bluuebunny/crossref_metadata_2025_split huggingface dataset:
A biodiversity evaluation framework for restoration of aquatic macrophyte communities in shallow lakes driven by hydrological process management
Authors: Li Shuhan , Sun Tao , Yang Wei , Cui Baoshan , Yin Xinan 
Published: November 2020

AbstractMacrophyte community diversity and composition respond to ecosystem conservation and local environmental factors. In this study, we developed a multidimensional diversity framework for macrophyte communities, including the taxonomic and functional alpha and beta diversity. We used the framework to explore the relationships among water level regimes and these diversity parameters in a case study of China's Baiyangdian Lake. Analysis of indicators of hydrologic alteration divided the water level from 1959 to 2019 into four regimes (dry, <6.42 m; low, 6.42–7.23 m; medium, 7.23–8.19 m; high, >8.19 m). Alpha and beta diversity were significantly higher in the medium regime than in the low and high regimes. Redundancy analysis indicated that the maximum water depth significantly affected taxonomic alpha diversity, and total nitrogen (TN) and chemical oxygen demand (COD) concentration significantly affected functional alpha diversity, respectively. Mantel tests showed that TN, Secchi depth (SD), and water depth in the high water level regime significantly increased the total beta diversity and turnover components. TN was the main factor that increased total taxonomic beta diversity. Water level regime mainly influenced interspecific relationships by changing the TN and COD concentration. The water level should be maintained between the medium and high water level regimes to promote restoration of the macrophyte community and improve ecosystem stability. The biodiversity evaluation framework would provide a deeper insight into the hydrological process management for restoration of aquatic macrophyte communities in shallow lakes.
New antiscatter grid design by optimization of strip thickness and height
Authors: Zhou Abel , Tan Qi , White Graeme L. , Davidson Rob 
Published: November 2020

AbstractAntiscatter grids are used in biomedical X‐ray imaging to improve image quality by reducing scatter radiation reaching the image receptor. However, this comes at the cost of increasing radiation exposure. Grid performance can be improved by optimizing strip‐thickness, which reduces radiation exposure, leading to greater benefits achieved by the grid. Evidence has shown that strip height may also affect grid performance. This work investigates optimization of grid performance by varying both the strip thickness and height for a constant grid‐ratio of 15:1 (r15). A series of grid designs using lead strips and carbon‐fiber‐interspace materials for grids for high‐energy use was evaluated. The performance of these designs was determined by adopting a Monte Carlo simulation. For each grid design, the signal‐to‐noise ratio improvement factor (KSNR) was determined. A maximum value of KSNR (1.895) was found among these designs at a strip height of 6.8 mm and a thickness of 66.8 μm. The best performance of the r15‐series grids is 6% greater than that of a grid design with a grid ratio of 15:1 and a strip frequency of 44 cm−1 (found in the literature); consequently, the transmission of scatter radiation is reduced by 40%. The results show that grid designs can be optimized by both the strip height and thickness. If the optimization of the strip height and thickness cannot be done simultaneously, the recommendation is to optimize the strip height for better radiation protection without compromising the grid performance. The findings provide useful guidance for designing high‐performance antiscatter grids to reduce radiation exposure of patients.
DementiaMRIimage classification using transformation technique based on elephant herding optimization with Randomized Adam method for updating the hyper‐parameters
Authors: Bharanidharan N , Rajaguru Harikumar 
Published: November 2020

AbstractThe primary objective of this research work is to build a binary classifier for categorizing the input brain magnetic resonanceimaging (MRI) images as either demented or nondemented with high accuracy. A novel hyper‐parameter updating method called Randomized Adam (RanAdam) is proposed for enhancing the dementia classification accuracy of elephant herding optimization algorithm and other swarm intelligence (SI) algorithms. Usually, Adam method is widely used in deep learning neural networks for hyper‐parameters updating, and it is ingenious to use Adam and its modified version called RanAdam as hyper‐parameters updating method for SI algorithms. The proposed RanAdam algorithm tries to find actual optimal values for hyper‐parameters near the optimal values given by Adam method through the Controlled Randomness procedure. This research work also compares dementia MRI image classification performance of elephant herding optimization‐based transformation technique with the standard clustering approaches and other transformation approaches. In this research work, 117 subjects (65 non‐dementia and 52 dementia subjects) acquired from the Open Access Series of Imaging Studies (OASIS) database is used. Two cases are analyzed in all the techniques: with and without statistical features. The highest accuracy of 90.6% is achieved by elephant herding optimization (EHO)‐based transformation technique combined with RanAdam for updating hyper‐parameters for the case without statistical features. To verify the efficiency of the proposed technique, a popular Pima diabetic dataset is considered in addition to the OASIS dementia dataset and 88% accuracy is earned for EHO‐based transformation technique combined with RanAdam.
A same‐day assay predicts apoptotic response to combined BCL‐2 and MCL‐1 BH3‐mimetic targeting in multiple myeloma cells
Authors: Grundy Martin , Al‐Kaisi Firas , Cull Joanna , Williams Cathy , Smith Dean , Seedhouse Claire H. 
Published: November 2020

