bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novelty and imitation within the brain: a Darwinian neurodynamic approach to combinatorial problems
Authors: Czégel Dániel , Giaffar Hamza , Csillag Márton , Futó Bálint , Szathmáry Eörs 
Published: June 2021

AbstractEfficient search in vast combinatorial spaces, such as those of possible action sequences, linguistic structures, or causal explanations, is an essential component of intelligence. Is there any computational domain that is flexible enough to provide solutions to such diverse problems and can be robustly implemented over neural substrates? Based on previous accounts, we propose that a Darwinian process, operating over sequential cycles of imperfect copying and selection of neural informational patterns, is a promising candidate. Here we implement imperfect information copying through one reservoir computing unit teaching another. Teacher and learner roles are assigned dynamically based on evaluation of the readout signal. We demonstrate that the emerging Darwinian population of readout activity patterns is capable of maintaining and continually improving upon existing solutions over rugged combinatorial reward landscapes. We also demonstrate the existence of a sharp error threshold, a neural noise level beyond which information accumulated by an evolutionary process cannot be maintained. We introduce a novel analysis method, neural phylogenies, that displays the unfolding of the neural-evolutionary process.
Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives
Authors: Iwata Mana , Gutiérrez Ana , Marques Gisela , Sabat Grzegorz , Kersten Philip J. , Cullen Daniel , Bhatnagar Jennifer M. , Yadav Jagjit , Lipzen Anna , Yoshinaga Yuko , Sharma Aditi , Adam Catherine , Daum Christopher , Ng Vivian , Grigoriev Igor V. , Hori Chiaki 
Published: June 2021

AbstractWood extractives, solvent-soluble fractions of woody biomass, are considered to be a factor impeding or excluding fungal colonization on the freshly harvested conifers. Among wood decay fungi, the basidiomycete Phlebiopsis gigantea has evolved a unique enzyme system to efficiently transform or degrade conifer extractives but little is known about the mechanism(s). In this study, to clarify the mechanism(s) of softwood degradation, we examined the transcriptome, proteome, and metabolome of P. gigantea when grown on defined media containing microcrystalline cellulose and pine sapwood extractives. Beyond the conventional enzymes often associated with cellulose, hemicellulose and lignin degradation, an array of enzymes implicated in the metabolism of softwood lipophilic extractives such as fatty and resin acids, steroids and glycerides was significantly up-regulated. Among these, a highly expressed and inducible lipase is likely responsible for lipophilic extractive degradation, based on its extracellular location and our characterization of the recombinant enzyme. Our results provide insight into physiological roles of extractives in the interaction between wood and fungi.
Doublons, topology and interactions in a one-dimensional lattice
Authors: Azcona P. Martínez , Downing C. A. 
Published: June 2021

AbstractWe investigate theoretically the Bose–Hubbard version of the celebrated Su-Schrieffer-Heeger topological model, which essentially describes a one-dimensional dimerized array of coupled oscillators with on-site interactions. We study the physics arising from the whole gamut of possible dimerizations of the chain, including both the weakly and the strongly dimerized limiting cases. Focusing on two-excitation subspace, we systematically uncover and characterize the different types of states which may emerge due to the competition between the inter-oscillator couplings, the intrinsic topology of the lattice, and the strength of the on-site interactions. In particular, we discuss the formation of scattering bands full of extended states, bound bands full of two-particle pairs (including so-called ‘doublons’, when the pair occupies the same lattice site), and different flavors of topological edge states. The features we describe may be realized in a plethora of systems, including nanoscale architectures such as photonic cavities, optical lattices and qubits, and provide perspectives for topological two-particle and many-body physics.
Pelvic floor dysfunction one year after first childbirth in relation to perineal tear severity
Authors: Huber Malin , Malers Ellen , Tunón Katarina 
Published: June 2021

