bluuebunny/crossref_metadata_2025_split huggingface dataset:
dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture
Authors: Mijangos Jose Luis , Gruber Bernd , Berry Oliver , Pacioni Carlo , Georges Arthur 
Published: June 2022

Abstract

Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of amplified sequence tags) by providing user‐friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities.

Here, we present Version 2 of dartR. In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting.

dartR provides many functions for importing, exporting and linking to other packages, to provide an easy‐to‐navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions.

As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.
Impacts of land cover on reptile movement and habitat use in farming landscapes
Authors: Balouch S. , Driscoll D. A. , Naseer A. , Rais M. , Doherty T. S. 
Published: June 2022

AbstractAgriculture is one of the greatest threats to biodiversity worldwide, but knowledge of how agriculture modifies animal movement, which is crucial for survival, is limited. Here, we examined the effect of landscape composition on the movements of the oriental garden lizard Calotes versicolor in agricultural landscapes of north‐central Pakistan. We radio‐tracked 32 individuals over 5 months to determine whether land cover type (farmland, tree patches, grassland) influences hourly movement rate, inter‐day distance moved, and activity area size. We found that hourly movement rates were higher in tree patches compared to grasslands, and higher when animals moved between land cover types rather than within individual land cover types. Activity area size and movement rates became smaller as the season progressed, but they did not differ according to animal sex or body size. Habitat selection analysis showed that lizards preferred tree patches, avoided farms, roads, water bodies and human dwellings, and used grasslands in proportion to availability. When lizards used farmlands, they were found in field margins 85% of the time. Our results emphasize the importance of treed areas as reptile habitat in these highly modified agricultural lands. Agricultural intensification that reduces the availability of tree patches and field margins will likely reduce the extent to which lizards can use the landscape by removing preferred habitat. Maintaining tree cover and small fields with field margins should promote the coexistence of wildlife conservation and food production in agricultural landscapes.
Thyroidectomy in Australia 2022: lessons from 21,000 consecutive cases
Authors: Papachristos Alexander James , Glover Anthony , Sywak Mark , Sidhu Stan B. 
Published: June 2022

AbstractIn this article, we aim to describe our modern‐day approach to total thyroidectomy, detailing the subtle refinements of our technique, as it has evolved over three decades and 21 000 cases. Since Delbridge's seminal paper in 2003, the major changes to our approach include a retrograde approach to the recurrent laryngeal nerve that allows dissection of the distal RLN from fascial bands within the ligament of Berry before medialisation of the thyroid lobe. Routine use of intraoperative nerve monitoring systems has increased our awareness of temporary neuropraxia, facilitated a reduction in the risk of bilateral RLN palsy and improved our identification and preservation of the external branch of the superior laryngeal nerve. The increasing use of advanced energy devices has been associated with a reduction in post‐operative haematoma rates. We adopt a low threshold to parathyroid auto‐transplantation, unless all glands are assessed to be clearly not at risk, and routinely supplement patients with Caltrate in the immediate post‐operative period to minimize the risk of symptomatic hypocalcaemia. Ultimately, when we reflect on the subtle refinements that have contributed to improved outcomes, the fundamental principles of exposure and dissection that have evolved over decades remain the basis of our surgical approach and must continue to do so.
Cervical cancer mortality in Norway according to screening attendance and age
Authors: Baasland Ingrid , Vie Gunnhild Å. , Romundstad Pål R. , Lönnberg Stefan 
Published: June 2022

