bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective evaluation of accuracy of fine needle aspiration biopsy for breast lesions using the International Academy of Cytology Yokohama System for reporting breast cytopathology
Authors: Agrawal Shruti , Anthony Michael Leonard , Pal Pranoy , Singh Divya , Mehan Anoushika , Singh Ashok , Joshi Prashant , Kumar Arvind , Ravi Bina , Rao Shalinee , Chowdhury Nilotpal 
Published: December 2020

AbstractBackgroundClassification of breast leasions into different cytological groups (1-5) can accurately be done using the International Academy of Cytology (IAC) Yokohama System for reporting breast cytopathology. Fine needle aspiration biopsy (FNAB) of breast leasions has been considered to be the primary investigation in detecting breast cancers, especially in low-cost settings. The main objective of this study was to prospectively re-confirm the diagnostic accuracy of breast FNAB using the IAC Yokohama system. Additionally, separate separate secondary subgroup analysis was done to confirm the accuracy of breast FNAB excluding lymph-node positive and lymphadenopathy positive tumors.Material and methodsA prospective study was done in a tertiary care centre in North India on patients undergoing core-needle /incisional/excisional biopsy of breast lesions between 1st September 2019 to 30th November,2020 (519 biopsies on 487 unique patients). Of these 519 histopathology biopsies, 505 had corresponding FNAB report of the same site. The FNAB was reported using the IAC Yokohama system and the most suitable category was allotted in every case. The rates of malignancy for each category and the accuracy of breast FNAB in diagnosing malignancy were calculated.ResultsOf the total 487 patients, 120 cases were benign on histology, while 367 were malignant. The rates of malignancy in benign, atypical, suspicious and malignant categories were 5%, 25%, 71% and 99.7% respectively. The diagnostic accuracy of atypical, suspicious and malignant categories was calculated as 90.1%, 95.2% and 93.3% respectively.ConclusionThe high sensitivity and specificity for each scenario for all tumors and for each examined BIRADS category/ies suggest excellent accuracy for Breast FNAB using the IAC Yokohama system.
Identification of SUMO targets required to maintain human stem cells in the pluripotent state
Authors: Mojsa Barbara , Tatham Michael H. , Davidson Lindsay , Liczmanska Magda , Branigan Emma , Hay Ronald T. 
Published: December 2020

AbstractTo determine the role of SUMO modification in the maintenance of pluripotent stem cells we used ML792, a potent and selective inhibitor of SUMO Activating Enzyme. Treatment of human induced pluripotent stem cells with ML792 initiated changes associated with loss of pluripotency such as reduced expression of key pluripotency markers. To identify putative effector proteins and establish sites of SUMO modification, cells were engineered to stably express either SUMO1 or SUMO2 with TGG to KGG mutations that facilitate GlyGly-K peptide immunoprecipitation and identification. A total of 976 SUMO sites were identified in 427 proteins. STRING enrichment created 3 networks of proteins with functions in regulation of gene expression, ribosome biogenesis and RNA splicing, although the latter two categories represented only 5% of the total GGK peptide intensity. The remainder have roles in transcription and chromatin structure regulation. Many of the most heavily SUMOylated proteins form a network of zinc-finger transcription factors centred on TRIM28 and associated with silencing of retroviral elements. At the level of whole proteins there was only limited evidence for SUMO paralogue-specific modification, although at the site level there appears to be a preference for SUMO2 modification over SUMO1 in acidic domains. We show that SUMO is involved in the maintenance of the pluripotent state in hiPSCs and identify many chromatin-associated proteins as bona fide SUMO substrates in human induced pluripotent stem cells.
Female meiosis II and pronuclear fusion require Bicaudal-D
Authors: Vazquez-Pianzola Paula , Beuchle Dirk , Saro Gabriella , Hernández Greco , Maldonado Giovanna , Brunßen Dominique , Meister Peter , Suter Beat 
Published: December 2020

