bluuebunny/crossref_metadata_2025_split huggingface dataset:
A randomised clinical trial of methotrexate points to possible efficacy and adaptive immune dysfunction in psychosis
Authors: Chaudhry I. B. , Husain M. O. , Khoso A. B. , Husain M. I. , Buch M. H. , Kiran T. , Fu B. , Bassett P. , Qurashi I. , ur Rahman R. , Baig S. , Kazmi A. , Corsi-Zuelli F. , Haddad P. M. , Deakin B. , Husain N. 
Published: November 2020

AbstractNMDA autoantibody encephalitis presenting as schizophrenia suggests the possible role of adaptive cell-mediated immunity in idiopathic schizophrenia. However, to our knowledge there have been no trials of the immune-suppressant methotrexate in schizophrenia. We tested if low-dose methotrexate as used in the treatment of systemic autoimmune disorders would be tolerable and effective in people with schizophrenia in a feasibility study. Ninety-two participants within 5 years of schizophrenia diagnosis were recruited from inpatient and outpatient facilities in Karachi, Pakistan. They were randomised to receive once weekly 10-mg oral methotrexate (n = 45) or matching placebo (n = 47) both with daily 5-mg folic acid, in addition to treatment as usual for 12 weeks. There were eight dropouts per group. Side effects were non-significantly more common in those on methotrexate and were not severe. One person developed leukopenia. Positive symptom scores improved more in those receiving methotrexate than placebo (β = −2.5; [95% CI −4.7 to −0.4]), whereas negative symptoms were unaffected by treatment (β = −0.39; [95% CI −2.01 to 1.23]). There were no immune biomarkers but methotrexate did not affect group mean leucocyte counts or C-reactive protein. We conclude that further studies are feasible but should be focussed on subgroups identified by advances in neuroimmune profiling. Methotrexate is thought to work in autoimmune disorders by resetting systemic regulatory T-cell control of immune signalling; we show that a similar action in the CNS would account for otherwise puzzling features of the immuno-pathogenesis of schizophrenia.
A novel lncRNA PTTG3P/miR-132/212-3p/FoxM1 feedback loop facilitates tumorigenesis and metastasis of pancreatic cancer
Authors: Liu Wenyu , Tang Jian , Zhang Huiqing , Kong Fanyang , Zhu Huiyun , Li Ping , Li Zhaoshen , Kong Xiangyu , Wang Kaixuan 
Published: November 2020

AbstractPseudogene pituitary tumor-transforming 3 (PTTG3P) is emerging as a key player in the development and progression of cancer. However, the biological role and clinical significance of PTTG3P in pancreatic ductal adenocarcinoma (PDAC) remain unclear. Here, we found that PTTG3P was significantly upregulated in PDAC tissues. Elevated PTTG3P expression correlated with larger tumor size and worse differentiation, and reduced overall survival. Bioinformatics and experimental evidence revealed that PTTG3P promoted malignant phenotypes and FoxM1 signaling pathway in PDAC cells. Mechanistically, PTTG3P functions as a microRNA sponge to positively regulate the expression of FoxM1 through sponging miR-132/212-3p. Moreover, it showed that FoxM1 transcriptionally activated PTTG3P expression, thus forming a feedback loop to promote the aggressiveness of PDAC cells. Taken together, our findings suggest that PTTG3P promotes PDAC progression through PTTG3P/miR-132/212-3p/FoxM1 feedforward circuitry and it may serve as a promising diagnostic marker or target for treatment in PDAC patients.
Validation of pore network modeling for determination of two-phase transport in fibrous porous media
Authors: Huang Xiang , Zhou Wei , Deng Daxiang 
Published: November 2020

AbstractPore network modeling (PNM) has been widely investigated in the study of multiphase transport in porous media due to its high computational efficiency. The advantage of PNM is achieved in part at the cost of using simplified geometrical elements. Therefore, the validation of pore network modeling needs further verification. A Shan-Chen (SC) multiphase lattice Boltzmann model (LBM) was used to simulate the multiphase flow and provided as the benchmark. PNM using different definitions of throat radius was performed and compared. The results showed that the capillary pressure and saturation curves agreed well when throat radius was calculated using the area-equivalent radius. The discrepancy of predicted phase occupations from different methods was compared in slice images and the reason can be attributed to the capillary pressure gradients demonstrated in LBM. Finally, the relative permeability was also predicted using PNM and provided acceptable predictions when compared with the results using single-phase LBM.
Mammographic tumour appearance is related to clinicopathological factors and surrogate molecular breast cancer subtype
Authors: Sturesdotter Li , Sandsveden Malte , Johnson Kristin , Larsson Anna-Maria , Zackrisson Sophia , Sartor Hanna 
Published: November 2020

