bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of iron-binding ligands in the corrosion of carbon steel driven by iron-reducing bacteria
Authors: Hernandez-Santana Alejandra , Kokbudak Hatice Nursah , Nanny Mark A. 
Published: February 2022

AbstractIron reducing bacteria (IRB) are thought to accelerate the corrosion of steel by removing the Fe(III)-oxide passivating layer through iron respiration. We investigated the effect of the iron-binding ligands oxalate, malonate, and succinate on the corrosion of carbon steel driven by the IRB Shewanella oneidensis. These dicarboxylates were found to accelerate the corrosion of carbon steel driven by IRB up to 2.6 times more than the abiotic experiment without dicarboxylates. Iron dissolution was enhanced by dicarboxylates, and this influenced the ability of planktonic cells to engage in iron respiration. The strong iron-binding ligands oxalate and malonate supported iron reduction by planktonic cells, whereas in the experiments with succinate or without dicarboxylate, a direct contact mechanism with the solid Fe(III)-oxide was observed. Faster microbial respiration rates were found in experiments with succinate than with oxalate or malonate, suggesting a competition for iron between the microbial cells and the strong iron-binding ligands.
Pair-density-wave in the strong coupling limit of the Holstein-Hubbard model
Authors: Huang Kevin S. , Han Zhaoyu , Kivelson Steven A. , Yao Hong 
Published: February 2022

AbstractA pair-density-wave (PDW) is a superconducting state with an oscillating order parameter. A microscopic mechanism that can give rise to it has been long sought but has not yet been established by any controlled calculation. Here we report a density-matrix renormalization-group (DMRG) study of an effective t-J-V model, which is equivalent to the Holstein-Hubbard model in a strong-coupling limit, on long two-, four-, and six-leg triangular cylinders. While a state with long-range PDW order is precluded in one dimension, we find strong quasi-long-range PDW order with a divergent PDW susceptibility as well as the spontaneous breaking of time-reversal and inversion symmetries. Despite the strong interactions, the underlying Fermi surfaces and electron pockets around the K and $${K}^{\prime}$$

K

′

points in the Brillouin zone can be identified. We conclude that the state is valley-polarized and that the PDW arises from intra-pocket pairing with an incommensurate center of mass momentum. In the two-leg case, the exponential decay of spin correlations and the measured central charge c ≈ 1 are consistent with an unusual realization of a Luther-Emery liquid.
Snow flea antifreeze peptide for cryopreservation of lactic acid bacteria
Authors: Chen Xu , Wu Jinhong , Li Xiaozhen , Yang Fujia , Huang Dan , Huang Jianlian , Wang Shaoyun , Guyonnet Vincent 
Published: February 2022

AbstractCryogenic machining is one of the most commonly used techniques for processing and preserving in food industry, and traditional antifreeze agents cannot regulate the mechanical stress damage caused by ice crystals formed during recrystallization or thawing. In this study, we successfully developed an express system of a novel recombinant snow flea antifreeze peptide (rsfAFP), which has significant ice recrystallization inhibition ability, thermal hysteresis activity and alters ice nucleation, thus regulating extracellular ice crystal morphology and recrystallization. We showed that rsfAFP improved the survival rate, acid-producing ability, freezing stability, and cellular metabolism activity of Streptococcus thermophilus. We further showed that rsfAFP interacts with the membrane and ice crystals to cover the outer layer of cells, forming a dense protective layer that maintains the physiological functions of S. thermophilus under freezing stress. These findings provide the scientific basis for using rsfAFP as an effective antifreeze agent for lactic acid bacteria cryopreservation or other frozen food.
Morphological and molecular features of early regeneration in the marine annelid Ophryotrocha xiamen
Authors: Chen Ruanni , Mukhtar Irum , Wei Shurong , Wu Siyi , Chen Jianming 
Published: February 2022

