bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial adhesive films by plasma-enabled polymerisation of m-cresol
Authors: Hartl Hugo , Li Wenshao , Michl Thomas Danny , Anangi Raveendra , Speight Robert , Vasilev Krasimir , Ostrikov Kostya Ken , MacLeod Jennifer 
Published: May 2022

AbstractThis work reveals a versatile new method to produce films with antimicrobial properties that can also bond materials together with robust tensile adhesive strength. Specifically, we demonstrate the formation of coatings by using a dielectric barrier discharge (DBD) plasma to convert a liquid small-molecule precursor, m-cresol, to a solid film via plasma-assisted on-surface polymerisation. The films are quite appealing from a sustainability perspective: they are produced using a low-energy process and from a molecule produced in abundance as a by-product of coal tar processing. This process consumes only 1.5 Wh of electricity to create a 1 cm2 film, which is much lower than other methods commonly used for film deposition, such as chemical vapour deposition (CVD). Plasma treatments were performed in plain air without the need for any carrier or precursor gas, with a variety of exposure durations. By varying the plasma parameters, it is possible to modify both the adhesive property of the film, which is at a maximum at a 1 min plasma exposure, and the antimicrobial property of the film against Escherichia coli, which is at a maximum at a 30 s exposure.
Ultrastructure of setae of a planktonic diatom, Chaetoceros coarctatus
Authors: Owari Yuka , Nakamura Fumi , Oaki Yuya , Tsuda Hiroyuki , Shimode Shinji , Imai Hiroaki 
Published: May 2022

AbstractSilica frustules of most planktonic diatoms have many shallow holes in which the length (L) is smaller than the width (W). The present study focuses on a silica ultrastructure of setae of a planktonic diatom having deep (L/W > 1) holes. Here, we characterized microscopically patterned nanoholes on the silica walls of thick, robust, and hollow setae of a colony of Chaetoceros coarctatus. Basically, tetragonal poroid arrangements with and without a costa pattern are observed on the inner and outer surfaces, respectively, for three kinds of curving hollow setae attached to the anterior, intercalary, and posterior parts of the colony. The seta structures including specific poroid arrangements and continuity of deep nanoholes depend on the location. The deep nanoholes ∼90 nm wide are elongated from 150 to 1500 nm (L/W ∼17) with an increase in the wall thickness of the polygonal tubes of the setae. The inside poroid array, with a period of 190 nm in the extension direction of setae, is lined by parallel plates of the costae. However, the poroid arrangement on the outer surface is disordered, with several holes obstructed with increasing wall thickness of the posterior terminal setae. According to the movement of a colony in a fluid microchannel, the thick curving terminal setae is suggested to involve attitude control and mechanical protection. Using an optical simulation, the patterned deep through-holes on the intercalary setae were suggested to contribute anti-reflection of blue light in the wavelength range of 400 to 500 nm for the promotion of photosynthesis in seawater.
Global coordination level in single-cell transcriptomic data
Authors: Amit Guy , Vaknin Ben Porath Dana , Levy Orr , Hamdi Omer , Bashan Amir 
Published: May 2022

AbstractGenes are linked by underlying regulatory mechanisms and by jointly implementing biological functions, working in coordination to apply different tasks in the cells. Assessing the coordination level between genes from single-cell transcriptomic data, without a priori knowledge of the map of gene regulatory interactions, is a challenge. A ‘top-down’ approach has recently been developed to analyze single-cell transcriptomic data by evaluating the global coordination level between genes (called GCL). Here, we systematically analyze the performance of the GCL in typical scenarios of single-cell RNA sequencing (scRNA-seq) data. We show that an individual anomalous cell can have a disproportionate effect on the GCL calculated over a cohort of cells. In addition, we demonstrate how the GCL is affected by the presence of clusters, which are very common in scRNA-seq data. Finally, we analyze the effect of the sampling size of the Jackknife procedure on the GCL statistics. The manuscript is accompanied by a description of a custom-built Python package for calculating the GCL. These results provide practical guidelines for properly pre-processing and applying the GCL measure in transcriptional data.
Chitinase-3-like protein-1 at hospital admission predicts COVID-19 outcome: a prospective cohort study
Authors: De Lorenzo Rebecca , Sciorati Clara , Lorè Nicola I. , Capobianco Annalisa , Tresoldi Cristina , Cirillo Daniela M. , Ciceri Fabio , Rovere-Querini Patrizia , Manfredi Angelo A. 
Published: May 2022

