bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular senescence of renal tubular epithelial cells in acute kidney injury
Authors: Chen Juan , Zhang Huhai , Yi Xiangling , Dou Qian , Yang Xin , He Yani , Chen Jia , Chen Kehong 
Published: February 2024

AbstractCellular senescence represents an irreversible state of cell-cycle arrest during which cells secrete senescence-associated secretory phenotypes, including inflammatory factors and chemokines. Additionally, these cells exhibit an apoptotic resistance phenotype. Cellular senescence serves a pivotal role not only in embryonic development, tissue regeneration, and tumor suppression but also in the pathogenesis of age-related degenerative diseases, malignancies, metabolic diseases, and kidney diseases. The senescence of renal tubular epithelial cells (RTEC) constitutes a critical cellular event in the progression of acute kidney injury (AKI). RTEC senescence inhibits renal regeneration and repair processes and, concurrently, promotes the transition of AKI to chronic kidney disease via the senescence-associated secretory phenotype. The mechanisms underlying cellular senescence are multifaceted and include telomere shortening or damage, DNA damage, mitochondrial autophagy deficiency, cellular metabolic disorders, endoplasmic reticulum stress, and epigenetic regulation. Strategies aimed at inhibiting RTEC senescence, targeting the clearance of senescent RTEC, or promoting the apoptosis of senescent RTEC hold promise for enhancing the renal prognosis of AKI. This review primarily focuses on the characteristics and mechanisms of RTEC senescence, and the impact of intervening RTEC senescence on the prognosis of AKI, aiming to provide a foundation for understanding the pathogenesis and providing potentially effective approaches for AKI treatment.
Orchestrating chromosome conformation capture analysis with Bioconductor
Authors: Serizay Jacques , Matthey-Doret Cyril , Bignaud Amaury , Baudry Lyam , Koszul Romain 
Published: February 2024

AbstractGenome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book (https://bioconductor.org/books/OHCA/) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data.
Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes
Authors: Company Carlos , Schmitt Matthias Jürgen , Dramaretska Yuliia , Serresi Michela , Kertalli Sonia , Jiang Ben , Yin Jiang-An , Aguzzi Adriano , Barozzi Iros , Gargiulo Gaetano 
Published: February 2024

AbstractDescriptive data are rapidly expanding in biomedical research. Instead, functional validation methods with sufficient complexity remain underdeveloped. Transcriptional reporters allow experimental characterization and manipulation of developmental and disease cell states, but their design lacks flexibility. Here, we report logical design of synthetic cis-regulatory DNA (LSD), a computational framework leveraging phenotypic biomarkers and trans-regulatory networks as input to design reporters marking the activity of selected cellular states and pathways. LSD uses bulk or single-cell biomarkers and a reference genome or custom cis-regulatory DNA datasets with user-defined boundary regions. By benchmarking validated reporters, we integrate LSD with a computational ranking of phenotypic specificity of putative cis-regulatory DNA. Experimentally, LSD-designed reporters targeting a wide range of cell states are functional without minimal promoters. Applied to broadly expressed genes from human and mouse tissues, LSD generates functional housekeeper-like sLCRs compatible with size constraints of AAV vectors for gene therapy applications. A mesenchymal glioblastoma reporter designed by LSD outperforms previously validated ones and canonical cell surface markers. In genome-scale CRISPRa screens, LSD facilitates the discovery of known and novel bona fide cell-state drivers. Thus, LSD captures core principles of cis-regulation and is broadly applicable to studying complex cell states and mechanisms of transcriptional regulation.
Subtractive transformation of cathode materials in spent Li-ion batteries to a low-cobalt 5 V-class cathode material
Authors: Ma Jun , Wang Junxiong , Jia Kai , Liang Zheng , Ji Guanjun , Ji Haocheng , Zhu Yanfei , Chen Wen , Cheng Hui-Ming , Zhou Guangmin 
Published: February 2024

