bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation profile and immunoscore signature in thymic carcinomas: An exploratory study and review of the literature
Authors: Asselta Rosanna , Di Tommaso Luca , Perrino Matteo , Destro Annarita , Giordano Laura , Cardamone Giulia , Rubino Luca , Santoro Armando , Duga Stefano , Zucali Paolo Andrea 
Published: March 2021

AbstractBackgroundSignificant efforts have been made to investigate the molecular pathways involved in thymic carcinogenesis. However, genetic findings have still not impacted clinical practice. The aim of this exploratory trial was to evaluate the immunoscore and molecular profile of a series of thymic carcinomas (TCs), correlating this data with clinical outcome.MethodsFormalin‐fixed, paraffin‐embedded (FFPE) TC tissues were retrieved from our center archive. The immunoscore was evaluated according to Angell and Gallon. DNA was extracted from FFPE tumor samples and, when available, from adjacent histologically normal tissues. Next‐generation sequencing (NGS) was performed targeting hotspot regions of 50 oncogenes and tumor suppressor genes.ResultsA series of 15 TCs were analyzed. After a median follow‐up of 82.4 months, the median overall survival was 104.7 months. The immunoscore was >2 in 5/15 patients (33%). Among the investigated genes, absence of mutations was observed in 5/15 patients (33%), whereas three variants in 1/15 (6%) patient, two variants in 4/15 (26%) patients, and one variant in 5/15 patients (33%) were found. The most recurrently mutated genes were FGFR3 (five mutations) and CDKN2A (three mutations, two of which were nonsense). Patients with CDKN2A loss showed a statistically significantly worse survival (P = 0.0013), whereas patients with FGFR3 mutations showed a statistically significantly better survival (P = 0.048).ConclusionsThis study adds data to the few existing reports on the mutational landscape of TCs, providing the first comprehensive analysis to date. Here, we confirm the low rate of mutations in TCs and suggest FGFR3 and CDKN2A mutations as intriguing potential therapeutic targets.
Effectively inferring overall spatial distribution pattern of species in a map when exact coordinate information is missing
Authors: Chen Youhua , Wu Yongbin , Zhou Jin , Zhang Wenyan , Lin Hong‐Da , Liu Xinke , Pan Kaiwen , Shen Tsung‐Jen , Pan Zhifen 
Published: March 2021

AbstractMapping and comparing biodiversity in space is a routine task in ecological research. However, accurate biodiversity mapping requires exact distributional information as inputs. When exact geographical coordinate information is missing or when only coarse distribution of species is available at the quadrat or plot level, how can we effectively infer and compare spatial distributional patterns of species with reasonable accuracy while controlling the confounding impacts of scale dependency?A crossing‐scale coefficient of variation (CCV) is calculated for three simple diversity indices, the Shannon, Gini–Simpson and reciprocal‐Simpson evenness indices, from the quadrat‐based biodiversity data over varying sampling grain sizes for subtly measuring overall spatial distributional pattern of species in a survey map.Extensive numerical simulations showed that, when the overall distribution of organisms was regular, CCV tended to be very small, for all the three evenness indices. By contrast, when the distribution was highly aggregate, CCV tended to be large. Finally, an intermediate CCV was observed when organism distribution was random. To this end, all the three evenness indices can detect the subtle change on aggregate or regular distribution. Among the indices, the Gini–Simpson evenness index is the most insensitive to both the change of population size of species and the number of sampling grain sizes used. Compared to available spatial statistic metrics that requires exact geographical coordinates as inputs, CCV is a useful metric for assessing the overall spatial distribution pattern of a species across sampling plots in which exact spatial coordinates of each individual are unavailable. Empirical applications of the CCV metric showed that plants in habitat patches extensively managed by humans can present very aggregate distributional pattern, being counterintuitive to the usual expectation that plants in cultivated or planted land should present regular distributional pattern.The present study recommends one effective tool, the combination of CCV and evenness indices, for exploring the overall spatial distributional pattern of a single species under the quadrat‐sampling scheme. The proposed method is particularly suitable to handle ecological data for which the finest‐scale distributional coordinate information of each individual of species is missing.
Potential and pitfalls of citizen science with children: Reflections on Pollinators in the Playground project
Authors: Prendergast Kit , Vanderstock Amelie , Neilly Heather , Ross Catherine , Pirotta Vanessa , Tegart Patrick 
Published: March 2021

