bluuebunny/crossref_metadata_2025_split huggingface dataset:
Range contractions of the Broad-winged Hawk in the Northeast United States
Authors: Pruitt Rachael , Goodrich Laurie , Shumar Matthew B. , Wilson Andrew M. 
Published: October 2021

ABSTRACTThe Broad-winged Hawk (BWHA,Buteo platypterus)is a small, secretive hawk with distinguishing broad black tail bands that breeds in northeastern North America. The hawk nests in deciduous or mixed forest, often near water, and close to clearings or forest edges. Land conversion and fragmentation alters the landscape and reduces the area of contiguous forest used by BWHA. This study seeks to determine the landscape characteristics influencing the apparent breeding range declines of the BWHA at the landscape scale. Landscape characteristics and BWHA presence data from 18,684 Breeding Bird Atlas blocks (each about 25km2) from Ohio, West Virginia, Maryland, Pennsylvania, and New York for two atlas period (1st Atlas: 1980s, 2nd Atlas: 2000s) were analyzed. Bayesian latent Gaussian models were fitted using INLA to determine best fit model for predicting the landscape characteristics associated with BWHA presence. The best models included landscape changes in land cover, including forest, water, urban, barren, farmland, and wetland and fragmentation of the landscape. Trends in loss were especially prevalent around the region’s largest cities: New York, Philadelphia, Baltimore and Washington DC. Loss of BWHA at the block-level was associated with areas with less forest in the 2000s, a decline in size of largest forest patches, lower elevations and lower latitudes. We suggest that both habitat loss and climate change may be contributing to the range contraction of the Broad-winged Hawk in the northeast United States.
The endemic plant species of Bali Ngemba Forest Reserve, Bamenda Highlands Cameroon, with a new Endangered cloud-forest tree speciesVepris onanae(Rutaceae)
Authors: Cheek Martin , Hatt Sebastian , Onana Jean Michel 
Published: October 2021

SummaryWe revise and update the records of strict and near-endemic species of the Bali Ngemba Forest Reserve, the largest known surviving patch (c. 8 km2in area) of submontane or cloud forest in the Bamenda Highlands, Cameroon which have lost >96 % of their original forest due to human activities. Nine strict endemics, and 11 near endemics are now documented, a drop from the number recorded after the first survey in 2004, since when five of the provisionally named species have been formally published.We test the hypothesis that a further one of the provisionally named putative Bali Ngemba new species,Veprissp. A, an 8 – 20 m tall tree from cloud forest in the 1310 – 1600 m altitudinal band, is indeed new to science. We compare it morphologically with other multicarpellate, apocarpous, trifoliolate Cameroon tree species formerly placed in the genusOriciaPierre until they were subsumed intoVeprisby Mziray (1992). These areVepris trifoliolata(Engl.) Mziray andV. gabonensis(Pierre) Mziray. We conclude thatVeprissp. A is a new undescribed species here named asVepris onanae. The new species is illustrated, mapped and its conservation status assessed as Endangered using the 2012 IUCN standard due to the threats of habitat clearance from agricultural pressures at its three locations all of which remain formally unprotected.Vepris onanaeappears unique among the Guineo-Congolian African oricioid species ofVeprisin occurring in cloud forest, the other species, apart fromV. renieriiof the Albertine Rift, occurring in lowland forest. It also differs in the very broad, (7.8 –) 11.3 – 18 cm wide leaflets of the flowering stems which have a 6-18(−30) mm long, narrowly triangular acumen (vs leaflets <12 cm wide, acumen absent or short) and in having both subsessile and pedicellate (pedicels 0.25 – 0.3 mm long and 1(– 2) mm long) male flowers (vs male flower pedicels all sessile, or all c. 3 mm long).We report for the first time on stage-dependent leaf heteromorphy inVeprisand characterise a level of sexual dimorphism more advanced than usual in the genus.We highlight the importance of protecting Bali Ngemba and other forest patches in the Bamenda Highlands if species such asVepris onanaeare not soon to become extinct.
Automated Optimization of Residual Reduction Algorithm Parameters in Opensim
Authors: Sturdy Jordan T. , Silverman Anne K. , Pickle Nathan T. 
Published: October 2021

