bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Naturally Occurring Deletion in FliE from Salmonella enterica Serovar Dublin Results in an Aflagellate Phenotype and Defective Proinflammatory Properties
Authors: Sasías Sebastián , Martínez-Sanguiné Adriana , Betancor Laura , Martínez Arací , D'Alessandro Bruno , Iriarte Andrés , Chabalgoity José A. , Yim Lucía 
Published: October 2017

ABSTRACT

Salmonella enterica
serovar Dublin is adapted to cattle but is able to infect humans with high invasiveness. An acute inflammatory response at the intestine helps to prevent
Salmonella
dissemination to systemic sites. Flagella contribute to this response by providing motility and FliC-mediated signaling through pattern recognition receptors. In a previous work, we reported a high frequency (11 out of 25) of
S
. Dublin isolates lacking flagella in a collection obtained from humans and cattle. The aflagellate strains were impaired in their proinflammatory properties
in vitro
and
in vivo
. The aim of this work was to elucidate the underlying cause of the absence of flagella in
S
. Dublin isolates. We report here that class 3 flagellar genes are repressed in the human aflagellate isolates, due to impaired secretion of FliA anti-sigma factor FlgM. This phenotype is due to an in-frame 42-nucleotide deletion in the
fliE
gene, which codes for a protein located in the flagellar basal body. The deletion is predicted to produce a protein lacking amino acids 18 to 31. The aflagellate phenotype was highly stable; revertants were obtained only when
fliA
was artificially overexpressed combined with several successive passages in motility agar. DNA sequence analysis revealed that motile revertants resulted from duplications of DNA sequences in
fliE
adjacent to the deleted region. These duplications produced a FliE protein of similar length to the wild type and demonstrate that amino acids 18 to 31 of FliE are not essential. The same deletion was detected in
S
. Dublin isolates obtained from cattle, indicating that this mutation circulates in nature.
Genomic and Transcriptomic Analysis of Escherichia coli Strains Associated with Persistent and Transient Bovine Mastitis and the Role of Colanic Acid
Authors: Lippolis John D. , Holman Devin B. , Brunelle Brian W. , Thacker Tyler C. , Bearson Bradley L. , Reinhardt Timothy A. , Sacco Randy E. , Casey Thomas A. 
Published: October 2017

ABSTRACTEscherichia coliis a leading cause of bacterial mastitis in dairy cattle. It is most often transient in nature, causing an infection that lasts 2 to 3 days. However,E. colihas been shown to cause a persistent infection in a minority of cases. Mechanisms that allow for a persistentE. coliinfection are not fully understood. The goal of this work was to determine differences betweenE. colistrains originally isolated from dairy cattle with transient and persistent mastitis. Using RNA sequencing, we show gene expression differences in nearly 200 genes when bacteria from the two clinical phenotypes are compared. We sequenced the genomes of theE. colistrains and report genes unique to the two phenotypes. Differences in thewcaoperon, which encodes colanic acid, were identified by DNA as well as RNA sequencing and differentiated the two phenotypes. Previous work demonstrated thatE. colistrains that cause persistent infections were more motile than those that cause transient infections. Deletion of genes in thewcaoperon from a persistent-infection strain resulted in a reduction of motility as measured in swimming and swarming assays. Furthermore, colanic acid has been shown to protect bacteria from complement-mediated killing. We show that transient-infectionE. colistrains were more sensitive to complement-mediated killing. The deletion of genes from thewcaoperon caused a persistent-infectionE. colistrain to become sensitive to complement-mediated killing. This work identifies important differences betweenE. colistrains that cause persistent and transient mammary infections in dairy cattle.
Temporal trends in cardiovascular disease risk factor profiles in a population-based schizophrenia sample: a repeat cross-sectional study
Authors: Chiu Maria , Rahman Farah , Vigod Simone , Wilton Andrew S , Kurdyak Paul 
Published: October 2017

