bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neck Pain Caused by Giant Dorsal Lipoma
Authors: Choi Jong Yun , Choi Young Jae , Seo Bommie Florence 
Published: July 2022

Giant lipomas are uncommon in the neck or craniofacial region. A 55-year-old male presented with a large pendulous mass arising from the dorsal aspect of his neck, which he had known about for 20 years. Discomfort during sleeping, frequent headaches, and chronic neck pain were his chief complaints. Computed topography revealed a well-circumscribed lipomatous lesion. A decrease in cervical spine lordosis was noted on sagittal x-rays. Surgical excision with local flap coverage was performed. The specimen weighed 2800 g. The patient reported immediate resolution of neck pain, and complete resolution of headaches following surgery. An increase in the degree of lordosis was seen in sagittal x-rays. Histopathological results confirmed the diagnosis of lipoma. Although most giant dorsal neck lipomas are benign, they may be a cause for neck pain, headaches and degenerative changes in the cervical spine, undermining the quality of life. Such symptoms should be assessed, and removal recommended.
Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovénbreen, Arctic
Authors: Huang Jun , Peng Xiaoya , Qin Kun , Liu Yixuan , Niu Jingjing , Liu Jia , Dong Jielin , Zhang Yongping , Peng Fang 
Published: July 2022

A rod-shaped, Gram-stain-negative, non-motile and aerobic bacterium, designated Q8-18T, was isolated from soil of glacier foreland in Austre Lovénbreen, Arctic, and subjected to a polyphasic taxonomic study. Strain Q8-18T grew optimally at 20 °C, pH 5.0–8.0 and in the presence of 0–1.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q8-18T belonged to the family

Sphingobacteriaceae

. Strain Q8-18T showed the highest sequence similarity to

Pedobacter mendelii

CCM 8685T (96.8%),

Pedobacter lithocola

CCM 8691T (96.8%),

Pedobacter roseus

CL-GP80T (96.7%),

Pedobacter changchengzhani

E01020T (96.7%),

Pedobacter alluvionis

DSM 19624T (96.6%),

Pedobacter jejuensis

THG-DR3T (96.3%),

Pedobacter ginsengiterrae

DCY49T (95.9%) and

Pedobacter jamesrossensis

CCM 8689T (95.9%). A whole genome-level comparison of strain Q8-18T with

P. roseus

CL-GP80T,

P. changchengzhani

E01020T,

P. alluvionis

DSM 19624T and

Pedobacter heparinus

LMG 10339T revealed average nucleotide identity values of 77.0, 76.0, 77.0 and 70.4%, respectively. The only respiratory isoprenoid quinone was menaquinone-7. The polar lipid profile of strain Q8-18T was found to contain one phosphatidylethanolamine, eight unidentified aminolipids, one aminophospholipids and five unidentified lipids. The G+C content of the genomic DNA was determined to be 35.4 mol%. The main fatty acids were summed feature 3 (comprising C16 : 1
ω7c and/or C16 : 1
ω6c), iso-C15 : 0 and anteiso-C15 : 0. On the basis of the evidence presented in this study, a novel species of the genus

Pedobacter

, Pedobacter mucosus sp. nov., is proposed, with the type strain Q8-18T (=CCTCC AB 2020009T=KCTC 82636T).
Sinomicrobium kalidii sp. nov., an indole-3-acetic acid-producing endophyte from a shoot of halophyte Kalidium cuspidatum
Authors: Li Lu-Fan , Xu Lian , Li Wen-Hao , Sun Ji-Quan 
Published: July 2022

To better understand the effects of endophytic bacteria on halophytes, a bacteria that produced indole-3-acetic acid and 1-aminocyclopropane-1-carboxylic acid deaminase, designated HD2P242T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. The cells of strain HD2P242T were Gram-stain-negative, strictly aerobic, motile by gliding, non-spore-forming and rod-shaped. Strain HD2P242T grew at pH 6.0–9.0 (optimum, pH 7.0) and 10–45 °C (optimum 37 °C), in the presence of 0–8 % (w/v) NaCl (optimum, 4 %). The strain was positive for oxidase and catalase. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both showed that strain HD2P242T clustered with

