bluuebunny/crossref_metadata_2025 huggingface dataset:
Burning the Rechtsstaat: legal institutions and protection of the rule of law
Authors: Hartwell Christopher A. , Urban Mateusz
Published: June 2020

The economic literature is clear that transparent and impartial rule of law is crucial for successful economic outcomes. However, how does one guarantee rule of law? This paper uses the idea of ‘self-reinforcing’ institutions to show how political institutions may derail rule of law if associated judicial institutions are not self-reinforcing. We illustrate this using the contrasting examples of Estonia and Poland to frame the importance of institutional context in determining both rule of law and the path of legal institutions. Although startingtabula rasafor a legal system is difficult, it worked well for rule of law in Estonia in the post-communist transition. Alternately, Poland pursued a much more gradualist strategy of reform of formal legal institutions; this approach meant that justice institutions, slow to shed their legacy and connection with the past, were relatively weak and susceptible to attack from more powerful (political) ones. We conclude that legal institutions can protect the rule of law but only if they are in line with political institutions, using their self-reinforcing nature as a shield from political whims of the day.
VOLUNTARY IMAGINATION: A FINE-GRAINED ANALYSIS
Authors: CANAVOTTO ILARIA , BERTO FRANCESCO , GIORDANI ALESSANDRO
Published: June 2020

We study imagination as reality-oriented mental simulation (ROMS): the activity of simulating nonactual scenarios in one’s mind, to investigate what would happen if they were realized. Three connected questions concerning ROMS are: What is the logic, if there is one, of such an activity? How can we gain new knowledge via it? What is voluntary in it and what is not? We address them by building a list of core features of imagination as ROMS, drawing on research in cognitive psychology and the philosophy of mind. We then provide a logic of imagination as ROMS which models such features, combining techniques from epistemic logic, action logic, and subject matter semantics. Our logic comprises a modal propositional language with non-monotonic imagination operators, a formal semantics, and an axiomatization.
Evolution of target and non-target based multiple herbicide resistance in a single Palmer amaranth (Amaranthus palmeri) population from Kansas
Authors: Chaudhari Sushila , Varanasi Vijay K. , Nakka Sridevi , Bhowmik Prasanta C. , Thompson Curtis R. , Peterson Dallas E. , Currie Randall S. , Jugulam Mithila
Published: June 2020

The evolution of resistance to multiple herbicides in Palmer amaranth is a major challenge for its management. In this study, a Palmer amaranth population from Hutchinson, Kansas (HMR), was characterized for resistance to inhibitors of photosystem II (PSII) (e.g., atrazine), acetolactate synthase (ALS) (e.g., chlorsulfuron), and EPSP synthase (EPSPS) (e.g., glyphosate), and this resistance was investigated. About 100 HMR plants were treated with field-recommended doses (1×) of atrazine, chlorsulfuron, and glyphosate, separately along with Hutchinson multiple-herbicide (atrazine, chlorsulfuron, and glyphosate)–susceptible (HMS) Palmer amaranth as control. The mechanism of resistance to these herbicides was investigated by sequencing or amplifying the psbA, ALS, and EPSPS genes, the molecular targets of atrazine, chlorsulfuron, and glyphosate, respectively. Fifty-two percent of plants survived a 1× (2,240 g ai ha−1) atrazine application with no known psbA gene mutation, indicating the predominance of a non–target site resistance mechanism to this herbicide. Forty-two percent of plants survived a 1× (18 g ai ha−1) dose of chlorsulfuron with proline197serine, proline197threonine, proline197alanine, and proline197asparagine, or tryptophan574leucine mutations in the ALS gene. About 40% of the plants survived a 1× (840 g ae ha−1) dose of glyphosate with no known mutations in the EPSPS gene. Quantitative PCR results revealed increased EPSPS copy number (50 to 140) as the mechanism of glyphosate resistance in the survivors. The most important finding of this study was the evolution of resistance to at least two sites of action (SOAs) (~50% of plants) and to all three herbicides due to target site as well as non–target site mechanisms. The high incidence of individual plants with resistance to multiple SOAs poses a challenge for effective management of this weed.
Treatment of bypass failure in patients with chronic limb threatening ischemia – open surgery vs. percutaneous mechanical thrombectomy
Authors: Migliara Bruno , Cappellari Tania Francesca , Mirandola Mattia , Griso Andrea , Kolasa Katarzyna , Zah Vladimir , Nicoletti Cristian , Lino Marcello
Published: June 2020

