bluuebunny/crossref_metadata_2025_split huggingface dataset:
An atlas of dynamic chromatin landscapes in mouse fetal development
Authors: Gorkin David U. , Barozzi Iros , Zhao Yuan , Zhang Yanxiao , Huang Hui , Lee Ah Young , Li Bin , Chiou Joshua , Wildberg Andre , Ding Bo , Zhang Bo , Wang Mengchi , Strattan J. Seth , Davidson Jean M. , Qiu Yunjiang , Afzal Veena , Akiyama Jennifer A. , Plajzer-Frick Ingrid , Novak Catherine S. , Kato Momoe , Garvin Tyler H. , Pham Quan T. , Harrington Anne N. , Mannion Brandon J. , Lee Elizabeth A. , Fukuda-Yuzawa Yoko , He Yupeng , Preissl Sebastian , Chee Sora , Han Jee Yun , Williams Brian A. , Trout Diane , Amrhein Henry , Yang Hongbo , Cherry J. Michael , Wang Wei , Gaulton Kyle , Ecker Joseph R. , Shen Yin , Dickel Diane E. , Visel Axel , Pennacchio Len A. , Ren Bing 
Published: July 2020

AbstractThe Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP–seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC–seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.
Landscape of cohesin-mediated chromatin loops in the human genome
Authors: Grubert Fabian , Srivas Rohith , Spacek Damek  V , Kasowski Maya , Ruiz-Velasco Mariana , Sinnott-Armstrong Nasa , Greenside Peyton , Narasimha Anil , Liu Qing , Geller Benjamin , Sanghi Akshay , Kulik Michael , Sa Silin , Rabinovitch Marlene , Kundaje Anshul , Dalton Stephen , Zaugg Judith B. , Snyder Michael 
Published: July 2020

AbstractPhysical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear. Here, to address these questions as part of phase III of the Encyclopedia of DNA Elements (ENCODE), we mapped cohesin-mediated chromatin loops, using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene expression in 24 diverse human cell types, including core ENCODE cell lines. Twenty-eight per cent of all chromatin loops vary across cell types; these variations modestly correlate with changes in gene expression and are effective at grouping cell types according to their tissue of origin. The connectivity of genes corresponds to different functional classes, with housekeeping genes having few contacts, and dosage-sensitive genes being more connected to enhancer elements. This atlas of chromatin loops complements the diverse maps of regulatory architecture that comprise the ENCODE Encyclopedia, and will help to support emerging analyses of genome structure and function.
The Late Triassic Ischigualasto Formation at Cerro Las Lajas (La Rioja, Argentina): fossil tetrapods, high-resolution chronostratigraphy, and faunal correlations
Authors: Desojo Julia B. , Fiorelli Lucas E. , Ezcurra Martín D. , Martinelli Agustín G. , Ramezani Jahandar , Da Rosa Átila. A. S. , von Baczko M. Belén , Trotteyn M. Jimena , Montefeltro Felipe C. , Ezpeleta Miguel , Langer Max C. 
Published: July 2020

AbstractPresent knowledge of Late Triassic tetrapod evolution, including the rise of dinosaurs, relies heavily on the fossil-rich continental deposits of South America, their precise depositional histories and correlations. We report on an extended succession of the Ischigualasto Formation exposed in the Hoyada del Cerro Las Lajas (La Rioja, Argentina), where more than 100 tetrapod fossils were newly collected, augmented by historical finds such as the ornithosuchidVenaticosuchus rusconiiand the putative ornithischianPisanosaurus mertii. Detailed lithostratigraphy combined with high-precision U–Pb geochronology from three intercalated tuffs are used to construct a robust Bayesian age model for the formation, constraining its deposition between 230.2 ± 1.9 Ma and 221.4 ± 1.2 Ma, and its fossil-bearing interval to 229.20 + 0.11/− 0.15–226.85 + 1.45/− 2.01 Ma. The latter is divided into a lowerHyperodapedonand an upperTeyumbaitabiozones, based on the ranges of the eponymous rhynchosaurs, allowing biostratigraphic correlations to elsewhere in the Ischigualasto-Villa Unión Basin, as well as to the Paraná Basin in Brazil. The temporally calibrated Ischigualasto biostratigraphy suggests the persistence of rhynchosaur-dominated faunas into the earliest Norian. Our ca. 229 Ma age assignment toPi. mertiipartially fills the ghost lineage between younger ornithischian records and the oldest known saurischians at ca. 233 Ma.
Offspring of obese mice display enhanced intake and sensitivity for palatable stimuli, with altered expression of taste signaling elements
Authors: Choo Ezen , Wong Lauren , Chau Patricia , Bushnell Jennifer , Dando Robin 
Published: July 2020

