bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps
Authors: Avelar-Barragan Julio , DeDecker Lauren , Lu Zachary N. , Coppedge Bretton , Karnes William E. , Whiteson Katrine L. 
Published: August 2022

AbstractColorectal cancer is the second most deadly and third most common cancer in the world. Its development is heterogenous, with multiple mechanisms of carcinogenesis. Two distinct mechanisms include the adenoma-carcinoma sequence and the serrated pathway. The gut microbiome has been identified as a key player in the adenoma-carcinoma sequence, but its role in serrated carcinogenesis is less clear. In this study, we characterized the gut microbiome of 140 polyp-free and polyp-bearing individuals using colon mucosa and fecal samples to determine if microbiome composition was associated with each of the two key pathways. We discovered significant differences between the microbiomes of colon mucosa and fecal samples, with sample type explaining 10–15% of the variation observed in the microbiome. Multiple mucosal brushings were collected from each individual to investigate whether the gut microbiome differed between polyp and healthy intestinal tissue, but no differences were found. Mucosal aspirate sampling revealed that the microbiomes of individuals with tubular adenomas and serrated polyps were significantly different from each other and polyp-free individuals, explaining 1–4% of the variance in the microbiome. Microbiome composition also enabled the accurate prediction of subject polyp types using Random Forest, which produced an area under curve values of 0.87–0.99. By directly sampling the colon mucosa and distinguishing between the different developmental pathways of colorectal cancer, our study helps characterize potential mechanistic targets for serrated carcinogenesis. This research also provides insight into multiple microbiome sampling strategies by assessing each method’s practicality and effect on microbial community composition.
Heuristic bounds on superconductivity and how to exceed them
Authors: Hofmann Johannes S. , Chowdhury Debanjan , Kivelson Steven A. , Berg Erez 
Published: August 2022

AbstractWhat limits the value of the superconducting transition temperature (Tc) is a question of great fundamental and practical importance. Various heuristic upper bounds onTchave been proposed, expressed as fractions of the Fermi temperature,TF, the zero-temperature superfluid stiffness,ρs(0), or a characteristic Debye frequency,ω0. We show that while these bounds are physically motivated and are certainly useful in many relevant situations, none of them serve as a fundamental bound onTc. To demonstrate this, we provide explicit models whereTc/TF(with an appropriately definedTF),Tc/ρs(0), andTc/ω0are unbounded.
Ultrafast coherent interlayer phonon dynamics in atomically thin layers of MnBi2Te4
Authors: Bartram F. Michael , Leng Yu-Chen , Wang Yongchao , Liu Liangyang , Chen Xue , Peng Huining , Li Hao , Yu Pu , Wu Yang , Lin Miao-Ling , Zhang Jinsong , Tan Ping-Heng , Yang Luyi 
Published: August 2022

AbstractThe atomically thin MnBi2Te4 crystal is a novel magnetic topological insulator, exhibiting exotic quantum physics. Here we report a systematic investigation of ultrafast carrier dynamics and coherent interlayer phonons in few-layer MnBi2Te4 as a function of layer number using time-resolved pump-probe reflectivity spectroscopy. Pronounced coherent phonon oscillations from the interlayer breathing mode are directly observed in the time domain. We find that the coherent oscillation frequency, the photocarrier and coherent phonon decay rates all depend sensitively on the sample thickness. The time-resolved measurements are complemented by ultralow-frequency Raman spectroscopy measurements, which both confirm the interlayer breathing mode and additionally enable observation of the interlayer shear mode. The layer dependence of these modes allows us to extract both the out-of-plane and in-plane interlayer force constants. Our studies not only reveal the interlayer van der Waals coupling strengths, but also shed light on the ultrafast optical properties of this novel two-dimensional material.
Real-world effectiveness of a social-psychological intervention translated from controlled trials to classrooms
Authors: Chen Patricia , Teo Dennis W. H. , Foo Daniel X. Y. , Derry Holly A. , Hayward Benjamin T. , Schulz Kyle W. , Hayward Caitlin , McKay Timothy A. , Ong Desmond C. 
Published: August 2022

