bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Impact of Lower Atmosphere Forecast Uncertainties on WACCM‐X Prediction of Ionosphere‐Thermosphere System During Geomagnetic Storms
Authors: Lee Wonseok , Song In‐Sun , Shim Ja Soon , Liu Guiping , Jee Geonhwa 
Published: December 2024

AbstractImpacts of lower atmosphere forecast uncertainties on the Ionosphere‐Thermosphere (IT) system are investigated using the Whole Atmosphere Community Climate Model with Thermosphere and Ionosphere eXtension (WACCM‐X) for April 2010 and March 2013 geomagnetic storms. For each storm, a specified‐dynamics simulation (analysis run) is carried out by constraining the model dynamics using reanalysis data. Results of the analysis runs are used as initial conditions for forecast runs initialized on 20, 10, 5, 2, and 1 day before the storm onset time. The forecast runs show that errors in TEC compared to the analysis run appear in the equatorial region within 1–2 days after forecast starts with differences of about 10%. These discrepancies gradually expand to high‐latitudes after 10 days. These errors in TECs could be due to the deviations in the semidiurnal (SW2) and non‐migrating (DE3) tides that also occur within 1–2 days after forecast starts. SW2 and DE3 tides could modify the E‐region wind driven dynamo at low latitudes, affecting the vertical plasma drift in the F‐region, leading to the forecast errors in TEC. The TEC forecast errors at high‐latitudes could be due to the change in the column integrated O/N2, associated with tidal wind variations and resultant delayed change in vertical motions. The SW2 and DE3 tides can be affected by uncertainties in winds in the mesosphere and lower thermosphere (MLT) in the mid‐to‐high latitudes. The MLT wind uncertainties are correlated with gravity wave drag (GWD), suggesting that the uncertainties in GWD can be one of the major sources of IT forecast errors.
Unlocking high-performance near-infrared photodetection: polaron-assisted organic integer charge transfer hybrids
Authors: Iqbal Muhammad Ahsan , Fang Xueqian , Abbas Yasir , Weng Xiaoliang , He Tingchao , Zeng Yu-Jia 
Published: December 2024

AbstractRoom temperature femtowatt sensitivity remains a sought-after attribute, even among commercial inorganic infrared (IR) photodetectors (PDs). While organic IR PDs are poised to emerge as a pivotal sensor technology in the forthcoming Fourth-Generation Industrial Era, their performance lags behind that of their inorganic counterparts. This discrepancy primarily stems from poor external quantum efficiencies (EQE), driven by inadequate exciton dissociation (high exciton binding energy) within organic IR materials, exacerbated by pronounced non-radiative recombination at narrow bandgaps. Here, we unveil a high-performance organic Near-IR (NIR) PD via integer charge transfer between Poly[2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene] (C-14PBTTT) donor (D) and Tetrafluorotetracyanoquinodimethane (TCNQF4) acceptor (A) molecules, showcasing strong low-energy subgap absorptions up to 2.5 µm. We observe that specifically, polaron excitation in these radical and neutral D-A blended molecules enables bound charges to exceed the Coulombic attraction to their counterions, leading to an elevated EQE (polaron absorption region) compared to Frenkel excitons. As a result, our devices achieve a high EQE of ∼107%, femtowatt sensitivity (NEP) of ~0.12 fW Hz-1/2 along a response time of ~81 ms, at room temperature for a wavelength of 1.0 µm. Our innovative utilization of polarons highlights their potential as alternatives to Frenkel excitons in high-performance organic IR PDs.
Efficacy and safety of lenvatinib plus gefitinib in lenvatinib-resistant hepatocellular carcinomas: a prospective, single-arm exploratory trial
Authors: Shi Yaoping , Cui Dan , Xia Lei , Shi Donghua , Jin Guangxin , Wang Siying , Lin Yan , Tang Xiaoyin , Chi Jiachang , Wang Tao , Li Meng , Lv Zicheng , Zheng Jiaojiao , Jia Qi , Yang Wu , Sun Zhen , Yang Fan , Feng Hao , Yuan Shengxian , Zhou Weiping , Qin Wenxin , Bernards Rene , Jin Haojie , Zhai Bo 
Published: December 2024