AbstractAdding extra raw materials for direct recycling or upcycling is prospective for battery recycling, but overlooks subtracting specific components beforehand can facilitate the recycling to a self-sufficient mode of sustainable production. Here, a subtractive transformation strategy of degraded LiNi0.5Co0.2Mn0.3O2 and LiMn2O4 to a 5 V-class disordered spinel LiNi0.5Mn1.5O4-like cathode material is proposed. Equal amounts of Co and Ni from degraded materials are selectively extracted, and the remaining transition metals are directly converted into Ni0.4Co0.1Mn1.5(CO3)2 precursor for preparing cathode material with in-situ Co doping. The cathode material with improved conductivity and bond strength delivers high-rate (10 C and 20 C) and high-temperature (60 °C) cycling stability. This strategy with no extra precursor input can be generalized to practical degraded black mass and reduces the dependence of current cathode production on rare elements, showing the potential of upcycling from the spent to a next-generation 5 V-class cathode material for the sustainable Li-ion battery industry.
Geographic pair matching in large-scale cluster randomized trials
Authors: Arnold Benjamin F. , Rerolle Francois , Tedijanto Christine , Njenga Sammy M. , Rahman Mahbubur , Ercumen Ayse , Mertens Andrew , Pickering Amy J. , Lin Audrie , Arnold Charles D. , Das Kishor , Stewart Christine P. , Null Clair , Luby Stephen P. , Colford John M. , Hubbard Alan E. , Benjamin-Chung Jade 
Published: February 2024

AbstractCluster randomized trials are often used to study large-scale public health interventions. In large trials, even small improvements in statistical efficiency can have profound impacts on the required sample size and cost. Location integrates many socio-demographic and environmental characteristics into a single, readily available feature. Here we show that pair matching by geographic location leads to substantial gains in statistical efficiency for 14 child health outcomes that span growth, development, and infectious disease through a re-analysis of two large-scale trials of nutritional and environmental interventions in Bangladesh and Kenya. Relative efficiencies from pair matching are ≥1.1 for all outcomes and regularly exceed 2.0, meaning an unmatched trial would need to enroll at least twice as many clusters to achieve the same level of precision as the geographically pair matched design. We also show that geographically pair matched designs enable estimation of fine-scale, spatially varying effect heterogeneity under minimal assumptions. Our results demonstrate broad, substantial benefits of geographic pair matching in large-scale, cluster randomized trials.
Unveiling the dynamics of little-bang nucleosynthesis
Authors: Sun Kai-Jia , Wang Rui , Ko Che Ming , Ma Yu-Gang , Shen Chun 
Published: February 2024

AbstractHigh-energy nuclear collisions provide a unique site for the synthesis of both nuclei and antinuclei at temperatures of kT ≈ 100 − 150 MeV. In these little bangs of transient collisions, a quark-gluon plasma (QGP) of nearly vanishing viscosity is created, which is believed to have existed in the early universe within the first few microseconds after the Big Bang. Analyses of identified particles produced in these little bangs based on the statistical hadronization model for the QGP have suggested that light (anti)nuclei are produced from the QGP as other hadrons and their abundances are little affected by later hadronic dynamics. Here, we find a strong reduction of the triton yield by about a factor of 1.8 in high-energy heavy-ion collisions based on a kinetic approach that includes the effects of hadronic re-scatterings, particularly that due to pion-catalyzed multi-body reactions. This finding is supported by the latest experimental measurements and thus unveils the important role of hadronic dynamics in the little-bang nucleosynthesis.
300 years of sclerosponge thermometry shows global warming has exceeded 1.5 °C
Authors: McCulloch Malcolm T. , Winter Amos , Sherman Clark E. , Trotter Julie A. 
Published: February 2024

