bluuebunny/crossref_metadata_2025_split huggingface dataset:
Normalizing single-cell RNA sequencing data with internal spike-in-like genes
Authors: Lin Li , Song Minfang , Jiang Yong , Zhao Xiaojing , Wang Haopeng , Zhang Liye 
Published: August 2020

Abstract
Normalization with respect to sequencing depth is a crucial step in single-cell RNA sequencing preprocessing. Most methods normalize data using the whole transcriptome based on the assumption that the majority of transcriptome remains constant and are unable to detect drastic changes of the transcriptome. Here, we develop an algorithm based on a small fraction of constantly expressed genes as internal spike-ins to normalize single-cell RNA sequencing data. We demonstrate that the transcriptome of single cells may undergo drastic changes in several case study datasets and accounting for such heterogeneity by ISnorm (Internal Spike-in-like-genes normalization) improves the performance of downstream analyses.
The Human, The Animal and the Prehistory of COVID-19*
Authors: Sivasundaram Sujit 
Published: August 2020

Abstract
In Asia, pangolins have generated a rich set of indigenous oral traditions. These contrast with the often confused, or failed, colonial and Western scientific practices of classifying, domesticating and collecting the pangolin. More recently this long-standing encounter between the pangolin and human has shifted into exponential killing. The pangolin has become the mammal which is most trafficked by humans. This trade has been a global one, a fact that is important to remember given the racist ideas and inequalities that have been highlighted through the experience of the COVID-19 pandemic. The changing relationship between the pangolin and the human in modern history is used here as a window onto the interlinked histories of the pandemic and environmental crisis, both of which arose partly from human encroachment into biodiverse and forested areas, including pangolin habitats. The phases of the pangolin–human relationship can be read for the preconditions of these interlinked crises that face the planet and its historians in 2020. It is vital that historians respond confidently and fully to causation at the interspecies frontier without using the pandemic to mount theoretically naive ‘compare and contrast’ exercises with past disease events to provide lessons for the present. A post-pandemic historiography will surely be interdisciplinary, with critical, philosophical and collaborative engagement with scientists.
Are Illness Perceptions Associated with Pain and Disability in Complex Regional Pain Syndrome? A Cross-Sectional Study
Authors: Antunovich Dana R , Horne Juliette C , Tuck Natalie L , Bean Debbie J 
Published: August 2020

Abstract

Objective
Complex regional pain syndrome (CRPS) is a complex and often poorly understood condition, and people with CRPS will have diverse beliefs about their symptoms. According to the self-regulation model, these beliefs (termed “illness perceptions”) influence health behaviors and outcomes. Previous studies have found that psychological factors influence CRPS outcomes, but few studies have investigated CRPS patients’ illness perceptions specifically. The present study examined whether illness perceptions were related to pain intensity and other relevant outcomes in people with CRPS.

Methods
In this cross-sectional study, 53 patients with CRPS (type 1 and type 2) completed questionnaires assessing illness perceptions, pain, disability, and psychological factors. Multiple regression analyses were used to determine whether illness perceptions were associated with pain intensity, disability, depression, and kinesiophobia, after controlling for possible covariates (including clinical and demographic factors, pain catastrophizing, and negative affect).

Results
Negative illness perceptions were associated with greater pain, disability, and kinesiophobia, but not depression. Specifically, attributing more symptoms to CRPS (more negative illness identity perceptions) was associated with greater pain intensity, and reporting a poorer understanding of CRPS (lower illness coherence scores) was associated with greater disability and kinesiophobia.

Conclusions
Patients with CRPS with more negative illness perceptions (particularly perceptions indicating a poor understanding of their condition) also experience greater pain, disability, and kinesiophobia. Future research could investigate whether altering CRPS patients’ illness perceptions influences clinical outcomes.
On the Compatibility of Rational Deliberation and Determinism: Why Deterministic Manipulation Is Not a Counterexample
Authors: Caruso Gregg D 
Published: August 2020