AbstractIntroductionThe association between cervical cancer screening and reduction of cervical cancer has been dealt with in much research. However, little has been published on the association between screening and cervical cancer mortality. We assessed cervical cancer deaths according to screening history, histopathology, and age among women in, under, and above screening age.Material and methodsIn this nationwide, registry‐based case–control study from Norway, we included 817 cervical cancer deaths in women diagnosed with cervical cancer in the period 1998–2009. We matched each case with 10 population‐based controls free from cervical cancer, obtained by density‐based sampling. Odds ratios (ORs) with 95% confidence intervals (CIs) for the association between screening attendance and cervical cancer mortality were estimated using conditional logistic regression models.ResultsOf all fatal cervical cancers, 35% were diagnosed among women over screening age and altogether, 83% were either in age groups not covered by the screening program or in non‐attenders of screening age. The estimated risk reduction associated with a cytology test in the preceding 3.5 years was 80% in screening age 25–69 years (OR 0.20; 95% CI 0.16–0.24) with the largest reduction in squamous cell carcinomas (84%) but also a substantial estimated risk reduction of 65% for adenocarcinomas. The associated risk reduction was strongest in women aged 45–69 years, with ORs in the range 0.09–0.18, compared with ORs 0.42–1.35 in women aged 25–39 years.ConclusionsTo reduce the mortality of cervical cancer, screening programs should focus on increasing adherence to the program, as half of all the fatal cases were in the non‐attender group. Further assessments regarding the potential preventive impact of extending screening to women over the current screening age should be considered.
PD‐L1 in gestational trophoblastic disease: an antibody evaluation
Authors: Hoeijmakers Yvonne M. , Simons Michiel , Bulten Johan , Gorris Mark A. J. , Ottevanger Petronella B. , de Vries I. Jolanda M. , Sweep Fred C. G. J. 
Published: June 2022

AbstractIntroductionTreatment with antibodies directed against programed‐cell death ligand 1 (PD‐L1) is a novel therapy for patients with gestational trophoblastic disease. Assessment of PD‐L1 expression in tumor tissue is commonly used to identify patients who might benefit from anti‐PD‐L1 treatment. Multiple antibodies are available to detect PD‐L1‐expressing cells, and percentages of PD‐L1‐expressing cells in samples of patients with gestational trophoblastic disease indicated by these antibodies differ substantially. This raises the question which PD‐L1 antibody best reflects PD‐L1 expression to select patients for treatment.Material and methodsSeven commercially available antibodies for PD‐L1 staining (E1L3N, 73–10, 22C3, CAL10, SP142, 28–8, SP263) were validated on Chinese hamster ovarian (CHO) cells transfected with PD‐L1, PD‐L2, wildtype CHO cells and tonsil tissue. Next, four complete hydatidiform moles and four choriocarcinomas were stained. Samples were independently assessed by two pathologists.ResultsAll seven antibodies showed membranous staining in the PD‐L1‐transfected CHO cells. E1L3N and 22C3 scored the highest percentages of PD‐L1‐positive cells (70%–90% and 60%–70%, respectively). E1L3N stained the cytoplasm of non‐transfected CHO cells and was excluded from analysis. The remaining six antibodies predominantly stained syncytiotrophoblast cells of both complete hydatidiform moles and choriocarcinomas. The percentage of PD‐L1‐stained trophoblast cells and staining intensity varied substantially per used PD‐L1 antibody and between complete hydatidiform moles and choriocarcinomas. Agreement between pathologists was best with 22C3 (intraclass correlation coefficient 0.94–0.96).ConclusionsBased on staining results of the CHO cells, gestational trophoblastic disease samples and intraclass correlation coefficient, 22C3 seems the most suitable for adequate detection of PD‐L1‐expressing trophoblast cells. All antibodies detected PD‐L1‐expressing cells in the gestational trophoblastic disease samples, though with great variability, hampering comparison of results between studies in this rare disease and emphasizing the need for uniformity in detecting PD‐L1‐expressing cells.
Editorial: group‐based hypnotherapy as good as individually delivered hypnotherapy for symptoms of irritable bowel syndrome
Authors: Mikocka‐Walus Antonina , Lores Taryn 
Published: June 2022

LINKED CONTENTThis article is linked to Lövdahl et al papers. To view these articles, visit https://doi.org/10.1111/apt.16934 and https://doi.org/10.1111/apt.16985
Letter: normalising the ileoanal pouch—more than a one‐step technique
Authors: Lo Sheng Wei , Garg Mayur , Segal Jonathan P. 
Published: June 2022

