bluuebunny/crossref_metadata_2025_split huggingface dataset:
TLR9 re-expression in cancer cells extends the S-phase and stabilizes p16INK4a protein expression
Authors: Parroche P , Roblot G , Le Calvez-Kelm F , Tout I , Marotel M , Malfroy M , Durand G , McKay J , Ainouze M , Carreira C , Allatif O , Traverse-Glehen A , Mendiola M , Pozo-Kreilinger J J , Caux C , Tommasino M , Goutagny N , Hasan U A 
Published: July 2016

AbstractToll-like receptor 9 (TLR9) recognizes bacterial, viral or cell damage-associated DNA, which initiates innate immune responses. We have previously shown that TLR9 expression is downregulated in several viral induced cancers including HPV16-induced cervical neoplasia. Findings supported that downregulation of TLR9 expression is involved in loss of anti-viral innate immunity allowing an efficient viral replication. Here we investigated the role of TLR9 in altering the growth of transformed epithelial cells. Re-introducing TLR9 under the control of an exogenous promoter in cervical or head and neck cancer patient-derived cells reduced cell proliferation, colony formation and prevented independent growth of cells under soft agar. Neither TLR3, 7, nor the TLR adapter protein MyD88 expression had any effect on cell proliferation, indicating that TLR9 has a unique role in controlling cell growth. The reduction of cell growth was not due to apoptosis or necrosis, yet we observed that cells expressing TLR9 were slower in entering the S-phase of the cell cycle. Microarray-based gene expression profiling analysis highlighted a strong interferon (IFN) signature in TLR9-expressing head and neck cancer cells, with an increase in IFN-type I and IL-29 expression (IFN-type III), yet neither IFN-type I nor IL-29 production was responsible for the block in cell growth. We observed that the protein half-life of p16INK4a was increased in TLR9-expressing cells. Taken together, these data show for the first time that TLR9 affects the cell cycle by regulating p16INK4a post-translational modifications and highlights the role of TLR9 in the events that lead to carcinogenesis.
Polaritonic Rabi and Josephson Oscillations
Authors: Rahmani Amir , Laussy Fabrice P. 
Published: July 2016

AbstractThe dynamics of coupled condensates is a wide-encompassing problem with relevance to superconductors, BECs in traps, superfluids, etc. Here, we provide a unified picture of this fundamental problem that includes i) detuning of the free energies, ii) different self-interaction strengths and iii) finite lifetime of the modes. At such, this is particularly relevant for the dynamics of polaritons, both for their internal dynamics between their light and matter constituents, as well as for the more conventional dynamics of two spatially separated condensates. Polaritons are short-lived, interact only through their material fraction and are easily detuned. At such, they bring several variations to their atomic counterpart. We show that the combination of these parameters results in important twists to the phenomenology of the Josephson effect, such as the behaviour of the relative phase (running or oscillating) or the occurence of self-trapping. We undertake a comprehensive stability analysis of the fixed points on a normalized Bloch sphere, that allows us to provide a generalized criterion to identify the Rabi and Josephson regimes in presence of detuning and decay.
A high-content image-based method for quantitatively studying context-dependent cell population dynamics
Authors: Garvey Colleen M. , Spiller Erin , Lindsay Danika , Chiang Chun-Te , Choi Nathan C. , Agus David B. , Mallick Parag , Foo Jasmine , Mumenthaler Shannon M. 
Published: July 2016

AbstractTumor progression results from a complex interplay between cellular heterogeneity, treatment response, microenvironment and heterocellular interactions. Existing approaches to characterize this interplay suffer from an inability to distinguish between multiple cell types, often lack environmental context and are unable to perform multiplex phenotypic profiling of cell populations. Here we present a high-throughput platform for characterizing, with single-cell resolution, the dynamic phenotypic responses (i.e. morphology changes, proliferation, apoptosis) of heterogeneous cell populations both during standard growth and in response to multiple, co-occurring selective pressures. The speed of this platform enables a thorough investigation of the impacts of diverse selective pressures including genetic alterations, therapeutic interventions, heterocellular components and microenvironmental factors. The platform has been applied to both 2D and 3D culture systems and readily distinguishes between (1) cytotoxic versus cytostatic cellular responses; and (2) changes in morphological features over time and in response to perturbation. These important features can directly influence tumor evolution and clinical outcome. Our image-based approach provides a deeper insight into the cellular dynamics and heterogeneity of tumors (or other complex systems), with reduced reagents and time, offering advantages over traditional biological assays.
Nano-Wilhelmy investigation of dynamic wetting properties of AFM tips through tip-nanobubble interaction
Authors: Wang Yuliang , Wang Huimin , Bi Shusheng , Guo Bin 
Published: July 2016

