bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial Intelligence Improves the Accuracy in Histologic Classification of Breast Lesions
Authors: Polónia António , Campelos Sofia , Ribeiro Ana , Aymore Ierece , Pinto Daniel , Biskup-Fruzynska Magdalena , Veiga Ricardo Santana , Canas-Marques Rita , Aresta Guilherme , Araújo Teresa , Campilho Aurélio , Kwok Scotty , Aguiar Paulo , Eloy Catarina 
Published: August 2020

Abstract

Objectives
This study evaluated the usefulness of artificial intelligence (AI) algorithms as tools in improving the accuracy of histologic classification of breast tissue.

Methods
Overall, 100 microscopic photographs (test A) and 152 regions of interest in whole-slide images (test B) of breast tissue were classified into 4 classes: normal, benign, carcinoma in situ (CIS), and invasive carcinoma. The accuracy of 4 pathologists and 3 pathology residents were evaluated without and with the assistance of algorithms.

Results
In test A, algorithm A had accuracy of 0.87, with the lowest accuracy in the benign class (0.72). The observers had average accuracy of 0.80, and most clinically relevant discordances occurred in distinguishing benign from CIS (7.1% of classifications). With the assistance of algorithm A, the observers significantly increased their average accuracy to 0.88. In test B, algorithm B had accuracy of 0.49, with the lowest accuracy in the CIS class (0.06). The observers had average accuracy of 0.86, and most clinically relevant discordances occurred in distinguishing benign from CIS (6.3% of classifications). With the assistance of algorithm B, the observers maintained their average accuracy.

Conclusions
AI tools can increase the classification accuracy of pathologists in the setting of breast lesions.
Out-of-Pocket Payment for Ambulatory Blood Pressure Monitoring Among Commercially Insured in the United States
Authors: Desai Raj , Dietrich Eric A , Park Haesuk , Smith Steven M 
Published: August 2020

Abstract

Background
Clinical guidelines increasingly recommended ambulatory blood pressure monitoring (ABPM) for hypertension diagnosis and management. Yet, ABPM is used infrequently in the United States, possibly because of low insurance coverage and high patient costs. We sought to analyze out-of-pocket payments (OPPs) for ABPM among privately insured patients.

Methods
We conducted a retrospective analysis using IBM® MarketScan® commercial claims of beneficiaries aged ≥18 years receiving ABPM from January 2012 to December 2018. The date of first ABPM claim (Healthcare Common Procedure Coding System codes 93784, 93786, 93788, or 93790) was considered the index date. Patients with 12 months of continuous enrollment preindex and 30-day postindex were included. Per beneficiary OPP was calculated by aggregating all ABPM-related OPPs within the 30-day postindex window (ABPM episode).

Results
Of 22,317 beneficiaries receiving ABPM, 62% had $0 OPP and 38% had OPP &gt;$0. Among the latter, median OPP per beneficiary for an ABPM episode was $23 (interquartile range [IQR], $14, $32), driven primarily by full ABPM claims (median, $22; IQR, $14, $24). Among individual components, scan analysis and report claims (median, $25; IQR, $13, $49) had the greatest OPP. The median OPP per ABPM episode did not change substantively from 2012 through 2018.

Conclusions
Among commercially insured in the United States, nearly 4-in-10 have an OPP for ABPM. Though most OPPs are relatively modest, some patients incur substantial OPP. Our findings highlight the need for policymakers to ensure adequate ABPM coverage in the commercial insurance marketplace.
Occupational Heat Stress and Practical Cooling Solutions for Healthcare and Industry Workers During the COVID-19 Pandemic
Authors: Foster Josh , Hodder Simon G , Goodwin James , Havenith George 
Published: August 2020

Abstract
Treatment and management of severe acute respiratory syndrome coronavirus-2, which causes coronavirus disease (COVID-19), requires increased adoption of personal protective equipment (PPE) to be worn by workers in healthcare and industry. In warm occupational settings, the added burden of PPE threatens worker health and productivity, a major lesson learned during the West-African Ebola outbreak which ultimately constrained disease control. In this paper, we comment on the link between COVID-19 PPE and occupational heat strain, cooling solutions available to mitigate occupational heat stress, and practical considerations surrounding their effectiveness and feasibility. While the choice of cooling solution depends on the context of the work and what is practical, mitigating occupational heat stress benefits workers in the healthcare and industrial sectors during the COVID-19 disease outbreak.
Functional–morphological analyses of the delicate snap-traps of the aquatic carnivorous waterwheel plant (Aldrovanda vesiculosa) with 2D and 3D imaging techniques
Authors: Westermeier Anna S , Hiss Natalie , Speck Thomas , Poppinga Simon 
Published: August 2020

