bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Pain Coping Questionnaire short-form: preliminary reliability and validity
Authors: Kohut Sara Ahola , Stinson Jennifer , Chambers Christine T. , Reid Graham J. , Pillai Riddell Rebecca R. 
Published: January 2022

Abstract

Introduction:
The Pain Coping Questionnaire (PCQ) has support for its validity and reliability as a tool to understand how a child copes with pain of an extended duration. However, measure length may limit feasibility in clinical settings.

Objectives:
The primary goal of this study was to develop a short-form (PCQ-SF) that could be used for screening how children cope with chronic or recurrent pain and examine its reliability and validity.

Methods:
The PCQ-SF was developed in a stepwise manner. First, a confirmatory factor analysis was computed using an amalgamated data set from the validation studies of the PCQ (N = 1225). Next, ratings from researchers and clinicians were obtained on PCQ item content and clarity (n = 12). Finally, the resulting 16-item short-form was tested in a pediatric sample living with chronic and recurrent pain (65 parent–child dyads; n = 128).

Results:
The PCQ-SF has acceptable preliminary reliability and validity. Both statistical and expert analyses support the collective use of the 16 items as an alternative to the full measure.

Conclusions:
The compact format of the PCQ-SF will allow practitioners in high-volume clinical environments to quickly determine a child's areas of strengths and weaknesses when coping with pain. Future research using larger more diverse samples to confirm clinical validity is warranted.
Angiofibroma of Soft Tissue on MRI and FDG PET/CT Image
Authors: Xiao Liu , Yang Liu , Wang Yueqi , Li Lin 
Published: January 2022

Abstract
Angiofibroma of soft tissue is a rare benign mesenchymal neoplasm. We reported a case of angiofibroma of soft tissue in a 61-year-old woman. MRI examination indicated a soft tissue mass in the right lower thigh, which showed isosignal intensity on T1-weighted imaging and heterogeneous high signal intensity on T2-weighted imaging. This lesion had intense tracer uptake, with an SUVmax of 7.24 on FDG PET/CT. Our case revealed that when soft tissue masses with intense FDG uptake on PET/CT are encountered, angiofibroma of soft tissue should be considered in the differential diagnosis.
Thyroid Scintigraphy of a Rare Case of Left Thyroid Lobe Hemiagenesis With Subacute Thyroiditis
Authors: Reya Nafisa , Posocco David , Dadparvar Simin 
Published: January 2022

Abstract
Thyroid hemiagenesis is a rare developmental anomaly. Patients with thyroid hemiagenesis have higher incidence of coexisting thyroid disorders in the remaining lobe. We present a rare case of a 21-year-old woman with subclinical hyperthyroidism incidentally found to have thyroid hemiagenesis on thyroid 123I-Na scan, which is confirmed on thyroid ultrasound. On scintigraphy, only the right lobe showed activity. Thyroid ultrasound demonstrated that the right lobe was normal without any nodule. The left lobe was not visualized. This patient's thyroid uptake and scan also revealed low uptake in the remaining right thyroid lobe in keeping with subacute thyroiditis.
Diagnosis of Pulmonary Embolism on 99mTc-Labeled Macroaggregated Albumin Lung Imaging After Hepatic Arterial Injection for Planning of Radioembolization
Authors: Frazzitta Aubrey E. , Kay Matthew D. , Warhadpande Devdutta , Kuo Phillip H. 
Published: January 2022

Abstract
A 54-year-old man with hepatocellular carcinoma from alcohol-induced cirrhosis presented with hepatic encephalopathy and refractory ascites related to decompensated liver disease. MRI confirmed disease progression adjacent the site of prior radiofrequency ablation, performed 2 years prior, with associated right hepatic vein tumor thrombus. 99mTc-labeled macroaggregated albumin lung shunt imaging performed before 90Y radioembolization identified a left lower lobe wedge-shaped defect, confirmed as pulmonary embolism on CT pulmonary angiography and MRI.
Use of 68Ga-FAPI PET/CT for Detecting Myeloid Sarcoma of the Breast and Assessing Early Response to Chemotherapy
Authors: Wu Simin , Lin Zhijuan , Shang Qihang , Pang Yizhen , Chen Haojun 
Published: January 2022

