bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel DNA methylation biomarkers show high sensitivity and specificity for blood-based detection of colorectal cancer—a clinical biomarker discovery and validation study
Authors: Jensen Sarah Østrup , Øgaard Nadia , Ørntoft Mai-Britt Worm , Rasmussen Mads Heilskov , Bramsen Jesper Bertram , Kristensen Helle , Mouritzen Peter , Madsen Mogens Rørbæk , Madsen Anders Husted , Sunesen Kåre Gotschalck , Iversen Lene Hjerrild , Laurberg Søren , Christensen Ib Jarle , Nielsen Hans Jørgen , Andersen Claus Lindbjerg 
Published: November 2019

Abstract
Background
Early detection plays an essential role to reduce colorectal cancer (CRC) mortality. While current screening methods suffer from poor compliance, liquid biopsy-based strategies for cancer detection is rapidly gaining promise. Here, we describe the development of TriMeth, a minimal-invasive blood-based test for detection of early-stage colorectal cancer. The test is based on assessment of three tumour-specific DNA methylation markers in circulating cell-free DNA.

Results
A thorough multi-step biomarker discovery study based on DNA methylation profiles of more than 5000 tumours and blood cell populations identified CRC-specific DNA methylation markers. The DNA methylation patterns of biomarker candidates were validated by bisulfite sequencing and methylation-specific droplet digital PCR in CRC tumour tissue and peripheral blood leucocytes. The three best performing markers were first applied to plasma from 113 primarily early-stage CRC patients and 87 age- and gender-matched colonoscopy-verified controls. Based on this, the test scoring algorithm was locked, and then TriMeth was validated in an independent cohort comprising 143 CRC patients and 91 controls. Three DNA methylation markers, C9orf50, KCNQ5, and CLIP4, were identified, each capable of discriminating plasma from colorectal cancer patients and healthy individuals (areas under the curve 0.86, 0.91, and 0.88). When combined in the TriMeth test, an average sensitivity of 85% (218/256) was observed (stage I: 80% (33/41), stage II: 85% (121/143), stage III: 89% (49/55), and stage IV: 88% (15/17)) at 99% (176/178) specificity in two independent plasma cohorts.

Conclusion
TriMeth enables detection of early-stage colorectal cancer with high sensitivity and specificity. The reported results underline the potential utility of DNA methylation-based detection of circulating tumour DNA in the clinical management of colorectal cancer.
Giant parathyroid adenoma: a case report and review of the literature
Authors: Al-Hassan Mohamed S. , Mekhaimar Menatalla , El Ansari Walid , Darweesh Adham , Abdelaal Abdelrahman 
Published: November 2019

Abstract
Background
Giant parathyroid adenoma is a rare type of parathyroid adenoma defined as weighing > 3.5 g. They present as primary hyperparathyroidism but with more elevated laboratory findings and more severe clinical presentations due to the larger tissue mass. This is the first reported case of giant parathyroid adenoma from the Middle East.

Case presentation
A 52-year-old Indian woman presented with a palpable right-sided neck mass and generalized fatigue. Investigations revealed hypercalcemia with elevated parathyroid hormone and an asymptomatic kidney stone. Ultrasound showed a complex nodule with solid and cystic components, and Sestamibi nuclear scan confirmed a giant parathyroid adenoma. Focused surgical neck exploration was done and a giant parathyroid adenoma weighing 7.7 gm was excised.

Conclusions
Giant parathyroid adenoma is a rare cause of primary hyperparathyroidism and usually presents symptomatically with high calcium and parathyroid hormone levels. Giant parathyroid adenoma is diagnosed by imaging and laboratory studies. Management is typically surgical, aiming at complete resection. Patients usually recover with no long-term complications or recurrence.
Greedy low-rank algorithm for spatial connectome regression
Authors: Kürschner Patrick , Dolgov Sergey , Harris Kameron Decker , Benner Peter 
Published: November 2019

