bluuebunny/crossref_metadata_2025_split huggingface dataset:
5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey
Authors: Chen Chih-Chieh , Liu Yen-Yi , Yang Ya-Chu , Hsu Chu-Yi 
Published: May 2022

Abstract
5NosoAE is a webserver that can be used for nosocomial bacterial analysis including the identification of similar strains based on antimicrobial resistance profiles (antibiogram) and the spatiotemporal distribution visualization and phylogenetic analysis of identified strains with similar antibiograms. The extensive use of antibiotics has caused many pathogenic bacteria to develop multiple drug resistance, resulting in clinical infection treatment challenges and posing a major threat to global public health. Relevant studies have investigated the key determinants of antimicrobial resistance in the whole-genome sequence of bacteria. However, a web server is currently not available for performing large-scale strain searches according to antimicrobial resistance profiles and visualizing epidemiological information including the spatiotemporal distribution, antibiogram heatmap, and phylogeny of identified strains. Here, we implemented these functions in the new server, referred to as 5NosoAE. This server accepts the genome sequence file in the FASTA format of five nosocomial bacteria, namely Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterococcus faecium and Staphylococcus aureus for query. All visualizations are implemented in JavaScript and PHP. This server will be useful for physicians and epidemiologists involved in research on infectious disease. The 5NosoAE platform is available at https://nosoae.imst.nsysu.edu.tw.
Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture
Authors: Zeng Qifan , Zhao Baojun , Wang Hao , Wang Mengqiu , Teng Mingxuan , Hu Jingjie , Bao Zhenmin , Wang Yangfan 
Published: May 2022

Abstract
It is of vital importance to understand the population structure, dissect the genetic bases of performance traits, and make proper strategies for selection in breeding programs. However, there is no single webserver covering the specific needs in aquaculture. We present Aquaculture Molecular Breeding Platform (AMBP), the first web server for genetic data analysis in aquatic species of farming interest. AMBP integrates the haplotype reference panels of 18 aquaculture species, which greatly improves the accuracy of genotype imputation. It also supports multiple tools to infer genetic structures, dissect the genetic architecture of performance traits, estimate breeding values, and predict optimum contribution. All the tools are coherently linked in a web-interface for users to generate interpretable results and evaluate statistical appropriateness. The webserver supports standard VCF and PLINK (PED, MAP) files, and implements automated pipelines for format transformation and visualization to simplify the process of analysis. As a demonstration, we applied the webserver to Pacific white shrimp and Atlantic salmon datasets. In summary, AMBP constitutes comprehensive resources and analytical tools for exploring genetic data and guiding practical breeding programs. AMBP is available at http://mgb.qnlm.ac.
MO119: Lupus Nephritis in Males: About 34 Cases
Authors: Afifi Rania , Elkhayat Ss , Medkouri G , Mtioui N , Zamd M , Ramdani B , Benghanem M 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Lupus nephritis (LN) is one of the most serious manifestations of systemic lupus erythematosus (SLE), affecting mainly young women, but can also affect men. It refers to the development of intrarenal tissue inflammation responsible for various damage at this level: glomerular, vascular and/or tubulointerstitial lesions.
This complication, which can be inaugural, occurs in the majority of cases early in the history of the disease, and constitutes a major evolutionary turning point, which can lead to end-stage chronic renal failure in 5–10% of cases.
The aim of our study was to analyse the different characteristics of NL in humans, since the latter is little studied due to the rarity of cases.

METHOD
We conducted a descriptive retrospective study at the nephrology departments of the Ibn Rochd University Hospital in Casablanca, from January 2011 to August 2021 (i.e. 10 years) on LN. All male patients (34 cases) who developed LN confirmed on renal biopsy.

