bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduction of physiological stress by urban green space in a multisensory virtual experiment
Authors: Hedblom Marcus , Gunnarsson Bengt , Iravani Behzad , Knez Igor , Schaefer Martin , Thorsson Pontus , Lundström Johan N. 
Published: July 2019

AbstractAlthough stress is an increasing global health problem in cities, urban green spaces can provide health benefits. There is, however, a lack of understanding of the link between physiological mechanisms and qualities of urban green spaces. Here, we compare the effects of visual stimuli (360 degree virtual photos of an urban environment, forest, and park) to the effects of congruent olfactory stimuli (nature and city odours) and auditory stimuli (bird songs and noise) on physiological stress recovery. Participants (N = 154) were pseudo-randomised into participating in one of the three environments and subsequently exposed to stress (operationalised by skin conductance levels). The park and forest, but not the urban area, provided significant stress reduction. High pleasantness ratings of the environment were linked to low physiological stress responses for olfactory and to some extent for auditory, but not for visual stimuli. This result indicates that olfactory stimuli may be better at facilitating stress reduction than visual stimuli. Currently, urban planners prioritise visual stimuli when planning open green spaces, but urban planners should also consider multisensory qualities.
A gene expression network analysis of the pancreatic islets from lean and obese mice identifies complement 1q like-3 secreted protein as a regulator of β-cell function
Authors: Koltes James E. , Arora Itika , Gupta Rajesh , Nguyen Dan C. , Schaid Michael , Kim Jeong-a , Kimple Michelle E. , Bhatnagar Sushant 
Published: July 2019

AbstractSecreted proteins are important metabolic regulators. Identifying and characterizing the role of secreted proteins from small tissue depots such as islets of Langerhans, which are required for the proper control of whole-body energy metabolism, remains challenging. Our objective was to identify islet-derived secreted proteins that affect islet function in obesity. Lean and obese mouse islet expression data were analyzed by weighted gene co-expression network analysis (WGCNA) to identify trait-associated modules. Subsequently, genes within these modules were filtered for transcripts that encode for secreted proteins based on intramodular connectivity, module membership, and differential expression. Complement 1q like-3 (C1ql3) secreted protein was identified as a hub gene affecting islet function in obesity. Co-expression network, hierarchal clustering, and gene-ontology based approaches identified a putative role for C1ql3 in regulating β-cell insulin secretion. Biological validation shows that C1ql3 is expressed in β-cells, it inhibits insulin secretion and key genes that are involved in β-cell function. Moreover, the increased expression of C1ql3 is correlated with the reduced insulin secretion in islets of obese mice. Herein, we demonstrate a streamlined approach to effectively screen and determine the function of secreted proteins in islets, and identified C1ql3 as a putative contributor to reduced insulin secretion in obesity, linking C1ql3 to an increased susceptibility to type 2 diabetes.
GeneHunt for rapid domain-specific annotation of glycoside hydrolases
Authors: Nguyen S. N. , Flores A. , Talamantes D. , Dar F. , Valdez A. , Schwans J. , Berlemont R. 
Published: July 2019

AbstractThe identification of glycoside hydrolases (GHs) for efficient polysaccharide deconstruction is essential for the development of biofuels. Here, we investigate the potential of sequential HMM-profile identification for the rapid and precise identification of the multi-domain architecture of GHs from various datasets. First, as a validation, we successfully reannotated >98% of the biochemically characterized enzymes listed on the CAZy database. Next, we analyzed the 43 million non-redundant sequences from the M5nr data and identified 322,068 unique GHs. Finally, we searched 129 assembled metagenomes retrieved from MG-RAST for environmental GHs and identified 160,790 additional enzymes. Although most identified sequences corresponded to single domain enzymes, many contained several domains, including known accessory domains and some domains never identified in association with GH. Several sequences displayed multiple catalytic domains and few of these potential multi-activity proteins combined potentially synergistic domains. Finally, we produced and confirmed the biochemical activities of a GH5-GH10 cellulase-xylanase and a GH11-CE4 xylanase-esterase. Globally, this “gene to enzyme pipeline” provides a rationale for mining large datasets in order to identify new catalysts combining unique properties for the efficient deconstruction of polysaccharides.
Cassava cell wall characterization and degradation by a multicomponent NSP-targeting enzyme (NSPase)
Authors: Staack Larissa , Della Pia Eduardo Antonio , Jørgensen Bodil , Pettersson Dan , Rangel Pedersen Ninfa 
Published: July 2019

