bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced Deep Convection and Bottom Water Formation Due To Antarctic Meltwater in a Multi‐Model Ensemble
Authors: Chen Jia‐Jia , Swart Neil C. , Beadling Rebecca , Cheng Xuhua , Hattermann Tore , Jüling André , Li Qian , Marshall John , Martin Torge , Muilwijk Morven , Pauling Andrew G. , Purich Ariaan , Smith Inga J. , Thomas Max 
Published: December 2023

AbstractThe additional water from the Antarctic ice sheet and ice shelves due to climate‐induced melt can impact ocean circulation and global climate. However, the major processes driving melt are not adequately represented in Coupled Model Intercomparison Project phase 6 (CMIP6) models. Here, we analyze a novel multi‐model ensemble of CMIP6 models with consistent meltwater addition to examine the robustness of the modeled response to meltwater, which has not been possible in previous single‐model studies. Antarctic meltwater addition induces a substantial weakening of open‐ocean deep convection. Additionally, Antarctic Bottom Water warms, its volume contracts, and the sea surface cools. However, the magnitude of the reduction varies greatly across models, with differing anomalies correlated with their respective mean‐state climatology, indicating the state‐dependency of the climate response to meltwater. A better representation of the Southern Ocean mean state is necessary for narrowing the inter‐model spread of response to Antarctic meltwater.
Geocoronal Solar Wind Charge Exchange Process Associated With the 2006‐December‐13 Coronal Mass Ejection Event
Authors: Zhou Yu , Yamasaki Noriko Y. , Toriumi Shin , Mitsuda Kazuhisa 
Published: December 2023

AbstractWe report the discovery of a geocoronal solar wind charge exchange (SWCX) event corresponding to the well‐known 2006 December 13th coronal mass ejection (CME) event. Strong evidence for the charge exchange origin of this transient diffuse emission is provided by prominent non‐thermal emission lines at energies of O7+, Ne9+, Mg11+, Si12+, Si13+. Especially, a 0.53 keV emission line that most likely arises from the N5+ 1s15p1 → 1s2 transition is detected. Previously, the forecastability of SWCX occurrence with proton flares has been disputed. In this particular event, we found that the SWCX signal coincided with the arrival of the magnetic cloud inside CME, triggered with a time delay after the proton flux fluctuation as the CME shock front passed through the Earth. Moreover, a spacecraft orbital modulation in SWCX light curve suggests that the emission arises close to the Earth. The line of sight was found to always pass through the northern magnetospheric cusp. The SWCX intensity was high when the line of sight passed the dusk side of the cusp, suggesting an azimuthal anisotropy in the flow of solar‐wind ions inside the cusp. An axisymmetric SWCX emission model is found to underestimate the observed peak intensity by a factor of about 50. We suggest this discrepancy is related to the azimuthal anisotropy of the solar‐wind flow in the cusp.
Combined Effects of Fronts, Upwelling and the Biological Pump on Organophosphate Esters in the Changjiang (Yangtze) River Estuary During Summer
Authors: Zhang Jinghua , Ma Yuxin , Zhong Yisen , Lohmann Rainer 
Published: December 2023

AbstractEstuarine and coastal environments are important transport pathways and regional sinks for anthropogenic pollutants. In this study, the occurrence and transport of the continuously released organophosphate esters (OPEs) was investigated together with physical and biochemical parameters throughout the water column in the Changjiang (Yangtze) River estuary during the summer. Total dissolved and particulate OPEs showed great spatial heterogeneity, with mean concentrations of 550 ± 280 ng/L in the estuary, 110 ± 270 ng/L in the front/upwelling zone, and 410 ± 450 ng/L in the continental shelf. OPE concentrations in the estuarine bottom waters were high due to massive terrestrial/sediment inputs. In contrast, the “surface enrichment and depth depletion” of OPEs in the continental shelf was closely related to seasonal stratification. Reduced OPE concentrations were observed in the frontal/upwelling zone due to isopycnal heaving. Frontal activity and upwelling induced phytoplankton blooms in the coastal regions, which jointly contributed to elevated OPEs beneath surface water with high phytoplankton aggregation. The OPEs mainly originated from wastewater treatment plant discharges, industrial pollution and consumer products. These OPEs generally posed a low ecological risk to aquatic lives, but their long‐term effects cannot be ignored due to their continuous high production, usage and release.
Composite healthy lifestyle, socioeconomic deprivation, and mental well-being during the COVID-19 pandemic: a prospective analysis
Authors: Hu Gang , Qin Huibo , Su Binbin , Bao Yanping , Liang Zhengting , Wang Yunhe 
Published: December 2023

