bluuebunny/crossref_metadata_2025_split huggingface dataset:
TREE SEEDLING EMERGENCE ON INTERACTIVE TEMPERATURE AND MOISTURE GRADIENTS AND IN PATCHES OF OLD‐FIELD VEGETATION
Authors: Burton Philip J. , Bazzaz F. A. 
Published: January 2018

Seeds of tree species commonly invading old‐fields (Fraxinus americana, Gleditsia triacanthos, Morus rubra, Platanus occidentalis, and Prunus serotina) were germinated at eight temperatures from 5 C to 40 C, with six moisture levels (2% to 18% gravimetric moisture content) at each temperature. For most species, total seedling emergence and emergence rate exhibited approximate bivariate Gaussian response surfaces. Emergence of all species, except Gleditsia, was much more sensitive to differences in temperature than to differences in moisture. Species differed considerably in their response breadths across the interactive gradients, with moisture response bearing little relationship to temperature response.Seeds of Acer saccharum, Crataegus mollis, Fraxinus americana, Gleditsia triacanthos, Morus rubra, and Prunus serotina were sown into old‐field vegetation patches dominated by eight different plant species, across three different soils. Acer and Morus emergence exhibited no significant differences among vegetation patches. Emergence of other tree species differed among patch types, but identity of the vegetation (often early successional) most conducive to emergence typically varied from year to year. Emergence of most species responded more strongly to vegetation than to soil series. High Fraxinus and Prunus emergence was associated with dampened temperature ranges, while high Crataegus emergence was associated with low amounts of plant litter. Despite great variability, vegetation differences can predict tree seedling emergence better than do year‐to‐year or soil differences. Extrapolations from the laboratory experiments predicted approximate levels of overall seedling emergence in the field, but prevailing temperatures and moisture differences among plant neighborhoods alone were not sufficient to explain observed differences in seedling emergence among these patches.
Generalized boosted modeling to identify subgroups where effect of dabigatran versus warfarin may differ: An observational cohort study of patients with atrial fibrillation
Authors: Wang Shirley V. , Huybrechts Krista F. , Fischer Michael A. , Franklin Jessica M. , Glynn Robert J. , Schneeweiss Sebastian , Gagne Joshua J. 
Published: January 2018

AbstractPurposeTo explore generalized boosted modeling (GBM) as a method for identifying subgroups with greater benefit or harm with dabigatran versus warfarin for treatment of atrial fibrillation.MethodsWe identified new initiators of warfarin or dabigatran with nonvalvular atrial fibrillation in 2 healthcare claims databases (2009–2013) and used GBM within 1 data source (development cohort) to explore subgroups where their effect on thromboembolism and major bleeding may differ. Identified subgroups were evaluated in the second data source (validation cohort) with stabilized‐inverse‐probability‐of‐treatment weights to adjust for confounding.ResultsDevelopment and validation cohorts included 13 624 (28% dabigatran) and 62 596 (29% dabigatran) initiators, respectively. In development data, the strongest exposure interactions were prior thromboembolism and renal disease. In validation data, reduction in thromboembolism with dabigatran was greater for patients with versus without a history of thromboembolism by 2.8 (95% CI, −0.5 to 5.4) events per 100 patient‐years. Major bleeding was reduced by 1.6/100 patient‐years for dabigatran compared to warfarin initiators, without evidence of variation by renal disease.ConclusionsWe explored use of GBM to identify potential subgroups with different treatment effect. Dabigatran's superiority to warfarin at prevention of thromboembolism may be greater in secondary than primary prevention. In practice, secondary prevention patients are more often treated with warfarin.
Label‐Free Quantitative Proteomic Screening of Candidate Plasma Biomarkers for the Prognosis of Breast Cancer with Different Lymph Node Statuses
Authors: Chen Ling , Zhao Weibo , He Jing , Li Liqi , Meng Dong , Cai Dongyan , Yu Jinjin , Chen Daozhen , Wu Yibo , Zhou Tao 
Published: January 2018

PurposeLymph node status is a crucial predictor for the overall survival of invasive breast cancer. However, lymph node involvement is only detected in about half of HER2‐positive patients. Since patients with lymph node involvement has less favorable prognosis and higher risk of recurrence, it is important to develop plasma protein biomarkers for distinguishing lymph node metastasis.Experimental designA label‐free quantitative proteomic strategy to construct plasma proteomes of ten patients with small size HER2‐positive breast cancer (five patients with lymph node metastasis versus five patients without lymph node metastasis) is applied.ResultsA total of 388 proteins are identified, of which 33 proteins are differentially expressed. Statistical analyses suggested the present strategy is low cost and highly efficient in initial screening of plasma biomarkers. In silico analyses using various bioinformatics databases show that these altered proteins are highly associated with breast disease, cancer pathway, lymph node morphology, metastasis, complement pathway, and immune regulation.Conclusions and clinical relevanceThe present dataset provides a list of candidate biomarkers that could be used for early differentiation diagnosis and prognosis of breast cancer with lymph node metastasis.
Global-Mode Analysis of Full-Disk Data from the Michelson Doppler Imager and the Helioseismic and Magnetic Imager
Authors: Larson Timothy P. , Schou Jesper 
Published: January 2018

