bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability of bacterial behavior in the mammalian gut captured using a growth-linked single-cell synthetic gene oscillator
Authors: Riglar David T , Richmond David L , Potvin-Trottier Laurent , Verdegaal Andrew A , Naydich Alexander D , Bakshi Somenath , Leoncini Emanuele , Paulsson Johan , Silver Pamela A 
Published: November 2018

AbstractThe dynamics of the bacterial population that comprises the gut microbiota plays key roles in overall mammalian health. However, a detailed understanding of bacterial growth within the gut is limited by the inherent complexity and inaccessibility of the gut environment. Here, we deploy an improved synthetic genetic oscillator to investigate dynamics of bacterial colonization and growth in the mammalian gut under both healthy and disease conditions. The synthetic oscillator, when introduced into both Escherichia coli and Salmonella Typhimurium maintains regular oscillations with a constant period in generations across growth conditions. We determine the phase of oscillation from individual bacteria using image analysis of resultant colonies and thereby infer the number of cell divisions elapsed. In doing so, we demonstrate robust functionality and controllability of the oscillator circuit’s activity during bacterial growth in vitro, in a simulated murine gut microfluidic environment, and in vivo within the mouse gut. We determine different dynamics of bacterial colonization and growth in the gut under normal and inflammatory conditions. Our results show that a precise genetic oscillator can function in a complex environment and reveal single cell behavior under diverse conditions where disease may create otherwise impossible-to-quantify variability in growth across the population.
SYNPLA: A synapse-specific method for identifying learning-induced synaptic plasticity loci
Authors: Dore Kim , Pao Yvonne , Lopez Jose Soria , Aronson Sage , Zhan Huiqing , Ghosh Sanchari , Merrill Sabina , Zador Anthony M. , Malinow Roberto , Kebschull Justus M. 
Published: November 2018

AbstractWhich neural circuits undergo synaptic changes when an animal learns? Although it is widely accepted that changes in synaptic strength underlie many forms of learning and memory, it remains challenging to connect changes in synaptic strength at specific neural pathways to specific behaviors and memories. Here we introduce SYNPLA (SYNaptic Proximity Ligation Assay), a synapse-specific, high-throughput and potentially brain-wide method capable of detecting circuit-specific learning-induced synaptic plasticity.
Cognitive and white-matter compartment models revealed the contribution of microstructural variability along sensorimotor tracts to simple reaction time
Authors: Karahan Esin , Costigan Alison G. , Graham Kim S. , Lawrence Andrew D. , Zhang Jiaxiang 
Published: November 2018

AbstractThe speed of voluntary reaction to an external stimulus varies substantially between individuals and is impaired in ageing. However, the neuroanatomical origins of inter-individual variability in reaction time (RT) remain largely unknown. Here, we combined a cognitive model of RT and a biophysical compartmental model of diffusion-weighted MRI (DWI) to characterize the relationship between RT and microstructure of the corticospinal tract (CST) and the optic radiation (OR), the primary motor output and visual input pathways associated with visual-motor responses.We fitted an accumulator model of RT to 46 female participants’ behavioral performance in a simple reaction time task. The non-decision time parameter (Ter) derived from the model was used to account for the latencies of stimulus encoding and action initiation. From multi-shell DWI data, we quantified tissue microstructure of the CST and OR with the neurite orientation dispersion and density imaging (NODDI) model as well as the conventional diffusion tensor imaging (DTI) model.Using novel skeletonization and segmentation approaches, we showed that DWI-based microstructure metrics varied substantially along CST and OR. The Ter of individual participants was negatively correlated with the NODDI measure of the neurite density in the bilateral superior CST. At an uncorrected threshold, the Ter positively correlated with the DTI measure of fractional anisotropy in an anterior segment of left OR. Further, we found no significant correlation between the microstructural measures and mean RT. Thus, our findings suggest a link between the inter-individual variability of sensorimotor speed and selective microstructural properties in white matter tracts.
APOBEC-mediated DNA alterations: a possible new mechanism of carcinogenesis in EBV-positive gastric cancer
Authors: Bobrovnitchaia Irina , Valieris Renan , Drummond Rodrigo , Lima João , Freitas Helano , Bartelli Thais , Amorin Maria , Nunes Diana , Dias-Neto Emmanuel , Silva Israel 
Published: November 2018