AbstractBackground and AimsThe endangered aquatic carnivorous waterwheel plant (Aldrovanda vesiculosa) catches prey with 3–5-mm-long underwater snap-traps. Trapping lasts 10–20 ms, which is 10-fold faster than in its famous sister, the terrestrial Venus flytrap (Dionaea muscipula). After successful capture, the trap narrows further and forms a ‘stomach’ for the digestion of prey, the so-called ‘sickle-shaped cavity’. To date, knowledge is very scarce regarding the deformation process during narrowing and consequent functional morphology of the trap.MethodsWe performed comparative analyses of virtual 3D histology using computed tomography (CT) and conventional 2D histology. For 3D histology we established a contrasting agent-based preparation protocol tailored for delicate underwater plant tissues.Key ResultsOur analyses reveal new structural insights into the adaptive architecture of the complex A. vesiculosa snap-trap. In particular, we discuss in detail the arrangement of sensitive trigger hairs inside the trap and present actual 3D representations of traps with prey. In addition, we provide trap volume calculations at different narrowing stages. Furthermore, the motile zone close to the trap midrib, which is thought to promote not only the fast trap closure by hydraulics but also the subsequent trap narrowing and trap reopening, is described and discussed for the first time in its entirety.ConclusionsOur research contributes to the understanding of a complex, fast and reversible underwater plant movement and supplements preparation protocols for CT analyses of other non-lignified and sensitive plant structures.
Reynolds Intellectual Screening Instrument 1st versus 2nd Edition in a Memory Disorder Sample
Authors: Ruchinskas Robert , Goette William 
Published: August 2020

Abstract

Objective
The Reynolds Intellectual Screening Instrument (RIST) and its second edition (RIST-2) are brief intelligence screening instruments that potentially have value in older populations as their norms extend over age 90. This study examined performance on these two instruments in a sample of individuals presenting for evaluation in a memory disorder clinic.

Method
A sample of 1,145 subjects over the age of 50 was chosen from 1,761 consecutive referrals. Individuals who obtained a consensus diagnosis of Mild Cognitive Impairment (MCI; n = 536), possible dementia of the Alzheimer Type (DAT; n = 400), or those with subjective cognitive complaints (SCC; n = 209) and who completed a neuropsychological battery that included either the RIST (n = 747) or the RIST-2 (n = 398) were included in the sample. No clinically significant demographic or neuropsychological performance differences were found for those taking either version of the RIST.

Results
Unlike the original version, RIST-2 Total and subtest scores were well below the mean for the DAT group and over 1 SD mean difference was seen for the DAT group when comparing the RIST and RIST-2 Totals. Diagnostic accuracy calculations suggested that the RIST-2 showed greater discrimination between the three groups although both versions achieved greater sensitivity than specificity.

Conclusions
Performance differences were evident when comparing the RIST and RIST-2, particularly for the DAT group. Although the RIST-2 evidenced greater diagnostic accuracy than its predecessor it should not be utilized in isolation for the clinical determination of DAT or MCI.
FastBMD: an online tool for rapid benchmark dose–response analysis of transcriptomics data
Authors: Ewald Jessica , Soufan Othman , Xia Jianguo , Basu Niladri 
Published: August 2020

Abstract

Motivation
Transcriptomics dose–response analysis is a promising new approach method for toxicity testing. While international regulatory agencies have spent substantial effort establishing a standardized statistical approach, existing software that follows this approach is computationally inefficient and must be locally installed.

Results
FastBMD is a web-based tool that implements standardized methods for transcriptomics benchmark dose–response analysis in R. It is &gt;60 times faster than the current leading software, supports transcriptomics data from 13 species, and offers a comprehensive analytical pipeline that goes from processing and normalization of raw gene expression values to interactive exploration of pathway-level benchmark dose results.

