Data Sanitization to Reduce Private Information Leakage from Functional Genomics.

The generation of functional genomics datasets is surging, because they provide insight into gene regulation and organismal phenotypes (e.g., genes upregulated in cancer). The intent behind functional genomics experiments is not necessarily to study genetic variants, yet they pose privacy concerns due to their use of next-generation sequencing. Moreover, there is a great incentive to broadly share raw reads for better statistical power and general research reproducibility. Thus, we need new modes of sharing beyond traditional controlled-access models. Here, we develop a data-sanitization procedure allowing raw functional genomics reads to be shared while minimizing privacy leakage, enabling principled privacy-utility trade-offs. Our protocol works with traditional Illumina-based assays and newer technologies such as 10x single-cell RNA sequencing. It involves quantifying the privacy leakage in reads by statistically linking study participants to known individuals. We carried out these linkages using data from highly accurate reference genomes and more realistic environmental samples.

The RNA-Binding Domain of hnRNP U Extends beyond the RGG/RG Motifs.

Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG motif within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV cross-linking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing 11 of these identified cross-link sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG motif is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG motif with RNA-binding properties comparable to those of the canonical RGG/RG motif. These RGG/RG motifs serve redundant functions, with neither serving as the primary RBD. While in isolation, each RGG/RG motif has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling the binding of most of the designed RNA set with low to midnanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlight the perils of a reductionist approach to defining biochemical activities in this system and pave the way for a detailed investigation of its RNA-binding specificity.

The Causes and Consequences of Drifting Expectations.

Awaiting news of uncertain outcomes is distressing because the news might be disappointing. To prevent such disappointments, people often "brace for the worst," pessimistically lowering expectations before news arrives to decrease the possibility of surprising disappointment (a negative prediction error, or PE). Computational decision-making research commonly assumes that expectations do not drift within trials, yet it is unclear whether expectations pessimistically drift in real-world, high-stakes settings, what factors influence expectation drift, and whether it effectively buffers emotional responses to goal-relevant outcomes. Moreover, individuals learn from PEs to accurately anticipate future outcomes, but it is unknown whether expectation drift also impedes PE-based learning. In a sample of students awaiting exam grades (N = 625), we found that expectations often drift and tend to drift pessimistically. We demonstrate that bracing is preferentially modulated by uncertainty; it transiently buffers the initial emotional impact of negative PEs but impairs PE-based learning, counterintuitively sustaining uncertainty into the future.

The role of area deprivation index in health care disruptions among cancer survivors during the SARS-CoV-2 pandemic.

OBJECTIVE: To examine the associations between demographic/medical and geographic factors with follow-up medical care and health-related quality of life (HRQoL) among cancer survivors during the SARS-CoV-2 pandemic. STUDY DESIGN: Cross-sectional survey. METHODS: An online survey was sent to cancer survivors between May 2020 and January 2021, exploring their experience with SARS-CoV-2, follow-up care, and HRQoL. PolicyMap was used to geocode home addresses. Both geographic and demographic/medical factors were examined for their associations with SARS-CoV-2 experience, follow-up care, and HRQoL (FACT-G7). RESULTS: Geographic data were available for 9651 participants. Patients living in the highest area deprivation index (ADI) neighborhoods (most deprived) had higher odds of avoiding in-person general (odds ratio [OR] = 7.20; 95% confidence interval [CI] = 2.79-18.60), cancer (OR = 8.47; 95% CI = 3.73-19.30), and emergency (OR = 14.2; 95% CI = 5.57-36.30) medical care, as well as lower odds of using telemedicine (OR = 0.61; 95% CI = 0.52-0.73) compared to the lowest ADI group. Race/ethnicity was not associated with follow-up care after controlling for ADI. The effect of ADI on HRQoL was generally in the expected direction, with higher ADI being associated with worse HRQoL. CONCLUSIONS: ADI influenced follow-up medical care more than age, race/ethnicity, or health insurance type. Healthcare providers and institutions should focus on decreasing barriers to in-person and telemedicine health care that disproportionally impact those living in more deprived communities, which are exacerbated by health care disruptions like those caused by the SARS-CoV-2 pandemic.

Evaluation of a head rest prototype for rotational corrections in three degrees of freedom.

