Impact of predictive selection of LbCas12a CRISPR RNAs upon on- and off-target editing rates in soybean.

Clustered regularly interspaced short palindromic repeats (CRISPR) technology has revolutionized creating targeted genetic variation in crops. Although CRISPR enzymes have been reported to have high sequence-specificity, careful design of the editing reagents can also reduce unintended edits at highly homologous sites. This work details the first large-scale study of the heritability of on-target edits and the rate of edits at off-target sites in soybean (), assaying ~700 T1 plants each resulting from transformation with LbCas12a constructs containing CRISPR RNAs (crRNAs) predicted to be either "unique" with no off-target sites or "promiscuous" with >10 potential off-targets in the soybean genome.

In Situ Dynamic Spectroscopic Ellipsometry Characterization of Cu-Ligated Mercaptoalkanoic Acid "Molecular" Ruler Multilayers.

Hybrid strategies that combine conventional top-down lithography with bottom-up molecular assembly are of interest for a range of applications including nanolithography and sensors. Interest in these strategies stems from the ability to create complex architectures over large areas with molecular-scale control and precision. The molecular-ruler process typifies this approach where the sequential layer-by-layer assembly of mercaptoalkanoic acid molecules and metal ions are combined with conventional top-down lithography to create precise, registered nanogaps.

Neuroimaging in Kabuki syndrome and another KMT2D-related disorder.

Recognition of distinct phenotypic features is an important component of genetic diagnosis. Although CHARGE syndrome, Kabuki syndrome, and a recently delineated KMT2D Ex 38/39 allelic disorder exhibit significant overlap, differences on neuroimaging may help distinguish these conditions and guide genetic testing and variant interpretation. We present an infant clinically diagnosed with CHARGE syndrome but subsequently found to have a de novo missense variant in exon 38 of KMT2D, the gene implicated in both Kabuki syndrome and a distinct KMT2D allelic disorder.

Novel methodology to assess the effect of contouring variation on treatment outcome.

Purpose: Contouring variation is one of the largest systematic uncertainties in radiotherapy, yet its effect on clinical outcome has never been analyzed quantitatively. We propose a novel, robust methodology to locally quantify target contour variation in a large patient cohort and find where this variation correlates with treatment outcome. We demonstrate its use on biochemical recurrence for prostate cancer patients.

Novel Variant Findings and Challenges Associated With the Clinical Integration of Genomic Testing: An Interim Report of the Genomic Medicine for Ill Neonates and Infants (GEMINI) Study.

Importance: A targeted genomic sequencing platform focused on diseases presenting in the first year of life may minimize financial and ethical challenges associated with rapid whole-genomic sequencing.

Objective: To report interim variants and associated interpretations of an ongoing study comparing rapid whole-genomic sequencing with a novel targeted genomic platform composed of 1722 actionable genes targeting disorders presenting in infancy.

Design, Setting, And Participants: The Genomic Medicine in Ill Neonates and Infants (GEMINI) study is a prospective, multicenter clinical trial with projected enrollment of 400 patients.

Influence of Contextual Factors, Technical Performance, and Movement Demands on the Subjective Task Load Associated With Professional Rugby League Match-Play.

Purpose: To identify the association between several contextual match factors, technical performance, and external movement demands on the subjective task load of elite rugby league players.

Methods: Individual subjective task load, quantified using the National Aeronautics and Space Administration Task Load Index (NASA-TLX), was collected from 29 professional rugby league players from one club competing in the European Super League throughout the 2017 season. The sample consisted of 26 matches (441 individual data points).

The Physiological and Perceptual Effects of Stochastic Simulated Rugby League Match Play.

Purpose: To examine responses to a simulated rugby league protocol designed to include more stochastic commands, and therefore require greater vigilance, than traditional team-sport simulation protocols.

Methods: Eleven male university rugby players completed 2 trials (randomized and control [CON]) of a rugby league movement simulation protocol, separated by 7 to 10 d. The CON trial consisted of 48 repeated ∼115-s cycles of activity.

Sequential targeted exome sequencing of 1001 patients affected by unexplained limb-girdle weakness.

Purpose: Several hundred genetic muscle diseases have been described, all of which are rare. Their clinical and genetic heterogeneity means that a genetic diagnosis is challenging. We established an international consortium, MYO-SEQ, to aid the work-ups of muscle disease patients and to better understand disease etiology.

Infant mortality: the contribution of genetic disorders.

Objective: To determine the proportion of infant deaths occurring in the setting of a confirmed genetic disorder.

Study Design: A retrospective analysis of the electronic medical records of infants born from 1 January, 2011 to 1 June, 2017, who died prior to 1 year of age.

Results: Five hundred and seventy three deceased infants were identified.

Stochastic ordering of simulated rugby match activity produces reliable movements and associated measures of subjective task load, cognitive and neuromuscular function.

The study assesses the test-retest reliability of movement and physiological measures during a simulated rugby match that employed activities performed in a stochastic order. Twenty male rugby players (21.4 ± 2.

BCL11B mutations in patients affected by a neurodevelopmental disorder with reduced type 2 innate lymphoid cells.

The transcription factor BCL11B is essential for development of the nervous and the immune system, and Bcl11b deficiency results in structural brain defects, reduced learning capacity, and impaired immune cell development in mice. However, the precise role of BCL11B in humans is largely unexplored, except for a single patient with a BCL11B missense mutation, affected by multisystem anomalies and profound immune deficiency. Using massively parallel sequencing we identified 13 patients bearing heterozygous germline alterations in BCL11B.

Expanding the molecular-ruler process through vapor deposition of hexadecanethiol.

