Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic ...variation.
We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation.
Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies.
Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Communities often unite during a crisis, though some cope by ascribing blame or stigmas to those who might be linked to distressing life events. In a preregistered two-wave survey, we evaluated the ...dehumanization of Asians and Asian Americans during the COVID-19 pandemic. Our first wave (March 26-April 2, 2020;
= 917) revealed dehumanization was prevalent, between 6.1% and 39% of our sample depending on measurement. Compared to non-dehumanizers, people who dehumanized also perceived the virus as less risky to human health and caused less severe consequences for infected people. They were more likely to be ideologically Conservative and believe in conspiracy theories about the virus. We largely replicated the results 1 month later in our second wave (May 6-May 13, 2020;
= 723). Together, many Americans dehumanize Asians and Asian Americans during the COVID-19 pandemic with related perceptions that the virus is less problematic. Implications and applications for dehumanization theory are discussed.
Abstract
Numeracy—the ability to understand and use numeric information—is linked to good decision-making. Several problems exist with current numeracy measures, however. Depending on the participant ...sample, some existing measures are too easy or too hard; also, established measures often contain items well-known to participants. The current article aimed to develop new numeric understanding measures (NUMs) including a 1-item (1-NUM), 4-item (4-NUM), and 4-item adaptive measure (A-NUM). In a calibration study, 2 participant samples (
n
= 226 and 264 from Amazon’s Mechanical Turk MTurk) each responded to half of 84 novel numeracy items. We calibrated items using 2-parameter logistic item response theory (IRT) models. Based on item parameters, we developed the 3 new numeracy measures. In a subsequent validation study, 600 MTurk participants completed the new numeracy measures, the adaptive Berlin Numeracy Test, and the Weller Rasch-Based Numeracy Test, in randomized order. To establish predictive and convergent validities, participants also completed judgment and decision tasks, Raven’s progressive matrices, a vocabulary test, and demographics. Confirmatory factor analyses suggested that the 1-NUM, 4-NUM, and A-NUM load onto the same factor as existing measures. The NUM scales also showed similar association patterns to subjective numeracy and cognitive ability measures as established measures. Finally, they effectively predicted classic numeracy effects. In fact, based on power analyses, the A-NUM and 4-NUM appeared to confer more power to detect effects than existing measures. Thus, using IRT, we developed 3 brief numeracy measures, using novel items and without sacrificing construct scope. The measures can be downloaded as Qualtrics files (
https://osf.io/pcegz/
).
Celotno besedilo
Dostopno za:
CEKLJ, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Background
Rates of contralateral prophylactic mastectomy (CPM)—removal of the healthy breast following breast cancer diagnosis—have increased, particularly among women for whom CPM provides no ...survival benefit. Affective (i.e., emotional) decision making is often blamed for this increase. We studied whether greater negative breast cancer affect could motivate uptake of CPM through increased cancer risk perceptions and biased treatment evaluations.
Methods
We randomly assigned healthy women with average breast-cancer risk (N = 1,030; Mage = 44.14, SD = 9.23 y) to 1 of 3 affect conditions (negative v. neutral v. positive narrative manipulation) in a hypothetical online experiment in which they were asked to imagine being diagnosed with cancer in one breast. We assessed 1) treatment choice, 2) affect toward CPM, and 3) perceived risk of future breast cancer in each breast (cancer affected and healthy) following lumpectomy, single mastectomy, and CPM.
Results
The manipulation caused women in the negative and neutral narrative conditions (26.9% and 26.4%, respectively) to choose CPM more compared with the positive narrative condition (19.1%). Across conditions, women’s CPM affect did not differ. However, exploratory analyses addressing a possible association of affect toward cancer-related targets suggested that women in the negative narrative condition may have felt more positively toward CPM than women in the positive narrative condition. The manipulation did not have significant effects on breast cancer risk perceptions.
Limitations
The manipulation of affect had a small effect size, possibly due to the hypothetical nature of this study and/or strong a priori knowledge and attitudes about breast cancer and its treatment options.
Conclusion
Increased negative affect toward breast cancer increased choice of CPM over other surgical options and might have motivated more positive affective evaluations of CPM.
