bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of bipartite network analyses to incomplete sampling and taxonomic uncertainty
Authors: Llopis-Belenguer Cristina , Balbuena Juan Antonio , Blasco-Costa Isabel , Karvonen Anssi , Sarabeev Volodimir , Jokela Jukka 
Published: July 2022

AbstractBipartite network analysis is a powerful tool to study the processes structuring interactions in antagonistic ecological communities. In applying the method, we assume that the sampled interactions provide an accurate representation of the actual community. However, acquiring a representative sample may be difficult as not all species are equally abundant or easily identifiable. Two potential sampling issues can compromise the conclusions of bipartite network analyses: failure to capture the full range of interactions of species (sampling completeness) and failure to identify species correctly (taxonomic resolution). These sampling issues are likely to co-occur in community ecology studies. We asked how commonly used descriptors (modularity, nestedness, connectance and specialisation (H2′)) of bipartite communities are affected by reduced host sampling completeness, parasite taxonomic resolution and their crossed effect. We used a quantitative niche model to generate replicates of simulated weighted bipartite networks that resembled natural host-parasite communities. The combination of both sampling issues had an additive effect on modularity and nestedness. The descriptors were more sensitive to uncertainty in parasite taxonomic resolution than to host sampling completeness. All descriptors in communities capturing less than 70% of correct taxonomic resolution strongly differed from correctly identified communities. When only 10% of parasite taxonomic resolution was retained, modularity and specialisation decreased ∼0.3 and ∼0.1-fold respectively, and nestedness and connectance changed ∼0.7 and ∼3.2-fold respectively. The loss of taxonomic resolution made the confidence intervals of estimates wider. Reduced taxonomic resolution led to smaller size of the communities, which emphasised the larger relative effect of taxonomic resolution on smaller communities. With regards to host sampling completeness, connectance and specialisation were robust, nestedness was reasonably robust (∼0.2-fold overestimation), and modularity was sensitive (∼0.5-fold underestimation). Nonetheless, most of the communities with low resolution for both sampling issues were structurally equivalent to correctly sampled communities (i.e., more modular and less nested than random assemblages). Therefore, modularity and nestedness were useful as categorical rather than quantitative descriptors of communities affected by sampling issues. We recommend evaluating both sampling completeness and taxonomic certainty when conducting bipartite network analyses. We also advise to apply the most robust descriptors in circumstances of unavoidable sampling issues.Open Research statementwe provide permanent and open access links to data sources and replication code in Appendix S1.
Individual reflectance of solar radiation confers a thermoregulatory benefit to dimorphic males bees (Centris pallida) using distinct microclimates
Authors: Barrett Meghan , O’Donnell Sean 
Published: July 2022

AbstractIncoming solar radiation (wavelengths 290 – 2500 nm) significantly affects an organism’s thermal balance via radiative heat gain. Species adapted to different environments can differ in solar reflectance profiles. We hypothesized that conspecific individuals using thermally distinct microhabitats to engage in fitness-relevant behaviors would show intraspecific differences in reflectance: we predicted individuals that use hot microclimates (where radiative heat gain represents a greater thermoregulatory challenge) would be more reflective across the entire solar spectrum than those using cooler microclimates. Differences in near-infrared (NIR) reflectance (700 - 2500 nm) are strongly indicative of thermoregulatory adaptation as, unlike differences in visible reflectance (400 - 700 nm), they are not perceived by ecological or social partners. We tested these predictions in maleCentris pallida(Hymenoptera: Apidae) bees from the Sonoran Desert. MaleC. pallidause alternative reproductive tactics that are associated with distinct microclimates: Large-morph males, with paler visible coloration, behave in an extremely hot microclimate close to the ground, while small-morph males, with a dark brown dorsal coloration, frequently use cooler microclimates above the ground near vegetation. We found that large-morph males had higher reflectance of solar radiation (UV through NIR) resulting in lower solar absorption coefficients. This thermoregulatory adaptation was specific to the dorsal surface, and produced by differences in hair, not cuticle, characteristics. Our results showed that intraspecific variation in behavior, particular in relation to microclimate use, can generate unique thermal adaptations that changes the reflectance of shortwave radiation among individuals within the same population.
Assessing jugular venous compliance with optical hemodynamic imaging by modulating intrathoracic pressure
Authors: Amelard Robert , Flannigan Nyan , Patterson Courtney A , Heigold Hannah , Hughson Richard L , Robertson Andrew D 
Published: July 2022

