bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo tumor immune microenvironment phenotypes correlate with inflammation and vasculature to predict immunotherapy response
Authors: Sahu Aditi , Kose Kivanc , Kraehenbuehl Lukas , Byers Candice , Holland Aliya , Tembo Teguru , Santella Anthony , Alfonso Anabel , Li Madison , Cordova Miguel , Gill Melissa , Fox Christi , Gonzalez Salvador , Kumar Piyush , Wang Amber Weiching , Kurtansky Nicholas , Chandrani Pratik , Yin Shen , Mehta Paras , Navarrete-Dechent Cristian , Peterson Gary , King Kimeil , Dusza Stephen , Yang Ning , Liu Shuaitong , Phillips William , Guitera Pascale , Rossi Anthony , Halpern Allan , Deng Liang , Pulitzer Melissa , Marghoob Ashfaq , Chen Chih-Shan Jason , Merghoub Taha , Rajadhyaksha Milind 
Published: September 2022

AbstractResponse to immunotherapies can be variable and unpredictable. Pathology-based phenotyping of tumors into ‘hot’ and ‘cold’ is static, relying solely on T-cell infiltration in single-time single-site biopsies, resulting in suboptimal treatment response prediction. Dynamic vascular events (tumor angiogenesis, leukocyte trafficking) within tumor immune microenvironment (TiME) also influence anti-tumor immunity and treatment response. Here, we report dynamic cellular-level TiME phenotyping in vivo that combines inflammation profiles with vascular features through non-invasive reflectance confocal microscopic imaging. In skin cancer patients, we demonstrate three main TiME phenotypes that correlate with gene and protein expression, and response to toll-like receptor agonist immune-therapy. Notably, phenotypes with high inflammation associate with immunostimulatory signatures and those with high vasculature with angiogenic and endothelial anergy signatures. Moreover, phenotypes with high inflammation and low vasculature demonstrate the best treatment response. This non-invasive in vivo phenotyping approach integrating dynamic vasculature with inflammation serves as a reliable predictor of response to topical immune-therapy in patients.
GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance
Authors: Chen Wenjun , Brown Jordan S. , He Tao , Wu Wei-Sheng , Tu Shikui , Weng Zhiping , Zhang Donglei , Lee Heng-Chi 
Published: September 2022

AbstractpiRNAs function as guardians of the genome by silencing non-self nucleic acids and transposable elements in animals. Many piRNA factors are enriched in perinuclear germ granules, but whether their localization is required for piRNA biogenesis or function is not known. Here we show that GLH/VASA helicase mutants exhibit defects in forming perinuclear condensates containing PIWI and other small RNA cofactors. These mutant animals produce largely normal levels of piRNA but are defective in triggering piRNA silencing. Strikingly, while many piRNA targets are activated in GLH mutants, we observe that hundreds of endogenous genes are aberrantly silenced by piRNAs. This defect in self versus non-self recognition is also observed in other mutants where perinuclear germ granules are disrupted. Together, our results argue that perinuclear germ granules function critically to promote the fidelity of piRNA-based transcriptome surveillance in C. elegans and preserve self versus non-self distinction.
High performance polymerized small molecule acceptor by synergistic optimization on π-bridge linker and side chain
Authors: Sun Guangpei , Jiang Xin , Li Xiaojun , Meng Lei , Zhang Jinyuan , Qin Shucheng , Kong Xiaolei , Li Jing , Xin Jingming , Ma Wei , Li Yongfang 
Published: September 2022

AbstractThe polymerized small-molecule acceptors have attracted great attention for application as polymer acceptor in all-polymer solar cells recently. The modification of small molecule acceptor building block and the π-bridge linker is an effective strategy to improve the photovoltaic performance of the polymer acceptors. In this work, we synthesized a new polymer acceptor PG-IT2F which is a modification of the representative polymer acceptor PY-IT by replacing its upper linear alkyl side chains on the small molecule building block with branched alkyl chains and attaching difluorene substituents on its thiophene π-bridge linker. Through this synergistic optimization, PG-IT2F possesses more suitable phase separation, increased charge transportation, better exciton dissociation, lower bimolecular recombination, and longer charge transfer state lifetime than PY-IT in their polymer solar cells with PM6 as polymer donor. Therefore, the devices based on PM6:PG-IT2F demonstrated a high power conversion efficiency of 17.24%, which is one of the highest efficiency reported for the binary all polymer solar cells to date. This work indicates that the synergistic regulation of small molecule acceptor building block and π-bridge linker plays a key role in designing and developing highly efficient polymer acceptors.
Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque
Authors: Fernández-Torras Adrià , Duran-Frigola Miquel , Bertoni Martino , Locatelli Martina , Aloy Patrick 
Published: September 2022

