bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating tumor DNA and magnetic resonance imaging to predict neoadjuvant chemotherapy response and recurrence risk
Authors: Magbanua Mark Jesus M. , Li Wen , Wolf Denise M. , Yau Christina , Hirst Gillian L. , Swigart Lamorna Brown , Newitt David C. , Gibbs Jessica , Delson Amy L. , Kalashnikova Ekaterina , Aleshin Alexey , Zimmermann Bernhard , Chien A. Jo , Tripathy Debu , Esserman Laura , Hylton Nola , van ‘t Veer Laura 
Published: March 2021

AbstractWe investigated whether serial measurements of circulating tumor DNA (ctDNA) and functional tumor volume (FTV) by magnetic resonance imaging (MRI) can be combined to improve prediction of pathologic complete response (pCR) and estimation of recurrence risk in early breast cancer patients treated with neoadjuvant chemotherapy (NAC). We examined correlations between ctDNA and FTV, evaluated the additive value of ctDNA to FTV-based predictors of pCR using area under the curve (AUC) analysis, and analyzed the impact of FTV and ctDNA on distant recurrence-free survival (DRFS) using Cox regressions. The levels of ctDNA (mean tumor molecules/mL plasma) were significantly correlated with FTV at all time points (p < 0.05). Median FTV in ctDNA-positive patients was significantly higher compared to those who were ctDNA-negative (p < 0.05). FTV and ctDNA trajectories in individual patients showed a general decrease during NAC. Exploratory analysis showed that adding ctDNA information early during treatment to FTV-based predictors resulted in numerical but not statistically significant improvements in performance for pCR prediction (e.g., AUC 0.59 vs. 0.69, p = 0.25). In contrast, ctDNA-positivity after NAC provided significant additive value to FTV in identifying patients with increased risk of metastatic recurrence and death (p = 0.004). In this pilot study, we demonstrate that ctDNA and FTV were correlated measures of tumor burden. Our preliminary findings based on a limited cohort suggest that ctDNA at surgery improves FTV as a predictor of metastatic recurrence and death. Validation in larger studies is warranted.
Optimal control for quantum detectors
Authors: Titum Paraj , Schultz Kevin , Seif Alireza , Quiroz Gregory , Clader B. D. 
Published: March 2021

AbstractQuantum systems are promising candidates for sensing of weak signals as they can be highly sensitive to external perturbations, thus providing excellent performance when estimating parameters of external fields. However, when trying to detect weak signals that are hidden by background noise, the signal-to-noise ratio is a more relevant metric than raw sensitivity. We identify, under modest assumptions about the statistical properties of the signal and noise, the optimal quantum control to detect an external signal in the presence of background noise using a quantum sensor. Interestingly, for white background noise, the optimal solution is the simple and well-known spin-locking control scheme. Using numerical techniques, we further generalize these results to the case of background noise with a Lorentzian spectrum. We show that for increasing correlation time, pulse based sequences, such as CPMG, are also close to the optimal control for detecting the signal, with the crossover dependent on the signal frequency. These results show that an optimal detection scheme can be easily implemented in near-term quantum sensors without the need for complicated pulse shaping.
An updated map of Trypanosoma cruzi histone post-translational modifications
Authors: de Almeida Rafael Fogaça , Fernandes Matheus , de Godoy Lyris Martins Franco 
Published: March 2021

AbstractIn humans and other eukaryotes, histone post-translational modifications (hPTMs) play an essential role in the epigenetic control of gene expression. In trypanosomatid parasites, conversely, gene regulation occurs mainly at the post-transcriptional level. However, our group has recently shown that hPTMs are abundant and varied in Trypanosoma cruzi, the etiological agent of Chagas Disease, signaling for possible conserved epigenetic functions. Here, we applied an optimized mass spectrometry-based proteomic workflow to provide a high-confidence comprehensive map of hPTMs, distributed in all canonical, variant and linker histones of T. cruzi. Our work expands the number of known T. cruzi hPTMs by almost 2-fold, representing the largest dataset of hPTMs available to any trypanosomatid to date, and can be used as a basis for functional studies on the dynamic regulation of chromatin by epigenetic mechanisms and the selection of candidates for the development of epigenetic drugs against trypanosomatids.
Creation and validation of a chest X-ray dataset with eye-tracking and report dictation for AI development
Authors: Karargyris Alexandros , Kashyap Satyananda , Lourentzou Ismini , Wu Joy T. , Sharma Arjun , Tong Matthew , Abedin Shafiq , Beymer David , Mukherjee Vandana , Krupinski Elizabeth A. , Moradi Mehdi 
Published: March 2021

