bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determining the importance of risk factors for the occurrence of temporomandibular disorders in the population and among exposed individuals
Authors: Miller James R. , Hass Zachary J. 
Published: February 2024

AbstractThere are many case-control (Ca-Co) studies in the literature on the importance of risk factors for the occurrence of temporomandibular disorders (TMD). These studies typically report the adjusted odds ratio (OR) for each risk factor being studied. This paper presents other epidemiological measurements for evaluating the importance of risk factors for the occurrence of TMD. These measurements include the population attributable risk percent (PAR%) and the attributable risk percent (AR%). The AR% for parafunctional habits, facial trauma, and orthopedic instability were estimated to be 86%, 80%, and 60%, respectively, while the corresponding PAR% were estimated to be 60%, 38%, and 7%. PAR% underestimates the importance of a risk factor for the occurrence of TMD among individuals exposed to the risk factor. The attributable risk percent (AR%) is an appropriate epidemiological measurement to evaluate the importance of a risk factor for TMD among individuals exposed to the risk factor.
Environmental, host, and symbiont drivers of heat tolerance in a species complex of reef-building corals
Authors: Naugle MS , Denis H , Mocellin VJL , Laffy PW , Popovic I , Bay LK , Howells EJ 
Published: February 2024

AbstractReef-building coral populations are under unprecedented threat from climate warming. Yet, variation in coral heat tolerance exists whereby some colonies can cope with higher sea temperatures than others and thus may hold unique value for conservation and restoration. Here, we quantify variation in heat tolerance of an ecologically important tabular coral species complex across the Great Barrier Reef (GBR) while also measuring genomic variation in the coral host and symbiont partners. Coral bleaching and photochemical traits were measured in 569 colonies within theAcropora hyacinthusspecies complex from 17 reefs following exposure to standardized acute heat stress assays. We detected substantial variation in heat tolerance, where individual colony thermal thresholds differed by up to 7.3°C and 5.7°C among and within reefs, respectively. Sea surface temperature climatology was the strongest predictor of heat tolerance, where colonies from warmer northern and inshore reefs typically exhibited the highest thermal thresholds, while colonies from cooler southern reefs were able to tolerate greater temperature increases relative to their local summer temperatures. Heat tolerance was also positively associated with exposure to thermal stress in the weeks preceding measurements. Assignment of colonies to host genomic clusters revealed four putative species within theA. hyacinthuscomplex that did not vary in their responses to experimental heat stress. Symbiodiniaceae communities within colonies were comprised primarily of Cladocopium ITS2 variants that differed spatially but had minimal effect on heat tolerance. Between 36 - 80% of heat tolerance variation was explained by environmental, host, and symbiont genomic predictors, leaving 20 - 64% to be explained by additional underlying drivers such as functional genomic variation not measured here. These results may be used to inform conservation and restoration actions, including targeting heat tolerant individuals for selective breeding, and will provide a foundation for evaluating the genomic basis of heat tolerance.
Landscape-scale spatial variations of pre-Columbian anthropogenic disturbances at three ring ditch sites in French Guiana
Authors: Marc Testé , Julien Engel , Kevin Mabobet , Mickael Mestre , Louise Brousseau 
Published: February 2024

