bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition
Authors: Ennis Dena , Shmorak Shimrit , Jantscher-Krenn Evelyn , Yassour Moran 
Published: January 2024

AbstractBreast milk contains human milk oligosaccharides (HMOs) that cannot be digested by infants, yet nourish their developing gut microbiome. While Bifidobacterium are the best-known utilizers of individual HMOs, a longitudinal study examining the evolving microbial community at high-resolution coupled with mothers’ milk HMO composition is lacking. Here, we developed a high-throughput method to quantify Bifidobacterium longum subsp. infantis (BL. infantis), a proficient HMO-utilizer, and applied it to a longitudinal cohort consisting of 21 mother-infant dyads. We observed substantial changes in the infant gut microbiome over the course of several months, while the HMO composition in mothers’ milk remained relatively stable. Although Bifidobacterium species significantly influenced sample variation, no specific HMOs correlated with Bifidobacterium species abundance. Surprisingly, we found that BL. infantis colonization began late in the breastfeeding period both in our cohort and in other geographic locations, highlighting the importance of focusing on BL. infantis dynamics in the infant gut.
The interplay of field-tunable strongly correlated states in a multi-orbital moiré system
Authors: Campbell Aidan J. , Vitale Valerio , Brotons-Gisbert Mauro , Baek Hyeonjun , Borel Antoine , Ivanova Tatyana V. , Taniguchi Takashi , Watanabe Kenji , Lischner Johannes , Gerardot Brian D. 
Published: January 2024

AbstractThe interplay of charge, spin, lattice and orbital degrees of freedom leads to a variety of emergent phenomena in strongly correlated systems. In transition-metal-dichalcogenide-based moiré heterostructures, recent observations of correlated phases can be described by triangular-lattice single-orbital Hubbard models based on moiré bands derived from the Brillouin-zone corners—the so-called K valleys. Richer phase diagrams described by multi-orbital Hubbard models are possible with hexagonal lattices that host moiré bands at the zone centre—called Γ valleys—or an additional layer degree of freedom. Here we report the tunable interaction between strongly correlated hole states hosted by Γ- and K-derived bands in a heterostructure of monolayer MoSe2 and bilayer 2H WSe2. We characterize the behaviour of exciton–polarons to distinguish the layer and valley degrees of freedom. The Γ band gives rise to a charge-transfer insulator described by a two-orbital Hubbard model. An out-of-plane electric field re-orders the Γ- and K-derived bands and drives the redistribution of carriers to the layer-polarized K orbital, generating Wigner crystals and Mott insulating states. Finally, we obtain degeneracy of the Γ and K orbitals at the Fermi level and observe interacting correlated states with phase transitions dependent on the doping density. Our results establish a platform to investigate multi-orbital Hubbard model Hamiltonians.
In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization
Authors: Oberbeckmann Elisa , Quililan Kimberly , Cramer Patrick , Oudelaar A. Marieke 
Published: January 2024

AbstractEukaryotic genomes are organized into chromatin domains. The molecular mechanisms driving the formation of these domains are difficult to dissect in vivo and remain poorly understood. Here we reconstitute Saccharomyces cerevisiae chromatin in vitro and determine its 3D organization at subnucleosome resolution by micrococcal nuclease-based chromosome conformation capture and molecular dynamics simulations. We show that regularly spaced and phased nucleosome arrays form chromatin domains in vitro that resemble domains in vivo. This demonstrates that neither loop extrusion nor transcription is required for basic domain formation in yeast. In addition, we find that the boundaries of reconstituted domains correspond to nucleosome-free regions and that insulation strength scales with their width. Finally, we show that domain compaction depends on nucleosome linker length, with longer linkers forming more compact structures. Together, our results demonstrate that regular nucleosome positioning is important for the formation of chromatin domains and provide a proof-of-principle for bottom-up 3D genome studies.
Inferring co-expression networks of Arabidopsis thaliana genes during their interaction with Trichoderma spp.
Authors: Vega-Arroy Javier-David , Herrera-Estrella Alfredo , Ovando-Vázquez Cesaré , Casas-Flores Sergio 
Published: January 2024

