bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of nitrite-degrading and biogenic amine-degrading strains and its involved genes
Authors: Li Yuxin , Yu Zhihui , Zhu Yingchun , Cao Zhixiang 
Published: October 2020

Abstract

Objectives
Accumulation of nitrite and biogenic amines (BAs) in fermented meat products is a matter of public health concern. The study aimed to screen nitrite-degrading and BA-degrading strains from sour porridges and sausages and bacon products in China.

Materials and Methods
After screening out 12 strains, the degradation of nitrite, the degradation of BAs, the activities of nitrite-reducing enzymes, and the detection of genes involved in the BAs were assessed by spectrophotometry method with hydrochloric acid naphthalene ethylenediamine, high-performance liquid chromatography, GENMED kit, and polymerase chain reaction, respectively.

Results
Pediococcus pentosaceus labelled M SZ1 2 and M GC 2, Lactobacillus plantarum labelled M SZ2 2, and Staphylococcus xylosus labelled Y CC 3 were selected. The activity of nitrite-reducing enzyme in M SZ2 2 was 2.663 units/mg. The degradation rate of total BAs of M SZ2 2 was 93.24%. The degradation rates of nitrite and BAs of M SZ1 2 were 86.49% and 37.87%, respectively. The activity of nitrite-reducing enzyme in M SZ1 2 was up to 1.962 units/mg. M GC 2 showed higher degradation rates of nitrite (89.19%) and Y CC 3 showed higher degradation rates of BAs (36.16%). The genes encoding the multicopper oxidases (suf I/D2EK17) were detected in the four strains, which also did not contain BAs (histidine decarboxylase (hdc), tyrosine decarboxylase (tdc), ornithine decarboxylase (odc), lysine decarboxylase (ldc)) formation encoding genes.

Conclusion
These four strains (M SZ1 2, M GC 2, M SZ2 2, and Y CC 3) are promising candidates to use as starter cultures for nitrite and BAs in fermented sausages.
The genetics-BIDS extension: Easing the search for genetic data associated with human brain imaging
Authors: Moreau Clara A , Jean-Louis Martineau , Blair Ross , Markiewicz Christopher J , Turner Jessica A , Calhoun Vince D , Nichols Thomas E , Pernet Cyril R 
Published: October 2020

Abstract
Metadata are what makes databases searchable. Without them, researchers would have difficulty finding data with features they are interested in. Brain imaging genetics is at the intersection of two disciplines, each with dedicated dictionaries and ontologies facilitating data search and analysis. Here, we present the genetics Brain Imaging Data Structure extension, consisting of metadata files for human brain imaging data to which they are linked, and describe succinctly the genomic and transcriptomic data associated with them, which may be in different databases. This extension will facilitate identifying micro-scale molecular features that are linked to macro-scale imaging repositories, facilitating data aggregation across studies.
NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
Authors: de Koning Willem , Miladi Milad , Hiltemann Saskia , Heikema Astrid , Hays John P , Flemming Stephan , van den Beek Marius , Mustafa Dana A , Backofen Rolf , Grüning Björn , Stubbs Andrew P 
Published: October 2020

Abstract

Background
Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In this respect, the Oxford Nanopore Technologies–based long-read sequencing “nanopore" platform is becoming a widely used tool with a broad range of applications and end-users. However, the need to explore and manipulate the complex data generated by long-read sequencing platforms necessitates accompanying specialized bioinformatics platforms and tools to process the long-read data correctly. Importantly, such tools should additionally help democratize bioinformatics analysis by enabling easy access and ease-of-use solutions for researchers.

Results
The Galaxy platform provides a user-friendly interface to computational command line–based tools, handles the software dependencies, and provides refined workflows. The users do not have to possess programming experience or extended computer skills. The interface enables researchers to perform powerful bioinformatics analysis, including the assembly and analysis of short- or long-read sequence data. The newly developed “NanoGalaxy" is a Galaxy-based toolkit for analysing long-read sequencing data, which is suitable for diverse applications, including de novo genome assembly from genomic, metagenomic, and plasmid sequence reads.

