bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Machine Learning Algorithm for Drug Screening Analysis on High-Resolution UPLC-MSE/QTOF Mass Spectrometry
Authors: Hao Ying , Lynch Kara , Fan Pengcheng , Jurtschenko Christopher , Cid Maria , Zhao Zhen , Yang He S 
Published: January 2023

Abstract

Background
Ultra-performance liquid chromatography (UPLC)-MSE/quadrupole time-of-flight (QTOF) high-resolution mass spectrometry employs untargeted, data-independent acquisition in a dual mode that simultaneously collects precursor ions and product ions at low and ramped collision energies, respectively. However, algorithmic analysis of large-scale multivariate data of comprehensive drug screening as well as the positivity criteria of drug identification have not been systematically investigated. It is also unclear whether ion ratio (IR), the intensity ratio of a defined product ion divided by the precursor ion, is a stable parameter that can be incorporated into the MSE/QTOF data analysis algorithm.

Methods
IR of 91 drugs were experimentally determined and variation of IR was investigated across 5 concentrations measured on 3 different days. A data-driven machine learning approach was employed to develop multivariate linear regression (MLR) models incorporating mass error, retention time, number of detected fragment ions and IR, accuracy of isotope abundance, and peak response using drug-supplemented urine samples. Performance of the models was evaluated in an independent data set of unknown clinical urine samples in comparison with the results of manual analysis.

Results
IR of most compounds acquired by MSE/QTOF were low and concentration-dependent (i.e., IR increased at higher concentrations). We developed an MLR model with composite score outputs incorporating 7 parameters to predict positive drug identification. The model achieved a mean accuracy of 89.38% in the validation set and 87.92% agreement in the test set.

Conclusions
The MLR model incorporating all contributing parameters can serve as a decision-support tool to facilitate objective drug identification using UPLC-MSE/QTOF.
Estimation of Reference Intervals from Routine Data Using the refineR Algorithm—A Practical Guide
Authors: Ammer Tatjana , Schützenmeister André , Rank Christopher M , Doyle Kelly 
Published: January 2023

AbstractBackgroundAccurate reference intervals are essential for the interpretation of laboratory test results. Typically, they are determined by the central 95% range of test results from a predefined reference population. As these direct studies can face practical and ethical challenges, indirect methods using routine measurements offer an alternative approach.MethodsWe provide step-by-step guidance on how to apply an indirect method in practice using refineR, the most recently published indirect method, and showcase the application by evaluating real-world data of 12 prespecified analytes. Measurements were retrieved from ARUP Laboratories’ data warehouse, and were obtained from routine patient testing on cobas c502 or e602 analyzers. Test results were prefiltered and cleaned and, if necessary, physiologically partitioned prior to estimating reference intervals using refineR. Estimated reference intervals were then compared to established intervals provided by the manufacturer.ResultsFor most analytes, the reference intervals estimated by refineR were comparable to those provided by the manufacturer, shown by overlapping confidence intervals at both reference limits, or only the upper or lower limit. For thyroid-stimulating hormone, refineR estimated higher reference limits, while estimates for prealbumin were lower compared to the established reference interval.ConclusionsWe applied the refineR algorithm to a variety of real-world data sets resulting in reference intervals similar to intervals previously established by direct methods. We further provide practical guidance and a code example on how to apply an indirect method in a real-world scenario facilitating their access and thus their use in laboratory settings.
End-to-End Data Automation for Pooled Sample SARS-CoV-2 Using R and Other Open-Source Tools
Authors: Mobini Mahdi , Matic Nancy , Gugten J Grace Van Der , Ritchie Gordon , Lowe Christopher F , Holmes Daniel T 
Published: January 2023

Abstract

Background
Due to supply chain shortages of reagents for real-time (RT)-PCR for SARS-CoV-2 and increasing demand on technical staff, an end-to-end data automation strategy for SARS-CoV-2 sample pooling and singleton analysis became necessary in the summer of 2020.