ABSTRACTDrosophilaClathrin heavy chain (Chc) is transported by the dynein/dynactin microtubule motor through its interaction with the adaptor protein Bicaudal-D (BicD). Here we show thatDrosophilaBicD and Chc localize to centrosomes and spindles during mitosis and to the tandem spindles during female meiosis II. Reducing the activity of BicD::GFP specifically in freshly laid eggs revealed that BicD is essential for the production of normal female meiosis II products and for pronuclear fusion. Chc interacts with BicD and D-TACC, and BicD is needed to correctly localize the microtubule-stabilizing factors D-TACC, clathrin, and Msps to the meiosis II spindles, suggesting that BicD acts by localizing these proteins. In unfertilized eggs, reduced BicD levels cause the female meiotic products to re-enter the cell cycle. As BicD is required to localize the spindle assembly checkpoint (SAC) components Mad2 and BubR1 to the female meiotic products, it appears that BicD functions to localize them to control metaphase arrest of polar bodies. Finally,DrosophilaandC. elegansorthologs ofBicDandtaccare also needed for pronuclear fusion.
Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence
Authors: Wei Chendan , Wang Zhenyi , Wang Jianyu , Teng Jia , Shen Shaoqi , Xiao Qimeng , Bao Shoutong , Feng Yishan , Zhang Yan , Li Yuxian , Sun Sangrong , Yue Yuanshuai , Wu Chunyang , Wang Yanli , Zhou Tianning , Xu Wenbo , Yu Jigao , Wang Li , Wang Jinpeng 
Published: December 2020

AbstractExtensive sequence similarity between duplicated gene pairs produced by paleo-polyploidization may result from illegitimate recombination between homologous chromosomes. The genomes of Asian cultivated rice Xian/indica(XI) and Geng/japonica(GJ) have recently been updated, providing new opportunities for investigating on-going gene conversion events. Using comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19%–5.77% of genes duplicated across three genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~0.4 mya, with more (7.77%–9.53%) showing conversion of only gene portions. Independently converted duplicates surviving in genomes of different subspecies often used the same donor genes. On-going gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes 11 and 12 in each genome most affected. Notably, on-going gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. Chromosome rearrangement after polyploidization may result in gene loss, providing a basis for on-going gene conversion, and may have contributed directly to restricted recombination/conversion between homoeologous regions. Gene conversion affected biological functions associated with multiple genes, such as catalytic activity, implying opportunities for interaction among members of large gene families, such as NBS-LRR disease-resistance genes, resulting in gene conversion. Duplicated genes in rice subspecies generated by grass polyploidization ~100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies.One-sentence summaryOn-going gene conversion between duplicated genes produced by 100 mya polyploidization contributes to rice subspecies divergence, often involving the same donor genes at chromosome termini.
Heterogeneity of Neuronal Populations Within Columns of Primate V1 Revealed by High-Density Recordings
Authors: Zhu Shude , Xia Ruobing , Chen Xiaomo , Moore Tirin 
Published: December 2020

AbstractPrimary visual cortex (V1) has been the focus of extensive neurophysiological investigation, and its laminar organization provides a key exemplar of the functional logic of neocortical microcircuits. Using newly developed high-density, linear array probes, we measured visual responses from large populations of simultaneously recorded neurons distributed across layers of macaque V1. In single recordings, myriad differences in the functional properties of neuronal subpopulations could be observed. In particular, we found that although standard measurements of orientation selectivity yielded only minor differences between laminar compartments, decoding of stimulus orientation from layer 4C responses was superior to that of both superficial and deep layers within the same cortical column. The superior orientation discrimination within layer 4C was associated with greater response reliability of individual neurons rather than lower correlated activity with neuronal populations. The results demonstrate the utility of high-density electrophysiology in revealing the functional organization and network properties of neocortical microcircuits in single experiments.
Repetitive mild traumatic brain injury causes synergistic effects on mortality
Authors: Willes Ashley M , Krcmarik Tori R , Daughtry Alexander E , Brusich Douglas J 
Published: December 2020

