bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics
Authors: Romero Irene Gallego , Pavlovic Bryan J. , Hernando-Herraez Irene , Banovich Nicholas E. , Kagan Courtney L. , Burnett Jonathan E. , Huang Constance H. , Mitrano Amy , Chavarria Claudia I. , Ben-Nun Inbar Friedrich , Li Yingchun , Sabatini Karen , Leonardo Trevor , Parast Mana , Marques-Bonet Tomas , Laurent Louise C. , Loring Jeanne F. , Gilad Yoav 
Published: September 2014

AbstractComparative genomics studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced pluripotent stem cell (iPSC) lines derived from fibroblasts of healthy donors. All lines appear to be free of integration from exogenous reprogramming vectors, can be maintained using standard iPSC culture techniques, and have proliferative and differentiation potential similar to human and mouse lines. To begin demonstrating the utility of comparative iPSC panels, we collected RNA sequencing data and methylation profiles from the chimpanzee iPSCs and their corresponding fibroblast precursors, as well as from 7 human iPSCs and their precursors, which were of multiple cell type and population origins. Overall, we observed much less regulatory variation within species in the iPSCs than in the somatic precursors, indicating that the reprogramming process has erased many of the differences observed between somatic cells of different origins. We identified 4,918 differentially expressed genes and 3,598 differentially methylated regions between iPSCs of the two species, many of which are novel inter-species differences that were not observed between the somatic cells of the two species. Our panel will help realise the potential of iPSCs in primate studies, and in combination with genomic technologies, transform studies of comparative evolution.
Prevalence and characteristics of metabolic syndrome in South‐East Asian psoriatic patients: A case–control study
Authors: Kokpol Chayada , Aekplakorn Wichai , Rajatanavin Natta 
Published: September 2014

AbstractThe prevalence of metabolic syndrome in Asian psoriatic patients compared with that of the general population shows variable results. This study aimed to examine the association between psoriasis and metabolic syndrome in a Thai population. This case–control study included 199 psoriatic patients and 199 controls matched for sex and age from the general Thai population. There were 111 men (55.8%) and 88 women (44.2%) in both the psoriatic and control groups. The mean age (± standard deviation) of both groups was 50.04 ± 13.81 and 49.96 ± 14.39 years (P = 0.91), respectively. The majority of psoriatic cases (82.9%) were of plaque type. The prevalence of metabolic syndrome was significantly higher in psoriatic patients than in the general population at 49.25% versus 30.65%. After controlling for age, sex, smoking and alcohol drinking the odds ratio was 2.25 (P < 0.0001). The metabolic components which were significantly higher in the cases than controls included hyperglycemia, high blood pressure (HBP) and abdominal obesity. No statistically significant difference was found between the cases and controls regarding prevalence of obesity, hypertriglyceridemia and low high‐density lipoprotein cholesterol. Thai psoriatic patients had a higher prevalence of metabolic syndrome than the general population. In conclusion, the prevalence of HBP, hyperglycemia and abdominal obesity was significantly higher in cases than in controls.
Image enhancement by multi‐parameter characterization of common image gathers
Authors: Dafni Raanan , Reshef Moshe 
Published: September 2014

ABSTRACTWe present an innovative approach for seismic image enhancement using multi‐parameter angle‐domain characterization of common image gathers. A special subsurface angle‐domain imaging system is used to generate the multi‐parameter common image gathers in a summation‐free image space. The imaged data associated with each common image gathers depth point contain direction‐dependent opening‐angle image contributions from all the available incident and scattered wave‐pairs at this point. Each direction‐dependent opening‐angle data can be differently weighted according to its coherency measure. Once the optimal migration velocity is used, it is assumed that in the actual specular direction, the coherency measure (semblance) along reflection events, from all available opening angles and opening azimuths, is larger than that along non‐specular directions. The computed direction‐dependent semblance attribute is designed to operate as an imaging filter which enhances specular migration contributions and suppresses all others in the final migration image. The ability to analyse the structural properties of the image points by the multi‐parameter common image gather allows us to better handle cases of complicated wave propagation and to improve the image quality at poorly illuminated regions or near complex structures. The proposed method and some of its practical benefits are demonstrated through detailed analysis of synthetic and real data examples.
Organic farming and heterogeneous landscapes positively affect different measures of plant diversity
Authors: Rader Romina , Birkhofer Klaus , Schmucki Reto , Smith Henrik G. , Stjernman Martin , Lindborg Regina 
Published: September 2014

Summary

Increasing landscape heterogeneity and organic farming practices are known to enhance species richness in agroecosystems. However, little is known about the consequences of these management options on other biodiversity components such as community composition, phylogenetic structure and functional diversity which may be more closely linked to ecosystem functioning.

