bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast Poisson solvers for spectral methods
Authors: Fortunato Daniel , Townsend Alex 
Published: July 2019

Abstract
Poisson’s equation is the canonical elliptic partial differential equation. While there exist fast Poisson solvers for finite difference (FD) and finite element methods, fast Poisson solvers for spectral methods have remained elusive. Here we derive spectral methods for solving Poisson’s equation on a square, cylinder, solid sphere and cube that have optimal complexity (up to polylogarithmic terms) in terms of the degrees of freedom used to represent the solution. Whereas FFT-based fast Poisson solvers exploit structured eigenvectors of FD matrices, our solver exploits a separated spectra property that holds for our carefully designed spectral discretizations. Without parallelization we can solve Poisson’s equation on a square with 100 million degrees of freedom in under 2 min on a standard laptop.
Candidalysin Is Required for Neutrophil Recruitment and Virulence During Systemic Candida albicans Infection
Authors: Swidergall Marc , Khalaji Mina , Solis Norma V , Moyes David L , Drummond Rebecca A , Hube Bernhard , Lionakis Michail S , Murdoch Craig , Filler Scott G , Naglik Julian R 
Published: July 2019

AbstractBackgroundCandidalysin is a cytolytic peptide toxin secreted by Candida albicans hyphae and has significantly advanced our understanding of fungal pathogenesis. Candidalysin is critical for mucosal C albicans infections and is known to activate epithelial cells to induce downstream innate immune responses that are associated with protection or immunopathology during oral or vaginal infections. Furthermore, candidalysin activates the NLRP3 inflammasome and causes cytolysis in mononuclear phagocytes. However, the role of candidalysin in driving systemic infections is unknown.MethodsIn this study, using candidalysin-producing and candidalysin-deficient C albicans strains, we show that candidalysin activates mitogen-activated protein kinase (MAPK) signaling and chemokine secretion in endothelial cells in vitro.ResultsCandidalysin induces immune activation and neutrophil recruitment in vivo, and it promotes mortality in zebrafish and murine models of systemic fungal infection.ConclusionsThe data demonstrate a key role for candidalysin in neutrophil recruitment and fungal virulence during disseminated systemic C albicans infections.
Legionnaires’ Disease Mortality in Guinea Pigs Involves the p45 Mobile Genomic Element
Authors: Christensen Lanette M , Sule Preeti , Cirillo Suat L G , Strain Madison , Plumlee Quinci , Adams L Garry , Cirillo Jeffrey D 
Published: July 2019

AbstractBackgroundLegionella can cause Legionnaires’ disease, a potentially fatal form of pneumonia that occurs as sporadic epidemics. Not all strains display the same propensity to cause disease in humans. Because Legionella pneumophila serogroup 1 is responsible for >85% of infections, the majority of studies have examined this serogroup, but there are 3 commonly used laboratory strains: L pneumophila serogroup 1 Philadelphia (Phil-1)-derived strains JR32 and Lp01 and 130b-derived strain AA100.MethodsWe evaluated the ability of Phil-1, JR32, Lp01, and AA100 to cause disease in guinea pigs.ResultsWe found that, although Phil-1, JR32, and AA100 cause an acute pneumonia and death by 4 days postinfection (100%), strain Lp01 does not cause mortality (0%). We also noted that Lp01 lacks a mobile element, designated p45, whose presence correlates with virulence. Transfer of p45 into Lp01 results in recovery of the ability of this strain to cause mortality, leads to more pronounced disease, and correlates with increased interferon-γ levels in the lungs and spleens before death.ConclusionsThese observations suggest a mechanism of Legionnaires’ disease pathogenesis due to the presence of type IVA secretion systems that cause higher mortality due to overinduction of a proinflammatory response in the host.
In vitro unfermented fiber is a good predictor of the digestible and metabolizable energy content of corn distillers dried grains with solubles in growing pigs1
Authors: Zeng Zhikai , Jang Jae Cheol , Kerr Brian J , Shurson Gerald C , Urriola Pedro E 
Published: July 2019

Abstract
Characterizing fiber into fermentable and unfermentable fractions may enhance the accuracy of estimating DE and ME energy content in fiber-rich ingredients. Therefore, the objective of this study was to analyze the concentrations of NDF, representing both the fermentable (fNDFom) and unfermentable (uNDFom) portions among sources of corn distillers dried grains with solubles (DDGS), and determine their relative contributions to DE and ME content. The concentrations of DE and ME, as well as apparent total tract digestibility (ATTD) of GE, were measured in a previous experiment. Samples of DDGS (0.5 g) were mixed with fecal inoculum and incubated for 8, 12, and 72 h. The ash corrected NDF (NDFom) content of DDGS residues at each time point was determined. The fNDFom increased with fermentation time of 8 h (21.6%), 12 h (29.0%), and 72 h (68.6%). The ATTD of GE increased as the uNDFom decreased at 8 h (uNDFom8; R2 = 0.83; P &lt; 0.01) and 72 h (uNDFom72; R2 = 0.83; P &lt; 0.01). Likewise, ME content of DDGS increased as uNDFom72 decreased (R2 = 0.59; P &lt; 0.01). The best-fit DE equation was DE (kcal/kg DM) = 2,175 – 3.07 × uNDFom8 (g/kg, DM) – 1.50 × uNDFom72 (g/kg, DM) + 0.55 × GE (kcal/kg DM) (R2 = 0.94, SE = 36.21). The best-fit ME equation was ME (kcal/kg DM) = 1,643 – 2.31 × uNDFom8 (g/kg, DM) – 2.54 × uNDFom72 (g/kg, DM) + 0.65 × GE (kcal/kg DM) – 1.42 × crude protein (g/kg DM) (R2 = 0.94, SE = 39.21). These results indicate that in vitro unfermented fiber is negatively associated with GE and NDF digestibility, and therefore, is a good predictor of DE and ME content in corn-DDGS.
Effect of supplemental threonine above requirement on growth performance of Salmonella typhimurium challenged pigs fed high-fiber diets1
Authors: Wellington Michael O , Agyekum Atta K , Hamonic Kimberley , Htoo John K , Van Kessel Andrew G , Columbus Daniel A 
Published: July 2019

