EVI1 carboxy-terminal phosphorylation is ATM-mediated and sustains transcriptional modulation and self-renewal via enhanced CtBP1 association.

The transcriptional regulator EVI1 has an essential role in early hematopoiesis and development. However, aberrantly high expression of EVI1 has potent oncogenic properties and confers poor prognosis and chemo-resistance in leukemia and solid tumors. To investigate to what extent EVI1 function might be regulated by post-translational modifications we carried out mass spectrometry- and antibody-based analyses and uncovered an ATM-mediated double phosphorylation of EVI1 at the carboxy-terminal S858/S860 SQS motif. In the presence of genotoxic stress EVI1-WT (SQS), but not site mutated EVI1-AQA was able to maintain transcriptional patterns and transformation potency, while under standard conditions carboxy-terminal mutation had no effect. Maintenance of hematopoietic progenitor cell clonogenic potential was profoundly impaired with EVI1-AQA compared with EVI1-WT, in particular in the presence of genotoxic stress. Exploring mechanistic events underlying these observations, we showed that after genotoxic stress EVI1-WT, but not EVI1-AQA increased its level of association with its functionally essential interaction partner CtBP1, implying a role for ATM in regulating EVI1 protein interactions via phosphorylation. This aspect of EVI1 regulation is therapeutically relevant, as chemotherapy-induced genotoxicity might detrimentally sustain EVI1 function via stress response mediated phosphorylation, and ATM-inhibition might be of specific targeted benefit in EVI1-overexpressing malignancies.

Discovery and complete genome sequence of a novel circovirus-like virus in the endangered rowi kiwi, Apteryx rowi.

Circoviruses are circular, non-enveloped, single-stranded DNA viruses around 2000 nucleotides (nt) in length and include the pathogenic species, Porcine circovirus 1 and Beak and feather disease virus, capable of causing significant morbidity and mortality. This group of viruses may be robust to degradation by external environments, and avian circoviruses are known to move between closely related hosts. Using a de novo metagenomic approach, followed by confirmatory PCR, we identify for the first time a circular Rep-encoding single-stranded (CRESS) DNA virus in New Zealand kiwi, Apteryx spp., derived from faecal matter of the rowi kiwi (A. rowi) showing signs of verminous dermatitis. The entire 2085 nt genome was cloned and sequenced and contains both capsid and replicase genes, as well as a conserved 9 nt motif. Phylogenetic analyses place it within Circoviridae, adjacent to other environmental CRESS-DNA viruses, and most closely related to badger circovirus-like virus (Meles meles circovirus-like virus). As the rowi is the most critically endangered kiwi, it is vital to understand the role of rowi kiwi circovirus-like virus as a possible pathogen and also any potential cross-species transmission.

Discovery of novel virus sequences in an isolated and threatened bat species, the New Zealand lesser short-tailed bat (Mystacina tuberculata).

Bats harbour a diverse array of viruses, including significant human pathogens. Extensive metagenomic studies of material from bats, in particular guano, have revealed a large number of novel or divergent viral taxa that were previously unknown. New Zealand has only two extant indigenous terrestrial mammals, which are both bats, Mystacina tuberculata (the lesser short-tailed bat) and Chalinolobus tuberculatus (the long-tailed bat). Until the human introduction of exotic mammals, these species had been isolated from all other terrestrial mammals for over 1 million years (potentially over 16 million years for M. tuberculata). Four bat guano samples were collected from M. tuberculata roosts on the isolated offshore island of Whenua hou (Codfish Island) in New Zealand. Metagenomic analysis revealed that this species still hosts a plethora of divergent viruses. Whilst the majority of viruses detected were likely to be of dietary origin, some putative vertebrate virus sequences were identified. Papillomavirus, polyomavirus, calicivirus and hepevirus were found in the metagenomic data and subsequently confirmed using independent PCR assays and sequencing. The new hepevirus and calicivirus sequences may represent new genera within these viral families. Our findings may provide an insight into the origins of viral families, given their detection in an isolated host species.

