bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contaminations in (meta)genome data: An open issue for the scientific community
Authors: De Simone Giovanna , Pasquadibisceglie Andrea , Proietto Roberta , Polticelli Fabio , Aime Silvio , J.M. Op den Camp Huub , Ascenzi Paolo 
Published: December 2019

AbstractIn recent years, the high throughput and the low cost of next‐generation sequencing (NGS) technologies have led to an increase of the amount of (meta)genomic data, revolutionizing genomic research studies. However, the quality of sequencing data could be affected by experimental errors derived from defective methods and protocols. This represents a serious problem for the scientific community with a negative impact on the correctness of studies that involve genomic sequence analysis. As a countermeasure, several alignment and taxonomic classification tools have been developed to uncover and correct errors. In this critical review some of these integrated software tools and pipelines used to detect contaminations in reference genome databases and sequenced samples are reported. In particular, case studies of bacterial contaminations, contaminations of human origin, mitochondrial contaminations of ancient DNA, and cross contaminations are examined.
In utero and lactational exposure to triclocarban: reproductive effects on female rat offspring
Authors: Costa Nathália Orlandini , Borges Lorena Ireno , Cavalcanti Liara Freitas , Montagnini Bruno Garcia , Anselmo Franci Janete Aparecida , Kiss Ana Carolina Inhasz , Gerardin Daniela Cristina Ceccatto 
Published: December 2019

AbstractTriclocarban (TCC) is an antimicrobial compound widely used in personal care products such as soaps, toothpaste, and shampoo. This agent is incompletely removed by wastewater treatment and represents an environmental contaminant. Recent studies have shown that TCC is associated with some endocrine disruptions. The aim of the present study was to evaluate if TCC exposure during critical periods of development (gestation and lactation) could lead to adverse effects on reproductive and behavior parameters of female offspring. Pregnant female Wistar rats were divided into four groups (n = 8–11/group): Control; TCC 0.3 mg/kg (TCC 0.3); TCC 1.5 mg/kg; TCC 3.0 mg/kg (TCC 3.0); and treated daily by oral gavage from gestational day 0 to lactational day 21. The female pups (F1 generation) were weaned on post‐natal day 21 and included in the study. No litter‐mates were used for the same group. There was a decrease in estradiol levels in the TCC 0.3 and TCC 3.0 groups. Moreover, there was a decrease in progesterone levels and an increase in pre‐implantation loss in the TCC 3.0 group in adulthood. It is suggested, in this study, that the decrease in progesterone biosynthesis could interfere with implantation process. The exposure window to TCC is an important factor, as we found alterations only in the offspring.
Chitinous polymers: extraction from fungal sources, characterization and processing towards value‐added applications
Authors: Araújo Diana , Ferreira Inês C , Torres Cristiana AV , Neves Luísa , Freitas Filomena 
Published: December 2019

AbstractChitin, chitosan and their complexes with β‐glucan (chitin–glucan complex, CGC, and chitosan–glucan complex, ChGC) are value‐added polysaccharides extracted from the cell‐walls of many fungi. Commercial chitin and its deacetylated form, chitosan, are currently obtained from marine waste material, mostly animal sources (crustaceans and marine invertebrates), through harsh chemical procedures that have low reproducibility due to the variability of the composition of the sources and their seasonal character. These disadvantages are overcome by using fungi as sources of chitinous polymers. The extraction of chitin/chitosan from fungi cell‐walls has the great advantage of yielding products with stable composition and properties, using simpler procedures, with the added benefit of also generating CGC and ChGC, two copolymers that combine the proven properties of chitin/chitosan with those of β‐glucans. Over the last decades, fungal chitinous polymers have been the focus of extensive research that included optimization of the cultivation conditions of a wide range of species and the development of optimized extraction, purification and characterization techniques, as well as the demonstration of the biopolymers' biological properties, which include immunomodulatory, anticancer, antioxidant and antimicrobial activity. Given these properties, several attempts were made to develop applications for them in areas ranging from biomedicine and pharmaceuticals to food and agriculture. Despite their wide range of proven functional properties that include the ability to form different polymeric structures, as well as biological activity, fungal chitinous biopolymers are still underexplored. Nevertheless, these biopolymers hold great potential for development into valuable products or applications that are surely worth further investigation. © 2019 Society of Chemical Industry
Sonographic appearances of retained surgical sponges in the abdomen and pelvis
Authors: Li Qiu Yang , Wang Long Xia , An Ning Yu , Xu Hong 
Published: December 2019

