bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anomalous electrons in a metallic kagome ferromagnet
Authors: Ekahana Sandy Adhitia , Soh Y. , Tamai Anna , Gosálbez-Martínez Daniel , Yao Mengyu , Hunter Andrew , Fan Wenhui , Wang Yihao , Li Junbo , Kleibert Armin , Vaz C. A. F. , Ma Junzhang , Lee Hyungjun , Xiong Yimin , Yazyev Oleg V. , Baumberger Felix , Shi Ming , Aeppli G. 
Published: March 2024

AbstractOrdinary metals contain electron liquids within well-defined ‘Fermi’ surfaces at which the electrons behave as if they were non-interacting. In the absence of transitions to entirely new phases such as insulators or superconductors, interactions between electrons induce scattering that is quadratic in the deviation of the binding energy from the Fermi level. A long-standing puzzle is that certain materials do not fit this ‘Fermi liquid’ description. A common feature is strong interactions between electrons relative to their kinetic energies. One route to this regime is special lattices to reduce the electron kinetic energies. Twisted bilayer graphene1–4 is an example, and trihexagonal tiling lattices (triangular ‘kagome’), with all corner sites removed on a 2 × 2 superlattice, can also host narrow electron bands5 for which interaction effects would be enhanced. Here we describe spectroscopy revealing non-Fermi-liquid behaviour for the ferromagnetic kagome metal Fe3Sn2 (ref. 6). We discover three C3-symmetric electron pockets at the Brillouin zone centre, two of which are expected from density functional theory. The third and most sharply defined band emerges at low temperatures and binding energies by means of fractionalization of one of the other two, most likely on the account of enhanced electron–electron interactions owing to a flat band predicted to lie just above the Fermi level. Our discovery opens the topic of how such many-body physics involving flat bands7,8 could differ depending on whether they arise from lattice geometry or from strongly localized atomic orbitals9,10.
Synthetic reversed sequences reveal default genomic states
Authors: Camellato Brendan R. , Brosh Ran , Ashe Hannah J. , Maurano Matthew T. , Boeke Jef D. 
Published: March 2024

AbstractPervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or ‘noise’1–4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in ‘default genomic states’ between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.
Decoding chromatin states by proteomic profiling of nucleosome readers
Authors: Lukauskas Saulius , Tvardovskiy Andrey , Nguyen Nhuong V. , Stadler Mara , Faull Peter , Ravnsborg Tina , Özdemir Aygenli Bihter , Dornauer Scarlett , Flynn Helen , Lindeboom Rik G. H. , Barth Teresa K. , Brockers Kevin , Hauck Stefanie M. , Vermeulen Michiel , Snijders Ambrosius P. , Müller Christian L. , DiMaggio Peter A. , Jensen Ole N. , Schneider Robert , Bartke Till 
Published: March 2024

AbstractDNA and histone modifications combine into characteristic patterns that demarcate functional regions of the genome1,2. While many ‘readers’ of individual modifications have been described3–5, how chromatin states comprising composite modification signatures, histone variants and internucleosomal linker DNA are interpreted is a major open question. Here we use a multidimensional proteomics strategy to systematically examine the interaction of around 2,000 nuclear proteins with over 80 modified dinucleosomes representing promoter, enhancer and heterochromatin states. By deconvoluting complex nucleosome-binding profiles into networks of co-regulated proteins and distinct nucleosomal features driving protein recruitment or exclusion, we show comprehensively how chromatin states are decoded by chromatin readers. We find highly distinctive binding responses to different features, many factors that recognize multiple features, and that nucleosomal modifications and linker DNA operate largely independently in regulating protein binding to chromatin. Our online resource, the Modification Atlas of Regulation by Chromatin States (MARCS), provides in-depth analysis tools to engage with our results and advance the discovery of fundamental principles of genome regulation by chromatin states.
Selfish conflict underlies RNA-mediated parent-of-origin effects
Authors: Pliota Pinelopi , Marvanova Hana , Koreshova Alevtina , Kaufman Yotam , Tikanova Polina , Krogull Daniel , Hagmüller Andreas , Widen Sonya A. , Handler Dominik , Gokcezade Joseph , Duchek Peter , Brennecke Julius , Ben-David Eyal , Burga Alejandro 
Published: March 2024