Conclusions
A range of best-practice tools and workflows for long-read sequence genome assembly has been integrated into a NanoGalaxy platform to facilitate easy access and use of bioinformatics tools for researchers. NanoGalaxy is freely available at the European Galaxy server https://nanopore.usegalaxy.eu with supporting self-learning training material available at https://training.galaxyproject.org.
Political Comedy as a Gateway to News Use, Internal Efficacy, and Participation: A Longitudinal Mediation Analysis
Authors: Long Jacob A , Jeong Min Seon , Lavis Simon M 
Published: October 2020

Abstract
Despite a great deal of research, much about the effects of political comedy programming on its viewers remains uncertain. One promising line of work has focused on increased internal political efficacy—the sense that one is competent to engage with politics—as an outcome of exposure to political comedy programs. This may explain results showing that viewers are more likely to participate in politics. We extend this approach by considering the role of political comedy’s “gateway” effect in encouraging political media consumption, which can promote additional increases in efficacy and participation. This study provides a theoretical synthesis of prior research and a rigorous empirical test using a representative panel survey of adults in the United States, providing evidence of a relationship between political comedy and participation with both news use and internal efficacy serving as mediators. Furthermore, we find that only political satire, not late-night talk shows, appear to produce these effects.
Comparative evaluation of webinar, powerpoint presentation and lecture as oral health educational interventions among school children: a randomized controlled trial
Authors: Deokar Rahul , Dodamani Arun , Vishwakarma Prashanth , Jadhav Harish , Khairnar Mahesh , Marathe Pratiksha , Bhandari Rahul , Khobragade Vrushali 
Published: October 2020

AbstractThe study compared the effectiveness of three teaching methods on the oral health status of high school children. The study population of 791 school children selected from three different schools was randomly allocated to one of three intervention groups: (i) Webinar group (Online presentation)—260 subjects, (ii) Face to Face lecture using PowerPoint presentation (F2F PP group)—261 subjects and (iii) Control group (Only lecture)—270 subjects. Subjects from the Webinar group and F2F PP group received oral health education at an interval of 15 days starting from baseline. Subjects from the control group received oral health education only at baseline. Oral Hygiene Index (OHI) and Gingival Index (GI) were measured at baseline, at 1 month, 2 months’ and 3 months’ interval. OHI and GI showed a significant reduction (P = 0.001) in the Webinar group and F2F PP group; However, in the control group, OHI and GI reduced from baseline till second month and showed an increase at 3 months’ interval. F2F PP group showed a maximum reduction in OHI and GI followed by the Webinar group. It can be concluded that F2F PowerPoint-based oral health education was most effective followed by the webinar method.
Evaluation of mediastinoscopy in mediastinal lymph node staging for non-small-cell lung cancer
Authors: Diebels Ian , Hendriks Jeroen M H , Van Meerbeeck Jan P , Lauwers Patrick , Janssens Annelies , Yogeswaran Suresh K , Van Schil Paul E Y 
Published: October 2020

Abstract

OBJECTIVES
The purpose of this study was to assess the quality of video-assisted cervical mediastinoscopy (VACM) in the staging of non-small-cell lung cancer (NSCLC) at the Antwerp University Hospital with a focus on test effectiveness indicators, morbidity and unforeseen pN2 results.

METHODS
All consecutive VACM workups of cases of NSCLC performed between January 2010 and December 2015 were included to assess overall test quality and effectiveness. Quality assurance was performed in accordance with the recommendations of the European Society of Gastrointestinal Endoscopy and European Society of Thoracic Surgeons (ESTS) where appropriate.

RESULTS
A total of 168 video-assisted cervical mediastinoscopies were included. A total of 91.7% of the procedures were performed in accordance with the ESTS guideline. An unforeseen pN2 staging was identified in 10 anatomical lung resections (8.6%). Statistical analysis showed no significant association between VACM performed in accordance with the ESTS guideline and the presence of pN2 positive lymph nodes [χ2 (1) = 0.61; P = 0.57] and no association between VACM performed in accordance with the ESTS guideline and overall futile thoracotomy [χ2 (1) = 0.76; P = 0.50]. Calculations revealed a sensitivity of 81.8 [95% confidence interval (CI) 69.1–90.9], specificity of 100%, positive predictive value of 100%, negative predictive value of 91.9% (95% CI 86.6–95.2) and diagnostic accuracy of 94.1% (95% CI 89.33–97.11).