AbstractRecent advances in treatment options for multiple myeloma (MM) have positive impact on patient survival. However, there is a short fall of rapid and reliable assays that can predict patient response to novel agents. The anti‐apoptotic proteins B‐cell lymphoma‐2 (BCL‐2) and myeloid cell leukaemia‐1 (MCL‐1), are necessary for MM survival, although most myelomas are more dependent on MCL‐1. BCL‐2 inhibition alone yields significant cytotoxicity in only a minority of cases, therefore targeting both proteins simultaneously, is a therapeutic option. Venetoclax and S63845 are BCL‐2 and MCL‐1 targeting BH3‐mimetics which have demonstrated apoptotic synergy in MM. We investigated whether a novel short‐term flow cytometric cytochrome c release assay could predict response to dual BH3‐mimetic targeting in MM cells. Six human myeloma cell lines (HMCL) and seven primary samples were treated with venetoclax and S63845 alone or in combination. The 4‐hour assay confirmed the drug combination was synergistic in all HMCL tested. Annexin‐V data at 48 hours corresponded with 4‐hour response verifying the assay as a predictor of drug sensitivity. All primary samples responded to the drug combination, including samples with 1q gain and t(4;14) translocation. Normal stem cells were unaffected by the drug combination. We have developed a novel assay with the potential to predict response to therapy in MM cells.
Leishmania regulates host macrophage miRNAs expression by engaging transcription factor c-Myc
Authors: Nandan Devki , Rath Carolina Torturella , Reiner Neil E 
Published: November 2020

Abstract
Parasites of Leishmania genus have developed sophisticated strategies allowing them to deactivate their host macrophage to promote their survival. It has become clear that miRNAs play important roles in shaping innate and adaptive immune responses toward pathogens. It is not surprising that several pathogens including Leishmania have evolved the ability to regulate host macrophage miRNA expression in order to manipulate host cell phenotypes to their advantage. However, very little is known about the mechanisms used by intracellular pathogens to drive changes in host cell miRNA abundance. In this review, Leishmania exploitation of macrophage transcription factor c-Myc as a critical proxy virulence factor to regulate abundance of macrophage miRNAs influencing macrophage physiology to promote its survival will be discussed.
Non‐destructive detection of blueberry skin pigments and intrinsic fruit qualities based on deep learning
Authors: Mu Changhong , Yuan Zebin , Ouyang Xiuqin , Sun Pu , Wang Bo 
Published: November 2020

AbstractBACKGROUNDThis paper proposes a novel method to improve accuracy and efficiency in detecting the quality of blueberry fruit, taking advantage of deep learning in classification tasks. We first collected ‘Tifblue’ blueberries at seven different stages of maturity (10–70 days after full bloom) and measured the pigments of the blueberry skin and the total sugar and the total acid of the pulp. We then established a skin pigment contents prediction network (SPCPN), based on the correlation between the pigments and blueberry pictures, and also a fruit intrinsic qualities prediction network (FIQPN), based on the correlation between the pigments and fruit qualities. Finally, the SPCPN and FIQPN were consolidated into the blueberry quality parameters prediction network (BQPPN).RESULTSThe results showed that the anthocyanins in the blueberry skin were significantly correlated with the total sugar, total acid, and sugar / acid ratio of the fruit. After verification, the results also indicated that, for the prediction of anthocyanins, chlorophyll, and the anthocyanin / chlorophyll ratio, the SPCPN network model was found to achieve higher R2 (RMSE) values of 0.969 (0.139), 0.955 (0.005), 0.967 (15.4), respectively. The FIQPN network model was also able to evaluate the value of total sugar (R2 = 0.940, RMSE = 4.905), total acid (R2 = 0.930, RMSE = 2.034), and the sugar / acid ratio (R2 = 0.973, RMSE = 0.580).CONCLUSIONThe above results indicated the potential for utilizing deep learning technology to predict the quality indicators of blueberry before harvesting. © 2020 Society of Chemical Industry
Effect of microstructural features on the corrosion behavior of severely deformed Al–Mg–Si alloy
Authors: Orłowska Marta , Ura‐Bińczyk Ewa , Olejnik Lech , Lewandowska Małgorzata 
Published: November 2020

