bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inflammatory signature in acute-on-chronic liver failure includes increased expression of granulocyte genes ELANE, MPO and CD177
Authors: Saha Rohini , Pradhan Sai Sanwid , Shalimar  , Das Prasenjit , Mishra Priyanka , Singh Rohan , Sivaramakrishnan Venketesh , Acharya Pragyan 
Published: September 2021

AbstractAcute-on-Chronic Liver Failure (ACLF) is associated with innate immune dysfunction and high short-term mortality. Neutrophils have been identified to influence prognosis in ACLF. Neutrophil biology is under-evaluated in ACLF. Therefore, we investigated neutrophil-specific genes and their association with ACLF outcomes. This is an observational study. Enriched granulocytes, containing neutrophils, isolated from study participants in three groups- ACLF(n = 10), chronic liver disease (CLD, n = 4) and healthy controls (HC, n = 4), were analysed by microarray. Differentially expressed genes were identified and validated by qRT-PCR in an independent cohort of ACLF, CLD and HC (n = 30, 15 and 15 respectively). The association of confirmed overexpressed genes with ACLF 28-day non-survivors was investigated. The protein expression of selected neutrophil genes was confirmed using flow cytometry and IHC. Differential gene expression analysis showed 1140 downregulated and 928 upregulated genes for ACLF versus CLD and 2086 downregulated and 1091 upregulated genes for ACLF versus HC. Significant upregulation of neutrophilic inflammatory signatures were found in ACLF compared to CLD and HC. Neutrophil enriched genes ELANE, MPO and CD177 were highly upregulated in ACLF and their expression was higher in ACLF 28-day non-survivors. Elevated expression of CD177 protein on neutrophil surface in ACLF was confirmed by flow cytometry. IHC analysis in archival post mortem liver biopsies showed the presence of CD177+ neutrophils in the liver tissue of ACLF patients. Granulocyte genes ELANE, MPO and CD177 are highly overexpressed in ACLF neutrophils as compared to CLD or HC. Further, this three-gene signature is highly overexpressed in ACLF 28-day non-survivors.
Early postoperative urinary MCP-1 as a potential biomarker predicting acute rejection in living donor kidney transplantation: a prospective cohort study
Authors: Jang Hye Ryoun , Kim Minjung , Hong Sungjun , Lee Kyungho , Park Mee Yeon , Yang Kyeong Eun , Lee Cheol-Jung , Jeon Junseok , Lee Kyo Won , Lee Jung Eun , Park Jae Berm , Kim Kyunga , Kwon Ghee Young , Kim Yoon Goo , Kim Dae Joong , Huh Wooseong 
Published: September 2021

AbstractWe investigated the clinical relevance of urinary cytokines/chemokines reflecting intrarenal immunologic micromilieu as prognostic markers and the optimal measurement timing after living donor kidney transplantation (LDKT). This prospective cohort study included 77 LDKT patients who were followed for ≥ 5 years. Patients were divided into control (n = 42) or acute rejection (AR, n = 35) group. Early AR was defined as AR occurring within 3 months. Serum and urine cytokines/chemokines were measured serially as follows: intraoperative, 8/24/72 h, 1 week, 3 months, and 1 year after LDKT. Intrarenal total leukocytes, T cells, and B cells were analyzed with immunohistochemistry followed by tissueFAXS. Urinary MCP-1 and fractalkine were also analyzed in a validation cohort. Urinary MCP-1 after one week was higher in the AR group. Urinary MCP-1, fractalkine, TNF-α, RANTES, and IL-6 after one week were significantly higher in the early AR group. Intrarenal total leukocytes and T cells were elevated in the AR group compared with the control group. Urinary fractalkine, MCP-1, and IL-10 showed positive correlation with intrarenal leukocyte infiltration. Post-KT 1 week urinary MCP-1 showed predictive value in the validation cohort. One-week post-KT urinary MCP-1 may be used as a noninvasive diagnostic marker for predicting AR after LDKT.
Transparent qubit manipulations with spin-orbit coupled two-electron nanowire quantum dot
Authors: Hai Kuo , Wang Yifan , Chen Qiong , Hai Wenhua 
Published: September 2021

