bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pilot Study of Functional Magnetic Resonance Imaging Responses to Somatic Pain Stimuli in Youth With Functional and Inflammatory Gastrointestinal Disease
Authors: Huang Jeannie S. , Terrones Laura , Simmons Alan N. , Kaye Walter , Strigo Irina 
Published: August 2016

ABSTRACTBackground:Brain‐gut axis signaling modifies gastrointestinal symptomatology. Altered neural processing of intestinal pain signals involves interoceptive brain regions in adults with functional and inflammatory gastrointestinal disorders. Although these disorders frequently present in childhood, there are no published studies in youth. We determined whether neural processing of somatic pain stimuli differs in adolescents and young adults (AYA) with irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD), as compared to healthy controls (HC).Methods:IBS and IBD AYA (16–20 years) underwent anticipated and thermal pain stimuli of low and high intensity on their forearm and simultaneous blood oxygen level–dependent functional magnetic resonance imaging. Data from adult HC were used for comparison. Subjects answered surveys evaluating alexithymia, anxiety, depression, and pain catastrophizing. Group data were compared using linear mixed effects and analysis of variance.Results:Study groups were similar by sex but not age. Significant group by pain condition interactions were observed in interoceptive brain regions during pain anticipation, and within perceptual brain regions during perceived pain. Higher activation within interoceptive brain regions during anticipated pain was observed in IBS compared with IBD and HC subjects. IBD patients demonstrated increased activation in perceptual brain regions during experienced pain as compared to IBS and HC.Conclusions:IBS and IBD AYA demonstrate altered neural processing of somatic pain compared with each other and with HC. Our results suggest that neuromodulatory interventions targeting interoceptive brain circuits in IBS and perceptual brain regions in IBD may be effective.
Favorable Outcomes of Preterm Infants With Parenteral Nutrition–associated Liver Disease Treated With Intravenous Fish Oil–based Lipid Emulsion
Authors: Sorrell Michael , Moreira Alvaro , Green Kay , Jacob Rachel , Tragus Robin , Keller Laura , Quinn Amy , McCurnin Donald , Gong Alice , El Sakka Abeer , Mittal Naveen , Blanco Cynthia 
Published: August 2016

ABSTRACTObjectives:The aim of the study was to determine the acute and long‐term outcomes of preterm infants treated with an intravenous fish oil–based lipid emulsion (FishLE) for parenteral nutrition–associated liver disease (PNALD).Methods:Preterm infants 14 days to 24 months of age with anatomic short gut or severe intestinal dysmotility, serum direct bilirubin ≥4 mg/dL, and requiring >60% calories from parenteral nutrition were eligible. Enrolled infants received 1 g · kg–1 · day−1 of FishLE until resolution of direct hyperbilirubinemia or return of enteral nutrition. Acute clinical effects and biochemical markers of liver function were monitored. Growth and developmental scores at 6 and 12 months postmenstrual age (PMA) were assessed and compared with controls matched by gestational age (GA).Results:Thirteen patients with mean GA of 28 ± 4 weeks were treated and compared with 119 GA‐matched controls. Their mean direct bilirubin was 9.8 ± 6.4 mg/dL at enrollment. All infants had resolution of cholestasis after study completion. There were no acute adverse events, deaths, or liver/intestinal transplants. Weight and head circumference were similar between FishLE‐treated patients and controls at 6‐ and 12‐month PMA. Cognitive and motor scores were decreased at 6 and 12 months PMA in FishLE‐treated infants. Logistic regression analysis showed that prolonged hospitalization was detrimental to cognitive and motor development, whereas treatment was not.Conclusions:The use of intravenous FishLEs in premature infants appears to be safe and reverses PNALD despite significant liver disease and intestinal failure. This therapy should be used in preterm infants with PNALD and followed long term to evaluate development.
A Rare Presentation of Isolated Congenital Splenic Hemangioma With Kasabach-Merritt Syndrome
Authors: Dapaah-Siakwan Fredrick , Bryan Carleene , Walker Lashawndra S. , del Moral Teresa 
Published: August 2016

