Secondary mathematics teachers' descriptions of student engagement.

There is a need for a more robust conceptualization of engagement in mathematics education research. Investigating how teachers describe engagement can provide insight into relationships between purposes of engagement and dimensions of engagement. In this exploratory study, we examined how 28 secondary mathematics teachers in two states in the USA talked about their students' engagement. During interviews, we asked teachers to provide their definitions for engagement, describe their teaching strategies for engaging students, and describe their observations of engagement during a video clip from their own classroom. We interpreted teachers' talk to identify how they described the nature of mathematics engagement (dimensions such as behavioral, cognitive, affective, and/or social engagement) and purposes of engagement (engagement in learning or in schooling [Harris, 2011]). When teachers described the purpose of engagement as engagement in learning, they also tended to describe the nature of engagement with cognitive and social dimensions and with multiple dimensions of engagement.

Standoff detection of bacterial spores by field deployable coherent Raman spectroscopy.

Vibrational spectroscopies offer great potential for standoff detection of chemical and biological warfare agents, avoiding contamination to the operator and equipment. Among them, particularly promising is Coherent anti-Stokes Raman scattering (CARS) spectroscopy, using synchronized pump/Stokes laser pulses to set up a vibrational coherence of target molecules at a laser focus, which is read by further interaction with a probe pulse, resulting in the emission of a coherent beam detectable at a distance. CARS has previously demonstrated the capability to detect bacterial spores based on the Raman spectrum of the characteristic molecule calcium dipicolinate (CaDPA); however, a complex and bulky laser technology, which is only suitable for a laboratory environment, was employed. Here we develop a broadband CARS setup based on a compact, industrial grade ytterbium laser system. We demonstrate high signal-to-noise ratio detection of Bacillus atrophaeus spores at a concentration of 105 cfu/mm2, at a standoff distance of 1 m, and an acquisition time of 1 s. Our system, which combines chemical specificity and sensitivity along with improved ruggedness and portability, paves the way to a new generation of instruments for real-world standoff detection of chemical and biological threats.

Evaluation of the Abbott ARCHITECT HIV Ag/Ab combo assay for determining recent HIV-1 infection.

BACKGROUND: Given the challenges and costs associated with implementing HIV-1 incidence assay testing, there is great interest in evaluating the use of commercial HIV diagnostic tests for determining recent HIV infection. A diagnostic test with the capability of providing reliable data for the determination of recent HIV infection without substantial modifications to the test protocol would have a significant impact on HIV surveillance. The Abbott ARCHITECT HIV Ag/Ab Combo Assay is an antigen/antibody immunoassay, which meets the criteria as the first screening test in the recommended HIV laboratory diagnostic algorithm for the United States. METHODS: In this study, we evaluated the performance characteristics of the ARCHITECT HIV Ag/Ab Combo signal-to-cutoff ratio (S/Co) for determining recent infection, including estimation of the mean duration of recent infection (MDRI) and false recent rate (FRR), and selection of recency cutoffs. RESULTS: The MDRI estimates for the S/Co recency cutoff of 400 is within the 4 to 12 months range recommended for HIV incidence assays, and the FRR rate for this cutoff was 1.5%. Additionally, ARCHITECT Combo S/Co values were compared relative to diagnostic test results from two prior prospective HIV-1 diagnostic studies in order to validate the use of the S/Co for both diagnostic and recency determination. CONCLUSION: Dual-use of the ARCHITECT Combo assay data for diagnostic and incidence purposes would reduce the need for separate HIV incidence testing and allow for monitoring of recent infection for incidence estimation and other public health applications.

Multicenter, Open-Label, Phase I Study of DSP-7888 Dosing Emulsion in Patients with Advanced Malignancies.