Sinomicrobium pectinilyticum

5DNS001T and

S. oceani

SCSIO 03483T, and had 95.6, 94.3 and <94.3 % 16S rRNA gene similarities to

S. pectinilyticum

5DNS001T,

S. oceani

SCSIO 03483T and all the other current type strains. Strain HD2P242T contained menaquinone 6 as its sole respiratory quinone. Its major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and an unidentified lipid. The major fatty acids were iso-C17 : 0, iso-C16 : 0 3-OH, anteiso-C17 : 0 and summed feature 6 (C19 : 1
ω9c and/or C19 : 1
ω11c). The genome consisted of a 5 364 211 bp circular chromosome, with a G+C content of 45.1 mol%, predicting 4391 coding sequence genes, 47 tRNA genes and two rRNA operons. The average nucleotide identity based on blast and the digital DNA–DNA hybridization values of strain HD2P242T with

S. oceani

SCSIO 03483T and

S. pectinilyticum

5DNS001T were 73.8 and 77.0%, and 22.3 and 22.2%, respectively. The comparative genome analysis showed that the pan-genomes of strain HD2P242T and three

Sinomicrobium

type strains possessed 4236 clusters, whereas the core genome possessed 2162 clusters, which accounted for 52.3 % of all the clusters. The genomic analysis revealed that all four

Sinomicrobium

members could utilize d-glucose by the glycolysis–gluconeogenesis pathway or the pentose phosphate pathway. The tricarboxylic acid cycle was utilized as a metabolic centre. The phylogenetic, physiological and phenotypic characteristics allowed the discrimination of strain HD2P242T from its phylogenetic relatives. Therefore, Sinomicrobium kalidii sp. nov. is proposed, and the type strain is HD2P242T (=CGMCC 1.19025T=KCTC 92136T).
The specificity of different-distance connections in human structural connectomes
Authors: Yang Yaqian , Zheng Yi , Zhen Yi , Tang Shaoting , Zheng Hongwei , Zheng Zhiming 
Published: July 2022

AbstractBrain structural connectomes underpin complex cognitive processes. To date, abundant organizational features have been distilled by network-based tools, including hubs, modules, and small-worldness. However, these features are often devoid of spatial characteristics which directly shape connection formation. By considering the spatial embedding of brain networks, we reveal the connection specificity, that is, the similarity of similar-distance connections and the dissimilarity of different-distance connections. It is induced by the whole-brain connection length distribution, allowing areas to send and receive diverse signals through different-distance connections. Based on it, areas’ functional repertoires are associated with their connection length profiles, and meanwhile, length dispersion and clustering coefficients can be integrated into a hierarchy whose age-related degeneration may be related to cognitive decline. These results construct a putative bridge between brain spatial, topological, and functional features, expanding our understanding of how different architectures complement and reinforce each other to achieve complicated brain functions.
An Experimental Analysis of the Fine-Scale Effects of Nest Ectoparasites on Incubation Behavior
Authors: Hund Amanda K. , McCahill Kelley A. , Hernandez Mara , Turbek Sheela P. , Ardia Daniel R. , Terrien Ryan C. , Safran Rebecca J. 
Published: July 2022

