bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post-genomic progress in helminth parasitology
Authors: McVeigh Paul 
Published: April 2020

AbstractHelminth parasitology is an important discipline, which poses often unique technical challenges. One challenge is that helminth parasites, particularly those in humans, are often difficult to obtain alive and in sufficient quantities for study; another is the challenge of studying these organisms in vitro – no helminth parasite life cycle has been fully recapitulated outside of a host. Arguably, the key issue retarding progress in helminth parasitology has been a lack of experimental tools and resources, certainly relative to the riches that have driven many parasitologists to adopt free-living model organisms as surrogate systems. In response to these needs, the past 10–12 years have seen the beginnings of helminth parasitology's journey into the ‘omics’ era, with the release of abundant sequencing resources, and the functional genomics tools with which to test biological hypotheses. To reflect this progress, the 2019 Autumn Symposium of the British Society for Parasitology was held in Queen's University Belfast on the topic of ‘post-genomic progress in helminth parasitology’. This issue presents examples of the current state of play in the field, while this editorial summarizes how genomic datasets and functional genomic tools have stimulated impressive recent progress in our understanding of parasite biology.
Open Petri nets
Authors: Baez John C. , Master Jade 
Published: April 2020

AbstractThe reachability semantics for Petri nets can be studied using open Petri nets. For us, an “open” Petri net is one with certain places designated as inputs and outputs via a cospan of sets. We can compose open Petri nets by gluing the outputs of one to the inputs of another. Open Petri nets can be treated as morphisms of a category Open(Petri), which becomes symmetric monoidal under disjoint union. However, since the composite of open Petri nets is defined only up to isomorphism, it is better to treat them as morphisms of a symmetric monoidal double category
${\mathbb O}$
pen(Petri). We describe two forms of semantics for open Petri nets using symmetric monoidal double functors out of
${\mathbb O}$
pen(Petri). The first, an operational semantics, gives for each open Petri net a category whose morphisms are the processes that this net can carry out. This is done in a compositional way, so that these categories can be computed on smaller subnets and then glued together. The second, a reachability semantics, simply says which markings of the outputs can be reached from a given marking of the inputs.
An Event Study of Simultaneous Earthward and Tailward Reconnection Exhaust Flows in the Earth's Midtail
Authors: Wang Chih‐Ping , Liu Yi‐Hsin , Xing Xiaoyan , Runov Andrei , Artemyev Anton , Zhang Xiaojia 
Published: April 2020

AbstractWe report an event of two‐satellite measurements of simultaneous earthward and tailward fast flows of ~500 km/s in the midtail at X ~ −63 RE and evaluate magnetic reconnection as a responsible mechanism by comparing the observations with a particle‐in‐cell (PIC) simulation. The two satellites were near midnight separated mainly along the X direction by ~5 RE. As they moved across the current sheet from the northern to southern lobes, the one closer to the Earth crossed the x line with fast flows changing from tailward to earthward, while the other one simultaneously observed tailward flows. The observed plasma and fields showed several key reconnection signatures, including the Walén relation, the fast reconnection rate of ~0.1, the Hall magnetic and electric fields, and counterstreaming electrons in the separatrix, indicating the fast flow was the reconnection exhaust. The observed temporal variations of flow speeds and magnetic fields suggested that the x line was moving tailward to a location between the two satellites and the exhaust was moving up and down. Within the exhaust, plasma pressure was highly anisotropic, and the current sheet can be unstable to the mirror, ion cyclotron, and firehose instabilities. Current sheet flapping and enhanced compressional waves near proton's local gyro frequencies were observed around the current sheet. Comparing with the PIC simulation suggests that the waves were mainly a result of oblique firehose instability.
The Changing Relationship Between Rainfall and Surface Runoff on the Loess Plateau, China
Authors: Miao Chiyuan , Zheng Haiyan , Jiao Juying , Feng Xiaoming , Duan Qingyun , Mpofu Ephraim 
Published: April 2020

