bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of age on goal-dependent modulation of episodic memory retrieval
Authors: Srokova Sabina , Hill Paul F. , Elward Rachael L. , Rugg Michael D. 
Published: September 2020

AbstractRetrieval gating refers to the ability to modulate the retrieval of features of a single memory episode according to behavioral goals. Recent findings demonstrate that younger adults engage retrieval gating by attenuating the representation of task-irrelevant features of an episode. Here, we examine whether retrieval gating varies with age. Younger and older adults incidentally encoded words superimposed over scenes or scrambled backgrounds that were displayed in one of three spatial locations. Participants subsequently underwent fMRI as they completed two memory tasks: the background task, which tested memory for the word’s background, and the location task, testing memory for the word’s location. Employing univariate and multivariate approaches, we demonstrated that younger, but not older adults, exhibited attenuated reinstatement of scene information when it was goal-irrelevant (during the location task). Additionally, in younger adults only, the strength of scene reinstatement in the parahippocampal place area during the background task was related to item and source memory performance. Together, these findings point to an age-related decline in the ability to engage retrieval gating.
ClinePlotR: Visualizing genomic clines and detecting outliers in R
Authors: Martin Bradley T. , Chafin Tyler K. , Douglas Marlis R. , Douglas Michael E. 
Published: September 2020

AbstractPatterns of multi-locus differentiation (i.e., genomic clines) often extend broadly across hybrid zones and their quantification can help diagnose how species boundaries are shaped by adaptive processes, both intrinsic and extrinsic. In this sense, the transitioning of loci across admixed individuals can be contrasted as a function of the genome-wide trend, in turn allowing an expansion of clinal theory across a much wider array of biodiversity. However, computational tools that serve to interpret and consequently visualize ‘genomic clines’ are limited. Here, we introduce the ClinePlotR R-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages,bgcand Introgress. ClinePlotR bundles both input generation (i.e, filtering datasets and creating specialized file formats) and output processing (e.g., MCMC thinning and burn-in) with functions that directly facilitate interpretation and hypothesis testing. Tools are also provided for post-hoc analyses that interface with external packages such as ENMevaland RIdeogram. Our package increases the reproducibility and accessibility of genomic cline methods, thus allowing an expanded user base and promoting these methods as mechanisms to address diverse evolutionary questions in both model and non-model organisms.
Population receptive fields in non-human primates from whole-brain fMRI and large-scale neurophysiology in visual cortex
Authors: Klink P. Christiaan , Chen Xing , Vanduffel Wim , Roelfsema Pieter R. 
Published: September 2020

AbstractPopulation receptive field (pRF) modeling is a popular fMRI method to map the retinotopic organization of the human brain. While fMRI-based pRF-maps are qualitatively similar to invasively recorded single-cell receptive fields in animals, it remains unclear what neuronal signal they represent. We addressed this question in awake non-human primates comparing whole-brain fMRI and large-scale neurophysiological recordings in areas V1 and V4 of the visual cortex. We examined the fits of several pRF-models based on the fMRI BOLD-signal, multi-unit spiking activity (MUA) and local field potential (LFP) power in different frequency bands. We found that pRFs derived from BOLD-fMRI were most similar to MUA-pRFs in V1 and V4, while pRFs based on LFP gamma power also gave a good approximation. FMRI-based pRFs thus reliably reflect neuronal receptive field properties in the primate brain. In addition to our results in V1 and V4, the whole-brain fMRI measurements revealed retinotopic tuning in many other cortical and subcortical areas with a consistent increase in pRF-size with increasing eccentricity, as well as a retinotopically specific deactivation of default-mode network nodes similar to previous observations in humans.
Polygenic Risk Scores for Kidney Function to the Circulating Proteome, and Incident Kidney Diseases: the Atherosclerosis Risk in Communities Study
Authors: Yu Zhi , Jin Jin , Tin Adrienne , Köttgen Anna , Yu Bing , Chen Jingsha , Surapaneni Aditya , Zhou Linda , Ballantyne Christie M. , Hoogeveen Ron C. , Arking Dan E. , Chatterjee Nilanjan , Grams Morgan E. , Coresh Josef 
Published: September 2020