AbstractWe report on the first set of exact orthonormalized states to an ac driven one-dimensional (1D) two-electron nanowire quantum dot with the Rashba–Dresselhaus coexisted spin-orbit coupling (SOC) and the controlled magnetic field orientation and trapping frequency. In the ground state case, it is shown that the spatiotemporal evolutions of probability densities occupying internal spin states and the transfer rates between different spin states can be adjusted by the ac electric field and the intensities of SOC and magnetic field. Effects of the system parameters and initial-state-dependent constants on the mean entanglement are revealed, where the approximately maximal entanglement associated with the stronger SOC and its insensitivity to the initial and parametric perturbations are demonstrated numerically. A novel resonance transition mechanism is found, in which the ladder-like time-evolution process of expected energy and the transition time between two arbitrary exact states are controlled by the ac field strength. Using such maximally entangled exact states to encode qubits can render the qubit control more transparent and robust. The results could be extended to 2D case and to an array of two-electron quantum dots with weak neighboring coupling for quantum information processing.
Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis
Authors: Reis Ana C. , Cunha Mónica V. 
Published: September 2021

AbstractGenome sequencing has reinvigorated the infectious disease research field, shedding light on disease epidemiology, pathogenesis, host–pathogen interactions and also evolutionary processes exerted upon pathogens. Mycobacterium tuberculosis complex (MTBC), enclosing M. bovis as one of its animal-adapted members causing tuberculosis (TB) in terrestrial mammals, is a paradigmatic model of bacterial evolution. As other MTBC members, M. bovis is postulated as a strictly clonal, slowly evolving pathogen, with apparently no signs of recombination or horizontal gene transfer. In this work, we applied comparative genomics to a whole genome sequence (WGS) dataset composed by 70 M. bovis from different lineages (European and African) to gain insights into the evolutionary forces that shape genetic diversification in M. bovis. Three distinct approaches were used to estimate signs of recombination. Globally, a small number of recombinant events was identified and confirmed by two independent methods with solid support. Still, recombination reveals a weaker effect on M. bovis diversity compared with mutation (overall r/m = 0.037). The differential r/m average values obtained across the clonal complexes of M. bovis in our dataset are consistent with the general notion that the extent of recombination may vary widely among lineages assigned to the same taxonomical species. Based on this work, recombination in M. bovis cannot be excluded and should thus be a topic of further effort in future comparative genomics studies for which WGS of large datasets from different epidemiological scenarios across the world is crucial. A smaller M. bovis dataset (n = 42) from a multi-host TB endemic scenario was then subjected to additional analyses, with the identification of more than 1,800 sites wherein at least one strain showed a single nucleotide polymorphism (SNP). The majority (87.1%) was located in coding regions, with the global ratio of non-synonymous upon synonymous alterations (dN/dS) exceeding 1.5, suggesting that positive selection is an important evolutionary force exerted upon M. bovis. A higher percentage of SNPs was detected in genes enriched into “lipid metabolism”, “cell wall and cell processes” and “intermediary metabolism and respiration” functional categories, revealing their underlying importance in M. bovis biology and evolution. A closer look on genes prone to horizontal gene transfer in the MTBC ancestor and included in the 3R (DNA repair, replication and recombination) system revealed a global average negative value for Taijima’s D neutrality test, suggesting that past selective sweeps and population expansion after a recent bottleneck remain as major evolutionary drivers of the obligatory pathogen M. bovis in its struggle with the host.
Improvement of ligand-free modification strategy to obtain water-stable up-converting nanoparticles with bright emission and high reaction yield
Authors: Jurga Natalia , Przybylska Dominika , Kamiński Piotr , Grzyb Tomasz 
Published: September 2021

AbstractWater-dispersible up-converting nanoparticles (UCNPs) are known to be very effective in biomedical applications. Research groups have paid special attention to the synthesis of hydrophilic UCNPs with good physicochemical properties. Being aware of this, we decided to improve the ligand-free modification method of OA-capped NaYF4:Yb3+,Er3+/NaYF4 UCNPs prepared by precipitation in high-boiling-point solvents as the thus-far reported methods do not provide satisfactory results. Different molarities of hydrochloric acid and various mixing times were selected to remove the organic ligand from the NPs’ surface and to discover the most promising modification approach. Highly water-stable colloids were obtained with a very high reaction yield of up to 96%. Moreover, the acid treatment did not affect the morphology and the size of the product. All of the crystals exhibited a bright up-conversion emission under 975-nm excitation, which confirmed the two-photon excitation and effective energy transfer between the used dopant ions. Thus, we could establish the most successful ligand-free modification procedure.
High-fat diet increases the severity of Giardia infection in association with low-grade inflammation and gut microbiota dysbiosis
Authors: Allain Thibault , Fekete Elena , Sosnowski Olivia , Desmonts de Lamache Dimitri , Motta Jean-Paul , Leger Dezirae , Feener Troy , Reimer Raylene A. , Buret André G. 
Published: September 2021