AbstractRecovering brain connectivity from tract tracing data is an important computational problem in the neurosciences. Mesoscopic connectome reconstruction was previously formulated as a structured matrix regression problem (Harris et al. in Neural Information Processing Systems, 2016), but existing techniques do not scale to the whole-brain setting. The corresponding matrix equation is challenging to solve due to large scale, ill-conditioning, and a general form that lacks a convergent splitting. We propose a greedy low-rank algorithm for the connectome reconstruction problem in very high dimensions. The algorithm approximates the solution by a sequence of rank-one updates which exploit the sparse and positive definite problem structure. This algorithm was described previously (Kressner and Sirković in Numer Lin Alg Appl 22(3):564–583, 2015) but never implemented for this connectome problem, leading to a number of challenges. We have had to design judicious stopping criteria and employ efficient solvers for the three main sub-problems of the algorithm, including an efficient GPU implementation that alleviates the main bottleneck for large datasets. The performance of the method is evaluated on three examples: an artificial “toy” dataset and two whole-cortex instances using data from the Allen Mouse Brain Connectivity Atlas. We find that the method is significantly faster than previous methods and that moderate ranks offer a good approximation. This speedup allows for the estimation of increasingly large-scale connectomes across taxa as these data become available from tracing experiments. The data and code are available online.
Optimization of agro-residues as substrates for Pleurotus pulmonarius production
Authors: Wu Nan , Tian Fenghua , Moodley Odeshnee , Song Bing , Jia Chuanwen , Ye Jianqiang , Lv Ruina , Qin Zhi , Li Changtian 
Published: November 2019

AbstractThe “replacing wood by grass” project can partially resolve the conflict between mushroom production and balancing the ecosystem, while promoting agricultural economic sustainability.Pleurotus pulmonariusis an economically important edible and medicinal mushroom, which is traditionally produced using a substrate consisting of sawdust and cottonseed hulls, supplemented with wheat bran. A simplex lattice design was applied to systemically optimize the cultivation ofP. pulmonariususing agro-residues as the main substrate to replace sawdust and cottonseed hulls. The effects of differing amounts of wheat straw, corn straw, and soybean straw on the variables of yield, mycelial growth rate, stipe length, pileus length, pileus width, and time to harvest were demonstrated. Results indicated that a mix of wheat straw, corn straw, and soybean straw may have significantly positive effects on each of these variables. The high yield comprehensive formula was then optimized to include 40.4% wheat straw, 20.3% corn straw, 18.3% soybean straw, combined with 20.0% wheat bran, and 1.0% light CaCO3(C/N = 42.50). The biological efficiency was 15.2% greater than that of the control. Most encouraging was the indication that the high yield comprehensive formula may shorten the time to reach the reproductive stage by 6 days, compared with the control. Based on the results of this study, agro-residues may be used as a suitable substitution for sawdust and cottonseed hulls as the main cultivation substrates ofP. pulmonarius. These results provide a theoretical basis for the “replacing wood by grass” project on edible mushroom cultivation.
Development of a multiplex PCR assay for the simultaneous and rapid detection of six pathogenic bacteria in poultry
Authors: Wang Zhihao , Zuo Jiakun , Gong Jiansen , Hu Jiangang , Jiang Wei , Mi Rongsheng , Huang Yan , Chen Zhaoguo , Phouthapane Vanhnaseng , Qi Kezong , Wang Chen , Han Xiangan 
Published: November 2019

AbstractEscherichia coli, Pasteurella multocida, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella spp. and Staphylococcus aureus are six bacterial pathogens of avian. However, these pathogens may cause many similar pathological changes, resulting in clinical isolates that are difficult to quickly and simultaneously detect and identify. Here, a multiplex polymerase chain reaction (m-PCR) assay is reported to rapidly identify targets genes (phoA, KMT1, ureR, toxA, invA, and nuc) of these six pathogens in clinical samples. Six pairs of specific primers were designed. The optimal reaction conditions, specificity, and sensitivity of the m-PCR assay were investigated. The results showed that betaine remarkably improved amplification of the target genes. Specific test results showed that all six pathogens were detected by the proposed m-PCR protocol without cross-amplification with viruses or parasites. Sensitivity test results showed that the m-PCR system could amplify the six target genes from bacterial genomes or cultures with template amounts of 500 pg or 2.8–8.6 × 103 colony forming units, respectively. Furthermore, the six bacterial pathogens isolated from the infected tissue samples were successfully identified. The proposed m-PCR assay is a useful tool to monitor and diagnose bacterial infection in birds with high specificity, sensitivity and throughput.
Some Opial-type integral inequalities via $(p,q)$-calculus
Authors: Nasiruzzaman Md. , Mukheimer Aiman , Mursaleen M. 
Published: November 2019

AbstractIn this paper, we introduce a new Opial-type inequality by using$(p,q)$(p,q)-calculus and establish some integral inequalities. We find a$(p,q)$(p,q)-generalization of a Steffensens-type integral inequality and some other inequalities.
On statistical convergence and strong Cesàro convergence by moduli
Authors: León-Saavedra Fernando , Listán-García M. del Carmen , Pérez Fernández Francisco Javier , Romero de la Rosa María Pilar 
Published: November 2019

