bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pupil-linked Arousal Signals in the Midbrain Superior Colliculus
Authors: Wang Chin-An , White Brian , Munoz Douglas P. 
Published: May 2022

Abstract
The orienting response evoked by the appearance of a salient stimulus is modulated by arousal; however, neural underpinnings for the interplay between orienting and arousal are not well understood. The superior colliculus (SC), causally involved in multiple components of the orienting response including gaze and attention shifts, receives not only multisensory and cognitive inputs but also arousal-regulated inputs from various cortical and subcortical structures. To investigate the impact of moment-by-moment fluctuations in arousal on orienting saccade responses, we used microstimulation of the monkey SC to trigger saccade responses, and we used pupil size and velocity to index the level of arousal at stimulation onset because these measures correlate with changes in brain states and locus coeruleus activity. Saccades induced by SC microstimulation correlated with prestimulation pupil velocity, with higher pupil velocities on trials without evoked saccades than with evoked saccades. In contrast, prestimulation absolute pupil size did not correlate with saccade behavior. Moreover, pupil velocity correlated with evoked saccade latency and metrics. Together, our results demonstrated that small fluctuations in arousal, indexed by pupil velocity, can modulate the saccade response evoked by SC microstimulation in awake behaving monkeys.
Brain Functional Networks Involved in Different Premise Order in Conditional Reasoning: A Dynamic Causal Model Study
Authors: Wang Li , Zhang Meng , Zou Feng , Wu Xin , Wang Yufeng , Chen Jun 
Published: May 2022

Abstract
In conditional reasoning, the reasoner must draw a conclusion based on a conditional or “If…, then…” proposition. Previous studies have reported that reversing the premises can effectively promote modus tollens reasoning (a form of conditional reasoning), but subsequent experimental studies have found no such effect. Therefore, to further examine this issue and reveal the cognitive mechanism of conditional reasoning, we asked two groups of healthy volunteers (traditional and inverted premise order groups) to evaluate a set of visually presented conditional tasks (modus ponens/modus tollens) under fMRI. The results indicated that the inverted condition activated more brain regions associated with working memory, including the angular gyrus (BA 39), precuneus (BA 7), inferior parietal lobe, and middle frontal gyrus. The resulting common activation map was used to define the ROIs and perform dynamic causal modeling for the effective connectivity analysis, containing the medial frontal gyrus, hippocampus, cerebellum, and middle occipital gyrus in the right hemisphere and the inferior occipital gyrus in the left hemisphere. The results of intrinsic connections in the optimal model selected by Bayesian model selection showed that the connection strength was stronger in the inverted group rather than in the traditional group, which may indicate that the reversal of the premise order promotes connectivity between brain regions. Despite the lack of a premise order effect, we did discover a neuronal separation between the inverted and traditional conditions, which lends support to the mental model theory to some extent.
The Role of Action–Effect Contingency on Sensory Attenuation in the Absence of Movement
Authors: Han Nathan , Jack Bradley N. , Hughes Gethin , Whitford Thomas J. 
Published: May 2022

