bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salp metabolism: temperature and oxygen partial pressure effect on the physiology of Salpa fusiformis from the California Current
Authors: Trueblood Lloyd A 
Published: April 2019

AbstractSalps are pelagic tunicates that play an important role in carbon cycling by filter feeding and packaging waste into dense fecal pellets that sink rapidly to the deep ocean. There has been limited research on salp physiology and no studies that examine how changes in environmental factors such as temperature and dissolved oxygen impact basic physiological processes. Here I examine temperature and oxygen partial pressure effect on metabolism in blastozooids of Salpa fusiformis. Routine metabolic rates of 1.66 and 3.95 μmol O2 g−1 h−1 wet weight at 10°C and 17°C, respectively, resulted in a Q10 = 3.45. The observed decrease in metabolism associated with decreased temperature, as well as hypoxia tolerance, is explored in the context of observed vertical migrations into hypoxic waters in the California Current, and potential impacts on carbon output. Metabolic rates for S. fusiformis are compared to metabolic rates published for other species of salps and gelatinous zooplankton. Expansion of this work across a broader set of species is critical to quantify the impact climate change may have on salps and their role in marine carbon cycling.
Seasonal zooplankton development in a temperate semi-enclosed basin: two years with different spring bloom timing
Authors: Mahara Natalie , Pakhomov Evgeny A , Jackson Jennifer M , Hunt Brian Pv 
Published: April 2019

Abstract
Coastal temperate waters undergo considerable intra- and interannual environmental variations, which is reflected in the dynamic nature of their zooplankton communities. Since zooplankton phenology is dependent on several factors, particularly temperature and spring bloom timing, it is imperative to understand how zooplankton communities may shift under future climate conditions with warmer temperatures and more variable spring bloom initiation. To examine zooplankton phenology and response to shifts in bloom timing, we analyzed fortnightly zooplankton and environmental samples collected in the northern Strait of Georgia (B.C., Canada), a large semi-enclosed temperate basin, in 2015 and 2016. Despite a 5-week difference in spring bloom timing, zooplankton community succession was remarkably similar between years. In both years, biomass peaked within the same calendar week and communities were separated into winter, early spring and summer-autumn assemblages that formed independent of the spring bloom timing. Although some species-level phenological differences were observed between years, predominately delayed population development, zooplankton communities appeared to demonstrate resilience to interannual environmental variations on the whole. If ongoing warming shifts the timing of zooplankton consumers’ life history timing, it could lead to a mismatch with their zooplankton prey resource that exhibits comparatively less interannual variability.
Symbrachydactyly
Authors: Mills Janith K. , Butler Lesley , Mills Elisa M. , Oishi Scott N. 
Published: April 2019

ABSTRACT
Although congenital hand anomalies associated with finger nubbins may be produced by amniotic band disruption sequence (ABDS), symbrachydactyly should be considered in the differential diagnosis. ABDS usually affects more than one limb but symbrachydactyly largely is limited to one upper extremity, and has five distinct clinical presentations: short-fingered, atypical cleft, monodactylous, peromelic, and a forearm proximal transverse deficiency. This article discusses the diagnosis of symbrachydactyly compared with ABDS and outlines plans for managing patients with symbrachydactyly.
Prognostic Value of Tumor Heterogeneity and SUVmax of Pretreatment 18F-FDG PET/CT for Salivary Gland Carcinoma With High-Risk Histology
Authors: Cheng Nai-Ming , Hsieh Cheng-En , Liao Chun-Ta , Ng Shu-Hang , Wang Hung-Ming , Fang Yu-Hua Dean , Chou Wen-Chi , Lin Chien-Yu , Yen Tzu-Chen 
Published: April 2019

Purpose
Previous studies have shown that SUVmax on 18F-FDG PET/CT predicts prognosis in patients with salivary gland carcinoma (SGC). Here, we sought to evaluate whether texture features extracted from 18F-FDG PET/CT images may provide additional prognostic information for SGC with high-risk histology.