AbstractGenomic imprinting—the non-equivalence of maternal and paternal genomes—is a critical process that has evolved independently in many plant and mammalian species1,2. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles3,4. Yet, how these epigenetic differences evolve in the first place is poorly understood3,5,6. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals7–9. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs—but not SLOW-1 protein—are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.
Post-exercise heart rate recovery and its speed are associated with resting-reactivity cardiovagal modulation in healthy women
Authors: da Fonseca Richard Xavier , Gomes da Cruz Carlos Janssen , Soares Edgard de Melo Keene Von Koening , Garcia Giliard Lago , Porto Luiz Guilherme Grossi , Molina Guilherme Eckhardt 
Published: March 2024

AbstractThe present study sought to expand upon prior investigations of the relationship between post-exercise heart rate recovery (HRR) and cardiovagal resting-reactivity modulation. HRR from 1st to 5th min after maximal exercise test was correlated with a cardiovagal index of heart rate variability (SD1) at resting (supine and orthostatic positions) and its reactivity after the orthostatic stress test in 34 healthy women. Statistical analysis employed non-parametric tests with a p-value set at 5%. HRR, ∆%HRR, and coefficient of HRR (CHRR) at the 3rd and 5th min correlated with SD1 and SD1n (normalized units) in the supine position (rs = 0.36 to 0.47; p =  < 0.01). From the 1st to 5th min, HRR, ∆%HRR, and CHRR correlated with SD1 and SD1n in the orthostatic position (rs = 0.29 to 0.47; p =  ≤ 0.01 to 0.05), except for HRR at 5th min with SD1n (p = 0.06). Following the orthostatic stress test, HRR at 3rd and HRR, %∆HRR at 5th min correlated with ∆absSD1 (rs = 0.28 to 0.35; p = 0.02 to 0.05). All HRR measurements at 1st min correlated with ∆absSD1n (rs = 0.32 to 0.38; p = 0.01 to 0.03), and the CHRR at 1st min correlated with ∆%SD1(rs = 0.37; p = 0.01). After the sample was divided into high and low cardiovagal modulation subgroups, the subgroup with high modulation at rest (supine and orthostatic) and higher cardiovagal reactivity (reduction) showed faster HRR (p =  ≤ 0.01 to 0.05; ES:0.37 to 0.50). HRR throughout the 1st to 5th min positively correlates with cardiovagal modulation in the orthostatic position, and the 3rd and 5th min positively correlate with cardiovagal modulation in both postures at rest. Faster HRR following the maximal exercise test is associated with high resting-reactivity cardiovagal modulation in healthy women.
Multicenter study of the efficacy and safety of electrocautery-enhanced lumen-apposing metal stents for the internal drainage of pancreatic fluid collections
Authors: Chung Chen-Shuan , Kuo Yu-Ting , Chiu Yi-Chun , Lin Yang-Chao , Yang Chi-Ying , Chen Kuan-Chih , Liao Szu-Chia , Sun Cheuk-Kay , Lin Yen-Chih , Wang Hsiu-Po 
Published: March 2024

AbstractPancreatic fluid collections (PFCs) including pancreatic pseudocyst (PP) and walled-off necrosis (WON) are complications after acute pancreatitis. We aimed to evaluate the efficacy and safety of endoscopic ultrasound (EUS)-guided lumen-apposing metal stent (LAMS) placement to manage PFCs. Between June 2019 and May 2023, patients with symptomatic PFCs who underwent EUS-guided electrocautery-enhanced LAMS drainage were enrolled retrospectively from eight tertiary centers in Taiwan. In total, 33 [14 (42.42%) PP and 19 (57.58%) WON] patients were enrolled. Gallstones (27.27%) and abdominal pain (72.73%) were the most common etiology and indication for drainage. The technical and clinical success rates were 100% and 96.97%, respectively, and the mean procedure time was 30.55 (± 16.17) min. Complications included one (3.03%) case of self-limited bleeding; there were no cases of mortality. Seven (21.21%) patients had recurrence. Patients with disconnected pancreatic duct syndrome (DPDS) had a higher recurrence rate than those without (71.43% vs. 38.46%, p = 0.05). After replacing LAMSs with transmural double-pigtail plastic stents (DPSs) in the DPDS patients, the DPS migration rate was higher in the patients with recurrence (100% vs. 33.33%, p = 0.04). In conclusion, drainage of symptomatic PFCs with EUS-guided electrocautery-enhanced LAMS appears to be efficient and safe. Replacing LAMSs with DPSs in DPDS patients was associated with a lower recurrence rate.
Visual acuity prediction on real-life patient data using a machine learning based multistage system
Authors: Schlosser Tobias , Beuth Frederik , Meyer Trixy , Kumar Arunodhayan Sampath , Stolze Gabriel , Furashova Olga , Engelmann Katrin , Kowerko Danny 
Published: March 2024