AbstractWe developed a rich dataset of Chest X-Ray (CXR) images to assist investigators in artificial intelligence. The data were collected using an eye-tracking system while a radiologist reviewed and reported on 1,083 CXR images. The dataset contains the following aligned data: CXR image, transcribed radiology report text, radiologist’s dictation audio and eye gaze coordinates data. We hope this dataset can contribute to various areas of research particularly towards explainable and multimodal deep learning/machine learning methods. Furthermore, investigators in disease classification and localization, automated radiology report generation, and human-machine interaction can benefit from these data. We report deep learning experiments that utilize the attention maps produced by the eye gaze dataset to show the potential utility of this dataset.
Characterization of carrier behavior in photonically excited 6H silicon carbide exhibiting fast, high voltage, bulk transconductance properties
Authors: Sampayan S. E. , Grivickas P. V. , Conway A. M. , Sampayan K. C. , Booker I. , Bora M. , Caporaso G. J. , Grivickas V. , Nguyen H. T. , Redeckas K. , Schoner A. , Voss L. F. , Vengris M. , Wang L. 
Published: March 2021

AbstractUnabated, worldwide trends in CO2 production project growth to > 43-BMT per year over the next two decades. Efficient power electronics are crucial to fully realizing the CO2 mitigating benefits of a worldwide smart grid (~ 18% reduction for the United States alone). Even state-of-the-art SiC high voltage junction devices are inefficient because of slow transition times (~ 0.5-μs) and limited switching rates at high voltage (~ 20-kHz at ≥ 15-kV) resulting from the intrinsically limited charge carrier drift speed (< 2 × 107-cm-s−1). Slow transition times and limited switch rates waste energy through transition loss and hysteresis loss in external magnetic components. Bulk conduction devices, where carriers are generated and controlled nearly simultaneously throughout the device volume, minimize this loss. Such devices are possible using below bandgap excitation of semi-insulating (SI) SiC single crystals. We explored carrier dynamics with a 75-fs single wavelength pump/supercontinuum probe and a modified transient spectroscopy technique and also demonstrated a new class of efficient, high-speed, high-gain, bi-directional, optically-controlled transistor-like power device. At a performance level six times that of existing devices, for the first time we demonstrated prototype operation at multi-10s of kW and 20-kV, 125-kHz in a bulk conduction transistor-like device using direct photon-carrier excitation with below bandgap light.
eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants
Authors: Nørgaard Louise , Olesen Carsten Riis , Trøjelsgaard Kristian , Pertoldi Cino , Nielsen Jeppe Lund , Taberlet Pierre , Ruiz-González Aritz , De Barba Marta , Iacolina Laura 
Published: March 2021

AbstractWith an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as “biodiversity capsules” and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.
An intensity matched comparison of laser- and contact heat evoked potentials
Authors: De Schoenmacker Iara , Berry Carson , Blouin Jean-Sébastien , Rosner Jan , Hubli Michèle , Jutzeler Catherine R. , Kramer John L. K. 
Published: March 2021