ABSTRACTAvian incubation is a highly complex, adjustable behavior essential to embryo development and survival. When incubating, parents face a tradeoff between investing in incubation to maintain optimal temperatures for egg development or in self-maintenance behaviors to ensure their own survival and future reproduction. Because nest ectoparasites are costly and can reduce nestling quality and survival, infections could shift parental investment in current vs. future offspring. However, it is not well understood whether birds change investment in incubation in response to nest ectoparasitism, particularly in the context of other factors that are known to influence incubation behavior, such as ambient temperature, clutch size, and embryo development. We hypothesized that parents could respond to nest parasites by 1) investing more in incubation to promote the development of high-quality offspring to help offset the cost of parasites, 2) investing less in incubation or even abandoning their nest during incubation to save resources for future reproduction, or 3) being unresponsive to parasite infections, as incubation is more constrained by other factors. We tested these hypotheses by experimentally removing and adding mites in barn swallow nests at the start of incubation and deploying thermocouple eggs to measure egg temperatures at one-minute intervals until hatching. We found that while ambient temperature, clutch initiation date, embryo age, and clutch size were the main factors driving variation in egg conditions and parental incubation behavior, parasitized nests had higher mean egg temperatures, which could aid in nestling immune development. However, despite more optimal developmental temperatures, eggs in parasitized nests also had lower hatching success. Our results indicate that incubation is a dynamic behavior that is largely driven by the constraints of maintaining appropriate egg temperatures for development. Although quite costly upon hatching, ectoparasites appear to play a relatively minor role in driving variation in parental incubation investment.LAY SUMMARYIncubation is a complex behavior shaped by both internal and external factors.Ectoparasites often decrease quality and survival of nestlings and could influence investment in incubation because of tradeoffs in how parents spend energy.We manipulated parasites in barn swallow nests and used fake eggs with temperature sensors to collect data on egg temperatures and parental behavior throughout incubation.We found that other factors were the main drivers of variation in incubation behavior, but that eggs in parasite nests were warmer on average, which could help nestlings better cope with parasites upon hatching.Despite more optimal developmental temperatures, eggs in parasitized nests had lower hatching success.Although quite costly to nestlings, ectoparasites played a minor role in shaping parental incubation behavior.
Human iPSC-derived neuron of 16p11.2 deletion reveals haplotype-specific expression of MAPK3 and its contribution to variable NDD phenotypes
Authors: Liu Fang , Liang Chen , Li Zhengchang , Zhao Sen , Shangguan Shaofang , Yuan Haiming , Yao Ruen , Qin Zailong , Zhang Shujie , Zou Liping , Gao Zhijie , Chen Qian , Wen Suiwen , Peng Jing , Yin Fei , Chen Fei , Qiu Xiaoxia , Luo Jinsi , Xie Yingjun , Lu Dian , Zhang Yu , Xie Hua , Wang Hongying , Cui Xiaodai , Wang Jian , Huang Hailiang , Liu Ruize , Sun Xiaofang , Chen Chao , Wu Nan , Liu Chunyu , Shen Yiping , Gusella James F. , Chen Xiaoli 
Published: July 2022

ABSTRACTRecurrent proximal 16p11.2 deletion (16p11.2del) is risk factor of diverse neurodevelopmental disorders (NDDs) with variable penetrance. Although previous human induced pluripotent stem cell (hiPSC) models of 16p11.2del confirmed disrupted neuron development, it is not known which gene(s) at this interval are mainly responsible for the abnormal cellular phenotypes and how the NDD penetrance is regulated. After haplotype phasing of 16p11.2 region, we generated hiPSCs for two 16p11.2del families with distinct residual haplotypes and variable NDD phenotypes. We also differentiated the hiPSCs to cortical neural cells and demonstrated MAPK3 as a driver signal of 16p11.2 region contributing to the dysfunctions in multiple pathways related to neuron development, which leads to altered morphological or electrophysiological properties in neuron cells. Furthermore, residual haplotype-specific MAPK3 expression was identified in 16p11.2del neuron cells, associating MAPK3 down-expression with the minor allele of the residual haplotype. Ten SNPs of the residual haplotype are mapped as enhancer SNPs (enSNPs) of MAPK3, eight enSNPs were functionally validated by luciferase assays, implying enSNPs contribute to residual haplotype-specific MAPK3 expression via cis-regulation. Finally, the analyses of three different patient cohorts showed that the residual haplotype of 16p11.2del is associated with variable NDD phenotypes.
Layer-specific, retinotopically-diffuse modulation in human visual cortex by emotional faces
Authors: Liu Tina T. , Fu Jason Z , Chai Yuhui , Japee Shruti , Chen Gang , Ungerleider Leslie G. , Merriam Elisha P. 
Published: July 2022

