bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multimodality Multisystem Imaging of Pregnancy-Related Changes: Featuring Neurologic, Cardiothoracic, Breast, Gynecologic, and Musculoskeletal Issues
Authors: Dishuck Carolyn F. , Bass Rachel Z. , Allen Elizabeth M. , Andrikopoulou Efstathia F. , Galgano Samuel J. , Milner Desmin M. , Wright Ashley , Porter Kristin K. 
Published: March 2022

Abstract
Pregnancy and the puerperium are a time of significant physiologic change, and with an average of 4 million births in the United States yearly, radiologists encounter pregnancy-related imaging findings regularly. While many of these findings represent physiologic changes, a significant number represent pathology, making it paramount for radiologists to distinguish between the two. This case-based article reviews imaging findings within the nervous, cardiovascular, pulmonary, breast, gynecologic, musculoskeletal, digestive, hematologic, and integumentary systems throughout pregnancy and the postpartum period.
Computed Tomography and Magnetic Resonance Correlation and Agreement for Foot Muscle and Adipose Tissue Measurements
Authors: Commean Paul K. , Mueller Michael J. , Chen Ling , Wolfsberger Mary A. , Hastings Mary K. 
Published: March 2022

Background
Volumetric measures of intrinsic foot muscle and intermuscular adipose tissue (IMAT) infiltration are important in understanding foot injury and disease. We questioned whether measures of muscle and fat derived from computed tomography (CT) and magnetic resonance (MR) would be comparable.

Methods
This study determined the correlation and level of agreement between CT and MR measurements of foot muscle and IMAT from 32 subjects with diabetes and peripheral neuropathy. Volumetric CT and DIXON 3T MR scans were obtained. Intermuscular adipose tissue and muscle volumes used to create the IMAT to muscle ratio were obtained by segmenting the forefoot muscle compartment from each modality.

Results
Computed tomography IMAT ratios were significantly correlated (r = 0.85, P < 0.0001) with MR IMAT ratios. Computed tomography and MR IMAT ratio mean difference between CT and MR was small (0.044 unit, Bland-Altman plots).

Conclusions
The CT and MR IMAT ratio measurements were highly correlated, indicating both modalities represent tissue quantification similarly.
Level of Evidence: 2
Technical Efficacy: 1
Management of Patients With Common Bile Duct Dilatation Without a Sonographic Evident Cause: Evaluating the Yield of Subsequent Magnetic Resonance Imaging and Findings Correlated With Causative Pancreaticobiliary Pathology
Authors: Bezuidenhout Abraham Fourie , Lee Kristy , Nakhaei Masoud , Schawkat Khoschy , Wei Jesse , Lee Karen , Mortele Koenraad 
Published: March 2022

Objectives
The aims of the study were to evaluate the yield of magnetic resonance imaging (MRI) in patients with common bile duct (CBD) dilatation without a sonographic evident cause and to investigate sonographic and laboratory findings at presentation that might predict identification of underlying pancreaticobiliary pathology.

Methods
Included were consecutive patients in whom MRI was performed for further evaluation of CBD dilatation detected on ultrasound (US), without a sonographic evident cause, from January 1, 2014, to December 31, 2014. Magnetic resonance imaging and clinical data were retrospectively reviewed. Patients were divided into two groups: patients with and without identified underlying causative pancreaticobiliary pathology. Ultrasound findings and laboratory results at presentation were compared between groups to identify findings suggestive of underlying pancreaticobiliary pathology.

Results
Fifty-seven patients, with a mean age of 54 ± 16 years including 37 females (65%), underwent MRI. Specific pancreaticobiliary causes for CBD dilatation were identified in 38 patients (66%, 31 benign and 7 malignant). In the remaining patients, no cause was identified in 17 (30%) and MRIs were nondiagnostic in 2 patients. Magnetic resonance imaging accuracy for correctly identifying the underlying cause of CBD dilatation was 91%. Patients with associated intrahepatic bile duct dilatation on US and elevated alanine aminotransferase and alkaline phosphatase were more likely to have underlying pancreaticobiliary pathology (P < 0 .05). No patient with initial negative MRI had pancreaticobiliary malignancy.

