Measurement of very low-molecular weight metabolites by traveling wave ion mobility and its use in human urine samples

The collision cross-sections(CCS)measurement using ion mobility spectrometry(IMS)in combination with mass spectrometry(MS)offers a great opportunity to increase confidence in metabolite identification.However,owing to the lack of sensitivity and resolution,IMS has an analytical challenge in studying the CCS values of very low-molecular-weight metabolites(VLMs250 Da).Here,we describe an analytical method using ultrahigh-performance liquid chromatography(UPLC)coupled to a traveling wave ion mobility-quadrupole-time-of-flight mass spectrometer optimized for the measurement of VLMs in human urine samples.The experimental CCS values,along with mass spectral properties,were reported for the 174 metabolites.The experimental data included the mass-to-charge ratio(m/z),retention time(RT),tandem MS(MS/MS)spectra,and CCS values.Among the studied metabolites,263 traveling wave ion mobility spectrometry(TWIMS)-derived CCS values(TWCCSN2)were reported for the first time,and more than 70%of these were CCS values of VLMs.The TWCCSN2 values were highly repeatable,with inter-day variations of<1%relative standard deviation(RSD).The developed method revealed excellent TWCCSN2 accuracy with a CCS difference(DCCS)within±2%of the reported drift tube IMS(DTIMS)and TWIMS CCS values.The complexity of the urine matrix did not affect the precision of the method,as evidenced by DCCS within±1.92%.According to the Metabolomics Standards Initiative,55 urinary metabolites were identified with a confidence level of 1.Among these 55 metabolites,53(96%)were VLMs.The larger number of confirmed compounds found in this study was a result of the addition of TWCCSN2 values,which clearly increased metabolite identification confidence.

Learning Discriminatory Information for Object Detection on Urine Sediment Image

In clinical practice,the microscopic examination of urine sediment is considered an important in vitro examination with many broad applications.Measuring the amount of each type of urine sediment allows for screening,diagnosis and evaluation of kidney and urinary tract disease,providing insight into the specific type and severity.However,manual urine sediment examination is labor-intensive,time-consuming,and subjective.Traditional machine learning based object detection methods require hand-crafted features for localization and classification,which have poor generalization capabilities and are difficult to quickly and accurately detect the number of urine sediments.Deep learning based object detection methods have the potential to address the challenges mentioned above,but these methods require access to large urine sediment image datasets.Unfortunately,only a limited number of publicly available urine sediment datasets are currently available.To alleviate the lack of urine sediment datasets in medical image analysis,we propose a new dataset named UriSed2K,which contains 2465 high-quality images annotated with expert guidance.Two main challenges are associated with our dataset:a large number of small objects and the occlusion between these small objects.Our manuscript focuses on applying deep learning object detection methods to the urine sediment dataset and addressing the challenges presented by this dataset.Specifically,our goal is to improve the accuracy and efficiency of the detection algorithm and,in doing so,provide medical professionals with an automatic detector that saves time and effort.We propose an improved lightweight one-stage object detection algorithm called Discriminatory-YOLO.The proposed algorithm comprises a local context attention module and a global background suppression module,which aid the detector in distinguishing urine sediment features in the image.The local context attention module captures context information beyond the object region,while the global background suppression module emphasizes objects in uninformative backgrounds.We comprehensively evaluate our method on the UriSed2K dataset,which includes seven categories of urine sediments,such as erythrocytes(red blood cells),leukocytes(white blood cells),epithelial cells,crystals,mycetes,broken erythrocytes,and broken leukocytes,achieving the best average precision(AP)of 95.3%while taking only 10 ms per image.The source code and dataset are available at https://github.com/binghuiwu98/discriminatoryyolov5.