AbstractThe aim of this study was to determine the influence of severe plastic deformation processing and the changes in microstructure resulting therefrom on the corrosion resistance of an Al–Mg–Si alloy. The alloy was processed using incremental equal channel angular pressing, which caused a reduction in grain size from 15 to 0.9 µm. The grain refinement was accompanied by an increase in the number of grain boundaries and dislocations, and by changes in grain orientation. However, there was no change in the size and number of intermetallic particles, which presumably resulted in a constant number of galvanic couplings. Electrochemical experiments revealed only slight differences between the samples before and after processing. Higher potential transients/oscillations upon immersion and increased corrosion currents in the vicinity of corrosion potential point to slightly higher reactivity of the most refined material. This indicates that intermetallic particles are the most crucial microstructural elements in terms of corrosion resistance. Their impact exceeds that of grain boundaries, in particular, at the stage of corrosion initiation. The development of corrosion attack is controlled more by the microstructure of the matrix as the grain refinement resulted in a less pronounced corrosion attack in comparison with the coarse‐grained sample.
Spatial Distribution Changes and Habitat Use in Red Porgy in Waters off the Southeast U.S. Atlantic Coast
Authors: Smart Tracey I. , Bubley Walter J. , Glasgow Dawn M. , Reichert Marcel J. M. 
Published: November 2020

Abstract
Despite 30 years of relatively strict management measures, the Red Porgy Pagrus pagrus population off the southeast U.S. Atlantic coast has not met rebuilding goals and was still categorized as overfished over a decade after a moratorium (SEDAR 2020). The lack of recovery indicates that limiting fishing pressure is not enough to effectively manage population levels. Population size may be driven by spatial or habitat associations independent of fishing pressure. We defined spatial distribution and habitat associations of Red Porgy adults and recruits by using a 23-year, fishery-independent trap catch time series (1996–2019). Abundance of recruits was below the long-term average, and adults were declining for the last 8 years of the time series. In addition, the spatial distribution of recruits tended to contract to deeper waters in the center of the region when abundance was low, whereas adults remained relatively consistent in their spatial and depth distribution regardless of abundance. The independence between effective area occupied and adult abundance supports that adults persisted throughout the region, whereas recruit area occupied was proportional to abundance. Recruits and adults overlapped spatially, but there was some partitioning of habitats: recruits were more abundant in less-complex habitats (low benthic biota coverage and low availability of hard substrate) relative to more complex habitats, and adults were more abundant in more complex or warm habitats than in less-complex or cooler habitats. When overall abundance was reduced, adult abundance in more complex habitats became more similar to abundance in less-complex habitats, while there was little to no change in recruit habitat use. The center of the region had a high overlap of adults and recruits, particularly in times of reduced recruitment. If fishers cannot target adults only, there is high potential for bycatch mortality or reduced fitness for recruits, which would further reduce the likelihood of recovery.
Repeatability and reliability of GABA measurements with magnetic resonance spectroscopy in healthy young adults
Authors: Duda Jessica M. , Moser Amelia D. , Zuo Chun S. , Du Fei , Chen Xi , Perlo Sarah , Richards Christine E. , Nascimento Nara , Ironside Maria , Crowley David J. , Holsen Laura M. , Misra Madhusmita , Hudson James I. , Goldstein Jill M. , Pizzagalli Diego A. 
Published: November 2020