RESULTS
The average age of the patients was 29.41 years with extremes ranging from 15 to 56 years among them five black patients. The circumstance of discovery of LN was edematous syndrome in 46.87%, nephrotic syndrome 37.5% and renal failure in 15.62% of cases. The renal manifestations were made of arterial hypertension in 21.87% of cases, and haematuria in 15.62% of cases. The extrarenal manifestations were articular in 37.5% of cases, cutaneous in 56.25% of cases and 40.62% of cases had general signs. Biologically, on the blood count, haemolytic anaemia was observed in 87.5% of cases, lymphopenia in 31.25% of cases and thrombocytopaenia in 40.62%, while AANs were positive in 96.87% and anti-DNA antibody were positive in 93.75%. Hypocomplementemia was objectified in 84.37%. Histologically: according to the World Health Organization classification of LN, we have reported: LN class I in a single patient, i.e. 3.12%, and LN class III in 12.5% of cases, LN class IV in 53.12% and LN class V in 31.25%, while the combination of class V and III was seen in one patient and the combination of class IV and V in three cases. Concerning the evolution 34.37% progressed well with complete remission, 31.2% of patients relapsed, while three patients progressed to end-stage kidney disease (ESKD) and all of three from black. The evolution was also marked by death in eight patients; among them four were black.

CONCLUSION
Lupus disease is more aggressive in men and is characterized by a higher rate of complications, including kidney damage. In our study, we were able to deduce that LN in the black race has a bad prognosis.
MO139: Advance Care Planning in Hemodialysis: A Challenge for the Italian Nephrology
Authors: Simone Giuseppina , Toccafondi Alessandro , Ferro Giuseppe , Brogi Lorenzo , Gori Gabriele , Somma Chiara , Tsalouchos Aris , Mehmetaj Alma , Semeraro Francesca , Laudicina Selene , Dattolo Pietro 
Published: May 2022

Abstract

BACKGROUND
Advance care planning (ACP) enables competent patients to define goals and preferences for future treatments and care, to discuss these goals and preferences with relatives, and if appropriate to record these preferences [1]. After many years of political and social debates, in December 2017 the first advance directive and care planning legislation was approved in Italy. In the last years, several national recommendations released by political institutions and medical associations have underlined the importance of conducting ACP with chronic patients, included dialyses patients. Nevertheless, citizens’ awareness of these issues is scarce as well as the integration of the ACP process into clinical routine [2].

METHOD
Since November 2020, our nephrology unit adopted a protocol aimed to conduct ACP interventions with dialysis patients. Firstly, all patients were informed about the possibility to taking part in one or more ACP conversations with their nephrologist. Secondly, a semi-structured guide to the conversation was created in order to support physicians in conducting the ACP intervention. The guide is divided into three sections: (1) exploring patient's understanding of the disease and his/her hopes and life goals; (2) patient's social relationships; (3) preferences for future treatments and care (e.g. CPR, dialysis, palliative care, etc). Finally, patients along with nephrologist and their relatives can document their preferences.

RESULTS
Of 110 haemodialysis patients, 40 treated in our centre asked for an ACP intervention and filled-in an advance directive. Specifically, no patients required an immediate discontinuation of dialysis; nevertheless, 70% of them stated that would not like to continue with dialysis in case he/she was no longer able to self-determine (e.g. permanent loss of capacity to communicate with others). Most of patients (90%) have appointed a personal representative (usually their partner). In the eventuality of cardiac arrest, 55% of patients asked for cardiopulmonary resuscitation. Pain control and palliative care was the overall most cited topic. The fear of being a burden on family members has been frequently expressed by not independent patients. Regarding the last phase of life, 75% of patients expressed the desire to stay at home, the others in hospice.

CONCLUSION
ACP process is very recent in Italy and not well known by patients and healthcare providers (HCPs). As a result, discussions about future treatments and care are rarely included in the clinical routine with haemodialysis patients. Training of HCPs on these issues as well as the use of procedures tailored to the Italian context for conducting ACP interventions is needed.
MO221: Glomerulopathies After COVID-19 Vaccination. Report of Cases in Our Centre
Authors: Perea-Ortega Lara , Polo Criado Carolina , Hidalgo Guzman Pilar , Laura Fuentes Sanchez Maria , Toledo Rojas Remedios 
Published: May 2022

Abstract

BACKGROUND AND AIMS
After the start of the vaccination campaign against the SARS-COV-2 pandemic, it is possible that the number of cases of de novo and relapsing glomerulopathies will increase.
So far, most of the publications related to post-vaccination minimal change disease (also associated with other vaccines against influenza virus, hepatitis B, pneumococcus, etc.) and IgA nephropathy. However, post-vaccination cases of membranous nephropathy, ANCA vasculitis or anti-glomerular basement membrane glomerulonephritis are anecdotal.
Likewise, there are no cases of segmental and focal glomerulonephritis published in the literature.
We present the cases that have appeared in our centre in order to support the theory of a more than probably causal relationship. We highlight two cases of focal and segmental glomerulonephritis, making this publication the first to report this pathology post-vaccination.

