bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Preoperative Imaging Modalities for the Assessment of Malignant Potential of Pancreatic Cystic Lesions
Authors: Lee Sang-Woo , Shim Sung Ryul , Jeong Shin Young , Kim Seong-Jang 
Published: June 2022

Purpose
The aims of this study are to compare the performance of various preoperative imaging modalities for assessing the malignant potential of pancreatic cystic lesions (PCLs) through a network meta-analysis (NMA) and to clarify the role of 18F-FDG PET in the management of patients with PCL.

Methods
PubMed, EMBASE, and Cochrane Library were searched for the studies evaluating the performance of preoperative imaging modalities for identifying malignant PCLs. The NMA was performed for 4 representative categories of various imaging modalities in terms of diagnostic performance for differentiating malignant from benign PCL and intraductal papillary mucinous neoplasms only as a subgroup analysis. To calculate the probability of each imaging modality being the most effective diagnostic method, the surface under the cumulative ranking curve values were obtained.

Results
A total of 1018 patients from 17 direct comparison studies using 2 or more preoperative imaging modalities were included for differentiating malignant from benign PCL. The positive predictive value (PPV) and accuracy of 18F-FDG PET were significantly higher than that of CT (PPV: odds ratio [OR], 2.66; 95% credible interval [CrI], 1.21–6.17; accuracy: OR, 2.63; 95% CrI, 1.41–5.38) or MRI (PPV: OR, 2.50; 95% CrI, 1.09–6.26; accuracy: OR, 2.50; 95% CrI, 1.28–5.47) in all PCLs, as well as in the subgroup analysis for intraductal papillary mucinous neoplasm only. 18F-FDG PET showed the highest surface under the cumulative ranking curve values in all diagnostic performance areas of sensitivity, specificity, PPV, negative predictive value, and accuracy, followed by MRI or CT.

Conclusions
The results from this NMA suggest that 18F-FDG PET is the best preoperative imaging modality for differentiating malignant from benign PCLs and that it can be used for the preoperative evaluation of PCLs.
Establishing national stakeholder priorities for quality improvement in pediatric trauma care: Consensus results using a modified Delphi process
Authors: Melhado Caroline G. , Yorkgitis Brian K. , Patel Bhavin , Remick Katherine , Macias Charles G. , Dingeldein Michael W. , Gray Lisa , Jensen Aaron R. 
Published: June 2022

BACKGROUND
Quality improvement efforts within pediatric trauma centers (PTCs) are robust, but the majority of children do not receive initial postinjury care at PTCs. Disparities in access to quality trauma care remain, particularly for children who initially access the trauma system outside of a PTC. The purpose of this project was to identify unmet needs for injured children within the pediatric emergency care system and to determine national priorities for quality improvement across the continuum of pediatric trauma care.

METHODS
A panel of delegates representing patients and families, prehospital providers, federal funding partners, nurses, and physicians was recruited from 10 national stakeholder organizations. Potential targets were identified using an initial stakeholder meeting followed by a free text response survey. Free text items were coded and condensed as themes and then ranked by the panel using a modified Delphi approach to determine consensus priorities. Items not achieving >35% prioritization on a given iteration were dropped from subsequent iterations. Consensus was defined as 75% of members designating an item as a top-four priority.

RESULTS
Nineteen themes were identified as potential targets for QI initiatives. Four iterations of panel ranking were used to achieve consensus, with four priorities identified: (1) creation of a toolkit and standard provider training for pediatric trauma triage, shock recognition, and early recognition for need to transfer to higher level of care; (2) development of minimum standards for pediatric trauma resuscitation and stabilization capability in nonpediatric centers; (3) facilitating creation of local nursing and physician champions for pediatric trauma; and (4) development and dissemination of best-practice guidelines to improve imaging practices for injured children.

CONCLUSION
System-level quality improvement priorities for pediatric trauma care should focus resources on developing and implementing minimum pediatric standards for injury care, frontline provider training, stabilization protocols, imaging guidelines, and local pediatric champions.