AbstractIt was shown previously that high dietary fiber (DF) and immune system stimulation (ISS) with systemic Escherichia coli lipopolysaccharide independently increased the threonine (Thr) requirement to maximize growth performance and protein deposition (PD). However, no additive effects on the Thr requirement were observed when both DF and ISS were present. The objective of the present study was to investigate whether supplementing Thr to meet previously estimated requirements for high DF and systemic immune challenge would maintain performance of pigs exposed to an enteric immune challenge when fed high DF. A total of 128 pigs (22.6 ± SD = 1.6 kg initial BW) were assigned to 1 of 4 dietary treatments in a 2 × 2 factorial arrangement in a randomized complete block design (n = 8 pens/treatment and 4 pigs/pen) for 28 d. Treatments were a low-fiber (LF; 13% total DF) or high-fiber (HF; 20% total DF) diet with either a standard (STD; 0.65% SID) or supplemental (SUP; 0.78% SID) Thr level. After a 7-d adaptation, pigs were orally inoculated with 2 mL (2.3 × 109 CFU/mL) of Salmonella typhimurium (ST). Blood samples and rectal swabs were obtained and rectal temperature recorded to determine clinical responses and ST shedding. On day 7 postinoculation, 1 pig/pen was euthanized and mesenteric lymph nodes, spleen, and digesta (ileum, cecum, and colon) were sampled to assess ST colonization and translocation. Body weight and feed intake were recorded on day 0, 7, and 21 postinoculation to calculate ADG, ADFI, and G:F. Rectal temperature increased (P < 0.05) 24 h postinoculation and remained elevated at day 6. Serum albumin concentration decreased (P < 0.05), whereas haptoglobin concentration increased (P < 0.05) postinoculation. There was no fiber or Thr effect (P > 0.05) on ST counts in the ileum and cecum, but a fiber × Thr interaction (P < 0.05) was observed in the colon. Supplemental Thr improved (P < 0.05) growth performance in LF- and HF-fed challenged pigs. However, performance of supplemented HF challenged pigs was less than (P < 0.05) supplemented LF challenged pigs. These results suggest that Thr supplemented to meet requirements for high DF and systemic immune challenge was not sufficient to maintain growth performance of pigs fed HF diets and challenged with an enteric pathogen.
A Review of Adjunctive Therapies for Burn Injury Pain During the Opioid Crisis
Authors: Kim Daniel E , Pruskowski Kaitlin A , Ainsworth Craig R , Linsenbardt Hans R , Rizzo Julie A , Cancio Leopoldo C 
Published: July 2019

Abstract
Opioids are the mainstay of pain management after burn injury. The United States currently faces an epidemic of opioid overuse and abuse, while simultaneously experiencing a nationwide shortage of intravenous narcotics. Adjunctive pain management therapies must be sought and utilized to reduce the use of opioids in burn care to prevent the long-term negative effects of these medications and to minimize the dependence on opioids for analgesia. The purpose of this review was to identify literature on adjunctive pain management therapies that have been demonstrated to reduce pain severity or opioid consumption in adult burn patients. Three databases were searched for prospective studies, randomized controlled trials, and systematic reviews that evaluated adjunctive pain management strategies published between 2008 and 2019 in adult burn patients. Forty-six studies were analyzed, including 24 randomized controlled trials, six crossover trials, and 10 systematic reviews. Various adjunctive pain management therapies showed statistically significant reduction in pain severity. Only one randomized controlled trial on music therapy for acute background pain showed a reduction in opioid use. One cohort study on hypnosis demonstrated reduced opioid use compared with historical controls. We recommend the development of individualized analgesic regimens with the incorporation of adjunctive therapies in order to improve burn pain management in the midst of an abuse crisis and concomitant national opioid shortage.
Artificial Corn-Based Diet for Rearing Spodoptera frugiperda (Lepidoptera: Noctuidae)
Authors: Pinto José Ricardo Lima , Torres Aline Finotti , Truzi Caio Cesar , Vieira Natalia Fernanda , Vacari Alessandra Marieli , De Bortoli Sergio Antonio 
Published: July 2019