AbstractLenvatinib, a multi-kinase inhibitor, has been approved as first-line treatment for advanced hepatocellular carcinoma (HCC), but its efficacy is limited. We have shown previously that lenvatinib and epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) combination therapy overcomes lenvatinib resistance in HCC with high level of EGFR expression (EGFRhigh). We present here the results of a single-arm, open-label, exploratory study of lenvatinib plus the EGFR-TKI gefitinib for patients with HCC resistance to lenvatinib (NCT04642547; n = 30). Only patients with EGFRhigh HCC and progressive disease after lenvatinib treatment were recruited in the study. The most frequent adverse events of all grades were fatigue (27 patients; 90%), followed by rash (25 patients; 83.3%), diarrhea (24 patients; 80%), and anorexia (12 patients; 40%). Among 30 patients, 9 (30%) achieved a confirmed partial response and 14 (46.7%) had stable disease according to mRECIST criteria. Based on RECIST1.1, 5 (16.7%) achieved a confirmed partial response and 18 (60%) had stable disease. The estimated median progression free survival (PFS) and overall survival (OS) time were 4.4 months (95% CI: 2.5 to 5.9) and13.7 months (95% CI: 9.0 to NA), respectively. The objective response rate (ORR) of the patients in the present study compares very favorable to that seen for the two approved second line treatments for HCC (cabozantinib ORR of 4%; regorafenib ORR of 11%). Given that this combination was well-tolerated, a further clinical study of this combination is warranted.
The comprehensive SARS-CoV-2 ‘hijackome’ knowledge base
Authors: Huuskonen Sini , Liu Xiaonan , Pöhner Ina , Redchuk Taras , Salokas Kari , Lundberg Rickard , Maljanen Sari , Belik Milja , Reinholm Arttu , Kolehmainen Pekka , Tuhkala Antti , Tripathi Garima , Laine Pia , Belanov Sergei , Auvinen Petri , Vartiainen Maria , Keskitalo Salla , Österlund Pamela , Laine Larissa , Poso Antti , Julkunen Ilkka , Kakkola Laura , Varjosalo Markku 
Published: December 2024

AbstractThe continuous evolution of SARS-CoV-2 has led to the emergence of several variants of concern (VOCs) that significantly affect global health. This study aims to investigate how these VOCs affect host cells at proteome level to better understand the mechanisms of disease. To achieve this, we first analyzed the (phospho)proteome changes of host cells infected with Alpha, Beta, Delta, and Omicron BA.1 and BA.5 variants over time frames extending from 1 to 36 h post infection. Our results revealed distinct temporal patterns of protein expression across the VOCs, with notable differences in the (phospho)proteome dynamics that suggest variant-specific adaptations. Specifically, we observed enhanced expression and activation of key components within crucial cellular pathways such as the RHO GTPase cycle, RNA splicing, and endoplasmic reticulum-associated degradation (ERAD)-related processes. We further utilized proximity biotinylation mass spectrometry (BioID-MS) to investigate how specific mutation of these VOCs influence viral–host protein interactions. Our comprehensive interactomics dataset uncovers distinct interaction profiles for each variant, illustrating how specific mutations can change viral protein functionality. Overall, our extensive analysis provides a detailed proteomic profile of host cells for each variant, offering valuable insights into how specific mutations may influence viral protein functionality and impact therapeutic target identification. These insights are crucial for the potential use and design of new antiviral substances, aiming to enhance the efficacy of treatments against evolving SARS-CoV-2 variants.
The antitumor activity of TGFβ-specific T cells is dependent on IL-6 signaling
Authors: Perez-Penco Maria , Byrdal Mikkel , Lara de la Torre Lucia , Ballester Marta , Khan Shawez , Siersbæk Majken , Lecoq Inés , Madsen Cecilie Oelvang , Kjeldsen Julie Westerlin , Svane Inge Marie , Hansen Morten , Donia Marco , Johansen Julia Sidenius , Olsen Lars Rønn , Grøntved Lars , Chen Inna Markovna , Arnes Luis , Holmström Morten Orebo , Andersen Mads Hald 
Published: December 2024

