bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes
Authors: Li H. , Liu J. , Xiong L. , Zhang H. , Zhou H. , Yin H. , Jing W. , Li J. , Shi Q. , Wang Y. , Liu J. , Nie L. 
Published: March 2017

AbstractThe softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea + Pelodiscus + Dogania + Nilssonia + Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108 million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous–Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India–Asia collision and opening of the Bering Strait, which provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group.
Crystalline phases found in rapidly quenched Ni–Nb–Zr alloys
Authors: DEO L.P. , KAUFMAN M.J. , WANG B. , NIKODEMSKI S. , DE OLIVEIRA M.F. 
Published: March 2017

SummaryThe properties of metallic alloys can be significantly improved by developing non‐equilibrium phases in the microstructures through rapid solidification techniques, thus the characterisation of these unusual structures is extremely important. In this research, the microstructures of three rapidly quenched alloys, namely Ni65.2Nb33.8Zr1.0, Ni54.8Nb31.1Zr14.1 and Ni54.8Nb21.6Zr23.6 (at. %) were investigated in greater detail in order to determine the structures and compositions of their crystalline phases. These crystalline phases were characterised using a combination of scanning electron microscopy, energy dispersive x‐ray spectroscopy, x‐ray diffraction and transmission electron microscopy techniques. The phases were compared to the crystalline structures reported in the literature. Our results indicate some agreement with the Ni–Nb phase diagram and an isothermal section of the Ni–Nb–Zr phase diagram; however, it is detected zirconium solubility in the Ni3Nb phase, as well as, the absence of expected crystalline phases.
Taxation of firms with unknown mobility
Authors: Becker Johannes , Schneider Andrea 
Published: March 2017

AbstractWe analyze optimal business tax policy when some firms are able to escape taxation by moving abroad. In contrast to the existing literature, we assume that the true number of mobile firms is ex ante unknown. While the government may learn from the firms' location responses to past tax rate changes, firms may anticipate this and adjust their choices accordingly. We find that incomplete information on mobility substantially affects the properties and the implications of equilibrium policy choices. First, the government may find it optimal to set a tax rate that triggers partial firm migration but full revelation of the true number of mobile firms. Second, we show that, if the firms' outside option is attractive (i.e., relocation cost and foreign tax rates are low), expected tax rates and expected firm migration are higher if the degree of mobility is unknown. Third, there is a positive value of learning, i.e., commitment on future tax rates cannot increase the government's expected revenue. However, if the government can commit to a rule‐based learning mechanism, i.e., credibly tie its future tax policy to present policy outcomes, it may obtain a Pareto improvement.
Body Mass Index and Rural Status on Self‐Reported Health in Older Adults: 2004‐2013 Medicare Expenditure Panel Survey
Authors: Batsis John A. , Whiteman Karen L. , Lohman Matthew C. , Scherer Emily A. , Bartels Stephen J. 
Published: March 2017

AbstractPurposeTo ascertain whether rural status impacts self‐reported health and whether the effect of rural status on self‐reported health differs by obesity status.MethodsWe identified 22,307 subjects aged ≥60 from the Medical Expenditure Panel Survey 2004‐2013. Body mass index (BMI) was categorized as underweight, normal, overweight, or obese. Physical and mental component scores of the Short Form‐12 assessed self‐reported health status. Rural/urban status was defined using metropolitan statistical area. Weighted regression models ascertained the relative contribution of predictors (including rural and BMI) on each subscale.FindingsMean age was 70.7 years. Rural settings had higher proportions classified as obese (30.7 vs 27.6%; P < .001), and rural residents had lower physical health status (41.7 ± 0.3) than urban (43.4 ± 0.1; P < .001). Obese or underweight persons had lower physical health status (39.5 ± 0.20 and 37.0 ± 0.82, respectively) than normal (44.7 ± 0.18) or overweight (44.6 ± 0.16) persons (P < .001). BMI category stratification was associated with differences in physical health between rural/urban by BMI. Individuals classified as underweight or obese had lower physical health compared to normal, while the differences were less pronounced for mental health. No differences in mental health existed between rural/urban status. A BMI * rural interaction was significant for physical but not mental health.ConclusionsRural residents report lower self‐reported physical health status compared to urban residents, particularly older adults who are obese or underweight. No interaction was observed between BMI and rural status.
End‐product quality characteristics and consumer response of chickpea flour‐based gluten‐free muffins containing corn starch and egg white
Authors: Alvarez María Dolores , Herranz Beatriz , Jiménez María José , Canet Wenceslao 
Published: March 2017

