bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repeatability and agreement between methods for determining the Atterberg limits of fine‐grained soils
Authors: Rehman Hafeez Ur , Pouladi Nastaran , Pulido‐Moncada Mansonia , Arthur Emmanuel 
Published: January 2020

AbstractThe Atterberg limits (plastic limit [PL] and liquid limit [LL]) of fine‐grained soils are important for civil engineering and agronomic applications. Several methodologies exist to determine the PL and LL, each with associated merits and shortcomings. The reproducibility and uncertainties associated with the various methods have not been evaluated for different samples that differ in terms of clay mineralogy and geologic origin. The objectives were to (i) assess the repeatability of two methods each for determining the PL (thread rolling and rolling device) and LL (Casagrande cup and drop cone penetrometer), and compare the subsequent plasticity indexes for 30 samples from 10 countries; and (ii) evaluate the effect of particle size (2 mm and 425 µm) on the plastic and liquid limits for 28 Venezuelan samples. For the PL, the repeatability (estimated as the repeatability coefficient, RC, among replications) for the thread rolling and rolling device methods was similar (2.28 and 2.39%, respectively). For the LL, the drop cone method was 16% more repeatable than the Casagrande cup method. There was a strong correlation between the two respective methods for PL (r2 = 0.98) and LL (r2 = 0.99). For samples that have LL < 45, the LL from the Casagrande cup was slightly higher than LL from the drop cone, and vice versa for samples with LL > 45%. No significant differences were observed between PL measured on <2‐mm or <425‐µm samples; for samples with LL < 35% the two particle sizes gave similar values. There were however larger discrepancies between the two particle sizes for samples with LL > 36%.
Nitrogen fertilization changes the molecular composition of soil organic matter in a subtropical plantation forest
Authors: Geng Jing , Cheng Shulan , Fang Huajun , Pei Jie , Xu Meng , Lu Mingzhu , Yang Yan , Cao Zicheng 
Published: January 2020

AbstractThe biochemical mechanisms responsible for soil organic C (SOC) accumulation under N enrichment are not well understood. By examining two N types (NH4Cl and NaNO3) and three rates (0, 40, and 120 kg N ha−1 yr−1), we investigated the concentration and distribution of SOC by using soil aggregate separation and physical fractionation of soil organic matter (SOM). The molecular composition of SOM within bulk soil and each physical fraction was determined by pyrolysis–gas chromatography‐mass spectrometry. Nitrogen fertilization led to soil NO3−–N accumulation and intensified soil acidification. Four years of N fertilization did not change total SOC concentrations in the 0‐ to 20‐cm depth but a high rate of NaNO3 addition increased the concentrations of fine particulate organic C and microaggregate‐associated organic C by 133 and 83.4%, respectively. The change in SOC concentration was positively correlated with the change in fine particulate organic C and mineral‐associated organic C concentrations. Four years of N fertilization significantly changed the molecular composition of SOM, with an increase in the relative abundance of furfural and acetic acid and a decrease in pyrrole in the mineral‐associated organic matter (MAOM) fraction. Fertilization increased the furfural/pyrrole and aliphatic/aromatic ratios in the SOM and MAOM fractions, suggesting decreased stability of the passive SOM fraction. The SOC concentration was negatively correlated with the benzene/toluene ratio in both bulk soil and the MAOM fraction. Overall, exogenous N input to this subtropical plantation forest decreased the mineralization and humification of SOM, which could be detrimental to soil C accumulation.
Barriers, potentialities, and actions for implementation of sustainable energy procedures in Brazilian federal universities
Authors: Avila Lucas Veiga , da Silveira João Serafim Tusi , Neto Emitério da Rosa , Baggio Daniel Knebel 
Published: January 2020

AbstractMany universities around the world have served as active centers for research on climate change. However, there are several barriers to their activities, stemming from the nature of research, resources, and the structure of institutions. This document provides an overview of barriers, potential factors, and activities to develop and implement sustainable energy processes in public higher education institutions (HEIs) in Brazil. The research was conducted from March to April of 2018 with representatives of HEIs (rectors or prorectors of research). A total of 63 invitations to respond to the Survey‐monkey survey were emailed, and responses were received from 32 universities. The research concludes by proposing measures that can be taken to make the issue of climate change more present and effective in university research and teaching activities. This includes changes in research, information dissemination, and teaching approaches to better support actions to address climate change. In Brazil, there are many potentialities in terms of natural resources, but actions for implementation are still incipient. Further efforts and investment in research and development will be required.
Inference of Ancestral Recombination Graphs Using ARGweaver
Authors: Hubisz Melissa , Siepel Adam 
Published: January 2020

