bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Equatorial to Mid‐Latitudinal Global Night Time Ionospheric Plasma Irregularities Using Machine Learning
Authors: Seba Ephrem Beshir , Lapenta Giovanni 
Published: February 2024

AbstractThis study focuses on modeling the characteristics of nighttime topside Ionospheric Plasma Irregularities (PI) on a global scale. We utilize Random Forest (RF) and a one‐dimensional Convolutional Neural Network (1D‐CNN) model, incorporating data from the Swarm A, B, and C satellites, space weather data from the OMNIWeb data center, as well as zonal and meridional wind model data. Our objective is to simulate monthly global PI characteristics using a multilayer 1D‐CNN model trained on 12 space weather and ionospheric parameters. In addition, we investigate the most influential input parameters for predicting global nighttime PI characteristics. Our findings indicate that non‐equinox months exhibit the highest equatorial PI magnitude over the American‐African longitudinal sector, contrary to the expected higher Rayleigh‐Taylor instability growth rate during equinox months. Winter months display the most intense and widespread vertically and horizontally distributed equatorial PI patterns. We also observe double peaks across geomagnetic latitudes and longitudinally varying wavelike irregularity structures, particularly in May, August, and predominantly in September. Furthermore, north‐south hemispherical asymmetry in PI observed across different seasons. Through the RF parameter importance analysis method, we determine that temporal, geographical, and magnetic disturbance‐related factors play a crucial role in predicting global PI variabilities. These findings emphasize the significance of these variables in controlling the strongest PI characteristics observed in the Atlantic sector, which has garnered considerable attention in PI research. The employed 1D‐CNN model demonstrates exceptional predictive capabilities, exhibiting a strong correlation of 0.98 for global PI characteristics across all months and satellites.
APOE genotype-specific methylation patterns are linked to Alzheimer disease pathology and estrogen response
Authors: Panitch Rebecca , Sahelijo Nathan , Hu Junming , Nho Kwangsik , Bennett David A. , Lunetta Kathryn L. , Au Rhoda , Stein Thor D. , Farrer Lindsay A. , Jun Gyungah R. 
Published: February 2024

AbstractThe joint effects of APOE genotype and DNA methylation on Alzheimer disease (AD) risk is relatively unknown. We conducted genome-wide methylation analyses using 2,021 samples in blood (91 AD cases, 329 mild cognitive impairment, 1,391 controls) and 697 samples in brain (417 AD cases, 280 controls). We identified differentially methylated levels in AD compared to controls in an APOE genotype-specific manner at 25 cytosine-phosphate-guanine (CpG) sites in brain and 36 CpG sites in blood. Additionally, we identified seven CpG sites in the APOE region containing TOMM40, APOE, and APOC1 genes with P < 5 × 10−8 between APOE ε4 carriers and non-carriers in brain or blood. In brain, the most significant CpG site hypomethylated in ε4 carriers compared to non-carriers was from the TOMM40 in the total sample, while most of the evidence was derived from AD cases. However, the CpG site was not significantly modulating expression of these three genes in brain. Three CpG sites from the APOE were hypermethylated in APOE ε4 carriers in brain or blood compared in ε4 non-carriers and nominally significant with APOE expression in brain. Three CpG sites from the APOC1 were hypermethylated in blood, which one of the 3 CpG sites significantly lowered APOC1 expression in blood using all subjects or ε4 non-carriers. Co-methylation network analysis in blood and brain detected eight methylation networks associated with AD and APOE ε4 status. Five of the eight networks included genes containing network CpGs that were significantly enriched for estradiol perturbation, where four of the five networks were enriched for the estrogen response pathway. Our findings provide further evidence of the role of APOE genotype on methylation levels associated with AD, especially linked to estrogen response pathway.
Solar ultraviolet radiation exposure, and incidence of childhood acute lymphocytic leukaemia and non-Hodgkin lymphoma in a US population-based dataset
Authors: Little Mark P. , Mai Jim Z. , Fang Michelle , Chernyavskiy Pavel , Kennerley Victoria , Cahoon Elizabeth K. , Cockburn Myles G. , Kendall Gerald M. , Kimlin Michael G. 
Published: February 2024

Abstract
Background
Acute lymphocytic leukaemia (ALL) and non-Hodgkin lymphoma (NHL) are among the commonest types of childhood cancer. Some previous studies suggested that elevated ultraviolet radiation (UVR) exposures increase ALL risk; many more indicate NHL risk is reduced.

