Bacterial Protein Profiling——Comparison of Three Mass Spectrometry Methodologies

Profiling the protein composition of bacteria is essential for understanding their biology,physiology and interaction with environment.Mass spectrometry has become a pivotal tool for protein analysis,facilitating the examination of expression levels,molecular masses and structural modifications.In this study,we compared the performance of three widely-used mass spectrometry methods,i.e.,matrix-assisted laser desorption/ionization(MALDI)protein fingerprinting,top-down proteomics and bottom-up proteomics,in the profiling of bacterial protein composition.It was revealed that bottom-up proteomics provided the highest protein coverage and exhibited the greatest protein profile overlap between bacterial species.In contrast,MALDI protein fingerprinting demonstrated superior detection reproducibility and effectiveness in distinguishing between bacterial species.Although top-down proteomics identified fewer proteins than bottom-up approach,it complemented MALDI fingerprinting in the discovery of bacterial protein markers,both favoring abundant,stable,and hydrophilic bacterial ribosomal proteins.This study represents the most systematic and comprehensive comparison of mass spectrometry-based protein profiling methodologies to date.It provides valuable guidelines for the selection of appropriate profiling strategies for specific analytical purposes.This will facilitate studies across various fields,including infection diagnosis,antimicrobial resistance detection and pharmaceutical target discovery.

Predicting Age and Gender in Author Profiling: A Multi-Feature Exploration

Author Profiling (AP) is a subsection of digital forensics that focuses on the detection of the author’s personalinformation, such as age, gender, occupation, and education, based on various linguistic features, e.g., stylistic,semantic, and syntactic. The importance of AP lies in various fields, including forensics, security, medicine, andmarketing. In previous studies, many works have been done using different languages, e.g., English, Arabic, French,etc.However, the research on RomanUrdu is not up to the mark.Hence, this study focuses on detecting the author’sage and gender based on Roman Urdu text messages. The dataset used in this study is Fire’18-MaponSMS. Thisstudy proposed an ensemble model based on AdaBoostM1 and Random Forest (AMBRF) for AP using multiplelinguistic features that are stylistic, character-based, word-based, and sentence-based. The proposed model iscontrasted with several of the well-known models fromthe literature, including J48-Decision Tree (J48),Na飗e Bays(NB), K Nearest Neighbor (KNN), and Composite Hypercube on Random Projection (CHIRP), NB-Updatable,RF, and AdaboostM1. The overall outcome shows the better performance of the proposed AdaboostM1 withRandom Forest (ABMRF) with an accuracy of 54.2857% for age prediction and 71.1429% for gender predictioncalculated on stylistic features. Regarding word-based features, age and gender were considered in 50.5714% and60%, respectively. On the other hand, KNN and CHIRP show the weakest performance using all the linguisticfeatures for age and gender prediction.

Genomic profiling of colorectal cancer in large-scale Chinese patients:amplification and somatic mutations in ERBB2

Objectives:Human epidermal growth factor receptor 2(HER2)-targeted therapies have demonstrated potential benefits for metastatic colorectal cancer(mCRC)patients with HER2 amplification,but are not satisfactory in cases of HER2 mutant CRCs.Methods:Consequently,further elucidation of amplifications and somatic mutations in erythroblastic oncogene B-2(ERBB2)is imperative.Comprehensive genomic profiling was conducted on 2454 Chinese CRC cases to evaluate genomic alterations in 733 cancer-related genes,tumor mutational burden,microsatellite instability,and programmed death ligand 1(PD-L1)expression.Results:Among 2454 CRC patients,85 cases(3.46%)exhibited ERBB2 amplification,and 55 cases(2.24%)carried ERBB2 mutation.p.R678Q(28%),p.V8421(24%),and p.S310F/Y(12%)were the most prevalent of the 16 detected mutation sites.In comparison to the ERBB2 altered(alt)group,KRAS/BRAF mutations were more prevalent in ERBB2 wild-type(wt)samples(ERBB2wt vs.ERBB2alt,KRAS:50.9%vs.25.6%,p<0.05;BRAF:8.5%vs.2.3%,p<0.05).32.7%(18/55)of CRCs with ERBB2 mutation exhibited microsatellite instability high(MSI-H),while no cases with HER2 amplification displayed MSI-H.Mutant genes varied between ERBB2 copy number variation(CNV)and ERBB2 single nucleotide variant(SNV);TP53 alterations tended to co-occur with ERBB2 amplification(92.3%)as opposed to ERBB2 mutation(58.3%).KRAS and PIK3CA alterations were more prevalent in ERBB2 SNV cases(KRAS/PIK3CA:45.8%/31.2%)compared to ERBB2 amplification cases(KRAS/PIK3CA:14.1%/7.7%).Conclusion:Our study delineates the landscape of HER2 alterations in a large-scale cohort of CRC patients from China.These findings enhance our understanding of the molecular features of Chinese CRC patients and offer valuable implications for further investigation.

