bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long non-coding RNA H19 regulates matrisome signature and impacts cell behavior on MSC-engineered extracellular matrices
Authors: Moura Sara Reis , Freitas Jaime , Ribeiro-Machado Cláudia , Lopes Jorge , Neves Nuno , Canhão Helena , Rodrigues Ana Maria , Barbosa Mário Adolfo , Almeida Maria Ines 
Published: August 2022

Abstract
BackgroundProteins, protein-encoding transcripts and microRNAs have been investigated as molecular drivers of bone regeneration but few reached clinical relevance, while the vast and promising class of long non-coding RNAs (lncRNAs) remains poorly studied. The lncRNA H19 mediates osteogenic differentiation of Mesenchymal Stem/Stromal Cells (MSCs) through the control of intracellular pathways. However, the effect of H19 over the extracellular matrix (ECM) components remains largely unknown. This study was designed to decode the H19-mediated ECM regulatory network and to reveal how the decellularized siH19-engineered matrices influence MSC proliferation and fate. This is particularly relevant for diseases in which the ECM regulation and remodelling processes are disrupted, such as in osteoporosis.MethodsMass spectrometry-based quantitative proteomics analysis was used to identify ECM components, after oligonucleotides delivery to osteoporosis-derived hMSCs. qRT-PCR, immunofluorescence and proliferation, differentiation, apoptosis assays were performed. Engineered matrices were decellularized, characterized by atomic force microscopy and repopulated with hMSC and pre-adipocytes. Clinical bone samples were characterized by histomorphometry analysis. ResultsOur study provides an in-depth proteome-wide and matrisome-specific analysis of the ECM proteins controlled by the lncRNA H19. Using bone-marrow isolated MSC from osteoporosis patients, we identified fibrillin-1 (FBN1), vitronectin (VTN) and collagen triple helix repeat containing 1 (CTHRC1), among others, as having different pattern levels following H19 silencing. Decellularized siH19-engineered matrices are less dense and with a decreased collagen content compared with control matrices. Repopulation with naïve MSCs promotes a shift towards the adipogenic lineage in detriment of the osteogenic lineage and inhibits proliferation. In pre-adipocytes, these siH19-matrices enhance lipid droplets formation. Mechanistically, H19 is targeted by miR-29c, which expression is decreased in osteoporotic bone clinical samples. Accordingly, miR-29c impacts MSC proliferation and collagen production, but do not influence ALP staining or mineralization, revealing H19 silencing and miR-29c mimics have complementary but not overlapping functions.ConclusionOur data suggests H19 as a therapeutic target to engineer the bone ECM and control cell behaviour.
The expression of genes on chromosome 20q defines the mucinous characteristic of colorectal cancer
Authors: Seishima Ryo , Ogiri Masayo , Monno Masayoshi , Suzuki Yoshiyuki , Hattori Kaoru , Matsui Shimpei , Shigeta Kohei , Okabayashi Koji , Kitagawa Yuko 
Published: August 2022

Abstract
Colorectal mucinous adenocarcinoma (MAC) is one of the poorest prognostic types of histological diagnoses, and its mechanism of development is not well understood. In this study, we aimed to clarify the molecular characteristics of MAC from the perspective of chromosomal instability. In silico analysis using The Cancer Genome Atlas database revealed that there was a significant difference in copy number alteration of chromosome 20q (Chr20q) between MAC and nonmucinous adenocarcinoma (NMAC). In addition, the expression of genes on Chr20q was negatively associated with the expression of MUC2, which is a key molecule that can be used to distinguish the two histological types. We further identified 475 differentially expressed genes (DEGs) between MAC and NMAC, and some of the Chr20q genes in DEGs are considered to be pivotal genes used to define MAC. In vitro analysis showed that simultaneous knockdown of POFUT1 and PLAGL2, both of which are located on Chr20q, attenuated MUC2 expression. Moreover, these genes were highly expressed in NMAC but not in MAC according to the results of immunohistological studies using human samples. In conclusion, the genes on Chr20q are considered to be important for defining MAC.
Cholinergic signaling influences the expression of immune checkpoint inhibitors, PD-L1 and PD-L2, in human colorectal cancer tissues and cell lines
Authors: Kuol Nyanbol , Godlewski Janusz , Kmiec Zbigniew , Vogrin Sara , Fraser Sarah , Apostolopoulos Vasso , Nurgali Kulmira 
Published: August 2022

