bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serial analysis of cytokine and chemokine profiles and viral load in severe fever with thrombocytopenia syndrome
Authors: Fujikawa Keita , Koga Tomohiro , Honda Takahide , Uchida Toshihisa , Okamoto Momoko , Endo Yushiro , Mihara Tomo , Kondo Akira , Shimada Satoshi , Hayasaka Daisuke , Morita Kouichi , Mizokami Akinari , Kawakami Atsushi 
Published: October 2019

Abstract

Rationale:
Severe fever with thrombocytopenia syndrome (SFTS) is a recently recognized fatal infectious disease caused by the SFTS virus, and severe cases are complicated by the presence of hemophagocytic lymphohistiocytosis (HLH) associated with a cytokine storm. Herein, we report on serial changes of serum cytokine levels and viral load in a severe case of SFTS.

Patient concerns:
A 63-year-old Japanese woman presented with high-grade fever, abdominal pain, diarrhea, impaired consciousness, leukocytopenia, and thrombocytopenia.

Diagnosis:
SFTS was diagnosed based on a positive serum test for SFTS virus RNA and electroencephalogram (EEG) findings of encephalopathy.

Interventions:
The patient was treated with supportive therapy, including steroid pulse therapy (intravenous methylprednisolone 1 g/d for 3 days) for HLH and intravenous recombinant thrombomodulin 19200 U/d for 7 days for disseminated intravascular coagulation.

Outcomes:
Treatment for 7 days improved both symptoms and abnormal EEG findings, and SFTS virus RNA disappeared from the serum at day 10 from the onset of symptoms. The serum cytokines and chemokines analysis during the clinical course revealed 2 distinct phases: the acute phase and the recovery phase. The cytokines and chemokines elevated in the acute phase included interleukin (IL)-6, IL-10, interferon (IFN)-α2, IFN-γ, tumor necrosis factor-α, interferon-γ-induced protein-10, and fractalkine, while the IL-1β, IL-12p40, IL-17, and vascular endothelial growth factor levels were higher in the recovery phase.

Conclusion:
These observations suggest that the cytokines and chemokines elevated in the acute phase may reflect the disease severity resulted in a cytokine storm, while those in the recovery phase may be attributed to T-cell activation and differentiation.
The association of body composition with the risk of gestational diabetes mellitus in Chinese pregnant women
Authors: Wang Yan , Luo Bi-Ru 
Published: October 2019

Abstract
Studies have found that the measurement of body composition can be used to identify the gestational diabetes mellitus (GDM) risk in pregnant women. However, few studies focused on the relationship between body composition and GDM development in low GDM risk population. Thus, the objective of this study was to examine the association between body composition and the development of GDM in pregnant women with low risk of gestational diabetes.
A retrospective case-control study was conducted. We reviewed the medical records of 3965 pregnant women who had body composition measurement from March, 2016 to May, 2018 in our hospital. Their sociodemographic, clinical data, and body composition information were collected from medical record. Multiple logistic regression analyses were used.
A total of 2698 subjects were eligible for the study. The mean age of the gravidas was 30.95 ± 4.01 years old. Of all gravidas, 462 had gestational diabetes. Percentage body fat was the strongest risk factor for gestational diabetes after adjusting pre-pregnancy body mass index (BMI) (odds ratio = 1.786, 95% confidence interval = 1.112–2.866, P = .02). The age and extracellular water/intracellular water ratio were independently associated with gestational diabetes.
Percentage body fat was the strongest risk factor for gestational diabetes after adjusting pre-pregnancy BMI. Assessment of body composition may provide important guidance to identify gestational diabetes in pregnant women with low gestational diabetes risk.
Endometrial carcinoma complicated by malignant pericardial effusion
Authors: Liu Guang , Zhang Qianqian , Li Ze , Chen Xiaojun , Zhang Ning , Zhang Jinli 
Published: October 2019

Abstract

Rationale:
High-stage endometrial carcinoma is an aggressive tumor with a high propensity for distant spread. However, metastases to the pericardium are rare in gynecological cancer, and are usually fatal.

Patient concerns:
A 69-year-old woman was diagnosed with endometrial carcinoma with pericardium metastasis. The symptoms at presentation were panic and shortness of breath.

Diagnoses:
The cytologic examination of pericardial fluid obtained by pericardiocentesis confirmed metastasis.

