bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collective protection against the type VI secretion system in bacteria
Authors: Granato Elisa T , Smith William P J , Foster Kevin R 
Published: April 2023

Abstract
Bacteria commonly face attacks from other strains using the type VI secretion system (T6SS), which acts like a molecular speargun to stab and intoxicate competitors. Here we show how bacteria can work together to collectively defend themselves against these attacks. This project began with an outreach activity: while developing an online computer game of bacterial warfare, we noticed that one strategist (“Slimy”) that made extracellular polymeric substances (EPS) was able to resist attacks from another strategist that employed the T6SS (“Stabby”). This observation motivated us to model this scenario more formally, using dedicated agent-based simulations. The model predicts that EPS production can serve as a collective defence mechanism, which protects both producing cells and neighbouring cells that do not make EPS. We then tested our model with a synthetic community that contains a T6SS-wielding attacker (Acinetobacter baylyi), and two T6SS-sensitive target strains (Escherichia coli) that either secrete EPS, or not. As predicted by our modelling, we find that the production of EPS leads to collective protection against T6SS attacks, where EPS producers protect each other and nearby non-producers. We identify two processes that explain this protection: EPS sharing between cells and a second general mechanism whereby groups of resistant cells shield susceptible cells, which we call “flank protection”. Our work shows how EPS-producing bacteria can work together to defend themselves from the type VI secretion system.
CSF neurochemical profile and cognitive changes in Parkinson’s disease with mild cognitive impairment
Authors: Paolini Paoletti Federico , Gaetani Lorenzo , Bellomo Giovanni , Chipi Elena , Salvadori Nicola , Montanucci Chiara , Mancini Andrea , Filidei Marta , Nigro Pasquale , Simoni Simone , Tambasco Nicola , Di Filippo Massimiliano , Parnetti Lucilla 
Published: April 2023

AbstractPathophysiological substrate(s) and progression of Parkinson’s disease (PD) with mild cognitive impairment (PD-MCI) are still matter of debate. Baseline cerebrospinal fluid (CSF) neurochemical profile and cognitive changes after 2 years were investigated in a retrospective series of PD-MCI (n =48), cognitively normal PD (PD-CN,n = 40), prodromal Alzheimer’s disease (MCI-AD,n = 25) and cognitively healthy individuals with other neurological diseases (OND,n = 44). CSF biomarkers reflecting amyloidosis (Aβ42/40 ratio, sAPPα, sAPPβ), tauopathy (p-tau), neurodegeneration (t-tau, NfL, p-NfH), synaptic damage (α-syn, neurogranin) and glial activation (sTREM2, YKL-40) were measured. The great majority (88%) of PD-MCI patients was A-/T-/N-. Among all biomarkers considered, only NfL/p-NfH ratio was significantly higher in PD-MCI vs. PD-CN (p = 0.02). After 2 years, one-third of PD-MCI patients worsened; such worsening was associated with higher baseline levels of NfL, p-tau, and sTREM2. PD-MCI is a heterogeneous entity requiring further investigations on larger, longitudinal cohorts with neuropathological verification.
Tau-targeting antisense oligonucleotide MAPTRx in mild Alzheimer’s disease: a phase 1b, randomized, placebo-controlled trial
Authors: Mummery Catherine J. , Börjesson-Hanson Anne , Blackburn Daniel J. , Vijverberg Everard G. B. , De Deyn Peter Paul , Ducharme Simon , Jonsson Michael , Schneider Anja , Rinne Juha O. , Ludolph Albert C. , Bodenschatz Ralf , Kordasiewicz Holly , Swayze Eric E. , Fitzsimmons Bethany , Mignon Laurence , Moore Katrina M. , Yun Chris , Baumann Tiffany , Li Dan , Norris Daniel A. , Crean Rebecca , Graham Danielle L. , Huang Ellen , Ratti Elena , Bennett C. Frank , Junge Candice , Lane Roger M. 
Published: April 2023

