bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing the functional reserve of the kidney before hematopoietic stem cell transplantation: doubt remains
Authors: De Moor Bart , Sprangers Ben 
Published: April 2023

ABSTRACT
Acute kidney injury is a common and important complication following hematopoietic stem cell transplantation. In the nephrology community, acute kidney injury is no longer viewed as a simple temporary and potentially reversible decline in kidney clearance as acute kidney injury imposes a risk for immediate and future complications. Therefore, stratifying patients for the risk of acute kidney injury following stem cell transplantation would be very helpful to optimize peri-stem cell transplant management and could potentially improve outcomes in this patient population. In the current issue of CKJ, Mancianti et al. report on the testing of the kidney's functional reserve in patients planned for stem cell transplantation and demonstrate that stem cell transplant candidates with a preserved kidney response on a protein load had a higher chance of full kidney recovery after an episode of acute kidney injury. In this editorial, we discuss the kidney's functional reserve test and its limitations.
Validation of the German Registry for Acute Aortic Dissection Type A Score in predicting 30-day mortality after type A aortic dissection surgery
Authors: Gemelli Marco , Di Tommaso Ettorino , Natali Roberto , Dixon Lauren Kari , Mohamed Ahmed Eltayeb , Rajakaruna Cha , Bruno Vito D 
Published: April 2023

Abstract

OBJECTIVES
No reliable scores are available to predict mortality following surgery for type A acute aortic dissection (TAAAD). Recently, the German Registry of Acute Aortic Dissection Type A (GERAADA) score has been developed. We aim to compare how the GERAADA score performs in predicting operative mortality for TAAAD to the European System for Cardiac Operative Risk Evaluation (EuroSCORE) II.

METHODS
We calculated the GERAADA score and EuroSCORE II in patients who underwent TAAAD repair at the Bristol Heart Institute. As there are no precise criteria to calculate the GERAADA score, we used 2 methods: a Clinical-GERAADA score, which evaluated malperfusion with clinical and radiological evidence, and a Radiological-GERAADA score, where malperfusion was assessed by computed tomography scan alone.

RESULTS
207 consecutive patients had surgery for TAAAD, and the observed 30-day mortality was 15%. The Clinical-GERAADA score showed the strongest discriminative power with an area under the curve (AUC) of 0.80 [95% confidence interval (CI) 0.71–0.89], while the Radiological-GERAADA score had an AUC of 0.77 (95% CI 0.67–0.87). EuroSCORE II showed acceptable discriminative power with an AUC of 0.77 (95% CI 0.67–0.87).

CONCLUSIONS
Clinical GERAADA score performed better than the other scores and it is specific and easy to use in the context of a TAAAD. Further validation of the new criteria for malperfusion is needed.
Deletion of biofilm synthesis in Eubacterium limosum ATCC 8486 improves handling and transformation efficiency
Authors: Sanford Patrick A , Miller Katherine G , Hoyt Kathryn O , Woolston Benjamin M 
Published: April 2023

Abstract
Eubacterium limosum is an acetogenic bacterium of potential industrial relevance for its ability to efficiently metabolize a range of single carbon compounds. However, extracellular polymeric substance (EPS) produced by the type strain ATCC 8486 is a serious impediment to bioprocessing and genetic engineering. To remove these barriers, here we bioinformatically identified genes involved in EPS biosynthesis, and targeted several of the most promising candidates for inactivation, using a homologous recombination-based approach. Deletion of a single genomic region encoding homologues for epsABC, ptkA, and tmkA resulted in a strain incapable of producing EPS. This strain is significantly easier to handle by pipetting and centrifugation, and retains important wild-type phenotypes including the ability to grow on methanol and carbon dioxide and limited oxygen tolerance. Additionally, this strain is also more genetically tractable with a 2-fold increase in transformation efficiency compared to the highest previous reports. This work advances a simple, rapid protocol for gene knockouts in E. limosum using only the native homologous recombination machinery. These results will hasten the development of this organism as a workhorse for valorization of single carbon substrates, as well as facilitate exploration of its role in the human gut microbiota.
Evaluation of bacterial and fungal communities during the fermentation of pine needle
Authors: Xu Yinyu , Wen Qian , He Hao , Shi Hao , Chen Hongjun , Shi Pengtu , Zhou Wenhua 
Published: April 2023

