bluuebunny/crossref_metadata_2025_split huggingface dataset:
The selection landscape and genetic legacy of ancient Eurasians
Authors: Irving-Pease Evan K. , Refoyo-Martínez Alba , Barrie William , Ingason Andrés , Pearson Alice , Fischer Anders , Sjögren Karl-Göran , Halgren Alma S. , Macleod Ruairidh , Demeter Fabrice , Henriksen Rasmus A. , Vimala Tharsika , McColl Hugh , Vaughn Andrew H. , Speidel Leo , Stern Aaron J. , Scorrano Gabriele , Ramsøe Abigail , Schork Andrew J. , Rosengren Anders , Zhao Lei , Kristiansen Kristian , Iversen Astrid K. N. , Fugger Lars , Sudmant Peter H. , Lawson Daniel J. , Durbin Richard , Korneliussen Thorfinn , Werge Thomas , Allentoft Morten E. , Sikora Martin , Nielsen Rasmus , Racimo Fernando , Willerslev Eske 
Published: January 2024

AbstractThe Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer’s disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.
The demise of the giant ape Gigantopithecus blacki
Authors: Zhang Yingqi , Westaway Kira E. , Haberle Simon , Lubeek Juliën K. , Bailey Marian , Ciochon Russell , Morley Mike W. , Roberts Patrick , Zhao Jian-xin , Duval Mathieu , Dosseto Anthony , Pan Yue , Rule Sue , Liao Wei , Gully Grant A. , Lucas Mary , Mo Jinyou , Yang Liyun , Cai Yanjun , Wang Wei , Joannes-Boyau Renaud 
Published: January 2024

AbstractThe largest ever primate and one of the largest of the southeast Asian megafauna, Gigantopithecus blacki1, persisted in China from about 2.0 million years until the late middle Pleistocene when it became extinct2–4. Its demise is enigmatic considering that it was one of the few Asian great apes to go extinct in the last 2.6 million years, whereas others, including orangutan, survived until the present5. The cause of the disappearance of G. blacki remains unresolved but could shed light on primate resilience and the fate of megafauna in this region6. Here we applied three multidisciplinary analyses—timing, past environments and behaviour—to 22 caves in southern China. We used 157 radiometric ages from six dating techniques to establish a timeline for the demise of G. blacki. We show that from 2.3 million years ago the environment was a mosaic of forests and grasses, providing ideal conditions for thriving G. blacki populations. However, just before and during the extinction window between 295,000 and 215,000  years ago there was enhanced environmental variability from increased seasonality, which caused changes in plant communities and an increase in open forest environments. Although its close relative Pongo weidenreichi managed to adapt its dietary preferences and behaviour to this variability, G. blacki showed signs of chronic stress and dwindling populations. Ultimately its struggle to adapt led to the extinction of the greatest primate to ever inhabit the Earth.
The CRISPR effector Cam1 mediates membrane depolarization for phage defence
Authors: Baca Christian F. , Yu You , Rostøl Jakob T. , Majumder Puja , Patel Dinshaw J. , Marraffini Luciano A. 
Published: January 2024

AbstractProkaryotic type III CRISPR–Cas systems provide immunity against viruses and plasmids using CRISPR-associated Rossman fold (CARF) protein effectors1–5. Recognition of transcripts of these invaders with sequences that are complementary to CRISPR RNA guides leads to the production of cyclic oligoadenylate second messengers, which bind CARF domains and trigger the activity of an effector domain6,7. Whereas most effectors degrade host and invader nucleic acids, some are predicted to contain transmembrane helices without an enzymatic function. Whether and how these CARF–transmembrane helix fusion proteins facilitate the type III CRISPR–Cas immune response remains unknown. Here we investigate the role of cyclic oligoadenylate-activated membrane protein 1 (Cam1) during type III CRISPR immunity. Structural and biochemical analyses reveal that the CARF domains of a Cam1 dimer bind cyclic tetra-adenylate second messengers. In vivo, Cam1 localizes to the membrane, is predicted to form a tetrameric transmembrane pore, and provides defence against viral infection through the induction of membrane depolarization and growth arrest. These results reveal that CRISPR immunity does not always operate through the degradation of nucleic acids, but is instead mediated via a wider range of cellular responses.
Distributional reinforcement learning in prefrontal cortex
Authors: Muller Timothy H. , Butler James L. , Veselic Sebastijan , Miranda Bruno , Wallis Joni D. , Dayan Peter , Behrens Timothy E. J. , Kurth-Nelson Zeb , Kennerley Steven W. 
Published: January 2024