ABSTRACTGenome-wide association studies (GWAS) have revealed numerous loci for kidney function (estimated glomerular filtration rate, eGFR). The relationship of polygenic predictors of eGFR, risk of incident adverse kidney outcomes, and the plasma proteome is not known. We developed a genome-wide polygenic risk score (PRS) using a weighted average of 1.2 million SNPs for eGFR using the LDpred algorithm, summary statistics generated by a European-ancestry (EA) meta-analysis of the CKDGen Consortium (N=558,423) and UK Biobank GWAS for eGFR (90% of the cohort; N=289,432), followed by best parameter selection using data from the remaining 10% of the UK Biobank (N=32,159). We then tested the association of the PRS among 8,886 EA participants in the Atherosclerosis Risk in Communities (ARIC) study (mean age: 54±6 years, 53% female) with incident chronic kidney disease (CKD), end stage kidney disease (ESKD), kidney failure (KF), and acute kidney injury (AKI). We also examined 4,877 plasma proteins measured at two time points (visit 3 (1993-95) and visit 5 (2011-13)) in relation to the PRS and compared associations between the proteome and eGFR itself. All models were adjusted for age, sex, center, and the first 10 principal components of ancestry. The developed PRS had an R2for eGFR of 0.07 in ARIC. Over 30 years of follow up, the number of incident CKD, ESKD, KF, and AKI were 2,959, 137, 470, and 1,723, respectively. The PRS showed significant associations with all outcomes: hazard ratios (95% CI) per 1 SD lower PRS were 1.33 (1.28, 1.39), 1.20 (1.00, 1.42), 1.17 (1.06, 1.28), and 1.07 (1.02, 1.12) for incident CKD, ESKD, KF, and AKI respectively. The PRS was significantly associated (Bonferroni threshold P<1.02 × 10−5) with 108 proteins at both time points. The strongest associations were with cystatin-C (a marker of kidney function used in clinical practice), collagen alpha-1 (XV) chain, and desmocollin-2. All significant correlations with the PRS were negative, except those of testican-2 and angiostatin. Correlations of proteins with eGFR were much stronger than those with the PRS. Overall, we demonstrated that the PRS for eGFR is now sufficiently strong to capture risk for a spectrum of incident kidney diseases as well as broadly influence the plasma proteome.
A Spatiotemporal Molecular Switch Governs Plant Asymmetric Cell Division
Authors: Guo Xiaoyu , Park Chan Ho , Wang Zhi-Yong , Nickels Bryce E. , Dong Juan 
Published: September 2020

SummaryAsymmetric cell division (ACD) often requires protein polarization in the mother cell to produce daughter cells with distinct identities (“cell-fate asymmetry”). Here, we define a previously undocumented mechanism for establishing cell-fate asymmetry inArabidopsisstomatal stem cells. In particular, we show that polarization of BSL protein phosphatases promotes stomatal ACD by establishing a “kinase-based signaling asymmetry” in the two daughter cells. BSL polarization in the stomatal ACD mother cell is triggered upon commitment to cell division. Polarized BSL is inherited by the differentiating daughter cell where it suppresses cell division and promotes cell-fate determination. Plants lacking BSL exhibit stomatal over-proliferation, demonstrating BSL plays an essential role in stomatal development. Our findings establish that BSL polarization provides a spatiotemporal molecular switch that enables cell-fate asymmetry in stomatal ACD daughter cells. We propose BSL polarization is triggered by an ACD “checkpoint” in the mother cell that monitors establishment of division-plane asymmetry.
Household transmission in people infected with SARS-CoV-2 (COVID-19) in Metropolitan Lima
Authors: Angulo-Bazan Yolanda , Solis Gilmer , Cardenas Fany , Jorge Ana , Acosta Joshi , Cabezas Cesar 
Published: September 2020

