bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the genetic and genomic connection underlying neurodegeneration with brain iron accumulation and the risk for Parkinson’s disease
Authors: Alvarez Jerez Pilar , Alcantud Jose Luis , de los Reyes-Ramírez Lucia , Moore Anni , Ruz Clara , Vives Montero Francisco , Rodriguez-Losada Noela , Saini Prabhjyot , Gan-Or Ziv , Alvarado Chelsea X. , Makarious Mary B. , Billingsley Kimberley J. , Blauwendraat Cornelis , Noyce Alastair J. , Singleton Andrew B. , Duran Raquel , Bandres-Ciga Sara 
Published: April 2023

AbstractNeurodegeneration with brain iron accumulation (NBIA) represents a group of neurodegenerative disorders characterized by abnormal iron accumulation in the brain. In Parkinson’s Disease (PD), iron accumulation is a cardinal feature of degenerating regions in the brain and seems to be a key player in mechanisms that precipitate cell death. The aim of this study was to explore the genetic and genomic connection between NBIA and PD. We screened for known and rare pathogenic mutations in autosomal dominant and recessive genes linked to NBIA in a total of 4481 PD cases and 10,253 controls from the Accelerating Medicines Partnership Parkinsons’ Disease Program and the UKBiobank. We examined whether a genetic burden of NBIA variants contributes to PD risk through single-gene, gene-set, and single-variant association analyses. In addition, we assessed publicly available expression quantitative trait loci (eQTL) data through Summary-based Mendelian Randomization and conducted transcriptomic analyses in blood of 1886 PD cases and 1285 controls. Out of 29 previously reported NBIA screened coding variants, four were associated with PD risk at a nominalpvalue < 0.05. No enrichment of heterozygous variants in NBIA-related genes risk was identified in PD cases versus controls. Burden analyses did not reveal a cumulative effect of rare NBIA genetic variation on PD risk. Transcriptomic analyses suggested thatDCAF17is differentially expressed in blood from PD cases and controls. Due to low mutation occurrence in the datasets and lack of replication, our analyses suggest that NBIA and PD may be separate molecular entities.
Monitoring the impact of climate extremes and COVID-19 on statewise sentiment alterations in water pollution complaints
Authors: Liu Anqi , Kam Jonghun , Kwon Sae Yun , Shao Wanyun 
Published: April 2023

AbstractThe COVID-19 pandemic and associated prevention policies can directly or indirectly alter the sentiment of individuals while registering water pollution complaints, but observational evidence remains limited. Here, we conducted a sentiment analysis on over 10,000 water pollution complaints from residents in Alabama, USA (2012–2021) to better understand how and to what extent COVID-19 has altered emotion (polarity score-based) and attitude (subjectivity) of water pollution complaints. We found that the 2017 state-wise drought significantly increased the percentage of negative water pollution complaints by +35%, with no significant alternation in attitude before the COVID-19 pandemic. Since COVID-19, the percentage of negative and subjective water pollution complaints significantly decreased and increased by −30 and +20%, respectively, and these sentiment alternations were maintained by 2021. This study provides a new direction for environmental governance and management, requiring a timely response to changes in the public’s emotions and attitudes during the next climate extremes and pandemics.
Dynamic antagonism between key repressive pathways maintains the placental epigenome
Authors: Weigert Raha , Hetzel Sara , Bailly Nina , Haggerty Chuck , Ilik Ibrahim A. , Yung Philip Yuk Kwong , Navarro Carmen , Bolondi Adriano , Kumar Abhishek Sampath , Anania Chiara , Brändl Björn , Meierhofer David , Lupiáñez Darío G. , Müller Franz-Josef , Aktas Tugce , Elsässer Simon J. , Kretzmer Helene , Smith Zachary D. , Meissner Alexander 
Published: April 2023

