bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competition-driven eco-evolutionary feedback reshapes bacteriophage lambda’s fitness landscape and enables speciation
Authors: Doud Michael B. , Gupta Animesh , Li Victor , Medina Sarah J. , De La Fuente Caesar A. , Meyer Justin R. 
Published: January 2024

AbstractA major challenge in evolutionary biology is explaining how populations navigate rugged fitness landscapes without getting trapped on local optima. One idea illustrated by adaptive dynamics theory is that as populations adapt, their newly enhanced capacities to exploit resources alter fitness payoffs and restructure the landscape in ways that promote speciation by opening new adaptive pathways. While there have been indirect tests of this theory, to our knowledge none have measured how fitness landscapes deform during adaptation, or test whether these shifts promote diversification. Here, we achieve this by studying bacteriophage $$\lambda$$
λ
, a virus that readily speciates into co-existing receptor specialists under controlled laboratory conditions. We use a high-throughput gene editing-phenotyping technology to measure $$\lambda$$
λ
’s fitness landscape in the presence of different evolved-$$\lambda$$
λ
competitors and find that the fitness effects of individual mutations, and their epistatic interactions, depend on the competitor. Using these empirical data, we simulate $$\lambda$$
λ
’s evolution on an unchanging landscape and one that recapitulates how the landscape deforms during evolution. $$\lambda$$
λ
heterogeneity only evolves in the shifting landscape regime. This study provides a test of adaptive dynamics, and, more broadly, shows how fitness landscapes dynamically change during adaptation, potentiating phenomena like speciation by opening new adaptive pathways.
CaMK4 controls follicular helper T cell expansion and function during normal and autoimmune T-dependent B cell responses
Authors: Scherlinger Marc , Li Hao , Pan Wenliang , Li Wei , Karino Kohei , Vichos Theodoros , Boulougoura Afroditi , Yoshida Nobuya , Tsokos Maria G. , Tsokos George C. 
Published: January 2024

AbstractSystemic lupus erythematosus (SLE) is an autoimmune disease characterized by dysregulated B cell compartment responsible for the production of autoantibodies. Here, we show that T cell-specific expression of calcium/calmodulin-dependent protein kinase IV (CaMK4) leads to T follicular helper (Tfh) cells expansion in models of T-dependent immunization and autoimmunity. Mechanistically, CaMK4 controls the Tfh-specific transcription factor B cell lymphoma 6 (Bcl6) at the transcriptional level through the cAMP responsive element modulator α (CREMα). In the absence of CaMK4 in T cells, germinal center formation and humoral immunity is impaired in immunized mice, resulting in reduced anti-dsDNA titres, as well as IgG and complement kidney deposition in the lupus-prone B6.lpr mouse. In human Tfh cells, CaMK4 inhibition reduced BCL6 expression and IL-21 secretion ex vivo, resulting in impaired plasmablast formation and IgG production. In patients with SLE, CAMK4 mRNA levels in Tfh cells correlated with those of BCL6. In conclusion, we identify CaMK4/CREMα as a driver of T cell-dependent B cell dysregulation in autoimmunity.
A high affinity switch for cAMP in the HCN pacemaker channels
Authors: Porro Alessandro , Saponaro Andrea , Castelli Roberta , Introini Bianca , Hafez Alkotob Anahita , Ranjbari Golnaz , Enke Uta , Kusch Jana , Benndorf Klaus , Santoro Bina , DiFrancesco Dario , Thiel Gerhard , Moroni Anna 
Published: January 2024

AbstractBinding of cAMP to Hyperpolarization activated cyclic nucleotide gated (HCN) channels facilitates pore opening. It is unclear why the isolated cyclic nucleotide binding domain (CNBD) displays in vitro lower affinity for cAMP than the full-length channel in patch experiments. Here we show that HCN are endowed with an affinity switch for cAMP. Alpha helices D and E, downstream of the cyclic nucleotide binding domain (CNBD), bind to and stabilize the holo CNBD in a high affinity state. These helices increase by 30-fold cAMP efficacy and affinity measured in patch clamp and ITC, respectively. We further show that helices D and E regulate affinity by interacting with helix C of the CNBD, similarly to the regulatory protein TRIP8b. Our results uncover an intramolecular mechanism whereby changes in binding affinity, rather than changes in cAMP concentration, can modulate HCN channels, adding another layer to the complex regulation of their activity.
Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize
Authors: Wang Nanqi , Wang Tianqi , Chen Yu , Wang Ming , Lu Qiaofang , Wang Kunguang , Dou Zhechao , Chi Zhiguang , Qiu Wei , Dai Jing , Niu Lei , Cui Jianyu , Wei Zhong , Zhang Fusuo , Kümmerli Rolf , Zuo Yuanmei 
Published: January 2024

