bluuebunny/crossref_metadata_2025_split huggingface dataset:
Issues of Z-factor and an approach to avoid them for quality control in high-throughput screening studies
Authors: Zhang Xiaohua Douglas , Wang Dandan , Sun Shixue , Zhang Heping 
Published: December 2020

Abstract

Motivation
High-throughput screening (HTS) is a vital automation technology in biomedical research in both industry and academia. The well-known Z-factor has been widely used as a gatekeeper to assure assay quality in an HTS study. However, many researchers and users may not have realized that Z-factor has major issues.

Results
In this article, the following four major issues are explored and demonstrated so that researchers may use the Z-factor appropriately. First, the Z-factor violates the Pythagorean theorem of statistics. Second, there is no adjustment of sampling error in the application of the Z-factor for quality control (QC) in HTS studies. Third, the expectation of the sample-based Z-factor does not exist. Fourth, the thresholds in the Z-factor-based criterion lack a theoretical basis. Here, an approach to avoid these issues was proposed and new QC criteria under homoscedasticity were constructed so that researchers can choose a statistically grounded criterion for QC in the HTS studies. We implemented this approach in an R package and demonstrated its utility in multiple CRISPR/CAS9 or siRNA HTS studies.

Availability and implementation
The R package qcSSMDhomo is freely available from GitHub: https://github.com/Karena6688/qcSSMDhomo. The file qcSSMDhomo_1.0.0.tar.gz (for Windows) containing qcSSMDhomo is also available at Bioinformatics online. qcSSMDhomo is distributed under the GNU General Public License.

Supplementary information
Supplementary data are available at Bioinformatics online.
Higher Plasma Viremia in the Febrile Phase Is Associated With Adverse Dengue Outcomes Irrespective of Infecting Serotype or Host Immune Status: An Analysis of 5642 Vietnamese Cases
Authors: Vuong Nguyen Lam , Quyen Nguyen Than Ha , Tien Nguyen Thi Hanh , Tuan Nguyen Minh , Kien Duong Thi Hue , Lam Phung Khanh , Tam Dong Thi Hoai , Van Ngoc Tran , Yacoub Sophie , Jaenisch Thomas , Geskus Ronald B , Simmons Cameron P , Wills Bridget A 
Published: December 2020

Abstract

Background
One of the generally accepted constructs of dengue pathogenesis is that clinical disease severity is at least partially dependent upon plasma viremia, yet data on plasma viremia in primary versus secondary infections and in relation to clinically relevant endpoints remain limited and contradictory.

Methods
Using a large database comprising detailed clinical and laboratory characterization of Vietnamese participants enrolled in a series of research studies executed over a 15-year period, we explored relationships between plasma viremia measured by reverse transcription–polymerase chain reaction and 3 clinically relevant endpoints—severe dengue, plasma leakage, and hospitalization—in the dengue-confirmed cases. All 4 dengue serotypes and both primary and secondary infections were well represented. In our logistic regression models we allowed for a nonlinear effect of viremia and for associations between viremia and outcome to differ by age, serotype, host immune status, and illness day at study enrollment.

Results
Among 5642 dengue-confirmed cases we identified 259 (4.6%) severe dengue cases, 701 (12.4%) patients with plasma leakage, and 1441 of 4008 (40.0%) patients recruited in outpatient settings who were subsequently hospitalized. From the early febrile phase onwards, higher viremia increased the risk of developing all 3 endpoints, but effect sizes were modest (ORs ranging from 1.12–1.27 per 1-log increase) compared with the effects of a secondary immune response (ORs, 1.67–7.76). The associations were consistent across age, serotype, and immune status groups, and in the various sensitivity and subgroup analyses we undertook.

Conclusions
Higher plasma viremia is associated with increased dengue severity, regardless of serotype or immune status.
Bacterial and Fungal Profiles as Markers of Infliximab Drug Response in Inflammatory Bowel Disease
Authors: Ventin-Holmberg Rebecka , Eberl Anja , Saqib Schahzad , Korpela Katri , Virtanen Seppo , Sipponen Taina , Salonen Anne , Saavalainen Päivi , Nissilä Eija 
Published: December 2020

