bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Systematic Assessment Of Current Genome-Scale Metabolic Reconstruction Tools
Authors: Mendoza S. N. , Olivier B. G , Molenaar D , Teusink B 
Published: February 2019

AbstractSeveral genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools have been widely applied to reconstruct metabolic models for hundreds of microorganisms ranging from important human pathogens to species of industrial relevance. However, these platforms, as yet, have not been systematically evaluated with respect to software quality, best potential uses and intrinsic capacity to generate high-quality, genome-scale metabolic models. It is therefore unclear for potential users which tool best fits the purpose of their research. In this work, we performed a systematic assessment of the current genome-scale reconstruction software platforms. To meet our goal, we first defined a list of features for assessing software quality related to genome-scale reconstruction, which we expect to be useful for the potential users of these tools. Subsequently, we used the feature list to evaluate the performance of each tool. In order to assess the similarity of the draft reconstructions to high-quality models, we compared each tool’s output networks with that of the high-quality, manually curated, models of Lactobacillus plantarum and Bordetella pertussis, representatives of gram-positive and gram-negative bacteria, respectively. We showed that none of the tools outperforms the others in all the defined features and that model builders should carefully choose a tool (or combinations of tools) depending on the intended use of the metabolic model.Author SummaryMetabolic networks that comprise biochemical reactions at genome-scale have become very useful to study and predict the phenotype of important microorganisms. Several software platforms exist to build these metabolic networks. Based on different approaches and utilizing a variety of databases it is, unfortunately, unclear what are the best scenarios to use each of these tools. Hence, to understand the potential uses of these tools, we created a list of relevant features for metabolic reconstruction and we evaluated the tools in all these categories. Here, we show that none of the tools is better than the other in all the evaluated categories; instead, each tool is more suitable for particular purposes. Therefore, users should carefully select the tool(s) that best fit the purpose of their research. This is the first time these tools are systematically evaluated and this overview can be used as a guide for selecting the correct tool(s) for each case.
Consumers’ decisions in social commerce: the role of guanxi elements
Authors: Yang Xue 
Published: February 2019

Purpose
Recently, the popularity and growth of social media have boosted the development of social commerce (s-commerce). The purpose of this paper is to investigate consumers’ decisions in s-commerce, for which this study conducted empirical research on WeChat, a very popular social media in China, to validate how guanxi elements (e.g. ganqing, renqing and xinren) affect consumers’ decisions in s-commerce.

Design/methodology/approach
To examine the research model, an online survey instrument was developed to gather data. The hypotheses were tested using partial least squares modeling.

Findings
The results confirm that guanxi elements are positively related to eWOM sharing intention and social shopping intention. Moreover, these effects are mediated by a sense of belonging.

Originality/value
This study enhances the existing literature by introducing the concept of guanxi elements to the context of s-commerce, and linking the concept of guanxi elements and consumers’ decisions. Moreover, this study improves the theoretical and empirical understanding of guanxi elements by investigating its impact on eWOM sharing intention and social shopping intention. Third, the results confirm that guanxi elements not only influence a sense of belonging but also conjointly impacts eWOM sharing intention and social shopping intention in s-commerce.
De‐legitimising complementary medicine: framings of the Friends of Science in Medicine‐CAM debate in Australian media reports
Authors: Lewis Monique 
Published: February 2019

AbstractComplementary and alternative medicine (CAM) has developed into a complex and formidable commercial, sociocultural and political force in Australia, and given its influence, it is a relevant subject for scholars, health practitioners, health communicators, journalists, policy‐makers, and consumers of healthcare products and services. This research will consider a relative newcomer to the claims‐making space about CAM in the Australian health media‐scape; the Friends of Science in Medicine (FSM), an activist group of medical practitioners, researchers, and scientists, founded in late 2011. Using content analysis supported by NVivo, I searched for articles specifically referring to FSM and measured the patterns and frequencies of media frames, intonation and sources that are featured in Australian mainstream news reports between December 2011 and April 2017. The negative headlining and intonation of reports predominated, along with framing CAM as part of a lucrative, undisciplined and unethical industry as well as an illegitimate healthcare approach, more broadly. The findings offer insight into how journalists respond, replicate or reconstruct the framings that are provided by an influential and elite group of medical practitioners and scientists, and readdresses issues surrounding the need for more critical health reporting in Australia.
Sensory and Consumer Evaluation of Smoked Pulled Pork Prepared Using Different Smokers and Different Types of Wood
Authors: Swaney‐Stueve Marianne , Talavera Martin , Jepsen Tegan , Severns Bryan , Wise Robert , Deubler Grace 
Published: February 2019