AbstractDNA and Histone 3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb repressive complexes regulate the unmethylated CpG-rich promoters of developmental genes. In contrast to this general framework, the extra-embryonic lineages display non-canonical, globally intermediate DNA methylation levels, including disruption of local Polycomb domains. Here, to better understand this unusual landscape’s molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse trophoblast stem cells. We find that the extra-embryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized molecular appearance, our data point to a highly controlled equilibrium between counteracting repressors within extra-embryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.
CD-CODE: crowdsourcing condensate database and encyclopedia
Authors: Rostam Nadia , Ghosh Soumyadeep , Chow Chi Fung Willis , Hadarovich Anna , Landerer Cedric , Ghosh Rajat , Moon HongKee , Hersemann Lena , Mitrea Diana M. , Klein Isaac A. , Hyman Anthony A. , Toth-Petroczy Agnes 
Published: April 2023

AbstractThe discovery of biomolecular condensates transformed our understanding of intracellular compartmentalization of molecules. To integrate interdisciplinary scientific knowledge about the function and composition of biomolecular condensates, we developed the crowdsourcing condensate database and encyclopedia (cd-code.org). CD-CODE is a community-editable platform, which includes a database of biomolecular condensates based on the literature, an encyclopedia of relevant scientific terms and a crowdsourcing web application. Our platform will accelerate the discovery and validation of biomolecular condensates, and facilitate efforts to understand their role in disease and as therapeutic targets.
Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+
Authors: Zou Roger S. , Liu Yang , Gaido Oscar E. Reyes , Konig Maximilian F. , Mog Brian J. , Shen Leo L. , Aviles-Vazquez Franklin , Marin-Gonzalez Alberto , Ha Taekjip 
Published: April 2023

AbstractDiscovery of off-target CRISPR–Cas activity in patient-derived cells and animal models is crucial for genome editing applications, but currently exhibits low sensitivity. We demonstrate that inhibition of DNA-dependent protein kinase catalytic subunit accumulates the repair protein MRE11 at CRISPR–Cas-targeted sites, enabling high-sensitivity mapping of off-target sites to positions of MRE11 binding using chromatin immunoprecipitation followed by sequencing. This technique, termed DISCOVER-Seq+, discovered up to fivefold more CRISPR off-target sites in immortalized cell lines, primary human cells and mice compared with previous methods. We demonstrate applicability to ex vivo knock-in of a cancer-directed transgenic T cell receptor in primary human T cells and in vivo adenovirus knock-out of cardiovascular risk gene PCSK9 in mice. Thus, DISCOVER-Seq+ is, to our knowledge, the most sensitive method to-date for discovering off-target genome editing in vivo.
Characterizing uncertainty in Community Land Model version 5 hydrological applications in the United States
Authors: Yan Hongxiang , Sun Ning , Eldardiry Hisham , Thurber Travis B. , Reed Patrick M. , Malek Keyvan , Gupta Rohini , Kennedy Daniel , Swenson Sean C. , Wang Linying , Li Dan , Vernon Chris R. , Burleyson Casey D. , Rice Jennie S. 
Published: April 2023

AbstractLand surface models such as the Community Land Model Version 5 (CLM5) are essential tools for simulating the behavior of the terrestrial system. Despite the extensive application of CLM5, limited attention has been paid to the underlying uncertainties associated with its hydrological parameters and how these uncertainties affect water resource applications. To address this long-standing issue, we use five meteorological datasets to conduct a comprehensive hydrological parameter uncertainty characterization of CLM5 over the hydroclimatic gradients of the conterminous United States. Key datasets produced from the uncertainty characterization experiment include: a benchmark dataset of CLM5 default hydrological performance, parameter sensitivities for 28 hydrological metrics, and large-ensemble outputs for CLM5 hydrological predictions. The presented datasets will assist CLM5 calibration and support broad applications, such as evaluating drought and flood vulnerabilities. The datasets can be used to identify the hydroclimatological conditions under which parametric uncertainties demonstrate substantial effects on hydrological predictions and clarify where further investigations are needed to understand how hydrological prediction uncertainties interact with other Earth system processes.
The Materials Provenance Store
Authors: Statt Michael J. , Rohr Brian A. , Guevarra Dan , Suram Santosh K. , Morrell Thomas E. , Gregoire John M. 
Published: April 2023