AbstractBackground and AimsInflammatory bowel diseases [IBDs], Crohn’s disease [CD] and ulcerative colitis [UC], are globally increasing chronic gastro-intestinal inflammatory disorders associated with altered gut microbiota. Infliximab [IFX], a tumour necrosis factor [TNF]-alpha blocker, is used to treat IBD patients successfully, though one-third of the patients do not respond to therapy. No reliable biomarkers are available for prediction of IFX response. Our aims were to investigate the faecal bacterial and fungal communities during IFX therapy and find predictors for IFX treatment response in IBD patients.MethodsA total of 72 IBD patients [25 CD and 47 UC] started IFX therapy and were followed for 1 year or until IFX treatment was discontinued. An amplicon sequencing approach, targeting the bacterial 16S rRNA gene and fungal ITS 1 region separately, was used to determine the microbiota profiles in faecal samples collected before IFX therapy and 2, 6, and 12 weeks and 1 year after initiation of therapy. The response to IFX was evaluated by colonoscopy and clinically at 12 weeks after initiation.ResultsBoth faecal bacterial and fungal profiles differed significantly between response groups before start of IFX treatment. Non-responders had lower abundances of short chain fatty acid producers, particularly of the class Clostridia, and higher abundances of pro-inflammatory bacteria and fungi, such as the genus Candida, compared with responders. This was further indicated by bacterial taxa predicting the response in both CD and UC patients [area under the curve &gt;0.8].ConclusionsFaecal bacterial and fungal microbiota composition could provide a predictive tool to estimate IFX response in IBD patients.
Saddle pulmonary embolism and clot in transit in COVID-19 infection: a case report of catastrophic venous thromboembolism
Authors: Aoi Shunsuke , Kakkar Amit M , Golowa Yosef , Grushko Michael , Coyle Christina M , Elrafei Tarek , Langston Matthew D , Faillace Robert T , Bangalore Sripal , Sokol Seth I 
Published: December 2020

Abstract

Background
Coronavirus disease 2019 (COVID-19) is associated with a coagulopathy favouring thrombosis over bleeding that imparts a poor prognosis. Clot in transit (CIT) is considered a rare entity and the most severe form of venous thromboembolism (VTE), carrying a higher mortality than isolated pulmonary embolism (PE). The incidence of this phenomenon in patients with COVID-19 infection is unknown and likely under-recognized.

Case summary
During the peak of the COVID-19 pandemic in New York City, a 70-year-old Hispanic female presented with syncope due to a saddle PE further complicated by a highly mobile CIT. Polymerase chain reaction was positive for COVID-19 infection, however, there was no evidence of lung parenchymal involvement or hyper-inflammation. Based on consensus from a multidisciplinary team, aspiration thrombectomy was attempted to treat this extreme case of VTE, however, the patient died during the procedure.

Discussion
This case raises awareness to the most catastrophic form of VTE, presenting in an early phase of COVID-19 infection without the typical hyper-inflammation and severe lung injury associated with development of COVID-related coagulopathy. It also serves to inform on the critical role echocardiography has in the comprehensive evaluation and re-evaluation of hospitalized patients with COVID-19, and the importance of a multidisciplinary organized approach in clinical decision-making for this complex and poorly understood disease and its sequelae.
Disease and Human Capital Accumulation: Evidence from the Roll Back Malaria Partnership in Africa
Authors: Kuecken Maria , Thuilliez Josselin , Valfort Marie-Anne 
Published: December 2020

AbstractWe estimate the effects of a large-scale antimalaria campaign on a rich set of human capital outcomes in 27 sub-Saharan African countries. Using pre-campaign malaria risk as treatment probability, we exploit quasi-experimental variation in period and cohort exposure to antimalaria campaigns. A conservative interpretation of our results shows a globally positive impact of antimalaria campaigns: they reduced the probability of infant mortality (1 p.p.) and birth (0.4 p.p.) and increased educational attainment (0.4 years) and the likelihood of adult paid employment (6 p.p.). These findings demonstrate how the effects of sweeping disease reduction efforts extend beyond health outcomes.
British Universities and Transatlantic Slavery: the University of Glasgow Case
Authors: Mullen Stephen 
Published: December 2020