Methods
We assessed age<20 ALL/NHL incidence in Surveillance, Epidemiology and End Results data using AVGLO-derived UVR irradiance/cumulative radiant exposure measures, using quasi-likelihood models accounting for underdispersion, adjusted for age, sex, racial/ethnic group and other county-level socioeconomic variables.

Results
There were 30,349 cases of ALL and 8062 of NHL, with significant increasing trends of ALL with UVR irradiance (relative risk (RR) = 1.200/mW/cm2 (95% CI 1.060, 1.359, p = 0.0040)), but significant decreasing trends for NHL (RR = 0.646/mW/cm2 (95% CI 0.512, 0.816, p = 0.0002)). There was a borderline-significant increasing trend of ALL with UVR cumulative radiant exposure (RR = 1.444/MJ/cm2 (95% CI 0.949, 2.197, p = 0.0865)), and significant decreasing trends for NHL (RR = 0.284/MJ/cm2 (95% CI 0.166, 0.485, p < 0.0001)). ALL and NHL trend RR is substantially increased among those aged 0–3. All-age trend RRs are most extreme (increasing for ALL, decreasing for NHL) for Hispanics for both UVR measures.

Conclusions
Our more novel finding, of excess UVR-related ALL risk, is consistent with some previous studies, but is not clear-cut, and in need of replication.
Boosting exciton mobility approaching Mott-Ioffe-Regel limit in Ruddlesden−Popper perovskites by anchoring the organic cation
Authors: Gong Yiyang , Yue Shuai , Liang Yin , Du Wenna , Bian Tieyuan , Jiang Chuanxiu , Bao Xiaotian , Zhang Shuai , Long Mingzhu , Zhou Guofu , Yin Jun , Deng Shibin , Zhang Qing , Wu Bo , Liu Xinfeng 
Published: February 2024

AbstractExciton transport in two-dimensional Ruddlesden−Popper perovskite plays a pivotal role for their optoelectronic performance. However, a clear photophysical picture of exciton transport is still lacking due to strong confinement effects and intricate exciton-phonon interactions in an organic-inorganic hybrid lattice. Herein, we present a systematical study on exciton transport in (BA)2(MA)n−1PbnI3n+1 Ruddlesden−Popper perovskites using time-resolved photoluminescence microscopy. We reveal that the free exciton mobilities in exfoliated thin flakes can be improved from around 8 cm2 V−1 s−1 to 280 cm2V−1s−1 by anchoring the soft butyl ammonium cation with a polymethyl methacrylate network at the surface. The mobility of the latter is close to the theoretical limit of Mott-Ioffe-Regel criterion. Combining optical measurements and theoretical studies, it is unveiled that the polymethyl methacrylate network significantly improve the lattice rigidity resulting in the decrease of deformation potential scattering and lattice fluctuation at the surface few layers. Our work elucidates the origin of high exciton mobility in Ruddlesden−Popper perovskites and opens up avenues to regulate exciton transport in two-dimensional materials.
Probing molecules in gas cells of subwavelength thickness with high frequency resolution
Authors: Arellano Guadalupe Garcia , de Aquino Carvalho Joao Carlos , Mouhanna Hippolyte , Butery Esther , Billeton Thierry , Du-Burck Frederic , Darquié Benoit , Maurin Isabelle , Laliotis Athanasios 
Published: February 2024

AbstractMiniaturizing and integrating atomic vapor cells is widely investigated for the purposes of fundamental measurements and technological applications such as quantum sensing. Extending such platforms to the realm of molecular physics is a fascinating prospect that paves the way for compact frequency metrology as well as for exploring light-matter interactions with complex quantum objects. Here, we perform molecular rovibrational spectroscopy in a thin-cell of micrometric thickness, comparable to excitation wavelengths. We operate the cell in two distinct regions of the electromagnetic spectrum, probing ν1 + ν3 resonances of acetylene at 1.530 µm, within the telecommunications wavelength range, as well as the ν3 and ν2 resonances of SF6 and NH3 respectively, in the mid-infrared fingerprint region around 10.55 µm. Thin-cell confinement allows linear sub-Doppler transmission spectroscopy due to the coherent Dicke narrowing effect, here demonstrated for molecular rovibrations. Our experiment can find applications extending to the fields of compact molecular frequency references, atmospheric physics or fundamental precision measurements.
Specificity, synergy, and mechanisms of splice-modifying drugs
Authors: Ishigami Yuma , Wong Mandy S. , Martí-Gómez Carlos , Ayaz Andalus , Kooshkbaghi Mahdi , Hanson Sonya M. , McCandlish David M. , Krainer Adrian R. , Kinney Justin B. 
Published: February 2024

