bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinico-radiological features of brain metastases from thyroid cancer
Authors: Kim Song Soo , Kim Seok-Mo , Park Mina , Suh Sang Hyun , Ahn Sung Jun 
Published: December 2021

Abstract
The brain is an unusual site for distant metastases of thyroid cancer. The radiological features of brain metastases (BMs) have rarely been reported. Hemorrhage is frequently noted in BMs from thyroid cancer. This study aimed to investigate the clinico-radiological features of BMs from thyroid cancer and to determine the risk factors to predict BM hemorrhage.
We retrospectively evaluated the MR images of 35 patients with BMs from thyroid cancer at our hospital from 2013 to 2020. The number, size, site, presence of extra-cranial metastasis, presence of perilesional edema, intra-tumoral hemorrhage, enhancement pattern, and presence of diffusion restriction on MRI were described. We further classified the thyroid cancers into hemorrhagic and nonhemorrhagic groups to investigate the factors associated with hemorrhage.
54.29% of patients with thyroid BMs (19/35) had neurologic symptoms. 94.29% of patients (33/35) had extra-cranial metastases. The most common histology of primary thyroid cancer was papillary thyroid cancer (71.43%, 25/35), followed by anaplastic thyroid cancer (22.86%, 8/35). Thyroid cancer BMs were located mostly in the supra-tentorium (51.43%, 18/35) or both the supra and infra-tentorium (45.71%, 16/35). 60% of patients (21/35) showed hemorrhage within the BMs. The strongest predictor for BM hemorrhage was tumor size (variable importance: 50).
Thyroid cancer BMs exhibit a bleeding tendency. Furthermore, larger BMs are more likely to have an intra-tumoral hemorrhage.
Antiphospholipid syndrome with mesenteric vein thrombosis and hepatic nodular regenerative hyperplasia in a child
Authors: Han Seung Hyung , Park Kyung Duk , Kim Soon Chul 
Published: December 2021

Abstract

Rationale:
Hepatic nodular regenerative hyperplasia (NRH), a nonspecific change in the liver parenchyma, is very rare in children. Hepatic microvascular changes may be the cause, as these vascular changes are uncommon in children. Antiphospholipid syndrome (APS), an autoimmune disease characterized by vascular thromboembolism, is extremely unusual in children.

Patient concerns:
A 13-year-old girl who presented with abdominal pain and elevated liver enzymes was transferred to our hospital. Abdominal computed tomography and magnetic resonance imaging showed a massive mesenteric venous thrombus and a malignant mass with liver metastasis.

Diagnoses:
Her immunological profile was positive for antinuclear antibodies (ANA) at a titer of 1/160 (nucleolar pattern), anticardiolipin antibodies (aCL) immunoglobulin G, and anti-histone antibody. A liver biopsy revealed hepatic NRH.

Interventions:
The patient was initially started on heparin upon hospitalization and switched to warfarin and a vitamin K antagonist and continued treatment with international normalized ratio monitoring.

Outcomes:
Her symptoms improved after 9 months of anticoagulation therapy.

Lessons:
In the presence of hepatic NRH or vascular thrombosis in children, we recommend that APS be differentially diagnosed using lupus anticoagulant and aCL and appropriate management be implemented.
Leukocytes infiltration correlates intratumoral microvessel density and influence overall and late-phase disease-free survival in hepatocellular carcinoma
Authors: Yang Yuan , Fu Ning , Wang Haiqing , Hao Jingcheng 
Published: December 2021

