bluuebunny/crossref_metadata_2025_split huggingface dataset:
Old beagle dogs have lower faecal concentrations of some fermentation products and lower peripheral lymphocyte counts than young adult beagles
Authors: Gomes Márcia de Oliveira Sampaio , Beraldo Mariana Casteleti , Putarov Thaila Cristina , Brunetto Márcio Antônio , Zaine Leandro , Glória Maria Beatriz Abreu , Carciofi Aulus Cavalieri 
Published: October 2011

The effects of age on microbiota composition, gut fermentation end-product formation and peripheral lymphocyte numbers were compared between old and young adult Beagle dogs fed four kibble diets differing in yeast cell wall contents. The experiment had a double 4 × 4 Latin square design, one with four mature dogs (4 years old) and the other with four old dogs (10 years old), with four replicates (diets) per dog. In each period a 15 d adaptation period preceded a 5 d total collection of faeces for the digestibility trial. On day 21, fresh faecal samples were collected for the determination of bacterial enumeration, pH, biogenic amine and short-chain fatty acid. Flow cytometry was used for immunophenotypic evaluation. Dogs were fed four kibble diets with similar composition with 0, 0·15, 0·30 and 0·45 % of yeast cell wall (as-fed), respectively. Data were evaluated using general linear models of Statistical Analysis Systems statistical software (P < 0·05). No evidence of a difference in faecal bacteria counts between ages was found (total aerobes, total anaerobes,Bifidobacterium, Lactobacillus, ClostridiumandEscherichia coli:P>0·15). Faecal concentrations of butyrate, histamine, agmatine and spermine were lower (P ≤ 0·05) and faecal pH was higher (P = 0·03) in older dogs than in mature adult dogs, suggesting an alteration in bacterial metabolic activity, or in the rate of intestinal absorption of these compounds. Concentrations of T-lymphocytes, T-cytotoxic lymphocytes and B-lymphocytes were also lower (P ≤ 0·01) in older dogs than in mature adult dogs. The study confirmed alterations in peripheral lymphocytes and revealed a reduced concentration of some fermentation end products in the colon of old dogs.
Characteristics of ageing pets and their owners: dogsv.cats
Authors: Heuberger Roschelle , Wakshlag Joseph 
Published: October 2011

The purpose of the present cross-sectional, convenience sampled study was to ascertain differences in diet and lifestyle between cat (n155) and dog (n318) owners and their pets. Average cat ownership was 6·1 (sd5) years and average cat's age was 6·9 (sd5) years. Cats were reported to be overweight (14 %), fedad libitum(87 %), given medication (11 %) and had health conditions (24 %). Cat's age was significantly and positively related to cat's weight, duration of illness, owner's BMI and some owners' dietary characteristics. Overweight in cats was significantly associated with overweight in older owners ( ≥ 60 years). Younger cat owners ( < 60 years) showed non-statistically significant trends between the owner's BMI and cat's overweight. Cat's age was inversely correlated with cat's and owner's activity levels. Dogs were owned for 5·5 (sd4) years and mean dog's age was 5·9 (sd4) years. Dogs were reported to be overweight (18 %), fedad libitum(49 %), given medication (31 %) and had health conditions (34 %). Dog's age was positively associated with duration of illness. Dog's age was inversely correlated with amount of food fed, dog's activity and owner's exercise and intake of fruit, vegetables and whole grains. Dog's age was positively correlated with the owner's BMI and frequency of added fat consumption. Overweight in dogs was associated with overweight in older owners ( ≥ 60 years) and was correlated with poorer health in both the dog and the owner. Younger dog owners were more likely to have an overweight dog if they themselves were obese. Similarities were found in owner's and pet's diet and lifestyle issues with ageing. Overweight was associated with ageing, dietary, lifestyle and health issues in this sample. Older owners who were overweight had overweight pets. Strategies should be targeted towards decreasing both owner's and pet's overweight. The use of exercise and dietary interventions should be encouraged.
Effect of short-chain fructooligosaccharide-enriched energy-restricted diet on weight loss and serum haptoglobin concentration in Beagle dogs
Authors: Ricci Rebecca , Jeusette Isabelle , Godeau Jean-Marie , Contiero Barbara , Diez Marianne 
Published: October 2011