AbstractBiomedical data is accumulating at a fast pace and integrating it into a unified framework is a major challenge, so that multiple views of a given biological event can be considered simultaneously. Here we present the Bioteque, a resource of unprecedented size and scope that contains pre-calculated biomedical descriptors derived from a gigantic knowledge graph, displaying more than 450 thousand biological entities and 30 million relationships between them. The Bioteque integrates, harmonizes, and formats data collected from over 150 data sources, including 12 biological entities (e.g., genes, diseases, drugs) linked by 67 types of associations (e.g., ‘drug treats disease’, ‘gene interacts with gene’). We show how Bioteque descriptors facilitate the assessment of high-throughput protein-protein interactome data, the prediction of drug response and new repurposing opportunities, and demonstrate that they can be used off-the-shelf in downstream machine learning tasks without loss of performance with respect to using original data. The Bioteque thus offers a thoroughly processed, tractable, and highly optimized assembly of the biomedical knowledge available in the public domain.
Mitigation of China’s carbon neutrality to global warming
Authors: Li Longhui , Zhang Yue , Zhou Tianjun , Wang Kaicun , Wang Can , Wang Tao , Yuan Linwang , An Kangxin , Zhou Chenghu , Lü Guonian 
Published: September 2022

AbstractProjecting mitigations of carbon neutrality from individual countries in relation to future global warming is of great importance for depicting national climate responsibility but is poorly quantified. Here, we show that China’s carbon neutrality (CNCN) can individually mitigate global warming by 0.48 °C and 0.40 °C, which account for 14% and 9% of the global warming over the long term under the shared socioeconomic pathway (SSP) 3-7.0 and 5-8.5 scenarios, respectively. Further incorporating changes in CH4 and N2O emissions in association with CNCN together will alleviate global warming by 0.21 °C and 0.32 °C for SSP1-2.6 and SSP2-4.5 over the long term, and even by 0.18 °C for SSP2-4.5 over the mid-term, but no significant impacts are shown for all SSPs in the near term. Divergent responses in alleviated warming are seen at regional scales. The results provide a useful reference for the global stocktake, which assesses the collective progress towards the climate goals of the Paris Agreement.
Atherogenic potential of microgravity hemodynamics in the carotid bifurcation: a numerical investigation
Authors: Sucosky Philippe , Kalaiarasan Varun Vinayak , Quasebarth Graham B. , Strack Patricia , Shar Jason A. 
Published: September 2022

AbstractLong-duration spaceflight poses multiple hazards to human health, including physiological changes associated with microgravity. The hemodynamic adaptations occurring upon entry into weightlessness have been associated with retrograde stagnant flow conditions and thromboembolic events in the venous vasculature but the impact of microgravity on cerebral arterial hemodynamics and function remains poorly understood. The objective of this study was to quantify the effects of microgravity on hemodynamics and wall shear stress (WSS) characteristics in 16 carotid bifurcation geometries reconstructed from ultrasonography images using computational fluid dynamics modeling. Microgravity resulted in a significant 21% increase in flow stasis index, a 22–23% decrease in WSS magnitude and a 16–26% increase in relative residence time in all bifurcation branches, while preserving WSS unidirectionality. In two anatomies, however, microgravity not only promoted flow stasis but also subjected the convex region of the external carotid arterial wall to a moderate increase in WSS bidirectionality, which contrasted with the population average trend. This study suggests that long-term exposure to microgravity has the potential to subject the vasculature to atheroprone hemodynamics and this effect is modulated by subject-specific anatomical features. The exploration of the biological impact of those microgravity-induced WSS aberrations is needed to better define the risk posed by long spaceflights on cardiovascular health.
Corrosion behavior of TiZrHfBeCu(Ni) high-entropy bulk metallic glasses in 3.5 wt. % NaCl
Authors: Gong Pan , Wang Dongliang , Zhang Cheng , Wang Ying , Jamili-Shirvan Zahra , Yao Kefu , Wang Xinyun 
Published: September 2022