LINKED CONTENTThis article is linked to Quinn et al papers. To view these articles, visit https://doi.org/10.1111/apt.16859 and https://doi.org/10.1111/apt.16988
Editorial: chronic DILI and HILI—corticosteroid plus glycyrrhizin as standard therapy? Authors' reply
Authors: Wang Jia‐Bo , Huang Ang , Wang Yijin , Ji Dong , Zou Zhengsheng 
Published: June 2022

LINKED CONTENTThis article is linked to Wang et al papers. To view this article, visit https://doi.org/10.1111/apt.16902 and https://doi.org/10.1111/apt.16943
Letter: normalizing the ileoanal pouch—more than a one‐step technique. Authors' reply
Authors: Quinn Kevin P. , Busciglio Irene A. , Burton Duane D. , Inoue Akitoshi , Lee Yong S. , Heiken Jay P. , Sheedy Shannon P. , Fletcher Joel G. , Raffals Laura E. 
Published: June 2022

LINKED CONTENTThis article is linked to Quinn et al papers. To view these articles, visit https://doi.org/10.1111/apt.16859 and https://doi.org/10.1111/apt.16954
A BURST‐BAUS consensus document for best practice in the conduct of scrotal exploration for suspected testicular torsion: the Finding Consensus for Orchidopexy in Torsion (FIX‐IT) study
Authors: Clement Keiran D. , Light Alexander , Asif Aqua , Chan Vinson Wai‐Shun , Khadhouri Sinan , Shah Taimur T. , Banks Frederick , Dorkin Trevor , Driver Christopher P. , During Vinnie , Fraser Nia , Johnston Maximilian J. , Lucky Marc , Modgil Vaibhav , Muneer Asif , Parnham Arie , Pearce Ian , Shabbir Majed , Shenoy Manoj , Summerton Duncan J. , Undre Shabnam , Williams Alun , MacLennan Steven , Kasivisvanathan Veeru ,   the FIX‐IT collaborators
Published: June 2022

ObjectivesTo produce a best practice consensus guideline for the conduct of scrotal exploration for suspected testicular torsion using formal consensus methodology.Materials and MethodsA panel of 16 expert urologists, representing adult, paediatric, general and andrological urology used the RAND Corporation / University of California, Los Angeles (RAND/UCLA) Appropriateness Consensus Methodology to score a 184‐statement pre‐meeting questionnaire on the conduct of scrotal exploration for suspected testicular torsion. The collated responses were presented at a face‐to‐face online meeting and each item was rescored anonymously after a group discussion, facilitated by an independent chair with expertise in consensus methodology. Items were scored for agreement and consensus and the items scored with consensus were used to derive a set of best practice guidelines.ResultsStatements scored with consensus increased from Round 1 (122/184, 66.3%) to Round 2 (149/200, 74.5%). Recommendations were generated in 10 categories: consent; assessment under anaesthetic; initial incision; intra‐operative decision making; fixation; medical photography; closure; operation note; logistics; and follow‐up after scrotal exploration. Our statements assume that the decision to operate has already been made. Key recommendations in the consent process included discussion of the possibility of orchidectomy and the possibility of subsequent infection of the affected testis or wound requiring antibiotic therapy. If after the examination under anaesthesia, the index of suspicion of testicular torsion is lower than previously thought, then the surgeon should still proceed to scrotal exploration as planned. A flow chart guiding decision making dependent on intra‐operative findings has been designed. If no torsion is present on exploration and bell clapper deformity is absent, the testis should not be fixed. When fixing a testis using sutures, a three‐ or four‐point method is acceptable and non‐absorbable sutures are preferred.ConclusionsWe have produced consensus recommendations to inform best practice in the conduct of scrotal exploration for suspected testicular torsion.
Corporate profit tax, firm entry with unemployment, and income inequality
Authors: Wang Leonard F. S. , Sun Ji 
Published: June 2022