ABSTRACTObjectiveDescribe the characteristics of SARS-CoV-2 infection among household members with a confirmed primary case of COVID-19 in low burden districts in Metropolitan Lima.Materials and MethodsA retrospective, secondary database review study was conducted. The information was collected from an epidemiological surveillance activity in close contacts (co-inhabitants) in 52 households in Metropolitan Lima with only one member with COVID-19. A reevaluation was carried out in 10 households. Epidemiological and clinical variables were evaluated and its association with the result of the rapid serological test (presence of IgG, IgM or both).ResultsSecondary cases were found in 40 households, which represents an average of 49.9% identification per household. A secondary attack rate of 53.0% (125 cases) was found among cohabitants, with 77.6% of cases being symptomatic (symptomatic / asymptomatic ratio: 3.5). The presence of fever and / or chills was found in 40.0% of people with a positive result, followed by a sore throat, in 39.2%. Ageusia and anosmia were present in 22.4% and 20.8% of cases, respectively. A reevaluation in 40 family members 33.6 ± 2.7 days after the first evaluation, show the persistence of positive IgM and IgG in the 20 positive cases in the first evaluation.ConclusionHaving a primary case of COVID-19 in home, the secondary attack rate of this infection is 53%; however, in a significant proportion of households evaluated there was no positive case, beyond the primary case. The epidemiological and clinical characteristics found in this case were in accordance with what has already been reported in other international series.
Efficiency ofSalicornia neeito treat aquaculture effluent from a hypersaline and artificial wetland
Authors: Diaz Mónica R. , Araneda Javier , Osses Andrea , Orellana Jaime , Gallardo José A. 
Published: September 2020

AbstractIn this study we evaluated the potential ofSalicornia neei, a halophyte plant native to South America, to treat saline effluents with simulated concentration of ammonium-N (Amm) and nitrate-N (Nit) similar to land-based marine aquaculture effluents. Plants were cultivated for 74 days in drainage lysimeters under three treatments of seawater fertilized with: 1) Nit+Amm, 2) Nit, or 3) without fertilizer (Control). Over 5 repetitions, nitrogen removal efficiency (RE) was high in both treatments (Nit + Amm = 89.6± 1,0 %; Nit 88.8 ± 0.9 %). While nitrogen removal rate (RR) was non linear and concentration-dependent (RRday 1-4: Nit+Amm= 2.9 ± 0.3 mg L−1d−1, Nit = 2.4 ± 0.5mg L−1d−1; RRday5-8: Nit + Amm = 0.8 ± 0.2mg L−1d−1, Nit=1.0 ± 0.2mg L−1d−1). Effluent salinity increased from 40.6 to 49.4 g L−1during the experiment, with no observed detrimental effects on RE or RR. High nitrogen removal efficiency and significant biomass production observed, Nit+Amm = 11.3 ± 2.0 kg m−2; Nit = 10.0 ± 0.8 kg m−2; Control = 4.6 ± 0.6 kg m−2, demonstrate that artificial wetlands ofS. neeican be used for wastewater treatment in saline aquaculture in South America.
Multivariate pattern analysis of brain structure predicts functional outcome after auditory-based cognitive training interventions
Authors: Kambeitz-Ilankovic Lana , Vinogradov Sophia , Wenzel Julian , Fisher Melissa , Haas Shalaila S. , Betz Linda , Penzel Nora , Nagarajan Srikantan , Koutsouleris Nikolaos , Subramaniam Karuna 
Published: September 2020

AbstractBackgroundCognitive gains following cognitive training interventions (CT) are associated with improved functioning in people with schizophrenia (SCZ). However, considerable inter-individual variability is observed. Here, we evaluate the sensitivity of brain structural features to predict functional response to auditory-based cognitive training (ABCT) at a single subject level.MethodsWe employed whole-brain multivariate pattern analysis (MVPA) with support vector machine (SVM) modeling to identify grey matter (GM) patterns that predicted ‘higher’ vs. ‘lower’ functioning after 40 hours of ABCT at the single subject level in SCZ patients. The generalization capacity of the SVM model was evaluated by applying the original model through an Out-Of-Sample Cross Validation analysis (OOCV) to unseen SCZ patients from an independent sample that underwent 50 hours of ABCT.ResultsThe whole-brain GM volume-based pattern classification predicted ‘higher’ vs. ‘lower’ functioning at follow-up with a balanced accuracy (BAC) of 69.4% (sensitivity 72.2%, specificity 66.7%) as determined by nested cross-validation. The neuroanatomical model was generalizable to an independent cohort with a BAC of 62.1% (sensitivity 90.9%, specificity 33.3%).ConclusionsIn particular, greater baseline GM volume in regions within superior temporal gyrus, thalamus, anterior cingulate and cerebellum -- predicted improved functioning at the single-subject level following ABCT in SCZ participants.
Phloem loading via the abaxial bundle sheath cells in maize leaves
Authors: Bezrutczyk Margaret , Zöllner Nora R. , Kruse Colin P. S. , Hartwig Thomas , Lautwein Tobias , Köhrer Karl , Frommer Wolf B. , Kim Ji-Yun 
Published: September 2020