AbstractIn this paper we will establish a result by Connor, Khan and Orhan (Analysis 8:47–63, 1988; Publ. Math. (Debr.) 76:77–88, 2010) in the framework of the statistical convergence and the strong Cesàro convergence defined by a modulus functionf. Namely, for every modulus functionf, we will prove that af-strongly Cesàro convergent sequence is alwaysf-statistically convergent and uniformly integrable. The converse of this result is not true even for bounded sequences. We will characterize analytically the modulus functionsffor which the converse is true. We will prove that these modulus functions are those for which the statistically convergent sequences aref-statistically convergent, that is, we show that Connor–Khan–Orhan’s result is sharp in this sense.
Oscillatory behavior of a second order nonlinear advanced differential equation with mixed neutral terms
Authors: Shi Hongwei , Bai Yuzhen 
Published: November 2019

AbstractIn this paper, we present several new oscillation criteria for a second order nonlinear differential equation with mixed neutral terms of the form
$$ \bigl(r(t) \bigl(z'(t)\bigr)^{\alpha }\bigr)'+q(t)x^{\beta } \bigl(\sigma (t)\bigr)=0,\quad t\geq t_{0}, $$(r(t)(z′(t))α)′+q(t)xβ(σ(t))=0,t≥t0, where $z(t)=x(t)+p_{1}(t)x(\tau (t))+p_{2}(t)x(\lambda (t))$z(t)=x(t)+p1(t)x(τ(t))+p2(t)x(λ(t)) and α, β are ratios of two positive odd integers. Our results improve and complement some well-known results which were published recently in the literature. Two examples are given to illustrate the efficiency of our results.
Lucas polynomials semi-analytic solution for fractional multi-term initial value problems
Authors: Mokhtar Mahmoud M. , Mohamed Amany S. 
Published: November 2019

AbstractHerein, we use the generalized Lucas polynomials to find an approximate numerical solution for fractional initial value problems (FIVPs). The method depends on the operational matrices for fractional differentiation and integration of generalized Lucas polynomials in the Caputo sense. We obtain these solutions using tau and collocation methods. We apply these methods by transforming the FIVP into systems of algebraic equations. The convergence and error analyses are discussed in detail. The applicability and efficiency of the method are tested and verified through numerical examples.
Occurrence and expression of genes encoding methyl-compound production in rumen bacteria
Authors: Kelly William J. , Leahy Sinead C. , Kamke Janine , Soni Priya , Koike Satoshi , Mackie Roderick , Seshadri Rekha , Cook Gregory M. , Morales Sergio E. , Greening Chris , Attwood Graeme T. 
Published: November 2019

Abstract
Background
Digestive processes in the rumen lead to the release of methyl-compounds, mainly methanol and methylamines, which are used by methyltrophic methanogens to form methane, an important agricultural greenhouse gas. Methylamines are produced from plant phosphatidylcholine degradation, by choline trimethylamine lyase, while methanol comes from demethoxylation of dietary pectins via pectin methylesterase activity. We have screened rumen metagenomic and metatranscriptomic datasets, metagenome assembled genomes, and the Hungate1000 genomes to identify organisms capable of producing methyl-compounds. We also describe the enrichment of pectin-degrading and methane-forming microbes from sheep rumen contents and the analysis of their genomes via metagenomic assembly.

Results
Screens of metagenomic data using the protein domains of choline trimethylamine lyase (CutC), and activator protein (CutD) found good matches only to Olsenella umbonata and to Caecibacter, while the Hungate1000 genomes and metagenome assembled genomes from the cattle rumen found bacteria within the phyla Actinobacteria, Firmicutes and Proteobacteria. The cutC and cutD genes clustered with genes that encode structural components of bacterial microcompartment proteins. Prevotella was the dominant genus encoding pectin methyl esterases, with smaller numbers of sequences identified from other fibre-degrading rumen bacteria. Some large pectin methyl esterases (> 2100 aa) were found to be encoded in Butyrivibrio genomes. The pectin-utilising, methane-producing consortium was composed of (i) a putative pectin-degrading bacterium (phylum Tenericutes, class Mollicutes), (ii) a galacturonate-using Sphaerochaeta sp. predicted to produce acetate, lactate, and ethanol, and (iii) a methylotrophic methanogen, Methanosphaera sp., with the ability to form methane via a primary ethanol-dependent, hydrogen-independent, methanogenesis pathway.