AbstractTau plays a key role in Alzheimer’s disease (AD) pathophysiology, and accumulating evidence suggests that lowering tau may reduce this pathology. We sought to inhibit MAPT expression with a tau-targeting antisense oligonucleotide (MAPTRx) and reduce tau levels in patients with mild AD. A randomized, double-blind, placebo-controlled, multiple-ascending dose phase 1b trial evaluated the safety, pharmacokinetics and target engagement of MAPTRx. Four ascending dose cohorts were enrolled sequentially and randomized 3:1 to intrathecal bolus administrations of MAPTRx or placebo every 4 or 12 weeks during the 13-week treatment period, followed by a 23 week post-treatment period. The primary endpoint was safety. The secondary endpoint was MAPTRx pharmacokinetics in cerebrospinal fluid (CSF). The prespecified key exploratory outcome was CSF total-tau protein concentration. Forty-six patients enrolled in the trial, of whom 34 were randomized to MAPTRx and 12 to placebo. Adverse events were reported in 94% of MAPTRx-treated patients and 75% of placebo-treated patients; all were mild or moderate. No serious adverse events were reported in MAPTRx-treated patients. Dose-dependent reduction in the CSF total-tau concentration was observed with greater than 50% mean reduction from baseline at 24 weeks post-last dose in the 60 mg (four doses) and 115 mg (two doses) MAPTRx groups. Clinicaltrials.gov registration number: NCT03186989.
A ubiquitous method for predicting underground petroleum deposits based on satellite data
Authors: Newaz Sarfaraz , Tahmid Md Toki , Al-Aboody Nadia , Islam A. B. M. Alim Al 
Published: April 2023

AbstractThe method of finding new petroleum deposits beneath the earth’s surface is always challenging for having low accuracy while simultaneously being highly expensive. As a remedy, this paper presents a novel way to predict the locations of petroleum deposits. Here, we focus on a region of the Middle East, Iraq to be specific, and conduct a detailed study on predicting locations of petroleum deposits there based on our proposed method. To do so, we develop a new method of predicting the location of a new petroleum deposit based on publicly available data sensed by an open satellite named Gravity Recovery and Climate Experiment (GRACE). Using GRACE data, we calculate the gravity gradient tensor of the earth over the region of Iraq and its surroundings. We use this calculated data to predict the locations of prospective petroleum deposits over the region of Iraq. In the process of our study for making the predictions, we leverage machine learning, graph-based analysis, and our newly-proposed OR-nAND method altogether. Our incremental improvement in the proposed methodologies enables us to predict 25 out of 26 existing petroleum deposits within the area under our study. Additionally, our method shows some prospective petroleum deposits that need to be explored physically in the future. It is worth mentioning that, as our study presents a generalized approach (demonstrated through investigating multiple datasets), we can apply it anywhere in the world beyond the area focused on in this study as an experimental case.
Altered oral microbiome in Sudanese Toombak smokeless tobacco users carries a newly emerging risk of squamous cell carcinoma development and progression
Authors: Sami Amel , Elimairi Imad , Ryan C. Anthony , Stanton Catherine , Patangia Dhrati , Ross R. Paul 
Published: April 2023

AbstractThere are an estimated 6–10 million smokeless tobacco (Toombak) users in Sudan, the majority being males. Toombak is known to be a carcinogenic product that is likely to modify the oral microbiome spatiality into a high-risk potential for the development and progression of oral cancer, but previous studies are lacking in this field. Here, we endeavour for the first time the exploration of the oral microbiome in key mucosal areas of the oral cavity and assess the microbiome variations in premalignant and oral squamous cell carcinoma (OSCC) samples from both users and non-users of Toombak. 16S rRNA sequencing was performed on DNA obtained from pooled saliva, oral mucosa and supragingival plaque from 78 Sudanese users and non-users of Toombak, aged between 20 and 70 years. In 32 of the pooled saliva samples, the mycobiome (fungal) environment was analysed through ITS sequencing. Then, 46 formalin-fixed paraffin-embedded samples of premalignant and OSCC samples were collected, and their associated microbiomes sequenced. The oral Sudanese microbiome was found to be enriched inStreptococcaceae, butStaphylococcaceaewere significantly more abundant amongst Toombak users. Genera enriched in the oral cavity of Toombak users includedCorynebacterium_1andCardiobacteriumwhile in non-users,Prevotella, LactobacillusandBifidobacteriumwere prominent.Aspergilluswas the most abundant fungus in the mouths of Toombak users with a marked loss ofCandida.The genusCorynebacterium_1was abundant in the buccal, floor of the mouth and saliva microbiomes as well as in oral cancer samples from Toombak users indicating a possible role for this genus in the early stages of oral cancer development. An oral cancer microbiome that favours poor survival and metastasis in those who use Toombak also emerged that includes the generaStenotrophomonasandSchlegelella. Those utilising Toombak carry an altered oral microbiome that may be an additional risk factor for this products carcinogenicity to the oral structures. These significant microbiome modulations are a newly emerging key driving factor in oral cancer development and progression in Toombak users while it is also shown that Toombak users carry an oral cancer microbiome that may increase the potential for a poorer prognosis.
Design and key construction technology of steel-concrete-steel sandwich composite pylon for a large span cable-stayed bridge
Authors: Pei Bida , Chong Aixiu , Xia Huan , Kang Xueyun 
Published: April 2023