AbstractDrugs that target pre-mRNA splicing hold great therapeutic potential, but the quantitative understanding of how these drugs work is limited. Here we introduce mechanistically interpretable quantitative models for the sequence-specific and concentration-dependent behavior of splice-modifying drugs. Using massively parallel splicing assays, RNA-seq experiments, and precision dose-response curves, we obtain quantitative models for two small-molecule drugs, risdiplam and branaplam, developed for treating spinal muscular atrophy. The results quantitatively characterize the specificities of risdiplam and branaplam for 5’ splice site sequences, suggest that branaplam recognizes 5’ splice sites via two distinct interaction modes, and contradict the prevailing two-site hypothesis for risdiplam activity at SMN2 exon 7. The results also show that anomalous single-drug cooperativity, as well as multi-drug synergy, are widespread among small-molecule drugs and antisense-oligonucleotide drugs that promote exon inclusion. Our quantitative models thus clarify the mechanisms of existing treatments and provide a basis for the rational development of new therapies.
Ferromagnetism on an atom-thick & extended 2D metal-organic coordination network
Authors: Lobo-Checa Jorge , Hernández-López Leyre , Otrokov Mikhail M. , Piquero-Zulaica Ignacio , Candia Adriana E. , Gargiani Pierluigi , Serrate David , Delgado Fernando , Valvidares Manuel , Cerdá Jorge , Arnau Andrés , Bartolomé Fernando 
Published: February 2024

AbstractFerromagnetism is the collective alignment of atomic spins that retain a net magnetic moment below the Curie temperature, even in the absence of external magnetic fields. Reducing this fundamental property into strictly two-dimensions was proposed in metal-organic coordination networks, but thus far has eluded experimental realization. In this work, we demonstrate that extended, cooperative ferromagnetism is feasible in an atomically thin two-dimensional metal-organic coordination network, despite only ≈ 5% of the monolayer being composed of Fe atoms. The resulting ferromagnetic state exhibits an out-of-plane easy-axis square-like hysteresis loop with large coercive fields over 2 Tesla, significant magnetic anisotropy, and persists up to TC ≈ 35 K. These properties are driven by exchange interactions mainly mediated by the molecular linkers. Our findings resolve a two decade search for ferromagnetism in two-dimensional metal-organic coordination networks.
Empirical data drift detection experiments on real-world medical imaging data
Authors: Kore Ali , Abbasi Bavil Elyar , Subasri Vallijah , Abdalla Moustafa , Fine Benjamin , Dolatabadi Elham , Abdalla Mohamed 
Published: February 2024

AbstractWhile it is common to monitor deployed clinical artificial intelligence (AI) models for performance degradation, it is less common for the input data to be monitored for data drift – systemic changes to input distributions. However, when real-time evaluation may not be practical (eg., labeling costs) or when gold-labels are automatically generated, we argue that tracking data drift becomes a vital addition for AI deployments. In this work, we perform empirical experiments on real-world medical imaging to evaluate three data drift detection methods’ ability to detect data drift caused (a) naturally (emergence of COVID-19 in X-rays) and (b) synthetically. We find that monitoring performance alone is not a good proxy for detecting data drift and that drift-detection heavily depends on sample size and patient features. Our work discusses the need and utility of data drift detection in various scenarios and highlights gaps in knowledge for the practical application of existing methods.
The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA
Authors: Lu Huizhi , Chen Zijing , Xie Teng , Zhong Shitong , Suo Shasha , Song Shuang , Wang Liangyan , Xu Hong , Tian Bing , Zhao Ye , Zhou Ruhong , Hua Yuejin 
Published: February 2024

