bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glucocorticoid treatment of suspected organizing pneumonia after H7N9 infection
Authors: Liu Huijiao , Li Jianwei , Chen Miaolian , Su Jiahao 
Published: August 2019

Abstract

Rationale:
H7N9 infection causes acute respiratory distress syndrome with high mortality. The use of glucocorticoids in the acute phase lessened inflammatory responses. Some case reports suggested that secondary organizing pneumonia (SOP) could occur at the recovery stage of the influenza virus infection, and the treatment with glucocorticoid was effective. However, the reports of organizing pneumonia after H7N9 infection are lacking. This study reported a patient with H7N9 virus infection who presented a suspected SOP during the recovery stage.

Patient concern:
A 68-year-old woman who was diagnosed with H7N9 viral pneumonia. After standard antiviral treatment, venous-venous extracorporeal membranous oxygenation (VV-ECMO) and other supportive treatment, the antigen in the alveolar lavage fluid turned negative, and the shadow in the lung was partially absorbed. However, the imaging manifestations were deteriorated at 3 weeks after disease onset, presented as exudation and consolidation shadow distributed under the pleura and along the bronchial vascular bundles. The oxygenation could not be improved. Repeated sputum, alveolar lavage fluid, and blood pathogen examinations showed negative results. Broad-spectrum anti-infective treatment was ineffective. However, the autoantibodies (ANA, anti-SSA/Ro60, anti-SSA/Ro52) were detected.

Diagnosis:
SOP was considered.

Interventions:
Glucocorticoid treatment begun at week 4 from the disease onset. The regimen was methylprednisolone at an initial dose of 40 mg twice a day for 1 week, tapering within 70 days until total withdrawal.

Outcomes:
The oxygenation was rapidly improved after initiation of methylprednisolone. The shadow in the lung gradually resolved, and the patient was discharged after improvement of the disease condition. The clinical disease course, imaging findings, and treatment effects in the previous cases of SOP after influenza virus infection were similar to those in this case, suggesting the occurrence of SOP after H7N9 virus infection.

Lessons:
Organizing pneumonia might occur during the recovery stage of influenza virus infection. When the clinical symptoms do not improve and the shadow in the lung shows no obvious absorption after elimination of the H7N9 influenza virus, or the clinical symptoms are aggravated again after improvement, the probability of transforming into the organizing pneumonia should be taken into consideration.
Hyperandrogenism in a girl with Turner syndrome
Authors: Diao Yuchao , Zheng Qingmei , Chen Zhihong , Dai Shuzhen , Yao Qin 
Published: August 2019

Abstract

Rationale:
The gonads of patients with Turner syndrome (TS) were previously thought to be funicular. There was no increase in androgen level. The gonad that is testis should be taken into account when the patient's serum testosterone level was abnormal and hypothalamic-pituitary-adrenal disease was excepted.

Patient concerns:
A 16-year-old girl was admitted to our hospital because of chromosomal abnormalities and elevated androgen levels.

Diagnosis:
Turner syndrome could be diagnosed since her chromosome karyotype was 45, XO.

Interventions:
The patient was given bilateral gonadectomy and hormone replacement therapies.

Outcome:
The level of the patient's serum testosterone was <0.45 nmol/L 2 days after the operation. Postoperative pathology showed that her right gonad was testicular tissue. The patient's menstruation was normal after the treatment of hormone replacement therapy.

Lessons:
All TS patients should get Y chromosome material screening. Gonadectomy could be done for Turner syndrome patients who have hyperandrogenism or Y chromosome material.
Intermittent alien hand syndrome caused by Marchiafava–Bignami disease
Authors: Shao Jie , Bai Rongrong , Duan Guangyu , Guan Yujia , Cui Li , Deng Hui 
Published: August 2019

Abstract

Rationale:
Alien Hand syndrome (AHS) is characterized in most patients by seemingly purposeful, involuntary movements of the extremities. It is not well known among physicians on account of its diverse clinical manifestations.