Cranial stereotactic irradiations require accurate reproduction of the planning CT patient position at the time of treatment, including removal of rotational offsets. A device prototype was evaluated for potential clinical use to correct rotational positional offsets in image-guided radiotherapy workflow. Analysis was carried out with a prototype device "RPS head" by gKteso GmbH, rotatable up to 4° in three dimensions by hand wheels. A software tool accounts for the nonrectangular rotation axes and also indicates translational motions to be performed with the standard couch to correct the initial offset and translational shifts introduced by the rotational motion. The accuracy of angular corrections and positioning of an Alderson RANDO head phantom using the prototype device was evaluated for nine treatment plans for cranial targets. Corrections were obtained from cone beam computed tomography (CBCT) imaging. The phantom position was adjusted and the final position was then verified by another CBCT. The long-term stability of the prototype device was evaluated. Attenuation by the device along its three main axes was assessed. A planning study was performed to evaluate if regions of high-density material can be avoided during plan generation. The device enabled the accurate correction of rotational offsets in a clinical setup with a mean residual angular difference of (0.0 ± 0.1)° and a maximum deviation of 0.2°. Translational offsets were less than 1 mm. The device was stable over a period of 20 min, not changing the head support plate position by more than (0.7 ± 0.6) mm. The device contains high-density material in the adjustment mechanism and slightly higher density in the support structures. These can be avoided during planning generation maintaining comparable plan quality. The head positioning device can be used to correct rotational offsets in a clinical setting.

Feasibility of Ethos adaptive treatments of lung tumors and associated quality assurance.

MOTIVATION: Online adaptive radiotherapy with Ethos is based on the anatomy determined from daily cone beam computed tomography (CBCT) images. Dose optimization and computation are performed on the density map of a synthetic CT (sCT), a deformable registration of the initial planning CT (pCT) onto the current CBCT. Large density changes as present in the lung region are challenging the system. METHODS: Treatment plans for Ethos were created and delivered for 1, 2, and 3 cm diameter lung lesions in an anthropomorphic phantom, combining different insets in the pCT and during adaptive and non-adaptive treatment sessions. Primary and secondary dose calculations as well as back-projected dose from portal images were evaluated. RESULTS: Density changes due to changed insets were not considered in the sCTs. This resulted in errors in the dose; for example, -15.9% of the mean dose for a plan when changing from a 3 cm inset in the pCT to 1 cm at the time of treatment. Secondary dose calculation is based on the sCT and could therefore not reveal these dose errors. However, dose calculation on the CBCT, either as a recalculation in the treatment planning system or as pre-treatment quality assurance (QA) before the treatment, indicated the differences. EPID in-vivo QA also reported discrepancies between calculated and delivered dose distributions. CONCLUSIONS: An incorrect density distribution in the sCT has an impact on the dose calculation accuracy in the adaptive treatment workflow with the Ethos system. Additional quality checks of the sCT can detect such errors.

More than a feeling: physiological measures of affect index the integration of effort costs and rewards during anticipatory effort evaluation.

The notion that humans avoid effortful action is one of the oldest and most persistent in psychology. Influential theories of effort propose that effort valuations are made according to a cost-benefit trade-off: we tend to invest mental effort only when the benefits outweigh the costs. While these models provide a useful conceptual framework, the affective components of effort valuation remain poorly understood. Here, we examined whether primitive components of affective response-positive and negative valence, captured via facial electromyography (fEMG)-can be used to better understand valuations of cognitive effort. Using an effortful arithmetic task, we find that fEMG activity in the corrugator supercilii-thought to index negative valence-1) tracks the anticipation and exertion of cognitive effort and 2) is attenuated in the presence of high rewards. Together, these results suggest that activity in the corrugator reflects the integration of effort costs and rewards during effortful decision-making.

Cognitive effort exertion enhances electrophysiological responses to rewarding outcomes.

Recent work has highlighted neural mechanisms underlying cognitive effort-related discounting of anticipated rewards. However, findings on whether effort exertion alters the subjective value of obtained rewards are inconsistent. Here, we provide a more nuanced account of how cognitive effort affects subsequent reward processing in a novel task designed to assess effort-induced modulations of the Reward Positivity, an event-related potential indexing reward-related neural activity. We found that neural responses to both gains and losses were significantly elevated in trials requiring more versus less cognitive effort. Moreover, time-frequency analysis revealed that these effects were mirrored in gain-related delta, but not in loss-related theta band activity, suggesting that people ascribed more value to high-effort outcomes. In addition, we also explored whether individual differences in behavioral effort discounting rates and reward sensitivity in the absence of effort may affect the relationship between effort exertion and subsequent reward processing. Together, our findings provide evidence that cognitive effort exertion can increase the subjective value of subsequent outcomes and that this effect may primarily rely on modulations of delta band activity.

