bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral History Research: Illuminating the Past: an Introduction
Authors: Stewart Mary , Liberman Dvora 
Published: November 2019

AbstractThis short piece makes reference to an event that was held in May 2019 at the London School of Economics. The occasion was entitled ‘Oral History Research: Illuminating the Past’. There were three speakers and the session was chaired by Professor Michael Lobban. One of the speakers that evening was Lesley Dingle and, following this introduction, her talk is featured in this issue of Legal Information Management.
Long‐Term Precipitation Estimates Generated by a Downscaling‐Calibration Procedure Over the Tibetan Plateau From 1983 to 2015
Authors: Ma Z. Q. , Ghent D. , Tan X. , He K. , Li H. Y. , Han X. Z. , Huang Q. T. , Peng J. 
Published: November 2019

AbstractThe World Meteorological Organization stipulates a minimum of 30 years of historical data is needed to obtain meaningful results in climatological research. However, large numbers of studies have explored downscaling approaches based on the TRMM Multi‐Satellite Precipitation Analysis (TMPA) data, which span only from 1998 to the present, to obtain the precipitation estimates (~1‐km resolution). The main aim of the present study was to develop a new method for obtaining long‐term (>30 years) precipitation estimates at ~1‐km resolution and to apply that method to a region with complex topography, the Tibetan Plateau. First, PERSIANN‐CDR (Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks—Climate Data Record) data were used for downscaling. Considering the characteristics of the PERSIANN‐CDR data, a new downscaling‐calibration procedure utilizing a combination of a spatial data mining downscaling algorithm (Cubist) and a geographical ratio analysis calibration method was proposed. We found that (1) both the original PERSIANN‐CDR data (Bias ~40.79%) and the downscaled results before calibration (Bias ~26.78%) overestimated the precipitation compared with ground observations; (2) the final downscaled results based on the PERSIANN‐CDR data after calibration were close to the ground observations (Bias ~5%); (3) compared to the results interpolated based on the PERSIANN‐CDR data (E <−1.0), both the downscaling procedure and calibration procedure contributed significantly to the accuracy of the final downscaled results (E ~0.83). These findings suggest that the proposed downscaling‐calibration procedure has great potential as an approach for retrieving long‐term precipitation estimates (~1‐km resolution) over the Tibetan Plateau.
Participatory Modeling Updates Expectations forIndividuals and Groups, Catalyzing BehaviorChange and Collective Action inWater‐Energy‐Food NexusGovernance
Authors: Kimmich C. , Gallagher L. , Kopainsky B. , Dubois M. , Sovann C. , Buth C. , Bréthaut C. 
Published: November 2019

AbstractParticipatory modeling is a potentially high‐impact approach for catalyzing fundamental sustainability transformations. We test if participation in a group system dynamics modeling exercise increases participants' agency through a novel method to evaluate potential behavioral change using expectation measures. A water‐energy‐food nexus—a functionally interdependent but underconceptualized system with low consensus and high scientific uncertainty—was mapped, and its evolution simulated by 46 participants in three interventions in a region undergoing hydropower infrastructure development in Northeastern Cambodia. Participants' system‐related expectations were measured before and after the interventions. Our results suggest that participants became significantly more optimistic about their individual agency to increase agricultural and fishing income and, interestingly, less likely to participate in local government development planning procedures. Findings also reveal how some uncertainties for multiple variables were reduced within and across the groups. Such converging expectations suggest that participatory modeling could contribute to making collective solutions and institutionalized agreements more likely. This research contributes to innovation in sustainability because it unpacks some underlying mechanics of how participatory processes can lead to new adaptive capacities, shared perspectives, and collective actions.
IMF By Influence on Magnetospheric Convection in Earth's Magnetotail Plasma Sheet
Authors: Pitkänen T. , Kullen A. , Laundal K. M. , Tenfjord P. , Shi Q. Q. , Park J.‐S. , Hamrin M. , De Spiegeleer A. , Chong G. S. , Tian A. M. 
Published: November 2019

