bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP
Authors: Reis Ana C. , Kolvenbach Boris A. , Chami Mohamed , Gales Luís , Egas Conceição , Corvini Philippe F.-X. , Nunes Olga C. 
Published: November 2019

Abstract
Background
Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified.

Results
Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements.

Conclusions
Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.
Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes
Authors: Deng Xiao , Zhao Xuechao , Liang Yuan , Zhang Liang , Jiang Jianping , Zhao Guoping , Zhou Yan 
Published: November 2019

AbstractBackgroundThe genome topology network (GTN) is a new approach for studying the phylogenetics of bacterial genomes by analysing their gene order. The previous GTN tool gives a phylogenetic tree and calculate the different degrees (DD) of various adjacent gene families with complete genome data, but it is limited to the gene family level.ResultIn this study, we collected 51 published complete and draft group BStreptococcus(GBS) genomes from the NCBI database as the case study data. The phylogenetic tree obtained from the GTN method assigned the genomes into six main clades. Compared with single nucleotide polymorphism (SNP)-based method, the GTN method exhibited a higher resolution in two clades. The gene families located at unique node connections in these clades were associated with the clusters of orthologous groups (COG) functional categories of “[G] Carbohydrate transport and metabolism,”, “[L] Replication, recombination, and repair” and “[J] translation, ribosomal structure and biogenesis”. Thus, these genes were the major factors affecting the differentiation of these six clades in the phylogenetic tree obtained from the GTN.ConclusionThe modified GTN analyzes draft genomic data and exhibits greater functionality than the previous version. The gene family clustering algorithm embedded in the GTN tool is optimized by introducing the Markov cluster algorithm (MCL) tool to assign genes to functional gene families. A bootstrap test is performed to verify the credibility of the clades when allowing users to adjust the relationships of the clades accordingly. The GTN tool gives additional evolutionary information that is a useful complement to the SNP-based method. Information on the differences in the connections between a gene and its adjacent genes in species or clades is easily obtained. The modified GTN tool can be downloaded fromhttps://github.com/0232/Genome_topology_network
Clinical operations of academic versus non-academic emergency departments: a descriptive comparison of two large emergency department operations surveys
Authors: Reznek Martin A. , Michael Sean S. , Harbertson Cathi A. , Scheulen James J. , Augustine James J. 
Published: November 2019

Abstract
Background
Academic and non-academic emergency departments (EDs) are regularly compared in clinical operations benchmarking despite suggestion that the two groups may differ in their clinical operations characteristics. and outcomes. We sought to describe and compare clinical operations characteristics of academic versus non-academic EDs.

Methods
We performed a descriptive, comparative analysis of academic and non-academic adult and general EDs with 40,000+ annual encounters, using the Academy of Academic Administrators of Emergency Medicine (AAAEM)/Association of Academic Chairs of Emergency Medicine (AACEM) and Emergency Department Benchmarking Alliance (EDBA) survey results. We defined academic EDs as primary teaching sites for emergency medicine (EM) residencies and non-academic EDs as sites with minimal resident involvement. We constructed the academic and non-academic cohorts from the AAAEM/AACEM and EDBA surveys, respectively, and analyzed metrics common to both surveys.

Results
Eighty and 454 EDs met inclusion criteria for academic and non-academic EDs, respectively. Academic EDs had more median annual patient encounters (73,001 vs 54,393), lower median proportion of pediatric patients (6.3% vs 14.5%), higher median proportion of EMS patients (27% vs 19%), and were more commonly designated as Level I or II Trauma Centers (94% vs 24%). Median patient arrival-to-provider times did not differ (26 vs 25 min). Median length-of-stay was longer (277 vs 190 min) for academic EDs, and left-before-treatment-complete was higher (5.7% vs 2.9%). MRI utilization was higher for academic EDs (2.2% patients with at least one MRI vs 1.0 MRIs performed per 100 patients). Patients-per-hour of provider coverage was lower for academic EDs with and without consideration for advanced practice providers and residents.

Conclusions
Demographic and operational performance measures differ between academic and non-academic EDs, suggesting that the two groups may be inappropriate operational performance comparators. Causes for the differences remain unclear but the differences appear not to be attributed solely to the academic mission.
Simultaneous dermatophytosis and keratomycosis caused by Trichophyton interdigitale infection: a case report and literature review
Authors: Zhang Mingrui , Jiang Lanxiang , Li Fuqiu , Xu Yangchun , Lv Sha , Wang Bing 
Published: November 2019

Abstract
Background
Dermatophytosis is a fungal infectious disease caused by dermatophytes, which produce protease and keratinase to digest keratin, leading to the colonization, invasion, and infection of the stratum corneum of the skin, hair shafts, and nails. Trichophyton interdigitale belongs to Trichophyton mentagrophytes complex, which is the common pathogen causing dermatophytosis. Fungal keratitis, also called keratomycosis, is an infectious disease of cornea.