AbstractInfectious and inflammatory stimuli elicit the generation of chitinase-3-like protein-1 (CHI3L1), involved in tissue damage, repair and remodeling. We evaluated whether plasma CHI3L1 at disease onset predicts clinical outcome of patients with Coronavirus 2019 (COVID-19) disease. Blood from 191 prospectively followed COVID-19 patients were collected at hospital admission between March 18th and May 5th, 2020. Plasma from 80 survivors was collected one month post-discharge. Forty age- and sex-matched healthy volunteers served as controls. Primary outcome was transfer to intensive care unit (ICU) or death. CHI3L1 was higher in COVID-19 patients than controls (p < 0.0001). Patients with unfavorable outcome (41 patients admitted to ICU, 47 died) had significantly higher CHI3L1 levels than non-ICU survivors (p < 0.0001). CHI3L1 levels abated in survivors one month post-discharge, regardless of initial disease severity (p < 0.0001), although remaining higher than controls (p < 0.05). Cox regression analysis revealed that CHI3L1 levels predict primary outcome independently of age, sex, comorbidities, degree of respiratory insufficiency and systemic inflammation or time from symptom onset to sampling (p < 0.0001). Kaplan–Meier curve analysis confirmed that patients with CHI3L1 levels above the median (361 ng/mL) had a poorer prognosis (log rank test, p < 0.0001). Plasma CHI3L1 is increased in COVID-19 patients and predicts adverse outcome.
Particulate matter (PM10) induces in vitro activation of human neutrophils, and lung histopathological alterations in a mouse model
Authors: Valderrama Andrés , Ortiz-Hernández Paul , Agraz-Cibrián Juan Manuel , Tabares-Guevara Jorge H. , Gómez Diana M. , Zambrano-Zaragoza José Francisco , Taborda Natalia A. , Hernandez Juan C. 
Published: May 2022

AbstractThe epidemiological association between exposure to particulate matter (PM10) and various respiratory and cardiovascular problems is well known, but the mechanisms driving these effects remain unclear. Neutrophils play an essential role in immune defense against foreign agents and also participate in the development of inflammatory responses. However, the role of these cells in the PM10induced inflammatory response is not yet fully established. Thus, this study aims to evaluate the effect of PM10on the neutrophil-mediated inflammatory response. For this, neutrophils from healthy adult human donors were in vitro exposed to different concentrations of PM10. The cell viability and cytotoxic activity were evaluated by MTT. LDH, propidium iodide and reactive oxygen species (ROS) were quantified by flow cytometry. Interleukin 8 (IL-8) expression, peptidyl arginine deiminase 4 (PAD4), myeloperoxidase (MPO), and neutrophil elastase (NE) expression were measured by RT-PCR. IL-8 was also quantified by ELISA. Fluorescence microscopy was used to evaluate neutrophil extracellular traps (NETs) release. The in vivo inflammatory responses were assessed in BALB/c mice exposed to PM10by histopathology and RT-PCR. The analysis shows that PM10exposure induced a cytotoxic effect on neutrophils, evidenced by necrosis and LDH release at high PM10concentrations. ROS production, IL-8, MPO, NE expression, and NETs release were increased at all PM10concentrations assessed. Neutrophil infiltration in bronchoalveolar lavage fluid (BALF), histopathological changes with inflammatory cell infiltration, and CXCL1 expression were observed in PM10-treated mice. The results suggest that lung inflammation in response to PM10could be mediated by neutrophils activation. In this case, these cells migrate to the lungs and release pro-inflamatory mediators, including ROS, IL-8, and NETs. Thus, contributing to the exacerbation of respiratory pathologies, such as allergies, infectious and obstructive diseases.
Phenomic data-facilitated rust and senescence prediction in maize using machine learning algorithms
Authors: DeSalvio Aaron J. , Adak Alper , Murray Seth C. , Wilde Scott C. , Isakeit Thomas 
Published: May 2022

