboratory to understand, in detail, the influence of the environment on the morphology and quenching of galaxies in dense environments. We study the Hydra cluster galaxies in the inner regions (1R200) of the cluster using data from the Southern Photometric Local Universe Survey, which uses 12 narrow and broad-band filters in the visible region of the spectrum. We analyse structural (Sérsic index, effective radius) and physical (colours, stellar masses, and star formation rates) properties. Based on this analysis, we find that ∼88 per cent of the Hydra cluster galaxies are quenched. Using the Dressler–Schectman test approach, we also find that the cluster shows possible substructures. Our analysis of the phase-space diagram together with density-based spatial clustering algorithm indicates that Hydra shows an additional substructure that appears to be in front of the cluster centre, which is still falling into it. Our results, thus, suggest that the Hydra cluster might not be relaxed. We analyse the median Sérsic index as a function of wavelength and find that for red [(u − r) ≥2.3] and early-type galaxies it displays a slight increase towards redder filters (13 and 18 per cent, for red and early type, respectively), whereas for blue + green [(u − r)&lt;2.3] galaxies it remains constant. Late-type galaxies show a small decrease of the median Sérsic index towards redder filters. Also, the Sérsic index of galaxies, and thus their structural properties, do not significantly vary as a function of clustercentric distance and density within the cluster; and this is the case regardless of the filter.
Community succession in phototrophic shell-degrading endoliths attacking intertidal mussels
Authors: Ndhlovu Aldwin , McQuaid Christopher D , Nicastro Katy R , Zardi Gerardo I 
Published: October 2020

ABSTRACT
Intertidal mussels are important ecosystem engineers that increase habitat complexity and provide shelter, substratum and food to associated communities. They thus play a key role in the maintenance of local biodiversity. Intertidal mussels are frequently parasitized by endolithic cyanobacteria that erode and significantly weaken their shells. We examined succession of cyanobacterial infestation in the shells of the mussels Perna perna and Mytilus galloprovincialis on the south coast of South Africa. We examined variations in species composition of the endolithic cyanobacterial community across regions of mussel shells of different ages (variation in space) and by exposing non-infested shells in field experiments for known periods (variation in time). The results on the spatial distribution of endolith species within a shell supported those from the field experiment evaluating temporal succession. Endolithic species that were early colonists of clean shells were similar to those that were found at the distal edge, the new and growing region of the shell. These species were also found near the umbo, the oldest region of the shell, but cyanobacterial communities near the umbo also included species that appeared late in time. Thus, succession when viewed in either time or space involved the accumulation, rather than the replacement of species. Species that arrived late in the succession were similar to endolithic species found near the umbo, the oldest region of the shell. Overall, the study shows clear patterns of endolithic cyanobacterial succession within mussel shells.
GenBank
Authors: Sayers Eric W , Cavanaugh Mark , Clark Karen , Pruitt Kim D , Schoch Conrad L , Sherry Stephen T , Karsch-Mizrachi Ilene 
Published: October 2020

Abstract
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. Recent updates include new resources for data from the SARS-CoV-2 virus, updates to the NCBI Submission Portal and associated submission wizards for dengue and SARS-CoV-2 viruses, new taxonomy queries for viruses and prokaryotes, and simplified submission processes for EST and GSS sequences.
GPCRdb in 2021: integrating GPCR sequence, structure and function
Authors: Kooistra Albert J , Mordalski Stefan , Pándy-Szekeres Gáspár , Esguerra Mauricio , Mamyrbekov Alibek , Munk Christian , Keserű György M , Gloriam David E 
Published: October 2020

AbstractG protein-coupled receptors (GPCRs) form both the largest family of membrane proteins and drug targets, mediating the action of one-third of medicines. The GPCR database, GPCRdb serves &gt;4 000 researchers every month and offers reference data, analysis of own or literature data, experiment design and dissemination of published datasets. Here, we describe new and updated GPCRdb resources with a particular focus on integration of sequence, structure and function. GPCRdb contains all human non-olfactory GPCRs (and &gt;27 000 orthologs), G-proteins and arrestins. It includes over 2 000 drug and in-trial agents and nearly 200 000 ligands with activity and availability data. GPCRdb annotates all published GPCR structures (updated monthly), which are also offered in a refined version (with re-modeled missing/distorted regions and reverted mutations) and provides structure models of all human non-olfactory receptors in inactive, intermediate and active states. Mutagenesis data in the GPCRdb spans natural genetic variants, GPCR-G protein interfaces, ligand sites and thermostabilising mutations. A new sequence signature tool for identification of functional residue determinants has been added and two data driven tools to design ligand site mutations and constructs for structure determination have been updated extending their coverage of receptors and modifications. The GPCRdb is available at https://gpcrdb.org.
PhycoCosm, a comparative algal genomics resource
Authors: Grigoriev Igor V , Hayes Richard D , Calhoun Sara , Kamel Bishoy , Wang Alice , Ahrendt Steven , Dusheyko Sergey , Nikitin Roman , Mondo Stephen J , Salamov Asaf , Shabalov Igor , Kuo Alan 
Published: October 2020