Availability and implementation
FastBMD is freely available at www.fastbmd.ca.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Quest for Indigenising Social Work Services for Disadvantaged Children in Vietnam
Authors: Thai Lan Nguyen Thi 
Published: August 2020

AbstractThis article presents a qualitative study about ways in which social work services for disadvantaged children can be indigenised in a Southeast Asian country. The research employed a multiple case study approach with five selected international organisations. Thirty-nine in-depth interviews, three group discussions combined with document analysis and participant observations being conducted. The findings have showcased Vietnamese social work professionalisation in the process of internationalisation through foreign influences. The study pictures the involvement of international organisations and its relation with local partners in the development of social work services in the local context. Importantly, the findings advocate for the complex process of indigenisation through the application of cultural relevance, contextual appropriateness and localisation of services for local disadvantaged children.
Ultrahigh-resolution MRI Reveals Extensive Cortical Demyelination in a Nonhuman Primate Model of Multiple Sclerosis
Authors: Donadieu Maxime , Kelly Hannah , Szczupak Diego , Lin Jing-Ping , Song Yeajin , Yen Cecil C C , Ye Frank Q , Kolb Hadar , Guy Joseph R , Beck Erin S , Jacobson Steven , Silva Afonso C , Sati Pascal , Reich Daniel S 
Published: August 2020

Abstract
Cortical lesions are a primary driver of disability in multiple sclerosis (MS). However, noninvasive detection of cortical lesions with in vivo magnetic resonance imaging (MRI) remains challenging. Experimental autoimmune encephalomyelitis (EAE) in the common marmoset is a relevant animal model of MS for investigating the pathophysiological mechanisms leading to brain damage. This study aimed to characterize cortical lesions in marmosets with EAE using ultrahigh-field (7 T) MRI and histological analysis. Tissue preparation was optimized to enable the acquisition of high-spatial resolution (50-μm isotropic) T2*-weighted images. A total of 14 animals were scanned in this study, and 70% of the diseased animals presented at least one cortical lesion on postmortem imaging. Cortical lesions identified on MRI were verified with myelin proteolipid protein immunostaining. An optimized T2*-weighted sequence was developed for in vivo imaging and shown to capture 65% of cortical lesions detected postmortem. Immunostaining confirmed extensive demyelination with preserved neuronal somata in several cortical areas of EAE animals. Overall, this study demonstrates the relevance and feasibility of the marmoset EAE model to study cortical lesions, among the most important yet least understood features of MS.
Qualitative and Quantitative Analysis of the New Sulfone Bactericide 2-(4-Fluorophenyl)-5-(Methylsulfonyl)-1,3,4-Oxadiazole and Identification of Its Degradation Pathways in Paddy Water
Authors: Meng Xingang , Wang Niao , Long Xiaofang , Chen Lingzhu , Hu Deyu 
Published: August 2020

AbstractRapid and simple methods for the determination of Jiahuangxianjunzuo (JHXJZ) in paddy water, brown rice, soil and rice straw was developed and validated. This method involved the use of ultrahigh-performance liquid chromatography equipped with photodiode array detector. The most important factor was chromatographic conditions, as identified through an orthogonal experimental design. This method showed good recoveries and precisions, thereby indicating its suitability for monitoring of JHXJZ residues in paddy water, brown rice, soil and rice straw. Furthermore, hydrolysis experiment was conducted in the laboratory under pH = 7 buffer solutions, and its degradation product was identified as 2-(4-fluorophenyl)-5-methoxy-1,3,4-oxadiazole by high-resolution mass spectrometry. JHXJZ has a major degradation pathway in the water which the OH− nucleophilic attack the C5 of 1,3,4-oxadiazole ring. Then it leaves mesyl to form intermediate 5-(4-fluorophenyl)-1,3,4-oxadiazol-2-ol and the intermediate combined with methanol formed the degradation product 2-(4-fluorophenyl)-5-methoxy-1,3,4-oxadiazole by the loss of one H2O.The degradation pathways of JHXJZ under the present indoor simulation conditions were proposed.
Human Immunodeficiency Virus (HIV) Infection Is Associated With Lower Risk of Hepatocellular Carcinoma After Sustained Virological Response to Direct-acting Antivirals in Hepatitis C Infected Patients With Advanced Fibrosis
Authors: Corma-Gómez Anaïs , Macías Juan , Lacalle-Remigio Juan Ramón , Téllez Francisco , Morano Luis , Rivero Antonio , Serrano Miriam , Ríos María José , Vera-Méndez Francisco Jesús , Alados Juan Carlos , Real Luis Miguel , Palacios Rosario , Santos Ignacio De Los , Imatz Arkaitz , Pineda Juan Antonio ,   RIS-HEP13 and GEHEP 011 study groups, Merino Dolores , Jose Galindo Maria , Galera Carlos , Ángel López-Ruz Miguel , Geijo Paloma , Javier Reus Bañuls Sergio , Pérez Camacho Inés 
Published: August 2020

Abstract

Background
The aim of this study was to assess the impact of human immunodeficiency virus (HIV) infection on the risk of developing hepatocellular carcinoma (HCC) in patients infected with hepatitis C virus (HCV) who achieve sustained virological response (SVR) with direct-acting antiviral (DAA).