Abstract
On 16 September 2018, the University of Glasgow released the report ‘Slavery, Abolition and the University of Glasgow’. This acknowledged that slave-owners, merchants and planters with connections to New World slavery – and their descendants – donated capital between 1697 and 1937 that influenced the development of the institution. In producing this report, the institution became the first British university to declare historical income derived from transatlantic slavery. In response, a nine-point programme reported as reparative justice was launched, the first British university to launch a project on such a scale. This article traces both the methodological approach undertaken in the study and the historical evidence related to the University of Glasgow. This provides insights into the process of collecting and analysing the evidence on which the report and strategy was based. Current understandings about British universities and transatlantic slavery are shaped by the institutional relationship with owners of enslaved people. This article underlines the importance of merchant capital – in this case, mainly via West India commerce – to the development of one institution.
Finite-time control of uncertain time-varying systems in p-normal form
Authors: Rattanamongkhonkun Kanya , Pongvuthithum Radom , Likasiri Chulin 
Published: December 2020

Abstract
This paper addresses a finite-time regulation problem for time-varying nonlinear systems in p-normal form. This class of time-varying systems includes a well-known lower-triangular system and a chain of power integrator systems as special cases. No growth condition on time-varying uncertainties is imposed. The control law can guarantee that all closed-loop trajectories are bounded and well defined. Furthermore, all states converge to zero in finite time.
Building longitudinal medication dose data using medication information extracted from clinical notes in electronic health records
Authors: McNeer Elizabeth , Beck Cole , Weeks Hannah L , Williams Michael L , James Nathan T , Bejan Cosmin A , Choi Leena 
Published: December 2020

Abstract

Objective
To develop an algorithm for building longitudinal medication dose datasets using information extracted from clinical notes in electronic health records (EHRs).

Materials and Methods
We developed an algorithm that converts medication information extracted using natural language processing (NLP) into a usable format and builds longitudinal medication dose datasets. We evaluated the algorithm on 2 medications extracted from clinical notes of Vanderbilt’s EHR and externally validated the algorithm using clinical notes from the MIMIC-III clinical care database.

Results
For the evaluation using Vanderbilt’s EHR data, the performance of our algorithm was excellent; F1-measures were ≥0.98 for both dose intake and daily dose. For the external validation using MIMIC-III, the algorithm achieved F1-measures ≥0.85 for dose intake and ≥0.82 for daily dose.

Discussion
Our algorithm addresses the challenge of building longitudinal medication dose data using information extracted from clinical notes. Overall performance was excellent, but the algorithm can perform poorly when incorrect information is extracted by NLP systems. Although it performed reasonably well when applied to the external data source, its performance was worse due to differences in the way the drug information was written. The algorithm is implemented in the R package, “EHR,” and the extracted data from Vanderbilt’s EHRs along with the gold standards are provided so that users can reproduce the results and help improve the algorithm.

Conclusion
Our algorithm for building longitudinal dose data provides a straightforward way to use EHR data for medication-based studies. The external validation results suggest its potential for applicability to other systems.
Effectiveness of Entomopathogenic Nematodes Against Ceratitis capitata (Diptera: Tephritidae) Pupae and Nematode Compatibility with Chemical Insecticides
Authors: Jean-Baptiste Maguintontz Cedney , de Brida Andressa Lima , Bernardi Daniel , da Costa Dias Sérgio , de Bastos Pazini Juliano , Leite Luis Garrigós , Wilcken Silvia Renata Siciliano , Garcia Flávio Roberto Mello 
Published: December 2020

Abstract
The Mediterranean fruit fly Ceratitis capitata (Wiedemann, 1824) (Diptera: Tephritidae) is among the main pests of fruit crops worldwide. Biological control using entomopathogenic nematodes (EPNs) may be an alternative to suppress populations of this pest. Thus, the aim of this study was to evaluate the pathogenicity and virulence of six EPN isolates (Heterorhabditis bacteriophora HB, H. amazonensis IBCB-n24, Steinernema carpocapsae IBCB-n02, S. rarum PAM-25, S. glaseri IBCB-n47, and S. brazilense IBCB-n06) against C. capitata pupae. The compatibility of EPNs with different chemical insecticides that are registered for management of C. capitata was also assessed. Isolates of H. bacteriophora HB and S. brazilense IBCB-n06 at a concentration of 1,000 infective juveniles (IJ)/ml proved to be most pathogenic to C. capitata (70 and 80% mortality, respectively). In contrast, the isolates H. amazonensis IBCB-n24, Steinernema carpocapsae IBCB-n02, S. rarum PAM-25, S. glaseri IBCB-n47 provided pupal mortality of less than 60%. Bioassays to determine lethal concentrations indicated that concentrations of 600 IJ/ml (H. bacteriophora HB) and 1,000 IJ/ml (S. brazilense IBCB-n06) showed the highest virulence against C. capitata pupae. In contrast, the highest numbers of IJs emerged at concentrations of 1,200 and 200 IJ/ml. In compatibility bioassays, malathion, spinetoram, phosmet, acetamiprid, and novaluron were considered compatible with and harmless (Class 1) to H. bacteriophora HB and S. brazilense IBCB-n06, according to IOBC/WPRS. This information is important for implementing integrated management programs for C. capitata, using biological control with EPNs, whether alone or in combination with chemical insecticides.
Assessing Cotton Genotypes for Resistance to Aphis gossypii (Hemiptera: Aphididae)
Authors: Morando Rafaela , da Silva Ivana Fernandes , da Silva Santana Alisson , Sampaio Guilherme Sicca Lopes , Lourenção André Luiz , Baldin Edson Luiz Lopes 
Published: December 2020