Methods
Using entirely open source software tools—Linux, bash, R, RShiny, ShinyProxy, and Docker—we developed a modular software application stack to manage the preanalytical, analytical, and postanalytical processes for singleton and pooled testing in a 5-week time frame.

Results
Pooling was operationalized for 81 days, during which time 64 pooled runs were performed for a total of 5320 sample pools and approximately 21 280 patient samples in 4:1 format. A total of 17 580 negative pooled results were released in bulk. After pooling was discontinued, the application stack was used for singleton analysis and modified to release all viral RT-PCR results from our laboratory. To date, 236 109 samples have been processed avoiding over 610 000 transcriptions.

Conclusions
We present an end-to-end data automation strategy connecting 11 devices, one network attached storage, 2 Linux servers, and the laboratory information system.
Cybersecurity and Information Assurance for the Clinical Laboratory
Authors: Patel Ankush U , Williams Christopher L , Hart Steven N , Garcia Christopher A , Durant Thomas J S , Cornish Toby C , McClintock David S 
Published: January 2023

Abstract

Background
Network-connected medical devices have rapidly proliferated in the wake of recent global catalysts, leaving clinical laboratories and healthcare organizations vulnerable to malicious actors seeking to ransom sensitive healthcare information. As organizations become increasingly dependent on integrated systems and data-driven patient care operations, a sudden cyberattack and the associated downtime can have a devastating impact on patient care and the institution as a whole. Cybersecurity, information security, and information assurance principles are, therefore, vital for clinical laboratories to fully prepare for what has now become inevitable, future cyberattacks.

Content
This review aims to provide a basic understanding of cybersecurity, information security, and information assurance principles as they relate to healthcare and the clinical laboratories. Common cybersecurity risks and threats are defined in addition to current proactive and reactive cybersecurity controls. Information assurance strategies are reviewed, including traditional castle-and-moat and zero-trust security models. Finally, ways in which clinical laboratories can prepare for an eventual cyberattack with extended downtime are discussed.

Summary
The future of healthcare is intimately tied to technology, interoperability, and data to deliver the highest quality of patient care. Understanding cybersecurity and information assurance is just the first preparative step for clinical laboratories as they ensure the protection of patient data and the continuity of their operations.
Use of Computer Simulation for Calculating Reference Limits for Distribution Overlap
Authors: Vidali Matteo 
Published: January 2023

Abstract

Background
In laboratory medicine, data collected in different settings or under different conditions are frequently analyzed to obtain meaningful information. Evaluation based only on location or variability measures, although useful, is not enough to extract all the value from data. Other mathematical or statistical approaches are possible, but the specific knowledge required is frequently out of the reach of most laboratorians. Computer simulation may help in solving the problem. The aim of this work was to use computer simulation for calculating reference limits for the overlap of 2 distributions.

Methods
Computer simulation was applied to find a reference value, and its confidence limits, from the overlapping area of 2 distributions when population means were allowed to differ by a pre-set amount. The allowable limits were compared with the overlapping area observed between data distributions reported from 3 laboratories. The simulation was run in R language. A description for the experimental setting was added, with the instructions for the simulation reported in structured English.

Results
The simulation allowed estimation of a limit to be used as a reference value when comparing two overlapping areas. Based on these limits, one laboratory in the study was found not to be aligned with the others.

Conclusions
Computer simulation is a low-cost, powerful, and easy to implement tool which may help in solving simple or complex problems, when assumptions are unrealistic or unmet, or when mathematical algorithms are not known or difficult to calculate.
Toward a contextualized understanding of well-being in the midwifery profession: An integrative review
Authors: Mharapara Tago L , Clemons Janine H , Greenslade-Yeats James , Ewertowska Tanya , Staniland Nimbus Awhina , Ravenswood Katherine 
Published: January 2023

