bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference standards for accurate validation and optimization of assays that determine integrated lentiviral vector copy number in transduced cells
Authors: Paugh Barbara S. , Baranyi Lajos , Roy Andre , He Hua-Jun , Harris Lindsay , Cole Kenneth D. , Artlip Moria , Raimund Caroline , Langan Patricia S. , Jana Srikanta , Orentas Rimas J. , Lin-Gibson Sheng , Krueger Winfried , Dropulić Boro 
Published: January 2021

AbstractLentiviral vectors (LV) have emerged as a robust technology for therapeutic gene delivery into human cells as advanced medicinal products. As these products are increasingly commercialized, there are concomitant demands for their characterization to ensure safety, efficacy and consistency. Standards are essential for accurately measuring parameters for such product characterization. A critical parameter is the vector copy number (VCN) which measures the genetic dose of a transgene present in gene-modified cells. Here we describe a set of clonal Jurkat cell lines with defined copy numbers of a reference lentiviral vector integrated into their genomes. Genomic DNA was characterized for copy number, genomic integrity and integration coordinates and showed uniform performance across independent quantitative PCR assays. Stability studies during continuous long-term culture demonstrated sustained renewability of the reference standard source material. DNA from the Jurkat VCN standards would be useful for control of quantitative PCR assays for VCN determination in LV gene-modified cellular products and clinical samples.
Association of GZMB polymorphisms and susceptibility to non-segmental vitiligo in a Korean population
Authors: Jeong Ki-Heon , Kim Su Kang , Seo Jong-Kil , Shin Min Kyung , Lee Mu-Hyoung 
Published: January 2021

AbstractNon-segmental vitiligo (NSV) is the most common type of vitiligo, which is characterized by chronic and progressive loss of melanocytes. Genetic factors have been shown to play a key role in NSV in association and family studies. Granzyme B is a serine protease found in the cytoplasmic granules of cytotoxic T lymphocytes and natural killer cells that play an important role in inducing apoptotic changes of target cells. Several recent studies have provided evidence that polymorphism in the GZMB gene might be associated with autoimmune disease. A total of 249 NSV patients and 455 healthy controls were recruited to determine whether single nucleotide polymorphisms (SNPs) [rs2236337 (3′ untranslated region, UTR), rs2236338 (Tyr247His), rs11539752 (Pro94Ala), rs10909625 (Lys80Lys), rs8192917 (Arg55Gln), and rs7144366 (5′ near gene)] in GZMB gene contribute to the risk of developing NSV. Genotyping was performed using a single 192.24 Dynamic Array IFC. Data were analyzed using EP1 SNP Genotyping Analysis software to obtain genotype calls. Among the six SNPs tested, five SNPs (rs2236337, rs2236338, rs11539752, rs10909625, and rs8192917) showed significant association with NSV susceptibility. Among them, rs2236338, rs11539752, rs10909625, and rs8192917 remained a statistically significant association following multiple correction test. The five SNPs were located within a block of linkage disequilibrium. Haplotypes T–A–G–T–T and C–G–C–C–C consisting of rs2236337, rs2236338, rs11539752, rs10909625, and rs8192917 demonstrated significant association with NSV. Our results suggest that GZMB polymorphisms are associated with the development of NSV.
Neon-green fluorescence in the desert gecko Pachydactylus rangei caused by iridophores
Authors: Prötzel David , Heß Martin , Schwager Martina , Glaw Frank , Scherz Mark D. 
Published: January 2021

AbstractBiofluorescence is widespread in the natural world, but only recently discovered in terrestrial vertebrates. Here, we report on the discovery of iridophore-based, neon-green flourescence in the gecko Pachydactylus rangei, localised to the skin around the eyes and along the flanks. The maximum emission of the fluorescence is at a wavelength of 516 nm in the green spectrum (excitation maximum 465 nm, blue) with another, smaller peak at 430 nm. The fluorescent regions of the skin show large numbers of iridophores, which are lacking in the non-fluorescent parts. Two types of iridophores are recognized, fluorescent iridophores and basal, non-fluorescent iridophores, the latter of which might function as a mirror, amplifying the omnidirectional fluorescence. The strong intensity of the fluorescence (quantum yield of 12.5%) indicates this to be a highly effective mechanism, unique among tetrapods. Although the fluorescence is associated with iridophores, the spectra of emission and excitation as well as the small Stokes shifts argue against guanine crystals as its source, but rather a rigid pair of fluorophores. Further studies are necessary to identify their morphology and chemical structures. We hypothesise that this nocturnal gecko uses the neon-green fluorescence, excited by moonlight, for intraspecific signalling in its open desert habitat.
Genetic and demographic history define a conservation strategy for earth’s most endangered pinniped, the Mediterranean monk seal Monachus monachus
Authors: Karamanlidis Alexandros A. , Skrbinšek Tomaž , Amato George , Dendrinos Panagiotis , Gaughran Stephen , Kasapidis Panagiotis , Kopatz Alexander , Stronen Astrid Vik 
Published: January 2021