AbstractThe prefrontal cortex is crucial for learning and decision-making. Classic reinforcement learning (RL) theories center on learning the expectation of potential rewarding outcomes and explain a wealth of neural data in the prefrontal cortex. Distributional RL, on the other hand, learns the full distribution of rewarding outcomes and better explains dopamine responses. In the present study, we show that distributional RL also better explains macaque anterior cingulate cortex neuronal responses, suggesting that it is a common mechanism for reward-guided learning.
Long non-coding RNAs and their potential function in response to postharvest senescence of Sparassis latifolia during cold storage
Authors: Weng Mengting , Zhang Di , Wang Hongyu , Yang Chi , Lin Hongyi , Pan Yanfang , Lin Yanquan 
Published: January 2024

AbstractLong non-coding RNAs (lncRNAs) have been shown to play crucial roles in response to aging processes. However, how lncRNAs regulate postharvest senescence of Sparassis latifolia (S. latifolia) with oriented polypropylene (OPP) film packing during cold storage remains unclear. In this study, we performed RNA-seq using the fruiting bodies of S. latifolia stored at 4 ℃ for 0, 8, 16 and 24 days after harvest, and profiled the lncRNA and mRNA transcriptome, respectively. In total, 1003 putative lncRNAs were identified, and there were 495, 483 and 162 differentially expressed (DE) lncRNAs, and 3680, 3941 and 1870 differentially expressed mRNAs after 8, 16 and 24 days of storage, respectively, compared to 0 day of storage. Target genes of differentially expressed lncRNAs were found to significantly associate with carbon and energy metabolism, response to abiotic stimulus, amino acid biosynthesis and metabolism, and protein synthesis and transcription. In addition, DE-lncRNA-mRNA co-expression networks in response to aging stress were also constructed. Taken together, these results confirm the regulatory role of lncRNAs in postharvest senescence of S. latifolia and will facilitate for improving preservation method.
Structural basis for the activity and specificity of the immune checkpoint inhibitor lirilumab
Authors: Lorig-Roach Nicholas , Harpell Nina M. , DuBois Rebecca M. 
Published: January 2024

AbstractThe clinical success of immune checkpoint inhibitors has underscored the key role of the immune system in controlling cancer. Current FDA-approved immune checkpoint inhibitors target the regulatory receptor pathways of cytotoxic T-cells to enhance their anticancer responses. Despite an abundance of evidence that natural killer (NK) cells can also mediate potent anticancer activities, there are no FDA-approved inhibitors targeting NK cell specific checkpoint pathways. Lirilumab, the most clinically advanced NK cell checkpoint inhibitor, targets inhibitory killer immunoglobulin-like receptors (KIRs), however it has yet to conclusively demonstrate clinical efficacy. Here we describe the crystal structure of lirilumab in complex with the inhibitory KIR2DL3, revealing the precise epitope of lirilumab and the molecular mechanisms underlying KIR checkpoint blockade. Notably, the epitope includes several key amino acids that vary across the human population, and binding studies demonstrate the importance of these amino acids for lirilumab binding. These studies reveal how KIR variations in patients could influence the clinical efficacy of lirilumab and reveal general concepts for the development of immune checkpoint inhibitors targeting NK cells.
How article category in Wikipedia determines the heterogeneity of its editors
Authors: Oeberst Aileen , Ridderbecks Till 
Published: January 2024