Abstract
Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other ‘omics’ data. PhycoCosm provides integration of genome sequence and annotation for &gt;100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.
Contemporary Analysis of Minimal Clinically Important Difference in the Neurosurgical Literature
Authors: Zervos Thomas M , Asmaro Karam , Air Ellen L 
Published: October 2020

Abstract

BACKGROUND
Minimal clinically important difference (MCID) is determined when a patient or physician defines the minimal change that outweighs the costs and untoward effects of a treatment. These measurements are “anchored” to validated quality-of-life instruments or physician-rated, disease-activity indices. To capture the subjective clinical experience in a measurable way, there is an increasing use of MCID.

OBJECTIVE
To review the overall concept, method of calculation, strengths, and weaknesses of MCID and its application in the neurosurgical literature.

METHODS
Recent articles were reviewed based on PubMed query. To illustrate the strengths and limitations of MCID, studies regarding the measurement of pain are emphasized and their impact on subsequent publications queried.

RESULTS
MCID varies by population baseline characteristics and calculation method. In the context of pain, MCID varied based on the quality of pain, chronicity, and treatment options.

CONCLUSION
MCID evaluates outcomes relative to whether they provide a meaningful change to patients, incorporating the risks and benefits of a treatment. Using MCID in the process of evaluating outcomes helps to avoid the error of interpreting a small but statistically significant outcome difference as being clinically important.
Posterior Vertebral Column Subtraction Osteotomy for Recurrent Tethered Cord Syndrome: A Multicenter, Retrospective Analysis
Authors: Theodore Nicholas , Cottrill Ethan , Kalb Samuel , Zygourakis Corinna , Jiang Bowen , Pennington Zach , Lubelski Daniel , Westbroek Erick M , Ahmed A Karim , Ehresman Jeff , Sciubba Daniel M , Witham Timothy F , Turner Jay D , Groves Mari , Kakarla U Kumar 
Published: October 2020

Abstract

BACKGROUND
Few have explored the safety and efficacy of posterior vertebral column subtraction osteotomy (PVCSO) to treat tethered cord syndrome (TCS).

OBJECTIVE
To evaluate surgical outcomes after PVCSO in adults with TCS caused by lipomyelomeningocele, who had undergone a previous detethering procedure(s) that ultimately failed.

METHODS
This is a multicenter, retrospective analysis of a prospectively collected cohort. Patients were prospectively enrolled and treated with PVCSO at 2 institutions between January 1, 2011 and December 31, 2018. Inclusion criteria were age ≥18 yr, TCS caused by lipomyelomeningocele, previous detethering surgery, and recurrent symptom progression of less than 2-yr duration. All patients undergoing surgery with a 1-yr minimum follow-up were evaluated.

RESULTS
A total of 20 patients (mean age: 36 yr; sex: 15F/5M) met inclusion criteria and were evaluated. At follow-up (mean: 23.3 ± 7.4 mo), symptomatic improvement/resolution was seen in 93% of patients with leg pain, 84% in back pain, 80% in sensory abnormalities, 80% in motor deficits, 55% in bowel incontinence, and 50% in urinary incontinence. Oswestry Disability Index improved from a preoperative mean of 57.7 to 36.6 at last follow-up (P < .01). Mean spinal column height reduction was 23.4 ± 2.7 mm. Four complications occurred: intraoperative durotomy (no reoperation), wound infection, instrumentation failure requiring revision, and new sensory abnormality.

CONCLUSION
This is the largest study to date assessing the safety and efficacy of PVCSO in adults with TCS caused by lipomyelomeningocele and prior failed detethering. We found PVCSO to be an excellent extradural approach that may afford definitive treatment in this particularly challenging population.