bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Does Motivation Modulate the Operation of the Mentalizing Network in Person Evaluation?
Authors: Nugiel Tehila , Beer Jennifer S. 
Published: November 2019

Abstract
The mentalizing network is theorized to play a central role in making sense of people (compared with nonsocial targets), but is its involvement affected when we make sense of people in a nondispassionate manner (e.g., favoritism toward others on the basis of group membership)? First, mixed findings and small samples have prevented strong conclusions about whether intergroup evaluation increases or decreases activation regions associated with the mentalizing network. Second, little is known about the psychological mechanism underlying mentalizing network activation shaped by ingroup versus outgroup evaluations. Psychological models suggest two hypotheses that can be challenging to disentangle with self-report: Ingroup trait evaluations may benefit from a priori expectations and/or preferential evidence accumulation. Therefore, the current study (n = 50) drew on a combination of drift diffusion modeling and fMRI to examine how group membership affects the engagement of the mentalizing network for trait evaluation and whether group-differentiated activation is associated with a priori expectations and/or preferential evidence accumulation. Outgroup trait evaluations engaged dorsomedial pFC activation, whereas ingroup trait evaluations engaged ventromedial pFC activation as well as other regions associated with mentalizing such as precuneus, posterior cingulate cortex, and right TPJ. Furthermore, the ventromedial pFC and posterior cingulate cortex activation was associated with differential expectations applied to ingroup trait evaluation. The current findings demonstrate the importance of combining motivational factors, computational modeling, and fMRI to deepen our understanding of the neural basis of person evaluation.
Effects of the invasive common milkweed (Asclepias syriaca) on nematode communities in natural grasslands
Authors: Jurová Jana , Renčo Marek , Gömöryová Erika , Čerevková Andrea 
Published: November 2019

Summary
Thousands of plant species have been introduced, both deliberately and accidentally, to native ecosystems across the globe. The common milkweed, Asclepias syriaca, is an invasive fast-growing plant species that has invaded natural and managed areas in Europe in recent years. However, only a few studies have investigated its impacts on above-ground and below-ground native biota. Soil nematodes are considered to be the most abundant metazoans, comprising different trophic groups. We examined soil nematode populations on several independent sites invaded and non-invaded by A. syriaca in southern Slovak Republic. We hypothesised that alteration of above-ground nutrient sources caused by invasion would alter nematode abundance, species diversity and trophic structure. Our study revealed that the nematode communities were not negatively affected by A. syriaca invasion over a period of two vegetation seasons. The most surprising results were that common milkweed did not decrease the abundance of plant parasites, bacterivores or fungivores and did not affect species diversity. Moreover, basic physicochemical soil parameters were similar in both invaded and non-invaded sites, although there is evidence that invasive milkweed considerably decreases native plant species cover. It is thus reasonable to conclude that A. syriaca does not pose a threat to soil nematode communities but has a negative impact on native plants. As there is an absence of nematological studies from A. syriaca-invaded ecosystems and considering it has invaded a wide range of habitats, it is impossible to generalise our findings and further studies are required.
Cosmology and Cosmic Order in Islamic Astronomy
Authors: Morrison Robert G. 
Published: November 2019

Abstract
This article analyzes how the astronomy of Islamic societies in the thirteenth and fourteenth centuries can be understood as cosmological. By studying the Arabic translations of the relevant Greek terms and then the definitions of the medieval Arabic dictionaries, the article finds that Arabic terms did not communicate order in the way implied by the Greek ho kósmos (ὁ κόσμος; the cosmos). Yet, astronomers of the period sometimes discussed cosmic order in addition to describing the cosmos. This article finds, too, that a new technical term, nafs al-amr (the fact of the matter) became part of later discussions of cosmic order.
Couleurs des urines et plantes tinctoriales dans le De Urinis Theophili: À propos du terme χυμένη
Authors: Vagenheim Ginette 
Published: November 2019