AbstractAlthough interleukin (IL)-6 is considered immunosuppressive and tumor-promoting, emerging evidence suggests that it may support antitumor immunity. While combining immune checkpoint inhibitors (ICIs) and radiotherapy in patients with pancreatic cancer (PC) has yielded promising clinical results, the addition of an anti-IL-6 receptor (IL-6R) antibody has failed to elicit clinical benefits. Notably, a robust TGFβ-specific immune response at baseline in PC patients treated solely with ICIs and radiotherapy correlated with improved survival. Recent preclinical studies demonstrated the efficacy of a TGFβ-based immune modulatory vaccine in controlling PC tumor growth, underscoring the important role of TGFβ-specific immunity in PC. Here, we explored the importance of IL-6 for TGFβ-specific immunity in PC. In a murine model of PC, coadministration of the TGFβ-based immune modulatory vaccine with an anti-IL-6R antibody rendered the vaccine ineffective. IL-6R blockade hampered the development of vaccine-induced T-cells and tumoral T-cell infiltration. Furthermore, it impaired the myeloid population, resulting in increased tumor-associated macrophage infiltration and an enhanced immunosuppressive phenotype. In PC patients, in contrast to those receiving only ICIs and radiotherapy, robust TGFβ-specific T-cell responses at baseline did not correlate with improved survival in patients receiving ICIs, radiotherapy and IL-6R blockade. Peripheral blood immunophenotyping revealed that IL-6R blockade altered the T-cell and monocytic compartments, which was consistent with the findings in the murine model. Our data suggest that the antitumor efficacy of TGFβ-specific T cells in PC depends on the presence of IL-6 within the tumor. Consequently, caution should be exercised when employing IL-6R blockade in patients receiving cancer immunotherapy.
Partitioned polygenic risk scores identify distinct types of metabolic dysfunction-associated steatotic liver disease
Authors: Jamialahmadi Oveis , De Vincentis Antonio , Tavaglione Federica , Malvestiti Francesco , Li-Gao Ruifang , Mancina Rosellina M. , Alvarez Marcus , Gelev Kyla , Maurotti Samantha , Vespasiani-Gentilucci Umberto , Rosendaal Frits Richard , Kozlitina Julia , Pajukanta Päivi , Pattou François , Valenti Luca , Romeo Stefano 
Published: December 2024

Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by an excess of lipids, mainly triglycerides, in the liver and components of the metabolic syndrome, which can lead to cirrhosis and liver cancer. While there is solid epidemiological evidence that MASLD clusters with cardiometabolic disease, several leading genetic risk factors for MASLD do not increase the risk of cardiovascular disease, suggesting no causal relationship between MASLD and cardiometabolic derangement. In this work, we leveraged measurements of visceral adiposity identifying 27 previously unknown genetic loci associated with MASLD (n = 36,394), six replicated in four independent cohorts (n = 3,903). Next, we generated two partitioned polygenic risk scores based on the presence of lipoprotein retention in the liver. The two polygenic risk scores suggest the presence of at least two distinct types of MASLD, one confined to the liver resulting in a more aggressive liver disease and one that is systemic and results in a higher risk of cardiometabolic disease. These findings shed light on the heterogeneity of MASLD and have the potential to improve the prediction of clinical trajectories and inform precision medicine approaches.
Soundboard-trained dogs produce non-accidental, non-random and non-imitative two-button combinations
Authors: Bastos Amalia P. M. , Houghton Zachary N. , Naranjo Lucas , Rossano Federico 
Published: December 2024

AbstractEarly studies attempting interspecies communication with great apes trained to use sign language and Augmented Interspecies Communication (AIC) devices were limited by methodological and technological constraints, as well as restrictive sample sizes. Evidence for animals’ intentional production of symbols was met with considerable criticisms which could not be easily deflected with existing data. More recently, thousands of pet dogs have been trained with AIC devices comprising soundboards of buttons that can be pressed to produce prerecorded human words or phrases. However, the nature of pets’ button presses remains an open question: are presses deliberate, and potentially meaningful? Using a large dataset of button presses by family dogs and their owners, we investigate whether dogs’ button presses are (i) non-accidental, (ii) non-random, and (iii) not mere repetitions of their owners’ presses. Our analyses reveal that, at the population level, soundboard use by dogs cannot be explained by random pressing, and that certain two-button concept combinations appear more often than expected by chance at the population level. We also find that dogs’ presses are not perfectly predicted by their owners’, suggesting that dogs’ presses are not merely repetitions of human presses, therefore suggesting that dog soundboard use is deliberate.
Optimal thresholds and key parameters for predicting influenza A virus transmission events in ferrets
Authors: Kieran Troy J. , Sun Xiangjie , Maines Taronna R. , Belser Jessica A. 
Published: December 2024