AbstractFungi of the Trichoderma genus are called "biostimulants" because they promote plant growth and development and induce disease resistance. We used conventional transcriptome and gene co-expression analyses to understand the molecular response of the plant Arabidopsis thaliana to inoculation with Trichoderma atroviride or Trichoderma virens. The transcriptional landscape of the plant during the interaction with these fungi showed a reduction in functions such as reactive oxygen species production, defense mechanisms against pathogens, and hormone signaling. T. virens, as opposed to T. atroviride, was more effective at downregulating genes related to terpenoid metabolism, root development, and chemical homeostasis. Through gene co-expression analysis, we found functional gene modules that closely link plant defense with hypoxia. Notably, we found a transcription factor (locus AT2G47520) with two functional domains of interest: a DNA-binding domain and an N-terminal cysteine needed for protein stability under hypoxia. We hypothesize that the transcription factor can bind to the promoter sequence of the GCC-box that is connected to pathogenesis by positioned weight matrix analysis.
A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds
Authors: Lin Kevin , Chang Ya-Chu , Billmann Maximilian , Ward Henry N. , Le Khoi , Hassan Arshia Z. , Bhojoo Urvi , Chan Katherine , Costanzo Michael , Moffat Jason , Boone Charles , Bielinsky Anja-Katrin , Myers Chad L. 
Published: January 2024

AbstractCurrent approaches to define chemical-genetic interactions (CGIs) in human cell lines are resource-intensive. We designed a scalable chemical-genetic screening platform by generating a DNA damage response (DDR)-focused custom sgRNA library targeting 1011 genes with 3033 sgRNAs. We performed five proof-of-principle compound screens and found that the compounds’ known modes-of-action (MoA) were enriched among the compounds’ CGIs. These scalable screens recapitulated expected CGIs at a comparable signal-to-noise ratio (SNR) relative to genome-wide screens. Furthermore, time-resolved CGIs, captured by sequencing screens at various time points, suggested an unexpected, late interstrand-crosslinking (ICL) repair pathway response to camptothecin-induced DNA damage. Our approach can facilitate screening compounds at scale with 20-fold fewer resources than commonly used genome-wide libraries and produce biologically informative CGI profiles.
Safety of ipsilesional anodal transcranial direct current stimulation in acute photothrombotic stroke: implications for early neurorehabilitation
Authors: Fritsch Brita , Mayer Marleen , Reis Janine , Gellner Anne-Kathrin 
Published: January 2024

AbstractEarly rehabilitation in the acute phase of stroke, that bears unique neuroplastic properties, is the current standard to reduce disability. Anodal transcranial direct current stimulation can augment neurorehabilitation in chronic stroke. Studies in the acute phase are sparse and held back by inconclusive preclinical data pointing towards potential negative interaction of the excitability increasing tDCS modality with stroke-induced glutamate toxicity. In this present study, we aimed to evaluate structural and behavioral safety of anodal tDCS applied in the acute phase of stroke. Photothrombotic stroke including the right primary motor cortex was induced in rats. 24 h after stroke anodal tDCS was applied for 20 min ipsilesionally at one of four different current densities in freely moving animals. Effects on the infarct volume and on stroke induced neuroinflammation were assessed. Behavioral consequences were monitored. Infarct volume and the modified Neurological Severity Score were not affected by anodal tDCS. Pasta handling, a more sensitive task for sensorimotor deficits, and microglia reactivity indicated potentially harmful effects at the highest tDCS current density tested (47.8 A/m2), which is more than 60 times higher than intensities commonly used in humans. Compared to published safety limits of anodal tDCS in healthy rats, recent stroke does not increase the sensitivity of the brain to anodal tDCS, as assessed by lesion size and neuroinflammatory response. Behavioral deficits only occurred at the highest intensity, which was associated with increased neuroinflammation. When safety limits of commonly used clinical tDCS are met, augmentation of early neurorehabilitation after stroke by anodal tDCS appears to be feasible.
Spatial hearing training in virtual reality with simulated asymmetric hearing loss
Authors: Valzolgher Chiara , Capra Sara , Sum Kevin , Finos Livio , Pavani Francesco , Picinali Lorenzo 
Published: January 2024

