bluuebunny/crossref_metadata_2025_split huggingface dataset:
Erbb4 deletion from fast-spiking interneurons causes psychosis-relevant neuroimaging phenotypes
Authors: Kiemes A. , Serrano Navacerrada M. E. , Kim E. , Randall K. , Simmons C. , Rojo Gonzalez L. , Petrinovic M.M. , Lythgoe D.J. , Rotaru D. , Di Censo D. , Hirshler L. , Barbier E. L. , Vernon A. C. , Stone J. M. , Davies C. , Cash D. , Modinos G. 
Published: March 2022

AbstractConverging lines of evidence suggest that dysfunction of cortical parvalbumin-expressing (PV+) GABAergic interneurons is a core feature of psychosis. This dysfunction is thought to underlie neuroimaging abnormalities commonly found in patients with psychosis, particularly in the hippocampus. These include increases in resting cerebral blood flow (CBF) and levels of glutamatergic metabolites, and decreases in binding of GABAA α5 receptors and the synaptic density marker synaptic vesicle glycoprotein 2A (SV2A). However, direct links between PV+ interneuron dysfunction and these neuroimaging readouts have yet to be established. Conditional deletion of a schizophrenia susceptibility gene, the tyrosine kinase receptor Erbb4, from cortical and hippocampal PV+ interneurons leads to several synaptic, behavioral and cognitive phenotypes relevant to psychosis in mice. Here, we investigated how this PV+ interneuron disruption affects the hippocampal in vivo neuroimaging readouts in the Erbb4 model. Adult Erbb4 conditional mutant mice (Lhx6-Cre;Erbb4F/F, n=12) and their wild-type littermates (Erbb4F/F, n=12) were scanned in a 9.4T magnetic resonance scanner to quantify CBF and glutamatergic metabolite levels (glutamine, glutamate, GABA). Subsequently, we assessed GABAA receptors and SV2A density using quantitative autoradiography. Erbb4 mutant mice showed significantly elevated CBF and glutamine levels, as well as decreased SV2A density compared to wild-type littermates. No significant GABAA receptor density differences were identified. These findings demonstrate that specific disruption of cortical PV+ interneurons in mice recapitulate some of the key neuroimaging findings in psychosis patients, and link PV+ interneuron deficits to non-invasive, translational measures of brain function and neurochemistry that can be used across species.
Algae community structure and relation to environmental factors in the Hulanhe Wetland, Northeast China
Authors: Hui Hongkuan , Wang Min , Li Yunlong , Liu Yubin 
Published: March 2022

AbstractThe distribution characteristic of algae community was evaluated in eight sampling sites based on a monthly survey during May to October 2020 and 2021 in the Hulanhe Wetland, Northeast China. Algae and water environmental factors including water temperature (T), pH, Conductivity (Cond.), biochemical oxygen demand (BOD), chemical oxygen demand (COD), total organic carbons (TOC), total phosphorus (TP) and nitrogen (TN) were investigated, and a total of 216 taxa were identified by microscope. The algae community was dominated by Bacillariophyta, Chlorophyta and Euglenophyta. Species such asMelosira granulate, Cyclotella meneghiniana, Navicula cryptocephalaandPandorina morumwere the most common species. Significant difference of the algae composition and abundance were found in the different sampling sites. Species composition in H8 were different variously with other sites, provide a good chance for us to study the tolerance of the species, compared with other sites, several pollution indicator species were observed. According to canonical correspondence analysis (CCA), TN and TP were the main environmental factors affecting the distribution of algae. Furthermore, temperature and dissolved oxygen were also important to the algae community. It is suggested that the relationship between algae community and environmental factors can point to new directions in future studies on the water quality and habitat conditions in a wetland.
The origin, epidemiology and phylodynamics of HIV-1 CRF47_BF
Authors: Hill Gracelyn , Pérez-Losada Marcos , Delgado Elena , Benito Sonia , Montero Vanessa , Gil Horacio , Sánchez Mónica , Cañada-García Javier , García-Bodas Elena , Crandall Keith A. , Thomson Michael M ,   The Spanish Group for the Study of New HIV Diagnoses
Published: March 2022