Methods
Multisite prospective cohort study, where HCV-monoinfected patients and HIV/HCV-coinfected individuals were included if they met: (1) SVR with DAA-based combination; (2) liver stiffness (LS) ≥9.5 kPa previous to treatment; (3) LS measurement at the SVR time-point. The main endpoint was the occurrence of HCC. Propensity score (PS) was calculated to address potential confounders due to unbalanced distribution of baseline characteristics of HIV/HCV-coinfected and HCV-monoinfected patients.

Results
In total, 1035 HCV-infected patients were included, 667 (64%) coinfected with HIV. After a median (Q1–Q3) follow-up time of 43 (31–49) months, 19 (1.8%) patients developed HCC (11 [3.0%]; HCV-monoinfected, 8[1.2%]; HIV/HCV-coinfected individuals; P = .013). In the multivariable analysis, HIV coinfection was associated with a lower adjusted risk of developing HCC (subhazard ratio [sHR] = 0.27, 95% confidence interval [CI]: .08–.90; P = .034). Predictors of HCC emergence were: HCV genotype 3 (sHR = 7.9, 95% CI: 2.5–24.9; P &lt; .001), MELD score at SVR &gt;10 (sHR = 1.37, 95% CI: 1.01–1.86; P = .043) and LS value at SVR (sHR = 1.03, 95% CI: 1.01–1.06, for 1 kPa increase; P = .011). Using inverse probability weighting method on the PS, HIV-infected patients had a lower risk of HCC (powered HR = 0.33, 95% CI: .11–.85).

Conclusions
Among HCV-infected patients with advanced fibrosis, who achieve SVR with DAA, HIV coinfection seems to be associated with a lower risk of HCC occurrence. The underlying causes for this finding need to be investigated.
Unique Clusters of Severe Acute Respiratory Syndrome Coronavirus 2 Causing a Large Coronavirus Disease 2019 Outbreak in Hong Kong
Authors: To Kelvin Kai-Wang , Chan Wan-Mui , Ip Jonathan Daniel , Chu Allen Wing-Ho , Tam Anthony Raymond , Liu Raymond , Wu Alan Ka-Lun , Lung Kwok-Cheung , Tsang Owen Tak-Yin , Lau Daphne Pui-Ling , To Wing-Kin , Kwan Mike Yat-Wah , Yau Yat-Sun , Ng Anthony Chin-Ki , Yip Cyril Chik-Yan , Chan Kwok-Hung , Tse Herman , Hung Ivan Fan-Ngai , Yuen Kwok-Yung 
Published: August 2020

Abstract
After 2 months of relative quiescence, a large coronavirus disease 2019 outbreak occurred in Hong Kong in July 2020 after gradual relaxation of social distancing policy. Unique severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) phylogenetic clusters have been identified among locally acquired cases, with most genomes belonging to cluster HK1, which is phylogenetically related to SARS-CoV-2 reported overseas.
Fatal Respiratory Diphtheria Caused by ß-Lactam–Resistant Corynebacterium diphtheriae
Authors: Forde Brian M , Henderson Andrew , Playford Elliott G , Looke David , Henderson Belinda C , Watson Catherine , Steen Jason A , Sidjabat Hanna E , Laurie Gordon , Muttaiyah Sharmini , Nimmo Graeme R , Lampe Guy , Smith Helen , Jennison Amy V , McCall Brad , Carroll Heidi , Cooper Matthew A , Paterson David L , Beatson Scott A 
Published: August 2020

Abstract

Background
Diphtheria is a potentially fatal respiratory disease caused by toxigenic Corynebacterium diphtheriae. Although resistance to erythromycin has been recognized, β-lactam resistance in toxigenic diphtheria has not been described. Here, we report a case of fatal respiratory diphtheria caused by toxigenic C. diphtheriae resistant to penicillin and all other β-lactam antibiotics, and describe a novel mechanism of inducible carbapenem resistance associated with the acquisition of a mobile resistance element.

Methods
Long-read whole-genome sequencing was performed using Pacific Biosciences Single Molecule Real-Time sequencing to determine the genome sequence of C. diphtheriae BQ11 and the mechanism of β-lactam resistance. To investigate the phenotypic inducibility of meropenem resistance, short-read sequencing was performed using an Illumina NextSeq500 sequencer on the strain both with and without exposure to meropenem.