Abstract
Stimuli that have been generated by a person's own willed motor actions generally elicit a suppressed electrophysiological, as well as phenomenological, response compared with identical stimuli that have been externally generated. This well-studied phenomenon, known as sensory attenuation, has mostly been studied by comparing ERPs evoked by self-initiated and externally generated sounds. However, most studies have assumed a uniform action–effect contingency, in which a motor action leads to a resulting sensation 100% of the time. In this study, we investigated the effect of manipulating the probability of action–effect contingencies on the sensory attenuation effect. In Experiment 1, participants watched a moving, marked tickertape while EEG was recorded. In the full-contingency (FC) condition, participants chose whether to press a button by a certain mark on the tickertape. If a button press had not occurred by the mark, a sound would be played a second later 100% of the time. If the button was pressed before the mark, the sound was not played. In the no-contingency (NC) condition, participants observed the same tickertape; in contrast, however, if participants did not press the button by the mark, a sound would occur only 50% of the time (NC-inaction). Furthermore, in the NC condition, if a participant pressed the button before the mark, a sound would also play 50% of the time (NC-action). In Experiment 2, the design was identical, except that a willed action (as opposed to a willed inaction) triggered the sound in the FC condition. The results were consistent across the two experiments: Although there were no differences in N1 amplitude between conditions, the amplitude of the Tb and P2 components were smaller in the FC condition compared with the NC-inaction condition, and the amplitude of the P2 component was also smaller in the FC condition compared with the NC-action condition. The results suggest that the effect of contingency on electrophysiological indices of sensory attenuation may be indexed primarily by the Tb and P2 components, rather than the N1 component which is most commonly studied.
Hierarchical Reinforcement Learning, Sequential Behavior, and the Dorsal Frontostriatal System
Authors: Janssen Miriam , LeWarne Christopher , Burk Diana , Averbeck Bruno B. 
Published: May 2022

Abstract
To effectively behave within ever-changing environments, biological agents must learn and act at varying hierarchical levels such that a complex task may be broken down into more tractable subtasks. Hierarchical reinforcement learning (HRL) is a computational framework that provides an understanding of this process by combining sequential actions into one temporally extended unit called an option. However, there are still open questions within the HRL framework, including how options are formed and how HRL mechanisms might be realized within the brain. In this review, we propose that the existing human motor sequence literature can aid in understanding both of these questions. We give specific emphasis to visuomotor sequence learning tasks such as the discrete sequence production task and the M × N (M steps × N sets) task to understand how hierarchical learning and behavior manifest across sequential action tasks as well as how the dorsal cortical–subcortical circuitry could support this kind of behavior. This review highlights how motor chunks within a motor sequence can function as HRL options. Furthermore, we aim to merge findings from motor sequence literature with reinforcement learning perspectives to inform experimental design in each respective subfield.
Social Prevalence Is Rationally Integrated in Belief Updating
Authors: Orticio Evan , Martí Louis , Kidd Celeste 
Published: May 2022

Abstract
People rely on social information to inform their beliefs. We ask whether and to what degree the perceived prevalence of a belief influences belief adoption. We present the results of two experiments that show how increases in a person’s estimated prevalence of a belief led to increased endorsement of said belief. Belief endorsement rose when impressions of the belief’s prevalence were increased and when initial beliefs were uncertain, as predicted by a Bayesian cue integration framework. Thus, people weigh social information rationally. An implication of these results is that social engagement metrics that prompt inflated prevalence estimates in users risk increasing the believability and adoption of viral misinformation posts.
Sensitivities of Maritime Tropical Trimodal Convection to Aerosols and Boundary Layer Static Stability
Authors: Sokolowsky G. Alexander , Freeman Sean W. , van den Heever Susan C. 
Published: May 2022

Abstract
A trimodal convective cloud distribution is commonly observed within the tropics due to the tropical-mean thermodynamic environment. The goal of this research has been to examine the integrated impacts of thermodynamic and aerosol properties on both the convective environment and the properties of the cloud modes themselves. This has been achieved by using LES experiments in which various thermodynamic and aerosol environments were independently and simultaneously perturbed. The key conclusions from this study are 1) large amounts of aerosol loading and low-level static stability suppress the bulk environment and the intensity and coverage of convective clouds; 2) cloud and environmental responses to aerosol loading tend to be stronger than those from static stability; 3) the effects of aerosol and stability perturbations modulate each other substantially; 4) the deepest convection and highest dynamical intensity occur at moderate aerosol loading, rather than at low or high loading; and 5) most of the strongest feedbacks due to aerosol and stability perturbations are seen in the boundary layer, though some are stronger above the freezing level. These results underscore the importance of considering the thermodynamic environment’s impact on aerosol-induced convective invigoration while highlighting the dominance of aerosol impacts on the trimodal distribution and revealing synergies between thermodynamics and aerosols.
Drivers of Biases in the CMIP6 Extratropical Storm Tracks. Part I: Northern Hemisphere
Authors: Priestley Matthew D. K. , Ackerley Duncan , Catto Jennifer L. , Hodges Kevin I. 
Published: May 2022