AbstractSmoked and barbecued meats have continued to gain popularity in recent years, however, no consensus exists on the best methods for preparation. Several smoker types and many varieties of wood are used for smoking meat in the restaurant industry and by amateur “pit‐masters.” In this research, pork was smoked with an outdoor offset smoker and an indoor electric smoker using four wood types: hickory, apple, oak, and mesquite. Descriptive and consumer acceptance tests were conducted to evaluate the different treatments and determine drivers of liking. Pork smoked with the offset smoker using hickory wood had the highest overall acceptance. Appearance characteristics, such as intensity of red color, were the top drivers of liking for the smoked pork product.Practical ApplicationThis research demonstrates the drivers of liking for smoked pork products commonly found in American barbecue, specifically Kansas City‐style barbecue. The results have application in both retail and restaurant environments and can be used to produce an optimized smoked pork product.
Twenty‐first‐century chemical odyssey: fuels versus commodities and cell factories versus chemical plants
Authors: Ramos Juan L. , Duque Estrella 
Published: February 2019

SummaryThe harmful effects of pollution from the massive and widespread use of fossil fuels have led various organizations and governments to search for alternative energy sources. To address this, a new energy bioprocess is being developed that utilizes non‐edible lignocellulose – the only sustainable source of organic carbon in nature. In this mini‐review, we consider the potential use of synthetic biology to develop new‐to‐nature pathways for the biosynthesis of chemicals that are currently synthesized using classical industrial approaches. The number of industrial processes based on starch or lignocellulose is still very modest. Advances in the area require the development of more efficient approaches to deconstruct plant materials, better exploitation of the catalytic potential of prokaryotes and lower eukaryotes and the identification of new and useful genes for product synthesis. Further research and progress is urgently needed in order for government and industry to achieve the major milestone of transitioning 30% of the total industry to renewable sources by 2050.
CRISPR interference‐mediated gene regulation in Pseudomonas putida KT2440
Authors: Kim Seong Keun , Yoon Paul K. , Kim Soo‐Jung , Woo Seung‐Gyun , Rha Eugene , Lee Hyewon , Yeom Soo‐Jin , Kim Haseong , Lee Dae‐Hee , Lee Seung‐Goo 
Published: February 2019

SummaryTargeted gene regulation is indispensable for reprogramming a cellular network to modulate a microbial phenotype. Here, we adopted the type II CRISPR interference (CRISPRi) system for simple and efficient regulation of target genes in Pseudomonas putida KT2440. A single CRISPRi plasmid was generated to express a nuclease‐deficient Cas9 gene and a designed single guide RNA, under control of l‐rhamnose‐inducible PrhaBAD and the constitutive Biobrick J23119 promoter respectively. Two target genes were selected to probe the CRISPRi‐mediated gene regulation: exogenous green fluorescent protein on the multicopy plasmid and endogenous glpR on the P. putida KT2440 chromosome, encoding GlpR, a transcriptional regulator that represses expression of the glpFKRD gene cluster for glycerol utilization. The CRISPRi system successfully repressed the two target genes, as evidenced by a reduction in the fluorescence intensity and the lag phase of P. putida KT2440 cell growth on glycerol. Furthermore, CRISPRi‐mediated repression of glpR improved both the cell growth and glycerol utilization, resulting in the enhanced production of mevalonate in an engineered P. putida KT2440 harbouring heterologous genes for the mevalonate pathway. CRISPRi is expected to become a robust tool to reprogram P. putida KT2440 for the development of microbial cell factories producing industrially valuable products.
Application of a real‐time pain monitoring system in Korean fibromyalgia patients: A pilot study
Authors: Lee Jennifer , Park Sung‐Hwan , Ju Ji Hyeon , Cho Jae Hyoung 
Published: February 2019