AbstractThe adverse psychological and social impacts of COVID-19 pandemic are well characterized, but the role of composite, modifiable lifestyle factors that may interact to mitigate these impacts is not. The effect of socioeconomic deprivation on these lifestyle risks also remains unclear. Based on a nationally representative, longitudinal cohort, we assessed the association between a combination of pre-pandemic lifestyle factors and mental health conditions during pandemic, and the contribution of deprivation to it. Composite lifestyle factors included BMI, smoking status, alcohol consumption, physical activity, sedentary time, sleep duration, and fruit and vegetable intake, with lifestyle scores and lifestyle categories calculated for each participant. Symptoms of depression and anxiety, and personal well-being were assessed by validated scales during the pandemic. Socioeconomic deprivation was characterized by both individual-level (income, wealth, and education) and group-level factors (Index of Multiple Deprivation). Of the 5049 eligible participants (mean [SD] age, 68.1 [10.9] years; 57.2% were female) included in the study, 41.6% followed a favorable lifestyle, 48.9% followed an intermediate lifestyle, and 9.5% followed an unfavorable lifestyle. Compared with favorable lifestyle category, participants in the intermediate and unfavorable lifestyle category were at increased risk of mental health conditions, with the hazard ratio (HR) for trend per increment change towards unfavorable category of 1.17 (95% CI 1.09–1.26) for depression, 1.23 (1.07–1.42) for anxiety, and 1.39 (1.20–1.61) for low well-being. A significant trend of lower risk for mental health conditions with increasing number of healthy lifestyle factors was observed (P < 0.001 for trend). There were no significant interactions between lifestyle factors and socioeconomic deprivation for any of the outcomes, with similar HRs for trend per one increment change in lifestyle category observed in each deprivation group. Compared with those in the least deprived group with favorable lifestyle, participants in the most deprived group adherent to unfavorable lifestyle had the highest risk of mental health outcomes. These results suggest that adherence to a broad combination of healthy lifestyle factors was associated with a significantly reduced risk of mental health conditions during the COVID-19 pandemic. Lifestyle factors, in conjunction with socioeconomic deprivation, independently contribute to the risk of mental health issues. Although further research is needed to assess causality, the current findings support public health strategies and individual-level interventions that provide enhanced support in areas of deprivation and target multiple lifestyle factors to reduce health inequalities and promote mental well-being during the ongoing COVID-19 pandemic.
Analysis of off-tumour toxicities of T-cell-engaging bispecific antibodies via donor-matched intestinal organoids and tumouroids
Authors: Harter Marius F. , Recaldin Timothy , Gerard Regine , Avignon Blandine , Bollen Yannik , Esposito Cinzia , Guja-Jarosz Karolina , Kromer Kristina , Filip Adrian , Aubert Julien , Schneider Anneliese , Bacac Marina , Bscheider Michael , Stokar-Regenscheit Nadine , Piscuoglio Salvatore , Beumer Joep , Gjorevski Nikolche 
Published: December 2023

AbstractPredicting the toxicity of cancer immunotherapies preclinically is challenging because models of tumours and healthy organs do not typically fully recapitulate the expression of relevant human antigens. Here we show that patient-derived intestinal organoids and tumouroids supplemented with immune cells can be used to study the on-target off-tumour toxicities of T-cell-engaging bispecific antibodies (TCBs), and to capture clinical toxicities not predicted by conventional tissue-based models as well as inter-patient variabilities in TCB responses. We analysed the mechanisms of T-cell-mediated damage of neoplastic and donor-matched healthy epithelia at a single-cell resolution using multiplexed immunofluorescence. We found that TCBs that target the epithelial cell-adhesion molecule led to apoptosis in healthy organoids in accordance with clinical observations, and that apoptosis is associated with T-cell activation, cytokine release and intra-epithelial T-cell infiltration. Conversely, tumour organoids were more resistant to damage, probably owing to a reduced efficiency of T-cell infiltration within the epithelium. Patient-derived intestinal organoids can aid the study of immune–epithelial interactions as well as the preclinical and clinical development of cancer immunotherapies.
Study of AEB and active seat belt on driver injury in vehicle–vehicle frontal oblique crash
Authors: Li Pingfei , Lei Yi , Liao Jingqian , Zhang Daowen , Dong Xinchi , Zhang Tianshu 
Published: December 2023