AbstractEmotionally expressive faces evoke enhanced neural responses in multiple brain regions, a phenomenon thought to depend critically on the amygdala. This emotion-related modulation is evident even in primary visual cortex (V1), providing a potential neural substrate by which emotionally salient stimuli can affect perception. How does emotional valence information, computed in the amygdala, reach V1? Here we use high-resolution functional MRI to investigate the layer profile and retinotopic distribution of neural activity specific to emotional facial expressions. Across three experiments, human participants viewed centrally presented face stimuli varying in emotional expression and performed a gender judgment task. We found that facial valence sensitivity was evident only in superficial cortical layers and was not restricted to the retinotopic location of the stimuli, consistent with diffuse feedback-like projections from the amygdala. Together, our results provide a feedback mechanism by which the amygdala directly modulates activity at the earliest stage of visual processing.
Parallel processing relies on a distributed, low-dimensional cortico-cerebellar architecture
Authors: Müller Eli J. , Hou Kevin Y. , Palesi Fulvia , Tan Joshua , Close Thomas , Gandini Wheeler-Kingschott Claudia A.M. , D’Angelo Egidio , Calamante Fernando , Shine James M. 
Published: July 2022

AbstractA characteristic feature of human cognition is our ability to ‘multi-task’ – performing two or more tasks in parallel – particularly when one task is well-learned. How the brain supports this capacity remains poorly understood. Most past studies have focussed on identifying the areas of the brain – typically the dorsolateral prefrontal cortex – that are required to navigate information processing bottlenecks. In contrast, we take a systems neuroscience approach to test the hypothesis that the capacity to conduct effective parallel processing relies on a distributed architecture that interconnects the cerebral cortex with the cerebellum. The latter structure contains over half of the neurons in the adult human brain, and is well-suited to support the fast, effective, dynamic sequences required to perform tasks relatively automatically. By delegating stereotyped within-task computations to the cerebellum, the cerebral cortex can be freed up to focus on the more challenging aspects of performing the tasks in parallel. To test this hypothesis, we analysed task-based fMRI data from 50 participants who performed a task in which they either balanced an avatar on a screen (‘Balance’), performed serial-7 subtractions (‘Calculation’) or performed both in parallel (‘Dual-Task’). Using a set of approaches that include dimensionality reduction, structure-function coupling and time-varying functional connectivity, we provide robust evidence in support of our hypothesis. We conclude that distributed interactions between the cerebral cortex and cerebellum are crucially involved in parallel processing in the human brain.
Structural epitope profiling identifies antibodies associated with critical COVID-19 and long COVID
Authors: Kearns Patrick K.A. , Dixon Charles , Badonyi Mihaly , Lee Kim , Czapiewski Rafal , Fleming Olivia , Nadukkandy Prajitha , Gerasimivicius Lukas , Sahputra Rinal , Potts Bethany , Benton Sam , Guy Jacky , Neilson Scott , Wise Helen , Jenks Sara , Templeton Kate ,   CIRCO, Dold Christina , Lambe Teresa , Pollard Andrew , Mentzer Alexander J , Knight Julian C ,   COMBAT, Dunachie Susanna , Klenerman Paul , Barnes Eleanor , Carson Alan , McWhirter Laura , Hussell Tracy , Fragkoudis Rennos , Rosser Susan , Cavanagh David , Cowan Graeme , Menon Madhvi , Marsh Joseph A. , Kleinjan Dirk A. , Gilbert Nick 
Published: July 2022

