bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomic analysis for identification of candidate sex-related genes and pathways in Crimson seabream (Parargyrops edita)
Authors: Shan Binbin , Liu Yan , Yang Changping , Zhao Yu , Sun Dianrong 
Published: January 2021

AbstractTeleost fishes display the largest array of sex-determining systems among animals, resulting in various reproductive strategies. Research on sex-related genes in teleosts will broaden our understanding of the process, and provide important insight into the plasticity of the sex determination process in vertebrates in general. Crimson seabream (Parargyrops edita Tanaka, 1916) is one of the most valuable and abundant fish resources throughout Asia. However, little genomic information on P. edita is available. In the present study, the transcriptomes of male and female P. edita were sequenced with RNA-seq technology. A total of 388,683,472 reads were generated from the libraries. After filtering and assembling, a total of 79,775 non redundant unigenes were obtained with an N50 of 2,921 bp. The unigenes were annotated with multiple public databases, including NT (53,556, 67.13%), NR (54,092, 67.81%), Swiss-Prot (45,265, 56.74%), KOG (41,274, 51.74%), KEGG (46,302, 58.04%), and GO (11,056, 13.86%) databases. Comparison of the unigenes of different sexes of P. edita revealed that 11,676 unigenes (9,335 in females, 2,341 in males) were differentially expressed between males and females. Of these, 5,463 were specifically expressed in females, and 1,134 were specifically expressed in males. In addition, the expression levels of ten unigenes were confirmed to validate the transcriptomic data by qRT-PCR. Moreover, 34,473 simple sequence repeats (SSRs) were identified in SSR-containing sequences, and 50 loci were randomly selected for primer development. Of these, 36 loci were successfully amplified, and 19 loci were polymorphic. Finally, our comparative analysis identified many sex-related genes (zps, amh, gsdf, sox4, cyp19a, etc.) and pathways (MAPK signaling pathway, p53 signaling pathway, etc.) of P. edita. This informative transcriptomic analysis provides valuable data to increase genomic resources of P. edita. The results will be useful for clarifying the molecular mechanism of sex determination and for future functional analyses of sex-associated genes.
A randomized clinical trial on the effect of a lidocaine patch on shoulder pain relief in laparoscopic cholecystectomy
Authors: Kim Ha Yeon , Choi Jong Bum , Min Sang Kee , Chang Min Ying , Lim Gang Mee , Kim Ji Eun 
Published: January 2021

AbstractThe incidence of laparoscopy-related shoulder pain reaches 90% in women. We evaluated the effect of lidocaine patch 5% on the shoulder pain after laparoscopic cholecystectomy (LC) in female patients. Total 63 female patients were randomly allocated to patch group (n = 31) and control group (n = 32). Patch group received lidocaine patch 5% and dressing retention tape on both shoulder, and control group received only dressing retention tape. Abdominal and shoulder pains were evaluated with rating on numeric rating scale (0 = no pain and 10 = the worst pain) at baseline and at 30 min, 6 h, 24 h, and 48 h after surgery. There were no significant differences in patient characteristics and operation details. The overall incidence of shoulder pain was significantly lower in patch group than in control group (42% vs. 78%, P = 0.005). The severity of shoulder pain also was significantly reduced in patch group compared to control group at 24 h and 48 h after surgery (P = 0.01 and P = 0.015, respectively). Complications related to lidocaine patch were not found except nausea. Lidocaine patch 5% reduced the incidence and severity of postoperative shoulder pain in female patients undergoing LC without complications.
Exosite inhibition of ADAMTS-5 by a glycoconjugated arylsulfonamide
Authors: Santamaria Salvatore , Cuffaro Doretta , Nuti Elisa , Ciccone Lidia , Tuccinardi Tiziano , Liva Francesca , D’Andrea Felicia , de Groot Rens , Rossello Armando , Ahnström Josefin 
Published: January 2021

