bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing physiological high-frequency oscillations using deep learning
Authors: Zhang Yipeng , Chung Hoyoung , Ngo Jacquline P , Monsoor Tonmoy , Hussain Shaun A , Matsumoto Joyce H , Walshaw Patricia D , Fallah Aria , Sim Myung Shin , Asano Eishi , Sankar Raman , Staba Richard J , Engel Jerome , Speier William , Roychowdhury Vwani , Nariai Hiroki 
Published: November 2022

Abstract

Objective. Intracranially-recorded interictal high-frequency oscillations (HFOs) have been proposed as a promising spatial biomarker of the epileptogenic zone. However, HFOs can also be recorded in the healthy brain regions, which complicates the interpretation of HFOs. The present study aimed to characterize salient features of physiological HFOs using deep learning (DL). Approach. We studied children with neocortical epilepsy who underwent intracranial strip/grid evaluation. Time-series EEG data were transformed into DL training inputs. The eloquent cortex (EC) was defined by functional cortical mapping and used as a DL label. Morphological characteristics of HFOs obtained from EC (ecHFOs) were distilled and interpreted through a novel weakly supervised DL model. Main results. A total of 63 379 interictal intracranially-recorded HFOs from 18 children were analyzed. The ecHFOs had lower amplitude throughout the 80–500 Hz frequency band around the HFO onset and also had a lower signal amplitude in the low frequency band throughout a one-second time window than non-ecHFOs, resembling a bell-shaped template in the time–frequency map. A minority of ecHFOs were HFOs with spikes (22.9%). Such morphological characteristics were confirmed to influence DL model prediction via perturbation analyses. Using the resection ratio (removed HFOs/detected HFOs) of non-ecHFOs, the prediction of postoperative seizure outcomes improved compared to using uncorrected HFOs (area under the ROC curve of 0.82, increased from 0.76). Significance. We characterized salient features of physiological HFOs using a DL algorithm. Our results suggested that this DL-based HFO classification, once trained, might help separate physiological from pathological HFOs, and efficiently guide surgical resection using HFOs.
Commissioning of the upgraded RICH system at the LHCb experiment
Authors: Okamura S. 
Published: November 2022

Abstract
The Ring-Imaging Cherenkov (RICH) system is an essential element of the LHCb experiment: it consists of an upstream detector (RICH 1), located close to the interaction point, and a downstream detector (RICH 2), placed after the tracking system and has the task of identifying charged hadrons over the momentum range 2–100 GeV/c. Currently, the LHCb experiment is completing an upgrade phase to allow data collection at a five-fold increase in instantaneous luminosity up to 2 × 1033 cm−2 s−1 and read out data at a rate of 40 MHz. The challenges of the higher luminosity are a significant increase in detector occupancy and a larger radiation dose. To match the new experimental requirements, both RICH detectors have been upgraded with a redesigned opto-electronic chain and new photon detectors. In addition, RICH 1 has a modified layout with new mechanics and spherical mirrors to reduce the maximum occupancy. A summary of the upgrade program and the current status of the commissioning operations will be presented.
Characterization of High-Flux CdZnTe with optimized electrodes for 4th generation synchrotrons
Authors: Baussens O. , Ponchut C. , Ruat M. , Bettelli M. , Zanettini S. , Zappettini A. 
Published: November 2022

Abstract
In this collaboration work between IMEM-CNR and the ESRF, we explore the potential of the Redlen Technologies High-Flux Cadmium Zinc Telluride (HF-CZT) material for direct X-ray detection at fluxes ranging from 10+7 to 10+12 photons mm−2 s−1. HF-CZT single crystals with optimized electroless gold and sputtered platinum electrodes are characterized both under dark conditions and under X-ray irradiation. We report low leakage current under dark conditions (<100 pA/mm2 at 5 kV/cm). We also report good linearity (R
2 > 0.999) under moderate to high incident X-ray flux (10+7 to 10+10 photons mm−2 s−1) as well as good stability and reproducibility for incident X-ray fluxes up to 10+12 photons mm−2 s−1. Finally, we study transient phenomena in the seconds time range and report fast stabilization time (<200 ms) and negligible afterglow in this time range.
Ultra-fast transverse beam orbit control in LCLS copper linac. Part I
Authors: Halavanau A. , Romero A. , Krasnykh A. , Lutman A. , Beukers T. , Hugyik J. , Le A. , Luchini K. , Jongewaard E. , Sy A. , Ibrahimov A. , Benwell A. , Marinelli A. , Decker F.-J. 
Published: November 2022

