bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus)
Authors: Minich David , Madden Christopher , Evans Morgan V. , Ballash Gregory A. , Barr Daniel J. , Poulsen Keith P. , Dennis Patricia M. , Hale Vanessa L. 
Published: June 2021

AbstractChronic wasting disease (CWD) is a fatal, contagious, neurodegenerative prion disease affecting both free-ranging and captive cervid species. CWD is spread via direct or indirect contact or oral ingestion of prions. In the gastrointestinal tract, prions enter the body through microfold cells (M-cells), and the abundance of these cells can be influenced by the gut microbiota. To explore potential links between the gut microbiota and CWD, we collected fecal samples from farmed and free-ranging white-tailed deer (Odocoileus virginianus) around the Midwest, USA. Farmed deer originated from farms that were depopulated due to CWD. Free-ranging deer were sampled during annual deer harvests. All farmed deer were tested for CWD via ELISA and IHC, and we used 16S rRNA gene sequencing to characterize the gut microbiota. We report significant differences in gut microbiota by provenance (Farm 1, Farm 2, Free-ranging), sex, and CWD status. CWD-positive deer from Farm 1 and 2 had increased abundances of Akkermansia, Lachnospireacea UCG-010, and RF39 taxa. Overall, differences by provenance and sex appear to be driven by diet, while differences by CWD status may be linked to CWD pathogenesis.
Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species
Authors: Petersen Anders Ø , Julienne Hanna , Hyötyläinen Tuulia , Sen Partho , Fan Yong , Pedersen Helle Krogh , Jäntti Sirkku , Hansen Tue H. , Nielsen Trine , Jørgensen Torben , Hansen Torben , Myers Pernille Neve , Nielsen H. Bjørn , Ehrlich S. Dusko , Orešič Matej , Pedersen Oluf 
Published: June 2021

AbstractKnowledge about in vivo effects of human circulating C-6 hydroxylated bile acids (BAs), also called muricholic acids, is sparse. It is unsettled if the gut microbiome might contribute to their biosynthesis. Here, we measured a range of serum BAs and related them to markers of human metabolic health and the gut microbiome. We examined 283 non-obese and obese Danish adults from the MetaHit study. Fasting concentrations of serum BAs were quantified using ultra-performance liquid chromatography-tandem mass-spectrometry. The gut microbiome was characterized with shotgun metagenomic sequencing and genome-scale metabolic modeling. We find that tauro- and glycohyocholic acid correlated inversely with body mass index (P = 4.1e-03, P = 1.9e-05, respectively), waist circumference (P = 0.017, P = 1.1e-04, respectively), body fat percentage (P = 2.5e-03, P = 2.3e-06, respectively), insulin resistance (P = 0.051, P = 4.6e-4, respectively), fasting concentrations of triglycerides (P = 0.06, P = 9.2e-4, respectively) and leptin (P = 0.067, P = 9.2e-4). Tauro- and glycohyocholic acids, and tauro-a-muricholic acid were directly linked with a distinct gut microbial community primarily composed of Clostridia species (P = 0.037, P = 0.013, P = 0.027, respectively). We conclude that serum conjugated C-6-hydroxylated BAs associate with measures of human metabolic health and gut communities of Clostridia species. The findings merit preclinical interventions and human feasibility studies to explore the therapeutic potential of these BAs in obesity and type 2 diabetes.
Behavior of light elements in iron-silicate-water-sulfur system during early Earth’s evolution
Authors: Iizuka-Oku Riko , Gotou Hirotada , Shito Chikara , Fukuyama Ko , Mori Yuichiro , Hattori Takanori , Sano-Furukawa Asami , Funakoshi Ken-ichi , Kagi Hiroyuki 
Published: June 2021