Abstract
The aim of this article is to draw the attention of scholars of ancient medicine to the need to consider the works of humanists in interpreting and editing medical treatises. Because humanists, especially those who had studied medicine and botany in the Italian universities, had acquired both a theoretical knowledge of ancient writings on medicine and a practical expertise in botany that allowed them to identify the plants mentioned in the major ancient sources such as Dioscorides, Theophrastus, Pliny and to understand their lexical uses in the Byzantine treatises on uroscopy. Such is the case for the word chyménè, which is nowadays completely misunderstood, as our examination of Theophilus Protospatharius’ De urinis (ca. seventh-ninth century) will show. That word, while obscure to the first translators of this treatise, such as Ambrogio Leone (1519), was correctly interpreted by the humanists Onorio Belli (1593), Claude Saumaise (1629) and Bodaeus de Stapel (1644), who were also the first to show us that the Latin version of Theophilus’ treatise on Urines had become corrupted in the course of the centuries.
OmicsARules: a R package for integration of multi-omics datasets via association rules mining
Authors: Chen Danze , Zhang Fan , Zhao Qianqian , Xu Jianzhen 
Published: November 2019

Abstract

Background
The improvements of high throughput technologies have produced large amounts of multi-omics experiments datasets. Initial analysis of these data has revealed many concurrent gene alterations within single dataset or/and among multiple omics datasets. Although powerful bioinformatics pipelines have been developed to store, manipulate and analyze these data, few explicitly find and assess the recurrent co-occurring aberrations across multiple regulation levels.

Results
Here, we introduced a novel R-package (called OmicsARules) to identify the concerted changes among genes under association rules mining framework. OmicsARules embedded a new rule-interestingness measure, Lamda3, to evaluate the associated pattern and prioritize the most biologically meaningful gene associations.
As demonstrated with DNA methlylation and RNA-seq datasets from breast invasive carcinoma (BRCA), esophageal carcinoma (ESCA) and lung adenocarcinoma (LUAD), Lamda3 achieved better biological significance over other rule-ranking measures. Furthermore, OmicsARules can illustrate the mechanistic connections between methlylation and transcription, based on combined omics dataset. OmicsARules is available as a free and open-source R package.

Conclusions
OmicsARules searches for concurrent patterns among frequently altered genes, thus provides a new dimension for exploring single or multiple omics data across sequencing platforms.
Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle
Authors: Zhou Jinghang , Liu Liyuan , Chen Chunpeng James , Zhang Menghua , Lu Xin , Zhang Zhiwu , Huang Xixia , Shi Yuangang 
Published: November 2019

Abstract

Background
Dual-purpose cattle are more adaptive to environmental challenges than single-purpose dairy or beef cattle. Balance among milk, reproductive, and mastitis resistance traits in breeding programs is therefore more critical for dual-purpose cattle to increase net income and maintain well-being. With dual-purpose Xinjiang Brown cattle adapted to the Xinjiang Region in northwestern China, we conducted genome-wide association studies (GWAS) to dissect the genetic architecture related to milk, reproductive, and mastitis resistance traits. Phenotypic data were collected for 2410 individuals measured during 1995–2017. By adding another 445 ancestors, a total of 2855 related individuals were used to derive estimated breeding values for all individuals, including the 2410 individuals with phenotypes. Among phenotyped individuals, we genotyped 403 cows with the Illumina 150 K Bovine BeadChip.

Results
GWAS were conducted with the FarmCPU (Fixed and random model circulating probability unification) method. We identified 12 markers significantly associated with six of the 10 traits under the threshold of 5% after a Bonferroni multiple test correction. Seven of these SNPs were in QTL regions previously identified to be associated with related traits. One identified SNP, BovineHD1600006691, was significantly associated with both age at first service and age at first calving. This SNP directly overlapped a QTL previously reported to be associated with calving ease. Within 160 Kb upstream and downstream of each significant SNP identified, we speculated candidate genes based on functionality. Four of the SNPs were located within four candidate genes, including CDH2, which is linked to milk fat percentage, and GABRG2, which is associated with milk protein yield.

