bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ppm1d truncating mutations promote the development of genotoxic stress-induced AML
Authors: Burocziova Monika , Danek Petr , Oravetzova Anna , Chalupova Zuzana , Alberich-Jorda Meritxell , Macurek Libor 
Published: September 2023

AbstractHematopoietic stem cells (HSCs) ensure blood cell production during the life-time of an organism, and to do so they need to balance self-renewal, proliferation, differentiation, and migration in a steady state as well as in response to stress or injury. Importantly, aberrant proliferation of HSCs leads to hematological malignancies, and thus, tight regulation by various tumor suppressor pathways, including p53, is essential. Protein phosphatase magnesium-dependent 1 delta (PPM1D) is a negative regulator of p53 and promotes cell survival upon induction of genotoxic stress. Truncating mutations in the last exon of PPM1D lead to the production of a stable, enzymatically active protein and are commonly associated with clonal hematopoiesis. Using a transgenic mouse model, we demonstrate that truncated PPM1D reduces self-renewal of HSCs in basal conditions but promotes the development of aggressive AML after exposure to ionizing radiation. Inhibition of PPM1D suppressed the colony growth of leukemic stem and progenitor cells carrying the truncated PPM1D, and remarkably, it provided protection against irradiation-induced cell growth. Altogether, we demonstrate that truncated PPM1D affects HSC maintenance, disrupts normal hematopoiesis, and that its inhibition could be beneficial in the context of therapy-induced AML.
Deciphering local and regional hydroclimate resolves contradicting evidence on the Asian monsoon evolution
Authors: Wolf Annabel , Ersek Vasile , Braun Tobias , French Amanda D. , McGee David , Bernasconi Stefano M. , Skiba Vanessa , Griffiths Michael L. , Johnson Kathleen R. , Fohlmeister Jens , Breitenbach Sebastian F. M. , Pausata Francesco S. R. , Tabor Clay R. , Longman Jack , Roberts William H. G. , Chandan Deepak , Peltier W. Richard , Salzmann Ulrich , Limbert Deborah , Trinh Hong Quan , Trinh Anh Duc 
Published: September 2023

AbstractThe winter and summer monsoons in Southeast Asia are important but highly variable sources of rainfall. Current understanding of the winter monsoon is limited by conflicting proxy observations, resulting from the decoupling of regional atmospheric circulation patterns and local rainfall dynamics. These signals are difficult to decipher in paleoclimate reconstructions. Here, we present a winter monsoon speleothem record from Southeast Asia covering the Holocene and find that winter and summer rainfall changed synchronously, forced by changes in the Pacific and Indian Oceans. In contrast, regional atmospheric circulation shows an inverse relation between winter and summer controlled by seasonal insolation over the Northern Hemisphere. We show that disentangling the local and regional signal in paleoclimate reconstructions is crucial in understanding and projecting winter and summer monsoon variability in Southeast Asia.
Model-free tracking control of complex dynamical trajectories with machine learning
Authors: Zhai Zheng-Meng , Moradi Mohammadamin , Kong Ling-Wei , Glaz Bryan , Haile Mulugeta , Lai Ying-Cheng 
Published: September 2023

AbstractNonlinear tracking control enabling a dynamical system to track a desired trajectory is fundamental to robotics, serving a wide range of civil and defense applications. In control engineering, designing tracking control requires complete knowledge of the system model and equations. We develop a model-free, machine-learning framework to control a two-arm robotic manipulator using only partially observed states, where the controller is realized by reservoir computing. Stochastic input is exploited for training, which consists of the observed partial state vector as the first and its immediate future as the second component so that the neural machine regards the latter as the future state of the former. In the testing (deployment) phase, the immediate-future component is replaced by the desired observational vector from the reference trajectory. We demonstrate the effectiveness of the control framework using a variety of periodic and chaotic signals, and establish its robustness against measurement noise, disturbances, and uncertainties.
Local flux coordination and global gene expression regulation in metabolic modeling
Authors: Li Gaoyang , Liu Li , Du Wei , Cao Huansheng 
Published: September 2023

