bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo transcriptomic subtyping of colorectal cancer liver metastases in the context of tumor heterogeneity
Authors: Moosavi Seyed H. , Eide Peter W. , Eilertsen Ina A. , Brunsell Tuva H. , Berg Kaja C. G. , Røsok Bård I. , Brudvik Kristoffer W. , Bjørnbeth Bjørn A. , Guren Marianne G. , Nesbakken Arild , Lothe Ragnhild A. , Sveen Anita 
Published: September 2021

Abstract
Background
Gene expression-based subtyping has the potential to form a new paradigm for stratified treatment of colorectal cancer. However, current frameworks are based on the transcriptomic profiles of primary tumors, and metastatic heterogeneity is a challenge. Here we aimed to develop a de novo metastasis-oriented framework.

Methods
In total, 829 transcriptomic profiles from patients with colorectal cancer were analyzed, including primary tumors, liver metastases, and non-malignant liver samples. High-resolution microarray gene expression profiling was performed of 283 liver metastases from 171 patients treated by hepatic resection, including multiregional and/or multi-metastatic samples from each of 47 patients. A single randomly selected liver metastasis sample from each patient was used for unsupervised subtype discovery by nonnegative matrix factorization, and a random forest prediction model was trained to classify multi-metastatic samples, as well as liver metastases from two independent series of 308 additional patients.

Results
Initial comparisons with non-malignant liver samples and primary colorectal tumors showed a highly variable degree of influence from the liver microenvironment in metastases, which contributed to inter-metastatic transcriptomic heterogeneity, but did not define subtype distinctions. The de novo liver metastasis subtype (LMS) framework recapitulated the main distinction between epithelial-like and mesenchymal-like tumors, with a strong immune and stromal component only in the latter. We also identified biologically distinct epithelial-like subtypes originating from different progenitor cell types. LMS1 metastases had several transcriptomic features of cancer aggressiveness, including secretory progenitor cell origin, oncogenic addictions, and microsatellite instability in a microsatellite stable background, as well as frequent RAS/TP53 co-mutations. The poor-prognostic association of LMS1 metastases was independent of mutation status, clinicopathological variables, and current subtyping frameworks (consensus molecular subtypes and colorectal cancer intrinsic subtypes). LMS1 was also the least heterogeneous subtype in comparisons of multiple metastases per patient, and tumor heterogeneity did not confound the prognostic value of LMS1.

Conclusions
We report the first large study of multi-metastatic gene expression profiling of colorectal cancer. The new metastasis-oriented subtyping framework showed potential for clinically relevant transcriptomic classification in the context of metastatic heterogeneity, and an LMS1 mini-classifier was constructed to facilitate prognostic stratification and further clinical testing.
Late chronotype predicts more depressive symptoms in bipolar disorder over a 5 year follow-up period
Authors: Vidafar Parisa , Yocum Anastasia K. , Han Peisong , McInnis Melvin G. , Burgess Helen J. 
Published: September 2021

Abstract
Background
There is increasing evidence that bipolar disorder is influenced by circadian timing, including the timing of sleep and waking activities. Previous studies in bipolar disorder have shown that people with later timed daily activities, also known as late chronotypes, are at higher risk for subsequent mood episodes over the following 12–18 months. However, these studies were limited to euthymic patients and smaller sample sizes. The aim of the current study was to further examine baseline chronotype as a potentially important predictor of mood-related outcomes in a larger sample of individuals with bipolar disorder and over the longest follow up period to date, of 5 years. Participants included 318 adults diagnosed with bipolar I and II (19–86 years) who were enrolled in the Prechter Longitudinal Study of Bipolar Disorder.

Results
Participants with a late chronotype were found to be more likely to have mild to more severe depressive symptoms (PHQ-9 ≥ 5) as captured with PHQ-9 assessments every 2 months over the 5 year follow up period. This higher risk for depressive symptoms remained even after adjusting for age, sex and mood at baseline. Additionally, late chronotypes reported fewer hypomania/mania episodes during the 5 year follow up, as derived from clinical interviews every two years.