AbstractPurposeTo describe the sonographic (ultrasound—US) features of retained surgical sponges (RSSs) and compare them with the pathological findings.MethodsUltrasound features of RSSs in nine patients (seven women and two men) identified between June 1996 and July 2015 were retrospectively analyzed. Patient characteristics including gender and age, location of the sponge, time interval until diagnosis, clinical presentation, and patient complaints were evaluated.ResultsThe US appearances of RSSs could be classified into three types. Type I (five cases): an echogenic arc with a strong posterior shadow; type II (two cases): US appearance mimicked a cystic teratoma; type III (two cases): a cystic mass with zigzag‐shaped internal contents. CT and/or MRI showed a mass with density/signal intensity similar to that of the adjacent soft tissues.ConclusionThe characteristic US findings along with a history of surgery can help reach a correct diagnosis of RSS.
Rainbow saturation of graphs
Authors: Girão António , Lewis David , Popielarz Kamil 
Published: December 2019

AbstractIn this paper, we study the following problem proposed by Barrus, Ferrara, Vandenbussche, and Wenger. Given a graph and an integer , what is , the minimum number of edges in a ‐edge‐colored graph on vertices such that does not contain a rainbow copy of , but adding to a new edge in any color from creates a rainbow copy of ? Here, we completely characterize the growth rates of as a function of , for any graph belonging to a large class of connected graphs and for any . This classification includes all connected graphs of minimum degree 2. In particular, we prove that , for any and , thus resolving a conjecture of Barrus, Ferrara, Vandenbussche, and Wenger. We also pose several new problems and conjectures.
Preliminary investigation on the molecular mechanisms underlying the correlation between VDR‐FokI genotype and periodontitis
Authors: Liu Kaining , Han Bing , Hou Jianxia , Meng Huanxin 
Published: December 2019

AbstractBackgroundThe only polymorphism that could change the protein structure in vitamin D receptor (VDR) is the FokI polymorphism (rs2228570). The FF genotype has the strongest transcriptional activity of VDR and is correlated with higher susceptibility to periodontitis. To reveal the possible molecular mechanisms for the correlation preliminarily, the influence of VDR‐FokI genotype on the expression of osteoprotegerin (OPG) and receptor activator of nuclear factor kappa B ligand (RANKL) in human gingival fibroblasts (hGFs) and human periodontal ligament cells (hPDLCs) was investigated in this study.MethodshGFs and hPDLCs from 15 donors (five FF, seven Ff, and three ff) were treated with 1,25OH2D3, with or without the specific knockdown of VDR using siRNA. The mRNA and protein expression of OPG and RANKL were detected using real‐time PCR and enzyme‐linked immunosorbent assay, respectively.ResultsBoth in hGFs and hPDLCs, 1,25OH2D3 could significantly induce the mRNA and protein expression of RANKL, and FF genotype had significantly higher induction than the other genotypes, however, neither 1,25OH2D3 nor VDR‐FokI had significant influence on the OPG expression. As a result, the RANKL/OPG ratio was significantly elevated under 1,25OH2D3 stimulation and FF genotype had the most remarkable elevation. When VDR was knocked down, all the differences among the three genotypes disappeared.ConclusionThe strongest transcriptional activity of FF genotype might contribute to the strongest enhancement of RANKL expression and RANKL/OPG ratio in hGFs and hPDLCs stimulated by 1,25OH2D3, which might help to reveal the mechanisms of the correlation between FF genotype and susceptibility to periodontitis.
Effect of urease and nitrification inhibitors on ammonia volatilization and abundance of N‐cycling genes in an agricultural soil
Authors: Castellano-Hinojosa Antonio , González-López Jesús , Vallejo Antonio , Bedmar Eulogio J. 
Published: December 2019