Conclusions
These findings are beneficial not only for breeding through marker-assisted selection, but also for genome editing underlying the related traits to enhance the overall performance of dual-purpose cattle.
Mining and genomic characterization of resistance to tan spot, Stagonospora nodorum blotch (SNB), and Fusarium head blight in Watkins core collection of wheat landraces
Authors: Halder Jyotirmoy , Zhang Jinfeng , Ali Shaukat , Sidhu Jagdeep S. , Gill Harsimardeep S. , Talukder Shyamal K. , Kleinjan Jonathan , Turnipseed Brent , Sehgal Sunish K. 
Published: November 2019

AbstractBackgroundIn the late 1920s, A. E. Watkins collected about 7000 landrace cultivars (LCs) of bread wheat (Triticum aestivumL.) from 32 different countries around the world. Among which 826 LCs remain viable and could be a valuable source of superior/favorable alleles to enhance disease resistance in wheat. In the present study, a core set of 121 LCs, which captures the majority of the genetic diversity of Watkins collection, was evaluated for identifying novel sources of resistance against tan spot, Stagonospora nodorum blotch (SNB), and Fusarium Head Blight (FHB).ResultsA diverse response was observed in 121 LCs for all three diseases. The majority of LCs were moderately susceptible to susceptible to tan spot Ptr race 1 (84%) and FHB (96%) whereas a large number of LCs were resistant or moderately resistant against tan spot Ptr race 5 (95%) and SNB (54%). Thirteen LCs were identified in this study could be a valuable source for multiple resistance to tan spot Ptr races 1 and 5, and SNB, and another five LCs could be a potential source for FHB resistance. GWAS analysis was carried out using disease phenotyping score and 8807 SNPs data of 118 LCs, which identified 30 significant marker-trait associations (MTAs) with -log10 (p-value) > 3.0. Ten, five, and five genomic regions were found to be associated with resistance to tan spot Ptr race 1, race 5, and SNB, respectively in this study. In addition toTsn1, several novel genomic regionsQ.Ts1.sdsu-4BSandQ.Ts1.sdsu-5BS(tan spot Ptr race 1) andQ.Ts5.sdsu-1BL,Q.Ts5.sdsu-2DL,Q.Ts5.sdsu-3AL, andQ.Ts5.sdsu-6BL(tan spot Ptr race 5) were also identified. Our results indicate that these putative genomic regions contain several genes that play an important role in plant defense mechanisms.ConclusionOur results suggest the existence of valuable resistant alleles against leaf spot diseases in Watkins LCs. The single-nucleotide polymorphism (SNP) markers linked to the quantitative trait loci (QTLs) for tan spot and SNB resistance along with LCs harboring multiple disease resistance could be useful for future wheat breeding.
Did the ban on serving raw beef liver in restaurants decrease Enterohemorrhagic Escherichia coli infection in Japan?: an interrupted time-series analysis
Authors: Iwata Kentaro , Goto Michihiko 
Published: November 2019

Abstract

Background
Enterohemorrhagic Escherichia coli (EHEC) is an important pathogen that causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). After an EHEC outbreak involving uncooked beef, serving raw beef liver dishes at restaurants was completely banned starting on July 1, 2012 in Japan. However, its long-term associations with the incidence rates of EHEC infections have never been assessed by formal interrupted time-series analysis (ITSA).

Methods
A retrospective cohort study to assess the impact of banning raw beef liver provision at restaurants was conducted. The weekly incidence of asymptomatic and symptomatic EHEC infections, the incidence of HUS, and deaths were extracted from the national reportable diseases database from January 2008 to December 2017. ITSA was conducted to evaluate the impact of banning raw beef liver from July 2012. To account for a potential simultaneous external effect, the additional regulation on raw beef red meat handling (implemented in May 2011) and the seasonality were also incorporated into the model.

Results
There were 32,179 asymptomatic and 21,250 symptomatic EHEC infections (including 717 HUS cases and 26 deaths) reported during the study period. During the pre-intervention period (before week 27, 2012), there were 0.45 asymptomatic EHEC infections per million-persons per week. The mean post-intervention asymptomatic EHEC infections were 0.51 per million-persons per week. ITSA revealed no baseline trend or change in the intercept and trend (0.002 infections per million-persons per week, 95% Confidence interval − 0.03-0.04, p = 0.93, 1.22, CI -1.96-4.39, p = 0.45, and − 0.006, CI -0.003-0.02, p = 0.68, respectively). For symptomatic EHEC infections, there were 0.30 cases per million per week during the pre-intervention period, and it became 0.33 cases per million per week after the intervention. Time series modeling again did not show a significant baseline trend or changes in the intercept and trend (0.0005, CI -0.02-0.02, p = 0.96, 0.69, CI -1.75-3.12, p = 0.58, and − 0.003, CI -0.02-0.01, p = 0.76, respectively).

