bluuebunny/crossref_metadata_2025_split huggingface dataset:
Removal of an abluminal lining improves decellularization of human umbilical arteries
Authors: Tuan-Mu Ho-Yi , Chang Yi-Hao , Hu Jin-Jia 
Published: June 2020

AbstractThe decellularization of long segments of tubular tissues such as blood vessels may be improved by perfusing decellularization solution into their lumen. Particularly, transmural flow that may be introduced by the perfusion, if any, is beneficial to removing immunogenic cellular components in the vessel wall. When human umbilical arteries (HUAs) were perfused at a transmural pressure, however, very little transmural flow was observed. We hypothesized that a watertight lining at the abluminal surface of HUAs hampered the transmural flow and tested the hypothesis by subjecting the abluminal surface to enzyme digestion. Specifically, a highly viscous collagenase solution was applied onto the surface, thereby restricting the digestion to the surface. The localized digestion resulted in a water-permeable vessel without damaging the vessel wall. The presence of the abluminal lining and its successful removal were also supported by evidence from SEM, TEM, and mechanical testing. The collagenase-treated HUAs were decellularized with 1% sodium dodecyl sulfate (SDS) solution under either rotary agitation, simple perfusion, or pressurized perfusion. Regardless of decellularization conditions, the decellularization of HUAs was significantly enhanced after the abluminal lining removal. Particularly, complete removal of DNA was accomplished in 24 h by pressurized perfusion of the SDS solution. We conclude that the removal of the abluminal lining can improve the perfusion-assisted decellularization.
Differential expression of polyamine biosynthetic pathways in skin lesions and in plasma reveals distinct profiles in diffuse cutaneous leishmaniasis
Authors: Malta-Santos Hayna , França-Costa Jaqueline , Macedo Amanda , Queiroz Artur T. L. , Fukutani Kiyoshi F. , Muxel Sandra Marcia , Khouri Ricardo , Van Weyenbergh Johan , Boaventura Viviane , Barral Aldina , Costa Jackson M. , Floh Eny Iochevet Segal , Andrade Bruno B. , Floeter-Winter Lucile M. , Borges Valéria M. 
Published: June 2020

AbstractTegumentary leishmaniasis (TL) is a parasitic disease that can result in wide spectrum clinical manifestations. It is necessary to understand host and parasite determinants of clinical outcomes to identify novel therapeutic targets. Previous studies have indicated that the polyamine biosynthetic pathway is critical for Leishmania growth and survival. Despite its importance, expression of the such pathway has not been previously investigated in TL patients. We performed an exploratory analysis employing Systems Biology tools to compare circulating polyamines and amino acid concentration as well as polyamine pathway gene expression in cutaneous lesions patients presenting with distinct TL disease presentations. Diffuse cutaneous leishmaniasis (DCL) was associated with higher concentrations of amino acids, polyamines and its substrate transporters than mucosal cutaneous leishmaniasis or localized cutaneous leishmaniasis. In addition, the RNA expression of polyamine-related genes of patients lesions from two separate cohorts demonstrated that differential activation of this pathway is associated with parasite loads and able to discriminate the clinical spectrum of TL. Taken together, our findings highlight a new aspect of DCL immunopathogenesis indicating that the polyamine pathway may be explored as a novel therapeutic target to control disease burden.
In vitro evaluation and molecular docking of QS-21 and quillaic acid from Quillaja saponaria Molina as gastric cancer agents
Authors: Guzmán Leda , Villalón Katherine , Marchant María José , Tarnok María Elena , Cárdenas Pilar , Aquea Gisela , Acevedo Waldo , Padilla Leandro , Bernal Giuliano , Molinari Aurora , Corvalán Alejandro 
Published: June 2020