BACKGROUND: Wilms' tumor 1 (WT1) is overexpressed in various malignancies. DSP-7888 Dosing Emulsion, also known as ombipepimut-S (United States Adopted Name; International Nonproprietary Name: adegramotide/nelatimotide), is an investigational therapeutic cancer vaccine comprising two synthetic peptides derived from WT1 to promote both cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte-mediated immune responses against WT1-expressing tumors. OBJECTIVE: The aim of this study was to report the results from a phase I dose-escalation study (NCT02498665) that evaluated DSP-7888, administered either intradermally (ID) or subcutaneously (SC), in patients with recurrent or advanced malignancies associated with overexpression of WT1. PATIENTS AND METHODS: In this phase I dose-escalation study, patients with recurrent or advanced malignancies associated with overexpression of WT1 who progressed on, were intolerant to, or not a candidate for standard therapy or who presented with a malignancy that had no definite standard therapy received escalating doses of ID or SC DSP-7888 in a rolling-six study design. DSP-7888 3.5, 10.5, or 17.5 (ID only) mg was administered until disease progression or other discontinuation event. Primary objectives were safety, tolerability, and identification of the recommended phase II dose (RP2D). Overall survival (OS) and WT1-specific CTL induction were included as secondary and exploratory objectives, respectively. RESULTS: Twenty-four patients received either ID (3.5 mg, n = 4; 10.5 mg, n = 3; 17.5 mg, n = 3) or SC DSP-7888 (3.5 mg, n = 9; 10.5 mg, n = 5). No dose-limiting toxicity was observed. The most frequent treatment-emergent adverse event was injection site reactions (ID, 100% [10/10]; SC, 35.7% [5/14]); all were grade 1 or 2. Four patients (ID 17.5 mg, n = 1; SC 3.5 mg, n = 1; SC 10.5 mg, n = 2) had stable disease, 16 had progressive disease, and four were not evaluable. Median (95% confidence interval) OS duration was 180.0 (136.0-494.0) days. Among evaluable patients, WT1-specific CTL induction was observed in 66.7% (6/9) and 41.7% (5/12) of those administered ID and SC DSP-7888, respectively. CONCLUSIONS: DSP-7888 Dosing Emulsion was well tolerated, with no dose-limiting toxicities, in patients with recurrent or advanced malignancies. Higher WT1-specific CTL induction activity was noted with ID compared with SC administration; because of this, the ID route was selected for further evaluation in the clinical program. TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT02498665.

Altered Antibody Responses in Persons Infected with HIV-1 While Using Preexposure Prophylaxis.

Preexposure prophylaxis (PrEP) is an effective HIV prevention tool, although effectiveness is dependent upon adherence. It is important to characterize the impact of PrEP on HIV antibody responses in people who experience breakthrough infections to understand the potential impact on timely diagnosis and treatment. Longitudinal HIV-1-specific antibody responses were evaluated in 42 people who inject drugs (PWID) from the Bangkok Tenofovir Study (BTS) (placebo = 28; PrEP = 14) who acquired HIV while receiving PrEP. HIV-1 antibody levels and avidity to three envelope proteins (gp41, gp160, and gp120) were measured in the plasma using a customized Bio-Plex (Bio-Rad Laboratories, Hercules, CA) assay. A time-to-event analysis was performed for each biomarker to compare the distribution of times at which study subjects exceeded the recent/long-term assay threshold, comparing PrEP and placebo treatment groups. We fit mixed-effects models to identify longitudinal differences in antibody levels and avidity between groups. Overall, longitudinal antibody levels and avidity were notably lower in the PrEP breakthrough group compared to the placebo group. Time-to-event analyses demonstrated a difference in time to antibody reactivity between treatment groups for all Bio-Plex biomarkers. Longitudinal gp120 antibody levels within the PrEP breakthrough group were decreased compared to the placebo group. When accounting for PrEP adherence, both gp120 and gp160 antibody levels were lower in the PrEP breakthrough group compared to the placebo group. We demonstrate hindered envelope antibody maturation in PWID who became infected while receiving PrEP in the BTS, which has significant implications for HIV diagnosis. Delayed maturation of the antibody response to HIV may increase the time to detection for antibody-based tests. Clinical Trial Registration Number, NCT00119106.