Summary: Background: Lower limb bypass occlusion in patients with chronic limb threating ischemia remains a challenge. We can choose between different treatment options: open surgery, local thrombolysis, thrombectomy/atherectomy devices. In this pilot study, we compare clinical outcomes and treatment costs between open surgery (OS) and percutaneous mechanical thrombectomy (pMTH). Patients and methods: This pilot study represents a retrospective analysis of hospital data of 48 occluded bypasses admitted from 2013 to 2018. Only patients presenting with severe ischemia and recrudescence of symptoms (Rutherford 4–6) were included in the current analysis. Two cohorts of patients were analysed: patients who underwent OS and patients that underwent pMTH. Primary clinical outcomes were one-year cumulative patency and limb salvage rates. Total cost was calculated as a sum of intra- and post-operative costs. To weigh clinical benefits against the economic consequences of OS versus pMTH a cost-effectiveness framework was adopted. Results: We analysed a series of 48 occluded bypasses 17 treated with open surgery and 31 with pMTH. Procedural success was 100% in both groups. When comparing one-year death rates ( p-value = .22) and re-occlusion rates ( p-value = .43), no statistically significant differences were observed between the two cohorts. Mean patency duration in the surgery cohort was significantly shorter ( p-value < .05). Primary patency (OS 41.2% vs. pMTH 48.4%) and limb salvage rate (OS 88.2% vs. pMTH 90.3%) at one year are similar in both groups. The total cost of surgery was substantially higher (OS 10,159€ vs. pMTH 8,401€) Conclusions: This pilot study, although limited to 48 occluded bypasses, demonstrates that endovascular treatment with pMTH is less invasive, less time consuming and less expensive, and produces greater health benefits than traditional OS.
Why and How to Deal With Diurnal Cyclic Patterns in Ambulatory Assessment of Emotions
Authors: van de Maat Robin , Lataster Johan , Verboon Peter
Published: June 2020

Abstract. The use of ambulatory assessment (AA) based methods in emotion research has steadily increased over the past decades. Although having a number of benefits over other methods, the use and analysis of AA data may pose specific challenges. Among these, the issue of dealing with diurnal cycles in emotion data has received relative scant attention. This article therefore discusses why cyclic models may be considered for analyzing AA data on emotions, and describes how this approach can be applied to an empirical AA dataset. Results suggest that cyclic modeling may be a useful method for describing and accounting for (diurnal) cyclic patterns in AA data, but should be used with a number of considerations in mind.
Unprecedented Drought Challenges for Texas Water Resources in a Changing Climate: What Do Researchers and Stakeholders Need to Know?
Authors: Nielsen‐Gammon John W. , Banner Jay L. , Cook Benjamin I. , Tremaine Darrel M. , Wong Corinne I. , Mace Robert E. , Gao Huilin , Yang Zong‐Liang , Gonzalez Marisa Flores , Hoffpauir Richard , Gooch Tom , Kloesel Kevin
Published: June 2020

Long‐range water planning is complicated by factors that are rapidly changing in the 21st century, including climate, population, and water use. Here, we analyze climate factors and drought projections for Texas as an example of a diverse society straddling an aridity gradient to examine how the projections can best serve water stakeholder needs. We find that climate models are robust in projecting drying of summer‐season soil moisture and decreasing reservoir supplies for both the eastern and western portions of Texas during the 21st century. Further, projections indicate drier conditions during the latter half of the 21st century than even the most arid centuries of the last 1,000 years that included megadroughts. To illustrate how accounting for drought nonstationarity may increase water resiliency, we consider generalized case studies involving four key stakeholder groups: agricultural producers, large surface water suppliers, small groundwater management districts, and regional water planning districts. We also examine an example of customized climate information being used as input to long‐range water planning. We find that while stakeholders value the quantitative capability of climate model outputs, more specific climate‐related information better supports resilience planning across multiple stakeholder groups. New suites of tools could provide necessary capacity for both short‐ and long‐term, stakeholder‐specific adaptive planning.
NAC2H: The North American Climate Change and Hydroclimatology Data Set
Authors: Arsenault Richard , Brissette François , Chen Jie , Guo Qiang , Dallaire Gabrielle
Published: June 2020