AbstractThe Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species’ unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival.
Combining microcavity size selection with Raman microscopy for the characterization of Nanoplastics in complex matrices
Authors: Valsesia Andrea , Quarato Monica , Ponti Jessica , Fumagalli Francesco , Gilliland Douglas , Colpo Pascal 
Published: January 2021

AbstractNanoplastic particulates (pNP) are widely considered as being potentially harmful to the environment and living organisms while also being technically difficult to detect and identify in the presence of biological matrices. In this study, we describe a method for the extraction and subsequent Raman analysis of pNP present in the tissues of salt-water mussels. The process combines a step of enzymatic digestion/filtering to eliminate the biological matrix with a detection/identification procedure, which uses a micro-machined surface, composed of arrays of cavities with well-defined sub-micron depths and diameters. This sensor surface, exploits capillary forces in a drying droplet of analyte solution to drive the self-assembly of suspended nanoparticles into the cavities leaving the individual particles isolated from each other over the surface. The resulting array, when analysed using confocal Raman microscopy, permits the size selective analysis of the individual sub-micron pNP trapped in the cavities structure.
Lipoxygenase catalyzed metabolites derived from docosahexaenoic acid are promising antitumor agents against breast cancer
Authors: Chen Kun-Ming , Thompson Henry , Vanden-Heuvel John P. , Sun Yuan-Wan , Trushin Neil , Aliaga Cesar , Gowda Krishne , Amin Shantu , Stanley Bruce , Manni Andrea , El-Bayoumy Karam 
Published: January 2021

AbstractDocosahexaenoic acid (DHA) is known to inhibit breast cancer in the rat. Here we investigated whether DHA itself or select metabolites can account for its antitumor action. We focused on metabolites derived from the lipoxygenase (LOX) pathway since we previously showed that they were superior anti-proliferating agents compared to DHA; 4-OXO-DHA was the most potent. A lipidomics approach detected several LOX-metabolites in plasma and the mammary gland in rats fed DHA; we also identified for the first time, 4-OXO-DHA in rat plasma. In a reporter assay, 4-OXO-DHA and 4-HDHA were more effective activators of PPARɣ than DHA. In breast cancer cell lines, 4-OXO-DHA induced PPARɣ and 15-hydroxyprostaglandin dehydrogenase (15-PGDH) but inhibited the activity of NF-κB and suppressed PI3K and mTOR signaling. Because of the structural characteristics of 4-OXO-DHA (Michael acceptor), not shared by any of the other hydroxylated-DHA, we used MS and showed that it can covalently modify the cysteine residue of NF-κB. We have also shown that the chemopreventive effect of DHA is associated with significant reduction of PGE2 levels, in both rat mammary tumors induced by MNU and non-involved mammary tissues. Collectively, our results indicate that 4-OXO-DHA is the metabolite of choice in future chemoprevention studies.
A portable pen-sized instrumentation to measure stiffness of soft tissues in vivo
Authors: Li Zhengwei , Tofangchi Alireza , Stavins Robert A. , Emon Bashar , McKinney Ronald D. , Grippo Paul J. , Saif M. Taher A. 
Published: January 2021

AbstractQuantitative assessment of soft tissue elasticity is crucial to a broad range of applications, such as biomechanical modeling, physiological monitoring, and tissue diseases diagnosing. However, the modulus measurement of soft tissues, particularly in vivo, has proved challenging since the instrument has to reach the site of soft tissue and be able to measure in a very short time. Here, we present a simple method to measure the elastic modulus of soft tissues on site by exploiting buckling of a long slender bar to quantify the applied force and a spherical indentation to extract the elastic modulus. The method is realized by developing a portable pen-sized instrument (EPen: Elastic modulus pen). The measurement accuracies are verified by independent modulus measures using commercial nanoindenter. Quantitative measurements of the elastic modulus of mouse pancreas, healthy and cancerous, surgically exposed but attached to the body further confirm the potential clinical utility of the EPen.
Electrical tuning effect for Schottky barrier and hot-electron harvest in a plasmonic Au/TiO2 nanostructure
Authors: Sun Zhiguang , Fang Yurui 
Published: January 2021

