bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hall effect in gated single-wall carbon nanotube films
Authors: Yomogida Yohei , Horiuchi Kanako , Okada Ryotaro , Kawai Hideki , Ichinose Yota , Nishidome Hiroyuki , Ueji Kan , Komatsu Natsumi , Gao Weilu , Kono Junichiro , Yanagi Kazuhiro 
Published: January 2022

AbstractThe presence of hopping carriers and grain boundaries can sometimes lead to anomalous carrier types and density overestimation in Hall-effect measurements. Previous Hall-effect studies on carbon nanotube films reported unreasonably large carrier densities without independent assessments of the carrier types and densities. Here, we have systematically investigated the validity of Hall-effect results for a series of metallic, semiconducting, and metal–semiconductor-mixed single-wall carbon nanotube films. With carrier densities controlled through applied gate voltages, we were able to observe the Hall effect both in the n- and p-type regions, detecting opposite signs in the Hall coefficient. By comparing the obtained carrier types and densities against values derived from simultaneous field-effect-transistor measurements, we found that, while the Hall carrier types were always correct, the Hall carrier densities were overestimated by up to four orders of magnitude. This significant overestimation indicates that thin films of one-dimensional SWCNTs are quite different from conventional hopping transport systems.
Incidence and clearance of anal high-risk Human Papillomavirus infection and their risk factors in men who have sex with men living with HIV
Authors: Donà Maria Gabriella , Giuliani Massimo , Rollo Francesca , Vescio Maria Fenicia , Benevolo Maria , Giglio Amalia , Giuliani Eugenia , Morrone Aldo , Latini Alessandra 
Published: January 2022

AbstractHIV-infected men who have sex with men (MSM) display the highest prevalence of anal infection by high-risk Human Papillomaviruses (hrHPVs) and incidence of anal carcinoma. Anal specimens were genotyped by the Linear Array. Incidence and clearance of anal infection by hrHPVs, hrHPVs other than HPV16, low-risk HPVs, and four individual types (6,11,16,18) were estimated using a two-state Markov model. Determinants for incidence and clearance were assessed by logistic regression. Overall, 204 individuals were included (median age 42 years, IQR = 34–49). For hrHPVs, incidence and clearance rates were 36.1 × 1000 person-months (p-m) (95% CI 23.3–56.5) and 15.6 × 1000 p-m (95% CI 10.7–23.3), respectively. HPV16 showed a higher incidence than HPV18 (10.2 vs. 7.2 × 1000 p-m). Its clearance was more than twofold lower than that of HPV18 (30.1 vs. 78.2 × 1000 p-m). MSM receiving cART displayed a 68% to 88% decrease in risk of acquiring hrHPVs, hrHPVs other than HPV16, HPV16, and HPV18 (adjusted Hazard Ratio [aHR] 0.13, 95% CI 0.02–0.67; aHR 0.22, 95% CI 0.06–0.78; aHR 0.32, 95% CI 0.12–0.90; aHR 0.12, 95% CI 0.04–0.31, respectively) than patients not treated. A nadir CD4 + count < 200 cells/mm3 significantly reduced the clearance of hrHPVs other than HPV16 (aHR 0.39, 95% CI 0.17–0.90). cART use reduces the risk of acquiring anal infection by hrHPVs.
Selective dependence on IL-7 for antigen-specific CD8 T cell responses during airway influenza infection
Authors: Sheikh Abdalla , Jackson Jennie , Shim Hanjoo Brian , Yau Clement , Seo Jung Hee , Abraham Ninan 
Published: January 2022

AbstractInterleukin-7 (IL-7) is a cytokine known for its importance in T cell development and survival. How IL-7 shapes CD8 T cell responses during an acute viral infection is less understood. We had previously shown that IL-7 signaling deficient mice have reduced accumulation of influenza-specific CD8 T cells following influenza infection. We sought to determine whether IL-7 affects early CD8 T cell expansion in the mediastinal lymph node and effector function in the lungs. Using IL-7Rα signaling deficient mice, we show that IL-7 is required for a normal sized mediastinal lymph node and the early clonal expansion of influenza-specific CD8 T cells therein. We show that IL-7 plays a cell-intrinsic role in the accumulation of NP366–374 and PA224–233-specific CD8 T cells in the lymph node. We also found that IL-7 shapes terminal differentiation, degranulation and cytokine production to a greater extent in PA224–233-specific than NP366–374-specific CD8 T cells. We further demonstrate that IL-7 is induced in the lung tissue by viral infection and we characterize multiple cellular sources that contribute to IL-7 production. Our findings on IL-7 and its effects on lower respiratory diseases will be important for expanding the utility of therapeutics that are currently available.
Network models of prostate cancer immune microenvironments identify ROMO1 as heterogeneity and prognostic marker
Authors: Wang Lei , Liu Xudong , Liu Zhe , Wang Yafan , Fan Mengdi , Yin Jinyue , Zhang Yu , Ma Ying , Luo Jia , Li Rui , Zhao Xue , Zhang Peiju , Zhao Lijun , Fan Jinke , Chen Yuxuan , Lu Wei , Song Xinqiang 
Published: January 2022