AbstractEven within a single protein, antibody binding can have beneficial, neutral, or harmful effects during the response to infection. Resolving a polyclonal antibody repertoire across a pathogen’s proteome to specific epitopes may therefore explain much of the heterogeneity in susceptibility to infectious disease. However, the three-dimensional nature of antibody-epitope interactions makes the discovery of non-obvious targets challenging. We implemented a novel computational method and synthetic biology pipeline for identifying epitopes that are functionally important in the SARS-CoV-2 proteome and identified an IgM-dominant response to an exposed Membrane protein epitope which to our knowledge is the strongest correlate of severe disease identified to date (adjusted OR 72.14, 95% CI: 9.71 – 1300.15), stronger even than the exponential association of severe disease with age. We also identify persistence (> 2 years) of this IgM response in individuals with longCOVID, and a correlation with fatigue and depression symptom burden. The repetitive arrangement of this epitope and the pattern of isotype class switching is consistent with this being a previously unrecognized T independent antigen. These findings point to a coronavirus host-pathogen interaction characteristic of severe virus driven immune pathology. This epitope is a promising vaccine and therapeutic target as it is highly conserved through SARS-CoV-2 variant evolution in humans to date and in related coronaviruses (e.g. SARS-CoV), showing far less evolutionary plasticity than targets on the Spike protein. This provides a promising biomarker for longCOVID and a target to complement Spike-directed vaccination which could broaden humoral protection from severe or persistent disease or novel coronavirus spillovers.One-Sentence SummaryUsing a novel protein-structure-based B cell epitope discovery method with a wide range of possible applications, we have identified a simple to measure host-pathogen antibody signature associated with severe COVID-19 and longCOVID and suggest the viral Membrane protein contains an epitope that acts as a T independent antigen during infection triggering extrafollicular B cell activation.
Systems-level patterns in biological processes are changed under prolongevity interventions and across biological age
Authors: Watanabe Kengo , Wilmanski Tomasz , Baloni Priyanka , Robinson Max , Garcia Gonzalo G. , Hoopmann Michael R. , Midha Mukul K. , Baxter David H. , Maes Michal , Morrone Seamus R. , Crebs Kelly M. , Kapil Charu , Kusebauch Ulrike , Wiedrick Jack , Lapidus Jodi , Lovejoy Jennifer C. , Magis Andrew T. , Lausted Christopher , Roach Jared C. , Glusman Gustavo , Cummings Steven R. , Schork Nicholas J. , Price Nathan D. , Hood Leroy , Miller Richard A. , Moritz Robert L. , Rappaport Noa 
Published: July 2022

AbstractAging manifests as progressive deterioration in cellular and systemic homeostasis, requiring systems-level perspectives to understand the gradual molecular dysregulation of underlying biological processes. Here, we report systems-level changes in the molecular regulation of biological processes under multiple lifespan-extending interventions in mice and across age in humans. In mouse cohorts, Differential Rank Conservation (DIRAC) analyses of liver proteomics and transcriptomics show that mechanistically distinct prolongevity interventions tighten the regulation of aging-related biological modules, including fatty acid metabolism and inflammation processes. An integrated analysis of liver transcriptomics with mouse genome-scale metabolic model supports the shifts in fatty acid metabolism. Additionally, the difference in DIRAC patterns between proteins and transcripts suggests biological modules which may be tightly regulated via cap-independent translation. In a human cohort spanning the majority of the adult lifespan, DIRAC analyses of blood proteomics and metabolomics demonstrate that regulation of biological modules does not monotonically loosen with age; instead, the regulatory patterns shift according to both chronological and biological ages. Our findings highlight the power of systems-level approaches to identifying and characterizing the biological processes involved in aging and longevity.
Type 1 and type 2 diabetes mellitus: Clinical outcomes due to COVID-19. Protocol of a systematic literature review
Authors: Pérez Bedoya Juan Pablo , Muñoz Alejandro Mejía , Barengo Noël Christopher , Diaz Valencia Paula Andrea 
Published: July 2022

AbstractIntroductionDiabetes has been associated with an increased risk of complications in patients with COVID-19. Most studies do not differentiate between patients with type 1 and type 2 diabetes, which correspond to two pathophysiological distinct diseases that could represent different degrees of clinical compromise.ObjectiveTo identify if there are differences in the clinical outcomes of patients with COVID-19 and diabetes (type 1 and type 2) compared to patients with COVID-19 without diabetes.MethodsObservational studies of patients with COVID-19 and diabetes (both type 1 and type 2) will be included without restriction of geographic region, gender or age, whose outcome is hospitalization, admission to intensive care unit or mortality compared to patients without diabetes. Two authors will independently perform selection, data extraction, and quality assessment, and a third reviewer will resolve discrepancies. The data will be synthesized regarding the sociodemographic and clinical characteristics of patients with diabetes and without diabetes accompanied by the measure of association for the outcomes. The data will be synthesized regarding the sociodemographic and clinical characteristics of patients with diabetes and without diabetes accompanied by the measure of association for the outcomes.Expected resultsUpdate the evidence regarding the risk of complications in diabetic patients with COVID-19 and in turn synthesize the information available regarding type 1 and type 2 diabetes mellitus, to provide keys to a better understanding of the pathophysiology of diabetics.Systematic review registryThis study was registered at the International Prospective Registry for Systematic Reviews (PROSPERO) - CRD42021231942.