Introduction:Splenic hemangiomas (SHs) are the most common benign neoplasms of the spleen. However, they are rare in the newborn period. We present an extremely rare case of congenital SH complicated by Kasabach-Merritt syndrome.Case Presentation:A 2.93 kg male infant was delivered at term with a prenatal diagnosis of a left infrarenal mass diagnosed by ultrasound at 35 weeks of gestation. Magnetic resonance imaging demonstrated a well-defined splenic mass with multiple flow voids and scattered areas of high intensity suggestive of hemorrhage. He developed anemia, thrombocytopenia, and coagulopathy which required transfusion with packed red cells, platelets, cryoprecipitate, and fresh frozen plasma. Excision biopsy of the spleen led to resolution of anemia, thrombocytopenia, and coagulopathy. The diagnosis of SH was confirmed by histopathology. At 2 months outpatient follow-up, the patient was growing well without any evidence of tumor recurrence.Conclusions:Congenital SH is a rare entity that can be fatal if the potential complication of Kasabach-Merritt syndrome is not anticipated, evaluated, and promptly treated. Our patient had a favorable outcome with early surgical excision of the SH.
Early Therapeutic Alliance, Treatment Retention, and 12-Month Outcomes in a Healthy Lifestyles Intervention for People with Psychotic Disorders
Authors: Andrews Michelle , Baker Amanda L. , Halpin Sean A. , Lewin Terry J. , Richmond Robyn , Kay-Lambkin Frances J. , Filia Sacha L. , Castle David , Williams Jill M. , Clark Vanessa , Callister Robin 
Published: August 2016

Abstract
Engaging and retaining individuals with psychotic disorders in psychosocial treatments is difficult. Early therapeutic alliance, treatment retention, and 12-month outcomes were examined in a subsample of smokers with a psychotic disorder (N = 178) participating in a healthy lifestyles study comparing a telephone versus face-to-face delivered intervention. Therapeutic alliance was assessed using the Agnew Relationship Measure; primary outcomes were treatment retention and changes in symptoms and health behaviors. Contrary to expectations, early alliance did not predict treatment retention. However, elements of both client- and therapist-rated alliance predicted some clinical outcomes (e.g., higher confidence in the therapeutic alliance at session 1 predicted improvements in 12-month depression). Some modest interactions between early alliance and intervention condition were also identified (e.g., clients initially with lower self-perceived initiative, or higher therapist-perceived bonding benefited preferentially from the telephone-delivered intervention), highlighting the need to further examine the interplay between therapeutic alliance and treatment modality.
Mating promotes lactic-acid gut bacteria in a gift-giving insect
Authors: Smith Chad C. , Srygley Robert B. , Dietrich Emma I. , Mueller Ulrich G. 
Published: August 2016

ABSTRACTMating is a ubiquitous social interaction with the potential to influence the microbiome by facilitating transmission, modifying host physiology, and in species where males donate nuptial gifts to females, altering diet. We manipulated mating and nuptial gift consumption in two insects that differ in nuptial gift size, the Mormon cricketAnabrus simplexand the decorated cricketGryllodes sigillatus, with the expectation that larger gifts are more likely to affect the gut microbiome. Surprisingly, mating, but not nuptial gift consumption, affected bacterial community structure, and only in Mormon crickets. The change in structure was due to a precipitous drop in the abundance of lactic-acid bacteria in unmated females, a taxon known for their beneficial effects on nutrition and immunity. Mating did not affect phenoloxidase or lysozyme-like antibacterial activity in either species, suggesting that any physiological response to mating on host-microbe interactions is decoupled from the systemic immunity. Protein supplementation also did not affect the gut microbiome in decorated crickets, suggesting that insensitivity of gut microbes to dietary protein could contribute to the lack of an effect of nuptial gift consumption. Our study provides experimental evidence that sexual interactions can affect the microbiome and suggests mating can promote beneficial gut bacteria.
DNAmod: the DNA modification database
Authors: Sood Ankur Jai , Viner Coby , Hoffman Michael M. 
Published: August 2016