Abstract
Hepatocellular carcinoma (HCC) is a severe type of primary liver cancer with high postoperative recurrence. The prognosis predictability of tumor-infiltrating leukocytes (TILs) for patients who underwent HCC resection has been widely reported. However, limited information is available about TIL trafficking, which is also crucial for HCC patients.
We included tumor tissue samples and clinical data from 89 HCC patients in this study and performed immunohistochemistry for CD3, CD8, FoxP3, and CD31. TILs were measured using an algorithm for quantification of tumor immune stroma (QTiS). Intratumoral microvessels were counted using Weidner's method. We first examined correlations among them and analyzed their relationships with clinical and survival data.
Intratumoral microvessel density (iMVD) was significantly correlated with infiltration of CD3+ (r = 0.338, P = .001) and CD8+ (r = 0.320, P = .002) cells, but not FoxP3+ (r = 0.153, P = .152) cells. After multivariate analysis, higher infiltration of CD3+ (P = .038) independently showed significant predictability on better overall survival after resection of HCC. Although no influence of CD3+ (P = .386) and CD8+ (P = .648) cells were found on general disease-free survival, infiltration of CD3+ (P = .012), tumor size (P = .032) and albumin (P = .007) cells independently predicted late-phase disease-free survival. No significant relationships regarding iMVD, and infiltration of FoxP3+ cells with overall and disease-free survival were found.
Our data suggest that increased iMVD could enrich tumor-infiltrating CD3+ cells. Infiltrated CD3+ cells could help to better predict both the overall and late-phase disease-free survival after resection of HCC.
Clinical characteristics and prognostic factors for Crohn’s disease relapses using natural language processing and machine learning: a pilot study
Authors: Gomollón Fernando , Gisbert Javier P. , Guerra Iván , Plaza Rocío , Pajares Villarroya Ramón , Moreno Almazán Luis , López Martín Mª Carmen , Domínguez Antonaya Mercedes , Vera Mendoza María Isabel , Aparicio Jesús , Martínez Vicente , Tagarro Ignacio , Fernández-Nistal Alonso , Lumbreras Sara , Maté Claudia , Montoto Carmen 
Published: December 2021

Background
The impact of relapses on disease burden in Crohn’s disease (CD) warrants searching for predictive factors to anticipate relapses. This requires analysis of large datasets, including elusive free-text annotations from electronic health records. This study aims to describe clinical characteristics and treatment with biologics of CD patients and generate a data-driven predictive model for relapse using natural language processing (NLP) and machine learning (ML).

Methods
We performed a multicenter, retrospective study using a previously validated corpus of CD patient data from eight hospitals of the Spanish National Healthcare Network from 1 January 2014 to 31 December 2018 using NLP. Predictive models were created with ML algorithms, namely, logistic regression, decision trees, and random forests.

Results
CD phenotype, analyzed in 5938 CD patients, was predominantly inflammatory, and tobacco smoking appeared as a risk factor, confirming previous clinical studies. We also documented treatments, treatment switches, and time to discontinuation in biologics-treated CD patients. We found correlations between CD and patient family history of gastrointestinal neoplasms. Our predictive model ranked 25 000 variables for their potential as risk factors for CD relapse. Of highest relative importance were past relapses and patients’ age, as well as leukocyte, hemoglobin, and fibrinogen levels.

Conclusion
Through NLP, we identified variables such as smoking as a risk factor and described treatment patterns with biologics in CD patients. CD relapse prediction highlighted the importance of patients’ age and some biochemistry values, though it proved highly challenging and merits the assessment of risk factors for relapse in a clinical setting.
Emulsifiers and Intestinal Health
Authors: Richey Levine Arielle , Picoraro Joseph A. , Dorfzaun Sally , LeLeiko Neal S. 
Published: December 2021

ABSTRACTFood additives in general, and emulsifiers in particular, are considered to be important dietary components with a potential to harm the intestine, in part by promoting intestinal inflammation. There is inadequate objective information about the specific nature and the magnitude of the problem.The Food and Drug Administration (FDA) has recognized approximately 450 items added to our foods as being generally regarded as safe and has placed them on a generally regarded as safe (GRAS) list. Additionally, it has also approved approximately 3000 “food additives.” There is a general lack of transparency as to how either of these selections were and continue to be made. Once items are officially designated by the FDA as “food additives” or placed on the GRAS list, there is no regulatory mechanism for the ongoing monitoring of their safety.The most widely used emulsifier is “lecithin,” which is biochemically identified as phosphatidylcholine (PC). Regulatory guidelines allow manufacturers to use the label “lecithin” to be applied to emulsifiers that contain PC plus other phospholipids in a variety of unspecified concentrations. The PC used in experiments cited in the literature, is unlikely to be the same thing as the “lecithin” in our diets.The objective of this introduction to emulsifiers is to raise awareness of the current state of food additives in the USA and to encourage thoughtful approaches to the study of all additives found in our diets. The overriding goal should be to assure the safety of what we eat. As examples we discuss eight widely distributed food additives; four “natural” emulsifiers that are classified as GRAS as well as an additional emulsifier‐associated food additive that is also on the GRAS list, and three synthetic emulsifying agents that are FDA approved as “food additives.”
Interobserver and Intra-Observer Reliability of Eyelid Tests for Ocular Myasthenia Gravis
Authors: Jienmaneechotchai Thanchat , Apinyawasisuk Supanut , Jariyakosol Supharat , Hirunwiwatkul Parima 
Published: December 2021

