bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding enhancer complexity with machine learning and high-throughput discovery
Authors: Smith Gabrielle D. , Ching Wan Hern , Cornejo-Páramo Paola , Wong Emily S. 
Published: May 2023

AbstractEnhancers are genomic DNA elements controlling spatiotemporal gene expression. Their flexible organization and functional redundancies make deciphering their sequence-function relationships challenging. This article provides an overview of the current understanding of enhancer organization and evolution, with an emphasis on factors that influence these relationships. Technological advancements, particularly in machine learning and synthetic biology, are discussed in light of how they provide new ways to understand this complexity. Exciting opportunities lie ahead as we continue to unravel the intricacies of enhancer function.
Clinical characteristics and survival of pulmonary arterial hypertension with or without interstitial lung disease in systemic sclerosis
Authors: Fairley Jessica L. , Hansen Dylan , Ross Laura , Proudman Susanna , Sahhar Joanne , Ngian Gene-Siew , Walker Jennifer , Host Lauren V. , Morrisroe Kathleen , Apostolopoulous Diane , Ferdowsi Nava , Wilson Michelle , Tabesh Maryam , Stevens Wendy , Nikpour Mandana ,   Australian Scleroderma Interest Group, Cooley Helen , Croyle Lucy , Hill Catherine , Host Lauren , Lester Sue , Major Gabor , Nash Peter , Rischmueller Maureen , Roddy Janet , Strickland Gemma , Tay Tien , Tymms Kathleen , Youssef Peter 
Published: May 2023

Abstract
Objectives
To describe the clinical phenotype and prognosis of people in the Australian Scleroderma (SSc) Cohort Study with pulmonary arterial hypertension (PAH) with or without interstitial lung disease (ILD).

Methods
Participants meeting ACR/EULAR criteria for SSc were divided into four mutually exclusive groups: those meeting criteria for PAH (PAH-only), ILD (ILD-only), concurrent PAH and ILD (PAH-ILD) or neither PAH nor ILD (SSc-only). Logistic or linear regression analyses were used for associations between clinical features, health-related quality of life (HRQoL) and physical function. Survival analysis was performed using Kaplan–Meier estimates and Cox-regression modelling.

Results
Of 1561 participants, 7% fulfilled criteria for PAH-only, 24% ILD-only, 7% PAH-ILD and 62% SSc-only. People with PAH-ILD were more frequently male, with diffuse skin involvement, higher inflammatory markers, older age of SSc onset and higher frequency of extensive ILD than the cohort overall (p < 0.001). People of Asian race more frequently developed PAH-ILD (p < 0.001). People with PAH-ILD or PAH-only had worse WHO functional class and 6-min-walk-distance than ILD-only (p < 0.001). HRQoL scores were worst in those with PAH-ILD (p < 0.001).
Survival was reduced in the PAH-only and PAH-ILD groups (p < 0.01). Multivariable hazard modelling demonstrated the worst prognosis in extensive ILD and PAH (HR = 5.65 95% CI 3.50–9.12 p < 0.01), followed by PAH-only (HR = 4.21 95% CI 2.89–6.13 p < 0.01) and PAH with limited ILD (HR = 2.46 95% CI 1.52–3.99 p < 0.01).

Conclusions
The prevalence of concurrent PAH-ILD in the ASCS is 7%, with poorer survival in those patients with PAH-ILD compared to ILD or SSc alone. The presence of PAH confers a poorer overall prognosis than even extensive ILD; however, further data are required to better understand the clinical outcomes of this high-risk patient group.
Cervical and ocular vestibular evoked myogenic potentials in patients with Diabetic Peripheral Neuropathy
Authors: Zhang Jinying , Ye Lichao , Bai Xuefeng , Huang Yali , Lin Jiayu , Huang Huapin 
Published: May 2023

Abstract
Background
Diabetes causes impaired microarterial blood flow, demyelination and neuronal damage, which may lead to cochlear damage and vestibular malfunction. Vestibular evoked myogenic potentials (VEMP) is a simple, reproducible test. Cervical and ocular vestibular evoked myogenic potentials (cVEMP and oVEMP) can be explored in the saccadic-spinal and utriculo-ocular pathways in regular clinical practice.

Objective
To evaluate possible vestibular evoked myogenic potential (VEMP) abnormalities in patients with diabetic peripheral neuropathy.