Conclusion
We did not find a statistically significant reduction in the overall incidence rates of both asymptomatic and symptomatic EHEC infections in Japan after implementing measures, including a ban on serving raw beef liver dishes in the restaurant industry.
Involvement of SLC39A6 in gastric adenocarcinoma and correlation of the SLC39A6 polymorphism rs1050631 with clinical outcomes after resection
Authors: Gao Jian , Ren Wenjun , Xiao Chunhong , Wang Lie , Huang Qiaojia , Zhang Zaizhong , Dang Yuan , Weng Pengcheng , Wang Hui , Fang Xuehong , Zhuang Minxian , Lin Liying , Chen Shaoquan 
Published: November 2019

Abstract

Background
The single-nucleotide polymorphism SLC39A6 rs1050631 is strongly implicated in esophageal squamous cell carcinoma, leading us to question whether it may also play a role in gastric adenocarcima (GA).

Methods
We genotyped the SLC39A6 rs1050631 in 512 patients who underwent GA resection. All study subjects lived in an area of China with high GA incidence. Genotypes were examined for possible correlation with survival and recurrence. The potential involvement of SLC39A6 in gastric cancer was explored in clinical samples and cell culture studies.

Results
Multivariable analysis showed that patients with the CT + TT genotype at SLC39A6 rs1050631 were at greater risk of recurrence (hazard ratio, HR 1.387, p = 0.004) and death (HR 1.429, p = 0.002) than patients with CC genotype. Median recurrence-free and overall survival were significantly shorter in patients with the CT + TT genotype (20, 27 months) than in patients with the CC genotype (36, 43 months, p = 0.001, p < 0.001). Patients with the CT + TT genotype who were male or ≥ 60 years, or who had a tumor ≥5 cm or a moderately differentiated tumor were at significantly higher risk of recurrence and death. SLC39A6 was overexpressed in tissues from GA patients and in GA cell lines, and SLC39A6 knockdown in GA cell lines inhibited their proliferation, migration and invasion.

Conclusion
SLC39A6 rs1050631 correlates with post-resection prognosis of GA patients and SLC39A6 may participate in GA onset or progression.
CircAGFG1 promotes cervical cancer progression via miR-370-3p/RAF1 signaling
Authors: Wu Fengqin , Zhou Jingjing 
Published: November 2019

Abstract

Background
In past decades, circular RNAs (circRNAs) have achieved increasing attention because of its regulatory role in different kinds of cancers. However, how circAGFG1 regulates cervical cancer (CC) is still largely undiscovered. This study aims to evaluate the role of a novel circRNAs and related molecular mechanism in CC cells.

Methods
High or low level of circAGFG1 was detected in CC cells or normal cell line with qRT-PCR. The proliferative and migratory abilities of CC cells were assessed with loss-of function assays. The downstream miRNA and mRNA of circAGFG1 were searched out and proved by using bioinformatics analysis and mechanism experiments. Recue assays were designed to confirm the role of circAGFG1/miR-370-3p/RAF1 axis in CC cell activities.

Results
The levels of circAGFG1 was abundant in CC cells in comparison with normal cervical cell End1/E6E7. The inhibitory effect of decreased circAGFG1 level on the proliferative and migratory abilities of CC cells was assessed. CircAGFG1 and miR-370-3p were localized in the cytoplasm and they can interact with each other. Moreover, miR-370-3p was downregulated in CC cells. We also determined the negative effect of miR-370-3p on RAF1. CircAGFG1 could promote RAF1 expression by absorbing miR-370-3p, thereby activating RAF/MEK/ERK pathway. circAGFG1 promoted proliferation and migration of CC cells via enhancing the activity of RAF/MEK/ERK pathway by sponging miR-370-3p and further regulating RAF1.

