bluuebunny/crossref_metadata_2025_split huggingface dataset:
A blood-based metabolomics test to distinguish relapsing–remitting and secondary progressive multiple sclerosis: addressing practical considerations for clinical application
Authors: Yeo Tianrong , Sealey Megan , Zhou Yifan , Saldana Luisa , Loveless Samantha , Claridge Timothy D. W. , Robertson Neil , DeLuca Gabriele , Palace Jacqueline , Anthony Daniel C. , Probert Fay 
Published: July 2020

AbstractThe transition from relapsing–remitting multiple sclerosis (RRMS) to secondary progressive MS (SPMS) represents a huge clinical challenge. We previously demonstrated that serum metabolomics could distinguish RRMS from SPMS with high diagnostic accuracy. As differing sample-handling protocols can affect the blood metabolite profile, it is vital to understand which factors may influence the accuracy of this metabolomics-based test in a clinical setting. Herein, we aim to further validate the high accuracy of this metabolomics test and to determine if this is maintained in a ‘real-life’ clinical environment. Blood from 31 RRMS and 28 SPMS patients was subjected to different sample-handling protocols representing variations encountered in clinics. The effect of freeze–thaw cycles (0 or 1) and time to erythrocyte removal (30, 120, or 240 min) on the accuracy of the test was investigated. For test development, samples from the optimised protocol (30 min standing time, 0 freeze–thaw) were used, resulting in high diagnostic accuracy (mean ± SD, 91.0 ± 3.0%). This test remained able to discriminate RRMS and SPMS samples that had experienced additional freeze–thaw, and increased standing times of 120 and 240 min with accuracies ranging from 85.5 to 88.0%, because the top discriminatory metabolite biomarkers from the optimised protocol remained discriminatory between RRMS and SPMS despite these sample-handling variations. In conclusion, while strict sample-handling is essential for the development of metabolomics-based blood tests, the results confirmed that the RRMS vs. SPMS test is resistant to sample-handling variations and can distinguish these two MS stages in the clinics.
Identification of TNFAIP3 as relapse biomarker and potential therapeutic target for MOG antibody associated diseases
Authors: Saxena Shrishti , Lokhande Hrishikesh , Gombolay Grace , Raheja Radhika , Rooney Timothy , Chitnis Tanuja 
Published: July 2020

AbstractMOG-antibody associated disease (MOG-AAD) is a recently recognized demyelinating disorder predominantly affecting children but also occurs in adults, with a relapsing course in approximately 50% of patients. We evaluated peripheral blood mononuclear cells from MOG-AAD patients by flow cytometry and found a strong antigen specific central memory cell (CMC) response with increased Th1 and Th17 cells at the time of a relapse. Transcriptomic analysis of CMCs by three independent sequencing platforms revealed TNFAIP3 as a relapse biomarker, whose expression was down regulated at a relapse compared to remission in MOG-AAD patients. Serum in an additional cohort of patients showed decreased TNFAIP3 levels at relapse compared to remission state in MOG-AAD patients. Our studies suggest that alterations in TNFAIP3 levels are associated with relapses in MOG-AAD patients, which may have clinical utility as a disease course biomarker and therapeutic target.
Unique cysteine-enriched, D2L5 and D4L6 extracellular loops in CaV3 T-type channels alter the passage and block of monovalent and divalent ions
Authors: Guan Wendy , Stephens Robert F. , Mourad Omar , Mehta Amrit , Fux Julia , Spafford J. David 
Published: July 2020

