bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short‐chain fatty acids
Authors: Hackmann Timothy J. , Ngugi David Kamanda , Firkins Jeffrey L. , Tao Junyi 
Published: September 2017

SummaryBacteria have been thought to follow only a few well‐recognized biochemical pathways when fermenting glucose or other hexoses. These pathways have been chiseled in the stone of textbooks for decades, with most sources rendering them as they appear in the classic 1986 text by Gottschalk. Still, it is unclear how broadly these pathways apply, given that they were established and delineated biochemically with only a few model organisms. Here, we show that well‐recognized pathways often cannot explain fermentation products formed by bacteria. In the most extensive analysis of its kind, we reconstructed pathways for glucose fermentation from genomes of 48 species and subspecies of bacteria from one environment (the rumen). In total, 44% of these bacteria had atypical pathways, including several that are completely unprecedented for bacteria or any organism. In detail, 8% of bacteria had an atypical pathway for acetate formation; 21% of bacteria had an atypical pathway for propionate or succinate formation; 6% of bacteria had an atypical pathway for butyrate formation and 33% of bacteria had an atypical or incomplete Embden–Meyerhof–Parnas pathway. This study shows that reconstruction of metabolic pathways – a common goal of omics studies – could be incorrect if well‐recognized pathways are used for reference. Furthermore, it calls for renewed efforts to delineate fermentation pathways biochemically.
Swimming or Drowning in the Depths of Partnership
Authors: Sturup Sophie 
Published: September 2017

AbstractThis exploratory research paper seeks to consider the problems that may arise in the process of creating deep and lasting partnerships in public‐private partnerships (PPPs). It does this by contrasting two case studies of very different PPPs, Copenhagen's metro project and Melbourne City Link. The paper puts forward the case for the author's concern that a deep partnership could lead either to mercantile government or quasi‐governmental private parties and thus lead to a diminution of the benefits of PPPs. The paper concludes that these concerns are relevant and need to be considered and guarded against no matter the contract conditions.
Interaction effects between local flower richness and distance to natural woodland on pest and beneficial insects in apple orchards
Authors: Saunders Manu E. , Luck Gary W. 
Published: September 2017

Abstract

Local and landscape factors interact to influence animal populations and, ultimately, crop yields in agroecosystems. Yet few studies have considered interactions and trade‐offs between these factors within a single agroecosystem.
We sampled insect communities (fruit‐damaging pests and Diptera and Hymenoptera pollinator and natural enemy taxa) associated with focal apple trees in south‐eastern Australian orchards across a single growing season. We also measured marketable fruit yields on netted (preventing access to vertebrates) and open branches on each focal tree. We focused on relationships with local (ground cover attributes) and landscape (proximity to natural woodland) factors.
Importantly, we found that local flower richness in orchard understoreys may buffer the negative effects that isolation from natural woodland has on wild bee and natural enemy communities and the ecosystem services they provide.
The results of the present study suggest that floral diversity may be more effective in supporting beneficial insects in crop interiors, rather than at edges near natural vegetation.
More studies are needed that identify how local and landscape vegetation structure interact to influence communities of pest and beneficial taxa, and relevant ecosystem functions, in agroecosystems.
Performance of the Minto model for the target‐controlled infusion of remifentanil during cardiopulmonary bypass
Authors: Cho Y. J. , Jo W. Y. , Oh H. , Koo C.‐H. , Oh J. , Cho J.‐Y. , Yu K.‐S. , Jeon Y. , Kim T. K. 
Published: September 2017

SummaryWe studied the predictive performance of the Minto pharmacokinetic model during cardiopulmonary bypass in patients undergoing cardiac surgery. Patients received remifentanil target‐controlled infusion using the Minto model during total intravenous anaesthesia with propofol. From 56 patients, 275 arterial blood samples were drawn before, during and after bypass to determine the plasma concentration of remifentanil, and the predicted concentrations were recorded at each time. For pooled data, the median prediction error and median absolute prediction error were 21.3% and 21.8%, respectively, and 22.1% and 22.3% during bypass. Both were 148.4% during hypothermic circulatory arrest and measured concentrations were more than three times greater than predicted (26.9 (17.0) vs. 7.1 (1.6) ng.ml−1). The Minto model showed considerable bias but overall acceptable precision during bypass. The target concentration of remifentanil should be reduced when using the Minto model during hypothermic circulatory arrest.
Systematic review with meta‐analysis: breastfeeding and the risk of Crohn's disease and ulcerative colitis
Authors: Xu L. , Lochhead P. , Ko Y. , Claggett B. , Leong R. W. , Ananthakrishnan A. N. 
Published: September 2017

