bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic loss of norepinephrine does not alter adult hippocampal neurogenesis in dopamine β-hydroxylase deficient mice
Authors: Kapri Darshana , Vadodaria Krishna C. , Rommelfanger Karen S. , Ogbonmwan Yvonne E. , Liles L. Cameron , Fernandes-Thomas Kimberly A. , Salvi Sonali S. , Husain Basma F.A. , Weinshenker David , Vaidya Vidita A. 
Published: September 2022

AbstractNorepinephrine (NE), and specific adrenoceptors, have been reported to influence distinct aspects of adult hippocampal neurogenesis, including latent stem cell activation, progenitor proliferation, and differentiation. These findings are predominantly based on the use of pharmacological approaches in both in vitro and in vivo systems. Here, we sought to assess the consequences of genetic ablation of NE on adult hippocampal neurogenesis, by examining dopamine β hydroxylase knockout (Dbh-/-) mice, which lack NE from birth. We find that Dbh-/- mice exhibit no difference in adult hippocampal progenitor proliferation and survival. Further, the number of immature newborn neurons, labeled using stage-specific developmental markers within the hippocampal neurogenic niche, was also unaltered in Dbh -/- mice. In contrast, the noradrenergic neurotoxin DSP-4, which had previously been shown to reduce adult hippocampal neurogenesis in rats, also resulted in a decline in hippocampal progenitor proliferation in C57/Bl6N mice. These findings indicate that pharmacological lesioning of noradrenergic afferents in adulthood, but not the complete genetic loss of NE from birth, impairs adult hippocampal neurogenesis in mice.
The triplet codons across the watershed between the non-living and living matters
Authors: Li Dirson Jian 
Published: September 2022

AbstractThree nucleotides per codon had been determined before deciphering the genetic code. However, it is still a mystery why there are three nucleotides per codon. This is a deceptively simple problem, which need first to clarify the prebiotic picture that has been in debate for decades. The triplet nature of life has been observed not only in the triplet codons but also in the universal 3-base periodicity in genome sequences. Here, a statistical picture on the prebiotic sequence evolution has been proposed by ascertaining the profound relationship between the evolution of the genetic code and the diversification of life. There are indications that the triplet nature of the genetic code is due to a mixture of the periods in the superhelical structures of bent DNAs.
Hippocampal damage causes retrograde amnesia for objects’ visual, but not odour, properties in male rats
Authors: Lacoursiere Sean G. , McAllister Brendan B. , Hadikin Crystal , Tschetter Wayne W. , Lehmann Hugo , Sutherland Robert J. 
Published: September 2022

ABSTRACTDamage to the hippocampus produces profound retrograde amnesia, but odour and object discrimination memories can be spared in the retrograde direction. Prior lesion studies testing retrograde amnesia for object/odour discriminations are problematic due to sparing of large parts of the hippocampus, which may support memory recall, and/or the presence of uncontrolled, distinctive odours that may support object discrimination. To address these issues, we used a simple object discrimination test to assess memory in male rats. Two visually distinct objects, paired with distinct odour cues, were presented. One object was associated with a reward. Following training, neurotoxic hippocampal lesions were made usingN-methyl-D-aspartate(NMDA). The rats were then tested on the preoperatively learned object discrimination problem, with and without the availability of odour or visual cues during testing. The rats were also postoperatively trained on a new object discrimination problem. Lesion sizes ranged from 67-97% of the hippocampus (average of 87%). On the preoperatively learned discrimination problem, the rats with hippocampal lesions showed preserved object discrimination memory when tested in the dark (i.e., without visual cues) but not when the explicit odour cues were removed from the objects. Hippocampal lesions increased the number of trials required to reach criterion but did not prevent rats from solving the postoperatively learned discrimination problem. Our results support the idea that long-term memories for odours, unlike recall of visual properties of objects, does not depend on the hippocampus in rats, consistent with previous observations that hippocampal damage does not cause retrograde amnesia for odour memories.
Poly-omic risk scores predict inflammatory bowel disease diagnosis
Authors: Arehart Christopher H. , Sterrett John D. , Garris Rosanna L. , Quispe-Pilco Ruth E. , Gignoux Christopher R. , Evans Luke M. , Stanislawski Maggie A. 
Published: September 2022