AbstractMechanisms of viral oncogenesis are diverse and include the off-target activity of enzymes expressed by the infected cells, which evolved to target viral genomes for controlling their infection. Among these enzymes, the single-strand DNA editing capability of APOBECs represent a well-conserved viral infection response that can also cause untoward mutations in host DNA. Here we show, after evaluating somatic single-nucleotide variations and transcriptome data in 240 gastric cancer samples, a positive correlation between APOBEC3s mRNA-expression and the APOBEC-mutation signature, both increased in EBV+ tumors. The correlation was reinforced by the observation of APOBEC-mutations preferentially occuring in transcriptionally-active loci. The EBV-infection and APOBEC3 mutation-signature axis was confirmed in a validation cohort of 112 gastric cancer patients. Our findings suggest that APOBEC3 upregulation in EBV+ cancer may boost the mutation load, providing further clues to the mechanisms of EBV-induced gastric carcinogenesis. After further validation, this EBV-APOBEC axis may prove to be a secondary driving force in the mutational evolution of EBV+ gastric tumors, whose consequences in terms of prognosis and treatment implications should be vetted.
Error sensitivity and optimization of steady-state kinetic parameters using multidimensional chemical kinetic analysis
Authors: Eskew Joseph S. , Connell Christopher G. , Cochran Jared C. 
Published: November 2018

AbstractEnzyme behavior has been described using the Michaelis-Menten mechanism. The analysis of extended time domains provides a means to extract the Michaelis-Menten constants through direct fitting of raw data. We have developed a scheme for determining Michaelis-Menten rate constants by appropriate fitting of multidimensional experimental data sets to the closed form of the Michaelis-Menten model. We considered how varying parameters in experimental data affect the accuracy of the remaining parameter estimates. We determine how to improve experimental design to achieve a given accuracy, relative to the amount of intrinsic or external error. We analyze this scheme on data sets built around 20 hypothetical and 2 natural enzymes (kinesin and apyrase) to test error sensitivity in different parameter regimes. Overall, we provide evidence that our data fitting regime will tolerate significant experimental error in the raw data and still converge on the four Michaelis-Menten constants.
AICAR induces apoptosis and inhibits migration of prostate cancer cells through an AMPK/mTOR-dependent pathway
Authors: Su Chia-Cheng , Hsieh Kun-Lin , Wang Shu-Chi , Yeh Hsin-Chih , Huang Shu-Pin , Liu Po-Len , Fang Shih-Hua , Cheng Wei-Chung , Huang Kuan-Hua , Chiu Fang-Yen , Lin I-Ling , Huang Ming-Yii , Li Chia-Yang 
Published: November 2018

AbstractAICAR (5-aminoimidazole-4-carbox-amide-1-β-D-ribofuranoside), an AMP-activated protein kinase (AMPK) agonist, has demonstrated antitumor activities for several types of cancers. However, the activity of AICAR on the cell growth and metastasis of prostate cancer has not been extensively studied. Herein we examine the effects of AICAR on the cell growth and metastasis of prostate cancer cells, 22RV1 cells. Cell growth was performed by MTT assay and soft agar assay. Cell apoptosis was examined by Annexin V/PI staining and PARP cleavage Western blot. Cell migration was evaluated by wound-healing assay. The expression of EMT-related protein and the activity of the AMPK/ mTOR-dependent pathway were analyzed by Western blot. In addition, we also tested the effect of AICAR on the chemosensitivity to docetaxel using MTT assay. Our results indicated that AICAR inhibits cell growth, induces apoptosis, attenuates TGF-β-induced cell migration and EMT-related protein expression, and enhances the chemosensitivity to docetaxel through regulating the AMPK/mTOR-dependent pathway. Collectively, these findings support AICAR as a potential therapeutic agent for the treatment of prostate cancer.
Knockdown of DGKZ induces apoptosis and G2/M phase arrest in human acute myeloid leukemia HL-60 cells
Authors: Dong Changhu , Li Hong , Tian Yanning , Li Xiang , Wang Bing , Zhai Dongzhi , Bai Yingying , Chao Xu 
Published: November 2018