Abstract
Current and future experiments at LCLS require x-ray pulse trains of variable time separation on the nanosecond scale. For instance, the cavity-based XFEL (CBXFEL) will use up to 4 pulses separated by 218.5 ns, the X-ray Laser Oscillator (XLO) will use 15 to 25 ns spaced pulses, and the Matter under Extreme Conditions (MEC) experiments use pulse trains separated by 5 nanoseconds or less. In this paper, we demonstrate an ultra-fast e-beam trajectory control method based on transverse electro-magnetic (TEM) striplines and state-of-the-art power sources, to enhance LCLS operations in these regimes.
Design of a μSR spectrometer with ultrahigh arrays at China Spallation Neutron Source
Authors: Dong J.Y. , Pan Z.W. , Yang T.Y. , Lin Z.B. , Wang Z. , He Z.Y. , Chen Z. , Jing H.T. , Tang J.Y. , Liu J.D. , Zhang H.J. , Ye B.J. 
Published: November 2022

Abstract
A new muon source has been proposed to conduct muon spin
rotation/relaxation/ resonance (μSR) measurements at China Spallation Neutron Source (CSNS). Only 1 Hz of the CSNS proton beams (25 Hz in total) will be allocated for muon production. To make better use of muons in every pulse, an ultrahigh-array μSR spectrometer (UHAM) with thousands of detector channels is under design. Due to such a high granularity of detectors, multiple counting events generated from particle scattering or spiral motions of positrons in a strong longitudinal field should be carefully considered in the design. Six different structures were modeled and simulated based on two types of angular orientations (parallel arrangement and pointing arrangement) and three kinds of spectrometer geometries (cylinder, cone and sphere). A quality factor, Q, was proposed to evaluate the performance of these structures by integrating their impacts on the overall asymmetry, the counting rate and the percentage of multiple counts. According to the simulation, the conical structure with detectors pointing to the sample has the highest Q in both zero field and longitudinal field. The results also show that all kinds of structures cannot be operated under strong longitudinal fields with a strength over 2 T. The full simulation of a μSR spectrometer can provide good guidance for the construction of the UHAM in the upcoming upgrade of CSNS.
Spatial-temporal variations in green, blue and gray water footprints of crops: how do socioeconomic drivers influence?
Authors: Hu Mengmeng , Wu Wenbin , Yu Qiangyi , Tang Huajun , Wen Yanru , Zhao Fen 
Published: November 2022

Abstract
Nowadays, more than 70% of global freshwater is used for agriculture. The evaluation of the water footprint of crops (CWFs) is an important method to measure the effects of crop production on water resource utilization and water environmental pollution. However, little attention is paid to the impact of socioeconomic development differences on the water footprint of each crop. In this study, the green, blue, and gray water footprints of crop production were quantified, and the socioeconomic drivers of changes in the CWFs were revealed. It is of great significance to provide targeted guidance for agricultural water management in Heilongjiang, a province with the largest crop production in China. Here, we show that the total water footprint of crop production (TWF) increased from 62.2 billion m3 to 101.8 billion m3, and high-value areas were mainly concentrated in the west and south of Heilongjiang Province. Over 95% of the total grain crops sown were covered by maize, rice and soybean, which presented the greatest TWF. The share of green water footprint in TWF has increased, and crop growth is increasingly dependent on rainfall. Furthermore, our results highlight that the effective irrigated quota and crop-planting scale for maize and rice contribute to TWF increase. The TWF and agricultural value-added score were weakly decoupling in most municipalities, indicating the improved efficiency of crop water use; the TWF is growing slower than the economy, which is undesirable. Changes in TWF and agricultural value-added score were the same as the left half of the inverted ‘U of the ‘Environmental Kuznets Curve’, which has not reached the ‘inflection point’. More efforts to control the effective irrigated quota and crop-planting scale while improving effective irrigated efficiency are needed to ensure that economic growth does not come at the expense of consuming enormous quantities of water.
ENSO and QBO modulation of the relationship between Arctic sea ice loss and Eurasian winter climate
Authors: Ma Xuan , Wang Lei , Smith Doug , Hermanson Leon , Eade Rosie , Dunstone Nick , Hardiman Steven , Zhang Jiankai 
Published: November 2022