Conclusion
The results of this study provided new evidence that circAGFG1 acted as a vital regulator in cervical cancer proliferation and migration, giving great promise to apply it as a potential biomarker for diagnosis and therapy in CC treatment.
A reactive oxygen species scoring system predicts cisplatin sensitivity and prognosis in ovarian cancer patients
Authors: Sun Chaoyang , Guo Ensong , Zhou Bo , Shan Wanying , Huang Jia , Weng Danhui , Wu Peng , Wang Changyu , Wang Shixuan , Zhang Wei , Gao Qinglei , Xu Xiaoyan , Wang Beibei , Hu Junbo , Ma Ding , Chen Gang 
Published: November 2019

Abstract

Background
To reveal roles of reactive oxygen species (ROS) status in chemotherapy resistance and to develop a ROS scoring system for prognosis prediction in ovarian cancer.

Methods
We tested the sensitizing effects of ROS elevating drugs to cisplatin (cDDP) in ovarian cancer both in vitro and in vivo. A ROS scoring system was developed using The Cancer Genome Atlas (TCGA) database of ovarian cancer. The associations between ROS scores and overall survival (OS) were analyzed in TCGA, Tothill dataset, and our in-house dataset (TJ dataset).

Results
ROS-inducing drugs increased cisplatin-induced ovarian cancer cell injury in vitro and in vivo. ROS scoring system was established using 25 ROS-related genes. Patients were divided into low (scores 0–12) and high (scores 13–25) score groups. Improved patient survival was associated with higher scores (TCGA dataset hazard ratio (HR) = 0.43, P < 0.001; Tothill dataset HR = 0.65, P = 0.022; TJ dataset HR = 0.40, P = 0.003). The score was also significantly associated with OS in multiple datasets (TCGA dataset r2 = 0.574, P = 0.032; Thothill dataset r2 = 0.266, P = 0.049; TJ dataset r2 = 0.632, P = 0.001) and with cisplatin sensitivity in ovarian cancer cell lines (r2 = 0.799, P = 0.016) when used as a continuous variable. The scoring system showed better prognostic performance than other clinical factors by receiver operating characteristic (ROC) curves (TCGA dataset area under the curve (AUC) = 0.71 v.s. 0.65, Tothill dataset AUC = 0.73 v.s. 0.67, TJ dataset AUC = 0.74 v.s. 0.66).

Conclusions
ROS status is associated with chemotherapy resistance. ROS score system might be a prognostic biomarker in predicting the survival benefit from ovarian cancer patients.
Making the business case for an addiction medicine consult service: a qualitative analysis
Authors: Priest Kelsey C. , McCarty Dennis 
Published: November 2019

Abstract

Background
As the drug poisoning crisis worsens in North America and opioid use disorder (OUD)-related hospital admissions increase, policymakers and hospital administrators are beginning to recognize the important role of hospitals in the OUD care continuum. This study explores and describes how U.S. addiction medicine physicians created and presented business propositions to hospital administrators to support the development of addiction medicine consult (AMC) services.

Methods
Fifteen qualitative interviews were completed with board-certified or board-eligible addiction medicine physicians from 14 U.S. hospitals. The interviews occurred as part of a broader mixed methods study exploring hospital service delivery for patients admitted with OUD. Using a directed content analysis, the transcribed interviews were coded, analyzed, and final themes consolidated.

Results
Semi-structured interviews completed with addiction medicine physicians from established (n = 9) and developing (n = 5) AMC services at 14 U.S. hospitals explored how clinical champions persuaded hospital administrators to support AMC service development. Four elements were foundational to making the “business case”: 1) describing the prevalence of substance use disorder (SUD) or OUD in the hospital; 2) identifying the negative financial impacts of not treating SUDs during hospitalization; 3) highlighting the ongoing care quality and treatment gap for hospitalized patients with SUDs; and 4) noting the success of other institutional AMC services. Study findings informed the creation of tools to support AMC service development: 1) an AMC service business case template, and 2) an AMC service design and operations resource list.

Conclusions
OUD-related hospital admissions are unlikely to abate. Hospital administrators should consider innovative care delivery mechanisms to improve care for persons with OUD. AMC services may be a promising delivery mechanism to achieve this aim. For clinical and administrative champions, understanding how to communicate the potential effectiveness of this intervention to hospital leaders is an essential first step to AMC service creation.