AbstractIn ophthalmology, intravitreal operative medication therapy (IVOM) is a widespread treatment for diseases related to the age-related macular degeneration (AMD), the diabetic macular edema, as well as the retinal vein occlusion. However, in real-world settings, patients often suffer from loss of vision on time scales of years despite therapy, whereas the prediction of the visual acuity (VA) and the earliest possible detection of deterioration under real-life conditions is challenging due to heterogeneous and incomplete data. In this contribution, we present a workflow for the development of a research-compatible data corpus fusing different IT systems of the department of ophthalmology of a German maximum care hospital. The extensive data corpus allows predictive statements of the expected progression of a patient and his or her VA in each of the three diseases. For the disease AMD, we found out a significant deterioration of the visual acuity over time. Within our proposed multistage system, we subsequently classify the VA progression into the three groups of therapy “winners”, “stabilizers”, and “losers” (WSL classification scheme). Our OCT biomarker classification using an ensemble of deep neural networks results in a classification accuracy (F1-score) of over 98%, enabling us to complete incomplete OCT documentations while allowing us to exploit them for a more precise VA modelling process. Our VA prediction requires at least four VA examinations and optionally OCT biomarkers from the same time period to predict the VA progression within a forecasted time frame, whereas our prediction is currently restricted to IVOM/no therapy. We achieve a final prediction accuracy of 69% in macro average F1-score, while being in the same range as the ophthalmologists with 57.8 and $$50 \pm 10.7$$

50
±
10.7

% F1-score.
Factors associated to mortality in children with critical COVID-19 and multisystem inflammatory syndrome in a resource-poor setting
Authors: de Farias Emmerson C. F. , Pavão Junior Manoel J. C. , de Sales Susan C. D. , do Nascimento Luciana M. P. P. , Pavão Dalila C. A. , Pinheiro Anna P. S. , Pinheiro Andreza H. O. , Alves Marília C. B. , Ferraro Kíssila M. M. M. , Aires Larisse F. Q. , Dias Luana G. , Machado Mayara M. M. , Serrão Michaelle J. D. , Gomes Raphaella R. , de Moraes Sara M. P. , Moura Gabriella M. G. , de Sousa Adriana M. B. , Pontes Gabriela C. L. , Carvalho Railana D. F. P. , Silva Cristiane T. C. , Lemes Guilherme , da C. G. Diniz Bruna , Chermont Aurimery G. , de Almeida Kellen F. S. , Saraty Salma B. , Maia Mary L. F. , Lima Miriam R. C. , Carvalho Patricia B. , de B. Braga Renata , de O. Harada Kathia , Justino Maria C. A. , Clemente Gleice , Terreri Maria Teresa , Monteiro Marta C. 
Published: March 2024

AbstractSARS-CoV-2 infection in children is usually asymptomatic/mild. However, some patients may develop critical forms. We aimed to describe characteristics and evaluate the factors associated to in-hospital mortality of patients with critical COVID-19/MIS-C in the Amazonian region. This multicenter prospective cohort included critically ill children (1 mo–18 years old), with confirmed COVID-19/MIS-C admitted to 3 tertiary Pediatric Intensive Care Units (PICU) in the Brazilian Amazon, between April/2020 and May/2023. The main outcome was in-hospital mortality and were evaluated using a multivariable Cox proportional regression. We adjusted the model for pediatric risk of mortality score version IV (PRISMIV) score and age/comorbidity. 266 patients were assessed with 187 in the severe COVID-19 group, 79 included in the MIS-C group. In the severe COVID-19 group 108 (57.8%) were male, median age was 23 months, 95 (50.8%) were up to 2 years of age. Forty-two (22.5%) patients in this group died during follow-up in a median time of 11 days (IQR, 2–28). In the MIS-C group, 56 (70.9%) were male, median age was 23 months and median follow-up was 162 days (range, 3–202). Death occurred in 17 (21.5%) patients with a median death time of 7 (IQR, 4–13) days. The mortality was associated with higher levels of Vasoactive Inotropic-Score (VIS), presence of acute respiratory distress syndrome (ARDS), higher levels of Erythrocyte Sedimentation Rate, (ESR) and thrombocytopenia. Critically ill patients with severe COVID-19 and MIS-C from the Brazilian Amazon showed a high mortality rate, within 12 days of hospitalization.
Novel biosensor for high-throughput detection of progesterone receptor-interacting endocrine disruptors
Authors: Stavreva Diana A. , Varticovski Lyuba , Raziuddin Razi , Pegoraro Gianluca , Schiltz R. Louis , Hager Gordon L. 
Published: March 2024