AbstractThe objective of this work was to study changes in technological characteristics and sensory properties of gluten‐free muffins when using chickpea flour (CF) alone and/or with partial CF replacement by corn starch (CS). The effect of partial whole egg replacement by egg white (EW) was also investigated. Four different CF:CS ratios (100:0, 75:25, 50:50, and 25:75) were used in formulations with and without incorporated EW, and compared with wheat flour (WF) muffins (0:0). Muffins prepared from CF alone had lower hardness, springiness, cohesiveness, chewiness, and resilience than control ones. However, reducing protein content by CS addition significantly increased texture profile analysis parameters of muffin crumb. Muffins prepared with 25:75 ratio had a structure with springiness similar to muffins made with WF but were too hard. Reducing whole egg content by partial replacement with EW also significantly increased muffin hardness. Flash profile performed by consumers showed a clear discrimination of muffins according to CF:CS ratio. Muffins containing both CF and CS at 50:50 ratio had the same high overall acceptability and purchase intention as gluten ones. Gluten‐free CF‐based muffins of satisfactory quality can be manufactured by CS incorporation, either with or without EW.Practical applicationsBy decreasing and increasing protein and starch contents of chickpea flour (CF) by incorporation of corn starch (CS), muffins formulated from a combination of CF and CS at different CF:CS ratios, either with or without partial replacement of whole egg with egg white, result in high‐quality muffins with similar technological and sensory characteristics to those of their gluten counterparts. Sensory overall acceptability and purchase intention of muffins made with a 50:50 ratio did not differ significantly from those of the controls. These findings will benefit celiac population, while promoting the value and utilization of pulses through muffins.
The entry heating and abundances of basaltic micrometeorites
Authors: Genge Matthew J. 
Published: March 2017

AbstractBasaltic micrometeorites (MMs) derived from HED‐like parent bodies have been found among particles collected from the Antarctic and from Arctic glaciers and are to date the only achondritic particles reported among cosmic dust. The majority of Antarctic basaltic particles are completely melted cosmic spherules with only one unmelted particle recognized from the region. This paper investigates the entry heating of basaltic MMs in order to predict the relative abundances of unmelted to melted basaltic particles and to evaluate how mineralogical differences in precursor materials influence the final products of atmospheric entry collected on the Earth's surface. Thermodynamic modeling is used to simulate the melting behavior of particles with compositions corresponding to eucrites, diogenites, and ordinary chondrites in order to evaluate degree of partial melting and to make a comparison between the behavior of chondritic particles that dominate the terrestrial dust flux and basaltic micrometeroids. The results of 120,000 simulations were compiled to predict relative abundances and indicate that the phase relations of precursor materials are crucial in determining the relative abundances of particle types. Diogenite and ordinary chondrite materials exhibit similar behavior, although diogenite precursors are more likely to form cosmic spherules under similar entry parameters. Eucrite particles, however, are much more likely to melt due to their lower liquidus temperatures and small temperature interval of partial melting. Eucrite MMs, therefore, usually form completely molten cosmic spherules except at particle diameters <100 μm. The low abundance of unmelted basaltic MMs compared with spherules, if statistically valid, is also shown to be inconsistent with a low velocity population (12 km s−1) and is more compatible with higher velocities which may suggest a near‐Earth asteroid source dominates the current dust production of basaltic MMs.
Patient factors associated with unidentified reactivity in solid‐phase and polyethylene glycol antibody detection methods
Authors: Miller Nichole M. , Johnson Susan T. , Carpenter Erica , Naczek Christine A. , Karafin Matthew S. 
Published: March 2017

