bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential value of high-throughput single-cell DNA sequencing of Juvenile myelomonocytic leukemia: report of two cases
Authors: Volchkov E. V. , Khozyainova A. A. , Gurzhikhanova M. Kh. , Larionova I. V. , Matveev V. E. , Evseev D. A. , Ignatova A. K. , Menyailo M. E. , Venyov D. A. , Vorobev R. S. , Semchenkova A. A. , Olshanskaya Yu. V. , Denisov E. V. , Maschan M. A. 
Published: September 2023

AbstractJuvenile myelomonocytic leukemia (JMML) is a rare myeloproliferative disease of early childhood that develops due to mutations in the genes of the RAS-signaling pathway. Next-generation high throughput sequencing (NGS) enables identification of various secondary molecular genetic events that can facilitate JMML progression and transformation into secondary acute myeloid leukemia (sAML). The methods of single-cell DNA sequencing (scDNA-seq) enable overcoming limitations of bulk NGS and exploring genetic heterogeneity at the level of individual cells, which can help in a better understanding of the mechanisms leading to JMML progression and provide an opportunity to evaluate the response of leukemia to therapy. In the present work, we applied a two-step droplet microfluidics approach to detect DNA alterations among thousands of single cells and to analyze clonal dynamics in two JMML patients with sAML transformation before and after hematopoietic stem cell transplantation (HSCT). At the time of diagnosis both of our patients harbored only “canonical” mutations in the RAS signaling pathway genes detected by targeted DNA sequencing. Analysis of samples from the time of transformation JMML to sAML revealed additional genetic events that are potential drivers for disease progression in both patients. ScDNA-seq was able to measure of chimerism level and detect a residual tumor clone in the second patient after HSCT (sensitivity of less than 0.1% tumor cells). The data obtained demonstrate the value of scDNA-seq to assess the clonal evolution of JMML to sAML, response to therapy and engraftment monitoring.
Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells
Authors: Kim Heon Seok , Grimes Susan M. , Chen Tianqi , Sathe Anuja , Lau Billy T. , Hwang Gue-Ho , Bae Sangsu , Ji Hanlee P. 
Published: September 2023

AbstractGenome sequencing studies have identified numerous cancer mutations across a wide spectrum of tumor types, but determining the phenotypic consequence of these mutations remains a challenge. Here, we developed a high-throughput, multiplexed single-cell technology called TISCC-seq to engineer predesignated mutations in cells using CRISPR base editors, directly delineate their genotype among individual cells and determine each mutation’s transcriptional phenotype. Long-read sequencing of the target gene’s transcript identifies the engineered mutations, and the transcriptome profile from the same set of cells is simultaneously analyzed by short-read sequencing. Through integration, we determine the mutations’ genotype and expression phenotype at single-cell resolution. Using cell lines, we engineer and evaluate the impact of >100 TP53 mutations on gene expression. Based on the single-cell gene expression, we classify the mutations as having a functionally significant phenotype.
Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler
Authors: Abdulhay Nour J. , Hsieh Laura J. , McNally Colin P. , Ostrowski Megan S. , Moore Camille M. , Ketavarapu Mythili , Kasinathan Sivakanthan , Nanda Arjun S. , Wu Ke , Chio Un Seng , Zhou Ziling , Goodarzi Hani , Narlikar Geeta J. , Ramani Vijay 
Published: September 2023