AbstractMaternal body mass index and gestational weight gain predict future obesity status of the offspring. In studies of both rodents and non-human primates, maternal obesity also predicts a preference for palatable foods in the offspring. In this study, we used C57BL/6J mice to investigate whether an underlying cause for an increase in palatable food consumption in the offspring of obese mice was a change in taste function. Adult female mice were fed a normal chow (NC) or a high fat diet (HFD) for 5 weeks before mating, then also during the gestation (3 weeks) and lactation (3 weeks) periods, with offspring always maintained on a normal chow diet; thus the only experience offspring had with high fat food was via maternal exposure. Offspring exhibited similar weight, blood glucose levels and baseline water and chow intake in adulthood. Taste response was assessed after reaching maturity, using brief-access taste testing, with female offspring of obese dams showing an enhanced response to sucrose, and both sexes consuming more sucrose, sucralose and high fat diet if from obese mothers. Offspring also exhibited increased taste bud expression of mRNA for sweet receptor subunits T1R (Taste receptor type) 2 and 3, as well as other markers associated with taste signaling. Taste morphology in both groups appeared similar. Results indicate that obesity in the mother may lead to unhealthy feeding behavior in the offspring, correlating with altered expression of taste signaling elements, which likely drive increased avidity for palatable foods.
Transcriptome profiling and in silico detection of the antimicrobial peptides of red king crab Paralithodes camtschaticus
Authors: Yakovlev Igor A. , Lysøe Erik , Heldal Inger , Steen Hege , Hagen Snorre B. , Clarke Jihong Liu 
Published: July 2020

AbstractEndogenous antimicrobial peptides (AMPs) are evolutionarily ancient factors of innate immunity, which are produced by all multicellular organisms and play a key role in their protection against infection. Red king crab (Paralithodes camtschaticus), also called Kamchatka crab, is widely distributed and the best known species of all king crabs belonging to the family Lithodidae. Despite their economic importance, the genetic resources of king crabs are scarcely known and no full-genome sequences are available to date. Therefore, analysis of the red king crab transcriptome and identification and characterization of its AMPs could potentially contribute to the development of novel antimicrobial drug candidates when antibiotic resistance has become a global health threat. In this study, we sequenced the P. camtschaticus transcriptomes from carapace, tail flap and leg tissues using an Illumina NGS platform. Libraries were systematically analyzed for gene expression profiles along with AMP prediction. By an in silico approach using public databases we defined 49 cDNAs encoding for AMP candidates belonging to diverse families and functional classes, including buforins, crustins, paralithocins, and ALFs (anti-lipopolysaccharide factors). We analyzed expression patterns of 27 AMP genes. The highest expression was found for Paralithocin 1 and Crustin 3, with more than 8,000 reads. Other paralithocins, ALFs, crustins and ubiquicidins were among medium expressed genes. This transcriptome data set and AMPs provide a solid baseline for further functional analysis in P. camtschaticus. Results from the current study contribute also to the future application of red king crab as a bio-resource in addition to its being a known seafood delicacy.
The colours of Rome in the walls of Cástulo (Linares, Spain)
Authors: Tuñón José , Sánchez Alberto , Parras David J. , Amate Pilar , Montejo Manuel , Ceprián Bautista 
Published: July 2020