AbstractMammographic tumour appearance may provide prognostic useful information. For example, spiculation indicates invasiveness, but also better survival compared to tumours with other appearances. We aimed to study the relationship between mammographic tumour appearance and established clinicopathological factors, including surrogate molecular breast cancer subtypes, in the large Malmö Diet and Cancer Study. A total of 1116 women with invasive breast cancer, diagnosed between 1991 and 2014, were included. Mammographic tumour appearance in relation to status for oestrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2, histological grade, Ki67 and molecular subtype was analysed using various regression models. All models were adjusted for relevant confounders, including breast density, which can affect mammographic appearance. The results consistently showed that spiculated tumours are indicative of favourable characteristics, as they are more likely to be ER and PR positive, and more often exhibit lower histological grade and lower Ki67 expression. Furthermore, spiculated tumours tend to be of luminal A-like subtype, which is associated with a good prognosis. The establishment of associations between mammographic tumour appearance and clinico­pathological factors may aid in characterizing breast cancer at an earlier stage. This could contribute to more individualized breast cancer treatment in the future.
Network extraction by routing optimization
Authors: Baptista Diego , Leite Daniela , Facca Enrico , Putti Mario , De Bacco Caterina 
Published: November 2020

AbstractRouting optimization is a relevant problem in many contexts. Solving directly this type of optimization problem is often computationally intractable. Recent studies suggest that one can instead turn this problem into one of solving a dynamical system of equations, which can instead be solved efficiently using numerical methods. This results in enabling the acquisition of optimal network topologies from a variety of routing problems. However, the actual extraction of the solution in terms of a final network topology relies on numerical details which can prevent an accurate investigation of their topological properties. In fact, in this context, theoretical results are fully accessible only to an expert audience and ready-to-use implementations for non-experts are rarely available or insufficiently documented. In particular, in this framework, final graph acquisition is a challenging problem in-and-of-itself. Here we introduce a method to extract network topologies from dynamical equations related to routing optimization under various parameters’ settings. Our method is made of three steps: first, it extracts an optimal trajectory by solving a dynamical system, then it pre-extracts a network, and finally, it filters out potential redundancies. Remarkably, we propose a principled model to address the filtering in the last step, and give a quantitative interpretation in terms of a transport-related cost function. This principled filtering can be applied to more general problems such as network extraction from images, thus going beyond the scenarios envisioned in the first step. Overall, this novel algorithm allows practitioners to easily extract optimal network topologies by combining basic tools from numerical methods, optimization and network theory. Thus, we provide an alternative to manual graph extraction which allows a grounded extraction from a large variety of optimal topologies. The analysis of these may open up the possibility to gain new insights into the structure and function of optimal networks. We provide an open source implementation of the code online.
Multiscale simulation of the focused electron beam induced deposition process
Authors: de Vera Pablo , Azzolini Martina , Sushko Gennady , Abril Isabel , Garcia-Molina Rafael , Dapor Maurizio , Solov’yov Ilia A. , Solov’yov Andrey V. 
Published: November 2020

AbstractFocused electron beam induced deposition (FEBID) is a powerful technique for 3D-printing of complex nanodevices. However, for resolutions below 10 nm, it struggles to control size, morphology and composition of the structures, due to a lack of molecular-level understanding of the underlying irradiation-driven chemistry (IDC). Computational modeling is a tool to comprehend and further optimize FEBID-related technologies. Here we utilize a novel multiscale methodology which couples Monte Carlo simulations for radiation transport with irradiation-driven molecular dynamics for simulating IDC with atomistic resolution. Through an in depth analysis of $$\hbox {W(CO)}_6$$