AbstractSignificanceThe internal jugular veins are critical cerebral venous drainage pathways that are affected by right heart function. Cardiovascular disease and microgravity can alter central venous pressure (CVP) and venous return, which may contribute to increased intracranial pressure and decreased cardiac output. Assessing jugular venous compliance may provide insight into cerebral drainage and right heart function, but monitoring changes in vessel volume is challenging.AimWe investigated the feasibility of quantifying jugular venous compliance from jugular venous attenuation (JVA), a non-contact optical measurement of blood volume, alongside CVP from antecubital vein cannulation.ApproachCVP was progressively increased through a guided graded Valsalva maneuver, increasing mouth pressure by 2 mmHg every 2 s until a maximum expiratory pressure of 20 mmHg. JVA was extracted from a 1 cm segment between the clavicle and mid-neck. Contralateral internal jugular vein cross-sectional area (CSA) was measured with ultrasound to validate changes in vessel size. Compliance was calculated using both JVA and CSA between four-beat averages over the duration of the maneuver.ResultsJVA and CSA were strongly correlated (median, interquartile range) over the Valsalva maneuver across participants (r=0.986, [0.983, 0.987]). CVP more than doubled on average between baseline and peak strain (10.7 ± 4.4 vs 25.8 ± 5.4 cmH2O; p<.01). JVA and CSA increased non-linearly with CVP, and both JVA- and CSA-derived compliance decreased progressively from baseline to peak strain (49% and 56% median reduction, respectively), with no significant difference in compliance reduction between the two measures (Z=–1.24, p=.21). Pressure-volume curves showed a logarithmic relationship in both CSA and JVA.ConclusionsOptical jugular vein assessment may provide new ways to assess jugular distention and cardiac function.
Endosymbiont strategic shifts inhibit cooperation during coral bleaching recovery
Authors: Allen-Waller Luella , Barott Katie L. 
Published: July 2022

ABSTRACTThe future of coral reefs in a warming world depends on corals’ ability to resist or recover from losing their photosynthetic algal endosymbionts (coral bleaching) during marine heatwaves. Heat-tolerant algal species can confer bleaching resistance by remaining in symbiosis during heat stress but tend to provide less photosynthate to the host than heat-sensitive species. Understanding this potential nutritional tradeoff is crucial for predicting coral success under climate change, but the energetic dynamics of corals hosting different algal species during bleaching recovery are poorly understood. To test how algal energetics affects coral recovery, we heat-stressed corals (Montipora capitata) hosting either heat-sensitive Cladocopium sp. or heat-tolerant Durusdinium glynni algae for two weeks, followed by a one-month recovery period. We found that while thermotolerant D. glynni regained density and photochemical efficiency faster after bleaching than Cladocopium, this algal recovery did not correspond with host physiological recovery, and D. glynni populations still contributed less photosynthate to the host relative to Cladocopium. Further, high-density algal populations of both species translocated a smaller proportion of their photosynthate than low-density populations, and corals receiving less photosynthate suffered reduced calcification rates and lower intracellular pH. This is the first evidence of a direct negative relationship between symbiont population size and ‘selfishness,’ and the first to establish a connection between Symbiodiniaceae carbon translocation and coral cellular homeostasis. Together, these results suggest that algal energy reallocation towards regrowth after bleaching can harm coral physiology, and that reestablishing a beneficial endosymbiosis can pose a secondary challenge for holobionts surviving stress.
Text mining and portal development for gene-specific publications on Alzheimer’s disease and other neurodegenerative diseases
Authors: Liu Jiannan , Wu Huanmei , Robertson Daniel H. , Zhang Jie 
Published: July 2022