AbstractWe use Geotail, Cluster, and Time History of Events and Macroscale Interactions during Substorms data over 15 years (1995–2009) to statistically investigate convective ion flows (V⊥xy<200 km/s) in the magnetotail plasma sheet under the influence of a clearly nonzero dawn‐dusk interplanetary magnetic field (IMF By). We find that IMF By causes an interhemispheric asymmetry in the flows, which depends on the direction of IMF By. On the average, one magnetic hemisphere is dominated by a dawn‐dusk flow component, which is oppositely directed compared to that in the other hemisphere. This asymmetry is observed for both earthward and tailward flows. A comparison to tail By reveals that the region where the asymmetry in the average flows appears agrees with the appearance of the tail By direction collinear to IMF By. The results imply that IMF By has a major influence on the direction of the magnetic flux transport in the magnetotail.
Spectral tomographic imaging with aplanatic metalens
Authors: Chen Chen , Song Wange , Chen Jia-Wern , Wang Jung-Hsi , Chen Yu Han , Xu Beibei , Chen Mu-Ku , Li Hanmeng , Fang Bin , Chen Ji , Kuo Hsin Yu , Wang Shuming , Tsai Din Ping , Zhu Shining , Li Tao 
Published: November 2019

AbstractTomography is an informative imaging modality that is usually implemented by mechanical scanning, owing to the limited depth-of-field (DOF) in conventional systems. However, recent imaging systems are working towards more compact and stable architectures; therefore, developing nonmotion tomography is highly desirable. Here, we propose a metalens-based spectral imaging system with an aplanatic GaN metalens (NA = 0.78), in which large chromatic dispersion is used to access spectral focus tuning and optical zooming in the visible spectrum. After the function of wavelength-switched tomography was confirmed on cascaded samples, this aplanatic metalens is utilized to image microscopic frog egg cells and shows excellent tomographic images with distinct DOF features of the cell membrane and nucleus. Our approach makes good use of the large diffractive dispersion of the metalens and develops a new imaging technique that advances recent informative optical devices.
Brain structural changes in cannabis dependence: association with MAGL
Authors: Manza Peter , Yuan Kai , Shokri-Kojori Ehsan , Tomasi Dardo , Volkow Nora D. 
Published: November 2019

AbstractCannabis use is rising, yet there is poor understanding of biological processes that might link chronic cannabis use to brain structural abnormalities. To lend insight into this topic, we examined white matter microstructural integrity and gray matter cortical thickness/density differences between 89 individuals with cannabis dependence (CD) and 89 matched controls (64 males, 25 females in each group) from the Human Connectome Project. We tested whether cortical patterns for expression of genes relevant for cannabinoid signaling (from Allen Human Brain Atlas postmortem tissue) were associated with spatial patterns of cortical thickness/density differences in CD. CD had lower fractional anisotropy than controls in white matter bundles innervating posterior cingulate and parietal cortex, basal ganglia, and temporal cortex. The CD group also had significantly less gray matter thickness and density in precuneus, relative to controls. Sibling-pair analysis found support for causal and graded liability effects of cannabis on precuneus structure. Spatial patterns of gray matter differences in CD were significantly associated with regional differences in monoacylglycerol lipase (MAGL) expression in postmortem brain tissue, such that regions with higher MAGL expression (but not fatty-acid amide hydrolase or FAAH) were more vulnerable to cortical thinning. In sum, chronic cannabis use is associated with structural differences in white and gray matter, which was most prominent in precuneus and associated white matter tracts. Regions with high MAGL expression, and therefore with potentially physiologically restricted endogenous cannabinoid signaling, may be more vulnerable to the effects of chronic cannabis use on cortical thickness.
Developmental vitamin D and autism spectrum disorders: findings from the Stockholm Youth Cohort
Authors: Lee Brian K. , Eyles Darryl W. , Magnusson Cecilia , Newschaffer Craig J. , McGrath John J. , Kvaskoff David , Ko Pauline , Dalman Christina , Karlsson Håkan , Gardner Renee M. 
Published: November 2019