Patient concerns:
We present a 57-year-old Chinese man who could not stop or turn himself around as he involuntarily and uncontrollably walked forward, which had happened frequently in the month prior to treatment. He had been a heavy drinker for thirty years before the onset of the disease, with an alcohol intake of 600 to 800 ml/day.

Diagnoses:
History of alcohol intake and the brain magnetic resonance imaging findings indicated a diagnosis of Marchiafava–Bignami disease. The patient was additionally diagnosed with Alien Hand Syndrome according to his clinical symptoms.

Interventions:
The patient was treated with high doses of vitamin B for 1 month.

Outcomes:
The patient's abnormal behaviors never appeared during the treatment, and no instance of recurrence was observed during the 6 months of follow-up.

Lessons:
The clinical manifestation of AHS is non-specific. Only by considering its diverse manifestation can doctors better understand the disease and achieve early intervention.
Lateral ventriculo-peritoneal shunt treating delayed cerebrospinal fluid leak after cervical laminoplasty
Authors: Gao Wenshan , Ren Bao , Wang Xiaodong , Zhou Xiaozhe , Han Ye , An Jilong 
Published: August 2019

Abstract

Rationale:
Delayed cerebrospinal fluid (CSF) leak is a rare and terrible complication after cervical surgery, potentially causing morbidity or even threatening life.

Patient concerns:
A 55-year-old Chinese male, with a history of hypertension for 8 years, complained of numbness and weakness of both upper limbs for 10 years. Strength of right upper limb triceps and wrist extensor muscle was slight weakness. Bilateral Hoffman sign was positive. Cervical magnetic resonance imaging (MRI) indicated multilevel cervical spondylotic myelopathy. We performed cervical laminoplasty for that patient on August 23, 2018. Nevertheless, he abruptly complained of dizziness and vision, but the wound condition was good. Cervical MRI showed delayed cerebrospinal fluid leak on October 15, 2018.

Diagnoses:
He was diagnosed with delayed CSF leak after cervical laminoplasty.

Interventions:
We performed lateral ventriculo-peritoneal shunt (LVPS) for that patient on October 17, 2018.

Outcomes:
At 3-month follow-up, the treatment has a good outcome and there is no recurrence of clinical symptoms.

Lessons:
Delayed CSF leak after cervical laminoplasty is rare. Once diagnosed, surgery is needed as soon as possible. LVPS has been proven an effective treatment for this server disease.
Imaging findings of IgG4-related kidney disease without extrarenal organ involvement
Authors: Zhang ShuiXia , Yang Qian 
Published: August 2019

Abstract

Rationale:
IgG4-related disease (IgG4-RD) is a systemic chronic inflammatory disorder that can affect almost every organ. IgG4-RD includes IgG4-related kidney disease (IgG4-RKD), but lesions affecting the kidney alone or first are very rare, and a complete understanding is lacking. Computed tomography (CT) and magnetic resonance imaging (MRI) findings can show the typical characteristics of IgG4-RKD and provide information for accurate and rapid diagnosis.

Patient concerns:
We report a case of a 60-year-old woman who was admitted to our hospital for dizziness and instability while walking, her bilateral eyelids were also slightly swollen. She had no medical history.

Diagnoses:
CT and MRI images of the patient revealed multiple local and diffuse patchy lesions in the bilateral renal parenchyma and mass-like tissue in the bilateral renal pelvis, accompanied by right hydronephrosis. A pathological examination of renal samples showed numerous lymphocyte and plasma cell infiltration. Immunohistochemistry demonstrated approximately 50% of the IgG-positive plasma cells to be IgG4+. The serum IgG level was obviously elevated, with both C3and C4 levels were reduced. The patient was diagnosed with IgG4-RKD.

Interventions:
The patient received corticosteroid therapy at another hospital.

Outcomes:
The bilateral kidney lesions were smaller on follow-up CT images.

Lessons:
IgG4-RKD exhibits some characteristic imaging features. Despite the relatively low incidence of IgG4-RKD, it should be included in differential diagnoses when images show multiple lesions in kidneys with mild and delayed enhancement and hypointensity on T2WI in middle-aged to elderly patients
Challenges and Strategies for Conducting Research With Grandparent–Grandchild Dyads
Authors: Song MinKyoung , Bonds Kalisha 
Published: August 2019

Background
Given a marked increase in the number of grandparents who play a caregiving role for their grandchildren, there is a parallel urgency for more research involving grandparent–grandchild dyads.