AbstractCRF47_BF is a circulating recombinant form (CRF) of the human immunodeficiency virus type 1 (HIV-1), the etiological agent of AIDS. CRF47_BF represents one of 19 CRFx_BFs and has a geographic focus in Spain, where it was first identified in 2010. Since its discovery, CRF47_BF has expanded considerably in Spain, predominantly through heterosexual contact (∼56% of the infections). Little is known, however, about the origin and diversity of this CRF or its epidemiological correlates, as very few samples have been available so far. This study conducts a phylogenetic analysis with representatives of all CRFx_BF sequence types along with HIV-1 M Group subtypes to place the CRF47_BF sequences in a definitive phylogenetic context. The CRFx_BF sequences cluster into a single, not well supported, clade that includes their dominant parent subtypes (subtype B and subtype F). This clade also includes subtype D and excludes subsubtype F2. The CRF47_BF sequences all share a most recent common ancestor. Further analysis of this clade couples CRF47_BF protease-reverse transcriptase sequences and epidemiological data from an additional 87 samples collected throughout Spain, coupled with additional CRF47_BF database sequences from Brazil and Spain to investigate the origin and phylodynamics of CRF47_BF. The Spanish region with the highest proportion of CRF47_BF samples in the data set was the Basque Country (43.7%) with Navarre next highest at 19.5%. We include in our analysis epidemiological data on host sex, mode of transmission, time of collection, and geographic region. The phylodynamic analysis indicates that CRF47_BF originated in Brazil around 1993-1994 and spread to Spain from Brazil in approximately 1999-2000. The virus spread rapidly throughout Spain with increasing population sizes prior to 2010 and again between 2010 and 2017 with population declines to 2019 and a steady state through 2020. Three strongly supported clusters associated with Spanish regions (Basque Country, Navarre, and Aragon), together comprising 60.8% of the Spanish samples, were identified, one of which was also associated with transmission among men who have sex with men. The expansion in Spain of CRF47_BF, together with that of other CRFs and subtype variants of South American origin, previously reported, reflects the increasing relationship between the South American and European HIV-1 epidemics.
A non-coding single nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation
Authors: Yanchus Connor , Drucker Kristen L. , Kollmeyer Thomas M. , Tsai Ricky , Liang Minggao , Jiang Lingyan , Pawling Judy , Ali Asma , Decker Paul , Kosel Matt , Panda Arijit , Malik Ahmad , Al-Zahrani Khalid N. , Hernandez J. Javier , Ahmed Musaddeque , Loganathan Sampath Kumar , Trcka Daniel , Michaelraj Antony , Fortin Jerome , Mazrooei Parisa , Zhou Lily , Elia Andrew , Lupien Mathieu , He Housheng Hansen , Wang Liguo , Abyzov Alexej , Dennis James W. , Wilson Michael D. , Wrana Jeffrey , Lachance Daniel , Wrensch Margaret , Wiencke John , Pennacchio Len A. , Dickel Diane E. , Visel Axel , Taylor Michael , Zadeh Gelareh , Dirks Peter , Eckel-Passow Jeanette E. , Mak Tak , Kvon Evgeny , Jenkins Robert B. , Schramek Daniel 
Published: March 2022

AbstractEstablishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single nucleotide polymorphism rs55705857 (A>G), which confers a 6-fold increased risk of IDH-mutant low-grade glioma (LGG) and is amongst the highest genetic associations with cancer. By fine-mapping the locus, we reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the Myc promoter and increased Myc expression. To functionally test rs55705857, we generated an IDH1R132H-driven LGG mouse model and show that mutating the highly conserved, orthologous mouse rs55705857 locus dramatically accelerated tumor development from 463 to 172 days and increased penetrance from 30% to 75%. Overall, our work generates new LGG models and reveals mechanisms of the heritable predisposition to lethal glioma in ∼40% of LGG-patients.
Non-literal language processing is jointly supported by the language and Theory of Mind networks: Evidence from a novel meta-analytic fMRI approach
Authors: Hauptman Miriam , Blank Idan , Fedorenko Evelina 
Published: March 2022