BACKGROUNDSeveral publications have reported an increase in nonspecific reactions when automated technologies such as solid phase are used for the detection of red blood cell alloantibodies. However, there is little known about patient‐specific factors associated with these reactions and the clinical importance of these nonspecific reactions.STUDY DESIGN AND METHODSWe performed a 6‐year retrospective review of our blood bank records and all newly reported unidentified (UID) reactivity using a test tube polyethylene glycol (t‐PEG) and solid‐phase method for the detection and identification of alloantibodies was recorded. Patient factors, such as underlying diagnosis, age, sex, ABO, Rh type, ethnicity, and subsequent antibody formation were recorded in each case.RESULTSWe determined that there was a significant increase in new UID reactions recorded in solid phase (20 per 10,000 tests) when compared to the t‐PEG (1.8 per 10,000 tests) method for the detection of antibodies (p ≤ 0.0001). Solid‐phase UID reactions were significantly associated with female sex (p = 0.04) and certain diagnoses, such as chronic or autoimmune disease, cancer, pregnancy, surgery, and trauma. Approximately 16% of patients developed a new auto‐ or alloantibody subsequent to their detected UID using solid phase.CONCLUSIONSWhen solid phase is used for antibody identification, there is greater sensitivity toward nonspecific reactivity when compared to the t‐PEG method. Patient sex and underlying diagnosis may explain the increased incidence of new UID reactivity in the solid‐phase technology. Finally, UID reactivity should not be overlooked due to a notable percentage of subsequent clinically significant antibodies after UID detection.
Binding of
Candida albicans
to Human CEACAM1 and CEACAM6 Modulates the Inflammatory Response of Intestinal Epithelial Cells
Authors: Klaile Esther , Müller Mario M. , Schäfer Miriam R. , Clauder Ann-Katrin , Feer Sabina , Heyl Kerstin A. , Stock Magdalena , Klassert Tilman E. , Zipfel Peter F. , Singer Bernhard B. , Slevogt Hortense 
Published: March 2017

ABSTRACT

Candida albicans
colonizes human mucosa, including the gastrointestinal tract, as a commensal. In immunocompromised patients,
C. albicans
can breach the intestinal epithelial barrier and cause fatal invasive infections. Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1; CD66a), CEACAM5 (CEA), and CEACAM6 (CD66c) are immunomodulatory receptors expressed on human mucosa and are recruited by bacterial and viral pathogens. Here we show for the first time that a fungal pathogen (i.e.,
C. albicans
) also binds directly to the extracellular domain of human CEACAM1, CEACAM3, CEACAM5, and CEACAM6. Binding was specific for human CEACAMs and mediated by the N-terminal IgV-like domain. In enterocytic C2BBe1 cells,
C. albicans
caused a transient tyrosine phosphorylation of CEACAM1 and induced higher expression of membrane-bound CEACAM1 and soluble CEACAM6. Lack of the CEACAM1 receptor after short hairpin RNA (shRNA) knockdown abolished CXCL8 (interleukin-8) secretion by C2BBe1 cells in response to
C. albicans
. In CEACAM1-competent cells, the addition of recombinant soluble CEACAM6 reduced the
C. albicans
-induced CXCL8 secretion.

IMPORTANCE
The present study demonstrates for the first time that fungal pathogens can be recognized by at least four members of the immunomodulatory CEACAM receptor family: CEACAM1, -3, -5, and -6. Three of the four receptors (i.e., CEACAM1, -5, and -6) are expressed in mucosal cells of the intestinal tract, where they are implicated in immunomodulation and control of tissue homeostasis. Importantly, the interaction of the major fungal pathogen in humans
Candida albicans
with CEACAM1 and CEACAM6 resulted in an altered epithelial immune response. With respect to the broad impact of CEACAM receptors on various aspects of the innate and the adaptive immune responses, in particular epithelial, neutrophil, and T cell behavior, understanding the role of CEACAMs in the host response to fungal pathogens might help to improve management of superficial and systemic fungal infections.
Genetic Determinants of 1,3-Butadiene Metabolism and Detoxification in Three Populations of Smokers with Different Risks of Lung Cancer
Authors: Boldry Emily J. , Patel Yesha M. , Kotapati Srikanth , Esades Amanda , Park Sungshim L. , Tiirikainen Maarit , Stram Daniel O. , Le Marchand Loïc , Tretyakova Natalia 
Published: March 2017