AbstractAnthropogenic emissions drive global-scale warming yet the temperature increase relative to pre-industrial levels is uncertain. Using 300 years of ocean mixed-layer temperature records preserved in sclerosponge carbonate skeletons, we demonstrate that industrial-era warming began in the mid-1860s, more than 80 years earlier than instrumental sea surface temperature records. The Sr/Ca palaeothermometer was calibrated against ‘modern’ (post-1963) highly correlated (R2 = 0.91) instrumental records of global sea surface temperatures, with the pre-industrial defined by nearly constant (<±0.1 °C) temperatures from 1700 to the early 1860s. Increasing ocean and land-air temperatures overlap until the late twentieth century, when the land began warming at nearly twice the rate of the surface oceans. Hotter land temperatures, together with the earlier onset of industrial-era warming, indicate that global warming was already 1.7 ± 0.1 °C above pre-industrial levels by 2020. Our result is 0.5 °C higher than IPCC estimates, with 2 °C global warming projected by the late 2020s, nearly two decades earlier than expected.
Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model
Authors: Marschmann Gianna L. , Tang Jinyun , Zhalnina Kateryna , Karaoz Ulas , Cho Heejung , Le Beatrice , Pett-Ridge Jennifer , Brodie Eoin L. 
Published: February 2024

AbstractSoil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.
A novel class of inhibitors that disrupts the stability of integrin heterodimers identified by CRISPR-tiling-instructed genetic screens
Authors: Mattson Nicole M. , Chan Anthony K. N. , Miyashita Kazuya , Mukhaleva Elizaveta , Chang Wen-Han , Yang Lu , Ma Ning , Wang Yingyu , Pokharel Sheela Pangeni , Li Mingli , Liu Qiao , Xu Xiaobao , Chen Renee , Singh Priyanka , Zhang Leisi , Elsayed Zeinab , Chen Bryan , Keen Denise , Pirrotte Patrick , Rosen Steven. T. , Chen Jianjun , LaBarge Mark A. , Shively John E. , Vaidehi Nagarajan , Rockne Russell C. , Feng Mingye , Chen Chun-Wei 
Published: February 2024

AbstractThe plasma membrane is enriched for receptors and signaling proteins that are accessible from the extracellular space for pharmacological intervention. Here we conducted a series of CRISPR screens using human cell surface proteome and integrin family libraries in multiple cancer models. Our results identified ITGAV (integrin αV) and its heterodimer partner ITGB5 (integrin β5) as the essential integrin α/β pair for cancer cell expansion. High-density CRISPR gene tiling further pinpointed the integral pocket within the β-propeller domain of ITGAV for integrin αVβ5 dimerization. Combined with in silico compound docking, we developed a CRISPR-Tiling-Instructed Computer-Aided (CRISPR-TICA) pipeline for drug discovery and identified Cpd_AV2 as a lead inhibitor targeting the β-propeller central pocket of ITGAV. Cpd_AV2 treatment led to rapid uncoupling of integrin αVβ5 and cellular apoptosis, providing a unique class of therapeutic action that eliminates the integrin signaling via heterodimer dissociation. We also foresee the CRISPR-TICA approach to be an accessible method for future drug discovery studies.
Designing a novel fractional order mathematical model for COVID-19 incorporating lockdown measures
Authors: Adel Waleed , Günerhan Hatıra , Nisar Kottakkaran Sooppy , Agarwal Praveen , El-Mesady A. 
Published: February 2024

AbstractThis research focuses on the design of a novel fractional model for simulating the ongoing spread of the coronavirus (COVID-19). The model is composed of multiple categories named susceptible $$S(t)$$

S
(
t
)

, infected $$I(t)$$

I
(
t
)

, treated $$T(t)$$

T
(
t
)

, and recovered $$R(t)$$

R
(
t
)

with the susceptible category further divided into two subcategories $${S}_{1} (t)$$

S
1

(
t
)

and $${S}_{2} (t)$$

S
2

(
t
)