AbstractOur integrative review synthesizes and evaluates two decades of empirical research on well-being in the midwifery profession to reveal (1) how researchers have studied midwives’ well-being; (2) key findings of research on midwives’ well-being; (3) underlying assumptions of this research; and (4) limitations of this research. We find that research on midwives’ well-being is disproportionately focused on individual midwives, who are assumed to be largely responsible for their own well-being, and that well-being in the midwifery profession is generally equated with the absence of mental health problems such as burnout, anxiety, and stress. Researchers have largely taken a narrow and instrumental approach to study midwives’ well-being, focusing on work-related antecedents and consequences, and overlooking the influence of nonwork factors embedded in the broader socioeconomic and cultural environment. Drawing on more comprehensive and contextualized well-being frameworks, we propose a research model that (1) expands the well-being construct as it applies to midwives and (2) situates midwives’ well-being in broader social, economic, political, and cultural contexts. Although developed in the midwifery context, our proposed research model can be applied to a host of professions.
The study of 11 contact binaries with mass ratios less than 0.1
Authors: Liu Xin-Yi , Li Kai , Michel Raul , Gao Xiang , Gao Xing , Liu Fei , Yin Shi-Peng , Wang Xi , Sun Guo-You 
Published: January 2023

ABSTRACT
Multi-band photometric observations of 11 totally eclipsing contact binaries were carried out. Applying the Wilson–Devinney program, photometric solutions were obtained. There are two W-subtype systems, which are CRTS J133031.1+161202 and CRTS J154254.0+324652, and the rest of the systems are A-subtype systems. CRTS J154254.0 + 324652 has the highest fill-out factor with 94.3 per cent, and the lowest object is CRTS J155009.2 + 493639 with only 18.9 per cent. The mass ratios of the 11 systems are all less than 0.1, which means that they are extremely low-mass ratio binary systems. We performed period variation investigation and found that the orbital periods of three systems decrease slowly, which may be caused by the materials may transfer from the primary component to the secondary component, and those of six systems increase slowly, which indicates that the materials may transfer from the secondary component to the primary component. LAMOST low-resolution spectra of four objects were analysed, and using the spectral subtraction technique, Hα emission line was detected, which means that the four objects exhibit chromospheric activity. In order to understand their evolutionary status, the mass–luminosity and mass–radius diagrams were plotted. The two diagrams indicate that the primary component is in the main sequence evolution stage, and the secondary component is above TAMS, indicating that they are over-luminous. To determine whether the 11 systems are in a stable state, the ratio of spin angular momentum to orbital angular momentum (Js/Jo) and the instability parameters were calculated, and we argued that CRTS J234634.7 + 222824 is on the verge of a merger.
Charge exchange between highly charged ions and atomic H for modelling comet C/1999 S4 X-ray emission
Authors: Zhang R T , Liao T , Zhang C J , Zou L P , Guo D L , Gao Y , Gu L Y , Zhu X L , Zhang S F , Ma X 
Published: January 2023

ABSTRACTSolar wind (SW) charge exchange (CX) is an important mechanism responsible for X-ray emissions in comets’ coma and many other astrophysical environments. By incorporating the experimentally derived total cross-sections and the tested state-selectivity models into the Kronos program, we generate X-ray spectra in H-like and fully stripped C, N, O ion CX collision with atomic H. Using these data, we revisit the fitting of Chandra X-ray data of Comet C/1999 S4 by considering the typical SW collision energies of 0.8 and 3 keV/u, respectively. Our results are in an excellent agreement with the astrophysical observation. We find that charge exchange between C5+,6+, N6+,7+, O7+,8+ and H significantly contributes to the comet’s spectrum ranging from 300 to 800 eV for both slow and fast SW ions, where N7+ abundance is underestimated in previous studies.
Unmet needs and wish for support of family caregivers of primary brain tumor patients
Authors: Pointon Lucy , Grant Robin , Peoples Sharon , Erridge Sara , Sherwood Paula , Klein Martin , Boele Florien 
Published: January 2023

