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Many treatments against breast cancer decrease the level of estrogen in blood, resulting in bone loss, osteoporosis and fragility fractures in breast cancer patients. This retrospective study aimed to evaluate a novel opportunistic screening for cancer treatment-induced bone loss (CTIBL) in breast cancer patients using CT radiomics. Between 2011 and 2021, a total of 412 female breast cancer patients who received treatment and were followed up in our institution, had post-treatment dual-energy X-ray absorptiometry (DXA) examination of the lumbar vertebrae and had post-treatment chest CT scan that encompassed the L1 vertebra, were included in this study. Results indicated that the T-score of L1 vertebra had a strongly positive correlation with the average T-score of L1–L4 vertebrae derived from DXA (r = 0.91, p < 0.05). On multivariable analysis, four clinical variables (age, body weight, menopause status, aromatase inhibitor exposure duration) and three radiomic features extracted from the region of interest of L1 vertebra (original_firstorder_RootMeanSquared, wavelet.HH_glcm_InverseVariance, and wavelet.LL_glcm_MCC) were selected for building predictive models of L1 T-score and bone health. The predictive model combining clinical and radiomic features showed the greatest adjusted R2 value (0.557), sensitivity (83.6%), specificity (74.2%) and total accuracy (79.4%) compared to models that relied solely on clinical data, radiomic features, or Hounsfield units. In conclusion, the clinical-radiomic predictive model may be used as an opportunistic screening tool for early identification of breast cancer survivors at high risk of CTIBL based on non-contrast CT images of the L1 vertebra, thereby facilitating early intervention for osteoporosis. [ABSTRACT FROM AUTHOR]

Prior research has shown that the deconvolution of cell-free RNA can uncover the tissue origin. The conventional deconvolution approaches rely on constructing a reference tissue-specific gene panel, which cannot capture the inherent variation present in actual data. To address this, we have developed a novel method that utilizes a neural network framework to leverage the entire training dataset. Our approach involved training a model that incorporated 15 distinct tissue types. Through one semi-independent and two complete independent validations, including deconvolution using a semi in silico dataset, deconvolution with a custom normal tissue mixture RNA-seq data, and deconvolution of longitudinal circulating tumor cell RNA-seq (ctcRNA) data from a cancer patient with metastatic tumors, we demonstrate the efficacy and advantages of the deep-learning approach which were exerted by effectively capturing the inherent variability present in the dataset, thus leading to enhanced accuracy. Sensitivity analyses reveal that neural network models are less susceptible to the presence of missing data, making them more suitable for real-world applications. Moreover, by leveraging the concept of organotropism, we applied our approach to trace the migration of circulating tumor cell-derived RNA (ctcRNA) in a cancer patient with metastatic tumors, thereby highlighting the potential clinical significance of early detection of cancer metastasis. [ABSTRACT FROM AUTHOR]

Motivation As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest disease and dictate prognosis. Previous studies that tried to correlate mutation with gene expression dysregulation neglected to adjust for the disparate multitudes of false positives associated with unequal sample sizes and uneven class balancing scenarios. Results To properly address this issue, we developed a statistical framework to rigorously assess the extent of mutation impact on microRNAs in relation to a permutation-based null distribution of a matching sample structure. Carrying out the framework in a pan-cancer study, we ascertained 9008 protein-coding genes with statistically significant mutation impacts on miRNAs. Of these, the collective miRNA expression for 83 genes showed significant prognostic power in nine cancer types. For example, in lower-grade glioma, 10 genes' mutations broadly impacted miRNAs, all of which showed prognostic value with the corresponding miRNA expression. Our framework was further validated with functional analysis and augmented with rich features including the ability to analyze miRNA isoforms; aggregative prognostic analysis; advanced annotations such as mutation type, regulator alteration, somatic motif, and disease association; and instructive visualization such as mutation OncoPrint, Ideogram, and interactive mRNA–miRNA network. Availability and implementation The data underlying this article are available in MutMix, at http://innovebioinfo.com/Database/TmiEx/MutMix.php. [ABSTRACT FROM AUTHOR]