SummaryBackgroundBreastfeeding is a modifiable factor that may influence development of inflammatory bowel diseases. However, literature on this has been inconsistent and not accounted for heterogeneity in populations and exposure.AimTo conduct a meta‐analysis to examine the association between breastfeeding in infancy and risk of Crohn's disease (CD) and ulcerative colitis (UC).MethodsA systematic search of Medline/PubMed and Embase was performed for full text, English‐language literature through November 2016. Studies were included if they described breastfeeding in infancy in patients with CD or UC, and healthy controls. Data were pooled using a random effects model for analysis.ResultsA total of 35 studies were included in the final analysis, comprising 7536 individuals with CD, 7353 with UC and 330 222 controls. Ever being breastfed was associated with a lower risk of CD (OR 0.71, 95% CI 0.59‐0.85) and UC (OR 0.78, 95% CI 0.67‐0.91). While this inverse association was observed in all ethnicity groups, the magnitude of protection was significantly greater among Asians (OR 0.31, 95% CI 0.20‐0.48) compared to Caucasians (OR 0.78, 95% CI 0.66‐0.93; P = .0001) in CD. Breastfeeding duration showed a dose‐dependent association, with strongest decrease in risk when breastfed for at least 12 months for CD (OR 0.20, 95% CI 0.08‐0.50) and UC (OR 0.21, 95% CI 0.10‐0.43) as compared to 3 or 6 months.ConclusionBreastfeeding in infancy protects against the development of CD and ulcerative colitis.
Systematic review with meta‐analysis: the global recurrence rate of Helicobacter pylori
Authors: Hu Y. , Wan J.‐H. , Li X.‐Y. , Zhu Y. , Graham D. Y. , Lu N.‐H. 
Published: September 2017

SummaryBackgroundUp‐to‐date information regarding the recurrence rate of Helicobacter pylori (H. pylori) after eradication therapy is not available.AimTo evaluate the global recurrence rate following H. pylori eradication therapy and confirm its association with socioeconomic and sanitary conditions.MethodsA systematic search of PubMed, EMBASE and the Cochrane library was performed to identify potentially relevant publications using the following keywords: “Helicobacter pylori” or “H. pylori” or “Hp” and “recurrence” or “recrudescence” or “reinfection” or “recurrent” or “recurred” or “re‐infect*” or “relapse*.”ResultsA total of 132 studies (53 934 patient‐years) were analysed. Each study was weighted according to the duration of patient‐years. The global annual recurrence, reinfection and recrudescence rate of H. pylori were 4.3% (95% CI, 4‐5), 3.1% (95% CI, 2‐5) and 2.2% (95% CI, 1‐3), respectively. The H. pylori recurrence rate was inversely related to the human development index (HDI) (ie, 3.1% [95% CI, 2‐4], 6.2% [95% CI, 4‐8] and 10.9% [95% CI, 6‐18] in countries with a very high, high and medium or low HDI) (P <.01) and directly related to H. pylori prevalence (10.9% [95% CI, 7‐16], 3.7% [95% CI, 3‐5], 3.4% [95% CI, 2‐5] and 1.6% [95% CI, 0.5‐3] in countries with a very high, high, medium or low local H. pylori prevalence) (P <.01). Global recurrence rates remained relatively stable between 1990s, 2000s and 2010s but varied across different regions (P <.05).ConclusionsH. pylori recurrence remains a problem closely associated with socioeconomic and sanitary conditions. Methods to reduce recurrence in developing countries are needed.
Short‐term results of self‐expanding metal stents for acute malignant large bowel obstruction
Authors: Kobborg M. , Broholm M. , Frostberg E. , Jeppesen M. , Gögenür I. 
Published: September 2017