Highlights
This study used narratives to elicit different levels of negative integral affect toward breast cancer to investigate the effects of affect on breast cancer treatment choices.
Increased negative affect toward breast cancer increased the choice of double mastectomy over lumpectomy and single mastectomy to treat a hypothetical, early-stage cancer.
The narrative manipulation of negative affect toward breast cancer did not change the perceived risks of future cancer following any of the surgical interventions.
Negative affect toward breast cancer may have biased affective evaluations of double mastectomy.
In two large-scale longitudinal datasets (combined N = 5761), we investigated ability-related political polarization in responses to the COVID-19 pandemic. We observed more polarization with greater ...ability in emotional responses, risk perceptions, and product-purchase intentions across five waves of data collection with a diverse, convenience sample from February 2020 through July 2020 (Study 1, N = 1267). Specifically, more liberal participants had more negative emotional responses and greater risk perceptions of COVID-19 than conservative participants. Compared to conservatives, liberal participants also interpreted quantitative information as indicating higher COVID-19 risk and sought COVID-related news more from liberal than conservative news media. Of key importance, we also compared verbal and numeric cognitive abilities for their independent capacity to predict greater polarization. Although measures of numeric ability, such as objective numeracy, are often used to index ability-related polarization, ideological differences were more pronounced among those higher in verbal ability specifically. Similar results emerged in secondary analysis of risk perceptions in a nationally representative longitudinal dataset (Study 2, N = 4494; emotions and purchase intentions were not included in this dataset). We further confirmed verbal-ability-related polarization findings on non-COVID policy attitudes (i.e., weapons bans and Medicare-for-all) measured cross-sectionally. The present Study 2 documented ability-related polarization emerging over time for the first time (rather than simply measuring polarization in existing beliefs). Both studies demonstrated verbal ability measures as the most robust predictors of ability-related polarization. Together, these results suggest that polarization may be a function of the amount and/or application of verbal knowledge rather than selective application of quantitative reasoning skills.
•People higher in verbal ability had more polarized responses to COVID-19.•Skill with numbers predicted lower risk perceptions, but not polarization.•People higher in verbal ability interpreted information to support beliefs.•People higher in verbal ability were more polarized in media consumption.
Abstract Test‐retest reliability—establishing that measurements remain consistent across multiple testing sessions—is critical to measuring, understanding, and predicting individual differences in ...infant language development. However, previous attempts to establish measurement reliability in infant speech perception tasks are limited, and reliability of frequently used infant measures is largely unknown. The current study investigated the test‐retest reliability of infants’ preference for infant‐directed speech over adult‐directed speech in a large sample ( N = 158) in the context of the ManyBabies1 collaborative research project. Labs were asked to bring in participating infants for a second appointment retesting infants on their preference for infant‐directed speech. This approach allowed us to estimate test‐retest reliability across three different methods used to investigate preferential listening in infancy: the head‐turn preference procedure, central fixation, and eye‐tracking. Overall, we found no consistent evidence of test‐retest reliability in measures of infants’ speech preference (overall r = 0.09, 95% CI −0.06,0.25). While increasing the number of trials that infants needed to contribute for inclusion in the analysis revealed a numeric growth in test‐retest reliability, it also considerably reduced the study's effective sample size. Therefore, future research on infant development should take into account that not all experimental measures may be appropriate for assessing individual differences between infants. Research Highlights We assessed test‐retest reliability of infants’ preference for infant‐directed over adult‐directed speech in a large pre‐registered sample ( N = 158). There was no consistent evidence of test‐retest reliability in measures of infants’ speech preference. Applying stricter criteria for the inclusion of participants may lead to higher test‐retest reliability, but at the cost of substantial decreases in sample size. Developmental research relying on stable individual differences should consider the underlying reliability of its measures.