AbstractProstate cancer (PCa) is the fifth leading cause of death from cancer in men worldwide. Its treatment remains challenging due to the heterogeneity of the tumor, mainly because of the lack of effective and targeted prognostic markers at the system biology level. First, the data were retrieved from TCGA dataset, and valid samples were obtained by consistent clustering and principal component analysis; next, key genes were analyzed for prognosis of PCa using WGCNA, MEGENA, and LASSO Cox regression model analysis, while key genes were screened based on disease-free survival significance. Finally, TIMER data were selected to explore the relationship between genes and tumor immune infiltration, and GSCAlite was used to explore the small-molecule targeted drugs that act with them. Here, we used tumor subtype analysis and an energetic co-expression network algorithm of WGCNA and MEGENA to identify a signal dominated by the ROMO1 to predict PCa prognosis. Cox regression analysis of ROMO1 was an independent influence, and the prognostic value of this biomarker was validated in the training set, the validated data itself, and external data, respectively. This biomarker correlates with tumor immune infiltration and has a high degree of infiltration, poor prognosis, and strong correlation with CD8+T cells. Gene function annotation and other analyses also implied a potential molecular mechanism for ROMO1. In conclusion, we putative ROMO1 as a portal key prognostic gene for the diagnosis and prognosis of PCa, which provides new insights into the diagnosis and treatment of PCa.
Comparative proteomic analysis of nuclear and cytoplasmic compartments in human cardiac progenitor cells
Authors: Albericio Guillermo , Aguilar Susana , Torán Jose Luis , Yañez Rosa , López Juan Antonio , Vázquez Jesús , Mora Carmen , Bernad Antonio 
Published: January 2022

AbstractClinical trials evaluating cardiac progenitor cells (CPC) demonstrated feasibility and safety, but no clear functional benefits. Therefore a deeper understanding of CPC biology is warranted to inform strategies capable to enhance their therapeutic potential. Here we have defined, using a label-free proteomic approach, the differential cytoplasmic and nuclear compartments of human CPC (hCPC). Global analysis of cytoplasmic repertoire in hCPC suggested an important hypoxia response capacity and active collagen metabolism. In addition, comparative analysis of the nuclear protein compartment identified a significant regulation of a small number of proteins in hCPC versus human mesenchymal stem cells (hMSC). Two proteins significantly upregulated in the hCPC nuclear compartment, IL1A and IMP3, showed also a parallel increase in mRNA expression in hCPC versus hMSC, and were studied further. IL1A, subjected to an important post-transcriptional regulation, was demonstrated to act as a dual-function cytokine with a plausible role in apoptosis regulation. The knockdown of the mRNA binding protein (IMP3) did not negatively impact hCPC viability, but reduced their proliferation and migration capacity. Analysis of a panel of putative candidate genes identified HMGA2 and PTPRF as IMP3 targets in hCPC. Therefore, they are potentially involved in hCPC proliferation/migration regulation.
Multiple bacterial partners in symbiosis with the nudibranch mollusk Rostanga alisae
Authors: Zhukova Natalia V. , Eliseikina Marina G. , Balakirev Evgeniy S. , Ayala Francisco J. 
Published: January 2022

AbstractThe discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host’s ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations. A total of 74 clones belonging to the phyla α-, β-, γ-Proteobacteria, Actinobacteria, and Cyanobacteria were identified. FISH confirmed that bacteriocytes were packed with Bradyrhizobium, Maritalea, Labrenzia, Bulkholderia, Achromobacter, and Stenotrophomonas mainly in the foot and notum epidermis, and also an abundance of Synechococcus cyanobacteria in the intestinal epithelium. An ultrastructural analysis showed several bacterial morphotypes of bacteria in epidermal cells, intestine epithelium, and in mucus layer covering the mollusk body. The high proportion of typical bacterial fatty acids in R. alisae indicated that symbiotic bacteria make a substantial contribution to its nutrition. Thus, the nudibranch harbors a high diversity of specific endo- and extracellular bacteria, which previously unknown as symbionts of marine invertebrates that provide the mollusk with essential nutrients. They can provide chemical defense against predators.
Integrated bioinformatics and network pharmacology to identify the therapeutic target and molecular mechanisms of Huangqin decoction on ulcerative Colitis
Authors: Wu Yi , Liu Xinqiao , Li Guiwei 
Published: January 2022