Landscape of urine biomarkers for bladder cancer:molecular function,cell-of-origin,and bibliometric trend

Background:The effective management of bladder cancer(BCa)depends on the early diagnosis and surveillance.Previous studies have explored numerous urinary molecules as potential biomarkers of BCa.However,the molecular functions and cell-of-origin profiles of these biomarkers are yet to be elucidated.In this study,we aimed to provide a comprehensive overview of the landscape of urinary biomarker genes for BCa.Methods:We conducted an exhaustive literature search in PubMed,through which 555 biomarker genes were identified.We then analyzed the BCa single-cell atlas to infer the cellular origin of these BCa urine biomarker genes and performed functional enrichment analysis to gain insights into the functional molecular implications of these biomarkers.Results:These genes are involved in tumor proliferation,angiogenesis,cellmigration,and cell death and are predominantly expressed in epithelial and stromal cells.Interestingly,our analysis ofmultiomics tumor data revealed a discordance between tissue and urine in terms of differential methylation and RNA expression,suggesting that biomarker discovery for liquid biopsies should ideally begin with the analysis of bodily fluids rather than relying interest and that test strategies incorporating multiple molecular markers represent an ongoing trend.Conclusions:Collectively,our study has built a landscape of BCa urine biomarker genes,uncovered molecular insights into these biomarkers,and revealed the bibliometric trends in this field,which will contribute to the discovery of novel biomarkers in the future.

Diagnosis of an intermediate case of maple syrup urine disease:A case report

BACKGROUND Maple syrup urine disease(MSUD)is an autosomal recessive genetic disorder caused by defects in the catabolism of the branched-chain amino acids(BCAAs).However,the clinical and metabolic screening is limited in identifying all MSUD patients,especially those patients with mild phenotypes or are asymptomatic.This study aims to share the diagnostic experience of an intermediate MSUD case who was missed by metabolic profiling but identified by genetic analysis.CASE SUMMARY This study reports the diagnostic process of a boy with intermediate MSUD.The proband presented with psychomotor retardation and cerebral lesions on magnetic resonance imaging scans at 8 mo of age.Preliminary clinical and metabolic profiling did not support a specific disease.However,whole exome sequencing and subsequent Sanger sequencing at 1 year and 7 mo of age identified bi-allelic pathogenic variants of the BCKDHB gene,confirming the proband as having MSUD with non-classic mild phenotypes.His clinical and laboratory data were retrospectively analyzed.According to his disease course,he was classified into an intermediate form of MSUD.His management was then changed to BCAAs restriction and metabolic monitoring conforming to MSUD.In addition,genetic counseling and prenatal diagnosis were provided to his parents.CONCLUSION Our work provides diagnostic experience of an intermediate MSUD case,suggesting that a genetic analysis is important for ambiguous cases,and alerts clinicians to avoid missing patients with non-classic mild phenotypes of MSUD.

Diagnostic value of matrix metalloproteinases 2, 7 and 9 in urine for early detection of colorectal cancer

BACKGROUND A noninvasive biomarker with high diagnostic performance is urgently needed for the early diagnosis of colorectal cancer(CRC).AIM To evaluate the diagnostic value of matrix metalloproteinases(MMPs)2,7 and 9 in urine for CRC.METHODS Of 59 healthy controls,47 patients with colon polyps and 82 patients with CRC were included in this study.Carcinoembryonic antigen(CEA)in serum and MMP2,MMP7,and MMP9 in urine were detected.The combined diagnostic model of the indicators was established by binary logistic regression.The receiver operating characteristic curve(ROC)of the subjects was used to evaluate the independent and combined diagnostic value of the indicators.RESULTS The MMP2,MMP7,MMP9,and CEA levels in the CRC group differed significantly from levels in the healthy controls(P<0.05).The levels of MMP7,MMP9,and CEA also differed significantly between the CRC group and the colon polyps group(P<0.05).The area under the curve(AUC)distinguishing between the healthy control and the CRC patients using the joint model with CEA,MMP2,MMP7 and MMP9 was 0.977,and the sensitivity and specificity were 95.10%and 91.50%,respectively.For early-stage CRC,the AUC was 0.975,and the sensitivity and specificity were 94.30%and 98.30%,respectively.For advanced stage CRC,the AUC was 0.979,and the sensitivity and specificity were 95.70%and 91.50%,respectively.Using CEA,MMP7 and MMP9 to jointly established a model distinguishing the colorectal polyp group from the CRC group,the AUC was 0.849,and the sensitivity and specificity were 84.10%and 70.20%,respectively.For early-stage CRC,the AUC was 0.818,and the sensitivity and specificity were 76.30%and 72.30%,respectively.For advanced stage CRC,the AUC was 0.875,and the sensitivity and specificity were 81.80%and 72.30%,respectively.CONCLUSION MMP2,MMP7 and MMP 9 may exhibit diagnostic value for the early detection of CRC and may serve as auxiliary diagnostic markers for CRC.

