bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy and Safety of Surgical Kidney Stone Interventions in Autosomal Dominant Polycystic Kidney Disease: A Systematic Review
Authors: Kalatharan Vinusha , Jandoc Racquel , Grewal Gary , Nash Danielle M. , Welk Blayne , Sarma Sisira , Pei York , Garg Amit X. 
Published: July 2020

Background: Reduced kidney function and distorted kidney anatomy in patients with autosomal dominant polycystic kidney disease (ADPKD) may complicate stone interventions more compared with the general population. Objectives: To review studies describing the safety and efficacy of the 3 main stone interventions in adults with ADPKD: shock wave lithotripsy (SWL), ureteroscopy, and percutaneous nephrolithotomy (PCNL). Design: Systematic review. Setting: Any country of origin. Patients: Adults with ADPKD who underwent SWL, ureteroscopy, or PCNL. Measurements: Being stone free after the intervention and postoperative complications as reported by each study, which included pain, bleeding, and fever. Methods: Relevant studies published until February 2019 were identified through a comprehensive search of MEDLINE, EMBASE, Web of Science, BIOSIS PREVIEW, and CINAHL. Studies were eligible for review if they reported at least one outcome following SWL, ureteroscopy, and/or PCNL in adults with ADPKD. We then abstracted information on study characteristics, patient characteristics, intervention details, and postintervention outcomes and assessed the methodological quality of each study using a modified Downs and Black checklist. Results: We screened 221 citations from which we identified 24 studies that met our review criteria. We identified an additional article when manually reviewing the reference list of an included article, yielding a total of 25 studies describing 311 patients (32 SWL, 42 ureteroscopy, and 237 PCNL). The percentage of patients who were stone free after 1 session ranged from 0% to 69% after SWL, 73% to 100% after ureteroscopy, and 45% to 100% after PCNL. The percentage of patients with ADPKD that experienced at least one postoperative complication ranged from 0% to 33% for SWL, 0% to 27% for ureteroscopy, and 0% to 100% for PCNL. Limitations: The number and quality of studies published to date are limited. Conclusions: The efficacy and safety of stone interventions in patients with ADPKD remains uncertain, with wide-ranging estimates reported in the literature. Trial Registration: We did not register the protocol of this systematic review.
High metabolic tumor volume is associated with decreased efficacy of axicabtagene ciloleucel in large B-cell lymphoma
Authors: Dean Erin A. , Mhaskar Rahul S. , Lu Hong , Mousa Mina S. , Krivenko Gabriel S. , Lazaryan Aleksandr , Bachmeier Christina A. , Chavez Julio C. , Nishihori Taiga , Davila Marco L. , Khimani Farhad , Liu Hien D. , Pinilla-Ibarz Javier , Shah Bijal D. , Jain Michael D. , Balagurunathan Yoganand , Locke Frederick L. 
Published: July 2020

Abstract
High metabolic tumor volume (MTV) predicts worse outcomes in lymphoma treated with chemotherapy. However, it is unknown if this holds for patients treated with axicabtagene ciloleucel (axi-cel), an anti-CD19 targeted chimeric antigen receptor T-cell therapy. The primary objective of this retrospective study was to investigate the relationship between MTV and survival (overall survival [OS] and progression-free survival [PFS]) in patients with relapsed/refractory large B-cell lymphoma (LBCL) treated with axi-cel. Secondary objectives included finding the association of MTV with response rates and toxicity. The MTV values on baseline positron emission tomography of 96 patients were calculated via manual methodology using commercial software. Based on a median MTV cutoff value of 147.5 mL in the first cohort (n = 48), patients were divided into high and low MTV groups. Median follow-up for survivors was 24.98 months (range, 10.59-51.02 months). Patients with low MTV had significantly superior OS (hazard ratio [HR], 0.25; 95% confidence interval [CI], 0.10-0.66) and PFS (HR, 0.40; 95% CI, 0.18-0.89). Results were successfully validated in a second cohort of 48 patients with a median follow-up for survivors of 12.03 months (range, 0.89-25.74 months). Patients with low MTV were found to have superior OS (HR, 0.14; 95% CI, 0.05-0.42) and PFS (HR, 0.29; 95% CI, 0.12-0.69). In conclusion, baseline MTV is associated with OS and PFS in axi-cel recipients with LBCL.
Men with sickle cell disease experience greater sexual dysfunction when compared with men without sickle cell disease
Authors: Idris Ibrahim M. , Abba Akib , Galadanci Jamil A. , Mashi Sharfuddeen A. , Hussaini Nafiu , Gumel Sagir Ahmed , Burnett Arthur L. , DeBaun Michael R. 
Published: July 2020