AbstractBackgroundMost primary brain tumor patients rely on family caregivers for support. Caregiving can be rewarding, but also leads to significant burden from unmet needs. We aimed to: (1) identify and characterize caregivers’ unmet needs; (2) determine associations between unmet needs and wish for support; (3) evaluate acceptability of the Caregiver Needs Screen (CNS) and perceived feasibility in clinical practice.MethodsFamily caregivers of primary brain tumor patients were recruited from outpatient clinics and asked to complete an adapted version of the CNS consisting of 33 common issues caregivers report (item scale 0–10), and the wish for support (yes/no). Participants ranked acceptability and feasibility (item scale 0–7; higher scores being positive) of the adapted CNS. Descriptive and non-parametric correlational analyses were applied.ResultsCaregivers (N = 71) reported 1–33 unmet caregiving needs (M = 17.20, sd = 7.98) but did not always wish for support (range 0–28, M = 5.82, sd = 6.96). A weak correlation was found between total number of unmet needs and wish for support (r = 0.296, P = .014). Most distressing items were patients’ changes in memory/concentration (M = 5.75, sd = 3.29), patients’ fatigue (M = 5.58, sd = 3.43), and signs of disease progression (M = 5.23, sd = 3.15).Caregivers most often wished support with recognizing disease progression (N = 24), and least often with managing spiritual issues (N = 0). Caregivers evaluated acceptability and feasibility of the CNS tool positively (mean scores ranged 4.2–6.2).ConclusionsFamily caregivers experience distress resulting from many neuro-oncology specific needs, but this is not directly related to wish for support. Family caregiver needs screening could be useful to tailor support to suit their preferences in clinical practice.
Mandatory Vaccinations, Religious Freedom, and Discrimination
Authors: Trispiotis Ilias 
Published: January 2023

Abstract
This article responds to the prevailing normative and doctrinal uncertainty over the compatibility of mandatory vaccination schemes with the right to freedom of religion or belief and the prohibition of discrimination on the grounds of religion or belief under the ECHR. The article develops an analytical framework that engages with the purpose of religious freedom and religious anti-discrimination; the scope of public health as a legitimate aim for state interference with those rights; the procedural fairness of mandatory vaccination schemes; and the empirical evidence underpinning those schemes. This multiprong analysis has important implications for any form of wide-ranging state restrictions on religious freedom and religious anti-discrimination, for reasons of public health, and more broadly.
Climate Risk Disclosure and Institutional Investors
Authors: Ilhan Emirhan , Krueger Philipp , Sautner Zacharias , Starks Laura T 
Published: January 2023

Abstract
Through a survey and analyses of observational data, we provide systematic evidence that institutional investors value and demand climate risk disclosures. The survey reveals the investors have a strong demand for climate risk disclosures, and many actively engage their portfolio firms for improvements. Empirical analyses of holdings data corroborate this evidence by showing a significantly positive association between climate-conscious institutional ownership and better firm-level climate risk disclosure. We establish further evidence of institutional investors’ influence on firms’ climate risk disclosures by examining a shock to the climate risk disclosure demand of French institutional investors (French Article 173).
Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Association between maternal plasma total antioxidant capacity and dietary antioxidants intake with birth size outcomes
Authors: Shokri-Mashhadi Nafiseh , Khoshhali Mehri , Heidari-Beni Motahar , Kelishadi Roya 
Published: January 2023

AbstractBackgroundMaternal antioxidants intake and plasma total antioxidant capacity (TAC) concentration during pregnancy might influence on birth outcomes. This study was conducted to determine the association between dietary antioxidants intake and plasma TAC during pregnancy with birth outcomes.MethodsOverall, 220 mother–infant pairs were recruited in the first trimester of pregnancy. Maternal whole blood was collected and TAC was determined by the ELISA kit. Food frequency questionnaire was used to collect information regarding usual dietary intake. Birth size measurements including birth weight, length and head circumference were measured according to standardized protocols.ResultsEnergy-adjusted intake of beta-carotene in the first trimester of gestation [beta (SE) = 0.0002 (0.00008); p = 0.016] and energy-adjusted intake of vitamin E in third trimester of pregnancy [beta (SE) = −0.31 (0.15); p = 0.046] had significantly positive and negative associations with birth length, respectively. The maternal plasma TAC was positively correlated with birth weight in both unadjusted and adjusted models [beta (SE) = 2.75 (1.35); p = 0.043 and beta (SE) = 3.43 (1.50); p = 0.023, respectively]. In addition, the adjusted model showed a significant positive relationship between the maternal plasma TAC and birth length [beta (SE) = 0.023 (0.009); p = 0.01].ConclusionThis study showed the positive association of maternal plasma TAC with birth weight and length. Moreover, maternal dietary intake of beta-carotene in the first trimester and vitamin E in the third trimester of pregnancy had significant positive and negative correlations with birth length, respectively.
Women Legislators in Africa and Foreign Aid
Authors: Annen Kurt , Asiamah Henrietta A 
Published: January 2023

