bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinicopathological Study of Mucinous Carcinoma of Breast with Emphasis on Cytological Features: A Study at Tertiary Care Teaching Hospital of South India
Authors: Chikkannaiah Panduranga , Thangngeo Deinu , Guruprasad Chanigaramaiah , Venkataramanappa Srinivasamurthy 
Published: August 2020

Abstract
Introduction Mucinous carcinoma (MC) is a rare form of breast cancer. It accounts for 1 to 7% of the cases and characterized by the presence of extracellular mucin (ECM). Depending on the amount of mucin, it is classified into pure mucinous carcinoma (> 90%, PMC) and mixed mucinous carcinoma (MMC; < 90%). In comparison to most common subtypes, MC is having better prognosis. There exist clinicopathological differences among PMC and MMC and also MC and IDC-NOS.
Materials and Methods MCs diagnosed between January 2012 and December 2017 were included. Fine needle aspiration cytology smears were screened for cellularity, ECM, nuclear pleomorphism, signet ring cells (SRC), mucinophages, and myxovascular fragments (MVF). Histopathology slides were screened to confirm the diagnosis. Immunohistochemistry slides were graded as per the standard protocol. Statistical analyses were performed by SPSS software.
Results In the present study, MC constituted 3.3%. The mean age of the patients was 50.9 years. ECM, mucinophages, and SRC were the key diagnostic cytological features. The PMC and MMC were clinicopathologically distinct with respect to gross findings and lymph node status. MMCs were highly proliferative. The mean duration of follow-up was 24.5 months. Complications were more common in MMC than PMC. Lymph node involvement is the key prognostic factor and it is independent of other prognostic factors like age, size, and hormonal receptor status.
Conclusion PMC are rare subtype of breast cancer. The diagnostic cytological features are ECM, MVF, and SRC. MMC and PMC are clinicopathologically and genetically distinct.
A 25-y longitudinal dolphin cohort supports that long-lived individuals in same environment exhibit variation in aging rates
Authors: Venn-Watson Stephanie , Jensen Eric D. , Schork Nicholas J. 
Published: August 2020

Significance
Aging is a degradative process that varies among individuals. Due to limitations in defining and differentiating aging rates in human populations, understanding why some people appear to age slower than others has proven difficult. We analyzed 44 blood-based indices of health as candidate aging rate biomarkers collected over a 25-y period on a relevant, long-lived population of dolphins. Evidence of subsets of dolphins exhibiting slow and accelerated aging rates were detected, despite sharing the same environment, diet, and health care. Furthermore, some dolphin subsets were more likely to develop clinically relevant conditions, including anemia and immunosenescence. Our results support the notion that aging rates in long-lived mammals may be defined and provide insight into novel interventions to delay aging.
Nucleosome allostery in pioneer transcription factor binding
Authors: Tan Cheng , Takada Shoji 
Published: August 2020

Significance
Upon binding of effectors, allosteric molecules change their structures and responses to the downstream molecules, which can be viewed as the molecular if−then device. Simulating binding of two pioneer transcription factors (TFs), Sox2 and Oct4, to a nucleosome, which is the fundamental unit of genome folding, we found that a nucleosome acts as a new type of allosteric molecule. Free nucleosomes exhibited rotation-coupled sliding of their DNA among metastable positions. The Sox2 binding on them selected a specific rotational phase of its motif, inducing global sliding of nucleosomal DNA. Consequently, the repositioned DNA affected the accessibility of another TF, Oct4, or the second molecule of Sox2 at a distant region within the nucleosome, which thus is a long-distance allosteric effect.
Noncovalent π-stacked robust topological organic framework
Authors: Meng Dong , Yang Jonathan Lee , Xiao Chengyi , Wang Rui , Xing Xiaofei , Kocak Olkan , Aydin Gulsevim , Yavuz Ilhan , Nuryyeva Selbi , Zhang Lei , Liu Guogang , Li Zhenxing , Yuan Shuai , Wang Zhao-Kui , Wei Wei , Wang Zhaohui , Houk K. N. , Yang Yang 
Published: August 2020