AbstractIn the past two decades, repeated discoveries of numerous geometric earthworks in interfluvial regions of Amazonia have shed new light onto the territorial extent and the long-term impact of pre-Columbian populations on contemporary landscapes. In particular, the recent development of LiDAR imagery has accelerated the discovery of earthworks in densely forested hinterlands throughout the Amazon basin and the Guiana Shield.This study aimed to evaluate the extent and landscape-scale spatial variations of pre-Columbian disturbances at three ring ditch sites in the French Guiana hinterland. We carried out extensive soil surveys along approximately 1 km-long transects spanning from ring ditches through the surrounding landscapes, and drawn upon multiple indicators, including archaeological artifacts, macro- and micro-charcoals, soil colorimetry, and physicochemical properties to retrace the pre-Columbian history of these sites in terms of occupation periods, anthropogenic soil alteration, and ancient land use.Our results revealed a perennial occupation of these sites over long periods ranging from the 5th and 15th centuries CE, with local enrichments in chemical indicators (Corg, N, Mg, K, Ca) both within the enclosures of ring ditches and in the surrounding landscapes. Physicochemical properties variations were accompanied by variations in soil colorimetry, with darker soils within the enclosure of ring ditches interra-firmeareas. Interestingly however, soil properties did not meet all the characteristics of the so-called Amazonian Dark Earths, thus advocating a paradigm shift towards a better integration of Amazonian Brown Earths into the definition of anthropogenic soils in Amazonia. Soil disturbances were also associated to local enrichments in macro- and micro-charcoals that supportin situfire management that could be attributed to forest clearance and/or slash-and-burn cultivation.Taken together, our results support the idea that pre-Columbian societies made extensive use of their landscapes in the interfluvial regions of the French Guiana hinterlands.
The proteome is a terminal electron acceptor
Authors: Flamholz Avi I. , Goyal Akshit , Fischer Woodward W. , Newman Dianne K. , Phillips Rob 
Published: February 2024

AbstractMicrobial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state.E. coli, for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation and respiration. To understand the limits on and evolutionary consequences of metabolic flexibility, we developed a mathematical model coupling redox chemistry with principles of cellular resource allocation. Our integrated model clarifies key phenomena, including demonstrating that autotrophs grow slower than heterotrophs because of constraints imposed by intracellular production of reduced carbon. Our model further indicates that growth is improved by adapting the redox state of biomass to nutrients, revealing an unexpected mode of evolution where proteins accumulate mutations benefiting organismal redox balance.One sentence summaryMicrobial proteins adapt their composition on physiological and evolutionary timescales to ensure organismal redox balance.
NELF coordinates Pol II transcription termination and DNA replication initiation
Authors: Nakayama Chihiro , Daigaku Yasukazu , Aoi Yuki , Fang Qi , Kimura Hiroshi , Shilatifard Ali , Tellier Michael , Nojima Takayuki 
Published: February 2024

SUMMARYRegulation of RNA polymerase II (Pol II) transcription is closely associated with cell proliferation. However, it remains unclear how the Pol II transcription program is altered in cancer to favour cell growth. Here, we find that gene expression ofNELFCD, a known negative elongation factor, is up-regulated in colorectal tumours. To dissect the direct role of NELF-C on Pol II transcription in such cancer, we employed an auxin-dependent protein degradation system for NELF-C in combination with nascent transcript sequencing technologies. Strikingly, we demonstrated that the acute loss of NELF-C protein globally perturbs Pol II transcription termination and also increases transcription elongation rate, independently of promoter-proximal Pol II pausing. This results in Pol II transcription into DNA replication initiation zones, and may link to failure of the cell cycle transition into S phase. We anticipate that NELF will be a potential therapeutic target to restrict colorectal cancers by promoting transcription-replication conflict.HIGHLIGHTSExpression ofNELFCDtranscript is up-regulated in colorectal tumorsNELF-C protein is mandatory for the transition between G1-S phases during cell cycleNELF-C loss impairs transcription termination independently of Pol II promoter-proximal pausingNELF-C loss leads Pol II to invade DNA replication initiation zones
Insights on the GPCR helix 8 solution structure and orientation using a neurotensin receptor 1 peptide
Authors: Bower James B. , Robson Scott A. , Ziarek Joshua J. 
Published: February 2024