AbstractADAMTS-5 is a major protease involved in the turnover of proteoglycans such as aggrecan and versican. Dysregulated aggrecanase activity of ADAMTS-5 has been directly linked to the etiology of osteoarthritis (OA). For this reason, ADAMTS-5 is a pharmaceutical target for the treatment of OA. ADAMTS-5 shares high structural and functional similarities with ADAMTS-4, which makes the design of selective inhibitors particularly challenging. Here we exploited the ADAMTS-5 binding capacity of β-N-acetyl-d-glucosamine to design a new class of sugar-based arylsulfonamides. Our most promising compound, 4b, is a non-zinc binding ADAMTS-5 inhibitor which showed high selectivity over ADAMTS-4. Docking calculations combined with molecular dynamics simulations demonstrated that 4b is a cross-domain inhibitor that targets the interface of the metalloproteinase and disintegrin-like domains. Furthermore, the interaction between 4b and the ADAMTS-5 Dis domain is mediated by hydrogen bonds between the sugar moiety and two lysine residues (K532 and K533). Targeted mutagenesis of these two residues confirmed their importance both for versicanase activity and inhibitor binding. This positively-charged cluster of ADAMTS-5 represents a previously unknown substrate-binding site (exosite) which is critical for substrate recognition and can therefore be targeted for the development of selective ADAMTS-5 inhibitors.
De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa
Authors: Zhang Cuiping , Wu Zhonglan , Jiang Xinqiang , Li Wei , Lu Yizeng , Wang Kuiling 
Published: January 2021

AbstractStephanandra incisa is a wild-type shrub with beautiful leaves and white flowers and is commonly used as a garden decoration accessory. However, the limited availability of genomic data of S. incisa has restricted its breeding process. Here, we identified EST-SSR markers using de novo transcriptome sequencing. In this study, a transcriptome database containing 35,251 unigenes, having an average length of 985 bp, was obtained from S. incisa. From these unigene sequences, we identified 5,555 EST-SSRs, with a distribution density of one SSR per 1.60 kb. Dinucleotides (52.96%) were the most detected SSRs, followed by trinucleotides (34.64%). From the EST-SSR loci, we randomly selected 100 sites for designing primer and used the DNA of 60 samples to verify the polymorphism. The average value of the effective number of alleles (Ne), Shannon’s information index (I), and expective heterozygosity (He) was 1.969, 0.728, and 0.434, respectively. The polymorphism information content (PIC) value was in the range of 0.108 to 0.669, averaging 0.406, which represented a middle polymorphism level. Cluster analysis of S. incisa were also performed based on the obtained EST-SSR data in our work. As shown by structure analysis, 60 individuals could be classified into two groups. Thus, the identification of these novel EST-SSR markers provided valuable sequence information for analyzing the population structure, genetic diversity, and genetic resource assessment of S. incisa and other related species.
Multi-critical topological transition at quantum criticality
Authors: Kumar Ranjith R. , Kartik Y. R. , Rahul S. , Sarkar Sujit 
Published: January 2021

AbstractThe investigation and characterization of topological quantum phase transition between gapless phases is one of the recent interest of research in topological states of matter. We consider transverse field Ising model with three spin interaction in one dimension and observe a topological transition between gapless phases on one of the critical lines of this model. We study the distinct nature of these gapless phases and show that they belong to different universality classes. The topological invariant number (winding number) characterize different topological phases for the different regime of parameter space. We observe the evidence of two multi-critical points, one is topologically trivial and the other one is topologically active. Topological quantum phase transition between the gapless phases on the critical line occurs through the non-trivial multi-critical point in the Lifshitz universality class. We calculate and analyze the behavior of Wannier state correlation function close to the multi-critical point and confirm the topological transition between gapless phases. We show the breakdown of Lorentz invariance at this multi-critical point through the energy dispersion analysis. We also show that the scaling theories and curvature function renormalization group can also be effectively used to understand the topological quantum phase transitions between gapless phases. The model Hamiltonian which we study is more applicable for the system with gapless excitations, where the conventional concept of topological quantum phase transition fails.
Regulation of trehalase activity by multi-site phosphorylation and 14-3-3 interaction
Authors: Dengler Lisa , Örd Mihkel , Schwab Lucca M. , Loog Mart , Ewald Jennifer C. 
Published: January 2021