AbstractBackgroundTremendous research efforts have been made in the Alzheimer’s disease (AD) field to understand the disease etiology, progression and discover treatments for AD. Many mechanistic hypotheses, therapeutic targets and treatment strategies have been proposed in the last few decades. Reviewing previous work and staying current on this ever-growing body of AD publications is an essential yet difficult task for AD researchers.MethodsIn this study, we designed and implemented a natural language processing (NLP) pipeline to extract gene-specific neurodegenerative disease (ND) -focused information from the PubMed database. The collected publication information was filtered and cleaned to construct AD-related gene-specific publication profiles. Six categories of AD-related information are extracted from the processed publication data: publication trend by year, dementia type occurrence, brain region occurrence, mouse model information, keywords occurrence, and co-occurring genes. A user-friendly web portal is then developed using Django framework to provide gene query functions and data visualizations for the generalized and summarized publication information.ResultsBy implementing the NLP pipeline, we extracted gene-specific ND-related publication information from the abstracts of the publications in the PubMed database. The results are summarized and visualized through an interactive web query portal. Multiple visualization windows display the ND publication trends, mouse models used, dementia types, involved brain regions, keywords to major AD-related biological processes, and co-occurring genes. Direct links to PubMed sites are provided for all recorded publications on the query result page of the web portal.ConclusionThe resulting portal is a valuable tool and data source for quick querying and displaying AD publications tailored to users’ interested research areas and gene targets, which is especially convenient for users without informatic mining skills. Our study will not only keep AD field researchers updated with the progress of AD research, assist them in conducting preliminary examinations efficiently, but also offers additional support for hypothesis generation and validation which will contribute significantly to the communication, dissimilation and progress of AD research.
GLT8D1 mutations cause amyotrophic lateral sclerosis via disruption of neurotrophin signalling within membrane lipid rafts
Authors: Moll Tobias , Graves Emily , Urbanek Agnieszka , Soni Nikita , Ranganathan Ramya , Higginbottom Adrian , Wang Shanshan , Head Brian P , Cooper-Knock Johnathan , Shaw Pamela J 
Published: July 2022

AbstractMutations within GLT8D1 contribute to familial amyotrophic lateral sclerosis. Pathogenic mutations impair GLT8D1 glycosyltransferase enzymatic function via a dominant negative mechanism, yet the downstream mechanism leading to neurotoxicity is unclear. Here we show that a p.R92C mutation causes fragmentation of the Golgi network and reduces ganglioside expression within membrane lipid rafts (MLRs), leading to impaired neurotrophin signalling. Expression of p.R92C-GLT8D1 in HEK293 cells and mouse primary neurons reduces expression of GM1 gangliosides within the cell plasma membrane leading to disruption of MLRs. Furthermore, p.R92C-GLT8D1 reduces TrkB-mediated pro-survival signalling in MLRs isolated from primary neurons. Interestingly, up-regulation of wild-type GLT8D1 enhances MLRs and promotes pro-survival signalling through TrkB. This closely mirrors findings for another ALS gene, CAV1, suggesting convergence on a common pathogenic pathway. Other ALS genes have been associated with Golgi dysfunction and may disrupt the same pathway, suggesting a potential new therapeutic approach via upregulation of GLT8D1.Graphical Abstract
Microwell-Based Flow Culture Increases Viability and Restores Drug Response in Prostate Cancer Spheroids
Authors: Payne Marie C. , Ho Sum Yat , Hashimoto Takao , Imboden Sara , Diaz Johnny A. , Lee Brandon S. , Rupert Melissa J. , Cai Nathan Y. , Goldstein Andrew S. , Lin Neil Y.C. 
Published: July 2022