We surveyed semi‐natural plant communities within the uncultivated field margins of 18 arable farms in Skåne, south Sweden. We investigated how taxonomic, phylogenetic and functional diversity responds to landscape heterogeneity (presence of semi‐natural habitat) and farm management intensity (organic vs. conventional farming).

Plant species richness and functional diversity metrics all responded positively to landscape heterogeneity, with the strongest effect occurring on conventional farms. Community composition differed with farm management, and mean phylogenetic relatedness, an indicator of phylogenetic structure, was significantly higher on the field margins of organic compared to conventional farms. Individual plant functional groups themselves responded in unique ways to land management and landscape heterogeneity.

Synthesis and applications. Management strategies that promote the conservation of heterogeneous landscapes (i.e. a higher proportion of semi‐natural habitats) and organic farm management practices are important for maintaining plant phylogenetic, functional and taxonomic diversity in agroecosystems. Accommodating various forms of diversity is important to ensure that ecosystems have the greatest possible array of species ecologies’. Such measures will help to improve the capacity of these ecosystems to provide multiple ecosystem functions, including the sustaining and regulating services of benefit to people.
Revisiting Financial Conflicts of Interest in FDA Advisory Committees
Authors: PHAM‐KANTER GENEVIEVE 
Published: September 2014

Policy Points:

FDA Center for Drug Evaluation and Research advisory committee members who have financial ties solely to the firm sponsoring the drug under review are more likely to vote in ways favorable to the sponsor.
Committee members who serve on advisory boards for sponsoring firms show particularly strong pro‐sponsor bias.
Contrary to conventional wisdom, committee members who have financial ties to many different firms do not, on average, show pro‐industry bias in their voting behavior.
ContextThe Food and Drug Administration (FDA) Safety and Innovation Act has recently relaxed conflict‐of‐interest rules for FDA advisory committee members, but concerns remain about the influence of members’ financial relationships on the FDA's drug approval process. Using a large newly available data set, this study carefully examined the relationship between the financial interests of FDA Center for Drug Evaluation and Research (CDER) advisory committee members and whether members voted in a way favorable to these interests.MethodsThe study used a data set of voting behavior and reported financial interests of 1,379 FDA advisory committee members who voted in CDER committee meetings that were convened during the 15‐year period of 1997–2011. Data on 1,168 questions and 15,739 question‐votes from 379 meetings were used in the analyses. Multivariable logit models were used to estimate the relationship between committee members’ financial interests and their voting behavior.FindingsIndividuals with financial interests solely in the sponsoring firm were more likely to vote in favor of the sponsor than members with no financial ties (OR = 1.49, p = 0.03). Members with interests in both the sponsoring firm and its competitors were no more likely to vote in favor of the sponsor than those with no financial ties to any potentially affected firm (OR = 1.16, p = 0.48). Members who served on advisory boards solely for the sponsor were significantly more likely to vote in favor of the sponsor (OR = 4.97, p = 0.005).ConclusionsThere appears to be a pro‐sponsor voting bias among advisory committee members who have exclusive financial relationships with the sponsoring firm but not among members who have nonexclusive financial relationships (ie, those with ties to both the sponsor and its competitors). These findings point to important heterogeneities in financial ties and suggest that policymakers will need to be nuanced in their management of financial relationships of FDA advisory committee members.
Use of poisons information resources and satisfaction with electronic products by Victorian emergency department staff
Authors: Luke Stephen , Fountain John S , Reith David M , Braitberg George , Cruickshank Jaycen 
Published: September 2014