AbstractBuilding upon our previous work, in which we analyzed smoothed and subsampled velocity data from the Michelson Doppler Imager (MDI), we extend our analysis to unsmoothed, full-resolution MDI data. We also present results from the Helioseismic and Magnetic Imager (HMI), in both full resolution and processed to be a proxy for the low-resolution MDI data. We find that the systematic errors that we saw previously, namely peaks in both the high-latitude rotation rate and the normalized residuals of odd $a$
a
-coefficients, are almost entirely absent in the two full-resolution analyses. Furthermore, we find that both systematic errors seem to depend almost entirely on how the input images are apodized, rather than on resolution or smoothing. Using the full-resolution HMI data, we confirm our previous findings regarding the effect of using asymmetric profiles on mode parameters, and also find that they occasionally result in more stable fits. We also confirm our previous findings regarding discrepancies between 360-day and 72-day analyses. We further investigate a six-month period previously seen in $f$
f
-mode frequency shifts using the low-resolution datasets, this time accounting for solar-cycle dependence using magnetic-field data. Both HMI and MDI saw prominent six-month signals in the frequency shifts, but we were surprised to discover that the strongest signal at that frequency occurred in the mode coverage for the low-resolution proxy. Finally, a comparison of mode parameters from HMI and MDI shows that the frequencies and $a$
a
-coefficients agree closely, encouraging the concatenation of the two datasets.
FROM OVERT TO VEILED SEGREGATION: ISRAEL'S PALESTINIAN ARAB CITIZENS IN THE GALILEE
Authors: Shafir Gershon 
Published: January 2018

AbstractThis article's geographical focus is the Galilee, Israel's only region with a Palestinian Arab majority. Its sociological focus is the drive to Judaize this region, the mirror image of its de-Arabization, which I anchor in Israelis’ morbid fear of settler colonial reversal. Although direct legal discrimination—restriction of movement under a military government and exclusion from publicly administered land—was banned by the government and the High Court of Justice respectively, new modes of discrimination against Israel's Arab citizens have replaced the older forms. I demonstrate how policies that limit Arab middle-class citizens’ upwardly mobile migration into the Judaized spaces of communal settlements (or overlooks) and towns endure. I compare gatekeeping exercised by national-level indirect legal discrimination operating through the admission committees of communal settlements with the institutional discrimination practiced by municipalities of emerging mixed towns against new Arab residents’ public presence. Finally, I highlight the linkages between instances of Judaization across the Green Line, which make the unwinding of segregation, in all of its forms, that much harder.
THE MISSING TURKISH REVOLUTION: COMPARING VILLAGE-LEVEL CHANGE AND CONTINUITY IN REPUBLICAN TURKEY AND SOVIET CENTRAL ASIA, 1920–50
Authors: Tuna Mustafa 
Published: January 2018

AbstractThe Kemalist leadership of early Republican Turkey attempted to transform the country's Muslim populace with a heavy emphasis on secularism, scientific rationalism, and nationalism. Several studies have examined the effects of this effort, or the “Turkish Revolution,” at the central and more recently provincial levels. This article uses first-hand accounts and statistical data to carry the analysis to the village level. It argues that the Kemalist reforms failed to reach rural Turkey, where more than 80 percent of the population lived. A comparison with sedentary Soviet Central Asia's rural transformation in the same period reveals ideology and the availability of resources as the underlying causes of this failure. Informed by a Marxist–Leninist emphasis on the necessity of transforming the “substructure” for revolutionary change, the Soviet state undermined existing authority structures in Central Asia's villages to facilitate the introduction of communist ideals among their Muslim inhabitants. Turkey's Kemalist leadership, on the other hand, preserved existing authority structures in villages and attempted to change culture first. However, they lacked and could not create the resources to implement this change.
POINT OF NO RETURN? PROSPECTS OF EMPIRE AFTER THE OTTOMAN DEFEAT IN THE BALKAN WARS (1912–13)
Authors: Öztan Ramazan Hakkı 
Published: January 2018