AbstractCovalent DNA modifications, such as 5-methylcytosine (5mC), are increasingly the focus of numerous research programs. In eukaryotes, both 5mC and 5-hydroxymethylcytosine (5hmC) are now recognized as stable epigenetic marks, with diverse functions. Bacteria, archaea, and viruses contain various other modified DNA nucleobases. Numerous databases describe RNA and histone modifications, but no database specifically catalogues DNA modifications, despite their broad importance in epigenetic regulation. To address this need, we have developed DNAmod: the DNA modification database.DNAmod is an open-source database (https://dnamod.hoffmanlab.org) that catalogues DNA modifications and provides a single source to learn about their properties. DNAmod provides a web interface to easily browse and search through these modifications. The database annotates the chemical properties and structures of all curated modified DNA bases, and a much larger list of candidate chemical entities. DNAmod includes manual annotations of available sequencing methods, descriptions of their occurrence in nature, and provides existing and suggested nomenclature. DNAmod enables researchers to rapidly review previous work, select mapping techniques, and track recent developments concerning modified bases of interest.
Characterization of the pscC (Type III secretion) gene ofPseudomonas aeruginosa(PA01) and assessment of immunogenicity of pscC protein in rats
Authors: Bhuiyan SA. , Vanitha DJ. , Sultana H. , Opook F. , Rodrigues KF. 
Published: August 2016

ABSTRACTProteins associated with the bacterial membrane can be recruited for application as antigens for the development of vaccines. This preliminary study was directed towards evaluating the antigenic properties of thePseudomonas aeruginosa(PA01) pscC protein which is a component of the Type III secretion system. Gene specific primers were designed to isolate thepscCgene which was isolated, ligated onto the multiple cloning site of vector pGS21(a), cloned and expressed inEscherichia coli(BL21). The molecular weight of the expressed pscC protein was determined by SDS-PAGE (10% sodium dodecyl sulphate-polyacrylamide gel electrophoresis) and was found to be around 57 KDa and purified by the size exclusion chromatography. Finally, the purified pscC protein was injected subcutaneously into adult Sprague Dawley®rats with a range of concentrations (50, 100 and 150 µg per rat) respectively. Recombinant pscC antigen induced a specific humoral immune response against the antigen, which was validated by Enzyme-linked immunosorbent assay (ELISA). The results concluded that anti-pscC antibody was elicited in the animal model.
Deep Mutational Scanning Identifies Sites in Influenza Nucleoprotein That Affect Viral Inhibition by MxA
Authors: Ashenberg Orr , Padmakumar Jai , Doud Michael B. , Bloom Jesse D. 
Published: August 2016

AbstractThe innate-immune restriction factor MxA inhibits influenza replication by targeting the viral nucleoprotein (NP). Human influenza is more resistant than avian influenza to inhibition by human MxA, and prior work has compared human and avian viral strains to identify amino-acid differences in NP that affect sensitivity to MxA. However, this strategy is limited to identifying sites in NP where mutations that affect MxA sensitivity have fixed during the small number of documented zoonotic transmissions of influenza to humans. Here we use an unbiased deep mutational scanning approach to quantify how all ≈10,000 amino-acid mutations to NP affect MxA sensitivity. We both identify new sites in NP where mutations affect MxA resistance and re-identify mutations known to have increased MxA resistance during historical adaptations of influenza to humans. Most of the sites where mutations have the greatest effect are almost completely conserved across all influenza A viruses, and the amino acids at these sites confer relatively high resistance to MxA. These sites cluster in regions of NP that appear to be important for its recognition by MxA. Overall, our work systematically identifies the sites in influenza nucleoprotein where mutations affect sensitivity to MxA. We also demonstrate a powerful new strategy for identifying regions of viral proteins that affect interactions with host factors.Author SummaryDuring viral infection, human cells express proteins that can restrict virus replication. However, in many cases it remains unclear what determines the sensitivity of a given viral strain to a particular restriction factor. Here we use a high-throughput approach to measure how all amino-acid mutations to the nucleoprotein of influenza virus affect restriction by the human protein MxA. We find several dozen sites where mutations substantially affect influenza’s sensitivity to MxA. While a few of these sites are known to have fixed mutations during past adaptations of influenza to humans, most of the sites are broadly conserved across all influenza strains and have never previously been described as affecting MxA resistance. Our results therefore show that the known historical evolution of influenza has only involved substitutions at a small fraction of the sites where mutations can in principle affect MxA resistance. We suggest that this is because many sites are already broadly fixed at amino acids that confer high resistance.
Basosquamous carcinoma: Dermoscopic clues to diagnosis
Authors: Akay Bengu Nisa , Saral Secil , Heper Aylin O. , Erdem Cengizhan , Rosendahl Cliff 
Published: August 2016