AbstractLack of hydrological data of high spatiotemporal resolution has been a major challenge for understanding the rainfall‐runoff relationship on the Loess Plateau of China. In this study, we examined this relationship across 82 watersheds on the plateau for two time periods: P1 (1971–1987) and P2 (2008–2016). We found linear relationships between the annual rainfall series and annual surface runoff series in P1 that were stronger in the southeast and that declined toward the northwest, but this spatial pattern was slightly disrupted during P2. The mean annual runoff coefficient ranged from 0.056 to 0.126 for the 25th and 75th percentiles, respectively, during the P1 period, but the corresponding values were smaller in P2 (0.035 and 0.088, respectively). In total, the runoff coefficient decreased for 87% of the watersheds, with an average reduction of 0.033. For most watersheds of the plateau, we found a stable threshold value for the monthly runoff coefficient when monthly rainfall reached a certain value (i.e., a critical point). Between P1 and P2, the threshold value of the runoff coefficient decreased for 57 watersheds as a result of soil conservation measures. The rainfall critical point represents the minimum monthly rainfall to maintain the stable relationship between monthly infiltration and monthly rainfall in the process of runoff production. This value became greater on the middle regions of the plateau during P2 (increasing by 28% on average). Check dams, vegetation, and land use all have profoundly influenced the relationship between rainfall and surface runoff in this region.
Solid Ammonium Nitrate Aerosols as Efficient Ice Nucleating Particles at Cirrus Temperatures
Authors: Wagner Robert , Bertozzi Barbara , Höpfner Michael , Höhler Kristina , Möhler Ottmar , Saathoff Harald , Leisner Thomas 
Published: April 2020

AbstractRecent satellite observations and high‐altitude aircraft measurements have demonstrated the presence of solid ammonium nitrate particles in the Asian monsoon upper troposphere. Most likely, these particles are formed by a heterogeneous crystallization mechanism, given that efflorescence is strongly inhibited for pure ammonium nitrate solution droplets. Crystallization can be induced by the presence of ammonium sulfate, which more easily crystallizes and serves as a heterogeneous nucleus for the crystallization of ammonium nitrate. In the present study, we have investigated this crystallization pathway for different amounts of ammonium sulfate admixed to ammonium nitrate solution droplets and measured the heterogeneous ice nucleation ability of the crystallized particles at cirrus temperatures in a cloud chamber and with a continuous flow diffusion chamber. We found that an admixture of only 0.6 mol% of ammonium sulfate was sufficient to induce the crystallization of ammonium nitrate at 223 K and 22% RHw. These almost pure, crystalline ammonium nitrate particles showed the same temperature‐dependent ice nucleation behavior as observed for other inorganic salts like ammonium sulfate and sodium chloride. At temperatures above 230 K, the crystalline ammonium nitrate particles first deliquesced and nucleated ice homogeneously at ice saturation ratios between about 1.45 and 1.50. Below 230 K, heterogeneous ice nucleation was observed to start at an ice saturation ratio as low as 1.13. The deduced ice nucleation active surface site densities were in the range from 1010–1011 m−2 at ice saturation ratios between 1.2 and 1.4, thus similar in magnitude to those of desert dust particles.
Understanding the Impact of Observation Data Uncertainty on Probabilistic Streamflow Forecasts Using a Dynamic Hierarchical Model
Authors: Das Bhowmik Rajarshi , Ng Tze Ling , Wang Jui‐Pin 
Published: April 2020

AbstractEarlier researches have proposed algorithms to quantify the measurement uncertainty in rating curves and found that the magnitude of the uncertainty can be significant enough to impact hydrologic modeling. Therefore, they suggested frameworks to include measurement uncertainty in the rating curve to make it robust. Despite their efforts, a robust rating curve is often ignored in traditional practices, considering the investment of time and money as well as the resulting benefit from it. In the current research, we are interested in understanding the role of the measurement error variance in real‐time streamflow forecasting. Our objectives are (i) to employ a state‐of‐the‐art statistical forecasting model that can handle measurement uncertainty in daily streamflow and (ii) to understand the trade‐off in forecasting performance when substantial knowledge regarding the measurement uncertainty is provided to the modeler. We apply the Bayesian dynamic hierarchical model (BDHM) on four gauging sites in the United States. Results show that the BDHM performs better than the daily climatology and local linear regression model. Also, the forecast variance changes proportionally with the change in the error variance as an input in the observation equation. Following this, we design a simulation‐based study, which assigns the measurement error in the reported streamflow to obtain multiple realizations of the true streamflow. The inclusion of substantial knowledge about the true error improves the BDHM's performance by lowering the CRPS (continuous rank probability score) values. However, the inclusion increases the forecast variance to bring the true streamflow within the sampling variability of the forecasted streamflow. Overall, an improved trade‐off between the success rate of forecasts and the forecast variance can be achieved by including the measurement error in the BDHM for rivers that witness less dispersed streamflow data.
Simplified Green‐Ampt Model, Imbibition‐Based Estimates of Permeability, and Implications for Leak‐off in Hydraulic Fracturing
Authors: Tokunaga Tetsu K. 
Published: April 2020