AbstractAlthough assessments of influenza A virus transmissibility in the ferret model play a critical role in pandemic risk evaluations, few studies have investigated which virological data collected from virus-inoculated animals are most predictive of subsequent virus transmission to naïve contacts. We compiled viral titer data from >475 ferrets inoculated with 97 contemporary IAV (including high- and low-pathogenicity avian, swine-origin, and human viruses of multiple HA subtypes) that served as donors for assessments of virus transmission in the presence of direct contact (DCT) or via respiratory droplets (RDT). A diversity of molecular determinants, clinical parameters, and infectious titer measurements and derived quantities were examined to identify which metrics were most statistically supported with transmission outcome. Higher viral loads in nasal wash (NW) specimens were strongly associated with higher transmission frequencies in DCT, but not RDT models. However, viruses that reached peak titers in NW specimens early (day 1 p.i.) were strongly associated with higher transmission in both models. Interestingly, viruses with ‘intermediate’ transmission outcomes (33–66%) had NW titers and derived quantities more similar to non-transmissible viruses (<33%) in a DCT setting, but with efficiently transmissible viruses (>67%) in a RDT setting. Machine learning was employed to further assess the predictive role of summary measures and varied interpretation of intermediate transmission outcomes in both DCT and RDT models, with models employing these different thresholds yielding high performance metrics against both internal and external datasets. Collectively, these findings suggest that higher viral load in inoculated animals can be predictive of DCT outcomes, whereas the timing of when peak titers are detected in inoculated animals can inform RDT outcomes. Identification that intermediate transmission outcomes should be contextualized relative to the transmission mode assessed provides needed refinement towards improving interpretation of ferret transmission studies in the context of pandemic risk assessment.
The role of ER exit sites in maintaining P-body organization and integrity during Drosophila melanogaster oogenesis
Authors: Milano Samantha N , Bayer Livia V , Ko Julie J , Casella Caroline E , Bratu Diana P 
Published: December 2024

Abstract
Processing bodies (P-bodies) are cytoplasmic membrane-less organelles which host multiple mRNA processing events. While the fundamental principles of P-body organization are beginning to be elucidated in vitro, a nuanced understanding of how their assembly is regulated in vivo remains elusive. Here, we investigate the potential link between ER exit sites and P-bodies in Drosophila melanogaster egg chambers. Employing a combination of live and super-resolution imaging, we find that P-bodies associated with ER exit sites are larger and less mobile than cytoplasmic P-bodies, indicating that they constitute a distinct class of P-bodies. Moreover, we demonstrate that altering the composition of ER exit sites has differential effects on core P-body proteins (Me31B, Cup, and Trailer Hitch), suggesting a potential role for ER exit sites in P-body organization. Furthermore, we show that in the absence of ER exit sites, P-body integrity is compromised and the stability and translational repression efficiency of the maternal mRNA, oskar, are reduced. Together, our data highlights the crucial role of ER exit sites in governing P-body organization.
State of the interactomes: an evaluation of molecular networks for generating biological insights
Authors: Wright Sarah N , Colton Scott , Schaffer Leah V , Pillich Rudolf T , Churas Christopher , Pratt Dexter , Ideker Trey 
Published: December 2024

AbstractAdvancements in genomic and proteomic technologies have powered the creation of large gene and protein networks (“interactomes”) for understanding biological systems. However, the proliferation of interactomes complicates the selection of networks for specific applications. Here, we present a comprehensive evaluation of 45 current human interactomes, encompassing protein-protein interactions as well as gene regulatory, signaling, colocalization, and genetic interaction networks. Our analysis shows that large composite networks such as HumanNet, STRING, and FunCoup are most effective for identifying disease genes, while smaller networks such as DIP, Reactome, and SIGNOR demonstrate stronger performance in interaction prediction. Our study provides a benchmark for interactomes across diverse biological applications and clarifies factors that influence network performance. Furthermore, our evaluation pipeline paves the way for continued assessment of emerging and updated interaction networks in the future.
Device Use Among Spanish–English Bilingual and English Monolingual Children Who Are Deaf and Hard of Hearing
Authors: Wiseman Kathryn B. , Cowan Tiana M. , Calandruccio Lauren , Walker Elizabeth A. , Rodriguez Barbara , Oleson Jacob J. , McCreery Ryan W. , Leibold Lori J. , Buss Emily 
Published: December 2024

Purpose:
This report compares device use in a cohort of Spanish–English bilingual and English monolingual children who are deaf and hard of hearing, including children fitted with traditional hearing aids, cochlear implants (CIs), and/or bone-conduction hearing devices.