Interventions:
In addition to cisplatin instilled into the pericardial space, for systemic chemotherapy, we chose that gemcitabine and lobaplatin regimen be preferred.

Outcomes:
The patient has been participating in telephone follow-up for 8 months and has generally remained in a good condition.

Lessons:
Endometrial carcinoma can have pericardial metastases. When this happens, we recommend ultrasound-guided pericardial puncture and the pericardial injection of cisplatin, in combination with systemic chemotherapy that consists of gemcitabine and lobaplatin.
Efficacy and safety of tenofovir disoproxil fumarate in Chinese patients with chronic hepatitis B virus infection
Authors: Zheng Shuqin , Liu Longgen , Lu Jianchun , Zhang Xiujun , Shen Hongyu , Zhang Hongyu , Xue Yuan , Lin Lin 
Published: October 2019

Abstract
To date, a small number of studies concerning the effects and safety of tenofovir disoproxil fumarate (TDF) in Chinese individuals were conducted. In this study, we aimed to assess the antiviral effects and nephrotoxicity of TDF in Chinese patients with chronic hepatitis B virus (HBV) infection.
Patients with chronic HBV infection were prospectively recruited and TDF treatment was given for 96 weeks. HBV serologic markers, HBV DNA, creatinine and phosphorus were collected.
Fifty-seven treatment-naïve and 48 treatment-experienced patients were recruited. Irrespective of the prior treatment history, more than 95% of patients achieved virological response during 96 weeks treatment with TDF. Estimated glomerular filtration rate (eGFR) significantly declined in the first year of treatment in patients with chronic hepatitis B or younger age (<65 years old) (both P < .05), while that was not achieved in patients with liver cirrhosis or older age (≥65 years old) (both P > .05). For patients who were treatment-naïve or treated previously with adefovir dipivoxil, eGFR declined at the 48th week; however, eGFR was partially recovered at the 96th week. Furthermore, multivariable analysis showed that basal eGFR <90 mL/min/1.73 m2 (P = .001; odds ratio: 4.821; 95% confidence interval: 1.904–12.206) is the only independent risk factor for eGFR <90 mL/min/1.73 m2 at the 96th week.
TDF has potent antiviral effect in both treatment-naïve and treatment-experienced patients.
The peculiarities of Kawasaki disease at the extremes of age
Authors: Mărginean Cristina Oana , Meliţ Lorena Elena , Mărginean Maria Oana 
Published: October 2019

Abstract

Rationale:
Extremes of age is an important risk factor for the development of coronary arteries aneurysms (CAAs) associated to Kawasaki disease (KD) along with male gender, prolonged fever and a delay in diagnosis or treatment.

Patient concerns:
We report two cases of KD in the extremes of age, a 5-month-old male infant and a 9-year-old child in order to underline the features of this disorder outside the typical age range of 1 to 4 years. The 5-month-old male was admitted in our clinic for generalized polymorphous exanthema and fever for approximately 7 days. The laboratory test pointed out leukocytosis and increased inflammatory biomarkers. The 9-year-old male child was admitted in our clinic for fever and submandibular adenopathy. The onset was approximately 5 days before the admission with a sudden development of unilateral, painless, submandibular lymphadenopathy for which the ENT specialist recommended antibiotics and nonsteroid anti-inflammatory drugs. In the 2nd day of admission, he presented severe desquamation of hands and soles.

Diagnosis:
Both cases were diagnosed with KD. The echocardiography showed no cardiac impairment in the infant, while in the older patient it revealed mild dilation of the left coronary artery.

Interventions:
Both patients received intravenously immunoglobulin and pulsed methylprednisolone.

Outcomes:
The evolution was favorable in both cases, but in the infant, the C-reactive protein levels persisted mildly elevated for approximately 2 months after the diagnosis.

Lessons:
The peculiarities of KD in the extremes of age are related to a higher frequency of incomplete features and an increased incidence of coronary artery lesions resulting in a delay of the diagnosis, and subsequent poorer outcomes.
Circular RNA expression profile in peripheral whole blood of lung adenocarcinoma by high
Authors: Mu Yinyu , Xie Fuyi , Huang YunFei , Yang Dongdong , Xu Guodong , Wang Chunnian , Wu Qiaoping 
Published: October 2019

Abstract

Background:
Lung adenocarcinoma (LA) is a most common form of non-small cell lung cancer (NSCLC). To date, there are still no effective early diagnosis methods for patients to be cured in time. Noncoding RNA plays an important role in oncogenesis and tumor development. The expression profile of circular RNA (circRNA) in peripheral whole blood (PWB) of LA has not been systematically investigated. In this study, we identified the differentially expressed (DE) circRNAs in PWB of LA by high-throughput sequencing.