AbstractProtein phosphorylation enables a rapid adjustment of cellular activities to diverse intracellular and environmental stimuli. Many phosphoproteins are targeted on more than one site, which allows the integration of multiple signals and the implementation of complex responses. However, the hierarchy and interplay between multiple phospho-sites are often unknown. Here, we study multi‐site phosphorylation using the yeast trehalase Nth1 and its activator, the 14-3-3 protein Bmh1, as a model. Nth1 is known to be phosphorylated by the metabolic kinase PKA on four serine residues and by the cell cycle kinase CDK on one residue. However, how these five phospho-sites adjust Nth1 activity remains unclear. Using a novel reporter construct, we investigated the contribution of the individual sites for the regulation of the trehalase and its 14-3-3 interactor. In contrast to the constitutively phosphorylated S20 and S83, the weaker sites S21 and S60 are only phosphorylated by increased PKA activity. For binding Bmh1, S83 functions as the high‐affinity “gatekeeper” site, but successful binding of the Bmh1 dimer and thus Nth1 activation requires S60 as a secondary site. Under nutrient-poor conditions with low PKA activity, S60 is not efficiently phosphorylated and the cell cycle dependent phosphorylation of S66 by Cdk1 contributes to Nth1 activity, likely by providing an alternative Bmh1 binding site. Additionally, the PKA sites S20 and S21 modulate the dephosphorylation of Nth1 on downstream Bmh1 sites. In summary, our results expand our molecular understanding of Nth1 regulation and provide a new aspect of the interaction of 14-3-3 proteins with their targets.
The mammalian efferent vestibular system utilizes cholinergic mechanisms to excite primary vestibular afferents
Authors: Schneider Glenn T. , Lee Choongheon , Sinha Anjali K. , Jordan Paivi M. , Holt Joseph C. 
Published: January 2021

AbstractElectrical stimulation of the mammalian efferent vestibular system (EVS) predominantly excites primary vestibular afferents along two distinct time scales. Although roles for acetylcholine (ACh) have been demonstrated in other vertebrates, synaptic mechanisms underlying mammalian EVS actions are not well-characterized. To determine if activation of ACh receptors account for efferent-mediated afferent excitation in mammals, we recorded afferent activity from the superior vestibular nerve of anesthetized C57BL/6 mice while stimulating EVS neurons in the brainstem, before and after administration of cholinergic antagonists. Using a normalized coefficient of variation (CV*), we broadly classified vestibular afferents as regularly- (CV* < 0.1) or irregularly-discharging (CV* > 0.1) and characterized their responses to midline or ipsilateral EVS stimulation. Afferent responses to efferent stimulation were predominantly excitatory, grew in amplitude with increasing CV*, and consisted of fast and slow components that could be identified by differences in rise time and post-stimulus duration. Both efferent-mediated excitatory components were larger in irregular afferents with ipsilateral EVS stimulation. Our pharmacological data show, for the first time in mammals, that muscarinic AChR antagonists block efferent-mediated slow excitation whereas the nicotinic AChR antagonist DHβE selectively blocks efferent-mediated fast excitation, while leaving the efferent-mediated slow component intact. These data confirm that mammalian EVS actions are predominantly cholinergic.
Transcriptional analysis reveals key insights into seasonal induced anthocyanin degradation and leaf color transition in purple tea (Camellia sinensis (L.) O. Kuntze)
Authors: Maritim Tony Kipkoech , Masand Mamta , Seth Romit , Sharma Ram Kumar 
Published: January 2021

