Pan-cancer subclonal mutation analysis of 7,827 tumors predicts clinical outcome.

Intra-tumor heterogeneity is an important driver of tumor evolution and therapy response. Advances in precision cancer treatment will require understanding of mutation clonality and subclonal architecture. Currently the slow computational speed of subclonal reconstruction hinders large cohort studies.

Personalized prediction of survival rate with combination of penalized Cox models in patients with colorectal cancer.

The investigation into individual survival rates within the patient population was typically conducted using the Cox proportional hazards model. This study was aimed to evaluate the performance of machine learning algorithm in predicting survival rates more than 5 years for individual patients with colorectal cancer. A total of 475 patients with colorectal cancer (CRC) and complete data who had underwent surgery for CRC were analyze to measure individual's survival rate more than 5 years using a machine learning based on penalized Cox regression.

The effect of Bruton's tyrosine kinase (BTK) inhibitor in the eosinophilic asthma model of mouse.

Bruton's Tyrosine kinase (BTK) plays a pivotal role as the key mediator in B cell signaling. Recent research has revealed that it is also expressed in cells critical to asthma development, such as T cells, and eosinophils. This study aims to investigate the potential of BTK inhibitor in eosinophilic asthma mouse model.

Personalized Risk Prediction for Cancer Survivors: A Bayesian Semi-parametric Recurrent Event Model with Competing Outcomes.

Multiple primary cancers are increasingly more frequent due to improved survival of cancer patients. Characteristics of the first primary cancer largely impact the risk of developing subsequent primary cancers. Hence, model-based risk characterization of cancer survivors that captures patient-specific variables is needed for healthcare policy making.

A quantile-slicing approach for sufficient dimension reduction with censored responses.

Sufficient dimension reduction (SDR) that effectively reduces the predictor dimension in regression has been popular in high-dimensional data analysis. Under the presence of censoring, however, most existing SDR methods suffer. In this article, we propose a new algorithm to perform SDR with censored responses based on the quantile-slicing scheme recently proposed by Kim et al.

Association between fertilization success rate and ambient air pollution: a possible explanation of within-year variation of fertilization success rate.

Objective: To evaluate patterns in air pollution concentrations and fertilization (IVF) success rates using data from a large, long-term clinical database.

Methods: We conducted a retrospective cohort study investigating South Korean women who pursued IVF and embryo transfer (IVF-ET) between 2011 and 2017. Hourly concentrations of air pollutants measured at 318 air quality monitoring sites in South Korea between 2011 and 2017 were obtained from the National Institute of Environmental Research.

Penetrance of Different Cancer Types in Families with Li-Fraumeni Syndrome: A Validation Study Using Multicenter Cohorts.

Li-Fraumeni syndrome (LFS) is a rare hereditary cancer syndrome associated with an autosomal-dominant mutation inheritance in the tumor suppressor gene and a wide spectrum of cancer diagnoses. The previously developed R package, LFSPRO, is capable of estimating the risk of an individual being a mutation carrier. However, an accurate estimation of the penetrance of different cancer types in LFS is crucial to improve the clinical characterization and management of high-risk individuals.

Penetrance Estimates Over Time to First and Second Primary Cancer Diagnosis in Families with Li-Fraumeni Syndrome: A Single Institution Perspective.

Li-Fraumeni syndrome (LFS) is a rare autosomal dominant disorder associated with germline mutations and an increased lifetime risk of multiple primary cancers (MPC). Penetrance estimation of time to first and second primary cancer within LFS remains challenging because of limited data and the difficulty of characterizing the effects of a primary cancer on the penetrance of a second primary cancer. Using a recurrent events survival modeling approach that incorporates a family-wise likelihood to efficiently integrate the pedigree structure, we estimated the penetrance for both first and second primary cancer diagnosis from a pediatric sarcoma cohort at MD Anderson Cancer Center [MDACC, Houston, TX; number of families = 189; single primary cancer (SPC) = 771; and MPC = 87].

Bayesian Semiparametric Estimation of Cancer-specific Age-at-onset Penetrance with Application to Li-Fraumeni Syndrome.

Penetrance, which plays a key role in genetic research, is defined as the proportion of individuals with the genetic variants (i.e., genotype) that cause a particular trait and who have clinical symptoms of the trait (i.

Simulating a Virtual Machining Model in an Agent-Based Model for Advanced Analytics.

Monitoring the performance of manufacturing equipment is critical to ensure the efficiency of manufacturing processes. Machine-monitoring data allows measuring manufacturing equipment efficiency. However, acquiring real and useful machine-monitoring data is expensive and time consuming.

Bayesian estimation of a semiparametric recurrent event model with applications to the penetrance estimation of multiple primary cancers in Li-Fraumeni syndrome.

A common phenomenon in cancer syndromes is for an individual to have multiple primary cancers (MPC) at different sites during his/her lifetime. Patients with Li-Fraumeni syndrome (LFS), a rare pediatric cancer syndrome mainly caused by germline TP53 mutations, are known to have a higher probability of developing a second primary cancer than those with other cancer syndromes. In this context, it is desirable to model the development of MPC to enable better clinical management of LFS.

Principal weighted support vector machines for sufficient dimension reduction in binary classification.