Sensitivity and specificity of secondary dose calculation for head and neck treatment plans.

PURPOSE: Secondary dose calculation (SDC) with an independent algorithm is one option to perform plan-specific quality assurance (QA). While measurement-based QA can potentially detect errors in plan delivery, the dose values are typically only compared to calculations on homogeneous phantom geometries instead of patient CT data. We analyzed the sensitivity and specificity of an SDC software by purposely introducing different errors and determined thresholds for optimal decisions. METHODS: Thirty head and neck VMAT plans and 30 modifications of those plans, including errors related to density and beam modelling, were recalculated using RadCalc with a Monte Carlo algorithm. Decision thresholds were obtained by receiver operating characteristics (ROC) analysis. For comparison, measurement-based QA using the ArcCHECK phantom was carried out and evaluated in the same way. RESULTS: Despite optimized decision thresholds, none of the systems was able to reliably detect all errors. ArcCHECK analysis using a 2%/2 mm criterion with a threshold of 91.1% had an area under the curve (AUC) of 0.80. Evaluating differences in recalculated and planned DVH parameter of the target structures in RadCalc with a 2% threshold an AUC of 0.86 was achieved. Out-of-field deviations could be attributed to weaknesses in the beam model. CONCLUSIONS: Secondary dose calculation with RadCalc is an alternative to established measurement-based phantom QA. Different tools catch different errors; therefore, a combination of approaches should be preferred.

Sensitivity and specificity of Varian Halcyon's portal dosimetry for plan-specific pre-treatment QA.

PURPOSE: Developed as a plan-specific pre-treatment QA tool, Varian portal dosimetry promises a fast, high-resolution, and integrated QA solution. In this study, the agreement between predicted fluence and measured cumulative portal dose was determined for the first 140 patient plans at our Halcyon linear accelerator. Furthermore, the capability of portal dosimetry to detect incorrect plan delivery was compared to that of a common QA phantom. Finally, tolerance criteria for verification of VMAT plan delivery with Varian portal dosimetry were derived. METHODS: All patient plans and the corresponding verification plans were generated within the Eclipse treatment planning system. Four representative plans of different treatment sites (prostate, prostate with lymphatic drainage, rectum, and head & neck) were intentionally altered to model incorrect plan delivery. Investigated errors included both systematic and random errors. Gamma analysis was conducted on both portal dose (criteria γ2%/2 mm , γ2%/1 mm , and γ1%/1 mm ) and ArcCHECK measurements (criteria γ3%/3 mm , γ3%/2 mm , and γ2%/2 mm ) with a 10% low-dose threshold. Performance assessment of various acceptance criteria for plan-specific treatment QA utilized receiver operating characteristic (ROC) analysis. RESULTS: Predicted and acquired portal dosimetry fluences demonstrated a high agreement evident by average gamma passing rates for the clinical patient plans of 99.90%, 96.64%, and 91.87% for γ2%/2 mm , γ2%/1 mm , and γ1%/1 mm , respectively. The ROC analysis demonstrated a very high capability of detecting erroneous plan delivery for portal dosimetry (area under curve (AUC) > 0.98) and in this regard outperforms QA with the ArcCHECK phantom (AUC ≈ 0.82). With the suggested optimum decision thresholds excellent sensitivity and specificity is simultaneously possible. CONCLUSIONS: Owing to the high achievable spatial resolution, portal dosimetry at the Halcyon can reliably be deployed as plan-specific pre-treatment QA tool to screen for errors. It is recommended to support the fluence integrated portal dosimetry QA by independent phantom-based measurements of a random sample survey of treatment plans.

The Average Reward Rate Modulates Behavioral and Neural Indices of Effortful Control Allocation.

People tend to avoid exerting cognitive effort, and findings from recent behavioral studies suggest that effort allocation is in part determined by the opportunity cost of slothful responding-operationalized as the average reward rate per unit time. When the average rate of reward is high, individuals make more errors in cognitive control tasks, presumably owing to a withdrawal of costly cognitive processing. An open question remains whether the presumed modulations of cognitively effortful control processes are observable at the neural level. Here, we measured EEG while participants completed the Simon task, a well-known response conflict task, while the experienced average reward rate fluctuated across trials. We examined neural activity associated with the opportunity cost of time by applying generalized eigendecomposition, a hypothesis-driven source separation technique, to identify a midfrontal component associated with the average reward rate. Fluctuations in average reward rate modulated not only component amplitude but also, most importantly, component theta power (4-8 Hz). Higher average reward rate was associated with reduced theta power, suggesting that the opportunity of time modulates effort allocation. These neural results provide evidence for the idea that people strategically modulate the amount of cognitive effort they exert based on the opportunity cost of time.