Case presentation
Here, we report a case of simultaneous dermatophytosis and keratomycosis caused by Trichophyton interdigitale. A 67-year-old man presented with extensive erythema all over the body since 4 years ago, fungal infection of left eye for 2 years, and loss of vision in the eye. These symptoms had become aggravated in the last month. Dermatological examinations showed extensive erythematous plaques with clear borders and scales, scattered red papules with ulceration, and scabs throughout the body. Onychomycosis was observed on the nails of left hand, conjunctival infection with secretion and loss of vision were noted in left eye. Hyaline septate hyphae were observed under direct microscopic examination, fungal culture and internal transcribed spacer sequencing revealed T. interdigitale. Histopathological examination suggested infectious granuloma. A diagnosis of dermatophytosis and keratomycosis caused by T. interdigitale with loss of vision in left eye was made. The patient was treated with luliconazole cream (two applications per day) and itraconazole (100 mg, BID, PO). Complete clinical remission was achieved after 1 month. Subsequently, the patient underwent left eye enucleation in the ophthalmology department.

Conclusions
In the present study, we reported a case of simultaneous dermatophytosis and keratomycosis caused by T. interdigitale, and reviewed the literature on corneal infection caused by Trichophyton. A total of 10 articles with 45 patients were published between 1973 and 2018. The pathogen of 27 patient were identified to species level. There were T. schoenleinii (17), T. mentagrophytes (4), T. verrucosum (3), T. rubrum (1), T. erinacei (1), and T. interdigitale (1). Five patients had corneal trauma, one had contact lens use history. Direct microscopic examination, fungal culture, and analysis of physiological characteristics were the main methods of identification. Early diagnosis and prompt treatment may help improve the management and outcomes.
Higher estimated net endogenous acid production with lower intake of fruits and vegetables based on a dietary survey is associated with the progression of chronic kidney disease
Authors: Toba Koji , Hosojima Michihiro , Kabasawa Hideyuki , Kuwahara Shoji , Murayama Toshiko , Yamamoto-Kabasawa Keiko , Kaseda Ryohei , Wada Eri , Watanabe Reiko , Tanabe Naohito , Suzuki Yoshiki , Narita Ichiei , Saito Akihiko 
Published: November 2019

Abstract
Background
Dietary acid load has been suggested to mediate the progression of chronic kidney disease (CKD). However, it is unclear what kinds of foods are actually associated with dietary acid load in patients with CKD. The self-administered diet history questionnaire (DHQ), which semi-quantitatively assesses the dietary habits of Japanese individuals through 150 question items, can estimate average daily intake of various foods and nutrients during the previous month. Using the DHQ, we investigated the association of dietary acid load with CKD progression. We also analyzed the kinds of food that significantly affect dietary acid load.

Methods
Subjects were 96 outpatients with CKD (average estimated glomerular filtration rate [eGFR], 53.0 ± 18.1 ml/min/1.73 m2) at Niigata University Hospital, who had completed the DHQ in 2011. We calculated net endogenous acid production (NEAP) from potassium and protein intake evaluated by the DHQ in order to assess dietary acid load. CKD progression was assessed by comparing eGFR between 2008 and 2014.

Results
NEAP was not correlated with protein intake (r = 0.088, p = 0.398), but was negatively correlated with potassium intake (r = − 0.748, p < 0.001). Reduction in eGFR from 2008 to 2014 was estimated to be significantly greater in patients with higher NEAP (NEAP > 50.1 mEq/day, n = 45) than in those with lower NEAP (NEAP ≤50.1 mEq/day, n = 50) by 5.9 (95% confidence interval [95%CI], 0.1 to 11.6) ml/min/1.73 m2. According to multiple logistic regression analysis, higher NEAP was significantly associated with lower intake of fruits (odds ratio [OR], 6.454; 95%CI, 2.19 to 19.00), green and yellow vegetables (OR, 5.18; 95%CI, 1.83 to14.66), and other vegetables (OR, 3.87; 95%CI, 1.29 to 11.62).

Conclusions
Elevated NEAP could be a risk factor for CKD progression. Low intake of fruits and vegetables would increase dietary acid load and might affect the progression of renal dysfunction in Japanese CKD patients.
A hemodialysis patient with bone disease after pregnancy: a case report
Authors: Sprenger-Mähr Hannelore , Zitt Emanuel , Kronbichler Andreas , Cejna Manfred , Lhotta Karl 
Published: November 2019

Abstract
Background
Pregnancy is rare in women on hemodialysis. Recommendations for the treatment of secondary hyperparathyroidism (sHPT) and preservation of bone health in pregnant dialysis patients are lacking.