AbstractThis paper introduces a new type of steel-concrete composite pylon that has been applied to Nanjing Fifth Yangtze River Bridge (a three-pylon cable-stayed bridge with a main span of 600 m). For this new type of pylon, the steel shells are connected with concrete through PBL shear connectors and studs, and the inner steel shells are connected with the outer steel shells by angle steels. Numerical analysis and full-scale model tests show that the pylon structure exhibits excellent mechanical properties and construction performance. The application of BIM technology, the research and development of special spreaders and construction platforms ensure the precise installation of structures. Highly factory-manufactured modular assembly of the reinforced steel shell structure can effectively reduce the intensity and difficulty of on-site operations, and improve the quality of the project, with low construction risks. Whereas, the successful application of this steel-concrete-steel sandwich composite pylon marks the formation of a complete set of construction technology of steel-concrete-steel sandwich composite pylon, which can be widely used in similar bridges.
Fungicidal activities of Cymbopogon winterianus against anthracnose of banana caused by Colletotrichum musae
Authors: Mangoba Mark Anthony Angeles , Alvindia Dionisio de Guzman 
Published: April 2023

AbstractThe genus Cymbopogon (Poaceae) species have been widely cultivated throughout the world for a wide range of uses in the pharmaceutical and agricultural fields. The current work investigates the fungicidal activities of Cymbopogon winterianus extract (CWE) in controlling the C. musae that caused anthracnose disease in banana fruit. In vitro assay results showed that CWE at 1.5–2.5 gL−1 concentrations controlled the development of the test pathogen. Mycelial blast, cytoplasmic discharge, and spore edema were noticed when CWE was applied. The Minimum Effective Concentration (MEC) of CWE for the in vivo assay was 1.50 gL−1 and can be used as a postharvest treatment on banana fruit to deter anthracnose infection. Moreover, no visible phytotoxicity or changes in aroma were observed on banana fruit treated with CWE, even at the highest concentration of 2.5 gL−1. The GCMS analysis revealed 41 chemical components associated with CWE. The five main compounds were the following: Methyl oleyl ether (40.20%), γ-Sitosterol (15.80%), 6-Methylheptan-3-ol (7.13%), α-Terpineol (5.56%), and n-Pentadecanol (4.05%). The CWE possesses excellent fungicidal effects against C. musae; in the near future, it can be used as an alternative to commercially available traditional fungicides on the market.
SARS-CoV-2 variants and mutational patterns: relationship with risk of ventilator-associated pneumonia in critically ill COVID-19 patients in the era of dexamethasone
Authors: Razazi Keyvan , Martins Bexiga Anissa , Arrestier Romain , Peiffer Bastien , Voiriot Guillaume , Luyt Charles-Edouard , Urbina Tomas , Mayaux Julien , Pham Tài , Roux Damien , Bellaiche Raphael , AIt Hamou Zakaria , Gaudry Stéphane , Azoulay Elie , Mekontso Dessap Armand , Rodriguez Christophe , Pawlotsky Jean-Michel , Fourati Slim , de Prost Nicolas 
Published: April 2023

AbstractWe aimed to explore the relationships between specific viral mutations/mutational patterns and ventilator-associated pneumonia (VAP) occurrence in COVID-19 patients admitted in intensive care units between October 1, 2020, and May 30, 2021. Full-length SARS-CoV-2 genomes were sequenced by means of next-generation sequencing. In this prospective multicentre cohort study, 259 patients were included. 222 patients (47%) had been infected with pre-existing ancestral variants, 116 (45%) with variant α, and 21 (8%) with other variants. 153 patients (59%) developed at least one VAP. There was no significant relationship between VAP occurrence and a specific SARS CoV-2 lineage/sublineage or mutational pattern.
Standardized Centella asiatica (ECa 233) extract decreased pain hypersensitivity development in a male mouse model of chronic inflammatory temporomandibular disorder
Authors: Rotpenpian Nattapon , Wanasuntronwong Aree , Tapechum Sompol , Vattarakorn Anchalee , Care Chit , Chindasri Wongsathit , Tilokskulchai Kanokwan , Tantisira Mayuree H. , Pakaprot Narawut 
Published: April 2023

