bluuebunny/crossref_metadata_2025_split huggingface dataset:
ADAD1 and ADAD2, testis-specific adenosine deaminase domain-containing proteins, are required for male fertility
Authors: Snyder Elizabeth , Chukrallah Lauren , Seltzer Kelly , Goodwin Leslie , Braun Robert E. 
Published: July 2020

AbstractAdenosine-to-inosine RNA editing, a fundamental RNA modification, is regulated by adenosine deaminase (AD) domain containing proteins. Within the testis, RNA editing is catalyzed by ADARB1 and is regulated in a cell-type dependent manner. This study examined the role of two testis-specific AD domain proteins, ADAD1 and ADAD2, on testis RNA editing and male germ cell differentiation. ADAD1, previously shown to localize to round spermatids, and ADAD2 had distinct localization patterns with ADAD2 expressed predominantly in mid- to late-pachytene spermatocytes suggesting a role for both in meiotic and post-meiotic germ cell RNA editing. AD domain analysis showed the AD domain of both ADADs was likely catalytically inactive, similar to known negative regulators of RNA editing. To assess the impact of Adad mutation on male germ cell RNA editing, CRISPR-induced alleles of each were generated in mouse. Mutation of either Adad resulted in complete male sterility with Adad1 mutants displaying severe teratospermia and Adad2 mutant germ cells unable to progress beyond round spermatid. However, mutation of neither Adad1 nor Adad2 impacted RNA editing efficiency or site selection. Taken together, these results demonstrate ADAD1 and ADAD2 are essential regulators of male germ cell differentiation with molecular functions unrelated to A-to-I RNA editing.
The social supergene dates back to the speciation time of two Solenopsis fire ant species
Authors: Cohen Pnina , Privman Eyal 
Published: July 2020

AbstractColony social organization of multiple Solenopsis fire ant species is determined by a supergene with two haplotypes SB and Sb, which are similar to X/Y sex chromosomes. The ancestral monogyne (single-queen) social form has been associated with homozygous SB/SB queens, while queens in colonies with the derived polygyne (multi-queen) social structure are heterozygous SB/Sb. By comparing 14 Solenopsis invicta genomes and the outgroup S. fugax, we dated the formation of the supergene to 1.1 (0.7–1.6) million years ago, much older than previous estimates, and close to the estimated time of speciation of the two socially polymorphic species S. invicta and S. richteri. We also used 12 S. invicta and S. richteri genomes to compare the evolutionary distances between these species and the distances between the social haplotypes, and found them to be similar. A phylogenetic analysis suggested that the monophyletic Sb clade is more closely related to S. richteri SB haplotypes than to S. invicta SB haplotypes. We conclude that the formation of the supergene occurred concomitantly with the process of speciation of the Solenopsis socially-polymorphic clade, and hypothesize that the Sb variant first arouse in one incipiently-speciating population and then introgressed into the other populations or species.
Kinome profiling of peripheral blood mononuclear cells collected prior to vaccination reveals biomarkers and potential mechanisms of vaccine unresponsiveness in pigs
Authors: Lipsit Sean W. L. , Wilkinson James , Scruten Erin , Facciuolo Antonio , Denomy Connor , Griebel Philip J. , Kusalik Anthony , Plastow Graham , Napper Scott 
Published: July 2020

AbstractInter-individual variance in host immune responses following vaccination can result in failure to develop protective immunity leaving individuals at risk for infection in addition to compromising herd immunity. While developing more efficacious vaccines is one strategy to mitigate this problem, predicting vaccine responsiveness prior to vaccination could inform which individuals require adjunct disease management strategies. To identify biomarkers of vaccine responsiveness, a cohort of pigs (n = 120) were vaccinated and pigs representing the high (n = 6; 90th percentile) and low (n = 6; 10th percentile) responders based on vaccine-specific antibody responses following vaccination were further analyzed. Kinase-mediated phosphorylation events within peripheral blood mononuclear cells collected prior to vaccination identified 53 differentially phosphorylated peptides when comparing low responders with high responders. Functional enrichment analysis revealed pro-inflammatory cytokine signaling pathways as dysregulated, and this was further substantiated by detection of higher (p < 0.01) concentrations of interferon-gamma in plasma of low responders compared to high responders prior to vaccination. In addition, low responder pigs with high plasma interferon-gamma showed lower (p < 0.01) birth weights than high responder pigs. These associations between vaccine responsiveness, cytokine signaling within peripheral immune cells, and body weight in pigs provide both evidence and insight into potential biomarkers for identifying low responders to vaccination.
GBA3: a polymorphic pseudogene in humans that experienced repeated gene loss during mammalian evolution
Authors: Lopes-Marques Monica , Serrano Catarina , Cardoso Ana R. , Salazar Renato , Seixas Susana , Amorim António , Azevedo Luisa , Prata Maria J. 
Published: July 2020