AbstractSound localization is essential to perceive the surrounding world and to interact with objects. This ability can be learned across time, and multisensory and motor cues play a crucial role in the learning process. A recent study demonstrated that when training localization skills, reaching to the sound source to determine its position reduced localization errors faster and to a greater extent as compared to just naming sources’ positions, despite the fact that in both tasks, participants received the same feedback about the correct position of sound sources in case of wrong response. However, it remains to establish which features have made reaching to sound more effective as compared to naming. In the present study, we introduced a further condition in which the hand is the effector providing the response, but without it reaching toward the space occupied by the target source: the pointing condition. We tested three groups of participants (naming, pointing, and reaching groups) each while performing a sound localization task in normal and altered listening situations (i.e. mild-moderate unilateral hearing loss) simulated through auditory virtual reality technology. The experiment comprised four blocks: during the first and the last block, participants were tested in normal listening condition, while during the second and the third in altered listening condition. We measured their performance, their subjective judgments (e.g. effort), and their head-related behavior (through kinematic tracking). First, people’s performance decreased when exposed to asymmetrical mild-moderate hearing impairment, more specifically on the ipsilateral side and for the pointing group. Second, we documented that all groups decreased their localization errors across altered listening blocks, but the extent of this reduction was higher for reaching and pointing as compared to the naming group. Crucially, the reaching group leads to a greater error reduction for the side where the listening alteration was applied. Furthermore, we documented that, across blocks, reaching and pointing groups increased the implementation of head motor behavior during the task (i.e., they increased approaching head movements toward the space of the sound) more than naming. Third, while performance in the unaltered blocks (first and last) was comparable, only the reaching group continued to exhibit a head behavior similar to those developed during the altered blocks (second and third), corroborating the previous observed relationship between the reaching to sounds task and head movements. In conclusion, this study further demonstrated the effectiveness of reaching to sounds as compared to pointing and naming in the learning processes. This effect could be related both to the process of implementing goal-directed motor actions and to the role of reaching actions in fostering the implementation of head-related motor strategies.
Dental implant as a potential risk factor for maxillary sinus fungus ball
Authors: Han Sun A. , Kim Sungtae , Seo Yuju , Yang Seung Koo , Rhee Chae-Seo , Han Doo Hee 
Published: January 2024

AbstractFungus ball is the most common form of non-invasive fungal sinusitis, and maxillary sinus is the most commonly involved site. Maxillary sinus fungus ball (MFB) accounts for a considerable proportion of unilateral maxillary sinusitis. The prevalence of MFB has recently increased; however, its contributing factors are unclear. This study analyzed the association between MFB and dental implants. One hundred one patients who underwent unilateral maxillary sinus surgery were divided into two groups based on surgical biopsy results: unilateral bacterial sinusitis (UBS, n = 45) and MFB (n = 56). Stratified random sampling of 30 patients from each group was performed to adjust for age. The number of dental implants on maxillary teeth and degree of penetration into the maxillary sinus was radiologically evaluated. The number of patients with dental implants was greater (P = 0.085) and the number of implants was significantly higher (P = 0.031) in the MFB group. Dental implant can be a potential risk factor for MFB development. Therefore, dental implant surgeons should take caution in penetrating the maxillary sinus floor during implant insertion and otolaryngologists should consider the possibility of fungus ball when assessing patients with sinusitis who have dental implants.
Soil characteristics and allometric models for biometric characteristics and nutrient amounts for high yielding “Bolaina” (Guazuma crinita) trees
Authors: Arévalo-Hernández C. O. , Arévalo-Gardini E. , Correa V. J. A. , Souza Júnior J. O. , Neves J. C. L. 
Published: January 2024