AbstractCollaboration is essential to advancing knowledge and, ultimately, entire societies. With the development of Web 2.0, the possibilities have risen to unprecedented levels and allowed for the collaborative creation of the world’s largest compendium of knowledge that ever existed – Wikipedia. Collaboration is not a safeguard of quality per se, however. Rather, the quality of Wikipedia articles rises with the number of editors per article as well as a greater diversity among them. Here, we address a not yet documented potential threat to those preconditions: self-selection of Wikipedia editors to articles. Specifically, we expected articles with a clear-cut link to a specific country (e.g., about its highest mountain, “national” article category) to attract a larger proportion of editors of that nationality when compared to articles without any specific link to that country (e.g., “gravity”, “universal” article category), whereas articles with a link to several countries (e.g., “United Nations”, “international” article category) should fall in between. Across several language versions, hundreds of different articles, and hundreds of thousands of editors, we find the expected effect within Wikipedia: The more exclusively an article topic is linked to a particular nation, the higher the proportion of editors from that country is among the contributors.
The development of an electrochemical immunosensor utilizing chicken IgY anti-spike antibody for the detection of SARS-CoV-2
Authors: Al-Qaoud Khaled M. , Obeidat Yusra M. , Al-Omari Tareq , Okour Mohammad , Al-Omari Mariam M. , Ahmad Mohammad I. , Alshadfan Raed , Rawashdeh AbdelMonem M. 
Published: January 2024

AbstractThis paper introduces a novel approach for detecting the SARS-CoV-2 recombinant spike protein combining a label free electrochemical impedimetric immunosensor with the use of purified chicken IgY antibodies. The sensor employs three electrodes and is functionalized with an anti-S IgY antibody, ELISA and immunoblot assays confirmed the positive response of chicken immunized with SARS-CoV2 S antigen. The developed immunosensor is effective in detecting SARS-CoV-2 in nasopharyngeal clinical samples from suspected cases. The key advantage of this biosensor is its remarkable sensitivity, and its capability of detecting very low concentrations of the target analyte, with a detection limit of 5.65 pg/mL. This attribute makes it highly suitable for practical point-of-care (POC) applications, particularly in low analyte count clinical scenarios, without requiring amplification. Furthermore, the biosensor has a wide dynamic range of detection, spanning from 11.56 to 740 ng/mL, which makes it applicable for sample analysis in a typical clinical setting.
Association of early cleavage, morula compaction and blastocysts ploidy of IVF embryos cultured in a time-lapse system and biopsied for genetic test for aneuploidy
Authors: De Martin H. , Bonetti T. C. S. , Nissel C. A. Z. , Gomes A. P. , Fujii M. G. , Monteleone P. A. A. 
Published: January 2024

AbstractIVF embryos have historically been evaluated by morphological characteristics. The time-lapse system (TLS) has become a promising tool, providing an uninterrupted evaluation of morphological and dynamic parameters of embryo development. Furthermore, TLS sheds light on unknown phenomena such as direct cleavage and incomplete morula compaction. We retrospectively analyzed the morphology (Gardner Score) and morphokinetics (KIDScore) of 835 blastocysts grown in a TLS incubator (Embryoscope+), which were biopsied for preimplantation genetic testing for aneuploidy (PGT-A). Only the embryos that reached the blastocyst stage were included in this study and time-lapse videos were retrospectively reanalysed. According to the pattern of initial cleavages and morula compaction, the embryos were classified as: normal (NC) or abnormal (AC) cleavage, and fully (FCM) or partially compacted (PCM) morulae. No difference was found in early cleavage types or morula compaction patterns between female age groups (< 38, 38–40 and > 40 yo). Most of NC embryos resulted in FCM (≅ 60%), while no embryos with AC resulted in FCM. Aneuploidy rate of AC-PCM group did not differ from that of NC-FCM group in women < 38 yo, but aneuploidy was significantly higher in AC-PCM compared to NC-FCM of women > 40 yo. However, the quality of embryos was lower in AC-PCM blastocysts in women of all age ranges. Morphological and morphokinetic scores declined with increasing age, in the NC-PCM and AC-PCM groups, compared to the NC-FCM. Similar aneuploidy rates among NC-FCM and AC-PCM groups support the hypothesis that PCM in anomalous-cleaved embryos can represent a potential correction mechanism, even though lower morphological/morphokinetic scores are seen on AC-PCM. Therefore, both morphological and morphokinetic assessment should consider these embryonic development phenomena.
Utilizing industrial byproducts for the manufacture of clay-cellulose nanocomposite cements with enhanced sustainability
Authors: El-Feky M. S. , Badawy Amr H. , Youssef Passant , Kohail Mohamed 
Published: January 2024

