bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ontogeny of Polycotylid Long Bone Microanatomy and Histology
Authors: O’Keefe F R , Sander P M , Wintrich T , Werning S 
Published: January 2019

Abstract
Plesiosauria is an extinct clade of diapsid marine reptiles that evolved in the Late Triassic and radiated globally for the remainder of the Mesozoic. The recent description of a pregnant specimen of Polycotylus latipinnis demonstrates that some plesiosaurs were viviparous. To establish a baseline of histological data on plesiosaur ontogeny, we sampled the mother and fetus of the gravid plesiosaur specimen. To widen the base of data concerning ontogeny and life history of plesiosaurs, we gathered additional morphologic and histologic data from a securely identified growth series of polycotylids from the Pierre Shale of South Dakota. Paleohistological thin sections were prepared from the three humeri. Both adults show a dense, heavily remodeled cortex consisting entirely of longitudinally oriented secondary osteons, except for a thin rind of superficial primary bone. The mother exhibits an external fundamental system, indicating it was fully mature; the other adult does not. In both adults the cortex grades into a spongy medulla, comprising large vascular canals and erosion rooms surrounded by secondary lamellar trabecular bone, and lacking a marrow cavity. The fetal humerus possesses a medullary region similar to that of the Dolichorhynchops bonneri adult, although its lamellar bone is primary and deposited around calcified cartilage. The medulla is demarcated from the cortex by a prominent Kastschenko’s line. The cortex of the fetus is a relatively thin layer of periosteal woven bone, longitudinally to radially vascularized, and interfingered with columns of osteoblasts surrounded by rapidly-deposited extracellular matrix. The neonate humerus resembles the fetus, with its trabeculae identical in both size and histology, although it lacks calcified cartilage. The cortex is also similar but much thicker, consisting entirely of rapidly deposited, radially vascularized, woven to fibrolamellar bone. The cortex carries a line near its surface. This feature is not a line of arrested growth, but a sudden change in vascular angle and increase in bone density. We argue this feature is a birth line indicating a change in growth regime, possibly in response to increased hydrodynamic forces after birth. The birth line indicates that the neonate was about 40% of maternal length when born. Our histological data demonstrate that polycotylids had very high fetal growth rates, and that birth size was large. Comparison with the geologically oldest plesiosaur confirms that rapid growth evolved in the Triassic, although histological details differ, and the degree to which the polycotylid ontogenetic pattern is generalizable to other plesiosaurs is currently unknown. Further histological research utilizing full growth series is needed, particularly for Jurassic taxa.
Clinical value of (1,3)-β-D-glucan, mannan, antimannan IgG and IgM antibodies in diagnosis of invasive candidiasis
Authors: Li Fengtian , Yu Xiaotian , Ye Liyan , Zhou Guang , Wang Leili , Luo Yanping 
Published: January 2019

Abstract
Diagnosis of invasive candidiasis (IC) is still challenging due to absence of specific clinical signs and symptoms. In this study we investigate the clinical value of (1,3)-β-D-glucan (BDG), mannan (MN), antimannan immunoglobulin G (AM-IgG), and antimannan immunoglobulin M (AM-IgM) assay in diagnosis of IC. During 2016 to 2018 serum samples from 71 patients with IC and 185 patients without IC were collected. Serum samples from 41 patients with bacteremia were also enrolled as additional control. Significant differences in mean serum biomarkers levels between IC and control group were observed. At low cutoff threshold the sensitivity and specificity of BDG (70 pg/ml), MN (50 pg/ml), AM-IgG (80 AU/ml), and AM-IgM (80 AU/ml) assay were 64.8% and 90.8%, 64.8 and 89.2%,74.6% and 87.0%, 57.7% and 60.0%, respectively. Combined use of BDG/MN, BDG/AM-IgG and MN/AM-IgG improved the sensitivity and specificity to 85.9% and 81.1%, 85.9% and 80.0%, 81.7% and 81.6%, respectively. The combination of BDG/MN, BDG/AM-IgG, or MN/AM-IgG may provide an encouraging approach for diagnosis of IC.
Dust bombardment can explain the extremely elongated shape of 1I/’Oumuamua and the lack of interstellar objects
Authors: Vavilov Dmitrii E , Medvedev Yurii D 
Published: January 2019