METHOD
We present a total of 8 cases reported in our centre since the start of the vaccination campaign. We only considered cases that started with symptoms within 1 month after the first or second dose of the SARS Cov2 vaccine.
Histological diagnosis was obtained in four patients with de novo glomerulopathy. In the other four patients with a flare of their baseline disease, renal biopsy was not performed. In these patients, the diagnosis of recurrence was made on the basis of laboratory and clinical data.

RESULTS
Five patients of the total that appeared in our centre developed minimal change disease (4 of them were recurrences and 1 de novo), 2 cases of de novo focal and segmental glomerulomephritis and 1 case of de novo IgA nephropathy.
Nephrotic range proteinuria and macroscopic haematuria were the most frequent symptoms in our patients and completely reversed after immunosuppressive treatment or, in some cases, with supportive care.
All of them received mRNA-based vaccines (six patients with Pfizer and two with Moderna). The mean time to onset of symptoms after vaccination was 13 days.
There was no difference in sex and the mean age was 40 years.

CONCLUSION
The development of vaccines has been a key factor in the control of the SARS Cov-2 pandemic. The cases reported so far are minimal, compared with the millions of doses administered, so the benefits exceed the risks.
However, according to the literature, we recommend closer follow-up in patients with known glomerulopathies and to perform renal biopsy as soon as possible after the onset of symptoms related to post-vaccination renal disease.
In our centre, most of the cases appeared after the first dose of vaccination and we induced the administration of the remaining doses because all our patients did well with treatment. However, we suggested that one option might be to delay, but not to stop, the second dose in order not to interfere with the immune response to vaccination in patients who are receiving immunosuppression.
MO334: Incidence of AKI Among Hospitalized COVID-19 Patients During the First and Sixth Waves of the Pandemic
Authors: Ardura Paula , Lorenzo Arturo , Martínez Manrique María , Lucía Valencia Ana , Acosta-Ochoa Isabel , Mendiluce Alicia , Fidalgo Veronica , Reinaldo Sanchez Gil Jimmy , Coca Armando 
Published: May 2022

Abstract

BACKGROUND AND AIMS
During the last 2 years, we have witnessed several waves of the COVID-19 pandemic characterized by massive infections among the general population, sudden increases in the number of hospitalizations and variable rates of complications and mortality among patients.
Acute kidney injury (AKI) has been described as a common and serious complication of COVID-19. However, multiple factors that are involved in the development of this complication have been modified throughout these months, including the appearance of new variants of the virus, the modification of treatment protocols or the advancement of vaccination among the general population.
In this study, we aimed to compare the rates of AKI among patients who required admission due to COVID-19 in the first and current (sixth) waves of the pandemic.

METHOD
Consecutive patients that required admission due to COVID-19 in a tertiary referral hospital during the first (March to May 2020) and current (December 2021) waves of the pandemic were enrolled in the study. Patient characteristics, rates of AKI incidence, 28-day mortality and in-hospital length of stay were compared between groups. Viral infection was confirmed by real-time RT-qPCR in all cases. AKI was defined according to the Kidney Disease: Improving Global Outcomes (KDIGO) guidelines using peak serum creatinine and acute dialysis criteria. Multivariate logistic regression was performed to define potential predictors of AKI.

RESULTS
Table 1 summarizes demographic and clinical characteristics among enrolled patients. Compared with the current wave, patients admitted during the first wave were older, had higher baseline serum creatinine and lower baseline eGFR. During the first wave, patients presented higher peak serum creatinine values and a higher incidence of in-hospital AKI. Age, male sex, hypertension, diabetes, CKD and pandemic wave were included in multivariate logistic regression analysis as potential predictors of AKI. Only past history of hypertension [OR 2.867; 95% confidence interval (95% CI) 1.279–6.424; P-value: .011] and CKD (OR 2.418; 95% CI 1.237–4.73; P-value: .01) independently predicted AKI in the sample.

