bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze)
Authors: Parmar Rajni , Seth Romit , Sharma Ram Kumar 
Published: January 2022

AbstractTea, being one of the most popular beverages requires large set of molecular markers for genetic improvement of quality, yield and stress tolerance. Identification of functionally relevant microsatellite or simple sequence repeat (SSR) marker resources from regulatory “Transcription factor (TF) genes” can be potential targets to expedite molecular breeding efforts. In current study, 2776 transcripts encoding TFs harbouring 3687 SSR loci yielding 1843 flanking markers were identified from traits specific transcriptome resource of 20 popular tea cultivars. Of these, 689 functionally relevant SSR markers were successfully validated and assigned to 15 chromosomes (Chr) of CSS genome. Interestingly, 589 polymorphic markers including 403 core-set of TF-SSR markers amplified 2864 alleles in key TF families (bHLH, WRKY, MYB-related, C2H2, ERF, C3H, NAC, FAR1, MYB and G2-like). Their significant network interactions with key genes corresponding to aroma, quality and stress tolerance suggests their potential implications in traits dissection. Furthermore, single amino acid repeat reiteration in CDS revealed presence of favoured and hydrophobic amino acids. Successful deployment of markers for genetic diversity characterization of 135 popular tea cultivars and segregation in bi-parental population suggests their wider utility in high-throughput genotyping studies in tea.
Working memory and pattern separation in founder strains of the BXD recombinant inbred mouse panel
Authors: Dickson Price E. , Mittleman Guy 
Published: January 2022

AbstractWorking memory and pattern separation are fundamental cognitive abilities which, when impaired, significantly diminish quality of life. Discovering genetic mechanisms underlying innate and disease-induced variation in these cognitive abilities is a critical step towards treatments for common and devastating neurodegenerative conditions such as Alzheimer's disease. In this regard, the trial-unique nonmatching-to-location assay (TUNL) is a touchscreen operant conditioning procedure allowing simultaneous quantification of working memory and pattern separation in mice and rats. In the present study, we used the TUNL assay to quantify these cognitive abilities in C57BL/6J and DBA/2J mice. These strains are the founders of the BXD recombinant inbred mouse panel which enables discovery of genetic mechanisms underlying phenotypic variation. TUNL testing revealed that pattern separation was significantly influenced by mouse strain, whereas working memory was not. Moreover, horizontal distance and vertical distance between choice-phase stimuli had dissociable effects on TUNL performance. These findings provide novel data on mouse strain differences in pattern separation and support previous findings of equivalent working memory performance in C57BL/6J and DBA/2J mice. Although working memory of the BXD founder strains was equivalent in this study, working memory of BXD strains may be divergent because of transgressive segregation. Collectively, data presented here indicate that pattern separation is heritable in the mouse and that the BXD panel can be used to identify mechanisms underlying variation in pattern separation.
Functional assays of non-canonical splice-site variants in inherited retinal dystrophies genes
Authors: Rodriguez-Muñoz Ana , Liquori Alessandro , García-Bohorquez Belén , Jaijo Teresa , Aller Elena , Millán José M. , García-García Gema 
Published: January 2022

AbstractInherited retinal dystrophies are a group of disorders characterized by the progressive degeneration of photoreceptors leading to loss of the visual function and eventually to legal blindness. Although next generation sequencing (NGS) has revolutionized the molecular diagnosis of these diseases, the pathogenicity of some mutations casts doubts. After the screening of 208 patients with a panel of 117 genes, we obtained 383 variants that were analysed in silico with bioinformatic prediction programs. Based on the results of these tools, we selected 15 variants for their functional assessment. Therefore, we carried out minigene assays to unveil whether they could affect the splicing of the corresponding gene. As a whole, seven variants were found to induce aberrant splicing in the following genes: BEST1, CACNA2D4, PRCD, RIMS1, FSCN2, MERTK and MAK. This study shows the efficacy of a workflow, based on the association of the Minimum Allele Frequency, family co-segregation, in silico predictions and in vitro assays to determine the effect of potential splice site variants identified by DNA-based NGS. These findings improve the molecular diagnosis of inherited retinal dystrophies and will allow some patients to benefit from the upcoming gene-based therapeutic strategies.
Transcranial direct current stimulation (tDCS) reduces motivation to drink ethanol and reacquisition of ethanol self-administration in female mice
Authors: Pedron Solène , Dumontoy Stéphanie , González-Marín Maria del Carmen , Coune Fabien , Van Schuerbeek Andries , Haffen Emmanuel , Naassila Mickael , Van Waes Vincent 
Published: January 2022