AbstractHydrogen (H) is considered to be one of the candidates for light elements in the Earth’s core, but the amount and timing of delivery have been unknown. We investigated the effects of sulfur (S), another candidate element in the core, on deuteration of iron (Fe) in iron–silicate–water system up to 6–12 GPa, ~ 1200 K using in situ neutron diffraction measurements. The sample initially contained saturated water (D2O) as Mg(OD)2 in the ideal composition (Fe–MgSiO3–D2O) of the primitive Earth. In the existence of water and sulfur, phase transitions of Fe, dehydration of Mg(OD)2, and formation of iron sulfide (FeS) and silicates occurred with increasing temperature. The deuterium (D) solubility (x) in iron deuterides (FeDx) increased with temperature and pressure, resulting in a maximum of x = 0.33(4) for the hydrous sample without S at 11.2 GPa and 1067 K. FeS was hardly deuterated until Fe deuteration had completed. The lower D concentrations in the S-containing system do not exceed the miscibility gap (x <  ~ 0.4). Both H and S can be incorporated into solid Fe and other light elements could have dissolved into molten iron hydride and/or FeS during the later process of Earth’s evolution.
Real-space observation of surface structuring induced by ultra-fast-laser illumination far below the melting threshold
Authors: Zaum Ch. , Osterloh N. , Darkins R. , Duffy D. M. , Morgenstern K. 
Published: June 2021

AbstractIntense short laser pulses are an intriguing tool for tailoring surface properties via ultra-fast melting of the surface layer of an irradiated target. Despite extensive studies on the interaction of femto-second laser interaction with matter, the initial steps of the morphological changes are not yet fully understood. Here, we reveal that substantial surface structure changes occur at energy densities far below the melting threshold. By using low-temperature scanning tunneling microscopy we resolve atomic-scale changes, i.e. the creation of nanosized adatom and vacancy clusters. The two cluster types have distinct non-linear fluence-dependencies. A theoretical analysis reveals their creation and motion to be non-thermal in nature. The formation of these atomistic changes, individually resolved here for the first time, recast our understanding of how surfaces respond to low-intensity ultra-short laser illumination. A visualization and control of the initial morphological changes upon laser illumination are not only of fundamental interest, but pave the way for the designing material properties through surface structuring.
Identification, characterization and control of a sequence variant in monoclonal antibody drug product: a case study
Authors: Thakur Anushikha , Nagpal Rekha , Ghosh Avik Kumar , Gadamshetty Deepak , Nagapattinam Sirisha , Subbarao Malini , Rakshit Shreshtha , Padiyar Sneha , Sreenivas Suma , Govindappa Nagaraja , Pai Harish V. , Melarkode Subbaraman Ramakrishnan 
Published: June 2021

AbstractSequence variants (SV) in protein bio therapeutics can be categorized as unwanted impurities and may raise serious concerns in efficacy and safety of the product. Early detection of specific sequence modifications, that can result in altered physicochemical and or biological properties, is therefore desirable in product manufacturing. Because of their low abundance, and finite resolving power of conventional analytical techniques, they are often overlooked in early drug development. Here, we present a case study where trace amount of a sequence variant is identified in a monoclonal antibody (mAb) based therapeutic protein by LC–MS/MS and the structural and functional features of the SV containing mAb is assessed using appropriate analytical techniques. Further, a very sensitive selected reaction monitoring (SRM) technique is developed to quantify the SV which revealed both prominent and inconspicuous nature of the variant in process chromatography. We present the extensive characterization of a sequence variant in protein biopharmaceutical and first report on control of sequence variants to < 0.05% in final drug product by utilizing SRM based mass spectrometry method during the purification steps.
A novel data-driven methodology for influenza outbreak detection and prediction
Authors: Du Lin , Pang Yan 
Published: June 2021

AbstractInfluenza is an infectious disease that leads to an estimated 5 million cases of severe illness and 650,000 respiratory deaths worldwide each year. The early detection and prediction of influenza outbreaks are crucial for efficient resource planning to save patient’s lives and healthcare costs. We propose a new data-driven methodology for influenza outbreak detection and prediction at very local levels. A doctor’s diagnostic dataset of influenza-like illness from more than 3000 clinics in Malaysia is used in this study because these diagnostic data are reliable and can be captured promptly. A new region index (RI) of the influenza outbreak is proposed based on the diagnostic dataset. By analysing the anomalies in the weekly RI value, potential outbreaks are identified using statistical methods. An ensemble learning method is developed to predict potential influenza outbreaks. Cross-validation is conducted to optimize the hyperparameters of the ensemble model. A testing data set is used to provide an unbiased evaluation of the model. The proposed methodology is shown to be sensitive and accurate at influenza outbreak prediction, with average of 75% recall, 74% precision, and 83% accuracy scores across five regions in Malaysia. The results are also validated by Google Flu Trends data, news reports, and surveillance data released by World Health Organization.
A computational model of the epidermis with the deformable dermis and its application to skin diseases
Authors: Ohno Kota , Kobayashi Yasuaki , Uesaka Masaaki , Gotoda Takeshi , Denda Mitsuhiro , Kosumi Hideyuki , Watanabe Mika , Natsuga Ken , Nagayama Masaharu 
Published: June 2021