Abstract
Background
Cancer cells express immunosuppressive molecules, such as programmed death ligands (PD-L)1 and PD-L2, enabling evasion from the host's immune system. Cancer cells synthesize and secrete acetylcholine (ACh), acting as an autocrine or paracrine hormone to promote their proliferation, differentiation, and migration.
Methods
We correlated the expression of PD-L1, PD-L2, cholinergic muscarinic receptor 3 (M3R), alpha 7 nicotinic receptor (α7nAChR), and choline acetyltransferase (ChAT) in colorectal cancer (CRC) tissues with the stage of disease, gender, age, risk, and patient survival. The effects of a muscarinic receptor blocker, atropine, and a selective M3R blocker, 4-DAMP, on the expression of immunosuppressive and cholinergic markers were evaluated in human CRC (LIM-2405, HT-29) and intestinal epithelial (T4056) cells.
Results
Increased expression of PD-L1, M3R, and ChAT at stages III-IV was associated with a high risk of CRC and poor survival outcomes independent of patients' gender and age. α7nAChR and PD-L2 were not changed at any CRC stages. Atropine and 4-DAMP suppressed proliferation and migration of human CRC and T4056 cells, induced apoptosis, and decreased PD-L1, PD-L2, and M3R expression in CRC cells via inhibition of EGFR and phosphorylation of ERK and STAT3.
Conclusions
The expression of immunosuppressive and cholinergic markers may increase the risk of recurrence of CRC. These markers might be used in determining prognosis and treatment regimens for CRC patients. Blocking cholinergic signaling may be a potential therapeutic for CRC through anti-proliferation and anti-migration via inhibition of EGFR and phosphorylation of ERK and STAT3. These effects allow the immune system to recognize and eliminate cancer cells.
Design for welding: an application in top class cars chassis
Authors: Renzi Cristina , Leali Francesco 
Published: August 2022

Abstract
High quality standards and components downsizing are two main quests of the engineering designers in the nowadays automotive industry. To this aim, lightweight materials as aluminum are used. Moreover, most parts of the automotive chassis made of aluminum are assembled by means of welding techniques. Lightweight materials, such as aluminum, are more and more adopted in chassis design even if the assembly process represents a challenge from a technological point of view, especially due to the distortions caused by the welding process. In case of thin aluminum structures, non-convenient distortions occur due to a combination of effects of fixturing and cooling (after welding) process. The reduction of distortions or almost their prediction is still a very challenging issue, so that no conclusive technique has been found to exclusively fix the problem yet. In this paper, a “design for welding” approach is proposed as an integrated product design and process simulation method, with the aim of predicting the final distortion of an aluminum welded automotive chassis. Thermal-Elastic-Plastic (TEP) finite element analyses (FEA) simulations are capable to provide acceptable results, but require high computational efforts, especially in case of complex geometries as car chassis. To overcome this problem, in this paper, the local-global FEA approach has been adopted with satisfactory results. A top-class car automotive aluminum chassis has been chosen as a case study.
Species-level drivers of avian centrality within seed-dispersal networks across different levels of organization
Authors: Moulatlet Gabriel , Dáttilo Wesley , Villalobos Fabricio 
Published: August 2022