Abstract
Background: 1,3-Butadiene (BD) is an important carcinogen in tobacco smoke that undergoes metabolic activation to DNA-reactive epoxides. These species can be detoxified via glutathione conjugation and excreted in urine as the corresponding N-acetylcysteine conjugates. We hypothesize that single nucleotide polymorphisms (SNPs) in BD-metabolizing genes may change the balance of BD bioactivation and detoxification in White, Japanese American, and African American smokers, potentially contributing to ethnic differences in lung cancer risk.
Methods: We measured the levels of BD metabolites, 1- and 2-(N-acetyl-L-cysteine-S-yl)-1-hydroxybut-3-ene (MHBMA) and N-acetyl-S-(3,4-dihydroxybutyl)-L-cysteine (DHBMA), in urine samples from a total of 1,072 White, Japanese American, and African American smokers and adjusted these values for body mass index, age, batch, and total nicotine equivalents. We also conducted a genome-wide association study to identify genetic determinants of BD metabolism.
Results: We found that mean urinary MHBMA concentrations differed significantly by ethnicity (P = 4.0 × 10−25). African Americans excreted the highest levels of MHBMA followed by Whites and Japanese Americans. MHBMA levels were affected by GSTT1 gene copy number (P &lt; 0.0001); conditional on GSTT1, no other polymorphisms showed a significant association. Urinary DHBMA levels also differed between ethnic groups (P = 3.3 × 10−4), but were not affected by GSTT1 copy number (P = 0.226).
Conclusions: GSTT1 gene deletion has a strong effect on urinary MHBMA levels, and therefore BD metabolism, in smokers.
Impact: Our results show that the order of MHBMA levels among ethnic groups is consistent with their respective lung cancer risk and can be partially explained by GSTT1 genotype. Cancer Epidemiol Biomarkers Prev; 26(7); 1034–42. ©2017 AACR.
Maltotriose Conjugation to a Chlorin Derivative Enhances the Antitumor Effects of Photodynamic Therapy in Peritoneal Dissemination of Pancreatic Cancer
Authors: Kato Akihisa , Kataoka Hiromi , Yano Shigenobu , Hayashi Kazuki , Hayashi Noriyuki , Tanaka Mamoru , Naitoh Itaru , Ban Tesshin , Miyabe Katsuyuki , Kondo Hiromu , Yoshida Michihiro , Fujita Yasuaki , Hori Yasuki , Natsume Makoto , Murakami Takashi , Narumi Atsushi , Nomoto Akihiro , Naiki-Ito Aya , Takahashi Satoru , Joh Takashi 
Published: March 2017

Abstract
Peritoneal dissemination is a major clinical issue associated with dismal prognosis and poor quality of life for patients with pancreatic cancer; however, no effective treatment strategies have been established. Herein, we evaluated the effects of photodynamic therapy (PDT) with maltotriose-conjugated chlorin (Mal3-chlorin) in culture and in a peritoneal disseminated mice model of pancreatic cancer. The Mal3-chlorin was prepared as a water-soluble chlorin derivative conjugated with four Mal3 molecules to improve cancer selectivity. In vitro, Mal3-chlorin showed superior uptake into pancreatic cancer cells compared with talaporfin, which is clinically used. Moreover, the strong cytotoxic effects of PDT with Mal3-chlorin occurred via apoptosis and reactive oxygen species generation, whereas Mal3-chlorin alone did not cause any cytotoxicity in pancreatic cancer cells. Notably, using a peritoneal disseminated mice model, we demonstrated that Mal3-chlorin accumulated in xenograft tumors and suppressed both tumor growth and ascites formation with PDT. Furthermore, PDT with Mal3-chlorin induced robust apoptosis in peritoneal disseminated tumors, as indicated by immunohistochemistry. Taken together, these findings implicate Mal3-chlorin as a potential next-generation photosensitizer for PDT and the basis of a new strategy for managing peritoneal dissemination of pancreatic cancer. Mol Cancer Ther; 16(6); 1124–32. ©2017 AACR.
Combinatorial Screening of Pancreatic Adenocarcinoma Reveals Sensitivity to Drug Combinations Including Bromodomain Inhibitor Plus Neddylation Inhibitor
Authors: Langdon Casey G. , Platt James T. , Means Robert E. , Iyidogan Pinar , Mamillapalli Ramanaiah , Klein Michael , Held Matthew A. , Lee Jong Woo , Koo Ja Seok , Hatzis Christos , Hochster Howard S. , Stern David F. 
Published: March 2017