Dopaminergic medication increases motivation to exert cognitive control by reducing subjective effort costs in Parkinson's patients.

Engaging in demanding mental activities requires the allocation of cognitive control, which can be effortful and aversive. Individuals thus tend to avoid exerting cognitive effort if less demanding behavioral options are available. Recent accounts propose a key role for dopamine in motivating behavior by increasing the sensitivity to rewards associated with effort exertion. Whether dopamine additionally plays a specific role in modulating the sensitivity to the costs of cognitive effort, even in the absence of any incentives, is much less clear. To address this question, we assessed cognitive effort avoidance in patients (n = 38) with Parkinson's disease, a condition characterized by loss of midbrain dopaminergic neurons, both ON and OFF dopaminergic medication and compared them to healthy controls (n = 24). Effort avoidance was assessed using the Demand Selection Task (DST), in which participants could freely choose between performing a high-demand or a low-demand version of a task-switching paradigm. Critically, participants were not offered any incentives to choose the more effortful option, nor for good performance. While healthy controls and patients OFF their dopaminergic medications consistently preferred the low-demand option, effort avoidance in patients ON dopaminergic medications was reduced compared to patients OFF, a difference which seems to lessen over trials. These differences in preference could not be explained by altered task-switching performance. Although patients ON were less accurate at detecting the different effort levels, as measured during instructed forced-choice blocks, their detection ability was not associated with effort avoidance, unlike in the healthy controls and the patients OFF. Our findings provide evidence that dopamine replacement in Parkinson's patients increases the willingness to engage in cognitively demanding behavior, and that this cannot be explained by possible effects of dopamine replacement on performance nor on the ability to detect effort demands. These results suggest that dopamine plays a role in reducing the sensitivity to effort costs that is independent of its role in enhancing the sensitivity to the benefits of effort exertion.

Implementing corrections of isocentric shifts for the stereotactic irradiation of cerebral targets: Clinical validation.

PURPOSE: Any Linac will show geometric imprecisions, including non-ideal alignment of the gantry, collimator and couch axes, and gantry sag or wobble. Their angular dependence can be quantified and resulting changes of the dose distribution predicted (Wack, JACMP 20(5), 2020). We analyzed whether it is feasible to correct geometric shifts during treatment planning. The successful implementation of such a correction procedure was verified by measurements of different stereotactic treatment plans. METHODS: Isocentric shifts were quantified for two Elekta Synergy Agility Linacs using the QualiForMed ISO-CBCT+ module, yielding the shift between kV and MV isocenters, the gantry flex and wobble as well as the positions of couch and collimator rotation axes. Next, the position of each field's isocenter in the Pinnacle treatment planning system was adjusted accordingly using a script. Fifteen stereotactic treatment plans of cerebral metastases (0.34 to 26.53 cm3 ) comprising 9-11 beams were investigated; 54 gantry and couch combinations in total. Unmodified plans and corrected plans were measured using the Sun Nuclear SRS-MapCHECK with the Stereophan phantom and evaluated using gamma analysis. RESULTS: Geometric imprecisions, such as shifts of up to 0.8 mm between kV and MV isocenter, a couch rotation axis 0.9 mm off the kV isocente,r and gantry flex with an amplitude of 1.1 mm, were found. For eight, mostly small PTVs D98 values declined more than 5% by simulating these shifts. The average gamma (2%/2 mm, absolute, global, 20% threshold) was reduced from 0.53 to 0.31 (0.32 to 0.30) for Linac 1 (Linac 2) when including the isocentric corrections. Thus, Linac 1 reached the accuracy level of Linac 2 after correction. CONCLUSION: Correcting for Linac geometric deviations during the planning process is feasible and was dosimetrically validated. The dosimetric impact of the geometric imperfections can vary between Linacs and should be assessed and corrected where necessary.

Task-evoked pupillary responses track effort exertion: Evidence from task-switching.