ABSTRACTLeaves are asymmetric, with differential functionalization of abaxial and adaxial tissues. The bundle sheath (BS) surrounding the vasculature of the C3 crop barley is dorsoventrally differentiated into three domains: adaxial structural, lateral S-type, and abaxial L-type. S-type cells seem to transfer assimilates towards the phloem. Here we used single-cell RNA sequencing to investigate BS differentiation in C4 maize. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, andc) and UmamiT amino acid efflux transporters.SWEET13a, b, cwere also identified in the phloem parenchyma (PP). Thus maize acquired a unique mechanism for phloem loading in whichabBS cells provide the main pathway for apoplasmic sucrose transfer towards the phloem. This pathway predominates in veins responsible for phloem loading (rank-2 intermediate), while rank-1 intermediate and major veins export sucrose from the phloem parenchyma (PP) adjacent to the sieve element companion cell (SE/CC) complex, as in Arabidopsis. We surmise thatabBS identity is subject to dorsoventral patterning and has components of PP identity. These observations provide first insights into the unique transport-specific properties ofabBS cells and support for a modification to the canonical phloem loading pathway of maize, which may be generalizable to other C4 monocots.
High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects
Authors: Larkin Alyse A. , Garcia Catherine A. , Brock Melissa L. , Lee Jenna A. , Garcia Nathan , Ustick Lucas J. , Barbero Leticia , Carter Brendan R. , Sonnerup Rolf E. , Talley Lynne , Tarran Glen A. , Volkov Denis L. , Martiny Adam C. 
Published: September 2020

AbstractDetailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 720 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 2.75 terabases of data, where the median number of base pairs per sample was 3.48 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or “Bio-GO-SHIP.” One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean.
Simplicial and Topological Descriptions of Human Brain Dynamics
Authors: Billings Jacob , Saggar Manish , Hlinka Jaroslav , Keilholz Shella , Petri Giovanni 
Published: September 2020

ABSTRACTWhereas brain imaging tools like functional Magnetic Resonance Imaging (fMRI) afford measurements of whole-brain activity, it remains unclear how best to interpret patterns found amid the data’s apparent self-organization. To clarify how patterns of brain activity support brain function, one might identify metric spaces that optimally distinguish brain states across experimentally defined conditions. Therefore, the present study considers the relative capacities of several metric spaces to disambiguate experimentally defined brain states. One fundamental metric space interprets fMRI data topographically, i.e, as the vector of amplitudes of a multivariate signal, changing with time. Another perspective considers the condition-dependency of the brain’s Functional Connectivity (FC), i.e., the similarity matrix computed across the variables of a multivariate signal. More recently, metric spaces that think of the data topologically, e.g., as an abstract geometric object, have become available. In the abstract, uncertainty prevails regarding the distortions imposed by the mode of measurement upon the object under study. Features that are invariant under continuous deformations, such as rotation and inflation, constitute the features of topological data analysis. While there are strengths and weaknesses of each metric space, we find that metric spaces that track topological features are optimal descriptors of the brain’s experimentally defined states.AUTHOR SUMMARYTime-Varying Functional Connectivity (TVFC) leverages brain imaging data to interpret brain function as time-varying patterns of coordinating activity among brain regions. While many questions remain regarding the organizing principles through which brain function emerges from multi-regional interactions, advances in the mathematics of Topological Data Analysis (TDA) may provide new insights into the brain’s functional self-organization. One tool from TDA, “persistent homology”, observes the occurrence and persistence ofn-dimensional holes in a sequence of simplicial complexes extracted from a weighted graph. The occurrence of such holes within the TVFC graph may indicate preferred routes of information flow among brain regions. In the present study, we compare the use of persistence homology versus more traditional metrics at the task of segmenting brain states that differ across experimental conditions. We find that the structures identified by persistence homology more accurately segment the stimuli, more accurately segment high versus low performance levels under common stimuli, and generalize better across volunteers. These findings support the topological interpretation of brain dynamics.
Biomechanical outcomes of the pendulum test characterize individual differences in activated versus resting leg rigidity in people with Parkinson’s disease
Authors: Martino Giovanni , McKay J. Lucas , Factor Stewart A. , Ting Lena H. 
Published: September 2020

