bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disease progression modelling from preclinical Alzheimer’s disease (AD) to AD dementia
Authors: Cho Soo Hyun , Woo Sookyoung , Kim Changsoo , Kim Hee Jin , Jang Hyemin , Kim Byeong C. , Kim Si Eun , Kim Seung Joo , Kim Jun Pyo , Jung Young Hee , Lockhart Samuel , Ossenkoppele Rik , Landau Susan , Na Duk L. , Weiner Michael , Kim Seonwoo , Seo Sang Won 
Published: February 2021

AbstractTo characterize the course of Alzheimer’s disease (AD) over a longer time interval, we aimed to construct a disease course model for the entire span of the disease using two separate cohorts ranging from preclinical AD to AD dementia. We modelled the progression course of 436 patients with AD continuum and investigated the effects of apolipoprotein E ε4 (APOE ε4) and sex on disease progression. To develop a model of progression from preclinical AD to AD dementia, we estimated Alzheimer’s Disease Assessment Scale-Cognitive Subscale 13 (ADAS-cog 13) scores. When calculated as the median of ADAS-cog 13 scores for each cohort, the estimated time from preclinical AD to MCI due to AD was 7.8 years and preclinical AD to AD dementia was 15.2 years. ADAS-cog 13 scores deteriorated most rapidly in women APOE ε4 carriers and most slowly in men APOE ε4 non-carriers (p < 0.001). Our results suggest that disease progression modelling from preclinical AD to AD dementia may help clinicians to estimate where patients are in the disease course and provide information on variation in the disease course by sex and APOE ε4 status.
Vivid biofluorescence discovered in the nocturnal Springhare (Pedetidae)
Authors: Olson Erik R. , Carlson Michaela R. , Ramanujam V. M. Sadagopa , Sears Lindsay , Anthony Sharon E. , Anich Paula Spaeth , Ramon Leigh , Hulstrand Alissa , Jurewicz Michaela , Gunnelson Adam S. , Kohler Allison M. , Martin Jonathan G. 
Published: February 2021

AbstractBiofluorescence has been detected in several nocturnal-crepuscular organisms from invertebrates to birds and mammals. Biofluorescence in mammals has been detected across the phylogeny, including the monotreme duck-billed platypus (Ornithorhyncus anatinus), marsupial opossums (Didelphidae), and New World placental flying squirrels (Gluacomys spp.). Here, we document vivid biofluorescence of springhare (Pedetidae) in both museum specimens and captive individuals—the first documented biofluorescence of an Old World placental mammal. We explore the variation in biofluorescence across our sample and characterize its physical and chemical properties. The striking visual patterning and intensity of color shift was unique relative to biofluorescence found in other mammals. We establish that biofluorescence in springhare likely originates within the cuticle of the hair fiber and emanates, at least partially, from several fluorescent porphyrins and potentially one unassigned molecule absent from our standard porphyrin mixture. This discovery further supports the hypothesis that biofluorescence may be ecologically important for nocturnal-crepuscular mammals and suggests that it may be more broadly distributed throughout Mammalia than previously thought.
CSF proteome in multiple sclerosis subtypes related to brain lesion transcriptomes
Authors: Elkjaer Maria L. , Nawrocki Arkadiusz , Kacprowski Tim , Lassen Pernille , Simonsen Anja Hviid , Marignier Romain , Sejbaek Tobias , Nielsen Helle H. , Wermuth Lene , Rashid Alyaa Yakut , Høgh Peter , Sellebjerg Finn , Reynolds Richard , Baumbach Jan , Larsen Martin R. , Illes Zsolt 
Published: February 2021

