bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA hypomethylation drives changes in MAGE-A gene expression resulting in alteration of proliferative status of cells
Authors: Colemon Ashley , Harris Taylor M. , Ramanathan Saumya 
Published: July 2020

AbstractMelanoma Antigen Genes (MAGEs) are a family of genes that have piqued the interest of scientists for their unique expression pattern. A subset of MAGEs (Type I) are expressed in spermatogonial cells and in no other somatic tissue, and then re-expressed in many cancers. Type I MAGEs are often referred to as cancer-testis antigens due to this expression pattern, while Type II MAGEs are more ubiquitous in expression. This study determines the cause and consequence of the aberrant expression of the MAGE-A subfamily of cancer-testis antigens. We have discovered that MAGE-A genes are regulated by DNA methylation, as revealed by treatment with 5-azacytidine, an inhibitor of DNA methyltransferases. Furthermore, bioinformatics analysis of existing methylome sequencing data also corroborates our findings. The consequence of expressing certain MAGE-A genes is an increase in cell proliferation and colony formation and resistance to chemo-therapeutic agent 5-fluorouracil and DNA damaging agent sodium arsenite. Taken together, these data indicate that DNA methylation plays a crucial role in regulating the expression of MAGE-A genes which then act as drivers of cell proliferation, anchorage-independent growth and chemo-resistance that is critical for cancer-cell survival.
Classification of archaic rice grains excavated at the Mojiaoshan site within the Liangzhu site complex reveals an Indica and Japonica chloroplast complex
Authors: Tanaka Katsunori , Zhao Chunfang , Wang Ningyuan , Kubota Shinji , Kanehara Masaaki , Kamijo Nobuhiko , Ishikawa Ryuji , Tasaki Hiroyuki , Kanehara Minako , Liu Bin , Chen Minghui , Nakamura Shin-ichi , Udatsu Tetsuro , Wang Cailin 
Published: July 2020

AbstractTo understand rice types that were utilized during postdomestication and in the modern age and the potential of genetic research in aged rice materials, archaeogenetic analysis was conducted for two populations of archaic rice grains from the Mojiaoshan site during the Liangzhu Period in China (2940 to 2840 BC). Sequencing after the PCR amplification of three regions of the chloroplast genome and one region of the nuclear genome showed recovery rates that were comparable to those in previous studies except for one chloroplast genome region, suggesting that the materials used in this work were appropriate for recovering genetic information related to domestication traits by using advanced technology. Classification after sequencing in these regions proved the existence ofJaponicaandIndicachloroplasts in archaic grains from the west trench, which were subsequently classified into eight plastid groups (type I–VIII), and indicated that these rice grains derived from different maternal lineages were stored together in storage houses at the Mojiaohsan site. Among these plastid groups, type V exhibited the same sequences as two modernIndicaaccessions that are utilized in basic studies and rice breeding. It was inferred that part of the chloroplast genome of archaic rice has been preserved in modern genetic resources in these two modernIndicaaccessions, and the results indicated that rice related to their maternal ancestor was present at the Mojiaoshan site during the Liangzhu Period in China. The usefulness of archaeogenetic analysis can be demonstrated by our research data as well as previous studies, providing encouragement for the possibility that archaeogenetic analysis can be applied to older rice materials that were utilized in the rice-domesticated period.Graphical abstract
18F-fluciclovine (Axumin) PET/CT detecting occult bone metastasis
Authors: Nepal Pankaj , Rodrigue Paul , Olsavsky Thomas 
Published: July 2020

Abstract
Background
18F-fluciclovine (Axumin) positron emission tomography (PET) is a novel agent for detection of biochemical recurrence of the prostate cancer. In this article, we present an interesting case of prostate cancer recurrence with bone metastasis not visualized with conventional CT, but detected with Axumin PET/CT. This case report will help reader to understand shortcomings of conventional modalities (CT/MRI/bone scan) in evaluation of biochemical recurrence of prostate cancer.