AbstractPurple-tea, an anthocyanin rich cultivar has recently gained popularity due to its health benefits and captivating leaf appearance. However, the sustainability of purple pigmentation and anthocyanin content during production period is hampered by seasonal variation. To understand seasonal dependent anthocyanin pigmentation in purple tea, global transcriptional and anthocyanin profiling was carried out in tea shoots with two leaves and a bud harvested during in early (reddish purple: S1_RP), main (dark gray purple: S2_GP) and backend flush (moderately olive green: S3_G) seasons. Of the three seasons, maximum accumulation of total anthocyanin content was recorded in S2_GP, while least amount was recorded during S3_G. Reference based transcriptome assembly of 412 million quality reads resulted into 71,349 non-redundant transcripts with 6081 significant differentially expressed genes. Interestingly, key DEGs involved in anthocyanin biosynthesis [PAL, 4CL, F3H, DFR and UGT/UFGT], vacuolar trafficking [ABC, MATE and GST] transcriptional regulation [MYB, NAC, bHLH, WRKY and HMG] and Abscisic acid signaling pathway [PYL and PP2C] were significantly upregulated in S2_GP. Conversely, DEGs associated with anthocyanin degradation [Prx and lac], repressor TFs and key components of auxin and ethylene signaling pathways [ARF, AUX/IAA/SAUR, ETR, ERF, EBF1/2] exhibited significant upregulation in S3_G, correlating positively with reduced anthocyanin content and purple coloration. The present study for the first-time elucidated genome-wide transcriptional insights and hypothesized the involvement of anthocyanin biosynthesis activators/repressor and anthocyanin degrading genes via peroxidases and laccases during seasonal induced leaf color transition in purple tea. Futuristically, key candidate gene(s) identified here can be used for genetic engineering and molecular breeding of seasonal independent anthocyanin-rich tea cultivars.
Discovery of a highly potent novel rifampicin analog by preparing a hybrid of the precursors of the antibiotic drugs rifampicin and clofazimine
Authors: Saravanan Pasupathy , Dusthackeer V. N. Azger , Rajmani R. S. , Mahizhaveni B. , Nirmal Christy R. , Rajadas Sam Ebenezer , Bhardwaj Neerupma , Ponnuraja C. , Bhaskar Adhin , Hemanthkumar A. K. , Ramachandran Geetha , Tripathy Srikanth P. 
Published: January 2021

AbstractTuberculosis (TB) is an infectious disease caused by the bacillus Mycobacterium tuberculosis (Mtb). The present work reports the design and synthesis of a hybrid of the precursors of rifampicin and clofazimine, which led to the discovery of a novel Rifaphenazine (RPZ) molecule with potent anti-TB activity. In addition, the efficacy of RPZ was evaluated in-vitro using the reference strain Mtb H37Rv. Herein, 2,3 diamino phenazine, a precursor of an anti-TB drug clofazimine, was tethered to the rifampicin core. This 2,3 diamino phenazine did not have an inherent anti-TB activity even at a concentration of up to 2 µg/mL, while rifampicin did not exhibit any activity against Mtb at a concentration of 0.1 µg/mL. However, the synthesized novel Rifaphenzine (RPZ) inhibited 78% of the Mtb colonies at a drug concentration of 0.1 µg/mL, while 93% of the bacterial colonies were killed at 0.5 µg/mL of the drug. Furthermore, the Minimum Inhibitory Concentration (MIC) value for RPZ was 1 µg/mL. Time-kill studies revealed that all bacterial colonies were killed within a period of 24 h. The synthesized novel molecule was characterized using high-resolution mass spectroscopy and NMR spectroscopy. Cytotoxicity studies (IC50) were performed on human monocytic cell line THP-1, and the determined IC50 value was 96 µg/mL, which is non-cytotoxic.
Performance simulation of polymer-based nanoparticle and void dispersed photonic structures for radiative cooling
Authors: Bijarniya Jay Prakash , Sarkar Jahar , Maiti Pralay 
Published: January 2021

AbstractPassive radiative cooling is an emerging field and needs further development of material. Hence, the computational approach needs to establish for effective metamaterial design before fabrication. The finite difference time domain (FDTD) method is a promising numerical strategy to study electromagnetic interaction with the material. Here, we simulate using the FDTD method and report the behavior of various nanoparticles (SiO2, TiO2, Si3N4) and void dispersed polymers for the solar and thermal infrared spectrums. We propose the algorithm to simulate the surface emissive properties of various material nanostructures in both solar and thermal infrared spectrums, followed by cooling performance estimation. It is indeed found out that staggered and randomly distributed nanoparticle reflects efficiently in the solar radiation spectrum, become highly reflective for thin slab and emits efficiently in the atmospheric window (8–13 µm) over the parallel arrangement with slight variation. Higher slab thickness and concentration yield better reflectivity in the solar spectrum. SiO2-nanopores in a polymer, Si3N4 and TiO2 with/without voids in polymer efficiently achieve above 97% reflection in the solar spectrum and exhibits substrate independent radiative cooling properties. SiO2 and polymer combination alone is unable to reflect as desired in the solar spectrum and need a highly reflective substrate like silver.
Drug related problems in clinical practice: a cross-sectional study on their prevalence, risk factors and associated pharmaceutical interventions
Authors: Garin Noe , Sole Nuria , Lucas Beatriz , Matas Laia , Moras Desiree , Rodrigo-Troyano Ana , Gras-Martin Laura , Fonts Nuria 
Published: January 2021

