bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parkin facilitates proteasome inhibitor-induced apoptosis via suppression of NF-κB activity in hepatocellular carcinoma
Authors: Zhang Xiaolan , Lin Chun , Song Junwei , Chen Han , Chen Xuhong , Ren Liangliang , Zhou Zhongqiu , Pan Jinyuan , Yang Zhenjun , Bao Wenhao , Ke Xueping , Yang Jianan , Liang Yingying , Huang Hongbiao , Tang Daolin , Jiang Lili , Liu Jinbao 
Published: September 2019

AbstractThe ubiquitin–proteasome system (UPS) is a tight homeostatic control mechanism of intracellular protein degradation and turnover involved in many human diseases. Proteasome inhibitors were initially developed as anticancer agents with potential benefits in the suppression of tumor growth. However, clinical trials of patients with solid tumors fail to demonstrate the same efficacy of these proteasome inhibitors. Here, we show that Parkin, an E3 ubiquitin ligase, is implicated in tumorigenesis and therapy resistance of hepatocellular carcinoma (HCC), the most common type of primary liver cancer in adults. Lower Parkin expression correlates with poor survival in patients with HCC. Ectopic Parkin expression enhances proteasome inhibitor-induced apoptosis and tumor suppression in HCC cells in vitro and in vivo. In contrast, knockdown of Parkin expression promotes apoptosis resistance and tumor growth. Mechanistically, Parkin promotes TNF receptor-associated factor (TRAF) 2 and TRAF6 degradation and thus facilitates nuclear factor-kappa-B (NF-κB) inhibition, which finally results in apoptosis. These findings reveal a direct molecular link between Parkin and protein degradation in the control of the NF-κB pathway and may provide a novel UPS-dependent strategy for the treatment of HCC by induction of apoptosis.
Cell necrosis, intrinsic apoptosis and senescence contribute to the progression of exencephaly to anencephaly in a mice model of congenital chranioschisis
Authors: Oria Marc , Duru Soner , Figueira Rebeca L. , Scorletti Federico , Turner Lucas E. , Fernandez-Alonso Irati , Fernandez-Martin Alejandra , Marotta Mario , Sbragia Lourenco , Shaaban Aimen F. , Peiro Jose L. 
Published: September 2019

AbstractExencephaly/anencephaly is one of the leading causes of neonatal mortality and the most extreme open neural tube defect with no current treatments and limited mechanistic understanding. We hypothesized that exencephaly leads to a local neurodegenerative process in the brain exposed to the amniotic fluid as well as diffuse degeneration in other encephalic areas and the spinal cord. To evaluate the consequences of in utero neural tissue exposure, brain and spinal cord samples from E17 exencephalic murine fetuses (maternal intraperitoneal administration of valproic acid at E8) were analyzed and compared to controls and saline-injected shams (n = 11/group). Expression of apoptosis and senescence genes (p53, p21, p16, Rbl2, Casp3, Casp9) was determined by qRT-PCR and protein expression analyzed by western blot. Apoptosis was measured by TUNEL assay and PI/AV flow cytometry. Valproic acid at E8 induced exencephaly in 22% of fetuses. At E17 the fetuses exhibited the characteristic absence of cranial bones. The brain structures from exencephalic fetuses demonstrated a loss of layers in cortical regions and a complete loss of structural organization in the olfactory bulb, hippocampus, dental gyrus and septal cortex. E17 fetuses had reduced expression of NeuN, GFAP and Oligodendrocytes in the brain with primed microglia. Intrinsic apoptotic activation (p53, Caspase9 and 3) was upregulated and active Caspase3 localized to the layer of brain exposed to the amniotic fluid. Senescence via p21-Rbl2 was increased in the brain and in the spinal cord at the lamina I-II of the somatosensory dorsal horn. The current study characterizes CNS alterations in murine exencephaly and demonstrates that degeneration due to intrinsic apoptosis and senescence occurs in the directly exposed brain but also remotely in the spinal cord.
RETRACTED ARTICLE: Long non-coding RNA linc00645 promotes TGF-β-induced epithelial–mesenchymal transition by regulating miR-205-3p-ZEB1 axis in glioma
Authors: Li Chenlong , Zheng Hongshan , Hou Weiliang , Bao Hongbo , Xiong Jinsheng , Che Wanli , Gu Yifei , Sun Haiming , Liang Peng 
Published: September 2019