Introduction: Cystic periventricular leukomalacia (PVL) is the most common white matter injury and a common cause of cerebral palsy in preterm infants. Postnatal epilepsy may occur after cystic PVL, but their causal relationship remains uncertain. Our aim was to validate the contribution of cystic PVL to postnatal epilepsy in very preterm infants and demonstrate their seizure characteristics. Methods: This prospective cohort study enrolled 1,342 preterm infants (birth weight <1,500 g and gestational age <32 weeks) from 2003 to 2015. Cystic PVL was diagnosed by serial cerebral ultrasound, and other comorbidities were recorded during hospitalization. Neurological developments and consequences, including epilepsy, were serially accessed until the age of 5. Results: A total of 976 preterm infants completed a 5-year neurological follow-up; 47 (4.8%) had cystic PVL. Preterm infants with cystic PVL were commonly associated with other comorbidities, including necrotizing enterocolitis stage III, neonatal seizures, and intraventricular hemorrhage during hospitalization. At age 5, 14 of the 47 (29.8%) preterm infants with cystic PVL had postnatal epilepsy. After adjusting for gender, gestational age, and three common comorbidities, cystic PVL was an independent risk factor for postnatal epilepsy (adjust OR: 16.2; 95% CI: 6.8–38.4; p < 0.001). Postnatal epilepsy after cystic PVL was commonly the generalized type (13 of 14, 92.9%), not intractable and most occurred after 1 year of age. Discussion/Conclusion: Cystic PVL would independently lead to postnatal epilepsy. Preterm infants with cystic PVL are at risk of postnatal epilepsy after age 1 in addition to cerebral palsy. [ABSTRACT FROM AUTHOR]

Background: The metabolome is the best representation of cancer phenotypes. Gene expression can be considered a confounding covariate affecting metabolite levels. Data integration across metabolomics and genomics to establish the biological relevance of cancer metabolism is challenging. This study aimed to eliminate the confounding effect of metabolic gene expression to reflect actual metabolite levels in microsatellite instability (MSI) cancers. Methods: In this study, we propose a new strategy using covariate-adjusted tensor classification in high dimensions (CATCH) models to integrate metabolite and metabolic gene expression data to classify MSI and microsatellite stability (MSS) cancers. We used datasets from the Cancer Cell Line Encyclopedia (CCLE) phase II project and treated metabolomic data as tensor predictors and data on gene expression of metabolic enzymes as confounding covariates. Results: The CATCH model performed well, with high accuracy (0.82), sensitivity (0.66), specificity (0.88), precision (0.65), and F1 score (0.65). Seven metabolite features adjusted for metabolic gene expression, namely, 3-phosphoglycerate, 6-phosphogluconate, cholesterol ester, lysophosphatidylethanolamine (LPE), phosphatidylcholine, reduced glutathione, and sarcosine, were found in MSI cancers. Only one metabolite, Hippurate, was present in MSS cancers. The gene expression of phosphofructokinase 1 (PFKP), which is involved in the glycolytic pathway, was related to 3-phosphoglycerate. ALDH4A1 and GPT2 were associated with sarcosine. LPE was associated with the expression of CHPT1, which is involved in lipid metabolism. The glycolysis, nucleotide, glutamate, and lipid metabolic pathways were enriched in MSI cancers. Conclusions: We propose an effective CATCH model for predicting MSI cancer status. By controlling the confounding effect of metabolic gene expression, we identified cancer metabolic biomarkers and therapeutic targets. In addition, we provided the possible biology and genetics of MSI cancer metabolism. [ABSTRACT FROM AUTHOR]

In some manufacturing processes, the quality of a product can be characterized by the functional relationship between the response variable and the explanatory variables. Profile monitoring is a tool used to examine the stability of the functional relationship over time. Many studies have pointed out that the measurements within a profile are uncorrelated. In this research, to take advantage of the ability to provide a comprehensive description of a wide variety of data, the Tweedie exponential dispersion process model is used to account for the within-profile correlation. Then, two exponentially weighted moving average control charts are developed to detect process changes during a Phase II application. In the simulation studies, we showed that our proposed control charts outperform the existing methods for monitoring linear and nonlinear profiles. Finally, two numerical examples are given to demonstrate the usefulness of our proposed control charts. [ABSTRACT FROM AUTHOR]