AbstractThis study investigates the influence of different nano clay contents (0, 1, 3, and 5 wt% of cement) on the microstructure and the mechanical properties of cement composites reinforced with varying Nano cellulose fiber contents (0, 0.5, 0.75, and 1 wt% of cement). Unlike previous research that employed sonication to improve dispersion in the cement matrix, this study explores the effects of unsonicated nano-cellulose addition and the combined incorporation of nano-cellulose and nano-clay. The results demonstrate that these additions significantly enhance the compressive strength, abrasion resistance, and water absorption ratios of the cement composites. Furthermore, the inclusion of nano-clay improves the microstructure of the cement matrix, strengthening the interfacial transition zone and reinforcing the bond between nano-cellulose and the cement matrix. The microstructural analysis using scanning electron microscopy (SEM) reveals the presence of a dense interconnected structure characterized by rod-like crystals. This research contributes to the development of sustainable construction materials by examining the effects of nano-cellulose and nano-clay on the properties and microstructure of cement composites. The utilization of industrial byproducts, such as wood sawdust, for the extraction of nano-cellulose offers an eco-friendly approach to enhance the performance of cement-based materials. The maximum compressive strength obtained, after 28 days, was at mix with 0.75% NCL + 5%NC with a gain of 53.5% than that of the control mix. In mixes containing only nano-clay (NCL), the increase in NCL content led to a higher rate of water absorption in the cement matrix, which reaches 4%. Confirming the results obtained from compressive strength and water absorption, mix with 0.75% NCL and 5% NC had obtained the optimum values with an improvement of 20% than that of the control mix.
Visualization and identification of components in a gigantic spherical dolomite concretion by Raman imaging in combination with MCR or CLS methods
Authors: Kitanaka Ryosuke , Tsuboi Motohiro , Numata Tomoko , Muramiya Yusuke , Yoshida Hidekazu , Ozaki Yukihiro 
Published: January 2024

AbstractThe combination of Raman imaging and multivariate curve resolution (MCR) or classical least squares (CLS) has allowed us to explore the distribution and identification of components in a gigantic spherical dolomite concretion. It has been found by the MCR and CLS analyses of imaging data that the concretion contains dolomite, kerogen, anatase, quartz, plagioclase, and carbon materials with considerably large distribution of dolomite. The existence of these components has also been confirmed by the point-by-point analysis of imaging data. The distributions of these components were clearly observed by Raman images. Of note is that the amount of carbon materials is considerably large, and they are buried among the matrix sedimentary grains in the concretion, suggesting that there exist soft tissues with biological origin. Moreover, one of the loading spectra of CLS shows intense bands in the region of 3000–2800 cm−1, and bands at ca. 1658, ca. 1585, 1455, 1323, and 1261 cm−1. These bands indicate the existence of decomposed organic materials in the concretion. Raman imaging of concretions provides direct evidence that concretions are of biological organic origin.
RETRACTED ARTICLE: Arsenic album 30C exhibits crystalline nano structure of arsenic trioxide and modulates innate immune markers in murine macrophage cell lines
Authors: Rath Suvasmita , Jema Jyoti Prava , Kesavan Kamali , Mallick Sagar , Pradhan Jyotsnarani , Chainy Gagan Bihari Nityananda , Nayak Debadatta , Kaushik Subhash , Dandapat Jagneshwar 
Published: January 2024