Abstract
Myeloid sarcoma is a rare presentation of acute myeloid leukemia as a solid tumor at various extramedullary sites. In this case, we report 18F-FDG and 68Ga-FAPI PET/CT findings in an 18-year-old woman with biopsy-proven myeloid sarcoma involving the left breast. 68Ga-FAPI PET/CT showed a far better tumor-to-background contrast than 18F-FDG PET/CT in the left breast mass. Moreover, follow-up 68Ga-FAPI PET/CT after 2 cycles of chemotherapy revealed a reduction in tumor size with decreasing activity in the myeloid sarcoma lesions.
Rare Case of Small Cell Metastatic Prostatic Adenocarcinoma, Properly Staged by 68Ga-PSMA PET/CT Scan
Authors: Golestani Zahra Bakhshi , Soltani Salman , Kalantari Mahmoud Reza , Ghorbani Hamid Reza , Aghaee Atena 
Published: January 2022

Abstract
Small cell carcinoma (SCC) of the prostate is a very rare entity and one of most aggressive neuroendocrine malignancies of prostate. We present a 60-year-old man with pathology-proven prostatic SCC by transrectal biopsy with ultrasonography guidance and Gleason score of 5 + 5. He was referred to perform 68Ga-PSMA PET/CT scan for staging. The scan showed PSMA uptake in the prostate bed and multiple large pelvic lymph nodes. As we know, 68Ga-PSMA uptake in the de novo form of SCC of prostate is not commonly found in the literature.
Pleural Metastasis of Papillary Thyroid Cancer Depicted by 68Ga-FAPI PET/CT
Authors: Chen Yun , Zheng Shan , Zhang Jiaying , Yao Shaobo , Miao Weibing 
Published: January 2022

Abstract
A 43-year-old woman with history of papillary thyroid cancer status post total thyroidectomy and neck dissection and multiple radioiodine therapy developed dyspnea and cough. CT scan of the chest showed left pleural thickening and pleural effusion. The pathology from pleural biopsy demonstrated the metastases from papillary thyroid cancer. 68Ga–fibroblast activation protein inhibitor PET/CT showed inhomogeneously increased uptake of fibroblast activation protein inhibitor in the thickened pleura.
Bilateral Testicular Mass Presenting as a Rare Manifestation of Extramedullary Plasmacytoma on 18F-FDG PET/CT
Authors: Civan Caner , Apaydin Arikan Evsen , Has Simsek Duygu , Sanli Oner , Kuyumcu Serkan 
Published: January 2022

Abstract
We present the case of a 48-year-old man diagnosed with metastatic Ewing sarcoma who was referred for 18F-FDG PET/CT for treatment response evaluation following chemoradiotherapy. The patient also had complaints of new-onset testicular swelling at the time of imaging. Although the metastatic bone disease showed a complete metabolic response to treatment, 18F-FDG PET/CT demonstrated significantly increased metabolic activity in bilateral testicular mass. Consequently, the patient underwent bilateral orchiectomy, and histopathologic examination revealed bilateral testicular plasmacytoma, a rare manifestation of extramedullary plasmacytoma.
68Ga-DOTATATE Uptake in an Intraosseous Hemangioma, as a Potential Cause of False-Positive PET/CT Finding, Simulating Tumoral Involvement
Authors: Saidi Bahare , Fallahi Babak , Manafi-Farid Reyhaneh , Fard-Esfahani Armaghan , Eftekhari Mohammad 
Published: January 2022

Abstract
We present the case of a 32-year-old man with a history of hypophosphatemia and multiple bone fractures, being evaluated at our center for a potential mesenchymal tumor. 68Ga-DOTATATE PET/CT revealed a highly 68Ga-DOTATATE–avid lesion in the ethmoidal sinus extending to the nasal cavity. Following resection, histologic examination of the specimen confirmed the diagnosis of “intraosseous hemangioma,” a potential cause of false-positive finding of 68Ga-DOTATATE PET/CT imaging in patients being evaluated for occult malignancies, especially at the traumatic/fractured sites.
Increased 68Ga-FAPI Uptake of Symptomatic Intracranial Atherosclerotic Plaque Revealed by PET/MR
Authors: Yang Qiao , Zhang Zongmuyu , Li Mingli , Xu Wei-Hai , Huo Li 
Published: January 2022