AbstractProgesterone receptor (PR)-interacting compounds in the environment are associated with serious health hazards. However, methods for their detection in environmental samples are cumbersome. We report a sensitive activity-based biosensor for rapid and reliable screening of progesterone receptor (PR)-interacting endocrine disrupting chemicals (EDCs). The biosensor is a cell line which expresses nuclear mCherry-NF1 and a green fluorescent protein (GFP)-tagged chimera of glucocorticoid receptor (GR) N terminus fused to the ligand binding domain (LBD) of PR (GFP-GR-PR). As this LBD is shared by the PRA and PRB, the biosensor reports on the activation of both PR isoforms. This GFP-GR-PR chimera is cytoplasmic in the absence of hormone and translocates rapidly to the nucleus in response to PR agonists or antagonists in concentration- and time-dependent manner. In live cells, presence of nuclear NF1 label eliminates cell fixation and nuclear staining resulting in efficient screening. The assay can be used in screens for novel PR ligands and PR-interacting contaminants in environmental samples. A limited screen of river water samples indicated a widespread, low-level contamination with PR-interacting contaminants in all tested samples.
Interleukin-10 enhances recruitment of immune cells in the neonatal mouse model of obstructive nephropathy
Authors: Wyczanska Maja , Thalmeier Franziska , Keller Ursula , Klaus Richard , Narasimhan Hamsa , Ji Xingqi , Schraml Barbara U. , Wackerbarth Lou M. , Lange-Sperandio Bärbel 
Published: March 2024

AbstractUrinary tract obstruction during renal development leads to inflammation, leukocyte infiltration, tubular cell death, and interstitial fibrosis. Interleukin-10 (IL-10) is an anti-inflammatory cytokine, produced mainly by monocytes/macrophages and regulatory T-cells. IL-10 inhibits innate and adaptive immune responses. IL-10 has a protective role in the adult model of obstructive uropathy. However, its role in neonatal obstructive uropathy is still unclear which led us to study the role of IL-10 in neonatal mice with unilateral ureteral obstruction (UUO). UUO serves as a model for congenital obstructive nephropathies, a leading cause of kidney failure in children. Newborn Il-10−/− and C57BL/6 wildtype-mice (WT) were subjected to complete UUO or sham-operation on the 2nd day of life. Neonatal kidneys were harvested at day 3, 7, and 14 of life and analyzed for different leukocyte subpopulations by FACS, for cytokines and chemokines by Luminex assay and ELISA, and for inflammation, programmed cell death, and fibrosis by immunohistochemistry and western blot. Compared to WT mice, Il-10−/− mice showed reduced infiltration of neutrophils, CD11bhi cells, conventional type 1 dendritic cells, and T-cells following UUO. Il-10−/− mice with UUO also showed a reduction in pro-inflammatory cytokine and chemokine release compared to WT with UUO, mainly of IP-10, IL-1α, MIP-2α and IL-17A. In addition, Il-10−/− mice showed less necroptosis after UUO while the rate of apoptosis was not different. Finally, α-SMA and collagen abundance as readout for fibrosis were similar in Il-10−/− and WT with UUO. Surprisingly and in contrast to adult Il-10−/− mice undergoing UUO, neonatal Il-10−/− mice with UUO showed a reduced inflammatory response compared to respective WT control mice with UUO. Notably, long term changes such as renal fibrosis were not different between neonatal Il-10−/− and neonatal WT mice with UUO suggesting that IL-10 signaling is different in neonates and adults with UUO.
Visual features are processed before navigational affordances in the human brain
Authors: Dwivedi Kshitij , Sadiya Sari , Balode Marta P. , Roig Gemma , Cichy Radoslaw M. 
Published: March 2024