Abstract
The ability of climate models to represent extratropical storm tracks is vital to provide useful projections. In previous work, the representation of the extratropical storm tracks in the Northern Hemisphere was found to have improved from phase 5 to phase 6 of the Coupled Model Intercomparison Project (CMIP). Here we investigate the remaining and persistent biases in models from phase 6 of CMIP, by contrasting the atmosphere-only simulations (AMIP6) with the historical coupled simulations (CMIP6). The comparison of AMIP6 and CMIP6 simulations reveals that biases in sea surface temperatures (SSTs) in the coupled simulations across the North Pacific Ocean in winter modify the atmospheric temperature gradient, which is associated with an equatorward bias of the storm track. In the North Atlantic Ocean, cyclones do not propagate poleward enough in coupled simulations, which is partly driven by cold SSTs to the south of Greenland, decreasing the latent heat fluxes. In summer, excessive heating across central Asia and the Tibetan Plateau reduces the local baroclinicity, causing fewer cyclones to form and propagate from eastern China into the North Pacific in both the coupled and atmosphere-only simulations. Several of the biases described in the coupled models are reduced considerably in the atmosphere-only models when the SSTs are prescribed. For example, the equatorward bias of the North Pacific storm track is reduced significantly. However, other biases are apparent in both CMIP6 and AMIP6 (e.g., persistent reduction in track density and cyclogenesis over eastern Asia in summer), which are associated with other processes (e.g., land surface temperatures).
Rivaroxaban vs placebo for extended antithrombotic prophylaxis after laparoscopic surgery for colorectal cancer
Authors: Becattini Cecilia , Pace Ugo , Pirozzi Felice , Donini Annibale , Avruscio Giampiero , Rondelli Fabio , Boncompagni Michela , Chiari Damiano , De Prizio Marco , Visonà Adriana , De Luca Raffaele , Guerra Francesco , Muratore Andrea , Portale Giuseppe , Milone Marco , Castagnoli Giampaolo , Righini Marc , Martellucci Jacopo , Persiani Roberto , Frasson Stefania , Dentali Francesco , Delrio Paolo , Campanini Mauro , Gussoni Gualberto , Vedovati Maria Cristina , Agnelli Giancarlo 
Published: May 2022

Abstract
The clinical benefit of extended prophylaxis for venous thromboembolism (VTE) after laparoscopic surgery for cancer is unclear. The efficacy and safety of direct oral anticoagulants for this indication are unexplored. PROphylaxis of venous thromboembolism after LAParoscopic Surgery for colorectal cancer Study II (PROLAPS II) was a randomized, double-blind, placebo-controlled, investigator-initiated, superiority study aimed at assessing the efficacy and safety of extended prophylaxis with rivaroxaban after laparoscopic surgery for colorectal cancer. Consecutive patients who had laparoscopic surgery for colorectal cancer were randomized to receive rivaroxaban (10 mg once daily) or a placebo to be started at 7 ± 2 days after surgery and given for the subsequent 3 weeks. All patients received antithrombotic prophylaxis with low-molecular-weight heparin from surgery to randomization. The primary study outcome was the composite of symptomatic objectively confirmed VTE, asymptomatic ultrasonography-detected deep vein thrombosis (DVT), or VTE-related death at 28 ± 2 days after surgery. The primary safety outcome was major bleeding. Patient recruitment was prematurely closed due to study drug expiry after the inclusion of 582 of the 646 planned patients. A primary study outcome event occurred in 11 of 282 patients in the placebo group compared with 3 of 287 in the rivaroxaban group (3.9 vs 1.0%; odds ratio, 0.26; 95% confidence interval [CI], 0.07-0.94; log-rank P = .032). Major bleeding occurred in none of the patients in the placebo group and 2 patients in the rivaroxaban group (incidence rate 0.7%; 95% CI, 0-1.0). Oral rivaroxaban was more effective than placebo for extended prevention of VTE after laparoscopic surgery for colorectal cancer without an increase in major bleeding. This trial was registered at www.clinicaltrials.gov as #NCT03055026.
Depletion of CLL cells by venetoclax treatment reverses oxidative stress and impaired glycolysis in CD4 T cells
Authors: van Bruggen J. A. C. , van der Windt G. J. W. , Hoogendoorn M. , Dubois J. , Kater Arnon P. , Peters F. S. 
Published: May 2022