Significance
A robust noncovalent π∙∙∙π interaction-stacked organic framework (OF), called πOF, consisting of a permanent three-dimensional porous structure that is held together by pure intralayer noncovalent π∙∙∙π interactions is synthesized and characterized. πOF shows excellent thermostability and high recyclability and exhibits self-healing properties by which the parent porosity is recovered upon solvent annealing at room temperature. We demonstrate remarkable transport properties of πOF in an organic-field-effect transistor, with mobility that is superior to traditional covalent OFs. πOF is a porous and conductive material for high-performance organic electronics.
Methodological concerns and their solutions in third-age language learning studies
Authors: van der Ploeg Mara , Keijzer Merel , Lowie Wander 
Published: August 2020

Abstract
With the average life expectancy in especially developed countries steadily increasing, healthy ageing is
prioritised on the research agenda. Various studies have looked into bilingualism as a possible anti-ageing tool to delay the
onset of symptoms of degenerative diseases like Alzheimer’s, with as perhaps the most promising recent line of work intervention
studies that introduce bilingual experiences to seniors in the form of foreign language courses meant to induce a protective
effect on cognitive decline. Unfortunately, the scant studies available have not found convincing results, most likely due to
several pitfalls in their designs, one of the most important being that method of instruction is rarely specified or controlled
for. In this paper, we identify methodological concerns that need to be addressed when conducting experimental work related to
third-age language learning, resulting in a research agenda for third-age language learning studies.
The cost of ignoring degrees of Abstand in defining a regional language
Authors: Leonardi Mara Maya Victoria , Tamburelli Marco 
Published: August 2020

Abstract
It is generally accepted that the concepts ‘language’ and ‘dialect’ are not entirely linguistic
notions, but also involve social, cultural and political factors. Nonetheless, it is still nowadays difficult to agree
upon a set of satisfying criteria by which ‘languages’ can be differentiated from ‘dialects’. In this chapter, we
analyse the linguistic context present in South Tyrol in order to highlight the consequences of these unsatisfying
definitions. Using the intelligibility criterion, we demonstrate that there is a certain degree of
Abstand between Standard German and the Bavarian variety spoken in South Tyrol. We then show how
this degree of Abstand affects the early stages of acquisition and the linguistic performance of
South Tyrolean children.
Surveying the ethnolinguistic vitality of two contested languages
Authors: Dołowy-Rybińska Nicole , Soria Claudia 
Published: August 2020

Abstract
In this chapter we present the results of a Polish-Italian research project aimed at evaluating and
comparing the vitality of two contested languages: Kashubian in Poland and Piedmontese in Italy.
Despite their different institutional status (Kashubian is a language recognised under the Polish
law while Piedmontese is a contested language that remains unrecognised under Italian law), they show similarities
with regard to their range of uses and speakers’ attitudes. The ethnolinguistic vitality of both communities is low,
and so are the status and prestige of both languages in their respective countries. Consciousness about the importance
of their maintenance is weakening, both within the communities and in wider social contexts. As they belong to the
same language family as their respective dominant languages, they were/are treated as dialects of the state languages
and thus not worthy of preservation. However, current accounts of language vitality for Kashubian and Piedmontese are
rather optimistic. We believe that this optimism is mainly due to an over-estimation of the importance of number of
speakers as a parameter for assessing vitality over others that address the ideology surrounding the language, such as
speakers’ attitudes, stigma, and the comparison between actual and perceived use of the language.
This chapter presents the preliminary results of a new survey addressing the vitality of these two
languages. The survey makes use of a new combination of ethnolinguistic vitality parameters and is specifically
focused on aspects related to language ideology.
Revitalising contested languages
Authors: Coluzzi Paolo , Brasca Lissander , Scuri Simona 
Published: August 2020

Abstract
This chapter opens with an introduction to the Lombard language and its institutional and
sociolinguistic situation, including the reasons why the term “language” is used and not the commonly used “dialect”.
The second and main part of the chapter looks at what has been done to date and what is currently being done to try to
reverse the ongoing language shift that is constantly reducing the number of speakers and the domains where the
language is used. This includes a detailed account of corpus planning, particularly the phase known as ‘graphisation’
(writing systems, including the latest polynomic system for all Lombard varieties), status planning and acquisition
planning, all of which have been carried out by committed individuals and private associations. The chapter closes
with a short discussion on the present status of Lombard with reference to the recent regional law for the protection
and promotion of the Lombard language.
Improving tolerance of cotton (
Gossypium hirsutum
L.) to drought and heat stress
Authors: Ul-Allah Sami , Iqbal Muhammad , Naeem Muhammad 
Published: August 2020