Abstract
This paper aims to defend deliberation-compatibilism against several objections, including a recent counterexample by Yishai Cohen that involves a deliberator who believes that whichever action she performs will be the result of deterministic manipulation. It begins by offering a Moorean-style proof of deliberation-compatibilism. It then turns to the leading argument for deliberation-incompatibilism, which is based on the presumed incompatibility of causal determinism and the ‘openness’ required for rational deliberation. The paper explains why this argument fails and develops a coherent account of how one can rationally deliberate and believe in causal determinism without inconsistency. The second half of the paper then takes up Cohen's proposed counterexample and his Four-Case Deliberation Argument (FCDA) against deliberation-compatibilism, which is meant to mirror Derk Pereboom's famous Four-Case Manipulation Argument. In response, the author defends a hard-line reply to FCDA but also argues that the notion of ‘sourcehood’ relevant to rational deliberation differs from that involved in free will.
Concordance in parent and offspring cortico-basal ganglia white matter connectivity varies by parental history of major depressive disorder and early parental care
Authors: Abraham Eyal , Posner Jonathan , Wickramaratne Priya J , Aw Natalie , van Dijk Milenna T , Cha Jiook , Weissman Myrna M , Talati Ardesheer 
Published: August 2020

AbstractSocial behavior is transmitted cross-generationally through coordinated behavior within attachment bonds. Parental depression and poor parental care are major risks for disruptions of such coordination and are associated with offspring’s psychopathology and interpersonal dysfunction. Given the key role of the cortico-basal ganglia (CBG) circuits in social communication, we examined similarities (concordance) of parent–offspring CBG white matter (WM) connections and how parental history of major depressive disorder (MDD) and early parental care moderate these similarities. We imaged 44 parent–offspring dyads and investigated WM connections between basal-ganglia seeds and selected regions in temporal cortex using diffusion tensor imaging (DTI) tractography. We found significant concordance in parent–offspring strength of CBG WM connections, moderated by parental lifetime-MDD and care. The results showed diminished neural concordance among dyads with a depressed parent and that better parental care predicted greater concordance, which also provided a protective buffer against attenuated concordance among dyads with a depressed parent. Our findings provide the first neurobiological evidence of concordance between parents-offspring in WM tracts and that concordance is diminished in families where parents have lifetime-MDD. This disruption may be a risk factor for intergenerational transmission of psychopathology. Findings emphasize the long-term role of early caregiving in shaping the neural concordance among at-risk and affected dyads.
Patent citations, knowledge flows, and catching-up: Evidences of different national experiences for the period 1982–2006
Authors: Britto Jorge Nogueira de Paiva , Ribeiro Leonardo Costa , Araújo Lucas Teixeira , Albuquerque Eduardo da Motta e 
Published: August 2020

AbstractThis paper uses information about patent citations to track the evolution of knowledge flows in selected countries engaged in catching-up processes. The analysis comprises patent citation data extracted from the USPTO database for the period 1982-2006. The data are presented through technological interaction matrices displaying the interaction between the technological fields of cited and citing patents. Each matrix cell matches the technological field(s) of one cited patent to the technological field(s) of its citing patent(s). The hypothesis is that the intensification and diversification of knowledge flows to a greater number of fields broadens the possibilities of identifying attractive opportunities for innovation, thereby multiplying the opportunities of development and catching-up. The analysis seeks to identify which technological fields concentrate the absorption and diffusion of knowledge in a given country over different periods, a consideration which tends to be related to the possibilities of catching-up processes.
Co-culture of human alveolar epithelial (A549) and macrophage (THP-1) cells to study the potential toxicity of ambient PM2.5: a comparison of growth under ALI and submerged conditions
Authors: Wang Guanghe , Zhang Xiaofeng , Liu Xinyan , Zheng Jing 
Published: August 2020