Case presentation
We report a case of 73-year-old male previously diagnosed with adenocarcinoma of prostate, status post-radiation treatment with excellent response to therapy. He presented with progressively increasing right groin pain and rising PSA level indicating biochemical recurrence. A bony metastasis to right inferior pubic ramus was diagnosed with Axumin PET/CT, not detected with conventional CT. He underwent local radiation treatment with excellent response to therapy.

Conclusion
18F-fluciclovine (Axumin) PET/CT is the most sensitive tool in detection of biochemical recurrence of prostate cancer. CT and MRI may not detect early cases of tumor recurrence which affects disease prognosis and patient management.
Arterial stiffness can occur early in mild-to-moderate chronic obstructive pulmonary disease
Authors: Mansour Waleed , El-Shabrawy Mohamed , Khalil Wael A. , Eldamanhory Ahmad S. , Embarak Sameh 
Published: July 2020

Abstract
Background
Chronic obstructive pulmonary disease (COPD) is a well-known respiratory system disorder impacting patient’s morbidity and mortality. Many COPD patients die from cardiovascular diseases. Criteria of arterial stiffness might be the early clue for cardiovascular affection in COPD patients. This study aimed to evaluate the occurrence of arterial stiffness as an early subclinical change in stable mild to moderate COPD patients.

Results
This cross-sectional study included 80 mild-to-moderate COPD patients and another 80 healthy controls. The carotid-femoral pulse wave velocity (cf-PWV) and the heart rate adjusted augmentation index (AIx75) were statistically significantly higher (13.8 ± 2.6 and 23.9 ± 10.8, respectively) among studied mild-to-moderate COPD patients when compared to healthy controls (10.7 ± 1.1 and 18.1 ± 8.9, respectively) (p < 0.001). FEV1 (forced expiratory volume in 1 s) % of predicted correlated negatively with both AIx75 (r = − 0.84, p < 0.001) and cf-PWV (r = − 0.85, p < 0.001), while BODE (body mass index, airflow obstruction, dyspnea, and exercise capacity) index correlated positively with both AIx75 (r = 0.58, p < 0.001) and cf-PWV (r = 0.52, p < 0.001) in patients with mild-to-moderate COPD.

Conclusions
Pulse wave velocity and augmentation index correlated with FEV1% of predicted and BODE index in patients with mild-to-moderate COPD.
Generative Adversarial Domain Adaptation for Nucleus Quantification in Images of Tissue Immunohistochemically Stained for Ki-67
Authors: Zhang Xuhong , Cornish Toby C. , Yang Lin , Bennett Tellen D. , Ghosh Debashis , Xing Fuyong 
Published: July 2020

PURPOSE We focus on the problem of scarcity of annotated training data for nucleus recognition in Ki-67 immunohistochemistry (IHC)–stained pancreatic neuroendocrine tumor (NET) images. We hypothesize that deep learning–based domain adaptation is helpful for nucleus recognition when image annotations are unavailable in target data sets. METHODS We considered 2 different institutional pancreatic NET data sets: one (ie, source) containing 38 cases with 114 annotated images and the other (ie, target) containing 72 cases with 20 annotated images. The gold standards were manually annotated by 1 pathologist. We developed a novel deep learning–based domain adaptation framework to count different types of nuclei (ie, immunopositive tumor, immunonegative tumor, nontumor nuclei). We compared the proposed method with several recent fully supervised deep learning models, such as fully convolutional network-8s (FCN-8s), U-Net, fully convolutional regression network (FCRN) A, FCRNB, and fully residual convolutional network (FRCN). We also evaluated the proposed method by learning with a mixture of converted source images and real target annotations. RESULTS Our method achieved an F1 score of 81.3% and 62.3% for nucleus detection and classification in the target data set, respectively. Our method outperformed FCN-8s (53.6% and 43.6% for nucleus detection and classification, respectively), U-Net (61.1% and 47.6%), FCRNA (63.4% and 55.8%), and FCRNB (68.2% and 60.6%) in terms of F1 score and was competitive with FRCN (81.7% and 70.7%). In addition, learning with a mixture of converted source images and only a small set of real target labels could further boost the performance. CONCLUSION This study demonstrates that deep learning–based domain adaptation is helpful for nucleus recognition in Ki-67 IHC stained images when target data annotations are not available. It would improve the applicability of deep learning models designed for downstream supervised learning tasks on different data sets.
Bortezomib, Melphalan, and Dexamethasone for Light-Chain Amyloidosis
Authors: Kastritis Efstathios , Leleu Xavier , Arnulf Bertrand , Zamagni Elena , Cibeira María Teresa , Kwok Fiona , Mollee Peter , Hájek Roman , Moreau Philippe , Jaccard Arnaud , Schönland Stefan O. , Filshie Robin , Nicolas-Virelizier Emmanuelle , Augustson Bradley , Mateos María-Victoria , Wechalekar Ashutosh , Hachulla Eric , Milani Paolo , Dimopoulos Meletios A. , Fermand Jean-Paul , Foli Andrea , Gavriatopoulou Maria , Klersy Catherine , Palumbo Antonio , Sonneveld Pieter , Johnsen Hans Erik , Merlini Giampaolo , Palladini Giovanni 
Published: July 2020