AbstractObjectivesChronic pain is a debilitating condition which should be managed with integrated multidisciplinary approaches. To this end, accurate pain assessment should be the first step, and self‐reporting pain assessment systems using smartphones or wearable devices are being introduced. The aim of the study was to evaluate the utility and efficacy of a real‐time pain monitoring system using a wearable device, referred to as the Pain Assessment and Analysis System (PAAS), in patients with fibromyalgia, which is characterized by widespread chronic pain.MethodsIn this pilot study, adult fibromyalgia patients were randomly assigned to use or to not use PAAS. Changes in the visual analog scale (VAS) were examined by rheumatologists at baseline and after 3 months, and correlations between conventional pain VAS or PAAS VAS and clinical parameters were investigated.ResultsA total of 24 fibromyalgia patients were enrolled in the study, with 14 patients assigned to the PAAS group, and 11 patients assigned to the control group. All patients completed the 3 month study. The reduction of pain on the VAS in patients who used PAAS for 3 months was significantly greater than that in the control group. The mean pain VAS calculated by PAAS showed good correlation with clinical parameters, including scores of the fibromyalgia impact questionnaire.ConclusionsThe proposed real‐time pain monitoring system can be utilized for pain assessment in Korean fibromyalgia patients. Moreover, the system accurately reflects pain status and may help to alleviate pain.
Cold treatment enhances low‐temperature flight performance in false codling moth, Thaumatotibia leucotreta (Lepidoptera: Tortricidae)
Authors: Boersma Nevill , Boardman Leigh , Gilbert Martin , Terblanche John S. 
Published: February 2019

Abstract
In sterile insect technique programmes, temperatures experienced by insects during rearing and handling, along with cool temperatures after release, can negatively affect performance and activity levels. Phenotypic plasticity (trait modifications caused by prior stress exposure) can offset these effects but is poorly understood in many species and traits.
We investigated the effects of a cold treatment (2 °C for 16 h) on flight performance in adult false codling moth, Thaumatotibia leucotreta. Using diverse methods, flight performance was tested using flight assays in the laboratory and in the field under varying environmental conditions.
The flight performance of T. leucotreta in the laboratory was affected by cold treatment (relative to a 25 °C control group), test temperature and their interaction. Field recapture of released moths was significantly affected by the interaction between cold treatment and environmental conditions.
Field recapture counts depended on the ambient temperature upon release. For example, under warmer conditions (>17 °C), the recapture count of cold‐treated moths was lower than that of the untreated control group, whereas the recapture count of cold‐treated moths at cooler temperatures was significantly higher.
Our results suggest a temperature‐dependent interaction between acute cold exposure and flight performance in adult T. leucotreta, which may be used to enhance the efficacy of the sterile insect technique under cooler environmental conditions.
Stricture rate after chemoradiotherapy and radiotherapy for oesophageal squamous cell carcinoma: a 20‐year experience
Authors: Hamer Peter W. , Hight Stephanie C. , Ward Ian G. , Harris Dean L. , Woodham Benjamin L. , Flint Richard S. 
Published: February 2019

BackgroundDefinitive chemoradiation for oesophageal squamous cell carcinoma (SCC) is the first‐line treatment in many centres. However, it is not without morbidity. We assess outcomes for patients treated with definitive chemoradiotherapy and radiotherapy.MethodsA retrospective review of a prospectively maintained database (Radiotherapy Department, Canterbury District Health Board) was undertaken. All patients who underwent definitive radiotherapy for oesophageal SCC between October 1996 and April 2015 were included.ResultsSixty patients underwent chemoradiotherapy with curative intent and 17 underwent definitive radiotherapy with curative intent. Median age was 69 years (44–84 years) for those undergoing chemoradiotherapy and 73 years (36–85 years) for those who underwent definitive radiotherapy. Tumour location in all patients was upper third in 14 (18%), middle third in 39 (51%), lower third in 22 (29%) cases and junctional tumour in two (3%). Staging information was complete for 73 of 77 patients (stage I 16/77 (21%), stage II 40/77 (52%), stage III 17/77 (22%)). Median dose of external beam radiotherapy for those who underwent definitive chemotherapy was 50.4 Gy (30–63 Gy) and 60 Gy (50–64 Gy) for definitive radiotherapy. Median length of follow‐up was 39 months (range 4–120 months). Strictures developed in 58% of all patients (52% chemoradiotherapy and 76% definitive radiotherapy). Twenty‐four (32%) patients were dilated and 14 (18%) stented. The chemoradiotherapy group had higher 5‐year survival than definitive radiotherapy group (34% versus 6%, P = 0.0034).ConclusionOesophageal SCC treated with chemoradiation has a 5‐year survival rate of 34%. Post‐treatment strictures occur in 52% of patients with chemoradiotherapy and 76% with definitive radiotherapy.
Vaginal or laparoscopic hysterectomy: Do perioperative outcomes differ? A propensity score‐matched analysis
Authors: Rademaker Doortje , Einarsson Jon I. , Huirne Judith A. F. , Gu XiangMei , Cohen Sarah L. 
Published: February 2019