Abstract
The causality between Arctic sea ice decline and cold boreal winters has been widely debated recently and remains controversial. A major source of uncertainty in the sea ice-cold winter relationship originates from that the stratosphere polar vortex (SPV) is not only affected by Arctic sea ice anomaly but can also be modulated by El Niño-Southern Oscillation (ENSO) and quasi-biennial oscillation (QBO). Using reanalysis data and hindcasts from the decadal prediction system version 4, here we show that both cold and warm winters occur over Eurasia when the Barents–Kara Sea sea ice is abnormally low. Warm winters occur during the La Niña-easterly QBO-low sea ice (LANINA-EQBO-LICE) years and cold winters during the neutral ENSO-neutral QBO (NENSO-NQBO)-LICE and El Niño (ELNINO)-NQBO-LICE years. During the LANINA-EQBO-LICE years, weakened upward-propagating planetary waves from the troposphere to the stratosphere strengthen the Arctic SPV and then weaken the Aleutian low and Siberian high, creating conditions favorable for Eurasian warming. The atmospheric responses are opposite in the NENSO-NQBO-LICE and ELNINO-NQBO-LICE years. This implies that care should be taken in using Arctic sea ice alone as the precursor to predict boreal winter climate.
Divergent runoff impacts of permafrost and seasonally frozen ground at a large river basin of Tibetan Plateau during 1960–2019
Authors: Song Lei , Wang Lei , Zhou Jing , Luo Dongliang , Li Xiuping 
Published: November 2022

Abstract
Since the 20th century, due to global warming, permafrost areas have undergone significant changes. The degradation of permafrost has complicated water cycle processes. Taking the upper Yellow River basin (UYRB) as a demonstration, this study discusses the long-term (1960–2019) changes in frozen ground and their hydrological effects with a cryosphere-hydrology model, in particular a permafrost version of the water and energy budget-based distributed hydrological model. The permafrost at the UYRB, with thickening active layer and lengthening thawing duration, has degraded by 10.8%. The seasonally frozen ground has a more pronounced intra-annual regulation that replenishes surface runoff in the warm season, while the degradation of permafrost leads to a runoff increase. The occurrence of extreme events at the UYRB has gradually decreased with the degradation of frozen ground, but spring droughts and autumn floods become more serious. The results may help better understand the hydrological impacts of permafrost degradation in the Tibetan Plateau.
Keratin intrinsic fluorescence as a mechanism for non-invasive monitoring of its glycation
Authors: Muir Rhona , Forbes Shareen , Birch David J S , Vyshemirsky Vladislav , Rolinski Olaf J 
Published: November 2022

Abstract
We have studied the evolution of keratin intrinsic fluorescence as an indicator of its glycation. Steady-state and time-resolved fluorescence of free keratin and keratin-glucose samples were detected in PBS solutions in vitro. The changes in the fluorescence response demonstrate that the effect of glucose is manifest in the accelerated formation of fluorescent cross-links with an emission peak at 460 nm and formation of new cross-links with emission peaks at 525 nm and 575 nm. The fluorescence kinetics of these structures is studied and their potential application for the detection of long-term complications of diabetes discussed.
Detection and quantification of Pb and Cr in oysters using laser-induced breakdown spectroscopy
Authors: YAN Qingxia , TIAN Ye , LI Ying , LIN Hong , JIA Ziwen , LU Yuan , YU Jin , SUN Chen , BAI Xueshi , DETALLE Vincent 
Published: November 2022

