bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiological Factors Associated With Intraductal Papillary Mucinous Neoplasm of the Pancreas
Authors: Bülow Robin , Tjaden Christine , Ittermann Till , Hinz Ulf , Klaiber Ulla , Weiss Frank-Ulrich , Aghdassi Ali , Heckler Max , Kromrey Marie-Luise , Völzke Henry , Hosten Norbert , Büchler Markus W. , Lerch Markus M. , Hackert Thilo 
Published: May 2022

Objective
The present study aimed to identify epidemiological factors associated with the development of intraductal papillary mucinous neoplasms (IPMN) of the pancreas comparing patients after IPMN resection with population-based controls.

Methods
Preoperative data of 811 patients undergoing pancreatic resection for IPMN were matched in a 1:1 ratio with a random sample of volunteers from the Study of Health in Pomerania, which showed no pancreatic cyst greater than 2 mm in magnetic resonance cholangiopancreaticography.

Results
A total of 811 controls with a mean age of 61.9 years (standard deviation, 8.4 years) were matched to cases with a mean age of 66.1 years (standard deviation, 9.3 years). A previous history of pancreatitis, endocrine pancreatic insufficiency was significantly more frequent in IPMN patients compared with controls (P = 0.001). Moreover, adjusted data revealed that urogenital cancer (P = 0.034), colorectal cancer (P = 0.021), as well as first-degree family history of colorectal cancer (P = 0.001) were significantly more frequent in IPMN patients.

Conclusions
A history of urogenital and colorectal cancer often coincides with IPMN, which have an indication for surgery and are associated with preoperative episodes of pancreatitis and with endocrine insufficiency. Prospective studies are needed to investigate the role of these factors in IPMN development.
Multidisciplinary Approach to the Care of Children With Acute Recurrent Pancreatitis and Chronic Pancreatitis
Authors: Dike Chinenye R. , Sellers Zachary M. , Husain Sohail Z. , Forsmark Christopher E. , Abu-El-Haija Maisam 
Published: May 2022

Objectives
The aim of this article is to provide guidance to centers and organizations on the personnel (both physician and nonphysician) needed to create and sustain an optimal team, along with potential alternatives, to provide care to children with acute recurrent pancreatitis and chronic pancreatitis.

Methods
This document was developed in collaboration with the North American Society of Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) Pancreas Committee and the National Pancreas Foundation (NPF) after several meetings.

Results
This document highlights both physician and nonphysician personnel needed to provide multidisciplinary care to children with pancreatitis per the recommendation of the NASPGHAN Pancreas Committee members in year 2021 and added to the currently published NPF criteria. We summarize how the NPF criteria would fit with the recently published pediatric pancreatitis society articles from the NASPGHAN.

Conclusions
It is important to manage children with acute recurrent pancreatitis and chronic pancreatitis in a multidisciplinary setting. There is need to study the impact of these personnel on the outcomes of children with pancreatitis.
Acute Pancreatitis in Japan
Authors: Ikeda Mio , Hamada Shin , Kikuta Kazuhiro , Takikawa Tetsuya , Yoshida Naoki , Matsumoto Ryotaro , Tanaka Yu , Kataoka Fumiya , Sasaki Akira , Tarasawa Kunio , Fujimori Kenji , Fushimi Kiyohide , Masamune Atsushi 
Published: May 2022

Objectives
Cases of acute pancreatitis (AP) are increasing worldwide, and mortality remains high in severe cases. In 2015, the Japanese guidelines for the management of AP were revised. We aimed to clarify the clinical practice of AP in Japan and its trend during the revision of the guidelines using a Japanese nationwide administrative database.

Methods
We retrospectively analyzed 102,119 patients with AP who were hospitalized between April 2014 and March 2018. The study period was divided into the first period (the time before the revision: fiscal years 2014 and 2015) and second period (after the revision: 2016 and 2017).

Results
Severe cases of AP accounted for 27.7% of total cases. The in-hospital mortality in severe cases was 5.7%. The mortality within 14 days of admission improved from 3.2% in the first period to 2.6% in the second period (P = 0.022). Referred patients had more severe diseases and a higher mortality. The mortality in patients who underwent endoscopic ultrasound-guided fistuloplasty for local complications (11.6%) was lower than that in patients who underwent percutaneous drainage (23.4%) or AP surgery (22.6%) (P < 0.001).