AbstractThe aims of this study were to evaluate pelvic floor dysfunction symptoms one year after delivery and investigate whether adverse functional outcomes after childbirth were related to the degree of perineal injury. A prospective cohort of 776 primiparas were included. Self-reported pelvic floor function data were obtained using a web-based questionnaire. Women with no/first-degree injuries, second-degree injuries, third-/fourth-degree injuries (obstetric anal sphincter injury, OASI) and cesarean section were compared. A total of 511 women (66%) responded. Second-degree tears were a risk factor for stress incontinence (aOR 2.6 (95% CI 1.3–5.1)). Cesarean section was protective against stress incontinence (aOR 0.2 (95% CI 0.1–0.9)). OASI was a risk factor for urge incontinence (aOR 4.8 (95% CI 1.6–15)), prolapse (aOR 7.7 (95% CI 2.1–29)) and pelvic pain (OR 3.3 (95% CI 1.1–10)). Dyspareunia was reported by 38% of women, 63% of women in the OASI group (aOR 3.1 (95% CI 1.1–9.0)). Women with OASI reported that the injury affected daily life (OR 18 (95% CI 5.1–59)). Pelvic floor dysfunction is common after childbirth, even in women with moderate injury. Women with OASI had significantly higher risks of symptoms of prolapse, urge urinary incontinence, pain, dyspareunia and impacts on daily life.
A dose response model for Staphylococcus aureus
Authors: Chandrasekaran Srikiran , Jiang Sunny C. 
Published: June 2021

AbstractDose-response models (DRMs) are used to predict the probability of microbial infection when a person is exposed to a given number of pathogens. In this study, we propose a new DRM forStaphylococcus aureus(SA), which causes skin and soft-tissue infections. The current approach to SA dose-response is only partially mechanistic and assumes that individual bacteria do not interact with each other. Our proposed two-compartment (2C) model assumes that bacteria that have not adjusted to the host environment decay. After adjusting to the host, they exhibit logistic/cooperative growth, eventually causing disease. The transition between the adjusted and un-adjusted states is a stochastic process, which the 2C DRM explicitly models to predict response probabilities. By fitting the 2C model to SA pathogenesis data, we show that cooperation between individual SA bacteria is sufficient (and, within the scope of the 2C model, necessary) to characterize the dose-response. This is a departure from the classical single-hit theory of dose-response, where complete independence is assumed between individual pathogens. From a quantitative microbial risk assessment standpoint, the mechanistic basis of the 2C DRM enables transparent modeling of dose-response of antibiotic-resistant SA that has not been possible before. It also enables the modeling of scenarios having multiple/non-instantaneous exposures, with minimal assumptions.
Cytokine signatures of end organ injury in COVID-19
Authors: Gómez-Escobar Luis G. , Hoffman Katherine L. , Choi Justin J. , Borczuk Alain , Salvatore Steven , Alvarez-Mulett Sergio L. , Galvan Manuel D. , Zhao Zhen , Racine-Brzostek Sabrina E. , Yang He S. , Stout-Delgado Heather W. , Choi Mary E. , Choi Augustine M. K. , Cho Soo Jung , Schenck Edward J. 
Published: June 2021

AbstractIncreasing evidence has shown that Coronavirus disease 19 (COVID-19) severity is driven by a dysregulated immunologic response. We aimed to assess the differences in inflammatory cytokines in COVID-19 patients compared to contemporaneously hospitalized controls and then analyze the relationship between these cytokines and the development of Acute Respiratory Distress Syndrome (ARDS), Acute Kidney Injury (AKI) and mortality. In this cohort study of hospitalized patients, done between March third, 2020 and April first, 2020 at a quaternary referral center in New York City we included adult hospitalized patients with COVID-19 and negative controls. Serum specimens were obtained on the first, second, and third hospital day and cytokines were measured by Luminex. Autopsies of nine cohort patients were examined. We identified 90 COVID-19 patients and 51 controls. Analysis of 48 inflammatory cytokines revealed upregulation of macrophage induced chemokines, T-cell related interleukines and stromal cell producing cytokines in COVID-19 patients compared to the controls. Moreover, distinctive cytokine signatures predicted the development of ARDS, AKI and mortality in COVID-19 patients. Specifically, macrophage-associated cytokines predicted ARDS, T cell immunity related cytokines predicted AKI and mortality was associated with cytokines of activated immune pathways, of which IL-13 was universally correlated with ARDS, AKI and mortality. Histopathological examination of the autopsies showed diffuse alveolar damage with significant mononuclear inflammatory cell infiltration. Additionally, the kidneys demonstrated glomerular sclerosis, tubulointerstitial lymphocyte infiltration and cortical and medullary atrophy. These patterns of cytokine expression offer insight into the pathogenesis of COVID-19 disease, its severity, and subsequent lung and kidney injury suggesting more targeted treatment strategies.
Attractive and repulsive residue fragments at the interface of SARS-CoV-2 and hACE2
Authors: Rodriguez Jorge H. 
Published: June 2021

