bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immune escape mutations in HIV-1 controllers in the Brazilian Amazon region
Authors: Gomes Samara Tatielle Monteiro , da Silva Graça Amoras Ednelza , Gomes Érica Ribeiro , Queiroz Maria Alice Freitas , Júnior Edivaldo Costa Sousa , de Vasconcelos Massafra Janaína Mota , da Silva Lemos Poliana , Júnior João Lídio Vianez , Ishak Ricardo , Vallinoto Antonio Carlos Rosário 
Published: July 2020

Abstract
Background
Human immunodeficiency virus (HIV-1) infection is characterized by high viral replication and a decrease in CD4+ T cells (CD4+TC), resulting in AIDS, which can lead to death. In elite controllers and viremia controllers, viral replication is naturally controlled, with maintenance of CD4+TC levels without the use of antiretroviral therapy (ART).

Methods
The aim of the present study was to describe virological and immunological risk factors among HIV-1-infected individuals according to characteristics of progression to AIDS. The sample included 30 treatment-naive patients classified into three groups based on infection duration (> 6 years), CD4+TC count and viral load: (i) 2 elite controllers (ECs), (ii) 7 viremia controllers (VCs) and (iii) 21 nonviremia controllers (NVCs). Nested PCR was employed to amplify the virus genome, which was later sequenced using the Ion PGM platform for subtyping and analysis of immune escape mutations.

Results
Viral samples were classified as HIV-1 subtypes B and F. Greater selection pressure on mutations was observed in the group of viremia controllers, with a higher frequency of immunological escape mutations in the genes investigated, including two new mutations in gag. The viral sequences of viremia controllers and nonviremia controllers did not differ significantly regarding the presence of immune escape mutations.

Conclusion
The results suggest that progression to AIDS is not dependent on a single variable but rather on a set of characteristics and pressures exerted by virus biology and interactions with immunogenetic host factors.
Differentiation of soft tissue and bone sarcomas from benign lesions utilizing 18F-FDG PET/CT-derived parameters
Authors: Chen Bo , Feng Hongbo , Xie Jinghui , Li Chun , Zhang Yu , Wang Shaowu 
Published: July 2020

Abstract
Background
Accurate differentiation between malignant and benign changes in soft tissue and bone lesions is essential for the prevention of unnecessary biopsies and surgical resection. Nevertheless, it remains a challenge and a standard diagnosis modality is urgently needed. The objective of this study was to evaluate the usefulness of 18F-fluorodeoxyglucose (18F-FDG) PET/CT-derived parameters to differentiate soft tissue sarcoma (STS) and bone sarcoma (BS) from benign lesions.

Methods
Patients who had undergone pre-treatment 18F-FDG PET/CT imaging and subsequent pathological diagnoses to confirm malignant (STS and BS, n = 37) and benign (n = 33) soft tissue and bone lesions were retrospectively reviewed. The tumor size, PET and low-dose CT visual characteristics, maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), total lesion glycolysis (TLG), and heterogeneous factor (HF) of each lesion were measured. Univariate and multivariate logistic regression analyses were conducted to determine the significant risk factors to distinguish sarcoma from benign lesions. To establish a regression model based on independent risk factors, and the receiver operating characteristic curves (ROCs) of individual parameters and their combination were plotted and compared. Conventional imaging scans were re-analyzed, and the diagnostic performance compared with the regression model.

Results
Univariate analysis results revealed that tumor size, SUVmax, MTV, TLG, and HF of 18F-FDG PET/CT imaging in the STS and BS group were all higher than in the benign lesions group (all P values were < 0.01). The differences in the visual characteristics between the two groups were also all statistically significant (P < 0.05). However, the multivariate regression model only included SUVmax and HF as independent risk factors, for which the odds ratios were 1.135 (95%CI: 1.026 ~ 1.256, P = 0.014) and 7.869 (95%CI: 2.119 ~ 29.230, P = 0.002), respectively. The regression model was constructed using the following expression: Logit (P) = − 2.461 + 0.127SUVmax + 2.063HF. The area under the ROC was 0.860, which was higher than SUVmax (0.744) and HF (0.790). The diagnostic performance of the regression model was superior to those of individual parameters and conventional imaging.