A data set containing hydrometeorological and hydroclimatological data for 3,540 watersheds in North America is described. The data set contains four main parts: (a) observed hydrometeorological data including daily streamflow observations, precipitation, minimum temperature, and maximum temperature; (b) 20 bias‐corrected climate model projections for two Representative Concentration Pathway (RCP) scenarios and five bias correction methods; (c) hydrological model calibration parameters and simulated streamflow for 4 hydrological models, 2 objective functions, and 10 calibration parameter sets for the reference period; and (d) hydrological simulations for each of the combinations of the abovementioned elements of the climate change impact study chain, for a total of 16,000 combinations. The data set also contains simulations and bias‐corrected climate for 30‐year horizons corresponding to 1.5°C and 2°C temperature increases for a subset of the climate models, for an additional 8,000 combinations. All simulations in the reference period are also provided. Fifty‐one precomputed hydrological indices are made available for each simulation. Overall, 2.89 × 1012 years of simulations are classified, analyzed, compressed, and made available for all researchers. This data set can be used to evaluate the uncertainty of various components in the impact study chain, to establish relationships between catchment properties and hydrological response to climate change, and to evaluate the spatial distribution of hydrological change according to a multitude of hydrological indices.
Assessing the Steady‐State Assumption in Water Balance Calculation Across Global Catchments
Authors: Han Juntai , Yang Yuting , Roderick Michael L. , McVicar Tim R. , Yang Dawen , Zhang Shulei , Beck Hylke E.
Published: June 2020

It has long been assumed that over a sufficiently long period of time, changes in catchment water storage (ΔS) are a relatively minor term compared to other fluxes and can be neglected in the catchment water balance equation. However, the validity of this fundamental assumption has rarely been tested, and the associated uncertainties in water balance calculations remain unknown. Here, we use long‐term (1982–2011) observations of monthly streamflow (Q) and precipitation (P) for 1,057 global unimpaired catchments, combined with four independent evapotranspiration (E) estimates to infer ΔS and to provide a global assessment of the steady‐state assumption in catchment water balance calculations. Results show that when the threshold for steady state is set to 5% of the mean monthly P, ~70% of the catchments attain steady state within 10 years while ~6% of the catchments fail to reach a steady state even after 30 years. The time needed for a catchment to reach steady state (τs) shows a close relationship with climatic aridity and vegetation coverage, with arid/semiarid and sparsely vegetated catchments generally having a longer τs. Additionally, increasing snowfall fraction also increases τs. The imbalance (ewb) caused by ignoring ΔS decreases as averaging period for water balance calculations increases as expected. For a typical 10‐year averaging period, ewb accounts for ~7% of P in arid, but that decreases to ~3% of P in humid catchments. These results suggest that catchment properties should be considered when applying the steady‐state assumption and call for caution when ignoring ΔS in arid/semiarid regions.
A rasterized building footprint dataset for the United States
Authors: Heris Mehdi P. , Foks Nathan Leon , Bagstad Kenneth J. , Troy Austin , Ancona Zachary H.
Published: June 2020

Microsoft released a U.S.-wide vector building dataset in 2018. Although the vector building layers provide relatively accurate geometries, their use in large-extent geospatial analysis comes at a high computational cost. We used High-Performance Computing (HPC) to develop an algorithm that calculates six summary values for each cell in a raster representation of each U.S. state, excluding Alaska and Hawaii: (1) total footprint coverage, (2) number of unique buildings intersecting each cell, (3) number of building centroids falling inside each cell, and area of the (4) average, (5) smallest, and (6) largest area of buildings that intersect each cell. These values are represented as raster layers with 30 m cell size covering the 48 conterminous states. We also identify errors in the original building dataset. We evaluate precision and recall in the data for three large U.S. urban areas. Precision is high and comparable to results reported by Microsoft while recall is high for buildings with footprints larger than 200 m2 but lower for progressively smaller buildings.
Functional kleptoplasts intermediate incorporation of carbon and nitrogen in cells of the Sacoglossa sea slug Elysia viridis
Authors: Cruz Sónia , LeKieffre Charlotte , Cartaxana Paulo , Hubas Cédric , Thiney Najet , Jakobsen Sofie , Escrig Stéphane , Jesus Bruno , Kühl Michael , Calado Ricardo , Meibom Anders
Published: June 2020

