A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry.

BACKGROUND: Label-free quantitation of mass spectrometric data is one of the simplest and least expensive methods for differential expression profiling of proteins and metabolites. The need for high accuracy and performance computational label-free quantitation methods is still high in the biomarker and drug discovery research field. However, recent most advanced types of LC-MS generate huge amounts of analytical data with high scan speed, high accuracy and resolution, which is often impossible to interpret manually. Moreover, there are still issues to be improved for recent label-free methods, such as how to reduce false positive/negatives of the candidate peaks, how to expand scalability and how to enhance and automate data processing. AB3D (A simple label-free quantitation algorithm for Biomarker Discovery in Diagnostics and Drug discovery using LC-MS) has addressed these issues and has the capability to perform label-free quantitation using MS1 for proteomics study. RESULTS: We developed an algorithm called AB3D, a label free peak detection and quantitative algorithm using MS1 spectral data. To test our algorithm, practical applications of AB3D for LC-MS data sets were evaluated using 3 datasets. Comparisons were then carried out between widely used software tools such as MZmine 2, MSight, SuperHirn, OpenMS and our algorithm AB3D, using the same LC-MS datasets. All quantitative results were confirmed manually, and we found that AB3D could properly identify and quantify known peptides with fewer false positives and false negatives compared to four other existing software tools using either the standard peptide mixture or the real complex biological samples of Bartonella quintana (strain JK31). Moreover, AB3D showed the best reliability by comparing the variability between two technical replicates using a complex peptide mixture of HeLa and BSA samples. For performance, the AB3D algorithm is about 1.2 - 15 times faster than the four other existing software tools. CONCLUSIONS: AB3D is a simple and fast algorithm for label-free quantitation using MS1 mass spectrometry data for large scale LC-MS data analysis with higher true positive and reasonable false positive rates. Furthermore, AB3D demonstrated the best reproducibility and is about 1.2- 15 times faster than those of existing 4 software tools.

Mass++: A Visualization and Analysis Tool for Mass Spectrometry.

We have developed Mass++, a plug-in style visualization and analysis tool for mass spectrometry. Its plug-in style enables users to customize it and to develop original functions. Mass++ has several kinds of plug-ins, including rich viewers and analysis methods for proteomics and metabolomics. Plug-ins for supporting vendors' raw data are currently available; hence, Mass++ can read several data formats. Mass++ is both a desktop tool and a software development platform. Original functions can be developed without editing the Mass++ source code. Here, we present this tool's capability to rapidly analyze MS data and develop functions by providing examples of label-free quantitation and implementing plug-ins or scripts. Mass++ is freely available at http://www.first-ms3d.jp/english/ .

The Factors Influencing Pregnant Women's Selection of Media Sources to Obtain Information on COVID-19 in Japan in 2021.

Pregnant women presumably gather information about the coronavirus disease 2019 (COVID-19) from various sources. However, it is difficult for pregnant women who are not medical professionals to source the appropriate information because of the infodemic related to the COVID-19 pandemic. Therefore, the objective of our study was to investigate how pregnant women gathered information about COVID-19 and COVID-19 vaccination. To address this issue, we conducted an online questionnaire survey between 5 October and 22 November 2021, which was approved by the Ethics Committee of Nihon University School of Medicine. We received 4962 responses after excluding 1179 insufficient answers. Our study found that age, occupation, and infection-risk anxiety influenced the selection of media for obtaining information. Pregnant women who were older, medical professionals, public servants, or educators tended to rely on specialized medical websites, whereas housewives tended to use mass media, social media, and sources with uncertain scientific evidence. Additionally, the number of weeks of gestation and the method of conception (natural or assisted reproductive conception) affected the selection of media. The accessibility of COVID-19 information for pregnant women was determined by their social background and pregnancy status. We need to continue making efforts to ensure that appropriate information is readily available to pregnant women and their families.

Eosinophilic gastroenteritis due to cow's milk allergy presenting with acute pancreatitis.