AbstractThis chapter describes the usage of the program ARGweaver, which estimates the ancestral recombination graph for as many as about 100 genome sequences. The ancestral recombination graph is a detailed description of the coalescence and recombination events that define the relationships among the sampled sequences. This rich description is useful for a wide variety of population genetic analyses. We describe the preparation of data and major considerations for running ARGweaver, as well as the interpretation of results. We then demonstrate an analysis using theDARC(Duffy) gene as an example, and show how ARGweaver can be used to detect signatures of natural selection and Neandertal introgression, as well as to estimate the dates of mutation events. This chapter provides sufficient detail to get a new user up and running with this complex but powerful analysis tool.
Genomics of Long- and Short-Term Adaptation in Maize and Teosintes
Authors: Lorant Anne , Ross-Ibarra Jeffrey , Tenaillon Maud 
Published: January 2020

AbstractMaize is an excellent model for the study of plant adaptation. Indeed, post domestication maize quickly adapted to a host of new environments across the globe. And work over the last decade has begun to highlight the role of the wild relatives of maize—the teosintes Zea mays ssp. parviglumis and ssp. mexicana—as excellent models for dissecting long-term local adaptation.Although human-driven selection associated with maize domestication has been extensively studied, the genetic basis of natural variation is still poorly understood. Here we review studies on the genetic basis of adaptation and plasticity in maize and its wild relatives. We highlight a range of different processes that contribute to adaptation and discuss evidence from natural, cultivated, and experimental populations. From an applied perspective, understanding the genetic bases of adaptation and the contribution of plasticity will provide us with new tools to both better understand and mitigate the effect of climate changes on natural and cultivated populations.
Population Genomics in the Great Apes
Authors: Castellano David , Munch Kasper 
Published: January 2020

AbstractThe great apes play an important role as model organisms. They are our closest living relatives, allowing us to identify the genetic basis of phenotypic traits that we think of as characteristically human. However, the most significant asset of great apes as model organisms is that they share with humans most of their genetic makeup. This means that we can extend our vast knowledge of the human genome, its genes, and the associated phenotypes to these species. Comparative genomic studies of humans and apes thus reveal how very similar genomes react when exposed to different population genetic regimes. In this way, each species represents a natural experiment, where a genome highly similar to the human one, is differently exposed to the evolutionary forces of demography, population structure, selection, recombination, and admixture/hybridization. The initial sequencing of reference genomes for chimpanzee, orangutan, gorilla, the bonobo, each provided new insights and a second generation of sequencing projects has provided diversity data for all the great apes. In this chapter, we will outline some of the findings that population genomic analysis of great apes has provided, and how comparative studies have helped us understand how the fundamental forces in evolution have contributed to shaping the genomes and the genetic diversity of the great apes.
Small RNA In Situ Hybridizations on Sections of Arabidopsis Embryos
Authors: Páldi Katalin , Mosiolek Magdalena , Nodine Michael D. 
Published: January 2020

AbstractSmall RNAs mediate posttranscriptional gene silencing in plants and animals. This often occurs in specific cell or tissue types and can be necessary for their differentiation. Determining small RNA (sRNA) localization patterns at cellular resolution can therefore provide information on the corresponding gene regulatory processes they are involved in. Recent improvements with in situ hybridization methods have allowed them to be applied to sRNAs. Here we describe an in situ hybridization protocol to detect sRNAs from sections of early staged Arabidopsis thaliana (Arabidopsis) embryos.
Prolegomena to the Study of Early Modern Commentators on Johannes de Sacrobosco’s Tractatus de sphaera
Authors: Valleriani Matteo 
Published: January 2020