AbstractTranscranial direct current stimulation (tDCS) is an emerging noninvasive brain neuromodulation technique aimed at relieving symptoms associated with psychiatric disorders, including addiction. The goal of the present study was to better identify which phase of alcohol-related behavior (hedonic effect, behavioral sensitization, self-administration, or motivation to obtain the drug) might be modulated by repeated anodal tDCS over the frontal cortex (0.2 mA, 20 min, twice a day for 5 consecutive days), using female mice as a model. Our data showed that tDCS did not modulate the hedonic effects of ethanol as assessed by a conditioned place preference test (CPP) or the expression of ethanol-induced behavioral sensitization. Interestingly, tDCS robustly reduced reacquisition of ethanol consumption (50% decrease) following extinction of self-administration in an operant paradigm. Furthermore, tDCS significantly decreased motivation to drink ethanol on a progressive ratio schedule (30% decrease). Taken together, our results show a dissociation between the effects of tDCS on “liking” (hedonic aspect; no effect in the CPP) and “wanting” (motivation; decreased consumption on a progressive ratio schedule). Our tDCS procedure in rodents will allow us to better understand its mechanisms of action in order to accelerate its use as a complementary and innovative tool to help alcohol-dependent patients maintain abstinence or reduce ethanol intake.
Calpain-mediated protein targets in cardiac mitochondria following ischemia–reperfusion
Authors: Li Ling , Thompson Jeremy , Hu Ying , Lesnefsky Edward J. , Willard Belinda , Chen Qun 
Published: January 2022

AbstractCalpain 1 and 2 (CPN1/2) are calcium-dependent cysteine proteases that exist in cytosol and mitochondria. Pharmacologic inhibition of CPN1/2 decreases cardiac injury during ischemia (ISC)–reperfusion (REP) by improving mitochondrial function. However, the protein targets of CPN1/2 activation during ISC–REP are unclear. CPN1/2 include a large subunit and a small regulatory subunit 1 (CPNS1). Genetic deletion of CPNS1 eliminates the activities of both CPN1 and CPN2. Conditional cardiomyocyte specific CPNS1 deletion mice were used in the present study to clarify the role of CPN1/2 activation in mitochondrial damage during ISC–REP with an emphasis on identifying the potential protein targets of CPN1/2. Isolated hearts from wild type (WT) or CPNS1 deletion mice underwent 25 min in vitro global ISC and 30 min REP. Deletion of CPNS1 led to decreased cytosolic and mitochondrial calpain 1 activation compared to WT. Cardiac injury was decreased in CPNS1 deletion mice following ISC–REP as shown by the decreased infarct size compared to WT. Compared to WT, mitochondrial function was improved in CPNS1 deletion mice following ischemia–reperfusion as shown by the improved oxidative phosphorylation and decreased susceptibility to mitochondrial permeability transition pore opening. H2O2 generation was also decreased in mitochondria from deletion mice following ISC–REP compared to WT. Deletion of CPNS1 also resulted in less cytochrome c and truncated apoptosis inducing factor (tAIF) release from mitochondria. Proteomic analysis of the isolated mitochondria showed that deletion of CPNS1 increased the content of proteins functioning in regulation of mitochondrial calcium homeostasis (paraplegin and sarcalumenin) and complex III activity. These results suggest that activation of CPN1 increases cardiac injury during ischemia–reperfusion by impairing mitochondrial function and triggering cytochrome c and tAIF release from mitochondria into cytosol.
Highly efficient removal of thallium(I) by facilely fabricated amorphous titanium dioxide from water and wastewater
Authors: Zhang Gaosheng , Luo Jinglin , Cao Hanlin , Hu Shengping , Li Huosheng , Wu Zhijing , Xie Yuan , Li Xiangping 
Published: January 2022

