bluuebunny/crossref_metadata_2025_split huggingface dataset:
Misidentification errors in reencounters result in biased estimates of survival probability from CJS models: Evidence and a solution using the robust design
Authors: Rakhimberdiev Eldar , Karagicheva Julia , Saveliev Anatoly , Loonstra A. H. Jelle , Verhoeven Mo A. , Hooijmeijer Jos C. E. W. , Schaub Michael , Piersma Theunis 
Published: February 2022

Abstract

Misidentification of marked individuals is unavoidable in most studies of wild animal populations. Models commonly used for the estimation of survival from such capture–recapture data ignore misidentification errors potentially resulting in biased parameter estimates. With a simulation study, we show that ignoring misidentification in Cormack–Jolly–Seber (CJS) models results in systematic positive biases in the estimates of survival and in spurious declines of survival over time.

We developed an extended robust design capture mark–resight (RDM) model that includes correct identification parameters to get unbiased survival estimates when resighting histories are prone to misidentification. The model assumes that resightings occur repeatedly within a season, which in practice is often the case when resightings of colour‐marked individuals are collected. We implemented the RDM model in a state‐space formulation and also an approximate, but computationally faster, model (RDMa) in JAGS and evaluated their performances using simulated and empirical capture–resight data on black‐tailed godwits Limosa limosa.

The CJS models applied to simulated data under an imperfect identification scenario data produced strongly positively biased estimates of survival. For a range of degrees of correct identification probabilities, the RDM model provided unbiased and accurate estimates of survival, reencounter and correct‐identification probabilities. The RDMa model performed well for large datasets (>25 individuals), with high resighting (>0.3) and high correct identification (>0.7) probabilities. For the empirical data, the CJS model estimated average juvenile survival at 0.997% and adult survival at 0.939% and also detected a strong decline in adult survival over time at a rate of −0.14 ± 0.029. In contrast, the RDMa model estimated a probability of correct identification of 0.94, annual juvenile survival at 0.234%, adult at 0.834% and less strong decline over time (−0.046 ± 0.016).

We conclude that estimates of survival probabilities obtained from data that include misidentification errors and analysed with standard CJS model are unlikely to be correct. The bias in survival increases with the magnitude of misidentification errors, which is inevitable as datasets become longer. Since misidentification due to tag misreads is common in empirical data, we recommend the use of the here presented RDM model to provide unbiased parameter estimates.
Patterns of recurrent preterm birth in Western Australia: A 36‐year state‐wide population‐based study
Authors: Adane Akilew A. , Shepherd Carrington C.J. , Farrant Brad M. , White Scott W. , Bailey Helen D. 
Published: February 2022

BackgroundIt is known that a previous preterm birth increases the risk of a subsequent preterm birth, but a limited number of studies have examined this beyond two consecutive pregnancies.AimsThis study aimed to assess the risk and patterns of (recurrent) preterm birth up to the fourth pregnancy.Materials and MethodsWe used Western Australian routinely linked population health datasets to identify women who had two or more consecutive singleton births (≥20 weeks gestation) from 1980 to 2015. A log‐binomial model was used to calculate risk ratios (RRs) and 95% confidence interval (CIs) for preterm birth risk in the third and fourth deliveries by the combined outcomes of previous pregnancies.ResultsWe analysed 255 435 women with 651 726 births. About 7% of women had a preterm birth in the first delivery, and the rate of continuous preterm birth recurrence was 22.9% (second), 44.9% (third) and 58.5% (fourth) deliveries. The risk of preterm birth at the third delivery was highest for women with two prior indicated preterm births (RR 12.5, 95% CI: 11.3, 13.9) and for those whose first pregnancy was 32–36 weeks gestation, and second pregnancy was less than 32 weeks gestation (RR 11.8, 95% CI: 10.3, 13.5). There were similar findings for the second and fourth deliveries.ConclusionsOur findings demonstrate that women with any prior preterm birth were at greater risk of preterm birth in subsequent pregnancies compared with women with only term births, and the risk increased with shorter gestational length, and the number of previous preterm deliveries, especially sequential ones.
Identification and functional analysis of two new de novo KCNMA1 variants associated with Liang–Wang syndrome
Authors: Liang Lina , Liu Huihui , Bartholdi Deborah , van Haeringen Arie , Fernandez‐Jaén Alberto , Peeters Els E. A. , Xiong Hongbo , Bai Xuemei , Xu Chengqi , Ke Tie , Wang Qing K. 
Published: February 2022

