bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of dynamic networks based on the Ising model for the case of study of co-authorship of scientific articles
Authors: Hurtado-Marín V. Andrea , Agudelo-Giraldo J. Dario , Robledo Sebastian , Restrepo-Parra Elisabeth 
Published: March 2021

AbstractTwo computational methods based on the Ising model were implemented for studying temporal dynamic in co-authorship networks: an interpretative for real networks and another for simulation via Monte Carlo. The objective of simulation networks is to evaluate if the Ising model describes in similar way the dynamic of the network and of the magnetic system, so that it can be found a generalized explanation to the behaviours observed in real networks. The scientific papers used for building the real networks were acquired from WoS core collection. The variables for each record took into account bibliographic references. The search equation for each network considered specific topics trying to obtain an advanced temporal evolution in terms of the addition of new nodes; that means 3 steps, a time to reach the interest of the scientific community, a gradual increase until reaching a peak and finally, a decreasing trend by losing of novelty. It is possible to conclude that both methods are consistent with each other, showing that the Ising model can predict behaviours such as the number and size of communities (or domains) according to the temporal distribution of new nodes.
Phylogeography and genetic diversity of the microbivalve Kidderia subquadrata, reveals new data from West Antarctic Peninsula
Authors: Levicoy Daniela , Flores Kamilla , Rosenfeld Sebastián , Cárdenas Leyla 
Published: March 2021

AbstractIt is well established that Antarctic biodiversity has been strongly influenced by rapid climatic fluctuations during the Quaternary. Marine invertebrates from Antarctica constitute an interesting lens through which to study the impacts of the last glacial periods as glaciation impacted the distribution and intraspecific genetic variation of these animals. However, the impact on the spatial genetic distribution and historical demography of local processes in areas adjacent to the West Antarctic Peninsula (WAP) is less clear. Here we present new genetic information on the bivalve Kidderia subquadrata, a small mollusk that inhabits intertidal rocky island ecosystems throughout the WAP. Using a phylogeographical approach, we examined the spatial patterns of genetic diversity in this brooder species to test the hypothesis of strong genetic structure in incubating organisms and the hypothesis of glacial refugia in organisms with limited dispersion. We found evidence of strong genetic structure among populations of the WAP and a recent expansion in the South Shetland Islands. Our findings are concordant with the predictions that incubating organisms, abundant in Antarctica, present a strong genetic structure among their populations and also support the hypothesis of glacial refugia in organisms with limited dispersion. The effect of the coastal current pattern in the WAP is suggested as a driver to the local spatial dynamics of the genetic diversity distribution. Although genetic information about this microbivalve is still scarce, the knowledge reported here has increased our understanding of the evolutionary patterns of this organism that is endemic to the Southern Ocean.
Influence of serum inflammatory cytokines on cytochrome P450 drug metabolising activity during breast cancer chemotherapy: a patient feasibility study
Authors: Crake Rebekah L. I. , Strother Matthew R. , Phillips Elisabeth , Doogue Matthew P. , Zhang Mei , Frampton Chris M. A. , Robinson Bridget A. , Currie Margaret J. 
Published: March 2021

AbstractIndividual response to chemotherapy in patients with breast cancer is variable. Obesity and exercise are associated with better and worse outcomes, respectively, and it is known that both impact the systemic cytokine milieu. Cytochrome P450 (CYP) enzymes are responsible for the metabolism of many chemotherapy agents, and CYP enzyme activity has been shown to be modified by inflammatory cytokines in vitro and in vivo. Cytokine-associated changes in CYP metabolism may alter chemotherapy exposure, potentially affecting treatment response and patient survival. Therefore, better understanding of these biological relationships is required. This exploratory single arm open label trial investigated changes in in vivo CYP activity in twelve women treated for stage II or III breast cancer, and demonstrated for the first time the feasibility and safety of utilising the Inje phenotyping cocktail to measure CYP activity in cancer patients receiving chemotherapy. Relative CYP activity varied between participants, particularly for CYP2C9 and CYP2D6, and changes in serum concentrations of the inflammatory cytokine monocyte chemoattractant protein 1 inversely correlated to CYP3A4 activity during chemotherapy. Future use of phenotyping cocktails in a clinical oncology setting may help guide drug dosing and improve chemotherapy outcomes.Clinical Trial Registration: Trial was retrospectively registered to the Australia New Zealand Clinical Trial Registry (ANZCTR). ACTRN12620000832976, 21 Aug 2020, https://www.anzctr.org.au/ACTRN12620000832976.aspx.
Nanostructure of bioactive glass affects bone cell attachment via protein restructuring upon adsorption
Authors: Thamma Ukrit , Kowal Tia J. , Falk Matthias M. , Jain Himanshu 
Published: March 2021