Conclusion
The regression model including SUVmax and HF based on 18F-FDG PET/CT imaging may be useful for differentiating STS and BS from benign lesions.
Trabecular bone score may indicate chronic kidney disease-mineral and bone disorder (CKD-MBD) phenotypes in hemodialysis patients: a prospective observational study
Authors: Yun Hyo Jin , Ryoo Soo Ryeong , Kim Jung-Eun , Choi Yong Jun , Park Inwhee , Shin Gyu-Tae , Kim Heungsoo , Jeong Jong Cheol 
Published: July 2020

Abstract
Background
In the general population, the trabecular bone score (TBS) represents the bone microarchitecture and predicts fracture risk independent of bone mineral density (BMD). A few studies reported that TBS is significantly reduced in dialysis patients. Chronic kidney disease-mineral and bone disorder (CKD-MBD) are accompanied by increased fracture risk, cardiovascular morbidity, and mortality. We investigated whether TBS is associated with comorbidity related to CKD-MBD or frailty in hemodialysis patients.

Methods
In this prospective observational study, TBS was obtained using the TBS iNsight software program (Med-Imaps) with BMD dual energy x-ray absorptiometry (DXA) images (L1–L4) from prevalent hemodialysis patients. A Tilburg frailty indicator was used to evaluate frailty, and hand grip strength and bio-impedance (InBody) were measured. A patient-generated subjective global assessment (PG-SGA) was used for nutritional assessment. The history of cardiovascular events (CVE) and demographic, clinical, laboratory, and biomarker data were collated. We then followed up patients for the occurrence of CKD-MBD related complications.

Results
We enrolled 57 patients in total. The mean age was 56.8 ± 15.9 years (50.9% female). Prevalence of Diabetes mellitus (DM) was 40.4% and CVE was 36.8%. Mean TBS was 1.44 ± 0.10. TBS significantly reduced in the CVE group (1.38 ± 0.08 vs. 1.48 ± 0.10, p <  0.001). Multivariable regression analysis was conducted adjusting for age, sex, dialysis vintage, DM, CVE, albumin, intact parathyroid hormone, fibroblast growth factor 23, handgrip strength, and phosphate binder dose. Age (ß = − 0.030; p = 0.001) and CVE (ß = − 0.055; p = 0.024) were significant predictors of TBS. During the follow up period after TBS measurements (about 20 months), four deaths, seven incident fractures, and six new onset CVE were recorded. Lower TBS was associated with mortality (p = 0.049) or new onset fracture (p = 0.007, by log-rank test).

Conclusion
Lower TBS was independently associated with increased age and CVE prevalence in hemodialysis patients. Mortality and fracture incidence were significantly higher in patients with lower TBS values. These findings suggest that TBS may indicate a phenotype of frailty and also a CKD-MBD phenotype reciprocal to CVE.
Thematic analysis of the medical records of patients evaluated for kidney transplant who did not receive a kidney
Authors: Butler Catherine R. , Taylor Janelle S. , Reese Peter P. , O’Hare Ann M. 
Published: July 2020

Abstract
Background
A potential pitfall of policies intended to promote referral for kidney transplant is that greater numbers of patients may be evaluated for transplant without experiencing the intended benefit of receiving a kidney. Little is known about the potential implications of this experience for patients.

Methods
We performed a thematic analysis of clinician documentation in the electronic medical records of all adults at a single medical center with advanced kidney disease who were referred to the local transplant coordinator for evaluation between 2008 and 2018 but did not receive a kidney.

Results
148 of 209 patients referred to the local kidney transplant coordinator at our center (71%) had not received a kidney by the end of follow-up. Three dominant themes emerged from qualitative analysis of documentation in the medical records of these patients: 1) Forward momentum: patients found themselves engaged in an iterative process of testing and treatment that tended to move forward unless an absolute contraindication to transplant was identified or patients disengaged; 2) Potential for transplant shapes other medical decisions: engagement in the transplant evaluation process could impact many other aspects of patients’ care; and 3) Personal responsibility and psychological burden for patients and families: clinician documentation suggested that patients felt personally responsible for the course of their evaluation and that the process could take an emotional toll on them and their family members.