AbstractThe residual reduction algorithm (RRA) in OpenSim is designed to improve dynamic consistency of kinematics and ground reaction forces in movement simulations of musculoskeletal models. RRA requires the user to select numerous tracking weights for the joint kinematics to reduce residual errors. Selection is often performed manually, which can be time-consuming and is unlikely to yield optimal tracking weights. A multi-heuristic optimization algorithm was used to expedite tracking weight decision making to reduce residual errors. This method produced more rigorous results than manual iterations and although the total computation time was not significantly reduced, this method does not require the user to monitor the algorithm’s progress to find a solution, thereby reducing manual tuning. Supporting documentation and code to implement this optimization is freely provided to assist the community with developing movement simulations.
Auto-encoded Latent Representations of White Matter Streamlines for Quantitative Distance Analysis
Authors: Zhong Shenjun , Chen Zhaolin , Egan Gary 
Published: October 2021

AbstractParcellation of whole brain tractograms is a critical step to study brain white matter structures and connectivity patterns. The existing methods based on supervised classification of streamlines into predefined streamline bundle types are not designed to explore sub-bundle structures, and methods with manually designed features are expensive to compute streamline-wise similarities. To resolve these issues, we propose a novel atlas-free method that learns a latent space using a deep recurrent auto-encoder. The method efficiently embeds any length of streamlines to fixed-size feature vectors, named streamline embedding, for tractogram parcellation using unsupervised clustering in the latent space. The method was evaluated on the ISMRM 2015 tractography challenge dataset with discrimination of major bundles using unsupervised clustering and streamline querying based on similarity. The learnt latent streamline and bundle representations open the possibility of quantitative studies of arbitrary granularity of sub-bundle structures using generic data mining techniques.
Cervicovaginal microbiota predicts Neisseria gonorrhoeae clinical presentation
Authors: Lovett Angela , Seña Arlene C. , Macintyre Andrew N. , Sempowski Gregory D. , Duncan Joseph A. , Waltmann Andreea 
Published: October 2021

AbstractNeisseria gonorrhoeae infection of the female lower genital tract can present with a spectrum of phenotypes ranging from asymptomatic carriage to symptomatic cervical inflammation, or cervicitis. The factors that contribute to the development of asymptomatic or symptomatic infections are largely uncharacterized. We conducted a pilot study to assess differences in the cervicovaginal microbial community of patients presenting with symptomatic vs. asymptomatic N. gonorrhoeae infections to a sexually transmitted infections (STI) clinic. DNA was isolated from cervicovaginal swab specimens from women who tested positive for N. gonorrhoeae infection using a clinical diagnostic nucleic acid amplification test. We performed deep sequencing of 16S ribosomal RNA gene amplicons, followed by microbiome analyses with QIIME, and species-specific real-time PCR to assess the composition of microbial communities cohabitating the lower genital tract with the infecting N. gonorrhoeae. Specimens collected from asymptomatic individuals with N. gonorrhoeae infection and no co-infection with Chlamydia trachomatis and/or Trichomonas vaginalis carried Lactobacillus-dominant microbial communities more frequently than symptomatic patients without co-infection. When compared to asymptomatic individuals, symptomatic women had microbial communities characterized by more diverse and heterogenous bacterial taxa, typically associated with bacterial vaginosis (BV) (Prevotella, Sneathia, Mycoplasma hominis and Bacterial Vaginosis-Associated Bacterium-1 (BVAB1)/”Candidatus Lachnocurva vaginae). Both symptomatic and asymptomatic N. gonorrhoeae patients with additional STI co-infection displayed a BV-like microbial community. We used a murine model of N. gonorrhoeae infection in mice pre-colonized with Lactobacillus crispatus to test whether pre-existing L. crispatus was protective from N. gonorrhoeae colonization or whether N. gonorrhoeae infection could drive the loss of L. crispatus during infection. Vaginal infection with either N. gonorrhoeae strain 1291 or an isogenic mutant known to exhibit lower inflammatory had no impact on Lactobacillus burden recovered from the mice. These data taken together suggest that Lactobacillus-dominant vaginal microbial community may protect individuals from developing symptoms during lower genital tract infection with N. gonorrhoeae.
Exo-enzymatic addition of diazirine-modified sialic acid to cell surfaces enables photocrosslinking of glycoproteins
Authors: Yarravarapu Nageswari , Reddy Konada Rohit Sai , Darabedian Narek , Pedowitz Nichole J. , Krishnamurthy Soumya N. , Pratt Matthew R. , Kohler Jennifer J. 
Published: October 2021