AbstractDiacylglycerol kinase zeta (DGKZ) is associated with the pathogenesis of a variety of malignant diseases, but its biological function on acute myeloid leukemia (AML) has not been explored. This study was aimed to analyze apoptosis induced by Knockdown of DGKZ and its mechanism in human acute myeloid leukemia HL-60 cells.In the present study qRT-PCR was used to detect the expression of DGKZ in HL-60, THP-1, K562, H9, Jurkat and CD34 cell lines. DGKZ-shRNA lentiviral vector was established and used to infect acute myeloid leukemia HL-60 cells. Cell Counting Kit-8 (CCK-8) assay was used to determine the viability of HL-60 cells DGKZ knocked down. Apoptosis and cell cycle phase of HL-60 cells after DGKZ knockdown were evaluated by flow cytometry. Western blot analysis was performed to investigated the protein expression related to apoptosis and cell cycle. Results showed DGKZ expression were stable and higher in Jurkat, HL-60, THP-1,K562 leukemia cells than those of H9 and CD34 cells. Compared with cells of the shCtrl group, DGKZ was markedly knocked down in cells which were transfected with lentivirus encoding shRNA of DGKZ in HL-60 cells. DGKZ knockdown significantly inhibited the proliferation and induced cycle arrest at the G2/M phase in HL-60 cells. Western blot results indicated the expressions of caspase-3, caspase-8, and survivin markedly increased in HL-60 cells after knockdown of DGKZ. The results suggest Knockdown of DGKZ can inhibit proliferation of acute myeloid leukemia HL-60 cell caused cell cycle arrest at the G2/M phase through caspases pathway.
Street fighters: Bite force, injury rates, and density of urban Australian water dragons (Intellagama lesueurii)
Authors: Baxter‐Gilbert James H. , Whiting Martin J. 
Published: November 2018

AbstractIn an increasingly urbanized world it is imperative that we understand how wildlife responds to this novel anthropogenic landscape, both at the individual‐ and population‐level. Urbanization generally reduces biodiversity, but can also favour particular species and increase their abundance relative to wild populations. When population density increases, so too does the frequency and cost of social interactions. We studied Australian water dragons (Intellagama lesueurii), a species common in urban, semi‐natural and natural areas, to firstly test the prediction that urban populations occur at higher densities, and then determine the consequences of urbanization for combat rates (quantified using wounding) and bite force. We established that urban populations are denser than ones from semi‐natural and natural habitats. We also recorded significantly more wounds in females from urban populations than females from both natural and semi‐natural populations. Urban males also had significantly higher incidence of wounding than males from natural populations. We did not find a difference in male or female bite force among any populations across the urban‐natural gradient. Overall, we found evidence that urbanization results in a higher population density of water dragons and more frequent conspecific combat, but this was not associated with an increase in bite force. These finding suggests that there may be a physiological cost to living in urban habitats related to increased contest rates and wounding.
Cannibalism or congeneric predation? The African clawed frog, Xenopus laevis (Daudin), preferentially predates on larvae of Cape platannas, Xenopus gilli Rose & Hewitt
Authors: Thorp Corey J. , Vonesh James R. , Measey John 
Published: November 2018

AbstractPredators are not limited to prey from other species as they can cannibalise vulnerable individuals within their own population. The African clawed frog, Xenopus laevis (Daudin), is a predator with a broad diet, known to consume multiple prey species, including congeners and conspecifics. African clawed frogs occur in sympatry with the Endangered Cape platanna, Xenopus gilli Rose & Hewitt, which are under threat through competition and predation from X. laevis. We investigated the threat of X. laevis predation on X. gilli using choice and no‐choice experiments to evaluate the relative vulnerability of X. laevis and X. gilli larvae. Results showed that large X. gilli larvae had a significantly higher vulnerability to X. laevis predation compared to small X. gilli larvae. However, the same discrimination was not discerned when offered large and small X. laevis larvae, or mixed larvae of the same size. We report ontogenic shifts in behaviour of X. gilli larvae that may be a factor in contributing to the vulnerability of large X. gilli larvae to adult X. leavis predation. Congeneric predation likely has negative implications for the population structure of the Endangered X. gilli. Our study underlines the call for the removal of X. laevis to conserve populations of X. gilli.
Analysis of implant loss risk factors especially in maxillary molar location: A retrospective study of 6977 implants in Chinese individuals
Authors: Zhou Na , Dong Heng , Zhu Yanxiang , Liu Hui , Zhou Nan , Mou Yongbin 
Published: November 2018