AbstractThe gene encoding the cytosolic β-glucosidase GBA3 shows pseudogenization due to a truncated allele (rs358231) that is polymorphic in humans. Since this enzyme is involved in the transformation of many plant β-glycosides, this particular case of gene loss may have been influenced by dietary adaptations during evolution. In humans, apart from the inactivating allele, we found that GBA3 accumulated additional damaging mutations, implying an extensive GBA3 loss. The allelic distribution of loss-of-function alleles revealed significant differences between human populations which can be partially related with their staple diet. The analysis of mammalian orthologs disclosed that GBA3 underwent at least nine pseudogenization events. Most events of pseudogenization occurred in carnivorous lineages, suggesting a possible link to a β-glycoside poor diet. However, GBA3 was also lost in omnivorous and herbivorous species, hinting that the physiological role of GBA3 is not fully understood and other unknown causes may underlie GBA3 pseudogenization. Such possibility relies upon a putative role in sialic acid biology, where GBA3 participates in a cellular network involving NEU2 and CMAH. Overall, our data shows that the recurrent loss of GBA3 in mammals is likely to represent an evolutionary endpoint of the relaxation of selective constraints triggered by diet-related factors.
Genomic imprinting analyses identify maternal effects as a cause of phenotypic variability in type 1 diabetes and rheumatoid arthritis
Authors: Blunk Inga , Thomsen Hauke , Reinsch Norbert , Mayer Manfred , Försti Asta , Sundquist Jan , Sundquist Kristina , Hemminki Kari 
Published: July 2020

AbstractImprinted genes, giving rise to parent-of-origin effects (POEs), have been hypothesised to affect type 1 diabetes (T1D) and rheumatoid arthritis (RA). However, maternal effects may also play a role. By using a mixed model that is able to simultaneously consider all kinds of POEs, the importance of POEs for the development of T1D and RA was investigated in a variance components analysis. The analysis was based on Swedish population-scale pedigree data. With P = 0.18 (T1D) and P = 0.26 (RA) imprinting variances were not significant. Explaining up to 19.00% (± 2.00%) and 15.00% (± 6.00%) of the phenotypic variance, the maternal environmental variance was significant for T1D (P = 1.60 × 10−24) and for RA (P = 0.02). For the first time, the existence of maternal genetic effects on RA was indicated, contributing up to 16.00% (± 3.00%) of the total variance. Environmental factors such as the social economic index, the number of offspring, birth year as well as their interactions with sex showed large effects.
Adaptive tuning of infrared emission using VO2 thin films
Authors: Larciprete M. C. , Centini M. , Paoloni S. , Fratoddi I. , Dereshgi S. A. , Tang K. , Wu J. , Aydin K. 
Published: July 2020

AbstractPhase-transition materials provide exciting opportunities for controlling optical properties of photonic devices dynamically. Here, we systematically investigate the infrared emission from a thin film of vanadium dioxide (VO2). We experimentally demonstrate that such thin films are promising candidates to tune and control the thermal radiation of an underlying hot body with different emissivity features. In particular, we studied two different heat sources with completely different emissivity features, i.e. a black body-like and a mirror-like heated body. The infrared emission characteristics were investigated in the 3.5–5.1 μm spectral range using the infrared thermography technique which included heating the sample, and then cooling back. Experimental results were theoretically analyzed by modelling the VO2 film as a metamaterial for a temperature range close to its critical temperature. Our systematic study reveals that VO2 thin films with just one layer 80 nm thick has the potential to develop completely different dynamic tuning of infrared radiation, enabling both black-body emission suppression and as well as mirror emissivity boosting, in the same single layer device. Understanding the dynamics and effects of thermal tuning on infrared emission will benefit wide range of infrared technologies including thermal emitters, sensors, active IR filters and detectors.
Force–frequency relationship during fatiguing contractions of rat medial gastrocnemius muscle
Authors: MacDougall Keenan B. , Devrome Andrea N. , Kristensen Anders M. , MacIntosh Brian R. 
Published: July 2020