AbstractObjectiveED staff use a range of poisons information resources of varying type and quality. The present study aims to identify those resources utilised in the state of Victoria, Australia, and assess opinion of the most used electronic products.MethodsA previously validated self‐administered survey was conducted in 15 EDs, with 10 questionnaires sent to each. The survey was then repeated following the provision of a 4‐month period of access to Toxinz™, an Internet poisons information product novel to the region. The study was conducted from December 2010 to August 2011.ResultsThere were 117 (78%) and 48 (32%) responses received from the first and second surveys, respectively, a 55% overall response rate. No statistically significant differences in professional group, numbers of poisoned patients seen or resource type accessed were identified between studies. The electronic resource most used in the first survey was Poisindex® (48.68%) and Toxinz™ (64.1%) in the second. There were statistically significant (P < 0.01) improvements in satisfaction in 26 of 42 questions between surveys, and no decrements. Although the majority of responders possessed mobile devices, less than half used them for poisons information but would do so if a reputable product was available.ConclusionThe order of poisons information sources most utilised was: consultation with a colleague, in‐house protocols and electronic resources. There was a significant difference in satisfaction with electronic poisons information resources and a movement away from existing sources when choice was provided. Interest in increased use of mobile solutions was identified.
Botanicals, selective insecticides, and predators to control Diaphorina citri (Hemiptera: Liviidae) in citrus orchards
Authors: Khan Azhar A. , Afzal Muhammad , Qureshi Jawwad A. , Khan Arif M. , Raza Abubakar M. 
Published: September 2014

AbstractThe Asian citrus psyllid (ACP) Diaphorina citri Kuwayama vectors pathogens that cause huanglongbing (HLB) or citrus greening devastating and economically important disease present in most citrus growing regions. Young citrus shoots are required for psyllid reproduction and development. During winter citrus trees produce little or no new growth. Overwintering adults reproduce in spring on newly emerging shoots also attractive to other pests and beneficial insects. Botanicals and relatively selective insecticides could help to conserve beneficial insects and reduce pest resistance to insecticides. Sprays of Azadirachtin (Neem), Tropane (Datura), Spirotetramat, Spinetoram, and broad‐spectrum Imidacloprid were evaluated to control ACP in spring and summer on 10‐year‐old “Kinow” Citrus reticulata Blanco trees producing new growth. Psyllid populations were high averaging 5–9 nymphs or adults per sample before treatment application. Nymphs or adults were significantly reduced to 0.5–1.5 per sample in all treatments for 3 weeks, average 61%–83% reduction. No significant reduction in ladybeetles Adalia bipunctata, Aneglei scardoni, Cheilomenes sexmaculata, and Coccinella septempunctata was observed. Syrphids, spiders and green lacewings were reduced in treated trees except with Tropane. Studies are warranted to assess impact of these predators on ACP and interaction with insecticides. Observed reduction in ACP populations may not be enough considering its reproductive potential and role in the spread of HLB. Follow‐up sprays may be required to achieve additional suppression using rotations of different insecticides.
Effect of Ascorbic Acid on the Properties of Ammonia Caramel Colorant Additives and Acrylamide Formation
Authors: Chen Hongxing , Gu Zhengbiao 
Published: September 2014

AbstractAmmonia caramels are among the most widely used colorant additives in the food industry. They are commonly prepared through the Maillard reaction and caramelization of mixtures of reducing sugars with ammonia or ammonium salts. Antioxidants are known to inhibit acrylamide formation during the Maillard reaction, and they may affect the properties of the ammonia caramel products. Thus, the objective of this study was to investigate the effect of the antioxidant ascorbic acid on the properties of ammonia caramel. A mixture of glucose and ammonia was allowed to react at 120 °C for 60 min in the presence of ascorbic acid at final concentrations of 0 to 0.08 M. The ammonia caramels obtained from these reactions were all positively charged. As the concentration of ascorbic acid increased, the color intensity of the ammonia caramel showed a decreasing trend, while the intensity of the fluorescence and total amount of pyrazines in the volatiles showed a tendency to increase. The addition of ascorbic acid did not result in obvious changes in the UV‐visible spectra of the ammonia caramels and the types of pyrazines in the volatiles were also unchanged. It is noteworthy that the addition of 0.02 to 0.08 M ascorbic acid did reduce the formation of the by‐product acrylamide, a harmful substance in food. When the concentration of ascorbic acid added reached 0.04 M, the content of acrylamide in the ammonia caramel was 20.53 μg/L, which was approximately 44% lower than that without ascorbic acid. As a result, ascorbic acid can be considered to improve the quality and safety of ammonia caramels.
Age‐associated reduction of cellular spreading/mechanical force up‐regulates matrix metalloproteinase‐1 expression and collagen fibril fragmentation via c‐Jun/AP‐1 in human dermal fibroblasts
Authors: Qin Zhaoping , Voorhees John J. , Fisher Gary J. , Quan Taihao 
Published: September 2014

