bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methods in Cognitive Pupillometry: Design, Preprocessing, and Statistical Analysis
Authors: Mathôt Sebastiaan , Vilotijević Ana 
Published: February 2022

AbstractCognitive pupillometry is the measurement of pupil size to investigate cognitive processes such as attention, mental effort, working memory, and many others. Currently, there is no commonly agreed-upon methodology for conducting cognitive-pupillometry experiments, and approaches vary widely between research groups and even between different experiments from the same group. This lack of consensus makes it difficult to know which factors to consider when conducting a cognitive-pupillometry experiment. Here we provide a comprehensive, hands-on guide to methods in cognitive pupillometry, with a focus on trial-based experiments in which the measure of interest is the task-evoked pupil response to a stimulus. We cover all methodological aspects of cognitive pupillometry: experimental design; preprocessing of pupil-size data; and statistical techniques to deal with multiple comparisons when testing pupil-size data. In addition, we provide code and toolboxes (in Python) for preprocessing and statistical analysis, and we illustrate all aspects of the proposed workflow through an example experiment and example scripts.
The estrous cycle modulates early-life adversity effects on mouse avoidance behavior through progesterone signaling
Authors: Laham Blake J. , Murthy Sahana S. , Hanani Monica , Clappier Mona , Boyer Sydney , Vasquez Betsy , Gould Elizabeth 
Published: February 2022

AbstractEarly-life adversity (ELA) predisposes individuals to develop neuropsychiatric conditions, which are more prevalent in women than men. Efforts to model this sex difference in rodents have produced mixed results, with some studies paradoxically showing stronger phenotypes in males than females. Since changes in reproductive hormone levels can increase the likelihood of anxiety disorders in women, we examined the effects of ELA on adult female mice across the estrous cycle. We found that during diestrus, when the ratio of progesterone to estrogen is relatively high, ELA mice exhibit increased avoidance behavior, altered activity levels in specific contexts, and increased theta oscillation power in the ventral hippocampus. Ovariectomy, which eliminates circulating estrogen but not progesterone, unexpectedly preserved some of the effects present in diestrus ELA mice. Progesterone receptor antagonism in diestrus normalized avoidance behavior in ELA mice, while treatment with a negative allosteric modulator of the progesterone metabolite allopregnanolone promoted avoidance behavior in control mice. These results suggest that altered progesterone and allopregnanolone signaling during diestrus increases avoidance behavior in ELA mice
Age-Related Central Gain with Degraded Neural Synchrony in the Auditory Brainstem of Mice and Humans
Authors: Rumschlag Jeffrey A. , McClaskey Carolyn M. , Dias James W. , Kerouac Lilyana B. , Noble Kenyaria V. , Panganiban Clarisse , Lang Hainan , Harris Kelly C. 
Published: February 2022

AbstractAging is associated with auditory nerve (AN) functional deficits and decreased inhibition in the central auditory system, amplifying central responses in a process known as central gain. Although central gain enhances response amplitudes, central gain may not restore disrupted response timing. In this translational study, we measured responses from the AN and auditory midbrain in younger and older mice and humans. We hypothesized that older mice and humans exhibit central gain without an improvement in inter-trial synchrony in the midbrain. Our data demonstrated greater age-related deficits in AN response amplitudes than auditory midbrain response amplitudes, as shown by significant interactions between neural generator and age group, indicating central gain in auditory midbrain. However, synchrony decreases with age in both the AN and midbrain responses. These results reveal age-related central gain without concomitant improvements in synchrony, consistent with those predictions based on decreases in inhibition. Persistent decreases in synchrony may contribute to auditory processing deficits in older mice and humans.
Olfactory responses ofDrosophilaare encoded in the organization of projection neurons
Authors: Choi Kiri , Kim Won Kyu , Hyeon Changbong 
Published: February 2022