AbstractPredicting water imbibition into porous materials is important in a wide variety of fields, and hydraulic fracturing of low permeability hydrocarbon reservoirs has emerged as an application that is imposing a large water footprint. Reliable predictions of imbibition are needed to better manage water use, yet are challenging because of uncertainties in both the permeability and capillary pressure driving force. Here, this uncertainty is reduced through evaluating correlations between the permeability and the effective capillary pressure associated with the wetting front, Pc,f. These correlations allow elimination of Pc,f from the Green and Ampt equation and concentrate all uncertainties in fluxes on the effective permeability k. Over a wide range of k and porosities n, imbibition scales approximately with k1/3. Although Leverett k1/4 scaling for predicting Pc,f is shown to be inferior when tested with data spanning a wide range of n, it nevertheless predicted imbibition fairly well. From simple imbibition measurements, both the empirical and Leverett scaling approaches allow estimates of k that have root‐mean‐square deviations of about one order of magnitude relative to measurements that ranged over 10 orders of magnitude in k.
Astrocytes with TDP-43 inclusions exhibit reduced noradrenergic cAMP and Ca2+ signaling and dysregulated cell metabolism
Authors: Velebit Jelena , Horvat Anemari , Smolič Tina , Prpar Mihevc Sonja , Rogelj Boris , Zorec Robert , Vardjan Nina 
Published: April 2020

AbstractMost cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) have cytoplasmic inclusions of TAR DNA-binding protein 43 (TDP-43) in neurons and non-neuronal cells, including astrocytes, which metabolically support neurons with nutrients. Neuronal metabolism largely depends on the activation of the noradrenergic system releasing noradrenaline. Activation of astroglial adrenergic receptors with noradrenaline triggers cAMP and Ca2+ signaling and augments aerobic glycolysis with production of lactate, an important neuronal energy fuel. Astrocytes with cytoplasmic TDP-43 inclusions can cause motor neuron death, however, whether astroglial metabolism and metabolic support of neurons is altered in astrocytes with TDP-43 inclusions, is unclear. We measured lipid droplet and glucose metabolisms in astrocytes expressing the inclusion-forming C-terminal fragment of TDP-43 or the wild-type TDP-43 using fluorescent dyes or genetically encoded nanosensors. Astrocytes with TDP-43 inclusions exhibited a 3-fold increase in the accumulation of lipid droplets versus astrocytes expressing wild-type TDP-43, indicating altered lipid droplet metabolism. In these cells the noradrenaline-triggered increases in intracellular cAMP and Ca2+ levels were reduced by 35% and 31%, respectively, likely due to the downregulation of β2-adrenergic receptors. Although noradrenaline triggered a similar increase in intracellular lactate levels in astrocytes with and without TDP-43 inclusions, the probability of activating aerobic glycolysis was facilitated by 1.6-fold in astrocytes with TDP-43 inclusions and lactate MCT1 transporters were downregulated. Thus, while in astrocytes with TDP-43 inclusions noradrenergic signaling is reduced, aerobic glycolysis and lipid droplet accumulation are facilitated, suggesting dysregulated astroglial metabolism and metabolic support of neurons in TDP-43-associated ALS and FTD.
Computational analysis of mechanical stress in colonic diverticulosis
Authors: Patel Bhavesh , Guo Xiaomei , Noblet Jillian , Chambers Sean , Gregersen Hans , Kassab Ghassan S. 
Published: April 2020