AbstractAnimal studies indicate that early life vitamin D is crucial for proper neurodevelopment. Few studies have examined whether maternal and neonatal vitamin D concentrations influence risk of autism spectrum disorders (ASD). Participants were sampled from the Stockholm Youth Cohort, a register-based cohort in Sweden. Concentrations of total 25-hydroxyvitamin D (25OHD) were assessed from maternal and neonatal biosamples using a highly sensitive liquid chromatography tandem mass spectrometry method. The maternal sample consisted of 449 ASD cases and 574 controls, the neonatal sample: 1399 ASD cases and 1607 controls; and the paired maternal-neonatal sample: 340 ASD cases and 426 controls. Maternal 25OHD was not associated with child ASD in the overall sample. However, in Nordic-born mothers, maternal 25OHD insufficiency (25 − <50 nmol/L) at ~11 weeks gestation was associated with 1.58 times higher odds of ASD (95% CI: 1.00, 2.49) as compared with 25OHD sufficiency (≥50 nmol/L). Neonatal 25OHD < 25 nmol/L was associated with 1.33 times higher odds of ASD (95% CI: 1.02, 1.75) as compared with 25OHD ≥ 50 nmol/L. Sibling-matched control analyses indicated these associations were not likely due to familial confounding. Children with both maternal 25OHD and neonatal 25OHD below the median had 1.75 (95% CI: 1.08, 2.86) times the odds of ASD compared with children with maternal and neonatal 25OHD both below the median. Our results are consistent with an increasing body of evidence suggesting that vitamin D concentrations in early life may be associated with increased risk of neurodevelopmental disorders including ASD.
HDAC5-mediated deacetylation and nuclear localisation of SOX9 is critical for tamoxifen resistance in breast cancer
Authors: Xue Yue , Lian Wenwen , Zhi Jiaqi , Yang Wenjuan , Li Qianjin , Guo Xingyi , Gao Jiahao , Qu Hao , Lin Weiqiang , Li Zhongqi , Lai Lihua , Wang Qingqing 
Published: November 2019

Abstract

Background
Tamoxifen resistance remains a significant clinical challenge for the therapy of ER-positive breast cancer. It has been reported that the upregulation of transcription factor SOX9 in ER+ recurrent cancer is sufficient for tamoxifen resistance. However, the mechanisms underlying the regulation of SOX9 remain largely unknown.

Methods
The acetylation level of SOX9 was detected by immunoprecipitation and western blotting. The expressions of HDACs and SIRTs were evaluated by qRT-PCR. Cell growth was measured by performing MTT assay. ALDH-positive breast cancer stem cells were evaluated by flow cytometry. Interaction between HDAC5 and SOX9 was determined by immunoprecipitation assay.

Results
Deacetylation is required for SOX9 nuclear translocation in tamoxifen-resistant breast cancer cells. Furthermore, HDAC5 is the key deacetylase responsible for SOX9 deacetylation and subsequent nuclear translocation. In addition, the transcription factor C-MYC directly promotes the expression of HDAC5 in tamoxifen resistant breast cancer cells. For clinical relevance, high SOX9 and HDAC5 expression are associated with lower survival rates in breast cancer patients treated with tamoxifen.

Conclusions
This study reveals that HDAC5 regulated by C-MYC is essential for SOX9 deacetylation and nuclear localisation, which is critical for tamoxifen resistance. These results indicate a potential therapy strategy for ER+ breast cancer by targeting C-MYC/HDAC5/SOX9 axis.
Genomic data integration by WON-PARAFAC identifies interpretable factors for predicting drug-sensitivity in vivo
Authors: Kim Yongsoo , Bismeijer Tycho , Zwart Wilbert , Wessels Lodewyk F. A. , Vis Daniel J. 
Published: November 2019