Case presentation
We present the case of a young woman with end-stage kidney disease (ESKD) due to lupus nephritis, who developed multiple brown tumors while on hemodialysis during her second pregnancy. During her first pregnancy sHPT was well controlled and no skeletal complications occurred. Before the second pregnancy she developed severe sHPT. During pregnancy, dialysis time was increased to 24 h per week, the patient was given oral calcitriol, and the dialysate calcium concentration was set at 1.5 mmol/l. In week 20 the patient complained about bone pain in her left hip. Magnetic resonance imaging revealed a cystic lesion compatible with a brown tumor. The baby was delivered in the 36th week by cesarean section. Further assessment identified multiple brown tumors of her skeleton, including the acetabulum, tibia, ribs, skull, thoracic spine and thumb. She required multiple orthopedic surgeries. Three months after pregnancy, etelcalcetide was started, which brought about a gradual improvement in her sHPT.

Conclusions
This case demonstrates that the combination of pregnancy and severe sHPT in dialysis patients can have deleterious consequences for bone health.
Effects of patient age on patency of chronic hemodialysis vascular access
Authors: Jeong Seonjeong , Kwon Hyunwook , Chang Jai Won , Kim Min-Ju , Ganbold Khaliun , Han Youngjin , Kwon Tae-Won , Cho Yong-Pil 
Published: November 2019

Abstract
Background
In this single-center, retrospective observational study, we assessed the long-term patency of vascular access (VA) after first VA placement to uncover independent risk factors associated with VA patency in Asian hemodialysis (HD) patients stratified by age. We also investigated factors associated with VA patency among older HD patients according to the type of VA in the overall study population.

Methods
The study period was from January 2011 to December 2013. A total of 651 chronic HD patients with confirmed first upper-extremity VA placement were enrolled, and their records were analyzed retrospectively. A total of 445 patients (68.4%) made up the nonelderly group (< 65 years), and 206 patients (31.6%) were in the elderly group (≥ 65 years). Study outcomes were defined as primary or secondary VA patency.

Results
Autologous arteriovenous fistula (AVF) was more common in the nonelderly group (P <  0.01). Kaplan–Meier curve survival analysis indicated that primary patency was longer in the nonelderly group (P <  0.01); secondary patency, however, was similar between groups (P = 0.37). The multivariate analysis of factors associated with primary VA patency revealed that increased age (hazard ratio [HR], 1.02; 95% confidence interval [CI], 1.01–1.03; P <  0.01) was associated with shorter primary patency, and AVF (HR, 0.38; 95% CI, 0.28–0.51; P <  0.01) was associated with longer primary patency. AVF (HR, 0.57; 95% CI, 0.37–0.87; P = 0.010) and diabetes mellitus (HR, 1.56; 95% CI, 1.07–2.29; P = 0.02) were independently associated with longer and shorter secondary patency periods, respectively; however, increased age was not a risk factor for decreased secondary patency.

Conclusions
Increased age was associated with shorter primary patency but not secondary patency, whereas AVF placement was associated with longer primary and secondary patency. Considering the similar rates of secondary patency between groups and the superior patency of AVF compared to arteriovenous graft, a fistula-first strategy should be applied to appropriate older patients.
Rare crystalline nephropathy leading to acute graft dysfunction: a case report
Authors: Bagai Sahil , Khullar Dinesh , Bansal Bhavna 
Published: November 2019

Abstract
Background
Adenine phosphoribosyl transferase (APRT) deficiency is a rare genetic form of kidney stones and/or kidney failure characterized by intratubular precipitation of 2,8 dihydroxyadenine crystals. Early diagnosis and prompt management can completely reverse the kidney injury.

Case presentation
44 year old Indian male, renal transplant recipient got admitted with acute graft dysfunction. Graft biopsy showed light brown refractile intratubular crystals with surrounding giant cell reaction, consistent with APRT deficiency. Patient improved after receiving allopurinol and hydration.