The effects of the dietary inclusion of two levels of short-chain fructooligosaccharides (sc-FOS) on weight loss, biochemical parameters and serum haptoglobin concentration were investigated in twelve experimental obese Beagle dogs. Dogs were randomised into two groups and submitted to a weight loss program (WLP): the control group (C) received a commercial energy-restricted high-protein diet containing 1 % DM sc-FOS, whereas the test group (T) received the same diet enriched with sc-FOS to attain a 3 % DM content. Body weight (BW) and body condition score were weekly assessed in each dog and blood was collected before and after WLP to measure total plasma cholesterol (CHOL), TAG, NEFA, glucose (GLUC), insulin, serum leptin and haptoglobin. Groups showed similar BW and blood parameters before treatment. When values before and after treatment of the dogs were compared, significant reductions were observed for all parameters, with the exception of NEFA and GLUC. However, when these reductions were compared between C and T groups, significant differences were detected only for haptoglobin (T beforev.T after: 1545v.605 mg/l,P = 0·03; C beforev.C after: 1635v.1400 mg/l,P = NS). Positive correlations between haptoglobin and CHOL and between haptoglobin and TAG were observed before but not after WLP. In conclusion, feeding obese dogs with the energy-restricted diet caused significant weight loss and reduction of blood parameters, irrespective of the sc-FOS content included. However, serum haptoglobin level, and the subclinical inflammatory condition associated with it, was significantly lowered in the T but not in the C group.
Effects of two commercially available feline diets on glucose and insulin concentrations, insulin sensitivity and energetic efficiency of weight gain
Authors: Coradini M. , Rand J. S. , Morton J. M. , Rawlings J. M. 
Published: October 2011

A low-carbohydrate, high-protein (LCHP) diet is often recommended for the prevention and management of diabetes in cats; however, the effect of macronutrient composition on insulin sensitivity and energetic efficiency for weight gain is not known. The present study compared the effect in adult cats (n32) of feeding a LCHP (23 and 47 % metabolisable energy (ME)) and a high-carbohydrate, low-protein (HCLP) diet (51 and 21 % ME) on fasting and postprandial glucose and insulin concentrations, and on insulin sensitivity. Tests were done in the 4th week of maintenance feeding and after 8 weeks ofad libitumfeeding, when weight gain and energetic efficiency of each diet were also measured. When fed at maintenance energy, the HCLP diet resulted in higher postprandial glucose and insulin concentrations. When fedad libitum, the LCHP diet resulted in greater weight gain (P < 0·01), and was associated with higher energetic efficiency. Overweight cats eating the LCHP diet had similar postprandial glucose concentrations to lean cats eating the HCLP diet. Insulin sensitivity was not different between the diets when cats were lean or overweight, but glucose effectiveness was higher after weight gain in cats fed the HCLP diet. According to the present results, LCHP diets fed at maintenance requirements might benefit cats with multiple risk factors for developing diabetes. However,ad libitumfeeding of LCHP diets is not recommended as they have higher energetic efficiency and result in greater weight gain.
CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0
Authors: Fricke W. Florian , White James , Arze Cesar , Matalka Malcom , Team The CloVR , White Owen , Angiuoli Samuel 
Published: October 2011

AbstractThe CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:A) UCLUST – a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates;B) BLASTX and BLASTN for functional and taxonomic assignment of sequences, respectively;C) Metastats and custom R scripts to generate additional statistical and graphical evaluation.The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples, which are used for comparative analysis. This protocol is available in CloVR beta version 0.5 and 0.6.
CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0
Authors: White Owen , Angiuoli Samuel , Fricke W. Florian , Galens Kevin , White James , Arze Cesar , Matalka Malcolm , Gwinn Giglio Michelle , Team The CloVR 
Published: October 2011