Methods:
Five paired LA and normal participants PWB samples were chosen to investigate the expression profile of circRNAs by high-throughput sequencing. Twenty LA and 10 normal controls PWB samples were subjected to reverse-transcription polymerase chain reaction (RT-PCR) for validation of circRNAs expression profile. Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and circRNA-miRNA network analysis was also performed to predict the function of circRNAs in PWB.

Results:
A total of 10566 circRNAs were identified and annotated, most of the circRNAs were exonic (78.14%). Statistical analysis revealed 4390 DE circRNAs, in which were 3009 upregulated circRNAs and1381downregulated circRNAs in LA. RT-PCR results showed that circRNA expression in LA was higher than that in controls. GO functional analysis, KEGG pathway analysis, and circRNA-miRNA network analysis all showed that circRNAs correlated with tumor development and progression to a certain degree. The current study is the first to systematically characterize and annotate circRNA expression in PWB of LA. Some host genes of the DE circRNAs were involved in tumor signaling pathway and had complicated correlations with tumor related miRNAs, indicating that circRNAs might involve in development and progression of LA.

Conclusions:
Our study revealed that circRNAs were abnormally expressed in PWB of LA, which might offer potential targets for the early diagnosis of the disease and new genetic insights into LA.
Outcomes of pathologically localized high-grade prostate cancer treated with radical prostatectomy
Authors: Heo Ji Eun , Park Jee Soo , Lee Jong Soo , Kim Jongchan , Jang Won Sik , Rha Koon Ho , Choi Young Deuk , Hong Sung Joon , Ham Won Sik 
Published: October 2019

Abstract
Adjuvant radiation therapy (ART) is recommended without consideration of radical prostatectomy Gleason score (RP GS) for cases with adverse features. We compared the outcomes of pathologically localized high-grade (GS 8–10) prostate cancer (PC) with those of pT3 GS 7 PC.
A total of 1585 men who underwent RP between 1995 and 2015 comprised the cohort, which was divided into group 1 (RP GS 7(3 + 4) and pT3; n = 760), group 2 (RP GS 7(4 + 3) and pT3; n = 565), and group 3 (RP GS 8–10 and pT2; n = 260). Biochemical recurrence (BCR), all-cause mortality (ACM), and PC-specific mortality (PCSM) risk were compared among groups using Cox regression and competing risk analysis.
At a median follow-up of 58 months (interquartile range: 37–85), 721 men experienced BCR and 84 died (22 due to PC). BCR-free survival rates were lower in group 3 than in group 1 (P < .001); nevertheless, no difference was observed between groups 2 and 3 (P = .638). Furthermore, no difference in ACM was noted among groups. PCSM rates were higher in group 3 than in groups 1 and 2 (P = .001 and P = .005, respectively). This association persisted in multivariate models after adjustment for clinicopathological variables.
Patients with RP GS 8–10 and pT2 PC had higher BCR and PCSM rates than those with RP GS 7 and pT3 PC. Localized high-grade PC should be considered in decision-making for ART.
Fall prevention initiative: A fall screening and intervention pilot study on the ambulatory setting
Authors: Kartiko Susan , Jeremitsky Elan , Cripps Michael W. , Konderwicz Ida , Jarosz Erin , Minshall Christian T. 
Published: October 2019

BACKGROUND
Falling is the most common cause of trauma in the geriatric population. To identify patients that were at-risk for falling, we implemented a provider-directed fall prevention screening initiative in the ambulatory setting of a large tertiary care referral center. We used three clinician-directed questions from the Stopping Elderly Accidents, Death and Injuries toolkit. Our goal was to intervene on patients who were screened as at-risk for falling by referring them to our physical therapy program and evaluating its effects to these patients.