Some sacoglossan sea slugs incorporate intracellular functional algal chloroplasts, a process termed kleptoplasty. “Stolen” chloroplasts (kleptoplasts) can remain photosynthetically active up to several months, contributing to animal nutrition. Whether this contribution occurs by means of translocation of photosynthesis-derived metabolites from functional kleptoplasts to the animal host or by simple digestion of such organelles remains controversial. Imaging of 13C and 15N assimilation over a 12-h incubation period of Elysia viridis sea slugs showed a light-dependent incorporation of carbon and nitrogen, observed first in digestive tubules and followed by a rapid accumulation into chloroplast-free organs. Furthermore, this work revealed the presence of 13C-labeled long-chain fatty acids (FA) typical of marine invertebrates, such as arachidonic (20:4n-6) and adrenic (22:4n-6) acids. The time frame and level of 13C- and 15N-labeling in chloroplast-free organs indicate that photosynthesis-derived primary metabolites were made available to the host through functional kleptoplasts. The presence of specific 13C-labeled long-chain FA, absent from E. viridis algal food, indicates animal based-elongation using kleptoplast-derived FA precursors. Finally, carbon and nitrogen were incorporated in organs and tissues involved in reproductive functions (albumin gland and gonadal follicles), implying a putative role of kleptoplast photosynthesis in the reproductive fitness of the animal host.
Tregitopes regulate the tolerogenic immune response and decrease the foetal death rate in abortion-prone mouse matings
Authors: Kedzierska Anna Ewa , Lorek Daria , Slawek Anna , Chelmonska-Soyta Anna
Published: June 2020

The imbalance in immune tolerance may cause the variety of reproductive failures. An intravenous immunoglobulin infusion (IVIg) therapy is used to improve the live birth rate in women suffering from recurrent pregnancy loss, recurrent spontaneous abortions and recurrent implantation failures. However, the results of IVIg studies are still inconclusive as IVIg infusion in women suffering from pregnancy loss is sometimes ineffective. One of the mechanisms of action of this treatment is inhibition of B cells differentiation and expansion of Tregs and secretion of interleukin 10. It was proposed that immunomodulatory effects of IVIg may be attributed to tregitopes - self-IgG-derived epitopes present in the structure of immunoglobulins. Similarly to IVIg, tregitopes cause the expansion of Tregs and secretion of antigen-specific effector cytokine response. Here, we studied whether the administration of mouse tregitope 167 and/or 289 can prevent abortions in mouse abortion-prone mouse matings. We revealed that tregitopes reduce the foetal death rate. This may be driven by observed higher pool of peripheral Tregs, increased production of IL-10 by Tregs and Bregs and/or maintaining the tolerogenic phenotype of antigen-presenting cells. We believe that our findings may indicate a potential alternative to IVIg for therapeutic intervention in case of pregnancy failures.
Age and Sex Influences Gamma-aminobutyric Acid Concentrations in the Developing Brain of Very Premature Infants
Authors: Basu Sudeepta K. , Pradhan Subechhya , Jacobs Marni B. , Said Mariam , Kapse Kushal , Murnick Jonathan , Whitehead Matthew T. , Chang Taeun , du Plessis Adre J. , Limperopoulos Catherine
Published: June 2020