. In light of the need for restrictive measures such as mandatory masks and social distancing to control the virus, the study of the dynamics and spread of the virus is an important topic. In addition, we investigate the positivity of the solution and its boundedness to ensure positive results. Furthermore, equilibrium points for the system are determined, and a stability analysis is conducted. Additionally, this study employs the analytical technique of the Laplace Adomian decomposition method (LADM) to simulate the different compartments of the model, taking into account various scenarios. The Laplace transform is used to convert the nonlinear resulting equations into an equivalent linear form, and the Adomian polynomials are utilized to treat the nonlinear terms. Solving this set of equations yields the solution for the state variables. To further assess the dynamics of the model, numerical simulations are conducted and compared with the results from LADM. Additionally, a comparison with real data from Italy is demonstrated, which shows a perfect agreement between the obtained data using the numerical and Laplace Adomian techniques. The graphical simulation is employed to investigate the effect of fractional-order terms, and an analysis of parameters is done to observe how quickly stabilization can be achieved with or without confinement rules. It is demonstrated that if no confinement rules are applied, it will take longer for stabilization after more people have been affected; however, if strict measures and a low contact rate are implemented, stabilization can be reached sooner.
AMMI and GGE biplot analysis of genotype by environment interaction for yield and yield contributing traits in confectionery groundnut
Authors: Kona Praveen , Ajay B. C. , Gangadhara K. , Kumar Narendra , Choudhary Raja Ram , Mahatma M. K. , Singh Sushmita , Reddy Kiran K. , Bera S. K. , Sangh Chandramohan , Rani Kirti , Chavada Zarana , Solanki K. D. 
Published: February 2024

AbstractThe global market has a high demand for premium edible grade groundnut, particularly for table use. India, in particular, exhibits significant potential for exporting confectionary grade large seeded groundnut. The environment plays a significant impact in influencing the expression of seed traits, which subsequently affects the confectionary quality of groundnut genotypes. The states of Gujarat and Rajasthan in India are prominent producers of high-quality groundnuts specifically used for confectionary purposes. The current study was conducted with 43 confectionery groundnut genotypes at Junagadh, Gujarat, and Bikaner, Rajasthan, with the goals of understanding genotype-by-environment interaction (GEI) effects and identifying stable, high yielding confectionery quality groundnut genotypes using AMMI and GGE biplot models. Pod yield per plant (PYP), number of pods per plant (NPP), hundred kernel weight (HKW), and shelling percent (SP) were estimated. The interplay between the environment and genotype has had a notable impact on the manifestation of confectionary grade characteristics in peanuts. The results from the Interaction Principal Component Analysis (IPCA) indicate that HKW contributed 76.68% and 18.95% towards the Global Environmental Index (GEI) through IPCA1 and IPCA2, respectively. Similarly, NPP contributed 87.52% and 8.65%, PYP contributed 95.87% and 2.1%, and SP contributed 77.4% and 16.22% towards GEI through IPCA1 and IPCA2, respectively. Based on the ranking of genotypes, the ideal genotypes were PBS 29079B for HKW, PBS 29230 for NPP. The genotypes PBS 29233 and PBS 29230 exhibited superior performance and stability in terms of pod yield, hundred kernel weight, number of pods per plant, and shelling percentage across various sites. These breeding lines have the potential to be developed for the purpose of producing confectionary grade groundnut with larger seeds, in order to fulfil the growing demand for export.
Nonarteritic anterior ischemic optic neuropathy and incidence of Parkinson’s disease based on a nationwide population based study
Authors: Ahn Jong Hyeon , Kang Min Chae , Youn Jinyoung , Park Kyung-Ah , Han Kyung-Do , Jung Jin-hyung 
Published: February 2024

AbstractThis study aimed to investigate the association between nonarteritic anterior ischemic optic neuropathy (NAION) and Parkinson's disease (PD) using a retrospective, nationwide, population-based cohort in South Korea. This study utilized data from the Korean National Health Insurance database, including 43,960 NAION patients and 219,800 age- and sex-matched controls. Cox proportional hazards regression models were used to assess the risk of developing PD in the NAION group compared to the control group after adjusting for various confounding factors. Subgroup analyses were conducted based on sex, age, and comorbidities. The incidence rate of PD was higher in the NAION group (1.326 per 1000 person-years) than in the control group (0.859 per 1000 person-years). After adjusting for confounding factors, the risk of developing PD was significantly higher in the NAION group (adjusted hazard ratio [aHR] 1.516, 95% confidence interval [CI] 1.300–1.769). Subgroup analyses did not reveal a significant difference in the risk of PD development based on sex, age, or comorbidities. This retrospective, nationwide, population-based cohort study revealed a significant association between NAION and an increased risk of developing PD in a South Korean population. The incidence rate of PD was observed to be higher in individuals diagnosed with NAION than in age- and sex-matched controls even after adjusting for potential confounding variables, with the risk being approximately 51.6% higher in the NAION group. Further research is necessary to elucidate the underlying pathophysiological mechanisms linking NAION to PD and to determine whether similar associations exist in other ethnic and geographical populations.
In-lab synthesized turn-off fluorescence sensor for estimation of Gemigliptin and Rosuvastatin polypill appraised by Spider diagram, AGREE and whiteness metrics
Authors: Mohyeldin Sara M. , Talaat Wael , Kamal Miranda F. , Daabees Hoda G. , El-Tahawy Mohsen M. T. , Keshk Reda M. 
Published: February 2024