AbstractSocial-psychological interventions have raised the learning and performance of students in rigorous efficacy trials. Yet, after they are distributed “in the wild” for students to self-administer, there has been little research following up on their translational effectiveness. We used cutting-edge educational technology to tailor, scale up, and track a previously-validated Strategic Resource Use intervention among 12,065 college students in 14 STEM and Economics classes. Students who self-administered this “Exam Playbook” benefitted by an average of 2.17 percentage points (i.e., a standardized effect size of 0.18), compared to non-users. This effect size was 1.65 percentage points when controlling for college entrance exam scores and 1.75 [−1.88] for adding [dropping] the Exam Playbook in stratified matching analyses. Average benefits differed in magnitude by the conduciveness of the class climate (including peer norms and incentives), gender, first-generation status, as well as how often and how early they used the intervention. These findings on how, when, and who naturally adopts these resources address a need to improve prediction, translation, and scalability of social-psychological intervention benefits.
Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated
Authors: Elhaik Eran 
Published: August 2022

AbstractPrincipal Component Analysis (PCA) is a multivariate analysis that reduces the complexity of datasets while preserving data covariance. The outcome can be visualized on colorful scatterplots, ideally with only a minimal loss of information. PCA applications, implemented in well-cited packages like EIGENSOFT and PLINK, are extensively used as the foremost analyses in population genetics and related fields (e.g., animal and plant or medical genetics). PCA outcomes are used to shape study design, identify, and characterize individuals and populations, and draw historical and ethnobiological conclusions on origins, evolution, dispersion, and relatedness. The replicability crisis in science has prompted us to evaluate whether PCA results are reliable, robust, and replicable. We analyzed twelve common test cases using an intuitive color-based model alongside human population data. We demonstrate that PCA results can be artifacts of the data and can be easily manipulated to generate desired outcomes. PCA adjustment also yielded unfavorable outcomes in association studies. PCA results may not be reliable, robust, or replicable as the field assumes. Our findings raise concerns about the validity of results reported in the population genetics literature and related fields that place a disproportionate reliance upon PCA outcomes and the insights derived from them. We conclude that PCA may have a biasing role in genetic investigations and that 32,000-216,000 genetic studies should be reevaluated. An alternative mixed-admixture population genetic model is discussed.
Improvement in fruit yield and tolerance to salinity of tomato plants fertigated with micronutrient amounts of iodine
Authors: Kiferle Claudia , Gonzali Silvia , Beltrami Sara , Martinelli Marco , Hora Katja , Holwerda Harmen Tjalling , Perata Pierdomenico 
Published: August 2022

AbstractIodine is an essential micronutrient for humans, but its role in plant physiology was debated for nearly a century. Recently its functional involvement in plant nutrition and stress-protection collected the first experimental evidence. This study wanted to examine in depth the involvement of iodine in tomato plant nutrition, also evaluating its potential on salt stress tolerance. To this end, iodine was administered at dosages effective for micronutrients to plants grown in different experimental systems (growth chamber and greenhouse), alone or in presence of a mild-moderate NaCl-salinity stress. Plant vegetative fitness, fruit yield and quality, biochemical parameters and transcriptional activity of selected stress-responsive genes were evaluated. In unstressed plants, iodine increased plant growth and fruit yield, as well as some fruit qualitative parameters. In presence of salt stress, iodine mitigated some of the negative effects observed, according to the iodine/NaCl concentrations used. Some fruit parameters and the expressions of the stress marker genes analyzed were affected by the treatments, explaining, at least in part, the increased plant tolerance to the salinity. This study thus reconfirms the functional involvement of iodine in plant nutrition and offers evidence towards the use of minute amounts of it as a beneficial nutrient for crop production.
Osteogenic transdifferentiation of primary human fibroblasts to osteoblast-like cells with human platelet lysate
Authors: Cayami Ferdy K. , Claeys Lauria , de Ruiter Ruben , Smilde Bernard J. , Wisse Lisanne , Bogunovic Natalija , Riesebos Elise , Eken Lyra , Kooi Irsan , Sistermans Erik A. , Bravenboer Nathalie , Pals Gerard , Faradz Sultana M. H. , Sie Daoud , Eekhoff E. Marelise W. , Micha Dimitra 
Published: August 2022