AbstractCassava (Manihot esculenta Crantz) is considered the third most important source of calories in tropical regions. Up to one third of cassava harvested worldwide is used in livestock production. The focus of this study was to characterize cassava cell wall structure to provide knowledge for a better application of cassava as an energy source in monogastric animal feed. A total of five cassava samples from different feed mills in South East Asia were investigated. On a dry matter basis, the cassava cell walls contained, on average, 640 mg g−1 glucose, 140 mg g−1 galactose, 50 mg g−1 mannose, 80 mg g−1 xylose, 60 mg g−1 arabinose, 10 mg g−1 fucose and 20 mg g−1 rhamnose. RONOZYME VP (DSM Nutritional Products, Switzerland), a non-specific multicomponent non-starch polysaccharide (NSP) degrading enzyme (NSPase) product from Aspergillus aculeatus, solubilized about 10% of cassava NSP content during 4 h incubations at 40 °C and pH 5. There was notable solubilization of polymers containing uronic acids, galactose, arabinose and rhamnose. Immuno-microscopy imaging indicated the solubilization of pectin, galactan and xyloglucan polysaccharides from cassava cell wall. As a consequence, the starch granules became more available to exogenous α-amylase degradation.
Microplastic contamination of table salts from Taiwan, including a global review
Authors: Lee Hyemi , Kunz Alexander , Shim Won Joon , Walther Bruno A. 
Published: July 2019

AbstractPlastic pollution is a rapidly worsening environmental problem, especially in oceanic habitats. Environmental pollution with microplastic particles is also causing food consumed by humans to be increasingly polluted, including table salts. Therefore, we present the first study which focuses only on table salt products purchased in Taiwan which we examined for the presence of microplastics. We used Fourier transform infrared spectroscopy to identify the polymer type of each particle. Within 4.4 kg of salt, we detected 43 microplastic particles which averages to 9.77 microplastic particles/kg. The identified polymer types were, in descending abundance, polypropylene, polyethylene, polystyrene, polyester, polyetherimide, polyethylene terephthalate, and polyoxymethylene. We combined our novel results with those of previous studies to provide the first global review of microplastic contamination of table salts. We found that 94% of salt products tested worldwide contained microplastics, with 3 out of 27 polymer types (polyethylene terephthalate, polypropylene, polyethylene) accounting for the majority of all particles. Averaging over seven separate studies, table salts contain a mean of 140.2 microplastic particles/kg. With a mean annual salt consumption of ~3.75 kg/year, humans therefore annually ingest several hundred microplastic particles from salt alone.
Peripheral Expression of Mutant Huntingtin is a Critical Determinant of Weight Loss and Metabolic Disturbances in Huntington’s Disease
Authors: Lakra Priya , Aditi Kumari , Agrawal Namita 
Published: July 2019

AbstractDeteriorating weight loss in patients with Huntington’s disease (HD) is a complicated peripheral manifestation and the cause remains poorly understood. Studies suggest that body weight strongly influences the clinical progression rate of HD and thereby offers a valuable target for therapeutic interventions. Mutant huntingtin (mHTT) is ubiquitously expressed and could induce toxicity by directly acting in the peripheral tissues. We investigated the effects of selective expression of mHTT exon1 in fat body (FB; functionally equivalent to human adipose tissue and liver) using transgenic Drosophila. We find that FB-autonomous expression of mHTT exon1 is intrinsically toxic and causes chronic weight loss in the flies despite progressive hyperphagia, and early adult death. Moreover, flies exhibit loss of intracellular lipid stores, and decline in the systemic levels of lipids and carbohydrates which aggravates over time, representing metabolic defects. At the cellular level, besides impairment, cell death also occurs with the formation of mHTT aggregates in the FB. These findings indicate that FB-autonomous expression of mHTT alone is sufficient to cause metabolic abnormalities and emaciation in vivo without any neurodegenerative cues.
A meta-barcoding analysis of soil mycobiota of the upper Andean Colombian agro-environment
Authors: Landinez-Torres Angela , Panelli Simona , Picco Anna Maria , Comandatore Francesco , Tosi Solveig , Capelli Enrica 
Published: July 2019