Materials and methods
89 patients with Type 2 Diabetes in the present study consisted of three groups: 29 patients with no peripheral neuropathy (NDPN group), 26 patients with asymptomatic neuropathy (SDPN group), 34 patients with symptomatic neuropathy (DPN group). Meanwhile, 42 healthy subjects were recruited as controls. The clinical characteristics (including gender, age, body mass index (BMI), and illness duration), as well as lipids (including triglyceride (TG), cholesterol (TC), low-density lipoprotein (LDL), and high-density lipoprotein (HDL)), uric acid, fasting blood glucose (FBG), and glycated hemoglobin (HbA1c) were compared among the four groups. Four groups were assessed using two vestibular tests including oVEMP and cVEMP. Latency and amplitude parameters were analyzed from VEMP plots.

Results
The latency of n10, p15 (oVEMP), p13, n23 (cVEMP) were significantly prolonged in the SDPN and DPN groups compared with the control and NDPN groups (p < 0.01), whereas latencies were similar in NDPN and the control groups. The amplitudes were not significantly different (p > 0.05). oVEMP latency p15 and cVEMP latency (p13, n23) were positively correlated with HbA1c, FBG, and illness duration, and oVEMP latency n10 was positively correlated with HbA1c and FBG. A nomogram, including FBG, HbA1C, HDL, TG, TC, LDL and group, was constructed to predict VEMP parameters and p13 was found to be independently associated with diabetic subgroups. Receiver operating characteristic curve (ROC) analysis showed good accuracy in predicting p13 in this nomogram. A user-friendly website has been created to facilitate the application of this prediction model ( https://fyey.shinyapps.io/VEMP_Model/ ).

Conclusion
Patients with diabetic peripheral neuropathy may have vestibular dysfunction. VEMP may be useful in assessing vestibular impairment in diabetic patients.
The reporting of neuropsychiatric symptoms in electronic health records of individuals with Alzheimer’s disease: a natural language processing study
Authors: Eikelboom Willem S. , Singleton Ellen H. , van den Berg Esther , de Boer Casper , Coesmans Michiel , Goudzwaard Jeannette A. , Vijverberg Everard G. B. , Pan Michel , Gouw Cornalijn , Mol Merel O. , Gillissen Freek , Fieldhouse Jay L. P. , Pijnenburg Yolande A. L. , van der Flier Wiesje M. , van Swieten John C. , Ossenkoppele Rik , Kors Jan A. , Papma Janne M. 
Published: May 2023

Abstract
Background
Neuropsychiatric symptoms (NPS) are prevalent in the early clinical stages of Alzheimer’s disease (AD) according to proxy-based instruments. Little is known about which NPS clinicians report and whether their judgment aligns with proxy-based instruments. We used natural language processing (NLP) to classify NPS in electronic health records (EHRs) to estimate the reporting of NPS in symptomatic AD at the memory clinic according to clinicians. Next, we compared NPS as reported in EHRs and NPS reported by caregivers on the Neuropsychiatric Inventory (NPI).

Methods
Two academic memory clinic cohorts were used: the Amsterdam UMC (n = 3001) and the Erasmus MC (n = 646). Patients included in these cohorts had MCI, AD dementia, or mixed AD/VaD dementia. Ten trained clinicians annotated 13 types of NPS in a randomly selected training set of n = 500 EHRs from the Amsterdam UMC cohort and in a test set of n = 250 EHRs from the Erasmus MC cohort. For each NPS, a generalized linear classifier was trained and internally and externally validated. Prevalence estimates of NPS were adjusted for the imperfect sensitivity and specificity of each classifier. Intra-individual comparison of the NPS classified in EHRs and NPS reported on the NPI were conducted in a subsample (59%).

Results
Internal validation performance of the classifiers was excellent (AUC range: 0.81–0.91), but external validation performance decreased (AUC range: 0.51–0.93). NPS were prevalent in EHRs from the Amsterdam UMC, especially apathy (adjusted prevalence = 69.4%), anxiety (adjusted prevalence = 53.7%), aberrant motor behavior (adjusted prevalence = 47.5%), irritability (adjusted prevalence = 42.6%), and depression (adjusted prevalence = 38.5%). The ranking of NPS was similar for EHRs from the Erasmus MC, although not all classifiers obtained valid prevalence estimates due to low specificity. In both cohorts, there was minimal agreement between NPS classified in the EHRs and NPS reported on the NPI (all kappa coefficients < 0.28), with substantially more reports of NPS in EHRs than on NPI assessments.