Abstract3D cancer spheroids represent a highly promising model for study of cancer progression and therapeutic development. Wide-scale adoption of cancer spheroids, however, remains a challenge due to the lack of control over hypoxic gradients that may cloud the assessment of cell morphology and drug response. Here, we present a Microwell Flow Device (MFD) that generates in-well laminar flow around 3D tissues via repetitive tissue sedimentation. Using a prostate cancer cell line, we demonstrate the spheroids in the MFD exhibit improved cell growth, reduced necrotic core formation, enhanced structural integrity, and down-regulated expression of cell stress genes. The flow-cultured spheroids also exhibit an improved sensitivity to chemotherapy with greater transcriptional response. These results demonstrate how fluidic stimuli reveal the cellular phenotype previously masked by severe necrosis. Our platform advances 3D cellular models and enables study into hypoxia modulation, cancer metabolism, and drug screening within pathophysiological conditions.
BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes
Authors: Pavia Michael J. , Chede Abhinav , Wu Zijun , Cadillo-Quiroz Hinsby , Zhu Qiyun 
Published: July 2022

AbstractExploring metagenomic contigs and “binning” them are essential for delineating functional and evolutionary guilds within microbial communities. Despite available automated binners, researchers often find human involvement necessary to achieve representative results. We present BinaRena, an interactive graphic interface dedicated to aiding human operators to explore contigs via customizable visualization and to associate them with bins based on various data types, including sequence metrics, coverage profiles, taxonomic assignments and functional annotations. Binning plans can be edited, inspected and compared visually or using algorithms. Completeness and redundancy of user-selected contigs can be calculated real-time. We show that BinaRena facilitated biological pattern discovery, hypothesis generation and bin refinement in a tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely-related populations from human gut samples. It significantly improved overall binning quality after curation using a simulated marine dataset. BinaRena is an installation-free, client-end web application for researchers of all levels.
Was fishing village of Lepenski Vir built by Europe’s first farmers?
Authors: Brami Maxime , Winkelbach Laura , Schulz Ilektra , Schreiber Mona , Blöcher Jens , Diekmann Yoan , Burger Joachim 
Published: July 2022

AbstractToday, it is widely accepted that agriculture and settled village life arrived in Europe as a cultural package, carried by people migrating from Anatolia and the Aegean Basin. The putative fisher-forager site of Lepenski Vir in Serbia has long been acknowledged as an exception to this model. Here, the Mesolithic-Neolithic transition - possibly inspired by interaction with the new arrivals - was thought to have taken place autochthonously on site. Our reinterpretation, based on ancient genomes, as well as archaeological and isotopic evidence, revisits this conclusion, indicating that here too, house construction, early village society and agriculture were primarily associated with Europe’s first farmers, thus challenging the long-held interpretation of Lepenski Vir as a Mesolithic community that adopted Neolithic practices. A detailed timeline of population changes at the site suggests that Aegean incomers did not simply integrate into an established Mesolithic society, rather founded new lineages and households. Iron Gates foragers and their admixed descendants appear to have been buried largely separately, on the fringes of the settlement, their diet showing no major shift from aquatic to terrestrial food resources.
Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection
Authors: Chaguza Chrispin , Hahn Anne M. , Petrone Mary E. , Zhou Shuntai , Ferguson David , Breban Mallery I. , Pham Kien , Peña-Hernández Mario A. , Castaldi Christopher , Hill Verity ,   Yale SARS-CoV-2 Genomic Surveillance Initiative, Schulz Wade , Swanstrom Ronald I. , Roberts Scott C. , Grubaugh Nathan D. 
Published: July 2022

SummaryThe chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral loads. During the infection, we found an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution led to the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, using unique molecular indexes for accurate intrahost viral sequencing, we tracked the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, ultimately providing opportunity for the emergence of genetically divergent and potentially highly transmissible variants as seen with Delta and Omicron.
Interpretable Radiomics Method for Predicting Human Papillomavirus Status in Oropharyngeal Cancer using Bayesian Networks
Authors: Altinok Oya , Guvenis Albert 
Published: July 2022