Abstract
To improve the quality and organoleptic properties of fermented pine needle, the physiological parameters and microbial communities must be explored. In this study, high-throughput sequencing was used to explore bacterial and fungal communities during the fermentation process of pine needle after adding starter culture of 0.8% activated dry yeast and Lactobacillus fermentum CECT5716 and Bifidobacterium Breve M-16 V. During the fermentation, the total flavonoid (from 0.049 to 111.404 mg/L) and polyphenol (from 19.412 to 183.399 mg/L) contents increased rapidly from 0 to 15 days. The total sugar increased from 0 to 3 days fermentation with a range from 3.359 mg/mL to 45.502 mg/mL in yeast fermentation stage, and reached the maximum value on day 3. The content of total acid (39.167 g/L) and amino acid nitrogen (1.185 g/L) gradually increased during the entire fermentation process and reached a maximum on day 7 of bacterial fermentation. Firmicutes and Proteobacteria phyla were the predominant bacteria in all time periods. At the genus level, well-known Lactobacillus was the most abundant bacterial strain on day 3, followed by Gluconobacter. The Acetobacter constituted more than 50% of the total bacterial abundance on day 1, but it decreased with the fermentation process. Exploration of fermented pine needle microbial community structure will expand the knowledge about their microbiota to manipulate the microbial community and improve their quality and organoleptic properties using different microbial recipes.
Increased Risks for Suicide, Self-Harm, Substance Use, and Psychiatric Disorders in Adults With Inflammatory Bowel Disease: A Nationwide Study in the United States From 2007 to 2017
Authors: Tse Chung Sang , Weng Chien-Hsiang , Kwon Michelle , Wolk Courtney Benjamin , Brown Lily A , Malani Kanika , Shah Samir A , Fine Sean D 
Published: April 2023

Lay Summary
In an analysis of over 260 million emergency department visits across the United States from 2007 to 2017, inflammatory bowel disease conferred &gt;10-fold risk for suicide deaths, self-harm, substance use, and psychiatric disorders, though the overall self-harm rates were low (&lt;1% of all-cause inflammatory bowel disease emergency department visits; total 56 suicide deaths).
Online Dictionaries and Accessibility for People with Visual Impairments
Authors: Rees Geraint Paul 
Published: April 2023

Abstract
Making information about language accessible to users has long been a key concern of lexicographic research. Adopting a narrower perspective, this examination of three dictionary websites (collinsdictionary.com, merriam-webster.com, and dle.rae.es) employs the Web Content Accessibility Guidelines (WCAG) to examine their accessibility for people with visual impairments. Dictionaries can be motors for social inclusion of this oft-marginalised group since, beyond resolving language doubts, they can also help affirm socio-cultural identities. Unlike paper dictionaries where space-saving conventions make accessibility a challenge, in principle, online resources are adaptable to the needs of users with visual impairments. In practice, although none of the websites evaluated meet any officially recognised WCAG conformance level, they do contain features aimed at improving accessibility for this group. Most impediments to accessibility are the result of ancillary elements such as advertising, social media, games, and word of the day features. Although these ancillary elements may not necessarily be the principal focus of dictionary use, they nonetheless have a negative effect on the accessibility of the dictionary entry itself. This article concludes with suggestions for solving several of these accessibility issues.
UnravelingAzospirillum’s colonization ability through microbiological and molecular evidence
Authors: Nievas S , Coniglio A , Takahashi W Y , López G A , Larama G , Torres D , Rosas S , Etto R M , Galvão C W , Mora V , Cassán F 
Published: April 2023

