bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses
Authors: Gross Sean M. , Dane Mark A. , Smith Rebecca L. , Devlin Kaylyn L. , McLean Ian C. , Derrick Daniel S. , Mills Caitlin E. , Subramanian Kartik , London Alexandra B. , Torre Denis , Evangelista John Erol , Clarke Daniel J. B. , Xie Zhuorui , Erdem Cemal , Lyons Nicholas , Natoli Ted , Pessa Sarah , Lu Xiaodong , Mullahoo James , Li Jonathan , Adam Miriam , Wassie Brook , Liu Moqing , Kilburn David F. , Liby Tiera A. , Bucher Elmar , Sanchez-Aguila Crystal , Daily Kenneth , Omberg Larsson , Wang Yunguan , Jacobson Connor , Yapp Clarence , Chung Mirra , Vidovic Dusica , Lu Yiling , Schurer Stephan , Lee Albert , Pillai Ajay , Subramanian Aravind , Papanastasiou Malvina , Fraenkel Ernest , Feiler Heidi S. , Mills Gordon B. , Jaffe Jake D. , Ma’ayan Avi , Birtwistle Marc R. , Sorger Peter K. , Korkola James E. , Gray Joe W. , Heiser Laura M. 
Published: October 2022

AbstractThe phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods (synapse.org/LINCS_MCF10A). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.
Multivalent binding kinetics resolved by fluorescence proximity sensing
Authors: Schulte Clemens , Soldà Alice , Spänig Sebastian , Adams Nathan , Bekić Ivana , Streicher Werner , Heider Dominik , Strasser Ralf , Maric Hans Michael 
Published: October 2022

AbstractMultivalent protein interactors are an attractive modality for probing protein function and exploring novel pharmaceutical strategies. The throughput and precision of state-of-the-art methodologies and workflows for the effective development of multivalent binders is currently limited by surface immobilization, fluorescent labelling and sample consumption. Using the gephyrin protein, the master regulator of the inhibitory synapse, as benchmark, we exemplify the application of Fluorescence proximity sensing (FPS) for the systematic kinetic and thermodynamic optimization of multivalent peptide architectures. High throughput synthesis of +100 peptides with varying combinatorial dimeric, tetrameric, and octameric architectures combined with direct FPS measurements resolved on-rates, off-rates, and dissociation constants with high accuracy and low sample consumption compared to three complementary technologies. The dataset and its machine learning-based analysis deciphered the relationship of specific architectural features and binding kinetics and thereby identified binders with unprecedented protein inhibition capacity; thus, highlighting the value of FPS for the rational engineering of multivalent inhibitors.
Rapid quantification of miRNAs using dynamic FRET-FISH
Authors: Kim Juyoung , Kang Chanshin , Shin Soochul , Hohng Sungchul 
Published: October 2022

AbstractMicroRNAs (miRNAs) are short regulatory RNAs that control gene expression at the post-transcriptional level. Various miRNAs playing important roles in cancer development are emerging as promising diagnostic biomarkers for early cancer detection. Accurate miRNA detection, however, remains challenging because they are small and highly homologous. Recently developed miRNA detection techniques based on single-molecule imaging enabled highly specific miRNA quantification without amplification, but the time required for these techniques to detect a single miRNA was larger than 10 minutes, making rapid profiling of numerous miRNAs impractical. Here we report a rapid miRNA detection technique, dynamic FRET-FISH, in which single-molecule imaging at high probe concentrations and thus high-speed miRNA detection is possible. Dynamic FRET-FISH can detect miRNAs in 10 s at 1.2 μM probe concentration while maintaining the high-specificity of single-nucleotide discrimination. We expect dynamic FRET-FISH will be utilized for early detection of cancers by profiling hundreds of cancer biomarkers in an hour.
Opposing comparable large effects of fine aerosols and coarse sea spray on marine warm clouds
Authors: Liu Fan , Mao Feiyue , Rosenfeld Daniel , Pan Zengxin , Zang Lin , Zhu Yannian , Yin Jianhua , Gong Wei 
Published: October 2022

AbstractFine aerosols, by acting as cloud condensation nuclei, suppress rainfall and enhance the albedo and coverage of marine warm clouds, thereby partly counteracting the greenhouse-induced warming. While this is relatively well documented, the co-existing opposite effects of giant cloud condensation nuclei from coarse sea spray aerosols are poorly quantified. Here, satellite measurements show that the effects of coarse sea spray aerosols have comparable magnitudes with opposite sign to those of fine aerosols. For fixed cloud liquid water path and coarse sea spray aerosols, increasing fine aerosols decreased rainfall flux and cloud drop effective radius by a factor of 1/4 and 40%, respectively. Conversely, for fixed fine aerosols and cloud liquid water path, added coarse sea spray aerosols enhanced rainfall flux and cloud drop effective radius by a factor of 4 and 35%, respectively. These large and contrasting effects are independent on meteorological conditions. These processes must be fully incorporated into climate models to faithfully represent aerosol effects on clouds, precipitation, and radiative forcing.
Ecosystem productivity has a stronger influence than soil age on surface soil carbon storage across global biomes
Authors: Plaza César , García-Palacios Pablo , Berhe Asmeret Asefaw , Barquero Jesús , Bastida Felipe , Png G. Kenny , Rey Ana , Bardgett Richard D. , Delgado-Baquerizo Manuel 
Published: October 2022