AbstractAcquired T-cell dysfunction is characteristic of chronic lymphocytic leukemia (CLL) and is associated with reduced efficacy of T cell–based therapies. A recently described feature of dysfunctional CLL-derived CD8 T cells is reduced metabolic plasticity. To what extend CD4 T cells are affected and whether CD4 T-cell metabolism and function can be restored upon clinical depletion of CLL cells are currently unknown. We address these unresolved issues by comprehensive phenotypic, metabolic, transcriptomic, and functional analysis of CD4 T cells of untreated patients with CLL and by analysis of the effects of venetoclax plus obinutuzumab on the CD4 population. Resting CD4 T cells derived from patients with CLL expressed lower levels of GLUT-1 and displayed deteriorated oxidative phosphorylation (OXPHOS) and overall reduced mitochondrial fitness. Upon T-cell stimulation, CLL T cells were unable to initiate glycolysis. Transcriptome analysis revealed that depletion of CLL cells in vitro resulted in upregulation of OXPHOS and glycolysis pathways and restored T-cell function in vitro. Analysis of CD4 T cells from patients with CLL before and after venetoclax plus obinutuzumab treatment, which led to effective clearance of CLL in blood and bone marrow, revealed recovery of T-cell activation and restoration of the switch to glycolysis, as well as improved T-cell proliferation. Collectively, these data demonstrate that CLL cells impose metabolic restrictions on CD4 T cells, which leads to reduced CD4 T-cell functionality. This trial was registered in the Netherlands Trial Registry as #NTR6043.
PGD: a machine learning-based photosynthetic-related gene detection approach
Authors: Wang Yunchuan , Dai Xiuru , Fu Daohong , Li Pinghua , Du Baijuan 
Published: May 2022

Abstract
Background
The primary determinant of crop yield is photosynthetic capacity, which is under the control of photosynthesis-related genes. Therefore, the mining of genes involved in photosynthesis is important for the study of photosynthesis. MapMan Mercator 4 is a powerful annotation tool for assigning genes into proper functional categories; however, in maize, the functions of approximately 22.15% (9520) of genes remain unclear and are labeled “not assigned”, which may include photosynthesis-related genes that have not yet been identified. The fast-increasing usage of the machine learning approach in solving biological problems provides us with a new chance to identify novel photosynthetic genes from functional “not assigned” genes in maize.

Results
In this study, we proved the ensemble learning model using a voting eliminates the preferences of single machine learning models. Based on this evaluation, we implemented an ensemble based ML(Machine Learning) methods using a majority voting scheme and observed that including RNA-seq data from multiple photosynthetic mutants rather than only a single mutant could increase prediction accuracy. And we call this approach “A Machine Learning-based Photosynthetic-related Gene Detection approach (PGD)”. Finally, we predicted 716 photosynthesis-related genes from the “not assigned” category of maize MapMan annotation. The protein localization prediction (TargetP) and expression trends of these genes from maize leaf sections indicated that the prediction was reliable and robust. And we put this approach online base on google colab.