AbstractCurrent methods in measuring maize (Zea mays L.) southern rust (Puccinia polyspora Underw.) and subsequent crop senescence require expert observation and are resource-intensive and prone to subjectivity. In this study, unoccupied aerial system (UAS) field-based high-throughput phenotyping (HTP) was employed to collect high-resolution aerial imagery of elite maize hybrids planted in the 2020 and 2021 growing seasons, with 13 UAS flights obtained from 2020 and 17 from 2021. In total, 36 vegetation indices (VIs) were extracted from mosaicked aerial images that served as temporal phenomic predictors for southern rust scored in the field and senescence as scored using UAS-acquired mosaic images. Temporal best linear unbiased predictors (TBLUPs) were calculated using a nested model that treated hybrid performance as nested within flights in terms of rust and senescence. All eight machine learning regressions tested (ridge, lasso, elastic net, random forest, support vector machine with radial and linear kernels, partial least squares, and k-nearest neighbors) outperformed a general linear model with both higher prediction accuracies (92–98%) and lower root mean squared error (RMSE) for rust and senescence scores (linear model RMSE ranged from 65.8 to 2396.5 across all traits, machine learning regressions RMSE ranged from 0.3 to 17.0). UAS-acquired VIs enabled the discovery of novel early quantitative phenotypic indicators of maize senescence and southern rust before being detectable by expert annotation and revealed positive correlations between grain filling time and yield (0.22 and 0.44 in 2020 and 2021), with practical implications for precision agricultural practices.
Fluoxetine exposure throughout neurodevelopment differentially influences basilar dendritic morphology in the motor and prefrontal cortices
Authors: Maloney Susan E. , Tabachnick Dora R. , Jakes Christine , Avdagic Selma , Bauernfeind Amy L. , Dougherty Joseph D. 
Published: May 2022

AbstractThe significance of serotonin (5HT) in mental health is underscored by the serotonergic action of many classes of psychiatric medication. 5HT is known to have a significant role in neurodevelopment, thus 5HT disruption during development may have a long term impact on brain structure and circuits. We previously generated a model of 5HT alteration throughout neurodevelopment by maternal administration of the selective serotonin reuptake inhibitor fluoxetine. We found resulting social behavior alterations in the offspring during both postnatal and adult ages. Previous work by others has indicated that early 5HT disruption influences neuronal morphology. Therefore, in the current study we sought to determine if dendritic morphological changes occur in areas involved in the social behavior deficits we previously observed, specifically the primary motor (M1) and medial prefrontal (mPFC) cortices. We quantified dendritic morphology of projection neurons in M1 and mPFC at postnatal day (P)10 and P79 in mice exposed to fluoxetine. Basilar dendritic complexity and spine density were persistently decreased in M1 fluoxetine-exposed neurons while in the mPFC, similar reductions were observed at P79 but were not present at P10. Our findings underscore that the developing brain, specifically the projection cortex, is vulnerable to 5HT system perturbation, which may be related to later behavioral disruptions.
Myofibrillar protein synthesis rates are increased in chronically exercised skeletal muscle despite decreased anabolic signaling
Authors: Langer Henning T. , West Daniel , Senden Joan , Spuler Simone , van Loon Luc J. C. , Baar Keith 
Published: May 2022

AbstractThe molecular responses to acute resistance exercise are well characterized. However, how cellular signals change over time to modulate chronic adaptations to more prolonged exercise training is less well understood. We investigated anabolic signaling and muscle protein synthesis rates at several time points after acute and chronic eccentric loading. Adult rat tibialis anterior muscle was stimulated for six sets of ten repetitions, and the muscle was collected at 0 h, 6 h, 18 h and 48 h. In the last group of animals, 48 h after the first exercise bout a second bout was conducted, and the muscle was collected 6 h later (54 h total). In a second experiment, rats were exposed to four exercise sessions over the course of 2 weeks. Anabolic signaling increased robustly 6 h after the first bout returning to baseline between 18 and 48 h. Interestingly, 6 h after the second bout mTORC1 activity was significantly lower than following the first bout. In the chronically exercised rats, we found baseline anabolic signaling was decreased, whereas myofibrillar protein synthesis (MPS) was substantially increased, 48 h after the last bout of exercise. The increase in MPS occurred in the absence of changes to muscle fiber size or mass. In conclusion, we find that anabolic signaling is already diminished after the second bout of acute resistance type exercise. Further, chronic exposure to resistance type exercise training results in decreased basal anabolic signaling but increased overall MPS rates.
The increased frequency of combined El Niño and positive IOD events since 1965s and its impacts on maritime continent hydroclimates
Authors: Xiao He-Ming , Lo Min-Hui , Yu Jin-Yi 
Published: May 2022