Fiber laser system for standoff coherent Raman spectroscopy.

A fiber laser system for standoff detection of chemical and biological species by coherent anti-Stokes Raman scattering is presented. The system is based on an ytterbium fiber laser and a hollow-core photonic crystal fiber for generation of broadband pump/Stokes pulses. High-resolution Raman spectra encompassing the fingerprint region (600-1600cm-1) are obtained for toluene, and two simulants of chemical and biological warfare agents, specifically dimethyl methylphosphonate and sodium dipicolinate. The system is operated at standoff distances of 2 m and integration times of 8 ms. The fiber technology makes the approach suitable for implementation as a compact standoff detection and identification system.

Machine learning utilising spectral derivative data improves cellular health classification through hyperspectral infra-red spectroscopy.

The objective differentiation of facets of cellular metabolism is important for several clinical applications, including accurate definition of tumour boundaries and targeted wound debridement. To this end, spectral biomarkers to differentiate live and necrotic/apoptotic cells have been defined using in vitro methods. The delineation of different cellular states using spectroscopic methods is difficult due to the complex nature of these biological processes. Sophisticated, objective classification methods will therefore be important for such differentiation. In this study, spectral data from healthy/traumatised cell samples using hyperspectral imaging between 2500-3500 nm were collected using a portable prototype device. Machine learning algorithms, in the form of clustering, have been performed on a variety of pre-processing data types including 'raw' unprocessed, smoothed resampling, background subtracted and spectral derivative. The resulting clusters were utilised as a diagnostic tool for the assessment of cellular health and quantified using both sensitivity and specificity to compare the different analysis methods. The raw data exhibited differences for one of the three different trauma types applied, although unable to accurately cluster all the traumatised samples due to signal contamination from the chemical insult. The background subtracted and smoothed data sets reduced the accuracy further, due to the apparent removal of key spectral features which exhibit cellular health. However, the spectral derivative data-types significantly improved the accuracy of clustering compared to other data types, with both sensitivity and specificity for the background subtracted data set being >94% highlighting its utility to account for unknown signal contamination while maintaining important cellular spectral features.

Nonlinear pulse compression to 22 fs at 15.6 µJ by an all-solid-state multipass approach.

We demonstrate nonlinear compression of pulses at 1.03 µm and repetition rate of 200 kHz generated by a ytterbium fiber laser using two cascaded all-solid-state multipass cells. The pulse duration has been compressed from 460 to 22 fs, corresponding to a compression factor of ∼21. The compressed pulse energy is 15.6 µJ, corresponding to an average power of 3.1 W, and the overall transmission of the two compression stages is 76%. The output beam quality factor is M2 ∼1.2 and the excess intensity noise introduced by nonlinear broadening is below 0.05%. These results show that nonlinear pulse compression down to ultrashort durations can be achieved with an all-solid-state approach, at pulse energies much higher than previously reported, while preserving the spatial characteristics of the laser.

Detecting malingered pain-related disability with the pain catastrophizing scale: a criterion groups validation study.

Objective: Intentional exaggeration of symptoms is a potential problem in contexts where there are financial incentives to appear disabled. Therefore, calibration of tools to accurately evaluate malingering in these contexts is important. The present study used a criterion groups validation design to determine the ability of the Pain Catastrophizing Scale (PCS) to detect Malingered Pain-Related Disability (MPRD). Method: Individuals meeting inclusionary/exclusionary criteria were selected for this study (n = 219) from a larger dataset of chronic pain patients referred for a psychological evaluation. Patients were classified into malingering groups using the Bianchini, Greve, and Glynn classification system for MPRD. PCS T scores were compared in patients who met MPRD criteria and those who showed no indication of malingering on multiple validity tests. Results: No group differences were observed regarding medicolegal and injury characteristics. Group analyses showed that the Not MPRD group had a significantly lower PCS score (Estimated Marginal Mean [EMM] = 62.3) than all other groups. The Probable and Definite MPRD groups (which together comprise the MPRD group) had the highest PCS T scores (EMM = 77.2 and EMM = 83.8, respectively). A PCS T score of 81 was associated with a 7% false-positive (FP) error rate, sensitivity of 47%, likelihood ratio (LR) of 6.7, and a positive predictive value (PPV) of .74 at base rates around 30%. Conclusions: PCS T scores greater than 81 should raise concerns about the validity of the PCS report and provide additional information that can be helpful in identifying intentional symptom exaggeration in patients with chronic pain.