BackgroundPeople with schizophrenia have an increased burden of cardiovascular diseases (CVD); however, little is known about the cardiovascular risk factor profiles of non-institutionalised individuals with schizophrenia. This study estimated the prevalence of CVD risk factors in a population-based sample of Canadians with and without schizophrenia.MethodsOntario respondents of the Canadian Community Health Survey were linked to administrative health databases; using a validated algorithm, we identified 1103 non-institutionalised individuals with schizophrenia and 156 376 without schizophrenia. We examined the prevalence of eight CVD risk factors: smoking, diabetes, hypertension, obesity, physical inactivity, fruit/vegetables consumption, psychosocial stress and binge drinking. To examine temporal trends, we compared prevalence estimates from 2001–2005 to 2007–2010.ResultsThe prevalence of most CVD risk factors was significantly higher among those with schizophrenia than the general population. Obesity and diabetes prevalence increased by 39% and 71%, respectively, in the schizophrenia group vs 11% and 24%, respectively, in the non-schizophrenia group between the two time periods. Unlike the general population, smoking rates among those with schizophrenia did not decline. Almost 90% of individuals with schizophrenia had at least one CVD risk factor and almost 40% had ≥3 co-occurring risk factors.ConclusionIndividuals with schizophrenia had a greater prevalence of individual and multiple CVD risk factors compared with those without schizophrenia, which persisted over time. Our findings suggest that public health efforts to reduce the burden of CVD risk factors have not been as effective in the schizophrenia population, thus highlighting the need for more targeted interventions and prevention strategies.
Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury
Authors: Howard Benjamin M , Kornblith Lucy Z , Christie Sabrinah A , Conroy Amanda S , Nelson Mary F , Campion Eric M , Callcut Rachael A , Calfee Carolyn S , Lamere Brandon J , Fadrosh Douglas W , Lynch Susan , Cohen Mitchell Jay 
Published: October 2017

BackgroundRecent studies have demonstrated the vital influence of commensal microbial communities on human health. The central role of the gut in the response to injury is well described; however, no prior studies have used culture-independent profiling techniques to characterize the gut microbiome after severe trauma. We hypothesized that in critically injured patients, the gut microbiome would undergo significant compositional changes in the first 72 hours after injury.MethodsTrauma stool samples were prospectively collected via digital rectal examination at the time of presentation (0 hour). Patients admitted to the intensive care unit (n=12) had additional stool samples collected at 24 hours and/or 72 hours. Uninjured patients served as controls (n=10). DNA was extracted from stool samples and 16S rRNA-targeted PCR amplification was performed; amplicons were sequenced and binned into operational taxonomic units (OTUs; 97% sequence similarity). Diversity was analyzed using principle coordinates analyses, and negative binomial regression was used to determine significantly enriched OTUs.ResultsCritically injured patients had a median Injury Severity Score of 27 and suffered polytrauma. At baseline (0 hour), there were no detectable differences in gut microbial community diversity between injured and uninjured patients. Injured patients developed changes in gut microbiome composition within 72 hours, characterized by significant alterations in phylogenetic composition and taxon relative abundance. Members of the bacterial orders Bacteroidales, Fusobacteriales and Verrucomicrobiales were depleted during 72 hours, whereas Clostridiales and Enterococcus members enriched significantly.DiscussionIn this initial study of the gut microbiome after trauma, we demonstrate that significant changes in phylogenetic composition and relative abundance occur in the first 72 hours after injury. This rapid change in intestinal microbiota represents a critical phenomenon that may influence outcomes after severe trauma. A better understanding of the nature of these postinjury changes may lead to the ability to intervene in otherwise pathological clinical trajectories.Level of evidenceIIIStudy typePrognostic/epidemiological
miR-6883 Family miRNAs Target CDK4/6 to Induce G1 Phase Cell-Cycle Arrest in Colon Cancer Cells
Authors: Lulla Amriti R. , Slifker Michael J. , Zhou Yan , Lev Avital , Einarson Margret B. , Dicker David T. , El-Deiry Wafik S. 
Published: October 2017