AbstractWall paintings have become one of the most relevant, complex and challenging research subjects in Archaeometry. Minimally- or non-invasive, accurate and multidisciplinary methods are needed to successfully address the problems posed by their physical and chemical properties and by their analysis techniques. Specifically, the analytical method implemented for the study of this type of samples must enable a precise separation of the chemical information from backgrounds and scenes, allowing the identification of pigment’s components in overlapping layers, the detection of minority components and the elucidation of pigment mixtures. Thus, this paper puts forward a multidisciplinary approach towards these goals by means of the combined use of micro Energy Dispersive X-ray Fluorescence (µEDXRF) surface mapping and single-spot micro-Raman spectroscopy and µEDXRF analysis. The samples under research come from the site of Cástulo (Linares, Spain), one of the most important Roman cities in the Iberian Peninsula. It must be emphasized the uniqueness of the walls of Cástulo, their optimal conservation state and the richness and variety of the colour’s palette used in their decoration, which make them an excellent and representative example of Roman wall paintings.
High fractional excretion of glycation adducts is associated with subsequent early decline in renal function in type 1 diabetes
Authors: Perkins Bruce A. , Rabbani Naila , Weston Andrew , Adaikalakoteswari Antonysunil , Lee Justin A. , Lovblom Leif E. , Cardinez Nancy , Thornalley Paul J. 
Published: July 2020

AbstractIncreased protein glycation, oxidation and nitration is linked to the development of diabetic nephropathy. We reported levels of serum protein glycation, oxidation and nitration and related hydrolysis products, glycation, oxidation and nitration free adducts in patients with type 1 diabetes (T1DM) during onset of microalbuminuria (MA) from the First Joslin Kidney Study, a prospective case–control study of patients with T1DM with and without early decline in GFR. Herein we report urinary excretion of the latter analytes and related fractional excretion values, exploring the link to MA and early decline in GFR. We recruited patients with T1DM and normoalbuminuria (NA) (n = 30) or new onset MA with and without early GFR decline (n = 22 and 33, respectively) for this study. We determined urinary protein glycation, oxidation and nitration free adducts by stable isotopic dilution analysis liquid chromatography-tandem mass spectrometry (LC–MS/MS) and deduced fractional excretion using reported plasma levels and urinary and plasma creatinine estimates. We found urinary excretion of pentosidine was increased ca. twofold in patients with MA, compared to normoalbuminuria (0.0442 vs 0.0103 nmol/mg creatinine, P < 0.0001), and increased ca. threefold in patients with early decline in GFR, compared to patients with stable GFR (0.0561 vs 0.0176 nmol/mg creatinine, P < 0.01). Urinary excretion of all other analytes was unchanged between the study groups. Remarkably, fractional excretions of 6 lysine and arginine-derived glycation free adducts were higher in patients with early decline in GFR, compared to those with stable GFR. Impaired tubular reuptake of glycation free adducts by lysine and arginine transporter proteins in patients with early GFR decline is likely involved. We conclude that higher fractional excretions of glycation adducts are potential biomarkers for early GFR decline in T1DM and MA. Measurement of these analytes could provide the basis for identifying patients at risk of early decline in renal function to target and intensify renoprotective treatment.
Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce
Authors: Chaudhary Rajiv , Lundén Karl , Dalman Kerstin , Dubey Mukesh , Nemesio-Gorriz Miguel , Karlsson Bo , Stenlid Jan , Elfstrand Malin 
Published: July 2020

AbstractThe Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.
Evaluation of qPCR reference genes in GH-overexpressing transgenic zebrafish (Danio rerio)
Authors: Rassier Gabriela T. , Silveira Tony L. R. , Remião Mariana H. , Daneluz Larissa O. , Martins Amanda W. S. , Dellagostin Eduardo N. , Ortiz Hadassa G. , Domingues William B. , Komninou Eliza R. , Kütter Mateus T. , Marins Luis F. F. , Campos Vinicius Farias 
Published: July 2020