LEVEL OF EVIDENCE
Therapeutic/Care Management; Level IV.
Clinical Utility in Adopting Race-free Kidney Donor Risk Index
Authors: Doshi Mona D. , Schaubel Douglas E. , Xu Yuwen , Rao Panduranga S. , Sung Randall S. 
Published: June 2022

Background.
Recent events of racial injustice prompted us to study potential impact of removing race from kidney donor risk index (KDRI) calculator.

Methods.
We used Scientific Registry for Transplant Recipients data to analyze outcomes of 66 987 deceased-donor kidney transplants performed in the United States between 2010 and 2016. Graft failure (GF) was defined as death or return to dialysis or requiring repeat transplant. We compared original KDRI and a race-free KDRI (Black donor coefficient zeroed out in the KDRI formula) with respect to recategorization of perceived GF risk (based on KDPI categories: ≤20, 21–34, 35–85, ≥86)‚ risk discrimination (using the C statistic) and predictive accuracy (using Brier score), and GF risk prediction (using Cox regression on time-to-GF). We used logistic regression to study the impact of donor race on discard probability.

Results.
There were 10 949 (16.3% of recipients) GF, and 1893 (17% of GFs) were among recipients of kidneys from Black donors. The use of race-free KDRI resulted in reclassification of 49% of kidneys from Black donors into lower GF risk categories. The impact on GF risk discrimination was minimal, with a relative decrease in C statistic of 0.16% and a change in GF predictive accuracy of 0.07%. For a given recipient/donor combination, transplants from Black (compared with non-Black) donors are estimated to decrease predicted graft survival at 1-y by 0.3%–3%, and 5-y by 1%–6%. Kidneys from Black donors are significantly more likely to be discarded (odds ratio adjusted for KDRI except race = 1.24). We estimate that an equal discard probability for Black and non-Black donors would yield 70 additional kidney transplants annually from Black donors.

Conclusions.
Use of race-free KDRI did not impact GF risk discrimination or predictive accuracy and may lower discard of kidneys from Black donors. We recommend use of race-free KDRI calculator acknowledging the possibility of miscalculation of GF risk in small proportion of kidneys from Black donors.
A GPU-based computational framework that bridges Neuron simulation and Artificial Intelligence
Authors: Zhang Yichen , He Gan , Liu Xiaofei , Johannes Hjorth J.J. , Kozlov Alexander , He Yutao , Zhang Shenjian , Ma Lei , Kotaleski Jeanette Hellgren , Tian Yonghong , Grillner Sten , Du Kai , Huang Tiejun 
Published: June 2022

AbstractBiophysically detailed multi-compartment models are powerful tools to explore computational principles of the brain and also serve as a theoretical framework to generate algorithms for artificial intelligence (AI) systems. However, the expensive computational cost severely limits the applications in both the neuroscience and AI fields. The major bottleneck during simulating detailed compartment models is the ability of a simulator to solve large systems of linear equations. Here, we present a novel Dendritic Hierarchical Scheduling (DHS) method to markedly accelerate such process. We theoretically prove that the DHS implementation is computationally optimal and accurate. This GPU-based method performs at 2-3 orders of magnitude higher speed than that of the classic serial Hines method in the conventional CPU platform. We build a DeepDendrite framework, which integrates the DHS method and the GPU computing engine of the NEURON simulator and demonstrate applications of DeepDendrite in neuroscience and AI tasks. We investigated how spatial patterns of spine inputs affect neuronal excitability in a detailed human pyramidal neuron model with 25,000 spines; and examined how dendrites protect morphologically detailed neural networks against adversarial attacks in typical image classification tasks.
Wide-Field Stokes Polarimetric Microscopy for Second Harmonic Generation Imaging
Authors: Castaño Leonardo Uribe , Mirsanaye Kamdin , Kontenis Lukas , Krouglov Serguei , Akens Margarete K. , Barzda Virginijus 
Published: June 2022