AbstractTo identify markers in the CSF of multiple sclerosis (MS) subtypes, we used a two-step proteomic approach: (i) Discovery proteomics compared 169 pooled CSF from MS subtypes and inflammatory/degenerative CNS diseases (NMO spectrum and Alzheimer disease) and healthy controls. (ii) Next, 299 proteins selected by comprehensive statistics were quantified in 170 individual CSF samples. (iii) Genes of the identified proteins were also screened among transcripts in 73 MS brain lesions compared to 25 control brains. F-test based feature selection resulted in 8 proteins differentiating the MS subtypes, and secondary progressive (SP)MS was the most different also from controls. Genes of 7 out these 8 proteins were present in MS brain lesions: GOLM was significantly differentially expressed in active, chronic active, inactive and remyelinating lesions, FRZB in active and chronic active lesions, and SELENBP1 in inactive lesions. Volcano maps of normalized proteins in the different disease groups also indicated the highest amount of altered proteins in SPMS. Apolipoprotein C-I, apolipoprotein A-II, augurin, receptor-type tyrosine-protein phosphatase gamma, and trypsin-1 were upregulated in the CSF of MS subtypes compared to controls. This CSF profile and associated brain lesion spectrum highlight non-inflammatory mechanisms in differentiating CNS diseases and MS subtypes and the uniqueness of SPMS.
Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects
Authors: Maldonado Lucas L. , Bertelli Andrea Mendoza , Kamenetzky Laura 
Published: February 2021

AbstractIn December 2019, rising pneumonia cases caused by a novel β-coronavirus (SARS-CoV-2) occurred in Wuhan, China, which has rapidly spread worldwide, causing thousands of deaths. The WHO declared the SARS-CoV-2 outbreak as a public health emergency of international concern, since then several scientists are dedicated to its study. It has been observed that many human viruses have codon usage biases that match highly expressed proteins in the tissues they infect and depend on the host cell machinery for the replication and co-evolution. In this work, we analysed 91 molecular features and codon usage patterns for 339 viral genes and 463 human genes that consisted of 677,873 codon positions. Hereby, we selected the highly expressed genes from human lung tissue to perform computational studies that permit to compare their molecular features with those of SARS, SARS-CoV-2 and MERS genes. The integrated analysis of all the features revealed that certain viral genes and overexpressed human genes have similar codon usage patterns. The main pattern was the A/T bias that together with other features could propitiate the viral infection, enhanced by a host dependant specialization of the translation machinery of only some of the overexpressed genes. The envelope protein E, the membrane glycoprotein M and ORF7 could be further benefited. This could be the key for a facilitated translation and viral replication conducting to different comorbidities depending on the genetic variability of population due to the host translation machinery. This is the first codon usage approach that reveals which human genes could be potentially deregulated due to the codon usage similarities between the host and the viral genes when the virus is already inside the human cells of the lung tissues. Our work leaded to the identification of additional highly expressed human genes which are not the usual suspects but might play a role in the viral infection and settle the basis for further research in the field of human genetics associated with new viral infections. To identify the genes that could be deregulated under a viral infection is important to predict the collateral effects and determine which individuals would be more susceptible based on their genetic features and comorbidities associated.
Identification of novel neuroblastoma biomarkers in urine samples
Authors: Yokota Kazuki , Uchida Hiroo , Sakairi Minoru , Abe Mayumi , Tanaka Yujiro , Tainaka Takahisa , Shirota Chiyoe , Sumida Wataru , Oshima Kazuo , Makita Satoshi , Amano Hizuru , Hinoki Akinari 
Published: February 2021