AbstractWe present a database resulting from high throughput experimentation, primarily on metal oxide solid state materials. The central relational database, the Materials Provenance Store (MPS), manages the metadata and experimental provenance from acquisition of raw materials, through synthesis, to a broad range of materials characterization techniques. Given the primary research goal of materials discovery of solar fuels materials, many of the characterization experiments involve electrochemistry, along with optical, structural, and compositional characterizations. The MPS is populated with all information required for executing common data queries, which typically do not involve direct query of raw data. The result is a database file that can be distributed to users so that they can independently execute queries and subsequently download the data of interest. We propose this strategy as an approach to manage the highly heterogeneous and distributed data that arises from materials science experiments, as demonstrated by the management of over 30 million experiments run on over 12 million samples in the present MPS release.
Contribution of serum lipids and cholesterol cellular metabolism in lung cancer development and progression
Authors: Hartmann Philipp , Trufa Denis I. , Hohenberger Katja , Tausche Patrick , Trump Sonja , Mittler Susanne , Geppert Carol I. , Rieker Ralf J. , Schieweck Oliver , Sirbu Horia , Hartmann Arndt , Finotto Susetta 
Published: April 2023

AbstractNeoplasms of the lungs are the leading cause of cancer incidence and mortality worldwide. Although immunotherapy has increased the overall survival of patients with lung cancer, there is the need to improve this treatment. At this regard, blood lipid levels are thought to be linked to cancer risk and thus a preventive intervention through regulation of the nutrition of patients with lung cancer is gaining much attention. In this study, we therefore asked about the contribution of serum lipids and cholesterol cellular metabolism in lung cancer development and progression. We measured different serum lipids and analyzed cholesterol synthesis enzymes 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGCR) and acetyl-coenzyme A cholesterol acetyltransferase 1 (ACAT1) as well as the cholesterol cellular export protein ATP-binding cassette (ABC) A-1 mRNA by quantitative PCR (qPCR) in the control and tumoral regions of post-surgery lung tissues to analyze the accumulation of cholesterol in cancer cells in a cohort of patients with lung adenocarcinoma (LUAD). We found that triglycerides in serum directly correlated with the body mass index (BMI) in patients with LUAD. By contrast, we found that high-density lipoprotein (HDL) cholesterol inversely correlated with the BMI, C-reactive protein (CRP) and overall survival and total cholesterol inversely correlated with the tumor diameter, serum CRP and overall survival in these LUAD patients. Functionally, the role of cholesterol is indispensable for the growth and development of normal animal cells where it is tightly regulated. Excess of cellular cholesterol regulated by HMGCR is converted to cholesteryl esters by the enzyme ACAT1 and exported extracellularly by the cholesterol transporter ABCA1. Here we found HMGCR and ACAT1 upregulated and ABCA1 downregulated in the lung’s tumoral region of our LUAD cohort, indicating cholesterol dysregulated cellular export in lung tumor cells.
A global analysis of the effectiveness of policy responses to COVID-19
Authors: Agyapon-Ntra Kwadwo , McSharry Patrick E. 
Published: April 2023

AbstractGovernments implemented many non-pharmaceutical interventions (NPIs) to suppress the spread of COVID-19 with varying results. In this paper, country-level daily time series from Our World in Data facilitates a global analysis of the propagation of the virus, policy responses and human mobility patterns. High death counts and mortality ratios influence policy compliance levels. Evidence of long-term fatigue was found with compliance dropping from over 85% in the first half of 2020 to less than 40% at the start of 2021, driven by factors such as economic necessity and optimism coinciding with vaccine effectiveness. NPIs ranged from facial coverings to restrictions on mobility, and these are compared using an empirical assessment of their impact on the growth rate of case numbers. Masks are the most cost-effective NPI currently available, delivering four times more impact than school closures, and approximately double that of other mobility restrictions. Gathering restrictions were the second most effective. International travel controls and public information campaigns had negligible effects. Literacy rates and income support played key roles in maintaining compliance. A 10% increase in literacy rate was associated with a 3.2% increase in compliance, while income support of greater than half of previous earnings increased compliance by 4.8%.
Textile dual-band NFC-A4WP (13.56–6.78 MHz) combiner for wireless energy and data transmission for connected clothing
Authors: Garnier Baptiste , Mariage Philippe , Rault François , Cochrane Cédric , Koncar Vladan 
Published: April 2023