Results
BQ11 demonstrated high-level resistance to penicillin (benzylpenicillin minimum inhibitory concentration [MIC] ≥ 256 μg/ml), β-lactam/β-lactamase inhibitors and cephalosporins (amoxicillin/clavulanic acid MIC ≥ 256 μg/mL; ceftriaxone MIC ≥ 8 μg/L). Genomic analysis of BQ11 identified acquisition of a novel transposon carrying the penicillin-binding protein (PBP) Pbp2c, responsible for resistance to penicillin and cephalosporins. When strain BQ11 was exposed to meropenem, selective pressure drove amplification of the transposon in a tandem array and led to a corresponding change from a low-level to a high-level meropenem-resistant phenotype.

Conclusions
We have identified a novel mechanism of inducible antibiotic resistance whereby isolates that appear to be carbapenem susceptible on initial testing can develop in vivo resistance to carbapenems with repeated exposure. This phenomenon could have significant implications for the treatment of C. diphtheriae infection, and may lead to clinical failure.
Differential diagnosis of perinatal Bartter, Bartter and Gitelman syndromes
Authors: Bamgbola Oluwatoyin Fatai , Ahmed Youssef 
Published: August 2020

AbstractThe common finding of hypokalemic alkalosis in several unrelated disorders may confound the early diagnosis of salt-losing tubulopathy (SLT). Antenatal Bartter syndrome (BS) must be considered in idiopathic early-onset polyhydramnios. Fetal megabladder in BS may allow its distinction from third-trimester polyhydramnios that occurs in congenital chloride diarrhea (CCD). Fetal megacolon occurs in CCD while fecal chloride &gt;90 mEq/L in infants is diagnostic. Failure-to-thrive, polydipsia and polyuria in early childhood are the hallmarks of classic BS. Unlike BS, there is low urinary chloride in hypokalemic alkalosis of intractable emesis and cystic fibrosis. Rarely, renal salt wasting may result from cystinosis, Dent disease, disorders of paracellular claudin-10b and Kir4.1 potassium-channel deficiency. Acquired BS may result from calcimimetic up-regulation of a calcium-sensing receptor or autoantibody inactivation of sodium chloride co-transporters in Sjögren syndrome. A relatively common event of heterozygous gene mutations for Gitelman syndrome increases the likelihood of its random occurrence in certain diseases of adult onset. Finally, diuretic abuse is the most common differential diagnosis of SLT. Unlike the persistent elevation in BS, urinary chloride concentration losses waxes and wanes on day-to-day assessment in patients with diuretic misuse.
Related Blogs’ Summarization With Natural Language Processing
Authors: Baliyan Niyati , Sharma Aarti 
Published: August 2020

Abstract
There is plethora of information present on the web, on a given topic, in different forms i.e. blogs, articles, websites, etc. However, not all of the information is useful. Perusing and going through all of the information to get the understanding of the topic is a very tiresome and time-consuming task. Most of the time we end up investing in reading content that we later understand was not of importance to us. Due to the lack of capacity of the human to grasp vast quantities of information, relevant and crisp summaries are always desirable. Therefore, in this paper, we focus on generating a new blog entry containing the summary of multiple blogs on the same topic. Different approaches of clustering, modelling, content generation and summarization are applied to reach the intended goal. This system also eliminates the repetitive content giving savings on time and quantity, thereby making learning more comfortable and effective. Overall, a significant reduction in the number of words in the new blog generated by the system is observed by using the proposed novel methodology.
OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques
Authors: R. Cerqueira Fabio , Vasconcelos Ana Tereza Ribeiro 
Published: August 2020

AbstractSmall open reading frames (ORFs) have been systematically disregarded by automatic genome annotation. The difficulty in finding patterns in tiny sequences is the main reason that makes small ORFs to be overlooked by computational procedures. However, advances in experimental methods show that small proteins can play vital roles in cellular activities. Hence, it is urgent to make progress in the development of computational approaches to speed up the identification of potential small ORFs. In this work, our focus is on bacterial genomes. We improve a previous approach to identify small ORFs in bacteria. Our method uses machine learning techniques and decoy subject sequences to filter out spurious ORF alignments. We show that an advanced multivariate analysis can be more effective in terms of sensitivity than applying the simplistic and widely used e-value cutoff. This is particularly important in the case of small ORFs for which alignments present higher e-values than usual. Experiments with control datasets show that the machine learning algorithms used in our method to curate significant alignments can achieve average sensitivity and specificity of 97.06% and 99.61%, respectively. Therefore, an important step is provided here toward the construction of more accurate computational tools for the identification of small ORFs in bacteria.