A spate of research has examined how individuals regulate effortful processing in service of goal-directed behaviors. One key challenge in developing an account of this regulation is quantifying the momentary amount of cognitive effort exerted by an individual in service of their goals. A growing body of literature has suggested using task-evoked pupil dilations as a potential psychophysiological index of cognitive effort; however, it remains unclear whether pupil diameter indexes effort exertion or merely reflects task load, as both are tightly intertwined. Here, we attempt to disentangle these disparate accounts of pupil diameter by leveraging individual differences in executive function (as measured by Stroop interference) and a motivational manipulation (i.e., monetary incentives) while participants complete a task-switching paradigm. In line with both the effort and demand accounts, we observed larger task-evoked pupillary responses (TEPRs) for trials in which there was a task switch versus a task repetition. Additionally, we found that larger phasic pupillary responses at baseline (without reward incentives) predicted smaller switch costs. Mirroring this pattern, individual differences in reward-induced switch cost reductions were predicted by reward-induced increases in phasic pupil diameter. Finally, we observed that the interrelationship between effort and pupil diameter at baseline was modulated by individual differences in Stroop interference costs. Together, these findings provide support for an effort account of TEPRs, and suggest that pupillometry is a viable index of cognitive effort.

Constraints on Ultralight Scalar Bosons within Black Hole Spin Measurements from the LIGO-Virgo GWTC-2.

Clouds of ultralight bosons-such as axions-can form around a rapidly spinning black hole, if the black hole radius is comparable to the bosons' wavelength. The cloud rapidly extracts angular momentum from the black hole, and reduces it to a characteristic value that depends on the boson's mass as well as on the black hole mass and spin. Therefore, a measurement of a black hole mass and spin can be used to reveal or exclude the existence of such bosons. Using the black holes released by LIGO and Virgo in their GWTC-2, we perform a simultaneous measurement of the black hole spin distribution at formation and the mass of the scalar boson. We find that the data strongly disfavor the existence of scalar bosons in the mass range between 1.3×10^{-13} and 2.7×10^{-13} eV. Our mass constraint is valid for bosons with negligible self-interaction, that is, with a decay constant f_{a}≳10^{14} GeV. The statistical evidence is mostly driven by the two binary black holes systems GW190412 and GW190517, which host rapidly spinning black holes. The region where bosons are excluded narrows down if these two systems merged shortly (∼10^{5} yr) after the black holes formed.

Acute Psychosocial Stress Increases Cognitive-Effort Avoidance.

Adverse effects following acute stress are traditionally thought to reflect functional impairments of central executive-dependent cognitive-control processes. However, recent evidence demonstrates that cognitive-control application is perceived as effortful and aversive, indicating that stress-related decrements in cognitive performance could denote decreased motivation to expend effort instead. To investigate this hypothesis, we tested 40 young, healthy individuals (20 female, 20 male) under both stress and control conditions in a 2-day study that had a within-subjects design. Cognitive-effort avoidance was assessed using the demand-selection task, in which participants chose between performing low-demand and high-demand variants of a task-switching paradigm. We found that acute stress indeed increased participants' preference for less demanding behavior, whereas task-switching performance remained intact. Additional Bayesian and multiverse analyses confirmed the robustness of this effect. Our findings provide novel insights into how stressful experiences shape behavior by modulating our motivation to employ cognitive control.

Imaging predictors of response to cardiac resynchronization therapy: left ventricular work asymmetry by echocardiography and septal viability by cardiac magnetic resonance.

AIMS: Left ventricular (LV) failure in left bundle branch block is caused by loss of septal function and compensatory hyperfunction of the LV lateral wall (LW) which stimulates adverse remodelling. This study investigates if septal and LW function measured as myocardial work, alone and combined with assessment of septal viability, identifies responders to cardiac resynchronization therapy (CRT). METHODS AND RESULTS: In a prospective multicentre study of 200 CRT recipients, myocardial work was measured by pressure-strain analysis and viability by cardiac magnetic resonance (CMR) imaging (n = 125). CRT response was defined as ≥15% reduction in LV end-systolic volume after 6 months. Before CRT, septal work was markedly lower than LW work (P < 0.0001), and the difference was largest in CRT responders (P < 0.001). Work difference between septum and LW predicted CRT response with area under the curve (AUC) 0.77 (95% CI: 0.70-0.84) and was feasible in 98% of patients. In patients undergoing CMR, combining work difference and septal viability significantly increased AUC to 0.88 (95% CI: 0.81-0.95). This was superior to the predictive power of QRS morphology, QRS duration and the echocardiographic parameters septal flash, apical rocking, and systolic stretch index. Accuracy was similar for the subgroup of patients with QRS 120-150 ms as for the entire study group. Both work difference alone and work difference combined with septal viability predicted long-term survival without heart transplantation with hazard ratio 0.36 (95% CI: 0.18-0.74) and 0.21 (95% CI: 0.072-0.61), respectively. CONCLUSION: Assessment of myocardial work and septal viability identified CRT responders with high accuracy.