Conclusions
Engagement in the kidney transplant evaluation process can be a significant undertaking for patients and families and may impact many other aspects of their care. Policies to promote referral for kidney transplant should be coupled with efforts to strengthen shared decision-making to ensure that the decision to undergo transplant evaluation is framed as an explicit choice with benefits, risks, and alternatives and patients have an opportunity to shape their involvement in this process.
Foods contributing to nutrients intake and assessment of nutritional status in pre-dialysis patients: a cross-sectional study
Authors: Seo Yeon Kyung , Lee Hyesu , Kim Hyunsuk , Kim Tae Yeon , Ryu Hyunjin , Ju Dal Lae , Jang Miyoung , Oh Kook-Hwan , Ahn Curie , Han Sung Nim 
Published: July 2020

AbstractBackgroundFor chronic kidney disease (CKD) patients, management of nutritional status is critical for delaying progression to end-stage renal disease. The purpose of this study is to provide the basis for personalized nutritional intervention in pre-dialysis patients by comparing the foods contributing to nutrients intake, nutritional status and potential dietary inflammation of CKD patients according to the diabetes mellitus (DM) comorbidity and CKD stage.MethodsTwo hundred fifty-six outpatients referred to the Department of Nephrology at SNUH from Feb 2016 to Jan 2017 were included. Subjects on dialysis and those who had undergone kidney transplantation were excluded. Bioelectrical impedance analysis (BIA), subjective global assessment (SGA), dietary intake, and biochemical parameters were collected. Subjects were classified into 4 groups according to DM comorbidity (DM or Non-DM) and CKD stage (Early or Late) by kidney function. Two-way analysis of variance and multinomial logistic regression analysis were performed for statistical analysis.ResultsTotal number of malnourished patients was 31 (12.1%), and all of them were moderately malnourished according to SGA. The body mass index (BMI) of the DM-CKD group was significantly higher than the Non-DM-CKD group. The contribution of whole grains and legumes to protein intake in the DM-CKD group was greater than that in the Non-DM-CKD group. The DM- Early-CKD group consumed more whole grains and legumes compared with the Non-DM-Early-CKD group. The subjects in the lowest tertile for protein intake had lower phase angle, SGA score and serum albumin levels than those in the highest tertile. The potential for diet-induced inflammation did not differ among the groups.ConclusionsSignificant differences in intakes of whole grains and legumes between CKD patients with or without DM were observed. Since contribution of whole grains and legumes to phosphorus and potassium intake were significant, advice regarding whole grains and legumes may be needed in DM-CKD patients if phosphorus and potassium intake levels should be controlled. The nutritional status determined by BIA, SGA and serum albumin was found to be different depending on the protein intake. Understanding the characteristics of food sources can provide a basis for individualized nutritional intervention for CKD patients depending on the presence of diabetes.
PhysIOpathology of NEuromuscular function rElated to fatigue in chronic Renal disease in the elderly (PIONEER): study protocol
Authors: Chatrenet Antoine , Beaune Bruno , Fois Antioco , Pouliquen Camille , Audebrand Jean-Michel , Torreggiani Massimo , Paris Damien , Durand Sylvain , Piccoli Giorgina Barbara 
Published: July 2020

Abstract
Background
Chronic Kidney Disease (CKD) is associated with reduced muscular strength resulting in profound fatigue. The physiopathology of these changes, their prevalence and evolution are still debated. Moreover, we have little data on elderly CKD patients. The present study protocol aims to 1) quantify the prevalence of low muscle strength (dynapenia) in a cohort of elderly patients with advanced CKD and to 2) characterize their force production coupled with electromyographic features and the symptoms of fatigue compared to a matched control group.

Methods
This is a case-control, prospective, interventional study. Inclusion criteria: age ≥ 60 years; CKD Stage 3b-5; clinical stability (i.e. no hospitalization and ≤ 25% in creatinine increase in the previous 3 months). Controls with normal kidney function will be matched in terms of age, gender and diabetes mellitus (requisite: estimated glomerular filtration rate ≥ 60 ml/min/1.73m2 available in the last 6 months). Exclusion criteria for cases and controls: neuromuscular disease, life expectancy < 3 months.
The handgrip strength protocol is an intermittent test consisting in 6 series of 9 repetitions of 3-s sub-maximum contractions at 40% of the maximum voluntary contraction (MVC) and 2 s of resting time between contractions. Each series is separated by one fast sub-maximum contraction and one MVC. Strength is assessed with a high-frequency handgrip dynamometer paired with surface electromyography. Symptoms of fatigue are assessed using MFI-20 and FACIT-F questionnaires. In order to reach a statistical power of 96%, we plan to enroll 110 subjects in each group.