METHODS
Patients 55 years or older who live in the community were screened from June 2017 to June 2018. Patients who answered yes to any of the three questions were identified as at-risk for falling, and referred to the Fall Prevention Initiative Physical Therapy Program (FPIPTP). The FPIPTP is a program that establishes a quantifiable fall risk using the Time Up and Go (TUG) test, which then initiates PT treatments, designed to prevent future falls by improving, gait, balance, and fitness. The Wilcoxon signed rank test was used to determine significance (p < 0.05).

RESULTS
We identified 112 patients with a median age of 76.5 years (IQR, 68–82 years) to be at-risk for falling. The initial median TUG score in this group of patients is 15.85 seconds (12–20.33 seconds), which is consistent with a high fall-risk (time >12 seconds). After completing the FPIPTP, the median TUG score significantly improved to 12 seconds (9–15 seconds, p < 0.0001).

CONCLUSION
We conclude that a provider can use the three specific questions from the Stopping Elderly Accidents, Death and Injuries toolkit to identify patients (≥55 years) that are at-risk for falling. Additionally, the FPIPTP is able to significantly improve the TUG score in this group. We will need to confirm this conclusion with a larger population study.

LEVEL OF EVIDENCE
Therapeutic, Level IV.
SMART: Statistical Mitogenome Assembly with Repeats
Authors: Alqahtani Fahad , Măndoiu Ion I. 
Published: October 2019

AbstractBy using next-generation sequencing technologies it is possible to quickly and inexpensively generate large numbers of relatively short reads from both the nuclear and mitochondrial DNA contained in a biological sample. Unfortunately, assembling such whole-genome sequencing (WGS) data with standard de novo assemblers often fails to generate high quality mitochondrial genome sequences due to the large difference in copy number (and hence sequencing depth) between the mitochondrial and nuclear genomes. Assembly of complete mitochondrial genome sequences is further complicated by the fact that many de novo assemblers are not designed for circular genomes, and by the presence of repeats in the mitochondrial genomes of some species.In this paper we describe the Statistical Mitogenome Assembly with Repeats (SMART) pipeline for automated assembly of complete circular mitochondrial genomes from WGS data. SMART uses an efficient coverage-based filter to first select a subset of reads enriched in mtDNA sequences. Contigs produced by an initial assembly step are filtered using BLAST searches against a comprehensive mitochondrial genome database, and used as “baits” for an alignment-based filter that produces the set of reads used in a second de novo assembly and scaffolding step. In the presence of repeats, the possible paths through the assembly graph are evaluated using a maximum-likelihood model. Additionally, the assembly process is repeated a user-specified number of times on re-sampled subsets of reads to select for annotation the reconstructed sequences with highest bootstrap support.Experiments on WGS datasets from a variety of species show that the SMART pipeline produces complete circular mitochondrial genome sequences with a higher success rate than current state-of-the art tools, even from low coverage WGS data. The pipeline is available through an easy-to-use web interface at https://neo.engr.uconn.edu/?tool_id=SMART.
Integrating healthcare and research genetic data empowers the discovery of 28 novel developmental disorders
Authors: Kaplanis Joanna , Samocha Kaitlin E. , Wiel Laurens , Zhang Zhancheng , Arvai Kevin J. , Eberhardt Ruth Y. , Gallone Giuseppe , Lelieveld Stefan H. , Martin Hilary C. , McRae Jeremy F. , Short Patrick J. , Torene Rebecca I. , de Boer Elke , Danecek Petr , Gardner Eugene J. , Huang Ni , Lord Jenny , Martincorena Iñigo , Pfundt Rolph , Reijnders Margot R. F. , Yeung Alison , Yntema Helger G. , Study DDD , Vissers Lisenka E. L. M. , Juusola Jane , Wright Caroline F. , Brunner Han G. , Firth Helen V. , FitzPatrick David R. , Barrett Jeffrey C. , Hurles Matthew E. , Gilissen Christian , Retterer Kyle 
Published: October 2019

SummaryDe novomutations (DNMs) in protein-coding genes are a well-established cause of developmental disorders (DD). However, known DD-associated genes only account for a minority of the observed excess of such DNMs. To identify novel DD-associated genes, we integrated healthcare and research exome sequences on 31,058 DD parent-offspring trios, and developed a simulation-based statistical test to identify gene-specific enrichments of DNMs. We identified 285 significantly DD-associated genes, including 28 not previously robustly associated with DDs. Despite detecting more DD-associated genes than in any previous study, much of the excess of DNMs of protein-coding genes remains unaccounted for. Modelling suggests that over 1,000 novel DD-associated genes await discovery, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of dominant DDs.
Pitch of Harmonic Complex Tones: Rate-Place Coding of Resolved Components in Harmonic and Inharmonic Complex Tones in Auditory Midbrain
Authors: Su Yaqing , Delgutte Bertrand 
Published: October 2019