AbstractNearly all essential nuclear processes act on DNA packaged into arrays of nucleosomes. However, our understanding of how these processes (for example, DNA replication, RNA transcription, chromatin extrusion and nucleosome remodeling) occur on individual chromatin arrays remains unresolved. Here, to address this deficit, we present SAMOSA-ChAAT: a massively multiplex single-molecule footprinting approach to map the primary structure of individual, reconstituted chromatin templates subject to virtually any chromatin-associated reaction. We apply this method to distinguish between competing models for chromatin remodeling by the essential imitation switch (ISWI) ATPase SNF2h: nucleosome-density-dependent spacing versus fixed-linker-length nucleosome clamping. First, we perform in vivo single-molecule nucleosome footprinting in murine embryonic stem cells, to discover that ISWI-catalyzed nucleosome spacing correlates with the underlying nucleosome density of specific epigenomic domains. To establish causality, we apply SAMOSA-ChAAT to quantify the activities of ISWI ATPase SNF2h and its parent complex ACF on reconstituted nucleosomal arrays of varying nucleosome density, at single-molecule resolution. We demonstrate that ISWI remodelers operate as density-dependent, length-sensing nucleosome sliders, whose ability to program DNA accessibility is dictated by single-molecule nucleosome density. We propose that the long-observed, context-specific regulatory effects of ISWI complexes can be explained in part by the sensing of nucleosome density within epigenomic domains. More generally, our approach promises molecule-precise views of the essential processes that shape nuclear physiology.
A 10-m resolution impervious surface area map for the greater Mekong subregion from remote sensing images
Authors: Sun Genyun , Li Zheng , Zhang Aizhu , Wang Xin , Yan Kai , Jia Xiuping , Liu Qinhuo , Li Jing 
Published: September 2023

AbstractHigh-resolution and multi-temporal impervious surface area maps are crucial for capturing rapidly developing urbanization patterns. However, the currently available relevant maps for the greater Mekong subregion suffer from coarse resolution and low accuracy. Addressing this issue, our study focuses on the development of accurate impervious surface area maps at 10-m resolution for this region for the period 2016–2022. To accomplish this, we present a new machine-learning framework implemented on the Google Earth Engine platform that merges Sentinel-1 Synthetic Aperture Radar images and Sentinel-2 Multispectral images to extract impervious surfaces. Furthermore, we also introduce a training sample migration strategy that eliminates the collection of additional training samples and automates multi-temporal impervious surface area mapping. Finally, we perform a quantitative assessment with validation samples interpreted from Google Earth. Results show that the overall accuracy and kappa coefficient of the final impervious surface area maps range from 92.75% to 92.93% and 0.854 to 0.857, respectively. This dataset provides comprehensive measurements of impervious surface coverage and configuration that will help to inform urban studies.
Analysis of compound health impacts of heatwave and COVID-19 in Korea from May to September in 2020
Authors: Park Haemin , Lee Sang-Min , Kim Woo Joong , Chae Yeora 
Published: September 2023

AbstractThe number of non-accidental deaths and heat-related illnesses due to the co-occurrence of heatwaves and COVID-19 has been identified to estimate compound health impacts between two risks. We have analyzed data from historical years (2013–2019) to calculate the baseline values of the number of non-accidental deaths and heat-related illness patients from May to September using a quasi-Poisson generalized linear model and compared them to data from 2020 in Korea. We also assessed the relative risk and absolute cumulative number of non-accidental deaths and heat-related illnesses in the summer of 2020 in Seoul, Daegu, and Gyeongnam region of Korea. In the Summer of 2020, Korea experienced 0.8% of non-accidental excess deaths, with the highest in August, and 46% of reduction was observed in heat-related throughout the study period, except in Daegu, where excess of heat-related illness occurred in August. The relative risk (RR) of non-accidental deaths at 33.1 °C, was 1.00 (CI 0.99–1.01) and 1.04 (CI 1.02–1.07) in 2013–2019 and 2020, respectively. The RR of heat-related illness at 33.1 °C, was 1.44 (CI 1.42–1.45) and 1.59 (CI 1.54–1.64) in 2013–2019 and 2020, respectively. The absolute cumulative trends of non-accidental deaths and heat-related illnesses were similar in the three regions, indicating increased non-accidental deaths and decreased heat-related illnesses at similar temperatures in 2020. During the COVID-19 pandemic, the fear of infection by the virus and the limited access to healthcare services led to changes in health-seeking behaviors. These results indicate social distancing could have had adverse impacts on other health conditions. A comprehensive health risk assessment is important when facing simultaneous risks, such as heatwaves and pandemics, in the implementation of effective countermeasures.
Automation of the control system for drying grain crops of the technological process for obtaining biodiesel fuels
Authors: Eremeeva Anzhelika M. , Ilyushin Yury V. 
Published: September 2023