ABSTRACT
Asteroid 1I/’Oumuamua is the first observed interstellar object. Its light-curve amplitude indicates that the object is highly elongated with an axial ratio of at least 5:1. The absence of such elongated asteroids in the Solar system and the apparent lack of observed interstellar objects are intriguing problems. Here we show that ’Oumuamua may have originated as a slightly elongated asteroid about 500 × 300 m in size. Surface erosion, caused by interstellar dust bombardment, subsequently increased the axial ratio. Simply travelling through the interstellar medium for 0.03 to 2 Gyr would have sufficed to give 1I its present shape. Passing through a 10 pc dust cloud with a grain density of 10−23 g cm−3 at 50 km s−1 would have had a similar effect on ’Oumuamua’s form. Smaller objects of around 100 m in diameter can travel the Galactic disc for merely 30 Myr before they are disrupted. This could explain the small number of interstellar objects observed to date.
PATIENT DOSE SURVEY BASED ON SIZE-SPECIFIC DOSE ESTIMATE AND ACCEPTABLE QUALITY DOSE IN CHEST AND ABDOMEN/PELVIS CT EXAMINATIONS
Authors: Mehdipour Ali , Parsi Masoumeh , Khorram Faezeh-Sadat 
Published: January 2019

AbstractThe practical aspects of two recently developed patient dose optimization methods in computed tomography (CT) examinations, size-specific dose estimate (SSDE) and acceptable quality dose (AQD), were verified for the chest and abdomen/pelvis examinations. A dose survey was performed in a CT institute by considering patients lateral diameter, weight and body mass index (BMI). The AQD tables for weight and BMI groups and SSDE threshold curves were obtained. The mean of volume CT dose index and dose length product for standard-size patients were compared with the national diagnostic reference levels (NDRLs) of Iran. The results show that patient doses are below the NDRLs. It is more reliable to report the AQDs based on SSDE and for BMI groups which can well take into account patient size in the dose optimization process. The SSDE threshold curves can be determined with more precision by including dose data of all possible sizes in the curves.
Factors Influencing Clinical and Setting Pathways After Discharge From an Acute Palliative/Supportive Care Unit
Authors: Mercadante Sebastiano , Adile Claudio , Ferrera Patrizia , Casuccio Alessandra 
Published: January 2019

Aim:
The aim of this study was to assess the factors which influence the care pathway after discharge from an acute palliative supportive care unit (APSCU).

Methods:
Patients’ demographics, indications for admission, kind of admission, the presence of a caregiver, awareness of prognosis, data on anticancer treatments in the last 30 days, ongoing treatment (on/off or uncertain), the previous care setting, analgesic consumption, and duration of admission were recorded. The Edmonton Symptom Assessment Scale (ESAS) at admission and at time of discharge (or the day before death), CAGE (cut down, annoy, guilt, eye-opener), and the Memorial Delirium Assessment Scale (MDAS), were used. At time of discharge, the subsequent referral to other care settings (death, home, home care, hospice, oncology), and the pathway of oncologic treatment were reconsidered (on/off, uncertain).

Results:
A total of 314 consecutive cancer patients admitted to the APSCU were surveyed. Factors independently associated with on-therapy were the lack of a caregiver, home discharge, and short hospital admission, in comparison with off-treatment, and less admission for other symptoms, shorter hospital admission, discharge at home, and better well-being, when compared with “uncertain.” Similarly, many factors were associated with discharge setting, but the only factor independently associated with discharge home was being “on-therapy.”

Conclusions:
The finding of this study is consistent with an appropriate selection of patients after being discharged by an APSCU, that works as a bridge between active treatments and supportive/palliative care, according the concept of early and simultaneous care.
Corpus Colossal: A Bibliometric Analysis of Neuroscience Abstracts and Impact Factor
Authors: Kenkel William M. 
Published: January 2019