AbstractDiverticulosis results from the development of pouch-like structures, called diverticula, over the colon. The etiology of the disease is poorly understood resulting in a lack of effective treatment approaches. It is well known that mechanical stress plays a major role in tissue remodeling, yet its role in diverticulosis has not been studied. Here, we used computational mechanics to investigate changes in stress distribution engendered over the colon tissue by the presence of a pouch-like structure. The objectives of the study were twofold: (1) observe how stress distribution changes around a single pouch and (2) evaluate how stress elevation correlates with the size of the pouch. Results showed that high stresses are concentrated around the neck of a pouch, and their values and propagation increase with the size of the pouch neck rather than the pouch surface area. These findings suggest that stress distribution may change in diverticulosis and a vicious cycle may occur where pouch size increases due to stress elevation, which in turn elevates stress further and so on. Significant luminal pressure reduction would be necessary to maintain stress at normal level according to our results and therapeutic approaches aimed directly at reducing stress should rather be sought after.
Complex intron generation in the yeast genus Lipomyces
Authors: Ág Norbert , Kavalecz Napsugár , Pénzes Fruzsina , Karaffa Levente , Scazzocchio Claudio , Flipphi Michel , Fekete Erzsébet 
Published: April 2020

AbstractIn primary transcripts of eukaryotic nuclear genes, coding sequences are often interrupted by U2-type introns. Such intervening sequences can constitute complex introns excised by consecutive splicing reactions. The origin of spliceosomal introns is a vexing problem. Sequence variation existent across fungal taxa provides means to study their structure and evolution. In one class of complex introns called [D] stwintrons, an (internal) U2 intron is nested within the 5'-donor element of another (external) U2 intron. In the gene for a reticulon-like protein in species of the ascomycete yeast genus Lipomyces, the most 5' terminal intron position is occupied by one of three complex intervening sequences consistent of differently nested U2 intron units, as demonstrated in L. lipofer, L. suomiensis, and L. starkeyi. In L. starkeyi, the donor elements of the constituent introns are abutting and the complex intervening sequence can be excised alternatively either with one standard splicing reaction or, as a [D] stwintron, by two consecutive reactions. Our work suggests how [D] stwintrons could emerge by the appearance of new functional splice sites within an extant intron. The stepwise stwintronisation mechanism may involve duplication of the functional intron donor element of the ancestor intron.
AF relay assisted multiuser MIMO‐DQSM downlink transmission system
Authors: Castillo‐Soria F.R. 
Published: April 2020

This Letter presents an amplify and forward (AF) relay assisted multiuser multiple input‐multiple output (MU‐MIMO) downlink transmission system based on a double quadrature spatial modulation (DQSM) scheme. The authors analyse and compared the bit error rate performance of the proposed AF‐MU‐MIMO‐DQSM system with its conventional counterpart AF‐MU‐MIMO system, which uses quadrature amplitude modulation/phase shift‐keying modulation. Results show that the utilised technique can effectively cancel the interference produced by multiple users and multiple relays in the system. The proposed AF‐MU‐MIMO‐DQSM system has up to 2 dB gain compared with the conventional system for the analysed cases.
Antiviral Potential of Spondias mombin L. Leaves Extract Against Herpes Simplex Virus Type-1 Replication Using In Vitro and In Silico Approaches
Authors: Siqueira Emerson M. da S. , Lima Tábata L. C. , Boff Laurita , Lima Sarah G. M. , Lourenço Estela M. G. , Ferreira Éder G. , Barbosa Euzébio G. , Machado Paula R. L. , Farias Kléber J. S. , Ferreira Leandro de S. , Rocha Hugo A. de O. , Simões Cláudia M. O. , Zucolotto Silvana M. 
Published: April 2020