Eosinophilic gastroenteritis (EGE) is characterized by eosinophilic infiltration of the digestive organs, most commonly of the stomach and the duodenum. Symptoms of EGE are nonspecific and include nausea, vomiting, abdominal pain, dyspepsia, malabsorption, ascites and weight loss. The various symptoms of EGE depend on its location and the depth of gastrointestinal eosinophil infiltration. We report a case presenting with acute pancreatitis caused by a milk allergy. The patient's symptoms rapidly improved after treatment with corticosteroids, and he remained symptom-free for more than 20 months by the elimination of cow's milk from his diet. Serum titers of pancreatic enzymes and total bilirubin simultaneously recovered and blood eosinophil counts normalized. The causative allergens of EGE are too various to detect; however, allergologic exams revealed that a cow's milk allergy had provoked EGE in our case. Adult-onset cow's milk allergies are rare; when seen, however, they may present severe complications such as anaphylaxis, gastroenteritis and pancreatitis. When unaccountable gastrointestinal symptoms are observed, EGE caused by food allergies should be included in the differential diagnosis.

Effects of lactic acid-fermented soymilk on lipid metabolism-related gene expression in rat liver.

We examined the effects of lactic acid fermentation of soymilk on the lipid profile and lipid metabolism-related gene expression in rat liver. Male Sprague-Dawley rats aged 7 weeks were fed a control diet (AIN-93), soymilk diet, or fermented soymilk diet for 1 week or 5 weeks. The hepatic triglyceride and cholesterol contents in the soymilk (SM) group and the fermented soymilk (FSM) group were significantly lower than those in the control group after 5 weeks, but these changes had not become apparent until after 1 week. The fatty acid synthesis-related genes were more markedly down-regulated after 1 week than after 5 weeks, whereas the cytochrome p450 family 7 subfamily a polypeptide 1 (CYP7al) gene related to cholesterol catabolism was more markedly up-regulated after 5 weeks than after 1 week. This up-regulation was higher in the FSM group than in the SM group. It is assumed that the bioactive components produced by lactic acid fermentation induced the up-regulation of CYP7a1.

[A case of severe asthma and peach allergy that improved with omalizumab therapy: a case report].

A 30-year-old woman had refractory asthma. She had also experienced twice severe anaphylaxis episodes after ingesting peaches. The patient was extremely wary about reoccurrence of anaphylaxis and avoided ingesting any fruits, including peaches. She visited our hospital for testing and treatment for asthma and the peach allergy. Skin and serologic testing showed that she had a severe allergy to house dust, mites, and peaches. The food challenge test results showed that ingesting 6.5 g of the peach fruit induced dyspnea in the patient. Her asthma could not be controlled despite treatment involving a leukotriene receptor antagonist and combination inhalation of high-dose salmeterol xinafoate/fluticasone propionate. We advised the patient to keep strict avoidance ingesting peaches because of her food allergy. However, she hoped to overcome her food restrictions, especially those for fruits. We initiated treatment involving the recombinant humanized monoclonal anti-IgE antibody omalizumab (150 mg, once a month) to ensure that the asthma was controlled well and to improve the patient's diet. The asthmatic symptoms ameliorated, and the peak expiratory flow increased in a short time. We gradually reduced the restriction on peach consumption. This was achieved by rechallenging the patient with increasing doses of 290 mg of the peach fruit and was initiated at 28 weeks after starting omalizumab therapy. The restriction on peach consumption was lifted eventually, and the patient did not experience any allergic symptoms subsequently on ingesting peaches. Thus, for our patient, omalizumab therapy was highly effective in achieving remission from both asthma and peach allergy.

Simultaneous removal of formaldehyde and benzene in indoor air with a combination of sorption- and decomposition-type air filters.

Urgent measures for indoor air pollution caused by volatile organic compounds are required in urban areas of China. Considering indoor air concentration levels and hazardous properties, formaldehyde and benzene should be given priority for pollution control in China. The authors proposed the use of air-cleaning devices, including stand-alone room air cleaners and in-duct devices. This study aimed to find the best combination of sorption and decomposition filters for the simultaneous removal of formaldehyde and benzene, employing four types of air filter units: an activated charcoal filter (ACF), an ACF impregnated with a trapping agent for acidic gases (ACID), a MnO2 filter (MDF) for oxidative decomposition of formaldehyde at room temperature and a photocatalyst filter (PHOTO) coupled with a parallel beam ultraviolet (UV) irradiation device. The performance of the combined systems under air flow rates of 35-165 m3 h(-1) was evaluated in a test chamber (2 m3) with a constant gas generation system. The experimental results and data analysis using a kinetic approach showed the combined system of ACF, PHOTO and MDF significantly reduced both concentrations of formaldehyde and benzene in air without any unpleasant odours caused by the UV-induced photocatalytic reaction. The system was then evaluated in a full-size laboratory (22 m3). This test proved the practical performance of the system even at full scale, and also suggested that the filters should be arranged in the order of PHOTO/ACF/MDF from upstream to downstream. The proposed system has the potential of being used for improving indoor air quality of houses and buildings in China.