AbstractBasosquamous carcinoma (BSC) is a rare skin cancer which has areas of basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) and a transition zone between them. However, dermoscopic features ofBSCare not well described in the published work, except one study. The aim of the present study was to better identify and clarify the dermoscopic findings ofBSCin the largest group of patients in the published work and to describe its dermoscopic features according to histopathologicallyBCC‐dominant,SCC‐dominant and intermediate categories. Dermoscopic features of 36 histopathologically provenBSCand their dermatopathological correlates were retrospectively analyzed. Dermoscopic features were evaluated by pattern analysis. Keratin mass (91.7%) was the most common dermoscopic feature. Surface scaling (77.8%), ulceration (69.4%), white structureless areas (69.4%), white clods (66.7%) and blood spots on keratin mass (66.7%) were the other frequent findings. Polymorphous vascular pattern consisting of various combinations of branched, serpentine, straight, coiled or looped vessels were detected in 61% of the lesions.BSChasBCC‐dominant vascular features together with otherwiseSCC‐dominant morphology, the common pattern seen inBSClesions beingBCC‐dominant polymorphous or monomorphous vasculature, together with dermoscopic findings of keratinization. White circles, known to be a valuable clue toSCCand keratoacanthoma, were present at the same magnitude inBSCin our study. The observed histological correlation of eosinophilic keratin overlying the epithelium which lined follicular infundibulae in these tumors, provides a plausible new perspective on dermoscopic white circles.
Endure and call for help: strategies of black mustard plants to deal with a specialized caterpillar
Authors: Lucas‐Barbosa Dani , Dicke Marcel , Kranenburg Twan , Aartsma Yavanna , van Beek Teris A. , Huigens Martinus E. , van Loon Joop J. A. 
Published: August 2016

SummaryPlants have evolved inducible resistance and tolerance mechanisms against insect herbivores. Resistance mechanisms that affect herbivorous insects directly can be effective against generalist herbivores, but will not deter specialist herbivores from attacking the plant. Tolerance mechanisms and indirect plant resistance are more likely effective strategies used by plants when dealing with specialist herbivores. However, inducible indirect resistance and tolerance mechanisms have rarely been investigated within the same study system.We studied multiple tolerance mechanisms and the role of natural enemies in reducing fitness loss ofBrassica nigraplants incurred by feeding by the specialist herbivorePieris brassicae. For this, we measured the changes in carbon and nitrogen triggered by herbivore attack and quantified plant biomass and seed production under field conditions, in the presence or absence of natural enemies of the herbivores. We also assessed whetherB. nigraincreased selfing rates when exposed to herbivore infestation, and investigated whether infestation byP. brassicaerenderedB. nigraplants more attractive to night‐active pollinators than control plants.We found thatB. nigraflowers are rarely visited by insects during the night, and exposure to herbivores did not influence selfing rates.Brassica nigraplants compensated for herbivory in terms of vegetative biomass. Seed set was negatively affected by herbivory in the absence of natural enemies, but not in the presence of natural enemies. Plants responded to herbivory with drastic changes in nitrogen contents of leaves and flowers, whereas no changes in carbon concentrations were detected.The investment in reproduction or re‐growth of vegetative tissues is not sufficient to sustain plant fitness. Reproductive output of flowering mustard plants is only sustained when interactions with the natural enemies of the herbivores are preserved. We conclude that natural enemies of herbivorous insects play an important role as component of the plant's defence strategy. This study reveals that both tolerance and indirect resistance are strategies of this plant species to sustain fitness.
Weak‐anisotropy approximation for P‐wave reflection coefficient at the boundary between two tilted transversely isotropic media
Authors: Ivanov Yuriy , Stovas Alexey 
Published: August 2016