Abstract
Spondias mobin leaves have been traditionally used for treating cold sores. The study investigated the mechanism of antiherpes action of S. mombin extract, fractions, and geraniin. Different concentrations of samples were used to evaluate the in vitro antiherpes activity (anti-HSV-1) in virucidal, post-infection, attachment, and penetration assays. The mechanism of action of geraniin was investigated considering the glycoproteins gB and gD of HSV-1 surface as potential molecular targets. Molecular docking simulations were carried out for both in order to determine the possible binding mode position of geraniin at the activity sites. The binding mode position was posteriorly optimized considering the flexibility of the glycoproteins. The chemical analysis of samples was performed by LC-MS and revealed the presence of 22 substances, which are hydrolysable tannins, O-glycosylated flavonoids, phenolic acids, and a carbohydrate. The extract, tannin-rich fraction and geraniin showed important in vitro virucidal activity through blocking viral attachment but showed no relevant inhibition of viral penetration. The in silico approaches demonstrated a high number of potential strong intermolecular interactions as hydrogen bonds between geraniin and the activity site of the glycoproteins, particularly the glycoprotein gB. In silico experiments indicated that geraniin is at least partially responsible for the anti-herpes activity through interaction with the viral surface glycoprotein gB, which is responsible for viral adsorption. These results highlight the therapeutic potential of S. mombin anti-herpes treatment and provides support for its traditional purposes. However, further studies are required to validate the antiviral activities in vivo, as well as efficacy in humans.
Textural features in FDG-PET/CT can predict outcome in melanoma patients to treatment with Vemurafenib and Ipililumab
Authors: Dittrich Daniela , Pyka Thomas , Scheidhauer Klemens , Lütje Susanne , Essler Markus , Bundschuh Ralph A. 
Published: April 2020

Abstract
Aim Recently, textural parameters assessed in FDG-PET/CT as surrogate marker for tumor heterogeneity have been shown to provide prognostic power. Therefore, we investigated the use of such parameters in FDG-PET/CT examinations before the start of immunotherapy with vemurafenib or ipilimumab in patients with malignant melanoma.
Methods In this retrospective analysis 26 patients with histologically proven advanced melanoma were included. FGD-PET/CT was performed before the start of treatment either with vemurafenib (n = 9) or ipilimumab (n = 17) and tumors were analyzed for textural parameters as well as conventional PET features. Lesions were classified as responding or not responding following PERCIST criteria. ROC analysis was performed to analyze the predictive power and cut-off values. In addition, the change of maximum SUV of the lesions between pretherapeutic PET/CT and another PET/CT performed about 12 weeks after start of treatment was evaluated and correlated with the pretreatment parameters.
Results In both groups, six textural parameters showed statistically significant predictive power as well as the metabolic tumor volume. In the group treated with vemurafenib eight additional textural parameters as well as the maximum and mean SUV and the TLG showed significance. A statistically significant correlation between the change of maximum SUV in the course of treatment and the pretherapeutic parameters was found in both treatment groups for three textural features.
Conclusion In patients with malignant melanoma textural parameters in pretherapeutic FDG-PET/CT examinations seem to have prognostic power for treatment response of immunotherapy with vemurafenib and ipilimumab. This can be an important step towards personalized tumor therapy.
Thrombocytopenia in Pregnancy: Approach to Diagnosis and Management
Authors: Fogerty Annemarie E. 
Published: April 2020

AbstractThe impact of thrombocytopenia varies widely depending on the underlying pathophysiology driving it. The biggest challenge in managing thrombocytopenia in pregnancy is accurately identifying the responsible pathophysiology—a task made difficult given the tremendous overlap in clinical and laboratory abnormalities associated with different thrombocytopenia processes. The most common etiologies of thrombocytopenia in pregnancy range from physiology deemed benign to those that are life-threatening to the mother and fetus. Even in cases in which the responsible etiology is deemed benign, such as gestational thrombocytopenia, there are still implications for the management of labor and delivery, a time where hemostatic challenges may prove life-threatening. In most institutions, a minimum platelet count will be mandated for epidural anesthesia to be deemed a safe option. The causes of thrombocytopenia can also include diagnoses that are pregnancy-specific (such as preeclampsia or gestational thrombocytopenia), potentially triggered by pregnancy (such as thrombotic thrombocytopenic purpura), or unrelated to or predating the pregnancy (such as liver disease, infections, or immune thrombocytopenia purpura). It is imperative that the source of thrombocytopenia is identified accurately and expeditiously, as intervention can range from observation alone to urgent fetal delivery. In this review, the approach to diagnosis and the pathophysiological mechanisms of the most common etiologies of thrombocytopenia in pregnancy and associated management issues are presented.