Abstract
Bird-plant seed-dispersal networks are structural components of ecosystems and have been used to assess species’ functional roles. The role that bird species play in seed-dispersal networks (from less connected [peripheral] to more connected [central]), determine the interaction patterns and their ecosystem services. These roles may be determined by drivers related to morphological and functional traits, evolutionary properties, geography, and environmental conditions acting at different spatial and temporal scales. However, it is still unknown if such drivers are equally important in determining species centrality at different network levels, from individual local networks to the global meta-network representing interactions across all local networks. Here, using a dataset of 314 local networks covering five continents and eleven biogeographic regions, we show that drivers related to geography are more important in explaining species centrality in the meta-network, but these drivers were not as important in local networks. At the global meta-network level, we found that species’ range size was the most important driver with more central species having larger range sizes, which would facilitate the interaction with a higher number of plant species and thus the maintenance of seed-dispersal interaction patterns at the global scale. Morphological traits such as beak width, body mass, and wing length had secondary explanatory power. At the local network level, none of the tested drivers of centrality had significant effects, perhaps because local factors related to resource availability are more important at this scale. Taken together, our results show that the drivers determining species centrality are scale dependent, suggesting that prediction and protection of species functional roles in seed-dispersal interactions requires a combined local and global approach.
A BLADE-ON-PETIOLE ortholog regulates floral proximodistal patterning in Torenia fournieri
Authors: SU Shihao , Lei Yawen , Zhou Xuan , Suzuki Takamasa , Xiao Wei , Higashiyama Tetsuya 
Published: August 2022

Abstract
The three-dimensional shape of a flower is integrated by morphogenesis along different independent floral axes. Differentiation along the floral proximodistal axis is tightly linked to specification of pollinators; however, it is still obscure how a flower patterns its proximodistal axis. The corolla of a Torenia fournieri flower exhibits strong differentiation along the proximodistal axis, including a distal petal lobe region, an intermediate corolla tube, and a proximal corolla neck region that is control by an ALOG (Arabidopsis LSH1 and Oryza G1) family homolog, TfALOG3. In this study, we report a floral specific BOP (BLADE-ON-PETIOLE) gene, TfBOP2, which is predominantly expressed in the proximal region of corolla. CRISPR knockout mutants of TfBOP2 have shorter proximal corolla tube and longer distal lobe region, with ectopic growth of conical cells in the fusion boundaries of corolla tube, consistent with its expression pattern as a proximal regulator. Mutants of BOP homologs in Arabidopsis thaliana also shows developmental defects in petal proximal region, favoring a conserved role of BOPs among different species. Genetic analysis demonstrates interaction between TfBOP2 and TfALOG3 in the control of corolla proximodistal patterning, since double mutants have shortest proximal corolla tube, while exhibiting normal boundary fusion. We further find that TfALOG3 physically interacts with TfBOP2, and can recruit TfBOP2 to the nucleus region, indicating their function possibly as a dimer. Our study unveils a plant universal BOP-ALOG complex being recruited to regulate flower proximodistal patterning of T. fournieri.
Transcriptional alteration in NF-κB-associated long noncoding RNAs in the gastric tissue of the Helicobacter pylori infected and non-infected patients with chronic gastritis
Authors: Ghanbarian Marzieh , Bakhtiari Ronak , Mirbagheri Seyedeh Zohre , Rezaei Fatemeh , Foroushani Abbas Rahimi , Alebouyeh Masoud 
Published: August 2022