A Multiplex HIV Incidence Assay for Inferring Recent HIV-1 Transmission and Time of Infection.

BACKGROUND: Laboratory assays for determining recent HIV-1 infection are an important public health tool for aiding in the estimation of HIV incidence. Some incidence assay analytes are remarkably predictive of time since seroconversion and may be useful for additional applications, such as predicting recent transmission events during HIV outbreaks and informing prevention strategies. METHODS: Plasma samples (n = 154) from a recent HIV-1 outbreak in a rural community in Indiana were tested with the customized HIV-1 Multiplex assay, based on the Bio-Rad Bio-Plex platform, which measures antibody response to HIV envelope antigens, gp120, gp160, and gp41. Assay cutoffs for each analyte were established to determine whether an individual seroconverted within 30, 60, or 90 days of the sample collection date. In addition, a novel bioinformatics method was implemented to infer infection dates of persons newly diagnosed with HIV during the outbreak. RESULTS: Sensitivity/specificity of the HIV-1 Multiplex assay for predicting seroconversion within 30, 60, and 90 days, based on a training data set, was 90.5%/95.4%, 94.1%/90%, and 89.4%/82.9%, respectively. Of 154 new diagnoses in Indiana between December 2014 and August 2016, the majority (71%) of recent infections (≤3 months since seroconversion) were identified between February and May 2016. The epidemiologic curve derived from the bioinformatics analysis indicated HIV transmission began as early as 2010, grew exponentially in 2014, and leveled off in April 2015. CONCLUSIONS: The HIV-1 Multiplex assay has the potential to identify and monitor trends in recent infection during an epidemic to assess the efficacy of programmatic or treatment interventions.

Characterization of real-time microarrays for simultaneous detection of HIV-1, HIV-2, and hepatitis viruses.

Real-time PCR assays for nucleic acid testing (NAT) of hepatitis viruses A-E and for HIV-1 and HIV-2 have been developed; however, a multiplex assay that can simultaneously detect all of these agents is not yet available. Standardized TaqMan assays for detection of hepatitis viruses A-E have been described and applied to TaqMan Array Cards (TAC) which are capable of multiple pathogen detection using a single set of optimized PCR conditions. Assays for three gene regions of HIV-1 (long-terminal repeat (LTR), gag, and polymerase) and HIV-2 (overlap of LTR and gag, protease and integrase) were designed using the hepatitis assay conditions. Nucleic acid extracts of HIV-1-infected samples (44 plasma, 41 whole blood, 20 HIV-1 viral stocks) were tested on the TAC cards; 98 were reactive (92%) with 70 in multiple gene regions. Twenty-four of the 27 (89%) HIV-2 specimens (10 plasma, 1 PBMC lysate, 6 whole blood and 10 plasmids containing HIV-2 polymerase) were detected on TAC. No HIV or hepatitis virus sequences were detected in 30 HIV-negative samples (specificity 100%). Three HBV and 18 HCV co-infections were identified in the HIV-1-infected specimens. Multi-pathogen detection using TAC could provide a rapid, sensitive and more efficient method of surveying for a variety of infectious disease nucleic acids.

A multiplexed RT-LAMP assay for detection of group M HIV-1 in plasma or whole blood.