AbstractRegeneration capability varies in the phylum Annelida making them an excellent group to investigate the differences between closely related organisms. Several studies have described the process of regeneration, while the underlying molecular mechanism remains unclear, especially during the early stage (wound healing and blastema formation). In this study, the newly identifiedOphryotrocha xiamenwas used to explore the early regeneration. The detailed morphological and molecular analyses positionedO. xiamenwithin ‘labronica’ clade. We analyzed the morphological changes during regeneration process (0–3 days post amputation) and molecular changes during the early regeneration stage (1 day post amputation). Wound healing was achieved within one day and a blastema formed one day later. A total of 243 DEGs were mainly involved in metabolism and signal transduction. Currently known regeneration-related genes were identified inO. xiamenwhich could help with exploring the functions of genes involved in regeneration processes. According to their conserved motif, we identified 8 differentHoxgene fragments andHox5andLox2were found to be absent in early regeneration and during regular growth. Our data can promote further use ofO. xiamenwhich can be used as an experimental model for resolving crucial problems of developmental biology in marine invertebrates.
A macroscopic Washburn approach of liquid imbibition in wood derived from X-ray tomography observations
Authors: Perré Patrick , Nguyen Dang Mao , Almeida Giana 
Published: February 2022

AbstractImbibition of water and silicone oil in poplar and spruce is investigated at the anatomical level by X-ray tomography observations and at the macroscopic level by imbibition kinetics. Imbibition mechanisms depend on both liquid and species. In poplar, oil penetrates vessels with a small contact angle, consistent with the value measured on solid wood (ca. $$20^{\circ }$$

20
∘

). Surprisingly, no direct penetration of water was observed in vessels. The large contact angle for water blocks the capillary rise at the scars between vessel cells. In spruce, oil and water penetrate primarily in latewood, where bordered pits remain open. Subsequently, water slowly invades the rest of the growth ring, while transversal migration is quasi-absent for oil. These 3D observations were quantified to feed a simple imbibition model that satisfactorily simulates macroscopic imbibition kinetics. A 1D approach is sufficient for oil imbibition while a 2D approach is required for water, revealing dual scale effects.
Nanostructured Ge and GeSn films by high-pressure He plasma sputtering for high-capacity Li ion battery anodes
Authors: Uchida Giichiro , Nagai Kenta , Habu Yuma , Hayashi Junki , Ikebe Yumiko , Hiramatsu Mineo , Narishige Ryota , Itagaki Naho , Shiratani Masaharu , Setsuhara Yuichi 
Published: February 2022

AbstractWe fabricated nanostructured Ge and GeSn films using He radio-frequency magnetron plasma sputtering deposition. Monodisperse amorphous Ge and GeSn nanoparticles of 30–40 nm size were arranged without aggregation by off-axis sputtering deposition in the high He-gas-pressure range of 0.1 Torr. The Ge film porosity was over 30%. We tested the charge/discharge cycle performance of Li-ion batteries with nanostructured Ge and GeSn anodes. The Ge anode with a dispersed arrangement of nanoparticles showed a Li-storage capacity of 565 mAh/g after the 60th cycle. The capacity retention was markedly improved by the addition of 3 at% Sn in Ge anode. The GeSn anode (3 at% Sn) achieved a higher capacity of 1128 mAh/g after 60 cycles with 92% capacity retention. Precise control of the nano-morphology and electrical characteristics by a single step procedure using low temperature plasma is effective for stable cycling of high-capacity Ge anodes.
Sensitivity of non-conditional climatic variables to climate-change deep uncertainty using Markov Chain Monte Carlo simulation
Authors: Zolghadr-Asli Babak , Bozorg-Haddad Omid , Enayati Maedeh , Loáiciga Hugo A. 
Published: February 2022