Gamma-aminobutyric acid (GABA) and glutamate are principal neurotransmitters essential for late gestational brain development and may play an important role in prematurity-related brain injury. In vivo investigation of GABA in the preterm infant with standard proton magnetic resonance spectroscopy (1H-MRS) has been limited due to its low concentrations in the developing brain, and overlap in the spectrum by other dominant metabolites. We describe early postnatal profiles of in vivo GABA and glutamate concentrations in the developing preterm brain measured by using the J-difference editing technique, Mescher-Garwood point resolved spectroscopy. We prospectively enrolled very preterm infants born ≤32 weeks gestational age and non-sedated 1H-MRS (echo time 68 ms, relaxation time 2000 ms, 256 signal averages) was acquired on a 3 Tesla magnetic resonance imaging scanner from a right frontal lobe voxel. Concentrations of GABA + (with macromolecules) was measured from the J-difference spectra; whereas glutamate and composite glutamate + glutamine (Glx) were measured from the unedited (OFF) spectra and reported in institutional units. We acquired 42 reliable spectra from 38 preterm infants without structural brain injury [median gestational age at birth of 28.0 (IQR 26.0, 28.9) weeks; 19 males (50%)] at a median postmenstrual age of 38.4 (range 33.4 to 46.4) weeks. With advancing post-menstrual age, the concentrations of glutamate OFF increased significantly, adjusted for co-variates (generalized estimating equation β = 0.22, p = 0.02). Advancing postnatal weeks of life at the time of imaging positively correlated with GABA + (β = 0.06, p = 0.02), glutamate OFF (β = 0.11, p = 0.02) and Glx OFF (β = 0.12, p = 0.04). Male infants had higher GABA + (1.66 ± 0.07 vs. 1.33 ± 0.11, p = 0.01) concentrations compared with female infants. For the first time, we report the early ex-utero developmental profile of in vivo GABA and glutamate stratified by age and sex in the developing brain of very preterm infants. This data may provide novel insights into the pathophysiology of neurodevelopmental disabilities reported in preterm infants even in the absence of structural brain injury.
Antioxidants help favorably regulate the kinetics of lipid peroxidation, polyunsaturated fatty acids degradation and acidic cannabinoids decarboxylation in hempseed oil
Authors: Pratap Singh Anubhav , Fathordoobady Farahnaz , Guo Yigong , Singh Anika , Kitts David D.
Published: June 2020

The seed of the hemp plant (Cannabis sativa L.) has been revered as a nutritional resource in Old World Cultures. This has been confirmed by contemporary science wherein hempseed oil (HSO) was found to exhibit a desirable ratio of omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) considered optimal for human nutrition. HSO also contains gamma-linoleic acid (GLA) and non-psychoactive cannabinoids, which further contribute to its’ potential bioactive properties. Herein, we present the kinetics of the thermal stability of these nutraceutical compounds in HSO, in the presence of various antioxidants (e.g. butylated hydroxytoluene, alpha-tocopherol, and ascorbyl palmitate). We focussed on oxidative changes in fatty acid profile and acidic cannabinoid stability when HSO was heated at different temperatures (25 °C to 85 °C) for upto 24 h. The fatty acid composition was evaluated using both GC/MS and 1H-NMR, and the cannabinoids profile of HSO was obtained using both HPLC-UV and HPLC/MS methods. The predicted half-life (DT50) for omega-6 and omega-3 PUFAs in HSO at 25 °C was about 3 and 5 days, respectively; while that at 85 °C was about 7 and 5 hours respectively, with respective activation energies (Ea) being 54.78 ± 2.36 and 45.02 ± 2.87 kJ/mol. Analysis of the conjugated diene hydroperoxides (CDH) and p-Anisidine value (p-AV) revealed that the addition of antioxidants significantly (p < 0.05) limited lipid peroxidation of HSO in samples incubated at 25–85 °C for 24 h. Antioxidants reduced the degradation constant (k) of PUFAs in HSO by upto 79%. This corresponded to a significant (p < 0.05) increase in color stability and pigment retention (chlorophyll a, chlorophyll b and carotenoids) of heated HSO. Regarding the decarboxylation kinetics of cannabidiolic acid (CBDA) in HSO, at both 70 °C and 85 °C, CBDA decarboxylation led to predominantly cannabidiol (CBD) production. The half-life of CBDA decarboxylation (originally 4 days) could be increased to about 17 days using tocopherol as an antioxidant. We propose that determining acidic cannabinoids decarboxylation kinetics is a useful marker to measure the shelf-life of HSO. The results from the study will be useful for researchers looking into the thermal treatment of hempseed oil as a functional food product, and those interested in the decarboxylation kinetics of the acidic cannabinoids.
Cavityless self-organization of ultracold atoms due to the feedback-induced phase transition
Authors: Ivanov Denis A. , Ivanova Tatiana Yu. , Caballero-Benitez Santiago F. , Mekhov Igor B.
Published: June 2020