AbstractBacteria have evolved various response systems to adapt to environmental stress. A protease-based derepression mechanism in response to DNA damage was characterized in Deinococcus, which is controlled by the specific cleavage of repressor DdrO by metallopeptidase PprI (also called IrrE). Despite the efforts to document the biochemical, physiological, and downstream regulation of PprI-DdrO, the upstream regulatory signal activating this system remains unclear. Here, we show that single-stranded DNA physically interacts with PprI protease, which enhances the PprI-DdrO interactions as well as the DdrO cleavage in a length-dependent manner both in vivo and in vitro. Structures of PprI, in its apo and complexed forms with single-stranded DNA, reveal two DNA-binding interfaces shaping the cleavage site. Moreover, we show that the dynamic monomer-dimer equilibrium of PprI is also important for its cleavage activity. Our data provide evidence that single-stranded DNA could serve as the signal for DNA damage sensing in the metalloprotease/repressor system in bacteria. These results also shed light on the survival and acquired drug resistance of certain bacteria under antimicrobial stress through a SOS-independent pathway.
Coherent control of enhanced second-harmonic generation in a plasmonic nanocircuit using a transition metal dichalcogenide monolayer
Authors: Wu Pei-Yuan , Lee Wei-Qing , Liu Chang-Hua , Huang Chen-Bin 
Published: February 2024

AbstractNonlinear nanophotonic circuits, renowned for their compact form and integration capabilities, hold potential for advancing high-capacity optical signal processing. However, limited practicality arises from low nonlinear conversion efficiency. Transition metal dichalcogenides (TMDs) could present a promising avenue to address this challenge, given their superior optical nonlinear characteristics and compatibility with diverse device platforms. Nevertheless, this potential remains largely unexplored, with current endeavors predominantly focusing on the demonstration of TMDs’ coherent nonlinear signals via free-space excitation and collection. In this work, we perform direct integration of TMDs onto a plasmonic nanocircuitry. By controlling the polarization angle of the input laser, we show selective routing of second-harmonic generation (SHG) signals from a MoSe2 monolayer within the plasmonic circuit. Routing extinction ratios of 14.86 dB are achieved, demonstrating good coherence preservation in this hybrid nanocircuit. Additionally, our characterization indicates that the integration of TMDs leads to a 13.8-fold SHG enhancement, compared with the pristine nonlinear plasmonic nanocircuitry. These distinct features—efficient SHG generation, coupling, and controllable routing—suggest that our hybrid TMD-plasmonic nanocircuitry could find immediate applications including on-chip optical frequency conversion, selective routing, switching, logic operations, as well as quantum operations.
CAMSAPs and nucleation-promoting factors control microtubule release from γ-TuRC
Authors: Rai Dipti , Song Yinlong , Hua Shasha , Stecker Kelly , Monster Jooske L. , Yin Victor , Stucchi Riccardo , Xu Yixin , Zhang Yaqian , Chen Fangrui , Katrukha Eugene A. , Altelaar Maarten , Heck Albert J. R. , Wieczorek Michal , Jiang Kai , Akhmanova Anna 
Published: February 2024

Abstractγ-Tubulin ring complex (γ-TuRC) is the major microtubule-nucleating factor. After nucleation, microtubules can be released from γ-TuRC and stabilized by other proteins, such as CAMSAPs, but the biochemical cross-talk between minus-end regulation pathways is poorly understood. Here we reconstituted this process in vitro using purified components. We found that all CAMSAPs could bind to the minus ends of γ-TuRC-attached microtubules. CAMSAP2 and CAMSAP3, which decorate and stabilize growing minus ends but not the minus-end tracking protein CAMSAP1, induced microtubule release from γ-TuRC. CDK5RAP2, a γ-TuRC-interactor, and CLASP2, a regulator of microtubule growth, strongly stimulated γ-TuRC-dependent microtubule nucleation, but only CDK5RAP2 suppressed CAMSAP binding to γ-TuRC-anchored minus ends and their release. CDK5RAP2 also improved selectivity of γ-tubulin-containing complexes for 13- rather than 14-protofilament microtubules in microtubule-capping assays. Knockout and overexpression experiments in cells showed that CDK5RAP2 inhibits the formation of CAMSAP2-bound microtubules detached from the microtubule-organizing centre. We conclude that CAMSAPs can release newly nucleated microtubules from γ-TuRC, whereas nucleation-promoting factors can differentially regulate this process.
A combinatorial genetic strategy for exploring complex genotype–phenotype associations in cancer
Authors: Li Shan , Wong Alicia , Sun Huiyun , Bhatia Vipul , Javier Gerardo , Jana Sujata , Wu Qian , Montgomery Robert B. , Wright Jonathan L. , Lam Hung-Ming , Hsieh Andrew C. , Faltas Bishoy M. , Haffner Michael C. , Lee John K. 
Published: February 2024