AbstractThe Peruvian amazon is very diverse in native forestry species, the Guazuma crinita “Bolaina” being one of the most planted species in the country; however, little or no information about soil requirements and nutrient demands is known. The objective of this work was to assess the general conditions of soil fertility, biomass and macro- and micronutrient amounts in high-productivity Guazuma crinita plantations. Fields of high yielding Bolaina of different ages (1–10 years) were sampled in two regions. Soil and plant samples were collected in each field and biometric measurements of fresh weight, diameter at breast height and height were performed. For soil and plant analysis, both macro- (N, P, K, Ca, Mg, S) and micronutrients (B, Cu, Fe, Mn, Zn) were determined. Finally, allometric equations were constructed for biometric and nutrient amounts. This study is the first to assess and model macro- and micronutrient amounts in the productive cycle in this species, which grows in fertile soils. In the case of biometric equations, the logarithmic and logistic models performed better. For nutrient amounts, this species followed a pattern of Ca > N > K > P > S > Mg for macronutrients and Fe > B > Mn > Zn > Cu for micronutrients. The best prediction models for nutrients were the square root and logistic models.
Right heart and left atrial strain to differentiate cardiac amyloidosis and Fabry disease
Authors: Mattig Isabel , Steudel Tilman , Klingel Karin , Barzen Gina , Frumkin David , Spethmann Sebastian , Romero Dorta Elena , Stangl Karl , Heidecker Bettina , Landmesser Ulf , Knebel Fabian , Canaan-Kühl Sima , Hahn Katrin , Brand Anna 
Published: January 2024

AbstractEchocardiographic differentiation of cardiac amyloidosis (CA) and Fabry disease (FD) is often challenging using standard echocardiographic parameters. We retrospectively analyzed the diagnostic accuracy of right heart and left atrial strain parameters to discriminate CA from FD using receiver operating characteristic curve analyses and logistic regression models. A total of 47 FD and 88 CA patients with left ventricular wall thickening were analyzed. The comparison of both cardiomyopathies revealed significantly reduced global and free wall longitudinal right ventricular strain (RVS; global RVS: CA − 13 ± 4%, n = 67, vs. FD − 18 ± 4%, n = 39, p < 0.001) as well as right atrial strain (RAS; reservoir RAS: CA 12 ± 8%, n = 70, vs. FD 26 ± 9%, n = 40, p < 0.001) and left atrial strain (LAS) in CA patients. Individually, global RVS as well as phasic LAS and RAS showed the highest diagnostic accuracy to distinguish CA and FD. The best diagnostic accuracy was achieved by combining the age, basal RV diameter, global RVS, and reservoir and conduit RAS (area under the curve 0.96 [95% CI 0.90–1.00]). Differential echocardiographic diagnostic work-up of patients with suspected CA or FD can be improved by integrating structural and functional parameters of the right heart and the left atrium.Trial registration: DRKS00027403.
Remote follow-up by pharmacists for blood pressure control in patients with hypertension: a systematic review and a meta-analysis of randomized controlled trials
Authors: Matsumoto Noriaki , Nakai Tsuyoshi , Sakakibara Mikio , Aimiya Yukinori , Sugiura Shinya , Lee Jeannie K. , Yamada Shigeki , Mizuno Tomohiro 
Published: January 2024

AbstractHypertension is a major cause of cardiovascular diseases. Several recent studies reported that pharmacists’ remote follow-up reduced hypertension patients’ blood pressure (BP). This meta-analysis aims to verify whether remote follow-up by pharmacists improves BP levels and reveal the factors that make the intervention effective. The search, conducted using PubMed/Medline, Embase, and Cochrane Library from June to July 2023, targeted articles published between October 1982 and June 2023, using terms including “pharmacist”, “hypertension”, and “randomized controlled trial (RCT)”. The inclusion criteria were: (a) RCTs involving hypertension patients with or without comorbidities, (b) pharmacists using remote communication tools to conduct follow-up encounter during the intervention period, (c) reporting systolic blood pressure (SBP) at baseline and during intervention. SBP was the primary outcome for the meta-analysis. Thirteen studies (3969 participants) were included in this meta-analysis. The mean difference of SBP between intervention group and control group was − 7.35 mmHg (P < 0.0001). Subgroup analyses showed the greater reduction of SBP in the “regularly scheduled follow-up cohort” (− 8.89 mmHg) compared with the “as needed follow-up cohort” (− 3.23 mmHg, P < 0.0001). The results revealed that remote follow-up by pharmacists reduced SBP levels in hypertension patients and scheduled remote follow-up may contribute to the effectiveness.
Diagnosing oral and maxillofacial diseases using deep learning
Authors: Kang Junegyu , Le Van Nhat Thang , Lee Dae-Woo , Kim Sungchan 
Published: January 2024