AbstractMacrophages are associated with innate immune response and M1-polarized macrophages exhibit pro-inflammatory functions. Nanoparticles of natural or synthetic compounds are potential triggers of innate immunity. As2O3 is the major component of the homeopathic drug, Arsenic album 30C.This has been claimed to have immune-boosting activities, however, has not been validated experimentally. Here we elucidated the underlying mechanism of Ars. alb 30C-mediated immune priming in murine macrophage cell line. Transmission Electron Microscopy (TEM) and X-ray diffraction (XRD) used for the structural analysis of the drug reveals the presence of crystalline As2O3 nanoparticles of cubic structure. Similarly, signatures of M1-macrophage polarization were observed by surface enhanced Raman scattering (SERS) in RAW 264.7 cells with concomitant over expression of M1 cell surface marker, CD80 and transcription factor, NF-κB, respectively. We also observed a significant increase in pro-inflammatory cytokines like iNOS, TNF-α, IL-6, and COX-2 expression with unaltered ROS and apoptosis in drug-treated cells. Enhanced expression of Toll-like receptors 3 and 7 were observed both in transcriptional and translational levels after the drug treatment. In sum, our findings for the first time indicated the presence of crystalline As2O3 cubic nanostructure in Ars. alb 30C which facilitates modulation of innate immunity by activating macrophage polarization.
Exercise-induced effects on asprosin and indices of atherogenicity and insulin resistance in males with metabolic syndrome: a randomized controlled trial
Authors: Suder Agnieszka , Makiel Karol , Targosz Aneta , Maciejczyk Marcin , Kosowski Piotr , Haim Alon 
Published: January 2024

AbstractMetabolic syndrome (MetS) development is associated with insulin resistance and obesity, with the progression of visceral adipose tissue playing a crucial role. Excessive adipose tissue is accompanied by an increase in the asprosin (ASP), which is responsible for carbohydrate metabolism and the regulation of hunger and satiety. Exercise affects the release of ASP, which may regulate metabolism accordingly. Due to the inconclusive results of the effect of exercise on ASP concentration in men with MetS, 12-week interventions were carried out in the following groups: EG1—aerobic training (n = 21, age: 34.21 ± 6.06, WC; waist circumference: 114.7 ± 10.93) and EG2—a combination of aerobic and resistance training (n = 21, age: 37.37 ± 7.08, WC: 114.8 ± 11.64) and compared with a control group (CG) of men with MetS without any intervention (n = 20, age: 38.26 ± 7.43, WC: 115.3 ± 10.54). Body composition, indicators of carbohydrate-lipid metabolism, and ASP were assessed four times: before the intervention, at 6 and 12 weeks of training, and 4 weeks after the training sessions. A comparison of the intervention influence on changes in the analyzed variables between the groups was performed using ANOVA test for dependent groups with post-hoc comparison. The effect size (ES) was also assessed using squared eta (η2). The implementation of aerobic training resulted in a decrease in ASP concentration (p = 0.03) within 6 weeks of the intervention, while in the CG a gradual increase in ASP was confirmed (p < 0.001). Aerobic-resistance training did not induce significant changes in ASP concentration but resulted in an increase in fat-free mass/fat mass (FFM/FM) ratio (p < 0.001), and a decrease (p = 0.04) in Homeostasis Model Assessment of Insulin Resistance (HOMA-IR). Changes in the visceral adipose tissue level indicate a gradual decrease in both the EG1 (p = 0.01) and EG2 (p = 0.04) groups. Both aerobic and aerobic-resistance exercises may have a regulatory effect, mainly by reducing visceral adipose tissue, on the improvement of metabolic disorders.