AbstractBy way of introduction to the present volume, a corpus of 359 treatises is described that was used in early modern educational institutions for introductory classes on cosmology and that is referenced by the following contributions. Following a taxonomy of early modern commentaries, central characteristics are analyzed in detail such as the rate of production of the treatises, the places where they were produced, and their various languages and formats. The focus then turns to the balance between the temporal dynamics of production of the treatises and the lifespans of their commentators. This reveals how the early modern textbooks first amplified medieval scientific knowledge and only slowly began to support and spread the echoes of scientific debate among contemporary scholars. The institutional and intellectual profiles of the commentary authors are then described on the basis of the results presented in the contributions to this volume. The commentators are described by referring on one hand to their relations to the universities, religious orders, and commercial institutions, and on the other to their engagement with disciplines both inside and outside the conceptual framework of the quadrivium. Finally, a quantitative summary of the results achieved by this volume is presented along with outlines for future research endeavors that will focus, consequently, on the role of the printers and publishers of the same commentaries.
The Use of Molecular Oxygen for Liquid Phase Aerobic Oxidations in Continuous Flow
Authors: Hone Christopher A. , Kappe C. Oliver 
Published: January 2020

AbstractMolecular oxygen (O2) is the ultimate “green” oxidant for organic synthesis. There has been recent intensive research within the synthetic community to develop new selective liquid phase aerobic oxidation methodologies as a response to the necessity to reduce the environmental impact of chemical synthesis and manufacture. Green and sustainable chemical processes rely not only on effective chemistry but also on the implementation of reactor technologies that enhance reaction performance and overall safety. Continuous flow reactors have facilitated safer and more efficient utilization of O2, whilst enabling protocols to be scalable. In this article, we discuss recent advancements in the utilization of continuous processing for aerobic oxidations. The translation of aerobic oxidation from batch protocols to continuous flow processes, including process intensification (high T/p), is examined. The use of “synthetic air”, typically consisting of less than 10% O2 in N2, is compared to pure O2 (100% O2) as an oxidant source in terms of process efficiency and safety. Examples of homogeneous catalysis and heterogeneous (packed bed) catalysis are provided. The application of flow photoreactors for the in situ formation of singlet oxygen (1O2) for use in organic reactions, as well as the implementation of membrane technologies, green solvents and recent reactor solutions for handling O2 are covered.
Affektive Epistemologien des Feldes
Authors: Shah Mira 
Published: January 2020

ZusammenfassungBevor mit Sherwood Washburn und Louis Leakey zwei Leitfiguren der Anthropologie in den 1950er bzw. 1960er Jahren auf die Idee kamen, junge Forscher/innen ‚ins Feld‘ zu schicken, wurde Wissen über Tiere überwiegend aus der Beobachtung gefangener oder der Autopsie toter Exemplare generiert.
The effect of fornix deep brain stimulation in brain diseases
Authors: Liu Huajie , Temel Yasin , Boonstra Jackson , Hescham Sarah 
Published: January 2020

AbstractDeep brain stimulation is used to alleviate symptoms of neurological and psychiatric disorders including Parkinson’s disease, epilepsy, and obsessive–compulsive-disorder. Electrically stimulating limbic structures has been of great interest, and in particular, the region of the fornix. We conducted a systematic search for studies that reported clinical and preclinical outcomes of deep brain stimulation within the fornix up to July 2019. We identified 13 studies (7 clinical, 6 preclinical) that examined the effects of fornix stimulation in Alzheimer’s disease (n = 9), traumatic brain injury (n = 2), Rett syndrome (n = 1), and temporal lobe epilepsy (n = 1). Overall, fornix stimulation can lead to decreased rates of cognitive decline (in humans), enhanced memory (in humans and animals), visuo-spatial memorization (in humans and animals), and improving verbal recollection (in humans). While the exact mechanisms of action are not completely understood, studies suggest fornix DBS to be involved with increased functional connectivity and neurotransmitter levels, as well as enhanced neuroplasticity.
P38 MAPK and glucocorticoid receptor crosstalk in bronchial epithelial cells
Authors: Lea Simon , Li Jian , Plumb Jonathan , Gaffey Kate , Mason Sarah , Gaskell Rosie , Harbron Chris , Singh Dave 
Published: January 2020