Abstract
Recurrent ischemic priapism is a common complication of sickle cell disease (SCD). We assessed the burden, characteristics, and types of priapism, including sexual dysfunction, in a cohort of men with and those without SCD, to test the hypothesis that sexual dysfunction is more prevalent in men with SCD. In Kano, Nigeria, we conducted a comparative cross-sectional survey that included 500 and 250 men 18 to 40 years of age, with and without SCD, respectively. The survey used the Priapism Questionnaire and the International Index of Erectile Function for sexual function assessment. All eligible participants approached for the study gave informed consent and were enrolled. Stuttering and major priapism were defined based on the average duration of priapism experiences that lasted ≤4 and &gt;4 hours, respectively. The prevalence of priapism was significantly higher in men with SCD than in those without it (32.6% vs 2%; P &lt; .001). Stuttering priapism accounted for 73.6% of the priapism episodes in men with SCD. Nearly 50% of the participants with SCD-related priapism had never sought medical attention for this complication. The majority of the men with SCD-related priapism used exercise as a coping mechanism. Priapism affected the self-image of the men with SCD, causing sadness, embarrassment, and fear. The percentage of the men with SCD who had erectile dysfunction was more than twofold higher than that of those without SCD who had erectile dysfunction (P = .01). The men with SCD had a higher prevalence of priapism and sexual dysfunction than the men without SCD.
Pirfenidone plus inhaled N-acetylcysteine for idiopathic pulmonary fibrosis: a randomised trial
Authors: Sakamoto Susumu , Kataoka Kensuke , Kondoh Yasuhiro , Kato Motoyasu , Okamoto Masaki , Mukae Hiroshi , Bando Masashi , Suda Takafumi , Yatera Kazuhiro , Tanino Yoshinori , Kishaba Tomoo , Hattori Noboru , Taguchi Yoshio , Saito Takefumi , Nishioka Yasuhiko , Kuwano Kazuyoshi , Kishi Kazuma , Inase Naohiko , Sasaki Shinichi , Takizawa Hajime , Johkoh Takeshi , Sakai Fumikazu , Homma Sakae 
Published: July 2020

BackgroundA randomised controlled trial in Japan showed that inhaled N-acetylcysteine monotherapy stabilised serial decline in forced vital capacity (FVC) in some patients with early idiopathic pulmonary fibrosis (IPF). However, the efficacy and tolerability of combination therapy with an antifibrotic agent and inhaled N-acetylcysteine are unknown.MethodsThis 48-week, randomised, open-label, multicentre phase 3 trial compared the efficacy and tolerability of combination therapy with pirfenidone plus inhaled N-acetylcysteine 352.4 mg twice daily with the results for pirfenidone alone in patients with IPF. The primary end-point was annual rate of decline in FVC. Exploratory efficacy measurements included serial change in diffusing capacity of the lung for carbon monoxide (DLCO) and 6-min walk distance (6MWD), progression-free survival (PFS), incidence of acute exacerbation, and tolerability.Results81 patients were randomly assigned in a 1:1 ratio to receive pirfenidone plus inhaled N-acetylcysteine (n=41) or pirfenidone (n=40). The 48-week rate of change in FVC was −300 mL and −123 mL, respectively (difference −178 mL, 95% CI −324–−31 mL; p=0.018). Serial change inDLCO, 6MWD, PFS and incidence of acute exacerbation did not significantly differ between the two groups. The incidence of adverse events (n=19 (55.9%) for pirfenidone plus N-acetylcysteine; n=18 (50%) for pirfenidone alone) was similar between groups.ConclusionsCombination treatment with inhaled N-acetylcysteine and pirfenidone is likely to result in worse outcomes for IPF.
The effect of pain conditioning on experimentally evoked cough: evidence of impaired endogenous inhibitory control mechanisms in refractory chronic cough
Authors: Hilton Emma , Satia Imran , Holt Kimberley , Woodcock Ashley A. , Belcher John , Smith Jaclyn A. 
Published: July 2020