AbstractIn this paper, we provide a general equilibrium analysis of corporate profit tax on income distribution, unemployment, and wage inequality. With firm dynamics in industrial sector, we identify a new channel through which profit tax affects income and wage inequality: profit tax cut will widen not only the wage gap between skilled and unskilled labor, but also exacerbate the wage inequality of unskilled labor among different sectors. The welfare effect of profit tax cut depends on unemployment deepening (labor‐distortion effect) and more manufacturing firms enter the market (business‐creation effect), eroding the market share of incumbent firms (business‐stealing effect).
Why is trust lower in Quebec? A cultural explanation
Authors: Wu Cary , Dawson Andrew 
Published: June 2022

AbstractIn this article, we provide a cultural explanation of a long‐standing trust puzzle in Canada—Quebecers trust much less than their fellow Canadians. Specifically, we develop a novel approach to empirically assess the historical influence of the Catholic Church, using the Quiet Revolution (a period of abrupt modernization in Quebec) as a natural experiment. We find that older cohorts socialized prior to the Quiet Revolution are significantly less trusting—a distinctive trend that is most pronounced among Catholics. Conversely, in the rest of Canada older cohorts are more trusting, following the trend commonly found in other countries. Furthermore, measures of both religious beliefs and modernization account for a large part of the birth cohort trust gap in Quebec. The findings suggest that low trust in Quebec is rooted in the province's Catholic cultural heritage, but that the legacy of the Quiet Revolution is gradually changing the trust culture.
Fading into the woodwork: Doula work and hospital‐based practice
Authors: Young Christina 
Published: June 2022

AbstractDoulas offer emotional support to women during pregnancy, childbirth, and the early postpartum period. In hospitals, doulas support their clients without holding formal status as employees or as a regulated profession. Drawing on interviews with 26 doulas in Toronto, Canada, along with analyses of the legacy of medical dominance in maternity care, I examine how doulas accomplish their work in hospitals. I find that doulas face challenges accessing physical resources and struggle to provide their model of care in light of routine hospital procedures and interventions. In response, many doulas develop strategies to address the constraints imposed by their work contexts. These findings suggest that the medical model of birth is resistant to even minor modifications or perspectives that view birth holistically rather than solely dependent on medical intervention.
BCL2‐associated athanogene 6 exon24 contributes to testosterone synthesis and male fertility in mammals
Authors: Song Huibin , Chen Dake , Bai Rong , Feng Yue , Wu Shang , Wang Tiansu , Xia Xuanyan , Li Jialian , Miao Yi‐Liang , Zuo Bo , Li Fenge 
Published: June 2022

AbstractObjectivesBCL2‐associated athanogene 6 (BAG6) plays critical roles in spermatogenesis by maintaining testicular cell survival. Our previous data showed porcine BAG6 exon24‐skipped transcript is highly expressed in immature testes compared with mature testes. The objective of this study is to reveal the functional significance of BAG6 exon24 in mammalian spermatogenesis.Materials and MethodsCRISPR/Cas9 system was used to generate Bag6 exon24 knockout mice. Testes and cauda epididymal sperm were collected from mice. TMT proteomics analysis was used to discover the protein differences induced by Bag6 exon24 deletion. Testosterone enanthate was injected into mice to generate a high‐testosterone mice model. H&E staining, qRT‐PCR, western blotting, vector/siRNA transfection, immunofluorescence, immunoprecipitation, transmission electron microscopy, TUNEL and ELISA were performed to investigate the phenotypes and molecular basis.ResultsBag6 exon24 knockout mice show sub‐fertility along with partially impaired blood‐testis barrier, increased apoptotic testicular cell rate and abnormal sperm morphology. Endoplasmic reticulum stress occurs in Bag6 exon24‐deficient testes and sterol regulatory element‐binding transcription factor 2 is activated; as a result, cytochrome P450 family 51 subfamily A member 1 expression is up‐regulated, which causes a high serum testosterone level. Additionally, serine/arginine‐rich splicing factor 1 down‐regulates BAG6 exon24‐skipped transcripts in porcine Sertoli cells by binding to 35–51 nt on BAG6 exon24 via its N‐terminal RNA‐recognition domain.ConclusionsOur findings reveal the critical roles of BAG6 exon24 in testosterone biosynthesis and male fertility, which provides new insights into the regulation of spermatogenesis and pathogenesis of subfertility in mammals.
1017. ASARUM SIEBOLDII FORMA MACULATUM: Aristolochiaceae
Authors: Moore Richard , King Christabel 
Published: June 2022