Conclusions
The main bacteria that produce methyl-compounds have been identified in ruminants. Their enzymatic activities can now be targeted with the aim of finding ways to reduce the supply of methyl-compound substrates to methanogens, and thereby limit methylotrophic methanogenesis in the rumen.
Factors During a Child’s Illness Are Associated With Levels of Prolonged Grief Symptoms in Bereaved Mothers and Fathers
Authors: Pohlkamp Lilian , Kreicbergs Ulrika , Sveen Josefin 
Published: November 2019

PURPOSE Previous research shows that bereaved parents are at an increased risk for intense and prolonged grief responses. To offer effective support to parents during a child’s cancer treatment and after their child’s death, more knowledge is needed about factors related to the child’s illness trajectory that may contribute to prolonged grief in bereaved parents and about possible sex differences related to such factors. Therefore, we examined possible contributing factors associated with prolonged grief in cancer-bereaved mothers and fathers 1 to 5 years after their child died of cancer. METHODS We studied data from a population-based nationwide survey, including 133 mothers and 92 fathers who had lost a child to cancer 1 to 5 years earlier, using univariable and multiple regression analyses to assess the associations between prolonged grief and possible contributing variables. RESULTS The variables associated with lower levels of prolonged grief symptoms for mothers were being able to talk about feelings within the family ( P = .00) and trusting that health care professionals made every possible effort to cure the child ( P = .01). The statistically significantly associated variables for fathers were having said farewell to the deceased child in the way they wanted ( P = .00) and feeling that they had received practical support from health care professionals during the child’s illness trajectory ( P = .01). CONCLUSION We found factors during the illness of children with cancer that contributed to prolonged grief for parents; these were different for mothers and fathers. The results may have implications for design of family bereavement support within pediatric oncology care, including addressing the differing needs of mothers and fathers more effectively.
International Waist Circumference Percentile Cutoffs for Central Obesity in Children and Adolescents Aged 6 to 18 Years
Authors: Xi Bo , Zong Xin’nan , Kelishadi Roya , Litwin Mieczysław , Hong Young Mi , Poh Bee Koon , Steffen Lyn M , Galcheva Sonya V , Herter-Aeberli Isabelle , Nawarycz Tadeusz , Krzywińska-Wiewiorowska Małgorzata , Khadilkar Anuradha , Schmidt Michael D , Neuhauser Hannelore , Schienkiewitz Anja , Kułaga Zbigniew , Kim Hae Soon , Stawińska-Witoszyńska Barbara , Motlagh Mohammad Esmaeil , Ruzita Abd Talib , Iotova Violeta M , Grajda Aneta , Ismail Mohd Noor , Krzyżaniak Alicja , Heshmat Ramin , Stratev Velin , Różdżyńska-Świątkowska Agnieszka , Ardalan Gelayol , Qorbani Mostafa , Świąder-Leśniak Anna , Ostrowska-Nawarycz Lidia , Yotov Yoto , Ekbote Veena , Khadilkar Vaman , Venn Alison J , Dwyer Terence , Zhao Min , Magnussen Costan G , Bovet Pascal 
Published: November 2019

Abstract

Context
No universal waist circumference (WC) percentile cutoffs used have been proposed for screening central obesity in children and adolescents.

Objective
To develop international WC percentile cutoffs for children and adolescents with normal weight based on data from 8 countries in different global regions and to examine the relation with cardiovascular risk.

Design and Setting
We used pooled data on WC in 113,453 children and adolescents (males 50.2%) aged 4 to 20 years from 8 countries in different regions (Bulgaria, China, Iran, Korea, Malaysia, Poland, Seychelles, and Switzerland). We calculated WC percentile cutoffs in samples including or excluding children with obesity, overweight, or underweight. WC percentiles were generated using the general additive model for location, scale, and shape (GAMLSS). We also estimated the predictive power of the WC 90th percentile cutoffs to predict cardiovascular risk using receiver operator characteristics curve analysis based on data from 3 countries that had available data (China, Iran, and Korea). We also examined which WC percentiles linked with WC cutoffs for central obesity in adults (at age of 18 years).

Main Outcome Measure
WC measured based on recommendation by the World Health Organization.

Results
We validated the performance of the age- and sex-specific 90th percentile WC cutoffs calculated in children and adolescents (6-18 years of age) with normal weight (excluding youth with obesity, overweight, or underweight) by linking the percentile with cardiovascular risk (area under the curve [AUC]: 0.69 for boys; 0.63 for girls). In addition, WC percentile among normal weight children linked relatively well with established WC cutoffs for central obesity in adults (eg, AUC in US adolescents: 0.71 for boys; 0.68 for girls).

