bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanistic and experimental models of cell migration reveal the importance of cell-to-cell pushing in cell invasion
Authors: Matsiaka Oleksii M , Baker Ruth E , Shah Esha T , Simpson Matthew J 
Published: April 2019

Abstract
Moving fronts of cells are essential for development, repair and disease progression. Therefore, understanding and quantifying the details of the mechanisms that drive the movement of cell fronts is of wide interest. Quantitatively identifying the role of intercellular interactions, and in particular the role of cell pushing, remains an open question. In this work, we report a combined experimental-modelling approach showing that intercellular interactions contribute significantly to the spatial spreading of a population of cells. We use a novel experimental data set with PC-3 prostate cancer cells that have been pretreated with Mitomycin-C to suppress proliferation. This allows us to experimentally separate the effects of cell migration from cell proliferation, thereby enabling us to focus on the migration process in detail as the population of cells recolonizes an initially-vacant region in a series of two-dimensional experiments. We quantitatively model the experiments using a stochastic modelling framework, based on Langevin dynamics, which explicitly incorporates random motility and various intercellular forces including: (i) long range attraction (adhesion); and (ii) finite size effects that drive short range repulsion (pushing). Quantitatively comparing the ability of this model to describe the experimentally observed population-level behaviour provides us with quantitative insight into the roles of random motility and intercellular interactions. To quantify the mechanisms at play, we calibrate the stochastic model to match experimental cell density profiles to obtain estimates of cell diffusivity, D, and the amplitude of intercellular forces, f
0. Our analysis shows that taking a standard modelling approach which ignores intercellular forces provides a poor match to the experimental data whereas incorporating intercellular forces, including short-range pushing and longer range attraction, leads to a faithful representation of the experimental observations. These results demonstrate a significant role of cell pushing during cell front movement and invasion.
Association Between Speed of Multimorbidity Accumulation in Old Age and Life Experiences: A Cohort Study
Authors: Dekhtyar Serhiy , Vetrano Davide Liborio , Marengoni Alessandra , Wang Hui-Xin , Pan Kuan-Yu , Fratiglioni Laura , Calderón-Larrañaga Amaia 
Published: April 2019

Abstract
Rapidly accumulating multiple chronic conditions (multimorbidity) during aging are associated with many adverse outcomes. We explored the association between 4 experiences throughout life—childhood socioeconomic circumstances, early-adulthood education, midlife occupational stress, and late-life social network—and the speed of chronic disease accumulation. We followed 2,589 individuals aged ≥60 years from the Swedish National Study on Aging and Care in Kungsholmen for 9 years (2001–2013). Information on life experiences was collected from detailed life-history interviews. Speed of disease accumulation was operationalized as the change in the count of chronic conditions obtained from clinical examinations, medical histories, laboratory data, drug use, and register linkages over 9 years. Linear mixed models were used to analyze the data. Speed of disease accumulation was lower in individuals with more than elementary education (for secondary, β × time = −0.065, 95% CI: −0.126, −0.004; for university, β × time = −0.118, 95% CI: −0.185, −0.050); for active occupations compared with high-strain jobs (β × time = −0.078, 95% CI: −0.138, −0.017); and for richer social networks (for moderate tertile, β × time = −0.102, 95% CI: −0.149, −0.055; for highest tertile, β × time = −0.135, 95% CI: −0.182, −0.088). The association between childhood circumstances and speed of disease accumulation was attenuated by later-life experiences. Diverse experiences throughout life might decelerate chronic disease accumulation during aging.
LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection
Authors: Johnson Travis S , Wang Tongxin , Huang Zhi , Yu Christina Y , Wu Yi , Han Yatong , Zhang Yan , Huang Kun , Zhang Jie 
Published: April 2019

Abstract

Motivation
Rapid advances in single cell RNA sequencing (scRNA-seq) have produced higher-resolution cellular subtypes in multiple tissues and species. Methods are increasingly needed across datasets and species to (i) remove systematic biases, (ii) model multiple datasets with ambiguous labels and (iii) classify cells and map cell type labels. However, most methods only address one of these problems on broad cell types or simulated data using a single model type. It is also important to address higher-resolution cellular subtypes, subtype labels from multiple datasets, models trained on multiple datasets simultaneously and generalizability beyond a single model type.