The pathophysiology of refractory chronic cough (RCC) is unclear. We hypothesised that endogenous inhibitory control mechanisms, such as those activated by noxious stimuli inducing pain (conditioned pain modulation) may be capable of inhibiting coughing and urge to cough evoked by inhaled capsaicin. Furthermore, these mechanisms may be impaired in patients with RCC.The objective was to investigate the effects of pain on cough and urge to cough in healthy volunteers and RCC patients. Healthy volunteers and RCC patients underwent a randomised, controlled, four-way crossover study comparing the effect of four interventions on capsaicin-evoked coughing and urge to cough. The interventions comprised immersing a hand in 1) noxious cold water; 2) warm water; 3) warm water, but subjects were instructed to voluntarily supress coughing; and 4) no intervention. The co-primary outcomes were numbers of evoked coughs and urge to cough scores.20 healthy volunteers (mean±sdage 50.1±14.2 years, male:female 10:10) and 20 RCC patients (age 60.1±7.9 years, male:female 9:11) participated. Overall, noxious cold water reduced capsaicin-evoked urge-to-cough scores and cough numbers compared with warm water (1.6 (95% CI 1.3–2.0)versus2.2 (1.8–2.6), p<0.001 and 4.8 (3.7–6.2) coughsversus7.9 (6.7–9.5) coughs, p<0.001, respectively). Healthy volunteers and RCC patients demonstrated similar reductions in the urge to cough during noxious cold-water immersion, but noxious cold water and voluntary suppression interventions were less effective at reducing capsaicin-evoked cough in RCC patients than in healthy volunteers (p=0.041).Endogenous inhibitory control mechanisms, specifically those activated by pain, can reduce both coughing and the urge to cough. Impairment of endogenous inhibitory control mechanisms may contribute to excessive coughing in RCC.
A performant bridge between fixed-size and variable-size seeding
Authors: Kutzner Arne , Kim Pok-Son , Schmidt Markus 
Published: July 2020

Abstract
Background
Seeding is usually the initial step of high-throughput sequence aligners. Two popular seeding strategies are fixed-size seeding (k-mers, minimizers) and variable-size seeding (MEMs, SMEMs, maximal spanning seeds). The former strategy supports fast seed computation, while the latter one benefits from a high seed uniqueness. Algorithmic bridges between instances of both seeding strategies are of interest for combining their respective advantages.

Results
We introduce an efficient strategy for computing MEMs out of fixed-size seeds (k-mers or minimizers). In contrast to previously proposed extend-purge strategies, our merge-extend strategy prevents the creation and filtering of duplicate MEMs. Further, we describe techniques for extracting SMEMs or maximal spanning seeds out of MEMs. A comprehensive benchmarking shows the applicability, strengths, shortcomings and computational requirements of all discussed seeding techniques. Additionally, we report the effects of seed occurrence filters in the context of these techniques.
Aside from our novel algorithmic approaches, we analyze hierarchies within fixed-size and variable-size seeding along with a mapping between instances of both seeding strategies.

Conclusion
Benchmarking shows that our proposed merge-extend strategy for MEM computation outperforms previous extend-purge strategies in the context of PacBio reads. The observed superiority grows with increasing read size and read quality. Further, the presented filters for extracting SMEMs or maximal spanning seeds out of MEMs outperform FMD-index based extension techniques. All code used for benchmarking is available via GitHub at https://github.com/ITBE-Lab/seed-evaluation.
SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles
Authors: Yu Zhenhua , Du Fang , Ban Rongjun , Zhang Yuanwei 
Published: July 2020

Abstract
Background
A number of simulators have been developed for emulating next-generation sequencing data by incorporating known errors such as base substitutions and indels. However, their practicality may be degraded by functional and runtime limitations. Particularly, the positional and genomic contextual information is not effectively utilized for reliably characterizing base substitution patterns, as well as the positional and contextual difference of Phred quality scores is not fully investigated. Thus, a more effective and efficient bioinformatics tool is sorely required.

Results
Here, we introduce a novel tool, SimuSCoP, to reliably emulate complex DNA sequencing data. The base substitution patterns and the statistical behavior of quality scores in Illumina sequencing data are fully explored and integrated into the simulation model for reliably emulating datasets for different applications. In addition, an integrated and easy-to-use pipeline is employed in SimuSCoP to facilitate end-to-end simulation of complex samples, and high runtime efficiency is achieved by implementing the tool to run in multithreading with low memory consumption. These features enable SimuSCoP to gets substantial improvements in reliability, functionality, practicality and runtime efficiency. The tool is comprehensively evaluated in multiple aspects including consistency of profiles, simulation of genomic variations and complex tumor samples, and the results demonstrate the advantages of SimuSCoP over existing tools.

