PatMatch: a program for finding patterns in peptide and nucleotide sequences

Here, we present PatMatch, an efficient, web-based pattern-matching program that enables searches for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences. The program can be used to find matches to a user-specified sequence pattern that can be described using ambiguous sequence codes and a powerful and flexible pattern syntax based on regular expressions. A recent upgrade has improved performance and now supports both mismatches and wildcards in a single pattern. This enhancement has been achieved by replacing the previous searching algorithm, scan_for_matches [D'Souza et al. (1997), Trends in Genetics, 13, 497–498], with nondeterministic-reverse grep (NR-grep), a general pattern matching tool that allows for approximate string matching [Navarro (2001), Software Practice and Experience, 31, 1265–1312]. We have tailored NR-grep to be used for DNA and protein searches with PatMatch. The stand-alone version of the software can be adapted for use with any sequence dataset and is available for download at The Arabidopsis Information Resource (TAIR) at . The PatMatch server is available on the web at for searching Arabidopsis thaliana sequences

Psychological Profile of Sasang Typology: A Systematic Review

A systematic review of studies related to the psychological characteristics of Sasang types was conducted with the goal of delineating generalizable psychological profiles based on Sasang typology, a traditional Korean medical typology with medical herbs and acupuncture that is characterized as personalized medicine. Journal articles pertaining to Sasang typology were collected using five electronic database systems in Korea and in the USA. As a result, 64 potentially relevant studies were identified and 21 peer-reviewed research articles that employed psychometric inventories were included. Beginning with the use of the Minnesota Multiphasic Personality Inventory in 1992, Myers-Briggs Type Indicator, NEO-Personality Inventory, Temperament and Character Inventory and other personality assessment tools were employed in the identified studies. Because data synthesis could not be carried out due to the heterogeneity of the studies, the present review article sought to delineate the mutual relevance of the studies based on research results pertaining to the correlation between the aforementioned psychological assessment instruments. Results of the review indicate that two super-factors, Extraversion and Neuroticism, serve as the foundation in regards to delineating personality constructs, such that the So-Yang type scored high on the Extraversion dimension and low on the Neuroticism dimension, while the So-Eum type scored low on the Extraversion dimension and high on the Neuroticism dimension. The present systematic review indicates that Sasang typology shares similarities with the Western psychological tradition

PD-1 blockade in recurrent or metastatic cervical cancer: Data from cemiplimab phase I expansion cohorts and characterization of PD-L1 expression in cervical cancer

Objectives: To characterize the safety, tolerability, and anti-tumor activity of cemiplimab as monotherapy or in combination with hypofractionated radiation therapy (hfRT) in patients with recurrent or metastatic cervical cancer. To determine the association between histology and programmed death-ligand 1 (PD-L1) expression. Methods: In non-randomized phase I expansion cohorts, patients (squamous or non-squamous histology) received cemiplimab 3 mg/kg intravenously every 2 weeks for 48 weeks, either alone (monotherapy cohort) or with hfRT during week 2 (combination cohort). Due to insufficient tissue material, PD-L1 protein expression was evaluated in commercially purchased samples and mRNA expression levels were analyzed from The Cancer Genome Atlas (TCGA). Results: Twenty patients enrolled in both cohorts in total; 10 had squamous histology. The most common adverse events of any grade were diarrhea, fatigue, and hypokalemia, occurring in 35%, 25%, and 25%, respectively. Objective response rate was 10% in each cohort; responders had squamous histology. Duration of response was 11.2 months and 6.4 months for the responder in the monotherapy and combination cohort, respectively. Irradiated lesions were not included in the response assessments. In separate archived specimens (N = 155), PD-L1 protein expression in tumor and immune cells was negative (<1%) more commonly in adenocarcinoma than in squamous tumors. PD-L1 mRNA levels were lower in adenocarcinoma than squamous cell tumors (1.2 vs 5.0 mean transcripts per million, respectively) in TCGA. Conclusions: Cemiplimab has activity in cervical squamous cell carcinoma. The phase I results, combined with results from other anti-PD-1 trials in cervical cancer and our biomarker analyses have informed the design of the ongoing phase III trial, with the primary overall survival hierarchical analyses being done first in patients with squamous histology

High-Speed Baud-Rate Clock and Data Recovery

This thesis presents an adaptive baud-rate CDR with CTLE and 1-tap DFE. The novelty in this design is the adaptation engine tailored for baud-rate clock and data recovery where the comparators for the DFE and the PD are shared to save power. A testchip was fabricated in TSMC 28nm CMOS. The adaptation engine is demonstrated for 34-36Gb/s operation with a Tyco 5" channel resulting in 15.05-18.25dB channel losses. At 35Gb/s, the total power consumption is measured to be 106.3mW or a FOM of 3.04pJ/bit. This thesis also presents a 2x half-baud-rate clock and data recovery technique with 2x oversampling at half-baud-rate (every other UI). A testchip was also fabricated in TSMC 28nm CMOS. A 30Gb/s 2x half-baud-rate CDR was tested with a Tyco 5" channel with 13.06dB of loss. The total power consumption is measured to be 79.2mW or a FOM of 2.64pJ/bit.M.A.S.2020-11-15 00:00:0

Shouldering the load of mandible reconstruction: 81 cases of oromandibular reconstruction with the scapular tip free flap

Background The scapular tip free flap (STFF) is becoming more popular for oromandibular reconstruction. This article reviewed the early and late outcomes in a larger series over 9 years. Methods We conducted a retrospective review of all consecutive patients who underwent oromandibular reconstruction using the STFF at London Health Sciences Centre. Demographic information, surgical data, and complications were collected and analyzed. Results From April 2008 to March 2017, 81 STFFs were performed in 80 patients. The average bony reconstruction measured 5.4 cm. Bone-only flaps were utilized in 24 cases (29.6%). Five cases (6.2%) required a single osteotomy. There were 3 (3.7%) flap failures. There were 7 plate extrusions and 11 cases of radiographic nonunion. Conclusion The STFF is a reliable option with acceptable early and long-term results. The STFF may be considered as a first line option especially for shorter bone defects or in conjunction with complex soft tissue requirements