Background:
Lid fatigability test (LFT), Cogan lid twitch (CLT), and forced eyelids closure test (FECT) are simple clinical screening tests for ocular myasthenia gravis (OMG). However, these tests are subjectively interpreted. We thus evaluated the interobserver and intra-observer reliability of each test.

Methods:
The 3 eyelid tests were performed in ptotic patients associated with various conditions, including OMG and others. Video clips of all tests were recorded using smartphone with built-in camera in the following order; LFT, CLT, and FECT. All video clips were distributed to 3 neuro-ophthalmologists and 3 general ophthalmologists, who were trained to evaluate the tests using a single standard instruction. After 3 months, all video clips were re-organized for the second evaluation. Interobserver and intra-observer reliability were calculated using Cohens' Kappa coefficient and Fleiss Kappa statistic.

Results:
The 3 eyelid tests were performed and recorded in 35 patients, which included the diagnosis of OMG, levator muscle dehiscence, partial oculomotor nerve palsy, and Horner syndrome. CLT received moderate-to-substantial interobserver reliability in neuro-ophthalmologist group (Fleiss Kappa 0.77 [95% CI 0.60–0.94] and 0.66 [95% CI 0.46–0.85] in first and second evaluation respectively), but the results varied in general ophthalmologist group (Fleiss Kappa 0.58 [95% CI 0.37–0.79] and 0.54 [95% CI 0.33–0.76] in first and second evaluation respectively). FECT and LFT received lower interobserver reliability in both groups. CLT also received moderate-to-almost perfect intra-observer reliability in neuro-ophthalmologist group (Cohen Kappa 0.55, 0.58, and 0.92), whereas FECT and LFT received lower intra-observer reliability. The intra-observer reliability varied among general ophthalmologists for all 3 eyelid tests.

Conclusions:
CLT is the most reliable test among the 3 eyelid tests. However, all tests should be interpreted with caution by general ophthalmologists.
Hemisphere-Dependent Ictal Tachycardia Versus Ictal Bradycardia in a Critically Ill Patient
Authors: Fong Michael W. K. , Norris Sarah , Percy Jennifer , Hirsch Lawrence J. , Herlopian Aline 
Published: December 2021

Summary:
Tachycardia is a common ictal phenomenon; however, ictal bradycardia is less commonly reported and rarely presents as ictal asystole/syncope. In critically ill patients, seizures are much less likely to manifest with overt clinical signs, i.e., are more likely to be subtle or nonconvulsive. In this setting, changes in heart rate may be the only clue that seizures are occurring. The authors report an exemplary case of a 78-year-old right-handed man who presented with spontaneous left frontal intraparenchymal hemorrhages. During standard clinical monitoring in the Neuro-Intensive Care Unit, the patient had discrete paroxysms of relative sinus tachycardia, independent episodes of sinus bradycardia, and 3 to 4 seconds of sinus pause. The cardiac investigation was unrevealing, but continuous EEG revealed the answer. The episodes of mild tachycardia were associated with seizures from the left temporal region, whereas those with bradycardia were associated with independent seizures from the right temporal region. The case stands as a stark reminder to remain vigilant of seizures in high-risk patients, especially as a cause for paroxysmal autonomic changes.
miR2Trait: an integrated resource for investigating miRNA-disease associations
Authors: Babu Poornima , Palaniappan Ashok 
Published: December 2021