Results
We developed a species- and dataset-independent transfer learning framework (LAmbDA) to train models on multiple datasets (even from different species) and applied our framework on simulated, pancreas and brain scRNA-seq experiments. These models mapped corresponding cell types between datasets with inconsistent cell subtype labels while simultaneously reducing batch effects. We achieved high accuracy in labeling cellular subtypes (weighted accuracy simulated 1 datasets: 90%; simulated 2 datasets: 94%; pancreas datasets: 88% and brain datasets: 66%) using LAmbDA Feedforward 1 Layer Neural Network with bagging. This method achieved higher weighted accuracy in labeling cellular subtypes than two other state-of-the-art methods, scmap and CaSTLe in brain (66% versus 60% and 32%). Furthermore, it achieved better performance in correctly predicting ambiguous cellular subtype labels across datasets in 88% of test cases compared with CaSTLe (63%), scmap (50%) and MetaNeighbor (50%). LAmbDA is model- and dataset-independent and generalizable to diverse data types representing an advance in biocomputing.

Availability and implementation
github.com/tsteelejohnson91/LAmbDA

Supplementary information
Supplementary data are available at Bioinformatics online.
The incorporation of cystine by the soluble carrier family 7 member 11 (SLC7A11) is a component of the redox regulatory mechanism in stallion spermatozoa†
Authors: Ortiz-Rodriguez José Manuel , Martín-Cano Francisco E , Ortega-Ferrusola Cristina , Masot Javier , Redondo Eloy , Gázquez Antonio , Gil María C , Aparicio Inés M , Rojo-Domínguez Patricia , Tapia José A , Rodriguez-Martínez Heriberto , Peña Fernando J 
Published: April 2019

Abstract
Oxidative stress is considered a major mechanism causing sperm damage during cryopreservation and storage, and underlies male factor infertility. Currently, oxidative stress is no longer believed to be caused only by the overproduction of reactive oxygen species, but rather by the deregulation of redox signaling and control mechanisms. With this concept in mind, here, we describe for the first time the presence of the soluble carrier family 7 member 11 (SLC7A11) antiporter, which exchanges extracellular cystine (Cyss) for intracellular glutamate, in stallion spermatozoa, as well as its impact on sperm function using the specific inhibitor sulfasalazine. Spermatozoa incubated with Cyss exhibited an increased intracellular GSH content compared with controls (P < 0.01): 50% in fresh extended stallion spermatozoa and 30% in frozen-thawed spermatozoa. This effect was prevented by the addition of sulfasalazine to the media. Cystine supplementation also reduced the oxidation–reduction potential of spermatozoa, with sulfasalazine only preventing this effect on fresh spermatozoa that were incubated for 3 h at 37°C, but not in frozen-thawed spermatozoa. While sulfasalazine reduced the motility of frozen-thawed spermatozoa, it increased motility in fresh samples. The present findings provide new and relevant data on the mechanism regulating the redox status of spermatozoa and suggest that a different redox regulatory mechanism exists in cryopreserved spermatozoa, thus providing new clues to improve current cryopreservation technologies and treat male factor infertility.
Whole-genome sequencing of human malignant mesothelioma tumours and cell lines
Authors: Oey Harald , Daniels Marissa , Relan Vandana , Chee Tian Mun , Davidson Morgan R , Yang Ian A , Ellis Jonathan J , Fong Kwun M , Krause Lutz , Bowman Rayleen V 
Published: April 2019