AbstractGoing beyond the literal meaning of utterances is key to communicative success. However, the mechanisms that support non-literal inferences remain debated. Using a novel meta-analytic approach, we evaluate the contribution of linguistic, social-cognitive, and executive mechanisms to non-literal interpretation. We identified 74 fMRI experiments (n=1,430 participants) from 2001-2021 that contrasted non-literal language comprehension with a literal control condition, spanning ten phenomena (e.g., metaphor, irony, indirect speech). Applying the activation likelihood estimation approach to the 825 activation peaks yielded six left-lateralized clusters. We then evaluated the locations of both the individual-study peaks and the clusters against probabilistic functional atlases (cf. macroanatomy, as is typically done) for three candidate brain networks—the language-selective network (Fedorenko et al., 2011), which supports language processing, the Theory of Mind (ToM) network (Saxe & Kanwisher, 2003), which supports social inferences, and the domain-general Multiple-Demand (MD) network (Duncan, 2010), which supports executive control. These atlases were created by overlaying individual activation maps of participants who performed robust and extensively validated ‘localizer’ tasks that target each network in question (n=806 for language; n=198 for ToM; n=691 for MD). We found that both the individual-study peaks and the ALE clusters fell primarily within the language network and the ToM network. These results suggest that non-literal processing is supported by both i) mechanisms that process literal linguistic meaning, and ii) mechanisms that support general social inference. They thus undermine a strong divide between literal and non-literal aspects of language and challenge the claim that non-literal processing requires additional executive resources.
A versatile pattern-forming cortical circuit based on Rho, F-actin, Ect2, and RGA-3/4
Authors: Michaud Ani , Leda Marcin , Swider Zachary T. , Kim Songeun , He Jiaye , Landino Jennifer , Valley Jenna R. , Huisken Jan , Goryachev Andrew B. , von Dassow George , Bement William 
Published: March 2022

AbstractMany cells can generate complementary traveling waves of actin filaments (F-actin) and cytoskeletal regulators. This phenomenon, termed cortical excitability, results from coupled positive and negative feedback loops of cytoskeletal regulators. The nature of these feedback loops, however, remains poorly understood. We assessed the role of the Rho GAP RGA-3/4 in the cortical excitability that accompanies cytokinesis in both frog and starfish. RGA-3/4 localizes to the cytokinetic apparatus, “chases” Rho waves in an F-actin-dependent manner and, when co-expressed with the Rho GEF Ect2, is sufficient to convert the normally quiescent, immature Xenopus oocyte cortex into a dramatically excited state. Experiments and modeling show that changing the ratio of RGA-3/4 to Ect2 produces a range of cortical behaviors from pulses to complex waves of Rho activity. We conclude that RGA-3/4, Ect2, Rho and F-actin form the core of a circuit that drives a diverse range of cortical behaviors, and demonstrate that the immature oocyte is a powerful model for characterizing these dynamics.SummaryMichaud et al. identify Ect2 and RGA-3/4 as core components of the cortical excitability circuit associated with cytokinesis. Additionally, they demonstrate that the immature Xenopus oocyte is a powerful model for characterizing excitable dynamics.
Neuroendocrinology of the lung revealed by single cell RNA sequencing
Authors: Kuo Christin S. , Darmanis Spyros , Diaz de Arce Alex , Liu Yin , Almanzar Nicole , Wu Timothy T.H. , Quake Stephen R. , Krasnow Mark A. 
Published: March 2022

ABSTRACTPulmonary neuroendocrine cells (PNECs) are sensory epithelial cells that transmit airway status to the brain via sensory neurons and locally via CGRP and GABA. Several other neuropeptides and neurotransmitters have been detected in various species, but the number, targets, functions, and conservation of PNEC signals are largely unknown. We used scRNAseq to profile hundreds of the rare mouse and human PNECs. This revealed >40 PNEC neuropeptide and peptide hormone genes, most cells expressing unique combinations of 5-18 genes. Peptides are packaged in separate vesicles, release presumably regulated by the distinct, multimodal combinations of sensors expressed by each PNEC. Expression of cognate receptors predicts an array of local targets, and we show the new PNEC signal angiotensin directly activates innervating sensory neurons. Many signals lack lung targets so may have endocrine activity like those of PNEC- derived carcinoid tumors. PNECs are an extraordinarily rich and diverse signaling hub rivaling the enteroendocrine system.
Ultrastructural characterisation of young and aged dental enamel by atomic force microscopy
Authors: Leiva-Sabadini Camila , Schuh Christina MAP , Barrera Nelson P , Aguayo Sebastian 
Published: March 2022