AbstractReference genes (RGs) must have a stable expression in tissues in all experimental conditions to normalize real-time quantitative reverse transcription PCR (qRT-PCR) data. F0104 is a highly studied lineage of zebrafish developed to overexpress the growth hormone (GH). It is assumed that the transgenic process may influence the expression levels of commonly used RGs. The objective of the present study was to make a comprehensive analysis of stability of canditade RGs actb1, actb2, b2m, eif2s2, eef1a1, gapdh, rplp2, rpl7, rpl13α, tuba1, and rps18, in gh-transgenic and non-transgenic zebrafish. Liver, brain, intestine and muscle samples from both groups had qRT-PCR results analyzed by dCt, geNorm, NormFinder, BestKeeper, and RefFinder softwares. Consensus analyses among software concluded that rpl13α, rpl7, and eef1a1 are the most stable genes for zebrafish, considering the studied groups and tissues. Gapdh, rps18, and tuba1 suffered variations in stability among different tissues of both groups, and so, they were listed as the genes with lowest stability. Results from an average pairwise variations test indicated that the use of two RGs would generate reliable results for gene expression analysis in the studied tissues. We conclude that genes that are commonly used in mammals for qRT-PCR assays have low stability in both non-transgenic and gh-transgenic zebrafish reinforcing the importance of using species-specific RGs.
Rituximab-containing therapy for cold agglutinin disease: a retrospective study of 16 patients
Authors: Jia Ming-nan , Qiu Yu , Wu Yan-yan , Cai Hao , Zhou Dao-bin , Cao Xin-xin , Li Jian 
Published: July 2020

AbstractCold agglutinin disease (CAD) is a rare form of autoimmune haemolytic anaemia, and because of its rareness, there is no standard treatment for CAD patients. We retrospectively analysed the response to rituximab-containing therapy in CAD patients at our hospital. All patients received rituximab-containing therapy for at least 1 month. A total of 16 patients (11 males and 5 females) were included. The median age at the onset of the disease was 63.5 years (range 41–79). Most patients had manifestations including anaemia (81.3%) or cold-induced circulatory symptoms (75.0%). The median haemoglobin level was 72 g/L (range 29–101), and the median cold agglutinin titre was 1,024 (range 64–2,048). Thirteen of 16 patients (81%) responded to the therapy. Responders achieved a median increase in haemoglobin levels of 45 g/L. Grade 3–4 neutropenia occurred in 3 patients (19%), but only 1 (6%) of them experienced infection. Anaphylaxis related to rituximab occurred in 1 patient. During follow-up, five patients experienced relapse, and two patients died. The estimated median progression-free survival was 36 months, and median overall survival was not yet reached. In conclusion, A rituximab-based therapy in accordance with individual patient characteristics may be a reasonable choice for CAD patients.
Noise suppression beyond the thermal limit with nanotransistor biosensors
Authors: Kutovyi Yurii , Madrid Ignacio , Zadorozhnyi Ihor , Boichuk Nazarii , Kim Soo Hyeon , Fujii Teruo , Jalabert Laurent , Offenhaeusser Andreas , Vitusevich Svetlana , Clément Nicolas 
Published: July 2020

AbstractTransistor biosensors are mass-fabrication-compatible devices of interest for point of care diagnosis as well as molecular interaction studies. While the actual transistor gates in processors reach the sub-10 nm range for optimum integration and power consumption, studies on design rules for the signal-to-noise ratio (S/N) optimization in transistor-based biosensors have been so far restricted to 1 µm2 device gate area, a range where the discrete nature of the defects can be neglected. In this study, which combines experiments and theoretical analysis at both numerical and analytical levels, we extend such investigation to the nanometer range and highlight the effect of doping type as well as the noise suppression opportunities offered at this scale. In particular, we show that, when a single trap is active near the conductive channel, the noise can be suppressed even beyond the thermal limit by monitoring the trap occupancy probability in an approach analog to the stochastic resonance effect used in biological systems.
Radiomics feature reproducibility under inter-rater variability in segmentations of CT images
Authors: Haarburger Christoph , Müller-Franzes Gustav , Weninger Leon , Kuhl Christiane , Truhn Daniel , Merhof Dorit 
Published: July 2020