Conclusions
We clarified the clinical practice of AP including the improved mortality after the revision of the guidelines.
The Scream: Benign Thyroid Tissue as a Lateral Neck Mass
Authors: Wiles Austin , Sayeed Sadia 
Published: May 2022

Abstract
Variant anatomy and cytomorphological overlap between benign and malignant conditions can coincide to produce diagnostic error. We report the case of an unusually shaped thyroid gland bearing a follicular adenoma interpreted as a metastatic papillary thyroid carcinoma. The shape of the gland had a striking resemblance to The Scream, a painting by Edvard Munch, and directly contributed to the misdiagnosis. We discuss the known embryological mechanisms of thyroid development, ultrasound radiological characteristics of thyroid examination, and the cytomorphologic interpretation of thyroid tissue. The constellation of these elements and the resultant error is eloquently illustrated by Munch’s artistic inspiration.
Pulmonary Oligometastasis From the Kidney Masquerading as Primary Carcinoma of the Lung
Authors: Fanaroff Rachel , Burke Allen 
Published: May 2022

Abstract
A biopsy of a solitary lung mass was diagnosed as a primary large cell carcinoma, favoring adenocarcinoma, based on positive epithelial markers, solid growth pattern, absence of squamous or endocrine differentiation, and relatively abundant eosinophilic cytoplasm. The immunohistochemical evaluation was initially confounded by misleading positive results for CD68 and calretinin. The diagnosis was changed to metastatic renal cell carcinoma, when further history and immunohistochemical stains were performed. This report underscores the utility of history and imaging findings in differentiating primary versus metastatic lung tumors and the need for judicious use of immunohistochemical stains. The differential diagnosis of carcinomas of the lung with solid growth pattern is discussed.
When Flow Is Turbulent: CD19 Intensity Is a Pitfall in Acute Leukemia Classification
Authors: Kallen Michael E. , Emadi Ashkan , Duong Vu H. , Baer Maria R. , Ning Yi , Singh Zeba N. , Koka Rima 
Published: May 2022

Abstract
Mixed phenotype acute leukemias (MPALs) are a rare category of acute leukemia with biologic and genetic heterogeneity and a prognosis generally inferior to those of single lineage leukemias. The diagnosis depends on immunophenotypic assessment with a comprehensive panel of monoclonal antibodies by multiparameter flow cytometry and lineage assignment by the World Health Organization criteria. CD19 assessment is required for establishing a B-cell component in MPALs, as is determination of its intensity of expression, and assessment of the additional B-cell markers CD79a, cytoplasmic CD22, and CD10. We report the case of an MPAL, initially classified as an acute myeloid leukemia with weak CD19 expression and later reclassified upon clear demonstration of a B-cell component; such cases highlight a pitfall in classification of acute leukemias, particularly given heterogeneous antigen expression between fluorochromes and subjectivity in judgment of intensity. Practical take-away points include the need for hypervigilance in marker performance patterns in flow cytometry, both between fluorochromes and over time, the benefits of repeat sampling and blast assessment between laboratories, and the potential quality improvements unlocked by expanded flow cytometry panels in diagnostic hematopathology.
Cutaneous Angiosarcoma Simulating Melanoma
Authors: Cockerell Clay J. , Abraham Akhil , Kingston Adean 
Published: May 2022

Abstract
Angiosarcoma is a rare and highly malignant neoplasm that commonly affects previously irradiated areas and areas of chronic lymphedema, classically presenting in the face and scalp. Angiosarcoma is estimated to have an incidence of .5 per 1,000,000 people in the United States, comprising fewer than 1% of all sarcomas. Epithelioid angiosarcoma is a rare, aggressive subtype that carries a poor prognosis and high mortality rate. Here, we present a case in which a lesion on the scalp was initially misdiagnosed as a malignant melanoma, but after further immunohistochemical stains and a wider excisional biopsy, a cutaneous angiosarcoma with epithelioid features simulating melanoma was revealed.
Room of Hazards: A Comparison of Differences in Safety Hazard Recognition Among Various Hospital-Based Healthcare Professionals and Trainees in a Simulated Patient Room
Authors: Wang Melinda , Banda Barbara , Rodwin Benjamin A. , Merchant Naseema B. 
Published: May 2022

Objectives
Adverse events in hospitals are common. While studies have used simulated patient rooms to assess healthcare trainees’ skills in detecting safety hazards, few have explored the characteristics of safety hazards that make them more or less identifiable to healthcare workers. We sought to determine differences in hospital-based safety hazard identification among physicians, nurses, and other staff members.