ABMRF:An Ensemble Model for Author Profiling Based on Stylistic Features Using Roman Urdu

This study explores the area of Author Profiling(AP)and its importance in several industries,including forensics,security,marketing,and education.A key component of AP is the extraction of useful information from text,with an emphasis on the writers’ages and genders.To improve the accuracy of AP tasks,the study develops an ensemble model dubbed ABMRF that combines AdaBoostM1(ABM1)and Random Forest(RF).The work uses an extensive technique that involves textmessage dataset pretreatment,model training,and assessment.To evaluate the effectiveness of several machine learning(ML)algorithms in classifying age and gender,including Composite Hypercube on Random Projection(CHIRP),Decision Trees(J48),Na飗e Bayes(NB),K Nearest Neighbor,AdaboostM1,NB-Updatable,RF,andABMRF,they are compared.The findings demonstrate thatABMRFregularly beats the competition,with a gender classification accuracy of 71.14%and an age classification accuracy of 54.29%,respectively.Additional metrics like precision,recall,F-measure,Matthews Correlation Coefficient(MCC),and accuracy support ABMRF’s outstanding performance in age and gender profiling tasks.This study demonstrates the usefulness of ABMRF as an ensemble model for author profiling and highlights its possible uses in marketing,law enforcement,and education.The results emphasize the effectiveness of ensemble approaches in enhancing author profiling task accuracy,particularly when it comes to age and gender identification.

AMachine Learning Approach to User Profiling for Data Annotation of Online Behavior

The user’s intent to seek online information has been an active area of research in user profiling.User profiling considers user characteristics,behaviors,activities,and preferences to sketch user intentions,interests,and motivations.Determining user characteristics can help capture implicit and explicit preferences and intentions for effective user-centric and customized content presentation.The user’s complete online experience in seeking information is a blend of activities such as searching,verifying,and sharing it on social platforms.However,a combination of multiple behaviors in profiling users has yet to be considered.This research takes a novel approach and explores user intent types based on multidimensional online behavior in information acquisition.This research explores information search,verification,and dissemination behavior and identifies diverse types of users based on their online engagement using machine learning.The research proposes a generic user profile template that explains the user characteristics based on the internet experience and uses it as ground truth for data annotation.User feedback is based on online behavior and practices collected by using a survey method.The participants include both males and females from different occupation sectors and different ages.The data collected is subject to feature engineering,and the significant features are presented to unsupervised machine learning methods to identify user intent classes or profiles and their characteristics.Different techniques are evaluated,and the K-Mean clustering method successfully generates five user groups observing different user characteristics with an average silhouette of 0.36 and a distortion score of 1136.Feature average is computed to identify user intent type characteristics.The user intent classes are then further generalized to create a user intent template with an Inter-Rater Reliability of 75%.This research successfully extracts different user types based on their preferences in online content,platforms,criteria,and frequency.The study also validates the proposed template on user feedback data through Inter-Rater Agreement process using an external human rater.