AbstractExogenous factors that may influence the pathophysiology of Giardia infection remain incompletely understood. We have investigated the role of dietary fat in the pathogenesis of Giardia infection. Male 3 to 4-week-old C57BL/6 mice were fed either a low fat (LF) or a high fat (HF) diet for 12 days and challenged with G. duodenalis. In infected animals, the trophozoite burden was higher in HF + Giardia mice compared to the LF + Giardia group at day 7 post infection. Fatty acids exerted direct pro-growth effects on Giardia trophozoites. Analysis of disease parameters showed that HF + Giardia mice exhibited more mucosal infiltration by inflammatory cells, decreased villus/crypt ratios, goblet cell hyperplasia, mucus disruption, increased gut motility, and elevated fecal water content compared with LF + Giardia. HF diet-dependent exacerbation of Giardia-induced goblet cell hyperplasia was associated with elevated Atoh1 and Muc2 gene expression. Gut microbiota analysis revealed that the HF diet alone induces a taxonomic shift. HF + Giardia mice exhibited microbiota dysbiosis characterized by an increase of Firmicutes and a decrease of Bacteroidetes and significant changes in α- and β-diversity metrics. Taken together, the findings suggest that a HF diet exacerbates the outcome of Giardia infection. The data demonstrate that elevated dietary fat represents an important exogenous factor promoting the pathophysiology of giardiasis.
Localization to delocalization probed by magnetotransport of hBN/graphene/hBN stacks in the ultra-clean regime
Authors: Iwasaki Takuya , Moriyama Satoshi , Ahmad Nurul Fariha , Komatsu Katsuyoshi , Watanabe Kenji , Taniguchi Takashi , Wakayama Yutaka , Hashim Abdul Manaf , Morita Yoshifumi , Nakaharai Shu 
Published: September 2021

AbstractWe report on magnetotransport in a high-quality graphene device, which is based on monolayer graphene (Gr) encapsulated by hexagonal boron nitride (hBN) layers, i.e., hBN/Gr/hBN stacks. In the vicinity of the Dirac point, a negative magnetoconductance is observed for high temperatures >  ~ 40 K, whereas it becomes positive for low temperatures ≤  ~ 40 K, which implies an interplay of quantum interferences in Dirac materials. The elastic scattering mechanism in hBN/Gr/hBN stacks contrasts with that of conventional graphene on SiO2, and our ultra-clean graphene device shows nonzero magnetoconductance for high temperatures of up to 300 K.
Faceting of Si and Ge crystals grown on deeply patterned Si substrates in the kinetic regime: phase-field modelling and experiments
Authors: Albani Marco , Bergamaschini Roberto , Barzaghi Andrea , Salvalaglio Marco , Valente Joao , Paul Douglas J. , Voigt Axel , Isella Giovanni , Montalenti Francesco 
Published: September 2021

AbstractThe development of three-dimensional architectures in semiconductor technology is paving the way to new device concepts for various applications, from quantum computing to single photon avalanche detectors. In most cases, such structures are achievable only under far-from-equilibrium growth conditions. Controlling the shape and morphology of the growing structures, to meet the strict requirements for an application, is far more complex than in close-to-equilibrium cases. The development of predictive simulation tools can be essential to guide the experiments. A versatile phase-field model for kinetic crystal growth is presented and applied to the prototypical case of Ge/Si vertical microcrystals grown on deeply patterned Si substrates. These structures, under development for innovative optoelectronic applications, are characterized by a complex three-dimensional set of facets essentially driven by facet competition. First, the parameters describing the kinetics on the surface of Si and Ge are fitted on a small set of experimental results. To this goal, Si vertical microcrystals have been grown, while for Ge the fitting parameters have been obtained from data from the literature. Once calibrated, the predictive capabilities of the model are demonstrated and exploited for investigating new pattern geometries and crystal morphologies, offering a guideline for the design of new 3D heterostructures. The reported methodology is intended to be a general approach for investigating faceted growth under far-from-equilibrium conditions.
Primate-specific stress-induced transcription factor POU2F1Z protects human neuronal cells from stress
Authors: Stepchenko Alexander G. , Portseva Tatiana N. , Glukhov Ivan A. , Kotnova Alina P. , Lyanova Bella M. , Georgieva Sofia G. , Pankratova Elizaveta V. 
Published: September 2021