AbstractIn this study, amorphous hydrous titanium dioxide was synthesized by a facile precipitation method at room temperature, aiming to effectively remove thallium(I) from water. The titanium dioxide prepared using ammonia as precipitant (TiO2I) is more effective for thallium(I) uptake than the one synthesized with sodium hydroxide (TiO2II). The TiO2 obtained particles are amorphous, aggregates of many nanoparticles and irregular in shape. The thallium(I) uptake increases with the rise of solution pH value. Under neutral pH conditions, the maximal thallium(I) adsorption capacities of TiO2I and TiO2II are 302.6 and 230.3 mg/g, respectively, outperforming most of the reported adsorbents. The amorphous TiO2 has high selectivity towards thallium(I) in the presence of multiple cations such as K+, Ca2+, Mg2+, Zn2+ and Ni2+. Moreover, the TiO2I is efficient in removing thallium(I) from real river water and mining wastewater. Additionally, the spent TiO2I can be regenerated using hydrochloric acid solution and reused. The Tl(I) adsorption is achieved via replacing the H+ in hydroxyl group on the surface of TiO2 and forming inner-sphere surface complexes. Owing to its high efficiency, facile synthesis and environmental friendliness, the TiO2I has the potential to be used as an alternative adsorbent to remove Tl(I) from water.
Comprehensive quantitative analysis of alternative splicing variants reveals the HNF1B mRNA splicing pattern in various tumour and non-tumour tissues
Authors: Hojny Jan , Michalkova Romana , Krkavcova Eva , Bui Quang Hiep , Bartu Michaela , Nemejcova Kristyna , Kalousova Marta , Kleiblova Petra , Dundr Pavel , Struzinska Ivana 
Published: January 2022

AbstractHepatocyte nuclear factor-1-beta (HNF1B) is a transcription factor and putative biomarker of solid tumours. Recently, we have revealed a variety ofHNF1BmRNA alternative splicing variants (ASVs) with unknown, but potentially regulatory, functions. The aim of our work was to quantify the most common variants and compare their expression in tumour and non-tumour tissues of the large intestine, prostate, and kidney. TheHNF1BmRNA variants 3p, Δ7, Δ7–8, and Δ8 were expressed across all the analysed tissues in 28.2–33.5%, 1.5–2%, 0.8–1.7%, and 2.3–6.9% of overallHNF1BmRNA expression, respectively, and occurred individually or in combination. The quantitative changes of ASVs between tumour and non-tumour tissue were observed for the large intestine (3p, Δ7–8), prostate (3p), and kidney samples (Δ7). Decreased expression of the overallHNF1BmRNA in the large intestine and prostate cancer samples compared with the corresponding non-tumour samples was observed (p = 0.019 and p = 0.047, respectively). The decreased mRNA expression correlated with decreased protein expression in large intestine carcinomas (p < 0.001). The qualitative and quantitative pattern of the ASVs studied by droplet digital PCR was confirmed by next-generation sequencing, which suggests the significance of the NGS approach for further massive evaluation of the splicing patterns in a variety of genes.
Three-step matching algorithm to enhance between-group comparability and minimize confounding in comparative effectiveness studies
Authors: Yang Chen-Yi , Kuo Shihchen , Lai Edward Chia-Cheng , Ou Huang-Tz 
Published: January 2022

AbstractWe developed a three-step matching algorithm to enhance the between-group comparability for comparative drug effect studies involving prevalent new-users of the newer study drug versus older comparator drug(s). The three-step matching scheme is to match on: (1) index date of initiating the newer study drug to align the cohort entry time between study groups, (2) medication possession ratio measures that consider prior exposure to all older comparator drugs, and (3) propensity scores estimated from potential confounders. Our approach is illustrated with a comparative cardiovascular safety study of glucagon-like peptide-1 receptor agonist (GLP-1ra) versus sulfonylurea (SU) in type 2 diabetes patients using Taiwan’s National Health Insurance Research Database 2003–2015. 66% of 3195 GLP-1ra users had previously exposed to SU. The between-group comparability was well-achieved after implementing the matching algorithm (i.e., standardized mean difference < 0.2 for all baseline patient characteristics). Compared to SU, the use of GLP-1ra yielded a significantly reduced risk of the primary composite cardiovascular events (hazard ratio [95% confidence interval]: 0.71 [0.54–0.95],p = 0.022). Our matching scheme can enhance the between-group comparability in prevalent new-user cohort designs to minimize time-related bias, improve confounder adjustment, and ensure the reliability and validity of study findings.
Intelligent pharmaceutical patent search on a near-term gate-based quantum computer
Authors: Wang Pei-Hua , Chen Jen-Hao , Tseng Yufeng Jane 
Published: January 2022