AbstractFine particulate matter (PM2.5) in the ambient atmosphere is strongly associated with detrimental health effects. However, these particles from various sources and regions are unlikely equally toxic. While animal studies are impractical for high-throughput toxicity testing, appropriate in vitro models are urgently needed. Co-culture of A549 and THP-1 macrophages grown at air–liquid interface (ALI) or under submerged conditions was exposed to same concentrations of ambient PM2.5 to provide accurate comparisons between culture methods. Following 24-h incubation with PM2.5 collected in Harbin in China, biological endpoints being investigated include cytotoxicity, reactive oxygen species (ROS) levels and pro-inflammatory mediators. The co-culture grown under submerged condition demonstrated a significant increase in ROS levels and all tested pro-inflammatory indicators [interleukin (IL)-1β, IL-6, IL-8 and tumor necrosis factor-α] in mRNA expression and released protein levels. Similar but a declining response trend was observed using the same PM2.5 incubation after grown at ALI. We further observed a significant increase of PM2.5-induced phosphorylation of p38 MAPK and activation of NF-κB p65 in a dose-dependent trend for co-cultures grown under submerged condition. These results provide important implications that culture conditions (ALI versus submerged) can induce different extents of biological responses to ambient PM2.5; the co-culture grown at ALI is less likely to produce false-positive results than submerged culture. Hence, culture conditions should be discussed when comparing in vitro methods used for high-throughput PM2.5 toxicity assessment in future.
The evolution of the nasopharyngeal carcinoma staging system over a 10-year period: implications for future revisions
Authors: Tang Si-Qi , Mao Yan-Ping , Xu Cheng , Guo Rui , Li Wen-Fei , Tang Ling-Long , Sun Ying , Ma Jun 
Published: August 2020

AbstractBackgroundThe classification criteria and staging groups for nasopharyngeal carcinoma described in the Union for International Cancer Control/American Joint Committee on Cancer (UICC/AJCC) staging system have been revised over time. This study assessed the proportion of patients whose staging and treatment strategy have changed due to revisions of the UICC/AJCC staging system over the past 10 years (ie, from the sixth edition to the eighth edition), to provide information for further refinement.MethodsWe retrospectively reviewed 1901 patients with non-metastatic nasopharyngeal carcinoma treated in our cancer center between November 2009 and June 2012. The Akaike information criterion and Harrell concordance index were applied to evaluate the performance of the staging system.ResultsIn total, 25 (1.3%) of the 1901 patients who were staged as T2a according to the sixth edition system were downgraded to T1 in the eighth edition; 430 (22.6%) staged as N0 in the sixth edition were upgraded to N1 in the eighth edition; 106 (5.6%) staged as N1/2 in the sixth edition were upgraded to N3 in the eighth edition. In addition, 51 (2.7%) and 25 (1.3%) of the study population were upstaged from stage I to stage II and stage II to stage IVa, respectively; 10 (0.5%) was downgraded from stage II to stage I. The survival curves of adjacent N categories and staging groups defined by eighth classification system were well-separated. However, there was no significant difference in the locoregional failure-free survival (P = 0.730) and disease-free survival (P = 0.690) rates between the T2 and T3 categories in the eighth edition classification system.ConclusionsModifications to the tumor-node-metastasis staging system over the past 10 years have resulted in N classification changes in numerous cases. Although the eighth edition tumor-node-metastasis staging system better predicts survival outcomes, the T classification could be simplified in future revisions.
Systemic lupus erythematosus: year in review 2019
Authors: Fan Yong , Hao Yan-Jie , Zhang Zhuo-Li 
Published: August 2020

Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with extreme heterogeneity and potentially involvement of any organ or system. Numerous unanswered questions and challenges in SLE always prompt further exploration. In 2019, great progress in various aspects of SLE emerged. Both the classification criteria and management recommendation for SLE were updated. New promising medications have been widely developed and tested, although subsequent clinical studies are warranted. As an emerging number of most notable studies in SLE were published in both clinical area and basic research in 2019, we aim to summarize the highest quality data on SLE regarding novel insights of pathogenesis, updated recommendations, hot-spot issues on clinical manifestations, new understanding of disease prognosis, and most importantly, the therapeutic advances in SLE in this review.
Kikuchi–Fujimoto Disease Triggered by Systemic Lupus Erythematosus and Mycoplasma pneumoniae Infection—A Report of a Case and a Review of the Literature
Authors: Müller Cornelia S. L. , Vogt Thomas , Becker Sören L. 
Published: August 2020