AbstractThe skin barrier is provided by the organized multi-layer structure of epidermal cells, which is dynamically maintained by a continuous supply of cells from the basal layer. The epidermal homeostasis can be disrupted by various skin diseases, which often cause morphological changes not only in the epidermis but in the dermis. We present a three-dimensional agent-based computational model of the epidermis that takes into account the deformability of the dermis. Our model can produce a stable epidermal structure with well-organized layers. We show that its stability depends on the cell supply rate from the basal layer. Modeling the morphological change of the dermis also enables us to investigate how the stiffness of the dermis affects the structure and barrier functions of the epidermis. Besides, we show that our model can simulate the formation of a corn (clavus) by assuming hyperproliferation and rapid differentiation. We also provide experimental data for human corn, which supports the model assumptions and the simulation result.
Activation and detoxification of cassava cyanogenic glucosides by the whitefly Bemisia tabaci
Authors: Easson Michael L. A. E. , Malka Osnat , Paetz Christian , Hojná Anna , Reichelt Michael , Stein Beate , van Brunschot Sharon , Feldmesser Ester , Campbell Lahcen , Colvin John , Winter Stephan , Morin Shai , Gershenzon Jonathan , Vassão Daniel G. 
Published: June 2021

AbstractTwo-component plant defenses such as cyanogenic glucosides are produced by many plant species, but phloem-feeding herbivores have long been thought not to activate these defenses due to their mode of feeding, which causes only minimal tissue damage. Here, however, we report that cyanogenic glycoside defenses from cassava (Manihot esculenta), a major staple crop in Africa, are activated during feeding by a pest insect, the whitefly Bemisia tabaci, and the resulting hydrogen cyanide is detoxified by conversion to beta-cyanoalanine. Additionally, B. tabaci was found to utilize two metabolic mechanisms to detoxify cyanogenic glucosides by conversion to non-activatable derivatives. First, the cyanogenic glycoside linamarin was glucosylated 1–4 times in succession in a reaction catalyzed by two B. tabaci glycoside hydrolase family 13 enzymes in vitro utilizing sucrose as a co-substrate. Second, both linamarin and the glucosylated linamarin derivatives were phosphorylated. Both phosphorylation and glucosidation of linamarin render this plant pro-toxin inert to the activating plant enzyme linamarase, and thus these metabolic transformations can be considered pre-emptive detoxification strategies to avoid cyanogenesis.
Molecular alterations in basal cell carcinoma subtypes
Authors: Di Nardo Lucia , Pellegrini Cristina , Di Stefani Alessandro , Ricci Francesco , Fossati Barbara , Del Regno Laura , Carbone Carmine , Piro Geny , Corbo Vincenzo , Delfino Pietro , De Summa Simona , Maturo Maria Giovanna , Rocco Tea , Tortora Giampaolo , Fargnoli Maria Concetta , Peris Ketty 
Published: June 2021

AbstractA number of genes have been implicated in the pathogenesis of BCC in addition to the Hedgehog pathway, which is known to drive the initiation of this tumour. We performed in-depth analysis of 13 BCC-related genes (CSMD1, CSMD2, DPH3 promoter, PTCH1, SMO, GLI1, NOTCH1, NOTCH2, TP53, ITIH2, DPP10, STEAP4, TERT promoter) in 57 BCC lesions (26 superficial and 31 nodular) from 55 patients and their corresponding blood samples. PTCH1 and TP53 mutations were found in 71.9% and 45.6% of BCCs, respectively. A high mutation rate was also detected in CSMD1 (63.2%), NOTCH1 (43.8%) and DPP10 (35.1%), and frequent non-coding mutations were identified in TERT (57.9%) and DPH3 promoter (49.1%). CSMD1 mutations significantly co-occurred with TP53 changes (p = 0.002). A significant association was observed between the superficial type of BCC and PTCH1 (p = 0.018) and NOTCH1 (p = 0.020) mutations. In addition, PTCH1 mutations were significantly associated with intermittent sun exposure (p = 0.046) and the occurrence of single lesions (p = 0.021), while NOTCH1 mutations were more frequent in BCCs located on the trunk compared to the head/neck and extremities (p = 0.001). In conclusion, we provide further insights into the molecular alterations underlying the tumorigenic mechanism of superficial and nodular BCCs with a view towards novel rationale-based therapeutic strategies.
Water﻿ vapor induced self-assembly of islands/honeycomb structure by secondary phase separation in polystyrene solution with bimodal molecular weight distribution
Authors: Łojkowski Maciej , Chlanda Adrian , Choińska Emilia , Swieszkowski Wojciech 
Published: June 2021