Sufficient dimension reduction is popular for reducing data dimensionality without stringent model assumptions. However, most existing methods may work poorly for binary classification. For example, sliced inverse regression (Li, 1991) can estimate at most one direction if the response is binary.

Manufacturing data analytics using a virtual factory representation.

Large manufacturers have been using simulation to support decision-making for design and production. However, with the advancement of technologies and the emergence of big data, simulation can be utilised to perform and support data analytics for associated performance gains. This requires not only significant model development expertise, but also huge data collection and analysis efforts.

TOWARDS A VIRTUAL FACTORY PROTOTYPE.

A virtual factory should represent most of the features and operations of the corresponding real factory. Some of the key features of the virtual factory include the ability to assess performance at multiple resolutions and generate analytics data similar to what is possible in a real factory. One should be able to look at the overall factory performance and be able to drill down to a machine and analyze its performance.

Two-Dimensional Solution Surface for Weighted Support Vector Machines.

The support vector machine (SVM) is a popular learning method for binary classification. Standard SVMs treat all the data points equally, but in some practical problems it is more natural to assign different weights to observations from different classes. This leads to a broader class of learning, the so-called weighted SVMs (WSVMs), and one of their important applications is to estimate class probabilities besides learning the classification boundary.

Continuous high-pressure negative suction drain: new powerful tool for closed wound management: clinical experience.

Background: Although various reconstructive flap surgeries have been successfully performed, there still are difficult wound complications, such as seroma formation, wound margin necrosis, delayed wound healing, and even flap failures. The negative-pressure wound therapy has been described in detail in the literature to assist open chronic/complex wound closure in reconstructive surgery. However, the negative-pressure wound therapy was difficult to be applied under the incisional closed wounds.

Probability-enhanced sufficient dimension reduction for binary classification.

In high-dimensional data analysis, it is of primary interest to reduce the data dimensionality without loss of information. Sufficient dimension reduction (SDR) arises in this context, and many successful SDR methods have been developed since the introduction of sliced inverse regression (SIR) [Li (1991) Journal of the American Statistical Association 86, 316-327]. Despite their fast progress, though, most existing methods target on regression problems with a continuous response.

Variable selection in large margin classifier-based probability estimation with high-dimensional predictors.

This is a discussion of the papers: "Probability estimation with machine learning methods for dichotomous and multicategory outcome: Theory" by Jochen Kruppa, Yufeng Liu, Gérard Biau, Michael Kohler, Inke R. König, James D. Malley, and Andreas Ziegler; and "Probability estimation with machine learning methods for dichotomous and multicategory outcome: Applications" by Jochen Kruppa, Yufeng Liu, Hans-Christian Diener, Theresa Holste, Christian Weimar, Inke R.

Long delayed traumatic carotid-cavernous sinus fistula.

Traumatic carotid-cavernous sinus fistula (TCCF) is a rare but significant vascular abnormality in the skull base found after craniomaxillofacial trauma. Although the direct type is usually caused by trauma, the onset of symptoms in TCCF may present several weeks after injury. We present the case of a patient who sustained a blunt head injury from falling down and was hospitalized with skull base fracture associated with zygomatic complex fractures on the right side.

New type of sauna-related burn: conductive contact burn.

A 70-year-old woman visited a Korean-style hot dry sauna room. The patient had a medical history of hypertension and hyperlipidemia. During the sauna, the patient slept for 30 minutes.

Dermatofibroma located on the tarsal plate after upper blepharoplasty?

Dermatofibroma is a firm, skin-colored or reddish-brown sessile papule or nodule. It arises spontaneously without a known cause or after a minor trauma, such as an insect bite. A 39-year-old Asian woman complained of a palpable mass and tenderness in the right upper eyelid.

Closed reduction of fractured anterior wall of the frontal sinus using threaded K-wires.

Classic approach of the anterior wall of frontal sinus fracture involves bicoronal or direct forehead incisions. However, these methods have some disadvantages, for example, paresthesia, scarring, and even alopecia. The purpose of this study was to introduce the simple and effective method of reduction of the anterior wall of frontal sinus fracture with threaded K-wires.

Mandibular tubercle resection: a means of maximizing the benefits of reduction mandibuloplasty.

Background: A square mandible is considered unattractive in Asia; as a result, mandibular reduction is the most common type of operation performed. The authors review the importance of mandibular tubercles in the lower margin of the parasymphysis area and introduce their resection techniques and results.

Methods: From April of 2005 to September of 2009, 178 patients underwent tubercle resection in the parasymphyseal area.

Multi-valued logic circuits using hybrid circuit consisting of three gates single-electron transistors (TG-SETs) and MOSFETs.

New multi-valued logic (MVL) families using the hybrid circuits consisting of three gates single-electron transistors (TG-SETs) and a metal-oxide-semiconductor field-effect transistor (MOSFET) are proposed. The use of SETs offers periodic literal characteristics due to Coulomb oscillation of SET, which allows a realization of binary logic (BL) circuits as well as multi-valued logic (MVL) circuits. The basic operations of the proposed MVL families are successfully confirmed through SPICE circuit simulation based on the physical device model of a TG-SET.