AbstractWe employ wide-field second harmonic generation (SHG) microscopy together with nonlinear Stokes polarimetry for quick ultrastructural investigation of large sample areas (700μmx 700μm) in thin histology sections. The Stokes vector components for SHG are obtained from the polarimetric measurements with incident and outgoing linear and circular polarization states. The Stokes components are used to construct the images of polarimetric parameters and deduce the sample maps of achiral and chiral nonlinear susceptibility tensor components ratios and cylindrical axis orientation in fibrillar materials. The imaged histology sections with polarimetric wide-field SHG microscopy provide large area maps of ultrastructural information about the collagenous tissue, which can be used for rapid histology investigations.
Fossil-explorer.com: An efficient interactive approach to exploring fossil data
Authors: Wu Junqi , Xu Honghe , Pan Zhaohui , Niu Zhibin 
Published: June 2022

ABSTRACTFossils today are increasingly being digitized and documented by multi-modal data obtained from visual data (i.e., photos and tomographic images), as well as text, locations, geological ages, and other chemical and physical measurements. Popular online websites such as PBDB and GBDB offer visual explorations of specimens’ localities, but they have limited multi-modal data visualization abilities and face challenges related to visual obscuration and insufficient interaction/exploration. Here, we present fossil-explorer.com, a continuously developing open-source online tool for assisting paleontologists with interactively exploring fossil collections. The tool is designed to address the issues of visual clutter, limited data types, and insufficient interactions. It is intuitive and endorsed by paleontologists. We have also quantitatively evaluated the tool by measuring the interaction scaling performance. The results show that it providessublinear interaction performanceand thus is able to deal efficiently with millions-level data. The currentfossil-explorer.comdemonstrates the Ordovician to Silurian graptolite fossil multimedia dataset, which is significant in global stratigraphy and shale gas exploration. The extended version also facilitates the use of Deepbone (http://deepbone.org), world’s most comprehensive database of vertebrate paleontology database. We developed the code forfossil-explorer.comto be open access and will continue to improve it.
A multiomics comparison of weight loss interventions shows the distinct effects of bariatric surgery and intermittent fasting on hepatic metabolism
Authors: Haran Arnon , Bergel Michael , Kleiman Doron , Hefetz Liron , Israeli Hadar , Weksler-Zangen Sarah , Agranovich Bella , Abramovich Ifat , Schyr Rachel Ben-Haroush , Gottlieb Eyal , Ben-Zvi Danny 
Published: June 2022

AbstractThe prevalence of obesity and non-alcoholic fatty liver (NAFL) is steadily increasing. Weight loss can lead to improvement in NAFL in patients and in model organisms. Weight loss can be achieved through either dietary and lifestyle interventions, pharmacotherapy, and bariatric surgery. Some interventions, such as intermittent fasting, have been purported to have benefits beyond those conferred by weight loss alone.In this study, rats were provided a high-fat, high-sucrose diet for 7 weeks and then were assigned to strict caloric restriction with intermittent fasting (IF-CR) or to sleeve gastrectomy (SG) bariatric surgery, achieving equivalent weight loss. The two interventions were compared to ad-libitum fed controls. The metabolome of the blood entering the liver was analyzed in the three experimental groups, as well as the metabolome and transcriptome of the liver under fasting conditions, to test how different means of weight loss affect the input of the liver and hepatic metabolism.Surprisingly, the two interventions had different and often opposite effects on the composition of portal blood and liver metabolites. IF-CR resulted in sweeping changes across multiple central metabolic pathways, including an increase in de novo lipogenesis and triglyceride export, and upregulation of glycolysis, citric acid cycle, and the pentose phosphate pathway, as well as an increase in glycogen storage. Meanwhile, the effects of SG concentrated on one-carbon metabolic pathways, with changes in metabolite and transcript levels pointing to decreased transmethylation and methionine cycle activity, with downstream effects on levels of glutathione and the hepatic oxidative state.In conclusion, our study highlights how different means of weight loss affect distinct metabolic pathways and demonstrates a unique effect of bariatric surgery on hepatic one-carbon and redox pathways.
G-quadruplex recognition by DARPIns through epitope/paratope analogy
Authors: Miclot Tom , Bignon Emmanuelle , Terenzi Alessio , Grandemange Stéphanie , Barone Giampaolo , Monari Antonio 
Published: June 2022