AbstractProcess of grain drying is discussed by the authors, which is considered one of the preliminary stages in the technology of biodiesel production. The drying process has a number of disadvantages that affect the quality and cost of biodiesel fuel. The impossibility of uniform heating and maintaining the required temperature with minimal energy costs is considered one of the most important defects that deserve scientific research. The authors propose a method for changing the heating system and preheating raw materials, based on world experience. We carried out mathematical calculations, provided the change in the temperature field of the drying chamber over time, and we also performed industrial experiment. Based on our results we determined the optimal number of heating sources of raw materials, taking into account the dimensions of the drying chamber. The authors propose a technical solution with which a uniform temperature field can be obtained in the drying chamber. Thus, the uniformity of the chamber heating will be increased, and large operating costs associated with leakage of oil from the grains will be disappeared.
The benefits of early continuous renal replacement therapy in critically ill patients with acute kidney injury at high-altitude areas: a retrospective multi-center cohort study
Authors: Wang Bowen , Peng Mengjia , Wei Hui , Liu Chang , Wang Juan , Jiang Liheng , Fang Fei , Wang Yuliang , Shen Yuandi 
Published: September 2023

AbstractSevere hypoxia would aggravate the acute kidney injury (AKI) in high-altitude areas and continuous renal replacement therapy (CRRT) has been used to treat critically ill patients with AKI. However, the characteristics and outcomes of CRRT in critically ill patients at AKI in high altitudes and the optimal timing of CRRT initiation remain unclear. 1124 patients were diagnosed with AKI and treated with CRRT in the ICU, comprising a high-altitude group (n = 648) and low-altitude group (n = 476). Compared with the low-altitude group, patients with AKI at high altitude showed longer CRRT (4.8 vs. 3.7, P = 0.036) and more rapid progression of AKI stages (P < 0.01), but without any significant minor or major bleeding episodes (P > 0.05). Referring to the analysis of survival and kidney recovery curves, a higher mortality but a lower possibility of renal recovery was observed in the high-altitude group (P < 0.001). However, in the high-altitude group, the survival rate of early CRRT initiation was significantly higher than that of delayed CRRT initiation (P < 0.001). The findings showed poorer clinical outcomes in patients undergoing CRRT for AKI at high altitudes. CRRT at high altitudes was unlikely to increase the adverse events. Moreover, early CRRT initiation might reduce the mortality and promote renal recovery in high-altitude patients.
Detecting potential causal relationship between inflammatory bowel disease and rosacea using bi-directional Mendelian randomization
Authors: Li Min , He Si Xian , He Yuan Xiong , Hu Xiao Han , Zhou Zhou 
Published: September 2023

AbstractThe association between rosacea and inflammatory bowel disease (IBD) has been studied in previous observational studies. It is unclear, however, whether the association is causal or not. Independent genetic variants for IBD were chosen as instruments from published Genome-wide association studies (GWAS) studies involving 38,155 cases with an IBD diagnosis and 48,485 controls in order to investigate the causal effect of IBD on rosacea. Summarized data for rosacea were gathered from various GWAS studies that included 1195 cases and 211,139 controls without rosacea. Reverse-direction Mendelian randomization (MR) analysis was done to investigate the relationship between genetically proxied rosacea and IBD. With the use of the inverse variance-weighted (IVW), MR-Egger, and weighted median approaches, a 2-sample Mendelian randomization study was carried out. Analysis of heterogeneity and sensitivity was performed to examine the pleiotropy and robustness of effect estimates. The forward-direction of the MR study was to reveal that genetic predisposition to IBD including its two main subtypes: Crohn’s disease (CD) and ulcerative colitis (UC) was associated with an increased risk of rosacea. The reverse-direction MR analyses did not demonstrate that a genetic predisposition to rosacea was associated with total IBD, UC and CD. Our findings provided evidence for a causal impact of IBD, UC, and CD on rosacea, but not vice versa. The elevated incidence of rosacea in patients with IBD should be recognized by doctors to make an early diagnosis and initiate specialized therapy.
Efficacy of hydroxyapatite-based skull base reconstruction for intraoperative high-flow cerebrospinal fluid leakage performed by less-experienced surgeons
Authors: Hong Inseo , Kim Kyung Hwan , Seo Youngbeom , Choo Yoon-Hee , Lee Han-Joo , Kim Seon-Hwan 
Published: September 2023