AbstractPleural mesothelioma is a cancer of serosal surfaces caused by environmental exposure to asbestos. Clinical outcome remains poor and while trials of new treatments are ongoing it remains an understudied cancer. Mesothelioma cell lines can readily be grown from primary tumour and from tumour cells shed into pleural effusion with the latter representing a particularly valuable source of DNA in clinical settings, procurable without the need for additional invasive procedures. However, it is not well understood how accurately patient-derived cultured tumour cells represent the molecular characteristics of their primary tumour. We used whole-genome sequencing of primary tumour and matched cultured cells to comprehensively characterize mutations and structural alterations. Most cases had complex rearranged genomes with evidence of chromoanagenesis and rearrangements reminiscent of chromoplexy. Many of the identified driver mutations were structural, indicating that mesothelioma is often caused by structural alterations and catastrophic genomic events, rather than point mutations. Because the majority of genomic changes detected in tumours were also displayed by the genomes of cultured tumour cells, we conclude that low-passage cultured tumour cells are generally suitable for molecular characterization of mesothelioma and may be particularly useful where tissue samples with high tumour cell content are not available. However, the subclonal compositions of the cell lines did not fully recapitulate the subclonal diversity of the primary tumours. Furthermore, longitudinal acquisition of major alterations in subclonal cell populations was observed after long-term passaging. These two factors define limitations of tumour-derived cell lines as genomic substrate for clinical purposes.
The Impact of Varicella Vaccination on the Incidence of Varicella and Herpes Zoster in the United States: Updated Evidence From Observational Databases, 1991–2016
Authors: Wolfson Lara J , Daniels Vincent J , Altland Alexandra , Black Wynona , Huang Wanjing , Ou Wanmei 
Published: April 2019

Abstract

Background
Universal childhood vaccination against varicella began in the United States as a 1-dose schedule in 1996, changing to a 2-dose schedule in 2006. The exogenous boosting hypothesis, which postulates that reexposure to circulating wild-type varicella delays the onset of herpes zoster, predicts a transient increase in the incidence of herpes zoster, peaking in adults 15–35 years after the start of varicella vaccination.

Methods
This was a retrospective study of administrative claims data from the MarketScan Commercial and Medicare databases between 1991–2016. Outcome measures were the incidences of herpes zoster per 100 000 person-years, by calendar year and age category, and the annual rates of change in herpes zoster by age category, in an interrupted time series regression analysis, for the periods of 1991–1995 (prevaccine), 1996–2006 (1-dose vaccination period), and 2007–2016 (2-dose vaccination period).

Results
The annual incidences of herpes zoster increased throughout the period of 1991–2012 in all adult age categories, with a plateau in 2013–2016 that was most evident in the ≥65 age group. In 1991–1995, the herpes zoster incidences increased at annual rates of 4–6% in age categories 18–34, 35–44, 45–54, and 55–64 years. In the same age categories during 1996–2006 and 2007–2016, the herpes zoster incidences increased at annual rates of 1–5%.

Conclusions
Although the annual incidence of herpes zoster in adults has continued to increase, the rates of change decreased during both the 1- and 2-dose vaccination periods. The hypothesized increase in herpes zoster predicted from modelling of the exogenous boosting hypothesis was not observed.
Trimethyllysine, a trimethylamine N-oxide precursor, provides near- and long-term prognostic value in patients presenting with acute coronary syndromes
Authors: Li Xinmin S , Obeid Slayman , Wang Zeneng , Hazen Benjamin J , Li Lin , Wu Yuping , Hurd Alex G , Gu Xiaodong , Pratt Alan , Levison Bruce S , Chung Yoon-Mi , Nissen Steven E , Tang Wai Hong Wilson , Mach François , Räber Lorenz , Nanchen David , Matter Christian M , Lüscher Thomas F , Hazen Stanley L 
Published: April 2019

Abstract

Aims
Trimethyllysine (TML) serves as a nutrient precursor of the gut microbiota-derived metabolite trimethylamine N-oxide (TMAO) and is associated with incident cardiovascular (CV) events in stable subjects. We examined the relationship between plasma TML levels and incident CV events in patients presenting with acute coronary syndromes (ACS).