AbstractThe projection neurons (PNs), reconstructed from electron microscope (EM) images of theDrosophilaolfactory system, offer a detailed view of neuronal anatomy, providing glimpses into information flow in the brain. About 150 uPNs constituting 58 glomeruli in the antennal lobe (AL) are bundled together in the axonal extension, routing the olfactory signal received at AL to mushroom body (MB) calyx and lateral horn (LH). Here we quantify the neuronal organization by inter-PN distances and examine its relationship with the odor types sensed byDrosophila. The homotypic uPNs that constitute glomeruli are tightly bundled and stereotyped in position throughout the neuropils, even though the glomerular PN organization in AL is no longer sustained in the higher brain center. Instead, odor-type dependent clusters consisting of multiple homotypes innervate the MB calyx and LH. Pheromone-encoding and hygro/thermo-sensing homotypes are spatially segregated in MB calyx, whereas two distinct clusters of food-related homotypes are found in LH in addition to the segregation of pheromone-encoding and hygro/thermo-sensing homotypes. We find that there are statistically significant associations between the spatial organization among a group of homotypic uPNs and certain stereotyped olfactory responses. Additionally, the signals from some of the tightly bundled homotypes converge to a specific group of lateral horn neurons (LHNs), which indicates that homotype (or odor type) specific integration of signals occurs at the synaptic interface between PNs and LHNs. Our findings suggest that before neural computation in the inner brain, some of the olfactory information are already encoded in the spatial organization of uPNs, illuminating that a certain degree of labeled-line strategy is at work in theDrosophilaolfactory system.
KIAA1109 is required for survival and for normal development and function of the neuromuscular junction in mice
Authors: Liu Yun , Lin Weichun 
Published: February 2022

AbstractKIAA1109 (4932438A13Rik) is a novel gene linked to Alkuraya-Kucinska Syndrome, an autosomal recessive disorder with severe brain malformations and arthrogryposis in humans. The role of KIAA1109 in mammalian development and function remains poorly understood. Here, we characterize mutant mice deficient in Kiaa1109 (Kiaa1109−/−). We report that Kiaa1109−/− mice died during perinatal stages. These Kiaa1109−/− embryos exhibited impaired intramuscular nerve growth and reduced sizes of the neuromuscular junction (NMJ) compared with their littermate controls. Electrophysiological analysis further revealed defects in neuromuscular synaptic transmission in Kiaa1109−/− embryos. Notably, the frequency of spontaneous neurotransmitter release was markedly increased, whereas evoked neurotransmitter release and quantal content were reduced. Furthermore, neuromuscular synapses in Kiaa1109−/− embryos failed to respond to a repetitive, low frequency stimulation (10Hz). These results demonstrate that KIAA1109 is required for survival in mice and for proper development and function of the NMJ.Significance StatementThis is the first report characterizing the phenotype of mutant mice deficient in KIAA1109 (4932438A13Rik), a novel gene in mammals. We show that KIAA1109 is required for survival in mice and that KIAA1109 plays important roles in normal development and function of the NMJ in mice.
A Geometric View of Signal Sensitivity Metrics in multi-echo fMRI
Authors: Liu Thomas T. , Li Bochao , Fernandez Brice , Banerjee Suchandrima 
Published: February 2022