AbstractUrine is a complex liquid containing numerous small molecular metabolites. The ability to non-invasively test for cancer biomarkers in urine is especially beneficial for screening child patients. This study attempted to identify neuroblastoma biomarkers by comprehensively analysing urinary metabolite samples from children. A total of 87 urine samples were collected from 54 participants (15 children with neuroblastoma and 39 without cancer) and used to perform a comprehensive analysis. Urine metabolites were extracted using liquid chromatography/mass spectrometry and analysed by Metabolon, Inc. Biomarker candidates were extracted using the Wilcoxon rank sum test, random forest method (RF), and orthogonal partial least squares discriminant analysis (OPLS-DA). RF identified three important metabolic pathways in 15 samples from children with neuroblastoma. One metabolite was selected from each of the three identified pathways and combined to create a biomarker candidate (3-MTS, CTN, and COR) that represented each of the three pathways; using this candidate, all 15 cases were accurately distinguishable from the control group. Two cases in which known biomarkers were negative tested positive using this new biomarker. Furthermore, the predictive value did not decrease in cases with a low therapeutic effect. This approach could be effectively applied to identify biomarkers for other cancer types.
Potential impact of a nonavalent anti HPV vaccine in Italian men with and without clinical manifestations
Authors: Bosco Liana , Serra Nicola , Fasciana Teresa , Pistoia Daniela , Vella Marco , Di Gregorio Leonardo , Schillaci Rosaria , Perino Antonino , Calagna Gloria , Firenze Alberto , Capra Giuseppina 
Published: February 2021

AbstractHuman papilloma virus infection (HPV) is the most common sexually transmitted disease. Little is known about male infection. Nonavalent vaccine against types 6/11/16/18/31/33/45/52/58 was approved and neutral gender immunization programs have been proposed. This study evaluates the potential impact of nonavalent vaccine compared to quadrivalent in male living in Sicily (Italy). 58.7% of samples were HPV positive and forty-four types of HPV were identified. A significant higher estimated coverage of nonavalent vaccine than quadrivalent was observed (64.3% vs. 45.8%), with absolute and relative additional impact of 20.1% and 47.2%, respectively. Low impact of the vaccine were calculated as the empirical probability of HPV genotypes 6/11/16/18/31/33/45/52/58 alone or in combination; the high impact as empirical probability of HPV6/11/16/18/31/33/45/52/58 genotypes alone or in association with other genotypes. The potential impact of the nonavalent vaccine vs quadrivalent was significant for low and high impact (29.7% > 18:8%; 34:6% > 26.6%, respectively). Particularly, in men with lesions and risky sexual contact was significant only for low impact (35.5% > 29.7%; 31.4% > 19.7%, respectively). In partners with positive females was significant for low impact (26.3% > 15.1%) and high impact (33.7% > 23.2%). Nonavalent vaccine offers broader protection in men with HPV positive partners, who would have a potential role in the transmission of the infection.
NIR light guided enhanced photoluminescence and temperature sensing in Ho3+/Yb3+/Bi3+ co-doped ZnGa2O4 phosphor
Authors: Monika  , Yadav Ram Sagar , Rai Anita , Rai Shyam Bahadur 
Published: February 2021

AbstractThe conversion of NIR light into visible light has been studied in Ho3+/Yb3+/Bi3+ co-doped ZnGa2O4 phosphor for the first time. The crystallinity and particles size of the phosphor increase through Bi3+ doping. The absorption characteristics of Ho3+, Yb3+ and Bi3+ ions are identified by the UV–vis-NIR measurements. The Ho3+ doped phosphor produces intense green upconversion (UC) emission under 980 nm excitations. The emission intensity ~ excitation power density plots show contribution of two photons for the UC emissions. The UC intensity of green emission is weak in the Ho3+ doped phosphor, which enhances upto 128 and 228 times through co-doping of Yb3+ and Yb3+/Bi3+ ions, respectively. The relative and absolute temperature sensing sensitivities of Ho3+/Yb3+/5Bi3+ co-doped ZnGa2O4 phosphor are calculated to be 13.6 × 10−4 and 14.3 × 10−4 K−1, respectively. The variation in concentration of Bi3+ ion and power density produces excellent color tunability from green to red via yellow regions. The CCT also varies with concentration of Bi3+ ion and power density from cool to warm light. The color purity of phosphor is achieved to 98.6% through Bi3+ doping. Therefore, the Ho3+/Yb3+/Bi3+:ZnGa2O4 phosphors can be suitable for UC-based color tunable devices, green light emitting diodes and temperature sensing.
The implications of subretinal fluid in pachychoroid neovasculopathy
Authors: Lee Geun Woo , Roh Hyeon Cheol , Kang Se Woong , Kim A. Young , Noh Hoon , Choi Kyung Jun 
Published: February 2021