Conclusions
NLP classifiers performed well in detecting a wide range of NPS in EHRs of patients with symptomatic AD visiting the memory clinic and showed that clinicians frequently reported NPS in these EHRs. Clinicians generally reported more NPS in EHRs than caregivers reported on the NPI.
Persistent and fatal severe acute respiratory syndrome coronavirus 2 infection in a patient with severe hypogammaglobulinemia: a case report
Authors: Bedoya-Joaqui Vanessa , Gutiérrez-López María I. , Caicedo Paola A. , Villegas-Torres María F. , Albornoz-Tovar Ludwig L. , Vélez Juan D. , Hidalgo-Cardona Alejandra , Tobón Gabriel J. , Cañas Carlos A. 
Published: May 2023

Abstract
Background
Viruses are constantly changing as a result of mutations, and new viral variants are expected to appear over time. The virus that causes coronavirus disease 2019, severe acute respiratory syndrome coronavirus 2, is not excluded from this condition. Patients with some types of immunodeficiency have been reported to experience symptoms that vary from mild to severe, or even death, after being infected with severe acute respiratory syndrome coronavirus 2. We report a case of a woman with severe hypogammaglobulinemia who developed a prolonged and fatal severe acute respiratory syndrome coronavirus 2 infection.

Case presentation
A 60-year-old mestizo female with a previous history of severe hypogammaglobulinemia manifested by recurrent pulmonary infections and follicular bronchiolitis. She received a monthly treatment of intravenous immunoglobulins and was admitted after report of a neurological manifestation related to a left thalamic inflammatory lesion, for a duration of 2 weeks of hospitalization, indicated for the study of her neurological condition, including brain biopsy. Both on admission and 1 week later, nasopharyngeal polymerase chain reaction tests for severe acute respiratory syndrome coronavirus 2 were performed and reported negative. In the third week of hospitalization, she developed pulmonary symptoms, and a positive test result for severe acute respiratory syndrome coronavirus 2 was evidenced. On Day 3, the patients’ condition worsened as the infection progressed to respiratory failure and required mechanical ventilation. On Day 8 after the coronavirus disease 2019 diagnosis, the polymerase chain reaction test for severe acute respiratory syndrome coronavirus 2 showed persistent detection of the virus. Various bacterial coinfections, including Klebsiella pneumoniae and Enterobacter cloacae, were diagnosed and treated. On Day 35, her pulmonary symptoms worsened, and the results of the severe acute respiratory syndrome coronavirus 2 polymerase chain reaction test remained positive. On Day 36, despite all the respiratory support, the patient died. The severe acute respiratory syndrome coronavirus 2 virus was sequenced at the beginning and 8 days after the onset of the disease, and the strain, without obvious mutations in the gene that encodes spike protein, was identified.

Conclusions
This clinical case showed persistent severe acute respiratory syndrome coronavirus 2 detection after 35 days of infection in a patient with severe hypogammaglobulinemia. The sequencing of the virus showed no mutations on the spike protein at 8 days, indicating that, in this case, the persistence of the viral detection was associated with immunodeficiency instead of changes in the viral components.
Speech emotion recognition based on emotion perception
Authors: Liu Gang , Cai Shifang , Wang Ce 
Published: May 2023

AbstractSpeech emotion recognition (SER) is a hot topic in speech signal processing. With the advanced development of the cheap computing power and proliferation of research in data-driven methods, deep learning approaches are prominent solutions to SER nowadays. SER is a challenging task due to the scarcity of datasets and the lack of emotion perception. Most existing networks of SER are based on computer vision and natural language processing, so the applicability for extracting emotion is not strong. Drawing on the research results of brain science on emotion computing and inspired by the emotional perceptive process of the human brain, we propose an approach based on emotional perception, which designs a human-like implicit emotional attribute classification and introduces implicit emotional information through multi-task learning. Preliminary experiments show that the unweighted accuracy (UA) of the proposed method has increased by 2.44%, and weighted accuracy (WA) 3.18% (both absolute values) on the Interactive Emotional Dyadic Motion Capture (IEMOCAP) dataset, which verifies the effectiveness of our method.
The effects of COVID-19 on European healthcare provision for working-age adults with major depressive disorder
Authors: Wong Win Lee Edwin , Sually Dilveer , Hidalgo-Mazzei Diego , Quoidbach Vinciane , Simon Judit , Boyer Patrice , Strawbridge Rebecca , Young Allan H. 
Published: May 2023

Abstract

Background
Major depressive disorder (MDD) is a leading cause of disability worldwide, and yet delivery of care for this illness is rife with gaps. The COVID-19 pandemic has had far reaching implications for every facet of healthcare, and MDD is no exception. This scoping review aimed to ascertain the impacts of COVID-19 on the delivery of MDD care in Europe, as well as to evaluate any novel MDD care strategies trialled in this period.