Isothermal nucleic acid amplification techniques, such as reverse-transcription loop-mediated isothermal amplification (RT-LAMP), exhibit characteristics that are suitable for the development of a rapid, low-cost NAT that can be used at the POC. For demonstration of utility for global use, studies are needed to validate the performance of RT-LAMP for the detection of divergent subtypes. In this study, we designed and evaluated multiplexed HIV-1 integrase RT-LAMP primers to detect subtypes within group M, along with an RNase P positive internal processing and amplification control. Using a panel of 26 viral isolates representing the major circulating subtypes, we demonstrated detection of all isolates of subtypes A1, C, D, F1, F2, G, CRF01_AE, CRF02_AG, and two unique recombinant forms (URFs). A whole blood panel created with one representative isolate of each subtype was successfully amplified with the group M HIV-1 integrase and RNase P internal control primers. The group M HIV-1 RT-LAMP assay was further evaluated on 61 plasma specimens obtained from persons from Cameroon and Uganda. The sequence-conserved group M HIV-1 RT-LAMP primers, coupled to a low-cost amplification device, may improve diagnosis of acute infection at the POC and provide timely confirmation of HIV status.

Further validation of booklet category test subscales for learning, set loss, and memory in a mixed clinical sample.

Although it has long been proposed that performance on the Booklet Category Test (BCT) relies on a number of different cognitive abilities, including executive functioning, perceptual reasoning, and memory, only a single total error score is typically derived and interpreted in clinical practice. BCT subscales based on factor analyses of subtest errors or designed specifically to measure specific cognitive domains have been proposed to better assess the multidimensional abilities underlying BCT performance. The aim of this study was to independently replicate and extend previous findings regarding the validity of these subscales. A mixed clinical sample of 137 patients completed the BCT and a number of additional measures used to assess neuropsychological domains of selective attention, various aspects of executive functioning, intellectual functioning, and memory. Correlation and regression analyses were used to explore the convergent and discriminant validity of each subscale. Subscales varied in the number and magnitude of their significant correlations with scores derived from traditional measures. In general, findings supported the convergent validity of BCT category learning, set loss, and memory subscales. However, findings regarding discriminant validity were more variable across subscales. Results provide additional support for the multidimensional nature of the BCT and the validity of derived subscales to measure specific aspects of cognitive functioning beyond what is measured by a total errors score. The recently proposed subscales examined in the current study appear to be worthy of further investigation by clinicians and researchers to determine their clinical utility.

Classification accuracy of the Minnesota Multiphasic Personality Inventory-2 (MMPI-2)-Restructured form validity scales in detecting malingered pain-related disability.

The symptom reports of individuals with chronic pain are multidimensional (e.g., emotional, cognitive, and somatic) and significantly contribute to increased morbidity and lost work productivity. When pain occurs in the context of a legally compensable event, reliable assessment of a patient's multifactorial symptom experience during psychological or neuropsychological evaluations is a necessity. The Validity Scales of the Minnesota Multiphasic Personality Inventory-2 (MMPI-2) have been shown useful in identifying symptom overreporting and feigning within chronic pain samples and a number of studies have emerged supporting the use of the MMPI-2-Restructured Form (MMPI-2-RF) in the detection of simulated or feigned impairment in a variety of populations. To date, only 1 other study exists examining the ability of the MMPI-2-RF to detect exaggerated complaints using a strict operationalization of malingering exclusive to chronic pain samples. The purpose of this study was to examine the classification accuracy of MMPI-2-RF Validity Scales in a group of patients with chronic pain using a criterion-groups design. The final sample consisted of 501 clinical chronic pain patients assigned to groups based on the Bianchini, Greve, and Glynn (2005) criteria for Malingered Pain-Related Disability (MPRD). Results showed that all MMPI-2-RF Validity Scales differentiated malingerers from nonmalingerers with a high degree of accuracy. At cut-offs associated with ≥95% Specificity, Sensitivities ranged from 15% (Fs) to 60% (Response Bias Scale; RBS). This study demonstrates that the MMPI-2-RF Validity Scales are capable of differentiating intentional symptom exaggeration from genuine complaints in a sample of incentivized chronic pain patients. (PsycINFO Database Record

Clusters of financially incentivized chronic pain patients using the Minnesota Multiphasic Personality Inventory-2 Restructured Form (MMPI-2-RF).