Abstract
Background
Helicobacter pylori could colonize the gastric mucosa and cause gastritis, gastric ulcer and gastric cancer. Numerous virulence factors have been identified in this bacterium that play important roles in the promotion of gastric disorders. Although the interaction of long noncoding RNAs (lncRNAs) with transcription, processing, and translation of genes associated with different diseases are described, their interaction with the inflammatory genes and H. pylori infection in the gastric tissue is not well known. In this study, H. pylori infection and its effect on the transcription of common lncRNAs that regulate NF-κB expression were analyzed relative to the non-infected patients.
Materials and Methods
Two groups of H. pylori-infected and non-infected patients with chronic gastritis were included in the study after general histopathological and microbiological analysis. Genotyping of the H. pylori strains was done by PCR and relative changes in the expression of NF-κB and regulatory lncRNAs, lincRNA-p21, MALAT1, NKILA, were measured by relative quantitative real time-PCR.
Results
Significant increase in the NF-κB gene expression was shown, while the expression level of MALAT1, lincRNA-p21 and NKILA genes decreased in the infected patients compared with the non-infected patients. Our results showed that the hypervirulent strain with oipA“on”/HP-NAP+/iceA1+/iceA2+/vacA s1m1/s1m2+/cagA+ genotype can promote a higher level of NF-κB transcription in the inflamed tissue.
Conclusion
H. pylori infection could promote down-regulation of lincRNA-p21, MALAT1 and NKILA in the infected gastric tissue that is correlated with upregulation of NF-κB. More detailed studies are needed to show link between the virulence genes and their impact on the deregulation of lncRNAs in the gastric tissue.
Cervical precancerous and cancerous lesions screening using Pap smear test at Provincial Referral Hospital of Bukavu, Eastern DR Congo: profile and recommendations to stakeholders
Authors: Mayeri Daniel Garhalangwanamuntu , Pierre Mulumeoderhwa Kahasha , Kibalama Isaac Barhishindi , Mongane Jules , Medina Louguè , Birindwa Etienne Kajibwami , Serge Chentwali Mwimangire , Claude Kalegamire Kikuru , Jeanne Maningo Materanya , Yvette Kujirakwinja Bisimwa , Benjamin Kasago , Léon-Emmanuel Mubenga Mukengeshai 
Published: August 2022

Abstract
Introduction: Cervical cancer is a health concern worldwide. The South Kivu Province in the Eastern DR Congo is facing many cases of this disease but poorly screened and reported. The objective of this was to determine the prevalence of cell abnormalities at cervical cytology in a tertiary teaching Hospital in Bukavu and their association with common risk factors of cervical cancer$Methods: A cross sectional study was conducted on 142 women attending the Provincial Referral Hospital of Bukavu (HPGRB) from February to December 2021. Quantitative variables were described by their median following their asymmetric distributions and the qualitative variables in absolute and relative frequencies. Then the Chi-square test was used for the comparison of proportion.ResultsForty-five per cent of the participants had between three and five children. Twenty-two (15.5%) of the 142 patients reported to have two or more sexual partners and 17.5% reported the use of hormonal contraception. The prevalence of cell abnormalities at cervical cytology was 17 % of which Low- Grade Squamous Intraepithelial Lesion (LSIL) was the most representative (12.9%).There was no statistically significant association between the common cervical risk factors and the occurrence of cell abnormalities.ConclusionCervical Pre (cancerous lesions are frequent in South Kivu province. The Pap smear test remains an early and affordable screening method and constitutes a secondary prevention strategy in women of 18 years and older in a low-income country such as DR Congo where vaccination against HPV is still hypothetic
Wild deer contribute to the sylvatic cycle of Neospora caninum in Australia
Authors: Huaman Jose L. , Pacioni Carlo , Doyle Mark , Forsyth David M. , Helbig Karla J. , Carvalho Teresa G. 
Published: August 2022

Abstract
Background
Infections with the coccidian parasite Neospora caninum affect domestic and wild animals worldwide. In Australia, N. caninum infections cause considerable losses to the cattle industry, but livestock infection source is contentious. Similarly, the role of wild animals, such as wild deer and kangaroos, in maintaining the parasite cycle is also unclear. It is possible that native or introduced herbivorous species could be reservoir hosts of N. caninum in Australia, but to date, this has not been investigated.
Results
We report here the first large-scale screening of the immune status of wild deer in Australia, spanning three species. In so doing, we also assessed two commercial cELISA tests validated for detecting N. caninum in cattle for their ability to detect N. caninum antibodies in serum samples of wild deer. N. caninum antibodies were detected in 3.7% of the wild deer serum samples collected in south-eastern Australia (n = 189), including 97 fallow deer, 14 red deer, and 78 sambar deer.
Conclusions
Overall, our study provides the first evidence of N. caninum antibody profiles in wild deer, quantifying deer's potential role in the sylvatic cycle of N. caninum, and epidemiological baseline information relevant for managing N. caninum infections in Australia.
Characterization of a polyclonal antibody that is highly selective for the D-isoAsp-25 variant of mammalian histone H2b
Authors: Aswad Dana W. , O'Leary Kevin S. , Williams Katherine 
Published: August 2022