AbstractThere is substantial evidence suggesting climate change is having an adverse impact on the world’s water resources. One must remember, however, that climate change is beset by uncertainty. It is therefore meaningful for climate change impact assessments to be conducted with stochastic-based frameworks. The degree of uncertainty about the nature of a stochastic phenomenon may differ from one another. Deep uncertainty refers to a situation in which the parameters governing intervening probability distributions of the stochastic phenomenon are themselves subjected to some degree of uncertainty. In most climatic studies, however, the assessment of the role of deep-uncertain nature of climate change has been limited. This work contributes to fill this knowledge gap by developing a Markov Chain Monte Carlo (MCMC) analysis involving Bayes’ theorem that merges the stochastic patterns of historical data (i.e., the prior distribution) and the regional climate models’ (RCMs’) generated climate scenarios (i.e., the likelihood function) to redefine the stochastic behavior of a non-conditional climatic variable under climate change conditions (i.e., the posterior distribution). This study accounts for the deep-uncertainty effect by evaluating the stochastic pattern of the central tendency measure of the posterior distributions through regenerating the MCMCs. The Karkheh River Basin, Iran, is chosen to evaluate the proposed method. The reason for selecting this case study was twofold. First, this basin has a central role in ensuring the region’s water, food, and energy security. The other reason is the diverse topographic profile of the basin, which imposes predictive challenges for most RCMs. Our results indicate that, while in most seasons, with the notable exception of summer, one can expect a slight drop in the temperature in the near future, the average temperature would continue to rise until eventually surpassing the historically recorded values. The results also revealed that the 95% confidence interval of the central tendency measure of computed posterior probability distributions varies between 0.1 and 0.3 °C. The results suggest exercising caution when employing the RCMs’ raw projections, especially in topographically diverse terrain.
Vertical stratification of insect abundance and species richness in an Amazonian tropical forest
Authors: de Souza Amorim Dalton , Brown Brian V. , Boscolo Danilo , Ale-Rocha Rosaly , Alvarez-Garcia Deivys Moises , Balbi Maria Isabel P. A. , de Marco Barbosa Alan , Capellari Renato Soares , de Carvalho Claudio José Barros , Couri Marcia Souto , de Vilhena Perez Dios Rodrigo , Fachin Diego Aguilar , Ferro Gustavo B. , Flores Heloísa Fernandes , Frare Livia Maria , Gudin Filipe Macedo , Hauser Martin , Lamas Carlos José Einicker , Lindsay Kate G. , Marinho Marco Antonio Tonus , Marques Dayse Willkenia Almeida , Marshall Stephen A. , Mello-Patiu Cátia , Menezes Marco Antônio , Morales Mírian Nunes , Nihei Silvio S. , Oliveira Sarah Siqueira , Pirani Gabriela , Ribeiro Guilherme Cunha , Riccardi Paula Raille , de Santis Marcelo Domingos , Santos Daubian , dos Santos Josenilson Rodrigues , Silva Vera Cristina , Wood Eric Matthew , Rafael José Albertino 
Published: February 2022

AbstractTropical forests are among the most biodiverse biomes on the planet. Nevertheless, quantifying the abundance and species richness within megadiverse groups is a significant challenge. We designed a study to address this challenge by documenting the variability of the insect fauna across a vertical canopy gradient in a Central Amazonian tropical forest. Insects were sampled over two weeks using 6-m Gressitt-style Malaise traps set at five heights (0 m–32 m–8 m intervals) on a metal tower in a tropical forest north of Manaus, Brazil. The traps contained 37,778 specimens of 18 orders of insects. Using simulation approaches and nonparametric analyses, we interpreted the abundance and richness of insects along this gradient. Diptera, Hymenoptera, and Coleoptera had their greatest abundance at the ground level, whereas Lepidoptera and Hemiptera were more abundant in the upper levels of the canopy. We identified species of 38 of the 56 families of Diptera, finding that 527 out of 856 species (61.6%) were not sampled at the ground level. Mycetophilidae, Tipulidae, and Phoridae were significantly more diverse and/or abundant at the ground level, while Tachinidae, Dolichopodidae, and Lauxaniidae were more diverse or abundant at upper levels. Our study suggests the need for a careful discussion of strategies of tropical forest conservation based on a much more complete understanding of the three-dimensional distribution of its insect diversity.
Poaching of protected wolves fluctuated seasonally and with non-wolf hunting
Authors: Santiago-Ávila Francisco J. , Treves Adrian 
Published: February 2022

AbstractPoaching is the main cause of mortality for many large carnivores, and mitigating it is imperative for the persistence of their populations. For Wisconsin gray wolves (Canis lupus), periods of increased risk in overall mortality and poaching seem to overlap temporally with legal hunting seasons for other large mammals (hunting wolves was prohibited). We analyzed monitoring data from adult, collared wolves in Wisconsin, USA (1979–2012, n = 495) using a competing-risk approach to test explicitly if seasons during which it was legal to train hunting hounds (hounding) or hunt other large mammals (hunting) affected wolves’ hazard of cause-specific mortality and disappearance. We found increases in hazard for disappearances and documented (‘reported’) poaching during seasons with hunting, hounding or snow cover relative to a season without these factors. The ‘reported poached’ hazard increased > 650% during seasons with hunting and snow cover, which may be due to a seasonal surge in numbers of potential poachers or to some poachers augmenting their activities. Snow cover was a major environmental factor contributing to poaching, presumably through increased detection of wolves. Our study suggests poaching is by far the highest mortality hazard for wolves and reinforces the need for protections and policies targeting poaching of protected populations.
Increased associative interference under high cognitive load
Authors: Baror Shira , Bar Moshe 
Published: February 2022