Methods
We searched the PubMed and PsycINFO databases up to January 2022 with a strategy centred around COVID-19 and MDD. Full texts of eligible studies examining working-age adults and conducted in Europe were evaluated against several criteria. All outcomes were then extracted and a narrative synthesis was constructed to summarise identified themes.

Results
Of 1,744 records identified in our search, 11 articles were eligible for inclusion in the review. In general, these studies reported a decrease in treatment rates, access to care, and perceived access to care during the COVID-19 pandemic. In addition, digital interventions trialled during the pandemic were broadly well-received by users, though their efficacy in improving MDD care was ambiguous.

Conclusions
Despite a limited number of pertinent studies, this scoping review identified a trend of exacerbated treatment gaps in MDD care during the pandemic. Several of our pre-specified gaps, including delays to detection or treatment of depression and rates of follow-up contacts, remained unexplored in the context of COVID-19. This highlights the need for further investigation to obtain a full understanding of the relationship between COVID-19 and MDD care in Europe.
Splitting probabilities for dynamics in corrugated channels: Passive vs. active Brownian motion
(a)
Authors: Malgaretti P. , Nizkaia T. , Oshanin G. 
Published: May 2023

Abstract
In many practically important problems which rely on particles' transport in realistic corrugated channels, one is interested in knowing the probability that either of the extremities (e.g., the one containing a chemically active site, or connected to a broader channel) is reached before the other one. In mathematical literature, the latter are called the “splitting” probabilities (SPs). Here, within the Fick-Jacobs approach, we study analytically the SPs as functions of system's parameters for dynamics in three-dimensional corrugated channels, confronting standard diffusion and active Brownian motion. Our analysis reveals some similarities in the behavior and also some markedly different features, which can be seen as fingerprints of the activity of particles.
Emergence of prethermal states in a driven dissipative system through cross-correlated dissipation
Authors: Chakrabarti Arnab , Bhattacharyya Rangeet 
Published: May 2023

Abstract
Periodically driven closed quantum many-body systems are known to exhibit prethermal or quasi-steady-state dynamics. In this work, we theoretically show that such prethermal phases can appear in the dynamics of a dipolar two-spin-1/2 system coupled to a heat bath if the cross terms between the drive and dipolar interactions are taken into consideration. To this end, we use our recently reported fluctuation-regulated quantum master equation (Chakrabarti A. and Bhattacharyya R., Phys. Rev. A
97 (2018) 063837), to show that the predicted dynamics can successfully explain the experimentally observed features of the transient and prethermal regime.
The Clinical Benefits of Antiresorptive Agents in Patients with Primary Breast Cancer Receiving Adjuvant Endocrine Therapy: A Systematic Review with Pairwise and Network Meta-analysis
Authors: Wang Sheng-Fan , Lin Yi-Sheng , Yeh Wan-Yu , Chang Yuh-Lih , Chiang Chern-En , Chen Chen-Huan , Tseng Ling-Ming , Lee Hsin-Chen , Liu Chun-Yu , Cheng Hao-Min 
Published: May 2023

Abstract

Context
Clinical trials have investigated the role of antiresorptive agents, including bisphosphonates and denosumab, in patients with primary breast cancer receiving adjuvant endocrine therapy, aiming for better bone protection and/or improving survival.

Objective
To summarize the clinical effects of antiresorptive agents in patients with early breast cancer receiving endocrine therapy.

Methods
We systematically reviewed and synthesized the clinical benefits and harms of antiresorptive agents in patients with early breast cancer receiving endocrine therapy by calculating the risk ratios (RRs).

Results
In the pooled meta-analysis, antiresorptive agents had significant clinical benefits on disease recurrence (RR 0.78, 95% CI 0.67-0.90) and locoregional recurrence (RR 0.69, 95% CI 0.49-0.95) in patients with breast cancer receiving endocrine therapy. Early use of antiresorptive agents has a beneficial effect on secondary endocrine therapy resistance instead of primary resistance. Safety analysis revealed that potential risk for osteonecrosis of the jaw (ONJ, RR 3.29, 95% CI 1.12-9.68) with antiresorptive agents; however, there is an insignificant difference in arthralgia. The subgroup analyses revealed that intervention with bisphosphonates might have profound clinical benefits, but also increased the occurrence of ONJ. A network meta-analysis further supported the clinical effects of early antiresorptive agent use compared with delayed use or placebo.