AbstractTo navigate through their immediate environment humans process scene information rapidly. How does the cascade of neural processing elicited by scene viewing to facilitate navigational planning unfold over time? To investigate, we recorded human brain responses to visual scenes with electroencephalography and related those to computational models that operationalize three aspects of scene processing (2D, 3D, and semantic information), as well as to a behavioral model capturing navigational affordances. We found a temporal processing hierarchy: navigational affordance is processed later than the other scene features (2D, 3D, and semantic) investigated. This reveals the temporal order with which the human brain computes complex scene information and suggests that the brain leverages these pieces of information to plan navigation.
Association of serum Ly6/PLAUR domain-containing protein 1 levels with skin sclerosis in systemic sclerosis
Authors: Sugimori Ayaka , Omori Issei , Iwasawa Okuto , Saito Hinako , Nakajima Hibari , Matsuno Ai , Sato Shinichi , Sumida Hayakazu 
Published: March 2024

AbstractSystemic sclerosis (SSc) is a connective tissue disease characterized by aberrant immune activation, vascular injury, and fibrosis of the skin and internal organs. Ly6/PLAUR domain-containing protein 1 (LYPD1) was reported to be secreted and to have various physiological functions such as anti-angiogenic effects. Here we investigated serum LYPD1 levels in SSc patients and the association of serum LYPD1 levels with clinical features of SSc. Serum samples were obtained from 75 SSc patients and 22 healthy individuals as controls. We measured serum LYPD1 levels using enzyme-linked immunosorbent assay kits. Then, the relationship between serum LYPD1 levels and clinical features of SSc was analyzed. Serum LYPD1 levels in diffuse cutaneous SSc (dcSSc) patients were significantly higher than those in the limited cutaneous SSc (lcSSc) patients (median [25–75th percentiles], 1693.43 [1086.61–1917.57] vs. 904.55 [714.356–1285.56] pg/mL), while there were no significant differences in the serum LYPD1 levels between lcSSc and healthy controls (904.55 [714.356–1285.56] vs. 750.71 pg/mL [544.00–912.14]). Further analysis revealed that serum LYPD1 levels in patients correlated with skin thickness scores and serum interleukin (IL)-6 levels, which were known to reflect the extent of skin thickening in SSc. Moreover, serum LYPD1 levels showed a decrease with improvement in skin thickness after treatment, along with a decrease in serum IL-6 levels. These results indicate that LYPD1 might be a potential marker for monitoring skin sclerosis and evaluating the efficacy of skin fibrosis treatment in SSc patients.
Development and validation of a novel overhead method for anteroposterior radiographs of fractured rat femurs
Authors: Sato Yosuke , Tagami Takashi , Akimoto Toshio , Takiguchi Toru , Endo Yusuke , Tsukamoto Takeshi , Hara Yoshiaki , Yokobori Shoji 
Published: March 2024

AbstractWe aimed to establish a new method of obtaining femur anteroposterior radiographs from live rats. We used five adult male Sprague–Dawley rats and created a femoral fracture model with an 8 mm segmental fragment. After the surgery, we obtained two femoral anteroposterior radiographs, a novel overhead method, and a traditional craniocaudal view. We obtained the overhead method three times, craniocaudal view once, and anteroposterior radiograph of the isolated femoral bone after euthanasia. We compared the overhead method and craniocaudal view with an isolated femoral anteroposterior view. We used a two-sample t-test and intraclass correlation coefficient (ICC) to estimate the intra-observer reliability. The overhead method had significantly smaller differences than the craniocaudal view for nail length (1.53 ± 1.26 vs. 11.4 ± 3.45, p < 0.001, ICC 0.96) and neck shaft angle (5.82 ± 3.8 vs. 37.8 ± 5.7, p < 0.001, ICC 0.96). No significant differences existed for intertrochanteric length/femoral head diameter (0.23 ± 0.13 vs. 0.23 ± 0.13, p = 0.96, ICC 0.98) or lateral condyle/medial condyle width (0.15 ± 0.16 vs. 0.13 ± 0.08, p = 0.82, ICC 0.99). A fragment displacement was within 0.11 mm (2.4%). The overhead method was closer to the isolated femoral anteroposterior view and had higher reliability.