AbstractThe nanostructure of engineered bioscaffolds has a profound impact on cell response, yet its understanding remains incomplete as cells interact with a highly complex interfacial layer rather than the material itself. For bioactive glass scaffolds, this layer comprises of silica gel, hydroxyapatite (HA)/carbonated hydroxyapatite (CHA), and absorbed proteins—all in varying micro/nano structure, composition, and concentration. Here, we examined the response of MC3T3-E1 pre-osteoblast cells to 30 mol% CaO–70 mol% SiO2 porous bioactive glass monoliths that differed only in nanopore size (6–44 nm) yet resulted in the formation of HA/CHA layers with significantly different microstructures. We report that cell response, as quantified by cell attachment and morphology, does not correlate with nanopore size, nor HA/CHO layer micro/nano morphology, or absorbed protein amount (bovine serum albumin, BSA), but with BSA’s secondary conformation as indicated by its β-sheet/α-helix ratio. Our results suggest that the β-sheet structure in BSA interacts electrostatically with the HA/CHA interfacial layer and activates the RGD sequence of absorbed adhesion proteins, such as fibronectin and vitronectin, thus significantly enhancing the attachment of cells. These findings provide new insight into the interaction of cells with the scaffolds’ interfacial layer, which is vital for the continued development of engineered tissue scaffolds.
Establishment and genomic characterization of a sporadic malignant peripheral nerve sheath tumor cell line
Authors: Longo Jody Fromm , Brosius Stephanie N. , Znoyko Iya , Alers Victoria A. , Jenkins Dorea P. , Wilson Robert C. , Carroll Andrew J. , Wolff Daynna J. , Roth Kevin A. , Carroll Steven L. 
Published: March 2021

AbstractMalignant peripheral nerve sheath tumors (MPNSTs) are aggressive Schwann cell-derived neoplasms that occur sporadically or in patients with neurofibromatosis type 1 (NF1). Preclinical research on sporadic MPNSTs has been limited as few cell lines exist. We generated and characterized a new sporadic MPNST cell line, 2XSB, which shares the molecular and genomic features of the parent tumor. These cells have a highly complex karyotype with extensive chromothripsis. 2XSB cells show robust invasive 3-dimensional and clonogenic culture capability and form solid tumors when xenografted into immunodeficient mice. High-density single nucleotide polymorphism array and whole exome sequencing analyses indicate that, unlike NF1-associated MPNSTs, 2XSB cells have intact, functional NF1 alleles with no evidence of mutations in genes encoding components of Polycomb Repressor Complex 2. However, mutations in other genes implicated in MPNST pathogenesis were identified in 2XSB cells including homozygous deletion of CDKN2A and mutations in TP53 and PTEN. We also identified mutations in genes not previously associated with MPNSTs but associated with the pathogenesis of other human cancers. These include DNMT1, NUMA1, NTRK1, PDE11A, CSMD3, LRP5 and ACTL9. This sporadic MPNST-derived cell line provides a useful tool for investigating the biology and potential treatment regimens for sporadic MPNSTs.
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility
Authors: Wang Jerry C. , Ramaswami Gokul , Geschwind Daniel H. 
Published: March 2021

AbstractAmyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss. Multiple genetic risk factors have been identified, implicating RNA and protein metabolism and intracellular transport, among other biological mechanisms. To achieve a systems-level understanding of the mechanisms governing ALS pathophysiology, we built gene co-expression networks using RNA-sequencing data from control human spinal cord samples, identifying 13 gene co-expression modules, each of which represents a distinct biological process or cell type. Analysis of four RNA-seq datasets from a range of ALS disease-associated contexts reveal dysregulation in numerous modules related to ribosomal function, wound response, and leukocyte activation, implicating astrocytes, oligodendrocytes, endothelia, and microglia in ALS pathophysiology. To identify potentially causal processes, we partitioned heritability across the genome, finding that ALS common genetic risk is enriched within two specific modules, SC.M4, representing genes related to RNA processing and gene regulation, and SC.M2, representing genes related to intracellular transport and autophagy and enriched in oligodendrocyte markers. Top hub genes of this latter module include ALS-implicated risk genes such as KPNA3, TMED2, and NCOA4, the latter of which regulates ferritin autophagy, implicating this process in ALS pathophysiology. These unbiased, genome-wide analyses confirm the utility of a systems approach to understanding the causes and drivers of ALS.
Ankle dorsiflexion deficit in the back leg is a risk factor for shoulder and elbow injuries in young baseball players
Authors: Shitara Hitoshi , Tajika Tsuyoshi , Kuboi Takuro , Ichinose Tsuyoshi , Sasaki Tsuyoshi , Hamano Noritaka , Endo Takafumi , Kamiyama Masataka , Honda Akira , Miyamoto Ryosuke , Nakase Kurumi , Yamamoto Atsushi , Kobayashi Tsutomu , Takagishi Kenji , Chikuda Hirotaka 
Published: March 2021

AbstractThe relationship between ankle joint function and throwing-related injuries has not been demonstrated. We hypothesized that limited ankle joint range of motion (ROM) was related to risk factors for shoulder and elbow injuries in young baseball players. This 12-month prospective cohort study evaluated the age, height, weight, playing position, shoulder, elbow, and ankle function of 228 enrolled baseball players. Shoulder and elbow injuries were tracked during the season. Univariate and multivariate analyses were performed to identify risk factors for shoulder and elbow injuries among participants divided into non-injured and injured groups. Univariate analysis showed that age, height, weight, ROM of elbow flexion in the dominant arm, muscle strength ratio of shoulder abduction, and the likelihood of being a pitcher or a catcher were significantly greater in the injured group than in the non-injured group. ROM of shoulder abduction-external/internal rotation, shoulder total arc on the dominant arm, ankle joint dorsiflexion, and plantar flexion on the back (non-lead) and front (lead) legs were significantly less in the injured group than in the non-injured group. In conclusion, ROM dorsiflexion deficits in the back leg, shoulder abduction-external rotation in the dominant arm, ROM increase in elbow flexion on the dominant side, older age, and being a pitcher were significant independent risk factors for injury.
RETRACTED ARTICLE: MicroRNA-205-5p inhibits skin cancer cell proliferation and increase drug sensitivity by targeting TNFAIP8
Authors: Ge Xinhong , Niture Suryakant , Lin Minghui , Cagle Patrice , Li P. Andy , Kumar Deepak 
Published: March 2021