AbstractAimLoss‐of‐function KCNMA1 variants cause Liang–Wang syndrome (MIM #618729), a newly identified multiple malformation syndrome with a broad spectrum of developmental and neurological phenotypes. However, the full spectrum of clinical features and underlying pathogenic mechanisms need full elucidation.MethodsExome sequencing was used to identify pathogenic variants. Patch‐clamp recordings were performed to access the effects of KCNMA1 variants on BK channels. Total and membrane protein expression levels of BK channels were characterized using Western blotting.ResultsWe report identification and functional characterization of two new de novo loss‐of‐function KCNMA1 variants p.(A172T) and p.(A314T) with characteristics of Liang–Wang syndrome. Variant p.(A172T) is associated with developmental delay, cognitive impairment and ataxia. Mechanistically, p.(A172T) abolishes BK potassium current, inhibits Mg2+‐dependent gating, but shifts conductance‐voltage (G‐V) curves to more positive potentials when complexed with WT channels. Variant p.(A314T) is associated with developmental delay, intellectual disability, cognitive impairment, mild ataxia and generalized epilepsy; suppresses BK current amplitude; and shifts G‐V curves to more positive potentials when expressed with WT channels. In addition, two new patients with previously reported gain‐of‐function variants p.(N536H) and p.(N995S) are found to show epilepsy and paroxysmal dyskinesia as reported previously, but also exhibit additional symptoms of cognitive impairment and dysmorphic features. Furthermore, variants p.(A314T) and p.(N536H) reduced total and membrane levels of BK proteins.ConclusionOur findings identified two new loss‐of‐function mutations of KCNMA1 associated with Liang–Wang syndrome, expanded the spectrum of clinical features associated with gain‐of‐function KCNMA1 variants and emphasized the overlapping features shared by gain‐of‐function and loss‐of‐function mutations.
A qualitative study utilizing Interpretative phenomenological analysis to explore disclosure in adolescents with turner syndrome
Authors: Nisbet Mhairi , O’Connor Rory , Mason Avril , Hunter Elizabeth 
Published: February 2022

ObjectivesTo explore the experiences of diagnostic disclosure and disclosure to others in adolescents with Turner syndrome (TS) and their parents/guardians. In addition, we sought to examine the impact of TS on girls with TS and their family’s lives.DesignA qualitative method utilizing interpretative phenomenological analysis (IPA) was employed.MethodsFive girls with TS and one parent/guardian of each girl completed dyadic and individual semi‐structured interviews. Interviews were audio recorded and analysed verbatim. Data were analysed in accordance with IPA guidelines, with a focus on the dynamic interactions within dyads.ResultsAnalyses identified three superordinate themes across the 10 participant accounts: communication and support, stigmatization of TS, and psychological consequences. Ten related subthemes are described alongside relevant quotations, highlighting a gradual process of diagnostic disclosure within families and wider health care systems. Both girls and their parents appeared to express a general desire to conceal TS from others, indicating possible TS‐related stigma. The results also demonstrate the varying impact TS can have within families.ConclusionsThe findings provide insight into the lived experience of receiving a diagnosis of TS and the possible difficulties around disclosure to others. Potential recommendations for clinicians and parents include ensuring direct conversations about infertility occur within treatment and facilitating open, honest communication.
Design, synthesis, and molecular modeling of coumarin derivatives as MDM2 inhibitors targeting breast cancer
Authors: Ahmed Eman Y. , Abdel Latif Nehad A. , Nasr Tamer , Awad Hanem M. , Abdelhafez Omaima M. 
Published: February 2022

AbstractThe coumarin ring was used as a central scaffold that was substituted with a variety of bioactive functional groups, for designing and synthesizing novel MDM2 inhibitors targeting breast cancer. The synthesized derivatives, 3c, 3d, 3g, 7b, 7c and 8 with IC50s ranging from 9.4 to 9.9 µM were evaluated for their safety on MCF10a normal breast cell line. The compounds showed selectivity indices of 2.15, 3.85, 2.75, 1.38, 3.72 and 5.20 respectively. 7c was selected for further investigation, the compound was capable of down‐regulating MDM2 and the anti‐apoptosis proteins Bcl‐2 and Bcl‐xL, up‐regulating the level of p53 and the pro‐apoptosis protein BAX, causing cell cycle arrest at G2/M phase and activating Caspase‐9 to induce apoptosis. Molecular docking study revealed the capability of derivative 7c to interact with the key amino acids in p53 binding pocket of MDM2 protein. Moreover, the physicochemical properties of compound 7c were studied in silico.
Evaluation of a blockchain‐based dynamic consent platform (METORY) in a decentralized and multicenter clinical trial using virtual drugs
Authors: Huh Ki Young , Moon Seol Ju , Jeong Sang‐un , Kim Min‐Ji , Yang Wooseok , Jeong Myeonggyu , Kim Min‐Gul , Lee SeungHwan 
Published: February 2022