Methods
We retrospectively examined pretreatment 18F-FDG PET/CT images obtained from 85 patients with nonmetastatic SGC showing high-risk histology. All patients were treated with curative intent. We used the fixed threshold of 40% of SUVmax for tumor delineation. PET texture features were extracted by using histogram analysis, normalized gray-level co-occurrence matrix, and gray-level size zone matrix. Optimal cutoff points for each PET parameter were derived from receiver operating characteristic curve analyses. Recursive partitioning analysis was used to construct a prognostic model for overall survival (OS).

Results
Receiver operating characteristic curve analyses revealed that SUVmax, SUV entropy, uniformity, entropy, zone-size nonuniformity, and high-intensity zone emphasis were significantly associated with OS. The strongest associations with OS were found for high SUVmax (>6.67) and high SUV entropy (>2.50). Multivariable Cox analysis identified high SUVmax, high SUV entropy, performance status, and N2c–N3 stage as independent predictors of survival. A prognostic model derived from multivariable analysis revealed that patients with high SUVmax and SUV entropy or with the presence of poor performance status or N2c–N3 were associated with worse OS.

Conclusions
A prognostic model that includes SUVmax and SUV entropy is useful for risk stratification and supports the additional benefit of texture analysis for SGC with high-risk histology.
68Ga-PSMA Uptake in Fibrous Dysplasia
Authors: Reale Maria Lucia , Buttigliero Consuelo , Tucci Marcello , Giardino Roberto , Poti Carlo 
Published: April 2019

Abstract
Prostate cancer is one of the most common malignancies. Imaging tools play an important role throughout the entire process of the disease. The scenario, however, is going to change. Thanks to a higher sensitivity and specificity, the use of the prostate-specific membrane antigen (PSMA) PET is of increasing importance, particularly at the time of diagnosis and in case of biochemical recurrence. Nevertheless, previous reports have described false-positive findings, as tracer-avid physiological findings or benign processes, potential pitfalls for interpretation of 68Ga-PSMA PET/CT. Here we report a case of PSMA uptake in a histologically proven fibrous dysplasia.
Tuberculosis Presenting as Cutaneous Erythema Nodosum on 18F-FDG PET/CT
Authors: Jain Tarun Kumar 
Published: April 2019

Abstract
The present article presented a 47-year-old woman with areas of nodular swelling and discoloration involving bilateral lower limbs since 12 months. Biopsy from skin lesions revealed erythema nodosum. As erythema nodosum can be secondary to multiple etiologies, whole-body 18F-FDG PET/CT was performed to assess the disease distribution and guide the site of biopsy. 18F-FDG PET/CT revealed metabolically active mediastinal lymphadenopathy in addition to the skin lesions. Endobronchial ultrasound–guided biopsy from subcarinal lymph node revealed tuberculosis.
18F–Prostate-Specific Membrane Antigen 1007 and 18F-FCH PET/CT in Local Recurrence of Prostate Cancer
Authors: Witkowska-Patena Ewa , Giżewska Agnieszka , Miśko Jolanta , Dziuk Mirosław 
Published: April 2019

Abstract

18F–prostate-specific membrane antigen (PSMA) 1007 is one of the most promising radiotracers for PET imaging of relapsing prostate cancer. Minimal urinary clearance seems to be its most valuable and outstanding feature. We present images of biochemically relapsed prostate cancer where 18F-PSMA-1007 PET/CT (performed to verify an ambiguous finding adjacent to the urinary bladder found in 18F-FCH PET/CT) proved superior to radiocholine and precisely visualized site of local recurrence.
Transient absorption spectroscopy using high harmonic generation: a review of ultrafast X-ray dynamics in molecules and solids
Authors: Geneaux Romain , Marroux Hugo J. B. , Guggenmos Alexander , Neumark Daniel M. , Leone Stephen R. 
Published: April 2019