AbstractIntercropping has the potential to improve plant nutrition as well as crop yield. However, the exact mechanism promoting improved nutrient acquisition and the role the rhizosphere microbiome may play in this process remains poorly understood. Here, we use a peanut/maize intercropping system to investigate the role of root-associated microbiota in iron nutrition in these crops, combining microbiome profiling, strain and substance isolation and functional validation. We find that intercropping increases iron nutrition in peanut but not in maize plants and that the microbiota composition changes and converges between the two plants tested in intercropping experiments. We identify a Pseudomonas secreted siderophore, pyoverdine, that improves iron nutrition in glasshouse and field experiments. Our results suggest that the presence of siderophore-secreting Pseudomonas in peanut and maize intercropped plays an important role in iron nutrition. These findings could be used to envision future intercropping practices aiming to improve plant nutrition.
Peculiar band geometry induced giant shift current in ferroelectric SnTe monolayer
Authors: Jin Gan , He Lixin 
Published: January 2024

AbstractThe bulk photovoltaic effect (BPVE) occurs when homogeneous noncentrosymmetric materials generate photocurrent or photovoltage under illumination. The intrinsic contribution to this effect is known as the shift current effect. We calculate the shift current conductivities of the ferroelectric SnTe monolayer using first-principles methods. Our results reveal a giant shift-current conductivity near the valley points in the SnTe monolayer. More remarkably, the linear optical absorption coefficient at this energy is very small, resulting in an enormous Glass coefficient that is four orders of magnitude larger than that of BaTiO3. To understand these giant shift-current effects, we employ a three-band model and find that they arise from the nontrivial energy band geometries near the valley points, where the shift-vector diverges. This serves as a prominent example highlighting the crucial role of band geometry in determining the fundamental properties of solids.
AutoTransOP: translating omics signatures without orthologue requirements using deep learning
Authors: Meimetis Nikolaos , Pullen Krista M. , Zhu Daniel Y. , Nilsson Avlant , Hoang Trong Nghia , Magliacane Sara , Lauffenburger Douglas A. 
Published: January 2024

AbstractThe development of therapeutics and vaccines for human diseases requires a systematic understanding of human biology. Although animal and in vitro culture models can elucidate some disease mechanisms, they typically fail to adequately recapitulate human biology as evidenced by the predominant likelihood of clinical trial failure. To address this problem, we developed AutoTransOP, a neural network autoencoder framework, to map omics profiles from designated species or cellular contexts into a global latent space, from which germane information for different contexts can be identified without the typically imposed requirement of matched orthologues. This approach was found in general to perform at least as well as current alternative methods in identifying animal/culture-specific molecular features predictive of other contexts—most importantly without requiring homology matching. For an especially challenging test case, we successfully applied our framework to a set of inter-species vaccine serology studies, where 1-to-1 mapping between human and non-human primate features does not exist.
Whole-genome resource sequences of 57 indigenous Ethiopian goats
Authors: Belay Shumuye , Belay Gurja , Nigussie Helen , Jian-Lin Han , Tijjani Abdulfatai , Ahbara Abulgasim M. , Tarekegn Getinet M. , Woldekiros Helina S. , Mor Siobhan , Dobney Keith , Lebrasseur Ophelie , Hanotte Olivier , Mwacharo Joram M. 
Published: January 2024