AbstractIn late 1912, the Ottoman imperial armies suffered a series of quick defeats at the hands of the Balkan League, comprising Greece, Serbia, Bulgaria, and Montenegro, resulting in significant territorial losses. The Ottoman defeat in the Balkan Wars (1912–13) often stands at the center of teleological accounts of a neat and linear transition from Ottoman Empire to Turkish Republic. These teleological readings see the Ottoman defeat as a historical turning point when Ottoman elites turned nationalist, discovered Anatolia, and embraced the Turkish core. This article contends that such approaches frame late Ottoman history in anticipation of the later reality of nation-states, and overlook the messy and historically complex nature of the collapse of empire and the emergence of the nation-state. Although the defeat was certainly shocking for the Ottoman ruling elite, I argue that it initiated an era of debate rather than one of broad consensus. Similarly, the defeat neither marked the end of the Ottoman Empire nor heralded the coming of the Turkish Republic, but rather reinvigorated the Ottoman imperialist project.
Modeling cancer using patient-derived induced pluripotent stem cells to understand development of childhood malignancies
Authors: Marin Navarro Ana , Susanto Evelyn , Falk Anna , Wilhelm Margareta 
Published: January 2018

AbstractIn vitro modeling of complex diseases is now a possibility with the use of patient-derived induced pluripotent stem (iPS) cells. Their stem cell properties, including self-renewal and their potential to virtually differentiate into any cell type, emphasize their importance as a translational tool for modeling disorders that so far have been limited by the unavailability of primary cell lines, animal models, or inaccessible human materials. Around 100 genes with germline mutations have been described to be responsible for cancer predisposition. Familial cancers are usually diagnosed earlier in life since these patients already carry the first transforming hit. Deriving iPS cells from patients suffering from familial cancers provides a valuable tool for understanding the mechanisms underlying pediatric cancer onset and progression since they require less mutation recurrence than adult cancers to develop. At the same time, some familial mutations are found in sporadic cases and are a valuable prognostic tool. Patient-derived iPS cells from germline malignancies can also create new tools in developing specific drugs with more personalized-therapy strategies.
Legionella DotM structure reveals a role in effector recruiting to the Type 4B secretion system
Authors: Meir Amit , Chetrit David , Liu Luying , Roy Craig R. , Waksman Gabriel 
Published: January 2018

AbstractLegionella pneumophila, a causative agent of pneumonia, utilizes the Type 4B secretion (T4BS) system to translocate over 300 effectors into the host cell during infection. T4BS systems are encoded by a large gene cluster termed dot/icm, three components of which, DotL, DotM, and DotN, form the “coupling complex”, which serves as a platform for recruitment of effector proteins. One class of effectors includes proteins containing Glu-rich/E-block sequences at their C terminus. However, the protein or region of the coupling complex mediating recruitment of such effectors is unknown. Here we present the crystal structure of DotM. This all alpha-helical structure exhibits patches of positively charged residues. We show that these regions form binding sites for acidic Glu-rich peptides and that mutants targeting these patches are defective in vivo in the translocation of acidic Glu-rich motif-containing effectors. We conclude that DotM forms the interacting surface for recruitment of acidic Glu-rich motif-containing Legionella effectors.
A roadmap towards personalized immunology
Authors: Delhalle Sylvie , Bode Sebastian F. N. , Balling Rudi , Ollert Markus , He Feng Q. 
Published: January 2018

AbstractBig data generation and computational processing will enable medicine to evolve from a “one-size-fits-all” approach to precise patient stratification and treatment. Significant achievements using “Omics” data have been made especially in personalized oncology. However, immune cells relative to tumor cells show a much higher degree of complexity in heterogeneity, dynamics, memory-capability, plasticity and “social” interactions. There is still a long way ahead on translating our capability to identify potentially targetable personalized biomarkers into effective personalized therapy in immune-centralized diseases. Here, we discuss the recent advances and successful applications in “Omics” data utilization and network analysis on patients’ samples of clinical trials and studies, as well as the major challenges and strategies towards personalized stratification and treatment for infectious or non-communicable inflammatory diseases such as autoimmune diseases or allergies. We provide a roadmap and highlight experimental, clinical, computational analysis, data management, ethical and regulatory issues to accelerate the implementation of personalized immunology.
Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach
Authors: Akberdin Ilya R. , Thompson Merlin , Hamilton Richard , Desai Nalini , Alexander Danny , Henard Calvin A. , Guarnieri Michael T. , Kalyuzhnaya Marina G. 
Published: January 2018

AbstractBiological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, 13C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confirmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. The computational framework of C1-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.
Oxidized Carbon Black: Preparation, Characterization and Application in Antibody Delivery across Cell Membrane
Authors: Amornwachirabodee Kittima , Tantimekin Nattapol , Pan-In Porntip , Palaga Tanapat , Pienpinijtham Prompong , Pipattanaboon Chonlatip , Sukmanee Thanyada , Ritprajak Patcharee , Charoenpat Promchat , Pitaksajjakul Pannamthip , Ramasoota Pongrama , Wanichwecharungruang Supason 
Published: January 2018