AbstractInvertebrate LCaV3 shares the quintessential features of vertebrate CaV3 T-type channels, with a low threshold of channel activation, rapid activation and inactivation kinetics and slow deactivation kinetics compared to other known Ca2+ channels, the CaV1 and CaV2 channels. Unlike the vertebrates though, CaV3 T-type channels in non-cnidarian invertebrates possess an alternative exon 12 spanning the D2L5 extracellular loop, which alters the invertebrate LCaV3 channel into a higher Na+ and lower Ca2+ current passing channel, more resembling a classical NaV1 Na+ channel. Cnidarian CaV3 T-type channels can possess genes with alternative cysteine-rich, D4L6 extracellular loops in a manner reminiscent of the alternative cysteine-rich, D2L5 extracellular loops of non-cnidarian invertebrates. We illustrate here that the preferences for greater Na+ or Ca2+ ion current passing through CaV3 T-type channels are contributed by paired cysteines within D2L5 and D4L6 extracellular loops looming above the pore selectivity filter. Swapping of invertebrate tri- and tetra-cysteine containing extracellular loops, generates higher Na+ current passing channels in human CaV3.2 channels, while corresponding mono- and di-cysteine loop pairs in human CaV3.2 generates greater Ca2+ current passing, invertebrate LCaV3 channels. Alanine substitutions of unique D2L5 loop cysteines of LCaV3 channels increases relative monovalent ion current sizes and increases the potency of Zn2+ and Ni2+ block by ~ 50× and ~ 10× in loop cysteine mutated channels respectively, acquiring characteristics of the high affinity block of CaV3.2 channels, including the loss of the slowing of inactivation kinetics during Zn2+ block. Charge neutralization of a ubiquitous aspartate residue of calcium passing CaV1, CaV2 and CaV3 channels, in the outer pore of the selectivity filter residues in Domain II generates higher Na+ current passing channels in a manner that may resemble how the unique D2L5 extracellular loops of invertebrate CaV3 channels may confer a relatively higher peak current size for Na+ ions over Ca2+ The extracellular loops of CaV3 channels are not engaged with accessory subunit binding, as the other Na+ (NaV1) and Ca2+ (CaV1/CaV2) channels, enabling diversity and expansion of cysteine-bonded extracellular loops, which appears to serve, amongst other possibilities, to alter to the preferences for passage of Ca2+ or Na+ ions through invertebrate CaV3 channels.
Validity of dynamical analysis to characterize heart rate and oxygen consumption during effort tests
Authors: Mongin D. , Chabert C. , Uribe Caparros A. , Collado A. , Hermand E. , Hue O. , Alvero Cruz J. R. , Courvoisier D. S. 
Published: July 2020

AbstractPerformance is usually assessed by simple indices stemming from cardiac and respiratory data measured during graded exercise test. The goal of this study is to characterize the indices produced by a dynamical analysis of HR and VO2 for different effort test protocols, and to estimate the construct validity of these new dynamical indices by testing their links with their standard counterparts. Therefore, two groups of 32 and 14 athletes from two different cohorts performed two different graded exercise testing before and after a period of training or deconditioning. Heart rate (HR) and oxygen consumption (VO2) were measured. The new dynamical indices were the value without effort, the characteristic time and the amplitude (gain) of the HR and VO2 response to the effort. The gain of HR was moderately to strongly associated with other performance indices, while the gain for VO2 increased with training and decreased with deconditioning with an effect size slightly higher than VO2 max. Dynamical analysis performed on the first 2/3 of the effort tests showed similar patterns than the analysis of the entire effort tests, which could be useful to assess individuals who cannot perform full effort tests. In conclusion, the dynamical analysis of HR and VO2 obtained during effort test, especially through the estimation of the gain, provides a good characterization of physical performance, robust to less stringent effort test conditions.
A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota
Authors: Aakko Juhani , Pietilä Sami , Toivonen Raine , Rokka Anne , Mokkala Kati , Laitinen Kirsi , Elo Laura , Hänninen Arno 
Published: July 2020

AbstractGut microbiota participates in diverse metabolic and homeostatic functions related to health and well-being. Its composition varies between individuals, and depends on factors related to host and microbial communities, which need to adapt to utilize various nutrients present in gut environment. We profiled fecal microbiota in 63 healthy adult individuals using metaproteomics, and focused on microbial CAZy (carbohydrate-active) enzymes involved in glycan foraging. We identified two distinct CAZy profiles, one with many Bacteroides-derived CAZy in more than one-third of subjects (n = 25), and it associated with high abundance of Bacteroides in most subjects. In a smaller subset of donors (n = 8) with dietary parameters similar to others, microbiota showed intense expression of Prevotella-derived CAZy including exo-beta-(1,4)-xylanase, xylan-1,4-beta-xylosidase, alpha-l-arabinofuranosidase and several other CAZy belonging to glycosyl hydrolase families involved in digestion of complex plant-derived polysaccharides. This associated invariably with high abundance of Prevotella in gut microbiota, while in subjects with lower abundance of Prevotella, microbiota showed no Prevotella-derived CAZy. Identification of Bacteroides- and Prevotella-derived CAZy in microbiota proteome and their association with differences in microbiota composition are in evidence of individual variation in metabolic specialization of gut microbes affecting their colonizing competence.
Functionalisation of a heat-derived and bio-inert albumin hydrogel with extracellular matrix by air plasma treatment
Authors: Ong John , Zhao Junzhe , Levy Galit Katarivas , Macdonald James , Justin Alexander W. , Markaki Athina E. 
Published: July 2020