AbstractThe formation of complex structures in thin films is of interest in many fields. Segregation of polymer chains of different molecular weights is a well-known process. However, here, polystyrene with bimodal molecular weight distribution, but no additional chemical modification was used. It was proven that at certain conditions, the phase separation occurred between two fractions of bimodal polystyrene/methyl ethyl ketone solution. The films were prepared by spin-coating, and the segregation between polystyrene phases was investigated by force spectroscopy. Next, water vapour induced secondary phase separation was investigated. The introduction of moist airflow induced the self-assembly of the lower molecular weight into islands and the heavier fraction into a honeycomb. As a result, an easy, fast, and effective method of obtaining island/honeycomb morphologies was demonstrated. The possible mechanisms of the formation of such structures were discussed.
A new pendulum motion with a suspended point near infinity
Authors: Ismail A. I. 
Published: June 2021

AbstractIn this paper, a pendulum model is represented by a mechanical system that consists of a simple pendulum suspended on a spring, which is permitted oscillations in a plane. The point of suspension moves in a circular path of the radius (a) which is sufficiently large. There are two degrees of freedom for describing the motion named; the angular displacement of the pendulum and the extension of the spring. The equations of motion in terms of the generalized coordinates $$\varphi$$
φ
and $$\xi$$
ξ
are obtained using Lagrange’s equation. The approximated solutions of these equations are achieved up to the third order of approximation in terms of a large parameter $$\varepsilon$$
ε
will be defined instead of a small one in previous studies. The influences of parameters of the system on the motion are obtained using a computerized program. The computerized studies obtained show the accuracy of the used methods through graphical representations.
Transmitting silks of maize have a complex and dynamic microbiome
Authors: Khalaf Eman M. , Shrestha Anuja , Rinne Jeffrey , Lynch Michael D. J. , Shearer Charles R. , Limay-Rios Victor , Reid Lana M. , Raizada Manish N. 
Published: June 2021

AbstractIn corn/maize, silks emerging from cobs capture pollen, and transmit resident sperm nuclei to eggs. There are > 20 million silks per U.S. maize acre. Fungal pathogens invade developing grain using silk channels, including Fusarium graminearum (Fg, temperate environments) and devastating carcinogen-producers (Africa/tropics). Fg contaminates cereal grains with mycotoxins, in particular Deoxynivalenol (DON), known for adverse health effects on humans and livestock. Fitness selection should promote defensive/healthy silks. Here, we report that maize silks, known as styles in other plants, possess complex and dynamic microbiomes at the critical pollen-fungal transmission interval (henceforth: transmitting style microbiome, TSM). Diverse maize genotypes were field-grown in two trial years. MiSeq 16S rRNA gene sequencing of 328 open-pollinated silk samples (healthy/Fg-infected) revealed that the TSM contains > 5000 taxa spanning the prokaryotic tree of life (47 phyla/1300 genera), including nitrogen-fixers. The TSM of silk tip tissue displayed seasonal responsiveness, but possessed a reproducible core of 7–11 MiSeq-amplicon sequence variants (ASVs) dominated by a single Pantoea MiSeq-taxon (15–26% of sequence-counts). Fg-infection collapsed TSM diversity and disturbed predicted metabolic functionality, but doubled overall microbiome size/counts, primarily by elevating 7–25 MiSeq-ASVs, suggestive of a selective microbiome response against infection. This study establishes the maize silk as a model for fundamental/applied research of plant reproductive microbiomes.
Time lapse synchrotron IR chemical imaging for observing the acclimation of a single algal cell to CO2 treatment
Authors: Azarfar Ghazal , Aboualizadeh Ebrahim , Ratti Simona , Olivieri Camilla , Norici Alessandra , Nasse Michael J. , Giordano Mario , Hirschmugl Carol J. 
Published: June 2021