AbstractModulating biomolecular networks in cells with peptides and proteins has become a promising therapeutic strategy and effective biological tools. A simple and effective reagent that can bring functional proteins into cells can increase efficacy and allow more investigations. Here we show that the relatively non-toxic and non-immunogenic oxidized carbon black particles (OCBs) prepared from commercially available carbon black can deliver a 300 kDa protein directly into cells, without an involvement of a cellular endocytosis. Experiments with cell-sized liposomes indicate that OCBs directly interact with phospholipids and induce membrane leakages. Delivery of human monoclonal antibodies (HuMAbs, 150 kDa) with specific affinity towards dengue viruses (DENV) into DENV-infected Vero cells by OCBs results in HuMAbs distribution all over cells’ interior and effective viral neutralization. An ability of OCBs to deliver big functional/therapeutic proteins into cells should open doors for more protein drug investigations and new levels of antibody therapies and biological studies.
Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid
Authors: Mendes Niege S. , Bitencourt Tamires A. , Sanches Pablo R. , Silva-Rocha Rafael , Martinez-Rossi Nilce M. , Rossi Antonio 
Published: January 2018

AbstractWhile fatty acids are known to be toxic to dermatophytes, key physiological aspects of the Trichophyton rubrum response to undecanoic acid (UDA), a medium chain saturated fatty acid (C11:0), are not well understood. Thus, we analysed RNA-seq data from T. rubrum exposed to sub-lethal doses of UDA for 3 and 12 h. Three putative pathways were primarily involved in UDA detoxification: lipid metabolism and cellular membrane composition, oxidative stress, and pathogenesis. Biochemical assays showed cell membrane impairment, reductions in ergosterol content, and an increase in keratinolytic activity following UDA exposure. Moreover, we assessed differential exon usage and intron retention following UDA exposure. A key enzyme supplying guanine nucleotides to cells, inosine monophosphate dehydrogenase (IMPDH), showed high levels of intron 2 retention. Additionally, phosphoglucomutase (PGM), which is involved in the glycogen synthesis and degradation as well as cell wall biosynthesis, exhibited a significant difference in exon 4 usage following UDA exposure. Owing to the roles of these enzymes in fungal cells, both have emerged as promising antifungal targets. We showed that intron 2 retention in impdh and exon 4 skipping in pgm might be related to an adaptive strategy to combat fatty acid toxicity. Thus, the general effect of UDA fungal toxicity involves changes to fungal metabolism and mechanisms for regulating pre-mRNA processing events.
A Longitudinal Investigation of Preferential Attention to Biological Motion in 2- to 24-Month-Old Infants
Authors: Sifre Robin , Olson Lindsay , Gillespie Scott , Klin Ami , Jones Warren , Shultz Sarah 
Published: January 2018

AbstractPreferential attention to biological motion is an early-emerging mechanism of adaptive action that plays a critical role in social development. The present study provides a comprehensive longitudinal mapping of developmental change in preferential attention to biological motion in 116 infants at 7 longitudinal time points. Tested repeatedly from 2 until 24 months of age, results reveal that preferential attention to biological motion changes considerably during the first months of life. Previously reported preferences in both neonates and older infants are absent in the second month but do reemerge by month 3 and become increasingly pronounced during the subsequent two years. These results highlight the second month of life as a potentially critical transition period in social visual engagement.
Anthropometry-based estimation of body heat capacity in individuals aged 7–69 years: the Size Korea Survey 2010
Authors: Pham Duong Duc , Lee Jeong Hoon , Kim Ka Yul , Song Ji Yeon , Kim Ji Eun , Leem Chae Hun 
Published: January 2018

AbstractAlthough our previously developed anthropometry-based calculation of heat capacity (HC) for adults appeared to be precise and valid, its use in children and adolescents may be associated with bias. This study investigated a large dataset from the Size Korea survey, a national anthropometric survey conducted in 2010, to revalidate our previous HC equation and to develop another one that is appropriate for children and adolescents. We enrolled 12,766 participants aged 7–69 years with body composition data measured by multi-frequency bioelectrical impedance analysis. Age was associated with HC in children aged 7–19 years (R2 = 0.58) but not in adults (R2 = 0.007). Linear regression was appropriate to describe the relationship between HC and body surface area (BSA) in adults, whereas the regression in children and adolescent was quadratic. The previously developed HC equation had high reliability (intra-class correlation coefficient = 0.995) and predictive power (accurate prediction rate = 86.1%) in the >20 age group. The model composed of sex, body weight, BSA, and BSA2 was appropriate for the prediction of HC in young individuals aged 7–19 years. In conclusion, anthropometric-based modelling is a simple, reliable, and useful method for the calculation of HC.