AbstractThe dynamic wetting properties of atomic force microscopy (AFM) tips are of much concern in many AFM-related measurement, fabrication, and manipulation applications. In this study, the wetting properties of silicon and silicon nitride AFM tips are investigated through dynamic contact angle measurement using a nano-Wilhelmy balance based method. This is done by capillary force measurement during extension and retraction motion of AFM tips relative to interfacial nanobubbles. The working principle of the proposed method and mathematic models for dynamic contact angle measurement are presented. Geometric models of AFM tips were constructed using scanning electronic microscopy (SEM) images taken from different view directions. The detailed process of tip-nanobubble interaction was investigated using force-distance curves of AFM on nanobubbles. Several parameters including nanobubble height, adhesion and capillary force between tip and nanobubbles are extracted. The variation of these parameters was studied over nanobubble surfaces. The dynamic contact angles of the AFM tips were calculated from the capillary force measurements. The proposed method provides direct measurement of dynamic contact angles for AFM tips and can also be taken as a general approach for nanoscale dynamic wetting property investigation.
Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives
Authors: Logacheva Maria D. , Schelkunov Mikhail I. , Shtratnikova Victoria Y. , Matveeva Maria V. , Penin Aleksey A. 
Published: July 2016

AbstractAlthough plastid genomes of flowering plants are typically highly conserved regarding their size, gene content and order, there are some exceptions. Ericaceae, a large and diverse family of flowering plants, warrants special attention within the context of plastid genome evolution because it includes both non-photosynthetic and photosynthetic species with rearranged plastomes and putative losses of “essential” genes. We characterized plastid genomes of three species of Ericaceae, non-photosynthetic Monotropa uniflora and Hypopitys monotropa and photosynthetic Pyrola rotundifolia, using high-throughput sequencing. As expected for non-photosynthetic plants, M. uniflora and H. monotropa have small plastid genomes (46 kb and 35 kb, respectively) lacking genes related to photosynthesis, whereas P. rotundifolia has a larger genome (169 kb) with a gene set similar to other photosynthetic plants. The examined genomes contain an unusually high number of repeats and translocations. Comparative analysis of the expanded set of Ericaceae plastomes suggests that the genes clpP and accD that are present in the plastid genomes of almost all plants have not been lost in this family (as was previously thought) but rather persist in these genomes in unusual forms. Also we found a new gene in P. rotundifolia that emerged as a result of duplication of rps4 gene.
Immune DNA signature of T-cell infiltration in breast tumor exomes
Authors: Levy Eric , Marty Rachel , Gárate Calderón Valentina , Woo Brian , Dow Michelle , Armisen Ricardo , Carter Hannah , Harismendy Olivier 
Published: July 2016

AbstractTumor infiltrating lymphocytes (TILs) have been associated with favorable prognosis in multiple tumor types. The Cancer Genome Atlas (TCGA) represents the largest collection of cancer molecular data, but lacks detailed information about the immune environment. Here, we show that exome reads mapping to the complementarity-determining-region 3 (CDR3) of mature T-cell receptor beta (TCRB) can be used as an immune DNA (iDNA) signature. Specifically, we propose a method to identify CDR3 reads in a breast tumor exome and validate it using deep TCRB sequencing. In 1,078 TCGA breast cancer exomes, the fraction of CDR3 reads was associated with TILs fraction, tumor purity, adaptive immunity gene expression signatures and improved survival in Her2+ patients. Only 2/839 TCRB clonotypes were shared between patients and none associated with a specific HLA allele or somatic driver mutations. The iDNA biomarker enriches the comprehensive dataset collected through TCGA, revealing associations with other molecular features and clinical outcomes.
Activation of α2A-adrenergic signal transduction in chondrocytes promotes degenerative remodelling of temporomandibular joint
Authors: Jiao Kai , Zeng Guang , Niu Li-Na , Yang Hong-xu , Ren Gao-tong , Xu Xin-yue , Li Fei-fei , Tay Franklin R. , Wang Mei-qing 
Published: July 2016