AbstractHarmonic complex tones (HCT) commonly occurring in speech and music evoke a strong pitch at their fundamental frequency (F0), especially when they contain harmonics individually resolved by the cochlea. When all frequency components of an HCT are shifted by the same amount, the pitch of the resulting inharmonic tone (IHCT) also shifts although the envelope repetition rate is unchanged. A rate-place code whereby resolved harmonics are represented by local maxima in firing rates along the tonotopic axis has been characterized in the auditory nerve and primary auditory cortex, but little is known about intermediate processing stages. We recorded single neuron responses to HCT and IHCT with varying F0 and sound level in the inferior colliculus (IC) of unanesthetized rabbits. Many neurons showed peaks in firing rates when a low-numbered harmonic aligned with the neuron’s characteristic frequency, demonstrating “rate-place” coding. The IC rate-place code was most prevalent for F0>800 Hz, was only moderately dependent on sound level over a 40 dB range, and was not sensitive to stimulus harmonicity. A spectral receptive-field model incorporating broadband inhibition better predicted the neural responses than a purely excitatory model, suggesting an enhancement of the rate-place representation by inhibition. Some IC neurons showed facilitation in response to HCT, similar to cortical “harmonic template neurons” (Feng and Wang 2017), but to a lesser degree. Our findings shed light on the transformation of rate-place coding of resolved harmonics along the auditory pathway, and suggest a gradual emergence of harmonic templates from low to high processing centers.Significance statementHarmonic complex tones are ubiquitous in speech and music and produce strong pitch percepts in human listeners when they contain frequency components that are individually resolved by the cochlea. Here, we characterize a “rate-place” code for resolved harmonics in the auditory midbrain that is more robust across sound levels than the peripheral rate-place code and insensitive to the harmonic relationships among frequency components. We use a computational model to show that inhibition may play an important role in shaping the rate-place code. We also show that midbrain auditory neurons can demonstrate similar properties as cortical harmonic template neurons. Our study fills a gap in understanding the transformation in neural representations of resolved harmonics along the auditory pathway.
Detecting dipicolinic acid production and biosynthesis pathways in Bacilli and Clostridia
Authors: Gordon Benjamin , Duellman Paul , Salvucci Anthony , De Lorme Marthah 
Published: October 2019

ABSTRACTBacterial endospores are highly resistant structures and dipicolinic acid is a key component of their resilience and stability. Due to the difficulty in controlling endospore contaminants, they are of interest in clean rooms, food processing, and production industries, while benefical endospore-formers are sought for potential utility. Dipicolinic acid production has traditionally been recognized in Bacilli, Clostridia, and Paenibacilli. Here, sixty-seven strains of aerobic and anaerobic endospore-forming bacteria belonging to the generaBacillus, Brevibacillus, Clostridium, Fontibacillus, Lysinibacillus, Paenibacillus, Rummeliibacillus, andTerribacilluswere grown axenically and sporulated biomasses were assayed for dipicolinic acid production using fluorimetric detection. Strains testing positive were sequenced and the genomes analyzed to identify dipicolinic acid biosynthesis genes. The well-characterized biosynthesis pathway was conserved in 59 strains of Bacilli and Paenibacilli as well as two strains of Clostridia; six strains of Clostridia lacked homologs to genes recognized as involved in dipicolinic acid biosynthesis. Our results confirm dipicolinic acid production across different classes and families of Firmicutes. We find that members ofClostridium(cluster I) lack recognized dipicolinic acid biosynthesis genes and propose an alternate genetic pathway in these strains. Finally, we explore why the extent and mechanism of dipicolinic acid production in endospore-forming bacteria should be fully understood. We believe that understanding the mechanism by which dipicolinic acid is produced can expand the methods to utilize endospore-forming bacteria, such as novel bacterial strains added to products, for genes to create inputs for the polymer industry and to be better equipped to control contaminating spores in industrial processes.