ABSTRACTA field’s priorities are thought to be reflected by the contents of its high-impact journals. Researchers in turn may choose to pursue research objectives based on what is believed to be most highly valued by their peers. By compiling a corpus of abstracts from within the field neuroscience, I was able to analyze which terms had differential frequencies between 12 high-impact and 13 medium-impact journals. Approximately 50,000 neuroscience abstracts were analyzed over the years 2014-2018. Several broad trends emerged from the analysis of which terms were biased towards high-impact journals. Generally speaking, high-impact journals tended to feature: genetic or psychiatric studies, use of the latest and most sophisticated methods, examinations of the orbitofrontal cortex or amygdala, and/or use of human or non-mammalian subjects. Medium-impact journals tended to feature motor or cardiovascular studies, use of older methods, examinations of caudal brain regions, and/or rats as subjects.
Disentangling sRNA-Seq data to study RNA communication between species
Authors: Bermúdez-Barrientos JR , Ramírez-Sánchez O , Chow FWN , Buck AH , Abreu-Goodger C 
Published: January 2019

ABSTRACTMany organisms exchange small RNAs during their interactions, and these RNAs can target or bolster defense strategies in host-pathogen systems. Current sRNA-Seq technology can determine the small RNAs present in any symbiotic system, but there are very few bioinformatic tools available to interpret the results. We show that one of the biggest challenges comes from sequences that map equally well to the genomes of both interacting organisms. This arises due to the small size of the sRNA compared to large genomes, and because many of the produced sRNAs come from genomic regions that encode highly conserved miRNAs, rRNAs or tRNAs. Here we present strategies to disentangle sRNA-Seq data from samples of communicating organisms, developed using diverse plant and animal species that are known to exchange RNA with their parasites. We show that sequence assembly, both de novo and genome-guided, can be used for sRNA-Seq data, greatly reducing the ambiguity of mapping reads. Even confidently mapped sequences can be misleading, so we further demonstrate the use of differential expression strategies to determine the true parasitic sRNAs within host cells. Finally, we validate our methods on new experiments designed to probe the nature of the extracellular vesicle sRNAs from the parasitic nematode H. bakeri that get into mouse epithelial cells.
Simultaneous proteomics and three PTMomics characterization of pro-inflammatory cytokines stimulated INS-1E cells using TiO2enrichment strategy
Authors: Huang Honggang , Drici Lylia , Lassen Pernille S. , Palmisano Giuseppe , Larsen Martin R. 
Published: January 2019

AbstractDiverse protein post-translational modifications (PTMs) in proteins form complex combinatorial patterns to regulate the protein function and biological processes in a fine-tuning manner. Reversible phosphorylation, cysteines (Cys) modification, and N-linked glycosylation are essentially involved in cellular signaling pathways of pro-inflammatory cytokines, which can induce beta cell death and diabetes. Here we developed a novel mass spectrometry–based proteomic strategy (termed TiCPG) for the simultaneous comprehensive characterization of the proteome and three post-translational modifications (PTMomes) by applying TiO2enrichment of peptides with reversibly modified Cysteine (rmCys), Phosphorylation, and sialylated N-linked (SAN-) Glycosylation from low amount of sample material with largely minimized sample loss. We applied this TiCPG strategy to quantitatively study the change of the three PTMs in β-cell-like INS-1E cells subject to pro-inflammatory cytokines stimulation. It enabled efficient enrichment and quantitative analysis of 8346 rmCys sites, 10321 phosphosites and 1906 SAN-glycosylation sites from 5853 proteins. Significant regulation was found on 100 proteins at the total protein level, while much higher degree of regulation was identified on 3025 peptides with PTMs from 1490 proteins. The three PTMs were co-regulated in proteins, but demonstrated differential spatial and temporal patterns related to protein cellular localization and function in the time course of cytokines stimulation, and they were extensively involved in essential signaling pathways related to pro-inflammatory cytokine mediated β-cell apoptosis, such as the inducible NO synthase (NOS2) signaling pathway, Overall, the TiCPG strategy is proved as a straight forward and powerful tool for multiple PTMomics studies.
Computational Analysis of Insulin-Glucagon Signalling Network: Implications of Bistability in Metabolic Homeostasis and Disease states
Authors: Somvanshi Pramod R , Tomar Manu , Kareenhalli Venkatesh 
Published: January 2019

