Oxford nanopore sequencing enables rapid discovery of single-domain antibodies from phage display libraries.

Antibody (Ab) repertoire sequencing using high-throughput massively parallel technologies has contributed substantially to the understanding of Ab responses following infection, vaccination and autoimmunity. Because individual B-cell receptors are recombined and diversified somatically, genomic comparisons are limited, and distinguishing rare variants from sequencing errors is a major challenge. Oxford Nanopore Technologies' MinION is a highly portable and cost-effective third-generation sequencing instrument, but has not been used for Ab repertoire sequencing due to its high error rate (approximately 1/10 bases). Here, we applied nanopore sequencing to single-domain Ab (sdAb) repertoires and phage-displayed sdAb libraries. We show that despite low overall data fidelity, sdAb sequences could be reconstructed above a frequency threshold (∼100 copies); however, distinguishing clonal sdAb variants was not always possible. The data quality was sufficient to enable rapid identification of antigen-specific sdAb sequences enriched during panning of phage display libraries, obviating the need for screening single clones

Phylogenetic Analysis of the Formin Homology 2 Domain

Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the “knob loop” region of the FH2 domain, with unknown functional consequences. Phylogenetic analysis using minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML) algorithms strongly supports the existence of seven metazoan groups. Yeast FH2 domains segregate from all other eukaryotes, including metazoans, other fungi, plants, and protists. Sequence comparisons of non-FH2 regions support relationships between three metazoan groups (Dia, DAAM, and FRL) and examine previously identified coiled-coil and Diaphanous auto-regulatory domain sequences. This analysis allows for a formin nomenclature system based on sequence relationships, as well as suggesting strategies for the determination of biochemical and cellular activities of these proteins

GRAND CHALLENGE No. 5: COMMUNICATING ARCHAEOLOGY Outreach and Narratives in Professional Practice

Communicating archaeology to non-expert audiences can convey the role and value of the discipline, implant respect for heritage, and connect descendant communities to their past. A challenge facing archaeology communicators is to translate complex ideas while retaining their richness and maximizing audience engagement. This article discusses how archaeologists can effectively communicate with non-experts using narrative and visual tools. We provide a communication strategy and three case studies from North America. The examples include the packaging of archaeological theory in the shape of mystery novels for student consumption; the use of artwork to anchor archaeological narratives in public outreach; and, the use of historical fiction to reformat archaeological content for Indigenous communities. We conclude with a discussion of outreach capacities and some of the risks and rewards of professional interactions with non-archaeologists

Curricular Satisfaction Levels of National Athletic Trainers\u27 Association- Accredited Postprofessional Athletic Training Graduates

Context: Academic programs rely on outcomes assessments to determine if changes in the curriculum are necessary. Objective: To examine the overall satisfaction levels of graduates (2005-2006) of National Athletic Trainers\u27 Association-accredited postprofessional athletic training education programs as related to the 2002 Standards and Guidelines for Development and Implementation of NATA-Accredited PostProfessional Graduate Athletic Training Education Programs. Design: Original survey instrument and demographic questionnaire. Setting: Online survey instrument. Patients or Other Participants: Of 211 survey recipients, 123 returned surveys (58.29% response rate). Main Outcome Measure(s): Demographic information and satisfaction levels in 10 standard areas (depth of learning, breadth of learning, critical thinking, instructor availability, theoretic basis, writing skills, scholarly growth, community return, leadership, and overall program satisfaction) were obtained. Satisfaction scores were categorized into 10 percentage brackets (eg, 80%-89%) for each standard area. Results: No differences were noted in relation to any of the standard satisfaction areas for evaluation of time off from school. However, graduates who required more than the allotted amount of time to complete their degree were less satisfied in the areas of depth of learning (P = .027), breadth of learning (P = .001), instructor availability (P = .005), writing (P = .022), and overall program satisfaction (P = .016). Conclusions: Graduates were generally satisfied across all areas of their didactic curriculum. However, satisfaction levels were affected if graduates required more than the allotted amount of time to complete their degrees

Resilient Aggregation in Simple Linear Sensor Networks

A sensor network is a network comprised of many small, wireless, resource-limited nodes that sense data about their environment and report readings to a base station. One technique to conserve power in a sensor network is to aggregate sensor readings hop-by-hop as they travel towards a base station, thereby reducing the total number of messages required to collect each sensor reading. In an adversarial setting, the ability of a malicious node to alter this aggregate total must be limited. We present three aggregation protocols inspired by three natural key pre-distribution schemes for linear networks. Assuming no more than $k$ consecutive nodes are malicious, each of these protocols limits the capability of a malicious node to altering the aggregate total by at most a single valid sensor reading. Additionally, our protocols are able to detect malicious behavior as it occurs, allowing the protocol to be aborted early, thereby conserving energy in the remaining nodes. A rigorous proof of security is also given for each protocol

Using Real Options Analysis for Evaluating Uncertain Investments in Information Technology: Insights from the ICIS 2001 Debate

Business and information systems (IS) executives continue to grapple with issues of risk and uncertainty in evaluating investments in information technology (IT). Despite the use of net present value (NPV) and other investment appraisal techniques, executives are often forced to rely on instinct when finalizing IT investment decisions. Recognizing the shortcomings of NPV, real options analysis has been suggested as an alternative approach, one that considers the risks associated with an investment while recognizing the ability of corporations to defer an investment until a later period or to make a partial investment instead. Responding to a growing interest in real options analysis among the IS community, a debate involving four prominent researchers was convened at the 2001 International Conference on Information Systems (ICIS). In addition to offering a tutorial overview of real options, the goal of the debate was to assess the state of research in this area and to identify avenues for future research. This paper describes the outcomes of the debate, culminating in a series of research questions and topics that set the stage for future research in IT and real options analysis. A transcript of the debate and an overview of real options analysis are included as appendices

Missense-depleted regions in population exomes implicate ras superfamily nucleotide-binding protein alteration in patients with brain malformation.

Genomic sequence interpretation can miss clinically relevant missense variants for several reasons. Rare missense variants are numerous in the exome and difficult to prioritise. Affected genes may also not have existing disease association. To improve variant prioritisation, we leverage population exome data to identify intragenic missense-depleted regions (MDRs) genome-wide that may be important in disease. We then use missense depletion analyses to help prioritise undiagnosed disease exome variants. We demonstrate application of this strategy to identify a novel gene association for human brain malformation. We identified de novo missense variants that affect the GDP/GTP-binding site of ARF1 in three unrelated patients. Corresponding functional analysis suggests ARF1 GDP/GTP-activation is affected by the specific missense mutations associated with heterotopia. These findings expand the genetic pathway underpinning neurologic disease that classically includes FLNA. ARF1 along with ARFGEF2 add further evidence implicating ARF/GEFs in the brain. Using functional ontology, top MDR-containing genes were highly enriched for nucleotide-binding function, suggesting these may be candidates for human disease. Routine consideration of MDR in the interpretation of exome data for rare diseases may help identify strong genetic factors for many severe conditions, infertility/reduction in reproductive capability, and embryonic conditions contributing to preterm loss