AbstractBackgroundThe knowledge of the potential risk factors associated with implant loss is crucial for dental clinicians, but the opinions about the risk factors are still diverse and controversial.PurposeThis retrospective study assessed the risk factors associated with implant loss, especially that in the maxillary molar location.Materials and MethodsFrom January 2015 to March 2017, 4338 Chinese patients received 6977 implants at Nanjing Stomatological Hospital. Information on patient age, gender, bone grafting procedure, implant location, length and diameter, and the records of lost implants were obtained. The Kaplan‐Meier method and log‐rank test were used to conduct a survival function analysis. Chi‐square test and multivariate Cox regression analysis were used to identify risk factors related to implant loss.ResultsThe cumulative survival rate (CSR) after 0‐32 months of observation period for all implants was 97.76%, and the CSR for maxillary molar implants was 97.00%. Maxillary molar implants showed a significantly lower CSR than the other implants (P < .05). Male sex, short implants (<10 mm) were considered as risk factors for implant loss. However, male sex and bone grafting procedure were regarded as risk factors for maxillary molar implant loss, which was slightly different from the result of all implants.ConclusionsMale sex, short implants (<10 mm) and maxillary molar location were considered as potential risk factors for implant loss, whereas male sex and bone grafting procedure were significantly associated with implant loss in maxillary molar location.
Patients with extensive regional lymph node involvement (pN2) following potentially curative surgery for colorectal cancer are at increased risk for developing peritoneal metastases: a retrospective single‐institution study
Authors: Bhatt A. , Bhamre R. , Rohila J. , Kalikar V. , Desouza A. , Saklani A. 
Published: November 2018

AbstractAimOur goal was to determine the incidence and clinical behaviour of peritoneal metastases (PM) in patients with colorectal cancer undergoing potentially curative surgery, comparing patients with extensive locoregional lymph node involvement (pN2) with those who have serosal involvement (pT4), a known risk factor for developing PM.MethodA retrospective analysis of a prospectively maintained database was performed. All patients with pT4 and pN2 were included in the analysis. The diagnostic criteria were the finding of PM during surgery with biopsy confirmation as well as imaging features suggestive of PM, including ovarian metastases and omental deposits.ResultsTwo hundred and fourteen patients treated between May 2010 and October 2015 were included. Of these, 110 (51.4%) had pT4 and 131 (61.2%) pN2 tumours: 17.2% of patients with pT4 tumours and 20.2% of patients with pN2 tumours developed PM (P = 0.53). The median time to detection of PM was 16.6 months and 11.8 months for pT4 and pN2 tumours, respectively. PM were isolated in 51.8% of patients with pN2 tumours. Nonperitoneal metastases developed in 37.5% of patients with pN2 tumours. In pN2 tumours, the incidence of PM was higher in signet ring cell and mucinous tumours (P < 0.01), positive surgical margins (P = 0.02), colonic versus rectal tumours (P = < 0.01) and right colon primary tumours (P = 0.01).ConclusionPatients with pN2 tumours are at an increased risk of developing PM, which is similar to the risk in pT4 tumours. pN2 tumours should be included in clinical trials evaluating preventive/proactive strategies. There is a need to identify predictive biomarkers for the development of PM versus other sites of metastasis.
Lipoprotein (a) and Low‐density lipoprotein apolipoprotein B metabolism following apheresis in patients with elevated lipoprotein(a) and coronary artery disease
Authors: Ma Louis , Waldmann Elisa , Ooi Esther M. M. , Chan Dick C. , Barrett Hugh P. R. , Watts Gerald F. , Parhofer Klaus G. 
Published: November 2018