AbstractInherited bone disorders account for about 10% of documented Mendelian disorders and are associated with high financial burden. Their study requires osteoblasts which play a critical role in regulating the development and maintenance of bone tissue. However, bone tissue is not always available from patients. We developed a highly efficient platelet lysate-based approach to directly transdifferentiate skin-derived human fibroblasts to osteoblast-like cells. We extensively characterized our in vitro model by examining the expression of osteoblast-specific markers during the transdifferentiation process both at the mRNA and protein level. The transdifferentiated osteoblast-like cells showed significantly increased expression of a panel of osteogenic markers. Mineral deposition and ALP activity were also shown, confirming their osteogenic properties. RNA-seq analysis allowed the global study of changes in the transcriptome of the transdifferentiated cells. The transdifferentiated cells clustered separately from the primary fibroblasts with regard to the significantly upregulated genes indicating a distinct transcriptome profile; transdifferentiated osteoblasts also showed significant enrichment in gene expression related to skeletal development and bone mineralization. Our presented in vitro model may potentially contribute to the prospect of studying osteoblast-dependent disorders in patient-derived cells.
Influence of long-term intensive use of irrigated meadow-chernozem soil on the biological activity and productivity of the arable layer
Authors: Shuliko Natalia Nikolaevna , Khamova Olga Fedorovna , Timokhin Artem Yur’yevich , Boiko Vasiliy Sergeyevich , Tukmacheva Elena Vasilevna , Krempa Anna 
Published: August 2022

AbstractThe research was carried out on the territory of the Russian Federation in the forest-steppe region of the south Western Siberia (Omsk state), in the long-term (43 years) stationary experiment. Sprinkling was used for irrigation in the experiment. The number of different physiological groups of microorganisms, the cellulolytic activity of the soil, and nitrification capacity were determined under the sowing of an eight-field grain-grass crop rotation (perennial grasses (Bunias orientalis L. + Bromopsis inermis L. + Galega orientalis Lam. 6–8 years old), spring barley Hordeum vulgare Leyss.—variety Sasha). Immobilization processes predominated in the soil under the sowed crops, it contributes to the preservation of soil organic matter (mineralization coefficient SAA/MPA < 1). The highest transformation ratio of soil organic matter, i.e. increased conversion of plant residues into organic matter, was noted with applying nitrogen-phosphorus fertilizers (N60P60) under the barley. The combination of irrigation factors and the use of mineral fertilizers (N30-60P60) were contributed to the growth of the microorganisms’ population, the amplification of decomposition of cellulose, and improvement of nitrification capacity in the soil. The perennial irrigation of the meadow-chernozem soil and the application of intensive technology of cultivation of crops in crop rotation stimulated the growth of the microorganisms’ population and didn’t detriment the ecological state of the soil.
Using a polygenic score in a family design to understand genetic influences on musicality
Authors: Wesseldijk Laura W. , Abdellaoui Abdel , Gordon Reyna L. ,   23andMe Research Team, Aslibekyan Stella , Auton Adam , Babalola Elizabeth , Bell Robert K. , Bielenberg Jessica , Bryc Katarzyna , Bullis Emily , Coker Daniella , Partida Gabriel Cuellar , Dhamija Devika , Das Sayantan , Elson Sarah L. , Filshtein Teresa , Fletez-Brant Kipper , Fontanillas Pierre , Freyman Will , Faaborg Anna , Fuller Shirin T. , Gandhi Pooja M. , Heilbron Karl , Hicks Barry , Jewett Ethan M. , Kukar Katelyn , Lin Keng-Han , Lowe Maya , McCreight Jey C. , McIntyre Matthew H. , Micheletti Steven J. , Moreno Meghan E. , Mountain Joanna L. , Nandakumar Priyanka , Noblin Elizabeth S. , O’Connell Jared , Huang Yunru , Petrakovitz Aaron A. , Lane Vanessa , Petrakovitz Aaron , Kim Joanne S. , Poznik G. David , Schumacher Morgan , Shastri Anjali J. , Shelton Janie F. , Shi Jingchunzi , Shringarpure Suyash , Tran Vinh , Tung Joyce Y. , Wang Xin , Wang Wei , Weldon Catherine H. , Wilton Peter , Hernandez Alejandro , Wong Corinna , Tchakouté Christophe Toukam , Ullén Fredrik , Mosing Miriam A. 
Published: August 2022