Conclusions
These results highlight the potential clinical usefulness of a single self-report question, in identifying patients at risk for a more depressive mood course. The results also suggest that circadian phase advancing treatments, that can shift circadian timing earlier, should be explored as a means to reduce depressive symptoms in late chronotypes with bipolar disorder.
Exploring the association between occupational complexity and numeracy
Authors: Billington Mary Genevieve , Foldnes Njål 
Published: September 2021

AbstractThe basic cognitive skill of numeracy is a recognized form of human capital, associated with economic and social well being for individuals and for nations. In this study, we explore how occupational complexity relates to proficiency in numeracy, among adults in full-time employment. We operationalize occupational complexity by constructing three measures of task complexity: complexity with data, complexity with people and complexity with things. Data from the international OECD survey of adult skills, 2012, is employed to investigate both the distribution of these three dimensions of occupational task complexity and how these relate to numeracy in 13 countries. The analysis indicates that data occupational complexity predicts numeracy scores, when controlling for age, gender and educational level. The findings open for a hypothesis that occupational activities may enhance basic skills in adult populations. If elaborated and supported through further studies this finding has practical implications for workplace organization and contributes to theoretical understandings of the development of basic skills in adults.
Social prediction: a new research paradigm based on machine learning
Authors: Chen Yunsong , Wu Xiaogang , Hu Anning , He Guangye , Ju Guodong 
Published: September 2021

AbstractSociology is a science concerned with both the interpretive understanding of social action and the corresponding causal explanation, process, and result. A causal explanation should be the foundation of prediction. For many years, due to data and computing power constraints, quantitative research in social science has primarily focused on statistical tests to analyze correlations and causality, leaving predictions largely ignored. By sorting out the historical context of "social prediction," this article redefines this concept by introducing why and how machine learning can help prediction in a scientific way. Furthermore, this article summarizes the academic value and governance value of social prediction and suggests that it is a potential breakthrough in the contemporary social research paradigm. We believe that through machine learning, we can witness the advent of an era of a paradigm shift from correlation and causality to social prediction. This shift will provide a rare opportunity for sociology in China to become the international frontier of computational social sciences and accelerate the construction of philosophy and social science with Chinese characteristics.
The biology of bone morphogenetic protein signaling pathway in cerebrovascular system
Authors: Tang Haishuang , Zhang Xiaoxi , Xue Gaici , Xu Fengfeng , Wang Qingsong , Yang Pengfei , Hong Bo , Xu Yi , Huang Qinghai , Liu Jianmin , Zuo Qiao 
Published: September 2021

AbstractBone morphogenetic protein belongs to transcription growth factor superfamily β; bone morphogenetic protein signal pathway regulates cell proliferation, differentiation, and apoptosis among different tissues. Cerebrovascular system supplies sufficient oxygen and blood into brain to maintain its normal function. The disorder of cerebrovascular system will result into serious cerebrovascular diseases, which is gradually becoming a major threat to human health in modern society. In recent decades, many studies have revealed the underlying biology and mechanism of bone morphogenetic protein signal pathway played in cerebrovascular system. This review will discuss the relationship between the two aspects, aiming to provide new perspective for non-invasive treatment and basic research of cerebrovascular diseases.
From mechanism-based to data-driven approaches in materials science
Authors: Hiemer Stefan , Zapperi Stefano 
Published: September 2021

AbstractA time-honored approach in theoretical materials science revolves around the search for basic mechanisms that should incorporate key feature of the phenomenon under investigation. Recent years have witnessed an explosion across areas of science of a data-driven approach fueled by recent advances in machine learning. Here we provide a brief perspective on the strengths and weaknesses of mechanism based and data-driven approaches in the context of the mechanics of materials. We discuss recent literature on dislocation dynamics, atomistic plasticity in glasses focusing on the empirical discovery of governing equations through artificial intelligence. We conclude highlighting the main open issues and suggesting possible improvements and future trajectories in the fields.
Current advances in pathogen-plant interaction between Verticillium dahliae and cotton provide new insight in the disease management
Authors: PALANGA Koffi Kibalou , LIU Ruixian , GE Qun , GONG Juwu , LI Junwen , LU Quanwei , LI Pengtao , YUAN Youlu , GONG Wankui 
Published: September 2021