AbstractPharmaceutical patent analysis is the key to product protection for pharmaceutical companies. In patent claims, a Markush structure is a standard chemical structure drawing with variable substituents. Overlaps between apparently dissimilar Markush structures are nearly unrecognizable when the structures span a broad chemical space. We propose a quantum search-based method which performs an exact comparison between two non-enumerated Markush structures with a constraint satisfaction oracle. The quantum circuit is verified with a quantum simulator and the real effect of noise is estimated using a five-qubit superconductivity-based IBM quantum computer. The possibilities of measuring the correct states can be increased by improving the connectivity of the most computation intensive qubits. Depolarizing error is the most influential error. The quantum method to exactly compares two patents is hard to simulate classically and thus creates a quantum advantage in patent analysis.
Non-invasive metabolomics biomarkers of production efficiency and beef carcass quality traits
Authors: Artegoitia Virginia M. , Newman J. W. , Foote A. P. , Shackelford S. D. , King D. A. , Wheeler T. L. , Lewis R. M. , Freetly H. C. 
Published: January 2022

AbstractThe inter-cattle growth variations stem from the interaction of many metabolic processes making animal selection difficult. We hypothesized that growth could be predicted using metabolomics. Urinary biomarkers of cattle feed efficiency were explored using mass spectrometry-based untargeted and targeted metabolomics. Feed intake and weight-gain was measured in steers (n = 75) on forage-based growing rations (stage-1, 84 days) followed by high-concentrate finishing rations (stage-2, 84 days). Urine from days 0, 21, 42, 63, and 83 in each stage were analyzed from steers with the greater (n = 14) and least (n = 14) average-daily-gain (ADG) and comparable dry-matter-intake (DMI; within 0.32 SD of the mean). Steers were slaughtered after stage-2. Adjusted fat-thickness and carcass-yield-grade increased in greater-ADG-cattle selected in stage-1, but carcass traits did not differ between ADG-selected in stage-2. Overall 85 untargeted metabolites segregated greater- and least-ADG animals, with overlap across diets (both stages) and breed type, despite sampling time effects. Total 18-bile acids (BAs) and 5-steroids were quantified and associated with performance and carcass quality across ADG-classification depending on the stage. Stepwise logistic regression of urinary BA and steroids had > 90% accuracy identifying efficient-ADG-steers. Urine metabolomics provides new insight into the physiological mechanisms and potential biomarkers for feed efficiency.
Predicting pathogenicity for novel hearing loss mutations based on genetic and protein structure approaches
Authors: Buonfiglio Paula I. , Bruque Carlos D. , Lotersztein Vanesa , Luce Leonela , Giliberto Florencia , Menazzi Sebastián , Francipane Liliana , Paoli Bibiana , Goldschmidt Ernesto , Elgoyhen Ana Belén , Dalamón Viviana 
Published: January 2022

AbstractHearing loss is a heterogeneous disorder. Identification of causative mutations is demanding due to genetic heterogeneity. In this study, we investigated the genetic cause of sensorineural hearing loss in patients with severe/profound deafness. After the exclusion of GJB2-GJB6 mutations, we performed whole exome sequencing in 32 unrelated Argentinean families. Mutations were detected in 16 known deafness genes in 20 patients: ACTG1, ADGRV1 (GPR98), CDH23, COL4A3, COL4A5, DFNA5 (GSDDE), EYA4, LARS2, LOXHD1, MITF, MYO6, MYO7A, TECTA, TMPRSS3, USH2A and WSF1. Notably, 11 variants affecting 9 different non-GJB2 genes resulted novel: c.12829C > T, p.(Arg4277*) in ADGRV1; c.337del, p.(Asp109*) and c.3352del, p.(Gly1118Alafs*7) in CDH23; c.3500G > A, p.(Gly1167Glu) in COL4A3; c.1183C > T, p.(Pro395Ser) and c.1759C > T, p.(Pro587Ser) in COL4A5; c.580 + 2 T > C in EYA4; c.1481dup, p.(Leu495Profs*31) in LARS2; c.1939 T > C, p.(Phe647Leu), in MYO6; c.733C > T, p.(Gln245*) in MYO7A and c.242C > G, p.(Ser81*) in TMPRSS3 genes. To predict the effect of these variants, novel protein modeling and protein stability analysis were employed. These results highlight the value of whole exome sequencing to identify candidate variants, as well as bioinformatic strategies to infer their pathogenicity.
Single-cell transcriptomics defines keratinocyte differentiation in avian scutate scales
Authors: Lachner Julia , Ehrlich Florian , Wielscher Matthias , Farlik Matthias , Hermann Marcela , Tschachler Erwin , Eckhart Leopold 
Published: January 2022