AbstractThis study tested whether activation of adrenoreceptors in chondrocytes has roles in degenerative remodelling of temporomandibular joint (TMJ) and to determine associated mechanisms. Unilateral anterior crossbite (UAC) was established to induce TMJ degeneration in rats. Saline vehicle, α2- and β-adrenoreceptor antagonists or agonists were injected locally into the TMJ area of UAC rats. Cartilage degeneration, subchondral bone microarchitecture and the expression of adrenoreceptors, aggrecans, matrix metalloproteinases (MMPs) and RANKL by chondrocytes were evaluated. Chondrocytes were stimulated by norepinephrine to investigate signal transduction of adrenoreceptors. Increased α2A-adrenoreceptor expression was observed in condylar cartilage of UAC rats, together with cartilage degeneration and subchondral bone loss. Norepinephrine depresses aggrecans expression but stimulates MMP-3, MMP-13 and RANKL production by chondrocytes through ERK1/2 and PKA pathway; these effects were abolished by an α2A-adrenoreceptor antagonist. Furthermore, inhibition of α2A-adrenoreceptor attenuated degenerative remodelling in the condylar cartilage and subchondral bone, as revealed by increased cartilage thickness, proteoglycans and aggrecan expression and decreased MMP-3, MMP-13 and RANKL expressions in cartilage, increased BMD, BV/TV and decreased Tb.Sp in subchondral bone. Conversely, activation of α2A-adrenoreceptor intensified aforementioned degenerative changes in UAC rats. It is concluded that activation of α2A-adrenergic signal in chondrocytes promotes TMJ degenerative remodelling by chondrocyte-mediated pro-catabolic activities.
A New Skin Tensiometer Device: Computational Analyses To Understand Biodynamic Excisional Skin Tension Lines
Authors: Paul Sharad P. , Matulich Justin , Charlton Nick 
Published: July 2016

AbstractOne of the problems in planning cutaneous surgery is that human skin is anisotropic, or directionally dependent. Indeed, skin tension varies between individuals and at different body sites. Many a surgeon has tried to design different devices to measure skin tension to help plan excisional surgery, or to understand wound healing. However, many of the devices have been beset with problems due to many confounding variables - differences in technical ability, material (sutures) used and variability between different users. We describe the development of a new skin tensiometer that overcomes many historical technical issues. A new skin tension measuring device is presented here. It was designed to be less user-dependent, more reliable and usable on different bodily sites. The design and computational optimizations are discussed. Our skin tensiometer has helped understand the differences between incisional and excisional skin lines. Langer, who pioneered the concept of skin tension lines, created incisional lines that differ from lines caused by forces that need to be overcome when large wounds are closed surgically (excisional tension). The use of this innovative device has led to understanding of skin biomechanics and best excisional skin tension (BEST) lines.
Serum bile acids and GLP-1 decrease following telemetric induced weight loss: results of a randomized controlled trial
Authors: Biemann Ronald , Penner Marina , Borucki Katrin , Westphal Sabine , Luley Claus , Rönicke Raik , Biemann Kathleen , Weikert Cornelia , Lux Anke , Goncharenko Nikolai , Marschall Hanns-Ulrich , Schneider Jochen G. , Isermann Berend 
Published: July 2016

AbstractBile acids (BAs) are increasingly recognised as metabolic regulators, potentially improving insulin sensitivity following bariatric surgery. However, physiological relevance of such observations remains unknown. Hence, we analysed serum BA composition and associated gut-derived hormone levels following lifestyle-induced weight loss in individuals with metabolic syndrome (MetS). 74 non-smoking men (45–55 yr) with MetS were randomised to a lifestyle-induced weight loss program (supervision via telemonitoring) or to a control arm. Before and after a 6 months intervention period clinical and laboratory parameters, body composition, serum BA profile, FGF-19 and GLP-1 concentrations were determined in fasting blood samples. 30 participants in the control and 33 participants in the treatment arm completed the study and were included in the data analysis. In participants of the treatment arm lifestyle-induced weight loss resulted in markedly improved insulin sensitivity. Serum levels of BA species and total GLP-1 decreased, while FGF-19 remained stable. Serum BA composition changed towards an increased 12α-hydroxylated/non-12α-hydroxylated ratio. None of these parameters changed in participants of the control arm. Our results demonstrate that improved metabolic control by lifestyle modifications lowers serum levels of BAs and GLP-1 and changes serum BA composition towards an increased 12α/non-12α ratio (ICTRP Trial Number: U1111-1158-3672).
Parallel Quantum Circuit in a Tunnel Junction
Authors: Faizy Namarvar Omid , Dridi Ghassen , Joachim Christian 
Published: July 2016