AbstractGenome-scale metabolic networks (GSMs) are fundamental systems biology representations of a cell’s entire set of stoichiometrically balanced reactions. However, such static GSMs do not incorporate the functional organization of metabolic genes and their dynamic regulation (e.g., operons and regulons). Specifically, there are numerous topologically coupled local reactions through which fluxes are coordinated; the global growth state often dynamically regulates many gene expression of metabolic reactions via global transcription factor regulators. Here, we develop a GSM reconstruction method, Decrem, by integrating locally coupled reactions and global transcriptional regulation of metabolism by cell state. Decrem produces predictions of flux and growth rates, which are highly correlated with those experimentally measured in both wild-type and mutants of three model microorganismsEscherichia coli,Saccharomyces cerevisiae, andBacillus subtilisunder various conditions. More importantly, Decrem can also explain the observed growth rates by capturing the experimentally measured flux changes between wild-types and mutants. Overall, by identifying and incorporating locally organized and regulated functional modules into GSMs, Decrem achieves accurate predictions of phenotypes and has broad applications in bioengineering, synthetic biology, and microbial pathology.
Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi
Authors: Duhamel Marine , Hood Michael E. , Rodríguez de la Vega Ricardo C. , Giraud Tatiana 
Published: September 2023

AbstractIn the absence of recombination, the number of transposable elements (TEs) increases due to less efficient selection, but the dynamics of such TE accumulations are not well characterized. Leveraging a dataset of 21 independent events of recombination cessation of different ages in mating-type chromosomes of Microbotryum fungi, we show that TEs rapidly accumulated in regions lacking recombination, but that TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 million years following recombination suppression. The same TE superfamilies have expanded in independently evolved non-recombining regions, in particular rolling-circle replication elements (Helitrons). Long-terminal repeat (LTR) retrotransposons of the Copia and Ty3 superfamilies also expanded, through transposition bursts (distinguished from gene conversion based on LTR divergence), with both non-recombining regions and autosomes affected, suggesting that non-recombining regions constitute TE reservoirs. This study improves our knowledge of genome evolution by showing that TEs can accumulate through bursts, following non-linear decelerating dynamics.
N-terminal α-amino SUMOylation of cofilin-1 is critical for its regulation of actin depolymerization
Authors: Weng Weiji , Gu Xiaokun , Yang Yang , Zhang Qiao , Deng Qi , Zhou Jie , Cheng Jinke , Zhu Michael X. , Feng Junfeng , Huang Ou , Li Yong 
Published: September 2023

AbstractSmall ubiquitin-like modifier (SUMO) typically conjugates to target proteins through isopeptide linkage to the ε-amino group of lysine residues. This posttranslational modification (PTM) plays pivotal roles in modulating protein function. Cofilins are key regulators of actin cytoskeleton dynamics and are well-known to undergo several different PTMs. Here, we show that cofilin-1 is conjugated by SUMO1 both in vitro and in vivo. Using mass spectrometry and biochemical and genetic approaches, we identify the N-terminal α-amino group as the SUMO-conjugation site of cofilin-1. Common to conventional SUMOylation is that the N-α-SUMOylation of cofilin-1 is also mediated by SUMO activating (E1), conjugating (E2), and ligating (E3) enzymes and reversed by the SUMO deconjugating enzyme, SENP1. Specific to the N-α-SUMOylation is the physical association of the E1 enzyme to the substrate, cofilin-1. Using F-actin co-sedimentation and actin depolymerization assays in vitro and fluorescence staining of actin filaments in cells, we show that the N-α-SUMOylation promotes cofilin-1 binding to F-actin and cofilin-induced actin depolymerization. This covalent conjugation by SUMO at the N-α amino group of cofilin-1, rather than at an internal lysine(s), serves as an essential PTM to tune cofilin-1 function during regulation of actin dynamics.
DNA methylation profiles in individuals with rare, atypical 7q11.23 CNVs correlate with GTF2I and GTF2IRD1 copy number
Authors: Strong Emma , Mervis Carolyn B. , Tam Elaine , Morris Colleen A. , Klein-Tasman Bonita P. , Velleman Shelley L. , Osborne Lucy R. 
Published: September 2023