AbstractVerticillium wilt is the second serious vascular wilt caused by the phytopathogenic fungus Verticillium dahliae Kleb. It has distributed worldwide, causing serious yield losses and fiber quality reduction in cotton production. The pathogen has developed different mechanisms like the production of cell wall degrading enzymes, activation of virulence genes and protein effectors to succeed in its infection. Cotton plant has also evolved multiple mechanisms in response to the fungus infection, including a strong production of lignin and callose deposition to strengthen the cell wall, burst of reactive oxygen species, accumulation of defene hormones, expression of defense-related genes, and target-directed strategies like cross-kingdom RNAi for specific virulent gene silencing. This review summarizes the recent progress made over the past two decades in understanding the interactions between cotton plant and the pathogen Verticillium dahliae during the infection process. The review also discusses the achievements in the control practices of cotton verticillium wilt in recent years, including cultivation practices, biological control, and molecular breeding strategies. These studies reveal that effective management strategies are needed to control the disease, while cultural practices and biological control approaches show promising results in the future. Furthermore, the biological control approaches developed in recent years, including antagonistic fungi, endophytic bacteria, and host induced gene silencing strategies provide efficient choices for integrated disease management.
Clinically relevant results of reverse total shoulder arthroplasty for patients younger than 65 years compared to the older patients
Authors: Hanisch Klaus , Holte Michael Boelstoft , Hvass Inge , Wedderkopp Niels 
Published: September 2021

Abstract
Background
Reverse total shoulder arthroplasty was originally designed for older patients with rotator cuff arthropathy and produces good results. The main objective of this retrospective study was to compare the patients younger than 65 years vs. the older patients in terms of the complications of reverse total shoulder arthroplasty and the functional recovery.

Methods
From January 2014 to January 2020, 566 patients who underwent the reverse total shoulder arthroplasty were divided into two groups (group A, ≥ 65 years, n = 506; group B, < 65 years, n = 60). The patients reported the quality of life using the patient-reported Western Ontario Osteoarthritis of the Shoulder index. The Constant score was obtained preoperatively and 3 months postoperatively. The complications and reoperations were compared. Statistical significance was set at P < 0.05.

Results
Clinically relevant improvements were found in group A and B. There was a multivariate statistically-significant but not clinically relevant difference in the change over time between group A and B. The mean 12-month Western Ontario Osteoarthritis of the Shoulder indexes were 58 in group B and 71 in group A. The mean Constant scores were 44 in group B vs. 43 in group A. Compared to group A, group B had a non-significant odds ratio of 1.9, which did not reach the clinically relevant Western Ontario Osteoarthritis of the Shoulder index of group A.

Conclusion
In patients younger than 65 years of age, RTSA seems to be a safe procedure in short term follow-up. After 1 year, we found no increased risk of complications, revision, or inferior outcomes compared to patients older than 65 years of age. Consequently, after one-year, RTSA provided clinically relevant improvements in the patients’ quality of life and shoulder strength regardless of age.
Superficial radial neuropathy: an unobserved etiology of chronic dorsoradial wrist pain
Authors: Saba Emmanuel Kamal Aziz 
Published: September 2021

Abstract
Background
Superficial radial neuropathy is considered an uncommon cause of chronic dorsoradial wrist pain. Its clinical diagnosis is usually missed. The purpose of the research was to investigate the existence of superficial radial neuropathy as a cause of chronic dorsoradial wrist pain. The study included 98 upper limbs obtained from 72 patients [58 women (80.6%)] with a primary complaint of chronic dorsoradial wrist pain and 91 asymptomatic upper limbs obtained from 63 apparently healthy individuals [46 women (73.0%)] as a control group. Clinical assessment and superficial radial nerve conduction study were done.

Results
No significant differences between patients and control group were present regarding sex and age. Among the participated patients, there were 29 upper limbs (29.6%) from 26 patients (36.1%) who had superficial radial neuropathy proved clinically and electrophysiologically. From them, three patients (11.5%) had bilateral superficial radial neuropathy. It was the solitary cause of chronic dorsoradial wrist pain in 15 upper limbs (51.7%) from 13 patients (50%). The remaining patients were associated with other musculoskeletal wrist conditions. The most common associated local wrist pathology was de Quervain’s disease in 8 upper limbs (27.6%) from 8 patients (30.8%).