Attosecond science opened the door to observing nuclear and electronic dynamics in real time and has begun to expand beyond its traditional grounds. Among several spectroscopic techniques, X-ray transient absorption spectroscopy has become key in understanding matter on ultrafast time scales. In this review, we illustrate the capabilities of this unique tool through a number of iconic experiments. We outline how coherent broadband X-ray radiation, emitted in high-harmonic generation, can be used to follow dynamics in increasingly complex systems. Experiments performed in both molecules and solids are discussed at length, on time scales ranging from attoseconds to picoseconds, and in perturbative or strong-field excitation regimes.
This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.
Chemical interactions and dynamics with femtosecond X-ray spectroscopy and the role of X-ray free-electron lasers
Authors: Wernet Philippe 
Published: April 2019

X-ray free-electron lasers with intense, tuneable and short-pulse X-ray radiation are transformative tools for the investigation of transition-metal complexes and metalloproteins. This becomes apparent in particular when combining the experimental observables from X-ray spectroscopy with modern theoretical tools for calculations of electronic structures and X-ray spectra from first principles. The combination gives new insights into how charge and spin densities change in chemical reactions and how they determine reactivity. This is demonstrated for the investigations of structural dynamics with metal K-edge absorption spectroscopy, spin states in excited-state dynamics with metal 3p-3d exchange interactions, the frontier-orbital interactions in dissociation and substitution reactions with metal-specific X-ray spectroscopy, and studies of metal oxidation states with femtosecond pulses for ‘probe-before-destroy’ spectroscopy. The role of X-ray free-electron lasers is addressed with thoughts about how they enable ‘bringing back together’ different aspects of the same problem and this is thought to go beyond a conventional review paper where these aspects are formulated in italic font type in a prequel, an interlude and in a sequel.
This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays'.
Domain-specific quantification of prion protein in cerebrospinal fluid by targeted mass spectrometry
Authors: Minikel Eric Vallabh , Kuhn Eric , Cocco Alexandra R , Vallabh Sonia M , Hartigan Christina R , Reidenbach Andrew G , Safar Jiri G , Raymond Gregory J , McCarthy Michael D , O’Keefe Rhonda , Llorens Franc , Zerr Inga , Capellari Sabina , Parchi Piero , Schreiber Stuart L , Carr Steven A 
Published: April 2019

AbstractTherapies currently in preclinical development for prion disease seek to lower prion protein (PrP) expression in the brain. Trials of such therapies are likely to rely on quantification of PrP in cerebrospinal fluid (CSF) as a pharmacodynamic biomarker and possibly as a trial endpoint. Studies using PrP ELISA kits have reproducibly shown that CSF PrP is lowered in the symptomatic phase of disease, a potential confounder for reading out the effect of PrP-lowering drugs in symptomatic patients. To date it has been unclear whether the reduced abundance of PrP in CSF results from its incorporation into plaques, retention in intracellular compartments, downregulation as a function of the disease process, or other factors. Because misfolding or proteolytic cleavage could potentially render PrP invisible to ELISA even if its concentration were constant or increasing in disease, we sought to establish an orthogonal method for CSF PrP quantification. We developed a targeted mass spectrometry method based on multiple reaction monitoring (MRM) of nine PrP tryptic peptides quantified relative to known concentrations of isotopically labeled standards. Analytical validation experiments showed process replicate coefficients of variation below 15%, good dilution linearity and recovery, and suitable performance for both CSF and brain homogenate and across humans as well as preclinical species of interest. InN=55 CSF samples from individuals referred to prion surveillance centers with rapidly progressive dementia, all six human PrP peptides, spanning the N- and C-terminal domains of PrP, were uniformly reduced in prion disease cases compared to individuals with non-prion diagnoses. This confirms the findings from ELISA studies, demonstrating that lowered CSF PrP concentration in prion disease is a genuine result of the disease process and not merely an artifact of ELISA-based measurement. We provide a targeted mass spectrometry-based method suitable for preclinical and clinical quantification of CSF PrP as a tool for drug development.
Characterization of LINE-1 transposons in a human genome at allelic resolution
Authors: Yang Lei , Metzger Genevieve A. , McLaughlin Richard N. 
Published: April 2019