AbstractThe cytotoxic mechanism of the saponin QS-21 and its aglycone quillaic acid (QA) was studied on human gastric cancer cells (SNU1 and KATO III). Both compounds showed in vitro cytotoxic activity with IC50values: 7.1 μM (QS-21) and 13.6 μM (QA) on SNU1 cells; 7.4 μM (QS-21) and 67 μM (QA) on KATO III cells. QS-21 and QA induce apoptosis on SNU1 and KATO III, as demonstrated by TUNEL, Annexin-V and Caspase Assays. Additionally, we performed in silico docking studies simulating the binding of both triterpenic compounds to key proteins involved in apoptotic pathways. The binding energies (∆Gbin) thus calculated, suggest that the pro-apoptotic protein Bid might be a plausible target involved in the apoptotic effect of both triterpenic compounds. Although QA shows some antiproliferative effects on SNU1 cells cultured in vitro, our results suggest that QS-21 is a more powerful antitumor agent,which merits further investigation regarding their properties as potential therapeutic agents for gastric cancer.
Persistence of environmental DNA in cultivated soils: implication of this memory effect for reconstructing the dynamics of land use and cover changes
Authors: Foucher Anthony , Evrard Olivier , Ficetola G. Francesco , Gielly Ludovic , Poulain Julie , Giguet-Covex Charline , Laceby J. Patrick , Salvador-Blanes Sébastien , Cerdan Olivier , Poulenard Jérôme 
Published: June 2020

AbstracteDNA refers to DNA extracted from an environmental sample with the goal of identifying the occurrence of past or current biological communities in aquatic and terrestrial environments. However, there is currently a lack of knowledge regarding the soil memory effect and its potential impact on lake sediment eDNA records. To investigate this issue, two contrasted sites located in cultivated environments in France were studied. In the first site, soil samples were collected (n = 30) in plots for which the crop rotation history was documented since 1975. In the second site, samples were collected (n = 40) to compare the abundance of currently observed taxa versus detected taxa in cropland and other land uses. The results showed that the last cultivated crop was detected in 100% of the samples as the most abundant. In addition, weeds were the most abundant taxa identified in both sites. Overall, these results illustrate the potential of eDNA analyses for identifying the recent (< 10 years) land cover history of soils and outline the detection of different taxa in cultivated plots. The capacity of detection of plant species grown on soils delivering sediments to lacustrine systems is promising to improve our understanding of sediment transfer processes over short timescales.
A tailored Cln3Q352X mouse model for testing therapeutic interventions in CLN3 Batten disease
Authors: Langin Logan , Johnson Tyler B. , Kovács Attila D. , Pearce David A. , Weimer Jill M. 
Published: June 2020

AbstractCLN3 Batten disease (CLN3 disease) is a pediatric lysosomal storage disorder that presents with progressive blindness, motor and cognitive decline, seizures, and premature death. CLN3 disease results from mutations in CLN3 with the most prevalent mutation, a 966 bp deletion spanning exons 7–8, affecting ~ 75% of patients. Mouse models with complete Cln3 deletion or Cln3Δex7/8 mutation have been invaluable for learning about both the basic biology of CLN3 and the underlying pathological changes associated with CLN3 disease. These models, however, vary in their disease presentation and are limited in their utility for studying the role of nonsense mediated decay, and as a consequence, in testing nonsense suppression therapies and read-through compounds. In order to develop a model containing a disease-causing nonsense point mutation, here we describe a first-of-its-kind Cln3Q352X mouse model containing a c.1054C > T (p.Gln352Ter) point mutation. Similar to previously characterized Cln3 mutant mouse lines, this novel model shows pathological deficits throughout the CNS including accumulation of lysosomal storage material and glial activation, and has limited perturbation in behavioral measures. Thus, at the molecular and cellular level, this mouse line provides a valuable tool for testing nonsense suppression therapies or read through compounds in CLN3 disease in the future.
Tools of the trade: MicroCT reveals native structure and functional morphology of organs that drive caterpillar–ant interactions
Authors: Basu Dipendra Nath , Kunte Krushnamegh 
Published: June 2020

AbstractCaterpillars of many lycaenid butterflies are tended by ants that offer protection from predators and parasitoids. Specialized structures such as glands, ciliary organs and chitinous ornamentation in caterpillars play key roles in the underlying tactile, acoustic, and chemical communication between caterpillars and ants. Although the ecological, evolutionary, and behavioural aspects of these interactions are well studied, the mechanisms (i.e., the functional morphology) that drive the specialized interactive organs are poorly characterized. We used advanced X-ray microtomography (MicroCT) to delineate internal, native morphology of specialized larval dew patches, nectar glands, and tactile ciliary organs that mediate interactions between Crematogaster ants and caterpillars of the obligate myrmecophilous Apharitis lilacinus butterfly. Our non-destructive MicroCT analysis provided novel 3-D insights into the native structure and positions of these specialized organs in unmatched detail. This analysis also suggested a functional relationship between organ structures and surrounding muscles and nervation that operate the glands and tactile organs, including a ‘lasso bag’ control mechanism for dew patches and muscle control for other organs. This provided a holistic understanding of the organs that drive very close caterpillar–ant interactions. Our MicroCT analysis opens a door for similar structural and functional analysis of adaptive insect morphology.
Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases
Authors: Barbosa Tiago M. , Baltazar Carla S. A. , Cruz Davide R. , Lousa Diana , Soares Cláudio M. 
Published: June 2020