AbstractThe force–frequency relationship presents the amount of force a muscle can produce as a function of the frequency of activation. During repetitive muscular contractions, fatigue and potentiation may both impact the resultant contractile response. However, both the apparent fatigue observed, and the potential for activity-dependent potentiation can be affected by the frequency of activation. Thus, we wanted to explore the effects that repetitive stimulation had on the force–frequency relationship. The force–frequency relationship of the rat medial gastrocnemius muscle was investigated during consecutive bouts of increasing fatigue with 20 to 100 Hz stimulation. Force was measured prior to the fatiguing protocol, during each of three levels of fatigue, and after 30 min of recovery. Force at each frequency was quantified relative to the pre-fatigued 100 Hz contractions, as well as the percentage reduction of force from the pre-fatigued level at a given frequency. We observed less reduction in force at low frequencies compared to high frequencies, suggesting an interplay of fatigue and potentiation, in which potentiation can “protect” against fatigue in a frequency-dependent manner. The exact mechanism of fatigue is unknown, however the substantial reduction of force at high frequency suggests a role for reduced force per cross-bridge.
Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells
Authors: Poisa-Beiro Laura , Thoma Judith , Landry Jonathan , Sauer Sven , Yamamoto Akihisa , Eckstein Volker , Romanov Natalie , Raffel Simon , Hoffmann Georg F. , Bork Peer , Benes Vladimir , Gavin Anne-Claude , Tanaka Motomu , Ho Anthony D. 
Published: July 2020

AbstractInspired by recent proteomic data demonstrating the upregulation of carbon and glycogen metabolism in aging human hematopoietic stem and progenitor cells (HPCs, CD34+ cells), this report addresses whether this is caused by elevated glycolysis of the HPCs on a per cell basis, or by a subpopulation that has become more glycolytic. The average glycogen content in individual CD34+ cells from older subjects (> 50 years) was 3.5 times higher and more heterogeneous compared to younger subjects (< 35 years). Representative glycolytic enzyme activities in HPCs confirmed a significant increase in glycolysis in older subjects. The HPCs from older subjects can be fractionated into three distinct subsets with high, intermediate, and low glucose uptake (GU) capacity, while the subset with a high GU capacity could scarcely be detected in younger subjects. Thus, we conclude that upregulated glycolysis in aging HPCs is caused by the expansion of a more glycolytic HPC subset. Since single-cell RNA analysis has also demonstrated that this subpopulation is linked to myeloid differentiation and increased proliferation, isolation and mechanistic characterization of this subpopulation can be utilized to elucidate specific targets for therapeutic interventions to restore the lineage balance of aging HPCs.
Combined use of GM2AP and TCP1-eta urinary levels predicts recovery from intrinsic acute kidney injury
Authors: Blanco-Gozalo Víctor , Casanova Alfredo G. , Sancho-Martínez Sandra M. , Prieto Marta , Quiros Yaremi , Morales Ana I. , Martínez-Salgado Carlos , Agüeros-Blanco Consuelo , Benito-Hernández Adalberto , Ramos-Barron María A. , Gómez-Alamillo Carlos , Arias Manuel , López-Hernández Francisco J. 
Published: July 2020

AbstractDeficient recovery from acute kidney injury (AKI) has immediate and long-term health, clinical and economic consequences. Pre-emptive recovery estimation may improve nephrology referral, optimize decision making, enrollment in trials, and provide key information for subsequent clinical handling and follow-up. For this purpose, new biomarkers are needed that predict outcome during the AKI episode. We hypothesized that damage pattern-specific biomarkers are expected to more closely associate to outcome within distinct subpopulations (i.e. those affected by specific pathological processes determining a specific outcome), as biomarker pleiotropy (i.e. associated to phenomena unrelated to AKI) introduced by unselected, heterogeneous populations may blur statistics. A panel of urinary biomarkers was measured in patients with AKI and their capacity to associate to normal or abnormal recovery was studied in the whole cohort or after sub-classification by AKI etiology, namely pre-renal and intrinsic AKI. A combination of urinary GM2AP and TCP1-eta best associates with recovery from AKI, specifically within the sub-population of renal AKI patients. This two-step strategy generates a multidimensional space in which patients with specific characteristics (i.e. renal AKI patients with good or bad prognosis) can be identified based on a collection of biomarkers working serially, applying pathophysiology-driven criteria to estimate AKI recovery, to facilitate pre-emptive and personalized handling.
Simultaneous wide-field imaging of phase and magnitude of AC magnetic signal using diamond quantum magnetometry
Authors: Mizuno Kosuke , Ishiwata Hitoshi , Masuyama Yuta , Iwasaki Takayuki , Hatano Mutsuko 
Published: July 2020