AbstractSpectral analysis of 1 and 2-states per line quantum bus are normally sufficient to determine the effective Vab(N) electronic coupling between the emitter and receiver states through the bus as a function of the number N of parallel lines. When Vab(N) is difficult to determine, an Heisenberg-Rabi time dependent quantum exchange process must be triggered through the bus to capture the secular oscillation frequency Ωab(N) between those states. Two different linear and "Equation missing" regimes are demonstrated for Ωab(N) as a function of N. When the initial preparation is replaced by coupling of the quantum bus to semi-infinite electrodes, the resulting quantum transduction process is not faithfully following the Ωab(N) variations. Because of the electronic transparency normalisation to unity and of the low pass filter character of this transduction, large Ωab(N) cannot be captured by the tunnel junction. The broadly used concept of electrical contact between a metallic nanopad and a molecular device must be better described as a quantum transduction process. At small coupling and when N is small enough not to compensate for this small coupling, an N2 power law is preserved for Ωab(N) and for Vab(N).
Human breast cancer-derived soluble factors facilitate CCL19-induced chemotaxis of human dendritic cells
Authors: Hwang Hyundoo , Shin Changsik , Park Juhee , Kang Enoch , Choi Bongseo , Han Jae-A , Do Yoonkyung , Ryu Seongho , Cho Yoon-Kyoung 
Published: July 2016

AbstractBreast cancer remains as a challenging disease with high mortality in women. Increasing evidence points the importance of understanding a crosstalk between breast cancers and immune cells, but little is known about the effect of breast cancer-derived factors on the migratory properties of dendritic cells (DCs) and their consequent capability in inducing T cell immune responses. Utilizing a unique 3D microfluidic device, we here showed that breast cancers (MCF-7, MDA-MB-231, MDA-MB-436 and SK-BR-3)-derived soluble factors increase the migration of DCs toward CCL19. The enhanced migration of DCs was mainly mediated via the highly activated JNK/c-Jun signaling pathway, increasing their directional persistence, while the velocity of DCs was not influenced, particularly when they were co-cultured with triple negative breast cancer cells (TNBCs or MDA-MB-231 and MDA-MB-436). The DCs up-regulated inflammatory cytokines IL-1β and IL-6 and induced T cells more proliferative and resistant against activation-induced cell death (AICD), which secret high levels of inflammatory cytokines IL-1β, IL-6 and IFN-γ. This study demonstrated new possible evasion strategy of TNBCs utilizing their soluble factors that exploit the directionality of DCs toward chemokine responses, leading to the building of inflammatory milieu which may support their own growth.
PACSIN2 polymorphism is associated with thiopurine-induced hematological toxicity in children with acute lymphoblastic leukaemia undergoing maintenance therapy
Authors: Smid Alenka , Karas-Kuzelicki Natasa , Jazbec Janez , Mlinaric-Rascan Irena 
Published: July 2016

AbstractAdequate maintenance therapy for childhood acute lymphoblastic leukemia (ALL), with 6-mercaptopurine as an essential component, is necessary for retaining durable remission. Interruptions or discontinuations of the therapy due to drug-related toxicities, which can be life threatening, may result in an increased risk of relapse. In this retrospective study including 305 paediatric ALL patients undergoing maintenance therapy, we systematically investigated the individual and combined effects of genetic variants of folate pathway enzymes, as well as of polymorphisms in PACSIN2 and ITPA, on drug-induced toxicities by applying a multi-analytical approach including logistic regression (LR), classification and regression tree (CART) and generalized multifactor dimensionality reduction (GMDR). In addition to the TPMT genotype, confirmed to be a major determinant of drug related toxicities, we identified the PACSIN2 rs2413739TT genotype as being a significant risk factor for 6-MP-induced toxicity in wild-type TPMT patients. A gene-gene interaction between MTRR (rs1801394) and MTHFR (rs1801133) was detected by GMDR and proved to have an independent effect on the risk of stomatitis, as shown by LR analysis. To our knowledge, this is the first study showing PACSIN2 genotype association with hematological toxicity in ALL patients undergoing maintenance therapy.
A novel gene OsAHL1 improves both drought avoidance and drought tolerance in rice
Authors: Zhou Liguo , Liu Zaochang , Liu Yunhua , Kong Deyan , Li Tianfei , Yu Shunwu , Mei Hanwei , Xu Xiaoyan , Liu Hongyan , Chen Liang , Luo Lijun 
Published: July 2016