Abstract
A 58-year-old man was enrolled in our 68Ga-FAPI PET/MR study for evaluation of stroke etiology. He had left thalamus and cerebellum infarction 6 months ago, and left occipital lobe infarction 2 years ago. 68Ga-FAPI PET/MR showed focal uptake along the low segment of the basilar artery. We hypothesize that the FAPI-avid plaque of basilar artery may account for the embolic events resulting in downstream infarction. Thus FAP-targeted imaging may have a potential for detection of vulnerable plaques.
FTY720 requires vitamin B12-TCN2-CD320 signaling in astrocytes to reduce disease in an animal model of multiple sclerosis
Authors: Jonnalagadda Deepa , Kihara Yasuyuki , Groves Aran , Ray Manisha , Saha Arjun , Lee-Okada Hyeon-Cheol , Furihata Tomomi , Yokomizo Takehiko , Quadros Edward V. , Rivera Richard , Chun Jerold 
Published: January 2022

SummaryFTY720 (fingolimod) is a sphingosine 1-phosphate (S1P) receptor modulator and sphingosine analogue approved for multiple sclerosis (MS) therapy, which can functionally antagonize the S1P receptor, S1P1. Vitamin B12 (B12) deficiency produces neurological manifestations resembling MS. Here, we report a new mechanism where FTY720 suppresses neuroinflammation by regulating B12 metabolic pathways. Nuclear RNA-seq of c-Fos-activated astrocytes (called ieAstrocytes) from experimental autoimmune encephalomyelitis (EAE) spinal cords identified up-regulation of CD320, a transcobalamin 2 (TCN2)-B12 receptor, by S1P1 inhibition. CD320 was reduced in MS plaques. Deficiency of CD320 or dietary B12 worsened EAE and eliminated FTY720’s efficacy, while concomitantly down-regulating type I interferon signaling. TCN2 functioned as a chaperone for FTY720 and sphingosine, which induced astrocytic CD320 internalization. An accompanying paper identified a requirement for astrocyte sphingosine kinases in FTY720 efficacy and its altered expression in MS brains, molecularly linking MS and B12 deficiency that can be accessed by sphingolipid/fingolimod metabolic pathways.
Heritable and climatic sources of variation in juvenile tree growth in an Austrian common garden experiment of Central European Norway spruce populations
Authors: Morales Laura , Swarts Kelly 
Published: January 2022

AbstractWe leveraged publicly available data on juvenile tree height of 299 Central European Norway spruce populations grown in a common garden experiment across 24 diverse trial locations in Austria and weather data from the trial locations and population provenances to parse the heritable and climatic components of juvenile tree height variation. Principal component analysis of geospatial and weather variables demonstrated high interannual variation among trial environments, largely driven by differences in precipitation, and separation of population provenances based on altitude, temperature, and snowfall. Tree height was highly heritable and modeling the covariance between populations and trial environments based on climatic data led to more stable estimation of heritability and population × environment variance. Climatic similarity among population provenances was highly predictive of population × environment estimates for tree height.
Elevated FAM84B promotes cell proliferation via interacting with NPM1 in esophageal squamous cell carcinoma
Authors: Wang Fang , Cheng Caixia , Wang Xinhui , Chen Fei , Li Hongyi , Zhou Yan , Wang Yanqiang , Hu Xiaoling , Kong Pengzhou , Zhang Ling , Cheng Xiaolong , Cui Yongping 
Published: January 2022

AbstractFamily with sequence similarity 84, member B (FAM84B) is a significant copy number amplification gene in the 8q24.21 locus identified by our previous WGS study in esophageal squamous cell carcinoma (ESCC). However, its clinical relevance and potential mechanisms have been elusive. Here, we performed the association analyses between FAM84BAmp and clinicopathological features using our dataset with 507 ESCC samples. The results indicated that, compared with the FAM84Bnon-Amp patients, the FAM84BAmp patients showed a more aggressive and a worse prognosis. Significant correlation was discovered between the expression level of FAM84B and FAM84BAmp in ESCC cohort. Furthermore, we found that the forced expression change of FAM84B can influence ESCC cell proliferation and cell cycle status, which is probably mediated by NPM1. A direct interaction between FAM84B and the C-terminal (189-294aa) of NPM1 was identified, which increased the NPM1 nuclear expression. Over-expression of NPM1 could inhibit the CDKN2A protein expression, which might affect the ESCC cell cycle. Our results indicate FAM84B CNA may be a potential diagnostic and therapeutic biomarker in ESCC, meanwhile, reveal a novel mechanism of FAM84B that it promotes tumorigenesis via interacting with NPM1 and suppressing CDKN2A.
Maternal first trimester metabolic profile in TGA pregnancies - a case-control study
Authors: Huida Johanna , Ojala Tiina , Hautala Johanna , Surcel Heljä-Marja , Priest James R , Helle Emmi 
Published: January 2022