SummaryThe dermal compartment of human skin is largely composed of dense collagen‐rich fibrils, which provide structural and mechanical support. Skin dermal fibroblasts, the major collagen‐producing cells, are interact with collagen fibrils to maintain cell spreading and mechanical force for function. A characteristic feature of aged human skin is fragmentation of collagen fibrils, which is initiated by matrix metalloproteinase 1 (MMP‐1). Fragmentation impairs fibroblast attachment and thereby reduces spreading. Here, we investigated the relationship among fibroblast spreading, mechanical force, MMP‐1 expression, and collagen fibril fragmentation. Reduced fibroblast spreading due to cytoskeletal disruption was associated with reduced cellular mechanical force, as determined by atomic force microscopy. These reductions substantially induced MMP‐1 expression, which led to collagen fibril fragmentation and disorganization in three‐dimensional collagen lattices. Constraining fibroblast size by culturing on slides coated with collagen micropatterns also significantly induced MMP‐1 expression. Reduced spreading/mechanical force induced transcription factor c‐Jun and its binding to a canonical AP‐1 binding site in the MMP‐1 proximal promoter. Blocking c‐Jun function with dominant negative mutant c‐Jun significantly reduced induction of MMP‐1 expression in response to reduced spreading/mechanical force. Furthermore, restoration of fibroblast spreading/mechanical force led to decline of c‐Jun and MMP‐1 levels and eliminated collagen fibril fragmentation and disorganization. These data reveal a novel mechanism by which alteration of fibroblast shape/mechanical force regulates c‐Jun/AP‐1‐dependent expression of MMP‐1 and consequent collagen fibril fragmentation. This mechanism provides a foundation for understanding the cellular and molecular basis of age‐related collagen fragmentation in human skin.
An individual patient data meta‐analysis on factors associated with adverse drug events in surgical and non‐surgical inpatients
Authors: Boeker Eveline B. , Ram Kim , Klopotowska Joanna E. , de Boer Monica , Creus Montse Tuset , de Andrés Ana L. , Sakuma Mio , Morimoto Takeshi , Boermeester Marja A. , Dijkgraaf Marcel G. W. 
Published: September 2014

AimThe incidence of adverse drug events (ADEs) in surgical and non‐surgical patients may differ. This individual patient data meta‐analysis (IPDMA) identifies patient characteristics and types of medication most associated with patients experiencing ADEs and suggests target areas for reducing harm and implementing focused interventions.MethodsAuthors of eligible studies on preventable ADEs (pADEs) were approached for collaboration. For assessment of differences among (non‐)surgical patients and identification of associated factors descriptive statistics, Pearson chi‐square, Poisson and logistic regression analyses were performed. For identification of high risk drugs (HRDs), a model was developed based on frequency, severity and preventability of medication related to ADEs.ResultsIncluded were 5367 patients from four studies. Patients aged ≥ 77 years experienced more ADEs and pADEs compared with patients aged ≤ 52 years (odds ratios (OR) 2.12 (95% CI 1.70, 2.65) and 2.55 (95% CI 1.70, 3.84), respectively, both P < 0.05). Polypharmacy on admission also increased the risk of ADEs (OR 1.21 (95% CI 1.03, 1.44), P < 0.05) and pADEs (OR 1.85 (95% CI 1.34, 2.56), P < 0.05). pADEs were associated with more severe harm than non‐preventable ADEs (54% vs. 32%, P < 0.05). The top five HRDs were antibiotics, sedatives, anticoagulants, diuretics and antihypertensives. Events associated with HRDs included diarrhoea or constipation, abnormal liver function test and central nervous system events. Most pADEs resulted from prescribing errors (90%).ConclusionElderly patients with polypharmacy on admission and receiving antibiotics, sedatives, anticoagulants, diuretics or antihypertensives were more prone to experiencing ADEs. Efficiency in prevention of ADEs may be improved by targeted vigilance systems for alertness of physicians and pharmacists.
Evaluation of graft stiffness using acoustic radiation force impulse imaging after living donor liver transplantation
Authors: Ijichi Hideki , Shirabe Ken , Matsumoto Yoshihiro , Yoshizumi Tomoharu , Ikegami Toru , Kayashima Hiroto , Morita Kazutoyo , Toshima Takeo , Mano Yohei , Maehara Yoshihiko 
Published: September 2014