AbstractThe effect of the combined application of urease and nitrification inhibitors on ammonia volatilization and the abundance of nitrifier and denitrifier communities is largely unknown. Here, in a mesocosm experiment, ammonia volatilization was monitored in an agricultural soil treated with urea and either or both of the urease inhibitor N‐(n‐butyl) thiophosphoric triamide (NBPT) and the nitrification inhibitor 3,4‐dimethylpyrazole phosphate (DMPP), with 50% and 80% water‐filled pore space (WFPS). The effect of the treatments on the abundance of bacteria and archaea was estimated by quantitative PCR (qPCR) amplification of their respective 16S rRNA gene, that of nitrifiers using amoA genes, and that of denitrifiers by qPCR of the norB and nosZI denitrification genes. After application of urea, N losses due to NH3 volatilization accounted for 23.0% and 9.2% at 50% and 80% WFPS, respectively. NBPT reduced NH3 volatilization to 2.0% and 2.4%, whereas DMPP increased N losses by up to 36.8% and 26.0% at 50% and 80% WFPS, respectively. The combined application of NBPT and DMPP also increased NH3 emissions, albeit to a lesser extent than DMPP alone. As compared with unfertilized control soil, both at 50% and 80% WFPS, NBPT strongly affected the abundance of bacteria and archaea, but not that of nitrifiers, and decreased that of denitrifiers at 80% WFPS. Regardless of moisture conditions, treatment with DMPP increased the abundance of denitrifiers. DMPP, both in single and in combined application with NBPT, increased the abundance of nitrification and denitrification genes.
Is N‐feedback involved in the regulation of nitrogenase activity in Medicago truncatula?
Authors: Sulieman Saad , Schulze Joachim , Mühling Karl H. , Tran Lam-Son Phan 
Published: December 2019

AbstractTo determine whether senescing leaves provoke an active nitrogen (N) remobilization that results in the reduction of nitrogenase activity, 60% of Medicago truncatula lower leaves were either darkened or individually excised for two weeks. Although a considerable amount of N was remobilized, N2 fixation activity was found to be increased to maintain the N source/sink balance, indicating an absence of the negative N‐feedback regulation of nitrogenase activity in the senescing M. truncatula.
Soluble levels of sCD40L and s4‐1BB are associated with a poor prognosis in elderly patients with colorectal cancer
Authors: Lima Petrus M. A. , Torres Leuridan C. , Martins Mário R. , da Matta Marina C. , Lima Jurema T. O. , de Mello Maria J. G. , da Silva Luciana M. , Cintra Evandro B. , Lira Clara C. R. , da Fonte Eduardo J. A. , Forones Nora M. 
Published: December 2019

AbstractBackground and ObjectivesThe prognosis of colorectal cancer (CRC) has improved in the last decades, however, a lower overall survival persists in the elderly. The understanding of immunity changes in the elderly with CRC will allow the emergence of new treatments with higher response rates. 4‐1BB and CD40L, an immune checkpoint stimulator, play an important role in T‐cell responses and platelets. Our aim was to characterize the soluble levels of CD40L and 4‐1BB in CRC elderly patients.MethodsA cross‐sectional study was performed in 41 patients with CRC and 35 healthy elderly controls. Patients with CRC were divided into three groups according to staging: 13 patients with advanced tumor restricted to the organ (stages II); 16 patients with lymph node metastasis (stage III); and 12 patients with distant metastasis (stage IV).ResultsThere were higher levels of soluble s4‐1BB and sCD40L in CRC elderly stage II patients when compared with healthy controls (P = .0009 and P < .0001, respectively), stage III patients (P = .008 and P < .0001, respectively) and stage IV patients (P = .007 and P < .0001, respectively).ConclusionsWe concluded that sCD40L and s4‐1BB molecules may be prognostic biomarkers, since the reduction in plasma levels of these molecules was associated with disease progression.
A metabolomics strategy for authentication of plant medicines with multiple botanical origins, a case study of Uncariae Rammulus Cum Uncis
Authors: Pan Huiqin , Yao Changliang , Yao Shuai , Yang Wenzhi , Wu Wanying , Guo Dean 
Published: December 2019