Abstractp38 MAPK inhibition may have additive and synergistic anti-inflammatory effects when used with corticosteroids. We investigated crosstalk between p38 MAPK inhibitors and corticosteroids in bronchial epithelial cells to investigate synergistic effects on cytokine production and the molecular mechanisms involved. Effects of the p38 MAPK inhibitor BIRB-796 and dexamethasone alone and in combination on LPS, polyI:C or TNFα -induced IL-6, CXCL8 and RANTES were assessed in 16HBEs (human epithelial cell line) and on TNFα-induced IL-6 and CXCL8 in primary human epithelial cells from asthma patients and healthy controls. 16HBEs were used to assess effects of BIRB-796 alone and in combination with dexamethasone on glucocorticoid receptor (GR) activity by reporter gene assay, expression of GR target genes and nuclear localisation using Western blot. The effects of BIRB-796 on TNFα stimulated phosphorylation of p38 MAPK and GR at serine (S) 226 by Western blot. Epithelial levels of phosphorylated p38 MAPK and GR S226 were determined by immunohistochemistry in bronchial biopsies from asthma patients and healthy controls. BIRB-796 in combination with dexamethasone increased inhibition of cytokine production in a synergistic manner. Combination treatment significantly increased GR nuclear localisation compared to dexamethasone alone. BIRB-796 inhibited TNFα-induced p38 MAPK and GR S226 phosphorylation. Phosphorylated GR S226 and p38 MAPK levels were increased in bronchial epithelium of more severe asthma patients. Molecular crosstalk exists between p38 MAPK activation and GR function in human bronchial epithelial cells, which alters GR activity. Combining a p38 MAPK inhibitor and a corticosteroid may demonstrate therapeutic potential in severe asthma.Key messages• Combination of corticosteroid and p38 inhibitor in human bronchial epithelial cells• Combination increased cytokine inhibition synergistically and nuclear GR• p38 MAPK inhibition reduced TNFα-induced phosphorylation of GR at S226 but not S211• Phosphorylated GRS226 and p38 is increased in bronchial epithelium in severe asthma• Combining a p38 inhibitor and a corticosteroid may be effective in asthma treatment
The EUropean Network of National Schizophrenia Networks Studying Gene–Environment Interactions (EU-GEI): Incidence and First-Episode Case–Control Programme
Authors:   EU-GEI WP2 Group, Gayer-Anderson Charlotte , Jongsma Hannah E. , Di Forti Marta , Quattrone Diego , Velthorst Eva , de Haan Lieuwe , Selten Jean-Paul , Szöke Andrei , Llorca Pierre-Michel , Tortelli Andrea , Arango Celso , Bobes Julio , Bernardo Miguel , Sanjuán Julio , Santos José Luis , Arrojo Manuel , Parellada Mara , Tarricone Ilaria , Berardi Domenico , Ruggeri Mirella , Lasalvia Antonio , Ferraro Laura , La Cascia Caterina , La Barbera Daniele , Menezes Paulo Rossi , Del-Ben Cristina Marta , Rutten Bart P. , van Os Jim , Jones Peter B. , Murray Robin M. , Kirkbride James B. , Morgan Craig 
Published: January 2020

Abstract
Purpose
The EUropean Network of National Schizophrenia Networks Studying Gene–Environment Interactions (EU-GEI) study contains an unparalleled wealth of comprehensive data that allows for testing hypotheses about (1) variations in incidence within and between countries, including by urbanicity and minority ethnic groups; and (2) the role of multiple environmental and genetic risk factors, and their interactions, in the development of psychotic disorders.

Methods
Between 2010 and 2015, we identified 2774 incident cases of psychotic disorders during 12.9 million person-years at risk, across 17 sites in 6 countries (UK, The Netherlands, France, Spain, Italy, and Brazil). Of the 2774 incident cases, 1130 cases were assessed in detail and form the case sample for case–control analyses. Across all sites, 1497 controls were recruited and assessed. We collected data on an extensive range of exposures and outcomes, including demographic, clinical (e.g. premorbid adjustment), social (e.g. childhood and adult adversity, cannabis use, migration, discrimination), cognitive (e.g. IQ, facial affect processing, attributional biases), and biological (DNA via blood sample/cheek swab). We describe the methodology of the study and some descriptive results, including representativeness of the cohort.