PurposeGamma‐aminobutyric acid (GABA) abnormalities have been implicated in a range of neuropsychiatric disorders. Despite substantial interest in probing GABA in vivo, human imaging studies relying on magnetic resonance spectroscopy (MRS) have generally been hindered by technical challenges, including GABA’s relatively low concentration and spectral overlap with other metabolites. Although past studies have shown moderate‐to‐strong test‐retest repeatability and reliability of GABA within certain brain regions, many of these studies have been limited by small sample sizes.MethodsGABA+ (macromolecular‐contaminated) test‐retest reliability and repeatability were assessed via a Meshcher‐Garwood point resolved spectroscopy (MEGA‐PRESS) MRS sequence in the rostral anterior cingulate cortex (rACC; n = 21) and dorsolateral prefrontal cortex (dlPFC; n = 20) in healthy young adults. Data were collected on a 3T scanner (Siemens Prisma, Siemens Healthcare, Erlangen, Germany) and GABA+ results were reported in reference to both total creatine (GABA+/tCr) and water (GABA+/water).ResultsResults showed strong test‐retest repeatability (mean GABA+/tCr coefficient of variation [CV] = 4.6%; mean GABA+/water CV = 4.0%) and reliability (GABA+/tCr intraclass correlation coefficient [ICC] = 0.77; GABA+/water ICC = 0.87) in the dlPFC. The rACC showed acceptable (but comparatively lower) repeatability (mean GABA+/tCr CV = 8.0%; mean GABA+/water CV = 7.5%), yet low‐moderate reliability (GABA+/tCr ICC = 0.40; GABA+/water ICC = 0.44).ConclusionThe present study found excellent GABA+ MRS repeatability and reliability in the dlPFC. The rACC showed inferior results, possibly because of a combination of shimming impedance and measurement error. These data suggest that MEGA‐PRESS can be utilized to reliably distinguish participants based on dlPFC GABA+ levels, whereas the mixed results in the rACC merit further investigation.
Utility of neuromuscular ultrasound in the investigation of common mononeuropathies in everyday neurophysiology practice
Authors: Pelosi Luciana , Leadbetter Ruth , Mulroy Eoin 
Published: November 2020

AbstractIntroductionIn everyday clinical neurophysiology practice, mononeuropathies are evaluated primarily by traditional electrodiagnostic testing. We sought to assess the additional benefit of neuromuscular ultrasound (US) in this scenario.MethodsAll consecutive mononeuropathies undergoing combined US and electrodiagnostic evaluation over a 23‐mo period at a single neurophysiology practice were reviewed. Three independent examiners assessed how often US was: (a) “contributory” ‐ enabling a definite diagnosis not made by electrophysiology alone and/or impacting on the therapeutic decision, (b) “confirmatory” of the electrodiagnostic findings, but not adding further diagnostic or therapeutic information, or (c) “negative” ‐ missed the diagnosis.ResultsThere were 385 studies included. US was “contributory” in 36%, “confirmatory” in 61% and “negative” in 3%.DiscussionIn this study of everyday neurophysiology practice, neuromuscular US contributed significant diagnostic or therapeutic information in over 1/3 of the investigations for common mononeuropathies. False negative US studies were uncommon in this setting.
Tumor Frameshift Mutation Proportion Predicts Response to Immunotherapy in Mismatch Repair-Deficient Prostate Cancer
Authors: Sena Laura A. , Fountain Julia , Isaacsson Velho Pedro , Lim Su Jin , Wang Hao , Nizialek Emily , Rathi Nityam , Nussenzveig Roberto , Maughan Benjamin L. , Velez Miguel Gonzalez , Ashkar Ryan , Larson Amanda C. , Pritchard Colin C. , Adra Nabil , Bryce Alan H. , Agarwal Neeraj , Pardoll Drew M. , Eshleman James R. , Lotan Tamara L. , Antonarakis Emmanuel S. 
Published: November 2020

Abstract

Background
Genomic biomarkers that predict response to anti-PD1 therapy in prostate cancer are needed. Frameshift mutations are predicted to generate more neoantigens than missense mutations; therefore, we hypothesized that the number or proportion of tumor frameshift mutations would correlate with response to anti-PD1 therapy in prostate cancer.

Methods
To enrich for response to anti-PD1 therapy, we assembled a multicenter cohort of 65 men with mismatch repair-deficient (dMMR) prostate cancer. Patient characteristics and outcomes were determined by retrospective chart review. Clinical somatic DNA sequencing was used to determine tumor mutational burden (TMB), frameshift mutation burden, and frameshift mutation proportion (FSP), which were correlated to outcomes on anti-PD1 treatment. We subsequently used data from a clinical trial of pembrolizumab in patients with nonprostatic dMMR cancers of various histologies as a biomarker validation cohort.