AbstractInteractions between soil organic matter and minerals largely govern the carbon sequestration capacity of soils. Yet, variations in the proportions of free light (unprotected) and mineral-associated (protected) carbon as soil develops in contrasting ecosystems are poorly constrained. Here, we studied 16 long-term chronosequences from six continents and found that the ecosystem type is more important than soil age (centuries to millennia) in explaining the proportion of unprotected and mineral-associated carbon fractions in surface soils across global biomes. Soil carbon pools in highly productive tropical and temperate forests were dominated by the unprotected carbon fraction and were highly vulnerable to reductions in ecosystem productivity and warming. Conversely, soil carbon in low productivity, drier and colder ecosystems was dominated by mineral-protected carbon, and was less responsive to warming. Our findings emphasize the importance of conserving ecosystem productivity to protect carbon stored in surface soils.
Eco-Evo-Devo of petal pigmentation patterning
Authors: Fairnie Alice L.M , Yeo May T.S. , Gatti Stefano , Chan Emily , Travaglia Valentina , Walker Joseph F. , Moyroud Edwige 
Published: October 2022

Abstract
Colourful spots, stripes and rings decorate the corolla of most flowering plants and fulfil important biotic and abiotic functions. Spatial differences in the pigmentation of epidermal cells can create these patterns. The last few years have yielded new data that have started to illuminate the mechanisms controlling the function, formation and evolution of petal patterns. These advances have broad impacts beyond the immediate field as pigmentation patterns are wonderful systems to explore multiscale biological problems: from understanding how cells make decisions at the microscale to examining the roots of biodiversity at the macroscale. These new results also reveal there is more to petal patterning than meets the eye, opening up a brand new area of investigation. In this mini-review, we summarise our current knowledge on the Eco-Evo-Devo of petal pigmentation patterns and discuss some of the most exciting yet unanswered questions that represent avenues for future research.
A modified extended min‐sum algorithm based on posterior probability thresholding for non‐binary low‐density parity‐check codes
Authors: Zhao Yatong , Wang Liqian , Zhu Miao , Wang Weiming , Tao Kai , Shi Yinlong , Chen Xue 
Published: October 2022

AbstractThis letter focuses on improving the error correction performance of the extended min‐sum (EMS) decoding algorithm. Introducing factor/offset modifications in the check node update process of the EMS algorithm can improve the performance. Based on this, the authors propose a novel threshold‐based modified EMS algorithm that introduces the factor/offset in a targeted manner by setting a threshold for the posterior probability. Simulation results show that an additional performance gain of the order of 0.08 dB is obtained with the proposed method without significantly increasing the complexity of the method.
Improving CME evolution and arrival predictions with AMR and grid stretching in Icarus
Authors: Baratashvili T. , Verbeke C. , Wijsen N. , Poedts S. 
Published: October 2022

Context.Coronal mass ejections (CMEs) are one of the main drivers of disturbances in interplanetary space. Strong CMEs, when directed towards the Earth, cause geomagnetic storms upon interacting with the Earth’s magnetic field, and can cause significant damage to our planet and affect everyday life. As such, efficient space weather prediction tools are necessary to forecast the arrival and impact of CME eruptions. Recently, a new heliospheric model called Icarus was developed based on MPI-AMRVAC, which is a 3D ideal magnetohydrodynamics model for the solar wind and CME propagation, and it introduces advanced numerical techniques to make the simulations more efficient. In this model the reference frame is chosen to be co-rotating with the Sun, and radial grid stretching together with adaptive mesh refinement (AMR) can be applied to the numerical domain.Aims.Grid stretching and AMR speed up simulation results and performance. Our aim is to combine the advanced techniques available in the Icarus model in order to obtain better results with fewer computational resources than with the equidistant grid. Different AMR strategies are suggested, depending on the purpose of the simulation.Methods.In this study, we model the CME event that occurred on July 12, 2012. A cone model was used to study the CME’s evolution through the background solar wind, and its arrival at and impact with the Earth. Grid stretching and AMR were combined in the simulations by using multiple refinement criteria, to assess its influence on the simulations’ accuracy and the required computational resources. We compare simulation results to the EUHFORIA model.Results.We applied different refinement criteria to investigate the potential of solution AMR for different applications. As a result, the simulations were sped up by a factor of ∼17 for the most optimal configuration in Icarus. For the cone CME model, we found that limiting the AMR to the region around the CME-driven shock yields the best results. The results modelled by the simulations with radial grid stretching and AMR level 4 are similar to the results provided by the original EUHFORIA and Icarus simulations with the ‘standard’ resolution and equidistant grids. The simulations with 5 AMR levels yielded better results than the simulations with an equidistant grid and standard resolution.Conclusions.Solution AMR is flexible and provides the user the freedom to modify and locally increase the grid resolution according to the purpose of the simulation. We find that simulations with a combination of grid stretching and AMR can reproduce the simulations performed on equidistant grids significantly faster. The advanced techniques implemented in Icarus can be further used to improve the forecasting procedures, since the reduced simulation time is essential to make physics-based forecasts less computationally expensive.
Vérités scientifiques et enjeux sociaux
Authors: Gargani Julien , Jacq Annick , Gispert Hélène , Brunet Philippe 
Published: October 2022