AbstractSpectroscopic analysis of AC magnetic signal using diamond quantum magnetometry is a promising technique for inductive imaging. Conventional dynamic decoupling like XY8 provides a high sensitivity of an oscillating magnetic signal with intricate dependence on magnitude and phase, complicating high throughput detection of each parameter. In this study, a simple measurement scheme for independent and simultaneous detection of magnitude and phase is demonstrated by a sequential measurement protocol. Wide-field imaging experiment was performed for an oscillating magnetic field with approximately $$100\,\upmu \hbox {m}$$100μm-squared observation area. Single pixel phase precision was $$2.1^{\circ }$$2.1∘ for $$0.76\,\upmu \hbox {T}$$0.76μT AC magnetic signal. Our method enables potential applications including inductive inspection and impedance imaging.
Uranium-free X solution: a new generation contrast agent for biological samples ultrastructure
Authors: Moscardini Aldo , Di Pietro Sebastiano , Signore Giovanni , Parlanti Paola , Santi Melissa , Gemmi Mauro , Cappello Valentina 
Published: July 2020

AbstractBiological samples are mainly composed of elements with a low atomic number which show a relatively low electron scattering power. For Transmission Electron Microscopy analysis, biological samples are generally embedded in resins, which allow thin sectioning of the specimen. Embedding resins are also composed by light atoms, thus the contrast difference between the biological sample and the surrounding resin is minimal. Due to that reason in the last decades, several staining solutions and approaches, performed with heavy metal salts, have been developed with the purpose of enhancing both the intrinsic sample contrast and the differences between the sample and resin. The best staining was achieved with the uranyl acetate (UA) solution, which has been the election method for the study of morphology in biological samples. More recently several alternatives for UA have been proposed to get rid of its radiogenic issues, but to date none of these solutions has achieved efficiencies comparable to UA. In this work, we propose a different staining solution (X Solution or X SOL), characterized by lanthanide polyoxometalates (LnPOMs) as heavy atoms source, which could be used alternatively to UA in negative staining (NS), in en bloc staining, and post sectioning staining (PSS) of biological samples. Furthermore, we show an extensive chemical characterization of the LnPOM species present in the solution and the detailed work for its final formulation, which brought remarkable results, and even better performances than UA.
Clinical significance of miR-1180-3p in hepatocellular carcinoma: a study based on bioinformatics analysis and RT-qPCR validation
Authors: Zhou Zihan , Zhou Xianguo , Jiang Yanji , Qiu Moqin , Liang Xiumei , Lin Qiuling , Guo Qian , Nong Cunli , Huo Rongrui , Chen Qian , Liu Haizhou , Liu Yingchun , Zhu Shaoliang , Wang Mengyun , Yu Hongping 
Published: July 2020

AbstractmiRNAs play an indispensable role in human carcinogenesis. Dysregulated miR-1180-3p has been observed in several types of cancer, including hepatocellular carcinoma (HCC). This study intends to correlate the expression level of miR-1180-3p with clinical features and overall survival in HCC patients. The expression and clinical significance of miR-1180-3p, selected from GEO and TCGA databases, were verified using an RT-qPCR method. The target genes of miR-1180-3p were obtained using 3 miRNA target gene prediction databases, and their functions were analyzed using the online tool WebGestalt. miR-1180-3p expression was significantly upregulated in 88 HCC tissues compared with non-tumor liver tissues (0.004 ± 0.009 vs. 0.002 ± 0.002, t = − 2.099, P = 0.038). Additionally, we found that the expression levels of miR-1180-3p were significantly correlated with tumor number (χ2 = 9.157, P = 0.006) and MVI (χ2 = 11.354, P = 0.003). Based on Kaplan–Meier analysis, patients with high miR-1180 expression had a shorter overall survival than those with low miR-1180-3p expression (P = 0.002). Furthermore, multivariate Cox analyses indicated that miR-1180-3p expression was an independent prognostic factor for overall survival (HR = 13.36, 95% CI 1.16, 153.69, P = 0.038). In addition, a total of 733 target genes of miR-1180-3p were found from three prediction databases. The GO analyses demonstrated that the target genes were closely related to the proliferation and malignancy of tumors. The KEGG analysis showed that target genes were enriched in several key cancer-related signaling pathways, including the Pathways in cancer, the Ras signaling pathway, and the MAPK signaling pathway. In conclusion, we demonstrate that miR-1180-3p is upregulated in HCC and is associated with a poor prognosis. Thus, miR-1180-3p might be useful as a prognostic marker for HCC.
Biomass addition alters community assembly in ultrafiltration membrane biofilms
Authors: Silva Marisa O. D. , Pernthaler Jakob 
Published: July 2020