AbstractChronic inflammatory temporomandibular disorder (TMD) pain has a high prevalence, and available nonspecific treatments have adverse side effects. ECa 233, a standardizedCentella asiaticaextract, is highly anti-inflammatory and safe. We investigated its therapeutic effects by injecting complete Freund’s adjuvant (CFA) into right temporomandibular joint of mice and administering either ibuprofen or ECa 233 (30, 100, and 300 mg/kg) for 28 days. Inflammatory and nociceptive markers, bone density, and pain hypersensitivity were examined. CFA decreased ipsilateral bone density, suggesting inflammation localization, which ipsilaterally caused immediate calcitonin gene-related peptide elevation in the trigeminal ganglia (TG) and trigeminal subnucleus caudalis (TNC), followed by late increase of NaV1.7 in TG and of p-CREB and activation of microglia in TNC. Contralaterally, only p-CREB and activated microglia in TNC showed delayed increase. Pain hypersensitivity, which developed early ipsilaterally, but late contralaterally, was reduced by ibuprofen and ECa 233 (30 or 100 mg/kg). However, ibuprofen and only 100-mg/kg ECa 233 effectively mitigated marker elevation. This suggests 30-mg/kg ECa 233 was antinociceptive, whereas 100-mg/kg ECa 233 was both anti-inflammatory and antinociceptive. ECa 233 may be alternatively and safely used for treating chronic inflammatory TMD pain, showing an inverted U-shaped dose–response relationship with maximal effect at 100 mg/kg.
Novel device for dividing core needle biopsy specimens to provide paired mirror image-like tissues for genetic and pathological tests
Authors: Nakamura Yuichi , Tsuji Keisuke , Shiraishi Takumi , Sako Satoshi , Ogura Ryota , Taga Hideto , Inoue Yuta , Ohashi Munehiro , Ueda Saya , Yamada Takeshi , Ueda Takashi , Fujihara Atsuko , Hongo Fumiya , Ukimura Osamu 
Published: April 2023

AbstractIn a world that seeks precision medicine, genetic testing is gaining importance in clinical decision making. We previously reported the utility of a novel tool for longitudinally dividing core needle biopsy (CNB) tissues into two filamentous tissues that can provide paired mirror image-like tissues (mirror-tissues) that spatially match each other. In this study, we investigated its application in gene panel testing in patients who underwent prostate CNB. Four hundred and forty-three biopsy cores were obtained from 40 patients. Of them, 361 biopsy cores (81.5%) were judged by a physician to be appropriate for dividing into two pieces using the new device, of which a histopathological diagnosis was successfully reached in 358 biopsy cores (99.2%). Among them, the quality and quantity of nucleic acid in 16 appropriately divided cores were assessed and found to be sufficient for gene panel testing, and histopathological diagnosis was successfully obtained from the remaining divided cores. The novel device for longitudinally-dividing CNB tissue provided mirror image-like paired-tissues for gene panel and pathology testing. The device might be a promising tool for obtaining genetic and molecular biological information, in addition to histopathological diagnosis, helping to advance personalized medicine.
Gut microbiota induces hepatic steatosis by modulating the T cells balance in high fructose diet mice
Authors: Zhou Xiaoqiong , Zhang Xianjuan , Niu Delei , Zhang Shuyun , Wang Hui , Zhang Xueming , Nan Fulong , Jiang Shasha , Wang Bin 
Published: April 2023

AbstractMetabolic diseases are often associated with high fructose (HF) consumption. HF has also been found to alter the gut microbiota, which then favors the development of nonalcoholic fatty liver disease. However, the mechanisms underlying of the gut microbiota on this metabolic disturbance are yet to be determined. Thus, in this study, we further explored the effect the gut microbiota concerning the T cells balance in an HF diet mouse model. We fed mice 60% fructose-enriched diet for 12 weeks. At 4 weeks, HF diet did not affect the liver, but it caused injury to the intestine and adipose tissues. After 12 weeks, the lipid droplet aggregation was markedly increased in the liver of HF-fed mice. Further analysis of the gut microbial composition showed that HF decreased theBacteroidetes/Firmicutesratio and increased the levels ofBlautia,Lachnoclostridium, andOscillibacter. In addition, HF can increase the expression of pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β) in the serum. T helper type 1 cells were significantly increased, and regulatory T(Treg) cells were markedly decreased in the mesenteric lymph nodes of the HF-fed mice. Furthermore, fecal microbiota transplantation alleviates systemic metabolic disorder by maintaining liver and intestinal immune homeostasis. Overall, our data indicated that intestinal structure injury and intestinal inflammation might be early, and liver inflammation and hepatic steatosis may be a subsequent effect following HF diets. Gut microbiota disorders impairing the intestinal barrier function and triggering immune homeostasis imbalance may be an importantly responsible for long-term HF diets induced hepatic steatosis.
Composites containing resins and carbon nano-onions as efficient porous carbon materials for supercapacitors
Authors: Siemiaszko Gabriela , Breczko Joanna , Hryniewicka Agnieszka , Ilnicka Anna , Markiewicz Karolina H. , Terzyk Artur P. , Plonska-Brzezinska Marta E. 
Published: April 2023