Objective
The aim of this study was to describe methodological challenges we encountered when conducting grandparent–grandchild dyadic research, some of which were challenges specific to working with dyads where the grandparents were caregivers to the child participants and others, which were challenges of a sort that might be encountered in any research involving data collection with multigenerational family units and, in particular, multigenerational family units including older adults.

Methods
During and after an observational study conducted by the researchers involving grandparent–grandchild dyads, we explored challenges we encountered and strategies for improving our research outcomes.

Results
We found several challenges specific to grandparent–grandchild dyads, including complications with reaching legal guardians to obtain permission for child participants; collecting accelerometer data from grandchildren was difficult, particularly if the grandparents did not live with their grandchildren; and participants who had various preferences for data collection methods. We also found challenges that might be found with any family context dyadic research, particularly involving older adults and across multiple generations, including relatively low follow-up response rates from those grandparents who initially expressed interest and a need for an extended data collection period. We employed targeted strategies to overcome those obstacles, and in this article, we describe the outcomes of those strategies.

Discussion
Recommendations from our results include the following: (a) find a way to involve the parents and/or legal guardian as early as possible, (b) have multiple team members involved in recruitment/data collection, (c) be flexible about data collection methods, (d) use flexible scheduling, and (e) use multiple simultaneous recruitment activities/multiple advertisement channels. Additional strategies include enhancing children’s sense of control during the consent process, simplifying study procedures, considering usability when creating online data surveys, and identifying power dynamics within the families.

Conclusion
The insights we gained will be useful for informing future family context dyadic research, in particular, research involving grandparent–grandchild dyads.
Cell death during complete metamorphosis
Authors: Tettamanti Gianluca , Casartelli Morena 
Published: August 2019

In insects that undergo complete metamorphosis, cell death is essential for reshaping or removing larval tissues and organs, thus contributing to formation of the adult's body structure. In the last few decades, the study of metamorphosis in Lepidoptera and Diptera has provided broad information on the tissue remodelling processes that occur during larva–pupa–adult transition and made it possible to unravel the underlying regulatory pathways. This review summarizes recent knowledge on cell death mechanisms in Lepidoptera and other holometabolous insects, highlighting similarities and differences withDrosophila melanogaster, and discusses the role of apoptosis and autophagy in this developmental setting.This article is part of the theme issue ‘The evolution of complete metamorphosis'.
Leveraging multiple data types to estimate the true size of the Zika epidemic in the Americas
Authors: Moore Sean M. , Oidtman Rachel J. , Soda K. James , Siraj Amir S. , Reiner Robert C. , Barker Christopher M. , Perkins T. Alex 
Published: August 2019

AbstractSince the first Zika virus (ZIKV) infection was confirmed in Brazil in May 2015, several hundred thousand cases have been reported across the Americas. This figure gives an incomplete picture of the epidemic, however, given that asymptomatic infections, imperfect surveillance, and variability in reporting rates imply that the incidence of infection was likely much higher. The infection attack rate (IAR)—defined as the proportion of the population that was infected over the course of the epidemic—has important implications for the longer-term epidemiology of Zika in the region, such as the timing, location, and likelihood of future outbreaks. To estimate the IAR and the total number of people infected, we leveraged multiple types of Zika case data from 15 countries and territories where subnational data were publicly available. Datasets included confirmed and suspected Zika cases in pregnant women and in the total population, Zika-associated Guillan-Barré syndrome cases, and cases of congenital Zika syndrome. We used a hierarchical Bayesian model with empirically-informed priors that leveraged the different case report types to simultaneously estimate national and subnational reporting rates, the fraction of symptomatic infections, and subnational IARs. In these 15 countries and territories, estimates of Zika IAR ranged from 0.084 (95% CrI: 0.067 − 0.096) in Peru to 0.361 (95% CrI: 0.214 − 0.514) in Ecuador, with significant subnational variability in IAR for every country. Totaling these infection estimates across these and 33 other countries and territories in the region, our results suggest that 132.3 million (95% CrI: 111.3-170.2 million) people in the Americas have been infected by ZIKV since 2015. These estimates represent the most extensive attempt to date to determine the size of the Zika epidemic in the Americas, and they offer an important baseline for assessing the risk of future Zika epidemics in this region.
Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics
Authors: Jiao Wen-Biao , Schneeberger Korbinian 
Published: August 2019