AbstractThe CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or HiSeq sequencing platforms or of combinations of Sanger and Roche/454 sequence data. The pipeline output consists of results and summary files generated during the different pipeline steps. Annotated sequence files are generated that are compatible with common genome browser tools and can be submitted to the GenBank repository at NCBI. This protocol is available in CloVR beta versions 0.5 and 0.6.
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.1
Authors: Fricke W. Florian , White James , Arze Cesar , Matalka Malcolm ,   The CloVR Team, White Owen , Angiuoli Samuel 
Published: October 2011

AbstractThe CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:A) Qiime – a Python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac, UCLUST, PyNAST and the RDP Bayesian classifier;B) UCHIME – a tool for rapid identification of chimeric 16S sequence fragments;C) Mothur – a C++-based software package for 16S analysis;D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.CloVR-16S accepts as input raw multiplex 454-pyrosequencer output (i.e. pooled pyrotagged sequences from multiple samples), or alternatively, pre-processed sequences from multiple samples in separate files. This protocol became first available in CloVR beta version 0.7.
Identification of a Gene for Pyruvate-Insensitive Mitochondrial Alternative Oxidase Expressed in the Thermogenic Appendices in Arum maculatum
Authors: Ito Kikukatsu , Ogata Takafumi , Kakizaki Yusuke , Elliott Catherine , Albury Mary S. , Moore Anthony L. 
Published: October 2011

Abstract
Heat production in thermogenic plants has been attributed to a large increase in the expression of the alternative oxidase (AOX). AOX acts as an alternative terminal oxidase in the mitochondrial respiratory chain, where it reduces molecular oxygen to water. In contrast to the mitochondrial terminal oxidase, cytochrome c oxidase, AOX is nonprotonmotive and thus allows the dramatic drop in free energy between ubiquinol and oxygen to be dissipated as heat. Using reverse transcription-polymerase chain reaction-based cloning, we reveal that, although at least seven cDNAs for AOX exist (AmAOX1a, -1b, -1c, -1d, -1e, -1f, and -1g) in Arum maculatum, the organ and developmental regulation for each is distinct. In particular, the expression of AmAOX1e transcripts appears to predominate in thermogenic appendices among the seven AmAOXs. Interestingly, the amino acid sequence of AmAOX1e indicates that the ENV element found in almost all other AOX sequences, including AmAOX1a, -1b, -1c, -1d, and -1f, is substituted by QNT. The existence of a QNT motif in AmAOX1e was confirmed by nano-liquid chromatography-tandem mass spectrometry analysis of mitochondrial proteins from thermogenic appendices. Further functional analyses with mitochondria prepared using a yeast heterologous expression system demonstrated that AmAOX1e is insensitive to stimulation by pyruvate. These data suggest that a QNT type of pyruvate-insensitive AOX, AmAOX1e, plays a crucial role in stage- and organ-specific heat production in the appendices of A. maculatum.
ArabidopsisSigma Factor Binding Proteins Are Activators of the WRKY33 Transcription Factor in Plant Defense
Authors: Lai Zhibing , Li Ying , Wang Fei , Cheng Yuan , Fan Baofang , Yu Jing-Quan , Chen Zhixiang 
Published: October 2011

AbstractNecrotrophic pathogens are important plant pathogens that cause many devastating plant diseases. Despite their impact, our understanding of the plant defense response to necrotrophic pathogens is limited. The WRKY33 transcription factor is important for plant resistance to necrotrophic pathogens; therefore, elucidation of its functions will enhance our understanding of plant immunity to necrotrophic pathogens. Here, we report the identification of two WRKY33-interacting proteins, nuclear-encoded SIGMA FACTOR BINDING PROTEIN1 (SIB1) and SIB2, which also interact with plastid-encoded plastid RNA polymerase SIGMA FACTOR1. Both SIB1 and SIB2 contain an N-terminal chloroplast targeting signal and a putative nuclear localization signal, suggesting that they are dual targeted. Bimolecular fluorescence complementation indicates that WRKY33 interacts with SIBs in the nucleus of plant cells. Both SIB1 and SIB2 contain a short VQ motif that is important for interaction with WRKY33. The two VQ motif–containing proteins recognize the C-terminal WRKY domain and stimulate the DNA binding activity of WRKY33. Like WRKY33, both SIB1 and SIB2 are rapidly and strongly induced by the necrotrophic pathogen Botrytis cinerea. Resistance to B. cinerea is compromised in the sib1 and sib2 mutants but enhanced in SIB1-overexpressing transgenic plants. These results suggest that dual-targeted SIB1 and SIB2 function as activators of WRKY33 in plant defense against necrotrophic pathogens.
INDEHISCENT and SPATULA Interact to Specify Carpel and Valve Margin Tissue and Thus Promote Seed Dispersal inArabidopsis
Authors: Girin Thomas , Paicu Teodora , Stephenson Pauline , Fuentes Sara , Körner Evelyn , O’Brien Martin , Sorefan Karim , Wood Thomas A. , Balanzá Vicente , Ferrándiz Cristina , Smyth David R. , Østergaard Lars 
Published: October 2011