AbstractThe initial stages of SARS-CoV-2 coronavirus attachment to human cells are mediated by non-covalent interactions of viral spike (S) protein receptor binding domains (S-RBD) with human ACE2 receptors (hACE2). Structural characterization techniques, such as X-ray crystallography (XRC) and cryoelectron microscopy (cryo-EM), previously identified SARS-CoV-2 spike protein conformations and their surface residues in contact with hACE2. However, recent quantum-biochemical calculations on the structurally related S-RBD of SARS-CoV-1 identified some contact-residue fragments as intrinsically attractive and others as repulsive. This indicates that not all surface residues are equally important for hACE2 attachment. Here, using similar quantum-biochemical methods, we report some four-residue fragments (i.e quartets) of the SARS-CoV-2 S-RBD as intrinsically attractive towards hACE2 and, therefore, directly promoting host–virus non-covalent binding. Other fragments are found to be repulsive although involved in intermolecular recognition. By evaluation of their respective intermolecular interaction energies we found two hACE2 fragments that include contact residues (ASP30, LYS31, HIS34) and (ASP38, TYR41, GLN42), respectively, behaving as important SARS-CoV-2 attractors. LYS353 also promotes viral binding via several mechanisms including dispersion van der Waals forces. Similarly, among others, three SARS-CoV-2 S-RBD fragments that include residues (GLN498, THR500, ASN501), (GLU484, PHE486, ASN487) and (LYS417), respectively, were identified as hACE2 attractors. In addition, key hACE2 quartets identified as weakly-repulsive towards the S-RBD of SARS-CoV-1 were found strongly attractive towards SARS-CoV-2 explaining, in part, the stronger binding affinity of hACE2 towards the latter coronavirus. These findings may guide the development of synthetic antibodies or identify potential viral epitopes.
Natural nutrient subsidies alter demographic rates in a functionally important coral-reef fish
Authors: Benkwitt Cassandra E. , Taylor Brett M. , Meekan Mark G. , Graham Nicholas A. J. 
Published: June 2021

AbstractBy improving resource quality, cross-ecosystem nutrient subsidies may boost demographic rates of consumers in recipient ecosystems, which in turn can affect population and community dynamics. However, empirical studies on how nutrient subsidies simultaneously affect multiple demographic rates are lacking, in part because humans have disrupted the majority of these natural flows. Here, we compare the demographics of a sex-changing parrotfish (Chlorurus sordidus) between reefs where cross-ecosystem nutrients provided by seabirds are available versus nearby reefs where invasive, predatory rats have removed seabird populations. For this functionally important species, we found evidence for a trade-off between investing in growth and fecundity, with parrotfish around rat-free islands with many seabirds exhibiting 35% faster growth, but 21% lower size-based fecundity, than those around rat-infested islands with few seabirds. Although there were no concurrent differences in population-level density or biomass, overall mean body size was 16% larger around rat-free islands. Because the functional significance of parrotfish as grazers and bioeroders increases non-linearly with size, the increased growth rates and body sizes around rat-free islands likely contributes to higher ecosystem function on coral reefs that receive natural nutrient subsidies. More broadly, these results demonstrate additional benefits, and potential trade-offs, of restoring natural nutrient pathways for recipient ecosystems.
Adipogenesis in triple-negative breast cancer is associated with unfavorable tumor immune microenvironment and with worse survival
Authors: Oshi Masanori , Tokumaru Yoshihisa , Angarita Fernando A. , Lee Lan , Yan Li , Matsuyama Ryusei , Endo Itaru , Takabe Kazuaki 
Published: June 2021