Conclusion
APRT forms a reversible cause of crystalline nephropathy. High index of suspicion is required for the correct diagnosis as timely diagnosis has therapeutic implications.
Chronic treatment of curcumin improves hepatic lipid metabolism and alleviates the renal damage in adenine-induced chronic kidney disease in Sprague-Dawley rats
Authors: Ghelani Hardik , Razmovski-Naumovski Valentina , Chang Dennis , Nammi Srinivas 
Published: November 2019

AbstractBackgroundChronic kidney disease (CKD), including nephrotic syndrome, is a major cause of cardiovascular morbidity and mortality. The literature indicates that CKD is associated with profound lipid disorders due to the dysregulation of lipoprotein metabolism which progresses kidney disease. The objective of this study is to evaluate the protective effects of curcumin on dyslipidaemia associated with adenine-induced chronic kidney disease in rats.MethodsMale SD rats (n = 29) were divided into 5 groups for 24 days: normal control (n = 5, normal diet), CKD control (n = 6, 0.75% w/w adenine-supplemented diet), CUR 50 (n = 6, 50 mg/kg/day curcumin + 0.75% w/w adenine-supplemented diet), CUR 100 (n = 6, 100 mg/kg/day curcumin + 0.75% w/w adenine-supplemented diet), and CUR 150 (n = 6, 150 mg/kg/day curcumin + 0.75% w/w adenine-supplemented diet). The serum and tissue lipid profile, as well as the kidney function test, were measured using commercial diagnostic kits.ResultsThe marked rise in total cholesterol, low-density lipoprotein (LDL) cholesterol, very low-density lipoprotein (VLDL) cholesterol, triglycerides and free fatty acids in serum, as well as hepatic cholesterol, triglyceride and free fatty acids of CKD control rats were significantly protected by curcumin co-treatment (at the dose of 50, 100 and 150 mg/kg). Furthermore, curcumin significantly increased the serum high-density lipoprotein (HDL) cholesterol compared to the CKD control rats but did not attenuate the CKD-induced weight retardation. Mathematical computational analysis revealed that curcumin significantly reduced indicators for the risk of atherosclerotic lesions (atherogenic index) and coronary atherogenesis (coronary risk index). In addition, curcumin improved kidney function as shown by the reduction in proteinuria and improvement in creatinine clearance.ConclusionThe results provide new scientific evidence for the use of curcumin in CKD-associated dyslipidaemia and substantiates the traditional use of curcumin in preventing kidney damage.
Susceptibility of BAFF-var allele carriers to severe SLE with occurrence of lupus nephritis
Authors: Friebus-Kardash Justa , Trendelenburg Marten , Eisenberger Ute , Ribi Camillo , Chizzolini Carlo , Huynh-Do Uyen , Lang Karl Sebastian , Wilde Benjamin , Kribben Andreas , Witzke Oliver , Dolff Sebastian , Hardt Cornelia 
Published: November 2019

Abstract
Background
Dysregulation of the B-cell activating factor (BAFF) system is involved in the pathogenesis of systemic lupus erythematosus (SLE). Increased serum concentrations of BAFF are related to lupus nephritis and disease activity among SLE patients. Recently, a variant of the BAFF-encoding gene, BAFF-var, was identified to be associated with autoimmune diseases, in particular SLE, and to promote the production of soluble BAFF. The present study aimed to assess the prevalence of BAFF-var in a cohort of 195 SLE patients and to analyze the association of the BAFF-var genotype (TNSF13B) with various manifestations of SLE.

Methods
A cohort of 195 SLE patients from Central Europe, including 153 patients from the Swiss SLE Cohort Study and 42 patients from the University Hospital Essen, Germany, underwent genotyping for detection of BAFF-var allele.

Results
Of the 195 patients, 18 (9.2%) tested positive for BAFF-var variant according to the minor allele frequency of 4.6%. The presence of BAFF-var was associated with the occurrence of lupus nephritis (p = 0.038) (p = 0.03 and p = 0.003). Among various organ manifestations of SLE, the presence of BAFF-var was associated with the occurrence of lupus nephritis (p = 0.038; odds ratio [OR], 2.4; 95% confidence interval [CI], 0.89–6.34) and renal activity markers such as proteinuria and hematuria (p = 0.03; OR, 2.4; 95% CI, 0.9–6.4 for proteinuria; p = 0.003; OR, 3.9; 95% CI, 1.43–10.76 for hematuria). SLE patients carrying the BAFF-var allele exhibited increased disease activity at study entry, as determined by the physician’s global assessment (PGA: p = 0.002; OR, 4.8; 95% CI, 1.54–14.93) and the SLE Disease Activity Index (p = 0.012; OR, 3.5; 95% CI, 1.12–11.18). Consistent with that, the percentage of patients treated with immunosuppressive agents at study entry was higher among those carrying the BAFF-var allele than among those tested negative for BAFF-var (p = 0.006; OR, 3.7; 95% CI, 1.27–10.84).

Conclusions
Our results indicate an association between the BAFF-var genotype and increased severity of SLE. Determining the BAFF-var status of SLE patients may improve the risk stratification of patients for whom the development of lupus nephritis is more likely and thus may be helpful in the follow-up care and treatment of SLE patients.