Methods
Healthcare workers were invited to identify safety hazards in a simulated patient room with intentionally placed hazards. Responses were transcribed and compared between physicians (MD), nurses (RN), and other hospital-based healthcare professionals and trainees (other). Data were analyzed using nonparametric statistical analysis.

Results
Twelve physicians, 29 nurses, and 26 other staff members participated in this study. Different professions identified different numbers of total hazards with nurses identifying more hazards than other professions (RN: 9.59, MD: 9.17, other: 6.35; P = 0.001). All professions had difficulty identifying hazards associated with omission (e.g., no precaution sign: MD: 8.3%, RN: 3.4%, other: 0%) or hazards requiring 2-step logical thinking (e.g., intravenous heparin for patient with head laceration: MD: 0%, RN: 6.9%, other: 0%).

Conclusions
Physicians, nurses, and others identified different numbers of total hazards, and few participants identified hazards associated with omission or 2-step logical thinking. While previous studies have found differences in types of hazards identified among different healthcare members, we identified hazards that were collectively challenging for all participants to identify. Future studies should target identification of these types of hazards, using human factor engineering to decrease risk of patient harm.
Predicting Perceived Reporting Complexity of Abdominopelvic Computed Tomography With Deep Learning
Authors: Cheng Phillip M. , Whang Gilbert , Allgood Evan , Tejura Tapas K. 
Published: May 2022

Objective
The purpose of this pilot study was to examine human and automated estimates of reporting complexity for computed tomography (CT) studies of the abdomen and pelvis.

Methods
A total of 1019 CT studies were reviewed and categorized into 3 complexity categories by 3 abdominal radiologists, and the majority classification was used as ground truth. Studies were randomized into a training set of 498 studies and a test set of 521 studies. A 2-stage neural network model was trained on the training set; the first-stage image-level classifier produces image embeddings that are used in the second-stage sequential model to provide a study-level prediction.

Results
All 3 human reviewers agreed on ratings for 470 of the 1019 studies (46%); at least 2 of the 3 reviewers agreed on ratings for 1010 studies (99%). After training, the neural network model predicted complexity labels that agreed with the radiologist consensus rating on 55% of the studies; 90% of the incorrect predicted categories were errors where the predicted category differed from the consensus rating by one level of complexity.

Conclusions
There is moderate interrater agreement in radiologist-perceived reporting complexity for CT studies of the abdomen and pelvis. Automated prediction of reporting complexity in radiology studies may be a useful adjunct to radiology practice analytics.
Examining the association between genetic risk for depression, wellbeing and schizophrenia, and proximity to greenspace
Authors: Reed Zoe E. , Morris Tim T. , Davis Oliver S.P. , Smith George Davey , Munafò Marcus R. , Griffith Gareth J. 
Published: May 2022

AbstractPrevious studies indicate that residing in areas with greater greenspace is associated with better mental health and wellbeing. It is unclear whether these associations reflect those with better mental health seeking out greener environments.To examine this we 1) test associations between depression, wellbeing and schizophrenia polygenic scores (PGS) with two greenspace measures in UK Biobank (N=238,306 and 293,922), 2) estimate multilevel-models (MLM), clustering individuals by local geography to investigate whether observed global effect estimates may be capturing between area differences and, 3) conduct one-sample Mendelian randomisation (MR) to estimate causal effects.Depression and schizophrenia PGS were associated with residing in areas with lower greenspace, whilst wellbeing PGS was associated with higher greenspace. Locally-clustered MLM demonstrated attenuation for the individual wellbeing PGS association and a reversal of effect for the schizophrenia PGS association. MR revealed evidence of a causal effect of increased depression liability on decreased greenspace.Our study provides evidence for a putative causal relationship whereby people with greater liability to depression may select into less green neighbourhoods. Our results also highlight the potential for apparently individual-level PGS effect estimates to be biased by contextual, between-area differences in outcome, which are not effectively addressed using traditional principal component adjustment.
Macroecological variation in movement profiles: body size does not explain it all
Authors: Straus Samantha , Forbes Coreen , Little Chelsea J. , Germain Rachel M. , Main Danielle A. , O’Connor Mary I. , Thompson Patrick L. , Ford Adam T. , Gravel Dominique , Guzman Laura Melissa 
Published: May 2022