AbstractTumor necrosis factor-α-induced protein 8 (TNFAIP8) is a member of the TIPE/TNFAIP8 family which regulates tumor growth and survival. Our goal is to delineate the detailed oncogenic role of TNFAIP8 in skin cancer development and progression. Here we demonstrated that higher expression of TNFAIP8 is associated with basal cell carcinoma (BCC), squamous cell carcinoma (SCC), and melanoma development in patient tissues. Induction of TNFAIP8 expression by TNFα or by ectopic expression of TNFAIP8 in SCC or melanoma cell lines resulted in increased cell growth/proliferation. Conversely, silencing of TNFAIP8 decreased cell survival/cell migration in skin cancer cells. We also showed that miR-205-5p targets the 3′UTR of TNFAIP8 and inhibits TNFAIP8 expression. Moreover, miR-205-5p downregulates TNFAIP8 mediated cellular autophagy, increased sensitivity towards the B-RAFV600E mutant kinase inhibitor vemurafenib, and induced cell apoptosis in melanoma cells. Collectively our data indicate that miR-205-5p acts as a tumor suppressor in skin cancer by targeting TNFAIP8.
Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing
Authors: Ahmed Syed A. K. Shifat , Rudden Michelle , Elias Sabrina M. , Smyth Thomas J. , Marchant Roger , Banat Ibrahim M. , Dooley James S. G. 
Published: March 2021

AbstractPseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than deletion of lasR. In PA80, no QS regulatory genes were expressed, which we attribute to the inactivation of the RhlRI QS system by deletion of rhlR and mutation of rhlI. This study demonstrates that inactivation of the LasRI system does not impact RhlRI regulated virulence factors. PA80 has bypassed the common pathoadaptive mutations observed in LasR by targeting the RhlRI system. This suggests that RhlRI is a significant target for the long-term persistence of P. aeruginosa in chronic CF patients. This raises important questions in targeting QS systems for therapeutic interventions.
Canine mammary cancer tumour behaviour and patient survival time are associated with collagen fibre characteristics
Authors: Garcia Ana P. V. , Reis Luana A. , Nunes Fernanda C. , Longford Francis G. J. , Frey Jeremy G. , de Paula Ana M. , Cassali Geovanni D. 
Published: March 2021

AbstractPrecise diagnosis and prognosis are key in prevention and reduction of morbidity and mortality in all types of cancers. Here we show that changes in the collagen fibres in the main histological subtypes of canine mammary gland carcinomas are directly associated with the tumour behaviour and the animal survival time and could become a useful tool in helping with diagnosis. Imaging by second harmonic generation and multiphoton excited fluorescence microscopy were performed to evaluate the collagen and cellular segment parameters in cancer biopsies. We present a retrospective study of 45 cases of canine mammary cancer analysing 836 biopsies regions including normal mammary gland tissue, benign mixed tumours, carcinoma in mixed tumour, carcinosarcoma, micropapillary carcinoma and solid carcinoma. The image analyses and the comparison between the tumour types allowed to assess the collagen fibre changes during tumour progression. We demonstrate that the collagen parameters correlate with the clinical and pathological data, the results show that in neoplastic tissues, the collagen fibres are more aligned and shorter as compared to the normal tissues. There is a clear association of the mean fibre length with the dogs survival times, the carcinomas presenting shorter collagen fibres indicate a worse survival rate.
Influence of alkaline modification on selected properties of banana fiber paperbricks
Authors: Akinwande Abayomi A. , Adediran Adeolu A. , Balogun Oluwatosin A. , Olusoju Oluwaseyi S. , Adesina Olanrewaju S. 
Published: March 2021

AbstractIn a bid to develop paper bricks as alternative masonry units, unmodified banana fibers (UMBF) and alkaline (1 Molar aqueous sodium hydroxide) modified banana fibers (AMBF), fine sand, and ordinary Portland cement were blended with waste paper pulp. The fibers were introduced in varying proportions of 0, 0.5, 1.0 1.5, 2.0, and 2.5 wt% (by weight of the pulp) and curing was done for 28 and 56 days. Properties such as water and moisture absorption, compressive, flexural, and splitting tensile strengths, thermal conductivity, and specific heat capacity were appraised. The outcome of the examinations carried out revealed that water absorption rose with fiber loading while AMBF reinforced samples absorbed lesser water volume than UMBF reinforced samples; a feat occasioned by alkaline treatment of banana fiber. Moisture absorption increased with paper bricks doped with UMBF, while in the case of AMBF-paper bricks, property value was noted to depreciate with increment in AMBF proportion. Fiber loading resulted in improvement of compressive, flexural, and splitting tensile strengths and it was noted that AMBF reinforced samples performed better. The result of the thermal test showed that incorporation of UMBF led to depreciation in thermal conductivity while AMBF infusion in the bricks initiated increment in value. Opposite behaviour was observed for specific heat capacity as UMBF enhanced heat capacity while AMBF led to depreciation. Experimental trend analysis carried out indicates that curing length and alkaline modification of fiber were effective in maximizing the properties of paperbricks for masonry construction.
Spatio-temporal alterations in retinal and choroidal layers in the progression of age-related macular degeneration (AMD) in optical coherence tomography
Authors: Vogl Wolf-Dieter , Bogunović Hrvoje , Waldstein Sebastian M. , Riedl Sophie , Schmidt-Erfurth Ursula 
Published: March 2021