AbstractAlbumin-based hydrogels are increasingly attractive in tissue engineering because they provide a xeno-free, biocompatible and potentially patient-specific platform for tissue engineering and drug delivery. The majority of research on albumin hydrogels has focused on bovine serum albumin (BSA), leaving human serum albumin (HSA) comparatively understudied. Different gelation methods are usually employed for HSA and BSA, and variations in the amino acid sequences of HSA and BSA exist; these account for differences in the hydrogel properties. Heat-induced gelation of aqueous HSA is the easiest method of synthesizing HSA hydrogels however hydrogel opacity and poor cell attachment limit their usefulness in downstream applications. Here, a solution to this problem is presented. Stable and translucent HSA hydrogels were created by controlled thermal gelation and the addition of sodium chloride. The resulting bio-inert hydrogel was then subjected to air plasma treatment which functionalised its surface, enabling the attachment of basement membrane matrix (Geltrex). In vitro survival and proliferation studies of foetal human osteoblasts subsequently demonstrated good biocompatibility of functionalised albumin hydrogels compared to untreated samples. Thus, air plasma treatment enables functionalisation of inert heat-derived HSA hydrogels with extracellular matrix proteins and these may be used as a xeno-free platform for biomedical research or cell therapy.
Dendritic spine density is increased on nucleus accumbens D2 neurons after chronic social defeat
Authors: Fox Megan E. , Figueiredo Antonio , Menken Miriam S. , Lobo Mary Kay 
Published: July 2020

AbstractStress alters the structure and function of brain reward circuitry and is an important risk factor for developing depression. In the nucleus accumbens (NAc), structural and physiological plasticity of medium spiny neurons (MSNs) have been linked to increased stress-related and depression-like behaviors. NAc MSNs have opposing roles in driving stress-related behaviors that is dependent on their dopamine receptor expression. After chronic social defeat stress, NAc MSNs exhibit increased dendritic spine density. However, it remains unclear if the dendritic spine plasticity is MSN subtype specific. Here we use viral labeling to characterize dendritic spine morphology specifically in dopamine D2 receptor expressing MSNs (D2-MSNs). After chronic social defeat, D2-MSNs exhibit increased spine density that is correlated with enhanced social avoidance behavior. Together, our data indicate dendritic spine plasticity is MSN subtype specific, improving our understanding of structural plasticity after chronic stress.
Preparation and evaluation of zeolites for ammonium removal from municipal wastewater through ion exchange process
Authors: Guida Samuela , Potter Chris , Jefferson Bruce , Soares Ana 
Published: July 2020

AbstractThe application of ion exchange process for ammonium (NH4+-N) removal from wastewater is limited due to the lack of suppliers of engineered zeolites which present high ammonium exchange capacity (AEC) and mechanical strength. This study focuses on the preparation and evaluation of synthetic zeolites (Zeolite1-6) by measuring AEC and resistance to attrition and compression, against natural (clinoptilolite) and engineered zeolite (reference, Zeolite-N). At high NH4+-N concentrations, Zeolite6 and Zeolite2 showed capacities of 4.7 and 4.5 meq NH4+-N/g media, respectively. In secondary effluent wastewater (initial NH4+-N of 0.7 meq NH4+-N/L), Zeolite1, 2 and 6 showed an AEC of 0.05 meq NH4+-N/g media, similar to Zeolite-N (0.06 meq NH4+-N /g media). Among the synthetic zeolites, Zeolite3 and 6 showed higher resistance to attrition (disintegration rate = 2.7, 4.1 NTU/h, respectively) when compared with Zeolite-N (disintegration rate = 13.2 NTU/h). Zeolite4 and 6 showed higher resistance to compression (11 N and 6 N, respectively). Due its properties, Zeolite6 was further tested in an ion exchange demonstration scale plant treating secondary effluent from a municipal wastewater treatment plant. However, Zeolite6 disintegrated after 2 months of operation, whilst Zeolite-N remained stable for 1.5 year. This highlighted the importance of the zeolite’s mechanical strength for successful application. In particular, future work should focus on the optimization of the zeolite production process (temperature, time and dimension of the kiln during calcination) to obtain an engineered zeolite with a spherical shape thus reducing eventual sharp edges which can affect mechanical strength.
A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics
Authors: Lv Honghao , Wang Yong , Han Fengqing , Ji Jialei , Fang Zhiyuan , Zhuang Mu , Li Zhansheng , Zhang Yangyong , Yang Limei 
Published: July 2020