Abstract

Drought and heat stress are burning issues for agriculture in the climate change scenario due to which lower yield and production of crops have been projected. In this situation, sustainable production of food and fiber crops is a challenge. Cotton (
Gossypium hirsutum
L.) is a major cash crop of the world including Pakistan, and its growth and yield are highly influenced by drought and heat stress. Development of drought and heat stress tolerant genotype is the most sustainable way to cope with this stress. In this review, different tolerance mechanisms of the cotton plant against heat and drought stress are discussed. These tolerance mechanisms include morphological, physiological, biochemical, and genetic adaptations of cotton plant to the external stress. Moreover, different strategies to improve the tolerance of cotton against heat and drought stress have also been discussed. As both stresses complement each other in most of the cases and some mechanisms are the same for both stresses, therefore, both are discussed together. Prospects and challenges have also been discussed.
Modified forward and inverse Born series for the Calderon and diffuse-wave problems
Authors: Abhishek Anuj , Bonnet Marc , Moskow Shari 
Published: August 2020

Abstract
We propose a new direct reconstruction method based on series inversion for electrical impedance tomography (EIT) and the inverse scattering problem for diffuse waves. The standard Born series for the forward problem has the limitation that the series requires that the contrast lies within a certain radius for convergence. Here, we instead propose a modified Born series which converges for the forward problem unconditionally. We then invert this modified Born series and compare reconstructions with the usual inverse Born series. We also show that the modified inverse Born series has a larger radius of convergence.
Equilibrium shape of misfitting precipitates with anisotropic elasticity and anisotropic interfacial energy
Authors: Joshi Tushar , Arora Rajat , Basak Anup , Gupta Anurag 
Published: August 2020

Abstract
Extended finite element method and anisotropic level set method are coupled to determine locally stable equilibrium shapes of homogeneous and inhomogeneous precipitates in a large matrix. The bulk elasticity and the interfacial energy density are both allowed to be anisotropic while the misfit strain is kept dilatational. The anisotropy in the crystalline interfacial energies, incorporated through a dependence on the orientation, renders the evolution equation unstable for certain orientation regimes. The equation is regularized by adding a curvature term in the interface energy density which in turn requires the level set method to be modified suitably. The developed methodology is verified for several existing solutions before obtaining new results in the presence of anisotropic interfacial energy. Equilibrium shapes are obtained both for single and multiple precipitates with an emphasis on the interplay between the anisotropies in bulk elasticity and interface energy density.
Peatland protection and restoration are key for climate change mitigation
Authors: Humpenöder Florian , Karstens Kristine , Lotze-Campen Hermann , Leifeld Jens , Menichetti Lorenzo , Barthelmes Alexandra , Popp Alexander 
Published: August 2020

Abstract
Peatlands cover only about 3% the global land area, but store about twice as much carbon as global forest biomass. If intact peatlands are drained for agriculture or other human uses, peat oxidation can result in considerable CO2 emissions and other greenhouse gases (GHG) for decades or even centuries. Despite their importance, emissions from degraded peatlands have so far not been included explicitly in mitigation pathways compatible with the Paris Agreement. Such pathways include land-demanding mitigation options like bioenergy or afforestation with substantial consequences for the land system. Therefore, besides GHG emissions owing to the historic conversion of intact peatlands, the increased demand for land in current mitigation pathways could result in drainage of presently intact peatlands, e.g. for bioenergy production. Here, we present the first quantitative model-based projections of future peatland dynamics and associated GHG emissions in the context of a 2 °C mitigation pathway. Our spatially explicit land-use modelling approach with global coverage simultaneously accounts for future food demand, based on population and income projections, and land-based mitigation measures. Without dedicated peatland policy and even in the case of peatland protection, our results indicate that the land system would remain a net source of CO2 throughout the 21st century. This result is in contrast to the outcome of current mitigation pathways, in which the land system turns into a net carbon sink by 2100. However, our results indicate that it is possible to reconcile land use and GHG emissions in mitigation pathways through a peatland protection and restoration policy. According to our results, the land system would turn into a global net carbon sink by 2100, as projected by current mitigation pathways, if about 60% of present-day degraded peatlands would be rewetted in the coming decades, next to the protection of intact peatlands.
The effect of cold and hot pressing on mechanical properties and tribological behavior of Mg-Al2O3 nanocomposites
Authors: Rahmani Kaveh , Sadooghi Ali , Hashemi Seyed Jalal 
Published: August 2020