AbstractGlycan binding often mediates extracellular macromolecular recognition events. Accurate characterization of these binding interactions can be difficult because of dissociation and scrambling that occur during purification and analysis steps. Use of photocrosslinking methods has been pursued to covalently capture glycan-dependent interactionsin situhowever use of metabolic glycan engineering methods to incorporate photocrosslinking sugar analogs is limited to certain cell types. Here we report an exo-enzymatic labeling method to add a diazirine-modified sialic acid (SiaDAz) to cell surface glycoconjugates. The method involves chemoenzymatic synthesis of diazirine-modified CMP-sialic acid (CMP-SiaDAz), followed by sialyltransferase-catalyzed addition of SiaDAz to desialylated cell surfaces. Cell surface SiaDAz-ylation is compatible with multiple cell types and is facilitated by endogenous extracellular sialyltransferase activity present in Daudi B cells. This method for extracellular addition of α2-6-linked SiaDAz enables UV-induced crosslinking of CD22, demonstrating the utility for covalent capture of glycan-mediated binding interactions.
Identification of Key Ischemic Stroke Genes by Computational Systems Biology
Authors: Yue Rongting , Dutta Abhishek 
Published: October 2021

AbstractStroke is one of the leading causes of death in humans. Even if patients survive from stroke, they may suffer sequelae such as disability. Treatment for strokes remains unsatisfactory due to an incomplete understanding of its mechanisms. This study investigates Ischemic Stroke (IS), a primary subtype of stroke, through analyses based on microarray data. Limma (in R)derives differentially expressed genes, and the protein-protein interaction (PPI) network is mapped from the database. Gene co-expression patterns are obtained for clustering gene modules by the Weighted Correlation Network Analysis (WGCNA), and genes with high connectivity in the significantly co-expressed modules are selected as key regulators. Common hubs are identified as Cdkn1a, Nes and Anxa2. Based on our analyses, we hypothesize that these hubs might play a key role in the onset and progression of IS. Result suggests the potential of identifying unexplored key regulators by the systemic method used in this work. Further analyses aim at expanding candidate genes for screening biomarkers for IS, and experimental validation is required on identified potential hubs.
Comparison Between Lotka-Volterra and Multivariate Autoregressive Models of Ecological Interaction Systems
Authors: Olivença Daniel V. , Davis Jacob D. , Voit Eberhard O. 
Published: October 2021

AbstractLotka-Volterra (LV) and Multivariate Autoregressive (MAR) models are computational frameworks with different mathematical structures that have both been proposed for the same purpose of extracting governing features of dynamic interactions among coexisting populations of different species from observed time series data.We systematically compare the feasibility of the two modeling approaches, using four synthetically generated datasets and seven ecological datasets from the literature.The overarching result is that LV models outperform MAR models in most cases and are generally superior for representing cases where the dependent variables deviate greatly from their steady states. A large dynamic range is particularly prevalent when the populations are highly abundant, change considerably over time, and exhibit a large signal-to-noise ratio. By contrast, MAR models are better suited for analyses of populations with low abundances and for investigations where the quantification of noise is important.We conclude that the choice of either one or the other modeling framework should be guided by the specific goals of the analysis and the dynamic features of the data.Availability of algorithms usedhttps://github.com/LBSA-VoitLab/Comparison-Between-LV-and-MAR-Models-of-Ecological-Interaction-Systems
Multi-omics analysis of multiple glucose-sensing receptor systems in yeast
Authors: Li Shuang , Li Yuanyuan , Rushing Blake R. , Harris Sarah E. , McRitchie Susan L. , Dominguez Daniel , Sumner Susan J. , Dohlman Henrik G. 
Published: October 2021