There is a growing need for integrated approaches that align community priorities with strategies that build resilience to climate hazards, societal shocks, and economic crises to ensure more ...equitable and sustainable outcomes. We anticipate that adaptive management and resilience learning are central elements for these approaches. In this paper, we describe an approach to build and test a Resilience Learning System to support research and implementation of a resilience strategy developed for the Greater Miami and the Beaches or the Resilient305 Strategy. Elements foundational to the design of this integrated research strategy and replicable Resilience Learning System are: (1) strong partnerships among community members, government and non-government organization leaders, and researchers from multiple academic institutions; (2) contributions of subject matter expertise and local knowledge to identify information and translational gaps, formulate metrics and evaluate outcomes of Resilient305 Strategy actions from the community perspective; and (3) a comprehensive understanding of civic engagement activities, technological tools, and resilience-building capacities, including policy and financial innovations, from which to advance socio-technological, smart and connected regional-to-hyperlocal community translation through co-design/co-production. Initial results on co-produced metrics are provided. This work produces a new, replicable framework for resilience research that includes a comprehensive set of metrics, translation to communities through structured dialogues, a collaborative process involving all stakeholders and researchers, and evaluation of resilience actions to inform new investments and improve understanding and effectiveness over time.
Evaluate the safety and effectiveness of an ab interno implanted (iStent inject) Trabecular Micro-Bypass System (Glaukos Corporation, San Clemente, CA) in combination with cataract surgery in ...subjects with mild to moderate primary open-angle glaucoma (POAG).
Prospective, randomized, single-masked, concurrently controlled, multicenter clinical trial.
Eyes with mild to moderate POAG and preoperative intraocular pressure (IOP) ≤24 mmHg on 1 to 3 medications, unmedicated diurnal IOP (DIOP) 21 to 36 mmHg, and cataract requiring surgery.
After uncomplicated cataract surgery, eyes were randomized 3:1 intraoperatively to ab interno implantation of iStent inject (Model G2-M-IS; treatment group, n = 387) or no stent implantation (control group, n = 118). Subjects were followed through 2 years postoperatively. Annual washout of ocular hypotensive medication was performed.
Effectiveness end points were ≥20% reduction from baseline in month 24 unmedicated DIOP and change in unmedicated month 24 DIOP from baseline. Safety measures included best spectacle-corrected visual acuity (BSCVA), slit-lamp and fundus examinations, gonioscopy, pachymetry, specular microscopy, visual fields, complications, and adverse events.
The groups were well balanced preoperatively, including medicated IOP (17.5 mmHg in both groups) and unmedicated DIOP (24.8±3.3 mmHg vs. 24.5±3.1 mmHg in the treatment and control groups, respectively, P = 0.33). At 24 months, 75.8% of treatment eyes versus 61.9% of control eyes experienced ≥20% reduction from baseline in unmedicated DIOP (P = 0.005), and mean reduction in unmedicated DIOP from baseline was greater in treatment eyes (7.0±4.0 mmHg) than in control eyes (5.4±3.7 mmHg; P < 0.001). Of the responders, 84% of treatment eyes and 67% of control eyes were not receiving ocular hypotensive medication at 23 months. Furthermore, 63.2% of treatment eyes versus 50.0% of control eyes had month 24 medication-free DIOP ≤18 mmHg (difference 13.2%; 95% confidence interval, 2.9–23.4). The overall safety profile of the treatment group was favorable and similar to that in the control group throughout the 2-year follow-up.
Clinically and statistically greater reductions in IOP without medication were achieved after iStent inject implantation with cataract surgery versus cataract surgery alone, with excellent safety through 2 years.
Kistin and Silverstein talk about pilot intervention studies, which commonly defined as small studies carried out in preparation for larger investigations. These are essential precursors to ...high-quality clinical trials. Although not all trials are preceded by pilot investigations when they are, pilot studies inform how subsequent trials are conducted and have an important role in controlling the pipeline of intervention development and dissemination by influencing which large-scale trials are ultimately carried out and which are never brought to fruition.
Social cognition has become a high priority area for the study of schizophrenia. However, despite developments in this area, progress remains limited by inconsistent terminology and differences in ...the way social cognition is measured. To address these obstacles, a consensus-building meeting on social cognition in schizophrenia was held at the National Institute of Mental Health in March 2006. Agreement was reached on several points, including definitions of terms, the significance of social cognition for schizophrenia research, and suggestions for future research directions. The importance of translational interdisciplinary research teams was emphasized. The current article presents a summary of these discussions.
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