Can the Urine Dipstick Test Be an Alternative in the Screening of Urinary Tract Infections for Inpatients in the Context of a Low-Income Country?

Background: Urinary Tract Infection (UTI), a prevalent bacterial infection in adults, heavily relies on cytobacteriological examination of urine (CBEU) for diagnosis. However, in resource-limited countries, accessibility to CBEU remains hindered by cost and availability. This study aims to assess the utility of the Urinary Dipstick Test (UDT) in diagnosing UTIs among hospitalized patients in the context of limited resources. Methods: A cross-sectional study was conducted from February to May 2019, encompassing hospitalized patients who underwent CBEU at the bacteriology unit of Sour? Sanou University Hospital. UDT and CBEU were concurrently performed, and UDT’s analytical and diagnostic performance was evaluated against CBEU, considered the gold standard. Results: A total of 274 CBEU requests were registered, involving 274 patients (159 males) with a mean age of 45.8 ± 21.3 years (ranging from 1 to 90 years). UTI was confirmed in 90 patients, yielding a frequency of 32.85%. The UTI bacteriological profile was dominated by Enterobacteriaceae (75.23%), primarily Escherichia coli (60.55%). Nitrite and Leukocytes were positive in 54 (19.8%) and 157 (53.6%) of the samples tested. Among patients with confirmed UTI, Nitrite, and Leukocytes were positive in 30 (33%) and 71 (79%) patients respectively. UDT demonstrated variable performance based on nitrite and leukocyte combination: Sensitivity (57%-82%), Specificity (7%-98%), Positive Predictive Value (PPV) (43%-57%), Negative Predictive Value (NPV) (43%-67%). UDT performed slightly better in women (NPV = 88%) and inpatients without urinary catheters (NPV = 75% and PPV = 80%). Conclusion: This study underscores UDT’s potential utility in excluding UTIs among women, younger patients, and inpatients without urinary catheters, albeit with limited confidence. The UDT emerges as a complementary tool for UTI screening, particularly in resource-limited settings.

Effects of Inhabiting and Life Patterns on the UV Spectral Properties of Small Mammalian Herbivores’ Urine

It is well known that avian predators can use prey excretions such as urine and feces to track their prey, and the urine and feces of small mammalian herbivores can reflect ultraviolet (UV) light and emit fluorescent light. There are still some debates as to whether UV visibility of small mammalian herbivores’ urine is used as a hunting cue by avian raptors. Some studies in Europe have demonstrated that diurnal raptors are capable of utilizing these cues to target key prey species. However, researchers in Australia have argued that raptors do not use the UV visibility of urine while hunting. To our knowledge, there are no reports from Asia concerning the ultraviolet spectral characteristics of small mammal herbivores’ urine. This study examined the UV spectral properties of urine from 6 small mammal herbivores species by comparing the UV reflectance and fluorescence spectra of urine from small mammalian herbivores living in plateau meadows, plateau shrubs, open marshland, farmland, and semi-desert grassland in China. In addition, we compared the UV spectral properties of urine from ground-dwelling species of rodents and subterranean species to determine whether ultraviolet visibility of small mammal herbivores’ urine could be used as a visual signal by Asian vole-eating raptors. The results showed that: 1) the SC370 values of urine from four small mammal herbivores species were ordered as plateau pika (plateau meadow) > root voles (plateau bush) > reed voles (swampland) > Brandt’s vole (desert grassland);and 2) UV fluorescence peak intensity and the wavelengths of urine from ground-dwelling species (such as the root vole, plateau pika, or Brandt’s vole) were significantly higher than those of subterranean-dwelling species (mandarin vole and plateau zokor). These results indicate that UV visibility of small mammal herbivores’ urine may act as a visual cue for raptors.