AbstractPrevious studies comparing laser (LEPs) and contact heat evoked potentials (CHEPs) consistently reported higher amplitudes following laser compared to contact heat stimulation. However, none of the studies matched the perceived pain intensity, questioning if the observed difference in amplitude is due to biophysical differences between the two methods or a mismatch in stimulation intensity. The aims of the current study were twofold: (1) to directly compare the brain potentials induced by intensity matched laser and contact heat stimulation and (2) investigate how capsaicin-induced secondary hyperalgesia modulates LEPs and CHEPs. Twenty-one healthy subjects were recruited and measured at four experimental sessions: (1) CHEPs + sham, (2) LEPs + sham, (3) CHEPs + capsaicin, and (4) LEPs + capsaicin. Baseline (sham) LEPs latency was significantly shorter and amplitude significantly larger compared to CHEPs, even when matched for perceived pain. Neither CHEPs nor LEPs was sensitive enough to detect secondary hyperalgesia. These differences provide evidence that a faster heating rate results in an earlier and more synchronized LEPs than CHEPs. To our knowledge, this was the first study to match perceived intensity of contact heat and laser stimulations, revealing distinct advantages associated with the acquisition of LEPs.
Anthropogenic nutrient loads and season variability drive high atmospheric N2O fluxes in a fragmented mangrove system
Authors: Hershey N. Regina , Nandan S. Bijoy , Vasu K. Neelima , Tait Douglas R. 
Published: March 2021

AbstractFragmented mangroves are generally ignored in N2O flux studies. Here we report observations over the course of a year from the Mangalavanam coastal wetland in Southern India. The wetland is a fragmented mangrove stand close to a large urban centre with high anthropogenic nitrogen inputs. The study found the wetland was a net source of N2O to the atmosphere with fluxes ranging between 17.5 to 117.9 µmol m−2 day−1 which equated to high N2O saturations of between 697 and 1794%. The average dissolved inorganic nitrogen inputs (80.1 ± 18.1 µmol L−1) and N2O emissions (59.2 ± 30.0 µmol m−2 day−1) were highest during the monsoon season when the rainfall and associated river water inputs and terrestrial runoff were highest. The variation in N2O dynamics was shown to be driven by the changes in rainfall, water column depth, salinity, dissolved oxygen, carbon, and substrate nitrogen. The study suggests that fragmented/minor mangrove ecosystems subject to high human nutrient inputs may be a significant component of the global N2O budget.
Expression analysis of selected genes involved in tryptophan metabolic pathways in Egyptian children with Autism Spectrum Disorder and learning disabilities
Authors: Higazi Aliaa M. , Kamel Hanan M. , Abdel-Naeem Emad A. , Abdullah Noha M. , Mahrous Doaa M. , Osman Ashraf M. 
Published: March 2021

AbstractAutism Spectrum Disorder (ASD) and learning disabilities are neurodevelopmental disabilities characterized by dramatically increasing incidence rates, yet the exact etiology for these disabilities is not identified. Impairment in tryptophan metabolism has been suggested to participate in the pathogenesis of ASD, however, further validation of its involvement is required. Additionally, its role in learning disabilities is still uninvestigated. Our objective was to evaluate some aspects of tryptophan metabolism in ASD children (N = 45) compared to children with learning disabilities (N = 44) and healthy controls (N = 40) by measuring the expression levels of the MAOA, HAAO and AADAT genes using real-time RT-qPCR. We also aimed to correlate the expression patterns of these genes with parental ages at the time of childbirth, levels of serum iron, and vitamin D3 and zinc/copper ratio, as possible risk factors for ASD. Results demonstrated a significant decrease in the expression of the selected genes within ASD children (p < 0.001) relative to children with learning disabilities and healthy controls, which significantly associated with the levels of our targeted risk factors (p < 0.05) and negatively correlated to ASD scoring (p < 0.001). In conclusion, this study suggests that the expression of the MAOA, HAAO and AADAT genes may underpin the pathophysiology of ASD.
Untangling the multi-regime molecular mechanism of verbenol-chemotype Zingiber officinale essential oil against Aspergillus flavus and aflatoxin B1
Authors: Singh Prem Pratap , Jaiswal Atul Kumar , Kumar Akshay , Gupta Vishal , Prakash Bhanu 
Published: March 2021