Abstract
There has been a significant rise in the share of women legislators in Africa. What makes this fact puzzling is that it cannot be attributed to an African electorate that values gender equality and having women in political leadership positions. In stark contrast to this, gender equality and women’s empowerment have successively moved up in the priority list of the international donor community over the last two decades. This raises the question of whether there is a relationship between women legislators in Africa and foreign-aid allocations. This study finds a strong and statistically robust relationship: an increase in the share of women legislators from 15 to 20 percent is associated with an increase of about 4 percent in aid conditional on current levels of aid. Additionally, the study finds that democratic countries receive more aid but does not find an interaction effect between democracy and the share of women legislators, which suggests that donors do not tailor their gender-selective aid towards more democratic countries. The results provide evidence in support of aid selectivity for policies that improve gender equality in aid-recipient countries in Sub-Saharan Africa.
Carbon Burial in Sediments below Seaweed Farms
Authors: Duarte Carlos M. , Delgado-Huertas Antonio , Marti Elisa , Gasser Beat , San Martin Isidro , Cousteau Alexandra , Neumeyer Fritz , Reilly-Cayten Megan , Boyce Joshua , Kuwae Tomohiro , Hori Masakazu , Miyajima Toshihiro , Price Nichole N. , Arnold Suzanne , Ricart Aurora M. , Davis Simon , Surugau Noumie , Abdul Al-Jeria , Wu Jiaping , Xiao Xi , Chung Ik Kyo , Choi Chang Geun , Sondak Calvyn F.A. , Albasri Hatim , Krause-Jensen Dorte , Bruhn Annette , Boderskov Teis , Hancke Kasper , Funderud Jon , Borrero-Santiago Ana R. , Pascal Fred , Joanne Paul , Ranivoarivelo Lanto , Collins William T. , Clark Jennifer , Gutierrez Juan Fermin , Riquelme Ricardo , Avila Marcela , Macreadie Peter I. , Masque Pere 
Published: January 2023

AbstractThe hypothesis that seaweed farming contributes to carbon burial below the farms was tested by quantifying burial rates in 20 seaweed farms distributed globally, ranging from 2 to 300 years in operation and from 1 ha to 15,000 ha in size. This involved combining analyses of organic carbon density with sediment accumulation rate in sediments below seaweed farms relative to reference sediments beyond the farm and/or prior to the farm operation. One in every four farms sampled was set over environments that export, rather than retain materials. For the farms that were placed over depositional environments, where sediment accumulation could be quantified, the thickness of sediment layers and stocks of carbon accumulated below the farms increased with farm age, reaching 140 ton C ha-1for the oldest farm, and tended to exceed those in reference sediments beyond the farm and/or prior to the operation of the farms. Organic carbon burial rates in the farm sediments averaged (± SE) 1.87 ± 0.73 ton CO2equivalent (CO2-eq) ha-1year-1(median 0.83, range 0.10 – 8.99 ton CO2-eqha-1year-1), twice the average (± SE) burial rate in reference sediments (0.90 ± 0.27, median 0.64, range 0.10-3.00 ton CO2-eqha-1year-1), so that the excess organic carbon burial attributable to the seaweed farms averaged 1.06 ± 0.74 ton CO2-eqha-1year-1(median 0.09, range −0.13-8.10 ton CO2-eqha-1year-1). This first direct quantification of carbon burial in sediments below seaweed farms confirms that, when placed over depositional environments, seaweed farming tend to sequester carbon in the underlying sediments, but do so at widely variable rates, increasing with farm yield.