AbstractRepetitive mild TBI (rmTBI) events are common in the U.S. However, rmTBI is challenging to study and this contributes to a poor understanding of mechanistic bases for disease following these injuries. We used fruit flies(D. melanogaster)and a modified version of the high-impact trauma (HIT) method of TBI to assess the pattern of mortality observed after rmTBI. We found that the pattern of mortality was synergistic after a critical number of injuries, similar to that observed previously at more moderate levels of TBI severity. The identity of cellular and molecular factors which contribute to the synergistic effect on mortality remain unknown, but this model offers a platform for investigation into such factors.
Environmental uncertainty and cross-buying in logistics outsourcing arrangements: a resource dependence perspective
Authors: Hofer Adriana Rossiter , Jin Yao Henry , Knemeyer A. Michael 
Published: December 2020

PurposeThis study follows the tenets of the resource dependence theory (RDT) to investigate the effects of four dimensions of industry-level environmental uncertainty – munificence, dynamism, complexity and innovative intensity – on a shipper's cross-buying (i.e. outsourcing across multiple service categories) in logistics outsourcing arrangements.Design/methodology/approachNegative binomial regression was used to test the hypotheses with a sample of US manufacturers. Measures were developed through information acquired from a proprietary database of 3PL companies obtained through Armstrong and Associates, Inc. and publicly available industry measures from the US Manufacturing Census and Compustat.FindingsThe findings indicate that individual dimensions of environmental uncertainty exhibit distinct influences on shippers' cross-buying in their logistics outsourcing arrangements. Specifically, the growth and initial innovative intensity of shippers' industries lead to an increased number of logistics service categories outsourced to 3PLs, while industry dynamism and exceptionally high innovative intensity drive the opposite effect.Practical implicationsThese findings provide valuable guidance to 3PLs with respect to decisions related to the acquisition of specialized transportation, storage, information systems and personnel assets to serve specific industries. The findings highlight industry conditions that are more likely to lead shippers to outsource across a wider array of logistics service categories and, as a result, potentially yield higher customer retention and profit margins.Originality/valueWhile extant 3PL literature posits that shippers' individual strategic orientations and capabilities impact their outsourcing strategy, this study contributes to the literature by providing a theoretical-based empirical examination of the industry-level influencers of such behavior.
Dutch investment advisors’ perceptions towards the MiFID II directive
Authors: Loonen Tom 
Published: December 2020

Purpose
The Markets in Financial Instruments Directive (MiFID) II directive was enforced in the EU in January 2018. While EU-member states implemented this directive in their national legislation, investment firms are still enforcing compliance. With the purpose of “investor protection”, the purpose of this study is to investigate the effectiveness of transparency, suitability, warning and information requirements. How do investment advisers view and embrace these MiFID II requirements? Are differences evident within this group of professionals?

Design/methodology/approach
In total, 267 Dutch investment advisors serving non-professional investors daily completed structured surveys on their opinion of the acceptance and effectiveness of the MiFID II requirements. The findings are compared with existing literature to examine similarities with other legislation.

Findings
The results demonstrated differences depending on the investment firms’ size and investment advisors’ seniority and gender. Professionals should be critical of new legislation and regulations, as it limits their autonomy. However, female investment advisors and those with up to ten years’ experience are less critical of the effectiveness of the MiFID II requirements, embracing them without discussion. Investment advisors in large investment firms believe that MiFID II contributes to investors’ interests, whereas those in small and medium-sized investment firms often do not share this opinion. For example, respondents considered cost transparency an effective requirement to achieve better investment services and protect investors’ interests.

Originality/value
The effectiveness and applicability of legislation are often viewed from a legal perspective, and enforcement is essential. However, this study explores legislation from the perspective of professionals under supervision.
Determinants of SMEs intention to adopt Islamic crowdfunding model in Northwestern Nigeria
Authors: Kazaure Mansur Ahmed , Abdullah Abdul Rashid , Zawawi Dahlia Binti , Hamzah Amer 
Published: December 2020

Purpose
The study aims is to examine the determinant factors of small and medium enterprises’ (SMEs’) intention to adopt the Islamic crowdfunding model as alternative sources of finance.

Design/methodology/approach
Using a survey questionnaire, 385 responses were received from owners and managers of SMEs in three states (Kano, Kaduna and Katsina) of northwestern Nigeria and analyses using PLS-SEM 3.0 software.