AbstractBlockchain is a novel data architecture characterized by a chronological sequence of blocks in a decentralized manner. We aimed to evaluate the real‐world feasibility of a blockchain‐based dynamic consent platform (METORY) in a decentralized and multicenter trial. The study consisted of three visits (i.e., screening and 2 follow‐up visits) with a 2‐week interval. Each subject was required to report the self‐measured body temperatures and take a virtual investigational drug by entering the unique drug code on the application. To simulate real‐world study settings, two major (i.e., changes in the schedule of body temperature measurement) and three minor protocol amendments (i.e., nonsignificant changes without any changes in the procedures) were set. Overall study completion rates, proportion of consent, and response time to each protocol amendment and adherence were evaluated. A total of 60 subjects (30 in each center) were enrolled in two study centers. All subjects completed the study, and the overall proportion of consent to each protocol amendment was 95.7 ± 13.7% (mean ± SD), with a median response time of 0.2 h. Overall, subjects took 90.8% ± 19.2% of the total drug, whereas compliance with the schedule was 69.1% ± 27.0%. Subjects reported 96.7% ± 4.2% of the total body temperature measurements whereas the adherence to the schedule was 59.0% ± 25.0%, which remarkably decreased after major protocol amendments. In conclusion, we evaluated a blockchain‐based dynamic consent platform in real clinical trial settings. The results suggested that major changes should be avoided unless subjects’ proper understanding is warranted.
A phase I evaluation of the effect of curcumin on dose‐limiting toxicity and pharmacokinetics of irinotecan in participants with solid tumors
Authors: Gbolahan Olumide B. , O’Neil Bert H. , McRee Autumn J. , Sanoff Hanna K. , Fallon John K. , Smith Philip C. , Ivanova Anastasia , Moore Dominic T. , Dumond Julie , Asher Gary N. 
Published: February 2022

AbstractCurcumin inhibits UDP‐glucuronyltransferases, a primary metabolic pathway for cancer chemotherapeutic agents like irinotecan. Concurrent administration of both agents may exacerbate irinotecan toxicity. We conducted this phase I study to determine the safety of concurrent curcumin and irinotecan administration. Ten participants with advanced solid tumors received one of four doses (1, 2, 3, and 4 g) of a curcumin phosphatidylcholine complex (PC) orally daily, and 200 mg/m2 of i.v. infusion irinotecan on days 1 and 15 of a 28‐day cycle, to determine the maximum tolerated dose (MTD) of PC. Thirteen participants received 4 g of PC (MTD) to assess the effect on the pharmacokinetic (PK) properties of irinotecan and its metabolites, SN‐38 and SN‐38G. Irinotecan, SN‐38, and SN‐38G exposure equivalence with and without curcumin was assessed using area under the plasma concentration‐time curves from 0 to 6 h (AUC0‐6h). Safety assessments and disease responses were also evaluated. The combination of irinotecan and PC was well‐tolerated. Because there was no dose limiting toxicity, the maximum dose administered (4 g) was defined as the recommended phase II dose of PC. PC did not significantly alter the plasma exposure and other PK properties of irinotecan and its metabolites. There was no apparent increase in the incidence of irinotecan‐associated toxicities. The objective response rate was 3/19 (22%, 95% confidence interval [CI]: 5–39%), median progression free survival and overall survival (n = 23) were 4 months (95% CI: 2.9–8.9 months) and 8.4 months (95% CI: 3.7 – not evaluable [NE]), respectively. Future studies are required to evaluate the efficacy of this combination.
BNT162b2 Vaccine‐Associated Myo/Pericarditis in Adolescents: A Stratified Risk‐Benefit Analysis
Authors: Krug Allison , Stevenson Josh , Høeg Tracy Beth 
Published: February 2022