Conclusions
Superficial radial neuropathy is common among patients with chronic dorsoradial wrist pain and should be considered in the differential diagnosis.
An fMRI study of cognitive reappraisal in major depressive disorder and borderline personality disorder
Authors: De la Peña-Arteaga Víctor , Berruga-Sánchez Mercedes , Steward Trevor , Martínez-Zalacaín Ignacio , Goldberg Ximena , Wainsztein Agustina , Abulafia Carolina , Cardoner Narcís , Castro Mariana N. , Villarreal Mirta , Menchón José M. , Guinjoan Salvador M. , Soriano-Mas Carles 
Published: September 2021

Abstract

Background
One common denominator to the clinical phenotypes of borderline personality disorder (BPD) and major depressive disorder (MDD) is emotion regulation impairment. Although these two conditions have been extensively studied separately, it remains unclear whether their emotion regulation impairments are underpinned by shared or distinct neurobiological alterations.

Methods
We contrasted the neural correlates of negative emotion regulation across an adult sample of BPD patients (n = 19), MDD patients (n = 20), and healthy controls (HCs; n = 19). Emotion regulation was assessed using an established functional magnetic resonance imaging cognitive reappraisal paradigm. We assessed both task-related activations and modulations of interregional connectivity.

Results
When compared to HCs, patients with BPD and MDD displayed homologous decreased activation in the right ventrolateral prefrontal cortex (vlPFC) during cognitive reappraisal. In addition, the MDD group presented decreased activations in other prefrontal areas (i.e., left dorsolateral and bilateral orbitofrontal cortices), while the BPD group was characterized by a more extended pattern of alteration in the connectivity between the vlPFC and cortices of the visual ventral stream during reappraisal.

Conclusions
This study identified, for the first time, a shared neurobiological contributor to emotion regulation deficits in MDD and BPD characterized by decreased vlPFC activity, although we also observed disorder-specific alterations. In MDD, results suggest a primary deficit in the strength of prefrontal activations, while BPD is better defined by connectivity disruptions between the vlPFC and temporal emotion processing regions. These findings substantiate, in neurobiological terms, the different profiles of emotion regulation alterations observed in these disorders.
Pretest Genetic Education Video Versus Genetic Counseling for Men Considering Prostate Cancer Germline Testing: A Patient-Choice Study to Address Urgent Practice Needs
Authors: Russo Jessica , McDougall Carey , Bowler Nicholas , Shimada Ayako , Gross Laura , Hyatt Colette , Kelly William K. , Calvaresi Anne , Handley Nathan R. , Hirsch Irvin H. , Izes Joseph K. , Lallas Costas D. , Mann Mark , Mark James Ryan , Mille Patrick J. , Preate Donald , Trabulsi Edouard J. , Tsang Miranda , Chandrasekar Thenappan , Weiner Perry R. , Gomella Leonard G. , Giri Veda N. 
Published: September 2021

PURPOSE Germline testing (GT) for prostate cancer (PCA) is now central to treatment and hereditary cancer assessment. With rising demand for and shortage of genetic counseling (GC), tools to deliver pretest informed consent across practice settings are needed to improve access to GT and precision care. Here, we report on Evaluation and Management for Prostate Oncology, Wellness, and Risk (EMPOWER), a patient-choice study for pretest video-based genetic education (VBGE) versus GC to inform urgent practice needs. PATIENTS AND METHODS Men with PCA or at risk for PCA (family history of PCA) were eligible and could choose pretest VBGE or GC. Outcomes included decisional conflict for GT, change in genetics knowledge, satisfaction, and intention to share results with family and/or providers. Descriptive statistics summarized results with counts and percentages for categorical variables and mean ± standard deviation for continuous variables. Data were compared with Fisher's exact, chi-squared, or Wilcoxon two-sample tests. Mean change in genetics knowledge was compared with t tests. The significance level was set a priori at .05. RESULTS Data on the first 127 participants were analyzed. Characteristics were White (85.8%), bachelor's degree (66.9%), and PCA diagnosis (90.6%). The majority chose VBGE (71%) versus GC (29%; P < .001). No differences were observed in decisional conflict for GT or satisfaction. Cancer genetics knowledge improved in both groups without significant difference (+0.9 VBGE, +1.8 GC, P = .056). Men who chose VBGE had higher intention to share GT results (96.4% VBGE v 86.4% GC, P = .02). Both groups had high rates of GT uptake (VBGE 94.4%, GC 92%). CONCLUSION A substantial proportion of men opted for pretest VBGE, with comparable patient-reported outcomes and uptake of GT. The results support the use of pretest video to address the critical GC shortage in the precision era.
Dysbetalipoproteinemia: Differentiating Multifactorial Remnant Cholesterol Disease From Genetic ApoE Deficiency
Authors: Paquette Martine , Bernard Sophie , Paré Guillaume , Baass Alexis 
Published: September 2021