Abstract
In this research, pure powder of Mg was mixed with 0, 1.5, 3, 5%vol. of Aluminium oxide in a planetary mill. Next, the powder mixture was poured in a mold and pressed in two diverse conditions of (1) hot pressing at 600 MPa pressure and 450 °C temperature for 25 min and (2) cold pressing at 600 MPa pressure in the room temperature and samples sintered in a furnace under Argon gas at 450 °C temperature for 2 h. Density and mechanical properties, e.g., microhardness, and wear properties of the produced samples were assessed. Also, metallographic photography and SEM analysis were done on the samples to investigate their microstructure properties and analyze their worn surfaces. The results revealed that with an increase in the volume of the reinforcement particles, the experimental density and microhardness soared, on the contrary, the relative density showed a decreasing trend. Moreover, the results of the microhardness analysis for the produced samples via hot pressing method were achieved better than those of cold pressing, as the highest hardness 81HV was achieved for %5 vol. Al2O3 containing samples produced through the hot pressing method, which was about %18 more than that of the %5 vol. Al2O3 containing samples produced via the cold pressing method and was about %85 more than of the pure Mg samples produced via the hot pressing method. The results of the samples’ wear properties also signified the improvement of wear resistance and decrease of mass loss with an increase in the volume fraction of the reinforcement particles. The lowest mass loss of 2.5 g was obtained for the sample containing %5 vol. of the reinforcement particle which was produced via the hot pressing method. This value was less about %40 and %80 compared to pure Mg samples produced via hot and cold pressing methods, respectively.
Cadmium (II) removal from aqueous solution using magnetic spent coffee ground biochar: Kinetics, isotherm and thermodynamic adsorption
Authors: Hussain Naeem , Chantrapromma Suchada , Suwunwong Thitipone , Phoungthong Khamphe 
Published: August 2020

Abstract
Spent coffee grounds are a waste generated in large amounts by the food industry producing instant coffee. While it is used as animal feed, mostly spent coffee grounds are burned. In this study, The spent coffee grounds were modified to be magnetic in order to remove cadmium (II) ion. The magnetic solids are easy to separate from water with a magnet. The biochar was prepared at 400 °C. Several factors that affect the adsorption were studied, such as adsorbent dosage, contact time, initial metal ion concentration and effect of solution pH. At the optimum conditions (the adsorbent dosage 0.1 g l−1, pH 7, time 30 min and the initial concentration 40 mg l−1), the percentage removal of Cd(II) was ∼96%. The surface morphology of the adsorbent showed iron particles with a cubical shape on the adsorbent, with 3–20 μm average diameter. The adsorption data was well fit by a pseudo-second order and a Langmuir isotherm, with the maximum adsorption capacity 10.42 mg/g. The adsorption process was spontaneous and endothermic. The main goal of the study is to re-use the spent coffee grounds waste and use low-cost adsorbent for cadmium (II) removal in aqueous solution. The magnetic biochar was easily manipulated by external magnetic fields after treatment. With good adsorbent performance of the magnetic biochar, spent coffee grounds could be used to treat Cd(II) contamination.
An approach for normalization and quality control for NanoString RNA expression data
Authors: Bhattacharya Arjun , Hamilton Alina M , Furberg Helena , Pietzak Eugene , Purdue Mark P , Troester Melissa A , Hoadley Katherine A , Love Michael I 
Published: August 2020