AbstractAflatoxin B1 (AFB1), the natural polyketide produced by Aspergillus flavus, has a potent carcinogenic effect on humans as well as animals. In the present study, the antifungal and anti-aflatoxigenic B1 activity of chemically characterized Zingiber officinale essential oil (ZOEO) was investigated via in vitro analysis aided with molecular dynamics (MD) approaches. The GC–MS results revealed verbenol (52.41%) as the major component of oil. The antifungal and anti-aflatoxigenic activity of ZOEO was found to be 0.6 µl/ml and 0.5 µl/ml respectively. In-vitro analysis targeting the cell membrane, mitochondria and carbohydrate catabolism elucidated the probable antifungal mode of action. Further, docking and MD simulation results confirmed the inhibitory action of verbenol on the structural gene products (Nor-1, Omt-1, and Vbs) of aflatoxin biosynthetic machinery. Biochemical assays revealed the fungitoxic potential of the ZOEO while, computational results infers the stabilizing effects on the gene products upon verbenol binding leads to the impairment in its functionality. This is the first attempt to assess the multi-regime anti-AFB1 mechanism of verbenol chemotype-ZOEO targeting the Nor-1, Omt-1, and Vbs via computational approaches.
Seasonal patterns of bison diet across climate gradients in North America
Authors: Craine Joseph M. 
Published: March 2021

AbstractNorth American plains bison (Bison bison) have been reintroduced across their former range, yet we know too little about their current diet to understand what drove their past migrations as well as observed continental-scale variation in weight gain and reproduction. In order to better understand the seasonal diets of bison at the continental scale, bison fecal material was collected monthly from April to September in 2019 across 45 sites throughout the conterminous United States. Fecal material was analyzed for dietary quality using near infrared spectroscopy and dietary composition with DNA metabarcoding. As observed in previous research, dietary quality peaked in June and was on average greatest for sites with cold, wet climates. Yet, in April, dietary quality was highest in warmer regions, likely reflecting earlier phenology of plants in southern than northern regions. Independent of climate and season, bison that consumed more warm-season grasses had lower dietary protein concentrations. Interpreting the relative abundance of sequences from different plant species as the relative intake of protein from those species, only 38% of bison protein intake came from grasses. An equal amount of dietary protein came from legumes (38%) and 22% from non-leguminous forbs. Seasonal shifts in bison diet were also clear, in part, following the phenology of functional groups. For example, cool-season grass protein intake was highest in May, while legume protein intake was highest in August. Comparing data taken in June and September 2018 in a previous study with corresponding data in 2019, on average, June [CP] was 20% higher in 2019 than 2018, while September [CP] did not differ between years. Dietary functional group composition was generally similar in amounts and relationships with climate between years, yet in September 2019, legumes contributed 20% more protein and warm-season grasses 14% less than in September 2018. In all, this research demonstrates that bison consistently rely on eudicots for protein with the functional group composition of their diet in some ways consistent across space and time, but also spatially and temporally variable. The early-season inversion of plant quality gradients would have been a strong driver of migratory behavior for large numbers of bison optimizing protein intake. As most bison currently experience protein deficiency, optimizing protein intake under current non-migratory conditions will require increasing the relative abundance of high-protein species such as N2-fixing species.
New Permian radiolarians from east Asia and the quantitative reconstruction of their evolutionary and ecological significances
Authors: Xiao Yifan , Suzuki Noritoshi , Ito Tsuyoshi , He Weihong 
Published: March 2021

AbstractThe biostratigraphically important Permian radiolarian generaPseudoalbaillellasensu stricto andFollicucullus(Follicucullidae, Polycystinea) are discriminated by morphological gaps in their wings and segmentation. Previous statistical analyses demonstrated thatLongtanellafills morphological gaps between these two genera.Longtanellahas long been regarded as a junior synonym ofParafollicucullus, and only a few species have been described. Herein several trueLongtanellaspecies are recognized from South China, and eight new species and five indeterminate species are described and illustrated to prove the validity of the genusLongtanella. In addition, a new genus,Parafollicucullinoidesgen. nov., is described. Their palaeogeographic distributions and living environments are explored by applying correspondence analysis (CA), with occurrence datasets of selected fusulinacean genera from the Japanese Islands, China and Sundaland. CA results indicate thatLongtanellawas present to a limited extent in warmer conditions in the fusulinacean Province B and C during Kungurian–Roadian time, and possibly lived above the thermocline and below the deepest limit of fusulinaceans. ThePseudoalbaillellaand theFollicucullusgroup preferred open ocean conditions, living below the thermocline and distributed not only in the ‘Equatorial Warm Water Province’, but also the northern peri-Gondwana Cool Water Province and the southern North Cool Water Province.
Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts
Authors: Shortt Jonathan A. , Timm Laura E. , Hales Nicole R. , Nikolakis Zachary L. , Schield Drew R. , Perry Blair W. , Liu Yang , Zhong Bo , Castoe Todd A. , Carlton Elizabeth J. , Pollock David D. 
Published: March 2021