ABSTRACTG-protein coupled receptors (GPCRs) are the largest class of membrane proteins in the human genome with high pharmaceutical relevance and implications to human health. These receptors share a prevalent architecture of seven transmembrane helices followed by an intracellular, amphipathic helix 8 (H8) and a disordered C-terminus. Technological advancements have led to over 1000 receptor structures in the last two decades, yet frequently H8 and the C-tail are conformationally heterogeneous or altogether absent. Here we synthesize a peptide comprising the neurotensin receptor 1 (NTS1) H8 and C-terminus (H8-Ctail) to investigate its structural stability, conformational dynamics and orientation in the presence of detergent and phospholipid micelles, which mimic the membrane. Circular dichroism (CD) and nuclear magnetic resonance (NMR) measurements confirm that zwitterionic 1,2-diheptanoyl-sn-glycero-3-phosphocholine is a potent stabilizer of H8 structure, whereas the commonly-used branched detergent lauryl maltose neopentyl glycol (LMNG) is unable to completely stabilize the helix – even at amounts four orders of magnitude greater than its critical micellar concentration. We then used NMR spectroscopy to assign the backbone chemical shifts. A series of temperature and lipid titrations were used to define the H8 boundaries as F376-R392 from chemical shift perturbations, changes in resonance intensity, and chemical-shift derived phi/psi angles. Finally, the H8 azimuthal and tilt angles, defining the helix orientation relative of the membrane normal were measured using paramagnetic relaxation enhancement (PRE) NMR. Taken together, our studies reveal the H8C-tail region is sensitive to membrane physicochemical properties and is capable of more adaptive behavior than previously suggested by static structural techniques.
Ophthalmic Manifestations of NAA10-Related and NAA15-Related Neurodevelopmental Syndrome: Analysis of Cortical Visual Impairment and Refractive Errors
Authors: Patel Rahi , Park Agnes Y. , Marchi Elaine , Gropman Andrea L. , Whitehead Matthew T. , Lyon Gholson J. 
Published: February 2024

AbstractNAA10-related andNAA15-related neurodevelopmental syndrome, otherwise known as Ogden Syndrome, is known to present with varying degrees of intellectual disability, hypotonia, congenital cardiac abnormalities, seizures, and delayed speech and motor development. However, the ophthalmic manifestations ofNAA10andNAA15mutations are not yet fully characterized or understood. This study analyzed the prevalence of six ophthalmic conditions (cortical visual impairment, myopia, hyperopia, strabismus, nystagmus, and astigmatism) in 67 patients with pathogenic mutations in theNAA10cohort (54 inherited, 10 de novo; 65 missense, 2 frameshift) and 19 patients with pathogenic mutations in theNAA15cohort (18 de novo; 8 frameshift, 4 missense, 4 nonsense, and 1 splice site). Patients were interviewed virtually or in-person to collect a comprehensive medical history verified by medical records. These records were then analyzed to calculate the prevalence of these ophthalmic manifestations in each cohort. Analysis revealed a higher prevalence of ophthalmic conditions in ourNAA10cohort compared to existing literature (myopia 25.4% vs. 4.7%; astigmatism 37.3% vs. 13.2%; strabismus 28.4% vs. 3.8%; CVI 22.4% vs. 8.5%, respectively). No statistically significant differences were identified between theNAA10andNAA15mutations. Our study includes novel neuroimaging of 13NAA10and 5NAA15probands, which provides no clear correlation between globe size and severity of comorbid ophthalmic disease. Finally, anecdotal evidence was compiled to underscore the importance of early ophthalmologic evaluations and therapeutic interventions.
Effects of water nutrient concentrations on stream macroinvertebrate community stoichiometry: a large-scale study
Authors: Beck M. , Billoir E. , Usseglio-Polatera P. , Meyer A. , Gautreau E. , Danger M. 
Published: February 2024