BioImageXD: an open, general-purpose and high-throughput image-processing platform.

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

Molecular mechanism of alpha2beta1 integrin interaction with human echovirus 1.

Conformational activation increases the affinity of integrins to their ligands. On ligand binding, further changes in integrin conformation elicit cellular signalling. Unlike any of the natural ligands of alpha2beta1 integrin, human echovirus 1 (EV1) seemed to bind more avidly a 'closed' than an activated 'open' form of the alpha2I domain. Furthermore, a mutation E336A in the alpha2 subunit, which inactivated alpha2beta1 as a collagen receptor, enhanced alpha2beta1 binding to EV1. Thus, EV1 seems to recognize an inactive integrin, and not even the virus binding could trigger the conformational activation of alpha2beta1. This was supported by the fact that the integrin clustering by EV1 did not activate the p38 MAP kinase pathway, a signalling pathway that was shown to be dependent on E336-related conformational changes in alpha2beta1. Furthermore, the mutation E336A did neither prevent EV1 induced and alpha2beta1 mediated protein kinase C activation nor EV1 internalization. Thus, in its entry strategy EV1 seems to rely on the activation of signalling pathways that are dependent on alpha2beta1 clustering, but do not require the conformational regulation of the receptor.

A cfDNA methylation-based tissue-of-origin classifier for cancers of unknown primary.

Cancers of Unknown Primary (CUP) remains a diagnostic and therapeutic challenge due to biological heterogeneity and poor responses to standard chemotherapy. Predicting tissue-of-origin (TOO) molecularly could help refine this diagnosis, with tissue acquisition barriers mitigated via liquid biopsies. However, TOO liquid biopsies are unexplored in CUP cohorts. Here we describe CUPiD, a machine learning classifier for accurate TOO predictions across 29 tumour classes using circulating cell-free DNA (cfDNA) methylation patterns. We tested CUPiD on 143 cfDNA samples from patients with 13 cancer types alongside 27 non-cancer controls, with overall sensitivity of 84.6% and TOO accuracy of 96.8%. In an additional cohort of 41 patients with CUP CUPiD predictions were made in 32/41 (78.0%) cases, with 88.5% of the predictions clinically consistent with a subsequent or suspected primary tumour diagnosis, when available (23/26 patients). Combining CUPiD with cfDNA mutation data demonstrated potential diagnosis re-classification and/or treatment change in this hard-to-treat cancer group.

Low-power analog processing for sensing applications: low-frequency harmonic signal classification.

A low-power analog sensor front-end is described that reduces the energy required to extract environmental sensing spectral features without using Fast Fouriér Transform (FFT) or wavelet transforms. An Analog Harmonic Transform (AHT) allows selection of only the features needed by the back-end, in contrast to the FFT, where all coefficients must be calculated simultaneously. We also show that the FFT coefficients can be easily calculated from the AHT results by a simple back-substitution. The scheme is tailored for low-power, parallel analog implementation in an integrated circuit (IC). Two different applications are tested with an ideal front-end model and compared to existing studies with the same data sets. Results from the military vehicle classification and identification of machine-bearing fault applications shows that the front-end suits a wide range of harmonic signal sources. Analog-related errors are modeled to evaluate the feasibility of and to set design parameters for an IC implementation to maintain good system-level performance. Design of a preliminary transistor-level integrator circuit in a 0.13 µm complementary metal-oxide-silicon (CMOS) integrated circuit process showed the ability to use online self-calibration to reduce fabrication errors to a sufficiently low level. Estimated power dissipation is about three orders of magnitude less than similar vehicle classification systems that use commercially available FFT spectral extraction.

Cross-validating the Dot Counting Test Among an Adult ADHD Clinical Sample and Analyzing the Effect of ADHD Subtype and Comorbid Psychopathology.