AbstractThe safety of vehicle occupants in oblique collision scenarios continues to pose challenges, even with the implementation of Automatic Emergency Braking (AEB) systems. While AEB reduces collision risks, studies indicate it may heighten injury risks for out-of-position (OOP) occupants. To counteract this issue, the integration of active seat belts in vehicles equipped with AEB systems is recommended. Firstly, this study established an oblique angle collision scenario post-AEB activation using data from the Chinese National Automobile Accident In-depth Investigation System (NAIS) database, analyzed through Prescan software. The dynamic response of the vehicle was examined. Following this, finite element (FE) models were validated to assess the effects of collision overlap rate, AEB braking strategy, and active seat belt pre-tensioning on occupant injuries and kinematics. Under specific collision conditions, the impact of the timing and amount of seat belt pre-tensioning, as well as airbag deployment timing on occupant injuries, was also explored. Findings revealed that a 75% collision overlap rate significantly increases driver injury risk. Active seat belts effectively mitigate injuries caused by OOP statuses during AEB interventions, with the lowest Weighted Injury Criterion (WIC) observed at a pre-tensioning time of 200 ms for active seat belts. The study further suggests that optimal results in reducing occupant injuries are achieved when active pre-tensioning seat belts are complemented by appropriately timed airbag deployment.
Insights into isotherms, kinetics, and thermodynamics of adsorption of acid blue 113 from an aqueous solution of nutraceutical industrial fennel seed spent
Authors: Taqui Syed Noeman , Syed Akheel Ahmed , Mubarak Nabisab Mujawar , Farade Rizwan Abutaleeb , Khan M. A. Majeed , Kalam Md. Abul , Dehghani Mohammad Hadi , Soudagar Manzoore Elahi Mohammad , Rather Rauoof Ahmad , Shamshuddin Sathgatta Zaheeruddin Mohamed , Karri Rama Rao 
Published: December 2023

AbstractResearch studies have been carried out to accentuate Fennel Seed Spent, a by-product of the Nutraceutical Industry, as an inexpensive, recyclable and operational biosorbent for bioremediation of Acid Blue 113 (AB113) in simulated water-dye samples and textile industrial effluent (TIE). The physical process of adhesion of AB113 on the surface of the biosorbent depends on various parameters, such as the initial amount of the dye, amount and expanse of the biosorbent particles, pH of the solution and temperature of the medium. The data obtained was analyzed using three two-parameter and five three-parameter adsorption isotherm models to glean the adsorbent affinities and interaction mechanism of the adsorbate molecules and adsorbent surface. The adsorption feature study is conducted employing models of Weber-Morris, pseudo 1st and 2nd order, diffusion film model, Dumwald-Wagner and Avrami model. The study through 2nd order pseudo and Avrami models produced complementary results for the authentication of experimental data. The thermodynamic features, ΔG0, ΔH0, and ΔS0 of the adsorption process are acclaimed to be almost spontaneous, physical in nature and endothermic in their manifestation. Surface characterization was carried out using Scanner Electron Microscopy, and identification and determination of chemical species and molecular structure was performed using Infrared Spectroscopy (IR). Maximum adsorption evaluated using statistical optimization with different combinations of five independent variables to study the individual as well as combined effects by Fractional Factorial Experimental Design (FFED) was 236.18 mg g−1 under optimized conditions; pH of 2, adsorbent dosage of 0.500 g L−1, and an initial dye concentration of 209.47 mg L−1 for an adsorption time of 126.62 min with orbital shaking of 165 rpm at temperature 49.95 °C.
Return to work after traumatic spinal fractures and spinal cord injuries: a retrospective cohort study
Authors: Keihanian Fateme , Homaie Rad Enayatollah , Samadi Shal Simin , Pourreza Nooshin , Eramsadati Leila Khoochakinejad , Hosseini Malekroudi Seyedeh Mitra , Khodadadi-Hassankiadeh Naema 
Published: December 2023