AbstractLeg rigidity is associated with frequent falls in people with Parkinson’s disease (PD), suggesting a potential role in functional balance and gait impairments. Changes in neural state due to secondary tasks, e.g. activation maneuvers, can exacerbate (or “activate”) rigidity, possibly increasing the risk of falls. However, the subjective interpretation and coarse classification of the standard clinical rigidity scale has prohibited the systematic, objective assessment of resting and activated leg rigidity. The pendulum test is an objective diagnostic method that we hypothesized would be sensitive enough to characterize resting and activated leg rigidity.We recorded kinematic data during the pendulum test in 15 individuals with PD, spanning a range of leg rigidity severity (slight to severe). From the recorded data of leg swing kinematics we measured biomechanical outcomes including first swing excursion, first extension peak, number and duration of the oscillations, resting angle, relaxation index, maximum and minimum angular velocity. We examined associations between biomechanical outcomes and clinical leg rigidity score. We evaluated the effect of increasing rigidity through activation maneuvers on biomechanical outcomes. Finally, we assessed whether either biomechanical outcomes or changes in outcomes with activation were associated with fall history.Our results suggest that the biomechanical assessment of the pendulum test can objectively quantify leg rigidity among people with PD. We found that the presence of marked rigidity during clinical exam significantly impacted biomechanical outcomes, i.e. first extension peak, number of oscillations, relaxation index and maximum angular velocity. No differences in the effect of activation maneuvers between groups with clinically assessed moderate and marked rigidity were observed, suggesting that activated rigidity may be independent of resting rigidity and should be scored as independent variables. Moreover, we found that fall history was more common among people whose rigidity was increased with a secondary task, as measured by biomechanical outcomes.We conclude that different mechanisms contributing to resting and activated rigidity may play an important yet unexplored functional role in balance impairments. The pendulum test may contribute to a better understanding of fundamental mechanisms underlying motor symptoms in PD, evaluating the efficacy of treatments, and predicting the risk of falls.
Tracking Smell Loss to Identify Healthcare Workers with SARS-CoV-2 Infection
Authors: Weiss Julian J. , Attuquayefio Tuki N. , White Elizabeth B. , Li Fangyong , Herz Rachel S. , White Theresa L. , Campbell Melissa , Geng Bertie , Datta Rupak , Wyllie Anne L. , Grubaugh Nathan D. , Casanovas-Massana Arnau , Catherine Muenker M. , Handoko Ryan , Iwasaki Akiko ,   the Yale IMPACT Research Team, Martinello Richard A. , Ko Albert I. , Small Dana M. , Farhadian Shelli F. 
Published: September 2020

AbstractBackgroundHealthcare workers (HCW) treating COVID-19 patients are at high risk for infection and may also spread infection through their contact with vulnerable patients. Smell loss has been associated with SARS-CoV-2 infection, but it is unknown whether monitoring for smell loss can be used to identify asymptomatic infection among high risk individuals, like HCW.MethodsWe performed a prospective cohort study, tracking 473 HCW across three months to determine if smell loss could predict SARS-CoV-2 infection in this high-risk group. HCW subjects completed a longitudinal, novel behavioral at-home assessment of smell function with household items, as well as detailed symptom surveys that included a parosmia screening questionnaire, and RT-qPCR testing to identify SARSCoV-2 infection.ResultsSARS-CoV-2 was identified in 17 (3.6%) of 473 HCW. Among the 17 infected HCW, 53% reported smell loss, and were more likely to report smell loss than COVID-negative HCW on both the at-home assessment and the screening questionnaire (P< .01). 67% reported smell loss prior to having a positive SARS-CoV-2 test, and smell loss was reported a median of two days before testing positive. Neurological symptoms were reported more frequently among COVID-positive HCW who reported smell loss (P< .01).ConclusionsIn this prospective study of HCW, self-reported changes in smell using two different measures were predictive of COVID-19 infection. Smell loss frequently preceded a positive test and was associated with neurological symptoms.