AbstractHydrogenases are efficient biocatalysts for H2 production and oxidation with various potential biotechnological applications.[NiFe]-class hydrogenases are highly active in both production and oxidation processes—albeit primarily biased to the latter—but suffer from being sensitive to O2.[NiFeSe] hydrogenases are a subclass of [NiFe] hydrogenases with, usually, an increased insensitivity to aerobic environments. In this study we aim to understand the structural causes of the low sensitivity of a [NiFeSe]-hydrogenase, when compared with a [NiFe] class enzyme, by studying the diffusion of O2. To unravel the differences between the two enzymes, we used computational methods comprising Molecular Dynamics simulations with explicit O2 and Implicit Ligand Sampling methodologies. With the latter, we were able to map the free energy landscapes for O2 permeation in both enzymes. We derived pathways from these energy landscapes and selected the kinetically more relevant ones with reactive flux analysis using transition path theory. These studies evidence the existence of quite different pathways in both enzymes and predict a lower permeation efficiency for O2 in the case of the [NiFeSe]-hydrogenase when compared with the [NiFe] enzyme. These differences can explain the experimentally observed lower inhibition by O2 on [NiFeSe]-hydrogenases, when compared with [NiFe]-hydrogenases. A comprehensive map of the residues lining the most important O2 pathways in both enzymes is also presented.
Impact of habitat alteration on amphibian diversity and species composition in a lowland tropical rainforest in Northeastern Leyte, Philippines
Authors: Decena Syrus Cesar Pacle , Avorque Carlo Aguirre , Decena Ian Christopher Pacle , Asis Pol Delbert , Pacle Bryan 
Published: June 2020

AbstractThe impact of anthropogenic habitat alteration on amphibians was investigated, employing an investigative focus on leaf-litter and semi-aquatic species across different habitat alteration types. The habitat alteration types which include primary forest, selectively logged primary forest, secondary forest, abandoned farm areas and pasture (this represents a gradient of habitat alteration ranging from least altered to most altered, respectively) also encompass two habitat types: stream and terrestrial. Species assemblage was compared between habitat alteration types and habitat types, where a total 360 leaf-litter and semi-aquatic amphibians were observed (15 species, 6 families). It was found that amphibian abundance was significantly higher in both forest and stream habitat, and species richness did not differ with respect to habitat alteration type. It was determined, however, that species richness was highly dependent on habitat type (significantly higher in stream habitat). Meanwhile, diversity (Shannon–Wiener) was significantly higher in both forest and stream habitat, and species composition differed markedly between habitat alteration types for stream strip plots. Forest habitat exhibited domination by forest specialist species, while altered habitat (abandoned farm areas and pasture) exhibited domination by open-habitat specialist species. Additionally, strong relationships were found between species composition and abundance, as well as richness and diversity (within the measured habitat structures and observed microclimatic conditions). Analyses determined that the higher abundance of leaf-litter and semi-aquatic amphibians was best explained by higher DBH (1.3 m from the ground) and lower temperature and the higher species richness was best explained by higher understorey density. Additionally, higher diversity was associated with increasing understorey density, tree density and temperature. In general, the assemblage of leaf-litter and semi-aquatic amphibians in the lowland tropical rainforest in northeastern Leyte was affected by habitat alteration, highlighting the on-going importance of conservation efforts.
Simulation acceleration for transmittance of electromagnetic waves in 2D slit arrays using deep learning
Authors: Kim Wonsuk , Seok Junhee 
Published: June 2020