Abstract
Aphis gossypii Glover (Hemiptera: Aphididae) is a polyphagous species frequently associated with the presence of sooty mold and viruses lethal to plants. The purpose of this work was to characterize possible resistance categories of cotton genotypes against A. gossypii. Initially, a preliminary test was carried out with 78 genotypes, 15 of which were selected for infestation ability assays and the determination of the cumulative aphid-day rates. Posteriorly, these genotypes were also evaluated through antixenosis and antibiosis assays. The genotypes FM 910, FM 966 LL, Mocó, Gossypium hirsutum var. punctatum L. (Malvaceae), Variedade Reba = BTK-12, Deltapine, Hi-Bred, Acala 4–42, IAC PV010-1664, IAC 21, Reba B-50 PR and FMT 709 inhibited the aphid colonization. In the infestation ability assay, G. hirsutum punctatum, IAC PV010-1664 and Acala 4–42 were the least infested. In a multiple-choice assay, Deltapine Smooth Leaf and Variedade Reba = BTK-12 were significantly less infested, suggesting antixenosis. In the antibiosis assay, Gossypium arboreum L. (Malvaceae) 1 showed the lowest number of nymphs, number of nymphs per adult per day and, number of nymphs at 10 d after the birth of the first nymph in addition to reducing the reproductive period, nymphal survival, adult longevity and, developmental time. In the FM 910, the number of nymphs produced per day and, at 10 d after the birth of the first nymph decreased, which also indicated resistance. The results obtained here are unprecedented and can be explored in breeding programs to develop insect-resistant cotton cultivars.
Bernini’s painting collection: a reconstructed inventory raisonné
Authors: Mormando Franco 
Published: December 2020

Abstract
Here presented is the first comprehensive inventory of the paintings on display in Gian Lorenzo Bernini’s home by artists other than himself at the time of his death in November 1680. Although inventories of Bernini’s household dating from 1681 to 1771 have previously been published, none by itself is sufficient to provide a complete catalogue of the artist’s collection. By collating the family inventories with what is known of Bernini’s career, personal and professional relationships, the oeuvre of the artists identified in the inventories, and data from art market records and provenance databases, the author has compiled the most detailed description of Bernini’s collection so far available, including, wherever possible, proposed new attributions, more accurate subject descriptions, and indications of the present whereabouts of the works.
21-Gene Assay and Breast Cancer Mortality in Ductal Carcinoma In Situ
Authors: Rakovitch Eileen , Sutradhar Rinku , Nofech-Mozes Sharon , Gu Sumei , Fong Cindy , Hanna Wedad , Paszat Lawrence 
Published: December 2020

Abstract

Background
The inability to identify individuals with ductal carcinoma in situ (DCIS) who are at risk of breast cancer (BC) mortality have hampered efforts to reduce the overtreatment of DCIS. The 21-gene recurrence score (RS) predicts distant metastases for individuals with invasive BC, but its prognostic utility in DCIS is unknown.

Methods
We performed a population-based analysis of 1362 individuals of DCIS aged 75 years or younger at diagnosis treated with breast-conserving therapy. We examined the association between a high RS (defined a priori as &gt;25) and the risk of BC mortality by using a propensity score-adjusted model accounting for the competing risk of death from other causes, testing for interactions. All statistical tests were 2-sided.