Le colloque « Vérités scientifiques et enjeux sociaux » a permis de nourrir une réflexion sur l’organisation des sciences en lien avec la production des preuves scientifiques et leurs modes de partage. Comment faire émerger la diversité des enjeux sociaux dans les sciences ? Comment partager plus largement la production scientifique et celle des preuves ? Les modes de production, de validation et de partage des preuves ne sont pas figés, ce qui les rend difficiles à appréhender. Les écueils et les mécanismes favorisant la fabrication de l’ignorance ont ainsi été abordés. L’interdisciplinarité, les sciences inclusives et les synthèses scientifiques collectives, thèmes évoqués lors du colloque, sont autant de pistes pour éclairer les débats publics, partager autrement les preuves et la capacité d’expertise, et définir collectivement les enjeux.
Head and Neck Ultrasound – EFSUMB Training Recommendations
for the Practice of Medical Ultrasound in Europe
Authors: Todsen Tobias , Ewertsen Caroline , Jenssen Christian , Evans Rhodri , Kuenzel Julian 
Published: October 2022

AbstractDifferent surgical and medical specialists increasingly use head and neck
ultrasound and ultrasound-guided interventions as part of their clinical
practice. We need to ensure high quality and standardized practice across
specialties, and this position paper of the European Federation of Societies for
Ultrasound in Medicine and Biology (EFSUMB) describes the training requirements
for head and neck ultrasound. Traditionally, a minimum number of ultrasound
examinations indicates competence, but this is unreliable, and a general shift
towards competence-based training is ongoing. For each EFSUMB level, we will
outline the theoretical knowledge and skills needed for clinical practice. The
recommendations follow the three EFSUMB competency levels for medical ultrasound
practice. Level 1 describes the skills required to perform essential head and
neck ultrasound examinations independently, level 2 includes ultrasound-guided
interventions, while level 3 involves the practice of high-level neck ultrasound
and use of advanced technologies. Our goal is to ensure high quality and
standardized head and neck ultrasound practice performed by different clinical
specialists with these recommendations.
Associations of PNPLA3 rs738409 Polymorphism with Plasma Lipid
Levels: A Systematic Review and Meta-Analysis
Authors: Luo Zhi , Liu Yang , Li Hang , Zhou Yawen , Peng Yuanyuan , Lin Xuan , Fang Ying , Wan Jing , Wei Baozhu 
Published: October 2022

AbstractAccumulating evidence has shown that the rs738409 polymorphism of patatin-like
phospholipase domain-containing 3 (PNPLA3) is associated with non-alcoholic
fatty liver disease (NAFLD). Since NAFLD has been reported to be associated with
lipid metabolism, this study is conducted to explore whether the rs738409
polymorphism of PNPLA3 was associated with lipid levels. By searching PubMed and
the Cochrane database from May 31, 2020, to June 30, 2021. Sixty-three studies
(81 003 subjects) were included for the analysis. The consistent findings for
the associations of rs738409 polymorphism with lipid levels were the
significantly decreased triglycerides (TG) (SMD=−0.04,
95% CI=−0.07 to −0.01, p=0.02) and total
cholesterol (TC) (SMD=−0.03, 95%
CI=−0.05 to −0.01, p<0.01) levels. Subgroup
analysis indicated that the associations of rs738409 polymorphism with TG and TC
levels were stronger in Caucasians, obesity patients, and adult subjects than in
Asians, T2DM patients, and children subjects. The rs738409 polymorphism of
PNPLA3 was associated with lower TG and TC levels in Caucasians, obese and adult
subjects, which may contribute to the reduced coronary artery disease (CAD) risk
between PNPLA3 rs738409 polymorphism and CAD.
Effect of Cabergoline Treatment on Disease Control in Acromegaly
Patients
Authors: Hacisahinogullari Hulya , Yalin Gulsah Yenidunya , Selcukbiricik Ozlem Soyluk , Gul Nurdan , Bilgic Bilge , Uzum Ayse Kubat , Tanakol Refik , Aral Ferihan 
Published: October 2022