AbstractDomestic goats are distributed worldwide, with approximately 35% of the one billion world goat population occurring in Africa. Ethiopia has 52.5 million goats, ~99.9% of which are considered indigenous landraces deriving from animals introduced to the Horn of Africa in the distant past by nomadic herders. They have continued to be managed by smallholder farmers and semi-mobile pastoralists throughout the region. We report here 57 goat genomes from 12 Ethiopian goat populations sampled from different agro-climates. The data were generated through sequencing DNA samples on the Illumina NovaSeq 6000 platform at a mean depth of 9.71x and 150 bp pair-end reads. In total, ~2 terabytes of raw data were generated, and 99.8% of the clean reads mapped successfully against the goat reference genome assembly at a coverage of 99.6%. About 24.76 million SNPs were generated. These SNPs can be used to study the population structure and genome dynamics of goats at the country, regional, and global levels to shed light on the species’ evolutionary trajectory.
T7 phage-assisted evolution of riboswitches using error-prone replication and dual selection
Authors: Goicoechea Serrano Eduardo , Blázquez-Bondia Carlos , Jaramillo Alfonso 
Published: January 2024

AbstractLeveraging riboswitches, non-coding mRNA fragments pivotal to gene regulation, poses a challenge in effectively selecting and enriching these functional genetic sensors, which can toggle between ON and OFF states in response to their cognate inducers. Here, we show our engineered phage T7, enabling the evolution of a theophylline riboswitch. We have replaced T7’s DNA polymerase with a transcription factor controlled by a theophylline riboswitch and have created two types of host environments to propagate the engineered phage. Both types host an error-prone T7 DNA polymerase regulated by a T7 promoter along with another critical gene—either cmk or pifA, depending on the host type. The cmk gene is necessary for T7 replication and is used in the first host type for selection in the riboswitch's ON state. Conversely, the second host type incorporates the pifA gene, leading to abortive T7 infections and used for selection in the riboswitch’s OFF state. This dual-selection system, termed T7AE, was then applied to a library of 65,536 engineered T7 phages, each carrying randomized riboswitch variants. Through successive passage in both host types with and without theophylline, we observed an enrichment of phages encoding functional riboswitches that conferred a fitness advantage to the phage in both hosts. The T7AE technique thereby opens new pathways for the evolution and advancement of gene switches, including non-coding RNA-based switches, setting the stage for significant strides in synthetic biology.
Formal optimization techniques select hydrogen to decarbonize California
Authors: Thai Clinton , Brouwer Jack 
Published: January 2024

AbstractSystem planning across economic sectors is becoming increasingly necessary. Building upon existing solutions for deep decarbonization, the inclusion of renewable capacity to meet up to 8 MMT/year hydrogen demand is carried out. An hourly economic dispatch problem modeling the 2050 California electric grid given this hydrogen demand constraint is solved. Hydrogen demand outside of the power generation sector is fixed, but the demand for power generation is endogenously determined. The factor to consider offshore wind capacity, in addition to a conservative and an aggressive hydrogen technology adoption approach, creates four distinct scenarios to evaluate. The difference in results then provides a basis for discussing the costs and benefits associated with using hydrogen to further decarbonize across all sectors. The carbon reduction achieved outside of the power generation sector is 27 MMT despite a slight increase in carbon within the power generation sector. The seasonal storage requirement for hydrogen spans from 72 to 149 TBtu dependent upon the renewable capacity mix. This level of hydrogen demand results in 21% to 41% of total electric load being dedicated to hydrogen production. Battery energy storage has the lowest energy throughput in the middle of the year coinciding with peak electrolyzer operation.
Neurochemical differences in core regions of the autistic brain: a multivoxel 1H-MRS study in children
Authors: Dionísio Ana , Espírito Ana , Pereira Andreia C. , Mouga Susana , d’Almeida Otília C. , Oliveira Guiomar , Castelo-Branco Miguel 
Published: January 2024