AbstractThe NanoString RNA counting assay for formalin-fixed paraffin embedded samples is unique in its sensitivity, technical reproducibility and robustness for analysis of clinical and archival samples. While commercial normalization methods are provided by NanoString, they are not optimal for all settings, particularly when samples exhibit strong technical or biological variation or where housekeeping genes have variable performance across the cohort. Here, we develop and evaluate a more comprehensive normalization procedure for NanoString data with steps for quality control, selection of housekeeping targets, normalization and iterative data visualization and biological validation. The approach was evaluated using a large cohort ($N=\kern0.5em 1649$) from the Carolina Breast Cancer Study, two cohorts of moderate sample size ($N=359$ and$130$) and a small published dataset ($N=12$). The iterative process developed here eliminates technical variation (e.g. from different study phases or sites) more reliably than the three other methods, including NanoString’s commercial package, without diminishing biological variation, especially in long-term longitudinal multiphase or multisite cohorts. We also find that probe sets validated for nCounter, such as the PAM50 gene signature, are impervious to batch issues. This work emphasizes that systematic quality control, normalization and visualization of NanoString nCounter data are an imperative component of study design that influences results in downstream analyses.
Identification of the RNase-binding site of SARS-CoV-2 RNA for anchor primer-PCR detection of viral loading in 306 COVID-19 patients
Authors: Xu Tao , Wang Jingu , Hu Bingjie , Zhang Guosi , Zhou Wu , Zheng Meiqin , Shen Bo , Sun Baochang , Zhang Yanjun , Chen Yin , Yu Jian , Liang Min , Pan Jingye , Chen Chengshui , Chen Haixiao , Jiang Minghua , Xu Liangde , Qu Jia , Chen Jiang-Fan 
Published: August 2020

Abstract
The pandemic of coronavirus disease 2019 (COVID-19) urgently calls for more sensitive molecular diagnosis to improve sensitivity of current viral nuclear acid detection. We have developed an anchor primer (AP)-based assay to improve viral RNA stability by bioinformatics identification of RNase-binding site of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and implementing AP dually targeting the N gene of SARS-CoV-2 RNA and RNase 1, 3, 6. The arbitrarily primed polymerase chain reaction (AP-PCR) improvement of viral RNA integrity was supported by (a) the AP increased resistance of the targeted gene (N gene) of SARS-CoV-2 RNA to RNase treatment; (b) the detection of SARS-CoV-2 RNA by AP-PCR with lower cycle threshold values (−2.7 cycles) compared to two commercially available assays; (c) improvement of the viral RNA stability of the ORF gene upon targeting of the N gene and RNase. Furthermore, the improved sensitivity by AP-PCR was demonstrated by detection of SARS-CoV-2 RNA in 70–80% of sputum, nasal, pharyngeal swabs and feces and 36% (4/11) of urine of the confirmed cases (n = 252), 7% convalescent cases (n = 54) and none of 300 negative cases. Lastly, AP-PCR analysis of 306 confirmed and convalescent cases revealed prolonged presence of viral loading for &gt;20 days after the first positive diagnosis. Thus, the AP dually targeting SARS-CoV-2 RNA and RNase improves molecular detection by preserving SARS-CoV-2 RNA integrity and reveals the prolonged viral loading associated with older age and male gender in COVID-19 patients.
DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method
Authors: Chu Yanyi , Shan Xiaoqi , Chen Tianhang , Jiang Mingming , Wang Yanjing , Wang Qiankun , Salahub Dennis Russell , Xiong Yi , Wei Dong-Qing 
Published: August 2020

Abstract
Identifying drug-target interactions (DTIs) is an important step for drug discovery and drug repositioning. To reduce the experimental cost, a large number of computational approaches have been proposed for this task. The machine learning-based models, especially binary classification models, have been developed to predict whether a drug-target pair interacts or not. However, there is still much room for improvement in the performance of current methods. Multi-label learning can overcome some difficulties caused by single-label learning in order to improve the predictive performance. The key challenge faced by multi-label learning is the exponential-sized output space, and considering label correlations can help to overcome this challenge. In this paper, we facilitate multi-label classification by introducing community detection methods for DTI prediction, named DTI-MLCD. Moreover, we updated the gold standard data set by adding 15,000 more positive DTI samples in comparison to the data set, which has widely been used by most of previously published DTI prediction methods since 2008. The proposed DTI-MLCD is applied to both data sets, demonstrating its superiority over other machine learning methods and several existing methods. The data sets and source code of this study are freely available at https://github.com/a96123155/DTI-MLCD.