Results
With 16 years median follow-up, 36 (2.6%) died of BC, and 200 (14.7%) died of other causes. The median value of the RS was 15 (range = 0-84); 29.6% of individuals had a high RS. A high RS was associated with an 11-fold increased risk of BC mortality (hazard ratio = 11.27, 95% confidence interval [CI] = 3.00 to 42.33; P &lt; .001) in women aged 50 years or younger at diagnosis treated with breast-conserving surgery alone, culminating in a 9.4% (95% CI = 2.3% to 22.5%) 20-year risk of BC death. For women with a high RS, treatment with radiotherapy was associated with a 71% (hazard ratio = 0.29, 95% CI = 0.10 to 0.89; P = .03) relative and a 5% absolute reduction in the 20-year cumulative risk of death from BC.

Conclusion
The 21-gene RS predicts BC mortality in DCIS and combined with age (50 years or younger) at diagnosis can identify individuals for whom radiotherapy reduces the risk of death from BC.
Grids of stellar models with rotation – V. Models from 1.7 to 120 M⊙ at zero metallicity
Authors: Murphy Laura J , Groh Jose H , Ekström Sylvia , Meynet Georges , Pezzotti Camila , Georgy Cyril , Choplin Arthur , Eggenberger Patrick , Farrell Eoin , Haemmerlé Lionel , Hirschi Raphael , Maeder André , Martinet Sebastién 
Published: December 2020

ABSTRACT
Understanding the nature of the first stars is key to understanding the early Universe. With new facilities such as James Webb Space Telescope (JWST) we may soon have the first observations of the earliest stellar populations, but to understand these observations we require detailed theoretical models. Here we compute a grid of stellar evolution models using the Geneva code with the aim to improve our understanding of the evolution of zero-metallicity stars, with particular interest in how rotation affects surface properties, interior structure, and metal enrichment. We produce a range of models of initial masses (Mini) from $1.7$ to $120\, \mathrm{M}_{\odot }$, focusing on massive models of $9 \le M_{\rm ini}\le 120\, \mathrm{M}_{\odot }$. Our grid includes models with and without rotation, with rotating models having an initial velocity of 40 per cent of the critical velocity. We find that rotation strongly impacts the evolution of the first stars, mainly through increased core size and stronger H-burning shells during core He-burning. Without radiative mass loss, angular momentum builds at the surface in rotating models, thus models of initial masses $M_{\rm ini}\ge 60 \, \mathrm{M}_{\odot }$ reach critical rotation on the main sequence and experience mass loss. We find that rotational mixing strongly affects metal enrichment, but does not always increase metal production as we see at higher metallicities. This is because rotation leads to an earlier CNO boost to the H shell during He-burning, which may hinder metal enrichment depending on initial mass and rotational velocity. Electronic tables of this new grid of Population III models are publicly available.
A complete search for redshift z ≳ 6.5 quasars in the VIKING survey
Authors: Barnett R , Warren S J , Cross N J G , Mortlock D J , Fan X , Wang F , Hewett P C 
Published: December 2020

ABSTRACT
We present the results of a new, deeper, and complete search for high-redshift 6.5 &lt; z &lt; 9.3 quasars over 977 deg2 of the VISTA Kilo-Degree Infrared Galaxy (VIKING) survey. This exploits a new list-driven data set providing photometry in all bands Z, Y, J, H, Ks, for all sources detected by VIKING in J. We use the Bayesian model comparison (BMC) selection method of Mortlock et al., producing a ranked list of just 21 candidates. The sources ranked 1, 2, 3, and 5 are the four known z &gt; 6.5 quasars in this field. Additional observations of the other 17 candidates, primarily DESI Legacy Survey photometry and ESO FORS2 spectroscopy, confirm that none is a quasar. This is the first complete sample from the VIKING survey, and we provide the computed selection function. We include a detailed comparison of the BMC method against two other selection methods: colour cuts and minimum-χ2 SED fitting. We find that: (i) BMC produces eight times fewer false positives than colour cuts, while also reaching 0.3 mag deeper, (ii) the minimum-χ2 SED-fitting method is extremely efficient but reaches 0.7 mag less deep than the BMC method, and selects only one of the four known quasars. We show that BMC candidates, rejected because their photometric SEDs have high χ2 values, include bright examples of galaxies with very strong [O iii] λλ4959,5007 emission in the Y band, identified in fainter surveys by Matsuoka et al. This is a potential contaminant population in Euclid searches for faint z &gt; 7 quasars, not previously accounted for, and that requires better characterization.