Conclusions
Magnetic resonance imaging seems to be an accurate noninvasive method for identifying the underlying cause in most patients with CBD dilatation on US and in excluding pancreaticobiliary malignancy. Patients with associated intrahepatic bile duct dilatation and/or elevated liver enzymes are at higher risk of harboring underlying pancreaticobiliary pathology.
Computed Tomography Assessment of Sarcopenic Myosteatosis for Predicting Overall Survival in Colorectal Carcinoma: Systematic Review
Authors: Franco Valle Kevin , Lubner Meghan G. , Pickhardt Perry J. 
Published: March 2022

Background
As the US population ages, cancer incidence and prevalence are projected to increase. In the last decade, there has been an increased interest in the opportunistic use of computed tomography (CT) scan data to predict cancer prognosis and inform treatment based on body composition measures, especially muscle measures for sarcopenia.

Objective
This article aimed to perform a systematic review of current literature related to CT assessment of muscle attenuation values for myosteatosis in colorectal cancer (CRC) survival prediction.

Results
Initial broad search of CT and CRC yielded 4234 results. A more focused search strategy narrowed this to 129 research papers, and 13 articles met the final inclusion criteria. Twelve of 13 studies found a statistically significant decrease in overall survival according to Hounsfield unit (HU)–based sarcopenia, with hazard ratios ranging from 1.36 to 2.94 (mean, 1.78). However, the specific criteria used to define myosteatosis by CT varied widely, with attenuation thresholds ranging from 22.5 to 47.3 HU, often further subdivided by sex and/or body mass index.

Conclusions
Current evidence suggests that a strong association between CT-based muscle attenuation values for myosteatosis assessment correlates with overall survival in CRC. However, more research is needed to verify these findings and determine appropriate threshold values for more diverse patient populations. Because CRC patients are staged and followed by CT, the opportunity exists for routine objective myosteatosis assessment in the clinical setting.
Suicide Risk in Rheumatoid Arthritis Patients is Associated With Suboptimal Vitamin D Levels
Authors: Calderón Espinoza Ivette , Chavarria-Avila Efrain , Pizano-Martinez Oscar , Martínez-García Erika Aurora , Armendariz-Borunda Juan , Marquez-Aguirre Ana Laura , Llamas-García Arcelia , Corona-Sánchez Esther Guadalupe , Toriz González Guillermo , Vazquez-Del Mercado Monica 
Published: March 2022

Background/Objective
Rheumatoid arthritis (RA) patients might experience anxiety and depressive symptoms. Deficient vitamin D levels may be a trigger for these conditions. The aim of this study was to determine the frequency of depression, anxiety symptoms, and suicidal risk or ideation in patients with RA associated with vitamin D serum levels.

Methods
In this cross-sectional study, we recruited RA patients older than 18 years, classified into 3 groups according to serum vitamin D levels: sufficient, ≥30 ng/mL; insufficient, 20–29 ng/mL; and deficient, <20 ng/mL. Based on the self-reported Plutchik and the Hospital Anxiety and Depression Scale, we evaluated the association of suicidal risk, depression, and anxiety with the vitamin D levels in RA and the Rheumatoid Arthritis Quality-of-Life Questionnaire.

Results
We studied 72 patients with RA between January and October 2019. We found an inverse correlation between Plutchik score and suicidal risk with inadequate vitamin D levels, but not with the Hospital Anxiety and Depression Scale. Suicidal ideation was associated with a higher score on the Rheumatoid Arthritis Quality-of-Life Questionnaire.

Conclusions
Despite the high prevalence of depressive and anxiety symptoms in RA patients, a Plutchik low correlation coefficient with inadequate serum levels of vitamin D was found. However, in the analysis of covariance, we were able to find that vitamin D levels remain associated with a reduction of suicide ideation. Further studies are needed to identify a risk profile for early psychological interventions to improve the quality of life in RA patients.
Systemic Lupus Erythematosus and Antiphospholipid Antibody Syndrome as Risk Factors for Acute Coronary Syndrome in Young Patients
Authors: Whittier Millan , Bautista Sanchez Rocio , Arora Shilpa , Manadan Augustine Mathew 
Published: March 2022

Objective
This study aimed to compare the odds of acute coronary syndrome (ACS) in patients aged 18 to 40 years to patients older than 40 years with and without secondary diagnoses of systemic lupus erythematosus (SLE) or antiphospholipid antibody syndrome (APLS) while controlling for traditional cardiovascular (CV) risk factors.