Assessment of spermatogenesis in camels via seminiferous tubule staging and testosterone profiling

Objective:To investigate the successive morphological stages of spermatogenesis,hormonal regulation,and testosterone profile in dromedary camel reproduction.Methods:Testicular tissue samples were obtained from 12 dromedary bull camels aged 7 to 8 at a local abattoir.The histological assessment involved tissue processing,hematoxylin and eosin(H&E)staining,and examination under a microscope.Stereological analysis,germ cell identification,and assessment of seminiferous tubules and maturation were conducted.Testosterone assay was performed by radioimmunoassay using blood samples collected at regular intervals.Results:The study revealed 12 phases of the dromedary camel's seminiferous epithelium cycle,highlighting distinct morphological characteristics and cellular processes.Acrosomal migration,maturation,cap formation,and the Golgi-mediated synthesis of proacrosomal vesicles were also explained in dimension,as were the steps of acrosome biogenesis.Spermatids and mature sperm cells were present when spermatogenesis phases were examined.An analysis of the dimensions of seminiferous tubules revealed specific measures for diameter,area,and epithelial height about luminal characteristics.Moreover,there were noticeable variations in the serum testosterone concentrations during the study period,indicating temporal dynamics.Conclusions:This study outlines the spermatogenesis process in dromedary camels across 12 stages,emphasizing cellular dynamics and acrosomal biogenesis.It also provides seminiferous tubule measurements and observes seasonal testosterone fluctuations,offering insights into reproductive regulation and potential strategies for camel breeding conservation.

基于部分调用图的线程敏感Profiling技术

Profiling技术能提供程序实际执行时的相关信息。在动态编译环境中,Profiling的运行时开销导致难以收集较为复杂的运行时信息。该文提出一种基于部分调用图的Profiling技术,在收集多线程程序中线程相关的各种执行信息时,能有效减少运行时开销。在开放源码的虚拟机上实现了该Profiling技术。实验表明,其运行时开销只有原来的2%-4%。

基于OPT Cache替换Profiling的Cache提示生成

提出了一个基于最优Cache替换(OPT)Profiling的静态Cache提示生成方法,并通过模拟SPEC2000Int测试程序,对该方法与LRUCache替换策略进行了性能比较。

指导cache静态划分的程序性能profiling优化技术

对于共享cache的多核处理器,如何管理好各个核对cache的利用,对于充分发挥多核处理器性能是很关键的问题.目前采用的cache替换方法程序间会出现性能干扰,cache静态划分技术则是通过为同时运行的程序分配不同的空间来解决性能干扰问题.为了给程序分配合适大小的cache空间,需要对程序进行性能profiling,即事先多遍运行收集程序在各种cache容量下的性能数据,这种性能profiling方法开销巨大,影响实用.为了解决性能profiling需要多遍运行程序的问题,提出了只需单遍运行的程序性能profiling优化技术.该技术利用在线的phase分析技术识别程序的运行阶段,避免对相同阶段的重复profiling;同时分析程序各phase的性能同cache容量变化的关系趋势,对于性能不敏感的容量变化则不进行profiling,降低开销.在程序运行结束后通过程序各phase在cache各种容量下的性能来估计程序在各容量下的整体性能,以指导cache静态划分.实验表明,该技术的开销仅为7%,而该方法指导的cache划分比未划分时有8%的性能改进,同多遍运行的程序性能profiling指导的cache划分性能相比仅有1%的下降.

Cache Profiling技术

如何减少和隐藏cache失效的延迟,是人们关注的热点。编译器为了得到cache访问命中的情况,往往使用模拟器去跑一遍来得到结果,这样的速度很慢。为了克服以上缺点,提出了在编译器中作cache profiling来获取cache访问的信息。类似于value profiling和strideprofiling,cache profiling对访存指令作插装,可以有效地提高速度,并且只需要编译器的支持即可。Cache profiling获得的信息可以用来改进指令调度、软件预取、生成cache hint和辅助线程等。