AbstractThe emergence of new primate-specific genes is an essential factor in human and primate brain development and functioning. POU2F1/Oct-1 is a transcription regulator in higher eukaryotes which is involved in the regulation of development, differentiation, stress response, and other processes. We have demonstrated that the Tigger2 transposon insertion into the POU2F1 gene which occurred in the primate lineage led to the formation of an additional exon (designated the Z-exon). Z-exon-containing primate-specific Oct-1Z transcript includes a short upstream ORF (uORF) located at its 5’-end and the main ORF encoding the Oct-1Z protein isoform (Pou2F1 isoform 3, P14859-3), which differs from other Oct-1 isoforms by its N-terminal peptide. The Oct-1Z-encoding transcript is expressed mainly in human brain cortex. Under normal conditions, the translation of the ORF coding for the Oct-1Z isoform is repressed by uORF. Under various stress conditions, uORF enables a strong increase in the translation of the Oct-1Z-encoding ORF. Increased Oct-1Z expression levels in differentiating human neuroblasts activate genes controlling stress response, neural cell differentiation, brain formation, and organogenesis. We have shown that the Oct-1Z isoform of the POU2F1/Oct-1 transcription factor is an example of a primate-specific genomic element contributing to brain development and cellular stress defense.
The relationship between major dietary patterns and fertility status in iranian men: a case–control study
Authors: Haeri Farahnaz , Pourmasoumi Makan , Ghiasvand Reza , Feizi Awat , Salehi-Abargouei Amin , Marvast Laleh Dehghan , Clark Cain C. T. , Mirzaei Masoud 
Published: September 2021

AbstractIn this case–control study, we aimed to investigate the association between major dietary patterns and fertility status in Iranian men. The study population included 400 newly diagnosed infertile men and 537 healthy individuals without a history of infertility in Yazd, Iran. Infertility was confirmed clinically, based on the World Health Organization (WHO) criteria. Dietary intake was assessed using a 168-item semi-quantitative food frequency questionnaire (FFQ), and dietary patterns were determined based on a principal component analysis. Four major dietary patterns were found in this study, including healthy, Western, mixed, and traditional dietary patterns. After adjustments for potential confounders, men above the median of a healthy dietary pattern showed a reduced risk of infertility compared to those below the median (OR 0.52; 95% CI 0.33–0.83). In contrast, men with greater adherence to Western and mixed dietary patterns were more likely to be infertile (OR 2.66; 95% CI 1.70–4.17 and OR 2.82; 95% CI 1.75–4.56, respectively). Also, there was no significant association between the traditional dietary pattern and the odds of infertility. The present study suggests that greater adherence to a healthy dietary pattern may have an inverse association with the odds of infertility; however, Western and mixed dietary patterns may be associated with an increased risk of infertility.
Fabrication of a state of the art mesh lock polymer for water based solid free drilling fluid
Authors: Wang Chaoqun , Ding Wei 
Published: September 2021