AbstractInsulin and glucagon control plasma macronutrient homeostasis through their signalling network composed of multiple feedback and crosstalk mechanisms. To understand how these interactions contribute to metabolic homeostasis and disease states, we analysed the steady state response of metabolic regulation (catabolic or anabolic) with respect to structural and input perturbations in the integrated signalling network, for varying levels of plasma glucose. Structural perturbations revealed: the positive feedback of AKT on IRS is responsible for the bistability in anabolic zone (glucose >5.5 mmol); the positive feedback of calcium on cAMP is responsible for ensuring ultrasensitive response in catabolic zone (glucose <4.5 mmol); the crosstalk between AKT and PDE3 is responsible for efficient catabolic response under low glucose condition; the crosstalk between DAG and PKC regulates the span of anabolic bistable region with respect to plasma glucose levels. The macronutrient perturbations revealed: varying plasma amino acids and fatty acids from normal to high levels gradually shifted the bistable response towards higher glucose range eventually making the response catabolic or unresponsive to increasing glucose levels. The analysis reveals that certain macronutrient composition may be more conducive to homeostasis than others. The network perturbations that may contribute to disease states such as diabetes, obesity and cancer are discussed.
Automated methods for 3D Segmentation of Focused Ion Beam-Scanning Electron Microscopic Images
Authors: Caffrey Brian , Maltsev Alexander V. , Gonzalez-Freire Marta , Hartnell Lisa M. , Ferrucci Luigi , Subramaniam Sriram 
Published: January 2019

AbstractFocused Ion Beam Scanning Electron Microscopy (FIB-SEM) is an imaging approach that enables analysis of the 3D architecture of cells and tissues at resolutions that are 1-2 orders of magnitude higher than that possible with light microscopy. The slow speeds of data collection and analysis are two critical problems that limit more extensive use of FIB-SEM technology. Here, we present a robust method that enables rapid, large-scale acquisition of data from tissue specimens, combined with an approach for automated data segmentation using machine learning, which dramatically increases the speed of image analysis. We demonstrate the feasibility of these methods through the 3D analysis of human muscle tissue by showing that our process results in an improvement in speed of up to three orders of magnitude as compared to manual approaches for data segmentation. All programs and scripts we use are open source and are immediately available for use by others.Impact StatementThe high-throughput, easy-to-use and versatile segmentation pipeline described in our manuscript will enable rapid, large-scale statistical analysis of sub-cellular structures in tissues.
Image-based metric of invasiveness predicts response to adjuvant temozolomide for primary glioblastoma
Authors: Massey Susan Christine , White Haylye , Whitmire Paula , Doyle Tatum , Johnston Sandra K. , Singleton Kyle W. , Jackson Pamela R. , Hawkins-Daarud Andrea , Bendok Bernard R. , Porter Alyx B. , Vora Sujay , Sarkaria Jann N. , Mrugala Maciej M. , Swanson Kristin R. 
Published: January 2019

AbstractTemozolomide (TMZ) has been the standard-of-care chemotherapy for glioblastoma (GBM) patients for more than a decade. Despite this long time in use, significant questions remain regarding how best to optimize TMZ therapy for individual patients. Understanding the relationship between TMZ response and factors such as number of adjuvant TMZ cycles, patient age, patient sex, and image-based tumor features, might help predict which GBM patients would benefit most from TMZ, particularly for those whose tumors are not MGMT methylated. Using a cohort of 90 newly-diagnosed GBM patients treated according to the Stupp protocol, we examined the relationships between several patient and tumor characteristics and volumetric and survival outcomes during adjuvant chemotherapy. Volumetric changes in MR imaging abnormalities during adjuvant therapy were used to assess TMZ response. T1Gd volumetric response is associated with younger patient age, increased number of TMZ cycles, longer time to nadir volume, and decreased tumor invasiveness. Moreover, increased adjuvant TMZ cycles corresponded with improved volumetric response only among more nodular tumors, and this volumetric response was associated with improved survival outcomes. Finally, in a subcohort of patients with known MGMT methylation status, MGMT methylated tumors were more diffusely invasive than unmethylated tumors, suggesting that the improved response in nodular tumors is not driven by a preponderance of MGMT methylated tumors. Our finding that less diffusely invasive tumors are associated with greater volumetric response to TMZ suggests that patients with these tumors may benefit from additional cycles of adjuvant TMZ, even for those without MGMT methylation.
Highly Heritable and Functionally Relevant Breed Differences in Dog Behavior
Authors: MacLeant Evan L , Snyder-Mackler Noah , vonHoldt Bridgett M. , Serpell James A. 
Published: January 2019