This study cross-validated the dot counting test (DCT) as a performance validity test (PVT) in an adult attention-deficit/hyperactivity disorder (ADHD) clinical population and examined the effect of ADHD subtype and psychiatric comorbidity on accuracy for detecting invalidity. DCT performance was assessed among 210 consecutive adult ADHD referrals who underwent neuropsychological evaluation and were classified into valid (n = 175) or invalid (n = 35) groups based on seven independent criterion PVTs. The invalid group had significantly worse DCT performance than the valid group using both the standard and unrounded scoring procedure (ηp2=.28). Classification accuracy was excellent, with 54.3% sensitivity/92% specificity at optimal cut-scores of ≥14 (rounded) and ≥13.38 (unrounded). Nonsignificant DCT performance differences emerged based on ADHD subtype or the presence/absence of comorbid psychopathology. The DCT functions well as a nonmemory-based PVT in an ethnoracially diverse ADHD population, supporting its clinical utility for detecting invalid neurocognitive performance during ADHD evaluations.

Multi-Maintenance Olaparib Therapy in Relapsed, Germline BRCA1/2-Mutant High-Grade Serous Ovarian Cancer (MOLTO): A Phase II Trial.

PURPOSE: A single maintenance course of a PARP inhibitor (PARPi) improves progression-free survival (PFS) in germline BRCA1/2-mutant high-grade serous ovarian cancer (gBRCAm-HGSOC). The feasibility of a second maintenance course of PARPi was unknown. PATIENTS AND METHODS: Phase II trial with two entry points (EP1, EP2). Patients were recruited prior to rechallenge platinum. Patients with relapsed, gBRCAm-HGSOC were enrolled at EP1 if they were PARPi-naïve. Patients enrolled at EP2 had received their first course of olaparib prior to trial entry. EP1 patients were retreated with olaparib after RECIST complete/partial response (CR/PR) to platinum. EP2 patients were retreated with olaparib ± cediranib after RECIST CR/PR/stable disease to platinum and according to the platinum-free interval. Co-primary outcomes were the proportion of patients who received a second course of olaparib and the proportion who received olaparib retreatment for ≥6 months. Functional homologous recombination deficiency (HRD), somatic copy-number alteration (SCNA), and BRCAm reversions were investigated in tumor and liquid biopsies. RESULTS: Twenty-seven patients were treated (EP1 = 17, EP2 = 10), and 19 were evaluable. Twelve patients (63%) received a second course of olaparib and 4 received olaparib retreatment for ≥6 months. Common grade ≥2 adverse events during olaparib retreatment were anemia, nausea, and fatigue. No cases of MDS/AML occurred. Mean duration of olaparib treatment and retreatment differed (12.1 months vs. 4.4 months; P < 0.001). Functional HRD and SCNA did not predict PFS. A BRCA2 reversion mutation was detected in a post-olaparib liquid biopsy. CONCLUSIONS: A second course of olaparib can be safely administered to women with gBRCAm-HGSOC but is only modestly efficacious. See related commentary by Gonzalez-Ochoa and Oza, p. 2563.

Using PVA and captive breeding to balance trade-offs in the rescue of the island dibbler onto a new island ark.

In the face of the current global extinction crisis, it is critical we give conservation management strategies the best chance of success. Australia is not exempt from global trends with currently the world's greatest mammal extinction rate (~ 1 per 8 years). Many more are threatened including the dibbler (Parantechinus apicalis) whose remnant range has been restricted to Western Australia at just one mainland site and two small offshore islands-Whitlock Island (5 ha) and Boullanger Island (35 ha). Here, we used 14 microsatellite markers to quantify genetic variation in the remaining island populations from 2013 to 2018 and incorporated these data into population viability analysis (PVA) models, used to assess factors important to dibbler survival and to provide guidance for translocations. Remnant population genetic diversity was low (< 0.3), and populations were highly divergent from each other (pairwise FSTs 0.29-0.52). Comparison of empirical data to an earlier study is consistent with recent declines in genetic diversity and models projected increasing extinction risk and declining genetic variation in the next century. Optimal translocation scenarios recommend 80 founders for new dibbler populations-provided by captive breeding-and determined the proportion of founders from parental populations to maximise genetic diversity and minimise harvesting impact. The goal of our approach is long-term survival of genetically diverse, self-sustaining populations and our methods are transferable. We consider mixing island with mainland dibblers to reinforce genetic variation.