AbstractPolymers are used widely in various kinds of drilling fluid to maintain the proper rheological properties. However, most of them are not available for high-temperature or salt solutions due to poor temperature and salt resistance. To ameliorate the temperature and salt resistance of polymer used in the solid-free water-based drilling fluid, a novel polymer with a kind of "Mesh-Lock" reinforced network cross structure, named PLY-F [main monomer acrylic acid (AA), acrylamide (AM), functional monomers 2-acrylamide-2-methylpropanesulfonic acid (AMPS)N-vinylpyrrolidone (NVP) and C16DMAAC] were prepared through free radical polymerization of an aqueous solution of organic cross-linking agent pentaerythritol triallyl ether (PTE) as a cross-linking system, Potassium persulfate (KPS) and sodium bisulfite as the initiator for the first time. The surface morphology, crosslinking architecture and temperature and salt resistance of the PLY-F were fully characterized with several means including SEM, FT-IR,13CNMR, dynamic rheology, and long-term thermal stability. The SEM observation indicated that the PLY-F exhibits a regular “Mesh-Lock” reinforced network cross structure. FT-IR,13CNMR analysis indicated that the characteristic functional groups of each monomer such as AM, AA, AMPS and NVP were all together in the polymer. The results show that the apparent viscosity retention rate of the PLY-F in the potassium formate solution (with a density of 1.3 g/cm3) was more than 80% after heat rolling for 72 h at 200 °C and the plastic viscosity retention rate reached 90.3%. Moreover, the salt resistance of the polymer can reach the density of 1.4 g/cm3(potassium formate solution) under 200 °C and the temperature resistance can reach 220 °C under the density of 1.3 g/cm3(potassium formate solution). Besides, the PLY-F still has good rheological properties in other saturated solutions (NaCl, HCOONa) under 210 °C.
Experimental and empirical investigation of a CI engine fuelled with blends of diesel and roselle biodiesel
Authors: Verma Tikendra Nath , Rajak Upendra , Dasore Abhishek , Afzal Asif , Manokar A. Muthu , Aabid Abdul , Baig Muneer 
Published: September 2021

AbstractThe continuous rise in demand, combined with the depletion of the world's fossil fuel reserves, has forced the search for alternative fuels. The biodiesel produced from Roselle is one such indigenous biodiesel with tremendous promise, and its technical ability to operate with compression ignition engines is studied in this work. To characterize the fuel blends, researchers used experimental and empirical approaches while operating at engine loads of 25, 50, 75, and 100%, and with fuel injection timings of 19°, 21°, 23°, 25°, and 27° before top dead center. Results indicate that for 20% blend with the change of injection timing from 19° bTDC to 27° bTDC at full load, brake specific fuel consumption and exhaust gas temperature was increased by 15.84% and 4.60% respectively, while brake thermal efficiency decreases by 4.4%. Also, an 18.89% reduction in smoke, 5.26% increase in CO2, and 12.94% increase in NOx were observed. In addition, an empirical model for full range characterization was created. With an r-squared value of 0.9980 ± 0.0011, the artificial neural network model constructed to characterize all 10 variables was able to predict satisfactorily. Furthermore, substantial correlation among specific variables suggested that empirically reduced models were realistic.
Mechanism of the fungal-like particles in the inhibition of adipogenesis in 3T3-L1 adipocytes
Authors: Jakkawanpitak Chanawee , Inafuku Masashi , Oku Hirosuke , Hutadilok-Towatana Nongporn , Bunkrongcheap Ruthaiwan , Sermwittayawong Natthawan , Aiemchareon Piyapat , Sermwittayawong Decha 
Published: September 2021

AbstractThe dynamic ability of adipocytes in adipose tissue to store lipid in response to changes in the nutritional input and inflammatory elicitors has a major impact on human health. Previously, we established laminarin-coated beads or LCB as an inflammatory elicitor for adipocytes. However, it was not clear whether LCB inhibits lipid accumulation in adipocytes. Here, we show that LCB acts in the early stage of adipogenesis through both interleukin-1 receptor-associated kinases (IRAK) and spleen tyrosine kinase (SYK) pathways, resulting in the activation of the AMP-activated protein kinase (AMPK) and nuclear factor-κB (NF-κB) complexes, which subsequently cause cell cycle arrest, downregulation of the key transcription factors and enzymes responsible for adipogenesis, inhibition of adipogenesis, and stimulation of an inflammatory response. While LCB could effectively block lipid accumulation during the early stage of adipogenesis, it could stimulate an inflammatory response at any stage of differentiation. Additionally, our results raise a possibility that toll-like receptor 2 (TLR2) and C-type lectin domain family 7 member A (CLEC7A/Dectin-1) might be potential β-glucan receptors on the fat cells. Together, we present the mechanism of LCB, as fungal-like particles, that elicits an inflammatory response and inhibits adipogenesis at the early stage of differentiation.