AbstractFreshwater biofilms assemble from a pool of rare water column genotypes. Random density fluctuations and temporal species turnover of functionally equivalent potential colonizers result in compositional variability of newly formed biofilm communities. We hypothesized that stronger environmental filtering as induced by enhanced substrate levels might reduce the impact of a locally variable pool of colonizers and instead select for more universal habitat specialists. Our model were heterotrophic biofilms that form on membranes during gravity-driven ultrafiltration of lake water. In four separate experiments, biomass of the cyanobacterium Microcystis was added to the feed water of one set of treatments (BM) and the resulting biofilm communities were compared to unamended controls (CTRL). Biomass addition led to a significant shift of community assembly processes: Replicate BM biofilms were more similar to each other than by chance in 3 of 4 experiments, whereas the opposite was the case for CTRL communities. Moreover, BM communities were more stochastically assembled across experiments from a common ‘regional’ pool of biofilm colonizers, whereas the composition of CTRL communities was mainly determined by experiment-specific ‘local’ genotypes. Interestingly, community assembly processes were also related to both, physiology (aerobic vs. anaerobic lifestyle) and the phylogenetic affiliation of biofilm bacteria.
Standardization procedure for flow cytometry data harmonization in prospective multicenter studies
Authors: Le Lann Lucas , Jouve Pierre-Emmanuel , Alarcón-Riquelme Marta , Jamin Christophe , Pers Jacques-Olivier ,   PRECISESADS Flow Cytometry Study Group, Alvarez Montserrat , Alvarez-Errico Damiana , Azevedo Nancy , Barbarroja Nuria , Buttgereit Anne , Cheng Qingyu , Chizzolini Carlo , Cremer Jonathan , De Groof Aurélie , De Langhe Ellen , Ducreux Julie , Dufour Aleksandra , Gerl Velia , Hernandez-Fuentes Maria , Khodadadi Laleh , Kniesch Katja , Li Tianlu , Lopez-Pedrera Chary , Makowska Zuzanna , Marañón Concepción , Muchmore Brian , Neves Esmeralda , Rouvière Bénédicte , Simon Quentin , Trombetta Elena , Varela Nieves , Witte Torsten ,   PRECISESADS Clinical Consortium, Aguilar-Quesada Rocío , Aguirre-Zamorano Maria Angeles , Almeida Isabel , Baerlecken Niklas , Balog Attila , Belz Doreen , Beretta Lorenzo , Alonso Ricardo Blanco , Bocskai Márta , Brandão Mariana , Rubio José Luis Callejas , Campar Ana , Castro-Villegas Maria-Carmen , Cervera Ricardo , Collantes Eduardo , Cornec Divi , Martínez Alfonso Corrales , Deák Magdolna , Devauchelle-Pensec Valérie , Dulic Sonja , Escudero-Contreras Alejandro , Espinosa Gerard , Faria Raquel , Farinha Fátima , Roldán María Concepción Fernández , Anjos Tania Gomes , González-Gay Miguel A. , Hiepe Falk , Hunzelmann Nicolas , Jousse-Joulin Sandrine , Kádár Gabriella , Kovács Laszló , Lauwerys Bernard , Lehner Michaela , López-Berrio Antonio , Lories Rik , Marinho António , Marovac Jacqueline , Meroni Pier Luigi , Miranda Blanca , Moleón Immaculada Jiménez , Navarro-Linares Héctor , Ortega-Castro Rafaela , Ortego Norberto , Garrido Enrique Ramón , Raya Enrique , Fernández Raquel Ríos , Rodríguez-Pintó Ignasi , Saraux Alain , Stummvoll Georg , Vasconcelos Carlos , Zauner Michael 
Published: July 2020

AbstractOne of the most challenging objective for clinical cytometry in prospective multicenter immunomonitoring trials is to compare frequencies, absolute numbers of leukocyte populations and further the mean fluorescence intensities of cell markers, especially when the data are generated from different instruments. Here, we describe an innovative standardization workflow to compare all data to carry out any large-scale, prospective multicentric flow cytometry analysis whatever the duration, the number or type of instruments required for the realization of such projects.