AbstractHuangqin decoction (HQD) is a Traditional Chinese Medicine formula for ulcerative colitis. However, the pharmacology and molecular mechanism of HQD on ulcerative colitis is still unclear. Combined microarray analysis, network pharmacology, and molecular docking for revealing the therapeutic targets and molecular mechanism of HQD against ulcerative colitis. TCMSP, DrugBank, Swiss Target Prediction were utilized to search the active components and effective targets of HQD. Ulcerative colitis effective targets were obtained by microarray data from the GEO database (GSE107499). Co-targets between HQD and ulcerative colitis are obtained by Draw Venn Diagram. PPI (Protein–protein interaction) network was constructed by the STRING database. To obtain the core target, topological analysis is exploited by Cytoscape 3.7.2. GO and KEGG enrichment pathway analysis was performed to Metascape platform, and molecular docking through Autodock Vina 1.1.2 finished. 161 active components with 486 effective targets of HQD were screened. 1542 ulcerative colitis effective targets were obtained with |Log2FC|> 1 and adjusted P-value < 0.05. The Venn analysis was contained 79 co-targets. Enrichment analysis showed that HQD played a role in TNF signaling pathway, IL-17 signaling pathway, Th17 cell differentiation, etc. IL6, TNF, IL1B, PTGS2, ESR1, and PPARG with the highest degree from PPI network were successfully docked with 19 core components of HQD, respectively. According to ZINC15 database, quercetin (ZINC4175638), baicalein (ZINC3871633), and wogonin (ZINC899093) recognized as key compounds of HQD on ulcerative colitis. PTGS2, ESR1, and PPARG are potential therapeutic targets of HQD. HQD can act on multiple targets through multi-pathway, to carry out its therapeutic role in ulcerative colitis.
Whole-genome-scale identification of novel non-protein-coding RNAs controlling cell proliferation and survival through a functional forward genetics strategy
Authors: Tonge D. P. , Darling D. , Farzaneh F. , Williams G. T. 
Published: January 2022

AbstractIdentification of cell fate-controlling lncRNAs is essential to our understanding of molecular cell biology. Here we present a human genome-scale forward-genetics approach for the identification of lncRNAs based on gene function. This approach can identify genes that play a causal role, and immediately distinguish them from those that are differentially expressed but do not affect cell function. Our genome-scale library plus next-generation-sequencing and bioinformatic approach, radically upscales the breadth and rate of functional ncRNA discovery. Human gDNA was digested to produce a lentiviral expression library containing inserts in both sense and anti-sense orientation. The library was used to transduce human Jurkat T-leukaemic cells. Cell populations were selected using continuous culture ± anti-FAS IgM, and sequencing used to identify sequences controlling cell proliferation. This strategy resulted in the identification of thousands of new sequences based solely on their function including many ncRNAs previously identified as being able to modulate cell survival or to act as key cancer regulators such as AC084816.1*, AC097103.2, AC087473.1, CASC15*, DLEU1*, ENTPD1-AS1*, HULC*, MIRLET7BHG*, PCAT-1, SChLAP1, and TP53TG1. Independent validation confirmed 4 out of 5 sequences that were identified by this strategy, conferred a striking resistance to anti-FAS IgM-induced apoptosis.
Ultra-fast data sanitization of SRAM by back-biasing to resist a cold boot attack
Authors: Han Seong-Joo , Han Joon-Kyu , Yun Gyeong-Jun , Lee Mun-Woo , Yu Ji-Man , Choi Yang-Kyu 
Published: January 2022

AbstractAlthough SRAM is a well-established type of volatile memory, data remanence has been observed at low temperature even for a power-off state, and thus it is vulnerable to a physical cold boot attack. To address this, an ultra-fast data sanitization method within 5 ns is demonstrated with physics-based simulations for avoidance of the cold boot attack to SRAM. Back-bias, which can control device parameters of CMOS, such as threshold voltage and leakage current, was utilized for the ultra-fast data sanitization. It is applicable to temporary erasing with data recoverability against a low-level attack as well as permanent erasing with data irrecoverability against a high-level attack.
Prediction scenarios of past, present, and future environmental suitability for the Mediterranean species Arbutus unedo L.
Authors: Almeida Alice Maria , Martins Maria João , Campagnolo Manuel Lameiras , Fernandez Paulo , Albuquerque Teresa , Gerassis Saki , Gonçalves José Carlos , Ribeiro Maria Margarida 
Published: January 2022