AbstractThis study aimed to determine the factors associated with return to work (RTW) after traumatic spinal fracture and spinal cord injury. It provided a predictive model for RTW among patients with spinal fractures and spinal cord injury and determined important factors influencing the time to RTW after injury. A retrospective cohort study was conducted in Poursina Tertiary Hospital, Guilan, Iran between May 2017 and May 2020. Patients aged 18 to 65 who were hospitalized with traumatic spinal fractures and spinal cord injuries were included. Demographic and clinical data were collected from the National Spinal Column/Cord Injury Registry of Iran (NSCIR-IR). A researcher-administered questionnaire was used through a telephone interview to obtain complementary data on social and occupational variables. Kaplan–Meier survival analysis was used to estimate the average time to RTW and the predictors of RTW were determined by multivariate Cox regression model. Of the 300 patients included, 78.6% returned to work and the average time to RTW was about 7 months. The mean age of the participants was 45.63 ± 14.76 years old. Among the study variables, having a Bachelor’s degree (HR 2.59; 95% CI 1.16–5.77; P = 0.019), complications after injury (HR 0.47; 95% CI 0.35–0.62; P = 0.0001), full coverage health insurance (HR 1.73; 95% CI 1.10–2.72; P = 0.016), opium use (HR 0.48; 95% CI 0.26–0.90; P = 0.023), number of vertebral fractures (HR 0.82; 95% CI 0.67–0.99; P = 0.046), and length of hospital stay (HR 0.95; 95% CI 0.93–0.98; P = 0.001) were found to be significant in predicting RTW in Cox regression analysis. Our analysis showed that wealthier people and those with high job mobility returned to work later.
Protein–protein interaction network module changes associated with the vertebrate fin-to-limb transition
Authors: Fernando Pasan C. , Mabee Paula M. , Zeng Erliang 
Published: December 2023

AbstractEvolutionary phenotypic transitions, such as the fin-to-limb transition in vertebrates, result from modifications in related proteins and their interactions, often in response to changing environment. Identifying these alterations in protein networks is crucial for a more comprehensive understanding of these transitions. However, previous research has not attempted to compare protein–protein interaction (PPI) networks associated with evolutionary transitions, and most experimental studies concentrate on a limited set of proteins. Therefore, the goal of this work was to develop a network-based platform for investigating the fin-to-limb transition using PPI networks. Quality-enhanced protein networks, constructed by integrating PPI networks with anatomy ontology data, were leveraged to compare protein modules for paired fins (pectoral fin and pelvic fin) of fishes (zebrafish) to those of the paired limbs (forelimb and hindlimb) of mammals (mouse). This also included prediction of novel protein candidates and their validation by enrichment and homology analyses. Hub proteins such as shh and bmp4, which are crucial for module stability, were identified, and their changing roles throughout the transition were examined. Proteins with preserved roles during the fin-to-limb transition were more likely to be hub proteins. This study also addressed hypotheses regarding the role of non-preserved proteins associated with the transition.
Topographic comparison of the retinal microvascular changes between patients with compressive and glaucomatous optic neuropathies
Authors: Lim Hyunah , Lee Byung Joo , Kook Michael S. , Sung Kyung Rim , Kim Ko Eun , Moon Yeji 
Published: December 2023

AbstractWe investigated the difference in optical coherence tomography angiography characteristics between the patients with compressive optic neuropathy (CON, n = 26) and glaucomatous optic neuropathy (GON, n = 26), who were matched for the severity of visual field defect. The peripapillary retinal nerve fiber layer (pRNFL) thickness in the nasal and temporal sectors was thinner in the CON group, whereas the inferior pRNFL thickness was thinner in the GON group. Accordingly, the CON group had lower peripapillary vessel density (pVD) in the nasal and temporal sectors, and the GON group in the inferior sector. In the macular area, the CON group had a thinner macular ganglion cell-inner plexiform layer in the superior and nasal sectors, whereas the GON group in the inferior sector. However, the CON group did not have a lower macular VD than the GON group in any sector, whereas the GON group exhibited lower superficial capillary plexus VD in the superior, inferior, and temporal sectors. Comparison of the structure–vasculature correlation revealed a significant difference in the nasal and temporal peripapillary areas and superior and nasal macular sectors; a decrease in VD was greater in the GON group than in the CON group when the comparable structural change occurred.
Enantiomorph conversion in single crystals of the Weyl semimetal CoSi
Authors: Carrillo-Cabrera Wilder , Simon Paul , Schmidt Marcus , König Markus , Borrmann Horst , Winkelmann Aimo , Burkhardt Ulrich , Grin Yuri 
Published: December 2023