AbstractTo further our understanding of the genetics of musicality, we explored associations between a polygenic score for self-reported beat synchronization ability (PGSrhythm) and objectively measured rhythm discrimination, as well as other validated music skills and music-related traits. Using family data, we were able to further explore potential pathways of direct genetic, indirect genetic (through passive gene–environment correlation) and confounding effects (such as population structure and assortative mating). In 5648 Swedish twins, we found PGSrhythm to predict not only rhythm discrimination, but also melody and pitch discrimination (betas between 0.11 and 0.16, p < 0.001), as well as other music-related outcomes (p < 0.05). In contrast, PGSrhythm was not associated with control phenotypes not directly related to music. Associations did not deteriorate within families (N = 243), implying that indirect genetic or confounding effects did not inflate PGSrhythm effects. A correlation (r = 0.05, p < 0.001) between musical enrichment of the family childhood environment and individuals' PGSrhythm, suggests gene–environment correlation. We conclude that the PGSrhythm captures individuals' general genetic musical propensity, affecting musical behavior more likely direct than through indirect or confounding effects.
Mixed convection flow of an electrically conducting viscoelastic fluid past a vertical nonlinearly stretching sheet
Authors: Jafar Ahmad Banji , Shafie Sharidan , Ullah Imran , Safdar Rabia , Jamshed Wasim , Pasha Amjad Ali , Rahman Mustafa Mutiur , Hussain Syed M. , Rehman Aysha , El Din El Sayed M. Tag , Eid Mohamed R. 
Published: August 2022

AbstractThe study of hydromagnetic mixed convection flow of viscoelastic fluid caused by a vertical stretched surface is presented in this paper. According to this theory, the stretching velocity varies as a power function of the displacement from the slot. The conservation of energy equation includes thermal radiation and viscous dissipation to support the mechanical operations of the heat transfer mechanism. Through the use of an adequate and sufficient similarity transformation for a nonlinearly stretching sheet, the boundary layer equations governing the flow issue are converted into a set of ordinary differential equations. The Keller box technique is then used to numerically solve the altered equations. To comprehend the physical circumstances of stretching sheets for variations of the governing parameters, numerical simulations are made. The influence and characteristic behaviours of physical parameters were portrayed graphically for the velocity field and temperature distributions. The research shows that the impact of the applied magnetic parameter is to improve the distribution of the viscoelastic fluid temperature and reduce the temperature gradient at the border. Temperature distribution and the associated thermal layer are shown to have improved because of radiative and viscous dissipation characteristics. Radiation causes additional heat to be produced in liquid, raising the fluid's temperature. It was also found that higher velocities are noticed in viscoelastic fluid as compared with Newtonian fluid (i.e., when K = 0).
Small molecule mediated inhibition of protein cargo recognition by peroxisomal transport receptor PEX5 is toxic to Trypanosoma
Authors: Napolitano Valeria , Softley Charlotte A. , Blat Artur , Kalel Vishal C. , Schorpp Kenji , Siebenmorgen Till , Hadian Kamyar , Erdmann Ralf , Sattler Michael , Popowicz Grzegorz M. , Dubin Grzegorz 
Published: August 2022