AbstractInflammatory Bowel Disease (IBD) is characterized by complex etiology and a disrupted colonic ecosystem. We provide a framework for the analysis of multi-omic data, which we apply to study the gut ecosystem in IBD. Specifically, we train and validate models using data on the metagenome metatranscriptome, virome, and metabolome from the Human Microbiome Project 2 IBD Multi-omics Database, with 1,785 repeated samples from 131 individuals (103 cases, 27 controls). After splitting the participants into training and testing groups, we used mixed effects least absolute shrinkage and selection operator (LASSO) regression to select features for each -omic. These features, with demographic covariates, were used to generate separate single-omic prediction scores. All four single-omic scores were then combined into a final regression to assess the relative importance of the individual -omics and the predictive benefits when considered together. We identified several species, pathways, and metabolites known to be associated with IBD risk, and we explored the connections between datasets. Individually, metabolomics and viromics scores were more predictive than metagenomics or metatranscriptomics, and when all four scores were combined, we predicted disease diagnosis with a Nagelkerke’s R2of 0.46 and an AUC of 0.80 [95% CI: 0.63, 0.98]. Our work suggests that some single-omic models for complex traits are more predictive than others, that incorporating multiple -omics datasets may improve prediction, and that each -omic data type provides a combination of unique and redundant information. This modeling framework can be extended to other complex traits and multi-omic datasets.ImportanceComplex traits are characterized by many biological and environmental factors, such that multi-omics datasets are well-positioned to help us understand their underlying etiologies. We applied a prediction framework across multiple -omics (metagenomics, metatranscriptomics, metabolomics, and viromics) from the gut ecosystem to predict inflammatory bowel disease (IBD) diagnosis. The predicted scores from our models highlighted key features and allowed us to compare the relative utility of each -omic dataset in single-omic versus multi-omics models. Our results emphasized the importance of metabolomics and viromics over metagenomics and metatranscriptomics for predicting IBD status. The greater predictive capability of metabolomics and viromics is likely because these -omics serve as markers of lifestyle factors such as diet. This study provides a modeling framework for multi-omic data, and our results show the utility of combining multiple -omic data types to disentangle complex disease etiologies and biological signatures.
A Structural Heart-Brain Axis Mediates the Association Between Cardiovascular Risk and Cognitive Function
Authors: Jaggi Akshay , Conole Eleanor L.S. , Raisi-Estabragh Zahra , Gkontra Polyxeni , McCracken Celeste , Neubauer Stefan , Petersen Steffen E. , Cox Simon , Lekadir Karim 
Published: September 2022

AbstractElevated vascular disease risk associates with poorer cognitive function, but the mechanism for this link is poorly understood. A leading theory, the structural-functional model argues that vascular risk may drive adverse cardiac remodelling, which in turn leads to chronic cerebral hypoperfusion and subsequent brain structural damage. This model predicts that variation in heart and brain structure should associate with both greater vascular risk and lower cognitive function. This study tests that prediction in a large sample of the UK Biobank (N=11,962). We assemble and summarise vascular risk factors, cardiac magnetic resonance radiomics, brain structural and diffusion MRI indices, and cognitive assessment. We also extract ‘heart-brain axes’ capturing the covariation in heart and brain structure. Many heart and brain measures partially explain the vascular risk – cognitive function association, like left ventricular end-diastolic volume and grey matter volume. Notably, a heart-brain axis, capturing correlation between lower myocardial intensity, lower grey matter volume, and poorer thalamic white matter integrity, completely mediates the association, supporting the structural-functional model. Our findings also complicate this theory by finding that brain structural variation cannot completely explain the heart structure – cognitive function association. Our results broadly offer evidence for the structural functional hypothesis, identify imaging biomarkers for this association by considering covariation in heart and brain structure, and generate novel hypotheses about how cardiovascular risk may link to cognitive function.
Tailored Magnetic Resonance Fingerprinting
Authors: Poojar Pavan , Qian Enlin , Fung Maggie , Quarterman Patrick , Jambawalikar Sachin R. , Lignelli Angela , Geethanath Sairam 
Published: September 2022