PURPOSE Oral melphalan and dexamethasone (MDex) were considered a standard of care in light-chain (AL) amyloidosis. In the past decade, bortezomib has been increasingly used in combination with alkylating agents and dexamethasone. We prospectively compared the efficacy and safety of MDex and MDex with the addition of bortezomib (BMDex). METHODS This was a phase III, multicenter, randomized, open-label trial. Patients were stratified according to cardiac stage. Patients with advanced cardiac stage (stage IIIb) amyloidosis were not eligible. The primary end point was hematologic response rate at 3 months. This trial is registered with ClinicalTrials.gov identifier NCT01277016 . RESULTS A total of 109 patients, 53 in the BMDex and 56 in the MDex group, received ≥ 1 dose of therapy (from January 2011 to February 2016). Hematologic response rate at 3 months was higher in the BMDex arm (79% v 52%; P = .002). Higher rates of very good partial or complete response rates (64% v 39%; hazard ratio [HR], 2.47; 95% CI, 1.30 to 4.71) and improved overall survival, with a 2-fold decrease in mortality rate (HR, 0.50; 95% CI, 0.27 to 0.90), were observed in the BMDex arm. Grade 3 and 4 adverse events (the most common being cytopenia, peripheral neuropathy, and heart failure) were more common in the BMDex arm, occurring in 20% versus 10% of cycles performed. CONCLUSION BMDex improved hematologic response rate and overall survival. To our knowledge, this is the first time a controlled study has demonstrated a survival advantage in AL amyloidosis. BMDex should be considered a new standard of care for AL amyloidosis.
Optimizing Behavioral Sleep Strategies
Authors: Ong Jason C. , Gamaldo Charlene 
Published: July 2020

ABSTRACT
Patients are increasingly looking to optimize sleep as a health and wellness strategy. Sleep health is often individualized based on three elements that correspond to overall physical and mental well-being: (1) sleep quality, which refers to the continuity and depth of sleep as well as a feeling of restoration upon awakening; (2) sleep quantity, which refers to the duration of sleep that is appropriate for a given age group; and (3) timing of the sleep window, which refers to the positioning of sleep that is aligned with an individual’s circadian rhythm for sleep or an ideal circadian zone. In the past, prescribing hypnotic medications was considered the primary approach for improving sleep. However, there has been a recent paradigm shift to favor behavioral approaches, particularly in the case of insomnia where cognitive-behavioral therapy has been shown to have a more favorable benefit-to-harm profile than medications. The clinical vignette is presented here as a springboard for discussion regarding the latest evidence and efficacy for sleep behavior techniques and consumer monitoring devices developed to improve sleep health and awareness for clinicians to consider when educating their patients on maximizing sleep health behaviors.
Parasomnias Occurring in Non–Rapid Eye Movement Sleep
Authors: Silber Michael H. 
Published: July 2020

ABSTRACT

PURPOSE OF REVIEW
This article discusses the clinical manifestations, diagnosis and differential diagnosis, pathophysiology, and management of parasomnias occurring in non–rapid eye movement (REM) sleep.