Feedback is a general idea of modifying system behavior depending on the measurement outcomes. It spreads from natural sciences, engineering, and artificial intelligence to contemporary classical and rock music. Recently, feedback has been suggested as a tool to induce phase transitions beyond the dissipative ones and tune their universality class. Here, we propose and theoretically investigate a system possessing such a feedback-induced phase transition. The system contains a Bose-Einstein condensate placed in an optical potential with the depth that is feedback-controlled according to the intensity of the Bragg-reflected probe light. We show that there is a critical value of the feedback gain where the uniform gas distribution loses its stability and the ordered periodic density distribution emerges. Due to the external feedback, the presence of a cavity is not necessary for this type of atomic self-organization. We analyze the dynamics after a sudden change of the feedback control parameter. The feedback time constant is shown to determine the relaxation above the critical point. We show as well that the control algorithm with the derivative of the measured signal dramatically decreases the transient time.
Fourier analysis of circumpapillary retinal nerve fiber layer thickness in optical coherence tomography for differentiating myopia and glaucoma
Authors: Hsieh Ming-Hung , Chang Yu-Fan , Liu Catherine Jui-Ling , Ko Yu-Chieh
Published: June 2020

Differentiating glaucoma from myopic eye is a challenge to ophthalmologists. We try to develop a new discrete Fourier transform (DFT) model for analyzing optical coherence tomography data for the circumpapillary retinal nerve fiber layer (cpRNFL), and investigate DFT as a new diagnostic tool for glaucomatous myopic eyes. The thicknesses of 12 equidistant cpRNFL points were transformed into 6 signals in the frequency domain, ranging from 1 to 6 Hz. In all 232 eyes, generalized linear model showed that 1 Hz, 2 Hz, and 4 Hz were associated with glaucoma, high myopia, and the interaction between glaucoma and high myopia. The 3 Hz signal was associated with glaucoma and high myopia exclusively. A receiver operating characteristic curve analysis of the 3 Hz signals showed areas under the curves of 0.93 (95% CI 0.90–0.96) and 0.93 (95% CI 0.88–0.98), for diagnosing glaucoma in all subjects and in the highly myopic group, respectively. The DFT model is useful to differentiate glaucoma from non-glaucomatous change and showed potential as a diagnostic tool for glaucomatous myopic eyes.
Cerebral autoregulation and response to intravenous thrombolysis for acute ischemic stroke
Authors: Nogueira Ricardo C. , Lam Man Y. , Llwyd Osian , Salinet Angela S. M. , Bor-Seng-Shu Edson , Panerai Ronney B. , Robinson Thompson G.
Published: June 2020

We hypothesized that knowledge of cerebral autoregulation (CA) status during recanalization therapies could guide further studies aimed at neuroprotection targeting penumbral tissue, especially in patients that do not respond to therapy. Thus, we assessed CA status of patients with acute ischemic stroke (AIS) during intravenous r-tPA therapy and associated CA with response to therapy. AIS patients eligible for intravenous r-tPA therapy were recruited. Cerebral blood flow velocities (transcranial Doppler) from middle cerebral artery and blood pressure (Finometer) were recorded to calculate the autoregulation index (ARI, as surrogate for CA). National Institute of Health Stroke Score was assessed and used to define responders to therapy (improvement of ≥ 4 points on NIHSS measured 24–48 h after therapy). CA was considered impaired if ARI < 4. In 38 patients studied, compared to responders, non-responders had significantly lower ARI values (affected hemisphere: 5.0 vs. 3.6; unaffected hemisphere: 5.4 vs. 4.4, p = 0.03) and more likely to have impaired CA (32% vs. 62%, p = 0.02) during thrombolysis. In conclusion, CA during thrombolysis was impaired in patients who did not respond to therapy. This variable should be investigated as a predictor of the response to therapy and to subsequent neurological outcome.
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

The 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

Tegumentary 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

The 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

eDNA 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

CLN3 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

Caterpillars 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

Hydrogenases 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

The 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

When 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

To 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

Taxol 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

Agriculture 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

A 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.