AbstractObjectiveTo evaluate the association between maternal first trimester metabolic profile and transposition of the great arteries (TGA) in the offspring.DesignA matched case-control study using national register data and maternal first trimester blood samples.SettingsFinlandPatientsA total of 100 mothers with TGA in their offspring and 200 controls matched by the year of birth and sex of the child, and the age and the body mass index (BMI) of the mother.InterventionsNone.Main outcome measuresTo identify the impact of 73 metabolic measure concentrations on the likelihood that a child would be born with TGA.ResultsA higher concentration of four subtypes in extremely large very-low-density lipoprotein (VLDL) particles and one in large VLDL particles were observed in mothers with TGA in their offspring. This finding did not reach statistical significance after multiple testing correction. In the analysis of the subgroups of maternal BMI over 25 and 30 only, the odds ratios (OR) of the metabolic variables were higher compared to the original population. In the group with a BMI over 25 the mean OR was 1.3 (N= 111, total) and in the group with a BMI over 30 the mean OR was 2.1 (N= 42, total).ConclusionsWe found no statistically significant difference between the metabolic profiles of mothers with TGA in their offspring, and their controls. However, the trend in our BMI-matched study potentially indicates that the likelihood of TGA development associates with maternal early-pregnancy metabolic profile, and the association is more pronounced in the subgroups of BMI over 25 and 30. Further studies are needed especially in the higher BMI groups.What is already known on this topic?The most important structures of the heart develop during early pregnancy, but studies on the association of maternal metabolomics during the first trimester with CHD development are scarce.Maternal obesity and diabetes are known risk factors for CHD in the offspring but the precise developmental mechanisms underlying this risk remain unknown.What this study adds to this topic?The maternal metabolomic profile in early pregnancy is potentially associated with the likelihood of TGA development in the offspring.Metabolic markers in obese women may have a stronger association with the development of TGA but this connection requires further studies.
NNeurite: artificial neuronal networks for the unsupervised extraction of axonal and dendritic time-lapse signals
Authors: Chenouard Nicolas , Kouskoff Vladimir , Tsien Richard W. , Gambino Frédéric 
Published: January 2022

AbstractFluorescence microscopy of Ca2+ transients in small neurites of the behaving mouse provides an unprecedented view of the micrometer-scale mechanisms supporting neuronal communication and computation, and therefore opens the way to understanding their role in cognition. However, the exploitation of this growing and precious experimental data is impeded by the scarcity of methods dedicated to the analysis of images of neurites activity in vivo. We present NNeurite, a set of mathematical and computational techniques specialized for the analysis of time-lapse microscopy images of neurite activity in small behaving animals. Starting from noisy and unstable microscopy images containing an unknown number of small neurites, NNeurite simultaneously aligns images, denoises signals and extracts the location and the temporal activity of the sources of Ca2+ transients. At the core of NNeurite is a novel artificial neuronal network (NN) which we have specifically designed to solve the non-negative matrix factorization (NMF) problem modeling source separation in fluorescence microscopy images. For the first time, we have embedded non-rigid image alignment in the NMF optimization procedure, hence allowing to stabilize images based on the transient and weak neurite signals. NNeurite processing is free of any human intervention as NN training is unsupervised and the unknown number of Ca2+ sources is automatically obtained by the NN-based computation of a low-dimensional representation of time-lapse images. Importantly, the spatial shapes of the sources of Ca2+ fluorescence are not constrained in NNeurite, which allowed to automatically extract the micrometer-scale details of dendritic and axonal branches, such dendritic spines and synaptic boutons, in the cortex of behaving mice. We provide NNeurite as a free and open-source library to support the efforts of the community in advancing in vivo microscopy of neurite activity.
Uncovering potential interventions for pancreatic cancer patients via mathematical modeling
Authors: Plaugher Daniel , Aguilar Boris , Murrugarra David 
Published: January 2022