AbstractGemigliptin-Rosuvastatin single-pill combination is a promising therapeutic tool in the effective control of hyperglycemia and hypercholesterolemia. Organic sensors with high quantum yields have profoundly significant applications in the pharmaceutical industry, such as routine quality control of marketed formulations. Herein, the fluorescence sensor, 2-Morpholino-4,6-dimethyl nicotinonitrile 3, (λex; 226 nm, λem; 406 nm), was synthesized with a fluorescence quantum yield of 56.86% and fully characterized in our laboratory. This sensor showed high efficiency for the determination of Gemigliptin (GEM) and Rosuvastatin (RSV) traces through their stoichiometric interactions and simultaneously fractionated by selective solvation. The interaction between the stated analytes and sensor 3 was a quenching effect. Various experimental parameters and the turn-off mechanism were addressed. The adopted approach fulfilled the ICH validation criteria and showed linear satisfactory ranges, 0.2–2 and 0.1–1 μg/mL for GEM and RSV, respectively with nano-limits of detection less than 30 ng/mL for both analytes. The synthesized sensor has been successfully applied for GEM and RSV co-assessment in their synthetic polypill with excellent % recoveries of 98.83 ± 0.86 and 100.19 ± 0.64, respectively. No statistically significant difference between the results of the proposed and reported spectrophotometric methods in terms of the F- and t-tests. Ecological and whiteness appraisals of the proposed study were conducted via three novel approaches: the Greenness Index via Spider Diagram, the Analytical Greenness Metric, and the Red–Green–Blue 12 model. The aforementioned metrics proved the superiority of the adopted approach over the previously published one regarding eco-friendliness and sustainability. Our devised fluorimetric turn-off sensing method showed high sensitivity, selectivity, feasibility, and rapidity with minimal cost and environmental burden over other sophisticated techniques, making it reliable in quality control labs.
Western Caucasus regional hydroclimate controlled by cold-season temperature variability since the Last Glacial Maximum
Authors: Wolf Annabel , Baker Jonathan Lloyd , Tjallingii Rik , Cai Yanjun , Osinzev Alexander , Antonosyan Mariya , Amano Noel , Johnson Kathleen Rose , Skiba Vanessa , McCormack Jeremy , Kwiecien Ola , Chervyatsova Olga Yakovlevna , Dublyansky Yuri Viktorovich , Dbar Roman Saidovich , Cheng Hai , Breitenbach Sebastian Franz Martin 
Published: February 2024

AbstractThe Caucasus region is key for understanding early human dispersal and evolution in Eurasia, and characterizing the environmental contrast between Last Glacial Maximum and Holocene is crucial for investigating human adaptation strategies to large climatic shifts. However, a paucity of high-resolution paleoclimate records leave this context largely unknown for early human populations in the Caucasus region. Based on our model-proxy comparison of high- and low-resolution records of 24 stalagmites from three caves, we find spatially distinct changes in vegetation and seasonality of precipitation, especially under glacial conditions. Supported by modern oxygen-isotope data and climate modeling, we identify a supraregional cold-season temperature control for oxygen isotopes in Black Sea speleothems, which previously had been interpreted as a local moisture-source signal. Carbon-isotope and trace-element data further suggest disproportionate changes in vegetation cover and soil dynamics at high altitudes, which would have resulted in a reduction but not a disappearance of human refugia during the Last Glacial Maximum, relative to the current interglacial. Our findings imply that abrupt climatic pressures from harsh conditions were overcome by adaptive strategies in the past.