Conclusions
SimuSCoP, a new bioinformatics tool is developed to learn informative profiles from real sequencing data and reliably mimic complex data by introducing various genomic variations. We believe that the presented work will catalyse new development of downstream bioinformatics methods for analyzing sequencing data.
The NETest liquid biopsy is diagnostic for gastric neuroendocrine tumors: observations on the blood-based identification of microscopic and macroscopic residual disease
Authors: Malczewska A. , Procner A. , Walter A. , Kusnierz K. , Zajecki W. , Aslanian H. , Kos-Kudla B. 
Published: July 2020

Abstract
Background
NETest, a novel multi-gene liquid biopsy has utility in neuroendocrine tumor (NET) diagnosis and identification of residual disease. We independently assessed utility of the NETest to diagnose gastric neuroendocrine neoplasms (GNENs) and identify micro- and macroscopic residual disease.

Methods
Cohorts comprised histologically confirmed GNENs at biopsy, n = 46; GNETs Type 1: 42 (32 NET G1, 10 NET G2), a GNET Type 3: 1 well-differentiated NET G3, neuroendocrine carcinomas (NECs) (n = 3), and controls (n = 63). Disease status at sampling was assessed by gastroscopy, histology (resection margin [R] positivity of polypectomy or biopsy), EUS, CT or MRI, and/or 68Ga-DOTA-TATE PET/CT. Groups included image- (gastroscopy, EUS, and anatomical and/or functional imaging) positive or image negative disease. NETest assay by PCR (spotted plates, normal cut-off: 20). Data: mean ± SD.

Results
Disease extent: Image-negative (n = 30) (21 R0, 9 R1); Image-positive, n = 16.
Diagnosis: NETest was increased in GNETs (23 ± 11) vs. controls (7 ± 4, p < 0.0001). In histology-positive, the NETest accuracy was 100% (25/25).
Microscopic disease: In image-negative but R1, NETest was elevated in 100% (9/9; 28 ± 9). Levels were elevated vs. controls (7 ± 4, p < 0.0001), or R0 (16 ± 11, p = 0.02). Eight of 21 R0, exhibited positive NETest.
Macroscopic disease: Gastric lesions were multiple: 38%, single: 62%, submucosal: 13%, or ulcerated: 13%. Lesions size was ≤5 mm (50%), > 5–9.9 mm (17%), 10–19.9 mm (17%), ≥20 mm (17%) [≥10 mm: 34%). The NETest accuracy was 100% (16/16). Levels (28 ± 7) were higher than controls (7 ± 4, p < 0.0001) or R0 (16 ± 11, p = 0.002) but not to R1 (28 ± 9, p = 0.5).

Conclusions
NETest is diagnostic for gastric NETs. Elevated levels identify both microscopic and macroscopic residual disease. In histology/image-negative disease, elevated NETest may reflect early evidence of increased neuroendocrine gene expression of hypergastrinemia-induced neoplastic transformation of enterochromaffin-like (ECL) cells to tumor status. A sensitive liquid biopsy has utility in the management and surveillance of gastric NET disease.
Healthy aging in elderly cochlear implant recipients: a multinational observational study
Authors: Marx M. , Mosnier I. , Belmin J. , Wyss J. , Coudert-Koall C. , Ramos A. , Manrique Huarte R. , Khnifes R. , Hilly O. , Martini A. , Cuda D. 
Published: July 2020

Abstract
Background
Given an increase in the aging population and its impact on healthcare systems, policy makers for provision of health and social services are aiming to keep older adults in good health for longer, in other words towards ‘healthy aging’. Our study objective is to show that rehabilitation with cochlear implant treatment in the elderly with hearing impairment improves the overall health-related quality of life and general well-being that translate into healthy aging.

Methods
The multicentre, prospective, repeated measures, single-subject, clinical observational study will accrue 100 elderly, first-time, unilateral CI recipients (≥ 60 years) and analyze changes on specific measurement tools over ca. 20 months from preimplant to postimplant. Evaluations will consist of details collected through case history and interview questionnaires by clinicians, data logging, self-report questionnaires completed by the recipients and a series of commonly used audiometric measures and geriatric assessment tools. The primary indicator of changes in overall quality of life will be the HUI-3.