AbstractThe corrosion behavior of TiZrHfBeCu(Ni) high-entropy bulk metallic glasses (HE-BMGs) has been investigated. The TiZrHfBeCu(Ni) HE-BMGs exhibited high corrosion resistance in 3.5 wt. % NaCl solution because of accumulation of ZrO2 and TiO2 in the passive film. Ni promoted increases of the ZrO2, TiO2, and HfO2 contents and a decrease of the BeO content, which improved the HE-BMG corrosion behavior. Compared with Zr41.2Ti13.8Ni10Cu12.5Be22.5 BMG, the high-entropy effect of HE-BMGs can significantly reduce the atomic mobility, which inhibits outward migration of Cu, reduces the kinetics of the dissolution reaction, and inhibits inward erosion by Cl−, thereby improving the corrosion performance.
Nanoscale electric field imaging with an ambient scanning quantum sensor microscope
Authors: Qiu Ziwei , Hamo Assaf , Vool Uri , Zhou Tony X. , Yacoby Amir 
Published: September 2022

AbstractNitrogen-vacancy (NV) center in diamond is a promising quantum sensor with remarkably versatile sensing capabilities. While scanning NV magnetometry is well-established, NV electrometry has been so far limited to bulk diamonds. Here we demonstrate imaging external alternating (AC) and direct (DC) electric fields with a single NV at the apex of a diamond scanning tip under ambient conditions. A strong electric field screening effect is observed at low frequencies. We quantitatively measure its frequency dependence and overcome this screening by mechanically oscillating the tip for imaging DC fields. Our scanning NV electrometry achieved an AC E-field sensitivity of 26 mV μm−1 Hz−1/2, a DC E-field gradient sensitivity of 2 V μm−2 Hz−1/2, and sub-100 nm resolution limited by the NV-sample distance. Our work represents an important step toward building a scanning-probe-based multimodal quantum sensing platform.
Socioeconomic and genomic roots of verbal ability from current evidence
Authors: Guo Guang , Lin Meng-Jung , Harris Kathleen Mullan 
Published: September 2022

AbstractThis research examines how the human genome and SES jointly and interactively shape verbal ability among youth in the U.S. The youth are aged 12–18 when the study starts. The research draws on findings from the latest GWAS as well as a rich set of longitudinal SES measures at individual, family and neighborhood levels from Add Health (N = 7194). Both SES and genome measures predict verbal ability well separately and jointly. More interestingly, the inclusion of both sets of predictors in the same model corrects for about 20% upward bias in the effect of the education PGS, and implies that about 20–30% of the effects of parental SES are not environmental, but parentally genomic. The three incrementalR2s that measure the relative contributions of the two PGSs, the genomic component in parental SES, and the environmental component in parental SES are estimated to be about 1.5%, 1.5%, and 7.8%, respectively. The total environmentalR2and the total genomicR2are, thus, 7.8% and 3%, respectively. These findings confirm the importance of SES environment and also pose challenges to traditional social-science research. Not only does an individual’s genome have an important direct influence on verbal ability, parental genomes also influence verbal ability through parental SES. The decades-long blueprint of including SES in a model and interpreting their effects as those of SES needs to be amended accordingly. A straightforward solution is to routinely collect DNA data for large social-science studies granted that the primary purpose is to understand social and environmental influences.
The personality and cognitive traits associated with adolescents’ sensitivity to social norms
Authors: Tate Christopher , Kumar Rajnish , Murray Jennifer M. , Sanchez-Franco Sharon , Sarmiento Olga L. , Montgomery Shannon C. , Zhou Huiyu , Ramalingam Abhijit , Krupka Erin , Kimbrough Erik , Kee Frank , Hunter Ruth F. 
Published: September 2022