W(CO)
6

deposition on $$\hbox {SiO}_2$$

SiO
2

and its subsequent irradiation with electrons, we provide a comprehensive description of the FEBID process and its intrinsic operation. Our analysis reveals that simulations deliver unprecedented results in modeling the FEBID process, demonstrating an excellent agreement with available experimental data of the simulated nanomaterial composition, microstructure and growth rate as a function of the primary beam parameters. The generality of the methodology provides a powerful tool to study versatile problems where IDC and multiscale phenomena play an essential role.
Topical delivery of a small molecule RUNX1 transcription factor inhibitor for the treatment of proliferative vitreoretinopathy
Authors: Delgado-Tirado Santiago , Amarnani Dhanesh , Zhao Guannan , Rossin Elizabeth J. , Eliott Dean , Miller John B. , Greene Whitney A. , Ramos Leslie , Arevalo-Alquichire Said , Leyton-Cifuentes David , Gonzalez-Buendia Lucia , Isaacs-Bernal Daniela , Whitmore Hannah A. B. , Chmielewska Natalia , Duffy Brandon V. , Kim Eric , Wang Heuy-Ching , Ruiz-Moreno Jose M. , Kim Leo A. , Arboleda-Velasquez Joseph F. 
Published: November 2020

AbstractProliferative vitreoretinopathy (PVR) is the leading cause of retinal detachment surgery failure. Despite significant advances in vitreoretinal surgery, it still remains without an effective prophylactic or therapeutic medical treatment. After ocular injury or retinal detachment, misplaced retinal cells undergo epithelial to mesenchymal transition (EMT) to form contractile membranes within the eye. We identified Runt-related transcription factor 1 (RUNX1) as a gene highly expressed in surgically-removed human PVR specimens. RUNX1 upregulation was a hallmark of EMT in primary cultures derived from human PVR membranes (C-PVR). The inhibition of RUNX1 reduced proliferation of human C-PVR cells in vitro, and curbed growth of freshly isolated human PVR membranes in an explant assay. We formulated Ro5-3335, a lipophilic small molecule RUNX1 inhibitor, into a nanoemulsion that when administered topically curbed the progression of disease in a novel rabbit model of mild PVR developed using C-PVR cells. Mass spectrometry analysis detected 2.67 ng/mL of Ro5-3335 within the vitreous cavity after treatment. This work shows a critical role for RUNX1 in PVR and supports the feasibility of targeting RUNX1 within the eye for the treatment of an EMT-mediated condition using a topical ophthalmic agent.
IL-10 based immunomodulation initiated at birth extends lifespan in a familial mouse model of amyotrophic lateral sclerosis
Authors: Strickland Michael R. , Ibanez Kristen R. , Yaroshenko Mariya , Diaz Carolina Ceballos , Borchelt David R. , Chakrabarty Paramita 
Published: November 2020

AbstractInflammatory signaling is thought to modulate the neurodegenerative cascade in amyotrophic lateral sclerosis (ALS). We have previously shown that expression of Interleukin-10 (IL-10), a classical anti-inflammatory cytokine, extends lifespan in the SOD1-G93A mouse model of familial ALS. Here we test whether co-expression of the decoy chemokine receptor M3, that can scavenge inflammatory chemokines, augments the efficacy of IL-10. We found that recombinant adeno-associated virus (AAV)-mediated expression of IL-10, alone, or in combination with M3, resulted in modest extension of lifespan relative to control SOD1-G93A cohort. Interestingly neither AAV-M3 alone nor AAV-IL-10 + AAV-M3 extend survival beyond that of the AAV-IL-10 alone cohort. Focused transcriptomic analysis revealed induction of innate immunity and phagocytotic pathways in presymptomatic SOD1-G93A mice expressing IL-10 + M3 or IL-10 alone. Further, while IL-10 expression increased microglial burden, the IL-10 + M3 group showed lower microglial burden, suggesting that M3 can successfully lower microgliosis before disease onset. Our data demonstrates that over-expression of an anti-inflammatory cytokine and a decoy chemokine receptor can modulate inflammatory processes in SOD1-G93A mice, modestly delaying the age to paralysis. This suggests that multiple inflammatory pathways can be targeted simultaneously in neurodegenerative disease and supports consideration of adapting these approaches to treatment of ALS and related disorders.
Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease
Authors: Dolan Mary E. , Hill David P. , Mukherjee Gaurab , McAndrews Monica S. , Chesler Elissa J. , Blake Judith A. 
Published: November 2020