AbstractCerebrospinal fluid (CSF) leakage after endoscopic skull base surgery remains a challenge despite multilayer reconstruction including nasoseptal flap (NSF) has become a standard technique. Injectable hydroxyapatite (HXA) has shown promising results to prevent CSF leakage. This study aimed to validate the efficacy of HXA-based skull base reconstruction performed by less-experienced neurosurgeons who had short-term clinical experiences as independent surgeons. Between March 2018 and November 2022, 41 patients who experienced intraoperative high-flow CSF leakage following endoscopic endonasal surgery at two independent tertiary institutions were enrolled. Skull base reconstruction was performed using conventional multilayer techniques combined with or without HXA. The primary outcome was postoperative CSF leakage. The surgical steps and nuances were described in detail. The most common pathology was craniopharyngioma. Injectable HXA was used in 22 patients (HXA group) and conventional techniques were performed in 19 patients (control group). The HXA group achieved a significantly lower incidence of postoperative CSF leakage than the control group (0% vs. 26.3%, p = 0.016). No HXA-related complications were observed. The use of injectable HXA in skull base reconstruction was highly effective and safe. This technique and its favorable results might be readily reproduced by less-experienced neurosurgeons.
Effects of movement congruence on motor resonance in early Parkinson’s disease
Authors: Gentile Eleonora , Brunetti Antonio , Ricci Katia , Vecchio Eleonora , Santoro Carlo , Sibilano Elena , Bevilacqua Vitoantonio , Iliceto Giovanni , Craighero Laila , de Tommaso Marina 
Published: September 2023

AbstractThe observation of action seems to involve the generation of the internal representation of that same action in the observer, a process named motor resonance (MR). The objective of this study was to verify whether an experimental paradigm of action observation in a laboratory context could elicit cortical motor activation in 21 early Parkinson’s disease (PD) patients compared to 22 controls. Participants were instructed to simply observe (observation-only session) or to respond (Time-to-contact detection session) at the instant the agent performed a grasping action toward a graspable or ungraspable object. We used functional near-infrared spectroscopy with 20 channels on the motor and premotor brain areas and event-related desynchronization of alpha-mu rhythm. In both groups, response times were more accurate in graspable than ungraspable object trials, suggesting that motor resonance is present in PD patients. In the Time-to-contact detection session, the oxyhemoglobin levels and alpha-mu desynchronization prevailed in the graspable object trials rather than in the ungraspable ones. This study demonstrates the preservation of MR mechanisms in early PD patients. The action observation finalized to a consequent movement can activate cortical networks in patients with early PD, suggesting early rehabilitation interventions taking into account specific observation paradigms preceding motor production.
Quantifying the impact of Wolbachia releases on dengue infection in Townsville, Australia
Authors: Ogunlade Samson T. , Adekunle Adeshina I. , Meehan Michael T. , McBryde Emma S. 
Published: September 2023

AbstractFrom October 2014 to February 2019, local authorities in Townsville, North Queensland, Australia continually introduced Wolbachia-infected mosquitoes to control seasonal outbreaks of dengue infection. In this study, we develop a mathematical modelling framework to estimate the effectiveness of this intervention as well as the relative dengue transmission rates of Wolbachia-infected and wild-type mosquitoes. We find that the transmission rate of Wolbachia-infected mosquitoes is reduced approximately by a factor of 20 relative to the uninfected wild-type population. In addition, the Townsville Wolbachia release program led to a 65% reduction in predicted dengue incidence during the release period and over 95% reduction in the 24 months that followed. Finally, to investigate the potential impact of other Wolbachia release programs, we use our estimates of relative transmissibility to calculate the relationship between the reproductive number of dengue and the proportion of Wolbachia-infected mosquitoes in the vector population.
Global increase in destructive potential of extratropical transition events in response to greenhouse warming
Authors: Cheung Hung Ming , Chu Jung-Eun 
Published: September 2023