AbstractThe activity of the retrotransposon LINE-1 has created a substantial portion of the human genome. Most of this sequence comprises fractured and debilitated LINE-1s. An accurate approximation of the number, location, and sequence of the LINE-1 elements present in any single genome has proven elusive due to the difficulty of assembling and phasing the repetitive and polymorphic regions of the human genome. Through an in-depth analysis of publicly-available, deep, long-read assemblies of nearly homozygous human genomes, we defined the location and sequence of all intact LINE-1s in these assemblies. We found 148 and 142 intact LINE-1s in two nearly homozygous assemblies. A combination of these assemblies suggests a diploid human genome contains at least 50% more intact LINE-1s than previous estimates – in this case, 290 intact LINE-1s at 194 loci. We think this is the best approximation, to date, of the number of intact LINE-1s in a single diploid human genome. In addition to counting intact LINE-1 elements, we resolved the sequence of each element, including some LINE-1 elements in unassembled, presumably centromeric regions of the genome. A comparison of the intact LINE-1s in each assembly shows the specific pattern of variation between these genomes, including LINE-1s that remain intact in only one genome, allelic variation in shared intact LINE-1s, and LINE-1s that are unique (presumably young) insertions in only one genome. We found that many old elements (> 6 million years old) remain intact, and comparison of the young and intact LINE-1s across assemblies reinforces the notion that only a small portion of all LINE-1 sequences that may be intact in the genomes of the human population has been uncovered. This dataset provides the first nearly comprehensive estimate of LINE-1 diversity within an individual, an important dataset in the quest to understand the functional consequences of sequence variation in LINE-1 and the complete set of LINE-1s in the human population.
Integrating multiple data sources to fit matrix population models for interacting species
Authors: Barraquand Frédéric , Gimenez Olivier 
Published: April 2019

AbstractInferring interactions between populations of different species is a challenging statistical endeavour, which requires a large amount of data. There is therefore some incentive to combine all available sources of data into a single analysis to do so. In demography and single-population studies, Integrated Population Models combine population counts, capture-recapture and reproduction data to fit matrix population models. Here, we extend this approach to the community level in a stage-structured predator-prey context. We develop Integrated Community Models (ICMs), implemented in a Bayesian framework, to fit multispecies nonlinear matrix models to multiple data sources. We assessed the value of the different sources of data using simulations of ICMs under different scenarios contrasting data availability. We found that combining all data types (capture-recapture, counts, and reproduction) allows the estimation of both demographic and interaction parameters, unlike count-only data which typically generate high bias and low precision in interaction parameter estimates for short time series. Moreover, reproduction surveys informed the estimation of interactions particularly well when compared to capture-recapture programs, and have the advantage of being less costly. Overall, ICMs offer an accurate representation of stage structure in community dynamics, and foster the development of efficient observational study designs to monitor communities in the field.
Parallel Group ICA + ICA: Joint Estimation of Linked Functional Network Variability and Structural Covariation with Application to Schizophrenia
Authors: Qi Shile , Sui Jing , Chen Jiayu , Liu Jingyu , Jiang Rongtao , Silva Rogers , Iraji Armin , Damaraju Eswar , Salman Mustafa , Lin Dongdong , Fu Zening , Zhi Dongmei , Turner Jessica A. , Bustillo Juan , Ford Judith M. , Mathalon Daniel H. , Voyvodic James , McEwen Sarah , Preda Adrian , Belger Aysenil , Potkin Steven G. , Mueller Bryon A. , Adali Tulay , Calhoun Vince D. 
Published: April 2019