Abstract
The quantitative determination of heavy metals in aquatic products is of great importance for food security issues. Laser-induced breakdown spectroscopy (LIBS) has been used in a variety of foodstuff analysis, but is still limited by its low sensitivity when targeting trace heavy metals. In this work, we compare three sample enrichment methods, namely drying, carbonization, and ashing, for increasing detection sensitivity by LIBS analysis for Pb and Cr in oyster samples. The results demonstrate that carbonization can remove a significant amount of the contributions of organic elements C, H, N and O; meanwhile, the signals of the metallic elements such as Cu, Pb, Sr, Ca, Cr and Mg are enhanced by 3–6 times after carbonization, and further enhanced by 5–9 times after ashing. Such enhancement is not only due to the more concentrated metallic elements in the sample compared to the dried ones, but also the unifying of the matter in carbonized and ashed samples from which higher plasma temperature and electron density are observed. This condition favors the detection of trace elements. According to the calibration curves with univariate and multivariate analysis, the ashing method is considered to be the best choice. The limits of detection of the ashing method are 0.52 mg kg−1 for Pb and 0.08 mg kg−1 for Cr, which can detect the presence of heavy metals in the oysters exceeding the maximum limits of Pb and Cr required by the Chinese national standard. This method provides a promising application for the heavy metal contamination monitoring in the aquatic product industry.
Preprint Highlight: Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer
Authors: Lim Grace 
Published: November 2022

Standard genomic and proteomic profiling methods for colorectal tumors do not always translate into reliable precision medicine outcomes. Tumor plasticity mechanisms can result in nongenetic responses to targeted therapies, calling for a functional approach using dynamic and physiologically relevant patient models. This study establishes a functional precision medicine workflow by combining the application of kinase inhibitors with quantitative and spatial proteomics to reveal both intrinsic and extrinsic signaling crosstalk in a living biobank of patient-derived colorectal cancer organoid models. The data and methods used here provide a framework for a better understanding of colorectal cancers that accounts for off-target effects of kinase inhibitors and patient-specific plasticity mechanisms that influence downstream cell signaling responses. This preprint has been assigned the following badges: New Methods, New Materials, Open Data, Open Software. Read the preprint on bioRxiv ( Plattner et al., 2022 ): https://doi.org/10.1101/2022.09.16.508204 .
Preprint Highlight: Actomyosin cables position cell cohorts during Drosophila germband retraction by entraining their morphodynamic and mechanical properties
Authors: Ríos-Barrera Luis Daniel 
Published: November 2022

Midway through embryonic development in Drosophila melanogaster, the germband retracts to relocate the body segments to their final position. This process requires complex cell rearrangements and tissue-scale coordination, but the cellular behaviors and forces that drive it have not been characterized in detail. This work shows that proper tissue retraction requires coordination between distinct supracellular actomyosin cables at the posterior-most segment of the germband: nonconstricting circumferential cables mechanically isolate cell subpopulations within the germband, and constricting cables accelerate overall tissue retraction. Force propagation drives morphogenesis of a wide range of organs and tissues. This work provides a model to understand how forces are coordinated between adjacent tissues but also restrained to specific tissue compartments during development. This preprint has been assigned the following badges: New Hypothesis, Cross-Validation, Open Data. Read the preprint on bioRxiv ( Nandi et al., 2022 ): https://doi.org/10.1101/2022.09.23.509113 .
Prescribing and deprescribing in very old age: perceptions of very old adults, caregivers and health professionals
Authors: Ouellet Nicole , Bergeron Anne-Sophie , Gagnon Eric , Cossette Benoit , Labrecque Cory A , Sirois Caroline 
Published: November 2022

Abstract

Background
although they are major consumers of medications, there is little evidence-based data to guide prescribing and deprescribing of medications for very old adults (80+ years).

Objectives
to discover the perceptions of very old adults, caregivers and health professionals in order to further examine the clinical and ethical issues raised by prescribing and deprescribing in very old age.

Methods
individual interviews were conducted with very old adults (n = 10) and caregivers (n = 6), whereas group interviews were conducted with health professionals (n = 11). The themes covered included perceptions of medication use, polypharmacy, deprescribing and patient-health professional relationships. Thematic analysis was used to identify areas of convergence and divergence.