Containing the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of Dendrobium catenatum, Phalaenopsis equestris, and Apostasia shenzhenica which belong to two different subfamilies of Orchidaceae, and developed user-friendly tools to explore the orchid genetic sequences in the OrchidBase 4.0. The OrchidBase 4.0 offers the opportunity for plant science community to compare orchid genomes and transcriptomes and retrieve orchid sequences for further study. In the year 2022, two whole-genome sequences of Orchidoideae species, Platanthera zijinensis and Platanthera guangdongensis, were de novo sequenced, assembled and analyzed. In addition, systemic transcriptomes from these two species were also established. Therefore, we included these datasets to develop the new version of OrchidBase 5.0. In addition, three new functions including synteny, gene order, and miRNA information were also developed for orchid genome comparisons and miRNA characterization. OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/ [ABSTRACT FROM AUTHOR]

Simple Summary: Using the covariate-adjusted tensor classification in the high-dimension (CATCH) model, we integrated adjusted radiomics-based CT images into RNA immune genomic expression data to achieve the accurate classification of recurrent CRC. The correlation between radiomic features and immune gene expression identifies potential therapeutic targets in CRC. We provide individualized cancer therapeutic strategies based on adjusted radiomic features in recurrent stage III CRC. To evaluate whether adjusted computed tomography (CT) scan image-based radiomics combined with immune genomic expression can achieve accurate stratification of cancer recurrence and identify potential therapeutic targets in stage III colorectal cancer (CRC), this cohort study enrolled 71 patients with postoperative stage III CRC. Based on preoperative CT scans, radiomic features were extracted and selected to build pixel image data using covariate-adjusted tensor classification in the high-dimension (CATCH) model. The differentially expressed RNA genes, as radiomic covariates, were identified by cancer recurrence. Predictive models were built using the pixel image and immune genomic expression factors, and the area under the curve (AUC) and F1 score were used to evaluate their performance. Significantly adjusted radiomic features were selected to predict recurrence. The association between the significantly adjusted radiomic features and immune gene expression was also investigated. Overall, 1037 radiomic features were converted into 33 × 32-pixel image data. Thirty differentially expressed genes were identified. We performed 100 iterations of 3-fold cross-validation to evaluate the performance of the CATCH model, which showed a high sensitivity of 0.66 and an F1 score of 0.69. The area under the curve (AUC) was 0.56. Overall, ten adjusted radiomic features were significantly associated with cancer recurrence in the CATCH model. All of these methods are texture-associated radiomics. Compared with non-adjusted radiomics, 7 out of 10 adjusted radiomic features influenced recurrence-free survival. The adjusted radiomic features were positively associated with PECAM1, PRDM1, AIF1, IL10, ISG20, and TLR8 expression. We provide individualized cancer therapeutic strategies based on adjusted radiomic features in recurrent stage III CRC. Adjusted CT scan image-based radiomics with immune genomic expression covariates using the CATCH model can efficiently predict cancer recurrence. The correlation between adjusted radiomic features and immune genomic expression can provide biological relevance and individualized therapeutic targets. [ABSTRACT FROM AUTHOR]

Background: The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages of Phalaenopsis as well as biotic and abiotic stress-treated Phalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae. Description: Recently, the whole-genome sequences of Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris were de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species. Conclusions: OrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available at http://orchidbase.itps.ncku.edu.tw/ [ABSTRACT FROM AUTHOR]

Orchid gynostemium, the fused organ of the androecium and gynoecium, and ovule development are unique developmental processes. Two DROOPING LEAF / CRABS CLAW (DL / CRC) genes, PeDL1 and PeDL2, were identified from the Phalaenopsis orchid genome and functionally characterized. Phylogenetic analysis indicated that the most recent common ancestor of orchids contained the duplicated DL/CRC -like genes. Temporal and spatial expression analysis indicated that PeDL genes are specifically expressed in the gynostemium and at the early stages of ovule development. Both PeDL s could partially complement an Arabidopsis crc-1 mutant. Virus-induced gene silencing (VIGS) of PeDL1 and PeDL2 affected the number of protuberant ovule initials differentiated from the placenta. Transient overexpression of PeDL1 in Phalaenopsis orchids caused abnormal development of ovule and stigmatic cavity of gynostemium. PeDL1, but not PeDL2, could form a heterodimer with Phalaenopsis equestris CINCINNATA 8 (PeCIN8). Paralogous retention and subsequent divergence of the gene sequences of PeDL1 and PeDL2 in P. equestris might result in the differentiation of function and protein behaviors. These results reveal that the ancestral duplicated DL/CRC -like genes play important roles in orchid reproductive organ innovation. [ABSTRACT FROM AUTHOR]