ABSTRACTExisting and commonly used in industry nowadays, closed‐form approximations for a P‐wave reflection coefficient in transversely isotropic media are restricted to cases of a vertical and a horizontal transverse isotropy. However, field observations confirm the widespread presence of rock beds and fracture sets tilted with respect to a reflection boundary. These situations can be described by means of the transverse isotropy with an arbitrary orientation of the symmetry axis, known as tilted transversely isotropic media. In order to study the influence of the anisotropy parameters and the orientation of the symmetry axis on P‐wave reflection amplitudes, a linearised 3D P‐wave reflection coefficient at a planar weak‐contrast interface separating two weakly anisotropic tilted tranversely isotropic half‐spaces is derived. The approximation is a function of the incidence phase angle, the anisotropy parameters, and symmetry axes tilt and azimuth angles in both media above and below the interface. The expression takes the form of the well‐known amplitude‐versus‐offset “Shuey‐type” equation and confirms that the influence of the tilt and the azimuth of the symmetry axis on the P‐wave reflection coefficient even for a weakly anisotropic medium is strong and cannot be neglected. There are no assumptions made on the symmetry‐axis orientation angles in both half‐spaces above and below the interface. The proposed approximation can be used for inversion for the model parameters, including the orientation of the symmetry axes. Obtained amplitude‐versus‐offset attributes converge to well‐known approximations for vertical and horizontal transverse isotropic media derived by Rüger in corresponding limits. Comparison with numerical solution demonstrates good accuracy.
Determination of Inorganic Ion Profiles of Illicit Drugs by Capillary Electrophoresis
Authors: Evans Elizabeth , Costrino Carolina , do Lago Claudimir L. , Garcia Carlos D. , Roux Claude , Blanes Lucas 
Published: August 2016

AbstractA portable capillary electrophoresis instrument with dual capacitively coupled contactless conductivity detection (C4D) was used to determine the inorganic ionic profiles of three pharmaceutical samples and precursors of two illicit drugs (contemporary samples of methylone and para‐methoxymethamphetamine). The LODs ranged from 0.10 μmol/L to 1.25 μmol/L for the 10 selected cations, and from 0.13 μmol/L to 1.03 μmol/L for the eight selected anions. All separations were performed in less than 6 min with migration times and peak area RSD values ranging from 2 to 7%. The results demonstrate the potential of the analysis of inorganic ionic species to aid in the identification and/or differentiation of unknown tablets, and real samples found in illicit drug manufacture scenarios. From the resulting ionic fingerprint, the unknown tablets and samples can be further classified.
Experimental conditions improving in‐solution target enrichment for ancient DNA
Authors: Cruz‐Dávalos Diana I. , Llamas Bastien , Gaunitz Charleen , Fages Antoine , Gamba Cristina , Soubrier Julien , Librado Pablo , Seguin‐Orlando Andaine , Pruvost Mélanie , Alfarhan Ahmed H. , Alquraishi Saleh A. , Al‐Rasheid Khaled A. S. , Scheu Amelie , Beneke Norbert , Ludwig Arne , Cooper Alan , Willerslev Eske , Orlando Ludovic 
Published: August 2016

AbstractHigh‐throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best‐suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture‐enrichment methods represent cost‐effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in‐solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self‐annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.