Findings
All hypotheses were found to be significant.

Research limitations/implications
The research focused only on northwestern Nigeria; there is a need for further research to focus on other geographical zones in Nigeria.

Practical implications
Crowd funders and policymakers can use these findings to enable the adoption of the Islamic crowdfunding model.

Originality/value
The previous study has not examined the role of technology acceptance model in the adoption of the financial model; these findings contribute to the crowdfunding literature by filling this gap.
Characteristics of Aboriginal and Torres Strait Islander peoples attending Australian emergency departments
Authors: Lim Jolene CJ , Harrison Glenn , Raos Maximilian , Moore Katie 
Published: December 2020

AbstractObjectiveAboriginal and Torres Strait Islander patients are overrepresented in Australian EDs. The present study aimed to assess their characteristics in utilising ED services at a national level.MethodsThis exploratory, quantitative study used 2016–2017 de‐identified data from the National Non‐admitted Patient Emergency Department Care Database to assess the proportions (with 95% confidence interval) of Indigenous and non‐Indigenous Australians across various aspects of ED presentations, including mode of arrival, triage scale, diagnosis information, episode end status and ED length of stay. Episode level ED data were compared by Indigenous status and geographical remoteness of EDs.ResultsOf 7.4 million presentations, 6.58% were Indigenous presentations, with over two‐thirds occurring in regional and remote EDs. Indigenous patients were more likely than non‐Indigenous patients to arrive to EDs by ambulance and police/correctional services vehicle across all remoteness areas. Additionally, they were more likely to present with respiratory system illness, illness of the skin/subcutaneous tissue/breast and mental/behavioural disorders. Indigenous Australians were more likely to leave EDs before being seen or care complete (odds ratio 1.73, 95% confidence interval 1.71–1.74), and this was observed for patients classified across all levels of triage scale.ConclusionsThis is the first national study looking at the characteristics of and reasons for presenting to Australian EDs for Indigenous and non‐Indigenous patients. Our findings provide important insight into the potential factors affecting Indigenous patient care, and an impetus for ongoing research and advocacy work to improve the quality of emergency care provided to Indigenous Australians.
Effective double‐digest RAD sequencing and genotyping despite large genome size
Authors: Gargiulo Roberta , Kull Tiiu , Fay Michael F. 
Published: December 2020

AbstractObtaining informative data is the ambition of any genomic project, but in nonmodel species with very large genomes, pursuing such a goal requires surmounting a series of analytical challenges. Double‐digest RAD sequencing is routinely used in nonmodel organisms and offers some control over the volume of data obtained. However, the volume of data recovered is not always an indication of the reliability of data sets, and quality checks are necessary to ensure that true and artefactual information is set apart. In the present study, we aim to fill the gap existing between the known applicability of RAD sequencing methods in plants with large genomes and the use of the retrieved loci for population genetic inference. By analysing two populations of Cypripedium calceolus, a nonmodel orchid species with a large genome size (1C ~ 31.6 Gbp), we provide a complete workflow from library preparation to bioinformatic filtering and inference of genetic diversity and differentiation. We show how filtering strategies to dismiss potentially misleading data need to be explored and adapted to data set‐specific features. Moreover, we suggest that the occurrence of organellar sequences in libraries should not be neglected when planning the experiment and analysing the results. Finally, we explain how, in the absence of prior information about the genome of the species, seeking high standards of quality during library preparation and sequencing can provide an insurance against unpredicted technical or biological constraints.
Prediction of photofading of N‐β‐hydroxyethylamino‐o‐nitrophenyl derivatives: a theoretical study
Authors: Wojciechowski Krzysztof , Szuster Lucjan 
Published: December 2020