AbstractAlgae are the main primary producers in aquatic environments and therefore of fundamental importance for the global ecosystem. Mid-infrared (IR) microspectroscopy is a non-invasive tool that allows in principle studying chemical composition on a single-cell level. For a long time, however, mid-infrared (IR) imaging of living algal cells in an aqueous environment has been a challenge due to the strong IR absorption of water. In this study, we employed multi-beam synchrotron radiation to measure time-resolved IR hyperspectral images of individual Thalassiosira weissflogii cells in water in the course of acclimation to an abrupt change of CO2 availability (from 390 to 5000 ppm and vice versa) over 75 min. We used a previously developed algorithm to correct sinusoidal interference fringes from IR hyperspectral imaging data. After preprocessing and fringe correction of the hyperspectral data, principal component analysis (PCA) was performed to assess the spatial distribution of organic pools within the algal cells. Through the analysis of 200,000 spectra, we were able to identify compositional modifications associated with CO2 treatment. PCA revealed changes in the carbohydrate pool (1200–950 cm$$^{-1}$$

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1

), lipids (1740, 2852, 2922 cm$$^{-1}$$

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1

), and nucleic acid (1160 and 1201 cm$$^{-1}$$

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1

) as the major response of exposure to elevated CO2 concentrations. Our results show a local metabolism response to this external perturbation.
High electrochemical and mechanical performance of zinc conducting-based gel polymer electrolytes
Authors: Dueramae Isala , Okhawilai Manunya , Kasemsiri Pornnapa , Uyama Hiroshi 
Published: June 2021

AbstractZinc ionic conducting-based gel polymer electrolytes (GPEs) were fabricated from carboxymethyl cellulose (CMC) and three different zinc salts in a mass ratio ranging within 0–30 wt%. The effects of zinc salt and loading level on the structure, thermal, mechanical, mechanical stability, and morphological properties, as well as electrochemical properties of the GPEs films, were symmetrically investigated. The mechanical properties and mechanical stability of CMC were improved with the addition of zinc acetate, zinc sulphate, and zinc triflate, approaching the minimum requirement of a solid state membrane for battery. The maximum ionic conductivity of 2.10 mS cm−1 was achieved with the addition of 15 wt% zinc acetate (ZnA), GPEA15. The supported parameters, indicating the presence of the amorphous region that likely supported Zn2+ movement in the CMC chains, were clearly revealed with the increase in the number of mobile Zn2+ carriers in FT-IR spectra and the magnitude of ionic transference number, the decrease of the enthalpy of fusion in DSC thermogram, and the shifting to lower intensity of 2θ in XRD pattern. The developed CMC/ZnA complex-based GPEs are very promising for their high ionic conductivity as well as good mechanical properties and the ability for long-term utilization in a zinc ion battery.
The global impact of wild pigs (Sus scrofa) on terrestrial biodiversity
Authors: Risch Derek R. , Ringma Jeremy , Price Melissa R. 
Published: June 2021

AbstractThe International Union for the Conservation of Nature’s (IUCN) Red List of Threatened Species is a comprehensive database of over 120,000 species and is a powerful tool to evaluate the threat of invasive species to global biodiversity. Several problematic species have gained global recognition due to comprehensive threat assessments quantifying the threat these species pose to biodiversity using large datasets like the IUCN Red List of Threatened Species. However, the global threat of wild pigs (Sus scrofa) to biodiversity is still poorly understood despite well-documented ecosystem level impacts. In this study, we utilized the IUCN Red List to quantify the impacts of this globally distributed species throughout its native and non-native range. Here we show that wild pigs threaten 672 taxa in 54 different countries across the globe. Most of these taxa are listed as critically endangered or endangered and 14 species have been driven to extinction as a direct result of impacts from wild pigs. Our results show that threats from wild pigs are pervasive across taxonomic groups and that island endemics and taxa throughout the non-native range of wild pigs are particularly vulnerable.