AbstractThis study aimed to identify the clinical characteristics and longitudinal changes in exudative pachychoroid neovasculopathy (PNV) and non-exudative PNV. This retrospective cohort study involved 81 eyes of PNV diagnosed by multimodal imaging including optical coherence tomography angiography. At baseline, they were divided into exudative PNV group and non-exudative PNV group depending on the presence of subretinal fluid. The clinical features of both groups and the longitudinal changes were investigated and compared. There were 55 eyes with non-exudative PNV and 26 eyes with exudative PNV. Individuals with non-exudative PNV were older, more frequently asymptomatic and had a higher prevalence of polypoidal choroidal vasculopathy in the opposite eye (all P’s < 0.05). Whereas individuals with exudative PNV showed thicker choroid and more frequent history of central serous chorioretinopathy (all P’s < 0.001). During about 12 months of longitudinal observation, the transformation into polypoidal choroidal vasculopathy was noted in 4 eyes of non-exudative PNV group, whereas in none of the exudative PNV group. Exudative PNV and non-exudative PNV seem to be separate entities with different epidemiological parameters. Non-exudative PNV, which is frequently found without symptoms at an older age, is suspected to be the significant precursor lesion of polypoidal choroidal vasculopathy. In contrast, exudative PNV may share the same pathophysiology as central serous chorioretinopathy.
Optical and surface energy probe of Hamaker constant in copper oxide thin films for NEMS and MEMS stiction control applications
Authors: Ogwu Abraham , Darma T. H. 
Published: February 2021

AbstractCopper oxide films hold substantial promise as anti-stiction coatings in micro-electromechanical (MEMS) devices and with shrinking dimensions on the nanometre scale on nano electromechanical (NEMS) devices. The Hamaker constant will play a very significant role in understanding stiction and tribology in these devices. We used an approximate but sufficiently accurate form of the Lifshitz theory using the multiple oscillator model to calculate the Hamakers constant of symmetric copper oxide thin films based on experimentally obtained dielectric data in the wavelength range 190-850 nm using spectroscopic ellipsometry. We also used the Tabor–Winterton approximation (TWA) and Surface energy measurements to determine the Hamaker constant. There was better agreement in the Hamaker constant values obtained by the limited Lifshitz theory and TWA approach than with the Surface energy approach. The difference is explained through the influence of surface roughness on the surface energy using extensions of the stochastic KPZ growth model and the Family-Vicsek scaling relation and rigorous treatment of the Cassie-Baxter and Wenzel models as optimisations of a surface free energy functional linking roughness and surface tension. The dominance of the Cu2O phase in the films and of the London dispersion force on the surface of the films was previously confirmed by FTIR Cu(I)–O vibrational mode observation and XPS Cu 2p3/2 binding energy peak and its fitted satellites. The use of the limited Lifshitz theory and ellipsometry data would seem to provide a suitable best first approximation for determining the Hamaker constant of predominantly dispersive anti-stiction coatings in technologically important MEMS/NEMS devices.
Morphological features of large layer V pyramidal neurons in cortical motor-related areas of macaque monkeys: analysis of basal dendrites
Authors: Takata Yu , Nakagawa Hiroshi , Ninomiya Taihei , Yamanaka Hajime , Takada Masahiko 
Published: February 2021