AbstractIntegrative analyses that summarize and link molecular data to treatment sensitivity are crucial to capture the biological complexity which is essential to further precision medicine. We introduce Weighted Orthogonal Nonnegative parallel factor analysis (WON-PARAFAC), a data integration method that identifies sparse and interpretable factors. WON-PARAFAC summarizes the GDSC1000 cell line compendium in 130 factors. We interpret the factors based on their association with recurrent molecular alterations, pathway enrichment, cancer type, and drug-response. Crucially, the cell line derived factors capture the majority of the relevant biological variation in Patient-Derived Xenograft (PDX) models, strongly suggesting our factors capture invariant and generalizable aspects of cancer biology. Furthermore, drug response in cell lines is better and more consistently translated to PDXs using factor-based predictors as compared to raw feature-based predictors. WON-PARAFAC efficiently summarizes and integrates multiway high-dimensional genomic data and enhances translatability of drug response prediction from cell lines to patient-derived xenografts.
Evaluation of narrow band imaging in the assessment of laryngeal granuloma
Authors: Klimza H. , Pietruszewska W. , Jackowska J. , Piersiala K. , Wierzbicka M. 
Published: November 2019

AbstractLaryngeal granulomas belong to common complications following trans-oral laser microsurgery (TLM). The aim of this study was to evaluate NBI in the differentiation between granuloma-like lesions and local tumor recurrence. 154 consecutive patients after TLM due to early laryngeal cancer were enrolled. In the group, a monthly follow-up including NBI endoscopy was performed. Moderate and severe dysplasia, carcinoma in situ and invasive cancer were defined as positive histology, laryngeal granuloma and other benign laryngeal lesions as negative histology and premalignant lesions as suspicious histology. In 47/154 (31%) cases, granuloma-like lesion (GLL) was found. Patients with GLL were divided into two groups based on the NBI classification. In all patients, the microvascular pattern in NBI was compared with the final histology. In group A, with suspicious, perpendicular vessels, 13/13 (100%) samples were positive. In group B, with normal vascular pattern 3/34 (9%) samples were positive and 31/34 (91%) samples were negative. There was a significant correlation between the positive NBI vascular pattern and the final histology (p = 0.00001). Sensitivity, specificity, accuracy of NBI were as follows: 81%, 100%, 94%, respectively.Based on our results, NBI can reliably differentiate between postoperative laryngeal granuloma and local tumor recurrence. In such a manner, this method is very helpful in the follow-up of tumor patients.
Chemical activation of divergent protein tyrosine phosphatase domains with cyanine-based biarsenicals
Authors: Plaman Bailey A. , Chan Wai Cheung , Bishop Anthony C. 
Published: November 2019

AbstractStrategies for the direct chemical activation of specific signaling proteins could provide powerful tools for interrogating cellular signal transduction. However, targeted protein activation is chemically challenging, and few broadly applicable activation strategies for signaling enzymes have been developed. Here we report that classical protein tyrosine phosphatase (PTP) domains from multiple subfamilies can be systematically sensitized to target-specific activation by the cyanine-based biarsenical compounds AsCy3 and AsCy5. Engineering of the activatable PTPs (actPTPs) is achieved by the introduction of three cysteine residues within a conserved loop of the PTP domain, and the positions of the sensitizing mutations are readily identifiable from primary sequence alignments. In the current study we have generated and characterized actPTP domains from three different subfamilies of both receptor and non-receptor PTPs. Biarsenical-induced stimulation of the actPTPs is rapid and dose-dependent, and is operative with both purified enzymes and complex proteomic mixtures. Our results suggest that a substantial fraction of the classical PTP family will be compatible with the act-engineering approach, which provides a novel chemical-biological tool for the control of PTP activity and the study of PTP function.
Athena: Automated Tuning of k-mer based Genomic Error Correction Algorithms using Language Models
Authors: Abdallah Mustafa , Mahgoub Ashraf , Ahmed Hany , Chaterji Somali 
Published: November 2019