AbstractNeuroimaging of certain pathologies requires both multi-parametric qualitative and quantitative imaging. The role of the quantitative MRI (qMRI) is well accepted but suffers from long acquisition times leading to patient discomfort, especially in geriatric and pediatric patients. Previous studies show that synthetic MRI can be used in order to reduce the scan time and provide qMRI as well as multi-contrast data. However, this approach suffers from artifacts such as partial volume and flow. In order to increase the scan efficiency (the number of contrasts and quantitative maps acquired per unit time), we designed, simulated, and demonstrated rapid, simultaneous, multi-contrast qualitative (T1 weighted, T1 fluid attenuated inversion recovery (FLAIR), T2 weighted, water, and fat), and quantitative imaging (T1 and T2 maps) through the approach of tailored MR fingerprinting (TMRF) to cover whole-brain in approximately four minutes.We performed TMRF on in vivo four healthy human brains and in vitro ISMRM/NIST phantom and compared with vendor supplied gold standard (GS) and MRF sequences. All scans were performed on a 3T GE Premier system and images were reconstructed offline using MATLAB. The reconstructed qualitative images were then subjected to custom DL denoising and gradient anisotropic diffusion denoising. The quantitative tissue parametric maps were reconstructed using a dense neural network to gain computational speed compared to dictionary matching. The grey matter and white matter tissues in qualitative and quantitative data for the in vivo datasets were segmented semi-automatically. The SNR and mean contrasts were plotted and compared across all three methods. The GS images show better SNR in all four subjects compared to MRF and TMRF (GS>TMRF>MRF). The T1 and T2 values of MRF are relatively overestimated as compared to GS and TMRF. The scan efficiency for TMRF is 1.72 min-1 which is higher compared to GS (0.32 min-1) and MRF (0.90 min-1).
Differential contagiousness of respiratory disease across the United States
Authors: Mallela Abhishek , Lin Yen Ting , Hlavacek William S. 
Published: September 2022

AbstractThe initial contagiousness of a communicable disease within a given population is quantified by the basic reproduction number, denoted R0. The value of R0 gives the expected number of new cases generated by an infectious person in a wholly susceptible population and depends on both pathogen and population properties. On the basis of compartmental models that reproduce Coronavirus Disease 2019 (COVID-19) surveillance data, we estimated region-specific R0 values for 280 of 384 metropolitan statistical areas (MSAs) in the United States (US), which account for 95% of the US population living in urban areas and 82% of the total population. Our estimates range from 1.9 to 7.7 and quantify the relative susceptibilities of regional populations to spread of respiratory diseases.One-Sentence SummaryInitial contagiousness of Coronavirus Disease 2019 varied over a 4-fold range across urban areas of the United States.LA-UR-22-29514
Long-term air pollution, cardiometabolic multimorbidity, and genetic susceptibility: a multi-state modeling study of 415,855 participants
Authors: Gao Xu , Jiang Meijie , Huang Ninghao , Guo Xinbiao , Baccarelli Andrea A. , Huang Tao 
Published: September 2022

AbstractBackgroundCardiometabolic multimorbidity (CMM) with at least two cardiometabolic diseases (CMDs) including type II diabetes (T2D), ischemic heart disease (IHD), and stroke, is a global health problem with multiplicative mortality risk and deserves to be investigated as a top priority. Although air pollution is a leading modifiable environmental risk for individual CMD, its impacts on CMM progression were poorly understood.ObjectiveTo elucidate the impact of air pollution on CMM progression, individually and in the context of genetic preposition.DesignMulti-state modeling cohort study.SettingData were extracted from the UK Biobank.Participants415,855 eligible UK Biobank adults that were free of CMDs at baseline.MeasurementsAnnual concentrations of particulate matter (PM) with a diameter of ≤2.5 μm (PM2.5), 2.5-10 μm (PM2.5-10), and ≤10 μm (PM10), and nitrogen oxides (NOx and NO2) were estimated using Land Use Regression model.ResultsDuring a median follow-up of 8.93 years, 33,375 participants had a first CMD (FCMD), and 3,257 subsequently developed CMM. PM2.5, PM10, NO2, and NOx levels, as well as their combined exposure were associated with increased FCMD risks and even higher risks of CMM. Particularly, per a 5-μg/m3 increase in PM2.5, risks for FCMD and CMM increased by 27% (95% confidence interval: 20%-34%) and 41% (18%-68%), respectively. By FCMD types, participants with IHD had a higher risk of CMM than those with T2D or stroke. Eighty-five CMD-related genetic variants were associated with CMM trajectories in our study and associations of air pollution with FCMD and CMM risks could be aggravated progressively with increasing genetic risks.LimitationsOther major air pollutants including ozone and SO2 were not considered due to the data availability.ConclusionsAir pollution has profound adverse health impacts on the progression of CMM through multi-stage dynamics, especially for individuals with IHD and high genetic risk.
Germ cell-specific proteins ACRV1 and AKAP4 facilitate identification of rare spermatozoa in semen of non-obstructive azoospermia patients
Authors: Zhang Junyan , Kanoatov Mirzo , Jarvi Keith , Gauthier-Fisher Andrée , Moskovtsev Sergey I. , Librach Clifford , Drabovich Andrei P. 
Published: September 2022