AbstractAssociative processing is central for human cognition, perception and memory. But while associations often facilitate performance, processing irrelevant associations can interfere with performance, for example when learning new information. The aim of this study was to explore whether associative interference is influenced by contextual factors such as resources availability. Experiments 1–3 show that associative interference increases under high cognitive load. This result generalized to both long-term and short-term memory associations, and to both explicitly learned as well as incidentally learned associations in the linguistic and pictorial domains. Experiment 4 further revealed that attention to associative information can delay one’s perceptual processing when lacking resources. Taken together, when resources diminish associative interference increases, and additionally, processing novel and ambiguous information is hindered. These findings bare relevance to other domains as well (e.g., social, educational), in which increased load or stress may prompt an undesirable bias towards prior, misleading information.
Incorporating uncertainty in learning to defer algorithms for safe computer-aided diagnosis
Authors: Liu Jessie , Gallego Blanca , Barbieri Sebastiano 
Published: February 2022

AbstractDeep neural networks are increasingly being used for computer-aided diagnosis, but erroneous diagnoses can be extremely costly for patients. We propose a learning to defer with uncertainty (LDU) algorithm which identifies patients for whom diagnostic uncertainty is high and defers them for evaluation by human experts. LDU was evaluated on the diagnosis of myocardial infarction (using discharge summaries), the diagnosis of any comorbidities (using structured data), and the diagnosis of pleural effusion and pneumothorax (using chest x-rays), and compared with ‘learning to defer without uncertainty information’ (LD) and ‘direct triage by uncertainty’ (DT) methods. LDU achieved the same F1 score as LD but deferred considerably fewer patients (e.g. 36% vs. 69% deferral rate for diagnosing pleural effusion with an F1 score of 0.96). Furthermore, even when many patients were assigned the wrong diagnosis with high confidence (e.g. for the diagnosis of any comorbidities) LDU achieved a 17% increase in F1 score, whereas DT was not applicable. Importantly, the weight of the defer loss in LDU can be easily adjusted to obtain the desired trade-off between diagnostic accuracy and deferral rate. In conclusion, LDU can readily augment any existing diagnostic network to reduce the risk of erroneous diagnoses in clinical practice.
Photothermal inactivation of universal viral particles by localized surface plasmon resonance mediated heating filter membrane
Authors: Yoo Seunghwan , Yoon Sun-Woo , Jung Woo-Nam , Chung Moon Hyun , Kim Hyunjun , Jeong Hagkeun , Yoo Kyung-Hwa 
Published: February 2022

AbstractThis study introduces localized surface plasmon resonance (L-SPR) mediated heating filter membrane (HFM) for inactivating universal viral particles by using the photothermal effect of plasmonic metal nanoparticles (NPs). Plasmonic metal NPs were coated onto filter membrane via a conventional spray-coating method. The surface temperature of the HFM could be controlled to approximately 40–60 °C at room temperature, owing to the photothermal effect of the gold (Au) NPs coated on them, under irradiation by visible light-emitting diodes. Due to the photothermal effect of the HFMs, the virus titer of H1Npdm09 was reduced by > 99.9%, the full inactivation time being < 10 min, confirming the 50% tissue culture infective dose (TCID50) assay. Crystal violet staining showed that the infectious samples with photothermal inactivation lost their infectivity against Mardin-Darby Canine Kidney cells. Moreover, photothermal inactivation could also be applied to reduce the infectivity of SARS-CoV-2, showing reduction rate of 99%. We used quantitative reverse transcription polymerase chain reaction (qRT-PCR) techniques to confirm the existence of viral genes on the surface of the HFM. The results of the TCID50 assay, crystal violet staining method, and qRT-PCR showed that the effective and immediate reduction in viral infectivity possibly originated from the denaturation or deformation of membrane proteins and components. This study provides a new, simple, and effective method to inactivate viral infectivity, leading to its potential application in various fields of indoor air quality control and medical science.
Computational discovery of binding mode of anti-TRBC1 antibody and predicted key amino acids of TRBC1
Authors: Saetang Jirakrit , Sangkhathat Surasak , Jangphattananont Nawaphat , Khopanlert Wannakorn , Julamanee Jakrawadee , Tipmanee Varomyalin 
Published: February 2022