AbstractCabbage (Brassica oleracea var. capitata) is an important vegetable crop widely grown throughout the world, providing plentiful nutrients and health-promoting substances. To facilitate further genetics and genomic studies and crop improvement, we present here a high-quality reference genome for cabbage. We report a de novo genome assembly of the cabbage double-haploid line D134. A combined strategy of single-molecule real-time (SMRT) sequencing, 10× Genomics and chromosome conformation capture (Hi-C) produced a high quality cabbage draft genome. The chromosome-level D134 assembly is 529.92 Mb in size, 135 Mb longer than the current 02-12 reference genome, with scaffold N50 length being raised as high as 38 times. We annotated 44,701 high-quality protein-coding genes, and provided full-length transcripts for 45.59% of the total predicted gene models. Moreover, we identified novel genomic features like underrated TEs, as well as gene families and gene family expansions and contractions during B. oleracea evolution. The D134 draft genome is a cabbage reference genome assembled by SMRT long-read sequencing combined with the 10× Genomics and Hi-C technologies for scaffolding. This high-quality cabbage reference genome provides a valuable tool for improvement of Brassica crops.
Metallic glass coating for improving diamond dicing performance
Authors: Chu Jinn P. , Lai Bo-Zhang , Yiu Pakman , Shen Yu-Lin , Chang Chia-Wei 
Published: July 2020

AbstractThis is the first report on the coating of diamond dicing blades with metallic glass (MG) coating to reduce chipping when used to cut Si, SiC, sapphire, and patterned sapphire substrates (PSS). The low coefficient-of-friction (CoF) of Zr-based MG-coated dicing blades was shown to reduce the number and size of chips, regardless of the target substrate. Overall, SiC, sapphire and PSS were most affected by chipping, due to the fact that higher cutting forces were needed for the higher hardness of SiC, sapphire and PSS. Compared to the bare blade, the MG coating provided the following reductions in chipping area: Si (~ 23%), SiC (~ 36%), sapphire (~ 45%), and PSS (~ 33%). The proposed coating proved particularly effective in reducing chips of larger size (> 41 µm in chipping width), as indicated by an ~ 80% reduction when cutting sapphire. Small variations in kerf angle and depth demonstrate the durability of the coated blades, which would no doubt enhance consistency in dicing performance and extend the blade lifespan. Finite-element modeling revealed significant reductions in tensile stress and elastic–plastic deformation during dicing, thanks to a lower CoF.
Biological characteristics of Trissolcus urichi (Crawford) (Hymenoptera: Scelionidae) on Euschistus heros (Fabricius) and Dichelops melacanthus (Dallas) (Hemiptera: Pentatomidae) Eggs
Authors: de Queiroz Ana Paula , Bueno Adeney de Freitas , Panizzi Antônio Ricardo , Favetti Bruna Magda , Grande Marcela Lais Mora , Luski Pamela Gislaine Gellert 
Published: July 2020

AbstractSpecies of the genus Trissolcus are effective as egg parasitoids of Euschistus heros and can potentially be used in a multispecies pest management approach. However, in order to successfully use those biocontrol agents in the field, previous detailed knowledge about their life history are necessary. Therefore, we evaluate some biological characteristics of Trissolcus urichi on Euschistus heros and Dichelops melacanthus eggs. Three independent experiments were performed: (1) T. urichi host preference between E. heros and D. melacanthus eggs. (2) T. urichi eggs-adult period (days), number of parasitized eggs in 24 h, emergence rate (%) and sex ratio of the parasitoid in E. heros and D. melacanthus eggs. (3) Morphometric characteristics of T. urichi grown on E. heros and D. melacanthus eggs. Trissolcus urichi preferred to parasitize E. heros eggs, exhibiting a higher number of parasitized eggs, higher rate of emergence (%) and faster development, as well as producing progeny of larger size than the parasitoids emerged from eggs of D. melacanthus in relation to body length, wing length and width. Thus, it can be concluded that T. urichi had better performance on E. heros eggs, although the parasitoid had also acceptable parasitism capacity and development in D. melacanthus eggs.
AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq
Authors: Arrigoni L. , Ferrari F. , Weller J. , Bella C. , Bönisch U. , Manke T. 
Published: July 2020

AbstractChromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide. Restriction Enzyme-based Labeling of Chromatin in Situ (RELACS) is a recently developed ChIP-seq protocol that deploys a chromatin barcoding strategy to enable standardized and high-throughput generation of ChIP-seq data. The manual implementation of RELACS is constrained by human processivity in both data generation and data analysis. To overcome these limitations, we have developed AutoRELACS, an automated implementation of the RELACS protocol using the liquid handler Biomek i7 workstation. We match the unprecedented processivity in data generation allowed by AutoRELACS with the automated computation pipelines offered by snakePipes. In doing so, we build a continuous workflow that streamlines epigenetic profiling, from sample collection to biological interpretation. Here, we show that AutoRELACS successfully automates chromatin barcode integration, and is able to generate high-quality ChIP-seq data comparable with the standards of the manual protocol, also for limited amounts of biological samples.
Infrared spectroscopy refines chronological assessment, depositional environment and pyrolysis conditions of archeological charcoals
Authors: Smidt E. , Tintner J. , Nelle O. , Oliveira R. R. , Patzlaff R. , Novotny E. H. , Klemm S. 
Published: July 2020

AbstractBased on infrared spectral characteristics, six archeological sample sets of charcoals from German (5) and Brazilian (1) sites, covering the time span from the nineteenth century CE to 3950 BCE, were compared to a chronological (present to the fifteenth century BCE) series of Austrian charcoals. A typical chronological trend of several bands (stretch vibrations: O–C–O of carboxylates at 1,585–1,565 and 1,385–1,375 cm−1, C–O carboxylic acids at 1,260–1,250 cm−1) that indicate oxidation and subsequently increasing hydrophilicity (O–H stretch vibration at about 3,400 cm−1) was also contained in the archive samples. Three sample sets fit in the typical band development according to their age. For three sample sets this conformity was not observed. Despite the age of two sample sets (3950–2820 BCE), most charcoals were assigned to the Modern Period. Apart from the high degree of carbonization, anaerobic depositional conditions over a longer period of time seem to contribute to the surprising conservation. Non-removable mineral components in charcoals, as observed in a third sample set, strongly influence infrared band intensities and positions of organic compounds. The role of inorganic components in terms of charcoal aging, and the information we can obtain from spectral characteristics in an archeological context, are discussed.
EEG dynamics and neural generators of psychological flow during one tightrope performance
Authors: Leroy A. , Cheron G. 
Published: July 2020

AbstractPsychological “flow” emerges from a goal requiring action, and a match between skills and challenge. Using high-density electroencephalographic (EEG) recording, we quantified the neural generators characterizing psychological “flow” compared to a mindful “stress” state during a professional tightrope performance. Applying swLORETA based on self-reported mental states revealed the right superior temporal gyrus (BA38), right globus pallidus, and putamen as generators of delta, alpha, and beta oscillations, respectively, when comparing “flow” versus “stress”. Comparison of “stress” versus “flow” identified the middle temporal gyrus (BA39) as the delta generator, and the medial frontal gyrus (BA10) as the alpha and beta generator. These results support that “flow” emergence required transient hypo-frontality. Applying swLORETA on the motor command represented by the tibialis anterior EMG burst identified the ipsilateral cerebellum and contralateral sensorimotor cortex in association with on-line control exerted during both “flow” and “stress”, while the basal ganglia was identified only during “flow”.
The carbon footprint of the carbon feedstock CO2
Authors: Müller Leonard Jan , Kätelhön Arne , Bringezu Stefan , McCoy Sean , Suh Sangwon , Edwards Robert , Sick Volker , Kaiser Simon , Cuéllar-Franca Rosa , El Khamlichi Aïcha , Lee Jay H. , von der Assen Niklas , Bardow André 
Published: July 2020

This paper reviews methodological approaches for determining the carbon footprint of captured CO2 as carbon feedstock, and shows why some approaches lead to suboptimal choices of CO2 sources and that increased consistency in life cycle assessment (LCA) studies on CCU is needed.