The Divergent Roles of Symptom and Performance Validity in the Assessment of ADHD.

OBJECTIVE: This study examined concordance between symptom and performance validity among clinically-referred patients undergoing neuropsychological evaluation for Attention-Deficit/Hyperactivity Disorder (ADHD). METHOD: Data from 203 patients who completed the WAIS-IV Working Memory Index, the Clinical Assessment of Attention Deficit-Adult (CAT-A), and ≥4 criterion performance validity tests (PVTs) were analyzed. RESULTS: Symptom and performance validity were concordant in 76% of cases, with the majority being valid performance. Of the remaining 24% of cases with divergent validity findings, patients were more likely to exhibit symptom invalidity (15%) than performance invalidity (9%). Patients demonstrating symptom invalidity endorsed significantly more ADHD symptoms than those with credible symptom reporting (ηp2 = .06-.15), but comparable working memory test performance, whereas patients with performance invalidity had significantly worse working memory performance than those with valid PVT performance (ηp2 = .18). CONCLUSION: Symptom and performance invalidity represent dissociable constructs in patients undergoing neuropsychological evaluation of ADHD and should be evaluated independently.

Impaired or invalid? Limitations of assessing performance validity using the Boston Naming Test.

The Boston Naming Test (BNT) has been proposed as an embedded performance validity test (PVT), though replication is needed to provide further empirical support of its simultaneous use as a cognitive ability measure and embedded PVT. This cross-sectional study examined BNT performance in a mixed neuropsychiatric sample of 137 patients with/without cognitive impairment. Four independent criterion PVTs classified 109 (80%) as valid and 28 (20%) as invalid. BNT raw and demographically-corrected T-scores were significantly higher among the valid group with small effect sizes (ηp2 = 0.04-0.05). Raw/T-scores differentiated valid/invalid groups, but with low classification accuracy (areas under the curve [AUCs] = 0.68/0.63), and unacceptably weak sensitivities (i.e. 7%/18%). When separated by impairment status, raw score accuracy appreciably increased (AUC = 0.87; 61% sensitivity/89% specificity) among unimpaired patients, whereas T-score accuracy, while significant, remained low (AUC = 0.68; 21% sensitivity/89% specificity). Conversely, among impaired patients, neither the raw (AUC = 0.59) nor T-score (AUC = 0.60) accurately identified invalid performance. In sum, BNT scores were not able to differentiate valid from invalid performance when cognitive impairment was present, and therefore showed limited overall utility as embedded PVTs. These findings further caution against inferring performance validity from measures in which a single score is used to assess both cognitive ability and validity.

Examining independent and combined accuracy of embedded performance validity tests in the California Verbal Learning Test-II and Brief Visuospatial Memory Test-Revised for detecting invalid performance.

The California Verbal Learning Test-Second Edition (CVLT-II) Forced Choice Recognition (FC) and Brief Visuospatial Memory Test-Revised (BVMT-R) Recognition Discrimination Index (RD) are embedded performance validity tests (PVTs) assessing material-specific neuropsychological processes (i.e., verbal and visual memory, respectively). Prior research demonstrated the utility of these PVTs independently; however, no study has compared their diagnostic accuracy for identifying invalid performance relative to each other and in combination within a single sample. This cross-sectional study included an adult neuropsychiatric sample who underwent neuropsychological evaluation. Validity groups were determined via independent criterion PVT performance, and consisted of 103 participants with valid and 25 with invalid neurocognitive performance. FC and RD were not significantly correlated (r = .154), yet both differed between validity groups (ηp2 = .14-.19). Previously established FC (≤14) and RD (≤4) cutoffs evidenced 32-40% sensitivity/90-98% specificity, though receiver operating characteristic (ROC) analyses indicated a more liberal FC cutoff (≤15) was optimal. Logistic regression models utilizing both embedded PVTs indicated that FC did not significantly improve classification accuracy above and beyond RD. Results support the clinical utility of existing cutoffs for FC and RD for independently identifying invalid performance, though the latter showed relatively better ability to detect invalid performance when both are used together.