The Minnesota Multiphasic Personality Inventory (MMPI)-2 Restructured Form (MMPI-2-RF) has been shown to have clinical utility in the assessment of individuals with chronic pain (e.g., predicting surgical outcomes). The purpose of this study was to explore the ability of the MMPI-2-RF Validity Scales in profiling patients with chronic pain who had external financial incentive (e.g., workers' compensation claims) and determine the associations between Validity Scale response patterns and important outcomes. Cluster analysis identified 2 similarly sized clusters of patients with very different MMPI-2-RF profiles. Cluster 1 was characterized by valid responding and showed mean elevations on the somatic and low positive emotion Restructured Clinical scales. Cluster 2 was characterized by patients overreporting on the MMPI-2-RF Validity Scales, who also demonstrated elevations on 7 of the 9 RC scales. Cluster membership was differentially associated with clinical variables: patients in Cluster 2 had greater self-reported pain and disability, were less likely to have spine-related findings on imaging and were more likely to be classified as probable or definite malingerers. These results support the utility of the MMPI-2-RF Validity scales in distinguishing between credible and noncredible responses from patients with chronic pain seen within a medico-legal context. (PsycINFO Database Record

A multiplex assay for detection of SHIV plasma and mucosal IgG and IgA.

Evaluating antibody maturation provides valuable data to characterize immune responses to HIV infection and can provide insight into biomedical intervention efficacy. It is important to develop assays that evaluate antibody maturation in both plasma and mucosal compartments. The nonhuman primate model provides a controlled system to collect temporal data that are integral to assessing intervention strategies. We report the development of a novel multiplex assay, based on the Bio-Plex platform, to evaluate plasma and mucosal IgG and IgA avidity and maturation against simian/human immunodeficiency virus (SHIV) in this controlled system. Vaginal mucosa and plasma samples were collected from a prior study evaluating the efficacy of a tenofovir disoproxil fumarate (TDF) intravaginal ring (IVR) against SHIVSF162P3 challenge in female pigtailed macaques. For validation of the multiplex assay, specimens from six SHIV-infected placebo animals and one TDF breakthrough animal were evaluated. For SHIV and HIV envelope analytes, antibody levels and avidity in both compartments continued to mature post-infection. Maturation of IgG and IgA levels was similar in each compartment, however, mucosal antibody levels tended to be more variable. This SHIV assay elucidates IgG/IgA antibody kinetics in the plasma and vaginal mucosa and will be a valuable tool in vaccine and other biomedical intervention studies in the nonhuman primate model.

Performance characteristics of an antibody-based multiplex kit for determining recent HIV-1 infection.

The availability of reliable laboratory methods for determining recent HIV infection is vital for accurate estimation of population-based incidence. The mean duration of recent infection (MDRI) and false recent rate (FRR) are critical parameters for HIV incidence assays, as they impact HIV incidence estimates and provide a measure of assay performance. The HIV-1 Multiplex assay is an in-house developed, magnetic bead-based assay that measures virus-specific antibody levels and avidity to multiple analytes. To ensure quality control and to facilitate transfer of the assay to external laboratories or testing facilities, the in-house assay has been adapted and produced in kit form. Here, we describe the performance characteristics of the multiplex kit and demonstrate the stability of the kit components over a one-year period. Two statistical methods were employed to estimate the MDRI of the individual analytes and five different algorithms, combining multiple analyte values. The MDRI estimates for the individual analytes and five algorithms were all between 200 and 300 days post-seroconversion, with no notable difference between the two statistical approaches. All five algorithms exhibited a 0% FRR with specimens from long-term, subtype B HIV-1-infected individuals. The assay parameters described in this study provide the necessary tools to implement the HIV-1 multiplex assay and improves the utility of the assay for field use.

Mucosal Sparing Radiation Therapy in Resected Oropharyngeal Cancer.