Methods
Data were extracted from the National Inpatient Sample database from 2016 to 2018. The National Inpatient Sample was searched for hospitalizations of adult patients with ACS as the principal diagnosis, with and without SLE or APLS as secondary diagnoses. Age was divided categorically into 2 groups: adults aged 18 to 40 years and those older than 40 years. The primary outcome was the development of ACS. Multivariate logistic regression analyses were used to adjust for confounders.

Results
There were 90,879,561 hospital discharges in the 2016 to 2018 database. Of those, 55,050 between the ages of 18 to 40 years and 1,966,234 aged older than 40 years were hospitalized with a principal diagnosis of ACS. Traditional CV risk factors were associated with ACS hospitalizations in both age groups. In multivariate analysis of the 18 to 40 years age group, both SLE (odds ratio, 2.18; 95% confidence interval, 1.814–2.625) and APLS (odds ratio, 2.18; 95% confidence interval, 1.546–3.087) were strongly associated with ACS hospitalizations. After the age of 40 years, there were no increased odds of ACS hospitalizations for SLE or APLS.

Conclusions
In the younger population, SLE and APLS were strongly associated with ACS hospitalizations in addition to the traditional CV risk factors. In the older age group, traditional CV risk factors dominated and diluted the effect of SLE and APLS.
18F-FDG PET/CT Imaging in Sarcomatoid Hepatocellular Carcinoma
Authors: Yang Ting , Zou Min-Hong , Zou Qiong , Jiao Ju , Zhang Yong 
Published: March 2022

Abstract
Sarcomatoid hepatocellular carcinoma is a rare subtype of hepatocellular carcinoma. We present a 53-year-old man with a hepatic IV/VIII segment neoplasm whose tumor markers were all in the reference range. The neoplasm presented intense uptake of 18F-FDG and was confirmed as sarcomatoid hepatocellular carcinoma by immunohistochemistry. After 6 cycles of PD-1 treatment, no recurrence or metastasis was found by follow-up CT over 2 years. Thus, we reported a case of sarcomatoid hepatocellular carcinoma with complete remission to PD-1 treatment and provided some help for the diagnosis and treatment of sarcomatoid hepatocellular carcinoma.
Primary Solitary Tuberculosis in the Hepatic Round Ligament Detected by 68Ga-FAPI PET/CT
Authors: Deng Ying , Wu Junhao , Xu Chuanqi , Zhang Wei 
Published: March 2022

Abstract
A 45-year-old woman recently complained of abdominal pain, poor appetite, and weight loss. Her serum ferritin, CA199, and CA242 levels were elevated. 68Ga-FAPI PET/CT revealed a subcapsular mass in the liver, which showed a significant FAPI uptake without other abnormal activity. Postoperative pathological examination confirmed tuberculosis in the hepatic round ligament.
Metal Coordinating Inhibitors of Rift Valley Fever virus Replication
Authors: Geerling Elizabeth , Murphy Valerie , Stone E. Taylor , Casals Andreu Gazquez , Hassert Mariah , O’Dea Austin T. , Cao Feng , Donlin Maureen J. , Elagawany Mohamed , Elgendy Bahaa , Pardali Vasiliki , Giannakopoulou Erofili , Zoidis Grigoris , Schiavone Daniel V. , Berkowitz Alex J. , Agyemang Nana B. , Murelli Ryan P. , Tavis John E. , Pinto Amelia K. , Brien James D. 
Published: March 2022

AbstractRift Valley Fever Virus (RVFV) is a veterinary and human pathogen and is an agent of bioterrorism concern. Currently, RVFV treatment is limited to supportive care, so new drugs to control RVFV infection are urgently needed. RVFV is a member of the Bunyavirales order, and replication of these viruses depends on the viral endonuclease activity of the viral L protein. Screening for RVFV replication inhibitors among compounds with divalent cation-coordinating motifs similar to known viral nuclease inhibitors identified 31 novel RVFV inhibitors with selective indexes from 5 – 402 and 50% effective concentrations of 0.54 – 56 µM in Vero cells, primarily α-Hydroxytropolones and N-Hydroxypyridinediones. Inhibitor activity and selective index was validated in the human cell line A549. To evaluate specificity, select compounds were tested against another Bunyavirus, La Crosse Virus (LACV). Conservation of the enzymatic activity such as the cap-snatching mechanism among the Bunyavirales implies that the α-Hydroxytropolone and N-Hydroxypyridinedione chemotypes hold potential for development into treatments for related pathogens, including Hantaan Virus, Severe fever with thrombocytopenia syndrome virus, Crimean-Congo Hemorrhagic Fever Virus, and LACV. Keywords: Rift Valley Fever Virus 1, La Crosse virus 2, Cap-snatching endonuclease 3, Replication inhibitors 4, α-Hydroxytropolones 5, N-Hydroxypyridinediones 6.
An end-to-end deep learning method for rotamer-free protein side-chain packing
Authors: McPartlon Matt , Xu Jinbo 
Published: March 2022