AbstractWhen designing new optical devices, many simulations must be conducted to determine the optimal design parameters. Therefore, fast and accurate simulations are essential for designing optical devices. In this work, we introduce a deep learning approach that accelerates a simulator solving frequency-domain Maxwell equations. Our model achieves high accuracy while predicting transmittance per wavelength in 2D slit arrays under certain conditions to achieve 160,000 times faster results than the simulator. We generated a dataset using an open-source simulator and compared its performance with those of other machine learning models. Additionally, we propose a new loss function and performance evaluation method for creating better performance models with multiple regression outputs from one input source. We observed that using a loss function that adds binary cross-entropy loss, which predicts whether the differential of the transmittance is positive or negative at wavelengths adjacent to the root mean-squared error of the transmittance value, is more effective for predicting variations in multiple regression outputs. The simulation results show that a four-layer convolutional neural network model demonstrates the best accuracy (R2score: 0.86). The overall approach presented here is expected to be useful for simulating and designing optical devices.
Lung cancer prediction in Lambert-Eaton myasthenic syndrome in a prospective cohort
Authors: Maddison Paul , Lipka Alexander F. , Gozzard Paul , Sadalage Girija , Ambrose Philip A. , Lang Bethan , Verschuuren Jan J. 
Published: June 2020

AbstractTo evaluate the Dutch-English Lambert-Eaton Myasthenic Syndrome (LEMS) Tumour Association Prediction (DELTA-P) score in a prospective cohort of patients with newly diagnosed LEMS to assess the clinical validity of this tool in a real-world setting. Clinical features from 87 patients with LEMS, occurring within three months from disease onset, were collated to produce a DELTA-P score for each patient. Lung cancer was detected in 44/87 (51%) LEMS patients. Weight loss ≥ 5%, tobacco use at LEMS onset and age at onset ≥ 50 years were independent predictors for the development of small-cell lung cancer (SCLC) in LEMS patients in multivariable analysis. Median DELTA-P scores were significantly higher in SCLC-LEMS patients (3.5, 95% CI 3 to 4) compared to non-tumour-LEMS (2, 95% CI 1 to 2) (P < 0.0001). Higher DELTA-P scores increased the risk of SCLC stepwise (score 0 = 0%, 1 = 18.8%, 2 = 45%, 3 = 55.5%, 4 = 85.7%, 5 = 87.5%, 6 = 100%). The area under the curve of the receiver operating curve was 82.5% (95% CI 73.9% to 91%). The DELTA-P cancer prediction score, calculated at the time of LEMS diagnosis, is an effective tool for cancer screening in an independent, prospective study setting.
Comparative transcriptome analysis of a taxol-producing endophytic fungus, Aspergillus aculeatinus Tax-6, and its mutant strain
Authors: Qiao Weichuan , Tang Tianhao , Ling Fei 
Published: June 2020

AbstractTaxol is a rare but extremely effective antitumor agent extracted from Taxus yew barks. Taxus plants are valuable and rare species, and the production of taxol from them is a complex process. Therefore, taxol-producing endophytic fungi seem to be a promising alternative because of their high practical value and convenient progress. In this study, the transcriptome of an endophytic fungus, Aspergillus aculeatinus Tax-6 was analyzed in order to understand the molecular mechanisms of producing fungal taxol. The results showed that genes involved in the mevalonate (MVA) pathway and non-mevalonate (MEP) pathway were expressed, including isopentenyl pyrophosphate transferase, geranyl pyrophosphate transferase, and geranylgeranyl pyrophosphate synthetase. However, those downstream genes involved in the conversion of taxa-4(5)-11(12)-diene from geranylgeranyl pyrophosphate were not expressed except for taxane 10-beta-hydroxylase. Additionally, a mutant strain, A. aculeatinus BT-2 was obtained from the original strain, A. aculeatinus Tax-6, using fungicidin as the mutagenic agent. The taxol yield of BT-2 was 560 µg L−1, which was higher than that of Tax-6. To identify the mechanism of the difference in taxol production, we compared the transcriptomes of the two fungi and explored the changes in the gene expression between them. When compared with the original strain, Tax-6, most genes related to the MVA pathway in the mutant strain BT-2 showed upregulation, including GGPPS. Moreover, most of the downstream genes were not expressed in the mutant fungi as well. Overall, the results revealed the pathway and mechanism of taxol synthesis in endophytic fungi and the potential for the construction of taxol-producing genetic engineering strains.
Integration of fish culture and poultry rearing in transplanted rice for nutritional security in smallholder farms
Authors: Ramanathan Kathiresan , Sangeeviraman Vishnudevi , Chandrahasan Prabakar , Chaudhary Badri Narayan , Ramachandra Srikrishna Sulgodu 
Published: June 2020