基于动态profiling技术的流水粒度调优

结点间流水是解决数据分布和计算分割不一致时的一种重要的并行发掘技术.结点间流水通过计算与通信的重叠获得并行度.精确的流水粒度是获得良好的流水性能的关键.流水分块取决于很多因素,如程序规模、程序的访问模式、结点规模、结点的计算能力和存储体系、通信系统的性能、通信库开销等等.提出了动态profiling方式并实现在流水粒度的推导中,运行时信息收集部分典型分块,结合代价模型推导流水粒度,该模型考虑局部性优化;探索如何减少插桩执行的开销的同时保证代价模型的精度.实验证明,这种方式有更好的适应性,能获得较好的流水并行.

cache profiling信息指导的软件流水

软件流水是一种重要的指令调度技术,它通过同时执行来自不同循环迭代的指令来加快循环的执行时间.随着处理器速度和访存速度差距越拉越大,访存指令尤其是cache miss的访存指令日益成为系统性能提高的瓶颈.由于这些指令的延迟不是固定的,如何在软件流水中预测并掩盖这些访存指令的延迟是非常重要的.与前人预测访存延迟的方法不同,引入cache profiling技术,通过动态收集到profile信息来预测访存延迟,并进行适当的调度.当增加模调度循环中的访存指令的延迟时,启动间隔也会随之增大,导致性能不会随之上升.CSMS算法和FLMS算法在尽量不增大启动间隔的情况下,改变访存指令的延迟.改进了CSMS算法和FLMS算法,根据cache profiling的信息来改变访存延迟,所以比前人的方法更为准确.实验表明,新方法可以有效地提高程序性能,对SPEC2000测试程序平均性能提高1%左右,个别例子的性能改进高达11%.

Gene expression profiling:Canonical molecular changes and clinicopathological features in sporadic colorectal cancers

AIM： To investigate alternative or subordinate pathways involved in colorectal tumorigenesis and tumor growth, possibly determining at-risk populations and predicting responses to treatment. METHODS： Using microarray gene-expression analysis, we analyzed patterns of gene expression relative to canonical molecular changes and clinicopathological features in 84 sporadic colorectal cancer patients, standardized by tumor location. Subsets of differentially expressed genes were confirmed by real-time reverse-transcript polymerase chain reaction （RT-PCR）. RESULTS： The largest number of genes identified as being differentially expressed was by tumor location, and the next largest number by lymphovascular or neural invasion of tumor cells and by mismatch repair （NMR） defects. Amongst biological processes, the immune response was significantly implicated in entire molecular changes observed during colorectal tumorigenesis （P 〈 0.001）. Amongst 47 differentially expressed genes, seven （PISD, NIBP, BAI2, STOML1, MRPL21, MRPL16, and MKKS） were newly found to correlate with tumorigenesis and tumor growth. Most location-associated molecular changes had distinct effects on gene expression, but the effects of the latter were sometimes contradictory. CONCLUSION： We show that several differentially expressed genes were associated with canonical molecular changes in sporadic colorectal cancers, possibly constituting alternative or subordinate pathways of tumorigenesis. As tumor location was the dominant factor influencing differential gene expression, location-specific analysis may identify location-associated pathways and enhance the accuracy of class prediction.