AbstractIdentifying image features that are robust with respect to segmentation variability is a tough challenge in radiomics. So far, this problem has mainly been tackled in test–retest analyses. In this work we analyse radiomics feature reproducibility in two phases: first with manual segmentations provided by four expert readers and second with probabilistic automated segmentations using a recently developed neural network (PHiseg). We test feature reproducibility on three publicly available datasets of lung, kidney and liver lesions. We find consistent results both over manual and automated segmentations in all three datasets and show that there are subsets of radiomic features which are robust against segmentation variability and other radiomic features which are prone to poor reproducibility under differing segmentations. By providing a detailed analysis of robustness of the most common radiomics features across several datasets, we envision that more reliable and reproducible radiomic models can be built in the future based on this work.
The relationship between blood metabolites of the tryptophan pathway and kidney function: a bidirectional Mendelian randomization analysis
Authors: Cheng Yurong , Li Yong , Benkowitz Paula , Lamina Claudia , Köttgen Anna , Sekula Peggy 
Published: July 2020

AbstractBlood metabolites of the tryptophan pathway were found to be associated with kidney function and disease in observational studies. In order to evaluate causal relationship and direction, we designed a study using a bidirectional Mendelian randomization approach. The analyses were based on published summary statistics with study sizes ranging from 1,960 to 133,413. After correction for multiple testing, results provided no evidence of an effect of metabolites of the tryptophan pathway on estimated glomerular filtration rate (eGFR). Conversely, lower eGFR was related to higher levels of four metabolites: C-glycosyltryptophan (effect estimate = − 0.16, 95% confidence interval [CI] (− 0.22; − 0.1); p = 9.2e−08), kynurenine (effect estimate = − 0.18, 95% CI (− 0.25; − 0.11); p = 1.1e−06), 3-indoxyl sulfate (effect estimate = − 0.25, 95% CI (− 0.4; − 0.11); p = 6.3e−04) and indole-3-lactate (effect estimate = − 0.26, 95% CI (− 0.38; − 0.13); p = 5.4e−05). Our study supports that lower eGFR causes higher blood metabolite levels of the tryptophan pathway including kynurenine, C-glycosyltryptophan, 3-indoxyl sulfate, and indole-3-lactate. These findings aid the notion that metabolites of the tryptophan pathway are a consequence rather than a cause of reduced eGFR. Further research is needed to specifically examine relationships with respect to chronic kidney disease (CKD) progression among patients with existing CKD.
Electronic phase shift measurement for the determination of acoustic wave DOA using single MEMS biomimetic sensor
Authors: Rabelo Renato C. , Alves Fabio D. , Karunasiri Gamani 
Published: July 2020

AbstractMEMS acoustic sensors have been developed to mimic the highly-accurate sound-locating system of the Ormia ochracea fly, which detects sound wavelengths much larger than its hearing organ. A typical ormia-based MEMS directional sound sensor possesses two coupled wings that vibrate in response to sound according to a superposition of its two main resonant modes, rocking and bending. Vibrations are transduced into electronic signals by interdigitated comb finger capacitors at each wing’s end along with a capacitance measuring circuitry. A sensor designed to exhibit resonant modes closely placed in frequency, enhancing their coupling, was operated with a closed cavity behind the wings. Simultaneous and independent measurements of electronic signals generated at each of the single sensor wings were used to determine incident sound direction of arrival (DOA). DOA was found proportional to the phase shift between them and to the difference over the sum of their amplitudes as well. Single sensor phase shift DOA measurement presented a resolution better than 3° for sound pressure levels of 25 mPa or greater. These results indicate that a single sensor operating in closed-cavity configuration can provide hemispherical unambiguous direction of arrival of sound waves which wavelength is much larger than the sensor size.