AbstractIt is known that members of the bacterial genus Azospirillum can promote the growth of a great variety of plants, an ability harnessed by the industry to create bioproducts aimed to enhance the yield of economically relevant crops. Its versatile metabolism allows this bacterium to adapt to numerous environments, from optimal to extreme or highly polluted. The fact of having been isolated from soil and rhizosphere samples collected worldwide and many other habitats proves its remarkable ubiquity. Azospirillum rhizospheric and endophytic lifestyles are governed by several mechanisms, leading to efficient niche colonization. These mechanisms include cell aggregation and biofilm formation, motility, chemotaxis, phytohormone and other signaling molecules production, and cell-to-cell communication, in turn, involved in regulating Azospirillum interactions with the surrounding microbial community. Despite being infrequently mentioned in metagenomics studies after its introduction as an inoculant, an increasing number of studies detected Azospirillum through molecular tools (mostly 16S rRNA sequencing) as part of diverse, even unexpected, microbiomes. This review focuses on Azospirillum traceability and the performance of the available methods, both classical and molecular. An overview of Azospirillum occurrence in diverse microbiomes and the less-known features explaining its notorious ability to colonize niches and prevail in multiple environments is provided.
Machine-learning enhancement of urine dipstick tests for chronic kidney disease detection
Authors: Jang Eun Chan , Park Young Min , Han Hyun Wook , Lee Christopher Seungkyu , Kang Eun Seok , Lee Yu Ho , Nam Sang Min 
Published: April 2023

Abstract

Objective
Screening for chronic kidney disease (CKD) requires an estimated glomerular filtration rate (eGFR, mL/min/1.73 m2) from a blood sample and a proteinuria level from a urinalysis. We developed machine-learning models to detect CKD without blood collection, predicting an eGFR less than 60 (eGFR60 model) or 45 (eGFR45 model) using a urine dipstick test.

Materials and Methods
The electronic health record data (n = 220 018) obtained from university hospitals were used for XGBoost-derived model construction. The model variables were age, sex, and 10 measurements from the urine dipstick test. The models were validated using health checkup center data (n = 74 380) and nationwide public data (KNHANES data, n = 62 945) for the general population in Korea.

Results
The models comprised 7 features, including age, sex, and 5 urine dipstick measurements (protein, blood, glucose, pH, and specific gravity). The internal and external areas under the curve (AUCs) of the eGFR60 model were 0.90 or higher, and a higher AUC for the eGFR45 model was obtained. For the eGFR60 model on KNHANES data, the sensitivity was 0.93 or 0.80, and the specificity was 0.86 or 0.85 in ages less than 65 with proteinuria (nondiabetes or diabetes, respectively). Nonproteinuric CKD could be detected in nondiabetic patients under the age of 65 with a sensitivity of 0.88 and specificity of 0.71.

Discussion and Conclusions
The model performance differed across subgroups by age, proteinuria, and diabetes. The CKD progression risk can be assessed with the eGFR models using the levels of eGFR decrease and proteinuria. The machine-learning-enhanced urine-dipstick test can become a point-of-care test to promote public health by screening CKD and ranking its risk of progression.
Comprehensive Quality Evaluation of Qizhi Xiangfu Pills Based on Quantitative Analysis of Multi-Components by a Single Marker Combined with GC Fingerprints and Chemometrics
Authors: Zou Jia-Jia , Xu Xiao-Li , Yang Lin , Wang Yi-Wu , Li Yan , Dai Lei , He Dan 
Published: April 2023

Abstract

Background
Qizhi Xiangfu Pills (QXPs) are a traditional Chinese medicine (TCM) used clinically for qi stagnation and blood stasis. The current quality control of QXPs in the ministry standards and the reported literature is minimal, and requires improvement.

Objective
This study aimed to analyze and determine the active ingredients in QXPs for its overall evaluation.

Methods
In this study, a quantitative analysis of multi-components by a single marker (QAMS) method was established to simultaneously determine caryophyllene oxide, cyperotundone, ligustilide, and α-cyperone in QXPs by GC. Moreover, the GC fingerprints of 22 batches of samples were also established, and the common peaks were initially identified by GC–MS, then classified in various dimensions using chemometric methods, and the main markers causing the discrepancies between groups were analyzed by orthogonal partial least-squares discrimination analysis (OPLS-DA).

Results
Compared with an internal standard method (ISM), the determination results obtained by QAMS had no significant difference. Twenty-two common peaks were distinguished in the fingerprint of 22 batches of QXPs, 17 of which were identified, and the similarity of the fingerprints was greater than 0.898. The 22 batches of QXPs were roughly divided into 3 categories, and 12 main markers causing the discrepancies were discovered.

Conclusion
The established QAMS method combined with the GC fingerprint and chemometrics is convenient and feasible, which helps to improve the quality evaluation of QXPs and provides a demonstration for the related study of compound preparations and single herbs.