AbstractAccumulating evidence indicates long noncoding RNAs (lncRNA) play a vital role in tumor progression. However, the role of linc00645-induced accelerated malignant behavior in glioblastoma (GBM) remains unknown. In the present study, linc00645 expression was significantly upregulated in GBM tissues and cell lines. High level of linc00645 was associated with poor overall survival in GBM patients. Knockdown of linc00645 suppressed the proliferation, stemness, migration, invasion, and reversed transforming growth factor (TGF)-β-induced motility of glioma cell lines. Furthermore, linc00645 directly interacted with miR-205-3p and upregulated of miR-205-3p impeded efficiently the increase of ZEB1 induced by linc00645 overexpression. Moreover, knockdown of linc00645 significantly suppressed the progression of glioma cells in vivo. miR-205-3p was a target of linc00645 and linc00645 modulates TGF-β-induced glioma cell migration and invasion via miR-205-3p. Taken together, our findings identified the linc00645/miR-205-3p/ZEB1 signaling axis as a key player in EMT of glioma cells triggered by TGF-β. These data elucidated that linc00645 plays an oncogenic role in glioma and it may serve as a prognostic biomarker and a potential therapeutic target for the treatment of glioma in humans.
Large linear magnetoelectric effect and field-induced ferromagnetism and ferroelectricity in DyCrO4
Authors: Shen Xudong , Zhou Long , Chai Yisheng , Wu Yan , Liu Zhehong , Yin Yunyu , Cao Huibo , Cruz Clarina Dela , Sun Young , Jin Changqing , Muñoz Angel , Alonso José Antonio , Long Youwen 
Published: September 2019

AbstractAll the magnetoelectric properties of scheelite-type DyCrO4 are characterized by temperature- and field-dependent magnetization, specific heat, permittivity, electric polarization, and neutron diffraction measurements. Upon application of a magnetic field within ±3 T, the nonpolar collinear antiferromagnetic structure leads to a large linear magnetoelectric effect with a considerable coupling coefficient. An applied electric field can induce the converse linear magnetoelectric effect, realizing magnetic field control of ferroelectricity and electric field control of magnetism. Furthermore, a higher magnetic field (>3 T) can cause a metamagnetic transition from the initially collinear antiferromagnetic structure to a canted structure, generating a large ferromagnetic magnetization up to 7.0 μB f.u.−1. Moreover, the new spin structure can break the space inversion symmetry, yielding ferroelectric polarization, which leads to coupling of ferromagnetism and ferroelectricity with a large ferromagnetic component.
Functional interpretation of single cell similarity maps
Authors: DeTomaso David , Jones Matthew G. , Subramaniam Meena , Ashuach Tal , Ye Chun J. , Yosef Nir 
Published: September 2019

AbstractWe present Vision, a tool for annotating the sources of variation in single cell RNA-seq data in an automated and scalable manner. Vision operates directly on the manifold of cell-cell similarity and employs a flexible annotation approach that can operate either with or without preconceived stratification of the cells into groups or along a continuum. We demonstrate the utility of Vision in several case studies and show that it can derive important sources of cellular variation and link them to experimental meta-data even with relatively homogeneous sets of cells. Vision produces an interactive, low latency and feature rich web-based report that can be easily shared among researchers, thus facilitating data dissemination and collaboration.
Flotillins promote T cell receptor sorting through a fast Rab5–Rab11 endocytic recycling axis
Authors: Redpath Gregory M. I. , Ecker Manuela , Kapoor-Kaushik Natasha , Vartoukian Haig , Carnell Michael , Kempe Daryan , Biro Maté , Ariotti Nicholas , Rossy Jérémie 
Published: September 2019