AbstractStructural organization of organs in multicellular organisms occurs through intricate patterning mechanisms that often involve complex interactions between transcription factors in regulatory networks. For example, INDEHISCENT (IND), a basic helix-loop-helix (bHLH) transcription factor, specifies formation of the narrow stripes of valve margin tissue, where Arabidopsis thaliana fruits open on maturity. Another bHLH transcription factor, SPATULA (SPT), is required for reproductive tissue development from carpel margins in the Arabidopsis gynoecium before fertilization. Previous studies have therefore assigned the function of SPT to early gynoecium stages and IND to later fruit stages of reproductive development. Here we report that these two transcription factors interact genetically and via protein–protein contact to mediate both gynoecium development and fruit opening. We show that IND directly and positively regulates the expression of SPT, and that spt mutants have partial defects in valve margin formation. Careful analysis of ind mutant gynoecia revealed slight defects in apical tissue formation, and combining mutations in IND and SPT dramatically enhanced both single-mutant phenotypes. Our data show that SPT and IND at least partially mediate their joint functions in gynoecium and fruit development by controlling auxin distribution and suggest that this occurs through cooperative binding to regulatory sequences in downstream target genes.
Do proteolytic antibodies complete the panoply of the autoimmune response in acquired haemophilia A?
Authors: Mahendra Ankit , Padiolleau‐Lefevre Séverine , Kaveri Srinivas V. , Lacroix‐Desmazes Sébastien 
Published: October 2011

SummaryAcquired haemophilia A (AHA) is a rare bleeding disorder characterized by the sudden generation of autoantibodies against factor VIII (FVIII) in individuals with no previous history of abnormal haemostasis. Understanding the pathogenesis of this disease has been hampered by the rarity of the patients and the difficulty in obtaining biological material from untreated patients. Still, progress has been made recently in understanding the pathogenesis of AHA. In particular, the importance of CD4+ T cells in AHA development has been documented and the epitopes targeted by T cells on FVIII have been delineated. Accordingly, a polymorphism in the cytotoxic T‐lymphocyte‐associated protein 4 gene (CTLA4), known to participate in the regulation of CD4+ T‐cell responses, and a preferential usage of certain human leukocyte antigen class II haplotypes, have been associated with the disease. Recent findings have documented the presence of immunoglobulin G (IgG) with proteolytic activity against FVIII and factor IX (FIX) in patients with AHA. While FVIII‐hydrolysing IgG has been shown to inactivate FVIII, FIX‐hydrolysing IgG from AHA patients activate FIX in vitro. Here, we describe the latest findings on the immuno‐pathogenesis of AHA, with a special focus on the potential role played by antibodies endowed with proteolytic properties.
Child coping, parent coping assistance, and post‐traumatic stress following paediatric physical injury
Authors: Marsac M. L. , Donlon K. A. , Winston F. K. , Kassam‐Adams N. 
Published: October 2011