AbstractAn original fully textile combiner is proposed to power supply sensors close to a body with only one centralized source of energy like a smartphone, for instance. A solution is provided for taking into account the requirements of an industrial production process that need to minimize needle movements during an embroidery process. Moreover, the paper shows how to support several wireless power transmission standards that already exist, i.e. NFC and A4WP, or will exist to satisfy the tremendous needs of energy for distributed systems in the IoT domain. In this paper, a new textile-based flexible wireless system enabling communication and energy harvesting is proposed. Analytical, numerical, and experimental studies have been conducted to demonstrate that the structure has two resonant frequencies at 6.8 MHz and 13.6 MHz, which make it suitable for NFC and A4WP standards. Moreover, the losses caused by the system are 2.76 dB and 1.91 dB for A4WP and NFC, respectively. The results are successively presented to highlight the specificities of such textile multi-coils combiners. A method for gaining a resonant structure without any solid electronic component is explained.
Access, timeliness and retention for HIV testing under early infant diagnosis (EID) program, India
Authors: Kamble Suchit , Gawde Nilesh , Goel Noopur , Thorwat Mohan , Nikhare Kalyani , Bembalkar Shilpa , Kamble Sushmita , Brahme Radhika , Pawar Swapna , Sahoo Rakesh , Rana Manish , Singh Manishkumar , Mohiuddin Syed Ahmed , Hatnoor Shivappa , Narapureddy Bayapa Reddy , Saleem M. , Shekhawat Kirti , Verma Vinita , Kapoor Neha , Das Chinmoyee , Gangakhedkar Raman 
Published: April 2023

AbstractEarly Infant Diagnosis of HIV infection services are crucial for managing the perinatally acquired HIV infection. Assessing the performance of the EID services and its underlying determinants is important for the National AIDS Control Program, India. The objectives of this study were to find out access to HIV testing, the timeliness of the testing cascade, and the proportion of HIV exposed infants who are followed up to 18 months for a definitive diagnosis of HIV. The study design was a mixed method. A total of 11 states accounting for 80% of HIV-positive pregnant women were selected. Program records from a total of 62 Integrated counselling and testing centres (ICTCs) served as the source of information. The qualitative component included interviews of program managers at the state and district level, service providers at the ICTC level, and caregivers of HIV exposed infants. In the sampled 62 ICTCs, 78% of the HIV exposed infants had at least one HIV test. Of the infants who had HIV tests, 50% had at first sample collected by 8 weeks of age. The median turnaround time from sample collection to DNA PCR testing was 36 (IQR 19–70) days and that to next sample collection in case of detection of virus in the first sample was 66 (IQR 55–116) days. At 18 months of age, 544 (62%) HIV exposed infants were retained in the EID testing cascade. A total of 30 infants were diagnosed with HIV at a median age of 421 (IQR 149–650) days. More than three fourth of the HIV exposed infants had access to early infant diagnosis (EID) services. Both demand and supply-side factors contribute to access, timeliness and retention and there is a need to address these factors.
Access to germasiloxanes and alkynylgermanes mediated by earth-abundant species
Authors: Stachowiak-Dłużyńska Hanna , Kuciński Krzysztof , Broniarz Konstancja , Szafoni Ewelina , Gruszczyński Marcin , Lewandowski Dariusz , Consiglio Giuseppe , Hreczycho Grzegorz 
Published: April 2023

AbstractThe reactions between silanols or terminal acetylenes with alkynylgermanes have been accomplished using potassium bis(trimethylsilyl)amide as the catalyst. This strategy has provided an entry point into various organogermanes including germasiloxanes and alkynylgermanes. Remarkably, not only KHMDS but also simple bases such as KOH can serve as efficient catalysts in this process.
On good encodings for quantum annealer and digital optimization solvers
Authors: Ceselli Alberto , Premoli Marco 
Published: April 2023