AbstractIn multi-echo fMRI (ME-fMRI), two metrics have been widely used to measure the performance of various acquisition and analysis approaches. These are temporal SNR (tSNR) and differential contrast-to-noise ratio (dCNR). A key step in ME-fMRI is the weighted combination of the data from multiple echoes, and prior work has examined the dependence of tSNR and dCNR on the choice of weights. However, most studies have focused on only one of these two metrics, and the relationship between the two metrics has not been examined. In this work, we present a geometric view that offers greater insight into the relation between the two metrics and their weight dependence. We identify three major regimes: (1) a tSNR robust regime in which tSNR is robust to the weight selection with most weight variants achieving close to optimal performance, whereas dCNR shows a pronounced dependence on the weights with most variants achieving suboptimal performance; (2) a dCNR robust regime in which dCNR is robust to the weight selection with most weight variants achieving close to optimal performance, while tSNR exhibits a strong dependence on the weights with most variants achieving significantly lower than optimal performance; and (3) a within-type robust regime in which both tSNR and dCNR achieve nearly optimal performance when the form of the weights are variants of their respective optimal weights and exhibit a moderate decrease in performance for other weight variants. Insight into the behavior observed in the different regimes is gained by considering spherical representations of the weight dependence of the components used to form each metric. For multi-echo acquisitions, dCNR is shown to be more directly related than tSNR to measures of CNR and signal-to-noise ratio (SNR) for both task-based and resting-state fMRI scans, respectively.
Single-deletion-mutant, third-generation rabies viral vectors allow nontoxic retrograde targeting of projection neurons with greatly increased efficiency
Authors: Jin Lei , Sullivan Heather A. , Zhu Mulangma , Lea Nicholas E. , Lavin Thomas K. , Fu Xin , Matsuyama Makoto , Hou YuanYuan , Feng Guoping , Wickersham Ian R. 
Published: February 2022

SUMMARYRabies viral vectors have become important components of the systems neuroscience toolkit, allowing both direct retrograde targeting of projection neurons and monosynaptic tracing of inputs to defined postsynaptic populations, but the rapid cytotoxicity of first-generation (ΔG) vectors limits their use to short-term experiments. We recently introduced second-generation, double-deletion-mutant (ΔGL) rabies viral vectors, showing that they efficiently retrogradely infect projection neurons and express recombinases effectively but with little to no detectable toxicity; more recently, we have shown that ΔGL viruses can be used for monosynaptic tracing with far lower cytotoxicity than the first-generation system. Here we introduce third-generation (ΔL) rabies viral vectors, which, like first-generation vectors, have only a single gene deleted from their genomes (in this case the viral polymerase gene L) but which appear to be as nontoxic as second-generation ones, based onin vivolongitudinal structural and functional two-photon imaging andex vivoelectrophysiology. Although third-generation vectors are therefore phenotypically very similar to second-generation ones, we show that they have the major advantage of growing to much higher titers, and this key difference results in significantly increased numbers of retrogradely labeled neuronsin vivo. These ΔL rabies viral vectors therefore constitute a new state of the art for minimally perturbative, pathway-specific expression of recombinases and transactivators in mammalian neurons selected on the basis of their axonal projections. Because replication of deletion-mutant rabies viruses within complementing cells is precisely the process that underlies monosynaptic tracing, the higher replication efficiency of this new class of rabies viral vectors furthermore suggests the potential to provide the foundation of an improved nontoxic monosynaptic tracing system.
A real-world evaluation of the implementation of NLP technology in abstract screening of a systematic review
Authors: Perlman-Arrow Sara , Loo Noel , Bobrovitz Niklas , Yan Tingting , Arora Rahul K. 
Published: February 2022

AbstractThe laborious and time-consuming nature of systematic review production hinders the dissemination of up-to-date evidence synthesis. Well-performing natural language processing (NLP) tools for systematic reviews have been developed, showing promise to improve efficiency. However, the feasibility and value of these technologies have not been comprehensively demonstrated in a real-world review. We developed an NLP-assisted abstract screening tool that provides text inclusion recommendations, keyword highlights, and visual context cues. We evaluated this tool in a living systematic review on SARS-CoV-2 seroprevalence, conducting a quality improvement assessment of screening with and without the tool. We evaluated changes to abstract screening speed, screening accuracy, characteristics of included texts, and user satisfaction. The tool improved efficiency, reducing screening time per abstract by 45.9% and decreasing inter-reviewer conflict rates. The tool conserved precision of article inclusion (positive predictive value; 0.92 with tool vs 0.88 without) and recall (sensitivity; 0.90 vs 0.81). The summary statistics of included studies were similar with and without the tool. Users were satisfied with the tool (mean satisfaction score of 4.2/5). We evaluated an abstract screening process where one human reviewer was replaced with the tool’s votes, finding that this maintained recall (0.92 one-person, one-tool vs 0.90 two tool-assisted humans) and precision (0.91 vs 0.92) while reducing screening time by 70%. Implementing an NLP tool in this living systematic review improved efficiency, maintained accuracy, and was well-received by researchers, demonstrating the real-world effectiveness of NLP in expediting evidence synthesis.
Examining the Association between the Gastrointestinal Microbiota and Gulf War Illness: A Prospective Cohort Study
Authors: Kates Ashley , Keating Julie , Baubie Kelsey , Putman-Buehler Nathan , Watson Lauren , Godfrey Jared , Deblois Courtney L. , Suen Garret , Cook Dane B. , Rabago David , Gangnon Ronald , Safdar Nasia 
Published: February 2022