AbstractThe aim of this study was to evaluate the efficacy of cabergoline in normalizing
plasma IGF-I levels in acromegaly patients with elevated IGF-I levels after
surgery and/or SRL therapy. Acromegaly patients (n: 143) were evaluated
retrospectively. Patients with elevated IGF-I levels after surgery
and/or SRLs therapy and a fixed dose of SRLs treatment for the last six
months with no history of radiotherapy in the last three years were included in
the study (n: 12). Previous treatment regimens, baseline PRL and IGF-I levels
(ULNR), sella MRI, and immunohistochemical findings were evaluated. Cabergoline
was used as an add on (n: 11) or single medical treatment (n: 1). The median
duration of treatment with SRL alone was 12 months (range 6–48 months).
The mean IGF-I value before cabergoline therapy was 1.45±0.4 ULNR. The
mean cabergoline dose and duration of treatment were
1.55±0.75 mg/week and 9±6.3 months,
respectively. IGF-I normalization was only achieved in patients with serum IGF-I
concentration<1.5×ULNR before the onset of cabergoline treatment
(n: 9). In some of the patients with IGF-I normalization, baseline prolactin
levels were normal (n: 3). Immunopositivity for prolactin in adenoma tissue was
found in three patients with IGF-I normalization. Cabergoline therapy is
effective in the normalization of IGF-I levels even in normoprolactinemic
acromegaly patients when IGF-I levels are mildly or moderately elevated during
SRL therapy.
Relations Between Body Fat Mass and Insulin Resistance in Non-Obese
Patients with Idiopathic Hypogonadotropic Hypogonadism and Normal Glucose
Tolerance
Authors: Yang Xubin , Chen Xueyan , Xu Huan , Deng Hongrong , Yao Bin , Xu Wen , Lin Qiongyan 
Published: October 2022

AbstractThe purpose of this study was to investigate the relationship between body fat
mass and insulin resistance in non-obese patients with idiopathic
hypogonadotropic hypogonadism (IHH) and normal glucose tolerance. A total of 42
patients with IHH and normal glucose tolerance, and BMI lower than
28 kg/m2 were recruited. Patients were required
to have a normal glucose tolerance test for inclusion in the study. Ten Healthy
subjects were recruited as control group. Laboratory studies included fasting
insulin, testosterone, and lipids. Waist circumference (WC), weight, and body
fat mass were measured, and waist-to-hip ratio (WHR), body mass index (BMI),
HOMA-IR, and logHOMA-B were calculated. Data were compared between groups, and
linear regression was used to determine relations. Blood pressure, fasting
glucose, BMI, WHR, and lipids were similar between the groups. Fasting insulin
levels (15.61±7.66 mIU/l vs.
7.60±3.84 mIU/l), logHOMA-B (2.39±0.29 vs.
2.03±0.21), HOMA-IR (3.38±1.71 vs. 1.64±0.91), and body
fat mass (30.49±9.46% vs. 21.11±4.31%) were
significantly greater in the IHH group compared with those in control group (all
p<0.05). Multivariable linear regression showed that in IHH patients
body fat mass was an independent predictor of fasting insulin level
(β=0.71, p<0.01), logHOMA-B (β=0.02,
p<0.05), and HOMA-IR (β=0.14, p<0.05). Body fat
mass is an independent predictor of insulin resistance in non-obese IHH patients
with normal glucose tolerance.
An Unusual Clinical Presentation of Budd–Chiari Syndrome in an Adolescent Boy
Authors: Agrawal Shreyash , Pathania Garima , Mittal Richa , Mehndiratta Sumit , Singh Amitabh 
Published: October 2022

AbstractWe report an unusual case of massive splenomegaly with pancytopenia without ascites, which was referred to us with suspicion of a myeloproliferative disorder in an adolescent boy. The work-up done was noncontributory to a hematological disorder. On further work-up, liver biopsy depicted sinusoidal congestion, with Doppler study suggestive of nonvisualization of hepatic veins. There was hypertrophy of the right lobe and the presence of venovenous collaterals. Janus kinase 2 (JAK2) V617F mutation was negative, which confirmed the absence of unidentified myeloproliferative disorder. This was an atypical presentation of Budd–Chiari syndrome (BCS) in children. The absence of ascites could be due to more efficient collateral formation in adolescent age groups due to angiogenesis. Underlying thrombophilia was detected as methylenetetrahydrofolate reductase mutation 677C > T with raised serum homocysteine levels. It is imperative to be aware of the diverse clinical manifestations in children for early detection and appropriate intervention to prevent catastrophic results in pediatric BCS.