AbstractLittle is known about the personality and cognitive traits that shape adolescents’ sensitivity to social norms. Further, few studies have harnessed novel empirical tools to elicit sensitivity to social norms among adolescent populations. This paper examines the association between sensitivity to norms and various personality and cognitive traits using an incentivised rule-following task grounded in Game Theory. Cross-sectional data were obtained from 1274 adolescents. Self-administered questionnaires were used to measure personality traits as well as other psychosocial characteristics. Incentivised rule-following experiments gauged sensitivity to social norms. A series of multilevel mixed effects ordered logistic regression models were employed to assess the association between sensitivity to norms and the personality and cognitive traits. The results highlighted statistically significant univariate associations between the personality and cognitive traits and sensitivity to norms. However, in the multivariate adjusted model, the only factor associated with sensitivity to norms was gender. The gender-stratified analyses revealed differences in the personality and cognitive traits associated with sensitivity to norms across genders. For males need to belong was significantly negatively associated with sensitivity to norms in the multivariate model. By comparison, emotional stability was negatively associated with sensitivity to norms for females. This study reinforced the findings from an earlier study and suggested female adolescents had higher levels of sensitivity to norms. The results indicated no consistent pattern between sensitivity to norms and the personality and cognitive traits. Our findings provide a basis for further empirical research on a relatively nascent construct, and bring a fresh perspective to the question of norm-following preferences among this age group.
Deep learning multi-organ segmentation for whole mouse cryo-images including a comparison of 2D and 3D deep networks
Authors: Liu Yiqiao , Gargesha Madhusudhana , Scott Bryan , Tchilibou Wane Arthure Olivia , Wilson David L. 
Published: September 2022

AbstractCryo-imaging provided 3D whole-mouse microscopic color anatomy and fluorescence images that enables biotechnology applications (e.g., stem cells and metastatic cancer). In this report, we compared three methods of organ segmentation: 2D U-Net with 2D-slices and 3D U-Net with either 3D-whole-mouse or 3D-patches. We evaluated the brain, thymus, lung, heart, liver, stomach, spleen, left and right kidney, and bladder. Training with 63 mice, 2D-slices had the best performance, with median Dice scores of > 0.9 and median Hausdorff distances of < 1.2 mm in eightfold cross validation for all organs, except bladder, which is a problem organ due to variable filling and poor contrast. Results were comparable to those for a second analyst on the same data. Regression analyses were performed to fit learning curves, which showed that 2D-slices can succeed with fewer samples. Review and editing of 2D-slices segmentation results reduced human operator time from ~ 2-h to ~ 25-min, with reduced inter-observer variability. As demonstrations, we used organ segmentation to evaluate size changes in liver disease and to quantify the distribution of therapeutic mesenchymal stem cells in organs. With a 48-GB GPU, we determined that extra GPU RAM improved the performance of 3D deep learning because we could train at a higher resolution.
Association of Toll-like receptors polymorphisms with the risk of acute lymphoblastic leukemia in the Brazilian Amazon
Authors: Xabregas Lilyane Amorim , Hanna Fabíola Silva Alves , Magalhães-Gama Fábio , Souza Gláucia Lima , Pereira Daniele Sá , de Lima Amanda Barros , Toro Diana Mota , Santiago Mirian Rodrigues Ribeiro , da Motta Passos Leny Nascimento , Tarragô Andréa Monteiro , Malheiro Adriana , Costa Allyson Guimarães 
Published: September 2022

AbstractAcute lymphoblastic leukemia (ALL) is the most common hematologic malignancy in children in childhood. Single-nucleotide polymorphism (SNPs) in key molecules of the immune system, such as Toll-like receptors (TLRs) and CD14 molecules, are associated with the development of several diseases. However, their role in ALL is unknown. A case–control study was performed with 152 ALL patients and 187 healthy individuals to investigate the role of SNPs in TLRs and the CD14 gene in ALL. In this study, TLR6 C > T rs5743810 [OR: 3.20, 95% CI: 1.11–9.17, p = 0.003) and TLR9 C > T rs187084 (OR: 2.29, 95% CI: 1.23–4.26, p = 0.000) seems to be a risk for development of ALL. In addition, the TLR1 T > G rs5743618 and TLR6 C > T rs5743810 polymorphisms with protection against death (OR: 0.17, 95% IC: 0.04–0.79, p = 0.008; OR: 0.48, 95% IC: 0.24–0.94, p = 0.031, respectively). Our results show that SNPs in TLRs genes may be involved in the pathogenesis of ALL and may influence clinical prognosis; however, further studies are necessary to elucidate the role of TLR1, TLR4, TLR5, TLR6, TLR9 and CD14 polymorphisms in this disease.
Athleticism and sex impact neural processing of sound
Authors: Krizman Jennifer , Bonacina Silvia , Colegrove Danielle , Otto-Meyer Rembrandt , Nicol Trent , Kraus Nina 
Published: September 2022