Effects of Lactobacillus fermented soymilk and soy yogurt on hepatic lipid accumulation in rats fed a cholesterol-free diet.

We examined the effects of lactic acid fermented soymilk, in which part of the soymilk was replaced with okara (soy yogurt), on plasma and hepatic lipid profiles in rats fed a cholesterol-free diet. Additionally, we investigated the effects of soy yogurt on hepatic gene expression in rats using DNA microarray analysis. Male Sprague-Dawley rats aged 5 weeks (n=5/group) were fed a control diet (AIN-93) or a test diet in which 20% of the diet was replaced by soy yogurt for 7 weeks. Soy yogurt consumption did not affect body weight or adipose tissue weight as compared with control diet. In the soy yogurt group, the liver weight and hepatic triglyceride content were significantly lower than the control group, and the level of plasma cholesterol was also lower. Furthermore, DNA microarray analysis indicated that soy yogurt ingestion down-regulated the expression of the SREBP-1 gene and enzymes related to lipogenesis in the rat liver, while expression of beta-oxidation-related genes was up-regulated. These results suggest that soy yogurt is beneficial in preventing hepatic lipid accumulation in rats.

Isoflavone and protein constituents of lactic acid-fermented soy milk combine to prevent dyslipidemia in rats fed a high cholesterol diet.

A high cholesterol diet induces dyslipidemia. This study investigated whether isoflavone aglycones in lactic acid-fermented soy milk (LFS) improve lipid metabolism in rats fed a high cholesterol diet. Male Sprague-Dawley rats aged seven weeks were fed an AIN-93G diet, a 1% cholesterol diet (a high cholesterol diet), a high-cholesterol diet containing 4% isoflavone extract of LFS (LFS extract diet), a high-cholesterol diet containing 19.4% ethanol-washed LFS (ethanol-washed LFS diet, isoflavone-poor diet), or a high cholesterol diet containing 23.2% intact LFS (intact LFS diet) for five weeks. The plasma total cholesterol (TC) level was increased in the rats fed the LFS extract diet compared with those fed the high cholesterol diet. The TC level was decreased by the intact LFS and ethanol-washed LFS diets. The cholesterol-lowering effect was stronger in the rats fed the intact LFS diet than those fed the ethanol-washed LFS diet. The plasma triglyceride (TG) level was unchanged in the rats fed the LFS extract diet, but it decreased in rats fed the intact LFS and ethanol-washed LFS diets. Although, compared with the high cholesterol diet, the LFS extract and ethanol-washed LFS diets did not reduce hepatic cholesterol and TG, both levels were remarkably lowered by the intact LFS diet. These results suggest that the improvement in lipid metabolism of rats fed a high-cholesterol diet containing LFS isoflavone aglycones is not due to an independent effect but due to a cooperative effect with soy protein.

Hypocholesterolemic effects of lactic acid-fermented soymilk on rats fed a high cholesterol diet.

The effect of fermented soymilk on rats fed a high cholesterol diet was investigated to clarify the cholesterol-lowering function. Male Sprague-Dawley rats aged 7 weeks were fed a control diet (1% cholesterol, high cholesterol diet), high cholesterol diet containing 11.7% fermented soymilk diet (5% soy protein as final concentration, F-5), or high cholesterol diet containing 23.4% fermented soymilk diet (10% soy protein as final concentration, F-10) for 5 weeks. The liver weight and fat mass were decreased by the ingestion of fermented soymilk. The hepatic triglyceride and cholesterol levels in the F-5 and F-10 groups were significantly lowered compared to those in the control group. The plasma total cholesterol level of the F-10 group was significantly decreased. The expression of SREBP-2, a cholesterol synthesis-related gene, was significantly decreased in liver of the F-5 group, but the expression of CYP7a1, a cholesterol catabolism-related gene, was significantly increased. These results suggest that fermented soymilk can modulate the cholesterol metabolism in rats fed a high cholesterol diet.