AbstractThe emergence of the SARS-CoV-2 virus and subsequent COVID-19 pandemic initiated intense research into the mechanisms of action for this virus. It was quickly noted that COVID-19 presents more seriously in conjunction with other human disease conditions such as hypertension, diabetes, and lung diseases. We conducted a bioinformatics analysis of COVID-19 comorbidity-associated gene sets, identifying genes and pathways shared among the comorbidities, and evaluated current knowledge about these genes and pathways as related to current information about SARS-CoV-2 infection. We performed our analysis using GeneWeaver (GW), Reactome, and several biomedical ontologies to represent and compare common COVID-19 comorbidities. Phenotypic analysis of shared genes revealed significant enrichment for immune system phenotypes and for cardiovascular-related phenotypes, which might point to alleles and phenotypes in mouse models that could be evaluated for clues to COVID-19 severity. Through pathway analysis, we identified enriched pathways shared by comorbidity datasets and datasets associated with SARS-CoV-2 infection.
Targeting the endothelin axis as a therapeutic strategy for oral cancer metastasis and pain
Authors: Dang Dongmin , Ye Yi , Aouizerat Bradley E. , Patel Yogin K. , Viet Dan T. , Chan King Chong , Ono Kentaro , Doan Coleen , Figueroa Johnny D. , Yu Gary , Viet Chi T. 
Published: November 2020

AbstractMetastasis reduces survival in oral cancer patients and pain is their greatest complaint. We have shown previously that oral cancer metastasis and pain are controlled by the endothelin axis, which is a pathway comprised of the endothelin A and B receptors (ETAR and ETBR). In this study we focus on individual genes of the pathway, demonstrating that the endothelin axis genes are methylated and dysregulated in cancer tissue. Based on these findings in patients, we hypothesize that ETAR and ETBR play dichotomous roles in oral carcinogenesis and pain, such that ETAR activation and silenced ETBR expression result in increased carcinogenesis and pain. We test a treatment strategy that targets the dichotomous functions of the two receptors by inhibiting ETAR with macitentan, an ETAR antagonist approved for treatment of pulmonary hypertension, and re-expressing the ETBR gene with adenovirus transduction, and determine the treatment effect on cancer invasion (i.e., metastasis), proliferation and pain in vitro and in vivo. We demonstrate that combination treatment of macitentan and ETBR gene therapy inhibits invasion, but not proliferation, in cell culture and in a mouse model of tongue cancer. Furthermore, the treatment combination produces an antinociceptive effect through inhibition of endothelin-1 mediated neuronal activation, revealing the analgesic potential of macitentan. Our treatment approach targets a pathway shown to be dysregulated in oral cancer patients, using gene therapy and repurposing an available drug to effectively treat both oral cancer metastasis and pain in a preclinical model.
TERT promoter alterations could provide a solution for Peto’s paradox in rodents
Authors: Vedelek Balázs , Maddali Asha Kiran , Davenova Nurgul , Vedelek Viktor , Boros Imre M. 
Published: November 2020

AbstractCancer is a genetic disease caused by changes in gene expression resulting from somatic mutations and epigenetic changes. Although the probability of mutations is proportional with cell number and replication cycles, large bodied species do not develop cancer more frequently than smaller ones. This notion is known as Peto’s paradox, and assumes stronger tumor suppression in larger animals. One of the possible tumor suppressor mechanisms involved could be replicative senescence caused by telomere shortening in the absence of telomerase activity. We analysed telomerase promoter activity and transcription factor binding in mammals to identify the key element of telomerase gene inactivation. We found that the GABPA transcription factor plays a key role in TERT regulation in somatic cells of small rodents, but its binding site is absent in larger beavers. Protein binding and reporter gene assays verify different use of this site in different species. The presence or absence of the GABPA TF site in TERT promoters of rodents correlates with TERT promoter activity; thus it could determine whether replicative senescence plays a tumor suppressor role in these species, which could be in direct relation with body mass. The GABPA TF binding sites that contribute to TERT activity in somatic cells of rodents are analogous to those mutated in human tumors, which activate telomerase by a non-ALT mechanism.
Genome-wide association analysis of the strength of the MAMP-elicited defense response and resistance to target leaf spot in sorghum
Authors: Samira Rozalynne , Kimball Jennifer A. , Samayoa Luis Fernando , Holland James B. , Jamann Tiffany M. , Brown Patrick J. , Stacey Gary , Balint-Kurti Peter J. 
Published: November 2020