CONCLUSION
Despite multiple changes that have occurred throughout the pandemic, including new treatment protocols, the appearance of new variants of the virus with different clinical profiles or the extensive application of vaccines, these changes have not translated into a significant decrease in the risk of AKI among patients admitted due to COVID-19, which appears to still be conditioned mainly by comorbidities of each patient, including past history of CKD.
MO385: Performance of Creatinine-Based Equations to Estimate Glomerular Filtration Rate in White and Black Subjects From Europe, Brazil and Africa
Authors: Delanaye Pierre , Bjork Jonas , Vidal-Petiot Emmanuelle , Ebert Natalie , Odvar Eriksen Bjørn , Dubourg Laurence , Grubb Anders , Hansson Magnus , Lamb Edmund , Littman Karin , Mariat Christophe , Melsom Toralf , Schaeffner Elke , Sundin Per-Ola , Bokenkamp Arend , Berg Ulla , Asling-Monemi Kasja , Åkesson Anna , Larsson Anders , Cavalier Etienne , Dalton Neil , Courbebaisse Marie , Couzi Lionel , Gaillard François , Garrouste Cyril , Jacquemont Lola , Kamar Nassim , Legendre Christophe , Rostaing Lionel , Stehlé Thomas , Haymann Jean-Philippe , Selistre Luciano , Strogoff-de-Matos Jorge , Bukabau Justine , Sumaili Ernest , Yayo Eric , Monnet Dagui , Nyman Ulf , Pottel Hans , Flamant Martin 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Current Glomerular filtration rate (GFR) estimating equations based on serum creatinine are facing increased criticism due to the inclusion of a race correction in black Americans with the CKD-EPI equation (CKD-EPIASR, A = Age, S = Sex, R = Race). A new equation without race (CKD-EPIAS) has been proposed. However, this equation was developed mainly from US cohorts. The performance of this new equation has been poorly compared with current European-developed creatinine-based equations, i.e. the Lund-Malmö Revised (LMR), and the new European Kidney Function Consortium (EKFC)

METHOD
Data from subjects over 18 years, representing 11 cohorts from Europe (previously described as the EKFC dataset, n = 13 856), and enhanced with data from Brazil (n = 100), France (n = 4429) and Africa [Democratic Republic of Congo (DRC) and Côte d'Ivoire, n = 508] were considered (n = 18 893 for the whole cohort). The EKFC cohort was considered as non-black population. All data from Africa derived from black individuals. From France, 964 subjects were self-reported as black (=Blacks from Paris). Measured GFR as a reference method and IDMS creatinine results were available. Median bias (eGFR—mGFR) with 95% confidence intervals (CI), imprecision (interquartile range: IQR), and P30 accuracy (percentage of eGFR-values within ± 30% of mGFR) with 95% CI were calculated.

RESULTS
Results are summarized in Table.

CONCLUSION
The new CKD-EPIAS has been launched in the USA for societal reasons and is now recommended by US guidelines. However, in Europe and Africa, its performance was suboptimal. The EKFC equation, using the usual Q values, or population-specific Q values (when available), displays the best performance over the whole age range for populations in Europe and Africa.
MO493: Covid-19 Among Romanian HAemodialysis Patients: Risk Factors and Outcomes. Data From the Romanian Renal Registry
Authors: Stefan Gabriel , Garneata Liliana , Podgoreanu Eugen , Mircescu Gabriel 
Published: May 2022

Abstract

BACKGROUND AND AIMS
During the COVID-19 pandemic, patients on maintenance heamodialysis (HD) are vulnerable due to their comorbidities, uremia-impaired immunity and limited physical distancing. We aimed to evaluate the risk factors and outcomes of SARS-CoV-2 infection in HD patients in our country.

METHOD
All HD patients enrolled in the national COVID-19 screening programme between 1 September 2020 and 28 February 2021, were included in this retrospective 6-month cohort study, with outcomes ascertained through 28 February 2021.
We excluded patients under 18 years who received a preemptive kidney graft, recovered kidney function or were lost to follow-up during the first 90 days of HD.
Screening for COVID-19 infection was performed by RT-PCR on nasopharyngeal swabs, every 14 days or at staff indication.
SARS-CoV-2 infection severity was defined as mild, moderate, severe and critical as previously described.
We aimed to evaluate the risk factors for COVID-19 as well as for all-causes of death within 90 days of COVID-19.

