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Predicting mutations deleterious to function in beta-lactamase TEM1 using MM-GBSA

Missense mutations can have disastrous effects on the function of a protein. And as a result, they have been implicated in numerous diseases. However, the majority of missense variants only have a nominal impact on protein function. Thus, the ability to distinguish these two classes of missense mutations would greatly aid drug discovery efforts in target identification and...

Rumination in bereaved parents: Psychometric evaluation of the Swedish version of the Utrecht Grief Rumination Scale (UGRS)

Background Bereaved parents may be at higher risk to develop persistent, severe and disabling grief, termed prolonged grief. Grief rumination, repetitive thinking about the causes and consequences of the loss, is a malleable cognitive process that maintains prolonged grief. Grief rumination can be measured with the Utrecht Grief Rumination Scale (UGRS). The present study aimed to...

Host Cell Deoxyribonucleic Acid Methylation Markers for the Detection of High-grade Anal Intraepithelial Neoplasia and Anal Cancer

High-grade anal intraepithelial neoplasia (AIN2/3; HGAIN) is highly prevalent in human immunodeficiency virus positive (HIV+) men who have sex with men (MSM), but only a minority will eventually progress to cancer. Currently, the cancer risk cannot be established, and therefore all HGAIN is treated, resulting in overtreatment. We assessed host cell deoxyribonucleic acid (DNA...

Plasma cytokine levels and the presence of colorectal cancer

Background/Aims Cancer-related activation of cytokine networks are central aspects of tumor development. The goal of the study was to examine the possibility of plasma cytokines for the screening of colorectal cancer (CRC). Methods We carried out a multicenter, hospital-based case-control study in 66 adult Japanese patients with CRC and 87 healthy adult Japanese. A multiplex bead...

DNA Ligase 1 is an essential mediator of sister chromatid telomere fusions in G2 cell cycle phase

Fusion of critically short or damaged telomeres is associated with the genomic rearrangements that support malignant transformation. We have demonstrated the fundamental contribution of DNA ligase 4-dependent classical non-homologous end-joining to long-range inter-chromosomal telomere fusions. In contrast, localized genomic recombinations initiated by sister chromatid fusion are...

A closed-loop, music-based brain-computer interface for emotion mediation

Emotions play a critical role in rational and intelligent behavior; a better fundamental knowledge of them is indispensable for understanding higher order brain function. We propose a non-invasive brain-computer interface (BCI) system to feedback a person’s affective state such that a closed-loop interaction between the participant’s brain responses and the musical stimuli is...

Enhancing naked oat (Avena nuda L.) productivity with minimal indirect nitrogen loss and maximum nitrogen use efficiency through integrated use of different nitrogen sources

Oat (Avena nuda L.) is a nutritious grain crop, rich in dietary fibers and phytochemicals. Application of efficient nitrogen (N) sources and dose is very important to obtain higher crop productivity and to achieve environmental sustainability. The exploitation of natural beneficial microbes and organic nitrogen in combination with chemical nitrogen would be effective to boost...

Two-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure

In the promoter of c-KIT proto-oncogene, whose deregulation has been implicated in many cancers, three G-rich regions (kit1, kit* and kit2) are able to fold into G-quadruplexes. While kit1 and kit2 have been studied in depth, little information is available on kit* folding behavior despite its key role in regulation of c-KIT transcription. Notably, kit* contains consensus sites...

Randomized controlled comparison of cross-sectional survey approaches to optimize follow-up completeness in clinical studies

Introduction In outcome research, incomplete follow-up is a major, yet potentially correctable source of bias. Cross-sectional surveys may theoretically increase completeness of follow-up, but low response rates are reported typically. We investigated whether a pre-notification letter improved patient availability for follow-up phone interviews and thereby improved cross...

Virtual navigation tested on a mobile app is predictive of real-world wayfinding navigation performance

Virtual reality environments presented on tablets and smartphones have potential to aid the early diagnosis of conditions such as Alzheimer’s dementia by quantifying impairments in navigation performance. However, it is unclear whether performance on mobile devices can predict navigation errors in the real world. We compared the performance of 49 participants (25 females, 18-35...

Color-coded molecular beacons for multiplex PCR screening assays

The number of different fluorescent colors that can be distinguished in a PCR screening assay restricts the number of different targets that can be detected. If only six colors can be distinguished, and the probe for each target is labeled with a unique color, then only six different targets can be identified. Yet, it is often desirable to identify more targets. For instance, the...

Complications of CT-guided lung biopsy with a non-coaxial semi-automated 18 gauge biopsy system: Frequency, severity and risk factors

Objectives To evaluate frequency and severity of complications after CT-guided lung biopsy using the Society of Interventional Radiology (SIR) classification, and to assess risk factors for overall and major complications. Materials and methods 311 consecutive biopsies with a non-coaxial semi-automated 18 gauge biopsy system were retrospectively evaluated. Complications after...

Determining the effects of DNA sequence on Hel308 helicase translocation along single-stranded DNA using nanopore tweezers

Motor enzymes that process nucleic-acid substrates play vital roles in all aspects of genome replication, expression, and repair. The DNA and RNA nucleobases are known to affect the kinetics of these systems in biologically meaningful ways. Recently, it was shown that DNA bases control the translocation speed of helicases on single-stranded DNA, however the cause of these effects...

InDel markers: An extended marker resource for molecular breeding in chickpea

Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands...

Engagement of DNA and H3K27me3 by the CBX8 chromodomain drives chromatin association

Polycomb repressive complex 1 (PRC1) is critical for mediating gene repression during development and adult stem cell maintenance. Five CBX proteins, CBX2,4,6,7,8, form mutually exclusive PRC1 complexes and are thought to play a role in the association of PRC1 with chromatin. Specifically, the N-terminal chromodomain (CD) in the CBX proteins is thought to mediate specific...

Polymerization kinetics stability, volumetric changes, apatite precipitation, strontium release and fatigue of novel bone composites for vertebroplasty

Purpose The aim was to determine effects of diluent monomer and monocalcium phosphate monohydrate (MCPM) on polymerization kinetics and volumetric stability, apatite precipitation, strontium release and fatigue of novel dual-paste composites for vertebroplasty. Materials and methods Polypropylene (PPGDMA) or triethylene (TEGDMA) glycol dimethacrylates (25 wt%) diluents were...

Bayesian inference of origin firing time distributions, origin interference and licencing probabilities from Next Generation Sequencing data

DNA replication is a stochastic process with replication forks emanating from multiple replication origins. The origins must be licenced in G1, and the replisome activated at licenced origins in order to generate bi-directional replication forks in S-phase. Differential firing times lead to origin interference, where a replication fork from an origin can replicate through and...

Phenotypic plasticity influences the success of clonal propagation in industrial pharmaceutical Cannabis sativa

The burgeoning cannabis market requires evidence-based science such that farmers can quickly and efficiently generate new plants. In part, horticultural operations are limited by the success of cloning procedures. Here, we measured the role of environmental conditions and cultivar identity on the success of generating long branch material with many meristems in planting stock...