AbstractBackgroundMale patients ages 12–17 years have an elevated risk of mRNA vaccination‐associated myo/pericarditis. A risk‐benefit analysis of first and second doses of mRNA vaccination in adolescent boys by health status and history of SARS‐CoV‐2 infection has not been performed.MethodsUsing the Vaccine Adverse Event Reporting System (VAERS), we identified BNT162b2 [Pfizer‐BioNTech] myo/pericarditis occurrence according to CDC criteria. Main outcomes were as follows: 1) post‐vaccination myo/pericarditis crude incidence in adolescents aged 12–15 and 16–17; and 2) two risk‐benefit analyses by age, sex, comorbidity, variant and history of infection.ResultsCases of myo/pericarditis (n = 253) included 129 after dose 1 and 124 after dose 2; 86.9% were hospitalized. Incidence per million after dose two in male patients aged 12–15 and 16–17 was 162.2 and 93.0, respectively. Weighing post‐vaccination myo/pericarditis against COVID‐19 hospitalization during delta, our risk‐benefit analysis suggests that among 12–17‐year‐olds, two‐dose vaccination was uniformly favourable only in nonimmune girls with a comorbidity. In boys with prior infection and no comorbidities, even one dose carried more risk than benefit according to international estimates. In the setting of omicron, one dose may be protective in nonimmune children, but dose two does not appear to confer additional benefit at a population level.ConclusionsOur findings strongly support individualized paediatric COVID‐19 vaccination strategies which weigh protection against severe disease vs. risks of vaccine‐associated myo/pericarditis. Research is needed into the nature and implications of this adverse effect as well as immunization strategies which reduce harms in this overall low‐risk cohort.
Epidemiological characterization of a disease associated with phytoplasmas in Andean oak, Quercus humboldtii Bonpland, in Bogotá—Colombia
Authors: Lamilla Julian , Solano Cindy Julieth , Franco‐Lara Liliana 
Published: February 2022

AbstractQuercus humboldtii is the dominant tree species in oak forest ecosystems in the Colombian Andes, and approximately 15,000 trees have been planted in urban Bogotá. In Bogotá, Q. humboldtii is affected by phytoplasmas. The management of phytoplasmas relies mainly on control of the insect vectors. The aim of this work was to generate information on phytoplasmas affecting Q. humboldtii and the potential insect vectors involved. Phytoplasmas were detected by nested PCR and identified by restriction fragment length polymorphism or sequencing analysis of the 16S rRNA gene in 238 randomly selected urban trees, from 17 city zones. The prevalence of the disease was 80%, with phytoplasmas detected in 94% of trees. ‘Candidatus Phytoplasma fraxini’ was found in 54.6%, ‘Candidatus Phytoplasma asteris’ in 30.7% and mixed infections of both phytoplasmas in 8.8% of the trees. Phytoplasmas were observed in the phloem of infected trees by electron microscopy. ‘Ca. P. fraxini’ was more common than ‘Ca. P. asteris’ in both street and parks trees, but correlations between the phytoplasma and disease‐associated variables were not observed. The entomofauna of a subsample of 102 of these trees was examined. Representative specimens of seven orders were collected, with Hemiptera the most prevalent. Specimens of 17 Cicadellidae, one Membracidae and one Psyllidae species were collected. Cicadellidae species from subfamilies Aphrodinae, Deltocephalinae, Iassinae, Eurymelinae, Megophthalminae and Typhlocybinae were found, in which phytoplasma vectors have been reported previously. Specimens of two known Cicadellidae vector species were collected: Amplicephalus funzaensis (Deltochephalinae) and Exitianus atratus (Deltochephalinae). Phytoplasmas were assessed in 103 Cicadellidae specimens. ‘Candidatus P. asteris’ was detected in A. funzaensis (n = 3/16 tested), E. atratus (n = 2/10 tested) and Alebrini sp. 1 (n = 1/11) tested). The possible epidemiological implications of these findings are discussed.
Impact of infectious comorbidity and overall time of hospitalization in total outpatient management of acute myeloid leukemia patients following venetoclax and hypomethylating agents
Authors: Papayannidis Cristina , Nanni Jacopo , Cristiano Gianluca , Marconi Giovanni , Sartor Chiara , Parisi Sarah , Zannoni Letizia , Saed Rashed , Ottaviani Emanuela , Bandini Lorenza , Testoni Nicoletta , Baldazzi Carmen , Solli Vincenza , Ricci Paolo , Di Giovanni Bezzi Chiara , Abd‐alatif Rania , Stanzani Marta , Paolini Stefania , Cavo Michele , Curti Antonio 
Published: February 2022