AbstractAimSelf‐expanding metal stents (SEMSs) can be used as a palliative treatment or to initially decompress colon prior to definitive surgery (as a so‐called ‘bridge to surgery’). The purpose of this study was to investigate the efficacy and safety of SEMS used as palliation and bridge to surgery for malignant large bowel obstruction.MethodA multicentre retrospective study was conducted from January 2010 to December 2013 to identify patients undergoing stent placement for acute large bowel obstruction. Patients were included from four Danish colorectal centres. Outcomes identified included clinical success, 30‐day mortality, stent related complications and surgery related complications. Furthermore, we analysed for predictive factors for successful stenting. Clinical success was defined as relief of obstructive symptoms, without the need of other additional surgical interventions during the hospital stay.ResultsSEMSs were inserted in 239 patients for whom the indication was as a bridge to surgery in 112 patients (47%) and as palliation in 127 (53%) patients. Clinical success was achieved in 90 patients (80.4%) in the bridge to surgery group and in 105 patients (82.8%) in the palliation group. The 30‐day mortality rates in the two groups were 5.4% and 11.8% for bridge to surgery and palliation respectively. A total of 17.8% of the patients in the bridge to surgery group had a stent related complication and in the palliation group it was 20.4%. Multivariate analysis demonstrated that clinical failure is a predictive factor of 30‐day mortality (OR 11.1, 95% CI: 4.1–30.0).ConclusionThe use of a SEMS to relieve a malignant large bowel obstruction is generally an effective and safe method, but complications are seen in about 20% of patients. Further investigations are required to determine the role of SEMSs in the treatment of acute, malignant, large bowel obstruction.
A Pilot Dose‐Finding Study of Etanercept in Rheumatoid Arthritis
Authors: Breedveld Ferdinand C. , Jones Heather E. , Peifer Kim , Korth‐Bradley Joan 
Published: September 2017

AbstractA randomized, parallel‐dose study assessed the pharmacokinetics (PK) and pharmacodynamics (PD) of etanercept in 61 patients with rheumatoid arthritis (RA) who received doses from 10 mg once‐weekly to 50 mg twice‐weekly for 4 weeks. Empiric application of a maximal‐effect (Emax) model to pooled steady‐state concentrations (Css) and PD markers provided half‐maximal‐effect concentration estimates of 567, 573, 465, 87, and 159 ng/mL for change from baseline in number of swollen joints, number of painful joints, erythrocyte sedimentation rate, interleukin‐6, and matrix metalloproteinase‐3, respectively. Css >∼2,000 ng/mL did not appear to offer additional benefit. It was concluded that the middle doses, 10 mg twice‐weekly, 50 mg every 2 weeks, and 50 mg once‐weekly, would provide Css in the target range of 500–2,000 ng/mL. The revised US Food and Drug Administration guideline for development of medicines for treatment of RA encourages a study design incorporating PK/PD assessment to inform later studies.
Histopathologic features of cutaneous leishmaniasis and use of CD1a staining for amastigotes in Old World and New World leishmaniasis
Authors: Sundharkrishnan Lohini , North Jeffrey P. 
Published: September 2017

BackgroundPositive CD1a staining of Leishmania has been reported in Old World leishmaniasis, but the sensitivity of such staining for other Leishmania species is unknown.MethodsA retrospective review was done on skin biopsies of proven cutaneous leishmaniasis based on histology, immunohistochemistry, culture and/or polymerase chain reaction (PCR). We assessed the pattern of inflammation present and assessed for CD1a (MTB1 clone) positivity in amastigotes. Patients without a clearly documented travel history to delineate Old vs New World leishmaniasis and cases without tissue for CD1a staining were excluded.ResultsVarious patterns of granulomatous inflammation were observed including sarcoidal (31%), diffuse (25%), suppurative and granulomatous (25%), palisaded (13%) and lichenoid (6%). CD1a staining was positive in amastigotes in 9 of 16 cases (56%). Five of 7 (71%) cases of Old World disease were CD1a positive, while 4 of 9 cases (44%) of New World cases were positive.ConclusionsMultiple patterns of granulomatous inflammation occur in cutaneous leishmaniasis. Our results confirm CD1a (MTB1 clone) can be a diagnostic adjunct to highlight amastigotes in biopsies of cutaneous leishmaniasis, with variable positivity in both Old World and New World forms of the disease. As 44% of cases were CD1a negative in our cohort, there are significant limitations to this screening approach.
Sitagliptin and Roux‐en‐Y gastric bypass modulate insulin secretion via regulation of intra‐islet PYY
Authors: Guida Claudia , McCulloch Laura J. , Godazgar Mahdieh , Stephen Sam D. , Baker Charlotte , Basco Davide , Dong Jiawen , Chen Duan , Clark Anne , Ramracheya Reshma D 
Published: September 2017