An upper ocean response to Typhoon Bolaven analyzed with Argo profiling floats

In situ observations from Argo profiling floats combined with satellite retrieved SST and rain rate are used to investigate an upper ocean response to Typhoon Bolaven from 20 through 29 August 2012. After the passage of Typhoon Bolaven, the deepening of mixed layer depth（MLD）, and the cooling of mixed layer temperature（MLT） were observed. The changes in mixed layer salinity（MLS） showed an equivalent number of increasing and decreasing because the typhoon-induced salinity changes in the mixed layer were influenced by precipitation, evaporation, turbulent mixing and upwelling of thermocline water. The deepening of the MLD and the cooling of the MLT indicated a significant rightward bias, whereas the MLS was freshened to the left side of the typhoon track and increased on the other side. Intensive temperature and salinity profiles observed by Iridium floats make it possible to view response processes in the upper ocean after the passage of a typhoon. The cooling in the near-surface and the warming in the subsurface were observed by two Iridium floats located to the left side of the cyclonic track during the development stage of the storm, beyond the radius of maximum winds relative to the typhoon center. Water salinity increases at the base of the mixed layer and the top of the thermocline were the most obvious change observed by those two floats. On the right side of the track and near the typhoon center when the typhoon was intensified, the significant cooling from sea surface to a depth of 200×10^4 Pa, with the exception of the water at the top of the thermocline, was observed by the other Iridium float. Owing to the enhanced upwelling near the typhoon center, the water salinity in the near-surface increased noticeably. The heat pumping from the mixed layer into the thermocline induced by downwelling and the upwelling induced by the positive wind stress curl are the main causes for the different temperature and salinity variations on the different sides of the track. It seems that more time is required for the anomalies in the subsurface to be restored to pretyphoon conditions than for the anomalies in the mixed layer.

基于edge profiling的循环运行时信息分析方法

应用程序中循环部分往往是计算密集型应用的主要工作负载,随着基于FPGA的可重构计算系统的出现,循环的静态分析技术已不能满足可重构计算系统根据程序当前行为模式进行特定优化的要求。针对现有的程序动态分析技术无法直接获取循环动态信息的问题,提出一种循环信息分析算法,根据支配关系在控制流图中识别循环,通过edge profiling的结果分析计算得到循环调用次数、循环平均迭代次数及循环运行时间等关键信息,并在LLVM(Low Level Virtual Machine)平台上实现该算法。实验结果表明,该算法能够自动识别所有循环结构,并对循环部分进行精确分析,分析结果能够为可重构计算系统待加速计算密集型循环的选择提供较全面、精确的信息支持,对程序员进行可重构系统中软硬件划分技术的研究具有重要作用。

Identification of epididymis-specific transcripts in the mouse and rat by transcriptional profiling

As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetrix whole genome microarrays. A total of 17 096 and 16 360 probe sets representing transcripts were identified as being expressed in the segmented mouse and rat epididymal transcriptomes, respectively. Comparison of the expressed murine transcripts against a mouse transcriptional profiling database derived from 22 other mouse tissues identified 77 transcripts that were expressed uniquely in the epididymis. The expression of these genes was further evaluated by reverse transcription polymerase chain reaction （RT-PCR） analysis of RNA from 21 mouse tissues. RT-PCR analysis confirmed epididymis-specific expression of Defensin Beta 13 and identified two additional genes with expression restricted only to the epididymis and testis. Comparison of the 16 360 expressed transcripts in the rat epididymis with data of 21 other tissues from a rat transcriptional profiling database identified 110 transcripts specific for the epididymis. Sixty-two of these transcripts were further investigated by qPCR analysis. Only Defensin 22 （E3 epididymal protein） was shown to be completely specific for the epididymis. In addition, 14 transcripts showed more than 100-fold selective expression in the epididymis. The products of these genes might play important roles in epididymal and/or sperm function and further investigation and validation as contraceptive targets are warranted. The results of the studies described in this report are available at the Mammalian Reproductive Genetics （MRG） Database （http：//mrg. genetics.washington.edu/）. （Asian J Androl 2007July; 9： 522-527）

NBS profiling技术在小麦抗叶锈病研究中的应用初探

为了研究NBS profiling技术在小麦(Triticum aestivumL.)抗叶锈病基因中应用的可行性,本研究选用15个小麦抗叶锈病近等基因系和感病亲本Thatcher为材料,建立NBS profiling体系,并进行多态性分析;同时选取含有成株抗叶锈病基因Lr35的近等基因系TcLr35和Thatcher为材料,进行cDNA NBS profiling,从转录水平上寻找与目的基因Lr35相关的RGA片段。研究结果表明:基因组NBS profiling中所选的16对酶/引物组合中MseⅠ/NBS2、MseⅠ/NBS5和MseⅠ/NBS7均得到了较好扩增结果,多态性高,多态性检出率分别为26.4%、26.4%和23.5%;cDNA NBS profiling中共筛选了52对酶/引物组合进行差异片段的扩增,有多对组合能成功揭示抗感间差异。NBS profiling技术可应用于小麦叶锈病抗病基因的研究中,为该技术在小麦抗叶锈病基因筛选及分子标记研究中的应用奠定了基础。