ABSTRACTThe yeast Saccharomyces cerevisiae has long been used to produce alcohol from glucose and other sugars. While much is known about glucose metabolism, relatively little is known about the receptors and signaling pathways that indicate glucose availability. Here we compare the two glucose receptor systems in S. cerevisiae. The first is a heterodimer of transporter-like proteins (transceptors), while the second is a seven-transmembrane receptor coupled to a large G protein (Gpa2) and two small G proteins (Ras1 and Ras2). Through comprehensive measurements of glucose-dependent transcription and metabolism, we demonstrate that the two receptor systems have distinct roles in glucose signaling: the G protein-coupled receptor directs carbohydrate and energy metabolism, while the transceptors regulate ancillary processes such as ribosome, amino acids, cofactor and vitamin metabolism. The large G protein transmits the signal from its cognate receptor, while the small G protein Ras2 (but not Ras1) integrates responses from both receptor pathways. Collectively, our analysis reveals the molecular basis for glucose detection and the earliest events of glucose-dependent signal transduction in yeast.
Txn1 mutation causes epilepsy associated with vacuolar degeneration in the midbrain
Authors: Ohmori Iori , Ouchida Mamoru , Imai Hirohiko , Ishida Saeko , Toyokuni Shinya , Mashimo Tomoji 
Published: October 2021

AbstractThioredoxin (TXN), encoded by Txn1, acts as a critical antioxidant in the defense against oxidative stress by regulating the dithiol/disulfide balance of interacting proteins. The role of TXN in the central nervous system (CNS) is largely unknown. A phenotype-driven study of N-ethyl-N-nitrosourea-mutated rats with running seizures at around five-week of age revealed the relevance of Txn1 mutations to CNS disorders. Genetic mapping identified Txn1-F54L in epileptic rats. The insulin-reducing activity of Txn1-F54L rats was approximately one-third that of the wild-type. Vacuolar degeneration in the midbrain, mainly in the thalamus and the inferior colliculus, was observed in the Txn1-F54L rats. The lesions displayed neuronal and oligodendrocyte cell death. Neurons in Txn1-F54L rats showed morphological changes in the mitochondria. Vacuolar degeneration began at three weeks of age, and spontaneous repair began at seven weeks; a dramatic change from cell death to repair occurred in the midbrain during a restricted period. In conclusion, Txn1 is essential for the development of the midbrain in juvenile rats.
Assessing the Live Decellularized Renal Microvasculature Post-Transplantation Using Intravital Microscopy
Authors: Corridon Peter R. , Khan Anousha A. 
Published: October 2021

AbstractTransplantation is the ideal solution for end-stage renal failure, but the growing mismatch between organ supply and demand accentuates the need for alternative solutions like the bioartificial kidney. Several approaches to developing this technology have been demonstrated, and whole organ decellularization appears to be a promising methodology. One major challenge to this strategy is maintaining vascular integrity and functionality post-transplantation. Most models to examine the microvasculature have primarily utilized in vitro or in vivo techniques that are incapable of providing adequate spatial and temporal resolution. Here, we show that decellularized scaffolds orthotopically transplanted into rats initially retain microvascular structure in vivo using intravital two-photon microscopy, as previously identified in vitro. Large molecular weight dextran molecules also provide real-time evidence of the onset of ischemia and increases in microvascular permeability, support substantial translocation of dextran macromolecules from glomerular and peritubular capillary tracks as early as 12 hours after transplantation. Macromolecular extravasation continued across a week, at which time the decellularized microarchitecture was significantly compromised. These results indicate that a in vivo method capable of tracking microvascular integrity represents a powerful interdisciplinary approach for studying scaffold viability and identifying ways to promote scaffold longevity and angiogenesis in bioartificial organs.
CircHIPK3 dysregulation of the miR-30c/DLL4 axis is essential for KSHV lytic replication
Authors: Harper Katherine L. , Mottram Timothy J. , Anene Chinedu A. , Foster Becky , Patterson Molly R. , McDonnell Euan , Macdonald Andrew , Westhead David , Whitehouse Adrian 
Published: October 2021