AbstractTrypanosomiases are life-threatening infections of humans and livestock, and novel effective therapeutic approaches are needed. Trypanosoma compartmentalize glycolysis into specialized organelles termed glycosomes. Most of the trypanosomal glycolytic enzymes harbor a peroxisomal targeting signal-1 (PTS1) which is recognized by the soluble receptor PEX5 to facilitate docking and translocation of the cargo into the glycosomal lumen. Given its pivotal role in the glycosomal protein import, the PEX5–PTS1 interaction represents a potential target to inhibit import of glycolytic enzymes and thus kill the parasite. We developed a fluorescence polarization (FP)-based assay for monitoring the PEX5–PTS1 interaction and performed a High Throughput Screening (HTS) campaign to identify small molecule inhibitors of the interaction. Six of the identified hits passed orthogonal selection criteria and were found to inhibit parasite growth in cell culture. Our results validate PEX5 as a target for small molecule inhibitors and provide scaffolds suitable for further pre-clinical development of novel trypanocidal compounds.
Practical counting of substitutive paths on a planar infrastructure network
Authors: Hayashi Yukio , Tanaka Atsushi 
Published: August 2022

AbstractWhen there are many non-intersecting paths between two vertices on a network, the connectivity is fault-tolerant. Because of no common vertices on these paths, they can be emergently used in avoiding destroyed parts on the usual paths by any disasters or attacks. It gives a tolerance index whether the combination of non-intersecting paths is many or few. However, to enumerate such paths is an intractable combinatorial problem, no practical algorithm has been known. On the other hand, many socio-technological infrastructure networks are embedded on the surface of Earth. Thus, as an approximate solution, we extendedly apply the counting method based on a path matrix with our proposed mapping to directed acyclic graphs from a planar network according to each pair of source and terminal vertices. The tendency of many or few combinations of the paths is clearly investigated through computer simulations for realistic networks. This approach will be useful for evaluating the existence of substitutive paths to improve the tolerance in risk management.
Semi-supervised classifier guided by discriminator
Authors: Jamroziński Sebastian , Markowska-Kaczmar Urszula 
Published: August 2022

AbstractSome machine learning applications do not allow for data augmentation or are applied to modalities where the augmentation is difficult to define. Our study aimed to develop a new method in semi-supervised learning (SSL) applicable to various modalities of data (images, sound, text), especially when augmentation is hard or impossible to define, i.e., medical images. Assuming that all samples, labeled and unlabeled, come from the same data distribution, we can say that labeled and unlabeled data sets used in the semi-supervised learning tasks are similar. Based on this observation, the data embeddings created by the classifier should also be similar for both sets. In our method, finding these embeddings is achieved based on two models—classifier and an auxiliary discriminator model, inspired by the Generative Adversarial Network (GAN) learning process. The classifier is trained to build embeddings for labeled and unlabeled datasets to cheat discriminator, which recognizes whether the embedding comes from a labeled or unlabeled dataset. The method was named the DGSSC from Discriminator Guided Semi-Supervised Classifier. The experimental research aimed evaluation of the proposed method on the classification task in combination with the teacher-student approach and comparison with other SSL methods. In most experiments, training the networks with the DGSSC method improves accuracy with the teacher-student approach. It does not deteriorate the accuracy of any experiment.
Tumor spheroids accelerate persistently invading cancer cells
Authors: Audoin Melanie , Søgaard Maria Tangen , Jauffred Liselotte 
Published: August 2022

AbstractGlioblastoma brain tumors form in the brain’s white matter and remain one of the most lethal cancers despite intensive therapy and surgery. The complex morphology of these tumors includes infiltrative growth and gain of cell motility. Therefore, various brain-mimetic model systems have been developed to investigate invasion dynamics. Despite this, exactly how gradients of cell density, chemical signals and metabolites influence individual cells’ migratory behavior remains elusive. Here we show that the gradient field induced by the spheroid—accelerates cells’ invasion of the extracellular matrix. We show that cells are pushed away from the spheroid along a radial gradient, as predicted by a biased persistent random walk. Thus, our results grasp in a simple model the complex behavior of metastasizing cells. We anticipate that this well-defined and quantitative assay could be instrumental in the development of new anti-cancer strategies.