AbstractBasal resources generally mirror environmental nutrient concentrations in the elemental composition of their tissue, meaning that nutrient alterations can directly reach consumer level. An increased nutrient content (e.g. phosphorus) in primary and detrital resources under nutrient enriched conditions should favour taxa with a high demand for this nutrient. With the nutrient demand of a taxon being correlated to the elemental composition of its body tissue (e.g. phosphorus content), such above described species shifts likely alter the overall community stoichiometry. However, studies addressing stoichiometry at community level are rare and most often restricted to lacustrine planktonic systems, single streams or limited experimental setups.Relying on a stoichiometric database for >200 taxa and >1300 standardized sampling events of macroinvertebrate assemblages from the French national monitoring programme, we investigated the effect of water phosphorus and nitrogen load on stream macroinvertebrate community stoichiometry.Community stoichiometry was significantly affected by water phosphorus concentration and the effect was strongest at low levels of nitrogen. While we could not confirm our hypothesis of increasing community %P (and decreasing C:P, N:P) with increasing water phosphorus concentrations for the overall community, it clearly followed this pattern for both Insecta and Malacostraca. General differences in the elemental composition among major taxonomic groups and a shift among these groups over the nutrient gradient probably explain the response of community stoichiometry. Our results show that assumptions from Ecological Stoichiometry Theory also hold at the community level, at least for two dominant taxa, and on a large spatial scale, with likely consequences for nutrient cycling and ecosystem function.
Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease
Authors: Zhou Xin , Shen Xiaotao , Johnson Jethro S. , Spakowicz Daniel J. , Agnello Melissa , Zhou Wenyu , Avina Monica , Honkala Alexander , Chleilat Faye , Chen Shirley Jingyi , Cha Kexin , Leopold Shana , Zhu Chenchen , Chen Lei , Lyu Lin , Hornburg Daniel , Wu Si , Zhang Xinyue , Jiang Chao , Jiang Liuyiqi , Jiang Lihua , Jian Ruiqi , Brooks Andrew W. , Wang Meng , Contrepois Kévin , Gao Peng , Schüssler-Fiorenza Rose Sophia Miryam , Binh Tran Thi Dong , Nguyen Hoan , Celli Alessandra , Hong Bo-Young , Bautista Eddy J. , Dorsett Yair , Kavathas Paula , Zhou Yanjiao , Sodergren Erica , Weinstock George M. , Snyder Michael P. 
Published: February 2024

SummaryTo understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.Study HighlightsThe stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility
Authors: Feng Yuzhen , van Bodegraven Dominik , Kádek Alan , Munguira Ignacio L.B. , Soria-Martinez Laura , Nentwich Sarah , Kavan Daniel , Uetrecht Charlotte , Schelhaas Mario , Roos Wouter H. 
Published: February 2024

AbstractHigh-risk human papillomaviruses (HPVs) cause various cancers. While type-specific prophylactic vaccines are available, additional anti-viral strategies are highly desirable. Initial HPV cell entry involves receptor-switching induced by structural capsid modifications. These modifications are initiated by interactions with cellular heparan sulphates (HS), however, their molecular nature and functional consequences remain elusive. Combining virological assays with hydrogen/deuterium exchange mass spectrometry, and atomic force microscopy, we investigated the effect of capsid-HS binding and structural activation. We show how HS-induced structural activation requires a minimal HS-chain length and simultaneous engagement of several binding sites by a single HS molecule. This engagement introduces a pincer-like force that stabilizes the capsid in a conformation with extended capsomer linkers. It results in capsid enlargement and softening, thereby facilitating L1 proteolytic cleavage and subsequent L2-externalization, as needed for cell entry. Our data will help further devising prophylactic strategies against HPV infections.
Ultra-sensitive water contaminant detection with transcription factor interfaced microcantilevers
Authors: Agarwal Dilip K. , Lucci Tyler J. , Jung Jaeyoung K. , Shekhawat Gajendra S. , Lucks Julius B. , Dravid Vinayak P. 
Published: February 2024