Background and Objective. The main purpose of this study was to develop a simple automatic diagnostic classification scheme for chemotherapy-induced peripheral neuropathy. Methods. This was a prospective cohort study that enrolled patients with colorectal or gynecologic cancer post chemotherapy for more than 1 year. The patients underwent laboratory examinations (nerve conduction studies and quantitative sensory tests), and a questionnaire about the quality of life. An unsupervised classification algorithm was used to classify the patients into groups using a small number of variables derived from the laboratory tests. A panel of five neurologists also diagnosed the types of neuropathies according to the laboratory tests. The results by the unsupervised classification algorithm and the neurologists were compared. Results. The neurologists' diagnoses showed much higher rates of entrapment syndromes (66.1%) and radiculopathies (55.1%) than polyneuropathy (motor/sensory: 33.1%/29.7%). A multivariate analysis showed that the questionnaire was not significantly correlated with the results of quantitative sensory tests (r = 0.27) or the neurologists' diagnoses (r = 0.2). All of the patients were classified into four groups by the unsupervised classification algorithm. The classification corresponded to the severity of neuropathy and correlated well with the neurologists' diagnoses and the scales of neurological examinations. The overall correct rate of classification by the unsupervised classification algorithm was 78.8% (95% confidence interval: 73.1%-88.3%). Conclusion. The results of our unsupervised classification algorithm based on three variables of laboratory tests correlated well with the neurologists' diagnoses. [ABSTRACT FROM AUTHOR]

Profile monitoring is a technique to test the stability of the relationship between a response variable and explanatory variables over time. The most relevant linear profile monitoring methods have been constructed using the normality assumption. However, the normality assumption could be violated in many quality control applications. In this study, we consider a situation in which the random errors in a linear profile model follow a skew‐normal distribution. The skew‐normal distribution is a generalized version of the normal distribution. A new Shewhart‐type chart and exponentially weighted moving average (EWMA) chart, named the ShewhartR and EWMAR charts, respectively, are constructed based on residuals to monitor the parameters of linear profile model. The simulation results show that the multivariate EWMA chart is sensitive to the normality assumption and that the proposed ShewhartR and EWMAR charts have good ability to detect big and small‐to‐moderate process shifts, respectively. An example using photo mask techniques in semiconductor manufacturing is provided to illustrate the applications of the ShewhartR and EWMAR charts. [ABSTRACT FROM AUTHOR]

In profile monitoring for a multivariate manufacturing process, the functional relationship of the multivariate profiles rarely occurs in linear form, and the real data usually do not follow a multivariate normal distribution. Thus, in this paper, the functional relationship of multivariate nonlinear profile data is described via a nonparametric regression model. We first fit the multivariate nonlinear profile data and obtain the reference profiles through support vector regression (SVR) model. The differences between the observed multivariate nonlinear profiles and the reference profiles are used to calculate the vector of metrics. Then, a nonparametric revised spatial rank exponential weighted moving average (RSREWMA) control chart is proposed in the phase II monitoring. Moreover, a simulation study is conducted to evaluate the detecting performance of our proposed nonparametric RSREWMA control chart under various process shifts using out‐of‐control average run length (ARL1). The simulation results indicate that the SREWMA control chart coupled with the metric of mean absolute deviation (MAD) can be used to monitor the multivariate nonlinear profile data when a common fixed design (CFD) is not applicable in the phase II study. Finally, a realistic multivariate nonlinear profile example is used to demonstrate the usefulness of our proposed RSREWMA control chart and its monitoring schemes. [ABSTRACT FROM AUTHOR]