AbstractWe investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4s specific sensors. To this end we carried out all-atom molecular dynamic simulations to unravel the interactions between specific nucleic acids, including human-telomeric (h-telo), Bcl-2, and c-Myc, with different peptides, forming a DARPin/G4 complex. By comparing the sequences of DARPin with that of a peptide known for its high affinity for c-Myc, we show that the recognition cannot be ascribed to sequence similarity but, instead, depends on the complementarity between the three-dimensional arrangement of the molecular fragments involved: the α-helix/loops domain of DARPin and the G4 backbone. Our results reveal that DARPins tertiary structure presents a charged hollow region in which G4 can be hosted, thus the more complementary the structural shapes, the more stable the interaction.
Dose-dependent suppression of hippocampal contextual memory formation, place cells, and spatial engrams by the NMDAR antagonist (R)-CPP
Authors: Zhu Mengwen , Perkins Mark G. , Lennertz Richard , Abdulzahir Alifayez , Pearce Robert A. 
Published: June 2022

ABSTRACTA common way to study the functional importance of N-methyl-D-aspartate receptors (NMDARs) in hippocampal memory-encoding circuits is by administering NMDAR antagonists. We recently compared the effects of (R,S)-3-(2-carboxypiperazin-4-yl)-propyl-1-phosphonic acid (CPP), a competitive NMDAR antagonist, on suppression of memory in vivo versus suppression of NMDAR-mediated field EPSPs (fEPSPNMDA) and long-term potentiation (LTP) in vitro. Surprisingly, we found that concentrations that block contextual conditioning in vivo are ineffective at blocking the fEPSPNMDA or LTP in vitro. Here we tested one possible explanation for the mismatch – that the hippocampus is relatively resistant to CPP compared to other brain structures engaged in contextual fear conditioning. We used the context pre-exposure facilitation effect (CPFE) paradigm to isolate the hippocampal component of contextual learning, and in-vivo calcium imaging of place cells and spatial engrams to directly assess hippocampal spatial coding. We found that, by both measures, the active enantiomer (R)-CPP did interfere with hippocampal function at concentrations below those that block fEPSPs or LTP. We conclude that the alternative – that CPP interferes with memory by targeting NMDARs in interneurons rather than pyramidal neurons – is the more likely explanation.
Simulation of Energy Regeneration in Human Locomotion for Efficient Exoskeleton Actuation
Authors: Laschowski Brokoslaw , Inkol Keaton A. , Mihailidis Alex , McPhee John 
Published: June 2022

AbstractBackdriveable actuators with energy regeneration can improve the efficiency and extend the battery-powered operating times of robotic lower-limb exoskeletons by converting some of the otherwise dissipated energy during negative mechanical work into electrical energy. However, previous related studies have focused on steady-state level-ground walking. To better encompass real-world community mobility, here we developed a feedforward human-exoskeleton energy regeneration system model to simulate energy regeneration and storage during other daily locomotor activities. Data from inverse dynamics analyses of 10 healthy young adults walking at variable speeds and slopes were used to calculate the negative joint mechanical power and work (i.e., the mechanical energy theoretically available for electrical energy regeneration). These human joint mechanical energetics were then used to simulate backdriving a robotic exoskeleton and regenerating energy. An empirical characterization of the exoskeleton device was carried out using a joint dynamometer system and an electromechanical motor model to calculate the actuator efficiency and to simulate energy regeneration. Our performance calculations showed that regenerating energy at slower walking speeds and decline slopes could significantly extend the battery-powered operating times of robotic lower-limb exoskeletons (i.e., up to 99% increase in total number of steps), therein improving locomotor efficiency.
Comprehensive Characterisation of Fetal and Mature Retinal Cell Identity to Assess the Fidelity of Retinal Organoids
Authors: Kim Hani Jieun , O’Hara-Wright Michelle , Kim Daniel , Loi To Ha , Lim Benjamin Y. , Jamieson Robyn V. , Gonzalez-Cordero Anai , Yang Pengyi 
Published: June 2022