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental condition which compromises various cognitive and behavioural domains. The understanding of the pathophysiology and molecular neurobiology of ASD is still an open critical research question. Here, we aimed to address ASD neurochemistry in the same time point at key regions that have been associated with its pathophysiology: the insula, hippocampus, putamen and thalamus. We conducted a multivoxel proton magnetic resonance spectroscopy (1H-MRS) study to non-invasively estimate the concentrations of total choline (GPC + PCh, tCho), total N-acetyl-aspartate (NAA + NAAG, tNAA) and Glx (Glu + Gln), presenting the results as ratios to total creatine while investigating replication for ratios to total choline as a secondary analysis. Twenty-two male children aged between 10 and 18 years diagnosed with ASD (none with intellectual disability, in spite of the expected lower IQ) and 22 age- and gender-matched typically developing (TD) controls were included. Aspartate ratios were significantly lower in the insula (tNAA/tCr: p = 0.010; tNAA/tCho: p = 0.012) and putamen (tNAA/tCr: p = 0.015) of ASD individuals in comparison with TD controls. The Glx ratios were significantly higher in the hippocampus of the ASD group (Glx/tCr: p = 0.027; Glx/tCho: p = 0.011). Differences in tNAA and Glx indices suggest that these metabolites might be neurochemical markers of region-specific atypical metabolism in ASD children, with a potential contribution for future advances in clinical monitoring and treatment.
Anomalous intralayer growth of epitaxial Si on Ag(111)
Authors: Wang Kejian , Prévot Geoffroy , Aqua Jean-Noël 
Published: January 2024

AbstractThe epitaxial growth of silicene has been the subject of many investigations, controversies and non-classical results. In particular, the initially promising deposition of Si on a metallic substrate such as Ag(111) has revealed unexpected growth modes where Si is inserted at the beginning of the growth in the first atomic plane of the substrate. In order to rationalize this anomalous growth mode, we develop an out-of-equilibrium description of a lattice-based epitaxial growth model, which growth dynamics are analyzed via kinetic Monte-Carlo simulations. This model incorporates several effects revealed by the experiments such as the intermixing between Si and Ag, and surface effects. It is parametrized thanks to an approach in which we show that relatively precise estimates of energy barriers can be deduced by meticulous analysis of atomic microscopy images. This analysis enables us to reproduce both qualitatively and quantitatively the anomalous growth patterns of Si on Ag(111). We show that the dynamics results in two modes, a classical sub-monolayer growth mode at low temperature, and an inserted growth mode at higher temperatures, where the deposited Si atoms insert in the first layer of the substrate by replacing Ag atoms. Furthermore, we reproduce the non-standard $$\Lambda $$
Λ
shape of the experimental plot of the island density as a function of temperature, with a shift in island density variation during the transition between the submonoloyer and inserted growth modes.
Visual hallucinations induced by Ganzflicker and Ganzfeld differ in frequency, complexity, and content
Authors: Shenyan Oris , Lisi Matteo , Greenwood John A. , Skipper Jeremy I. , Dekker Tessa M. 
Published: January 2024

AbstractVisual hallucinations can be phenomenologically divided into those of a simple or complex nature. Both simple and complex hallucinations can occur in pathological and non-pathological states, and can also be induced experimentally by visual stimulation or deprivation—for example using a high-frequency, eyes-open flicker (Ganzflicker) and perceptual deprivation (Ganzfeld). Here we leverage the differences in visual stimulation that these two techniques involve to investigate the role of bottom-up and top-down processes in shifting the complexity of visual hallucinations, and to assess whether these techniques involve a shared underlying hallucinatory mechanism despite their differences. For each technique, we measured the frequency and complexity of the hallucinations produced, utilising button presses, retrospective drawing, interviews, and questionnaires. For both experimental techniques, simple hallucinations were more common than complex hallucinations. Crucially, we found that Ganzflicker was more effective than Ganzfeld at eliciting simple hallucinations, while complex hallucinations remained equivalent across the two conditions. As a result, the likelihood that an experienced hallucination was complex was higher during Ganzfeld. Despite these differences, we found a correlation between the frequency and total time spent hallucinating in Ganzflicker and Ganzfeld conditions, suggesting some shared mechanisms between the two methodologies. We attribute the tendency to experience frequent simple hallucinations in both conditions to a shared low-level core hallucinatory mechanism, such as excitability of visual cortex, potentially amplified in Ganzflicker compared to Ganzfeld due to heightened bottom-up input. The tendency to experience complex hallucinations, in contrast, may be related to top-down processes less affected by visual stimulation.
Analysis of anemia and iron supplementation among glioblastoma patients reveals sex-biased association between anemia and survival
Authors: Shenoy Ganesh , Slagle-Webb Becky , Khunsriraksakul Chachrit , Pandya Shesh Bhavyata , Luo Jingqin , Khristov Vladimir , Smith Nataliya , Mansouri Alireza , Zacharia Brad E. , Holder Sheldon , Lathia Justin D. , Barnholtz-Sloan Jill S. , Connor James R. 
Published: January 2024