Methods and results
Plasma levels of TML were quantified in two independent cohorts using mass spectrometry, and its relationship with CV events was investigated. In a Cleveland Cohort (N = 530), comprised of patients presenting to the emergency department with chest pain and suspected ACS, TML was associated with major adverse cardiac events (MACE, myocardial infarction, stroke, need for revascularization, or all-cause mortality) over both 30 days [3rd tertile (T3), adjusted odds ratio (OR) 1.77, 95% confidence interval (CI) 1.04–3.01; P &lt; 0.05] and 6 months (T3, adjusted OR 1.95, 95% CI 1.15–3.32; P &lt; 0.05) of follow-up independent of traditional CV risk factors and indices of renal function. Elevated TML levels were also associated with incident long-term (7-year) all-cause mortality [T3, adjusted hazard ratio (HR) 2.52, 95% CI 1.50–4.24; P &lt; 0.001], and MACE even amongst patients persistently negative for cardiac Troponin T at presentation (e.g. 30-day MACE, T3, adjusted OR 4.49, 95% CI 2.06–9.79; P &lt; 0.001). Trimethyllysine in combination with TMAO showed additive significance for near- and long-term CV events, including patients with ‘negative’ high-sensitivity Troponin T levels. In a multicentre Swiss Cohort (N = 1683) comprised of ACS patients, similar associations between TML and incident 1-year adverse cardiac risks were observed (e.g. mortality, adjusted T3 HR 2.74, 95% CI 1.28–5.85; P &lt; 0.05; and MACE, adjusted T3 HR 1.55, 95% CI 1.04–2.31; P &lt; 0.05).

Conclusion
Plasma TML levels, alone and together with TMAO, are associated with both near- and long-term CV events in patients with chest pain and ACS.
Characteristics, transcriptional patterns and possible physiological significance of glycoside hydrolase family 16 members in Coprinopsis cinerea
Authors: Kang Liqin , Zhu Yiting , Bai Yang , Yuan Sheng 
Published: April 2019

ABSTRACT
The glycoside hydrolase (GH) 16 family of Coprinopsis cinerea includes 15 members distributed in four subgroups (A1, A2, B and D) by phylogenetic analysis. The expression patterns match well with the requirement of wall-softening in the germination of basidiospores, hyphal growth and branching, primordium formation, stipe elongation, pileus expansion and autolysis. Remarkably, expression levels of different GH16 members varied with different morphogenetic events. Like orthologs of Aspergillus fumigatus GH16 glucanases (ENG2–5), which were expressed in the dormant conidia and conidiogenesis, and essential for segregation of conidia, some members such as ENG in the subgroup A1 in C. cinerea were also predominantly expressed in dormant basidiospores, primordia and maturing pilei during basidiosporogenesis. In contrast, other members in subgroup A2, subgroup B or D were dominantly expressed in the germinating basidiospores, the growing mycelia, and the elongating stipes. We did not find the members of the GH81 or GH55 family in C. cinerea genome, which was different from A. fumigatus. However, C. cinerea contains an extra three subgroups (A2, B and D) compared with A. fumigatus. These extra subgroups of GH16 family members may function as those endo-β-1,3-glucanases belonging to other GH families in the development and growth of C. cinerea.
Music Hall, Jigs and Strippers: English Low-Brow Music in French Nineteenth-Century Travel Writing
Authors: Scott Hannah 
Published: April 2019

Abstract
It is a commonplace to remark that nineteenth-century England was a land without music. Yet French travel writers in the fin de siècle remark again and again on their astonishing, low-brow musical encounters in the nation’s capital. The present article examines such experiences in the writing of Jules Vallès and Hector France, as they turn their steps away from the refinement of Covent Garden to seek out more esoteric musical experiences in the music halls, tawdry bars, minor theatres and strip joints of London. These texts present an intriguing and ambivalent textual form to the reader. Though being based on – and structured as – travel anecdotes, they no less insistently reach beyond the anecdotal experience to extrapolate overarching conclusions about the English and their character relative to France. Yet in doing so, their texts reveal inconsistencies and contradictions as they try to reconcile these strange musical experiences with the stereotypes of Englishness that had solidified over the generations; these alien musical experiences resist conceptualization and challenge the tropes that had for so long underwritten French ideas of the English Other.
Simulation of fine-scale electrical conductivity fields using resolution-limited tomograms and area-to-point kriging
Authors: Nussbaumer Raphaël , Linde Niklas , Mariethoz Grégoire , Holliger Klaus 
Published: April 2019