AbstractSource authentication of herbal medicines was essential for ensuring their safety, efficacy and quality consistency, especially those with multiple botanical origins. This study proposed a metabolomics strategy for species discrimination and source recognition. Uncariae Rammulus Cum Uncis, officially stipulating the stems with hooks of five Uncaria species as its origins, was taken as a case study. Firstly, an untargeted MSE method was developed by ultra‐high performance liquid chromatography hyphenated with quadrupole time‐of‐flight mass spectrometry for global metabolite characterization. Subsequently, data pretreatment was conducted by using Progenesis QI software and screening rules. The obtained metabolite features were defined as variables for statistical analyses. Principal component analysis and chemical fingerprinting spectra suggested that five official species were differentiated from each other except for Uncaria hirsuta and Uncaria sinensis. Furthermore, orthogonal partial least squares discrimination analysis was performed to discriminate confused two species, and resulted in the discovery of nine contributing markers. Ultimately, a Support Vector Machine model was developed to recognize five species and predict origins of commercial materials. The study demonstrated that the developed strategy was effective in discrimination and recognition of confused species, and promising in tracking botanical origins of commercial materials.
Assessment of land levelling effects on lowland soil quality indicators and water retention evaluated by multivariate and geostatistical analyses
Authors: Timm Luís Carlos , Pires Luiz Fernando , Centeno Luana Nunes , Bitencourt Dioni Glei Bonini , Parfitt José Maria Barbat , de Campos Alexssandra Dayanne Soares 
Published: December 2019

AbstractStudies focusing on the impact of levelling on the management of available water for rice growth and on soil hydro‐physical quality indicators cultivated in lowland soils under aerobic conditions are still scarce. The objective of this study was to evaluate the levelling impact on soil water retention and soil quality indicators by multivariate and geostatistical analyses. A 10 × 10 m grid was used to sample the 0‐ to 20‐cm layer in a 1.0‐ha experimental field, before and after levelling. Sand and clay contents, macroporosity, bulk density (Bd), organic matter (OM), weighted average diameter of aggregates, and the water retention curve were measured. Available water capacity, structural stability, and S indexes and relative field capacity were calculated. Descriptive statistics, Kolmogorov–Smirnov test, and geostatistical analysis were used. Maps of all data sets significantly correlated with Bd and OM after levelling were constructed using ordinary and indicator kriging. Kaiser–Meyer–Olkin and Bartlett tests were performed for factorial and principal component analyses which were used to reduce the dimensionality of data and of main principal component maps. Levelling negatively affected the majority of soil quality indicators, caused an increase of their spatial range, and an improved the goodness of fit of the semivariogram models used. The majority of variables were best fitted by the Gaussian model after levelling. Bd and OM probability maps were found to be useful tools for farmers wanting to utilize different strategies for topsoil management, with the goal of improving soil quality of levelled areas for future land recuperation operations.
Length-Based Assessment of an Artisanal Albulid Fishery in the South Pacific: a Data-Limited Approach for Management and Conservation
Authors: Filous Alexander , Lennox Robert J. , Clua Eric E. G. , Cooke Steven J. , Danylchuk Andy J. 
Published: December 2019