AbstractSchistosomiasis persists in Asian regions despite aggressive elimination measures. To identify factors enabling continued parasite transmission, we performed reduced representation genome sequencing on Schistosoma japonicum miracidia collected across multiple years from transmission hotspots in Sichuan, China. We discovered strong geographic structure, suggesting that local, rather than imported, reservoirs are key sources of persistent infections in the region. At the village level, parasites collected after referral for praziquantel treatment are closely related to local pre-treatment populations. Schistosomes within villages are also highly related, suggesting that only a few parasites from a limited number of hosts drive re-infection. The close familial relationships among miracidia from different human hosts also implicate short transmission routes among humans. At the individual host level, genetic evidence indicates that multiple humans retained infections following referral for treatment. Our findings suggest that end-game schistosomiasis control measures should focus on completely extirpating local parasite reservoirs and confirming successful treatment of infected human hosts.
Nucleation of Ga droplets self-assembly on GaAs(111)A substrates
Authors: Tuktamyshev Artur , Fedorov Alexey , Bietti Sergio , Vichi Stefano , Tambone Riccardo , Tsukamoto Shiro , Sanguinetti Stefano 
Published: March 2021

AbstractWe investigated the nucleation of Ga droplets on singular GaAs(111)A substrates in the view of their use as the seeds for the self-assembled droplet epitaxial quantum dots. A small critical cluster size of 1–2 atoms characterizes the droplet nucleation. Low values of the Hopkins-Skellam index (as low as 0.35) demonstrate a high degree of a spatial order of the droplet ensemble. Around $$350\,^{\circ }\hbox {C}$$

350

∘

C

the droplet size distribution becomes bimodal. We attribute this observation to the interplay between the local environment and the limitation to the adatom surface diffusion introduced by the Ehrlich–Schwöbel barrier at the terrace edges.
Applying a bagging ensemble machine learning approach to predict functional outcome of schizophrenia with clinical symptoms and cognitive functions
Authors: Lin Eugene , Lin Chieh-Hsin , Lane Hsien-Yuan 
Published: March 2021

AbstractIt has been suggested that the relationship between cognitive function and functional outcome in schizophrenia is mediated by clinical symptoms, while functional outcome is assessed by the Quality of Life Scale (QLS) and the Global Assessment of Functioning (GAF) Scale. To determine the outcome assessed by QLS and GAF, we established a bagging ensemble framework with a feature selection algorithm resulting from the analysis of factors such as 3 clinical symptom scales and 11 cognitive function scores of 302 patients with schizophrenia in the Taiwanese population. We compared our bagging ensemble framework with other state-of-the-art algorithms such as multilayer feedforward neural networks, support vector machine, linear regression, and random forests. The analysis revealed that the bagging ensemble model with feature selection performed best among predictive models in predicting the QLS functional outcome by using 20-item Scale for the Assessment of Negative Symptoms (SANS20) and 17-item Hamilton Depression Rating Scale (HAMD17). Moreover, to predict the GAF outcome, the bagging ensemble model with feature selection performed best among predictive models by using SANS20 and the Positive and Negative Syndrome Scale-Positive (PANSS-Positive) subscale. The study indicates that there are synergistic effects between negative (SANS20) and depressive (HAMD17) symptoms as well as between negative and positive (PANSS-Positive) symptoms in influencing functional outcome of schizophrenia using the bagging ensemble framework with feature selection.