AbstractBackground  Following a physical injury, many children exhibit long‐term psychological reactions such as post‐traumatic stress symptoms (PTSS). Children's coping strategies, and the ways that others help them cope with injury (i.e. coping assistance), are understudied, potentially malleable variables that could be targeted in preventive interventions. The objectives of the current research were to describe child coping behaviour and parent coping assistance following a child's injury, and to investigate the relationships among coping, coping assistance and child PTSS.Method  Participants included 82 children with injuries and one parent of each child. Children completed measures of coping and coping assistance 2 weeks after their injury (T1). Children also completed measures of coping and PTSS at a 3‐month follow‐up (T2). Parents reported on the coping assistance they provided to their child at T1.Results  Children reported using an average of six coping strategies (out of 10) with wishful thinking, social support, distraction, and cognitive restructuring endorsed most frequently. Child‐reported social withdrawal and resignation 2 weeks after his or her injury (T1) were related to subsequent PTSS (T2). Social withdrawal at T2 was related to concurrent child PTSS (T2). Children were more likely to seek social support when their parents reported helping their child cope. No relationships were identified between active coping behaviours or parent coping assistance and PTSS outcomes.Conclusions  Findings suggest that children's coping strategies (particularly social withdrawal and resignation) play a possibly important, complex role in the development of traumatic stress symptoms. When parents help their child cope, children are more likely to seek out social support, suggesting that they will be more able to ask their parents for help as needed. Future research should identify effective strategies to prevent PTSS including how parents can best support their child following paediatric injury.
Immunology in the Clinic Review Series; focus on metabolic diseases: development of islet autoimmune disease in type 2 diabetes patients: potential sequelae of chronic inflammation
Authors: Brooks-Worrell B , Palmer J P 
Published: October 2011

SummaryOTHER THEMES PUBLISHED IN THIS IMMUNOLOGY IN THE CLINIC REVIEW SERIESAllergy, Host Responses, Cancer, Autoinflammatory Diseases, Type 1 diabetes and viruses.Historically, the development of type 2 diabetes has been considered not to have an autoimmune component, in contrast to the autoimmune pathogenesis of type 1 diabetes. In this review we will discuss the accumulating data supporting the concept that islet autoreactivity and inflammation is present in type 2 diabetes pathogenesis, and the islet autoimmunity appears to be one of the factors associated with the progressive nature of the type 2 diabetes disease process.
Infiltrating cellular pattern in kidney graft biopsies translates into forkhead box protein 3 up-regulation and p16INK4α senescence protein down-regulation in patients treated with belatacept compared to cyclosporin A
Authors: Furuzawa-Carballeda J , Lima G , Alberú J , Palafox D , Uribe-Uribe N , Morales-Buenrostro L E , Reyes Acevedo R , Mondragón G , Chevaile A , Llorente L 
Published: October 2011

Summary
Renal allograft survival is related directly to cell senescence. In the transplantation scenario many cellular events – participating as immunological and non-immunological factors – could contribute to accelerate this biological process, responsible for the ultimate fate of the graft. Mechanisms concerned in tolerance versus rejection are paramount in this outcome. For this reason, immunosuppressive treatment constitutes an extremely important decision to prevent organ dysfunction and, finally, graft loss. This study was conducted to document the proportion of CD4+/interleukin (IL)-17A+-, CD16+/indoleamine 2, 3-dioxygenase (IDO+)-, forkhead box protein P3 (FoxP3+)-expressing cells, senescent cells (p16INK4α) and the percentage of interstitial fibrosis (IF) in graft biopsies of kidney transplant recipients participating in the BENEFIT (Bristol-Myers Squibb IM103008) study. CD4+/IL-17A+, CD16+/IDO+, FoxP3+ and p16INK4α+ cells were evaluated by immunohistochemistry, and the percentage of IF by morphometry on graft biopsies obtained at time 0 (pre-implantation) and at 12 months post-transplant. Senescent cells and CD4+/IL-17A+ cells were increased among graft biopsies in subjects receiving cyclosporin A (CsA) compared to those under belatacept treatment. Meanwhile, CD16+/IDO+ and FoxP3+-expressing cells were lower in biopsies from CsA treatment compared to patients treated with Belatacept. Histological morphometric analyses disclosed more IF in 12-month CsA-treated patients in comparison to pre-implantation biopsy findings. Summing up, renal biopsies from patients receiving belatacept showed greater amounts of FoxP3+ cells and lower amounts of CD4+/IL-17A+ and senescent cells compared to patients under CsA treatment. Along with these findings, an increase in IF in annual CsA-treated-patients biopsies compared to pre-implantation and belatacept-treated patients were observed.