CONCLUSIONS
Overall, 91.7% of the VACM were performed in accordance with the ESTS guideline. This process resulted in a sensitivity of 81.8%, a negative predictive value of 91.9% and an unforeseen pN2 rate of 8.6%.
Faster Johnson–Lindenstrauss transforms via Kronecker products
Authors: Jin Ruhui , Kolda Tamara G , Ward Rachel 
Published: October 2020

AbstractThe Kronecker product is an important matrix operation with a wide range of applications in signal processing, graph theory, quantum computing and deep learning. In this work, we introduce a generalization of the fast Johnson–Lindenstrauss projection for embedding vectors with Kronecker product structure, the Kronecker fast Johnson–Lindenstrauss transform (KFJLT). The KFJLT reduces the embedding cost by an exponential factor of the standard fast Johnson–Lindenstrauss transform’s cost when applied to vectors with Kronecker structure, by avoiding explicitly forming the full Kronecker products. We prove that this computational gain comes with only a small price in embedding power: consider a finite set of $p$ points in a tensor product of $d$ constituent Euclidean spaces $\bigotimes _{k=d}^{1}{\mathbb{R}}^{n_k}$, and let $N = \prod _{k=1}^{d}n_k$. With high probability, a random KFJLT matrix of dimension $m \times N$ embeds the set of points up to multiplicative distortion $(1\pm \varepsilon )$ provided $m \gtrsim \varepsilon ^{-2} \, \log ^{2d - 1} (p) \, \log N$. We conclude by describing a direct application of the KFJLT to the efficient solution of large-scale Kronecker-structured least squares problems for fitting the CP tensor decomposition.
Administering an appeasing substance to optimize performance and health responses in feedlot receiving cattle
Authors: Colombo Eduardo A , Cooke Reinaldo F , Brandão Alice P , Wiegand Jacob B , Schubach Kelsey M , Duff Glenn C , Gouvêa Vinícius N , Cappellozza Bruno I 
Published: October 2020

AbstractThis experiment evaluated the impacts of administering a bovine appeasing substance (BAS) at feedlot entry to receiving cattle. Angus-influenced steers (n = 342) from 16 sources were purchased from an auction yard on day –1, and transported (12 hr; 4 trucks) to the feedlot. Upon arrival on day 0, shrunk body weight (BW; 240 ± 1 kg) was recorded and steers were ranked by load, shrunk BW, and source and assigned to receive BAS (IRSEA Group, Quartier Salignan, France; n = 171) or placebo (diethylene glycol monoethyl ether; CON; n = 171). The BAS is a mixture of fatty acids that replicate the composition of the bovine appeasing pheromone. Treatments (5 mL) were topically applied to each individual steer on their nuchal skin area. Steers were allocated to 1 of 24 drylot pens (12 pens/treatment) and received a free-choice diet until day 46. Steers were assessed daily for bovine respiratory disease (BRD) signs, and feed intake was recorded from each pen daily. Steer unshrunk BW was recorded on days 7, 17, 31, 45, and 46. Shrunk BW on day 0 was added an 8% shrink to represent initial BW, and final BW was calculated by averaging BW from days 45 and 46. Blood samples were collected from 5 steers/pen on days 0, 7, 11, 31, and 45. Pen was considered the experimental unit. Steer BW gain was greater (P = 0.04) in BAS vs. CON (1.01 vs. 0.86 kg/d, SEM = 0.05). Feed intake did not differ (P = 0.95) between treatments, resulting in greater (P = 0.05) feed efficiency in BAS vs. CON (171 vs. 142 g/kg, SEM = 10). Plasma cortisol concentration was greater (P = 0.05) and plasma glucose concentration was less in CON vs. BAS on day 7 (treatment × day; P = 0.07 and &lt;0.01, respectively). Mean plasma β-hydroxybutyrate concentration was greater (P &lt; 0.01) in BAS vs. CON (3.23 and 2.75 mg/mL; SEM = 0.12). Incidence of BRD was greater (P ≤ 0.05) in BAS vs. CON from days 6 to 10 and days 19 to 23 (treatment × day; P &lt; 0.01), although overall BRD incidence did not differ (P = 0.20) between treatments (82.4% vs. 76.6%, respectively; SEM = 3.2). A greater proportion (P = 0.04) of BAS steers diagnosed with BRD required one antimicrobial treatment to regain health compared with CON (59.3% vs. 47.6%, SEM = 4.2). Hence, BAS administration to steers upon feedlot arrival improved BW gain during a 45-d receiving period by enhancing feed efficiency. Moreover, results suggest that BAS improved steer performance by facilitating early detection of BRD signs, lessening the disease recurrence upon first antimicrobial treatment.
Clinical Course of Cancer Patients With COVID-19: A Retrospective Cohort Study
Authors: Alpert Naomi , Rapp Joseph L , Marcellino Bridget , Lieberman-Cribbin Wil , Flores Raja , Taioli Emanuela 
Published: October 2020