Dose rate correction for a silicon diode detector array.

PURPOSE: A signal dependence on dose rate was reported for the ArcCHECK array due to recombination processes within the diodes. The purpose of our work was to quantify the necessary correction and apply them to quality assurance measurements. METHODS: Static 10 × 10 cm2 6-MV fields delivered by a linear accelerator were applied to the detector array while decreasing the average dose rate, that is, the pulse frequency, from 500 to 30 MU/min. An ion chamber was placed inside the ArcCHECK cavity as a reference. Furthermore, the instantaneous dose rate dependence (DRD) was studied. The position of the detector was adjusted to change the dose-per-pulse, varying the distance between the focus and the diode closest to the focus between 69.6 and 359.6 cm. Reference measurements were performed with an ion chamber placed inside a PMMA slab phantom at the same source-to-detector distances ( S D D s ) . Exponential saturation functions were fitted to the data, with different parameters to account for two generations of ArcCHECK detectors (types 2 and 3) and both DRDs. Corrections were applied to 12 volumetric modulated arc therapy plans. RESULTS: The sensitivity decreased by up to 2.8% with a decrease in average dose rate and by 9% with a decrease in instantaneous dose rate. Correcting the average DRD, the mean gamma pass rates (2%/2-mm criterion) of the treatment plans were improved by 5 percentage points (PP) for diode type 3 and 0.4 PP for type 2. Correcting the instantaneous DRD, the improvement was 8.4 PP for type 3 and 0.9 PP for type 2. CONCLUSIONS: The instantaneous DRD was identified as the prevailing effect on the diode sensitivity. We developed and validated a method to correct this behavior. The number of falsely not passed treatment plans could be considerably reduced.

A functional genetic screen reveals sequence preferences within a key tertiary interaction in cobalamin riboswitches required for ligand selectivity.

Riboswitches are structured mRNA sequences that regulate gene expression by directly binding intracellular metabolites. Generating the appropriate regulatory response requires the RNA rapidly and stably acquire higher-order structure to form the binding pocket, bind the appropriate effector molecule and undergo a structural transition to inform the expression machinery. These requirements place riboswitches under strong kinetic constraints, likely restricting the sequence space accessible by recurrent structural modules such as the kink turn and the T-loop. Class-II cobalamin riboswitches contain two T-loop modules: one directing global folding of the RNA and another buttressing the ligand binding pocket. While the T-loop module directing folding is highly conserved, the T-loop associated with binding is substantially less so, with no clear consensus sequence. To further understand the functional role of the binding-associated module, a functional genetic screen of a library of riboswitches with the T-loop and its interacting nucleotides was used to build an experimental phylogeny comprised of sequences that possess a wide range of cobalamin-dependent regulatory activity. Our results reveal conservation patterns of the T-loop and its interaction with the binding core that allow for rapid tertiary structure formation and demonstrate its importance for generating strong ligand-dependent repression of mRNA expression.

Stress promotes generalization of older but not recent threat memories.

Stress broadly affects the ability to regulate emotions and may contribute to generalization of threat-related behaviors to harmless stimuli. Behavioral generalization also tends to increase over time as memory precision for recent events gives way to more gist-like representations. Thus, acute stress coupled with a delay in time from a negative experience may be a strong predictor of the transition from normal to generalized fear expression. Here, we investigated the effect of a single-episode acute stressor on generalization of aversive learning when stress is administered either immediately after an aversive learning event or following a delay. In a between-subjects design, healthy adult volunteers underwent threat (fear) conditioning using a tone-conditioned stimulus paired with an electric shock to the wrist and another tone not paired with shock. Behavioral generalization was tested to a range of novel tones either on the same day (experiment 1) or 24 h later (experiment 2) and was preceded by either an acute stress induction or a control task. Anticipatory sympathetic arousal [i.e., skin conductance responses (SCRs)] and explicit measures of shock expectancy served as dependent measures. Stress administered shortly after threat conditioning did not affect behavioral generalization. In contrast, stress administered following a delay led to heightened arousal and increased generalization of SCRs and explicit measures of shock expectancy. These findings show that acute stress increases generalization of older but not recent threat memories and have clinical relevance to understanding overgeneralization characteristics of anxiety and stress-related disorders.