AimsThe gut hormone peptide tyrosine tyrosine (PYY) is critical for maintaining islet integrity and restoring islet function following Roux‐en‐Y gastric bypass (RYGB). The expression of PYY and its receptors (NPYRs) in islets has been documented but not fully characterized. Modulation of islet PYY by the proteolytic enzyme dipeptidyl peptidase IV (DPP‐IV) has not been investigated and the impact of DPP‐IV inhibition on islet PYY function remains unexplored. Here we have addressed these gaps and their effects on glucose‐stimulated insulin secretion (GSIS). We have also investigated changes in pancreatic PYY in diabetes and following RYGB.MethodsImmunohistochemistry and gene expression analysis were used to assess PYY, NPYRs and DPP‐IV expression in rodent and human islets. DPP‐IV activity inhibition was achieved by sitagliptin. Secretion studies were used to test PYY and the effects of sitagliptin on insulin release, and the involvement of GLP‐1. Radioimmunoassays were used to measure hormone content in islets.ResultsPYY and DPP‐IV localized in different cell types in islets while NPYR expression was confined to the beta‐cells. Chronic PYY application enhanced GSIS in rodent and diabetic human islets. DPP‐IV inhibition by sitagliptin potentiated GSIS; this was mediated by locally‐produced PYY, and not GLP‐1. Pancreatic PYY was markedly reduced in diabetes. RYGB strongly increased islet PYY content, but did not lead to full restoration of pancreatic GLP‐1 levels.ConclusionLocal regulation of pancreatic PYY, rather than GLP‐1, by DPP‐IV inhibition or RYGB can directly modulate the insulin secretory response to glucose, indicating a novel role of pancreatic PYY in diabetes and weight‐loss surgery.
CO2 evasion from boreal lakes: Revised estimate, drivers of spatial variability, and future projections
Authors: Hastie Adam , Lauerwald Ronny , Weyhenmeyer Gesa , Sobek Sebastian , Verpoorter Charles , Regnier Pierre 
Published: September 2017

AbstractLakes (including reservoirs) are an important component of the global carbon (C) cycle, as acknowledged by the fifth assessment report of the IPCC. In the context of lakes, the boreal region is disproportionately important contributing to 27% of the worldwide lake area, despite representing just 14% of global land surface area. In this study, we used a statistical approach to derive a prediction equation for the partial pressure of CO2 (pCO2) in lakes as a function of lake area, terrestrial net primary productivity (NPP), and precipitation (r2 = .56), and to create the first high‐resolution, circumboreal map (0.5°) of lake pCO2. The map of pCO2 was combined with lake area from the recently published GLOWABO database and three different estimates of the gas transfer velocity k to produce a resulting map of CO2 evasion (FCO2). For the boreal region, we estimate an average, lake area weighted, pCO2 of 966 (678–1,325) μatm and a total FCO2 of 189 (74–347) Tg C year−1, and evaluate the corresponding uncertainties based on Monte Carlo simulation. Our estimate of FCO2 is approximately twofold greater than previous estimates, as a result of methodological and data source differences. We use our results along with published estimates of the other C fluxes through inland waters to derive a C budget for the boreal region, and find that FCO2 from lakes is the most significant flux of the land‐ocean aquatic continuum, and of a similar magnitude as emissions from forest fires. Using the model and applying it to spatially resolved projections of terrestrial NPP and precipitation while keeping everything else constant, we predict a 107% increase in boreal lake FCO2 under emission scenario RCP8.5 by 2100. Our projections are largely driven by increases in terrestrial NPP over the same period, showing the very close connection between the terrestrial and aquatic C cycle.
Effect of the addition of soluble (nutriose, inulin and polydextrose) and insoluble (bamboo, potato and pea) fibres on the quality of sugar‐snap cookies
Authors: Mancebo Camino M. , Rodríguez Patricia , Martínez Mario M. , Gómez Manuel 
Published: September 2017