ABSTRACTMicroRNAs are key components of cellular regulatory networks, and breakdown in miRNA function could lead to cascading effects culminating in pathophenotypes. A better understanding of the role of miRNAs in diseases would aid human health. Here, we have devised a method for comprehensively mapping the associations between miRNAs and diseases by merging on a common key between two curated omics databases. The resulting bidirectional resource, miR2Trait, is more detailed than earlier catalogues, uncovers new relationships, and includes analytical utilities to interrogate and extract knowledge from these datasets. The resource could aid in identifying the disease enrichment of a user-given set of miRNAs and analyzing the miRNA profile of a specified diseasome. miR2Trait is available as both a web-server (https://sas.sastra.edu/pymir18) and an open-source command-line interface (https://github.com/miR2Trait) under MIT license for both commercial and non-commercial use. The datasets are available for download at: https://doi.org/10.6084/m9.figshare.8288825.
Crowding changes appearance systematically in peripheral, amblyopic, and developing vision
Authors: Kalpadakis-Smith A.V. , Tailor V.K. , Dahlmann-Noor A.H. , Greenwood J.A. 
Published: December 2021

AbstractVisual crowding is the disruptive effect of clutter on object recognition. Although most prominent in adult peripheral vision, crowding also disrupts foveal vision in typically-developing children and those with strabismic amblyopia. Do these crowding effects share the same mechanism? Here we exploit observations that crowded errors in peripheral vision are not random: target objects appear either averaged with the flankers (assimilation), or replaced by them (substitution). If amblyopic and developmental crowding share the same mechanism then their errors should be similarly systematic. We tested foveal vision in children aged 3-8 years with typical vision or strabismic amblyopia, and peripheral vision in typical adults. The perceptual effects of crowding were measured by requiring observers to adjust a reference stimulus to match the perceived orientation of a target ‘Vac-Man’ element. When the target was surrounded by flankers that differed by ±30°, all three groups (adults and children with typical or amblyopic vision) reported orientations between the target and flankers (assimilation). Errors were reduced with ±90° differences, but primarily matched the flanker orientation (substitution) when they did occur. A population pooling model of crowding successfully simulated this pattern of errors in all three groups. We conclude that the perceptual effects of amblyopic and developing crowding are systematic and resemble the near periphery in adults, suggesting a common underlying mechanism.PrecisCrowding strongly disrupts peripheral vision, as well as the foveal vision of children with typical vision and amblyopia. We show that typically developing and amblyopic children make the same crowded errors as adults in the visual periphery, consistent with a common mechanism in all three cases.
Medical Students’ Perceptions of Learning and Working on the COVID-19 Frontlines: “… a confirmation that I am in the right place professionally.”
Authors: Klasen Jennifer M. , Schoenbaechler Zoe , Bogie Bryce , Meienberg Andrea , Nickel Christian , Bingisser Roland , LaDonna Kori 
Published: December 2021

AbstractIntroductionThe COVID-19 pandemic caused complex and enduring challenges for health care providers and medical educators and changed the medical education landscape for learners. Medical students were required to adapt and learn in a novel learning environment while universities paused their formal medical training. The current study sought to investigate medical students’ experiences working on a pandemic frontline to understand how they perceived this novel learning environment influenced both their learning and their developing professional identity.MethodsWe conducted semi-structured interviews with 21 medical students who worked in a COVID-19 testing facility at the University Hospital of Basel. Using constructivist grounded theory methodology, we collected and analyzed data iteratively using a constant comparative approach to develop codes and theoretical categories.ResultsParticipants described improvements in their technical and communication skills, consequently impacting their professional development. The presence of a perceived flat hierarchy between the physicians and medical students promoted professional identity development amongst the medical students. Most participants perceived working on the pandemic frontlines as a positive learning experience, which seemed supported by a flatter hierarchy and open communication compared to their usual learning environment.ConclusionSince medical students reported that their work on the pandemic frontlines positively affected their learning, the need to create hands-on learning opportunities for medical students challenge curriculum developers. Medical students wish to feel like full-fledged care team members rather than observing learners. Performing simple clinical tasks and collaborative moments in a supportive learning environment may promote learning and professional development.
Draft genome of the Brazilian railroad worm Phrixothrix hirtus E.Olivier (Phengodidae: Coleoptera)
Authors: Amaral Danilo Trabuco , Mitani Yasuo , Silva Bonatelli Isabel Aparecida , Cerri Ricardo , Ohmiya Yoshihiro , Viviani Vadim 
Published: December 2021