Abstract:
Kikuchi–Fujimoto disease (KFD) is a necrotizing histiocytic lymphadenitis that was described for the first time in 1972 in Japan. Its etiology is still not fully understood. It has been reported in association with many different agents, diseases, and triggering factors without any conclusive result. To the best of our knowledge, we report for the first time a case of KFD with systemic lupus erythematosus in a child in association with a polymerase chain reaction (PCR)-positive throat swab for Mycoplasma pneumoniae. Although difficult to prove, the acute M. pneumoniae infection might have served as a triggering event for the development of KFD in our case. We encourage further studies to investigate a potential relationship between KFD and M. pneumoniae, which should also use PCR-based testing for this pathogen in patients with KFD.
Hypertensive disorders of pregnancy and menopausal symptoms: a cross-sectional study from the data registry on experiences of aging, menopause, and sexuality
Authors: Faubion Stephanie S. , King Amanda , Kattah Andrea G. , Kuhle Carol L. , Sood Richa , Kling Juliana M. , Mara Kristin C. , Kapoor Ekta 
Published: August 2020

Abstract

Objective:
Hypertensive disorders of pregnancy and menopausal symptoms, specifically vasomotor symptoms, have both been associated with cardiovascular disease risk in women. However, data are sparse on the association between these two female-specific cardiovascular risk factors. This study was conducted to investigate the association between a history of a hypertensive disorder of pregnancy and menopausal symptoms.

Methods:
This was a cross-sectional study of women aged 40 to 65 years seen for specialty consultation in women's health clinics at Mayo Clinic Rochester, MN and Scottsdale, AZ, between May, 2015 and September, 2019. A self-reported history of hypertensive disorders of pregnancy served as the independent variable, and menopause symptoms as assessed by the Menopause Rating Scale were the primary outcome measure.

Results:
Of 2,684 women included in the analysis, 180 had a self-reported history of a hypertensive disorder of pregnancy. The total menopausal symptom scores as well as somatic and psychological domain scores were higher in women with a history of a hypertensive disorder of pregnancy compared to women without a history of a hypertensive disorder of pregnancy or to women without a pregnancy. On multivariable analysis, women with a hypertensive disorder of pregnancy using hormone therapy had significantly higher total menopause symptom scores than women with no such history.

Conclusions:
In this large cross-sectional study, a history of hypertensive disorders of pregnancy was associated with more bothersome menopausal symptoms. Additional study is needed to determine the strength of this association, underlying mechanisms of the association, and clinical implications for cardiovascular risk prediction in women.
The effect of pathophysiological changes in the vaginal milieu on the signs and symptoms of genitourinary syndrome of menopause (GSM)
Authors: Qi Wenhui , Li Huiyang , Wang Chen , Li Huanrong , Fan Aiping , Han Cha , Xue Fengxia 
Published: August 2020

Abstract

Importance and objective:
The aim of this study was to provide an overview of the most recent literature on genitourinary syndrome of menopause (GSM), to explore the key elements of GSM diagnosis, and the potential impact of pathophysiological changes in the vaginal milieu on vulvovaginal symptoms.

Methods:
The MEDLINE database was searched, and only articles written in English were considered. Additional references were identified by hand searching the bibliographies of the included articles.

Discussions and conclusion:
The vaginal milieu plays important roles in producing bothersome symptoms in the host. In women with GSM, low hormone states can result in pathophysiological changes in the vaginal milieu, including the vaginal microbiome and the mucosal immunity. Hormone-associated disruption of the balance of the indigenous microbiota and the dysregulation of these immune responses are the pathophysiological basis of GSM symptoms. However, whether the microbiome and mucosal immunity are markers of vulvovaginal disorder or agents actively promoting a healthy vagina are still not fully understood. It is an important area of focus.
The Academic Fellowship in Physician Assistant Education
Authors: Herrick Amber , Leiken Shuli , Hoover Eve B. , Feirstein Jennifer , Bonnin Kirsten J. , Stoehr James D. 
Published: August 2020