AbstractIntroductionThere are assertions that vaginal mode may be the preferred approach of minimally invasive hysterectomy, yet rates of laparoscopic hysterectomy (LH) continue to rise while vaginal hysterectomy (VH) rate remains relatively unchanged. The aim of this study is to compare the perioperative outcomes of LH vs VH.Material and methodsWe identified women who underwent either LH or VH for benign indications between 2009 and 2015 at a large academic institution. A propensity score‐matched analysis was used to adjust for differences between women undergoing VH vs LH. Outcome parameters were perioperative complications (both intraoperative and postoperative), operative time, blood loss, hospital length of stay, conversion and readmission.ResultsA total of 1921 patients underwent either LH or VH during the study period. In all, 155 patients from each group were successfully matched using propensity score match analysis. While most intra‐ and postoperative characteristics did not differ between groups, LH was associated with lower blood loss during surgery (102.8 ± 166.5 mL vs 185.0 ± 179.0 mL, P < 0.001) and shorter hospital stay (0.9 ± 1 days vs 1.2 ± 0.9 days, P < 0.0001). Concomitant adnexal surgery was performed more frequently during LH (47.7% vs 12.3%, P < 0.0001), and concomitant prolapse surgery was performed more frequently at the time of VH (14.2% vs 68.4%, P < 0.0001).ConclusionsBoth VH and LH have overall favorable perioperative outcomes; however, LH is associated with lower blood loss and a shorter hospital stay. The results support the trend toward increasing rates of laparoscopic approach to hysterectomy when appropriate.
Wuzhi capsule regulates chloroacetaldehyde pharmacokinetics behaviour and alleviates high‐dose cyclophosphamide‐induced nephrotoxicity and neurotoxicity in rats
Authors: Chen Li , Xiong Xiaojuan , Hou Xingyun , Wei Hua , Zhai Jianxiu , Xia Tianyi , Gong Xiaobin , Gao Shouhong , Feng Ge , Tao Xia , Zhang Feng , Chen Wansheng 
Published: February 2019

AbstractHigh‐dose cyclophosphamide (HD‐CTX) treatment often leads to severe nephrotoxicity and neurotoxicity, which are mainly caused by one of its metabolites, chloroacetaldehyde (CAA). However, there are no effective antidotes to prevent these side effects. The objective of this study was to evaluate the effect of Wuzhi Capsule (WZC) on the pharmacokinetics of CTX and its metabolites in rats, and the attenuation of CAA induced kidney and brain injuries, which was produced at equimolar with 2‐dechloroethylcyclophosphamide. Rats were treated with single‐ or multiple‐dose of WZC when giving HD‐CTX, and the plasma concentration of CTX and its metabolites were quantitated by UHPLC‐MS/MS Single‐dose, not multiple‐dose of WZC co‐administration (300 mg/kg) significantly reduced Cmax and AUC0→24 h of DC‐CTX by 33.10% and 35.51%, respectively. Biochemical assay suggested oxidative stress was involved in kidney and brain injuries by HD‐CTX, which were attenuated by single‐dose WZC (300 mg/kg) pre‐treatment, with increased glutathione, glutathione peroxidase and superoxide dismutase contents/or activities in both tissues and plasma (P < 0.05). Meanwhile, WZC pre‐treatment could also significantly decrease the plasma levels of creatinine, blood urea nitrogen and malondialdehyde (P < 0.05). Additionally, WZC treatment improved the morphology and pathology condition of the kidneys and brains in rats. In conclusion, single‐dose WZC co‐administration decreased CAA production and exerted protective effect on CTX‐induced oxidative stress in kidney and brain, whereas repetitive WZC co‐administration with CTX was probably not recommended.
CDKL5 deficiency predisposes neurons to cell death through the deregulation of SMAD3 signaling
Authors: Fuchs Claudia , Medici Giorgio , Trazzi Stefania , Gennaccaro Laura , Galvani Giuseppe , Berteotti Chiara , Ren Elisa , Loi Manuela , Ciani Elisabetta 
Published: February 2019