AbstractDrug-related problems (DRP) cause preventable negative health outcomes, especially during hospital admissions. The aim of our study was to examine the prevalence and characteristics of DRP in regular clinical pharmacy, as well as to determine those factors associated with a higher risk of DRP in the hospital setting. We analyzed data from a standardized registry database of regular pharmacy practice (2015- 2016). DRP were classified according to the Pharmaceutical Care Network Europe v6.2 classification. Cross-sectional data were obtained from 1602 adults admitted to medical wards. Crude and adjusted binary logistic regressions were performed to identify associations between potential risk factors and DRP. Overall DRP prevalence was high across medical specialties (45,1%), in a population characterized by advanced age, polypharmacy and multimorbidity. Problems leading to DRP were mainly classified into two domains (effectiveness and adverse reactions), being drug and dose selection the most frequent causes. Interventions were accepted and DRP were totally or partially solved in 74.1% and 4.81% of cases, respectively. In the adjusted model polypharmacy, allergies, BMI > 25 kg/m2 and clearance < 30 mL/min were associated with a higher risk of DRP. The participation of clinical pharmacists into multidisciplinary teams promotes the detection and solution of DRP. Polypharmacy, obesity, renal impairment and allergy are associated with a higher risk of DRP during admission.
Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery
Authors: Chang Lyra , Campbell James , Raji Idris O. , Guduru Shiva K. R. , Kandel Prasanna , Nguyen Michelle , Liu Steven , Tran Kevin , Venugopal Navneet K. , Taylor Bethany C. , Holt Matthew V. , Young Nicolas L. , Samuel Errol L. G. , Jain Prashi , Santini Conrad , Sankaran Banumathi , MacKenzie Kevin R. , Young Damian W. 
Published: January 2021

AbstractDespite the established roles of the epigenetic factor UHRF1 in oncogenesis, no UHRF1-targeting therapeutics have been reported to date. In this study, we use fragment-based ligand discovery to identify novel scaffolds for targeting the isolated UHRF1 tandem Tudor domain (TTD), which recognizes the heterochromatin-associated histone mark H3K9me3 and supports intramolecular contacts with other regions of UHRF1. Using both binding-based and function-based screens of a ~ 2300-fragment library in parallel, we identified 2,4-lutidine as a hit for follow-up NMR and X-ray crystallography studies. Unlike previous reported ligands, 2,4-lutidine binds to two binding pockets that are in close proximity on TTD and so has the potential to be evolved into more potent inhibitors using a fragment-linking strategy. Our study provides a useful starting point for developing potent chemical probes against UHRF1.
Investigating real-life emotions in romantic couples: a mobile EEG study
Authors: Packheiser Julian , Berretz Gesa , Rook Noemi , Bahr Celine , Schockenhoff Lynn , Güntürkün Onur , Ocklenburg Sebastian 
Published: January 2021

AbstractThe neural basis of emotional processing has been largely investigated in constrained spatial environments such as stationary EEGs or fMRI scanners using highly artificial stimuli like standardized pictures depicting emotional scenes. Typically, such standardized experiments have low ecological validity and it remains unclear whether their results reflect neuronal processing in real-life affective situations at all. Critically, emotional situations do not only encompass the perception of emotions, but also behavioral components associated with them. In this study, we aimed to investigate real-life emotions by recording couples in their homes using mobile EEG technology during embracing, kissing and emotional speech. We focused on asymmetries in affective processing as emotions have been demonstrated to be strongly lateralized in the brain. We found higher alpha and beta power asymmetry during kissing and embracing on frontal electrodes during emotional kisses and speech compared to a neutral control condition indicative of stronger left-hemispheric activation. In contrast, we found lower alpha power asymmetry at parieto-occipital electrode sites in the emotional compared to the neutral condition indicative of stronger right-hemispheric activation. Our findings for alpha power asymmetries are in line with models of emotional lateralization that postulate a valence-specific processing over frontal cortices and right-hemispheric dominance in emotional processing in parieto-occipital regions. In contrast, beta power asymmetries pointed more towards valence-specific processing indicating that, while alpha and beta frequencies seem to be functionally associated, they are not reflecting identical cognitive processing.