ABSTRACTNon-obstructive azoospermia (NOA), the most severe form of male infertility due to testicular failure, could be treated with intra-cytoplasmic sperm injection (ICSI), providing spermatozoa were retrieved with the microdissection testicular sperm extraction (mTESE). Here, we hypothesized that some testis- and germ cell-specific proteins would facilitate flow cytometry-assisted identification of rare spermatozoa in semen cell pellets of NOA patients, thus enabling non-invasive diagnostics prior to mTESE. Data mining and extensive verification by targeted proteomic assays and immunofluorescent microscopy revealed a panel of testis-specific proteins expressed at the continuum of germ cell differentiation, including the late germ cell-specific proteins AKAP4_HUMAN and ASPX_HUMAN (ACRV1 gene) with the exclusive expression in spermatozoa tails and acrosomes, respectively. A multiplex imaging flow cytometry assay revealed low numbers of the morphologically intact AKAP4+/ASPX+/Hoechst+ spermatozoa in semen pellet of NOA patients. While the previously suggested soluble markers for spermatozoa retrieval suffered from low diagnostic specificity, our multi-step gating strategy and visualization of AKAP4+/ASPX+/Hoechst+ cells bearing elongated tails and acrosome-capped nuclei facilitated fast and unambiguous identification of the mature intact spermatozoa. Pending further validation, our assay may emerge as a non-invasive test to predict the retrieval of morphologically intact spermatozoa by mTESE, thus improving diagnostics and treatment of the severe forms of male infertility.
Viable Monkeypox virus in the environment of a patient room
Authors: Marimuthu Kalisvar , Ching Wong Judith Chui , Lim Poh Lian , Octavia Sophie , Huan Xiaowei , Ng Yi Kai , Yang Jun Jing , Sutjipto Stephanie , Linn Kyaw Zaw , Setoh Yin Xiang , Ong Chong Hui Clara , Griffiths Jane , Farhanah Sharifah , Cheok Thai Shawn , Binti Sulaiman Nur Ashikin , Congcong Sipaco Barbara , Neves Erica Sena , Loo Liang Hui , Hakim Luqman , Sim Shuzhen , Lim Merrill , Nazeem Mohammad , Vasoo Shawn , Tham Kwok Wai , Ng Oon Tek , Ng Lee Ching 
Published: September 2022

AbstractWe conducted a prospective environmental surveillance study to investigate the air, surface, dust and water contamination of a room occupied by a patient infected with Monkeypox virus (MPXV) at various stages of his illness. The patient tested positive for MPXV from a throat swab and skin lesions. Environmental sampling was conducted in a negative pressure room with 12 unidirectional HEPA air changes per hour and daily cleaning of the surfaces. A total of 179 environmental samples were collected on days 7, 8, 13, and 21 of his illness. Air, surface, and dust contamination was highest during the first eight days of the illness, with a gradual decline to the lowest contamination level by day 21. Viable MPXV was isolated from surfaces and dust samples and no viable virus was isolated from the air and water samples.SynopsisInadequate research prevail on the mode of transmission for monkeypox virus. This study reports the findings of viable monkeypox virus from the patient environment, highlighting its implications for human health and impact on infection and prevention control measures.
Neural Correlates of Impulsive Compulsive Behaviors in Parkinson’s Disease: A Japanese Retrospective Study
Authors: Kimura Ikko , Revankar Gajanan S. , Ogawa Kotaro , Amano Kaoru , Kajiyama Yuta , Mochizuki Hideki 
Published: September 2022