AbstractThe Neotropical region is the richest in bioluminescent Coleoptera species, however, its bioluminescence megadiversity is still underexplored in terms of genomic organization and evolution, mainly within the Phengodidae family. The railroad worm Phrixothrix hirtus is an important biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed the partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing an important source of genomic information and a framework for comparative genomic analyses for the evaluation of the bioluminescent system in Elateroidea. The estimated genome size has ∼3.4Gb, 32% of GC content, and 67% of repetitive elements, being the largest genome described in the Elateroidea superfamily. Several events of gene family expansions associated with anatomical development and morphogenesis, as well as distinct odorant-binding receptors and retrotransposable elements were found in this genome. Similar molecular functions and biological processes are shared with other studied species of Elateriformia. Common genes putatively associated with bioluminescence production and control, including two luciferase genes that displayed 7 exons and 6 introns, and genes that could be involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea. In P. hirtus the conversion of L- to D-luciferin seems to involve additional steps using a Palmitoyl-CoA thioesterase instead of an Acyl-CoA synthetase, which was found in Lampyridae species.HighlightsFirst draft genome assembly of Phengodidae, the largest one described in Coleoptera;Gene family expansions associated with anatomical development and morphogenesis;Bioluminescent control and luciferin biosynthesis genes are common within Elateroidea;Despite similar bioluminescent system, metabolic routes may have evolved independently;
Mechanistic investigation of SARS-CoV-2 Omicron variant spike mutants via full quantum mechanical modeling
Authors: Zaccaria Marco , Genovese Luigi , Lawhorn Brigitte E. , Dawson William , Joyal Andrew S. , Hu Jingqing , Autissier Patrick , Nakajima Takahito , Johnson Welkin E. , Fofana Ismael , Farzan Michael , Momeni Babak 
Published: December 2021

AbstractAb initioquantum mechanical models can characterize and predict intermolecular binding, but only recently have models including more than a few hundred atoms gained traction. Here, we simulate ∼13,000 atoms to predict and characterize binding of SARS-CoV-2 spike variants to the human receptor ACE2 (hACE2). We compare four spike variants in our analysis: Wuhan, Omicron, and two Omicron-based variants. To assess binding, we mechanistically characterize the energetic contribution of each amino acid involved, and predict the effect of select single point mutations. We validate our computational predictions experimentally by comparing binding efficacy of spike variants to cells expressing hACE2. We argue that this computational model, QM-CR, can identify mutations critical for intermolecular interactions and inform the engineering of high-specificity interactors.One-Sentence SummaryAb initiomodeling can predict the strength of SARS-CoV-2 variants’ binding to human cell receptor.
No part gets left behind: Tiled nanopore sequencing of whole ASFV genomes stitched together using Lilo
Authors: Warr Amanda , Newman Caitlin , Craig Nicky , Vendelė Ingrida , Pilare Rizalee , Cruz Lilet Cariazo , Barangan Twinkle Galase , Morales Reildrin G , Opriessnig Tanja , Venturina Virginia Mauro , Mananggit Milagros R , Lycett Samantha , Domingo Clarissa YJ , Tait-Burkard Christine 
Published: December 2021

AbstractAfrican Swine Fever virus (ASFV) is the causative agent of a deadly, panzootic disease, infecting wild and domesticated suid populations. Contained for a long time to the African continent, an outbreak of a particularly infectious variant in Georgia in 2007 initiated the spread of the virus around the globe, severely impacting pork production and local economies. The virus is highly contagious and has a mortality of up to 100% in domestic pigs. It is critical to track the spread of the virus, detect variants associated with pathology, and implement biosecurity measures in the most effective way to limit its spread. Due to its size and other limitations, the 170-190kbp large DNA virus has not been well sequenced with fewer than 200 genome sequences available in public repositories. Here we present an efficient, low-cost method of sequencing ASFV at scale. The method uses tiled PCR amplification of the virus to achieve greater coverage, multiplexability and accuracy on a portable sequencer than achievable using shotgun sequencing. We also present Lilo, a pipeline for assembling tiled amplicon data from viral or microbial genomes without relying on polishing against a reference, allowing for structural variation and hypervariable region assembly other methods fail on. The resulting ASFV genomes are near complete, lacking only parts of the highly repetitive 3’- and 5’telomeric regions, and have a high level of accuracy. Our results will allow sequencing of ASFV at optimal efficiency and high throughput to monitor and act on the spread of the virus.