Pancreatic acinar cell carcinoma: A review on molecular profiling of patient tumors

Pancreatic carcinomas with acinar differentiation are rare,accounting for 1%-2% of adult pancreatic tumors; they include pancreatic acinar cell carcinoma(PACC),pancreatoblastoma,and carcinomas of mixed differentiation. Patients with PACC have a prognosis better than pancreatic ductal adenocarcinomas but worse than pancreatic neuroendocrine tumors. Reports of overall survival range from 18 to 47 mo. A literature review on PACCs included comprehensive genomic profiling and whole exome sequencing on a series of more than 70 patients as well as other diagnostic studies including immunohistochemistry. Surgical resection of PACC is the preferred treatment for localized and resectable tumors. The efficacy of adjuvant treatment is unclear. Metastatic PACCs are generally not curable and treated with systemic chemotherapy. They are moderately responsive to chemotherapy with different regimens showing various degrees of response in case reports/series. Most of these regimens were developed to treat patients with pancreatic ductal adenocarcinomas or colorectal adenocarcinomas. Review of PACC's molecular profiling showed a number of gene alterations such as: SMAD4,BRAF,BRCA2,TP53,RB1,MEN1,JAK-1,BRCA-1,BRCA-2,and DNA mismatch repair abnormalities. PACCs had multiple somatic mutations with some targetable with available drugs. Therefore,molecular profiling of PACC should be an option for patients with refractory PACC.

Advances of supercritical fluid chromatography in lipid profiling

Supercritical fluid chromatography(SFC) meets with great favor due to its high efficiency, low organic solvent consumption, and the specialty for the identification of the isomeric species. This review describes the advances of SFC in targeted and untargeted lipid profiling. The advancement of the SFC instruments and the stationary phases are summarized. Typical applications of SFC to the targeted and untargeted lipid profiling are discussed in detail. Moreover, the perspectives of SFC in the lipid profiling are also proposed. As a useful and promising tool for investigating lipids in vitro and in vivo, SFC will predictably obtain further development.

Gene expression profiling of the rat sciatic nerve in early Wallerian degeneration after injury

Wallerian degeneration is an important area of research in modern neuroscience. A large number of genes are differentially regulated in the various stages of Wallerian degeneration, especially during the early response. In this study, we analyzed gene expression in early Wallerian degeneration of the distal nerve stump at 0, 0.5, 1,6, 12 and 24 hours after rat sciatic nerve injury using gene chip microarrays. We screened for differentially-expressed genes and gene expression patterns. We examined the data for Gene Ontology, and explored the Kyoto EncycLopedia of Genes and Genomes Pathway. This allowed us to identify key regulatory factors and recurrent network motifs. We identified 1 546 differentially-expressed genes and 21 distinct patterns ofgene expression in early Wallerian degeneration, and an enrichment of genes associated with the immune response, acute inflammation, apoptosis, cell adhesion, ion transport and the extracellular matrix. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed components involved in the Jak-STAT, ErbB, transforming growth factor-13, T cell receptor and calcium signaling pathways. Key factors included interleukin-6, interleukin-1, integrin, c-sarcoma, carcinoembryonic antigen-related cell adhesion molecules, chemokine （C-C motif） ligand, matrix metalloproteinase, BH3 interacting domain death agonist, baculoviral lAP repeat-containing 3 and Rac. The data were validated with real-time quantitative PCR. This study provides a global view of gene expression profiles in eady Wallerian degeneration of the rat sciatic nerve. Our findings provide insight into the molecular mechanisms underlying early Wallerian degeneration, and the regulation of nerve degeneration and regeneration.