AbstractPeripheral T-cell lymphoma (PTCL) is a type of non-Hodgkin lymphoma that progresses aggressively with poor survival rate. CAR T cell targeting T-cell receptor β-chain constant domains 1 (TRBC1) of malignant T cells has been developed recently by using JOVI.1 monoclonal antibody as a template. However, the mode of JOVI.1 binding is still unknown. This study aimed to investigate the molecular interaction between JOVI.1 antibody and TRBC1 by using computational methods and molecular docking. Therefore, the TRBC protein crystal structures (TRBC1 and TRBC2) as well as the sequences of JOVI.1 CDR were chosen as the starting materials. TRBC1 and TRBC2 epitopes were predicted, and molecular dynamic (MD) simulation was used to visualize the protein dynamic behavior. The structure of JOVI.1 antibody was also generated before the binding mode was predicted using molecular docking with an antibody mode. Epitope prediction suggested that the N3K4 region of TRBC1 may be a key to distinguish TRBC1 from TCBC2. MD simulation showed the major different surface conformation in this area between two TRBCs. The JOVI.1-TRBC1 structures with three binding modes demonstrated JOVI.1 interacted TRBC1 at N3K4 residues, with the predicted dissociation constant (Kd) ranging from 1.5 × 108to 1.1 × 1010 M. The analysis demonstrated JOVI.1 needed D1 residues of TRBC1 for the interaction formation to N3K4 in all binding modes. In conclusion, we proposed the three binding modes of the JOVI.1 antibody to TRBC1 with the new key residue (D1) necessary for N3K4 interaction. This data was useful for JOVI.1 redesign to improve the PTCL-targeting CAR T cell.
Impact of extractive industries on malaria prevalence in the Democratic Republic of the Congo: a population-based cross-sectional study
Authors: Mitchell Cedar L. , Janko Mark M. , Mwandagalirwa Melchior K. , Tshefu Antoinette K. , Edwards Jessie K. , Pence Brian W. , Juliano Jonathan J. , Emch Michael 
Published: February 2022

AbstractExtraction of natural resources through mining and logging activities provides revenue and employment across sub-Saharan Africa, a region with the highest burden of malaria globally. The extent to which mining and logging influence malaria transmission in Africa remains poorly understood. Here, we evaluate associations between mining, logging, and malaria in the high transmission setting of the Democratic Republic of the Congo using population-representative malaria survey results and geographic data for environmental features and mining and logging concessions. We find elevated malaria prevalence among individuals in rural areas exposed to mining; however, we also detect significant spatial confounding among locations. Upon correction, effect estimates for mining and logging shifted toward the null and we did not find sufficient evidence to detect an association with malaria. Our findings reveal a complex interplay between mining, logging, space, and malaria prevalence. While mining concessions alone may not drive the high prevalence, unobserved features of mining-exposed areas, such as human migration, changing vector populations, or parasite genetics, may instead be responsible.
Nanoscale transformations of amphiboles within human alveolar epithelial cells
Authors: Vigliaturo Ruggero , Jamnik Maja , Dražić Goran , Podobnik Marjetka , Žnidarič Magda Tušek , Ventura Giancarlo Della , Redhammer Günther J. , Žnidaršič Nada , Caserman Simon , Gieré Reto 
Published: February 2022

AbstractAmphibole asbestos is related to lung fibrosis and several types of lung tumors. The disease-triggering mechanisms still challenge our diagnostic capabilities and are still far from being fully understood. The literature focuses primarily on the role and formation of asbestos bodies in lung tissues, but there is a distinct lack of studies on amphibole particles that have been internalized by alveolar epithelial cells (AECs). These internalized particles may directly interact with the cell nucleus and the organelles, exerting a synergistic action with asbestos bodies (AB) from a different location. Here we document the near-atomic- to nano-scale transformations induced by, and taking place within, AECs of three distinct amphiboles (anthophyllite, grunerite, “amosite”) with different Fe-content and morphologic features. We show that: (i) an Fe-rich layer is formed on the internalized particles, (ii) particle grain boundaries are transformed abiotically by the internal chemical environment of AECs and/or by a biologically induced mineralization mechanism, (iii) the Fe-rich material produced on the particle surface does not contain large amounts of P, in stark contrast to extracellular ABs, and (iv) the iron in the Fe-rich layer is derived from the particle itself. Internalized particles and ABs follow two distinct formation mechanisms reaching different physicochemical end-states.