AbstractWilliams-Beuren syndrome (WBS) and 7q11.23 duplication syndrome (Dup7) are rare neurodevelopmental disorders caused by deletion and duplication of a 1.5 Mb region that includes at least five genes with a known role in epigenetic regulation. We have shown that CNV of this chromosome segment causes dose-dependent, genome-wide changes in DNA methylation, but the specific genes driving these changes are unknown. We measured genome-wide whole blood DNA methylation in six participants with atypical CNV of 7q11.23 (three with deletions and three with duplications) using the Illumina HumanMethylation450k array and compared their profiles with those from groups of individuals with classic WBS or classic Dup7 and with typically developing (TD) controls. Across the top 1000 most variable positions we found that only the atypical rearrangements that changed the copy number of GTF2IRD1 and/or GTF2I (coding for the TFII-IRD1 and TFII-I proteins) clustered with their respective syndromic cohorts. This finding was supported by results from hierarchical clustering across a selection of differentially methylated CpGs, in addition to pyrosequencing validation. These findings suggest that CNV of the GTF2I genes at the telomeric end of the 7q11.23 interval is a key contributor to the large changes in DNA methylation that are seen in blood DNA from our WBS and Dup7 cohorts, compared to TD controls. Our findings suggest that members of the TFII-I protein family are involved in epigenetic processes that alter DNA methylation on a genome-wide level.
A pseudoproxy emulation of the PAGES 2k database using a hierarchy of proxy system models
Authors: Zhu Feng , Emile-Geay Julien , Anchukaitis Kevin J. , McKay Nicholas P. , Stevenson Samantha , Meng Zilu 
Published: September 2023

AbstractPaleoclimate reconstructions are now integral to climate assessments, yet the consequences of using different methodologies and proxy data require rigorous benchmarking. Pseudoproxy experiments (PPEs) provide a tractable and transparent test bed for evaluating climate reconstruction methods and their sensitivity to aspects of real-world proxy networks. Here we develop a dataset that leverages proxy system models (PSMs) for this purpose, which emulates the essential physical, chemical, biological, and geological processes that translate climate signals into proxy records, making these synthetic proxies more relevant to the real world. We apply a suite of PSMs to emulate the widely-used PAGES 2k dataset, including realistic spatiotemporal sampling and error structure. A hierarchical approach allows us to produce many variants of this base dataset, isolating the impact of sampling bias in time and space, representation error, sampling error, and other assumptions. Combining these various experiments produces a rich dataset (“pseudoPAGES2k”) for many applications. As an illustration, we show how to conduct a PPE with this dataset based on emerging climate field reconstruction techniques.
Spatiotemporal trends of carbon stock in wood and bamboo products in China during 1987–2020
Authors: Zhang Luyang , Zhang Shuaikun , Chen Dongdong , Li Tianrun , Wang Shiyi , Xu Zhiyuan , Wang Yuchao , Liu Zhihua , Zhang Shaoliang 
Published: September 2023

AbstractHarvested wood/bamboo products (HWP/HBP) constitute a large global carbon stock. However, the contribution of HBP to carbon stocks has been neglected in mixed wood and bamboo data, especially in China. Therefore, the production approach and the first-order decay method were used to estimate the spatiotemporal carbon stock change in HWP/HBP based on provincial production data from the China Forestry Statistical Yearbooks for 1987–2020. The results showed that China’s total carbon stocks of HWP and HBP were 328.7 teragram carbon (TgC) and 129.7 TgC between 1987 and 2020. Of this, the HWP carbon stock was mainly sourced from three provinces across the north and south: Guangxi (60.8 TgC), Heilongjiang (37.2 TgC), and Fujian (24.2 TgC), and HBP carbon stock was mainly sourced from three southern provinces: Fujian (33.4 TgC), Guangxi (20.3 TgC), and Zhejiang (13.7 TgC). The proportion of the HBP carbon stock in the total carbon stock increased from 20% in 2010 to 28% in 2020, indicating that bamboo products play an important role in the accumulation of carbon stocks in China. The differences in contributions to spatiotemporal trends between the provinces provide more specific information to make precise decisions about forest management and carbon sequestration.
Quantum computation at the edge of a disordered Kitaev honeycomb lattice
Authors: Timoshuk Igor , Tikhonov Konstantin , Makhlin Yuriy 
Published: September 2023