Discussion
The protocol is designed to make use of measurement tools that have already been applied to the hearing-impaired population in order to compare effects of CI rehabilitation in adults immediately before their implantation, (pre-implant) and after gaining 1–1.5 years of experience (post-implant). The broad approach will lead to a greater understanding of how useful hearing impacts the quality of life in elderly individuals, and thus improves potentials for healthy aging. Outcomes will be described and analyzed in detail.

Trial registration
This research has been registered in ClinicalTrials.gov (http://www.clinicaltrials.gov/), 7 March 2017 under the n° NCT03072862.
Cerebral and pulmonary aspergillosis, treatment and diagnostic challenges of mixed breakthrough invasive fungal infections: case report study
Authors: Amanati Ali , Lotfi Mehrzad , Masoudi Mohammad Sadegh , Jafarian Hadis , Ghasemi Fatemeh , Bozorgi Haleh , Badiee Parisa 
Published: July 2020

Abstract
Background
Breakthrough invasive fungal infections (bIFIs) are an area of concern in the scarcity of new antifungals. The mixed form of bIFIs is a rare phenomenon but could be potentially a troublesome challenge when caused by azole-resistant strains or non-Aspergillus fumigatus. To raise awareness and emphasize diagnostic challenges, we present a case of mixed bIFIs in a child with acute lymphoblastic leukemia.

Case presentation
A newly diagnosed 18-month-old boy with acute lymphoblastic leukemia was complicated with prolonged severe neutropenia after induction chemotherapy. He experienced repeated episodes of fever due to extended-spectrum beta-lactamase-producing Escherichia coli bloodstream infection and pulmonary invasive fungal infection with Aspergillus fumigatus (early-type bIFIs) while receiving antifungal prophylaxis. Shortly after pulmonary involvement, his condition aggravated by abnormal focal movement, loss of consciousness and seizure. Cerebral aspergillosis with Aspergillus niger diagnosed after brain tissue biopsy. The patient finally died despite 108-day antifungal therapy.

Conclusions
Mixed bIFIs is a rare condition with high morbidity and mortality in the patients receiving immunosuppressants for hematological malignancies. This case highlights the clinical importance of Aspergillus identification at the species level in invasive fungal infections with multiple site involvement in the patients on antifungal prophylaxis.
Analysis of 4 imaging features in patients with COVID-19
Authors: Jin Jun , Gao De-hong , Mo Xin , Tan Si-ping , Kou Zhen-xia , Chen Yi-bo , Cao Jin-bo , Chen Wen-jing , Zhang Ya-ming , Li Bing-qing , Huang Kuan-long , Xu Bing-ren , Tang Xiao-li , Wang Yu-li 
Published: July 2020

Abstract
Background
The aim of this was to analyze 4 chest CT imaging features of patients with coronavirus disease 2019 (COVID-19) in Shenzhen, China so as to improve the diagnosis of COVID-19.

Methods
Chest CT of 34 patients with COVID-19 confirmed by the nucleic acid test (NAT) were retrospectively analyzed. Analyses were performed to investigate the pathological basis of four imaging features(“feather sign”,“dandelion sign”,“pomegranate sign”, and “rime sign”) and to summarize the follow-up results.

Results
There were 22 patients (65.2%) with typical “feather sign”and 18 (52.9%) with “dandelion sign”, while few patients had “pomegranate sign” and “rime sign”. The “feather sign” and “dandelion sign” were composed of stripe or round ground-glass opacity (GGO), thickened blood vessels, and small-thickened interlobular septa. The “pomegranate sign” was characterized as follows: the increased range of GGO, the significant thickening of the interlobular septum, complicated with a small amount of punctate alveolar hemorrhage. The “rime sign” was characterized by numerous alveolar edemas. Microscopically, the wall thickening, small vascular proliferation, luminal stenosis, and occlusion, accompanied by interstitial infiltration of inflammatory cells, as well as numerous pulmonary interstitial fibrosis and partial hyaline degeneration were observed. Repeated chest CT revealed the mediastinal lymphadenectasis in one patient. Re-examination of the NAT showed another positive anal swab in two patients.

Conclusion
“Feather sign” and “dandelion sign” were typical chest CT features in patients withCOVID-19; “pomegranate sign” was an atypical feature, and “rime sign” was a severe feature. In clinical work, accurate identification of various chest CT signs can help to improve the diagnostic accuracy of COVID-19 and reduce the misdiagnosis or missed diagnosis rate.