AbstractThe targeted endocytic recycling of the T cell receptor (TCR) to the immunological synapse is essential for T cell activation. Despite this, the mechanisms that underlie the sorting of internalised receptors into recycling endosomes remain poorly understood. To build a comprehensive picture of TCR recycling during T cell activation, we developed a suite of new imaging and quantification tools centred on photoactivation of fluorescent proteins. We show that the membrane-organising proteins, flotillin-1 and -2, are required for TCR to reach Rab5-positive endosomes immediately after endocytosis and for transfer from Rab5- to Rab11a-positive compartments. We further observe that after sorting into in Rab11a-positive vesicles, TCR recycles to the plasma membrane independent of flotillin expression. Our data suggest a mechanism whereby flotillins delineate a fast Rab5-Rab11a endocytic recycling axis and functionally contribute to regulate the spatial organisation of these endosomes.
Methionine in a protein hydrophobic core drives tight interactions required for assembly of spider silk
Authors: Heiby Julia C. , Goretzki Benedikt , Johnson Christopher M. , Hellmich Ute A. , Neuweiler Hannes 
Published: September 2019

AbstractWeb spiders connect silk proteins, so-called spidroins, into fibers of extraordinary toughness. The spidroin N-terminal domain (NTD) plays a pivotal role in this process: it polymerizes spidroins through a complex mechanism of dimerization. Here we analyze sequences of spidroin NTDs and find an unusually high content of the amino acid methionine. We simultaneously mutate all methionines present in the hydrophobic core of a spidroin NTD from a nursery web spider’s dragline silk to leucine. The mutated NTD is strongly stabilized and folds at the theoretical speed limit. The structure of the mutant is preserved, yet its ability to dimerize is substantially impaired. We find that side chains of core methionines serve to mobilize the fold, which can thereby access various conformations and adapt the association interface for tight binding. Methionine in a hydrophobic core equips a protein with the capacity to dynamically change shape and thus to optimize its function.
Electrochemical Redox Refrigeration
Authors: McKay Ian S. , Kunz Larissa Y. , Majumdar Arun 
Published: September 2019

AbstractThe high conformational entropy change of the Fe(CN)63−/4− redox reaction can be used as the basis for a compact electrochemical refrigerator. This device is comparable to a liquid version of a Peltier cooler, with two distinct advantages: (1) the entropy change per carrier (1.5 mV/K) of the electrochemical refrigerant is more than 5 times larger than that of state-of-the-art solid thermoelectric materials; and (2) the liquid electrolyte can be advected continuously away from the cooling junction, so that Joule heating in the bulk element does not diminish the delivered cooling effect. In this work, we use infrared microscopy to visualize the thermal aspects of Fe(CN)63−/4− redox, and compare the estimated cooling to calculated values with and without electrolyte flow. While the temperature differences achieved in a single cell are small (~50 mK) and not enhanced by electrolyte flow, the cooling power density (~0.5 W/cm3) is high when normalized to the small electrode volume. Non-dimensional figures of merit are proposed to identify electrochemical redox species for maximizing the cooling effect.
Introducing a Bayesian model of selective attention based on active inference
Authors: Mirza M. Berk , Adams Rick A. , Friston Karl , Parr Thomas 
Published: September 2019

AbstractInformation gathering comprises actions whose (sensory) consequences resolve uncertainty (i.e., are salient). In other words, actions that solicit salient information cause the greatest shift in beliefs (i.e., information gain) about the causes of our sensations. However, not all information is relevant to the task at hand: this is especially the case in complex, naturalistic scenes. This paper introduces a formal model of selective attention based on active inference and contextual epistemic foraging. We consider a visual search task with a special emphasis on goal-directed and task-relevant exploration. In this scheme, attention modulates the expected fidelity (precision) of the mapping between observations and hidden states in a state-dependent or context-sensitive manner. This ensures task-irrelevant observations have little expected information gain, and so the agent – driven to reduce expected surprise (i.e., uncertainty) – does not actively seek them out. Instead, it selectively samples task-relevant observations, which inform (task-relevant) hidden states. We further show, through simulations, that the atypical exploratory behaviours in conditions such as autism and anxiety may be due to a failure to appropriately modulate sensory precision in a context-specific way.
An in vitro assay and artificial intelligence approach to determine rate constants of nanomaterial-cell interactions
Authors: Price Edward , Gesquiere Andre J. 
Published: September 2019