Abstract
The rapid growth of the physician assistant (PA) profession has required PA programs to increase their efforts in the recruitment and retention of experienced faculty. One approach was the establishment of the academic fellowship concept in 1998. Since then, 5 PA programs have designed fellowships, 3 of which were implemented and graduated fellows. To institute and develop an academic fellowship takes time, resources, and buy-in from faculty and students. The structure of the curricula within the fellowships has been similar since 1998 and includes faculty development opportunities, lecture development and delivery, student assessment, small group facilitation, interprofessional education, and committee work. Most fellowship-trained educators have entered faculty positions after completion of their fellowship. They appear to use sound educational strategies in their teaching and are successful in their scholarly productivity. Academic fellowships are just one route in the transition to PA education, and while they may require a significant investment from the sponsoring institution and program, they can provide a unique opportunity for PAs to immerse themselves in the faculty experience before the full commitment to a career change.
Effect of Electrode to Modiolus Distance on Electrophysiological and Psychophysical Parameters in CI Patients With Perimodiolar and Lateral Electrode Arrays
Authors: Degen Chantal Vanessa , Büchner Andreas , Kludt Eugen , Lenarz Thomas 
Published: August 2020

Objectives:
To investigate the intracochlear position of the latest Cochlear Nucleus 532 electrode array compared with the straight Nucleus 522 and the precurved 512 arrays and determine the effect of the electrode–modiolus distance on electrically evoked compound action potential, C-levels, electrically evoked stapedius reflex thresholds (ESRTs), and impedances.

Methods:
Postoperative high-resolution cone beam computational tomography images of 30 patients with Cochlear Nucleus 532, 522, and 512 implants were evaluated using the Comet (Cochlea Measurement Tool) program to determine the distance between the 22 individual electrode contacts and the medial wall. ESRTs were documented intraoperatively and electrophysiological as well as psychophysical parameters were measured at multiple time points including the first fitting after the initial activation.

Results:
The electrode–modiolus distance in perimodiolar arrays is uniformly small across the array, whereas in a straight electrode carrier it varies significantly along the length of the array. Electrically evoked compound action potential thresholds and C-levels are larger with increased distance to the modiolus. Impedances and stapedius reflex thresholds do not differ significantly between the arrays. Our results show that the electrode position has a significant effect on both electrophysiological and psychophysical parameters, while impedances and ESRTs are not impacted.

Conclusion:
Novel tools can be used in the evaluation of high resolution cone beam computational tomography images to determine individual electrode–modiolus distances after cochlear implantation. The results of this study suggest that the correlations between electrode–modiolus distance and electrophysiological and psychophysical parameters are not sufficiently strong to adjust CI-fitting based on imaging data.
Changes in the Auditory Association Cortex in Dementing Illnesses
Authors: Aylward Alana , Auduong Priscilla , Anderson Jeffrey S. , Zielinski Brandon A. , Wang Angela Y. , Weng Cindy , Foster Norman L. , Gurgel Richard K. 
Published: August 2020

Objective:
To evaluate the relationship between degree of cognitive impairment and gray-matter density changes in the auditory cortex.

Study Design:
Retrospective case-control.

Patients:
Six hundred sixty-three patients of a tertiary referral center cognitive disorders clinic.

Intervention:
Magnetic resonance imaging.

Main Outcome Measures:
Ratios of gray matter density of the primary auditory cortex (A1) to whole brain and auditory association cortex (AAC) to whole brain in patients with Alzheimer's disease (AD) compared with mild cognitive impairment (MCI) and patients with a mini-mental state exam (MMSE) scores ≤25 versus >25.

Results:
After multivariate analysis, a statistically significant difference between AAC to brain ratios for patients with a MMSE ≤25 (n = 325) compared with >25 (n = 269) was found, with values −0.03 (95% CI −0.04 to −0.02, p < 0.0001) on the left and −0.04 (95% CI −0.06 to −0.03, p < 0.0001) on the right. The adjusted average difference of left and right AAC to brain ratios between AD patients (n = 218) compared with MCI patients (n = 121) was also statistically significant, at −0.03 (95% CI −0.05 to −0.01, p = 0.004) and −0.05 (95% CI −0.07 to −0.03, p < 0.0001), respectively. There was no statistically significant difference in the left or right A1 to brain ratios between the MMSE groups or between the AD and MCI groups.

Conclusions:
The AAC for patients with MMSE ≤25 and for those with AD shows decreased gray matter density when compared with patients with better cognitive function. No difference was detected in A1, raising the possibility that patients may have intact neural hearing, but impaired ability to interpret sounds.