Abstract
Pancreatic adenocarcinoma (PDAC) is the fourth most common cause of cancer-related death in the United States. PDAC is difficult to manage effectively, with a five-year survival rate of only 5%. PDAC is largely driven by activating KRAS mutations, and as such, cannot be directly targeted with therapeutic agents that affect the activated protein. Instead, inhibition of downstream signaling and other targets will be necessary to effectively manage PDAC. Here, we describe a tiered single-agent and combination compound screen to identify targeted agents that impair growth of a panel of PDAC cell lines. Several of the combinations identified from the screen were further validated for efficacy and mechanism. Combination of the bromodomain inhibitor JQ1 and the neddylation inhibitor MLN4294 altered the production of reactive oxygen species in PDAC cells, ultimately leading to defects in the DNA damage response. Dual bromodomain/neddylation blockade inhibited in vivo growth of PDAC cell line xenografts. Overall, this work revealed novel combinatorial regimens, including JQ1 plus MLN4294, which show promise for the treatment of RAS-driven PDAC. Mol Cancer Ther; 16(6); 1041–53. ©2017 AACR.
Unwarranted Variation in the Quality of Care for Patients With Diseases of the Thoracic Aorta
Authors: Bottle Alex , Mariscalco Giovanni , Shaw Matthew A. , Benedetto Umberto , Saratzis Athanasios , Mariani Silvia , Bashir Mohamad , Aylin Paul , Jenkins David , Oo Aung Y. , Murphy Gavin J. , Tsang Geoff , Bryan Alan J. , Cooper Graham , Duncan Andrew , Harrington Deborah , Kuduvalli Manoj , Mascaro Jorge , Rosendahl Ulrich , Unsworth‐White Jonathan 
Published: March 2017

Background
Thoracic aortic disease has a high mortality. We sought to establish the contribution of unwarranted variation in care to regional differences in outcomes observed in patients with thoracic aortic disease in England.

Methods and Results

Data from the Hospital Episode Statistics (
HES
) and the National Adult Cardiac Surgery Audit (
NACSA
) were extracted. A parallel systematic review/meta‐analysis through December 2015, and structure and process questionnaire of English cardiac surgery units were also accomplished. Treatment and mortality rates were investigated. A total of 24 548 adult patients in the
HES
study, 8058 in the
NACSA
study, and 103 543 from a total of 33 studies in the systematic review were obtained. Treatment rates for thoracic aortic disease within 6 months of index admission ranged from 7.6% to 31.5% between English counties. Risk‐adjusted 6‐month mortality in untreated patients ranged from 19.4% to 36.3%. Regional variation persisted after adjustment for disease or patient factors. Regional cardiac units with higher case volumes treated more‐complex patients and had significantly lower risk‐adjusted mortality relative to low‐volume units. The results of the systematic review indicated that the delivery of care by multidisciplinary teams in high‐volume units resulted in better outcomes. The observational analyses and the online survey indicated that this is not how services are configured in most units in England.

Conclusions
Changes in the organization of services that address unwarranted variation in the provision of care for patients with thoracic aortic disease in England may result in more‐equitable access to treatment and improved outcomes.