AbstractAcoustic radiation force impulse (ARFI) imaging is an ultrasound‐based modality to evaluate tissue stiffness using short‐duration acoustic pulses in the region of interest. Virtual touch tissue quantification (VTTQ), which is an implementation of ARFI, allows quantitative assessment of tissue stiffness. Twenty recipients who underwent living donor liver transplantation (LDLT) for chronic liver diseases were enrolled. Graft types included left lobes with the middle hepatic vein and caudate lobes (n = 11), right lobes (n = 7), and right posterior segments (n = 2). They underwent measurement of graft VTTQ during the early post‐LDLT period. The VTTQ value level rose after LDLT, reaching a maximum level on postoperative day 4. There were no significant differences in the VTTQ values between the left and right lobe graft types. Significant correlations were observed between the postoperative maximum value of VTTQ and graft volume‐to‐recipient standard liver volume ratio, portal venous flow to graft volume ratio, and post‐LDLT portal venous pressure. The postoperative maximum serum alanine aminotransferase level and ascites fluid production were also significantly correlated with VTTQ. ARFI may be a useful diagnostic tool for the noninvasive and quantitative evaluation of the severity of graft dysfunction after LDLT.
Utility of pre‐procurement bedside liver biopsy in the deceased extended‐criteria liver donor
Authors: Mangus Richard S. , Borup Tim C. , Popa Sam , Saxena Romil , Cummings Oscar , Tector A. Joseph 
Published: September 2014

AbstractIntroductionThe Indiana Organ Procurement Organization (IOPO) utilizes preoperative bedside liver biopsies in certain extended‐criteria donors (ECDs), obtained by the on‐site coordinator, to determine the utility of pursuing donation. This study reports the clinical and financial outcomes for this management strategy.MethodsAll bedside liver biopsies obtained in ECDs over a five‐yr period were reviewed. Study variables included the following: indication for biopsy, biopsy results, taking the case to the operating room, transplantation of the donor liver, and graft survival. All biopsies were processed at a single university center.ResultsThere were 110 donors biopsied. Primary indications included the following: old age (29%), extensive/current alcohol abuse (26%), hepatitis C‐positive serology (21%), obesity (25%), and severely elevated liver function enzymes (18%). Biopsy results demonstrated a potentially transplantable liver in 73 cases (66%), all of whom were taken to the OR (while 37 ruled out for donation based upon liver biopsy [34%]). Of all biopsied livers, 49 ultimately were transplanted (45%). Intra‐operative decisions included the following: transplant 51/73 (70%), surgeon decision to exclude 20/73 (27%), nonuse due to finding of malignancy two (3%).ConclusionsBedside liver biopsy may be a valuable tool to determine the utility in pursuing donation in ECDs, particularly with liver‐only donors.
Jesus' Prophethood and Islam: Insights from the Risale‐i Nur
Authors: Largen Kristin Johnston 
Published: September 2014

AbstractWhile Jesus’ prophethood is an indisputable component of his identity in the Christian tradition, it has been marginalized for centuries in favor of his identity as savior. In this article, I argue that an engagement with an understanding of Jesus’ prophethood in Islam, particularly as explicated by the Turkish thinker Bediüzzaman Said Nursi, can help Christians recover a more robust interpretation of Jesus as prophet that has a positive impact on a Christian articulation of the church and of discipleship today.