AbstractProtein side-chain packing (PSCP), the task of determining amino acid side-chain conformations, has important applications to protein structure prediction, refinement, and design. Many methods have been proposed to resolve this problem, but their accuracy is still unsatisfactory. To address this, we present AttnPacker, an end-to-end, SE(3)-equivariant deep graph transformer architecture for the direct prediction of side-chain coordinates. Unlike existing methods, AttnPacker directly incorporates backbone geometry to simultaneously compute all amino acid side-chain atom coordinates without delegating to a rotamer library, or performing expensive conformational search or sampling steps. Tested on the CASP13 and CASP14 native and non-native protein backbones, AttnPacker predicts side-chain conformations with RMSD significantly lower than the best side-chain packing methods (SCWRL4, FASPR, Rosetta Packer, and DLPacker), and achieves even greater improvements on surface residues. In addition to RMSD, our method also achieves top performance in side-chain dihedral prediction across both data sets.
Deep learning based feature extraction for prediction and interpretation of sharp-wave ripples
Authors: Navas-Olive Andrea , Amaducci Rodrigo , Jurado-Parras Teresa , Sebastian Enrique R , de la Prida Liset M 
Published: March 2022

AbstractLocal field potential (LFP) deflections and oscillations define hippocampal sharp-wave ripples (SWR), one of the most synchronous events of the brain. SWR reflect firing and synaptic current sequences emerging from cognitively relevant neuronal ensembles. Current spectral methods fail to capture their mechanistic complexity, thus limiting progress. Here, we show how one-dimensional convolutional networks operating over high-density LFP hippocampal recordings allowed for automatic identification of SWR. When applied to ultra-dense hippocampus-wide recordings, we discovered physiologically relevant processes associated to the emergence of SWR, prompting for novel classification criteria. To gain interpretability, we developed a method to interrogate the operation of the artificial network. We found it relied in feature-based specialization, which permit identification of spatially segregated oscillations and deflections, as well as synchronous population firing. Thus, using deep learning based approaches may change the current heuristic for a better mechanistic interpretation of these relevant neurophysiological events.
dialogi: Utilising NLP with chemical and disease similarities to drive the identification of Drug-Induced Liver Injury literature
Authors: Katritsis Nicholas M , Liu Anika , Youssef Gehad , Rathee Sanjay , MacMahon Méabh , Hwang Woochang , Wollman Lilly , Han Namshik 
Published: March 2022

ABSTRACTDrug-Induced Liver Injury (DILI), despite its low occurrence rate, can cause severe side effects or even lead to death. Thus, it is one of the leading causes for terminating the development of new, and restricting the use of already-circulating, drugs. Moreover, its multifactorial nature, combined with a clinical presentation that often mimics other liver diseases, complicate the identification of DILI-related literature, which remains the main medium for sourcing results from the clinical practice and experimental studies. In this work– contributing to the ‘Literature AI for DILI Challenge’ of the Critical Assessment of Massive Data Analysis (CAMDA) 2021– we present an automated pipeline for distinguishing between DILI-positive and negative papers. We used Natural Language Processing (NLP) to filter out the uninformative parts of a text, and identify and extract mentions of chemicals and diseases. We combined that information with small-molecule and disease embeddings, which are capable of capturing chemical and disease similarities, to improve classification performance. The former are directly sourced from the Chemical Checker (CC). For the latter, we collected data that encode different aspects of disease similarity from the National Library of Medicine’s (NLM) Medical Subject Headings (MeSH) thesaurus and the Comparative Toxicogenomics Database (CTD). Following a similar procedure as the one used in the CC, vector representations for diseases were learnt and evaluated. Two Neural Network (NN) classifiers were developed: one that only accepts texts as input (baseline model) and an augmented classifier that also utilises chemical and disease embeddings (extended model). We trained, validated, and tested the models through a Nested Cross-Validation (NCV) scheme with 10 outer and 5 inner folds. During this, the baseline and extended models performed virtually identically, with macro F1-scores of 95.04 ± 0.61% and 94.80 ± 0.41%, respectively. Upon validation on an external, withheld, dataset, representing imbalanced data, the extended model achieved an F1-score of 91.14 ± 1.62%, outperforming its baseline counterpart, which got a lower score of 88.30 ± 2.44%. We make further comparisons between the classifiers and discuss future improvements and directions, including utilising chemical and disease embeddings for visualisation and exploratory analysis of the DILI-positive literature.
Coherent multi-level network oscillations create neural filters to favor quiescence over navigation in Drosophila
Authors: Raccuglia Davide , Suárez-Grimalt Raquel , Krumm Laura , Brodersen Cedric B , Ender Anatoli , Jagannathan Sridhar R. , Winter York , Yvon-Durocher Genevieve , Kempter Richard , Geiger Jörg RP , Owald David 
Published: March 2022