SummaryDietary fibre intake can help to improve the health of the population. Cookies are one of the most consumed bakery products. The aim of this study was to investigate the influence of different fibres on cookie quality. Soluble fibres (nutriose, inulin and polydextrose) decreased dough consistency favoured cookie spread during baking and produced wider and thinner cookies. In contrast, insoluble fibres (elongated and rounded) showed an opposite trend increasing dough consistency and giving rise to cookies with higher moisture, lower spread factor and higher hardness. Long insoluble fibres gave rise to harder cookies and with lower spread factor. Cookies made with soluble fibres were darker than the control cookie and cookies containing insoluble fibres. Therefore, solubility and shape of insoluble fibres play an important role in cookie quality. Fibre selection will be key to enriched cookies development.
Microwave‐assisted degradation of chitosan with hydrogen peroxide treatment using Box‐Behnken design for enhanced antibacterial activity
Authors: Zhang Yiwen , Zhang Hongcai , Chen Shunsheng , Fu Hao , Zhao Yanyun 
Published: September 2017

SummaryLow molecular mass (MM) chitosan with high degree of deacetylation (DDA) has excellent bioactivity including antioxidant, antibacterial and encapsulation properties. In this work, to reduce the MM of chitosan, microwave‐assisted heating treatment (MAHT) conditions were investigated using three factors at three levels Box‐Behnken design (BBD). Microwave heating (MH) time, H2O2 concentration and solid‐to‐liquid ratio significantly affected the DDA and MM of chitosan. The antibacterial activities of chitosan before and after degradation were investigated based on minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The results showed that a second‐order polynomial equation fitted the observed values using multiple regression analysis and had a high coefficient of determination (R2 = 0.9591 and 0.9161 for the DDA and MM of chitosan, respectively). An optimisation study was performed using Derringer's desirability function methodology, and the optimal conditions were 80‐s MH time, 1.5% H2O2 concentration and 1:40 solid‐to‐liquid ratio. The MIC and MBC of chitosan before and after degradation against Escherichia coli and Salmonella typhimurium were 0.031 and 0.063 mg mL−1, and 0.25 and 0.125 mg mL−1, respectively. The optimised DDA and MM of chitosan were 90.58 ± 2.04% and 124.25 ± 14.36 kDa, respectively, which significantly reduces the use of oxidant reagent.
Impact of feedback on adenoma detection rates: Outcomes of quality improvement program
Authors: Gurudu Suryakanth R , Boroff Erika S , Crowell Michael D , Atia Mary , Umar Sarah B , Leighton Jonathan A , Faigel Douglas O , Ramirez Francisco C 
Published: September 2017

AbstractBackground and AimFeedback has been shown to improve performance in colonoscopy including adenoma detection rate (ADR). The frequency at which feedback should be given is unknown. As part of a quality improvement program, we sought to measure the outcome of providing quarterly and monthly feedback on colonoscopy quality measures.MethodsAll screening colonoscopies performed at endoscopy unit at Mayo Clinic Arizona by gastroenterologists between October 2010 and December 2012 were reviewed. Quality indicators, including ADR, were extracted for each individual endoscopist, and feedback was provided. The study period was divided into four distinct groups: pre‐intervention that served as baseline, quarterly feedback, monthly feedback, and post‐intervention. Based on ADR, endoscopists were grouped into “low detectors” (≤ 25%), “average detectors” (26–35%), and “high detectors” (> 35%).ResultsA total of 3420 screening colonoscopies were performed during the study period (555 patients during pre‐intervention, 1209 patients during quarterly feedback, 599 during monthly feedback, and 1057 during the post‐intervention period) by 16 gastroenterologists. The overall ADR for the group improved from 30.5% to 37.7% (P = 0.003). Compared with the pre‐interventional period, all quality indicators measured significantly improved during the monthly feedback and post‐intervention periods but not in the quarterly feedback period.ConclusionsIn our quality improvement program, monthly feedback significantly improved colonoscopy quality measures, including ADR, while quarterly feedback did not. The impact of the intervention was most prominent in the “low detectors” group. Results were durable up to 6 months following the intervention.