Concordance between the Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF) and Clinical Assessment of Attention Deficit-Adult (CAT-A) over-reporting validity scales for detecting invalid ADHD symptom reporting.

This study investigated the relationship between symptom validity scales on the Clinical Assessment of Attention Deficit-Adult (CAT-A) and the Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF) in the context of Attention-Deficit/Hyperactivity Disorder (ADHD) evaluation. The sample comprised 140 consecutive patients referred for a neuropsychological evaluation of ADHD and were administered the CAT-A and the MMPI-2-RF and a battery of performance-based neurocognitive tests. Results indicated CAT-A/MMPI-2-RF symptom validity concordance of 51% between measures, with 38% concordant valid and 13% concordant invalid responses. Among those with discordance symptom validity results, rates of valid CAT-A/invalid MMPI-2-RF responding (41%) were more common than invalid CAT-A/valid MMPI-2-RF responding (8%). Results also indicated higher levels of ADHD symptoms among invalid responding within the CAT-A, whereas the MMPI-2-RF Cognitive Complaints scale did not differ by CAT-A validity status. Finally, symptom validity scales on both the CAT-A and MMPI-2-RF were largely discordant from neuropsychological test validity status per performance validity tests. Findings highlight the need for symptom validity testing when assessing ADHD and indicate that validity indices on broad personality assessments may assess different constructs than embedded validity indices in ADHD-specific measures.

cfDNA methylome profiling for detection and subtyping of small cell lung cancers.

Small cell lung cancer (SCLC) is characterized by morphologic, epigenetic and transcriptomic heterogeneity. Subtypes based upon predominant transcription factor expression have been defined that, in mouse models and cell lines, exhibit potential differential therapeutic vulnerabilities, with epigenetically distinct SCLC subtypes also described. The clinical relevance of these subtypes is unclear, due in part to challenges in obtaining tumor biopsies for reliable profiling. Here we describe a robust workflow for genome-wide DNA methylation profiling applied to both patient-derived models and to patients' circulating cell-free DNA (cfDNA). Tumor-specific methylation patterns were readily detected in cfDNA samples from patients with SCLC and were correlated with survival outcomes. cfDNA methylation also discriminated between the transcription factor SCLC subtypes, a precedent for a liquid biopsy cfDNA-methylation approach to molecularly subtype SCLC. Our data reveal the potential clinical utility of cfDNA methylation profiling as a universally applicable liquid biopsy approach for the sensitive detection, monitoring and molecular subtyping of patients with SCLC.

Live cell multicolor imaging of lipid droplets with a new dye, LD540.

A lipophilic dye based on the Bodipy fluorophore, LD540, was developed for microscopic imaging of lipid droplets. In contrast to previous lipid droplet dyes, it can spectrally be resolved from both green and red fluorophores allowing multicolor imaging in both fixed and living cells. Its improved specificity, brightness and photostability support live cell imaging, which was used to demonstrate by two-color imaging lipid droplet motility along microtubules.

Every second counts: A comparison of four dot counting test scoring procedures for detecting invalid neuropsychological test performance.

Although performance validity tests (PVTs) are an integral element of neuropsychological assessment, most PVTs have historically been restricted to the memory domain. The Dot Counting Test (DCT) is a nonmemory PVT shown to reliably identify invalid performance. Although several traditional and abbreviated scoring methods have been derived, no study to date has directly compared the available scoring approaches within a single sample. This cross-sectional study cross-validated 4 different DCT scoring approaches, including the traditional rounded E-score proposed within the manual, an unrounded E-score, and 2 abbreviated scoring procedures based on 4- and 6-card versions (DCT-4 and DCT-6, respectively) in a diverse mixed clinical neuropsychiatric sample (N = 132). Validity groups were established by 5 independent criterion PVTs (102 valid and 30 invalid). Receiver operating characteristic curve analyses yielded significant areas under the curve (AUCs = .84-.86) for the overall sample, with sensitivities of 50%-67% at ≥ 89% specificity. The DCT scores had outstanding classification accuracy (AUCs ≥ .92; sensitivities = 80%-83%) in the unimpaired group and excellent classification accuracy in the impaired group (AUCs = .79-.81; sensitivities = 43%-60%). Whereas negligible differences emerged between the 4 scoring methods for the cognitively intact group, the DCT-4 showed notably stronger psychometric properties among the overall sample in general and the mild cognitive impairment group in particular. Results corroborate previous findings suggesting that the DCT is a robust PVT, regardless of the employed scoring procedure, and replicate support for the abbreviated DCT-4 as the recommended validity indicator. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Cross-validation of non-memory-based embedded performance validity tests for detecting invalid performance among patients with and without neurocognitive impairment.