The development of methods to produce nanoscale features with tailored chemical functionalities is fundamental for applications such as nanoelectronics and sensor fabrication. The molecular-ruler process shows great utility for this purpose as it combines top-down lithography for the creation of complex architectures over large areas in conjunction with molecular self-assembly, which enables precise control over the physical and chemical properties of small local features. The molecular-ruler process, which most commonly uses mercaptoalkanoic acids and metal ions to generate metal-ligated multilayers, can be employed to produce registered nanogaps between metal features.

Heterozygous De Novo UBTF Gain-of-Function Variant Is Associated with Neurodegeneration in Childhood.

Ribosomal RNA (rRNA) is transcribed from rDNA by RNA polymerase I (Pol I) to produce the 45S precursor of the 28S, 5.8S, and 18S rRNA components of the ribosome. Two transcription factors have been defined for Pol I in mammals, the selectivity factor SL1, and the upstream binding transcription factor (UBF), which interacts with the upstream control element to facilitate the assembly of the transcription initiation complex including SL1 and Pol I.

Influence of Knowledge of Task Endpoint on Pacing and Performance During Simulated Rugby League Match Play.

Purpose: To examine the influence of knowledge of exercise duration on pacing and performance during simulated rugby league match play.

Methods: Thirteen male university rugby players completed 3 simulated rugby league matches (RLMSP-i) on separate days in a random order. In a control trial, participants were informed that they would be performing 2 × 23-min bouts (separated by 20 min) of the RLMSP-i (CON).

Juvenile myelomonocytic leukemia-associated variants are associated with neo-natal lethal Noonan syndrome.

Gain-of-function variants in some RAS-MAPK pathway genes, including PTPN11 and NRAS, are associated with RASopathies and/or acquired hematological malignancies, most notably juvenile myelomonocytic leukemia (JMML). With rare exceptions, the spectrum of germline variants causing RASopathies does not overlap with the somatic variants identified in isolated JMML. Studies comparing these variants suggest a stronger gain-of-function activity in the JMML variants.

Interrater reliability of a near-miss risk index for incident learning systems in radiation oncology.

Purpose: Tools for assessing the severity and risk of near-miss events in radiation oncology are few and needed. Recent work has described guidelines for the use of a 5-tier near-miss risk index (NMRI) for the classification of near-miss events. The purpose of this study was to assess the reliability of the NMRI among users in a radiation oncology department.

The Unsuitability of Energy Expenditure Derived From Microtechnology for Assessing Internal Load in Collision-Based Activities.

This aim of this study was to examine the validity of energy expenditure derived from microtechnology when measured during a repeated-effort rugby protocol. Sixteen male rugby players completed a repeated-effort protocol comprising 3 sets of 6 collisions during which movement activity and energy expenditure (EE) were measured using microtechnology. In addition, energy expenditure was estimated from open-circuit spirometry (EE).

Metrics of success: Measuring impact of a departmental near-miss incident learning system.

Purpose: There is a growing interest in the application of incident learning systems (ILS) to radiation oncology. The purpose of the present study is to define statistical metrics that may serve as benchmarks for successful operation of an incident learning system.

Methods And Materials: A departmental safety and quality ILS was developed to monitor errors, near-miss events, and process improvement suggestions.

The Internal and External Responses to a Forward-Specific Rugby League Simulation Protocol Performed With and Without Physical Contact.

It is important to understand the extent to which physical contact changes the internal and external load during rugby simulations that aim to replicate the demands of match play. Accordingly, this study examined the role of physical contact on the physiological and perceptual demands during and immediately after a simulated rugby league match. Nineteen male rugby players completed a contact (CON) and a noncontact (NCON) version of the rugby league match-simulation protocol in a randomized crossover design with 1 wk between trials.

1-Adamantanethiol as a versatile nanografting tool.

Strategies to regulate the self-assembly of adsorbates to create surface structures with molecular-scale features and organization are of broad interest to nanoscience, biochemistry, and engineering. One approach utilizes molecules with tailored intermolecular interaction strengths and topologies to direct molecular self-assembly as exemplified by the adsorption of 1-adamantanethiol molecules on Au{111} substrates. 1-Adamantanethiolate self-assembled monolayers exhibit decreased packing densities and weaker intermolecular interaction strengths than n-alkanethiolate self-assembled monolayers, which result in their complete displacement upon exposure to n-alkanethiol molecules.

Atomic force microscopy characterization and lithography of Cu-ligated mercaptoalkanoic acid "molecular ruler" multilayers.

Hybrid chemical patterning strategies that combine the sophistication of lithography with the intrinsic precision of molecular self-assembly are of broad interest for applications including nanoelectronics and bioactive surfaces. This approach is exemplified by the molecular-ruler process where the sequential deposition of mercaptoalkanoic acid molecules and coordinated metal ions is integrated with conventional lithographic techniques to fabricate registered, nanometer-scale spacings. Herein, we illustrate the capabilities of atomic force microscopy characterization and lithography to investigate the morphology, quality, and local thickness of Cu-ligated mercaptohexadecanoic acid multilayers on Au{111} substrates.

SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample.

mRNA synthesis, processing, and destruction involve a complex series of molecular steps that are incompletely understood. Because the RNA intermediates in each of these steps have finite lifetimes, extensive mechanistic and dynamical information is encoded in total cellular RNA. Here we report the development of SnapShot-Seq, a set of computational methods that allow the determination of in vivo rates of pre-mRNA synthesis, splicing, intron degradation, and mRNA decay from a single RNA-Seq snapshot of total cellular RNA.