Abstract
CDK4/6 targeting is a promising therapeutic strategy under development for various tumor types. In this study, we used computational methods and The Cancer Genome Atlas dataset analysis to identify novel miRNAs that target CDK4/6 and exhibit potential for therapeutic development in colorectal cancer. The 3′UTR of CDK4/6 mRNAs are targeted by a family of miRNAs, which includes miR-6883-5p, miR-149*, miR-6785-5p, and miR-4728-5p. Ectopic expression of miR-6883-5p or miR-149* downregulated CDK4 and CDK6 levels in human colorectal cancer cells. RNA-seq analysis revealed an inverse relationship between the expression of CDK4/6 and miR-149* and intronic miRNA-6883-5p encoding the clock gene PER1 in colorectal cancer patient samples. Restoring expression of miR-6883-5p and miR-149* blocked cell growth leading to G0–G1 phase cell-cycle arrest and apoptosis in colorectal cancer cells. CDK4/6 targeting by miR-6883-5p and miR-149* could only partially explain the observed antiproliferative effects. Notably, both miRNAs synergized with the frontline colorectal cancer chemotherapy drug irinotecan. Further, they resensitized mutant p53-expressing cell lines resistant to 5-fluorouracil. Taken together, our results established the foundations of a candidate miRNA-based theranostic strategy to improve colorectal cancer management. Cancer Res; 77(24); 6902–13. ©2017 AACR.
Phase Ib Study of Immune Biomarker Modulation with Neoadjuvant Cetuximab and TLR8 Stimulation in Head and Neck Cancer to Overcome Suppressive Myeloid Signals
Authors: Shayan Gulidanna , Kansy Benjamin A. , Gibson Sandra P. , Srivastava Raghvendra M. , Bryan James Kyle , Bauman Julie E. , Ohr James , Kim Seungwon , Duvvuri Umamaheswar , Clump David A. , Heron Dwight E. , Johnson Jonas T. , Hershberg Robert M. , Ferris Robert L. 
Published: October 2017

Abstract
Purpose: The response rate of patients with head and neck squamous cell carcinoma (HNSCC) to cetuximab therapy is only 15% to 20%, despite frequent EGFR overexpression. Because immunosuppression is common in HNSCC, we hypothesized that adding a proinflammatory TLR8 agonist to cetuximab therapy might result in enhanced T-lymphocyte stimulation and anti–EGFR-specific priming.
Experimental Design: Fourteen patients with previously untreated HNSCC were enrolled in this neoadjuvant trial and treated preoperatively with 3 to 4 weekly doses of motolimod (2.5 mg/m2) and cetuximab. Correlative tumor and peripheral blood specimens were obtained at baseline and at the time of surgical resection and analyzed for immune biomarker changes. Preclinical in vitro studies were also performed to assess the effect of cetuximab plus motolimod on myeloid cells.
Results: TLR8 stimulation skewed monocytes toward an M1 phenotype and reversed myeloid-derived suppressor cell (MDSC) suppression of T-cell proliferation in vitro. These data were validated in a prospective phase Ib neoadjuvant trial, in which fewer MDSC and increased M1 monocyte infiltration were found in tumor-infiltrating lymphocytes. Motolimod plus cetuximab also decreased induction of Treg and reduced markers of suppression, including CTLA-4, CD73, and membrane-bound TGFβ. Significantly increased circulating EGFR-specific T cells were observed, concomitant with enhanced CD8+ T-cell infiltration into tumors. These T cells manifested increased T-cell receptor (TCR) clonality, upregulation of the costimulatory receptor CD27, and downregulation of inhibitory receptor TIGIT.
Conclusions: Enhanced inflammatory stimulation in the tumor microenvironment using a TLR agonist overcomes suppressive myeloid and regulatory cells, enhancing the cellular antitumor immune response by therapeutic mAb in HNSCC. Clin Cancer Res; 24(1); 62–72. ©2017 AACR.
MODELING OF TREE GROWTH AFTER FOREST FIRE IN MOUNT CIREMAI NATIONAL PARK, INDONESIA
Authors: Rozak Andes Hamuraby , Setiadi Tedi 
Published: October 2017

Forest fire is a massive threat towards tropical forest causing various negative impacts to nature and human being.Â Forest fire often leads to alteration of forest structure and its functions.Â This study of tree growth after forest fire was conducted using a model simulation.Â The model was performed at the individual level of plant community and built to analyze the potential of tree growth and its scenario for post-fire recovery.Â Five important tree species from montane forest of Mount Ciremai were chosen to build the model based on four main parameters i.e. plant growth rate, diameter at breast height (DBH), tree-to-grass competition and tree-to-tree competition.Â The scenario of post-fire recovery was performed by replanting similar species with 5 cm DBH seedling.Â Prediction from our model showed that most of the chosen species would recover to its pre-fire condition after 37 - 50 years.Â Considering the limitation of competition after re-planting, it was suggested to minimize tree to tree competition and applied silvicultural treatments to maximize tree growth and tree community recovery.
INVASION OF Acacia decurrens WILLD. AFTER ERUPTION OF MOUNT MERAPI, INDONESIA
Authors: Sunardi Sunardi , Sulistijorini Sulistijorini , Setyawati Titiek 
Published: October 2017