AbstractIn primates, large layer V pyramidal neurons located in the frontal motor-related areas send a variety of motor commands to the spinal cord, giving rise to the corticospinal tract, for execution of skilled motor behavior. However, little is known about the morphological diversity of such pyramidal neurons among the areas. Here we show that the structure of basal dendrites of the large layer V pyramidal neurons in the dorsal premotor cortex (PMd) is different from those in the other areas, including the primary motor cortex, the supplementary motor area, and the ventral premotor cortex. In the PMd, not only the complexity (arborization) of basal dendrites, i.e., total dendritic length and branching number, was poorly developed, but also the density of dendritic spines was so low, as compared to the other motor-related areas. Regarding the distribution of the three dendritic spine types identified, we found that thin-type (more immature) spines were prominent in the PMd in comparison with stubby- and mushroom-type (more mature) spines, while both thin- and stubby-type spines were in the other areas. The differential morphological features of basal dendrites might reflect distinct patterns of motor information processing within the large layer V pyramidal neurons in individual motor-related areas.
Investigating an increase in Florida manatee mortalities using a proteomic approach
Authors: Lazensky Rebecca , Silva-Sanchez Cecilia , Kroll Kevin J. , Chow Marjorie , Chen Sixue , Tripp Katie , Walsh Michael T. , Denslow Nancy D. 
Published: February 2021

AbstractTwo large-scale Florida manatee (Trichechus manatus latirostris) mortality episodes were reported on separate coasts of Florida in 2013. The east coast mortality episode was associated with an unknown etiology in the Indian River Lagoon (IRL). The west coast mortality episode was attributed to a persistent Karenia brevis algal bloom or ‘red tide’ centered in Southwest Florida. Manatees from the IRL also had signs of cold stress. To investigate these two mortality episodes, two proteomic experiments were performed, using two-dimensional difference in gel electrophoresis (2D-DIGE) and isobaric tags for relative and absolute quantification (iTRAQ) LC–MS/MS. Manatees from the IRL displayed increased levels of several proteins in their serum samples compared to controls, including kininogen-1 isoform 1, alpha-1-microglobulin/bikunen precursor, histidine-rich glycoprotein, properdin, and complement C4-A isoform 1. In the red tide group, the following proteins were increased: ceruloplasmin, pyruvate kinase isozymes M1/M2 isoform 3, angiotensinogen, complement C4-A isoform 1, and complement C3. These proteins are associated with acute-phase response, amyloid formation and accumulation, copper and iron homeostasis, the complement cascade pathway, and other important cellular functions. The increased level of complement C4 protein observed in the red tide group was confirmed through the use of Western Blot.
Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss
Authors: Akhatar Javed , Goyal Anna , Kaur Navneet , Atri Chhaya , Mittal Meenakshi , Singh Mohini Prabha , Kaur Rimaljeet , Rialch Indu , Banga Surinder S. 
Published: February 2021

AbstractTimely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.
Infants with congenital heart defects have reduced brain volumes
Authors: Skotting Mikkel B. , Eskildsen S. F. , Ovesen A. S. , Fonov V. S. , Ringgaard S. , Hjortdal V. E. , Lauridsen M. H. 
Published: February 2021

AbstractChildren with congenital heart defects (CHDs) have increased risk of cognitive disabilities for reasons not fully understood. Previous studies have indicated signs of disrupted fetal brain growth from mid-gestation measured with ultrasound and magnetic resonance imaging (MRI) and infants with CHDs have decreased brain volumes at birth. We measured the total and regional brain volumes of infants with and without CHDs using MRI to investigate, if certain areas of the brain are at particular risk of disrupted growth. MRI brain volumetry analyses were performed on 20 infants; 10 with- (postmenstrual age 39–54 weeks, mean 44 weeks + 5 days) and 10 without CHDs (postmenstrual age 39–52 weeks, mean 43 weeks + 5 days). In six infants with- and eight infants without CHDs grey and white matter were also differentiated. Infants with CHDs had smaller brains (48 ml smaller; 95% CI, 6.1–90; p = 0.03), cerebrums (37.8 ml smaller; 95% CI, 0.8–74.8; p = 0.04), and cerebral grey matter (25.8 ml smaller; 95% CI, 3.5–48; p = 0.03) than infants without CHD. Brain volume differences observed within weeks after birth in children with CHDs confirm that the brain impact, which increase the risk of cognitive disabilities, may begin during pregnancy.