SummaryAsarum sieboldii f. maculatum (Nakai) Yamaji is a low growing, deciduous rhizomatous herb endemic to South Korea. It is illustrated here with a painting, a line drawing and a photograph in the wild; its introduction, horticultural merits and cultivation are discussed. Recent research has shown that the plain‐leaved A. sieboldii Miq. and A. maculatum Nakai are conspecific, and the rank of forma has been chosen here to denote the plant with mottled leaves.
Linked color imaging improves visibility of colorectal serrated lesion by high color contrast to surrounding mucosa
Authors: Murakami Takashi , Kamba Eiji , Nomura Kei , Kurosawa Taro , Haga Keiichi , Fukushima Hirofumi , Takeda Tsutomu , Shibuya Tomoyoshi , Yao Takashi , Nagahara Akihito 
Published: June 2022

ObjectivesThis study aimed to objectively evaluate the efficacy of linked color imaging (LCI) in diagnosing colorectal serrated lesions by utilizing visibility scores and color differences.MethodsWe examined 89 serrated lesions, including 36 hyperplastic polyps (HPs), 47 sessile serrated lesions (SSLs), and six traditional serrated adenomas (TSAs). Visibility changes were scored by six endoscopists as follows: 4, excellent; 3, good; 2, fair; and 1, poor. Furthermore, images obtained by white‐light imaging (WLI) or LCI were assessed using the CIELAB color space in the lesion and adjacent mucosa. We calculated the mean color values (L*, a*, and b*) measured at five regions of interest of the sample lesion and surrounding mucosa and derived the color difference (ΔE*).ResultsThe visibility scores of both HPs and SSLs in LCI were significantly higher than that in WLI (HPs, 3.67/2.89, P < 0.001; SSLs, 3.07/2.36, P < 0.001). Furthermore, SSLs showed a significantly higher L* value and significantly lower a* and b* values in LCI than the adjacent mucosae (L*, 61.76/58.23, P = 0.016; a*, 14.91/17.58, P = 0.019; b*, 20.42/24.21, P = 0.007), while WLI produced no significant difference in any color value. A similar trend was apparent in HPs. In all serrated groups, LCI revealed significantly greater ΔE* values between the lesion and adjacent mucosa than WLI (HPs, 11.54/6.12; SSLs, 13.43/7.67; TSAs, 35.00/22.48).ConclusionLinked color imaging showed higher color contrast between serrated lesions and the surrounding mucosae compared with WLI, indicating improved visibility of colorectal serrated lesion using LCI.
The perception and experience of young researchers in doctoral programmes in the context of recent reforms in Kazakhstan
Authors: Yelibay Moldir , Karabassova Laura , Mukhatayev Zhussipbek , Yermukhambetova Assiya 
Published: June 2022

AbstractHigher and doctoral education in Kazakhstan underwent a systemic reform since independence in 1990. Reforms have been determined by dynamic socio‐economic developments in Kazakhstan, the country's entry into the global market, and the need to increase the competitiveness of its human capital. Kazakhstan joined the Bologna Process and switched to a three‐cycle education system in 2010. However, the transition process did not happen smoothly. Doctoral education in the country is challenged by a low graduation rate of doctoral students. The purpose of the qualitative study on which this article reports was to explore doctoral students' perceptions of doctoral training and their experiences in Kazakhstani universities in the context of recent reforms.