AbstractRecent advances in atomic force microscopy (AFM) have allowed the characterisation of dental-associated biomaterials and biological surfaces with high-resolution and minimal sample preparation. In this context, the topography of dental enamel – the hardest mineralised tissue in the body – has been explored with AFM-based approaches at the micro-scale. With age, teeth are known to suffer changes that can impact their structural stability and function; however, changes in enamel structure because of ageing have not yet been explored with nanoscale resolution. Therefore, the aim of this exploratory work was to optimise an approach to characterise the ultrastructure of dental enamel and determine potential differences in topography, hydroxyapatite (HA) crystal size, and surface roughness at the nanoscale associated to ageing. For this, a total of six teeth were collected from human donors from which enamel specimens were prepared. By employing AC mode imaging, HA crystals were characterised in both transversal and longitudinal orientation with high-resolution in environmental conditions. Sound superficial enamel displayed the presence of a pellicle-like coating on its surface, that was not observable on cleaned specimens. Acidetching exposed crystals that were imaged and morphologically characterised in highresolution at the nanoscale in both the external and internal regions of enamel in older and younger specimens. Our results demonstrated important individual variations in HA crystal width and roughness parameters across the analysed specimens; however, an increase in surface roughness and decrease in HA width was observed for the pooled older external enamel group compared to younger specimens. Overall, high-resolution AFM was an effective approach for the qualitative and quantitative characterisation of human dental enamel ultrastructure at the nanometre range. Future work should focus on exploring the ageing of dental enamel with increased sample sizes to compensate for individual differences as well as other potential confounding factors such as behavioural habits and mechanical forces.
Automated detection of axonal damage along white matter tracts in acute severe traumatic brain injury
Authors: Maffei Chiara , Gilmore Natalie , Snider Samuel B. , Foulkes Andrea S. , Bodien Yelena G. , Yendiki Anastasia , Edlow Brian L. 
Published: March 2022

AbstractNew techniques for individualized assessment of white matter integrity are needed to detect traumatic axonal injury (TAI) and predict outcomes in critically ill patients with acute severe traumatic brain injury (TBI). Diffusion MRI tractography has the potential to quantify white matter microstructure in vivo and has been used to characterize tract-specific changes following TBI. However, tractography is not routinely used in the clinical setting to assess the extent of TAI, in part because focal lesions reduce the robustness of automated methods. Here, we propose a pipeline that combines automated tractography reconstructions of 40 white matter tracts with multivariate analysis of along-tract diffusion metrics to assess the presence of TAI in individual patients with acute severe TBI. We used the Mahalanobis distance to identify abnormal white matter tracts in each of 18 patients with acute severe TBI as compared to 33 healthy subjects. In all patients for which a FreeSurfer anatomical segmentation could be obtained (17 of 18 patients), including 13 with focal lesions, the automated pipeline successfully reconstructed a mean of 37.5 +/- 2.1 white matter tracts without the need for manual intervention. A mean of 2.5 +/- 2.1 tracts resulted in partial or failed reconstructions and needed to be reinitialized upon visual inspection. The pipeline detected at least one abnormal tract in all patients (mean: 9.07 +/- 7.91) and could accurately discriminate between patients and controls (AUC: 0.91). The individual patients’ profiles showed the number and neuroanatomic location of abnormal tracts varied across patients and levels of consciousness. The premotor, temporal, and parietal sections of the corpus callosum were the most commonly damaged tracts (in 10, 9, and 8 patients respectively), consistent with histological studies of TAI. TAI measures were not associated with concurrent behavioral measures of consciousness. In summary, we provide proof-of-principle evidence that an automated tractography pipeline has translational potential to detect and quantify TAI in individual patients with acute severe traumatic brain injury.
Accelerating Minimap2 for accurate long read alignment on GPUs
Authors: Sadasivan Harisankar , Maric Milos , Dawson Eric , Iyer Vishanth , Israeli Johnny , Narayanasamy Satish 
Published: March 2022