Method:
Participants were 84 Spanish–English bilingual children and 85 English monolingual children from clinical sites across the United States. The data represent a subset obtained in a larger clinical trial. Device use obtained via data logging was modeled as a function of language group, device type, child age, sex, and parental education.

Results:
Among children with traditional hearing aids, bilingual children wore their devices significantly fewer hours per day than monolingual children, but this group difference was not observed for children with CIs or bone-conduction hearing devices. In the monolingual group, older children wore their devices significantly more hours than younger children, but this effect of age was not present in the bilingual group. Parent report was consistent with data logging for bilingual and monolingual children.

Conclusions:
Spanish–English bilingual hearing aid users wore their devices less than their English monolingual peers, particularly among older children. This group effect was not observed for children with CIs or bone-conduction hearing devices. Additional studies are needed to identify factors that contribute to device use among bilingual children with hearing aids.
12b 500MS/s successive‐approximation‐register‐assisted pipeline analogue‐to‐digital convertor using a four‐stage ring amplifier with coarse‐analogue‐to‐digital convertor embedded
Authors: Liu Linghao , Ren Junyan , Ye Fan 
Published: December 2024

AbstractThis article presents a 12b 500MS/s successive‐approximation‐register‐assisted pipeline analogue‐to‐digital converter. By adopting a new auto‐zero scheme, a calibration‐free four‐stage ring residue amplifier with a small offset cancellation capacitor is proposed. In addition, the coarse‐analogue‐to‐digital converter of the second stage is embedded into the amplification phase, which relaxes the comparison periods of the first and second stages by 25.0% and 17.4%, respectively. Post‐simulated in 28‐nm CMOS technology with a 0.9 V supply, the analogue‐to‐digital converter achieves 62.2 dB SNDR and 78.1 dB SFDR. It consumes 8.45 mW with an on‐chip reference voltage buffer, resulting in Schreier's figure of merit (FoMS) of 166.9 dB.
A novel compact multifunctional coaxial to waveguide power combining transitions for X‐band applications
Authors: Kumar Manoj , Basavarajappa Gowrish 
Published: December 2024

AbstractThis paper presents the design of novel compact multifunctional coaxial to waveguide power combining transition (PCT) for X‐band applications. For the proof of the proposed concept, 2‐way PCT operating over the entire X‐band (8.2–12.4 GHz) and 4‐way PCT operation from 9.5 to 10.8 GHz are designed, developed, and characterised. Two‐way PCT achieves a measured return loss better than 14 dB over the operating band, and the measured amplitude imbalance and phase imbalance are within 0.25 dB and 4°, respectively. Four‐way PCT achieves a measured return loss better than 15 dB over the operating band, and the measured amplitude imbalance and phase imbalance are within 1 dB and 10°, respectively. Furthermore, a 6‐way PCT is also designed, fabricated, and measured to demonstrate the scalability of the proposed concept. The 6‐way PCT achieves the measured return loss better than 15 dB from 9.9 to 10.475 GHz, and measured amplitude and phase imbalances are within 0.6 dB and 10°, respectively. The designed power combining transition is proposed to be used in X‐band applications like antenna array applications and power combining applications.
Dual‐layer model predictive control‐based scheduling of integrated electricity‐hydrogen‐heat microgrid
Authors: Han Pengfei , Xu Xiaoyuan , Yan Zheng , Tan Zhenfei 
Published: December 2024

AbstractAs a newly widely used energy source, hydrogen has not yet been integrated with other energies efficiently, leading to low energy efficiency and high operating costs. This paper develops a novel cooperation model to coordinate electricity, hydrogen, and district heating systems and reduce operating costs. First, the mathematical model of electricity, hydrogen, and district heating systems coupled by electrolysers is established, and the bidirectional heat exchange (BHE) between hydrogen production and district heating networks (DHNs) is proposed. Then, a dual‐layer model predictive control (DLMPC) method is proposed for the integrated electricity, hydrogen, and heating microgrid (IEHHM) scheduling. The upper layer aims to deal with the hourly power variation and determine the IEHHM operation schedules, and the lower layer revises the power of electrolysers and combined heat and power (CHP) plants to follow the real‐time power variation of renewable energy generations (REGs). Simulation results show that: (1) BHE improves the thermal dynamics of electrolysers and DHNs, enhancing operational flexibility; (2) The DLMPC method enables timely adjustments to the dispatch schedule, reducing operating costs by responding to multi‐time‐scale power variations from REGs.