AbstractHerein, we report the functionalization of carbon nano-onions (CNOs) with the hydroxyaryl group and subsequent modifications with resins: resorcinol–formaldehyde using porogenic Pluronic F-127, resorcinol–formaldehyde-melamine, benzoxazine made of bisphenol A and triethylenetetramine, and calix[4]resorcinarene-derived using F-127. Following the direct carbonization, extensive physicochemical analysis was carried out, including Fourier transform infrared, Raman and X-ray photoelectron spectroscopy, scanning and transmission electron microscopy, and adsorption–desorption of N2. The addition of CNO to the materials significantly increases the total pore volume (up to 0.932 cm3 g−1 for carbonized resorcinol–formaldehyde resin and CNO (RF-CNO-C) and 1.242 cm3 g−1 for carbonized resorcinol–formaldehyde-melamine resin and CNO (RFM-CNO-C)), with mesopores dominating. However, the synthesized materials have poorly ordered domains with some structural disturbance; the RFM-CNO-C composite shows a more ordered structure with amorphous and semi-crystalline regions. Subsequently, cyclic voltammetry and galvanostatic charge–discharge method studied the electrochemical properties of all materials. The influence of resins' compositions, CNO content, and amount of N atoms in carbonaceous skeleton on the electrochemical performance was studied. In all cases, adding CNO to the material improves its electrochemical properties. The carbon material derived from CNO, resorcinol and melamine (RFM-CNO-C) showed the highest specific capacitance of 160 F g−1 at a current density of 2 A g−1, which is stable after 3000 cycles. The RFM-CNO-C electrode retains approximately 97% of its initial capacitive efficiency. The electrochemical performance of the RFM-CNO-C electrode results from the hierarchical porosity's stability and the presence of nitrogen atoms in the skeleton. This material is an optimal solution for supercapacitor devices.
A theoretical approach to zero-reflection toroidal curved metasurfaces
Authors: Allahverdizade Hosein , Aghdasinia Sina , Younesiraad Hemn , Bemani Mohammad 
Published: April 2023

AbstractIn this paper, we investigate the electromagnetic response of metasurfaces due to excitation of the toroidal moment. A toroidal curved metasurface analyzad using a novel theoretical solution based on the Fourier analysis to evaluate the localized fields. Analyzing localized near-field interactions are crucial in investigating the excited trapped modes and enables us to optimize the reflection properties of the proposed metasurface. Optimization is accomplished using graphene layer and resulted a hybrid dielectric-graphene structure with near-zero reflection properties.
Prevalence and hepatic histopathological findings of fascioliasis in sheep slaughtered in Jeddah, Saudi Arabia
Authors: Ashoor Safinaz J. , Wakid Majed H. 
Published: April 2023

AbstractHepatic fascioliasis is an important parasitic disease responsible for morbidity and mortality in many domestic ruminants, especially sheep, goats, and cattle, due to Fasciola (F.) hepatica and F. gigantica. This study aimed to determine the prevalence of fascioliasis in sheep slaughtered in Jeddah, Saudi Arabia, and to describe the morphological and histopathological changes in the liver. A total of 109,253 sheep slaughtered between July 2017 and July 2018 were screened to assess the prevalence of fascioliasis. The livers were grossly investigated for Fasciola infection and morphological changes. Tissue samples were collected for proper histopathological examinations. Livers of local and imported sheep represented infection rates of 0.67% and 2.12%, respectively, and the highest infection rate was in the spring season. Macroscopically, the affected liver showed hepatomegaly, thickened capsule and discoloration with necrosis, fibrosis, dilation of the bile duct, engorgement of the gallbladder and enlargement of the portal lymph nodes. Microscopic examination showed fibrotic thickening, calcification and hyperplasia of the bile ducts filled with debris, as well as massive hemorrhagic foci. Histopathological examinations of the infected liver showed a central vein region with disturbed parenchyma cells, focal lymphocytic infiltration, elongated endothelial cells, blood sinusoids that showed enlarged Kupffer cells, patches of lysed or necrotic hepatocytes, eosinophil infiltration, lymphocytes and proliferating fibroblast, thickening of hepatic artery and arteriolar walls. We concluded that fascioliasis among sheep slaughtered in Jeddah is not uncommon. The identified histopathological changes in the liver of infected sheep reflect tissue damage, which can lead to significant economic losses for the animals.