影响Urine-H-11干化学法检测尿液分析的因素

Urine—H—11尿液试纸是干化学法检测尿液分析的一种方法，利用干化学法进行尿液分析，能够简便，快速为临床诊断、治疗、预防和监测疾病提供可靠的实验依据，但是，Urine—H—11干化学法也受许多因素的影响，而导致结果的准确性，为了使大家更多的了解影响Urine-H—11干化学法检测尿液的各项因素，准确的为临床提供诊断依据，现将有关Urine—H—11干化学法检测尿液的影响因素总结如下：

Could natural phytochemicals be used to reduce nitrogen excretion and excreta‑derived N_(2)O emissions from ruminants?

Ruminants play a critical role in our food system by converting plant biomass that humans cannot or choose not to consume into edible high-quality food.However,ruminant excreta is a significant source of nitrous oxide(N_(2)O),a potent greenhouse gas with a long-term global warming potential 298 times that of carbon dioxide.Natural phytochemicals or forages containing phytochemicals have shown the potential to improve the efficiency of nitrogen(N)utilization and decrease N_(2)O emissions from the excreta of ruminants.Dietary inclusion of tannins can shift more of the excreted N to the feces,alter the urinary N composition and consequently reduce N_(2)O emissions from excreta.Essential oils or saponins could inhibit rumen ammonia production and decrease urinary N excretion.In grazed pastures,large amounts of glucosinolates or aucubin can be introduced into pasture soils when animals consume plants rich in these compounds and then excrete them or their metabolites in the urine or feces.If inhibitory compounds are excreted in the urine,they would be directly applied to the urine patch to reduce nitrification and subsequent N_(2)O emissions.The phytochemicals’role in sustainable ruminant production is undeniable,but much uncertainty remains.Inconsistency,transient effects,and adverse effects limit the effectiveness of these phytochemicals for reducing N losses.In this review,we will identify some current phytochemicals found in feed that have the potential to manipulate ruminant N excretion or mitigate N_(2)O production and deliberate the challenges and opportunities associated with using phytochemicals or forages rich in phytochemicals as dietary strategies for reducing N excretion and excreta-derived N_(2)O emissions.

Multivariate Analysis of Female Stress Urinary Incontinence and Establishment of a Prediction Model

Stress urinary incontinence(SUI)is a symptom of uncontrolled urine outflow that affects millions of women worldwide[1].SUI is a significant healthcare issue that affects the quality of life of women across numerous domains,including social activities,physical health,mental well-being,employment,and sexual life.

Metabolic dynamics in chronic gastritis:Examining urinary profiles post Helicobacter pylori eradication

Chronic gastritis is the persistent and insidious inflammation of the gastric lining.Helicobacter pylori(H.pylori)has been identified as the most common cause of chronic gastritis and consequently elimination of H.pylori can lead to its cure.This editorial explores the use of urinary metabolic profiles before and after eradication to identify biomarkers that can aid in prognosis and treatment.Despite providing promising insights,there are limitations such as a small sample size(17 patients),a narrow treatment period of 2 wk,and treatment heterogeneity,which raise concerns.Nevertheless,these findings have opened a gateway to enhancing the treatment and prognosis of chronic gastritis through urinary metabolomics.

Detection of Neisseria Gonorrhoeae from Urine with Ligase Chain Reaction

Objective: To evaluate the value of ligase chainreaction(LCR) in the diagnosis of diplococcusgonorrhoeae in urine. Methods: LCR detection of the urine for Neisseriagonorrhoeae and bacteria culture of discharge was per-formed simultaneously to 276 patients with urethritisor cervicitis seeking treatment in sex transmitted dis-eases (STDs) outpatient clinic. For specimens withdiscordant results, polymerase chain reaction wasconducted. The purpose was to detect the respectivesensitivity and specificity of bacteria culture and LCR. Results: 24 of 276(8.7%) patients had positive LCRresults and 21 of 276(7.6%) were positive for culture.5 specimens had discordant results from LCR andbacteria culture. The sensitivity and specificity of LCRin the diagnosis of gonorrhoeae were 92.3% and100% respectively. Conclusion: This study showed that LCR had ahigher sensitivity and specificity for the diagnosis ofgonorrhoeae from urine.