AbstractEngaging school‐age children in activities involving ‘real‐world’ science and interacting with scientific researchers can promote an interest in appreciating and understanding the natural world and the scientific method. Here, we describe a project involving five female early‐career and PhD researchers who facilitated a citizen science project with school‐age children. Under the guidance of the researchers, across five schools, children created artificial flowers and installed them on school ovals. Over repeated 10‐min observations, students recorded how colour (yellow vs. blue) and configuration (isolated, clumped adjacent, clumped mixed colour and clumped single colour) influenced how many and what taxa of insects visited. Here, we reflect on what we were able to achieve including creating a simple, fun, cost‐effective project; anecdotal student interest in insects, and positive female STEM role models. We also acknowledge constraints and shortcomings, including set curricula resulting in suboptimal season for pollinator studies; confounding of results due to children’s observations; and being unable to verify the data. We offer recommendations for more robust projects in future, which include collecting specimens to verify results, and measuring learning outcomes. If these recommendations are met, researcher–student projects can engage children in conducting scientific experiments with applications for home and school garden management.
Prevalence and experience of fatigue in survivors of critical illness: a mixed‐methods systematic review
Authors: Bench S. , Stayt L. , Shah A. , Dhiman P. , Czuber‐Dochan W. 
Published: March 2021

SummaryWe conducted a mixed methods systematic review to investigate the prevalence, experience and management of fatigue in survivors of critical illness. We identified 76 studies investigating fatigue or vitality in adults discharged from an intensive care unit and split the extracted data into three datasets: vitality scores from the Short Form Health Survey‐36 (n = 54); other quantitative data (n = 19); and qualitative data (n = 9). We assessed methodological quality using critical appraisal skills programme tools. We adopted a segregated approach to mixed‐methods synthesis. In a final step, we attributed combined results to one of four qualitative themes: prevalence and severity; contributing factors; impacts on quality of life; and assessment and management. Prevalence of fatigue ranged from 13.8 to 80.9%. Short Form Health Survey‐36 vitality scores were commonly used as a marker of fatigue. Vitality scores reached a nadir approximately one month following ICU discharge (mean (SD) 56.44 (32.30); 95%CI 52.92–59.97). They improved over time but seldom reached reference population scores. Associated biological, disease‐related and psychological factors included age, poor pre‐morbid status, sleep and psychological disturbance. Qualitative data highlight the profound negative impact of fatigue on survivors’ quality of life. Survivors seldom had any information provided on the potential impact of fatigue. No fatigue assessment tools specific to critical illness or evidence‐based interventions were reported. Fatigue is highly prevalent in survivors of critical illness, and negatively impacts recovery. Further research on developing fatigue assessment tools specifically for critically ill patients and evaluating the impact of pharmacological and non‐pharmacology interventions is needed.
Bariatric surgery has positive effects on patients’ and their partners’ sexual function: A prospective study
Authors: Gokalp Fatih , Koras Omer , Ugur Mustafa , Yildirak Ekrem , Sigva Hakan , Porgali Sefa B. , Tamkac Nezih , Gorur Sadik 
Published: March 2021

AbstractBackgroundObesity has been associated with severe conditions and sexual dysfunction. Bariatric surgery has effects positively patients’ sexual function.ObjectivesTo assess the effect of bariatric surgery on sexual functions of couples.Materials and MethodsThe study included 57 obese patients and their sexually active partners. Male participations were assessed with the International Index of Erectile Function (IIEF) and Male Sexual Health Questionaries (MSHQ‐4), and female participations were assessed with the Female Sexual Function Index (FSFI).ResultsThere were 31 (54.4%) male patients and 26 (45.6%) female patients in the study. The median IIEF score of the male patients statistically increased postoperatively (p < 0.001). The IIEF subgroup areas were found to have increased after surgery. The median FSFI score of the female patients statistically increased postoperatively (p < 0.001). The median FSFI of male patients’ partners significantly increased postoperatively (p < 0.001). All FSFI domains were statistically significantly increased (p < 0.001, all areas). The median IIEF value of the postoperative partners of the female patients also increased statistically significant (p < 0.001). In addition, the increases in the IIEF’s subdomains in terms of sexual desire (p < 0.001), intercourse satisfaction (p < 0.001), and general satisfaction (p < 0.001) were statistically significant.ConclusionThe sexual functions of both males and females and also their’ partners were improved after bariatric surgery. Patients with preoperative poor sexual function achieve significant benefits over patients without sexual dysfunction.
Protocol for the UK cohort study to investigate the prevention of parastomal hernia (the CIPHER study)
Authors: Tabusa Hana , Blazeby Jane M. , Blencowe Natalie , Callaway Mark , Daniels Ian R. , Gunning Amanda , Hollingworth William , McNair Augus G. , Murkin Charlotte , Pinkney Thomas D. , Rogers Chris A. , Smart Neil J. , Reeves Barnaby C. 
Published: March 2021