Abstract
Data-limited fisheries assessment methods have great potential to help inform small island communities on the status of their fisheries resources. In this paper, we provide a length-based assessment of an artisanal fishery that primarily targets spawning aggregations of Shortjaw Bonefish Albula glossodonta at Anaa Atoll in the Tuamotu Archipelago of French Polynesia. We assessed the length-frequency distribution of the spawning stock across a 3-year period (2016–2018). During this time, male and female Shortjaw Bonefish were fully recruited to the fishery at age 4 and age 5, respectively. Fishing mortality was over two times the range of natural mortality for this species (i.e., 0.21–0.32), and based on these estimates of natural mortality, the annual spawning potential ratio of the population was between 7% and 20% across the sampling years. The majority of the catch was sexually mature, with 78, 95, and 95% of the annual female catch in 2016, 2017, and 2018, respectively, being equal to or greater than the length of first maturity (i.e., 48 cm FL). However, every fisheries indicator and biological reference point suggested that the fishery was overexploited and in need of management intervention. To this aim, the community of Anaa (1) established an Educational Managed Marine Area, which overlaps with the Shortjaw Bonefish migratory corridor adjacent to Tukuhora village and (2) instated a temporal rahui (a traditional conservation method) inside the Educational Managed Marine Area during the peak months of the spawning season.
Assessing Polyunsaturated Fatty Acid Essentiality in Florida Pompano
Authors: Jackson Christopher J , Trushenski Jesse T , Schwarz Michael H 
Published: December 2019

Abstract
We evaluated the growth performance and fatty acid composition of juvenile Florida Pompano Trachinotus carolinus that were fed diets containing different combinations of n-3 and n-6 polyunsaturated fatty acids (PUFAs) to assess the relative importance of C18 PUFAs and long-chain (LC) PUFAs in meeting the essential fatty acid requirements of this species. Juvenile fish (mean ± SD =47.4 ± 0.6 g/fish) were fed diets containing different combinations of n-3 and n-6 PUFAs: a positive control containing menhaden fish oil, a negative control containing hydrogenated soybean oil, and experimental diets containing hydrogenated soybean oil amended with ethyl esters of 18:3(n-3); 18:3(n-3) and 18:2(n-6); 22:6(n-3); 22:6(n-3) and 20:4(n-6); or 20:5(n-3), 22:6(n-3), and 20:4(n-6). After 7 weeks, weight gain, feed conversion ratio, and specific growth rate were significantly greater among fish that were fed the positive control feed in comparison with those that received the negative control feed. The addition of n-3 and/or n-6 PUFAs to the negative control formulation did not significantly improve performance in any case, although numeric improvements observed for weight gain and feed conversion ratio appeared to suggest some advantage from providing a complement of both n-3 and n-6 LC-PUFAs in the diet. Fatty acid composition varied significantly between all tissues, generally reflecting dietary fatty acid profiles. Tissue fatty acid profiles suggest that Florida Pompano have some ability to elongate and desaturate fatty acids and may be able to survive on diets containing C18 PUFAs, but they perform optimally when provided with LC-PUFAs directly.
Failure to rescue and 30‐day in‐hospital mortality in hospitals with and without crew‐resource‐management safety training
Authors: Bacon Cynthia T. , McCoy Thomas P. , Henshaw Daryl S. 
Published: December 2019

AbstractFailure to rescue (FTR) occurs when a clinician is unable to save a hospitalized patient's life when they experience a complication that was not present on admission. Research suggests that a focus on patient safety, including implementing airline‐industry‐based‐crew‐resource management (CRM) training, can improve patient outcomes, however, the effects of CRM on FTR are unknown. This study examined FTR and 30‐day in‐hospital mortality (IM) outcomes in two hospitals to determine if differences existed in the treatment hospital (received CRM training) and the comparison hospital (did not receive CRM training). Researchers expected there would be lower rates of FTR and IM in the treatment hospital than the comparison hospital. The study utilized a matched two‐group comparison, cross‐sectional quasi‐experimental design. Over 10,000 patients (n = 10,823) comprised the study with 1,764 having at least one FTR complication. Adjusted odds of FTR were 2.9% higher for treatment versus comparison but these results did not reach significance. The adjusted odds of IM were 0.4% higher for treatment versus comparison but not significantly higher. Although the reasons for our findings remain unclear, previous researchers also found that CRM training improved staff outcomes but unexpectedly did not improve patient outcomes. CRM training may best be used to target changes in staff behaviors and improvement in staff outcomes. Refresher CRM training may be needed to prevent drifting back into longstanding behaviors. Reductions in FTR and patients with IM outcomes may require more comprehensive, multipronged interventions in addition to CRM training.