SUMMARY
Deterministic geophysical inversion approaches yield tomographic images with strong imprints of the regularization terms required to solve otherwise ill-posed inverse problems. While such tomograms enable an adequate assessment of the larger-scale features of the probed subsurface, the finer-scale details tend to be unresolved. Yet, representing these fine-scale structural details is generally desirable and for some applications even mandatory. To address this problem, we have developed a two-step methodology based on area-to-point kriging to generate fine-scale multi-Gaussian realizations from smooth tomographic images. Specifically, we use a co-kriging system in which the smooth, low-resolution tomogram is related to the fine-scale heterogeneity through a linear mapping operation. This mapping is based on the model resolution and the posterior covariance matrices computed using a linearization around the final tomographic model. This, in turn, allows us for analytical computations of covariance and cross-covariance models. The methodology is tested on a heterogeneous synthetic 2-D distribution of electrical conductivity that is probed with a surface-based electrical resistivity tomography (ERT) survey. The results demonstrate the ability of this technique to reproduce a known geostatistical model characterizing the fine-scale structure, while simultaneously preserving the large-scale structures identified by the smoothness-constrained tomographic inversion. Small discrepancies between the geophysical forward responses of the realizations and the reference synthetic data are attributed to the underlying linearization. Overall, the method provides an effective and fast alternative to more comprehensive, but computationally more expensive approaches, such as, for example, Markov chain Monte Carlo techniques. Moreover, the proposed method can be used to generate fine-scale multivariate Gaussian realizations from virtually any smoothness-constrained inversion results given the corresponding resolution and posterior covariance matrices.
Citrullus ecirrhosus: Wild Source of Resistance Against Bemisia tabaci (Hemiptera: Aleyrodidae) for Cultivated Watermelon
Authors: Simmons Alvin M , Jarret Robert L , Cantrell Charles L , Levi Amnon 
Published: April 2019

Abstract
Members of the highly polyphagous Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) species complex cause major crop damage by feeding and by transmitting plant viruses. The Middle East-Asia Minor 1 (MEAM1) of the B. tabaci complex is by far the most problematic whitefly affecting crops including cultivated watermelon (Citrullus lanatus; Cucurbitaceae: Cucurbitales). Watermelon cultivars share a narrow genetic base and are highly susceptible to whiteflies. We studied the potential of C. ecirrhosus, a perennial desert species that can be hybridized with C. lanatus, as a source of whitefly resistance for cultivated watermelon. The results of this study indicate that C. ecirrhosus offers resistance (although not total) against the MEAM1 B. tabaci based on, at least, antibiosis and antixenosis. Whitefly performance concerning developmental survival, body size attainment, and nonpreference were suppressed on C. ecirrhosus compared with the watermelon cultivar ‘Sugar Baby’. Also, our olfactometer results indicated that the adults were less attracted to leaf volatiles of C. ecirrhosus. Although there is a pungent odor associated with the leaves of C. ecirrhosus, the leaf volatiles had no toxic effect on adult whitefly survival as compared with cultivated watermelon. We also demonstrated that plants of C. ecirrhosus can be clonally propagated from vine cuttings of the parent plant. Using traditional breeding procedures, C. ecirrhosus was hybridized with C. lanatus and viable F1 and F2 seeds were produced. This is the first report of pest resistance in C. ecirrhosus. This wild species offers a source of resistance against whiteflies for the improvement of cultivated watermelon.
A Data Analysis of the Iran–US Claims Tribunal’s Jurisprudence—Lessons for International Dispute-Settlement Today
Authors: Charlotin Damien 
Published: April 2019

Abstract
The Iran–US Claims Tribunal was instituted in 1–981 to hear claims from the two governments and their nationals after they broke diplomatic and economic ties. Upon deciding hundreds of cases, the Tribunal has been hailed as an example of a successful international adjudicative body, and as a source of inspiration for international dispute-settlement scholars. Less often acknowledged, however, the Tribunal’s output also constitutes a formidable and under-investigated dataset, ripe for empirical and data-oriented analysis. Such an analysis confirms the Tribunal’s enduring relevance and sheds light on older and newer debates in international dispute-settlement scholarship. The oft-mentioned charge that the Tribunal’s party-appointed members were ‘political’, or the practice of issuing dissenting opinions, can be reviewed under this lens, as they lessons for international law scholars and practitioners today.