PURPOSE: To report the outcomes of patients with favorable risk oropharyngeal cancer that underwent adjuvant radiation therapy with omission of the primary site from the clinical target volume (CTV). MATERIAL/METHODS: A retrospective study of 40 patients treated with transoral surgery (TOS) followed by neck only radiation using intensity modulated radiation therapy (IMRT) with exclusion of the primary site. For all patients, a CTV of the primary surgical bed was contoured to obtain the estimated incidental dose to the primary site. RESULTS: Median follow-up was 51 months (range, 13-155 months). The median radiation therapy (RT) dose to the neck was 6000 cGy (range, 5400-6400 cGy). The mean incidental dose to the primary tonsillar site was 4320 cGy (SD ± 480 cGy) and to the primary base of tongue site was 4060 cGy (SD ± 420 cGy). There were no local failures and only 1 regional failure, resulting in 97.5% locoregional control rate at 4 years. Two patients developed distant metastases, without evidence of locoregional recurrence, for a 4-year overall survival rate of 97%. CONCLUSIONS: Our analysis suggests that mucosal sparing RT after TOS in favorable risk oropharyngeal cancer patients may provide comparable oncologic and improved functional outcomes compared to conventional treatment in selected patients.

Molecular Modeling and Functional Analysis of Exome Sequencing-Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma.

PURPOSE: Genomic testing has increased the quantity of information available to oncologists. Unfortunately, many identified sequence alterations are variants of unknown significance (VUSs), which thus limit the clinician's ability to use these findings to inform treatment. We applied a combination of in silico prediction and molecular modeling tools and laboratory techniques to rapidly define actionable VUSs. MATERIALS AND METHODS: Exome sequencing was conducted on 308 tumors from various origins. Most single nucleotide alterations within gene coding regions were VUSs. These VUSs were filtered to identify a subset of therapeutically targetable genes that were predicted with in silico tools to be altered in function by their variant sequence. A subset of receptor tyrosine kinase VUSs was characterized by laboratory comparison of each VUS versus its wild-type counterpart in terms of expression and signaling activity. RESULTS: The study identified 4,327 point mutations of which 3,833 were VUSs. Filtering for mutations in genes that were therapeutically targetable and predicted to affect protein function reduced these to 522VUSs of interest, including a large number of kinases. Ten receptortyrosine kinase VUSs were selected to explore in the laboratory. Of these, seven were found to be functionally altered. Three VUSs (FGFR2 F276C, FGFR4 R78H, and KDR G539R) showed increased basal or ligand-stimulated ERK phosphorylation compared with their wild-type counterparts, which suggests that they support transformation. Treatment of a patient who carried FGFR2 F276C with an FGFR inhibitor resulted in significant and sustained tumor response with clinical benefit. CONCLUSION: The findings demonstrate the feasibility of rapid identification of the biologic relevance of somatic mutations, which thus advances clinicians' ability to make informed treatment decisions.

Single-use, electricity-free amplification device for detection of HIV-1.

Early and accurate diagnosis of HIV is key for the reduction of transmission and initiation of patient care. The availability of a rapid nucleic acid test (NAT) for use at the point-of-care (POC) will fill a gap in HIV diagnostics, improving the diagnosis of acute infection and HIV in infants born to infected mothers. In this study, we evaluated the performance of non-instrumented nucleic acid amplification, single-use disposable (NINA-SUD) devices for the detection of HIV-1 in whole blood using reverse-transcription, loop-mediated isothermal amplification (RT-LAMP) with lyophilized reagents. The NINA-SUD heating device harnesses the heat from an exothermic chemical reaction initiated by the addition of saline to magnesium iron powder. Reproducibility was demonstrated between NINA-SUD units and comparable, if not superior, performance for detecting clinical specimens was observed as compared to the thermal cycler. The stability of the lyophilized HIV-1 RT-LAMP reagents was also demonstrated following storage at -20, 4, 25, and 30°C for up to one month. The single-use, disposable NAT minimizes hands-on time and has the potential to facilitate HIV-1 testing in resource-limited settings or at the POC.