Highlights
QAMS combined with a GC fingerprint and chemometrics method was established to evaluate the quality of QXPs for the first time.
A Helper Antibody-Based Competitive Fluorescence Immunochromatographic Assay for Quantitative Detection of Florfenicol in Poultry Eggs
Authors: Zhang Enhui , Liu Bochao , Lu Jinhui , Liang Chaolan , Zhao Fang , Li Jinfeng , Li Tingting , Li Chengyao , Zhang Ling 
Published: April 2023

Abstract

Background
Florfenicol (FF) is a chloramphenicol analogue used in animals, and florfenicol amine (FFA) is the main metabolite of FF. However, their residues in agricultural products are harmful to human health. A highly specific and sensitive assay for FF/FFA detection needs to be developed since the traditional detection methods are low in sensitivity.

Objective
In this study, a new method for rapid quantification of FF/FFA in poultry eggs by helper antibody-based fluorescent immunochromatographic assay (HAFIA) was established.

Methods
Triple antibodies including a primary monoclonal antibody (mAb) specific to the targets FF and FFA, a secondary polyclonal antibody (pAb) labeled with europium nanoparticles (EuNPs), and a helper monoclonal antibody (hAb), reacting with pAb but not with the mAb or the target antigen, are designed, which can form structural aggregation complexes in microwells with a single step of reactions. By loading the reaction sample solution, the triple-antibodies (mAb–pAb–hAb)–EuNPs complexes migrate to the test (T) line on the nitrocellulose membrane of testing strip and are competitively captured by the immobilized FF–bovine serum album (BSA) conjugates on the membrane and the FF/FFA targets in the sample solution.

Results
Fluorescence on the T line is read by a portable fluorescent strip reader in 10 min, and the result is given as the ratio of fluorescent intensities on the T and control (C) lines. This new fluorescent testing strip, with amplified signal from the triple-antibody complex, has 50-fold higher sensitivity than conventional colloidal gold-lateral flow immunoassays (CG-LFIAs), and can detect as low as 0.01 ng/mL FF and 0.1 ng/mL FFA targets from egg samples.

Conclusion
The developed competitive fluorescent immunochromatography method based on auxiliary antibodies has the advantages of high sensitivity and specificity for the rapid and quantitative detection of FF/FFA in poultry eggs.

Highlights
Newly designed helper antibody and portable device were applied to quantitative detection. HAFIA tests egg samples and results can be obtained in 10 minutes. HAFIA has the advantages of being more convenient, faster and does not require professional laboratory personnel.
Cost-effectiveness of Artificial Intelligence-Aided Colonoscopy for Adenoma Detection in Colon Cancer Screening
Authors: Barkun Alan N , von Renteln Daniel , Sadri Hamid 
Published: April 2023

Abstract

Background and Aims
Artificial intelligence-aided colonoscopy significantly improves adenoma detection. We assessed the cost-effectiveness of the GI Genius technology, an artificial intelligence-aided computer diagnosis for polyp detection (CADe), in improving colorectal cancer outcomes, adopting a Canadian health care perspective.

Methods
A Markov model with 1-year cycles and a lifetime horizon was used to estimate incremental cost-effectiveness ratio comparing CADe to conventional colonoscopy polyp detection amongst patients with a positive faecal immunochemical test. Outcomes were life years (LYs) and quality-adjusted life years (QALY) gained. The analysis applied costs associated with health care resource utilization, including procedures and follow-ups, from a provincial payer’s perspective using 2022 Canadian dollars. Effectiveness and cost data were sourced from the literature and publicly available databases. Extensive probabilistic and deterministic sensitivity analyses were performed, assessing model robustness.

Results
Life years and QALY gains for the CADe and conventional colonoscopy groups were 19.144 versus 19.125 and 17.137 versus 17.113, respectively. CADe and conventional colonoscopies’ overall per-case costs were $2990.74 and $3004.59, respectively. With a willingness-to-pay pre-set at $50,000/QALY, the incremental cost-effectiveness ratio was dominant for both outcomes, showing that CADe colonoscopy is cost-effective. Deterministic sensitivity analysis confirmed that the model was sensitive to the incidence risk ratio of adenoma per colonoscopy for large adenomas. Probabilistic sensitivity analysis showed that the CADe strategy was cost-effective in up to 73.4% of scenarios.