AbstractCancer-associated adipocytes are known to cause inflammation; however, the role of adipogenesis, the formation of adipocytes, in breast cancer is unclear. We hypothesized that intra-tumoral adipogenesis reflects a different cancer biology than abundance of intra-tumoral adipocytes. The Molecular Signatures Database Hallmark adipogenesis gene set of gene set variant analysis was used to quantify adipogenesis. Total of 5,098 breast cancer patients in multiple cohorts (training; GSE96058 (n = 3273), validation; TCGA (n = 1069), treatment response; GSE25066 (n = 508) and GSE20194 (n = 248)) were analyzed. Adipogenesis did not correlate with abundance of adipocytes. Adipogenesis was significantly lower in triple negative breast cancer (TNBC). Elevated adipogenesis was significantly associated with worse survival in TNBC, but not in the other subtypes. High adipogenesis TNBC was significantly associated with low homologous recombination deficiency, but not with mutation load. High adipogenesis TNBC enriched metabolism-related gene sets, but neither of cell proliferation- nor inflammation-related gene sets, which were enriched to adipocytes. High adipogenesis TNBC was infiltrated with low CD8+ T cells and high M2 macrophages. Although adipogenesis was not associated with neoadjuvant chemotherapy response, high adipogenesis TNBC was significantly associated with low expression of PD-L1 and PD-L2 genes, and immune checkpoint molecules index. In conclusion, adipogenesis in TNBC was associated with cancer metabolism and unfavorable tumor immune microenvironment, which is different from abundance of adipocytes.
Potential risk of disease modifying therapies on neoplasm development and coadjutant factors in multiple sclerosis outpatients
Authors: Gil-Bernal Rosalía , González-Caballero Juan Luis , Espinosa-Rosso Raúl , Gómez-Gómez Carmen 
Published: June 2021

AbstractNeoplasm development in Multiple Sclerosis (MS) patients treated with disease-modifying therapies (DMTs) has been widely discussed. The aim of this work is to determine neoplasm frequency, relationship with the prescription pattern of DMTs, and influence of the patients’ baseline characteristics. Data from 250 MS outpatients were collected during the period 1981–2019 from the medical records of the Neurology Service of the HUPM (Hospital Universitario Puerta del Mar)—in Southern Spain—and analysed using Cox models. Neoplasm prevalence was 24%, mainly located on the skin, with cancer prevalence as expected for MS (6.8%). Latency period from MS onset to neoplasm diagnosis was 10.4 ± 6.9 years (median 9.30 [0.9–30.5]). During the observation period β-IFN (70.4% of patients), glatiramer acetate (30.4%), natalizumab (16.8%), fingolimod (24.8%), dimethyl fumarate (24.0%), alemtuzumab (6.0%), and teriflunomide (4.8%) were administered as monotherapy. Change of pattern in step therapy was significantly different in cancer patients vs unaffected individuals (p = 0.011) (29.4% did not receive DMTs [p = 0.000]). Extended Cox model: Smoking (HR = 3.938, CI 95% 1.392–11.140, p = 0.010), being female (HR = 2.006, 1.070–3.760, p = 0.030), and age at MS diagnosis (AGE-DG) (HR = 1.036, 1.012–1.061, p = 0.004) were risk factors for neoplasm development. Secondary progressive MS (SPMS) phenotype (HR = 0.179, 0.042–0.764, p = 0.020) and treatment-time with IFN (HR = 0.923, 0.873–0.977, p = 0.006) or DMF (HR = 0.725, 0.507–1.036, p = 0.077) were protective factors. Tobacco and IFN lost their negative/positive influence as survival time increased. Cox PH model: Tobacco/AGE-DG interaction was a risk factor for cancer (HR = 1.099, 1.001–1.208, p = 0.049), followed by FLM treatment-time (HR = 1.219, 0.979–1.517). In conclusion, smoking, female sex, and AGE-DG were risk factors, and SPMS and IFN treatment-time were protective factors for neoplasm development; smoking/AGE-DG interaction was the main cancer risk factor.
Optimization of fins arrangements for the square light emitting diode (LED) cooling through nanofluid-filled microchannel
Authors: Hamida Mohamed Bechir Ben , Hatami Mohammad 
Published: June 2021

AbstractIn current paper, a finned micro-channel is designed for the cooling application in Light Emitting Diode (LED), numerically using Galerkin weighted residual Finite Element Method (GFEM). Selected materials for LED-chip is GaN, Die from Si, Die-attach is made by Au-20Sn, substrate is copper and heat sink material is considered to be Al. To make a convection heat transfer for cooling process, Al2O3-water nanofluid is used as the cooling fluid flow through the micro-channel and tried to maximize the heat transfer efficiency by optimized geometry. For this aim, there geometry variables from the microchannel were selected and minimum possible geometry cases (11 cases) were proposed by Central composite design (CCD) and variables were optimized by the Response Surface Method (RSM). As a main result, parameter B, i.e. fin length had the most effect on the Nusselt number and Al2O3 nanoparticles with φ = 0.05 stated greatest heat transfer value. Also, different designs of fins arrangements, caused up to 6.5% increase in the nanofluid temperature which enhanced the LED cooling process.
Lateral migration resistance of screw is essential in evaluating bone screw stability of plate fixation
Authors: Feng Xiaoreng , Qi Weichen , Zhang Teng , Fang Christian , Liang Hongfeng , Chen Bin , Leung Frankie 
Published: June 2021