AbstractNon-coding RNA (ncRNA) regulatory networks are emerging as critical regulators of gene expression. These intricate networks of ncRNA:ncRNA interactions modulate multiple cellular pathways and impact the development and progression of multiple diseases. Herpesviruses, including Kaposi’s sarcoma-associated herpesvirus, are adept at utilising ncRNAs, encoding their own as well as dysregulating host ncRNAs to modulate virus gene expression and the host response to infection. Research has mainly focused on unidirectional ncRNA-mediated regulation of target protein-coding transcripts; however, we have identified a novel host ncRNA regulatory network essential for KSHV lytic replication in B cells. KSHV-mediated upregulation of the host cell circRNA, circHIPK3, is a key component of this network, functioning as a competing endogenous RNA of miR-30c, leading to increased levels of the miR-30c target, DLL4. Dysregulation of this network highlights a novel mechanism of cell cycle control during KSHV lytic replication in B cells. Importantly, disruption at any point within this novel ncRNA regulatory network has a detrimental effect on KSHV lytic replication, highlighting the essential nature of this network and potential for therapeutic intervention.
Transgenic Drosophila lines for LexA-dependent gene and growth regulation
Authors: Chang Kathleen R. , Tsao Deborah D. , Bennett Celine , Wang Elaine , Floyd Jax F. , Tay Ashley S.Y. , Greenwald Emily , Kim Ella S. , Griffin Catherine , Morse Elizabeth , Chisholm Townley , Rankin Anne E. , Baena-Lopez Alberto , Lantz Nicole , Fox Elizabeth , Kockel Lutz , Kim Seung K. , Park Sangbin 
Published: October 2021

ABSTRACTConditional expression of short hairpin RNAs (shRNAs) with binary genetic systems is an indispensable tool for studying gene function. Addressing mechanisms underlying cell-cell communication in vivo benefits from simultaneous use of two independent gene expression systems. To complement the abundance of existing Gal4/UAS-based resources in Drosophila, we and others have developed LexA/LexAop-based genetic tools. Here, we describe experimental and pedagogical advances that promote the efficient conversion of Drosophila Gal4 lines to LexA lines, and the generation of LexAop-shRNA lines to suppress gene function. We developed a CRISPR/Cas9-based knock-in system to replace Gal4 coding sequences with LexA, and a LexAop-based shRNA expression vector to achieve shRNA-mediated gene silencing. We demonstrate the use of these approaches to achieve targeted genetic loss-of-function in multiple tissues. We also detail our development of secondary school curricula that enable students to create transgenic flies, thereby magnifying the production of well-characterized LexA/LexAop lines for the scientific community. The genetic tools and teaching methods presented here provide LexA/LexAop resources that complement existing resources to study intercellular communication coordinating metazoan physiology and development.
Growth and development of trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata) reflects locomotor behavior, life-history, and neuromuscular development
Authors: Saers Jaap P.P. , Gordon Adam D. , Ryan Timothy M. , Stock Jay T. 
Published: October 2021

AbstractWe aim to broaden the analysis of bone structure by suggesting a new way to incorporate the interactions between behavior, neuromuscular development, and life-history. We examine the associations between these variables and age-related variation in trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata). If skeletal markers linking these variables can be established, our inferences of the biology and behavior of fossil species would be significantly improved. We µCT scanned the calcaneus in a cross-sectional sample of 36 juveniles aged between 0 and 7 years old and 5 adults at the Primate Research Institute, Japan. We calculated whole bone averages of standard trabecular properties and generated whole-bone morphometric maps of bone volume fraction and Young’s modulus. Trabecular structure is increasingly heterogeneous in older individuals. BV/TV decreases during the first month of life and increases afterwards, coinciding with the onset of independent locomotion. At birth, primary Young’s modulus is oriented orthogonal to the ossification center, but after locomotor onset bone structure becomes stiffest in the direction of joint surfaces and muscle attachments. Age-related variation in bone volume fraction is best predicted by an interaction between neuromaturation, body mass, and locomotor independence. Results support the common assumption that trabecular structure dynamically adapts to novel joint loading conditions during ontogeny. The timing of independent locomotion, body size, and neuromuscular development, are all correlated to age-related variation in the trabecular structure of the macaque calcaneus. The causal mechanisms behind the observed patterns cannot be directly inferred from our cross-sectional study. If the model presented in this paper holds up under longitudinal experimental conditions, trabecular structure can be used both to infer behavior from fossil morphology and to serve as a valuable proxy for neuromuscular maturation and life history events like locomotor onset and the achievement of an adult-like gait.