ABSTRACTLong read sequencing technology is becoming increasingly popular for Precision Medicine applications like Whole Genome Sequencing (WGS) and microbial abundance estimation. Minimap2 is the state-of-the-art aligner and mapper used by the leading long read sequencing technologies, today. However, Minimap2 on CPUs is very slow for long noisy reads. ∼60-70% of the run-time on a CPU comes from the highly sequential chaining step in Minimap2. On the other hand, most Point-of-Care computational workflows in long read sequencing use Graphics Processing Units (GPUs). We present minimap2-accelerated (mm2-ax), a heterogeneous design for sequence mapping and alignment where minimap2’s compute intensive chaining step is sped up on the GPU and demonstrate its time and cost benefits.We extract better intra-read parallelism from chaining without loosing mapping accuracy by forward transforming Minimap2’s chaining algorithm. Moreover, we better utilize the high memory available on modern cloud instances apart from better workload balancing, data locality and minimal branch divergence on the GPU. We show mm2-ax on an NVIDIA A100 GPU improves the chaining step with 5.41 - 2.57X speedup and 4.07 - 1.93X speedup : costup over the fastest version of Minimap2, mm2-fast, benchmarked on a Google Cloud Platform instance of 30 SIMD cores.
Millennials' online perceptions: the role of cultural characteristics in creating e-loyalty
Authors: Li Jie , Ul Haq Junaid , Hussain Sajjad 
Published: March 2022

PurposeMillennials, a cohort of young consumers, are the primary group of shoppers via e-commerce. This study aims to identify Chinese individual cultural values in millennials and examine the role of perceived shopping (hedonic and utilitarian) values in creating e-loyalty.Design/methodology/approachData were collected from 296 Chinese millennials who use online shopping websites and apps. Confirmatory factor analysis was used to examine the validity and reliability of the methodology. Structural equation modeling was employed to test the proposed hypotheses.FindingsAll hypotheses were supported except one: the respondents rejected the impact of the face value on utilitarianism. The findings confirmed that Chinese individual cultural characteristics (face and Yuan) impact perceived shopping values (hedonic and utilitarian). Furthermore, these shopping values significantly influence e-loyalty.Research limitations/implicationsThe study's findings suggest some implications that academicians and market practitioners should consider. Additional implications for business managers focus on cultural characteristics, strong local teams, market-based approaches and long-term strategies.Originality/valueThe present work highlights the online shopping behavior of Chinese millennials by exploring e-loyalty, considering its two dimensions.
Effects of replacement of fat and NaCl by hydrolyzed collagen and mix of herbs on quality properties of chicken hamburger
Authors: Santana Neto Deocleciano Cassiano de , de Lima Flávio Bruno Soares , Freire Luís Flávio da Silva , Santos Vanessa da Costa , Rodrigues David Santos , Ferreira Valquiria Cardoso da Silva , Grisi Cristiani Viegas Brandão , Silva Fábio Anderson Pereira da 
Published: March 2022

PurposeThis study aims to assess the influence of partial and simultaneous substitution of fat and sodium by hydrolyzed collagen and mix of herbs (MH) in chicken hamburgers, on the physical properties and proximal composition.Design/methodology/approachFive formulations were developed: (1) HCON–without adding collagen and MH; (2) C25M25–adding 25% of collagen and 25% of MH; (3) C25M50–adding 25% of collagen and 50% of MH; (4) C50M25–adding 50% of collagen and 25% of MH and (5) C50M50–adding 50% of collagen and 50% of MH. Chicken hamburgers were analyzed by proximal composition, sodium content, collagen and color analysis. The influence of treatments on texture profile, cooking performance and lipid oxidation of chicken hamburger was also investigated.FindingsThere was reduction in lipid and sodium for modified formulations compared with the HCON. There was great influence for some parameters, such as luminosity, cooking performance and texture profile. The formulation C50M50 showed the best cooking performance when compared to the others.Originality/valueThe formulation adding 50% of collagen and 50% of MH showed the highest yield and water retention (WR), with the least reduction in diameter and shrinkage, as well as presenting the best indexes of the texture profile and the lowest oxidation index, being recommended as the best combination of fat and sodium replacement.