AbstractThe classification and localization of odontogenic lesions from panoramic radiographs is a challenging task due to the positional biases and class imbalances of the lesions. To address these challenges, a novel neural network,DOLNet, is proposed that uses mutually influencing hierarchical attention across different image scales to jointly learn theglobalrepresentation of the entire jaw and thelocaldiscrepancy between normal tissue and lesions. The proposed approach uses local attention to learn representations within a patch. From the patch-level representations, we generate inter-patch, i.e., global, attention maps to represent the positional prior of lesions in the whole image. Global attention enables the reciprocal calibration of path-level representations by considering non-local information from other patches, thereby improving the generation of whole-image-level representation. To address class imbalances, we propose an effective data augmentation technique that involves merging lesion crops with normal images, thereby synthesizing new abnormal cases for effective model training. Our approach outperforms recent studies, enhancing the classification performance by up to 42.4% and 44.2% in recall and F1 scores, respectively, and ensuring robust lesion localization with respect to lesion size variations and positional biases. Our approach further outperforms human expert clinicians in classification by 10.7 % and 10.8 % in recall and F1 score, respectively.
Studying the impact of phycoerythrin on antioxidant and antimicrobial activity of the fresh rainbow trout fillets
Authors: Nowruzi Bahareh , Ahmadi Mahsa , Bouaïcha Noureddine , Khajerahimi Amir Eghbal , Anvar Seyed Amir Ali 
Published: January 2024

AbstractMarine cyanobacteria present a significant potential source of new bioactive compounds with vast structural diversity and relevant antimicrobial and antioxidant activities. Phycobiliproteins (PBPs) like phycocyanin (PC), phycoerythrin (PE), and water-soluble cyanobacterial photosynthetic pigments, have exhibited strong pharmacological activities and been used as natural food additives. In this study, phycoerythrin (PE) isolated from a marine strain of cyanobacterium Nostoc sp. Ft salt, was applied for the first time as a natural antimicrobial as well as an antioxidant to increase the shelf life of fresh rainbow trout i.e., (Oncorhynchus mykiss) fillets. Fresh trout fillets were marinated in analytical grade PE (3.9 μg/mL) prepared in citric acid (4 mg/mL), and stored at 4 °C and 8 °C for 21 days. Microbiological analysis, antioxidant activity and organoleptic evaluation of both control and treated fish fillets were then statistically compared. The results demonstrated noticeable (P < 0.05) differences in the microbial counts, antioxidant activity, and organoleptic characteristic values between PE-treated and non-treated groups. In addition, we observed that treating fresh fish fillets with a PE solution leads to a significant increase in shelf life by at least 14 days. Consequently, PE could be an alternative to synthetic chemical additives since it does not contain the potentially dangerous residues of the synthetic chemical additives and is thus healthier to the consumers.
A numerical exploration of the comparative analysis on water and kerosene oil-based Cu–CuO/hybrid nanofluid flows over a convectively heated surface
Authors: Algehyne Ebrahem A. , Alamrani Fahad Maqbul , Saeed Anwar , Bognár Gabriella 
Published: January 2024

AbstractThe fluid flow over an extending sheet has many applications in different fields which include, manufacturing processes, coating, thin film decomposition, heat and mass transfer, biomedical applications, aerospace engineering, environmental science, energy production. Keeping in mind these applications, the non-Newtonian hybrid nanofluid flow comprising of Cu and CuO nanoparticles over an extending sheet is analyzed in this work. Two different base fluids called kerosene oil and water have been incorporated. The sheet is considered to be thermally convective along with zero mass flux condition. The main equations of modeled problem have been transformed to dimensionless form by using similarity variables. The designed problem is evaluated computationally by using bvp4c Matlab function. Validation of the present results is also performed. The impacts of magnetic, Brownian motion, chemical reaction, suction and thermophoresis factors are analyzed and discussed in details. The outcomes of the present investigation declare that the kerosene oil-based hybrid nanofluid flow has greater velocity and concentration profiles than that of the water-based hybrid nanofluid flow. The water-based hybrid nanofluid has greater temperature distribution than that of kerosene oil-based hybrid nanofluid flow. The streamlines of the kerosene oil-based Newtonian and non-Newtonian hybrid nanofluid flows are more stretched than water-based Newtonian and non-Newtonian hybrid nanofluid flows.