AbstractColombia is a country for which one of the highest biodiversity rates is reported, and one of the first in the tropical areas where an effort was made to gather information on indigenous fungi. Nevertheless, mycological data are still scarce and discontinuous, above all on soil fungi. The present study wanted to contribute to unveil the large soil fungal biodiversity in the upper Andean Colombian agro-ecosystems. The studied area is located in the department of Boyacà, considered with a notable economical value, partly devoted to subsistence agriculture. More than 150 described species were revealed in this study, belonging to 5 phyla with Ascomycota representing the dominant taxon. Basidiomycota and Zygomycota are also well represented, dominated by species of the genus Sebacina and Mortierella respectively, mainly distributed in the semi-natural plots (woodland and grassland). Most of the species are reported as first records for Colombia. Some of them are particularly interesting for their conservation significance such as Geoglossum fallax, which is the dominant species in the unimproved grassland plot. The bootstrap-based clustering analysis showed a different distribution of the species in orchards and non-cultivated areas as a possible response of the fungal community to different use of soil in the agro-environment.
Photobiomodulation (660 nm) therapy reduces oxidative stress and induces BDNF expression in the hippocampus
Authors: Heo Jin-Chul , Park Ji-Ae , Kim Dae-Kwang , Lee Jong-Ha 
Published: July 2019

AbstractPhotobiomodulation therapy (PBMT) effects an important role in neural regeneration and function enhancement, such as expression of nerve growth factor and nerve regeneration, in neuronal tissues, and inhibition of cell death by amyloid beta in neurons is inhibited by PBMT. However, there no studies evaluated the effects of PBMT on oxidative stress in the hippocampus. The aim of this study is to evaluate the effects of PBMT on oxidative stress in the hippocampus. This study assessed the anti-oxidative effect, the expression of BDNF and antioxidant enzymes, as well as the activation of cAMP response element binding (CREB) and extracellular signal-regulated kinase (ERK) signal transduction pathways assess using a hippocampal cell line (HT-22) and mouse organotypic hippocampal tissues by PBMT (LED, 660 nm, 20 mW/cm2). PBMT inhibited HT-22 cell death by oxidative stress and increased BDNF expression via ERK and CREB signaling pathway activation. In addition, PBMT increased BDNF expression in hippocampal organotypic slices and the levels of phosphorylated ERK and CREB, which were reduced by oxidative stress, as well as the expression of the antioxidant enzyme superoxide dismutase. These data demonstrate that PBMT inhibits hippocampal damage induced by oxidative stress and increases the expression of BDNF, which can be used as an alternative to treat a variety of related disorders that lead to nerve damage. Activation and redox homeostasis in neuronal cells may be a notable mechanism of the 660-nm PBMT-mediated photobioreactivity.
Role of Andaman and Nicobar Islands in eddy formation along western boundary of the Bay of Bengal
Authors: Mukherjee A. , Chatterjee Abhisek , Francis P. A. 
Published: July 2019