AbstractThe association between anemia and outcomes in glioblastoma patients is unclear. We analyzed data from 1346 histologically confirmed adult glioblastoma patients in the TriNetX Research Network. Median hemoglobin and hematocrit levels were quantified for 6 months following diagnosis and used to classify patients as anemic or non-anemic. Associations of anemia and iron supplementation of anemic patients with median overall survival (median-OS) were then studied. Among 1346 glioblastoma patients, 35.9% of male and 40.5% of female patients were classified as anemic using hemoglobin-based WHO guidelines. Among males, anemia was associated with reduced median-OS compared to matched non-anemic males using hemoglobin (HR 1.24; 95% CI 1.00–1.53) or hematocrit-based cutoffs (HR 1.28; 95% CI 1.03–1.59). Among females, anemia was not associated with median-OS using hemoglobin (HR 1.00; 95% CI 0.78–1.27) or hematocrit-based cutoffs (HR: 1.10; 95% CI 0.85–1.41). Iron supplementation of anemic females trended toward increased median-OS (HR 0.61; 95% CI 0.32–1.19) although failing to reach statistical significance whereas no significant association was found in anemic males (HR 0.85; 95% CI 0.41–1.75). Functional transferrin-binding assays confirmed sexually dimorphic binding in resected patient samples indicating underlying differences in iron biology. Anemia among glioblastoma patients exhibits a sex-specific association with survival.
A novel AllGlo probe-quantitative PCR method for detecting single nucleotide polymorphism in CYP2C19 to evaluate the antiplatelet activity of clopidogrel
Authors: Li Hongwei , Fang Yizhen , Chen Yongquan , Lin Yuning , Fang Zanxi , Lin Zhiyuan , Xie Huabin , Zhang Zhongying 
Published: January 2024

AbstractCYP2C19 gene has multiple single nucleotide polymorphism (SNP), which is the major determinant for clopidogrel treatment responses. Therefore, CYP2C19 SNP detection is essential for predicting clopidogrel efficacy. Currently, there is still no quick and effective method for routine detection of common CYP2C19 SNPs in clinical laboratories, which is critically needed prior to clopidogrel treatment. AllGlo™ based quantitative PCR was used to develop a novel genotyping method for CYP2C19 SNP detection, termed CyPAllGlo. The performance of CyPAllGlo was compared with that of the commonly used fluorescence in situ hybridization (FISH) method, and the data was verified by DNA sequencing. CyPallGlo was used to identify CYP2C19 polymorphisms in 363 patients with coronary heart disease. The univariate analysis was used to access the antiplatelet efficacy of clopidogrel in patients. The associations between CYP2C19 polymorphisms and clopidogrel efficacy were analyzed. Using CyPAllGlo to detect CYP2C19*2 and CYP2C19*3 alleles was highly specific and fast. The detection limit was approximately 0.07 µg/µl and 0.7 µg/µl for CYP2C19*2 and CYP2C19*3, respectively. The consistency between FISH and CyPAllGlo were 98.07% for CYP2C19*2 and 99.17% for CYP2C19*3. DNA sequencing showed that the accuracy of CyPAllGlo was 100%. The analysis time for the whole CyPAllGlo procedure was approximately 60 min. Univariate analysis showed that the anticoagulation efficacy of clopidogrel was related to patient age, CYP2C19 genotype, metabolic phenotype, and LDL level. The logistic regression analysis showed that the genotype of CYP2C19 and metabolic phenotype was the two risk factors for clopidogrel antiplatelet ineffectiveness. This novel CyPAllGlo is a rapid and accurate method for detection of CYP2C19 SNP. The specificity and consistency of CyPAllGlo are comparable with that of widely used DNA sequencing. These findings provide valuable rapid method for predicting clopidogrel efficacy, which can be quickly translated to improve personalized precision medicine for coronary heart disease treatment.