AbstractObjectivesTo develop a simple interpretable Bayesian Network (BN) to classify HPV status in patients with oropharyngeal cancer.MethodsTwo hundred forty-six patients, 216 of whom were HPV positive, were used in this study. We extracted 851 radiomics markers from patients’ contrast-enhanced Computed Tomography (CT) images. Mens eX Machina (MXM) approach selected two most relevant predictors: sphericity and max2DDiameterRow. The area under the curve (AUC) demonstrated BN model performance in 30% of the data reserved for testing. A Support Vector Machine (SVM) based method was also implemented for comparison purposes.ResultsThe Mens eX Machina (MXM) approach selected two most relevant predictors: sphericity and max2DDiameterRow. Areas under the Curves (AUC) were found 0.78 and 0.72 on the training and test data, respectively. When using support vector machine (SVM) and 25 features, the AUC was found 0.83 on the test data.ConclusionsThe straightforward structure and power of interpretability of our BN model will help clinicians make treatment decisions and enable the non-invasive detection of HPV status from contrast-enhanced CT images. Higher accuracy can be obtained using more complex structures at the expense of lower interpretability.Advances in KnowledgeDetermination of HPV status can be done by invasive laboratory techniques, which poses a potential risk to patients. Radiomics-based methods are non-invasive but are usually difficult to use because they are generally not interpretable. Therefore, there is a growing need to develop a non-invasive radiomics method that is simple and interpretable. This work accomplishes this objective while pointing out the limitations.
Modelling the contributions to hyperexcitability in a mouse model of Alzheimer’s disease
Authors: Mittag Martin , Mediavilla Laura , Remy Stefan , Cuntz Hermann , Jedlicka Peter 
Published: July 2022

AbstractNeuronal hyperexcitability is a feature of Alzheimer’s disease (AD). Three main mechanisms have been proposed to explain it: i), dendritic degeneration leading to increased input resistance, ii), ion channel changes leading to enhanced intrinsic excitability, and iii), synaptic changes leading to excitation-inhibition (E/I) imbalance. However, the relative contribution of these mechanisms is not fully understood. Therefore, we performed biophysically realistic multi-compartmental modelling of excitability in reconstructed CA1 pyramidal neurons of wild-type and APP/PS1 mice, a well-established animal model of AD. We show that, for synaptic activation, the excitability promoting effects of dendritic degeneration are cancelled out by excitability decreasing effects of synaptic loss. We find an interesting balance of excitability regulation with enhanced degeneration in the basal dendrites of APP/PS1 cells potentially leading to increased excitation by the apical but decreased excitation by the basal Schaffer collateral pathway. Furthermore, our simulations reveal that three additional pathomechanistic scenarios can account for the experimentally observed increase in firing and bursting of CA1 pyramidal neurons in APP/PS1 mice. Scenario 1: increased excitatory burst input; scenario 2: enhanced E/I ratio and scenario 3: alteration of intrinsic ion channels (IAHP down-regulated; INap, INa and ICaT up-regulated) in addition to enhanced E/I ratio. Our work supports the hypothesis that pathological network and ion channel changes are major contributors to neuronal hyperexcitability in AD. Overall, our results are in line with the concept of multi-causality and degeneracy according to which multiple different disruptions are separately sufficient but no single disruption is necessary for neuronal hyperexcitability.In briefUsing a computational model, we find that changes in the extrinsic network and intrinsic biophysical neuronal properties rather than dendritic degeneration alone explain the altered firing behaviour observed in Alzheimer’s disease (AD).HighlightsSimulations of synaptically driven responses in PCs with AD-related dendritic degeneration.Dendritic degeneration alone alters PC responses to layer-specific input but additional pathomechanistic scenarios are required to explain neuronal hyperexcitability in AD.Possible scenario 1: Burst hyperactivity of the surrounding network can explain hyper-excitability of PCs during AD.Possible scenario 2: AD-related increased excitatory input together with decreased inhibitory input (E/I imbalance) can lead to hyperexcitability in PCs.Possible scenario 3: Changes in E/I balance combined with altered ion channel properties can account for hyperexcitability in AD.