AbstractBackgroundLipoprotein apheresis effectively lowers lipoprotein(a) [Lp(a)] and low‐density lipoprotein (LDL) by approximately 60%‐70%. The rebound of LDL and Lp(a) particle concentrations following lipoprotein apheresis allows the determination of fractional catabolic rate (FCR) and hence production rate (PR) during non‐steady state conditions. We aimed to investigate the kinetics of Lp(a) and LDL apolipoprotein B‐100 (apoB) particles in patients with elevated Lp(a) and coronary artery disease undergoing regular apheresis.Patients and methodsA cross‐sectional study was carried out in 13 patients with elevated Lp(a) concentration (>500 mg/L) and coronary artery disease. Lp(a) and LDL‐apoB metabolic parameters, including FCR and PR were derived by the fit of a compartment model to the Lp(a) and LDL‐apoB concentration data following lipoprotein apheresis.ResultsThe FCR of Lp(a) was significantly lower than that of LDL‐apoB (0.39 [0.31, 0.49] vs 0.57 [0.46, 0.71] pools/day, P = 0.03) with no significant differences in the corresponding PR (14.80 [11.34, 19.32] vs 15.73 [11.93, 20.75] mg/kg/day, P = 0.80). No significant associations were observed between the FCR and PR of Lp(a) and LDL‐apoB.ConclusionsIn patients with elevated Lp(a), the fractional catabolism of Lp(a) is slower than that of LDL‐apoB particles, implying that different metabolic pathways are involved in the catabolism of these lipoproteins. These findings have implications for new therapies for lowering apolipoprotein(a) and apoB to prevent atherosclerotic cardiovascular disease.
A genetic algorithm‐based stacking algorithm for predicting soil organic matter from vis–NIR spectral data
Authors: Tsakiridis Nikolaos L. , Tziolas Nikolaos V. , Theocharis John B. , Zalidis George C. 
Published: November 2018

It has been demonstrated that diffuse reflectance spectroscopy in the visible and near‐infrared (vis–NIR) can be exploited to predict chemical and physical soil properties. Immense soil spectral libraries (SSL) are being developed; therefore, more elaborate tools that capitalize on contemporary knowledge and techniques need to be established to provide accurate predictions. In this paper, we propose a novel genetic algorithm‐based stacking model that makes synergetic use of multiple models developed from different preprocessed spectral sources (termed L1 models). This is a form of ensemble learning where multiple hypotheses are combined to create a more robust and more accurate ensemble hypothesis. The genetic algorithm automatically defines the configuration of the stacked model, by selecting the best cooperating subset of the initial models. Our methodology was tested on the newly developed GEO‐CRADLE SSL to predict soil organic matter (SOM). Results showed that the accuracy of prediction of the proposed method (
R2 = 0.76, and ratio of performance to interquartile range [RPIQ] = 2.22) was better than the one attained by the best L1 model (
R2 = 0.65, RPIQ = 1.93). This approach can thus be effectively utilized to enhance the predictions of soil properties in small and large soil spectral libraries alike.Highlights

A novel model stacking algorithm is proposed, combining spectral models from different sources and algorithms.
Use of a genetic algorithm is examined, accounting for the large number of possible model permutations.
The methodology was applied to the GEO‐CRADLE vis–NIR soil spectral library.
Results indicate that model stacking creates more accurate and robust models.
Provincializing the history of speculation from colonial South Asia
Authors: Bhattacharyya Debjani 
Published: November 2018

AbstractThis article proposes that South Asia has produced rich histories of economic practices understood variously as hoarding, speculation, and extortion. This essay frames the discussion of speculation in South Asian history along these three axes. First, it puts the term speculation under scrutiny to look at its changing meanings within the colonial and metropolitan context in order to assess how the term enters the colonial archive of law and finance. Especially, it looks at how the colonial officials created and sustained (mis)translations between indigenous practices and Anglo‐European categories of economic crimes. Second, it looks at the early scholarship on 18th and 19th century indigenous commercial practices that were coded as hoarding, speculating, profiteering, hedging, and squeezing in an attempt to rescue the colonial bazaar and what has been called its “inside history” alongside the development of market practices. This body of scholarship remains primarily focused on trading activities under the Mughals and East India Company. In the third and final section, we turn to the recent histories that have returned to vernacular commercial practices and the historical roots of India's market society to raise critical questions about how speculation and calculation shaped late colonial capitalism and governmentality.