AbstractWhen tropical cyclones (TCs) move to the mid-latitudes, they oftentimes undergo extratropical transition (ET) by which they lose their symmetry and warm-core characteristics. Upon transforming into extratropical cyclones (ETCs), they tend to impact larger areas and thus larger populations. In light of the increased TC intensity due to global warming identified in previous studies, here we examine its effect on the frequency and destructiveness of ET events globally using a high-resolution fully coupled Earth System model (0.25° for atmosphere; 0.1° for ocean) prescribed with present-day, doubling, and quadrupling CO2 concentrations. Our findings indicate that ETCs originated from the tropics with higher destructiveness (indicated by integrated kinetic energy) become more frequent in response to greenhouse warming, although the number of ET events does not change significantly. The key factor in the change in the destructiveness of ETCs is the increase in wind speed and the high-wind area at ET. Despite the uncertainty in the Northern Hemisphere, our results underscore the necessity for climate resilience in the mid-latitudes against global warming.
The mechanism of boreal summer SSTA phase-locking in the far eastern Pacific
Authors: Chen Han-Ching , Jin Fei-Fei 
Published: September 2023

AbstractIn observations, the boreal winter El Niño—Southern Oscillation (ENSO) phase-locking phenomenon is evident in the central-eastern Pacific. In the far eastern equatorial Pacific (FEP) and South American coastal regions, however, the peak of sea surface temperature anomalies (SSTA) tends to occur in the boreal summer, with fewer winter peak events. By separating the direct ENSO forcing from the FEP SSTA, we found that the summer peak preference is contributed by the residual SSTA component, while the ENSO forcing provides only a small probability of winter peak. The dynamics of FEP SSTA phase-locking in observations and its biases in the climate models are investigated by adopting a linear stochastic-dynamical model. In observations, the summer phase-locking of FEP SSTA is controlled by the seasonal modulation of the SSTA damping process. In contrast, in the climate models the strength of FEP SSTA phase-locking is much smaller than observed due to the overly negative SSTA damping rate.
Neural encoding of instantaneous kinematics of eye-head gaze shifts in monkey superior Colliculus
Authors: van Opstal A. John 
Published: September 2023

AbstractThe midbrain superior colliculus is a crucial sensorimotor stage for programming and generating saccadic eye-head gaze shifts. Although it is well established that superior colliculus cells encode a neural command that specifies the amplitude and direction of the upcoming gaze-shift vector, there is controversy about the role of the firing-rate dynamics of these neurons during saccades. In our earlier work, we proposed a simple quantitative model that explains how the recruited superior colliculus population may specify the detailed kinematics (trajectories and velocity profiles) of head-restrained saccadic eye movements. We here show that the same principles may apply to a wide range of saccadic eye-head gaze shifts with strongly varying kinematics, despite the substantial nonlinearities and redundancy in programming and execute rapid goal-directed eye-head gaze shifts to peripheral targets. Our findings could provide additional evidence for an important role of the superior colliculus in the optimal control of saccades.
The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse
Authors: Fernandez-Fuente Gonzalo , Overmyer Katherine A. , Lawton Alexis J. , Kasza Ildiko , Shapiro Samantha L. , Gallego-Muñoz Patricia , Coon Joshua J. , Denu John M. , Alexander Caroline M. , Puglielli Luigi 
Published: September 2023

AbstractCytosolic citrate is imported from the mitochondria by SLC25A1, and from the extracellular milieu by SLC13A5. In the cytosol, citrate is used by ACLY to generate acetyl-CoA, which can then be exported to the endoplasmic reticulum (ER) by SLC33A1. Here, we report the generation of mice with systemic overexpression (sTg) of SLC25A1 or SLC13A5. Both animals displayed increased cytosolic levels of citrate and acetyl-CoA; however, SLC13A5 sTg mice developed a progeria-like phenotype with premature death, while SLC25A1 sTg mice did not. Analysis of the metabolic profile revealed widespread differences. Furthermore, SLC13A5 sTg mice displayed increased engagement of the ER acetylation machinery through SLC33A1, while SLC25A1 sTg mice did not. In conclusion, our findings point to different biological responses to SLC13A5- or SLC25A1-mediated import of citrate and suggest that the directionality of the citrate/acetyl-CoA pathway can transduce different signals.