SummaryCharacterizing cell identity in complex tissues such as the human retina is essential for studying its development and disease. While retinal organoids derived from pluripotent stem cells have been widely used to model development and disease of the human retina, there is a lack of studies that have systematically evaluated molecular and cellular fidelity of the organoids derived from various culture protocols in recapitulating their in vivo counterpart. To this end, we performed an extensive meta-atlas characterisation of cellular identities of the human eye, covering a wide range of developmental stages. The resulting map uncovered previously unknown biomarkers of major retinal cell types and those associated with cell-type specific maturation. Using our retinal cell identity map from the fetal and adult tissues, we systematically assessed the fidelity of the retinal organoids to mimic the human eye, enabling us to comprehensively benchmark the current protocols for retinal organoid generation.
On the Interaction of Biopotential Sensing and Right Leg Drive System with Electro-Quasistatic Human Body Communication
Authors: Sriram Shreeya , Polachan Kurian , Sen Shreyas 
Published: June 2022

AbstractContinuous long-term sensing of biopotential signals is vital to facilitate accurate diagnosis. The current state of the art in wearable health monitoring relies on radiative technology for communication. Due to their radiative nature, these systems result in lossy and inefficient transmission, limiting the device’s life span. Human Body Communication has emerged as an energy-efficient secure communication modality, and literature has shown body communication to transmit biopotential signals at 100x lower power than traditional radiative technologies. Unlike radiative communication that uses airwaves, HBC, specifically Capacitive Electro-Quasistatic HBC (EQS-HBC), couple signals and confine them within the human body. In Capacitive EQS-HBC, the transmitter uses an electrode to modulate the body potential to transmit data. The modulation of body potential by HBC raises the following concerns. Will HBC transmissions affect the quality of biopotential signals sensed from the body? Additionally, since biopotential sensing systems commonly use Right Leg Drive (RLD) to bias body potential, there is also a concern if RLD can affect the quality of HBC transmissions.For the first time, our work studies the interactions between EQS-HBC and biopotential sensing. Our work is important since understanding HBC-RLD interactions is integral to developing EQS-HBC-based biosensors for Body Area Networks (BANs). For the studies, we conducted lab experiments and developed circuit theoretic models to back the experimental outcomes. We show that due to their higher frequency content and common-mode nature, HBC transmissions do not affect the differential sensing of low-frequency biopotential signals. We show that biopotential sensing using RLD affects HBC. RLD deteriorates the signal strength of HBC transmissions. We thus propose not to use RLD with HBC. We demonstrate our proposed solution by transmitting ECG signals using HBC with 96% correlation compared to the traditional wireless system at a fraction of the power.
Methamphetamine induced regional-specific transcriptomic and epigenetic changes in the rat brain
Authors: Miao Benpeng , Xing Xiaoyun , Bazylianska Viktoriia , Madden Pamela , Moszczynska Anna , Zhang Bo 
Published: June 2022

AbstractBackgroundMethamphetamine (METH) is a highly addictive central nervous system stimulant. Chronic use of METH is associated with multiple neurological and psychiatric disorders. An overdose of METH can cause brain damage and even death. Mounting evidence indicates that epigenetic changes and functional impairment in the brain occur due to addictive drug exposures. However, the responses of different brain regions to a METH overdose remain unclear.ResultsWe investigated the transcriptomic and epigenetic responses to a METH overdose in four regions of the rat brain, including the nucleus accumbens, dentate gyrus, Ammon’s horn, and subventricular zone. We found that 24 hours after METH overdose, 15.6% of genes showed changes in expression and 27.6% of open chromatin regions exhibited altered chromatin accessibility in all four rat brain regions. Interestingly, only a few of those differentially expressed genes and differentially accessible regions were affected simultaneously. Among four rat brain regions analyzed, 149 transcription factors and 31 epigenetic factors were significantly affected by METH overdose. METH overdose also resulted in opposite-direction changes in regulation patterns of both gene and chromatin accessibility between the dentate gyrus and Ammon’s horn. Approximately 70% of chromatin-accessible regions with METH-induced alterations in the rat brain are conserved at the sequence level in the human genome, and they are highly enriched in neurological processes. Many of these conserved regions are active brain-specific enhancers and harbor SNPs associated with human neurological functions and diseases.ConclusionOur results indicate strong region-specific transcriptomic and epigenetic responses to a METH overdose in distinct rat brain regions. We describe the conservation of region-specific gene regulatory networks associated with METH overdose. Overall, our study provides clues toward a better understanding of the molecular responses to METH overdose in the human brain.