AbstractAnimals couple habitats by three types of movement: dispersal, migration, and foraging, which dynamically link populations, communities, and ecosystems. Spatial distances of movement tend to correlate with each other, reflecting shared allometric scaling with body size, but may diverge due to biomechanical, phylogenetic, and ecological constraints. While these constraints have been investigated within specific taxa, the macroecological and macroevolutionary constraints on movement distances, and causes of those constraints, are still unknown. Here, we synthesized distances of all three movement types across 300+ vertebrate species, and investigated how the relationships between movement types and body size were modified by movement medium, taxonomy, and trophic guild (carnivore, herbivore, etc.). We found that the strength of relationships between movement types and body size varied among environments, taxa, and trophic guilds. Movement profiles interacted with physiological, taxonomic, and ecological traits to depart from expected body mass scaling. Overall, we find that there are systematic patterns to movement distances, and that movement types with very distinct ecological consequences (foraging, migration) can be correlated and subject to similar constraints. This implies that the scales of population dynamics in ecological communities are not entirely determined by the environment and likely reflect general biomechanical, evolutionary and metabolic constraints.
Mitigating pseudoreplication and bias in resource selection functions with autocorrelation-informed weighting
Authors: Alston Jesse M. , Fleming Christen H. , Kays Roland , Streicher Jarryd P. , Downs Colleen T. , Ramesh Tharmalingam , Calabrese Justin M. 
Published: May 2022

AbstractResource selection functions are among the most commonly used statistical tools in both basic and applied animal ecology. They are typically parameterized using animal tracking data, and advances in animal tracking technology have led to increasing levels of autocorrelation between locations in such data sets. Because resource selection functions assume that data are independent and identically distributed, such autocorrelation can cause misleadingly narrow confidence intervals and biased parameter estimates.Data thinning, generalized estimating equations, and step selection functions have been suggested as techniques for mitigating the statistical problems posed by autocorrelation, but these approaches have notable limitations that include statistical inefficiency, unclear or arbitrary targets for adequate levels of statistical independence, constraints in input data, and (in the case of step selection functions) scale-dependent inference. To remedy these problems, we introduce a method for likelihood weighting of animal locations to mitigate the negative consequences of autocorrelation on resource selection functions.In this study, we demonstrate that this method weights each observed location in an animal’s movement track according to its level of non-independence, expanding confidence intervals and reducing bias that can arise when there are missing data in the movement track.Ecologists and conservation biologists can use this method to improve the quality of inferences derived from resource selection functions. We also provide a complete, annotated analytical workflow to help new users apply our method to their own animal tracking data using thectmm Rpackage.
Unlocking the microblogging potential for science and medicine
Authors: Sarkar Aditya , Giros Augustin , Mockly Louis , Moore Jaden , Moore Andrew , Nagareddy Anish , Fu Boyang , Fiscutean Andrada , Chhugani Karishma , Darci-Maher Nicholas , Patel Yesha M. , Sarwal Varuni , Chang Yutong , Ginjala Srishti , Garmire Lana X. , Bao Riyue , Sankararaman Sriram , Chikhi Rayan , Mangul Serghei 
Published: May 2022