ABSTRACTThere is growing evidence that rather than using a single brain imaging modality to study its association with physiological or symptomatic features, the field is paying more attention to fusion of multimodal information. However, most current multimodal fusion approaches that incorporate functional magnetic resonance imaging (fMRI) are restricted to second-level 3D features, rather than the original 4D fMRI data. This trade-off is that the valuable temporal information is not utilized during the fusion step. Here we are motivated to propose a novel approach called “parallel group ICA+ICA” that incorporates temporal fMRI information from GICA into a parallel ICA framework, aiming to enable direct fusion of first-level fMRI features with other modalities (e.g.structural MRI), which thus can detect linked functional network variability and structural covariations. Simulation results show that the proposed method yields accurate inter-modality linkage detection regardless of whether it is strong or weak. When applied to real data, we identified one pair of significantly associated fMRI-sMRI components that show group difference between schizophrenia and controls in both modalities. Finally, multiple cognitive domain scores can be predicted by the features identified in the linked component pair by our proposed method. We also show these multimodal brain features can predict multiple cognitive scores in an independent cohort. Overall, results demonstrate the ability of parallel GICA+ICA to estimate joint information from 4D and 3D data without discarding much of the available information up front, and the potential for using this approach to identify imaging biomarkers to study brain disorders.
Is the addition of higher-order interactions in ecological models increasing the understanding of ecological dynamics?
Authors: AlAdwani Mohammad , Saavedra Serguei 
Published: April 2019

AbstractRecent work has shown that higher-order interactions can increase the stability, promote the diversity, and better explain the dynamics of ecological communities. Yet, it remains unclear whether the perceived benefits of adding higher-order terms into population dynamics models come from fundamental principles or a simple mathematical advantage given by the nature of multivariate polynomials. Here, we develop a general method to quantify the mathematical advantage of adding higher-order interactions in ecological models based on the number of free-equilibrium points that can be engineered in a system (i.e., equilibria that can be feasible or unfeasible by tunning model parameters). We apply this method to calculate the number of free-equilibrium points in Lotka-Volterra dynamics. While it is known that Lotka-Volterra models without higher-order interactions only have one free-equilibrium point regardless of the number of parameters, we find that by adding higher-order terms this number increases exponentially with the dimension of the system. Our results suggest that while adding higher-order interactions in ecological models may be good for prediction purposes, they cannot provide additional explanatory power of ecological dynamics if model parameters are not ecologically restricted.
Moiety Modeling Framework for Deriving Moiety Abundances from Mass Spectrometry Measured Isotopologues
Authors: Jin Huan , Moseley Hunter N.B. 
Published: April 2019

AbstractBackgroundStable isotope tracing can follow individual atoms through metabolic transformations through the detection of the incorporation of stable isotope within metabolites. This resulting data can be interpreted in terms related to metabolic flux. However, detection of a stable isotope in metabolites by mass spectrometry produces a profile of isotopologue peaks that requires deconvolution to ascertain the localization of isotope incorporation.ResultsTo aid the interpretation of the mass spectroscopy isotopologue profile, we have developed a moiety modeling framework for deconvoluting metabolite isotopologue profiles involving single and multiple isotope tracers. This moiety modeling framework provides facilities for moiety model representation, moiety model optimization, and moiety model selection. The moiety_modeling package was developed from the idea of metabolite decomposition into moiety units based on metabolic transformations, i.e. a moiety model. A SAGA-optimize package, solving a boundary-value inverse problem through a combined simulated annealing and genetic algorithm, was developed for model optimization. Additional optimization methods from the Python scipy library are utilized as well. Several forms of the Akaike information criterion and Bayesian information criterion are provided for selecting between moiety models. Moiety models and associated isotopologue data are defined in the JSON format.By testing the moiety modeling framework on the timecourses of 13C isotopologue data for UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) in human prostate cancer LnCaP-LN3 cells, we were able to confirm its robust performance in isotopologue deconvolution and moiety model selection.ConclusionsSAGA-optimize is a useful Python package for solving boundary-value inverse problems, and the moiety_modeling package is an easy-to-use tool for mass spectroscopy isotopologue profile deconvolution involving single and multiple isotope tracers. Both packages are freely freely available on GitHub and via the Python Package Index.