AbstractCDKL5 deficiency disorder (CDD) is a rare encephalopathy characterized by early onset epilepsy and severe intellectual disability. CDD is caused by mutations in the X‐linked cyclin‐dependent kinase‐like 5 (CDKL5) gene, a member of a highly conserved family of serine‐threonine kinases. Only a few physiological substrates of CDKL5 are currently known, which hampers the discovery of therapeutic strategies for CDD. Here, we show that SMAD3, a primary mediator of TGF‐β action, is a direct phosphorylation target of CDKL5 and that CDKL5‐dependent phosphorylation promotes SMAD3 protein stability. Importantly, we found that restoration of the SMAD3 signaling through TGF‐β1 treatment normalized defective neuronal survival and maturation in Cdkl5 knockout (KO) neurons. Moreover, we demonstrate that Cdkl5 KO neurons are more vulnerable to neurotoxic/excitotoxic stimuli. In vivo treatment with TGF‐β1 prevents increased NMDA‐induced cell death in hippocampal neurons from Cdkl5 KO mice, suggesting an involvement of the SMAD3 signaling deregulation in the neuronal susceptibility to excitotoxic injury of Cdkl5 KO mice. Our finding reveals a new function for CDKL5 in maintaining neuronal survival that could have important implications for susceptibility to neurodegeneration in patients with CDD.
Termite diversity in Neotropical dry forests of Colombia and the potential role of rainfall in structuring termite diversity
Authors: Casalla Robin , Korb Judith 
Published: February 2019

AbstractTermites are ecosystem engineers that play an important role in the biotransformation and re‐distribution of nutrients in soil. The dry forests are endemic repositories, but at same time, they are most threatened by extensive livestock and crop farming, fires, and climate change. In Colombia, the best‐protected dry forests are located in the north. The termite fauna of dry forests are poorly known. The aim was to identify the termite species occurring in tropical dry forests of the Colombian Caribbean coast in relation to diet and precipitation, temperature, elevation, and soil properties. A total of 32 species in 1,103 occurrences were found. Termitidae accounted for 78% of the species richness with the Anoplotermes‐group, Microcerotermes, and Nasutitermes being the dominant genera. Differences in species composition and abundance were found across sites. These differences may be linked to anthropogenic disturbance and polygyny and polydomy. Strikingly, our highest elevation site (334 m) had the highest species richness much higher than the two lower elevation sites. This implies an inversion of the common elevation‐diversity gradient, also found for termites which can be explained by increasing precipitation with elevation in the dry forest. An analysis of termite species richness at the global scale confirms that termite species richness correlates positively with rainfall. Hence, rainfall seems to positively affect termite diversity. In line, the studied Colombian tropical dry forests had low diversity compared to rain forests. A decline of species‐rich soil‐feeding termites with increasing aridity may explain why the highest termite diversity occurs in humid tropical rain forests.Abstract in Spanish is available with online material.
Lessons learned about steered molecular dynamics simulations and free energy calculations
Authors: Boubeta Fernando Martín , Contestín García Rocío María , Lorenzo Ezequiel Norberto , Boechi Leonardo , Estrin Dario , Sued Mariela , Arrar Mehrnoosh 
Published: February 2019

AbstractThe calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM‐MM tools, ligand migration, and conformational rearrangements that can be modeled using classical potentials. The use of steered molecular dynamics (sMD) together with the Jarzynski equality is a popular approach in calculating free energy profiles. Here, we first briefly review the application of the Jarzynski equality to sMD simulations, then revisit the so‐called stiff‐spring approximation and the consequent expectation of Gaussian work distributions and, finally, reiterate the practical utility of the second‐order cumulant expansion, as it coincides with the parametric maximum‐likelihood estimator in this scenario. We illustrate this procedure using simulations of CO, both in aqueous solution and in a carbon nanotube as a model system for biologically relevant nanoheterogeneous environments. We conclude the use of the second‐order cumulant expansion permits the use of faster pulling velocities in sMD simulations, without introducing bias due to large dispersion in the non‐equilibrium work distribution.