AbstractConventional evaluation of the stability of bone screws focuses on pullout strength, while neglecting lateral migration resistance. We measured pullout strength and lateral migration resistance of bone screws and determined how these characteristics relate to screw stability of locking plate (LP) and dynamic compression plate (DCP) fixation. Pullout strength and lateral migration resistance of individual bone screws with buttress, square, and triangular thread designs were evaluated in polyurethane foam blocks. The screw types with superior performance in each of these characteristics were selected. LP and DCP fixations were constructed using the selected screws and tested under cyclic craniocaudal and torsional loadings. Subsequently, the association between individual screws’ biomechanical characteristics and fixation stability when applied to plates was established. Screws with triangular threads had superior pullout strength, while screws with square threads demonstrated the highest lateral migration resistance; they were selected for LP and DCP fixations. LPs with square-threaded screws required a larger force and more cycles to trigger the same amount of displacement under both craniocaudal and torsional loadings. Screws with triangular and square threads showed no difference in DCP fixation stability under craniocaudal loading. However, under torsional loading, DCP fixation with triangular-threaded screws demonstrated superior fixation stability. Lateral migration resistance is the primary contributor to locking screw fixation stability when applied to an LP in resisting both craniocaudal and torsional loading. For compression screws applied to a DCP, lateral migration resistance and pullout strength work together to resist craniocaudal loading, while pullout strength is the primary contributor to the ability to resist torsional loading.
Realistic high-resolution lateral cephalometric radiography generated by progressive growing generative adversarial network and quality evaluations
Authors: Kim Mingyu , Kim Sungchul , Kim Minjee , Bae Hyun-Jin , Park Jae-Woo , Kim Namkug 
Published: June 2021

AbstractRealistic image generation is valuable in dental medicine, but still challenging for generative adversarial networks (GANs), which require large amounts of data to overcome the training instability. Thus, we generated lateral cephalogram X-ray images using a deep-learning-based progressive growing GAN (PGGAN). The quality of generated images was evaluated by three methods. First, signal-to-noise ratios of real/synthesized images, evaluated at the posterior arch region of the first cervical vertebra, showed no statistically significant difference (t-test, p = 0.211). Second, the results of an image Turing test, conducted by non-orthodontists and orthodontists for 100 randomly chosen images, indicated that they had difficulty in distinguishing whether the image was real or synthesized. Third, cephalometric tracing with 42 landmark points detection, performed on real and synthesized images by two expert orthodontists, showed consistency with mean difference of 2.08 ± 1.02 mm. Furthermore, convolutional neural network-based classification tasks were used to classify skeletal patterns using a real dataset with class imbalance and a dataset balanced with synthesized images. The classification accuracy for the latter case was increased by 1.5%/3.3% at internal/external test sets, respectively. Thus, the cephalometric images generated by PGGAN are sufficiently realistic and have potential to application in various fields of dental medicine.
Revealing the mystery of the cases where Nd–Fe–B magnetic like poles attract each other
Authors: Meng Hui , Tang Guiping , Shen Abby , Qian Michelle , Wei Qifeng , Mizzell George , Chen Christina H. 
Published: June 2021

AbstractThis investigation reveals the mystery of the cases where magnetic like poles attract each other, and unlike poles repel one another. It is identified that for two unequally sized like poles, the pole with a higherPc(permeance coefficient) causes a localized demagnetization (LD) to the pole with a lowerPc. If theLDis large enough, the polarity of a localized area can be reversed, resulting in an attraction between these two like poles in theLDarea in a small gap. Two unusual behaviors are observed: (1) an inflection pointIPappears on the force vs gap curves of all the unequally sized like poles since they have differentPc. Normally, the like poles’ repelling force increases when the gap decreases, but thisIPresults in nonmonotonic curves, even an attractive force in a small gap; (2) for some NdFeB magnets with a low coercivity and nonlinear B–H curve in the 2nd quadrant, a repulsion can occur for these unequal sized unlike poles, after previously pairing with their like poles that left an unrecoverableLDand reversed polarity area. The relationship of theLD, thePcratio, and the B–H curve are also explored in this paper.