AbstractAgriculture provides livelihood for 65% of Nepal’s population contributing for 27% of its GDP. Smallholder farms constitute 60% of farming segment. Distress farming, with inadequate minimum support price, subsidies and inadequate revenue generation force 29% of the general population to be malnourished. Farming system designs with integration of animal components would augment animal protein intake of these resource-poor populations, livelihood enhancement and sustainability of production system. On-farm field experiments in 75 participating farmers fields of Nepal with integration of fish culture and poultry rearing in transplanted rice showed appreciable (a significant) increase in nutritional status and livelihoods of participating farmers.
Low-level image statistics in natural scenes influence perceptual decision-making
Authors: Seijdel Noor , Jahfari Sara , Groen Iris I. A. , Scholte H. Steven 
Published: June 2020

AbstractA fundamental component of interacting with our environment is gathering and interpretation of sensory information. When investigating how perceptual information influences decision-making, most researchers have relied on manipulated or unnatural information as perceptual input, resulting in findings that may not generalize to real-world scenes. Unlike simplified, artificial stimuli, real-world scenes contain low-level regularities that are informative about the structural complexity, which the brain could exploit. In this study, participants performed an animal detection task on low, medium or high complexity scenes as determined by two biologically plausible natural scene statistics, contrast energy (CE) or spatial coherence (SC). In experiment 1, stimuli were sampled such that CE and SC both influenced scene complexity. Diffusion modelling showed that the speed of information processing was affected by low-level scene complexity. Experiment 2a/b refined these observations by showing how isolated manipulation of SC resulted in weaker but comparable effects, with an additional change in response boundary, whereas manipulation of only CE had no effect. Overall, performance was best for scenes with intermediate complexity. Our systematic definition quantifies how natural scene complexity interacts with decision-making. We speculate that CE and SC serve as an indication to adjust perceptual decision-making based on the complexity of the input.
Non-invasive red-light optogenetic control of Drosophila cardiac function
Authors: Men Jing , Li Airong , Jerwick Jason , Li Zilong , Tanzi Rudolph E. , Zhou Chao 
Published: June 2020

AbstractDrosophila is a powerful genetic model system for cardiovascular studies. Recently, optogenetic pacing tools have been developed to control Drosophila heart rhythm noninvasively with blue light, which has a limited penetration depth. Here we developed both a red-light sensitive opsin expressing Drosophila system and an integrated red-light stimulation and optical coherence microscopy (OCM) imaging system. We demonstrated noninvasive control of Drosophila cardiac rhythms using a single light source, including simulated tachycardia in ReaChR-expressing flies and bradycardia and cardiac arrest in halorhodopsin (NpHR)-expressing flies at multiple developmental stages. By using red excitation light, we were able to pace flies at higher efficiency and with lower power than with equivalent blue light excitation systems. The recovery dynamics after red-light stimulation of NpHR flies were observed and quantified. The combination of red-light stimulation, OCM imaging, and transgenic Drosophila systems provides a promising and easily manipulated research platform for noninvasive cardiac optogenetic studies.
Fast- and slow-light-enhanced light drag in a moving microcavity
Authors: Qin Tian , Yang Jianfan , Zhang Fangxing , Chen Yao , Shen Dongyi , Liu Wei , Chen Lei , Jiang Xiaoshun , Chen Xianfeng , Wan Wenjie 
Published: June 2020

AbstractFizeau’s experiment, inspiring Einstein’s special theory of relativity, reveals a small dragging effect acting on light inside a moving medium. Dispersion can enhance such light drag according to Lorentz’s predication. Here fast- and slow-light-enhanced light drag is demonstrated experimentally in a moving optical microcavity through stimulated Brillouin scattering induced transparency and absorption. The strong dispersion provides an enhancement factor up to ~104, greatly reducing the system size down to the micrometer range. These results may offer a unique platform for a compact, integrated solution to motion sensing and ultrafast signal processing applications.