In today's manufacturing industries, if the quality characteristic of a product or a process is assumed to be represented by a functional relationship between the response variable and one or more explanatory variables, then the data generated from such a relationship are called profile data. Generally speaking, the functional relationship of the profile data rarely occurs in linear form, and the real data usually do not follow normal distribution. Thus, in this paper, the functional relationship of profile data is described via a nonparametric regression model and a nonparametric exponentially weighted moving average (EWMA) control chart is developed for detecting the process shifts for nonlinear profile data in the Phase II monitoring. We first fit the nonlinear profile data via a support vector regression model and use the fitted values to calculate the five metrics. Then, the nonparametric EWMA control chart with the five metrics can be constructed accordingly. Moreover, a simulation study is conducted to evaluate the detecting performance of the new control chart under various process shifts using the out‐of‐control average run length. Finally, a realistic nonlinear profile example is used to demonstrate the usefulness of our proposed nonparametric EWMA control chart and its monitoring schemes. It is expected that the proposed nonparametric EWMA control chart can enhance the monitoring efficiency for nonlinear profile data in the phase II study. [ABSTRACT FROM AUTHOR]

Power/sample size (power) analysis estimates the likelihood of successfully finding the statistical significance in a data set. There has been a growing recognition of the importance of power analysis in the proper design of experiments. Power analysis is complex, yet necessary for the success of large studies. It is important to design a study that produces statistically accurate and reliable results. Power computation methods have been well established for both microarray-based gene expression studies and genotyping microarray-based genome-wide association studies. High-throughput sequencing (HTS) has greatly enhanced our ability to conduct biomedical studies at the highest possible resolution (per nucleotide). However, the complexity of power computations is much greater for sequencing data than for the simpler genotyping array data. Research on methods of power computations for HTS-based studies has been recently conducted but is not yet well known or widely used. In this article, we describe the power computation methods that are currently available for a range of HTS-based studies, including DNA sequencing, RNA-sequencing, microbiome sequencing and chromatin immunoprecipitation sequencing. Most importantly, we review the methods of power analysis for several types of sequencing data and guide the reader to the relevant methods for each data type. [ABSTRACT FROM AUTHOR]

Background: One of the most important and often neglected components of a successful RNA sequencing (RNA-Seq) experiment is sample size estimation. A few negative binomial model-based methods have been developed to estimate sample size based on the parameters of a single gene. However, thousands of genes are quantified and tested for differential expression simultaneously in RNA-Seq experiments. Thus, additional issues should be carefully addressed, including the false discovery rate for multiple statistic tests, widely distributed read counts and dispersions for different genes. Results: To solve these issues, we developed a sample size and power estimation method named RnaSeqSampleSize, based on the distributions of gene average read counts and dispersions estimated from real RNA-seq data. Datasets from previous, similar experiments such as the Cancer Genome Atlas (TCGA) can be used as a point of reference. Read counts and their dispersions were estimated from the reference's distribution; using that information, we estimated and summarized the power and sample size. RnaSeqSampleSize is implemented in R language and can be installed from Bioconductor website. A user friendly web graphic interface is provided at http://cqs.mc.vanderbilt.edu/shiny/RnaSeqSampleSize/. Conclusions: RnaSeqSampleSize provides a convenient and powerful way for power and sample size estimation for an RNAseq experiment. It is also equipped with several unique features, including estimation for interested genes or pathway, power curve visualization, and parameter optimization. [ABSTRACT FROM AUTHOR]

In some applications, the quality of the process or product is characterized and summarized by a functional relationship between a response variable and one or more explanatory variables. Profile monitoring is a technique for checking the stability of the relationship over time. Existing linear profile monitoring methods usually assumed the error distribution to be normal. However, this assumption may not always be true in practice. To address this situation, we propose a method for profile monitoring under the framework of generalized linear models when the relationship between the mean and variance of the response variable is known. Two multivariate exponentially weighted moving average control schemes are proposed based on the estimated profile parameters obtained using a quasi-likelihood approach. The performance of the proposed methods is evaluated by simulation studies. Furthermore, the proposed method is applied to a real data set, and the R code for profile monitoring is made available to users. [ABSTRACT FROM AUTHOR]