AbstractMicroblogging platform Twitter allows researchers to showcase their work, receive constructive feedback, find jobs, and build scientific collaborations. While existing literature has analyzed the benefits of Twitter in the development and distribution of scientific knowledge, most of the studies only took into account a limited number of researchers, which affected the generalizability of derived results. Our study analyzed the activity of 6,000 biomedical scientists on Twitter using data-driven approaches, a third of whom were female. Furthermore, we estimated that up to a quarter of the members of the scientific community are engaged on Twitter. While the number of male scientists joining the microblogging platform every year has decreased, the number of female scientists has remained roughly the same. Scientists are very selective in who they are following as compared to the general public. We also found that the type of tweets and retweets one posts may affect the number of followers, specifically, that a moderate to high level of professionalism and a high level of positivity is correlated with followers count. Moreover, female scientists send fewer negative tweets as compared to male scientists (31.1% for females and 34.7% for males). Our analysis could provide insights and launch a conversation on the advantages and limitations of using Twitter for disseminating scientific information and engaging in constructive discussion and collaborations within the scientific community.
Ecology and conservation status ofPhoebe hainesianaBrandis: a data deficit timber species from Indo-Myanmar biodiversity hotspot
Authors: Devajit Yengkhom , Aashish Lamabam , Wairokpam Benerjit , Vaishnav Vivek , Puni Lokho 
Published: May 2022

AbstractPhoebe hainesianaBrandis (Lauraceae) is an economically significant timber yielding forest species endemic to North-East India in Indo-Myanmar Biodiversity Hotspot (IMBH). The tree exhibits significant commercial importance in timber industries due to its peculiar wood qualities. The timber’s strength, toughness, and durability make it in high demand for furniture making. Despite its significance, the botanical description of the species is not well documented due to the confined distribution of the species in IMBH region. The natural population is rare, but it is the ‘least concerned’ species in the IUCN Red List. Moreover, no taxonomical description of the species is available for its distinct identity among the other species from the genus. In the present study, we conducted a taxonomic, ecological, and forestry assessment of the species in its natural environment, researching the literature and conducting a field survey. A significant variation in intra-specific wood density (450 kg/m3to 800 kg/m3) determines the scope of robust selection for the genetic improvement of the species. Its population has been severely fragmented due to over-harvesting in lack of sustainable management. According to our findings, the species is endangered due to a rapid decline in its population, a limited ‘extent of occurrence,’ and a small ‘area of occupancy.’ Among the other four species from the genus found in India,P. hainesianacan be identified based on its distinct lobes of the fruiting perianth. We recommend a sincere effort for the conservation of this key species of tropical evergreen forest in IMBH region.
Probabilistic mixture models improve calibration of panel-derived tumor mutational burden in the context of both tumor-normal and tumor-only sequencing
Authors: Anaya Jordan , Sidhom John-William , Cummings Craig A. , Baras Alexander S. ,   AACR Project GENIE Consortium
Published: May 2022

ABSTRACTBackgroundTumor mutational burden (TMB) has been investigated as a biomarker for immune checkpoint blockade (ICB) therapy. Increasingly, TMB is being estimated with gene panel-based assays (as opposed to full exome sequencing) and different gene panels cover overlapping but distinct genomic coordinates, making comparisons across panels difficult. Previous studies have suggested that standardization and calibration to exome-derived TMB be done for each panel to ensure comparability. With TMB cutoffs being developed from panel-based assays, there is a need to understand how to properly estimate exomic TMB values from different panel-based assays. Design: Our approach to calibration of panel-derived TMB to exomic TMB proposes the use of probabilistic mixture models that allow for nonlinear relationships along with heteroscedastic error. We examined various inputs including nonsynonymous, synonymous, and hotspot counts along with genetic ancestry. Using the TCGA cohort we generated a tumor-only version of the panel-restricted data by reintroducing private germline variants. Results: We were able to model more accurately the distribution of both tumor-normal and tumor-only data using the proposed probabilistic mixture models as compared to linear regression. Applying a model trained on tumor-normal data to tumor-only input results in biased TMB predictions. Including synonymous mutations resulted in better regression metrics across both data types, but ultimately a model able to dynamically weight the various input mutation types exhibited optimal performance. Including genetic ancestry improved model performance only in the context of tumor-only data, wherein private germline variants are observed.SignificanceA probabilistic mixture model better models the nonlinearity and heteroscedasticity of the data as compared to linear regression. Tumor-only panel data is needed to properly calibrate tumor-only panels to exomic TMB. Leveraging the uncertainty of point estimates from these models better informs cohort stratification in terms of TMB.