Results
Nineteen of 65 patients with dMMR metastatic castration-resistant prostate cancer were treated with anti-PD1 therapy. The PSA50 response rate was 65%, and the median progression-free survival (PFS) was 24 (95% confidence interval 16–54) weeks. Tumor FSP, more than overall TMB, correlated most strongly with prolonged PFS and overall survival (OS) on anti-PD1 treatment and with density of CD8+ tumor-infiltrating lymphocytes. High FSP similarly identified patients with longer PFS as well as OS on anti-PD1 therapy in a validation cohort.

Conclusion
Tumor FSP correlated with prolonged efficacy of anti-PD1 treatment among patients with dMMR cancers and may represent a new biomarker of immune checkpoint inhibitor sensitivity.

Implications for Practice
Given the modest efficacy of immune checkpoint inhibition (ICI) in unselected patients with advanced prostate cancer, biomarkers of ICI sensitivity are needed. To facilitate biomarker discovery, a cohort of patients with DNA mismatch repair-deficient (dMMR) prostate cancer was assembled, as these patients are enriched for responses to ICI. A high response rate to anti-PD1 therapy in these patients was observed; however, these responses were not durable in most patients. Notably, tumor frameshift mutation proportion (FSP) was identified as a novel biomarker that was associated with prolonged response to anti-PD1 therapy in this cohort. This finding was validated in a separate cohort of patients with nonprostatic dMMR cancers of various primary histologies. This works suggests that FSP predicts response to anti-PD1 therapy in dMMR cancers, which should be validated prospectively in larger independent cohorts.
Standardized Supportive Care Documentation Improves Safety of High-Dose Methotrexate Treatment
Authors: Alsdorf Winfried H. , Karagiannis Panagiotis , Langebrake Claudia , Bokemeyer Carsten , Frenzel Christian 
Published: November 2020

Abstract

Background
High-dose (HD) methotrexate (MTX) is an essential component of treatment protocols in acute lymphoblastic leukemia, aggressive lymphoma, and osteosarcoma. However, delayed MTX clearance may lead to life-threatening toxicities. Administration of supportive therapy for HD-MTX is complex, and insufficient supportive care increases the risk of MTX toxicity. To improve patient safety, we investigated the implementation of a checklist and urine alkalinization protocol in addition to standard supportive care during HD-MTX therapy.

Materials and Methods
The intervention included individualized patient checklists for control of adequate supportive care for every HD-MTX treatment cycle and a urine alkalinization protocol for documentation and guidance during urine alkalinization therapy. The impact of these tools on the rate of adverse events (acute renal injury, delayed MTX clearance) was retrospectively assessed in patients treated from April 2017 to April 2019 (intervention group) and compared with patients treated from January 2015 to March 2017 who received standard supportive care for HD-MTX according to a standard operating procedure (SOP).

Results
In total, 118 patients received 414 HD-MTX cycles in the intervention group compared with 108 patients with 332 treatment cycles in the SOP group. Delayed MTX clearance was observed in 2.6% of treatment cycles in the intervention cohort opposed to 15.2% of cycles in the SOP group. The rate of acute kidney injury was also significantly reduced in the intervention group (6.2%. vs. 0.7%). The use of carboxypeptidase as rescue treatment for severe renal impairment and insufficient MTX clearance was necessary in five cases in the SOP group and in only two cycles within the intervention group.

Conclusion
The use of standardized documentation for supportive care during HD-MTX therapy is recommended to minimize the risk of adverse events.

Implications for Practice
High-dose methotrexate (HD-MTX) is a commonly used treatment in several cancer types. Distinct supportive measures are necessary to minimize the risk of HD-MTX side effects, which can be life-threatening. Supportive care consists of certain examinations and interventions before starting HD-MTX and permanent alkalinization of the urine, as this greatly increases the elimination of MTX and decreases the risk of kidney injury. After implementing a checklist for control of supportive care and a urine alkalinization protocol to optimize urine alkalinization, a significant decrease of side effects was observed in comparison to the standard of care; therefore, the use of a safety checklist and alkalinization protocol is recommended for all patients who receive HD-MTX.