AbstractAge-related macular degeneration (AMD) is the predominant cause of vision loss in the elderly with a major impact on ageing societies and healthcare systems. A major challenge in AMD management is the difficulty to determine the disease stage, the highly variable progression speed and the risk of conversion to advanced AMD, where irreversible functional loss occurs. In this study we developed an optical coherence tomography (OCT) imaging based spatio-temporal reference frame to characterize the morphologic progression of intermediate age-related macular degeneration (AMD) and to identify distinctive patterns of conversion to the advanced stages macular neovascularization (MNV) and macular atrophy (MA). We included 10,040 OCT volumes of 518 eyes with intermediate AMD acquired according to a standardized protocol in monthly intervals over two years. Two independent masked retina specialists determined the time of conversion to MNV or MA. All scans were aligned to a common reference frame by intra-patient and inter-patient registration. Automated segmentations of retinal layers and the choroid were computed and en-face maps were transformed into the common reference frame. Population maps were constructed in the subgroups converting to MNV (n=135), MA (n=50) and in non-progressors (n=333). Topographically resolved maps of changes were computed and tested for statistical significant differences. The development over time was analysed by a joint model accounting for longitudinal and right-censoring aspect. Significantly enhanced thinning of the outer nuclear layer (ONL) and retinal pigment epithelium (RPE)–photoreceptorinner segment/outer segment (PR-IS/OS) layers within the central 3 mm and a faster thinning speed preceding conversion was documented for MA progressors. Converters to MNV presented an accelerated thinning of the choroid and appearance changes in the choroid prior to MNV onset. The large-scale automated image analysis allowed us to distinctly assess the progression of morphologic changes in intermediate AMD based on conventional OCT imaging. Distinct topographic and temporal patterns allow to prospectively determine eyes with risk of progression and thereby greatly improving early detection, prevention and development of novel therapeutic strategies.
Multilayer representation of collaboration networks with higher-order interactions
Authors: Vasilyeva E. , Kozlov A. , Alfaro-Bittner K. , Musatov D. , Raigorodskii A. M. , Perc M. , Boccaletti S. 
Published: March 2021

AbstractCollaboration patterns offer important insights into how scientific breakthroughs and innovations emerge in small and large research groups. However, links in traditional networks account only for pairwise interactions, thus making the framework best suited for the description of two-person collaborations, but not for collaborations in larger groups. We therefore study higher-order scientific collaboration networks where a single link can connect more than two individuals, which is a natural description of collaborations entailing three or more people. We also consider different layers of these networks depending on the total number of collaborators, from one upwards. By doing so, we obtain novel microscopic insights into the representativeness of researchers within different teams and their links with others. In particular, we can follow the maturation process of the main topological features of collaboration networks, as we consider the sequence of graphs obtained by progressively merging collaborations from smaller to bigger sizes starting from the single-author ones. We also perform the same analysis by using publications instead of researchers as network nodes, obtaining qualitatively the same insights and thus confirming their robustness. We use data from the arXiv to obtain results specific to the fields of physics, mathematics, and computer science, as well as to the entire coverage of research fields in the database.