Abstract

Background
Complications in cancer patients with coronavirus disease 2019 (COVID-19) have not been examined. This analysis aimed to compare characteristics of COVID-19 patients with and without cancer and assess whether cancer is associated with COVID-19 morbidity or mortality.

Methods
COVID-19–positive patients with an inpatient or emergency encounter at the Mount Sinai Health System between March 1, 2020, and May 27, 2020, were included and compared across cancer status on demographics and clinical characteristics. Multivariable logistic regressions were used to model the associations of cancer with sepsis, venous thromboembolism, acute kidney injury, intensive care unit admission, and all-cause mortality.

Results
There were 5556 COVID-19–positive patients included, 421 (7.6%) with cancer (325 solid, 96 nonsolid). Those with cancer were statistically significantly older, more likely to be non-Hispanic Black and to be admitted to the hospital during their encounter, and had more comorbidities than noncancer COVID-19 patients. Cancer patients were statistically significantly more likely to develop sepsis (adjusted odds ratio [ORadj] = 1.31, 95% confidence interval [CI] = 1.06 to 1.61) and venous thromboembolism (ORadj = 1.77, 95% CI = 1.01 to 3.09); there was no statistically significant difference in acute kidney injury (ORadj = 1.10, 95% CI = 0.87 to 1.39), intensive care unit admissions (ORadj = 1.04, 95% CI = 0.80 to 1.34), or mortality (ORadj = 1.02, 95% CI = 0.81 to 1.29).

Conclusions
COVID-19 patients with cancer may have a higher risk for adverse outcomes. Although there was no statistically significant difference in mortality, COVID-19 patients with cancer have statistically significantly higher risk of thromboembolism and sepsis. Further research is warranted into the potential effects of cancer treatments on inflammatory and immune responses to COVID-19 and on the efficacy of anticoagulant therapy in these patients.
Small bowel obstruction due to retroperitoneal hernia following renal transplant: a case report
Authors: Nawabi Atta , Kahle Adam C , King Clay D , Nawabi Perwaiz 
Published: October 2020

AbstractPara duodenal hernias, the most common type of retroperitoneal hernias, are thought to occur naturally from abnormal gut rotation because of fusion folds within the peritoneum. Retroperitoneal hernias are a rare postoperative complication and have not been described after renal transplantation via a retroperitoneal approach. This case report presents a 48-year-old male with intestinal obstruction after renal transplant due to herniation into the retroperitoneum via an incidentally created peritoneal defect. We suggest computed tomography with oral contrast be used in the early postoperative phase to assess for obstruction in patients with prolonged ileus of unclear etiology who have undergone retroperitoneal dissection. Small peritoneal defects should be closed during dissection. Larger, or multiple peritoneal defects should be extended to make a single, large defect to decrease the possibility of bowel herniating and becoming incarcerated.
Ten Zen Koans Translated from Japanese, Mandarin, Wu, Vietnamese, Thai, Fujian, Korean, Tibetan, Hakka, Javenese, Mizo, Nepal Bhasa, Khasi, Buryat, Malay, Paiwan, Burmese, Ryukyuan, and Okinawan by Jackson Bliss
Authors: Bliss Jackson 
Published: October 2020

Abstract
In this satirical short story about Zen poetry scholarship that explores the limited and often impossible process of linguistic and spiritual translation, the primary text does not exist at all, making this piece both a spiritual embodiment of Zen according to the writing of many of its most dedicated practitioners and devoted scholars, but also a textual and spatial oxymoron since footnotes are obviously ancillary information used to elaborate and contextualize arguments made on the primary text, which, in this case, does not exist; this poses a basic question: can there be footnotes without a primary text? The footnotes, in their own way, mock any attempt to transliterate a spiritual state of being or a school of thought such as Zen Buddhism since language is constrained by itself from adequately describing the very process that the text actively prevents the reader from doing at all.
A scalable random forest regressor for combining neutron-star equation of state measurements: a case study with GW170817 and GW190425
Authors: Hernandez Vivanco Francisco , Smith Rory , Thrane Eric , Lasky Paul D 
Published: October 2020