AbstractBiology and experience both influence the auditory brain. Sex is one biological factor with pervasive effects on auditory processing. Females process sounds faster and more robustly than males. These differences are linked to hormone differences between the sexes. Athleticism is an experiential factor known to reduce ongoing neural noise, but whether it influences how sounds are processed by the brain is unknown. Furthermore, it is unknown whether sports participation influences auditory processing differently in males and females, given the well-documented sex differences in auditory processing seen in the general population. We hypothesized that athleticism enhances auditory processing and that these enhancements are greater in females. To test these hypotheses, we measured auditory processing in collegiate Division I male and female student-athletes and their non-athlete peers (total n = 1012) using the frequency-following response (FFR). The FFR is a neurophysiological response to sound that reflects the processing of discrete sound features. We measured across-trial consistency of the response in addition to fundamental frequency (F0) and harmonic encoding. We found that athletes had enhanced encoding of the harmonics, which was greatest in the female athletes, and that athletes had more consistent responses than non-athletes. In contrast, F0 encoding was reduced in athletes. The harmonic-encoding advantage in female athletes aligns with previous work linking harmonic encoding strength to female hormone levels and studies showing estrogen as mediating athlete sex differences in other sensory domains. Lastly, persistent deficits in auditory processing from previous concussive and repetitive subconcussive head trauma may underlie the reduced F0 encoding in athletes, as poor F0 encoding is a hallmark of concussion injury.
Chromosomal microarray analyses from 5778 patients with neurodevelopmental disorders and congenital anomalies in Brazil
Authors: Krepischi Ana C. V. , Villela Darine , da Costa Silvia Souza , Mazzonetto Patricia C. , Schauren Juliana , Migliavacca Michele P. , Milanezi Fernanda , Santos Juliana G. , Guida Gustavo , Guarischi-Sousa Rodrigo , Campana Gustavo , Kok Fernando , Schlesinger David , Kitajima Joao Paulo , Campagnari Francine , Bertola Debora R. , Vianna-Morgante Angela M. , Pearson Peter L. , Rosenberg Carla 
Published: September 2022

AbstractChromosomal microarray analysis (CMA) has been recommended and practiced routinely since 2010 both in the USA and Europe as the first-tier cytogenetic test for patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies. However, in Brazil, the use of CMA is still limited, due to its high cost and complexity in integrating the results from both the private and public health systems. Although Brazil has one of the world’s largest single-payer public healthcare systems, nearly all patients referred for CMA come from the private sector, resulting in only a small number of CMA studies in Brazilian cohorts. To date, this study is by far the largest Brazilian cohort (n = 5788) studied by CMA and is derived from a joint collaboration formed by the University of São Paulo and three private genetic diagnostic centers to investigate the genetic bases of neurodevelopmental disorders and congenital abnormalities. We identified 2,279 clinically relevant CNVs in 1886 patients, not including the 26 cases of UPD found. Among detected CNVs, the corresponding frequency of each category was 55.6% Pathogenic, 4.4% Likely Pathogenic and 40% VUS. The diagnostic yield, by taking into account Pathogenic, Likely Pathogenic and UPDs, was 19.7%. Since the rational for the classification is mostly based on Mendelian or highly penetrant variants, it was not surprising that a second event was detected in 26% of those cases of predisposition syndromes. Although it is common practice to investigate the inheritance of VUS in most laboratories around the world to determine the inheritance of the variant, our results indicate an extremely low cost–benefit of this approach, and strongly suggest that in cases of a limited budget, investigation of the parents of VUS carriers using CMA should not be prioritized.