AbstractAimAbdominal surgery sometimes necessitates the creation of a stoma, which can cause future complications including parastomal hernia (PSH), an incisional hernia adjacent to and related to the stoma. PSH affects approximately 40% of patients within 2 years of stoma formation. Complications of PSH reduce a patient’s quality of life and can be severe (e.g. bowel obstruction). PSHs are difficult to manage and can recur after surgical repair. Therefore, it is very important to prevent a PSH. Surgeons create stomas in different ways and both patient and surgical factors are believed to influence the development of PSH. The aim of the CIPHER study is to investigate the influence of different surgical techniques on the development of PSH.MethodThe UK cohort study to investigate the prevention of parastomal hernia (the CIPHER study) aims to recruit 4000 patients undergoing elective or expedited surgery with the intention of forming an ileostomy or colostomy, irrespective of the primary indication for the planned surgery. For each patient, surgeons will describe their methods of trephine formation, mesh reinforcement of the stoma trephine, use of the stoma as a specimen extraction site and wound closure. The primary outcome will be incident PSH during follow‐up, defined as symptoms of PSH (custom‐designed questionnaire) and anatomical PSH, ascertained by independent reading of usual care CT scans. Secondary outcomes will include surgical site infection, the Comprehensive Complication Index, quality of life (EQ‐5D‐5L and SF‐12), PSH repair and use of NHS resources.ResultsResults of the study will be submitted for publication in peer‐reviewed journals. All publications relating to the results of CIPHER will use a corporate authorship, ‘The CIPHER Study Investigators’ with named writing committee members.ConclusionThe CIPHER study will be the first to investigate detailed surgical methods of stoma formation in a large, representative cohort of patients with a range of primary indications, both cancer and noncancer.
Separation and identification of commercial reactive dyes with hydrophilic interaction liquid chromatography and quadrupole time‐of‐flight mass spectrometry
Authors: Liu Yixin , Sui Xinyi , Terán Julio E. , Chapman Lisa P. , Ankeny Mary , Vinueza Nelson R. 
Published: March 2021

AbstractThe separation and identification of colourants from aqueous matrices could potentially benefit the coloration industry. In this work, we report a new method that combines hydrophilic interaction liquid chromatography (HILIC) and high‐resolution mass spectrometry (HRMS) for reactive dye separation and identification without employing ion‐pairing agents. The conditions outlined allowed the successful separation of a mixture of four commercial reactive dyes in an aqueous solution, which consisted of CI Reactive Black 5, CI Reactive Orange 35, CI Reactive Blue 49 and CI Reactive Red 31. To further demonstrate the feasibility of this new method, we conducted deeper research into the analysis of CI Reactive Red 31 and its hydrolysis products. Based on the high efficiency of HILIC for polar compounds, and its combination with HRMS, we were able to identify several isomers of CI Reactive Red 31 and its derivatives, which were further characterised by tandem mass spectrometry. This method could potentially benefit chemical evaluations in dye applications, including synthetic processes, because it provides reliable results and simplified operation conditions compared with common traditional high‐performance liquid chromatography methods.
Observed progression from melanosis with melanocyte hyperplasia to sinonasal melanoma with distant metastasis and a unique genetic rearrangement
Authors: Salari Behzad , Duncan Lyn M. , Lennerz Jochen K. , Holbrook Eric H. , Emerick Kevin S. , Foreman Ruth K. 
Published: March 2021