Results
very old adults are satisfied with the medications they are taking, do not see the need to reduce their medication use and consider their doctor as the expert who should make the decisions regarding treatment. The perceptions of caregivers are similar to those of older adults, whereas health professionals believe that very old adults take a lot of inappropriate medications and list multiple barriers to deprescribing. All participants describe a normalisation of medication use with ageing.

Conclusion
there is a dichotomy between the perception of the very old adults/caregivers and that of health professionals regarding the safety of medication in very old age. A cultural change regarding medication use seems essential to optimise therapy and support deprescribing in clinical practice since the potential issues raised by researchers do not resonate with the main stakeholders.
Deep learning-based classifier of diffuse large B-cell lymphoma cell-of-origin with clinical outcome
Authors: Viswanathan Aswathi , Kundal Kavita , Sengupta Avik , Kumar Ambuj , Kumar Keerthana Vinod , Holmes Antony B , Kumar Rahul 
Published: November 2022

Abstract
Diffuse large B-cell lymphoma (DLBCL) is an aggressive form of non-Hodgkin lymphoma with poor response to R-CHOP therapy due to remarkable heterogeneity. Based on gene expression, DLBCL cases were divided into two subtypes, i.e. ABC and GCB, where ABC subtype is associated with poor outcomes. Due to its association with clinical outcome, this classification, also known as cell-of-origin (COO), is an efficient way to predict the response to R-CHOP therapy. Previous COO classification methods have some shortcomings, e.g. limited number of samples in the training dataset. These shortcomings challenge the robustness of methods and make it difficult to implicate these methods at clinical level. To overcome the shortcomings of previous methods, we developed a deep learning-based classifier model on a cohort of 381 DLBCL patients using expression data of 20 genes. We implemented multilayer perceptron (MLP) to train deep learning-based classifier, named MLP-COO. MLP-COO achieved accuracy of 99.70% and 94.70% on training and testing datasets, respectively, with 10-fold cross-validation. We also assessed its performance on an independent dataset of 294 DLBCL patients. On independent dataset, we achieved an accuracy of 95.90% with MCC of 0.917. To show its broader applicability, we used this classifier to predict the clinical outcome using survival data from two large cohorts of DLBCL patients. In survival analysis, MLP-COO recapitulates the survival probabilities of DLBCL patients based on their COO in both cohorts. We anticipate that MLP-COO model developed in this study will benefit in the accurate COO prediction of DLBCL patients and their clinical outcomes.
An end-to-end multi-task system of automatic lesion detection and anatomical localization in whole-body bone scintigraphy by deep learning
Authors: Huang Kaibin , Huang Shengyun , Chen Guojing , Li Xue , Li Shawn , Liang Ying , Gao Yi 
Published: November 2022

Abstract

Summary
Limited by spatial resolution and visual contrast, bone scintigraphy interpretation is susceptible to subjective factors, which considerably affects the accuracy and repeatability of lesion detection and anatomical localization. In this work, we design and implement an end-to-end multi-task deep learning model to perform automatic lesion detection and anatomical localization in whole-body bone scintigraphy. A total of 617 whole-body bone scintigraphy cases including anterior and posterior views were retrospectively analyzed. The proposed semi-supervised model consists of two task flows. The first one, the lesion segmentation flow, received image patches and was trained in a supervised way. The other one, skeleton segmentation flow, was trained on as few as five labeled images in conjunction with the multi-atlas approach, in a semi-supervised way. The two flows joint in their encoder layers so each flow can capture more generalized distribution of the sample space and extract more abstract deep features. The experimental results show that the architecture achieved the highest precision in the finest bone segmentation task in both anterior and posterior images of whole-body scintigraphy. Such an end-to-end approach with very few manual annotation requirement would be suitable for algorithm deployment. Moreover, the proposed approach reliably balances unsupervised labels construction and supervised learning, providing useful insight for weakly labeled image analysis.

Supplementary information
Supplementary data are available at Bioinformatics online.