AbstractGulf War Illness (GWI) affects 25-35% of the 1991 Gulf War Veteran population. Patients with GWI experience pain, fatigue, cognitive impairments, gastrointestinal dysfunction, skin disorders, and respiratory issues. In longitudinal studies, many patients with GWI have shown little to no improvement in symptoms since diagnosis. The gut microbiome and diet play an important role in human health and disease, and preliminary studies suggest it may play a role in GWI. To examine the relationship between the gut microbiota, diet, and GWI, we conducted an eight-week prospective cohort study collecting stool samples, medications, health history, and dietary data. Sixty-nine participants were enrolled into the study, 36 of which met the case definition for GWI. The gut microbiota of participants, determined by 16S rRNA sequencing of stool samples, was stable over the duration of the study and showed no within person (alpha diversity) differences. Between group analyses (beta diversity) identified statistically significant different between those with and without GWI. Several taxonomic lineages were identified as differentially abundant between those with and without GWI (n=9) including a greater abundance of Lachnospiraceae and Ruminococcaceae in those without GWI. Additionally, there were taxonomic differences between those with high and low HEI scores including a greater abundance of Ruminococcaceae in those with higher HEI scores. This longitudinal cohort study of GWVs found that participants with GWI had significantly different microbiomes from those without GWI. Further studies are needed to determine the role these differences may play in the development and treatment of GWI.
Dynamic Epigenetic Changes during a Relapse and Recovery Cycle in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome
Authors: Helliwell A.M. , Stockwell P.A. , Edgar C.D. , Chatterjee A. , Tate W.P. 
Published: February 2022

AbstractBackgroundMyalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex disease with variable severity throughout the ongoing illness. Patients experience relapses where symptoms increase in severity, leaving them with a marked reduction in quality of life. Previous work has investigated molecular differences between ME/CFS patients and healthy controls, but the dynamic changes specific to each individual patient are unknown. Precision medicine can determine how each patient responds individually during variations in their long-term illness. We apply precision medicine here to map genomic changes in two selected ME/CFS patients through a relapse recovery cycle.ResultsDNA was isolated from Peripheral Blood Mononuclear Cells (PBMCs) from two patients and a healthy age/gender matched control in a longitudinal study to capture a patient relapse. Reduced representation DNA methylation sequencing profiles were obtained from each time point spanning the relapse recovery cycle. Both patients throughout the time course showed a significantly larger methylome variability (10-20 fold) compared with the control. During the relapse changes in the methylome profiles of the two patients were detected in regulatory-active regions of the genome that were associated respectively with 157 and 127 downstream genes, indicating disturbed metabolic, immune and inflammatory functions occurring during the relapse.ConclusionsSevere health relapses in ME/CFS patients result in functionally important changes in their DNA methylomes that, while differing among patients, lead to similar compromised physiology. DNA methylation that is a signature of disease variability in ongoing ME/CFS may have practical applications for strategies to decrease relapse frequency.
A mixture model to estimate SARS-CoV-2 seroprevalence in Chennai, India
Authors: Hitchings Matt D.T. , Patel Eshan U. , Khan Rifa , Srikrishnan Aylur K. , Anderson Mark , Kumar K.S. , Wesolowski Amy P. , Iqbal Syed H. , Rodgers Mary A. , Mehta Shruti H. , Cloherty Gavin , Cummings Derek A.T. , Solomon Sunil S. 
Published: February 2022