Conclusion
The addition of CADe solution to colonoscopy is a dominant, cost-effective strategy when used in faecal immunochemical test-positive patients in a Canadian health care setting.
Isoliquiritigenin regulates microglial M1/M2 polarisation by mediating the P38/MAPK pathway in cerebral stroke
Authors: Wang Ruixia , Zhang Weili 
Published: April 2023

Abstract

Objectives
Regulation of microglia polarisation may be a new way to treat ischaemic stroke based on its effects on brain injury. Isoliquiritigenin (ILG) is a flavonoid with neuroprotective function. The study investigated whether ILG regulated microglial polarisation and affects brain injury.

Methods
Here, a transient middle cerebral artery occlusion (tMCAO) model in vivo and lipopolysaccharide (LPS)-induced BV2 cells in vitro were established. Brain damage was assessed using a 2,3,5-triphenyl-tetrazolium-chloride staining assay. Microglial polarisation was analysed using enzyme linked immunosorbent assay, quantitative real-time polymerase chain reaction, and immunofluorescence assay. The levels of p38/MAPK pathway-related factors were measured by western blot.

Key findings
ILG suppressed infarct volume and neurological function of tMCAO rats. Moreover, ILG facilitated M2 microglia polarisation and suppressed M1 polarisation in the tMCAO model and LPS-induced BV2 cells. Moreover, ILG reduced the phosphorylation of p38, MAPK activated protein kinase 2, and heat shock protein 27 induced by LPS. Rescue study showed that activating the p38/MAPK pathway reversed the microglia polarisation induced by ILG and inactivating the p38/MAPK pathway enchanced the microglia polarisation.

Conclusion
ILG promoted microglia M2 polarisation by inactivating the p38/MAPK pathway, suggesting that ILG has the potential for the treatment of ischaemic stroke.
Electron transport in cyanobacterial thylakoid membranes: are cyanobacteria simple models for photosynthetic organisms?
Authors: Shimakawa Ginga 
Published: April 2023

Abstract
Cyanobacteria are structurally the simplest oxygenic phototrophs, but it is difficult to understand the regulation of their photosynthesis because the photosynthetic and respiratory processes share the same thylakoid membranes and cytosolic space. This review aims to summarize the molecular mechanisms and in vivo activities of electron transport in cyanobacterial thylakoid membranes based on the latest progress in photosynthesis research in cyanobacteria. Photosynthetic linear electron transport for CO2 assimilation is the dominant electron flux in the thylakoid membranes. The capacity for O2 photoreduction mediated by flavodiiron proteins is comparable to that for photosynthetic CO2 assimilation in cyanobacteria. Additionally, cyanobacterial thylakoid membranes harbour the significant electron flux of respiratory electron transport through a homologue of respiratory complex I, which is also recognized as forming part of the cyclic electron transport chain if it is coupled with photosystem I in the light. Further, O2-independent alternative electron transport through hydrogenase and nitrate reductase function with reduced ferredoxin as the electron donor. Whereas all these electron transport chains are understood individually, the regulatory complexity of the whole system remains to be uncovered in the near future.
New insights into the regulation of plant metabolism by O-acetylserine: sulfate and beyond
Authors: Apodiakou Anastasia , Hoefgen Rainer 
Published: April 2023

Abstract
Under conditions of sulfur deprivation, O-acetylserine (OAS) accumulates, which leads to the induction of a common set of six genes, called OAS cluster genes. These genes are induced not only under sulfur deprivation, but also under other conditions where OAS accumulates, such as shift to darkness and stress conditions leading to reactive oxygen species (ROS) or methyl-jasmonate accumulation. Using the OAS cluster genes as a query in ATTED-II, a co-expression network is derived stably spanning several hundred conditions. This allowed us not only to describe the downstream function of the OAS cluster genes but also to score for functions of the members of the co-regulated co-expression network and hence the effects of the OAS signal on the sulfate assimilation pathway and co-regulated pathways. Further, we summarized existing knowledge on the regulation of the OAS cluster and the co-expressed genes. We revealed that the known sulfate deprivation-related transcription factor EIL3/SLIM1 exhibits a prominent role, as most genes are subject to regulation by this transcription factor. The role of other transcription factors in response to OAS awaits further investigation.