AbstractBackgroundImpulsive compulsive behavior (ICB) often disturb patients with Parkinson’s Disease (PD), of which impulse control disorder (ICD) and dopamine dysregulation syndrome (DDS) are two major subsets. Although the nucleus accumbens (NAcc) is involved in ICB, it remains unclear how the NAcc affects cortical function and defines the different behavioral characteristics of ICD and DDS.ObjectivesTo identify the most involved cortico-striatal network in ICB and the differences in these networks between patients with ICD and those with DDS using structural and resting-state functional magnetic resonance imaging.MethodsPatients with PD were recruited using the data from a previous cohort study and were divided into patients with ICB (ICB group) and those without ICB (non-ICB group) using the Japanese version of the Questionnaire for Impulsive Compulsive Disorders in Parkinson’s Disease (J-QUIP). From these two groups, we extracted 37 pairs matched for age, sex, disease duration, and levodopa equivalent daily dose of dopamine agonists. Patients with ICB were further classified as either having ICD or DDS based on the J-QUIP subscore. General linear models were used to compare the gray matter volume and functional connectivity (FC) of the NAcc, caudate, and putamen between the ICB and non-ICB groups and between patients with ICD and those with DDS.ResultsWe found no significant differences in gray matter volume between the ICB and non-ICB groups or between patients with ICD and those with DDS. Compared with the non-ICB group, the FC of the right NAcc in the ICB group was lower in the bilateral ventromedial prefrontal cortex and higher in the left middle occipital gyrus. Patients with DDS showed higher FC between the right putamen and left superior temporal gyrus and higher FC between the left caudate and bilateral middle occipital gyrus than patients with ICD. In contrast, patients with ICD exhibited higher FC between the left NAcc and the right posterior cingulate cortex than patients with DSS.ConclusionsThe functionally altered network between the right NAcc and ventromedial prefrontal cortex was associated with the presence of ICB in PD, and the surrounding cortico-striatal networks may differentiate between the behavioral characteristics of patients with ICD and those with DDS.
The rapid radiation of Bomarea (Alstroemeriaceae: Liliales), driven by the rise of the Andes
Authors: Tribble Carrie M. , Alzate-Guarín Fernando , Gándara Etelvina , Vartoumian Araz , Burleigh J. Gordon , Zenil-Ferguson Rosana , Specht Chelsea D. , Rothfels Carl J. 
Published: September 2022

AbstractComplex geological events such as mountain uplift affect how, when, and where species originate and go extinct, but measuring those effects is a longstanding challenge. The Andes arose through a series of complex geological processes over the past c. 100 million years, impacting the evolution of regional biota by creating barriers to gene flow, opening up new habitats, and changing local climate patterns. Bomarea are tropical geophytes with ranges extending from central Mexico to central Chile. Of the roughly 120 species of Bomarea, most are found in the Andes, and previous work has suggested that Bomarea diversified rapidly and recently, corresponding with the uplift of the Andes. While many Bomarea species occur over small, isolated ranges, Bomarea edulis occurs significantly beyond the ranges of any other Bomarea species (from central Mexico to northern Argentina) and is thought to have potentially humanmediated dispersal, due to its status as a pre-Columbian food plant. To untangle the potential drivers of diversification and biogeographic history in Bomarea, we used a target-capture approach to sequence nuclear loci of 174 accessions of 124 species, including 16 outgroup species from across the family (Alstroemeriaceae). We included 43 individuals of B. edulis from across its range to assess species monophyly and identify infraspecific phylogeographic patterns. We model biogeographic range evolution in Bomarea and test if Andean orogeny has impacted its diversification. We find that Bomarea originated in the central Andes during the mid-Miocene, then spread north, following the trajectory of major mountain uplift events. Most observed speciation events occurred during the Pleistocene, while global climate cooled and oscillated and the northern Andes achieved their current form. Furthermore, we find that Andean lineages diversified faster than their non-Andean relatives. These results demonstrate a clear macroevolutionary signal of Andean orogeny on this neotropical radiation.