Conclusion
The international WC cutoffs developed in this study could be useful to screen central obesity in children and adolescents aged 6 to 18 years and allow direct comparison of WC distributions between populations and over time.
Orientation Order of Nonelectrically Poled FTC-Type Chromophores in PMMA on SiO2 Surfaces
Authors: Sugita Atsushi , Tsuruoka Miwa , Kinoshita Yuta , Futagami Yushi , Yoshimura Tomoyuki , Matsuo Jun-ichi 
Published: November 2019

Abstract
We present the orientation order of push-pull chromophores consisting of phenyl vinylene thiophene vinylene (FTC) bridges between the N,-N-bis-(2-hydroxyethyl)-amine electron donor and phenyl-trifluoromethyl-tricyanofuran (TCF-Ph-CF3) acceptor in poly (methyl methacrylate) (PMMA). The chromophores have attracted great attention as a guest material for nonlinear optical polymers for near-IR applications. Our experimental results demonstrated that the chromophores with relatively large molecular weights were oriented in a polar order with the aid of adsorption onto the surfaces of the SiO2 substrates, even without the conventional electrical poling procedure. The polar order of the chromophores extended approximately 50 nm vertically from the substrate surfaces. Polarized linear absorption and second harmonic generation spectroscopies were performed to determine the orientation distribution function of the chromophores in the PMMA. The average molecular tilt angle Θ, indicating the degree of the orientation order, was wider than the magic angle, and the chromophores were preferably oriented horizontally to the substrate surfaces. A relatively low orientation order was explained in terms of the strong dipole-dipole repulsions among the neighboring guest chromophores.
Method comparison of four clinically available assays for serum free light chain analysis
Authors: Fleming Chérina K.A. , Swarttouw Tim , de Kat Angelino Corrie M. , Jacobs Joannes F.M. , Russcher Henk 
Published: November 2019

Abstract

Background
Serum free light chain (sFLC) measurements are increasingly important in the context of screening for monoclonal gammopathies, prognostic stratification and monitoring of therapy responses. In this study we have performed a method comparison of four sFLC assays that are currently available for routine clinical use.

Methods
In a retrospective study, sFLC analyses were performed on a cohort that included 139 patients with various monoclonal gammopathies and 54 control sera without an M-protein. Method comparisons of the following four FLC assays were performed: Freelite (Binding Site), N-Latex FLC (Siemens), Seralite (Abingdon Health) and Sebia FLC (Sebia).

Results
Bland-Altman agreement analysis showed biases varying between −0.1 and 16.2 mg/L for κFLC, −6.0 and 6.8 mg/L for λFLC and −0.04 and 0.38 for the ratio of the involved to uninvolved FLC. Strong agreements were observed for FLC-concentrations below 100 mg/L. The clinical concordance of the κ/λFLC-ratio of the four methods varied between 86% and 92%. Significant quantitative differences were observed between the different methods, mainly in sera with high FLC concentrations. Most assays consistently overestimated FLC concentrations compared to SPE.

Conclusions
Good overall clinical concordances were observed between the four sFLC assays that were compared in this study. Although good agreements were observed between the FLC assays, significant absolute differences in FLC concentrations in individual patients can be seen, particularly at higher FLC concentrations. Because of inequivalent absolute sFLC values between the methods in individual patients, none of the four sFLC assays can be used interchangeably.
Ion Exchange of Benzoate in Ni-Al-Benzoate Layered Double Hydroxide by Amoxicillin
Authors: Dwiasi Dian Windy , Mudasir Mudasir , Roto Roto 
Published: November 2019

AbstractThe Ni-Al-NO3 layered double hydroxide (LDH) compound has been intercalated with benzoate anion through an anion exchange process for amoxicillin drug adsorption. The purpose of this research is to synthesize Ni-Al-NO3, ion exchange with benzoate anion to form Ni-Al-Benzoate, and then applying it as an adsorbent of amoxicillin. The adsorption process was carried out using the batch technique. The materials synthesized in this study were characterized by Fourier Transform Infrared Spectroscopy (FT-IR), X-ray ray diffraction (XRD), and Thermogravimetric Analysis/Differential Thermal Analysis (TGA/DTA). The exchange of benzoate in Ni-Al-Benzoate LDH by amoxicillin was followed by UV-Vis spectrophotometry. The pH, LDH amount, and contact time are optimized. The adsorption of amoxicillin by Ni-Al-Benzoate is fit to the pseudo-second-order kinetics model, with an adsorption capacity of 40 mg/ g. The results showed that anion exchange was successfully carried out between benzoate anion and amoxicillin.