ABSTRACT
Gravitational-wave observations of binary neutron star coalescences constrain the neutron-star equation of state by enabling measurement of the tidal deformation of each neutron star. This deformation is well approximated by the tidal deformability parameter Λ, which was constrained using the first binary neutron star gravitational-wave observation, GW170817. Now, with the measurement of the second binary neutron star, GW190425, we can combine different gravitational-wave measurements to obtain tighter constraints on the neutron-star equation of state. In this paper, we combine data from GW170817 and GW190425 to place constraints on the neutron-star equation of state. To facilitate this calculation, we derive interpolated marginalized likelihoods for each event using a machine learning algorithm. These likelihoods, which we make publicly available, allow for results from multiple gravitational-wave signals to be easily combined. Using these new data products, we find that the radius of a fiducial 1.4 M⊙ neutron star is constrained to $11.6^{+1.6}_{-0.9}$ km at 90 per cent confidence and the pressure at twice the nuclear saturation density is constrained to $3.1^{+3.1}_{-1.3}\times 10^{34}$ dyne cm−2 at 90 per cent confidence. Combining GW170817 and GW190425 produces constraints indistinguishable from GW170817 alone and is consistent with findings from other works.
Monism, Spinoza’s Way
Authors: Garrett Don 
Published: October 2020

AbstractMonism, characterized by Jonathan Schaffer as the thesis that the cosmos is the one and only basic actual concrete object, has been the subject of a great deal of recent interest. Spinoza is often taken, rightly, to be an important forebear. This article seeks to explain the distinctive content and basis of Spinoza’s monistic metaphysics and to compare it to contemporary Monism. It then argues that although Spinoza’s monistic metaphysics is not strictly a version of Monism as defined, it has a number of theoretical advantages that make central aspects of it worthy of serious consideration.
The World Just Is the Way It Is
Authors: Builes David 
Published: October 2020

Abstract
What is the relationship between objects and properties? According to a standard view, there are primitive individuals (or ‘particulars’, or ‘substrata’) that ‘instantiate’ or ‘have’ various properties. According to a rival view, objects are mere ‘bundles’ of properties. While there are a number of reasons to be skeptical of primitive individuals, there are also a number of challenges that the bundle theorist faces. The goal of this paper is to formulate a view about the relationship between objects and properties that avoids many of the problems inherent in both of these views. The view I will end up defending implies a particularly radical version of Monism, and it collapses the object-property distinction altogether.
deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
Authors: Xie Fangzhou , Liu Shurong , Wang Junhao , Xuan Jiajia , Zhang Xiaoqin , Qu Lianghu , Zheng Lingling , Yang Jianhua 
Published: October 2020

AbstractEukaryotic genomes encode thousands of small and large non-coding RNAs (ncRNAs). However, the expression, functions and evolution of these ncRNAs are still largely unknown. In this study, we have updated deepBase to version 3.0 (deepBase v3.0, http://rna.sysu.edu.cn/deepbase3/index.html), an increasingly popular and openly licensed resource that facilitates integrative and interactive display and analysis of the expression, evolution, and functions of various ncRNAs by deeply mining thousands of high-throughput sequencing data from tissue, tumor and exosome samples. We updated deepBase v3.0 to provide the most comprehensive expression atlas of small RNAs and lncRNAs by integrating ∼67 620 data from 80 normal tissues and ∼50 cancer tissues. The extracellular patterns of various ncRNAs were profiled to explore their applications for discovery of noninvasive biomarkers. Moreover, we constructed survival maps of tRNA-derived RNA Fragments (tRFs), miRNAs, snoRNAs and lncRNAs by analyzing &gt;45 000 cancer sample data and corresponding clinical information. We also developed interactive webs to analyze the differential expression and biological functions of various ncRNAs in ∼50 types of cancers. This update is expected to provide a variety of new modules and graphic visualizations to facilitate analyses and explorations of the functions and mechanisms of various types of ncRNAs.