AbstractThe Indian and Pacific Oceans surround the Maritime Continent (MC). Major modes of sea surface temperature variability in both oceans, including the Indian Ocean Dipole (IOD) and El Niño–Southern Oscillation (ENSO), can strongly affect precipitation on the MC. The prevalence of fires in the MC is closely associated with precipitation amount and terrestrial water storage in September and October. Precipitation and terrestrial water storage, which is a measurement of hydrological drought conditions, are significantly modulated by Indian Ocean Dipole (IOD) and El Niño events. We utilize long-term datasets to study the combined effects of ENSO and the IOD on MC precipitation during the past 100 years (1900–2019) and find that the reductions in MC precipitation and terrestrial water storage are more pronounced during years when El Niño and a positive phase of the IOD (pIOD) coincided. The combined negative effects are produced mainly through an enhanced reduction of upward motion over the MC. Coincident El Niño-pIOD events have occurred more frequently after 1965. However, climate models do not project a higher occurrence of coincident El Niño-pIOD events in a severely warming condition, implying that not the global warming but the natural variability might be the leading cause of this phenomenon.
No-ozone cold plasma can kill oral pathogenic microbes in H2O2-dependent and independent manner
Authors: Park Nam-Sook , Yun Se-Eun , Lee Hyun-Young , Lee Hae June , Choi Jeong-Hae , Kim Gyoo-Cheon 
Published: May 2022

AbstractTo apply the sterilisation effect of low-temperature plasma to the oral cavity, the issue of ozone from plasma must be addressed. In this study, a new technology for generating cold plasma with almost no ozone is developed and is named Nozone (no-ozone) Cold Plasma (NCP) technology. The antimicrobial efficacy of the NCP against four oral pathogens is tested, and its specific mechanism is elucidated. The treatment of NCP on oral pathogenic microbes on a solid medium generated a growth inhibition zone. When NCP is applied to oral pathogens in a liquid medium, the growth of microbes decreased by more than 105 colony forming units, and the bactericidal effect of NCP remained after the installation of dental tips. The bactericidal effect of NCP in the liquid medium is due to the increase in hydrogen peroxide levels in the medium. However, the bactericidal effect of NCP in the solid medium depends on the charged elements of the NCP. Furthermore, the surface bactericidal efficiency of the dental-tip-installed NCP is proportional to the pore size of the tips and inversely proportional to the length of the tips. Overall, we expect this NCP device to be widely used in dentistry in the near future.
A dual-band CPW-fed miniature planar antenna for S-, C-, WiMAX, WLAN, UWB, and X-band applications
Authors: Alam Md. Mottahir , Azim Rezaul , Sobahi Nebras M. , Khan Asif Irshad , Islam Mohammad Tariqul 
Published: May 2022

AbstractA miniature planar antenna is a vital component of any portable wireless communication device. The antenna in portable devices should provide wide/multiple operating bands to cover a good number of narrowband services as a multi-band antenna not only reduces the number of antennas but also lessens the system complexity, cost, and device size. To operate over S-, C-, WiMAX, WLAN, UWB, and X-communication bands, in this paper, a dual-band CPW-fed antenna is presented. The anticipated antenna is made up of a vertical bow-tie-shaped patch and two asymmetric ground planes and etched on the same side of the single-sided standard substrate material. To generate two distinct operating bands, an inverted L-shaped parasitic element is inserted within the modified U-shaped coplanar ground plane. The antenna achieved dual operating bands of 3.24–8.29 GHz and 9.12–11.25 GHz in measurement which helps the proposed antenna to cover S-, C-, WiMAX, WLAN, 4G LTE, 5G sub-6 GHz, UWB, and X-communication bands. In the two operating bands, the antenna realized a peak gain of 4.33 dBi, and 4.80 dBi, the maximum radiation efficiency of 86.6%, and 72.6%, and exhibits symmetric radiation patterns. In the operating bands, the antenna also exhibits good time-domain behavior which helps it to transmit the signal with minimum distortion.
Functional divergence of the pigmentation gene melanocortin-1 receptor (MC1R) in six endemic Macaca species on Sulawesi Island
Authors: Yan Xiaochan , Terai Yohey , Widayati Kanthi Arum , Itoigawa Akihiro , Purba Laurentia Henrieta Permita Sari , Fahri Fahri , Suryobroto Bambang , Imai Hiroo 
Published: May 2022