Eruption of Mount Merapi in 2010 caused a dense cover of Acacia decurrens Willd., which is an Invasive Alien Plant Species (IAPS). The dense cover happened in all areas of Mount Merapi National Park (MMNP) in Java, Indonesia. This study was aimed to describe the relationship between major natural disturbance from volcanic eruption in triggering the invasion of A.decurrens in Mount Merapi National Park. Vegetation data were collected using line transect in two different sites. The first site was Cangkringan which was affected by pyroclastic flow and the second site was Selo which was not affected by pyroclastic flow. Distribution patterns and association of A.decurrens with other species in each location was analyzed using ordination analysis of the Non-Metric Multidimensional Scaling (NMDS). Microclimate such as temperature, humidity, light density and soil humidity was recorded in each location. Correlation between species abundance and microclimate data was assessed using Canonical Correspondence Analysis (CCA). The results showed that the population of A. decurrens was more dominant in Cangkringan than in Selo site. Cangkringan site was impacted with pyroclastic flow during Mount Merapi eruption in 2010, while Selo site was not affected. In Cangkringan,Â A.decurrens was distributed in clump, while in Selo the plant was randomly distributed. Ordination analysis using NMDS showed that there was positive association between A.decurrens and herbaceous plant.Â Negative association was observed between A.decurrens and other tree species. CCA analysis showed that temperature and light density was positively correlated with A. decurrens abundance. This study showed that the IAPS invasion in MMNP was correlated with the eruption of Mount Merapi.
PREDICTING THE IMPACT OF CLIMATE CHANGE ON THE DISTRIBUTION OF Flindersia pimenteliana F. Muell. IN INDONESIAN PAPUA AND PAPUA NEW GUINEA
Authors: Robiansyah Iyan 
Published: October 2017

Population of Flindersia pimenteliana (Maple Silkwood) in Indonesian Papua and Papua New Guinea is severely fragmented and experiencing a continuing decline due to habitat destruction and illegal logging. This species is very susceptible to environmental changes and at greater risk of extinction due to its small and fragmented geographic ranges and low abundance. Using maximum entropy (MaxEnt) method, the present study predicted the impact of climate change on the distribution of the species across its native distribution area. Elevation and 19 bioclimatic variables commonly used in species distribution modeling were used as predictors. Â The prediction model of the current potential distribution identified a total area of 156,214 km2 in Indonesian Papua and Papua New Guinea (18% of total land area) as suitable habitat for F. pimenteliana. Elevation and precipitation of the wettest, coldest and warmest quarters contributed most to the model. Based on the average of HadGEM2-ES and MIROC-ESM models, potential distribution projections under RCP8.5 scenario suggested a habitat gain of 16% for 2050 and 8% for 2070 in the species distribution. Whereas under RCP4.5, an average habitat gain of 7% was predicted for both 2050 and 2070. The newly suitable habitats were predicted to be found mainly in Southern and Western Highland of Papua New Guinea. Protection of these areas from habitat destruction and land use change is needed to assist F. pimenteliana find the most suitable climate for its survival.
Eimeria SPECIES COMPOSITION AND FACTORS INFLUENCING OOCYSTS SHEDDING IN DAIRY FARM, BANDUNG, INDONESIA
Authors: Sufi Isrok Malikus , Cahyaningsih Umi , Sudarnika Etih 
Published: October 2017