AbstractClimate change is a challenge for forests in the coming decades, with a major impact on species adaptation and distribution. The Mediterranean Basin is one of the most vulnerable hotspots for biodiversity conservation under climate change in the world. This research aimed at studying a Mediterranean species well adapted to the region: the Arbutus unedo L. (strawberry tree). The MaxEnt, a presence-only species-distribution software, was used to model A. unedo’s environmental suitability. The current species potential distribution was accessed based on actual occurrences and selected environmental variables and subsequently projected for the Last Glacial Maximum (LGM), the Mid-Holocene (MH), and the years 2050 and 2070, considering the two Representative Concentration Pathways: RCP4.5 and RCP8.5. Results from the LGM projection suggest the presence of refugia in the core of the Mediterranean Basin, in particular the Iberian Peninsula (IP). The projections for the MH indicate increasing climatic suitability for the species and an eastward expansion, relatively to LGM. The predicted future environmental changes will most likely act as a catalyst for suitable habitat loss and a range shift towards the North is likely to occur.
Mortality associated with nonrestorative short sleep or nonrestorative long time-in-bed in middle-aged and older adults
Authors: Yoshiike Takuya , Utsumi Tomohiro , Matsui Kentaro , Nagao Kentaro , Saitoh Kaori , Otsuki Rei , Aritake-Okada Sayaka , Suzuki Masahiro , Kuriyama Kenichi 
Published: January 2022

AbstractAssociations of sleep duration with human health could differ depending on whether sleep is restorative. Using data from 5804 participants of the Sleep Heart Health Study, we examined the longitudinal association of sleep restfulness combined with polysomnography-measured total sleep time (TST) or time in bed (TIB), representing different sleeping behaviors, with all-cause mortality. Among middle-aged adults, compared with restful intermediate TST quartile, the lowest TST quartile with feeling unrested was associated with higher mortality (hazard ratio [HR], 1.54; 95% confidence interval [CI] 1.01–2.33); the highest TST quartile with feeling rested was associated with lower mortality (HR, 0.55; 95% CI 0.32–0.97). Among older adults, the highest TIB quartile with feeling unrested was associated with higher mortality, compared with restful intermediate TIB quartile (HR, 1.57; 95% CI 1.23–2.01). Results suggest a role of restorative sleep in differentiating the effects of sleep duration on health outcomes in midlife and beyond.
Regulation of gene expression by the APP family in the adult cerebral cortex
Authors: Cha Hye Ji , Shen Jie , Kang Jongkyun 
Published: January 2022

AbstractAmyloid precursor protein (APP) is associated with both familial and sporadic forms of Alzheimer’s disease. APP has two homologs, amyloid precursor-like protein 1 and 2 (APLP1 and APLP2), and they have functional redundancy. APP intracellular c-terminal domain (AICD), produced by sequential α- or β- and γ-secretase cleavages, is thought to control gene expression, similarly as the ICD of Notch. To investigate the role of APP family in transcriptional regulation, we examined gene expression changes in the cerebral cortex of APP/APLP1/APLP2 conditional triple knockout (cTKO) mice, in which APP family members are selectively inactivated in excitatory neurons of the postnatal forebrain. Of the 12 previously reported AICD target genes, only Nep and Npas4 mRNA levels were significantly reduced in the cerebral cortex of cTKO mice, compared to littermate controls. We further examined global transcriptional changes by RNA-seq and identified 189 and 274 differentially expressed genes in the neocortex and hippocampus, respectively, of cTKO mice relative to controls. Gene Ontology analysis indicated that these genes are involved in a variety of cellular functions, including extracellular organization, learning and memory, and ion channels. Thus, inactivation of APP family alters transcriptional profiles of the cerebral cortex and affects wide-ranging molecular pathways.
Effects of neighboring transitions on the mechanisms of electromagnetically induced absorption and transparency in an open degenerate multilevel system
Authors: Jadoon Zeeshan Ali Safdar , Noh Heung-Ryoul , Kim Jin-Tae 
Published: January 2022

AbstractIn this study, optical Bloch equations with and without neighboring hyperfine states near the degenerate two-level system (DTLS) in the challenging case of $$^{85}$$

85

Rb D2 transition, which involves the Doppler broadening effect, are solved. The calculated spectra agree well with the experimental results obtained based on the coupling-probe scheme with orthogonal linear polarizations of the coupling and probe fields. The mechanisms of electromagnetically induced absorption (electromagnetically induced transparency) for the open $$F_g=3 \rightarrow F_e=2$$