RECENT FINDINGS
Disorders of arousal are characterized by dissociated sleep, with wake and sleep phenomena intermingling, and local sleep, in which different areas of the brain exist simultaneously in different states of wakefulness or sleep. The frequency of arousals from slow-wave sleep with delta or mixed-frequency activity has a high sensitivity but relatively low specificity for the diagnosis of arousal parasomnias.

SUMMARY
Disorders of arousal (sleepwalking, sleep terrors, and confusional arousals) are characterized by incomplete awakenings from slow-wave sleep, limited recall of imagery, and partial or complete amnesia. They occur most frequently in childhood. Management includes correction of precipitating factors, attention to safety, behavioral techniques, and medications. Sleep-related eating disorder is a variant of arousal disorders and may be associated with the use of short-acting hypnotics and restless legs syndrome. Complex nocturnal visual hallucinations can occur with visual loss, dementia with Lewy bodies, use of β-adrenergic receptor antagonists, and anxiety. Exploding head syndrome occurs at wake-sleep transition or on waking during the night, is usually benign, and requires treatment only if significant sleep disruption occurs.
Insomnia
Authors: Perez Maria Nichole , Salas Rachel Marie E. 
Published: July 2020

ABSTRACT

PURPOSE OF REVIEW
This article provides updated information regarding the diagnosis and treatment of chronic insomnia disorder. In addition to discussing the latest recommendations regarding pharmacotherapeutic options for insomnia, this article also discusses the increased use of nonpharmacologic treatment approaches, including cognitive-behavioral therapy intervention, integrative medicine, mindfulness and meditation, and other therapeutic options in clinical practice.

RECENT FINDINGS
Insomnia is one of the most common sleep disorders in patients with other neurologic disorders. The definition and criteria for insomnia were updated with the release of the International Classification of Sleep Disorders, Third Edition. The American Academy of Sleep Medicine has updated clinical practice guidelines for the pharmacologic treatment of chronic insomnia in adults. New diagnostic and therapeutic options (eg, pharmacologic and behavioral therapies, at-home devices) have emerged to optimize and personalize the evaluation and management of sleep disorders such as insomnia. Although some of these devices and treatment options are still in the early stages of development, several are currently in clinical trials or will soon be available.

SUMMARY
This article emphasizes complexities related to the evaluation and management of patients with chronic insomnia disorder and describes alternative therapeutic options for patients with this common sleep disorder.
Central Disorders of Hypersomnolence
Authors: Trotti Lynn Marie 
Published: July 2020

ABSTRACT

PURPOSE OF REVIEW
This article discusses the central disorders of hypersomnolence, a group of disorders resulting in pathologic daytime sleepiness, particularly narcolepsy type 1 and narcolepsy type 2, idiopathic hypersomnia, and Kleine-Levin syndrome. Disease features, diagnostic testing, epidemiology, pathophysiology, and treatment are reviewed.

RECENT FINDINGS
Increasing evidence implicates autoimmunity in narcolepsy type 1, including a strong association with human leukocyte antigen–DQB1*06:02, association with a polymorphism in the T-cell receptor alpha locus in genome-wide association, and the identification of autoreactive T cells in patients with this type of narcolepsy. In contrast, the cause or causes of narcolepsy type 2 and idiopathic hypersomnia are unknown. Multiple treatment options exist, including two medications approved for the treatment of narcolepsy by the US Food and Drug Administration (FDA) in 2019. These include solriamfetol, a dopamine- and norepinephrine-reuptake inhibitor, and pitolisant, an H3-inverse agonist/antagonist that increases histaminergic neurotransmission.