AbstractPancreatic Ductal Adenocarcinoma (PDAC) is widely known for its poor prognosis because it is often diagnosed when the cancer is in a later stage. We built a Boolean model to analyze the microenvironment of pancreatic cancer in order to better understand the interplay between pancreatic cancer, stellate cells, and their signaling cytokines. Specifically, we have used our model to study the impact of inducing four common mutations: KRAS, TP53, SMAD4, and CDKN2A. After implementing the various mutation combinations, we used our stochastic simulator to derive aggressiveness scores based on simulated attractor probabilities and long-term trajectory approximations. These aggression scores were then corroborated with clinical data. Moreover, we found sets of control targets that are effective among common mutations. These control sets contain nodes within both the pancreatic cancer cell and the pancreatic stellate cell, including PIP3, RAF, PIK3 and BAX in pancreatic cancer cell as well as ERK and PIK3 in the pancreatic stellate cell. Many of these nodes were found to be differentially expressed among pancreatic cancer patients in the TCGA database. Furthermore, literature suggests that many of these nodes can be targeted by drugs currently in circulation. The results herein help provide a proof of concept in the path towards personalized medicine through a means of mathematical systems biology. All data and code used for running simulations, statistical analysis, and plotting is available on a GitHub repository at https://github.com/drplaugher/PCC_Mutations.
Predicting patient treatment response and resistance via single-cell transcriptomics of their tumors
Authors: Sinha Sanju , Vegesna Rahulsimham , Dhruba Saugato Rahman , Wu Wei , Kerr D. Lucas , Stroganov Oleg V. , Grishagin Ivan , Aldape Kenneth D. , Blakely Collin M. , Jiang Peng , Thomas Craig J. , Bivona Trever G. , Schäffer Alejandro A. , Ruppin Eytan 
Published: January 2022

AbstractTailoring the best treatments to cancer patients is an important open challenge. Here, we build a precision oncology data science and software framework for PERsonalized single-Cell Expression-based Planning for Treatments In Oncology (PERCEPTION). Our approach capitalizes on recently published matched bulk and single-cell transcriptome profiles of large-scale cell-line drug screens to build treatment response models from patients’ single-cell (SC) tumor transcriptomics. First, we show that PERCEPTION successfully predicts the response to monotherapy and combination treatments in screens performed in cancer and patient-tumor-derived primary cells based on SC-expression profiles. Second, it successfully stratifies responders to combination therapy based on the patients’ tumor’s SC-expression in two very recent multiple myeloma and breast cancer clinical trials. Thirdly, it captures the development of clinical resistance to five standard tyrosine kinase inhibitors using tumor SC-expression profiles obtained during treatment in a lung cancer patients’ cohort. Notably, PERCEPTION outperforms state-of-the-art bulk expression-based predictors in all three clinical cohorts. In sum, this study provides a first-of-its-kind conceptual and computational method that is predictive of response to therapy in patients, based on the clonal SC gene expression of their tumors.
Teasing apart the joint effect of demography and natural selection in the birth of a contact zone
Authors: Li Lili , Milesi Pascal , Tiret Mathieu , Chen Jun , Sendrowski Janek , Baison John , Chen Zhiqiang , Zhou Linghua , Karlsson Bo , Berlin Mats , Westin Johan , Garcia-Gil Rosario , Wu Harry , Lascoux Martin 
Published: January 2022

AbstractVast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. This is especially true in Scandinavia that was repeatedly glaciated. During glacial periods trees were confined to refugia, south and east of the ice sheet, from which they recolonized Scandinavia as the ice melted away. This multi-pronged recolonization led to large contact zones in most species. We leverage large genomic data from 5000 trees to reconstruct the demographic history of Norway spruce (Picea abies) and test for the presence of natural selection during the recolonization process and the establishment of the contact zone. Sweden is today made up of two large genetic clusters, a southern one originating from the Baltics and a Northern one originating from Northern Russia. The contact zone delineating these two clusters closely matches the limit between two major climatic regions. This suggests that natural selection contributed to the establishment and the maintenance of the contact zone. To test this hypothesis we first used Approximate Bayesian Computation; an Isolation-with migration model with genome-wide linked selection fits the data better than a purely neutral one. Secondly, we identified loci characterized by both extreme allele frequency differences between geographic regions and association to the variables defining the climatic zones. These loci, many of which are related to phenology, form clusters present on all linkage groups. Altogether, the current genetic structure reflects the joint effect of climatic cycles, recolonization and selection on the establishment of strong local adaptation and contact zones.Significance StatementUnderstanding how past climatic events, human actions and evolutionary forces contributed to the present distribution of genetic diversity is crucial to predict their reaction to the current climate crisis. Vast distribution shifts induced by past environmental changes, local ecological processes, natural selection and human transfers contributed to the current distribution of Norway spruce across Northern Europe. Genome-wide polymorphisms from thousands of individuals show that Scandinavia was recolonized after the Last Glacial from both south and north. This two-pronged recolonization established a contact zone between two genetic clusters that matches the limit between two major climate zones. The contact zone is shaped and maintained by natural selection on a large number of loci that form blocks of co-adapted loci spread genome-wide.