Discussion
The novelty of this study resides in the application of an already validated set of tests in a population in which this combination (dynamometer, electromyography and questionnaires) has not previously been explored. We expect a high prevalence of dynapenia and a higher fatigability in CKD patients. A positive correlation is expected between reported fatigue and fatigability.
Better appreciation of the prevalence and the relationship between fatigability and a sensation of fatigue can help us target interventions in CKD patients to improve quality of life and survival.

Trial registration
The study was approved by Ethical Committee EST III n°20.03.01 and was recorded as a Clinical Trial (NCT04330807) on April 2, 2020.
Factors influencing utilization of skilled birth attendant during childbirth in the Southern highlands, Tanzania: a multilevel analysis
Authors: Damian Damian J. , Tibelerwa Judges Y. , John Beatrice , Philemon Rune , Mahande Michael J. , Msuya Sia E. 
Published: July 2020

Abstract
Background
Use of skilled health provider (SBA) during and after childbirth has been reported to reduce maternal and newborn deaths; and is one of the key indicators monitored in Sustainable Development Goals (SDGs). Progress, levels and factors influencing utilization of SBA differ within and between countries. In Tanzania, SBA coverage stands at 64% while the national target is 80%; with wide variability between regions (42–96%). This study aimed at determining factors associated with utilization of skilled births providers during childbirth in Mbeya Region, Southern highlands, Tanzania.

Methods
This was a cross-sectional analytical study conducted in December 2015 to January 2016, in Mbeya Region. A total of 2844 women of reproductive age were enrolled, but only 1777 women who reported a live birth 5 years prior to the survey were included in this analysis. Multilevel logistic regression analyses were used to determine independent factors influencing utilization of SBA during childbirth. Random effects logistic model was used to assess the variability between clusters on the odds of using skilled birth attendants during delivery.

Results
In this setting, 81% of the women reported utilization of skilled births attendants during childbirth. ANC visits four times or more (aOR = 1.63–95% CI = 1.26, 2.10; p < 0.001) and having secondary education or higher (aOR = 2.16; 95% CI = 1.19–3.90; p = 0.011) were associated with increased SBA use during childbirth whereas having two (aOR = 0.51; 95% CI: 0.33–0.79; p = 0.003) or three children (aOR = 0.37; 95% CI: 0.27–0.58; p < 0.001) relative to one child, 30 to 60 min walking distance to the health facility (aOR = 0.66; 95% CI: 0.48–0.92; p = 0.012) and more than 1 h walking distance to the health facility (aOR = 0.43; 95% CI: 0.32–0.57; p < 0.001) compared to < 30 min; were associated with decreased SBA use during childbirth.

Conclusion
The proportion of births attended by skilled births attendants was high, but 19% of the women are still left behind. Concentrated efforts to improve utilization of SBA should be targeted to women with low education, with higher number of children, and with low frequency of ANC attendance. Furthermore, community and facility interventions addressing transport for pregnant women are needed. Qualitative study to explore the barriers of SBA use among the 19% who are not using skilled assistance during childbirth is needed.
Pregnancy induced Cushing’s syndrome and primary aldosteronism: a case report
Authors: Kersten Maria , Hancke Katharina , Janni Wolfgang , Kraft Katrina 
Published: July 2020

Abstract
Background
First manifestation of Cushing’s syndrome during pregnancy is rare. The diagnosis of both Cushing’s and primary aldosteronism within a pregnancy has not been previously documented. Diagnosis is especially challenging due to the normal physiological changes that occur during pregnancy. Consequently, many tests that are normally used for diagnosis are not reliable. Tumor based etiologies can be surgically removed. Etiologies that are not tumor based are challenging to treat during pregnancy.

Case presentation
A 25 year old G1P0 was admitted in the 22 5/7 week of pregnancy with elevated blood pressure (200/100 mm Hg), acne, moon facies, abdominal striae and hirsutism. With five antihypertensive medications her blood pressure remained 190/100 mm Hg. The patient was admitted to the ICU for intravenous medications and monitoring. She was diagnosed with Cushing’s syndrome and primary aldosteronism. In spite of therapy with spironolactone and metyrapone she developed preeclampsia and was delivered in the 26 0/7 week of pregnancy. At her follow up visit eight weeks postpartum she had blood pressure within normal limits, no clinical signs or symptoms, and all medications had been discontinued.