Coccidiosis is one of the most widely distributed parasitic diseases of cattle throughout the world. Coccidiosis infection in ruminants was caused by Eimeria spp. Â The objective of this study was to determine Eimeria species composition and various factors influencing Eimeria oocysts shedding in dairy farm.Â This study was conducted with a cross-sectional study design in dairy farm in South Bandung District from July 2014 to January 2015. Samples were obtained from 400 dairy cattle (196 cattle at age < 6 months, 37 cattle at age 6 - 12 months and 167 cattle at age > 12 months). Fecal samples were collected, examined and counted for Eimeria species composition and numbers of oocysts per gram of feces (OPG) using McMaster technique. A questionnaire was completed for individual dairy cattle farmer to record information about cattleâ€™s health and husbandry. The effect of cattleâ€™s sex, age and type of pen flooring to OPG values were analyzed using Mann-Whitney and Kruskal-Wallis tests. The Kruskal-Wallis test was performed followed by Dunn test as a multiple comparison test. Ten species of Eimeria were identified in all infected cattle. Among the Eimeria identified species, Eimeria bovis was found to have the highest prevalence (42.5%), followed subsequently by Eimeria wyomingensis (39.1%), Eimeria bukidnonensis (32.4%), Eimeria pellita (26.3%), Eimeria auburnensis (19.6%), Eimeria zuernii (17.3%), Eimeria cylindrica (3.9%), Eimeria canadensis (3.9%), Eimeria brasiliensis (3.4%) and Eimeria alabamensis (1.1%). The numbers of oocysts shed was correlated significantly (p < 0.05) with cattleâ€™s sex and age as well type of pen flooring which influenced the infection pressure. Younger calves aged less than 6 months shed the highest amount of Eimeria oocysts than older cattle. Many factors may cause the increasing number of OPG in fecal samples. Therefore, it is important to keep good sanitation and control of Eimeria among dairy cattle in the KPBS Pangalengan dairy farm.
PAYMENT FOR ENVIRONMENTAL SERVICES APPROACH TO REDUCE FLOOD IN CILIWUNG WATERSHED
Authors: Saridewi Tri Ratna , Hadi Setia , Fauzi Akhmad , Rusastra I Wayan 
Published: October 2017

Spatial planning has already been stipulated in Ciliwung Watershed, but its implementation is often not in line with the rapid development activities.Â To fulfill space demand, agricultural and forest areas are converted into open or built-up areas because the economic appreciation of forest and agricultural land is lower than that of open or built-up areas. Payment for Environmental Services (PES) is a tool designed to overcome environment mismanagement, which is beneficial for the lives of rural communities. Â PES should be considered in the formulation of spatial planning. This study was aimed to develop optimum land use pattern in reducing flood in Ciliwung Watershed, using PES approach. This study used a dynamic system approach, consisting of submodels for land use pattern change, runoff, value of farmland, upstream subsidy policy, population dynamics and environmental services.Â The results showed that the PES policy should be able to maintain the existence of paddy fields and dryland farming areas and to reduce runoff if it is implemented in the form of a guaranteed access to the market, and held in conjunction with efforts to prevent land conversion and to implement reforestation policies.Â The optimum land use pattern under this condition shall be reached in 2023, which consisted of 0.82% water bodies, 10.74% forest areas, 70.34 % built-up areas, 8.16% dryland farming areas, 4.97% grassland areas, 2.39% paddy fields areas and 2.58% open areas. This land use pattern can reduce runoff in Ciliwung River from 972.04 to 850 cm, and this level is considered to be flood-free.Â Communities living in the upstream areas are the most effective managers of the watershed.
DNA BARCODE CHARACTERIZATION OF MISTLETOE INFESTATION IN TEAK CLONAL SEED ORCHARD (CSO) IN PADANGAN, EAST JAVA PROVINCE, INDONESIA
Authors: Muttaqin Zainal , Budi Sri Wilarso , Wasis Basuki , Corryanti Corryanti , Siregar Iskandar Zulkarnaen 
Published: October 2017

For effective teak plantation management, early detection system in controlling teak mistletoe requires various basic information, including degree of infestation and accuracy of the species names. Mistletoe infestations in teak and mistletoe species name have been reported, but there are still problems in identifying the correct species or subspecies due to morphological similarity.Â The objective of this study was to clarify the species identity of hemi-parasitic mistletoe plants, which were found in teak Clonal Seed Orchard (CSO) in Padangan, East Java Province, Indonesia using DNA barcodes. Species identification of teak mistletoe based on leaf morphological characteristics and universal DNA barcode regions (i.e. matK and rbcL) were carried out. The results showed that the Canonical Discriminant Analysis (CDA) could differentiate Dendrophthoe pentandra and Macrosolen tetragonus based on leaf morphological characteristics. Variables having high correlation to distinguish both species were length of petiole, Â width of the widest leaf, number of secondary leaf veins, leaf base shape, aspect ratio, form factor and perimeter ratio of diameter.Â The results ofÂ DNA barcoding showed that the two DNA barcode regions presented good Â amplification and sequence results. Both DNA barcode regions successfully differentiated two species i.e. D. pentandra andÂ M. tetragonus which belong to Loranthaceae family and have similar leaf morphological characteristics. Those regions were also able to identify Viscum articulatum and other species belonging to Santalaceae family. These results suggested that the two DNA regions could become recommended universal DNA barcode for identifying teak mistletoe.