AbstractSchottky barrier controls the transfer of hot carriers between contacted metal and semiconductor, and decides the performance of plasmonic metal–semiconductor devices in many applications. It is immensely valuable to actively tune the Schottky barrier. In this work, electrical tuning of Schottky barrier in an Au-nanodisk/TiO2-film structure was demonstrated using a simple three-electrode electrochemical cell. Photocurrents excited at different wavelength significantly increase as the applied bias voltage increases. Analyzing and fitting of experimental results indicate that the photocurrent is mainly affected by the bias tuning position of Schottky barrier maximum, which shifts to metal–semiconductor interface as applied voltage increases, and enhances the collection efficiency of the barrier for plasmonic hot electrons. The conduction band curvature of 0.13 eV was simultaneously obtained from the fitting. This work provides a new strategy for facile tuning of Schottky barrier and hot-electron transfer across the barrier.
Image compression-encryption method based on two-dimensional sparse recovery and chaotic system
Authors: Ghaffari Aboozar 
Published: January 2021

AbstractIn this paper, we propose an image compression-encryption method based on two-dimensional (2D) sparse representation and chaotic system. In the first step of this method, the input image is extended in a transform domain to obtain a sparse representation. To achieve better performance of image compression by 2D sparse recovery, the sparse representation is scrambled via a chaotic confusion. This step helps the satisfaction of the uniqueness conditions for sparse recovery, and the security level of encryption is increased. Then, two orthogonal measurement matrices are generated using the chaotic time series. The singular value decomposition is used to compress the sparse scrambled representation in two dimensions. Finally, to reduce the correlation between adjacent pixels in the compressed matrix, and obtain a uniform distribution in the encrypted image, a compressed scrambling matrix based on chaotic confusion is used. Then, XOR operation is applied for final encryption. In the decryption process, to improve the compression efficiency, the total variation constraint is added to the 2D sparse recovery problem based on the smoothed norm. The simulation results demonstrate the satisfying performance of the proposed method for different compression ratios. Security analysis describes the effectiveness of the proposed encryption approach.
Novel circRNA discovery in sheep shows evidence of high backsplice junction conservation
Authors: Varela-Martínez Endika , Corsi Giulia I. , Anthon Christian , Gorodkin Jan , Jugo Begoña M. 
Published: January 2021

AbstractCircular RNAs (circRNAs) are covalently closed circular non-coding RNAs. Due to their structure, circRNAs are more stable and have longer half-lives than linear RNAs making them good candidates for disease biomarkers. Despite the scientific relevance of these molecules, the study of circRNAs in non-model organisms is still in its infancy. Here, we analyse total RNA-seq data to identify circRNAs in sheep from peripheral blood mononuclear cells (PBMCs) and parietal lobe cortex. Out of 2510 and 3403 circRNAs detected in parietal lobe cortex and in PBMCs, a total of 1379 novel circRNAs were discovered. Remarkably, around 63% of all detected circRNAs were found to be completely homologous to a circRNA annotated in human. Functional enrichment analysis was conducted for both tissues based on GO terms and KEGG pathways. The enriched terms suggest an important role of circRNAs from encephalon in synaptic functions and the involvement of circRNAs from PBMCs in basic immune system functions. In addition to this, we investigated the role of circRNAs in repetitive vaccination experiments via differential expression analysis and did not detect any significant relationship. At last, our results support both the miRNA sponge and the miRNA shuttle functions of CDR1-AS in sheep brain. To our knowledge, this is the first study on circRNA annotation in sheep PBMCs or parietal lobe cortex samples.
3D metal lattice structure manufacturing with continuous rods
Authors: Khoda Bashir , Ahsan A. M. M. Nazmul , Shovon Abu N. , Alam Adeeb I. 
Published: January 2021

AbstractIn this paper, a new possibility of fabricating a metal lattice structure with a continuous rod is demonstrated. A multi-layer, periodic, and aperiodic lattice structure can be manufactured with a continuous thin rod by bending it with a repetitive pattern. However, joining their nodes are challenging and an important problem to solve. This paper is investigating the joining of nodes in a loose lattice structure by delivering materials through the dipping process. Both liquid state (epoxy) and solid-state (inorganic particles) joining agents are considered for polymer–metal and metal–metal bonding, respectively. Liquid Carrier Systems (LCS) are designed considering their rheological behavior. We found 40% solid loading with the liquid carrier system provides sufficient solid particles transfer at dipping and join the lattice node using transient liquid phase bonding (TLP). 3D metal lattice structures are constructed, and their mechanical properties are investigated. The lattice structure shows comparable strength even with smaller relative density (< 10%). The strength and elastic modulus of all the fabricated samples decreases with the increase in cell size, which is consistent with the traditional wisdom.
Gene expression profiling of protease and non-protease genes in Trichophyton mentagrophytes isolates from dermatophytosis patients by qRT-PCR analysis
Authors: Datt Shyama , Das Shukla , Ahmad Ansari M. , Sharma Rahul , Datt Thakur , Bhattacharya S. N. 
Published: January 2021