AbstractWe analyze propagation of quantum information along chiral Majorana edge states in two-dimensional topological materials. The use of edge states may facilitate the braiding operation, an important ingredient in topological quantum computations. For the edge of the Kitaev honeycomb model in a topological phase, we discuss how the edge states can participate in quantum-information processing, and consider a two-qubit logic gate between distant external qubits coupled to the edge. Here we analyze the influence of disorder and noise on properties of the edge states and quantum-gate fidelity. We find that realistically weak disorder does not prevent one from implementation of a high-fidelity operation via the edge.
A novel nomogram predicting overt hepatic encephalopathy after transjugular intrahepatic portosystemic shunt in portal hypertension patients
Authors: Liao Yong , Zhang Lin , Wang Ji-tao , Yue Zhen-dong , Fan Zhen-hua , Wu Yi-fan , Zhang Yu , Dong Cheng-bin , Wang Xiu-qi , Cui Ting , Meng Ming-ming , Bao Li , Chen Shu-bo , Liu Fu-quan , Wang Lei 
Published: September 2023

AbstractWe aim to develop a nomogram to predict overt hepatic encephalopathy (OHE) after transjugular intrahepatic portosystemic shunt (TIPS) in patients with portal hypertension, according to demographic/clinical indicators such as age, creatinine, blood ammonia, indocyanine green retention rate at 15 min (ICG-R15) and percentage of Portal pressure gradient (PPG) decline. In this retrospective study, 296 patients with portal hypertension who received elective TIPS in Beijing Shijitan Hospital from June 2018 to June 2020 were included. These patients were randomly divided into a training cohort (n = 207) and a validation cohort (n = 89). According to the occurrence of OHE, patients were assigned to OHE group and non-OHE group. Both univariate and multivariate analyses were performed to determine independent variables for predicting OHE after TIPS. Accordingly, receiver operating characteristic (ROC) curve, calibration curve, and decision curve analysis (DCA) were used to compare the accuracy and superiority of a novel model with conventional Child–Pugh and MELD scoring model. Age (OR 1.036, 95% CI 1.002–1.070, p = 0.037), Creatinine (OR 1.011, 95% CI 1.003–1.019, p = 0.009), Blood ammonia (OR 1.025, 95% CI 1.006–1.044, p = 0.011), ICG-R15 (OR 1.030, 95% CI 1.009–1.052, p = 0.004) and Percentage decline in PPG (OR 1.068, 95% CI 1.029–1.109, p = 0.001) were independent risk factors for OHE after TIPS using multifactorial analysis. A nomogram was constructed using a well-fit calibration curve for each of these five covariates. When compared to Child–Pugh and MELD score, this new nomogram has a better predictive value (C-index = 0.828, 95% CI 0.761–0.896). Consistently, this finding was reproduceable in validation cohort and confirmed with DCA. A unique nomogram was developed to predict OHE after TIPS in patients with PHT, with a high prediction sensitivity and specificity performance than commonly applied scoring systems.
Telemedicine retinopathy of prematurity severity score (TeleROP-SS) versus modified activity score (mROP-ActS) retrospective comparison in SUNDROP cohort
Authors: Xu Christine L. , Adu-Brimpong Joel , Moshfeghi Henry P. , Rosenblatt Tatiana R. , Yu Michael D. , Ji Marco H. , Wang Sean K. , Zaidi Moosa , Ghoraba Hashem , Michalak Suzanne , Callaway Natalia F. , Kumm Jochen , Nudleman Eric , Wood Edward H. , Patel Nimesh A. , Stahl Andreas , Lepore Domenico , Moshfeghi Darius M. 
Published: September 2023

AbstractIdentifying and planning treatment for retinopathy of prematurity (ROP) using telemedicine is becoming increasingly ubiquitous, necessitating a grading system to help caretakers of at-risk infants gauge disease severity. The modified ROP Activity Scale (mROP-ActS) factors zone, stage, and plus disease into its scoring system, addressing the need for assessing ROP’s totality of binocular burden via indirect ophthalmoscopy. However, there is an unmet need for an alternative score which could facilitate ROP identification and gauge disease improvement or deterioration specifically on photographic telemedicine exams. Here, we propose such a system (Telemedicine ROP Severity Score [TeleROP-SS]), which we have compared against the mROP-ActS. In our statistical analysis of 1568 exams, we saw that TeleROP-SS was able to return a score in all instances based on the gradings available from the retrospective SUNDROP cohort, while mROP-ActS obtained a score of 80.8% in right eyes and 81.1% in left eyes. For treatment-warranted ROP (TW-ROP), TeleROP-SS obtained a score of 100% and 95% in the right and left eyes respectively, while mROP-ActS obtained a score of 70% and 63% respectively. The TeleROP-SS score can identify disease improvement or deterioration on telemedicine exams, distinguish timepoints at which treatments can be given, and it has the adaptability to be modified as needed.
Selective separation of chlorophyll-a using recyclable hybrids based on Zn-MOF@cellulosic fibers
Authors: Emam Hossam E. , Ahmed Hanan B. , El-Shahat Mahmoud , Abdel-Gawad Hassan , Abdelhameed Reda M. 
Published: September 2023