RESULTS
A total of 15 401 patients on maintenance HD were included. The median age was 64 years, and two-thirds were &gt;60 years old; 57% were male. Glomerular, diabetic kidney and tubulo-interstitial diseases were the main causes of CKD (18, 11 and 10%, respectively).
During the 6-months, 5386 patients (35%) were COVID-19 positive. Compared with negative patients, they had longer vintages, were more often treated by public dialysis providers and had a higher mortality.
Patients in the first 90 days of HD treated by public providers were more prone to SARS-CoV-2 infection in the multivariate logistic regression analysis (Table 1A).
A total of 15% of the COVID-19 patients died; those with the critical SARS-CoV-2 infection had the lowest survival of 8%, followed by those with severe (35%), medium (72%) and asymptomatic (89%) (Fig. 1).
COVID-19 patients &gt;70 years, of male sex, in the first 90 days of HD, with diabetic kidney disease, and from a public unit had higher mortality. Moreover, the same risk factors were retained in the multivariate Cox proportional hazard model (Table 1B).

CONCLUSION
The COVID-19 pandemic has had a substantial effect on mortality in HD patients affected by SARS-CoV-2 in Romania, especially those elderly and diabetic, with severe and critical clinical forms.
MO496: Serum Urea Levels and Cardiovascular Disease in Patients With Chronic Kidney Disease
Authors: Laville Solene , Couturier Aymeric , Lambert Oriane , Metzger Marie , Nicolas Mansencal , Jacquelinet Christian , Laville Maurice , Frimat Luc , Fouque Denis , Combe Christian , Robinson Bruce , Stengel Benedicte , Liabeuf Sophie , Massy Ziad 
Published: May 2022

Abstract

BACKGROUND AND AIMS
Elevated serum urea levels are common in moderate-to-advanced CKD. Several studies have shown that urea is a direct and indirect uremic toxin, especially with regard to cardiovascular disease. We sought to determine whether serum urea levels are associated with adverse cardiovascular events and death before kidney replacement therapy (KRT) in patients with CKD.

METHOD
CKD-REIN is a prospective cohort of CKD nephrology outpatients not receiving maintenance dialysis. The 2507 patients included in the analysis were divided into three groups according to the baseline serum urea level (T1 &lt; 10.5, T2:10.5–15.1 and T3 ≥ 15.1 mmol/L). Cause-specific Cox proportional hazard models were used to estimate hazard ratios (HRs) for the first atheromatous or nonatheromatous cardiovascular (CV) events and all-cause mortality before KRT. The models were adjusted for baseline comorbidities, laboratory data, and medications. Cardiovascular events of the first 3 years of follow-up in the CKD-REIN study were assessed carefully according to the Cardiovascular and Stroke Endpoint Definitions for Clinical Trials. Each death before KRT occurring during the 5-year follow-up period was used in the all-cause mortality model.

RESULTS
Of the 2507 included patients {median [first quartile–third quartile (Q1–Q3)] age: 69 (61–77); mean (standard deviation) eGFR 33.5(11.6) mL/min/1.73 m²}, 54% had a history of cardiovascular disease.
Over a median follow-up of 3.0 years [Q1–Q3, 2.2–3.1], 451 experienced their first atheromatous or nonatheromatous cardiovascular event (fatal or nonfatal), leading to an incidence rate (IR) [95% confidence interval (95% CI)] of 7.1 (6.4–7.7)/100 person-years (PYs) (Fig. 1).
Over a median follow-up period of 4.8 (3.3–5.1) years, 407 patients died before KRT, leading to an IR of 4.0 (3.6–4.3)/100 PYs.
After multiple adjustments for cardiovascular risk factors (including eGFR), patients in T3 had a higher risk of atheromatous and nonatheromatous cardiovascular events than patients in T1 [HR (95% CI), 2.08 (1.50–2.88), Fig. 1]. A nonsignificant trend towards a higher risk was also noted for patients in T2 [1.28 (0.96–1.71)]. The adjusted HRs for death before KRT were 1.30 (0.96–1.75] and 1.73 (1.22–2.45) for patients in T2 and those in T3, respectively.

CONCLUSION
Beyond CV risk factors including eGFR, this hypothesis-generating study suggests that serum urea level is a predictor of cardiovascular outcomes in patients with moderate to advanced CKD. Further research is needed to confirm current findings and explore mechanisms.