SUMMARY
The central disorders of hypersomnolence all cause severe sleepiness but can be differentiated based on ancillary symptoms, diagnostic testing, and pathophysiology. It is important that these disorders are identified because multiple treatments are available to improve functioning and quality of life.
Circadian Rhythm Sleep-Wake Disorders
Authors: Zee Phyllis C. , Abbott Sabra M. 
Published: July 2020

ABSTRACT

PURPOSE OF REVIEW
This article provides an overview of circadian physiology and discusses common presentations and treatment strategies for the circadian rhythm sleep-wake disorders.

RECENT FINDINGS
Circadian rhythms are present throughout the body, and appreciation for the role that circadian dysregulation plays in overall health is increasing, with mounting associations between circadian disruption and cardiometabolic disease risk.

SUMMARY
It is important to recognize the ubiquitous role that circadian rhythms play throughout the brain and body. An understanding of circadian neurophysiology will provide insight into the means by which patients with a variety of neuropathologies at the level of the retina, optic nerve, or hypothalamus may also be at risk for circadian dysfunction.
Obstructive Sleep Apnea
Authors: Kirsch Douglas B. 
Published: July 2020

ABSTRACT

PURPOSE OF REVIEW
Obstructive sleep apnea (OSA) is often overlooked by clinicians; however, undiagnosed OSA can lead to negative outcomes for patients, including patients with underlying neurologic conditions. Clinicians should be aware of what questions to ask, what diagnostic tests to use, and what treatments to consider in patients with OSA.

RECENT FINDINGS
OSA influences many neurologic conditions, including stroke, epilepsy, headache, and neuromuscular conditions. Treatment of OSA is effective, especially with patient-tailored options, the correct education, and support.

SUMMARY
OSA is a serious medical condition with impacts on patients’ health, safety, and quality of life. Clinicians should identify patients at high risk for OSA and arrange for appropriate diagnosis and treatment, which, in turn, may lead to the improvement of or reduction in risk for neurologic and other health conditions.
Imaging of COVID-19 pneumonia in children
Authors: Palabiyik Figen , Kokurcan Suna Ors , Hatipoglu Nevin , Cebeci Sinem Oral , Inci Ercan 
Published: July 2020

Objective:
Literature related to the imaging of COVID-19 pneumonia, its findings and contribution to diagnosis and its differences from adults are limited in pediatric patients. The aim of this study was to evaluate chest X-ray and chest CT findings in children with COVID-19 pneumonia.

Methods:
Chest X-ray findings of 59 pediatric patients and chest CT findings of 22 patients with a confirmed diagnosis of COVID-19 pneumonia were evaluated retrospectively.

Results:
COVID-19 pneumonia was most commonly observed unilaterally and in lower zones of lungs in chest X-ray examinations. Bilateral and multifocal involvement (55%) was the most observed involvement in the CT examinations, as well as, single lesion and single lobe (27%) involvement were also detected. Pure ground-glass appearance was observed in 41%, ground-glass appearance and consolidation together was in 36%. While peripheral and central co-distribution of the lesions (55%) were frequently observed, the involvement of the lower lobes (69%) was significant. In four cases,the coexistence of multiple rounded multifocal ground-glass appearance and rounded consolidation were observed.

Conclusion:
COVID-19 pneumonia imaging findings may differ in the pediatric population from adults. In diagnosis, chest X-ray should be preferred, CT should be requested if there is a pathologic finding on radiography that merits further evaluation and if clinically indicated.

Advances in knowledge:
Radiological findings of COVID-19 observed in children may differ from adults. Chest X-ray should often be sufficient in children avoiding additional irradiation, chest CT needs only be done in cases of clinical necessity.
The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction
Authors: Cohen Irun R. , Marron Assaf 
Published: July 2020

The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems:energy,entropy, andinteraction.Energyfrom the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements.Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not.Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosterssurvival-of-the-fitted– those entities that resist entropic destruction – and not only of the fittest – the entities with the greatest reproductive success. The “unit” of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are “fit enough”. We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.