Conclusion
Using antiresorptive agents early in patients with breast cancer receiving adjuvant endocrine therapy may provide additional benefits in risk reduction of recurrence, but there is a potential risk of ONJ.
Stem Cell–Derived Islet Transplantation in Patients With Type 2 Diabetes: Can Diabetes Subtypes Guide Implementation?
Authors: Verhoeff Kevin , Marfil-Garza Braulio A , Czarnecka Zofia , Cuesta-Gomez Nerea , Jasra Ila Tewari , Dadheech Nidheesh , Senior Peter A , Shapiro A M James 
Published: May 2023

Abstract
Historically, only patients with brittle diabetes or severe recurrent hypoglycemia have been considered for islet transplantation (ITx). This population has been selected to optimize the risk-benefit profile, considering risks of long-term immunosuppression and limited organ supply. However, with the advent of stem cell (SC)–derived ITx and the potential for immunosuppression-free ITx, consideration of a broader recipient cohort may soon be justified. Simultaneously, the classical categorization of diabetes is being challenged by growing evidence in support of a clustering of disease subtypes that can be better categorized by the All New Diabetics in Scania (ANDIS) classification system. Using the ANDIS classification, 5 subtypes of diabetes have been described, each with unique causes and consequences. We evaluate consideration for ITx in the context of this broader patient population and the new classification of diabetes subtypes.
In this review, we evaluate considerations for ITx based on novel diabetes subtypes, including their limitations, and we elaborate on unique transplant features that should now be considered to enable ITx in these “unconventional” patient cohorts. Based on evidence from those receiving whole pancreas transplant and our more than 20-year experience with ITx, we offer recommendations and potential research avenues to justify implementation of SC-derived ITx in broader populations of patients with all types of diabetes.
Forgotten Refugees and Erased “Multicultural” Subjects: The Vietnam War and South Korea's Subimperial Nation-Building
Authors: Kim Nora Hui-Jung 
Published: May 2023

Abstract
This article revisits South Korea's mostly forgotten involvement in the Vietnam War and examines lingering effects of the war on South Korea's subimperial nation-building in general and on its contemporary multicultural policies in particular. The Vietnam War served as a stepping stone for South Korea to transform itself from a war-torn country to an economic subempire in Asia. Encounters with Vietnamese refugees in the aftermath of the war helped form South Korea's subimperial gaze, solidifying the racial inferiority of South Koreans to the United States but establishing their superiority over the Vietnamese. Further, the resettlement of Vietnamese refugees laid the foundation for the practices of contemporary South Korean multiculturalism. In the aftermath of the Vietnam War, South Korea presented itself as a benevolent protector of Vietnamese refugees. The brutal acts committed on the battlefields and the neglect of the Vietnamese refugees living at the margins of South Korean society have been effaced from public memory. Through the work of selective memory, the “multicultural” South Korea presents itself yet again as a caring supporter of Vietnamese migrant wives. It is through this cultural amnesia that the myth of ethnic homogeneity was maintained, allowing the contemporary multiculturalism discourse and practice to be advertised as a novel cultural globalization project that is free of historical guilt or responsibility.
A Great, Restless Stream
Authors: Crowley Thomas 
Published: May 2023

Abstract
This article explores the thought of philosopher, historian, and activist Sharad Patil, particularly the way he constructs theoretical arguments by drawing on, expanding, and critiquing the insights of his predecessors in radical anti-caste thought, Jotirao Phule and B. R. Ambedkar. Patil advances a particular reading of Phule-Ambedkarism to sharpen his critique of orthodox Marxism and develop a philosophy that could undergird revolutionary egalitarian change in India. The article focuses on two key theoretical insights elaborated by Patil and his reading of Phule-Ambedkarism: one historical, centering on the methodological and ideological importance of rewriting longue durée history; the other political-economic, centering on the way that circuits of exploitation and rule get reproduced. The article attempts to read Patil according to his own methodological and analytic criteria. Patil had little interest in purity of theory or in defending the boundaries of the one true Marxism or Phule-Ambedkarism. Even while critiquing Phule and Ambedkar, Patil insistently asked (as this article too asks): what did their philosophies of history, of knowledge, and of political economy enable them to understand about the past, present, and future of egalitarian struggle in India and beyond?