Abstract

Context
Dysbetalipoproteinemia (DBL) is characterized by the accumulation of remnant lipoprotein particles and associated with an increased risk of cardiovascular and peripheral vascular disease (PVD). DBL is thought to be mainly caused by the presence of an E2/E2 genotype of the apolipoprotein E (APOE) gene, in addition to environmental factors. However, there exists considerable phenotypic variability among DBL patients.

Objective
The objectives were to verify the proportion of DBL subjects, diagnosed using the gold standard Fredrickson criteria, who did not carry E2/E2 and to compare the clinical characteristics of DBL patients with and without E2/E2.

Methods
A total of 12 432 patients with lipoprotein ultracentrifugation as well as APOE genotype or apoE phenotype data were included in this retrospective study.

Results
Among the 12 432 patients, 4% (n = 524) were positive for Fredrickson criteria (F+), and only 38% (n = 197) of the F+ individuals were E2/E2. The F+ E2/E2 group had significantly higher remnant cholesterol concentration (3.44 vs 1.89 mmol/L) and had higher frequency of DBL-related xanthomas (24% vs 2%) and floating beta (95% vs 11%) than the F+ non-E2/E2 group (P &lt; 0.0001). The F+ E2/E2 group had an independent higher risk of PVD (OR 11.12 [95% CI 1.87-66.05]; P = 0.008) events compared with the F+ non-E2/E2 group.

Conclusion
In the largest cohort of DBL worldwide, we demonstrated that the presence of E2/E2 was associated with a more severe DBL phenotype. We suggest that 2 DBL phenotypes should be distinguished: the multifactorial remnant cholesterol disease and the genetic apoE deficiency disease.
Acute Hepatitis due to Hepatic Glycogenosis After Insulin Overdose and Oral Glucose Administration in an Adolescent
Authors: Sasidharan Pillai Sabitha , Quintos Jose Bernardo , Topor Lisa Swartz 
Published: September 2021

Abstract

Background
Hepatic glycogenosis (HG) has been reported after intravenous (IV) dextrose administration to treat insulin overdose. We describe a case of HG in a patient with type 1 diabetes mellitus (T1DM) due to insulin overdose treated with oral glucose administration.

Case Presentation
An adolescent boy with T1DM on a basal bolus insulin regimen presented with abdominal discomfort, nausea, vomiting, and hypoglycemia of a few hours. His glucose was 71 mg/dL, aspartate transaminase (AST) 119 U/L, and alanine transaminase (ALT) 65 U/L. Hypoglycemia was treated with juice, and 12 hours later AST and ALT were 979 U/L and 700 U/L, respectively. Workup for infectious, autoimmune, metabolic, and toxic causes of hepatitis was negative. The transaminases improved by the next day and normalized within 3 weeks. Two weeks after discharge the patient returned with hypoglycemia, nausea, and right-sided abdominal pain of 13 hours. Hypoglycemia persisted despite multiple courses of glucose tablets and juice. Laboratory studies showed glucose of 58 mg/dL, AST of 776 U/L, ALT of 496 U/L, negative toxicology studies, and normal abdominal ultrasound. His serum insulin level was 249.7 mU/L and, C-peptide was less than 0.1 ng/mL, consistent with insulin overdose. He received IV fluids with dextrose, and insulin was held. Transaminases improved by the following day. Repeat serum insulin while on home regimen was normal.

Conclusion
Along with other diagnoses, HG should be considered in patients treated with insulin who present with hypoglycemia and acute hepatitis. HG can occur in cases of insulin overdose treated with repeated oral glucose administration.