Conclusions
This resource constitutes the largest and most extensive incidence and case–control study of psychosis ever conducted.
The neutrophil–lymphocyte ratio and locoregional melanoma: a multicentre cohort study
Authors: Robinson Alyss V. , Keeble Claire , Lo Michelle C. I. , Thornton Owen , Peach Howard , Moncrieff Marc D. S. , Dewar Donald J. , Wade Ryckie G. 
Published: January 2020

Abstract
Objectives
The neutrophil–lymphocyte ratio (NLR) is an inflammatory biomarker which is useful in cancer prognostication. We aimed to investigate the differences in baseline NLR between patients with localised and metastatic cutaneous melanoma and how this biomarker changed over time with the recurrence of disease.

Methods
This multicentre cohort study describes patients treated for Stage I–III cutaneous melanoma over 10 years. The baseline NLR was measured immediately prior to surgery and again at the time of discharge or disease recurrence. The odds ratios (OR) for sentinel node involvement are estimated using mixed-effects logistic regression. The risk of recurrence is estimated using multivariable Cox regression.

Results
Overall 1489 individuals were included. The mean baseline NLR was higher in patients with palpable nodal disease compared to those with microscopic nodal or localised disease (2.8 versus 2.4 and 2.3, respectively; p < 0.001). A baseline NLR ≥ 2.3 was associated with 30% higher odds of microscopic metastatic melanoma in the sentinel lymph node [adjusted OR 1.3 (95% CI 1.3, 1.3)]. Following surgery, 253 patients (18.7%) developed recurrent melanoma during surveillance although there was no statistically significant association between the baseline NLR and the risk of recurrence [adjusted HR 0.9 (0.7, 1.1)].

Conclusion
The NLR is associated with the volume of melanoma at presentation and may predict occult sentinel lymph metastases. Further prospective work is required to investigate how NLR may be modelled against other clinicopathological variables to predict outcomes and to understand the temporal changes in NLR following surgery for melanoma.
Improvement in Hyperglycemia Prevents Surgical Site Infection Irrespective of Insulin Therapy in Non‐diabetic Patients Undergoing Gastrointestinal Surgery
Authors: Yoneda Ayami , Takesue Yoshio , Takahashi Yoshiko , Ichiki Kaoru , Tsuchida Toshie , Ikeuchi Hiroki , Uchino Motoi , Hatano Etsuro , Shinohara Hisashi , Tomita Naohiro 
Published: January 2020

AbstractBackgroundIntensive glycemic control is recommended to prevent surgical site infections (SSI). Our aim was to evaluate retrospectively the effect of improvement in hyperglycemia irrespective of insulin use on the incidence of SSI in non‐diabetic patients.MethodsThe highest blood glucose (BG) concentration within 12 h (early peak BG) and the final BG from 12 to 24 h after surgery were evaluated in patients who underwent gastrointestinal surgery. Patients with an early peak BG of ≥150 mg/dL were divided into those with persistent (final BG of ≥150 mg/dL) and improved hyperglycemia (final BG of <150 mg/dL). Patients without hyperglycemia and those with late‐onset hyperglycemia were also assessed for SSI risk.ResultsOverall, 1612 patients were studied (diabetes, n = 293). Although hyperglycemia increased the SSI rates in non‐diabetic patients, no correlation was demonstrated in patients with diabetes at any cutoff final BG defining htperglycemia except for 180 mg/dL. Hyperglycemia improved without insulin therapy in 283 of 512 non‐diabetic patients who had early hyperglycemia. The adjusted standardized residual for those with SSI and persistent hyperglycemia was 5.2 (P < 0.05). In contrast, the absence of hyperglycemia was a significant preventive factor for SSI. In the multivariate analyses, persistent hyperglycemia was an independent risk factor for SSI (odds ratio 1.54; 95% confidence interval 1.03–2.31).ConclusionsRemission of hyperglycemia within 24 h after surgery prevented SSI in non‐diabetic patients. Considering that hyperglycemia improved in approximately half of patients without insulin therapy, commencement of insulin dosing after two consecutive BGs of ≥150 mg/dL might be reasonable, especially in general wards.