AbstractChlorophyll-a as pigments, exist in the green organelles for plants that act in photosynthesis. Different studies were considered with demonstration of an effective separation technique of Chlorophyll-a without decomposition; however, the reported methods were disadvantageous with expensiveness and low quantum yield. The current work uniquely represents an investigative method for the separation of Chlorophyll-a from spinach extract using cellulosic hybrids based on ZIF-8@cellulosic fibers (Zn-zeolitic imidazolate frameworks@cellulosic fibers) as a cost effective and recyclable absorbents. To obtain hybrids, ZIF-8 was in-situ prepared over the cellulosic fibers (bamboo, modal and cotton). The untreated and treated fibers were well characterized via FTIR, SEM, EDX, XRD, in order to approve the successive impregnation of ZIF-8. Whereas, the microscopic images showed that, microcrystalline ZIF-8 rods with length of 1.3–4.4 µm were grown over the cellulosic fibers. The obtained hybrids and the untreated fibers were exploited in the separation of Chlorophyll-a via the adsorption/desorption process. The chlorophyll-adsorption was followed Langmuir isotherm and pseudo-second order model. The Langmuir maximum capacities of Chlorophyll-a onto hybrids were followed the order of ZIF-8@cotton (583.6 mg/g) > ZIF-8@modal (561.3 mg/g) > ZIF-8@bamboo (528.7 mg/g). After incorporation of ZIF-8, the maximum adsorption capacities of cellulosic fibers were enhanced by 1.4–1.9 times. Adsorption of chlorophyll onto the applied hybrids was lowered by 27–28%, after five repetitive washing cycles. The data summarized that; chlorophyll was effectively separated by the synthesized ZIF-8@cellulosic fibers hybrids, whereas, the prepared hybrids showed good reusability for application on wider scaled purposes.
A survey on the awareness, current management, and barriers for non-alcoholic fatty liver disease among the general Korean population
Authors: Lee Jun-Hyuk , Jung Jang Han , Park Huiyul , Oh Joo Hyun , Ahn Sang Bong , Yoon Eileen Laurel , Jun Dae Won 
Published: September 2023

AbstractNon-alcoholic fatty liver disease (NAFLD) is often diagnosed incidentally during medical evaluation for diseases other than liver disease or during health checkups. This study aimed to investigate the awareness, current status, and barriers to the management of NAFLD in the general population. This cross-sectional study used an online survey, which consisted of 3-domain and 18-item questionnaires. The content validity index for each item of the questionnaire was rated above 0.80. Most respondents (72.8%) reported having heard of the term ‘NAFLD’, and a large proportion of the general population (85.7%) recognized the possibility of developing fatty liver without consuming alcohol. Awareness of the terminology of NAFLD and that NAFLD is a disease that needs to be managed is relatively high. However, the knowledge that NAFLD can progress to end-stage liver disease and new cardiovascular diseases is lacking. Only 25.7% of the general population is aware that NAFLD increases the incidence of heart and cerebrovascular diseases. Only 44.7% of those who were incidentally diagnosed during a health check-up were provided with any specific guidance on NAFLD, and more than half (55.3%) were not provided with education or guidance on NAFLD or did not remember it. Only 40.2% of people diagnosed with NAFLD incidentally visited a clinic. The reason for not visiting a clinic for the evaluation of NAFLD varied greatly depending on sex and age group. Only 40.2% of patients visited the clinic after being diagnosed with NAFLD. The reasons for not visiting the clinic after NAFLD diagnosis differed significantly according to sex and age.