AbstractChiral intermetallic phases may show unusual chemical and physical properties with nontrivial structure-property relationship. It is therefore of particular interest to study the structural conversion between domains of different handedness. Here, the atomic decoration of the enantiomorph exchange area within single crystal of the Weyl semimetal CoSi is determined by a combination of atomic-resolution scanning transmission electron microscopy imaging, single crystal X-ray diffraction and quantum chemical analysis of atomic interactions. Two-atomic [CoSi] units are shown to be the bonding base for the FeSi-type structure and may be considered as ‘pseudo-molecules’, thinking of molecular organic crystals. Tiny reorganisation of atomic interactions within these units results in the appearance of sequence ‘faults’ in the structure pattern i.e. in a different structural motif in the enantiomorph exchange area, which – contrary to the A and B enantiomorphs of CoSi – contains an inversion centre and allows a local enantiomorph ‘conversion’. Due to the special features of atomic interactions, the reorganisation of multi-atomic bonds leads to slightly higher total energy. This appears within one and the same grain which is prepared by the short distance chemical vapor transport.
Deep learning and transfer learning identify breast cancer survival subtypes from single-cell imaging data
Authors: Yadav Shashank , Zhou Shu , He Bing , Du Yuheng , Garmire Lana X. 
Published: December 2023

Abstract
Background
Single-cell multiplex imaging data have provided new insights into disease subtypes and prognoses recently. However, quantitative models that explicitly capture single-cell resolution cell-cell interaction features to predict patient survival at a population scale are currently missing.

Methods
We quantified hundreds of single-cell resolution cell-cell interaction features through neighborhood calculation, in addition to cellular phenotypes. We applied these features to a neural-network-based Cox-nnet survival model to identify survival-associated features. We used non-negative matrix factorization (NMF) to identify patient survival subtypes. We identified atypical subpopulations of triple-negative breast cancer (TNBC) patients with moderate prognosis and Luminal A patients with poor prognosis and validated these subpopulations by label transferring using the UNION-COM method.

Results
The neural-network-based Cox-nnet survival model using all cellular phenotype and cell-cell interaction features is highly predictive of patient survival in the test data (Concordance Index > 0.8). We identify seven survival subtypes using the top survival features, presenting distinct profiles of epithelial, immune, and fibroblast cells and their interactions. We reveal atypical subpopulations of TNBC patients with moderate prognosis (marked by GATA3 over-expression) and Luminal A patients with poor prognosis (marked by KRT6 and ACTA2 over-expression and CDH1 under-expression). These atypical subpopulations are validated in TCGA-BRCA and METABRIC datasets.

Conclusions
This work provides an approach to bridge single-cell level information toward population-level survival prediction.
The shelterin component TRF2 mediates columnar stacking of human telomeric chromatin
Authors: Wong Sook Yi , Soman Aghil , Korolev Nikolay , Surya Wahyu , Chen Qinming , Shum Wayne , van Noort John , Nordenskiöld Lars 
Published: December 2023

AbstractTelomere repeat binding factor 2 (TRF2) is an essential component of the telomeres and also plays an important role in a number of other non-telomeric processes. Detailed knowledge of the binding and interaction of TRF2 with telomeric nucleosomes is limited. Here, we study the binding of TRF2 to in vitro-reconstituted kilobasepair-long human telomeric chromatin fibres using electron microscopy, single-molecule force spectroscopy and analytical ultracentrifugation sedimentation velocity. Our electron microscopy results revealed that full-length and N-terminally truncated TRF2 promote the formation of a columnar structure of the fibres with an average width and compaction larger than that induced by the addition of Mg2+, in agreement with the in vivo observations. Single-molecule force spectroscopy showed that TRF2 increases the mechanical and thermodynamic stability of the telomeric fibres when stretched with magnetic tweezers. This was in contrast to the result for fibres reconstituted on the ‘Widom 601’ high-affinity nucleosome positioning sequence, where minor effects on fibre stability were observed. Overall, TRF2 binding induces and stabilises columnar fibres, which may play an important role in telomere maintenance.