ABSTRACTWater contamination is a growing global concern, creating a need to develop technologies that can detect a range of target compounds at the required thresholds. Here, we address this need by merging biological allosteric transcription factors with DNA coated nanomechanical microcantilevers to detect chemicals in water with digital readout. After proof-of-concept demonstration and optimization to detect tetracycline with the TetR transcription factor, we use the CadC transcription factor to detect Pb2+and Cd2+in water at concentrations down to 2 ppb and 1 ppb, respectively, in less than fifteen minutes. A computational model suggests this improvement in sensitivity could be achieved by the DNA coated microcantilever surface changing transcription factor binding properties. Our findings demonstrate a promising new approach for water quality monitoring with fast, highly sensitive, digital readouts.
The temporal specificity of BOLD fMRI is systematically related to anatomical and vascular features of the human brain
Authors: Gomez Daniel E. P. , Polimeni Jonathan R. , Lewis Laura D. 
Published: February 2024

AbstractThe ability to detect fast responses with functional MRI depends on the speed of hemodynamic responses to neural activity, because hemodynamic responses act as a temporal low-pass filter which blurs rapid changes. However, the shape and timing of hemodynamic responses are highly variable across the brain and across stimuli. This heterogeneity of responses implies that the temporal specificity of fMRI signals, or the ability of fMRI to preserve fast information, could also vary substantially across the cortex. In this work we investigated how local differences in hemodynamic response timing affect the temporal specificity of fMRI. We used ultra-high field (7T) fMRI at high spatiotemporal resolution, studying the primary visual cortex (V1) as a model area for investigation. We used visual stimuli oscillating at slow and fast frequencies to probe the temporal specificity of individual voxels. As expected, we identified substantial variability in temporal specificity, with some voxels preserving their responses to fast neural activity more effectively than others. We investigated which voxels had the highest temporal specificity, and tested whether voxel timing was related to anatomical and vascular features. We found that low temporal specificity is only weakly explained by the presence of large veins or cerebral cortical depth. Notably, however, temporal specificity depended strongly on a voxel’s position along the anterior-posterior anatomical axis of V1, with voxels within the calcarine sulcus being capable of preserving close to 25% of their amplitude as the frequency of stimulation increased from 0.05Hz to 0.20Hz, and voxels nearest to the occipital pole preserving less than 18%. These results indicate that detection biases in high-resolution fMRI will depend on the anatomical and vascular features of the area being imaged, and that these biases will differ depending on the timing of the underlying neuronal activity. While we attribute this variance primarily to hemodynamic effects, neuronal nonlinearities may also influence response timing. Importantly, this spatial heterogeneity of temporal specificity suggests that it could be exploited to achieve higher specificity in some locations, and that tailored data analysis strategies may help improve the detection and interpretation of fast fMRI responses.
Single-Stranded DNA with Internal Base Modifications Mediates Highly Efficient Gene Insertion in Primary Cells
Authors: Kanke Karen L. , Rayner Rachael E. , Abel Eli , Venugopalan Aparna , Suu Ma , Stack Jacob T. , Nouri Reza , Guo Gongbo , Vetter Tatyana A. , Cormet-Boyaka Estelle , Hester Mark E. , Vaidyanathan Sriram 
Published: February 2024

ABSTRACTSingle-stranded DNA (ssDNA) templates along with Cas9 have been used for gene insertion but suffer from low efficiency. Here, we show that ssDNA with chemical modifications in 10-17% of internal bases (eDNA) is compatible with the homologous recombination machinery. Moreover, eDNA templates improve gene insertion by 2-3 fold compared to unmodified and end-modified ssDNA in airway basal stem cells (ABCs), hematopoietic stem and progenitor cells (HSPCs), T-cells and endothelial cells. Over 50% of alleles showed gene insertion in three clinically relevant loci (CFTR, HBB, andCCR5) in ABCs using eDNA and up to 70% of alleles showed gene insertion in theHBBlocus in HSPCs. This level of correction is therapeutically relevant and is comparable to adeno-associated virus-based templates. Knocking out TREX1 nuclease improved gene insertion using unmodified ssDNA but not eDNA suggesting that chemical modifications inhibit TREX1. This approach can be used for therapeutic applications and biological modeling.