Conclusions
Early diagnosis of pregnancy induced Cushing’s syndrome and primary aldosteronism requires an interdisciplinary approach. Late detection has been associated with increased perinatal morbidity and mortality including but not limited to placental abruption and intrauterine demise. Collaboration is essential in the optimization of maternal and fetal outcomes.
Detection of genes mutations in cerebrospinal fluid circulating tumor DNA from neoplastic meningitis patients using next generation sequencing
Authors: Zhao Yue , He Jun Ying , Cui Jun Zhao , Meng Zi-Qi , Zou Yue Li , Guo Xiao Su , Chen Xin , Wang Xueliang , Yan Li-Tian , Han Wei Xin , Li Chunyan , Guo Li , Bu Hui 
Published: July 2020

Abstract
Background
This study profiled the somatic genes mutations and the copy number variations (CNVs) in cerebrospinal fluid (CSF)-circulating tumor DNA (ctDNA) from patients with neoplastic meningitis (NM).

Methods
A total of 62 CSF ctDNA samples were collected from 58 NM patients for the next generation sequencing. The data were bioinformatically analyzed by (Database for Annotation, Visualization and Integrated Discovery) DAVID software.

Results
The most common mutated gene was TP53 (54/62; 87.10%), followed by EGFR (44/62; 70.97%), PTEN (39/62; 62.90%), CDKN2A (32/62; 51.61%), APC (27/62: 43.55%), TET2 (27/62; 43.55%), GNAQ (18/62; 29.03%), NOTCH1 (17/62; 27.42%), VHL (17/62; 27.42%), FLT3 (16/62; 25.81%), PTCH1 (15/62; 24.19%), BRCA2 (13/62; 20.97%), KDR (10/62; 16.13%), KIT (9/62; 14.52%), MLH1 (9/62; 14.52%), ATM (8/62; 12.90%), CBL (8/62; 12.90%), and DNMT3A (7/62; 11.29%). The mutated genes were enriched in the PI3K-Akt signaling pathway by the KEGG pathway analysis. Furthermore, the CNVs of these genes were also identified in these 62 samples. The mutated genes in CSF samples receiving intrathecal chemotherapy and systemic therapy were enriched in the ERK1/2 signaling pathway.

Conclusions
This study identified genes mutations in all CSF ctDNA samples, indicating that these mutated genes may be acted as a kind of biomarker for diagnosis of NM, and these mutated genes may affect meningeal metastasis through PI3K-Akt signaling pathway.
Preoperative fibrinogen-to-albumin ratio, a potential prognostic factor for patients with stage IB-IIA cervical cancer
Authors: An Qiang , Liu Wei , Yang Yujia , Yang Bing 
Published: July 2020

AbstractBackgroundPrevious studies have shown that fibrinogen-to-albumin ratio (FAR) is a novel prognostic immune biomarker in various diseases. In this study, we investigated the role of FAR in the prognosis of patients with stage IB-IIA cervical cancer (CC).MethodsA total of 278 eligible participants with newly diagnosed CC (stage IB-IIA) who had undergone radical hysterectomy followed by adjuvant chemotherapy were enrolled in this study. Demographics, clinicopathological variables, and laboratory tests were obtained from the medical records. Risk factors for overall survival (OS) and recurrence-free survival (RFS) were evaluated by univariate and multivariate Cox proportional regression analyses. The association between OS, RFS, and FAR was assessed by the Kaplan–Meier method using log-rank test.ResultsFAR was associated with age, International Federation of Gynecology and Obstetrics (FIGO) stage, depth of the invasion, and C-reactive protein (CRP) level (P < 0.05). Preoperative FAR was an effective predictor for OS in CC patients with a cut-off value of 7.75 and an area under the curve (AUC) of 0.707 (P < 0.001). The univariate and multivariate Cox analyses indicated that FIGO stage and FAR were two independent risk factors for both OS and RFS (P < 0.05). Kaplan–Meier analysis confirmed that patients with high FAR levels showed significantly lower RFS (P = 0.004) and OS (P = 0.003) than those with low FAR levels.ConclusionsThis study indicated that elevated preoperative FAR might be a novel prognostic factor for CC patients with stage IB-IIA.