AbstractPlants have the capacity to respond to conserved molecular features known as microbe-associated molecular patterns (MAMPs). The goal of this work was to assess variation in the MAMP response in sorghum, to map loci associated with this variation, and to investigate possible connections with variation in quantitative disease resistance. Using an assay that measures the production of reactive oxygen species, we assessed variation in the MAMP response in a sorghum association mapping population known as the sorghum conversion population (SCP). We identified consistent variation for the response to chitin and flg22—an epitope of flagellin. We identified two SNP loci associated with variation in the flg22 response and one with the chitin response. We also assessed resistance to Target Leaf Spot (TLS) disease caused by the necrotrophic fungus Bipolaris cookei in the SCP. We identified one strong association on chromosome 5 near a previously characterized disease resistance gene. A moderately significant correlation was observed between stronger flg22 response and lower TLS resistance. Possible reasons for this are discussed.
Understanding the lost functionality of ethanol in non-alcoholic beer using sensory evaluation, aroma release and molecular hydrodynamics
Authors: Ramsey Imogen , Dinu Vlad , Linforth Rob , Yakubov Gleb E. , Harding Stephen E. , Yang Qian , Ford Rebecca , Fisk Ian 
Published: November 2020

AbstractConsumer sensory evaluation, aroma release analysis and biophysical protein analysis were used to investigate the effect of ethanol on the release and perception of flavour in beer (lager and stout) at different ethanol levels (0 and 5% ABV). Consumer study results showed no significant differences in orthonasal perception, yet retronasal results showed that 0% lager was perceived as maltier with reduced fruitiness, sweetness, fullness/body and alcohol warming sensation (p < 0.05). Whilst ethanol alone decreases the aroma release regardless of LogP, the presence of α-amylase selectively reduces the headspace concentration of hydrophobic compounds. It was found that ethanol has a subtle inhibitory effect on the binding of hydrophobic compounds to α-amylase, thereby increasing their headspace concentration in the 5% ABV as compared to the 0% beers. This synergistic ethanol * saliva effect is attributed to the changes in the conformation of α-amylase due to ethanol-induced denaturation. It is hypothesised that the partially unfolded protein structures have a lower number of hydrophobic pockets, leading to a lower capacity to entrap hydrophobic aroma compounds. This supports the hypothesis that ethanol * saliva interactions directly impact the sensory and flavour properties of beer, which would provide a basis for further investigations in reformulation of 0% ABV drinks.
Identification of distinct immune activation profiles in adult humans
Authors: Cezar Renaud , Winter Audrey , Desigaud Delphine , Pastore Manuela , Kundura Lucy , Dupuy Anne-Marie , Cognot Chantal , Vincent Thierry , Reynes Christelle , Dunyach-Remy Catherine , Lavigne Jean-Philippe , Sabatier Robert , Le Merre Patricia , Maggia Elisabeth , Corbeau Pierre 
Published: November 2020

AbstractLatent infectious agents, microbial translocation, some metabolites and immune cell subpopulations, as well as senescence modulate the level and quality of activation of our immune system. Here, we tested whether various in vivo immune activation profiles may be distinguished in a general population. We measured 43 markers of immune activation by 8-color flow cytometry and ELISA in 150 adults, and performed a double hierarchical clustering of biomarkers and volunteers. We identified five different immune activation profiles. Profile 1 had a high proportion of naïve T cells. By contrast, Profiles 2 and 3 had an elevated percentage of terminally differentiated and of senescent CD4+ T cells and CD8+ T cells, respectively. The fourth profile was characterized by NK cell activation, and the last profile, Profile 5, by a high proportion of monocytes. In search for etiologic factors that could determine these profiles, we observed a high frequency of naïve Treg cells in Profile 1, contrasting with a tendency to a low percentage of Treg cells in Profiles 2 and 3. Moreover, Profile 5 tended to have a high level of 16s ribosomal DNA, a direct marker of microbial translocation. These data are compatible with a model in which specific causes, as the frequency of Treg or the level of microbial translocation, shape specific profiles of immune activation. It will be of interest to analyze whether some of these profiles drive preferentially some morbidities known to be fueled by immune activation, as insulin resistance, atherothrombosis or liver steatosis.