AbstractIn vitro assays and simulation technologies are powerful methodologies that can inform scientists of nanomaterial (NM) distribution and fate in humans or pre-clinical species. For small molecules, less animal data is often needed because there are a multitude of in vitro screening tools and simulation-based approaches to quantify uptake and deliver data that makes extrapolation to in vivo studies feasible. Small molecule simulations work because these materials often diffuse quickly and partition after reaching equilibrium shortly after dosing, but this cannot be applied to NMs. NMs interact with cells through energy dependent pathways, often taking hours or days to become fully internalized within the cellular environment. In vitro screening tools must capture these phenomena so that cell simulations built on mechanism-based models can deliver relationships between exposure dose and mechanistic biology, that is biology representative of fundamental processes involved in NM transport by cells (e.g. membrane adsorption and subsequent internalization). Here, we developed, validated, and applied the FORECAST method, a combination of a calibrated fluorescence assay (CF) with an artificial intelligence-based cell simulation to quantify rates descriptive of the time-dependent mechanistic biological interactions between NMs and individual cells. This work is expected to provide a means of extrapolation to pre-clinical or human biodistribution with cellular level resolution for NMs starting only from in vitro data.
The effects of water temperature on the juvenile performance of two tropical damselfishes expatriating to temperate reefs
Authors: Djurichkovic Lucas D. , Donelson Jennifer M. , Fowler Ashley M. , Feary David A. , Booth David J. 
Published: September 2019

AbstractOcean warming associated with global climate change is already inducing geographic range shifts of marine species. Juvenile coral reef fishes transported into temperate latitudes (termed ‘vagrant’ fishes) can experience winter water temperatures below their normal thermal minimum. Such environmental extremes may increase energetic costs for such fishes, resulting in reduced performance, which may be the governing factor that limits the potential for poleward range expansion of such fishes. This study compared the juvenile physiological performance and behaviour of two congeneric tropical damselfishes which settle during austral summer months within temperate eastern Australia: Abudefduf vaigiensis have an extended southern range, and lower threshold survival temperature than the congeneric A. whitleyi. Physiological and behavioural performance parameters that may be affected by cooler temperature regimes at higher latitudes were measured in aquaria. Lower water temperature resulted in reduced growth rates, feeding rates, burst escape speed and metabolic rates of both species, with significantly reduced performance (up to six-fold reductions) for fishes reared at 18 °C relative to 22 °C and 26 °C. However, A. whitleyi exhibited lower growth rates than A. vaigiensis across all temperatures, and lower aerobic capacity at the lowest temperature (18 °C). This difference between species in growth and metabolic capacity suggests that the extended southern distribution and greater overwintering success of A. vaigiensis, in comparison to A. whitleyi is related to thermal performance parameters which are critical in maintaining individual health and survival. Our results support previous findings in the region that water temperature below 22 °C represents a critical physiological threshold for tropical Abudefduf species expatriating into temperate south-eastern Australia.
Dynamics of Singlet Oxygen-Triggered, RONS-Based Apoptosis Induction after Treatment of Tumor Cells with Cold Atmospheric Plasma or Plasma-Activated Medium
Authors: Bauer Georg , Sersenová Dominika , Graves David B. , Machala Zdenko 
Published: September 2019

AbstractTreatment of tumor cells with cold atmospheric plasma (CAP) or with plasma-activated medium (PAM) leads to a biochemical imprint on these cells. This imprint is mediated by primary singlet oxygen, which is mainly generated through the interaction between CAP-derived H2O2 and NO2−. This imprint is induced with a low efficiency as local inactivation of a few membrane-associated catalase molecules. As sustained generation of secondary singlet oxygen by the tumor cells is activated at the site of the imprint, a rapid bystander effect-like spreading of secondary singlet oxygen generation and catalase inactivation within the cell population is thus induced. This highly dynamic process is essentially driven by NOX1 and NOS of the tumor cells, and finally leads to intercellular RONS-driven apoptosis induction. This dynamic process can be studied by kinetic analysis, combined with the use of specific inhibitors at defined time intervals. Alternatively, it can be demonstrated and quantified by transfer experiments, where pretreated cells are mixed with untreated cells and bystander signaling is determined. These studies allow to conclude that the specific response of tumor cells to generate secondary singlet oxygen is the essential motor for their self-destruction, after a singlet oxygen-mediated triggering process by CAP or PAM.
Pre-operative Circulating Plasma Gelsolin Predicts Residual Disease and Detects Early Stage Ovarian Cancer
Authors: Asare-Werehene Meshach , Communal Laudine , Carmona Euridice , Le Tien , Provencher Diane , Mes-Masson Anne-Marie , Tsang Benjamin K. 
Published: September 2019