AbstractBackgroundSerological assays used to estimate SARS-CoV-2 seroprevalence rely on manufacturer cut-offs established based on more severe early cases who tended to be older.MethodsWe conducted a household-based serosurvey of 4,677 individuals from 2,619 households in Chennai, India from January to May, 2021. Samples were tested for SARS-CoV-2 IgG antibodies to the spike (S) and nucelocapsid (N) proteins. We calculated seroprevalence using manufacturer cut-offs and using a mixture model in which individuals were assigned a probability of being seropositive based on their measured IgG, accounting for heterogeneous antibody response across individuals.ResultsThe SARS-CoV-2 seroprevalence to anti-S and anti-N IgG was 62.0% (95% confidence interval [CI], 60.6 to 63.4) and 13.5% (95% CI, 12.6 to 14.5), respectively applying the manufacturer’s cut-offs, with low inter-assay agreement (Cohen’s kappa 0.15). With the mixture model, estimated anti-S IgG and anti-N IgG seroprevalence was 64.9% (95% Credible Interval [CrI], 63.8 to 66.0) and 51.5% (95% CrI, 50.2 to 52.9) respectively, with high inter-assay agreement (Cohen’s kappa 0.66). Age and socioeconomic factors showed inconsistent relationships with anti-S IgG and anti-N IgG seropositivity using manufacturer’s cut-offs, but the mixture model reconciled these differences. In the mixture model, age was not associated with seropositivity, and improved household ventilation was associated with lower seropositivity odds.ConclusionsWith global vaccine scale-up, the utility of the more stable anti-S IgG assay may be limited due to the inclusion of the S protein in several vaccines. SARS-CoV-2 seroprevalence estimates using alternative targets must consider heterogeneity in seroresponse to ensure seroprevalence is not underestimated and correlates not misinterpreted.
Protection of Omicron sub-lineage infection against reinfection with another Omicron sub-lineage
Authors: Chemaitelly Hiam , Ayoub Houssein H. , Coyle Peter , Tang Patrick , Yassine Hadi M. , Al-Khatib Hebah A. , Smatti Maria K. , Hasan Mohammad R. , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Butt Adeel A. , Al-Romaihi Hamad Eid , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J. 
Published: February 2022

AbstractBACKGROUNDThe SARS-CoV-2 Omicron (B.1.1.529) variant has two main sub-lineages, BA.1 and BA.2 with significant genetic distance between them. This study investigated protection of infection with one sub-lineage against reinfection with the other sub-lineage in Qatar during a large BA.1 and BA.2 Omicron wave, from December 19, 2021 to February 21, 2022.METHODSTwo national matched, retrospective cohort studies were conducted to estimate effectiveness of BA.1 infection against reinfection with BA.2 (N=20,197; BA.1-against-BA.2 study), and effectiveness of BA.2 infection against reinfection with BA.1 (N=100,925; BA.2-against-BA.1 study). Associations were estimated using Cox proportional-hazards regression models.RESULTSIn the BA.1-against-BA.2 study, cumulative incidence of infection was estimated at 0.03% (95% CI: 0.01-0.07%) for the BA.1-infected cohort and at 0.62% (95% CI: 0.51-0.75%) for the uninfected-control cohort, 15 days after the start of follow-up. Effectiveness of BA.1 infection against reinfection with BA.2 was estimated at 94.9% (95% CI: 88.4-97.8%). In the BA.2-against-BA.1 study, cumulative incidence of infection was estimated at 0.03% (95% CI: 0.02-0.04%) for the BA.2-infected cohort and at 0.17% (95% CI: 0.15-0.21%) for the uninfected-control cohort, 15 days after the start of follow-up. Effectiveness of BA.2 infection against reinfection with BA.1 was estimated at 85.6% (95% CI: 77.4-90.9%).CONCLUSIONSInfection with an Omicron sub-lineage appears to induce strong, but not full protection against reinfection with the other sub-lineage, for at least several weeks after the initial infection.