AbstractA novel gene, OsAHL1, containing an AT-hook motif and a PPC domain was identified through genome-wide profiling and analysis of mRNAs by comparing the microarray of drought-challenged versus normally watered rice. The results indicated OsAHL1 has both drought avoidance and drought tolerance that could greatly improve drought resistance of the rice plant. Overexpression of OsAHL1 enhanced multiple stress tolerances in rice plants during both seedling and panicle development stages. Functional studies revealed that OsAHL1 regulates root development under drought condition to enhance drought avoidance, participates in oxidative stress response and also regulates the content of chlorophyll in rice leaves. OsAHL1 specifically binds to the A/T rich sequence region of promoters or introns and hence directly regulates the expression of many stress related downstream genes.
Sestrin2 Silencing Exacerbates Cerebral Ischemia/Reperfusion Injury by Decreasing Mitochondrial Biogenesis through the AMPK/PGC-1α Pathway in Rats
Authors: Li Lingyu , Xiao Lina , Hou Yanghao , He Qi , Zhu Jin , Li Yixin , Wu Jingxian , Zhao Jing , Yu Shanshan , Zhao Yong 
Published: July 2016

AbstractSestrin2 (Sesn2) exerts neuroprotective properties in some neurodegenerative diseases. However, the role of Sesn2 in stroke is unclear. The AMP-activated protein kinase/peroxisome proliferator-activated receptor γ coactivator-1α (AMPK/PGC-1α) pathway plays an important role in regulating mitochondrial biogenesis, which helps prevent cerebral ischemia/reperfusion (I/R) injury. Here, we aimed to determine whether Sesn2 alleviated I/R damage by regulating mitochondrial biogenesis through the AMPK/PGC-1α signaling pathway. To be able to test this, Sprague-Dawley rats were subjected to middle cerebral artery occlusion (MCAO) for 1 h with Sesn2 silencing. At 24 h after reperfusion, we found that neurological deficits were exacerbated, infarct volume was enlarged, and oxidative stress and neuronal damage were greater in the Sesn2 siRNA group than in the MCAO group. To explore protective mechanisms, an AMPK activator was used. Expression levels of Sesn2, p-AMPK, PGC-1α, NRF-1, TFAM, SOD2, and UCP2 were significantly increased following cerebral I/R. However, upregulation of these proteins was prevented by Sesn2 small interfering RNA (siRNA). In contrast, activation of AMPK with 5′-aminoimidazole-4-carboxamide riboside weakened the effects of Sesn2 siRNA. These results suggest that Sesn2 silencing may suppress mitochondrial biogenesis, reduce mitochondrial biological activity, and finally aggravate cerebral I/R injury through inhibiting the AMPK/PGC-1α pathway.
ClC-3 Chloride Channel Proteins Regulate the Cell Cycle by Up-regulating cyclin D1-CDK4/6 through Suppressing p21/p27 Expression in Nasopharyngeal Carcinoma Cells
Authors: Ye Dong , Luo Hai , Lai Zhouyi , Zou Lili , Zhu Linyan , Mao Jianwen , Jacob Tim , Ye Wencai , Wang Liwei , Chen Lixin 
Published: July 2016

AbstractIt was shown in this study that knockdown of ClC-3 expression by ClC-3 siRNA prevented the activation of hypotonicity-induced chloride currents and arrested cells at the G0/G1 phase in nasopharyngeal carcinoma CNE-2Z cells. Reconstitution of ClC-3 expression with ClC-3 expression plasmids could rescue the cells from the cell cycle arrest caused by ClC-3 siRNA treatments. Transfection of cells with ClC-3 siRNA decreased the expression of cyclin D1, cyclin dependent kinase 4 and 6 and increased the expression of cyclin dependent kinase inhibitors (CDKIs), p21 and p27. Pretreatments of cells with p21 and p27 siRNAs depleted the inhibitory effects of ClC-3 siRNA on the expression of CDK4 and CDK6, but not on that of cyclin D1, indicating the requirement of p21 and p27 for the inhibitory effects of ClC-3 siRNA on CDK4 and CDK6 expression. ClC-3 siRNA inhibited cells to progress from the G1 phase to the S phase, but pretreatments of cells with p21 and p27 siRNAs abolished the inhibitory effects of ClC-3 siRNA on the cell cycle progress. Our data suggest that ClC-3 may regulate cell cycle transition between G0/G1 and S phases by up-regulation of the expression of CDK4 and CDK6 through suppression of p21 and p27 expression.