AbstractEddies along western boundary of the Bay of Bengal (WBoB) play an important role in regulating regional climate and marine productivity of the north Indian Ocean. In this paper, role of Andaman and Nicobar islands (ANIs) in the formation of eddies along the WBoB is studied using an ocean general circulation model. Our analysis shows that, in the absence of ANIs, there is a significant reduction in the total number of mesoscale eddies in this region. The impact is particularly evident for the cyclonic eddies as a reduction of ~50% can be noticed in the absence of the islands. In contrast, influence of ANIs on anticyclonic eddies is not homogeneous in the WBoB; while absence of ANIs significantly increases anticyclonic eddies in the central part of the WBoB, a decrease can be noticed in the southern part. We further show that the reduction in number of cyclonic eddies along the WBoB is primarily driven by reduced baroclinic and barotropic instabilities. This process is more conspicuous during winter (October–January) season compared to summer (June–September) and spring (February–May) seasons.
Analytical performance of a new automated chemiluminescent magnetic immunoassays for soluble PD-1, PD-L1, and CTLA-4 in human plasma
Authors: Goto Megumi , Chamoto Kenji , Higuchi Keiko , Yamashita Saya , Noda Kenta , Iino Takuya , Miura Masahiro , Yamasaki Toshinari , Ogawa Osamu , Sonobe Makoto , Date Hiroshi , Hamanishi Junzo , Mandai Masaki , Tanaka Yoshimasa , Chikuma Shunsuke , Hatae Ryusuke , Muto Manabu , Minamiguchi Sachiko , Minato Nagahiro , Honjo Tasuku 
Published: July 2019

AbstractCurrent clinically approved biomarkers for the PD-1 blockade cancer immunotherapy are based entirely on the properties of tumour cells. With increasing awareness of clinical responses, more precise biomarkers for the efficacy are required based on immune properties. In particular, expression levels of immune checkpoint-associated molecules such as PD-1, PD-L1, and CTLA-4 would be critical to evaluate the immune state of individuals. Although quantification of their soluble form leased from the membrane will provide quick evaluation of patients’ immune status, available methods such as enzyme-linked immunosorbent assays to measure these soluble factors have limitations in sensitivity and reproducibility for clinical use. To overcome these problems, we developed a rapid and sensitive immunoassay system based on chemiluminescent magnetic technology. The system is fully automated, providing high reproducibility. Application of this system to plasma of patients with several types of tumours demonstrated that soluble PD-1, PD-L1, and CTLA-4 levels were increased compared to those of healthy controls and varied among tumour types. The sensitivity and detection range were sufficient for evaluating plasma concentrations before and after the surgical ablation of cancers. Therefore, our newly developed system shows potential for accurate detection of soluble PD-1, PD-L1, and CTLA-4 levels in the clinical practice.
MMHelper: An automated framework for the analysis of microscopy images acquired with the mother machine
Authors: Smith Ashley , Metz Jeremy , Pagliara Stefano 
Published: July 2019

AbstractLive-cell imaging in microfluidic devices now allows the investigation of cellular heterogeneity within microbial populations. In particular, the mother machine technology developed by Wang et al. has been widely employed to investigate single-cell physiological parameters including gene expression, growth rate, mutagenesis, and response to antibiotics. One of the advantages of the mother machine technology is the ability to generate vast amounts of images; however, the time consuming analysis of these images constitutes a severe bottleneck. Here we overcome this limitation by introducing MMHelper (https://doi.org/10.5281/zenodo.3254394), a publicly available custom software implemented in Python which allows the automated analysis of brightfield or phase contrast, and any associated fluorescence, images of bacteria confined in the mother machine. We show that cell data extracted via MMHelper from tens of thousands of individual cells imaged in brightfield are consistent with results obtained via semi-automated image analysis based on ImageJ. Furthermore, we benchmark our software capability in processing phase contrast images from other laboratories against other publicly available software. We demonstrate that MMHelper has over 90% detection efficiency for brightfield and phase contrast images and provides a new open-source platform for the extraction of single-bacterium data, including cell length, area, and fluorescence intensity.
Neutrophil-derived miR-223 as local biomarker of bacterial peritonitis
Authors: Brook Amy C. , Jenkins Robert H. , Clayton Aled , Kift-Morgan Ann , Raby Anne-Catherine , Shephard Alex P. , Mariotti Barbara , Cuff Simone M. , Bazzoni Flavia , Bowen Timothy , Fraser Donald J. , Eberl Matthias 
Published: July 2019