AbstractWe report chromosome-level, reference-quality assemblies of sevenArabidopsis thalianaaccessions selected across the global range of this predominately ruderal plant. Each genome revealed between 13-17 Mb rearranged and 5-6 Mb novel sequence introducing copy-number changes in ∼5,000 genes, including ∼1,900 genes which are not part of the current reference annotation. Analyzing the collinearity between the genomes revealed ∼350 regions (4.1% of the euchromatin) where accession-specific tandem duplications destroyed the syntenic gene order between the genomes. Thesehotspots of rearrangementswere characterized by the loss of meiotic recombination in hybrids within these regions and the enrichment of genes implicated in biotic stress response. Together this suggests that hotspots of rearrangements are governed by altered evolutionary dynamics as compared to the rest of the genome, which are based on new mutations and not on the recombination of existing variation, and thereby enable a quick response to the ever-evolving challenges of biotic stress.
Cytoplasmic mRNA decay factors modulate RNA polymerase II processivity in 5’ and 3’ gene regions in yeast
Authors: Fischer Jonathan , Song Yun S. , Yosef Nir , di Iulio Julia , Churchman L. Stirling , Choder Mordechai 
Published: August 2019

AbstractmRNA levels are determined by the balance between mRNA synthesis and decay. Factors that mediate both processes, including the 5’ to 3’ exonuclease Xrn1, are responsible for the cross talk between the two processes in a manner that buffers steady-state mRNA levels. However, these proteins’ roles in transcription remain elusive and controversial. Applying NET-seq to yeast cells, we show that Xrn1 functions mainly as a transcriptional activator and that its disruption manifests via the reduction of RNA polymerase II (Pol II) occupancy downstream of transcription start sites. We combine our data and novel mathematical modeling of transcription to suggest that transcription initiation and elongation of targeted genes is modulated by Xrn1. Furthermore, Pol II occupancy markedly increases near cleavage and polyadenylation sites in xrn1Δ cells while its activity decreases, a characteristic feature of backtracked Pol II. We also provide indirect evidence that Xrn1 is involved in transcription termination downstream of polyadenylation sites. Two additional decay factors, Dhh1 and Lsm1, seem to function similarly to Xrn1 in transcription, perhaps as a complex, while the decay factors Ccr4 and Rpb4 also perturb transcription in other ways. Interestingly, DFs are capable of differentiating between SAGA- and TFIID-dominated promoters. These two classes of genes respond differently to XRN1 deletion in mRNA synthesis and differentially utilize mRNA decay pathways, raising the possibility that one distinction between the two types of genes lies in the mechanism(s) that balance these processes.
Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture
Authors: Zhu Yizhou , Suh Yousin 
Published: August 2019

AbstractThe resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here we report two 3C-derived methods, Tri-4C and Tri-HiC, which utilize mult-restriction enzyme digestions for ultrafine mapping of targeted and genome-wide chromatin interaction, respectively, at up to one hundred basepair resolution. Tri-4C identified CRE loop interaction networks and quantifatively revealed their alterations underlying dynamic gene control. Tri-HiC uncovered global fine-gage regulatory interaction networks, identifying > 20-fold more enhancer:promoter (E:P) loops than in situ HiC. In addition to vasly improved identification of subkilobase-sized E:P loops, Tri-HiC also uncovered interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically-associated domain (TAD) boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high resolution interactome maps required for characterizing fine-gage regulatory chromatin interactions in analysis of development, homeostasis and disease.
Investigating and Assessing the Dermoepidermal Junction with Multiphoton Microscopy and Deep Learning
Authors: Huttunen Mikko J. , Hristu Radu , Dumitru Adrian , Costache Mariana , Stanciu Stefan G. 
Published: August 2019