Purpose The purpose of this paper is to provide a new approach for detecting the small sustained process shifts in multistage systems with correlated multiple quality characteristics.Design/methodology/approach The authors propose a new multivariate linear regression model for a multistage manufacturing system with multivariate quality characteristics in which both the auto-correlated process outputs and the correlations occurring between neighboring stages are considered. Then, the multistage multivariate residual control charts are constructed to monitor the overall process quality of multistage systems with multiple quality characteristics. Moreover, an overall run length concept is adopted to evaluate the performances of the authors’ proposed control charts.Findings In the numerical example with cascade data, the authors show that the detecting abilities of the proposed multistage residual MEWMA and MCUSUM control charts outperform those of Phase II MEWMA and MCUSUM control charts. It further demonstrates the usefulness of the authors’ proposed control charts in the Phase II monitoring.Practical implications The research results of this paper can be applied to any multistage manufacturing or service system with multivariate quality characteristics. This new approach provides quality practitioners a better decision making tool for detecting the small sustained process shifts in multistage systems.Originality/value Once the multistage multivariate residual control charts are constructed, one can employ them in monitoring and controlling the process quality of multistage systems with multiple characteristics. This approach can lead to the direction of continuous improvement for any product or service within a company. [ABSTRACT FROM AUTHOR]

To assess the effect of chemotherapy on mitochondrial genome mutations in cancer survivors and their offspring, a study sequenced the full mitochondrial genome and determined the mitochondrial DNA heteroplasmic (mtDNA) mutation rate. To build a model for counts of heteroplasmic mutations in mothers and their offspring, bivariate Poisson regression was used to examine the relationship between mutation count and clinical information while accounting for the paired correlation. However, if the sequencing depth is not adequate, a limited fraction of the mtDNA will be available for variant calling. The classical bivariate Poisson regression model treats the offset term as equal within pairs; thus, it cannot be applied directly. In this research, we propose an extended bivariate Poisson regression model that has a more general offset term to adjust the length of the accessible genome for each observation. We evaluate the performance of the proposed method with comprehensive simulations, and the results show that the regression model provides unbiased parameter estimations. The use of the model is also demonstrated using the paired mtDNA dataset. [ABSTRACT FROM AUTHOR]

Purpose – In the past few years, several capability indices have been developed for evaluating the performance of multivariate manufacturing processes under the normality assumption. However, this assumption may not be true in most practical situations. Thus, the purpose of this paper is to develop new capability indices for evaluating the performance of multivariate processes subject to non-normal distributions. Design/methodology/approach – In this paper, the authors propose three non-normal multivariate process capability indices (MPCIs) RNMCp, RNMCpm and RNMCpu by relieving the normality assumption. Using the two normal MPCIs proposed by Pan and Lee, a weighted standard deviation method (WSD) is used to modify the NMCp and NMCpm indices for the-nominal-the-best case. Then the WSD method is applied to modify the multivariate ND index established by Niverthi and Dey for the-smaller-the-better case. Findings – A simulation study compares the performance of the various multivariate indices. Simulation results show that the actual non-conforming rates can be correctly reflected by the proposed capability indices. The numerical example further demonstrates that the actual quality performance of a non-normal multivariate process can properly reflected by the proposed capability indices. Practical implications – Process capability index is an important SPC tool for measuring the process performance. If the non-normal process data are mistreated as a normal one, it will result in an improper decision and thereby lead to an unnecessary quality loss. The new indices can provide practicing managers and engineers with a better decision-making tool for correctly measuring the performance for any multivariate process or environmental system. Originality/value – Once the existing multivariate quality/environmental problems and their Key Performance Indicators are identified, one may apply the new capability indices to evaluate the performance of various multivariate processes subject to non-normal distributions. [ABSTRACT FROM AUTHOR]

The Shewhart-type control chart is traditionally developed under the normality assumption. In practice, however, this assumption may not hold. Because the skew normal distribution represents a broad distribution class and is more flexible than is the normal distribution, we propose two new control charts to monitor process mean and spread for skew normal distributed data. Moreover, to facilitate practical implementation, tables of charting constants are provided. We conducted simulation studies to compare the false alarm rates, and the results show that new proposed charts perform better than others as skewness increases. Finally, an illustrative example is provided. [ABSTRACT FROM PUBLISHER]