AbstractFor all animals, undisturbed periods of rest are essential for undergoing recuperative processes. How neural interactions create brain states capable of dissociating an animal from its external world to promote quiescence remains a fundamental question. Here, we show how coherent network oscillations can create neural filters that favor a quiescent brain state over a state that promotes navigation. Circadian regulation and excitability of the Drosophila sleep homeostat (dFSB) generate nighttime specific slow-wave coherence between neural networks mediating sleep need (R5) and networks gating locomotion (helicon cells). Optogenetically mimicking coherent activity reveals that temporally fine-tuned R5 oscillations promote a quiescent state and reduce responsiveness to visual stimuli by hierarchically overruling locomotion-promoting helicon cells. We uncover that R5 and helicon bidirectionally regulate behavioral responsiveness by providing antagonistic inputs to head direction targets (EPG). Thus, coherent oscillations can form the mechanistic basis of neural filters by temporally associating antagonistic inputs and therefore reducing the functional connectivity between locomotion gating and navigational networks.
Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq
Authors: Hsu Yu-Ming , Wang Sheng-Shan , Tseng Yu-Chien , Lee Shin-Ruei , Fang Hsiang , Hung Wei-Chia , Kuo Hsin-I , Dai Hung-Yu 
Published: March 2022

AbstractThe cultivated peanut (Arachis hypogaeaL.) is an important oil crop but has a narrow genetic diversity. Molecular markers can be used to probe the genetic diversity of various germplasm. In this study, the restriction site associated DNA (RAD) approach was utilized to sequence 31 accessions of Taiwanese peanut germplasm, leading to the identification of a total of 17,610 single nucleotide polymorphisms (SNPs). The origin of these 31 accessions is contrasted so the global subset (n = 17) has greater genetic diversity than the local subset (n = 14). Concerning botanical varieties, the var.fastigiatasubset has greater genetic diversity than the other two subsets of var.vulgarisand var.hypogaea, suggesting that novel genetic resources should be introduced into breeding programs to enhance genetic diversity. Principal component analysis (PCA) using genotyping data separated the 31 accessions into three clusters largely according to the botanical varieties, consistent with the PCA result for 282 accessions genotyped by 14 kompetitive allele-specific PCR (KASP) markers developed in this study. The SNP markers identified in this work not only revealed the genetic relationship and population structure of current germplasm in Taiwan, but also offer an efficient tool for breeding and further genetic applications.
Do males know? Evidence-driven rainmaking mating strategy by male bonobos to meet the fertile window of females
Authors: Ryu Heungjin , Hashimoto Chie , Hill David A. , Mouri Keiko , Shimizu Keiko , Furuichi Takeshi 
Published: March 2022

AbstractFemale bonobos exhibit prolonged receptivity, one suggested function of which is to lower male mating competition. However, it is questionable whether easier access to receptive females can reduce male-male competition, given the exclusive nature of male reproductive success. We tested whether males could determine the fertile phase of females. We found that ovulation probability predicted male mating effort. High-ranking males copulated with females with higher fertility, and male-male agonistic interactions increased when there were fertile females in the party. When there were multiple females with maximal swelling, males concentrated their mating effort on females with an older infant whose maximal swelling started earlier, and they continued mating efforts until detumescence (rainmaking). These findings suggest that male bonobos distinguish between fertile and non-fertile phases of females and that having more receptive females in the party does not reduce male-male competition for fertile females.TeaserMales use the rainmaker’s rule to meet the periovulatory phase of the female bonobo for better reproductive success.