AbstractMelanosis, clinically presenting as a benign macular hyperpigmentation, consists of increased pigmentation (melanotic or melanocytic) either in the mucosal epithelial cells or as subepithelial pigment‐laden macrophages. On the other hand, primary sinonasal mucosal melanoma (SNMM) is a rare disease with poor prognosis and high rates of local recurrence and metastasis. We report follow‐up on a previously presented case of a 53‐year‐old man with recurrent clinical melanosis that progressed from histopathological melanocytic hyperplasia to melanoma in situ over a period of 4.8 years (Yao et al. Allergy Rhinol (Providence), 2016;7(3):164–167). The patient experienced multiple recurrences and local spread despite multiple extensive surgeries. We now report that this patient ultimately developed bilateral invasive SNMM and died with metastatic melanoma. Molecular analysis of the invasive melanoma revealed ALK rearrangement, specifically an EML4‐ALK fusion, which represents the first report of this particular genetic variant in mucosal melanoma.
Ossifying pyogenic granuloma: A rare variant usually not recognized
Authors: Dermawan Josephine K. , Kilpatrick Scott E. 
Published: March 2021

AbstractPyogenic granuloma (PG) represents a polypoid and lobular, capillary lesion, resembling granulation tissue, usually occurring on skin or mucosal surfaces. The occurrence of metaplastic ossification is extremely rare in PG. We present three cases of PG with metaplastic ossification. All three patients were men, aged 18‐66 years. In all cases, the lesions occurred on the digits, particularly in or around the nail bed. Histopathologically, these superficial dermal‐based tumors were characterized by classic features of PG, namely circumscribed, exophytic to polypoid proliferations of capillary‐sized blood vessels in a lobular arrangement. The characteristic vascular component also was intimately associated with spicules and trabeculae of metaplastic bone formation rimmed by osteoblasts and osteoclasts. This osseous component was diffusely distributed in two cases and more localized in another. We speculate that ossification in PGs possibly represents a reactive process in response to chronic injury. We believe that ossifying PG is likely under‐recognized and often mistaken for other entities also arising in the extremities and characterized by osseous metaplasia.
Development of equations and software for estimating weight in children with cerebral palsy
Authors: Ruiz Brunner Maria de las Mercedes , Cieri Maria Elisabeth , Butler Charlene , Cuestas Eduardo 
Published: March 2021

AimTo develop equations and software to estimate weight using segmental measures for children with cerebral palsy (CP).MethodThis was a cross‐sectional study. Children and adolescents with CP of both sexes from 2 to 19 years old from five cities in Argentina were included. Weight, mid‐upper arm circumference (MUAC), and clinical covariables were collected. Linear regression models with weight as the dependent variable and body segment lengths as predictors were developed and compared forR2, adjustedR2, and the root mean square of the error.ResultsIn total, 381 children and adolescents (mean age 10y 5mo [SD 4y 9mo], range 2–19y; 231 males, 150 females) with a confirmed diagnosis of CP were included. Gross motor function based on the Gross Motor Function Classification System (GMFCS) was as follows: level I, 59; II, 55; III, 59; IV, 69; V, 139. The interaction between weight and other variables such as MUAC, sex, GMFCS, and age was analysed. The concordance correlation coefficient between estimated and observed weight was 0.94 (95% CI 0.93–0.95). From the results of the equations, a free software tool, named Weight Calculator CP, was developed.InterpretationWeight in children with CP can be predicted using MUAC, GMFCS, and age. Weight Calculator CP can be used in clinical practice when direct weight cannot be obtained.What this paper addsEquations can be used to estimate weight in children with cerebral palsy via body segments.Weight can be estimated according to age and gross motor function.The average difference between estimated and observed weights was 119g.
Glycaemic control and hypoglycaemia risk with insulin glargine 300 U/mL and insulin degludec 100 U/mL in older participants in the BRIGHT trial
Authors: Bolli Geremia B. , Cheng Alice , Charbonnel Bernard , Aroda Vanita R. , Westerbacka Jukka , Bosnyak Zsolt , Boëlle‐Le Corfec Emmanuelle , Rosenstock Julio 
Published: March 2021