This trial was designed to assess efficacy and safety of erlotinib with sorafenib in the treatment of patients with advanced pancreatic adenocarcinoma. An exploratory correlative study analyzing pretreatment serum samples using a multivariate protein mass spectrometry-based test (VeriStrat®), previously shown to correlate with outcomes in lung cancer patients treated with erlotinib, was performed. Patients received sorafenib 400 mg daily along with erlotinib 150 mg daily with a primary endpoint of 8-week progression free survival ( PFS) rate. Pretreatment serum sample analysis by VeriStrat was done blinded to clinical and outcome data; the endpoints were PFS and overall survival ( OS). Difference between groups (by VeriStrat classification) was assessed using log-rank P values; hazard ratios ( HR) were obtained from Cox proportional hazards model. Thirty-six patients received study drug and were included in the survival analysis. Eight-week PFS rate of 46% (95% confidence interval ( CI): 0.32-0.67) did not meet the primary endpoint of a rate ≥70%. Thirty-two patients were included in the correlative analysis, and VeriStrat 'Good' patients had superior PFS (HR = 0.18, 95% CI: 0.06-0.57; P = 0.001) and OS (HR = 0.31 95% CI: 0.13-0.77, P = 0.008) compared to VeriStrat 'Poor' patients. Grade 3 toxicities of this regimen included fever, anemia, diarrhea, dehydration, rash, and altered liver function. This study did not meet the primary endpoint, and this combination will not be further pursued. In this small retrospective analysis, the proteomic classification was significantly associated with clinical outcomes and is being further evaluated in ongoing studies. [ABSTRACT FROM AUTHOR]

With the advent of modern technology, manufacturing processes have become very sophisticated; a single quality characteristic can no longer reflect a product's quality. In order to establish performance measures for evaluating the capability of a multivariate manufacturing process, several new multivariate capability (NMC) indices, such as NMC p and NMC pm , have been developed over the past few years. However, the sample size determination for multivariate process capability indices has not been thoroughly considered in previous studies. Generally, the larger the sample size, the more accurate an estimation will be. However, too large a sample size may result in excessive costs. Hence, the trade-off between sample size and precision in estimation is a critical issue. In this paper, the lower confidence limits of NMC p and NMC pm indices are used to determine the appropriate sample size. Moreover, a procedure for conducting the multivariate process capability study is provided. Finally, two numerical examples are given to demonstrate that the proper determination of sample size for multivariate process indices can achieve a good balance between sampling costs and estimation precision. [ABSTRACT FROM AUTHOR]

Background: Neonatal hypoxic-ischemic encephalopathy (HIE) is the most common cause of mortality and neurological disability in infancy after perinatal asphyxia. Reliable biomarkers to predict neurological outcomes of neonates after perinatal asphyxia are still not accessible in clinical practice. Methods: A prospective cohort study enrolled neonates with perinatal asphyxia. Biochemical blood tests and cerebral Doppler ultrasound were measured within 6 h of age and at the 4th day old. Neurological outcomes were assessed at 1 year old. Results: Sixty-four neonates with perinatal asphyxia were enrolled. Fifty-eight (90%) had hypoxic-ischemic encephalopathy (HIE) including 20 (34%) Stage I, 21 (36%) Stage II, and 17 (29%) Stage III. In the asphyxiated infants without therapeutic hypothermia, HIE stage, PH, and base excess levels within 6 h of age were the predictors of adverse outcomes. In the asphyxiated infants receiving therapeutic hypothermia, HIE stage failed to predict outcomes. Instead, blood lactate levels and pulsatility index (PI) of medial cerebral arteries (MCA) either in 6 h of age or at the 4th day old independently predicted adverse outcomes. Conclusions: Blood lactate, which is a common accessible test at the hospital and MCA PI on cerebral ultrasound could predict adverse outcomes in asphyxiated infants receiving therapeutic hypothermia. [ABSTRACT FROM AUTHOR]

Motivation: Exome capture kits have capture efficiencies that range from 40 to 60%. A significant amount of off-target reads are from the mitochondrial genome. These unintentionally sequenced mitochondrial reads provide unique opportunities to study the mitochondria genome.Results: MitoSeek is an open-source software tool that can reliably and easily extract mitochondrial genome information from exome and whole genome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers and detects heteroplasmy, somatic mutation and structural variants of the mitochondrial genome. MitoSeek can be set up to run in parallel or serial on large exome sequencing datasets.Availability: https://github.com/riverlee/MitoSeekContact: yan.guo@vanderbilt.eduSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]