AbstractVariation across dog breeds presents a unique opportunity for investigating the evolution and biological basis of complex behavioral traits. We integrated behavioral data from more than 17,000 dogs from 101 breeds with breed-averaged genotypic data (N = 5,697 dogs) from over 100,000 loci in the dog genome. Across 14 traits, we found that breed differences in behavior are highly heritable, and that clustering of breeds based on behavior accurately recapitulates genetic relationships. We identify 131 single nucleotide polymorphisms associated with breed differences in behavior, which are found in genes that are highly expressed in the brain and enriched for neurobiological functions and developmental processes. Our results provide insight into the heritability and genetic architecture of complex behavioral traits, and suggest that dogs provide a powerful model for these questions.
Regeneration in the absence of a blastema requires cell division but is not tied to wound healing in the ctenophoreMnemiopsis leidyi
Authors: Ramon-Mateu Julia , Ellison Tori , Angelini Thomas E. , Martindale Mark Q. 
Published: January 2019

ABSTRACTBackgroundThe ability to regenerate is a widely distributed but highly variable trait among metazoans. A variety of modes of regeneration has been described for different organisms, however, many questions regarding the origin and evolution of these strategies remain unanswered. Most species of ctenophore (or “comb jellies”), a clade of marine animals that branch off at the base of the animal tree of life, possess an outstanding capacity to regenerate. However, the cellular and molecular mechanisms underlying this ability are unknown. We have used the ctenophoreMnemiopsis leidyias a system to study wound healing and adult regeneration and provide some first-time insights of the cellular mechanisms involved in the regeneration of one of the most ancient extant group of multicellular animals.ResultsWe show that cell proliferation is activated at the wound site and is indispensable for whole-body regeneration. Wound healing occurs normally in the absence of cell proliferation forming a scar-less wound epithelium. No blastema-like structure is generated at the cut site, rather undifferentiated cells assume the correct location of missing structures and differentiate in place. Pulse-chase experiments and surgical intervention show that cells originating in the main regions of cell proliferation (the tentacle bulbs) do not seem to contribute to the formation of new structures after surgical challenge, suggesting a local source of cells during regeneration. While exposure to cell-proliferation blocking treatment inhibits regeneration, the ability to regenerate is recovered when the treatment ends (days after the original cut), suggesting that ctenophore regenerative capabilities are constantly ready to be triggered and they are somehow separable of the wound healing process.ConclusionsCtenophore regeneration takes place through a process of cell proliferation-dependent non blastemal-like regeneration and is temporally separable of the wound healing process. The remarkable ability to replace missing tissue, the many favorable experimental features (e.g. optical clarity, high fecundity, rapid regenerative performance, stereotyped cell lineage, sequenced genome), and the early branching phylogenetic position in the animal tree, all point to the emergence of ctenophores as a new model system to study the evolution of animal regeneration.
Nano-enhanced optical gene delivery to retinal degenerated mice
Authors: Batabyal Subrata , Gajjeraman Sivakumar , Bhattacharya Sulagna , Wright Weldon , Mohanty Samarendra 
Published: January 2019

ABSTRACTThe efficient and targeted delivery of genes and other impermeable therapeutic molecules into retinal cells is of immense importance for therapy of various visual disorders. Traditional methods for gene delivery require viral transfection, or chemical methods that suffer from one or many drawbacks such as invasiveness, low efficiency, lack of spatially targeted delivery, and can generally have deleterious effects such as unexpected inflammatory responses and immunological reactions. Here, we introduce a continuous wave near-infrared laser-based Nano-enhanced Optical Delivery (NOD) method for spatially controlled delivery of opsin-encoding genes into retinain-vivo. In this method, the optical field enhancement by gold nanorods is utilized to transiently permeabilize cell membrane enabling delivery of exogenous impermeable molecules to nanorod-binding cells in laser-irradiated regions. The successful delivery and expression of opsin in targeted retina after in-vivo NOD in the mice models of retinal degeneration opens new vista for re-photosensitizing retina with geographic atrophies as in dry age-related macular degeneration (AMD).