Study of the Optimal Conditions for Anaerobic Digestion of Cow Dung in Households in Cote d’Ivoire

This paper investigates the optimal conditions for methanisation applied to cow dung. Four experimental 25 liters digesters were used in this work. The best biogas yield is obtained when the digester is installed in a metal box and exposed to sunlight. The temperature in this digester varied between 25˚C and 37˚C. The dry matter content of the collected cow dung was 15.5%. The digester was fed with 9 kg of cow dung mixed with 8.5 litres of water, one litre of cassava effluent and 200 ml of human urine. After a retention period of 22 days, the biogas obtained was 67% methane and 21% carbon dioxide. The use of human urine and cassava effluent improved the quality of the biogas.

Metabolic phenotyping in health and disease

Analyzing metabolites(small molecules<1 kDa)in body fluids such as urine and plasma using various spectroscopic methods provides information on the metabotype(metabolic phenotype)of individuals or populations,information that can be applied to personalized medicine or public healthcare.

Swallowing Difficulties,Oral Symptoms,and Nutrition in Long-Term Care Elderly Residents-A Secondary Publication

Oral health is often impaired in people living in residential care.In older people,poor oral health is associated with functional deficits,multiple sclerosis,and memory disorders.Keeping one’s teeth healthy throughout life would promote both oral health and general health.Biting and swallowing problems in older people are also linked to oral health,limiting eating activities and requiring diet changes to softer foods that are easy to chew and swallow.This may limit dietary diversity and adequate nutrient intake.Although eating-related chewing and swallowing problems are common in institutionalized residents,they are often addressed too late,when the resident is already malnourished.Nutrition in nursing and retirement homes has been the subject of various studies since the 2000s.However,studies on swallowing and chewing difficulties are scarce and their link to adequate nutrient intake has received lesser attention[6,7].

Urological Complications of Female Genital Mutilation: A Case Report of 15 Patients

Objective background: This was a retrospective study of the clinical and therapeutic aspects of urological complications of female genital mutilation in the urology department of Bamako’s Gabriel Touré University Hospital. Methods: Our study took place from 2002 to 2017 in the urology department of the Gabriel Touré University Hospital in Bamako and concerned cases of complications of female genital mutilation. Our study included all girls or women presenting with urinary disorders related to complications of genital mutilation and received in urological consultation and surgical management. Results: The average age of our patients was 2.5 years, with extremes ranging from 3 months to 35 years. The oldest patient had presented with dystocia during both deliveries. Acute urine retention (n = 7) was the most frequent reason for consultation. Other signs included urinary incontinence, pollakiuria and burning. Physical examination revealed clitoridectomy and abrasion of the labia minora in 13 patients. Type III of the WHO classification of female genital mutilation was the most frequent and corresponded to infibulation.

Serum and urine metabolomic fingerprinting in diagnostics of inflammatory bowel diseases

AIM: To evaluate the utility of serum and urine metabolomic analysis in diagnosing and monitoring of inflammatory bowel diseases (IBD).

A Study on Bisphenol A,Nonylphenol,and Octylphenol in Human Urine amples Detected by SPE-UPLC-MS