AbstractVenetoclax (VEN) and hypomethylating agent (HMAs) regimens are emerging as the standard of care for unfit for chemotherapy acute myeloid leukemia (AML) patients, but the safety and feasibility of a total outpatient management have not been fully investigated. Fifty‐nine AML patients with active disease received VEN and HMAs. Nineteen out of 59 (32.2%) patients received the first cycle as inpatients, whereas 40/59 (67.8%) patients were treated in the outpatient setting. No significant differences were observed with regard to incidence of adverse events (AEs), including tumor lysis syndrome (TLS), and the 30‐day and 60‐day mortality was comparable. Notably, an infectious prophylaxis inspired to that adopted during intensive chemotherapy resulted in a low infection rate with a reduced bacterial infections incidence in out‐ versus hospitalized patients (p < .0001). The overall time of hospitalization was significantly shorter in patients who received a total outpatient treatment as compared to those who received the first cycle as inpatients (5.9 vs. 39.7 days, p < .0001). Despite the adopted differences in treatment management, the efficacy was similar. These data indicate that a total outpatient management of VEN and HMAs is feasible in AML patients without negatively impacting on treatment efficacy and may yield pharmacoeconomic and quality‐of‐life benefits.
Spatio‐temporal pattern and mechanism of coordinated development of “population–land–industry–money” in rural areas of three provinces in Northeast China
Authors: Lyu Xiao , Wang Yanan , Zhao Yuntai , Niu Shandong 
Published: February 2022

AbstractIn global pattern reconstruction, ecological civilization construction and integrated urban–rural development in the new era as well as outlining a new framework for rural development and promoting efficient operation of the coordination mechanism for rural development are urgently required. This paper considers three northeastern provinces of China as an example, attempts to analyze the relationship between the subsystems of rural development, and examines the coupling coordination mechanism of population, land, and industry money in the four‐dimensional system. It explores the evolution path and defects of rural development in Northeast China under the background of transformation from a systematic perspective. We found that the coupling degree of “population‐land‐industry‐money” in rural Northeast China is high, while the coordination degree is low. The degree of spatial and temporal differentiation of the coupling coordination degree gradually increases, and the rural development of each province is highly unbalanced. The results also indicate that the main reasons for the low level of the coupling coordination degree are improved land development levels, a relative shortage of labor force, backward industrial development, and increasingly weak rural investment levels. Finally, this paper illustrates that the main solutions to rural revitalization are stimulating rural investment through policies and promoting the revival of agriculture, with financial support as the starting point, before establishing the linkage and mutual feed development of “population‐land‐industry‐money” in rural areas. The results will help countries, especially developing countries, to further consider methods toward achieving rural development.
Visualization of Aqueous Geochemical Data Using Python and WQChartPy
Authors: Yang Jing , Liu Honghua , Tang Zhonghua , Peeters Luk , Ye Ming 
Published: February 2022

AbstractGraphical methods have been widely used for visualization, classification, and interpretation of aqueous geochemical data to obtain a better understanding of surface and subsurface hydrologic systems. This method note presents WQChartPy, an open‐source Python package developed to plot a total of 12 diagrams for analysis of aqueous geochemical data. WQChartPy can handle various data formats including Microsoft Excel, comma‐separated values (CSV), and general delimited text. The 12 diagrams include eight traditional diagrams (trilinear Piper, Durov, Stiff, Chernoff face, Schoeller, Gibbs, Chadha, and Gaillardet) and four recently proposed diagrams (rectangle Piper, color‐coded Piper, contour‐filled Piper, and HFE‐D) that have not been implemented in existing graphing software. The diagrams generated by WQChartPy can be saved as portable network graphics (PNG), scalable vector graphics (SVG), or portable document format (PDF) files for scientific publications. Jupyter and Google Colab notebooks are available online to illustrate how to use WQChartPy with example datasets. The geochemical diagrams can be generated with several lines of Python codes. Source codes of WQChartPy are publicly available at GitHub (https://github.com/jyangfsu/WQChartPy) and PyPI (https://pypi.org/project/wqchartpy/).