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g

=
3
→

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e

=
2

and 3 transitions (open $$F_g=2 \rightarrow F_e=2$$

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g

=
2
→

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e

=
2

and 3 transitions) are determined to be the effect of the strong closed $$F_g=3 \rightarrow F_e=4$$

F
g

=
3
→

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e

=
4

transition line (strong closed $$F_g=2 \rightarrow F_e=1$$

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g

=
2
→

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e

=
1

transition line); this finding is based on a comparison between the calculated absorption profiles of the DTLS without neighboring states and those of all levels with neighboring states, depending on the coupling and probe power ratios. Furthermore, based on the aforementioned comparison, the crucial factors that enhance or reduce the coherence effects and lead to the transformation between electromagnetically induced absorption and electromagnetically induced transparency, are (1) the power ratios between the coupling and probe beams, (2) the openness of the excited state, and (3) effects of the neighboring states due to Doppler broadening in a real atomic system.
MiR-29b may suppresses peritoneal metastases through inhibition of the mesothelial–mesenchymal transition (MMT) of human peritoneal mesothelial cells
Authors: Kimura Yuki , Ohzawa Hideyuki , Miyato Hideyo , Kaneko Yuki , Saito Akira , Takahashi Kazuya , Tojo Mineyuki , Yamaguchi Hironori , Kurashina Kentaro , Saito Shin , Hosoya Yoshinori , Lefor Alan Kawarai , Sata Naohiro , Kitayama Joji 
Published: January 2022

AbstractPeritoneal dissemination is a major metastatic pathway for gastrointestinal and ovarian malignancies. The miR-29b family is downregulated in peritoneal fluids in patients with peritoneal metastases (PM). We examined the effect of miR-29b on mesothelial cells (MC) which play critical a role in the development of PM through mesothelial-mesenchymal transition (MMT). Human peritoneal mesothelial cells (HPMCs) were isolated from surgically resected omental tissue and MMT induced by stimulation with 10 ng/ml TGF-β1. MiR-29b mimics and negative control miR were transfected by lipofection using RNAiMAX and the effects on the MMT evaluated in vitro. HPMC produced substantial amounts of miR-29b which was markedly inhibited by TGF-β1. TGF-β1 stimulation of HPMC induced morphological changes with decreased expression of E-cadherin and calretinin, and increased expression of vimentin and fibronectin. TGF-β1 also enhanced proliferation and migration of HPMC as well as adhesion of tumor cells in a fibronectin dependent manner. However, all events were strongly abrogated by simultaneous transfection of miR-29b. MiR-29b inhibits TGF-β1 induced MMT and replacement of miR-29b in the peritoneal cavity might be effective to prevent development of PM partly through the effects on MC.
High cell surface expression and peptide binding affinity of HLA-DQA1*05:03, a susceptible allele of neuromyelitis optica spectrum disorders (NMOSD)
Authors: Beppu Shohei , Kinoshita Makoto , Wilamowski Jan , Suenaga Tadahiro , Yasumizu Yoshiaki , Ogawa Kotaro , Ishikura Teruyuki , Tada Satoru , Koda Toru , Murata Hisashi , Shiraishi Naoyuki , Sugiyama Yasuko , Kihara Keigo , Sugimoto Tomoyuki , Arase Hisashi , Standley Daron M. , Okuno Tatsusada , Mochizuki Hideki 
Published: January 2022

AbstractNeuromyelitis optica spectrum disorder (NMOSD) is a relapsing autoimmune disease characterized by the presence of pathogenic autoantibodies, anti-aquaporin 4 (AQP4) antibodies. Recently, HLA-DQA1*05:03 was shown to be significantly associated with NMOSD in a Japanese patient cohort. However, the specific mechanism by which HLA-DQA1*05:03 is associated with the development of NMOSD has yet to be elucidated. In the current study, we revealed that HLA-DQA1*05:03 exhibited significantly higher cell surface expression levels compared to other various DQA1 alleles, and that its expression strongly depended on the amino acid sequence of the α1 domain, with a preference for leucine at position 75. Moreover, in silico analysis indicated that the HLA-DQ encoded by HLA-DQA1*05:03 preferentially presents immunodominant AQP4 peptides, and that the peptide major histocompatibility complexes (pMHCs) are more energetically stable in the presence of HLA-DQA1*05:03 than other HLA-DQA1 alleles. In silico 3D structural models were also applied to investigate the validity of the energetic stability of pMHCs. Taken together, our findings indicate that HLA-DQA1*05:03 possesses a distinct property to play a pathogenic role in the development of NMOSD.