INTRODUCTION: Embedded performance validity tests (PVTs) allow for continuous and economical validity assessment during neuropsychological evaluations; however, similar to their freestanding counterparts, a limitation of well-validated embedded PVTs is that the majority are memory-based. This study cross-validated several previously identified non-memory-based PVTs derived from language, processing speed, and executive functioning tests within a single mixed clinical neuropsychiatric sample with and without cognitive impairment. METHOD: This cross-sectional study included data from 124 clinical patients who underwent outpatient neuropsychological evaluation. Validity groups were determined by four independent criterion PVTs (failing ≤1 or ≥2), resulting in 98 valid (68% cognitively impaired) and 26 invalid performances. In total, 23 previously identified embedded PVTs derived from Verbal Fluency (VF), Trail Making Test (TMT), Stroop (SCWT), and Wisconsin Card Sorting Test (WCST) were examined. RESULTS: All VF, SCWT, and TMT PVTs, along with WCST Categories, significantly differed between validity groups (ηp2 =.05-.22) with areas under the curve (AUCs) of.65-.81 and 19-54% sensitivity (≥89% specificity) at optimal cut-scores. When subdivided by impairment status, all PVTs except for WCST Failures to Maintain Set were significant (AUCs =.75-94) with 33-85% sensitivity (≥90% specificity) in the cognitively unimpaired group. Among the cognitively impaired group, most VF, TMT, and SCWT PVTs remained significant, albeit with decreased accuracy (AUCs =.65-.76) and sensitivities (19-54%) at optimal cut-scores, whereas all WCST PVTs were nonsignificant. Across groups, SCWT embedded PVTs evidenced the strongest psychometric properties. CONCLUSION: VF, TMT, and SCWT embedded PVTs generally demonstrated moderate accuracy for identifying invalid neuropsychological performance. However, performance on these non-memory-based PVTs from processing speed and executive functioning tests are not immune to the effects of cognitive impairment, such that alternate cut-scores (with reduced sensitivity if adequate specificity is maintained) are indicated in cases where the clinical history is consistent with cognitive impairment. In contrast, WCST indices generally had poor accuracy.

The mixed liver and heart transcriptome dataset of the New Zealand brushtail possum, Trichosurus vulpecula.

New Zealand suffers greatly from invasive mammal predators including rats, stoats, feral cats and possums all of which not only damage or prey on New Zealand's unique terrestrial biodiversity, but also have huge impact on NZ's economy as many of these pests act as vectors of disease to farm and game animals. As such, the NZ government has invested nearly $90 m to support an ambitious plan to make the country predator free by 2050. Although there are adequate means to control invasive predator populations, it is widely agreed that current technologies are not sufficient for total eradication and that improved technologies are required. The Achilles Heel approach is one such developmental technology that attempts to exploit variation in the genes of target species that are vital to key physiological or cellular pathways within the body, such that interference with these genes will cause a species-specific death without the harmful effects on the environment and non-targets species that the current suite of control agents engender. Interference could either be through species-specific gene knock-down using such agents as siRNA and/or the use of species-selective chemical toxicants specifically developed against these targets. To assist with identifying species-specific gene targets in the New Zealand brushtail possum (Trichosurus vulpecula) we have assembled and annotated a possum mixed heart and liver transcriptome.