AbstractThe performance of most error-correction (EC) algorithms that operate on genomics reads is dependent on the proper choice of its configuration parameters, such as the value of k in k-mer based techniques. In this work, we target the problem of finding the best values of these configuration parameters to optimize error correction and consequently improve genome assembly. We perform this in an adaptive manner, adapted to different datasets and to EC tools, due to the observation that different configuration parameters are optimal for different datasets, i.e., from different platforms and species, and vary with the EC algorithm being applied. We use language modeling techniques from the Natural Language Processing (NLP) domain in our algorithmic suite, Athena, to automatically tune the performance-sensitive configuration parameters. Through the use of N-Gram and Recurrent Neural Network (RNN) language modeling, we validate the intuition that the EC performance can be computed quantitatively and efficiently using the “perplexity” metric, repurposed from NLP. After training the language model, we show that the perplexity metric calculated from a sample of the test (or production) data has a strong negative correlation with the quality of error correction of erroneous NGS reads. Therefore, we use the perplexity metric to guide a hill climbing-based search, converging toward the best configuration parameter value. Our approach is suitable for both de novo and comparative sequencing (resequencing), eliminating the need for a reference genome to serve as the ground truth. We find that Athena can automatically find the optimal value of k with a very high accuracy for 7 real datasets and using 3 different k-mer based EC algorithms, Lighter, Blue, and Racer. The inverse relation between the perplexity metric and alignment rate exists under all our tested conditions—for real and synthetic datasets, for all kinds of sequencing errors (insertion, deletion, and substitution), and for high and low error rates. The absolute value of that correlation is at least 73%. In our experiments, the best value of k found by Athena achieves an alignment rate within 0.53% of the oracle best value of k found through brute force searching (i.e., scanning through the entire range of k values). Athena’s selected value of k lies within the top-3 best k values using N-Gram models and the top-5 best k values using RNN models With best parameter selection by Athena, the assembly quality (NG50) is improved by a Geometric Mean of 4.72X across the 7 real datasets.
Therapeutic administration of Tregitope-Human Albumin Fusion with Insulin Peptides to promote Antigen-Specific Adaptive Tolerance Induction
Authors: De Groot Anne S. , Skowron Gail , White James Robert , Boyle Christine , Richard Guilhem , Serreze David , Martin William D. 
Published: November 2019

AbstractType 1 Diabetes (T1D) is an autoimmune disease that is associated with effector T cell (Teff) destruction of insulin-producing pancreatic beta-islet cells. Among the therapies being evaluated for T1D is the restoration of regulatory T cell (Treg) activity, specifically directed toward down-modulation of beta-islet antigen-specific T effector cells. This is also known as antigen-specific adaptive tolerance induction for T1D (T1D ASATI). Tregitopes (T regulatory cell epitopes) are natural T cell epitopes derived from immunoglobulin G (IgG) that were identified in 2008 and have been evaluated in several autoimmune disease models. In the T1D ASATI studies presented here, Tregitope peptides were administered to non-obese diabetic (NOD) mice at the onset of diabetes within two clinically-relevant delivery systems (liposomes and in human serum albumin [HSA]-fusion products) in combination with preproinsulin (PPI) target antigen peptides. The combination of Tregitope-albumin fusions and PPI peptides reduced the incidence of severe diabetes and reversed mild diabetes, over 49 days of treatment and observation. Combining HSA-Tregitope fusions with PPI peptides is a promising ASATI approach for therapy of T1D.
Climatic, physical, and biogeochemical changes drive rapid oxygen loss and recovery in a marine ecosystem
Authors: Wilson Jesse , Ucharm Gerda , Beman J. Michael 
Published: November 2019

AbstractDissolved oxygen (DO) concentrations shape the biogeochemistry and ecological structure of aquatic ecosystems; as a result, understanding how and why DO varies in space and time is of fundamental importance. Using high-resolution, in situ DO time-series collected over the course of a year in a novel marine ecosystem (Jellyfish Lake, Palau), we show that DO declined throughout the marine lake and subsequently recovered in the upper water column. These shifts were accompanied by variations in water temperature and were correlated to changes in wind, precipitation, and especially sea surface height that occurred during the 2015–2016 El Niño-Southern Oscillation event. Multiple approaches used to calculate rates of community respiration, net community production, and gross primary production from DO changes showed that DO consumption and production did not accelerate nor collapse; instead, their variance increased during lake deoxygenation and recovery, and then stabilized. Spatial and temporal variations in rates were significantly related to climatic variability and changes in DO, and causality testing indicated that these relationships were both correlative and causative. Our data indicate that climatic, physical, and biogeochemical properties and processes collectively regulated DO, producing linked feedbacks that drove DO decline and recovery.