AbstractAvailable genetically defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Here, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant bladder and prostate cancer models. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.
Enhanced risk of record-breaking regional temperatures during the 2023–24 El Niño
Authors: Jiang Ning , Zhu Congwen , Hu Zeng-Zhen , McPhaden Michael J. , Chen Deliang , Liu Boqi , Ma Shuangmei , Yan Yuhan , Zhou Tianjun , Qian Weihong , Luo Jingjia , Yang Xiuqun , Liu Fei , Zhu Yuejian 
Published: February 2024

AbstractIn 2023, the development of El Niño is poised to drive a global upsurge in surface air temperatures (SAT), potentially resulting in unprecedented warming worldwide. Nevertheless, the regional patterns of SAT anomalies remain diverse, obscuring where historical warming records may be surpassed in the forthcoming year. Our study underscores the significant influence of El Niño and the persistence of climate signals on the inter-annual variability of regional SAT, both in amplitude and spatial distribution. The likelihood of global mean SAT exceeding historical records, calculated from July 2023 to June 2024, is estimated at 90%, contingent upon annual-mean sea surface temperature anomalies in the eastern equatorial Pacific exceeding 0.6 °C. Regions particularly susceptible to recording record-high SAT include coastal and adjacent areas in Asia such as the Bay of Bengal and the South China Sea, as well as Alaska, the Caribbean Sea, and the Amazon. This impending warmth heightens the risk of year-round marine heatwaves and escalates the threat of wildfires and other negative consequences in Alaska and the Amazon basin, necessitating strategic mitigation measures to minimize potential worst-case impacts.
IL-6 and IL-17 as potential links between pre-existing hypertension and long-term COVID sequelae in patients undergoing hemodialysis: a multicenter cross-sectional study
Authors: Stepanova Natalia , Driianska Victoria , Rysyev Andriy , Ostapenko Tetyana , Kalinina Nataliia 
Published: February 2024

AbstractLong COVID, characterized by persistent symptoms following acute infection, poses a significant health challenge, particularly for patients with pre-existing chronic conditions such as hypertension. We hypothesized that an increase in the production of interleukins (IL)-6 and IL-17 could serve as a potential mechanism linking pre-existing uncontrolled blood pressure (BP) to the occurrence of long-term COVID sequelae in patients undergoing hemodialysis (HD). This cross-sectional study examined serum IL-6 and IL-17 levels in 80 patients undergoing HD, considering preinfection BP, the presence of long-term COVID sequelae, and the time interval after acute COVID-19 infection, which was either 5 or 10 months. Controlled BP was defined as a 3-month average pre-dialysis BP < 140/90 mmHg and post-dialysis < 130/80 mmHg. The findings suggest that the prevalence of long-term COVID sequelae was significantly higher in patients with uncontrolled BP than in the BP-controlled group. Both IL-6 and IL-17 concentrations were also significantly higher in patients with uncontrolled BP compared with the BP-controlled group. The patients with long-term COVID sequelae had higher IL-6 and IL-17 values than the fully recovered patients at both time points, but their concentrations decreased significantly over time. Further research and prospective studies are warranted to validate these findings.
Patient leaflets on respiratory tract infections did not improve shared decision making and antibiotic prescriptions in a low-prescriber setting
Authors: Plate Andreas , Di Gangi Stefania , Garzoni Christian , Selby Kevin , Pichierri Giuseppe , Senn Oliver , Neuner-Jehle Stefan 
Published: February 2024

AbstractPatient information leaflets can reduce antibiotic prescription rates by improving knowledge and encouraging shared decision making (SDM) in patients with respiratory tract infections (RTI). The effect of these interventions in antibiotic low-prescriber settings is unknown. We conducted a pragmatic pre-/post interventional study between October 2022 and March 2023 in Swiss outpatient care. The intervention was the provision of patient leaflets informing about RTIs and antibiotics use. Main outcomes were the extent of SDM, antibiotic prescription rates, and patients’ awareness/knowledge about antibiotic use in RTIs. 408 patients participated in the pre-intervention period, and 315 patients in the post- intervention period. There was no difference in the extent of SDM (mean score (range 0–100): 65.86 vs. 64.65, p = 0.565), nor in antibiotic prescription rates (no prescription: 89.8% vs. 87.2%, p = 0.465) between the periods. Overall awareness/knowledge among patients with RTI was high and leaflets showed only a small effect on overall awareness/knowledge. In conclusion, in an antibiotic low-prescriber setting, patient information leaflets may improve knowledge, but may not affect treatment decisions nor antibiotic prescription rates for RTIs.