Conclusions
This study reveals a new approach for mining novel genes related to a specific functional category and provides candidate genes for researchers to experimentally define their biological functions.
DeSP: a systematic DNA storage error simulation pipeline
Authors: Yuan Lekang , Xie Zhen , Wang Ye , Wang Xiaowo 
Published: May 2022

Abstract
Background
Using DNA as a storage medium is appealing due to the information density and longevity of DNA, especially in the era of data explosion. A significant challenge in the DNA data storage area is to deal with the noises introduced in the channel and control the trade-off between the redundancy of error correction codes and the information storage density. As running DNA data storage experiments in vitro is still expensive and time-consuming, a simulation model is needed to systematically optimize the redundancy to combat the channel's particular noise structure.

Results
Here, we present DeSP, a systematic DNA storage error Simulation Pipeline, which simulates the errors generated from all DNA storage stages and systematically guides the optimization of encoding redundancy. It covers both the sequence lost and the within-sequence errors in the particular context of the data storage channel. With this model, we explained how errors are generated and passed through different stages to form final sequencing results, analyzed the influence of error rate and sampling depth to final error rates, and demonstrated how to systemically optimize redundancy design in silico with the simulation model. These error simulation results are consistent with the in vitro experiments.

Conclusions
DeSP implemented in Python is freely available on Github (https://github.com/WangLabTHU/DeSP). It is a flexible framework for systematic error simulation in DNA storage and can be adapted to a wide range of experiment pipelines.
Deciphering resistance to Zymoseptoria tritici in the Tunisian durum wheat landrace accession ‘Agili39’
Authors: Ferjaoui Sahbi , Aouini Lamia , Slimane Rim B. , Ammar Karim , Dreisigacker Suzanne , Schouten Henk J. , Sapkota Suraj , Bahri Bochra A. , Ben M’Barek Sarrah , Visser Richard G. F. , Kema Gert H. J. , Hamza Sonia 
Published: May 2022

Abstract
Background
Septoria tritici blotch (STB), caused by Zymoseptoria tritici (Z. tritici), is an important biotic threat to durum wheat in the entire Mediterranean Basin. Although most durum wheat cultivars are susceptible to Z. tritici, research in STB resistance in durum wheat has been limited.

Results
In our study, we have identified resistance to a wide array of Z. tritici isolates in the Tunisian durum wheat landrace accession ‘Agili39’. Subsequently, a recombinant inbred population was developed and tested under greenhouse conditions at the seedling stage with eight Z. tritici isolates and for five years under field conditions with three Z. tritici isolates. Mapping of quantitative trait loci (QTL) resulted in the identification of two major QTL on chromosome 2B designated as Qstb2B_1 and Qstb2B_2. The Qstb2B_1 QTL was mapped at the seedling and the adult plant stage (highest LOD 33.9, explained variance 61.6%), conferring an effective resistance against five Z. tritici isolates. The Qstb2B_2 conferred adult plant resistance (highest LOD 32.9, explained variance 42%) and has been effective at the field trials against two Z. tritici isolates. The physical positions of the flanking markers linked to Qstb2B_1 and Qstb2B_2 indicate that these two QTL are 5 Mb apart. In addition, we identified two minor QTL on chromosomes 1A (Qstb1A) and chromosome 7A (Qstb7A) (highest LODs 4.6 and 4.0, and explained variances of 16% and 9%, respectively) that were specific to three and one Z. tritici isolates, respectively. All identified QTL were derived from the landrace accession Agili39 that represents a valuable source for STB resistance in durum wheat.

Conclusion
This study demonstrates that Z. tritici resistance in the ‘Agili39’ landrace accession is controlled by two minor and two major QTL acting in an additive mode. We also provide evidence that the broad efficacy of the resistance to STB in ‘Agili 39’ is due to a natural pyramiding of these QTL. A sustainable use of this Z. tritici resistance source and a positive selection of the linked markers to the identified QTL will greatly support effective breeding for Z. tritici resistance in durum wheat.