AbstractUntil now, the lightfastness of hair dyes had not been investigated using all‐valence molecular orbital methods. The results of calculations are used to obtain the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) frontier electron density, which can reflect the propensity for electrophilic or nucleophilic attack at an atom in a molecule. Using semi‐empirical quantum chemical methods AM1 and PM3, we have calculated the reactivity rates , superdelocalisability and electron density distribution in the tested dyes. We have found that the photooxidation of hair dyes (photochemical decomposition of hair dyes) and derivatives of N‐β‐hydroxyethylamino‐o‐nitrobenzene occurs through the degradation of the N‐β‐hydroxyethylamine substituent and on C2 or C4 atom (C4–NO2) in the process of electrophilic reaction with singlet oxygen 1O2 or nucleophilic reaction on the C1 carbon atom of the aromatic ring, with the use of superoxide anion radical O2●. The structures of the dyes were optimised using MM+, DM and AM1 or PM3 until constant energy value was realised with a 0.01 kcal/mol convergence criterion.
Preliminary survey of nematodes associated with broadleaved trees in İzmit Forest Management Directorate, Turkey
Authors: Taşdemir Sinan , Akbulut Süleyman , Kanzaki Natsumi , Öztürk Nuray 
Published: December 2020

AbstractA survey for Bursaphelenchus species was carried out in broadleaf forest sites of İzmit Forest Management Directorate. Nematodes were extracted from 128 wood samples, and 22 of them were cultured. Nematodes were identified using morphological characteristics and molecular analysis by amplifying D2‐D3 LSU with primers. Only one Bursaphelenchus species, Bursaphelenchus mucronatus kolymensis, was isolated from Quercus petraea representing the first report from broadleaved tree species in Turkey. Paraphelenchus acontioides and Aphelenchoides heidelbergi were identified and presented herein as the first reports of these two species from Turkey. In addition, five Aphelenchoides species were also found and reported as Aphelenchoides sp.
A delay in colonoscopy after positive fecal tests leads to higher incidence of colorectal cancer: A systematic review and meta‐analysis
Authors: Mutneja Hemant Raj , Bhurwal Abhishek , Arora Shilpa , Vohra Ishaan , Attar Bashar M 
Published: December 2020

AbstractBackground and AimA delay in performing colonoscopies after positive fecal tests in a screening program may risk neoplastic progression. Our objective is to conduct a systematic review and meta‐analysis to evaluate the effects of timing of a colonoscopy after a positive fecal test on the detection of colorectal cancer.MethodsCochrane guidelines and PRISMA statement were followed for this review. Digital dissertation databases were searched from inception to June 1, 2020, and all studies reporting the detection rates of colorectal cancer on the basis of different time intervals between a positive fecal test and the post‐test colonoscopy were included. We compared the detection rates of colorectal cancer (overall and advanced‐stage) and advanced adenoma based on different time intervals.ResultsA total of 361 637 patients from six observational studies were included for the analysis. The odds of detecting any colorectal cancer (odds ratio [OR] 1.58, 95% confidence interval [CI] 1.23–2.03, P < 0.001), advanced‐stage colorectal cancer (OR 2.16, 95% CI 1.47–3.16, P < 0.001), or advanced adenomas (OR 1.17, 95% CI 1.06–1.28, P = 0.001) are significantly higher if the colonoscopies are performed after 6 months from a positive fecal test, compared with within 6 months. There was no significant difference in the detection rates based on a 1‐month, a 2‐month, or a 3‐month cut‐off.ConclusionsA delay of colonoscopies beyond 6 months after positive fecal tests is associated with a higher odds of detecting colorectal cancer. A timely follow up of patients with positive fecal tests is warranted.
Stochastic dominance and decomposable measures of inequality and poverty
Authors: Zheng Buhong 
Published: December 2020

AbstractIn this paper, we characterize some new links between stochastic dominance and the measurement of inequality and poverty. We show that: for second‐degree normalized stochastic dominance (NSD), the weighted area between the NSD curve of a distribution and that of the equalized distribution is a decomposable inequality measure; for first‐degree and second‐degree censored stochastic dominance (CSD), the weighted area between the CSD curve of a distribution and that of the zero‐poverty distribution is a decomposable poverty measure. These characterizations provide graphical representations for decomposable inequality and poverty measures in the same manner as Lorenz curve does for the Gini index. The extensions of the links to higher degrees of stochastic dominance are also investigated.