AbstractCoat color is often highly variable within and between animal taxa. Among hundreds of pigmentation-related genes, melanocortin-1 receptor (MC1R) plays key roles in regulating the synthesis of the dark eumelanin and the red–yellow pheomelanin. The six species of macaques that inhabit Sulawesi Island diverged rapidly from their common ancestor, M. nemestrina. Unlike most macaques, Sulawesi macaques commonly have a dark coat color, with divergence in shade and color pattern. To clarify the genetic and evolutionary basis for coat color in Sulawesi macaques, we investigated the MC1R sequences and functional properties, including basal cAMP production and α-MSH-induced activity in vitro. We found fixed non-synonymous substitutions in MC1R in each species. Furthermore, we found that six species-specific variants corresponded with variation in agonist-induced and basal activity of MC1R. Inconsistent with the dark coat color, four substitutions independently caused decreases in the basal activity of MC1R in M. hecki, M. nigra, M. tonkeana, and M. ochreata. Selective analysis suggested MC1R of M. nigra and M. nigrescens underwent purifying selection. Overall, our results suggest that fixed differences in MC1R resulted in different functional characteristics and might contribute to divergence in color among the six Sulawesi macaque species.
Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment
Authors: Singh Jaspreet , Paliwal Kuldip , Litfin Thomas , Singh Jaswinder , Zhou Yaoqi 
Published: May 2022

AbstractProtein language models have emerged as an alternative to multiple sequence alignment for enriching sequence information and improving downstream prediction tasks such as biophysical, structural, and functional properties. Here we show that a method called SPOT-1D-LM combines traditional one-hot encoding with the embeddings from two different language models (ProtTrans and ESM-1b) for the input and yields a leap in accuracy over single-sequence-based techniques in predicting protein 1D secondary and tertiary structural properties, including backbone torsion angles, solvent accessibility and contact numbers for all six test sets (TEST2018, TEST2020, Neff1-2020, CASP12-FM, CASP13-FM and CASP14-FM). More significantly, it has a performance comparable to profile-based methods for those proteins with homologous sequences. For example, the accuracy for three-state secondary structure (SS3) prediction for TEST2018 and TEST2020 proteins are 86.7% and 79.8% by SPOT-1D-LM, compared to 74.3% and 73.4% by the single-sequence-based method SPOT-1D-Single and 86.2% and 80.5% by the profile-based method SPOT-1D, respectively. For proteins without homologous sequences (Neff1-2020) SS3 is 80.41% by SPOT-1D-LM which is 3.8% and 8.3% higher than SPOT-1D-Single and SPOT-1D, respectively. SPOT-1D-LM is expected to be useful for genome-wide analysis given its fast performance. Moreover, high-accuracy prediction of both secondary and tertiary structural properties such as backbone angles and solvent accessibility without sequence alignment suggests that highly accurate prediction of protein structures may be made without homologous sequences, the remaining obstacle in the post AlphaFold2 era.
Determination of a distinguished interferon gamma epitope recognized by monoclonal antibody relating to autoantibody associated immunodeficiency
Authors: Yasamut Umpa , Wisitponchai Tanchanok , Lee Vannajan Sanghiran , Yamabhai Montarop , Rangnoi Kuntalee , Thongkum Weeraya , Chupradit Koollawat , Tayapiwatana Chatchai 
Published: May 2022

AbstractAnti-interferon gamma autoantibodies (anti-IFN-γ autoAbs) neutralize the IFN-γ-mediated functions, contributing to immunodeficiency. A particular autoAb in patient serum had been previously demonstrated to recognize the same determinant on IFN-γ as the neutralizing anti-IFN-γ monoclonal antibody clone B27 (B27 mAb). This study explored the epitope recognized by B27 mAb. The specific peptide sequence recognized by B27 mAb, TDFLRMMLQEER, was retrieved from a phage display random peptide library. Sequence alignment and homology modeling demonstrated that the queried phage peptide sequence and structure were similar to amino acids at position 27–40 (TLFLGILKNWKEES) of the human IFN-γ. This determinant resides in the contact surface of IFN-γ and interferon gamma receptor 1. To elucidate the crucial amino acids, mutations were introduced by substituting T27 and T27F29L30 with alanine or deleting the amino acid residues T27–L33. The binding of B27 mAb to IFN-γ T27A using western blotting was lesser than that to wild-type. The interaction with triple mutant and T27–L33 deletion mutant using western blotting and sandwich ELISA was abolished. The finding demonstrated that T27, F29, and L30 are critical residues in the B27 antigenic determinant. Identification of the functional domain of IFN-γ decrypted the relevance of neutralizing autoAb in adult-onset immunodeficiency.