AbstractAimTo evaluate the efficacy and safety of insulin glargine 300 U/mL (Gla‐300) versus insulin degludec 100 U/mL (IDeg‐100) in predefined (</≥65 years) and post hoc (</≥70 years) age groups of people with type 2 diabetes (T2D) in the BRIGHT trial.Materials and MethodsBRIGHT was the first head‐to‐head randomized trial comparing Gla‐300 and Deg‐100 in insulin‐naïve adults with T2D. In this subanalysis, endpoints were studied by predefined (</≥65 years, N = 596/333) and post hoc (</≥70 years, N = 768/161) age groups.ResultsHeterogeneity of treatment effect was observed for HbA1c reductions across the </≥70 years subgroups, but not across the </≥ 65 years subgroups, with greater HbA1c reductions with Gla‐300 versus IDeg‐100 in those 70 years or older (least squares mean −0.34% [95% confidence interval: −0.589% to −0.100%]). There was no significant heterogeneity of treatment effect for incidence and rates of confirmed (≤3.9 mmol/L [≤70 mg/dL]) hypoglycaemia across any age subgroups over 24 weeks, but numerically lower incidence and rates were consistently observed for Gla‐300 versus IDeg‐100 in the 65 years or older and 70 years or older age groups in the initial 12 weeks.ConclusionsGla‐300 may be a suitable treatment option in the growing population of older people with T2D. Further investigation is required to determine Gla‐300 glycaemic benefits in high‐risk populations without increasing the risk of hypoglycaemia.
Left ventricular ejection fraction and Global Longitudinal Strain variability between methodology and experience
Authors: Kouris Nikos T. , Kostopoulos Vassilis S. , Psarrou Georgia A. , Kostakou Peggy M. , Tzavara Chara , Olympios Christoforos D. 
Published: March 2021

IntroductionAlthough ejection fraction (EF) is the cornerstone of the assessment of left ventricular (LV) systolic function, its measurement faces a number of challenges related to image quality, assumptions of LV geometry, and expertise. The aim of this study was to test the inter‐observer variability of EF and GLS measurement in patients with a broad spectrum of LV function, between physicians and investigators (Inv) with different levels of expertise.MethodsIn 122 patients, EF and GLS were measured by 4 Inv blinded to each other with different level of experience in echocardiography; EF was measured using 3 methods: visual assessment, biplane Simpson's method, and auto‐EF method. GLS was measured from the 3 apical views. A significant difference for LVEF and for LVGLS was considered to be >10 and >2 absolute values, respectively.ResultsIntra‐observer agreement was excellent for visually assessed EF (ICC = 0.87, P < .001) and GLS (ICC = 0.82, P < .001) and good for EF measured by Simpson's method (ICC = 0.70, P < .001) and auto‐EF (ICC = 0.72, P < .001). Intra‐observer and inter‐observer agreements were excellent for GLS with ICCs above 0.8. GLS discordance between the 4 Inv was not significant. Discordance in EF and GLS measurements among the Inv was not related to image quality or wall motion abnormalities.ConclusionAlthough EF has proved its prognostic value in various cardiovascular entities, GLS seems to be more reliable for serial assessment of LV function, demonstrating lower intra‐ and inter‐observer variability, even by different physicians with variant level of expertise.
Ecology and evolutionary biology must elevate BIPOC scholars
Authors: Duc Bo Massey Melanie , Arif Suchinta , Albury Catalina , Cluney Victoria A. 
Published: March 2021

AbstractBlack, Indigenous and people of colour (BIPOC) individuals are disproportionately impacted by the negative consequences of our ongoing environmental and climate crises, yet their valuable scientific voices are shockingly underrepresented within the fields of Ecology and Evolutionary Biology (EEB). As early‐career BIPOC EEB researchers, we recognise the key role that our fields play in understanding and mitigating the effects of our ongoing global crises, and are concerned about the lack of diversity we see among our own EEB cohorts and mentors. We present this piece as a call to action for the EEB Academy, drawing on our own experiences and the literature to suggest steps the Academy must take to increase representation of and equity for BIPOC graduate scholars in EEB. We synthesise these steps into four actionable ideas: anti‐racism education and practice, increased funding opportunities, integration of diverse cultural perspectives and a community‐minded shift in PhDs. Importantly, this advice is specifically directed at those who wield power in the Academy (e.g. funding agencies, societies, institutions, departments and faculty), rather than BIPOC scholars already struggling against inequitable frameworks in EEB.