AbstractTrichophyton mentagrophytes secretes Metallocarboxypeptidase A and B of the M14 family as endoproteases and exoprotease. T. mentagrophytes produce Metalloprotease 3 and 4 which degrades the protein into the short peptides and amino acids. To understand the host fungal relationship and identification of such genes expressed during infection is utmost important. T. mentagrophytes encodes some proteins which are associated with the glyoxylate cycle. The glyoxylate cycle enzymes have been involving in virulence of dermatophytes and their up-regulation during dermatophytes growth on keratin. On comparing the expression level of virulence protease and non-protease genes, we observed, among exoprotease protease genes, Metallocarboxypeptidase B was strongly up regulated (134.6 fold high) followed by Metallocarboxypeptidase A (115.6 fold high) and Di-peptidyl-peptidases V (10.1 fold high), in dermatophytic patients as compared to ATCC strain. Furthermore, among endoprotease, Metalloprotease 4 was strongly up regulated (131.6 fold high) followed by Metalloprotease 3 (16.7 fold high), in clinical strains as compared to T. mentagrophytes ATCC strain. While among non-protease genes, Citrate Synthase was highly expressed (118 fold high), followed by Isocitrate Lyase (101.6 fold high) and Malate Synthase (52.9 fold high). All the studied virulence genes were considered the best suitable ones by geNorm, Best keeper, Norm Finder and Ref finder.
Smoking, urinary cotinine levels and incidence of visual impairment
Authors: Han So Young , Chang Yoosoo , Shin Hocheol , Choi Chul Young , Ryu Seungho 
Published: January 2021

AbstractThe longitudinal relationship between smoking status and risk of developing visual impairment (VI) remains unclear. We examined the relationship of smoking status and urinary cotinine level, an objective measure of smoking, with incidence of VI. This cohort study included 279,069 individuals free of VI who were followed for up to 8.8 years (median 4.8 years). VI was defined as when bilateral visual acuity was worse than 0.5 (cutoffs of 0.3 Logarithm of the Minimum Angle of Resolution). During 1,324,429.8 person-years of follow-up, 7852 participants developed new-onset bilateral VI. Self-reported current smoking status was associated with increased risk of developing VI in both men and women, with a stronger association in women (P for interaction = 0.01). Multivariable adjusted hazard ratios (95% confidence intervals) for incident VI comparing current smokers to never-smokers were 1.14 (1.04–1.25) in men and 1.52 (1.28–1.80) in women. Urinary cotinine levels of ≥ 100 ng/ml were significantly associated with increased risk of incident VI, and these associations remained when introducing changes in urinary cotinine and other confounders during follow-up as time-varying covariates. Cigarette smoking assessed based on self-report and urinary cotinine level was associated with increased incidence of VI. Our findings identify smoking as an independent risk factor for VI.
Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients
Authors: Debesa-Tur Gabriela , Pérez-Brocal Vicente , Ruiz-Ruiz Susana , Castillejo Adela , Latorre Amparo , Soto José Luis , Moya Andrés 
Published: January 2021

AbstractAn increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples.
Deep learning-based computer-aided diagnosis in screening breast ultrasound to reduce false-positive diagnoses
Authors: Kim Soo -Yeon , Choi Yunhee , Kim Eun -Kyung , Han Boo-Kyung , Yoon Jung Hyun , Choi Ji Soo , Chang Jung Min 
Published: January 2021

AbstractA major limitation of screening breast ultrasound (US) is a substantial number of false-positive biopsy. This study aimed to develop a deep learning-based computer-aided diagnosis (DL-CAD)-based diagnostic model to improve the differential diagnosis of screening US-detected breast masses and reduce false-positive diagnoses. In this multicenter retrospective study, a diagnostic model was developed based on US images combined with information obtained from the DL-CAD software for patients with breast masses detected using screening US; the data were obtained from two hospitals (development set: 299 imaging studies in 2015). Quantitative morphologic features were obtained from the DL-CAD software, and the clinical findings were collected. Multivariable logistic regression analysis was performed to establish a DL-CAD-based nomogram, and the model was externally validated using data collected from 164 imaging studies conducted between 2018 and 2019 at another hospital. Among the quantitative morphologic features extracted from DL-CAD, a higher irregular shape score (P = .018) and lower parallel orientation score (P = .007) were associated with malignancy. The nomogram incorporating the DL-CAD-based quantitative features, radiologists’ Breast Imaging Reporting and Data Systems (BI-RADS) final assessment (P = .014), and patient age (P < .001) exhibited good discrimination in both the development and validation cohorts (area under the receiver operating characteristic curve, 0.89 and 0.87). Compared with the radiologists’ BI-RADS final assessment, the DL-CAD-based nomogram lowered the false-positive rate (68% vs. 31%, P < .001 in the development cohort; 97% vs. 45% P < .001 in the validation cohort) without affecting the sensitivity (98% vs. 93%, P = .317 in the development cohort; each 100% in the validation cohort). In conclusion, the proposed model showed good performance for differentiating screening US-detected breast masses, thus demonstrating a potential to reduce unnecessary biopsies.