Abstract
Approximately 12% of histone H2b molecules in mammalian brain contain a modification wherein Asp-25 is present as the D-enantiomer, and is mostly linked to Gly-26 via the side-chain carboxyl. Here we (1) demonstrate the high specificity of a polyclonal antibody to this modification, and (2) use this Ab to demonstrate that this modification is enriched in brain relative to liver, thymus, and HeLa cells.
Role of Gastric Aspirate Polymorphs in Diagnosis of Early Onset Neonatal Sepsis
Authors: Chaudhary¹ Dinesh , Basnet² Sahisnuta , Gauchan Eva , Gupta Binod Kumar , Chaudhary Nagendra , kafle Raju , Singh Shivani 
Published: August 2022

Abstract
Introduction
: Neonatal sepsis is one of the major causes of morbidity and mortality in the newborn. Early diagnosis of neonatal septicemia is the cornerstone for the successful management and favorable outcome. It is a challenge because of non-specific symptoms and signs of neonatal sepsis. Gastric aspirate cytology has been used for the diagnosis of neonatal infection. The presence of more than five polymorphs per high power field co-relate with neonatal infection.
Objective
To study correlation between positive gastric aspirate and development of early onset neonatal sepsis.
Methods
This is a Prospective Hospital based cross sectional Study conducted at Neonatal Intensive Care Unit (NICU) of Department of Pediatrics, Manipal Teaching Hospital, Pokhara, Nepal from November 2017 to May 2019. A total of 96 cases who were admitted in NICU suspected with EONS were included in the study. Under all aseptic conditions, nasogastric tube was inserted and gastric fluid was collected and sent to the pathology department. All slides were stained with Leishman’s stain and then examined for the presence of neutrophils under light microscope.
Results
Out of 96 neonates, 24 were blood culture positive and 72 were culture negative. Gastric aspirate examination was positive in 61 patients and negative in 35 patients. Gastric aspirate is more positive in term and normal birth weight babies. Among 61 gastric aspirate positive cases 21 are blood culture positive and 40 are culture negative (p = 0.005). Among other acute phase reactant, gastric aspirate has highest sensitivity (87.5%).
Conclusions
The present study concludes that gastric aspirate polymorphs are good screening tool in the early detection of early neonatal sepsis in a resource limited settings.
Global functional spectrum of soil bacterial communities
Authors: Piton Gabin , Allison Steven , Bahram Mohammad , Hildebrand Falk , Martiny Jennifer , Treseder Kathleen K. , Martiny Adam 
Published: August 2022

Abstract
Despite the tremendous importance of soil bacterial communities in biogeochemical cycles, the main functional variations developed by soil bacteria communities in-situ (as opposed to culture conditions) across the globe, and their environmental drivers has yet to be elucidated. Here we use shotgun metagenomes from all terrestrial biomes to characterize a genomic trait based soil bacteria’s functional spectrum, simplifying in two dimensions 53% of the global variation of their functional potential. Using machine learning, we show that soil pH, P content and climate (Precipitation patterns and temperature) predict 78% and 45% of the first and second dimension of the spectrum, respectively. The first dimension captures a continuum from small to large genomes associated with an increase of metabolism and resource acquisition complexity and versatility. Decrease in water stress and increased acidity drives this shift from small- to large-genome. The second dimension shows a continuum from microbial necromass and nutrient usage specialists to reactive degraders of simple carbons with more CAZy, rRNA and sigma factor genes. This shift to reactive bacteria was observed when climate restrains the growing window (low precipitation with high seasonality and extreme temperature) and pH becomes acidic. Overall, our study showed that metabolism versatility, reactivity and stoichiometry dominate soil bacteria functional spectrum across the globe.