AbstractHistopathological image analysis performed by a trained expert is currently regarded as the gold-standard in the case of many pathologies, including cancers. However, such approaches are laborious, time consuming and contain a risk for bias or human error. There is thus a clear need for faster, less intrusive and more accurate diagnostic solutions, requiring also minimal human intervention. Multiphoton Microscopy (MPM) can alleviate some of the drawbacks specific to traditional histopathology by exploiting various endogenous optical signals to provide virtual biopsies that reflect the architecture and composition of tissues, both in-vivo or ex-vivo. Here we show that MPM imaging of the dermoepidermal junction (DEJ) in unstained tissues provides useful cues for a histopathologist to identify the onset of non-melanoma skin cancers. Furthermore, we show that MPM images collected on the DEJ, besides being easy to interpret by a trained specialist, can be automatically classified into healthy and dysplastic classes with high precision using a Deep Learning method and existing pre-trained Convolutional Neural Networks. Our results suggest that Deep Learning enhanced MPM for in-vivo skin cancer screening could facilitate timely diagnosis and intervention, enabling thus more optimal therapeutic approaches.
Beyond accuracy: Measures for assessing machine learning models, pitfalls and guidelines
Authors: Dinga Richard , Penninx Brenda W.J.H. , Veltman Dick J. , Schmaal Lianne , Marquand Andre F. 
Published: August 2019

AbstractPattern recognition predictive models have become an important tool for analysis of neuroimaging data and answering important questions from clinical and cognitive neuroscience. Regardless of the application, the most commonly used method to quantify model performance is to calculate prediction accuracy, i.e. the proportion of correctly classified samples. While simple and intuitive, other performance measures are often more appropriate with respect to many common goals of neuroimaging pattern recognition studies. In this paper, we will review alternative performance measures and focus on their interpretation and practical aspects of model evaluation. Specifically, we will focus on 4 families of performance measures: 1) categorical performance measures such as accuracy, 2) rank based performance measures such as the area under the curve, 3) probabilistic performance measures based on quadratic error such as Brier score, and 4) probabilistic performance measures based on information criteria such as logarithmic score. We will examine their statistical properties in various settings using simulated data and real neuroimaging data derived from public datasets. Results showed that accuracy had the worst performance with respect to statistical power, detecting model improvement, selecting informative features and reliability of results. Therefore in most cases, it should not be used to make statistical inference about model performance. Accuracy should also be avoided for evaluating utility of clinical models, because it does not take into account clinically relevant information, such as relative cost of false-positive and false-negative misclassification or calibration of probabilistic predictions. We recommend alternative evaluation criteria with respect to the goals of a specific machine learning model.
Multidimensional Data Organization and Random Access in Large-Scale DNA Storage Systems
Authors: Song Xin , Shah Shalin , Reif John 
Published: August 2019

AbstractWith impressive density and coding capacity, DNA offers a promising solution for building long-lasting data archival storage systems. In recent implementations, data retrieval such as random access typically relies on a large library of non-interacting PCR primers. While several algorithms automate the primer design process, the capacity and scalability of DNA-based storage systems are still fundamentally limited by the availability of experimentally validated orthogonal primers. In this work, we combine the nested and semi-nested PCR techniques to virtually enforce multidimensional data organization in large DNA storage systems. The strategy effectively pushes the limit of DNA storage capacity and reduces the number of primers needed for efficient random access from very large address space. Specifically, our design requires k * n unique primers to index nk data entries, where k specifies the number of dimensions and n indicates the number of data entries stored in each dimension. We strategically leverage forward/reverse primer pairs from the same or different address layers to virtually specify and maintain data retrievals in the form of rows, columns, tables, and blocks with respect to the original storage pool. This architecture enables various random-access patterns that could be tailored to preserve the underlying data structures and relations (e.g., files and folders) within the storage content. With just one or two rounds of PCR, specific data subsets or individual datum from the large multidimensional storage can be selectively enriched for simple extraction by gel electrophoresis or readout via sequencing.Abstract Figure