Objective To establish a comprehensive analytical method based on SPE‐UPLC‐MS for the simultaneous determination of bisphenol A （BPA）, nonylphenol （NP）, and octylphenol （OP） in urine samples. Methods Sixty urine samples collected from healthy subjects were analyzed for BPA, NP, and OP concentrations. The samples were de‐conjugated by adding β‐glucuronidase and sulfatase. After the enzymatic treatment, the samples were subjected to the OASIS HLB column solid phase extraction cartridges so as to be cleaned and concentrated. The UPLC separation was performed on a Acquity UPLCTM BEH C18 column （2.1×100 mm, 1.7 μm） with a gradient elution system of methanol‐water as the mobile phase. Triple‐quadrupole mass spectrometry analyzer was used for the qualitative and quantitative analysis of UPLC‐MS/MS system. Results The limit of detection of BPA, NP, and OP was 0.10, 0.10, and 0.15 ng/mL, respectively. The recoveries of BPA, NP and OP were 80.1%‐108%, 81.3%‐109%, and 81.5%‐98.7%, respectively. Among the 60 urine samples, BPA was detected in 8 samples at the level of 0.297‐32.7ng/mL, NP was detected in 29 samples at the level of 1.69‐27.8 ng/mL, and OP was detected in 17 samples at the level of 0.407‐11.1 ng/mL. Conclusion The method is simple with high sensitivity and selectivity, and is suitable for the determination of BPA, NP, and OP in urine. As shown by our analysis , BPA, NP, and OP appear to be prevalent in human urine. This is particularly true for NP. The results from our study is therefore valuable for future studies to assess the exposure to BPA, NP, and OP in the general population.

Early diagnosis and prediction of severity in acute pancreatitis using the urine trypsinogen-2 dipstick test:A prospective study

AIM： To evaluate the use of the trypsinogen-2 dipstick （Actim Pancreatitis） test for early diagnosis and prediction of severity in acute pancreatitis （AP）. METHODS： Ninety-two patients with AP were included in this study. The control group was 25 patients who had acute abdominal pain from non-pancreatic causes. Urine trypsinogen-2 dipstick test （UTDT） and conventional diagnostic tests were performed in all patients. Patients were divided by the Atlanta classification into two groups as having mild or severe pancreatitis. RESULTS： UTDT was positive in 87 （94.6%） of the AP patients and in two （8%） controls （P 〈 0.05）. Positive UTDT was found in 61 （92.4%） of 66 （71.7%） patients with mild pancreatitis and in all （100%） of the 26 （28.3%） with severe pancreatitis （P 〉 0.05）. UTDT positivity lasted longer in severe pancreatitis compared with that in mild pancreatitis （6.2 ＋ 2.5 d vs 2.0 ＋ 1.43 d, P 〈 0.05）. The sensitivity, specificity, positive predictive value, negative predictive value （NPV）, positive likelihood ratio （PLR） and negative likelihood ratio （NLR） of UTDT were 91%, 72%, 96.6%, 70.4%, 3.4 and 0.1, respectively. CONCLUSION： UTDT is a simple, rapid and reliable method for use on admission. It has high specificity and low NLR for early diagnosis and prediction of severity in AP. However, its relatively low NPV does not allow trypsinogen-2 dipstick test to be a stand-alone tool for diagnosis of acute pancreatitis; the use of other conventional diagnostic tools remains a requirement.

Determination of urine catecholamines and metanephrines by reversed-phase liquid chromatography-tandem mass spectrometry

The measurement of urine catecholamine and metanephrine concentrations is important for biochemical screening and diagnosis of pheochromocytoma.The goal of this work was to develop a simple liquid chromatography-tandem mass spectrometry(LC-MS/MS)method for determining catecholamines and metanephrines in urine to replace an existing liquid chromatographic method using electrochemical detection.Urine samples were prepared using Oasis weak-cation-exchange cartridges.The eluate was analyzed on an Agilent ZORBAX Eclipse Plus Phenyl-Hexyl column in 3 min.Adrenaline,noradrenaline,dopamine,metanephrine,normetanephrine,and their deuterated internal standards were monitored in positive electrospray ionization mode by multiple reaction monitoring(MRM).No evidence of ion suppression was observed.The assay was linear up to 5μmol/L for adrenaline,5μmol/L for noradrenaline,6.1μmol/L for dopamine,5.6μmol/L for metanephrine,and 34.6μmol/L for normetanephrine,with lower limits of quantification of 5,5,12,6 and 7nmol/L,respectively.The intra-day and inter-day precisions for all analytes ranged from 0.59%to 4.64%and1.98%to 4.80%,respectively.External quality assurance samples were assayed and showed excellent agreement with the target values.This simple method provides an improved assay for determining urine catecholamines and metanephrines.