AbstractOvarian cancer (OVCA) patients with suboptimal residual disease (RD) and advanced stages have poor survival. pGSN is an actin binding protein which protects OVCA cells from cisplatin-induced death. There is an urgent need to discover reliable biomarkers to optimize individualized treatment recommendations. 99 plasma samples with pre-determined CA125 were collected from OVCA patients and pGSN assayed using sandwich-based ELISA. Associations between CA125, pGSN and clinicopathological parameters were examined using Fisher’s exact test, T test and Kruskal Wallis Test. Univariate and multivariate Cox proportional hazard models were used to statistically analyze clinical outcomes. At 64 µg/ml, pGSN had sensitivity and specificity of 60% and 60% respectively, for the prediction of RD where as that of CA125 at 576.5 U/mL was 43.5% and 56.5% respectively. Patients with stage 1 tumor had increased levels of pre-operative pGSN compared to those with tumor stage >1 and healthy subjects (P = 0.005). At the value of 81 µg/mL, pGSN had a sensitivity and specificity of 75% and 78.4%, respectively for the detection of early stage OVCA. At the value of 0.133, the Indicator of Stage 1 OVCA (ISO1) provided a sensitivity of 100% at a specificity of 67% (AUC, 0.89; P < 0.001). In the multivariate Cox regression analysis, pGSN (HR, 2.00; CI, 0.99–4.05; P = 0.05) was an independent significant predictor of progression free survival (PFS) but not CA125 (HR, 0.68; CI, 0.41–1.13; P = 0.13). Pre-operative circulating pGSN is a favorable and independent biomarker for early disease detection, RD prediction and patients’ prognosis.
Weather influences M. arvalis reproduction but not population dynamics in a 17-year time series
Authors: Giraudoux Patrick , Villette Petra , Quéré Jean-Pierre , Damange Jean-Pierre , Delattre Pierre 
Published: September 2019

AbstractRodent outbreaks have plagued European agriculture for centuries, but continue to elude comprehensive explanation. Modelling and empirical work in some cyclic rodent systems suggests that changes in reproductive parameters are partly responsible for observed population dynamics. Using a 17-year time series of Microtus arvalis population abundance and demographic data, we explored the relationship between meteorological conditions (temperature and rainfall), female reproductive activity, and population growth rates in a non-cyclic population of this grassland vole species. We found strong but complex relationships between female reproduction and climate variables, with spring female reproduction depressed after cold winters. Population growth rates were, however, uncorrelated with either weather conditions (current and up to three months prior) or with female reproduction (number of foetuses per female and/or proportion of females reproductively active in the population). These results, coupled with age-structure data, suggest that mortality, via predation, disease, or a combination of the two, are responsible for the large multi-annual but non-cyclic population dynamics observed in this population of the common vole.
The dynamics of memory retrieval for internal mentation
Authors: Stawarczyk David , D’Argembeau Arnaud 
Published: September 2019

AbstractDaily life situations often require people to remember internal mentation, such as their future plans or interpretations of events. Little is known, however, about the principles that govern memory for thoughts experienced during real-world events. In particular, it remains unknown whether factors that structure the retrieval of external stimuli also apply to thought recall, and whether some thought features affect their accessibility in memory. To examine these questions, we asked participants to undertake a walk on a university campus while wearing a lifelogging camera. They then received unexpected recall tasks about the thoughts they experienced during the walk, rated the phenomenological features of retrieved thoughts, and indicated the moment when they were experienced. Results showed that thought retrieval demonstrates primacy, recency, and temporal contiguity effects, and is also influenced by event boundaries. In addition, thoughts that involved planning and that were recurrent during the walk were more accessible in memory. Together, these results shed new light on the principles that govern memory for internal mentation and suggest that at least partially similar processes structure the retrieval of thoughts and stimuli from the external environment.