AbstractSeveral optimization solvers inspired by quantum annealing have been recently developed, either running on actual quantum hardware or simulating it on traditional digital computers. Industry and academics look at their potential in solving hard combinatorial optimization problems. Formally, they provide heuristic solutions for Ising models, which are equivalent to quadratic unconstrained binary optimization (QUBO). Constraints on solutions feasibility need to be properly encoded. We experiment on different ways of performing such an encoding. As benchmark we consider the cardinality constrained quadratic knapsack problem (CQKP), a minimal extension of QUBO with one inequality and one equality constraint. We consider different strategies of constraints penalization and variables encoding. We compare three QUBO solvers: quantum annealing on quantum hardware (D-Wave Advantage), probabilistic algorithms on digital hardware and mathematical programming solvers. We analyze their QUBO resolution quality and time, and the persistence values extracted in the quantum annealing sampling process. Our results show that a linear penalization of CQKP inequality improves current best practice. Furthermore, using such a linear penalization, persistence values produced by quantum hardware in a generic way allow to match a specific CQKP metric from literature. They are therefore suitable for general purpose variable fixing in core algorithms for combinatorial optimization.
Survival strategies of artificial active agents
Authors: Zanovello Luigi , Löffler Richard J. G. , Caraglio Michele , Franosch Thomas , Hanczyc Martin M. , Faccioli Pietro 
Published: April 2023

AbstractArtificial cells can be engineered to display dynamics sharing remarkable features in common with the survival behavior of living organisms. In particular, such active systems can respond to stimuli provided by the environment and undertake specific displacements to remain out of equilibrium, e.g. by moving towards regions with higher fuel concentration. In spite of the intense experimental activity aiming at investigating this fascinating behavior, a rigorous definition and characterization of such “survival strategies” from a statistical physics perspective is still missing. In this work, we take a first step in this direction by adapting and applying to active systems the theoretical framework of Transition Path Theory, which was originally introduced to investigate rare thermally activated transitions in passive systems. We perform experiments on camphor disks navigating Petri dishes and perform simulations in the paradigmatic active Brownian particle model to show how the notions of transition probability density and committor function provide the pivotal concepts to identify survival strategies, improve modeling, and obtain and validate experimentally testable predictions. The definition of survival in these artificial systems paves the way to move beyond simple observation and to formally characterize, design and predict complex life-like behaviors.
Prediction of anti-vascular endothelial growth factor agent-specific treatment outcomes in neovascular age-related macular degeneration using a generative adversarial network
Authors: Moon Sehwan , Lee Youngsuk , Hwang Jeongyoung , Kim Chul Gu , Kim Jong Woo , Yoon Won Tae , Kim Jae Hui 
Published: April 2023

AbstractTo develop an artificial intelligence (AI) model that predicts anti-vascular endothelial growth factor (VEGF) agent-specific anatomical treatment outcomes in neovascular age-related macular degeneration (AMD), thereby assisting clinicians in selecting the most suitable anti-VEGF agent for each patient. This retrospective study included patients diagnosed with neovascular AMD who received three loading injections of either ranibizumab or aflibercept. Training was performed using optical coherence tomography (OCT) images with an attention generative adversarial network (GAN) model. To test the performance of the AI model, the sensitivity and specificity to predict the presence of retinal fluid after treatment were calculated for the AI model, an experienced (Examiner 1), and a less experienced (Examiner 2) human examiners. A total of 1684 OCT images from 842 patients (419 treated with ranibizumab and 423 treated with aflibercept) were used as the training set. Testing was performed using images from 98 patients. In patients treated with ranibizumab, the sensitivity and specificity, respectively, were 0.615 and 0.667 for the AI model, 0.385 and 0.861 for Examiner 1, and 0.231 and 0.806 for Examiner 2. In patients treated with aflibercept, the sensitivity and specificity, respectively, were 0.857 and 0.881 for the AI model, 0.429 and 0.976 for Examiner 1, and 0.429 and 0.857 for Examiner 2. In 18.5% of cases, the fluid status of synthetic posttreatment images differed between ranibizumab and aflibercept. The AI model using GAN might predict anti-VEGF agent-specific short-term treatment outcomes with relatively higher sensitivity than human examiners. Additionally, there was a difference in the efficacy in fluid resolution between the anti-VEGF agents. These results suggest the potential of AI in personalized medicine for patients with neovascular AMD.