AbstractInfection remains a major cause of morbidity, mortality and technique failure in patients with end stage kidney failure who receive peritoneal dialysis (PD). Recent research suggests that the early inflammatory response at the site of infection carries diagnostically relevant information, suggesting that organ and pathogen-specific “immune fingerprints” may guide targeted treatment decisions and allow patient stratification and risk prediction at the point of care. Here, we recorded microRNA profiles in the PD effluent of patients presenting with symptoms of acute peritonitis and show that elevated peritoneal miR-223 and reduced miR-31 levels were useful predictors of bacterial infection. Cell culture experiments indicated that miR-223 was predominantly produced by infiltrating immune cells (neutrophils, monocytes), while miR-31 was mainly derived from the local tissue (mesothelial cells, fibroblasts). miR-223 was found to be functionally stabilised in PD effluent from peritonitis patients, with a proportion likely to be incorporated into neutrophil-derived exosomes. Our study demonstrates that microRNAs are useful biomarkers of bacterial infection in PD-related peritonitis and have the potential to contribute to disease-specific immune fingerprints. Exosome-encapsulated microRNAs may have a functional role in intercellular communication between immune cells responding to the infection and the local tissue, to help clear the infection, resolve the inflammation and restore homeostasis.
Reliable and early diagnosis of bacterial blight in pomegranate caused by Xanthomonas axonopodis pv. punicae using sensitive PCR techniques
Authors: Doddaraju Pushpa , Kumar Pavan , Gunnaiah Raghavendra , Gowda Abhishek A. , Lokesh Veeresh , Pujer Parvati , Manjunatha Girigowda 
Published: July 2019

AbstractBacterial blight caused by Xanthomonas axonopodis pv. punicae is a major disease of pomegranate. Bacterial blight drastically reduces the yield and quality of fruits, which are critical for pomegranate production. Precise and early diagnosis of bacterial blight is crucial for active surveillance and effective management of the disease. Symptoms based disease diagnostic methods are labor-intensive, time-consuming and may not detect disease on asymptomatic plants. DNA-based disease diagnostics using polymerase chain reaction (PCR) are reliable, precise, accurate and quick. PCR coupled with agarose gel electrophoresis (PCR-AGE), PCR coupled with capillary electrophoresis (PCR-CE) and real-time PCR (qPCR) were applied for the early and accurate diagnosis of bacterial blight in pomegranate. PCR-CE and qPCR were capable of diagnosing bacterial blight 6 to 10 days before symptom appearance, with detection limits of 100 fg and 10 fg of bacterial DNA respectively. However, conventional PCR-AGE detected pathogen at the onset of disease symptoms with a detection limit of 10 pg of bacterial DNA. qPCR detected bacterial blight in orchards that did not show any disease symptoms. Our data demonstrate that qPCR is more sensitive than other PCR methods along with being reliable for early diagnosis.
Anti-androgenic therapy with finasteride in patients with chronic heart failure - a retrospective propensity score based analysis
Authors: Kattih Badder , Elling Lukas Simon , Weiss Christel , Bea Marieke , Zwadlo Carolin , Bavendiek Udo , Bauersachs Johann , Heineke Joerg 
Published: July 2019

AbstractSex hormones influence the prevalence and the outcome of heart diseases. The conversion of testosterone to its more active metabolite dihydrotestosterone drives cardiac growth and dysfunction, while inhibition of this step by the anti-androgenic drug finasteride counteracts these pathological processes in preclinical models. In this retrospective, observational study, we aim to investigate whether finasteride, which is in clinical use mainly for prostate disease, might ameliorate cardiac hypertrophy and heart failure in patients. Retrospective chart review of 1041 medical cases with heart failure between 1995 and 2015 was conducted. Stratification was performed by concomitant prostate treatment status (tamsulosin versus finasteride). A propensity score analysis yielded a total of 328 matched medical cases without residual differences in the baseline patient characteristics. In this propensity score matched samples, anti-androgenic therapy with finasteride was associated with significantly reduced left ventricular hypertrophy (interventricular septal thickness 13.3 ± 2.4 mm control vs. 12.6 ± 2.1 mm finasteride group (p = 0.029); estimated average treatment effects on the treated: −0.7 mm, 95% CI mean difference −1.3 to −0.1). In this retrospective analysis anti-androgenic therapy with finasteride for prostate disease was associated with attenuated cardiac hypertrophy in patients with heart failure. Therefore, our data encourage further analysis of this approach in larger heart failure patient cohorts.