AbstractThe growth of skin appendages, such as hair, feathers and scales, depends on terminal differentiation of epidermal keratinocytes. Here, we investigated keratinocyte differentiation in avian scutate scales. Cells were isolated from the skin on the legs of 1-day old chicks and subjected to single-cell transcriptomics. We identified two distinct populations of differentiated keratinocytes. The first population was characterized by mRNAs encoding cysteine-rich keratins and corneous beta-proteins (CBPs), also known as beta-keratins, of the scale type, indicating that these cells form hard scales. The second population of differentiated keratinocytes contained mRNAs encoding cysteine-poor keratins and keratinocyte-type CBPs, suggesting that these cells form the soft interscale epidermis. We raised an antibody against keratin 9-like cysteine-rich 2 (KRT9LC2), which is encoded by an mRNA enriched in the first keratinocyte population. Immunostaining confirmed expression of KRT9LC2 in the suprabasal epidermal layers of scutate scales but not in interscale epidermis. Keratinocyte differentiation in chicken leg skin resembled that in human skin with regard to the transcriptional upregulation of epidermal differentiation complex genes and genes involved in lipid metabolism and transport. In conclusion, this study defines gene expression programs that build scutate scales and interscale epidermis of birds and reveals evolutionarily conserved keratinocyte differentiation genes.
Homogeneity of Arabian Peninsula dromedary camel populations with signals of geographic distinction based on whole genome sequence data
Authors: Bahbahani Hussain , Almathen Faisal 
Published: January 2022

AbstractDromedary camels in the Arabian Peninsula distribute along different geographical and ecological locations, e.g. desert, mountains and coasts. Here, we are aiming to explore the whole genome sequence data of ten dromedary populations from the Arabian Peninsula to assess their genetic structure, admixture levels, diversity and similarity indices. Upon including reference dromedary and Bactrian camel populations from Iran and Kazakhstan, we characterise inter-species and geographic genetic distinction between the dromedary and the Bactrian camels. Individual-based alpha genetic diversity profiles are found to be generally higher in Bactrian camels than dromedary populations, with the exception of five autosomes (NC_044525.1, NC_044534.1, NC_044540.1, NC_044542.1, NC_044544.1) at diversity orders (q ≥ 2). The Arabian Peninsula camels are generally homogenous, with a small degree of genetic distinction correlating with three geographic groups: North, Central and West; Southwest; and Southeast of the Arabian Peninsula. No significant variation in diversity or similarity indices are observed among the different Arabian Peninsula dromedary populations. This study contributes to our understanding of the genetic diversity of Arabian Peninsula dromedary camels. It will help conserve the genetic stock of this species and support the design of breeding programmes for genetic improvement of favorable traits.
Elucidation of contact state on various rough surfaces via highly robust colorimetric optical interferometry
Authors: Tomota Tatsunori , Tohyama Mamoru , Yagi Kazuyuki 
Published: January 2022

AbstractIn this study, we developed and practiced colorimetric optical interferometry for the direct observation of contact states to clarify contact phenomena. We theoretically demonstrated that the effect of roughness diffuse reflection could be neglected using interferometric light intensity according to the relationship between the optical film thickness and hue. Then, we measured the static contact surfaces of spherical test pieces of different root mean square roughnesses. Results indicate that the nominal contact area is significantly larger than that obtained from the Hertzian theory of smooth contact as the surface roughness increases. The contact film thickness on the nominal contact area increases almost in proportion to the root mean square roughness. Our experiment supports the validity of the contact theory and contact simulation with very small roughnesses, which have been difficult to verify experimentally. The advantage of this measurement is that it can simultaneously capture the macroscopic contact area and microscopic film thickness distribution, which is expected to further expand the range of application.