Abstract
Spodoptera frugiperda (J.E. Smith, 1797) is considered a key pest of maize. However, the artificial diets used for rearing this insect in the laboratory do not contain corn. The aim of this study was to evaluate the biology and to compare the food consumption by S. frugiperda, as well as the food preference of the larvae in the standard diet and the corn-based diet. Three of the following diets were evaluated: a standard diet based on beans (D1), a diet with corn flour as substitute for wheat germ (D2), and a diet replacing beans with green corn (D3). The biological parameters evaluated were period and survival of larvae and pupae; weight of male and female pupae; sex ratio; fecundity; egg incubation period; and adult longevity. The nutritional indices were determined and the biological data obtained were used to determine the parameters of fertility life tables; we also performed a multiple-choice test (feeding test). Larval development of S. frugiperda occurred in all three diets, although without oviposition by females developed from larval fed on D2. There was no difference among the diets in relation to the fertility life table parameters. The diet D2 resulted in better ingestion, digestion, assimilation, and conversion of food, but was associated with a metabolic cost to assimilate the food. Using a multiple-choice test, we observed that the larvae preferred diet D2. Based on our results, the most adequate diets for rearing S. frugiperda in the laboratory are D1 and D3.
Prognostic value of the expression of epithelial cell adhesion molecules in head and neck squamous cell carcinoma treated by definitive radiotherapy
Authors: Murakami Naoya , Mori Taisuke , Nakamura Satoshi , Yoshimoto Seiichi , Honma Yoshitaka , Ueno Takao , Kobayashi Kenya , Kashihara Tairo , Takahashi Kana , Inaba Koji , Okuma Kae , Igaki Hiroshi , Nakayama Yuko , Itami Jun 
Published: July 2019

Abstract
A reliable biomarker can contribute to appropriate treatment selection in the management of head and neck squamous cell carcinoma (HNSCC). Recently, epithelial cell adhesion molecule (EpCAM) was shown to have prognostic features in several malignancies. However, it remains to be elucidated whether EpCAM predicts prognosis of HNSCC after radiotherapy. Therefore, the prognostic potential of EpCAM in HNSCC patients treated by radiotherapy was investigated in this study. All HNSCCs patients examined between January 2013 and December 2015 were analyzed for the expression of EpCAM. One hundred HNSCC patients were identified who were treated by primary radiotherapy. Intense expression of EpCAM was found in 29 HNSCC patients. Two-year overall survival (OS) for patients with intense EpCAM expression was 62.2%, whereas it was 87.9% for those without (P = 0.011). In multivariate analysis, intense EpCAM expression was found to be an independent prognostic factors for OS (P = 0.036). Overall, EpCAM was found to be an independent prognostic factor for HNSCC.
Quantum mechanical study of the high-temperature H+ + HD → D+ + H2 reaction for the primordial universe chemistry
Authors: Lepers Maxence , Guillon Grégoire , Honvault Pascal 
Published: July 2019

ABSTRACT
We use the time-independent quantum-mechanical formulation of reactive collisions in order to investigate the state-to-state H+ + HD → D+ + H2 chemical reaction. We compute cross-sections for collision energies up to 1.8 eV and rate coefficients for temperatures up to 10 000 K. We consider HD in the lowest vibrational level v = 0 and rotational levels j = 0–6, and H2 in vibrational levels v′ = 0–3 and rotational levels j′ = 0–9. For temperatures below 4000 K, the rate coefficients strongly vary with the initial rotational level j, depending on whether the reaction is endothermic (j ≤ 2) or exothermic (j ≥ 3). The reaction is also found less and less probable as the final vibrational quantum number v′ increases. Our results illustrate the importance of studying state-to-state reactions, in the context of the chemistry of the primordial universe.
Correlated timing noise and high-precision pulsar timing: measuring frequency second derivatives as an example
Authors: Liu X J , Keith M J , Bassa C G , Stappers B W 
Published: July 2019

Abstract
We investigate the impact of noise processes on high-precision pulsar timing. Our analysis focuses on the measurability of the second spin frequency derivative $\ddot{\nu }$. This $\ddot{\nu }$ can be induced by several factors including the radial velocity of a pulsar. We use Bayesian methods to model the pulsar times-of-arrival in the presence of red timing noise and dispersion measure variations, modelling the noise processes as power laws. Using simulated times-of-arrival that both include red noise, dispersion measure variations, and non-zero $\ddot{\nu }$ values, we find that we are able to recover the injected $\ddot{\nu }$, even when the noise model used to inject and recover the input parameters are different. Using simulations, we show that the measurement uncertainty on $\ddot{\nu }$ decreases with the timing baseline T as Tγ, where γ = −7/2 + α/2 for power-law noise models with shallow power-law indices α (0 < α < 4). For steep power-law indices (α > 8), the measurement uncertainty reduces with T−1/2. We applied this method to times-of-arrival from the European Pulsar Timing Array and the Parkes Pulsar Timing Array and determined $\ddot{\nu }$ probability density functions for 49  millisecond pulsars. We find a statistically significant $\ddot{\nu }$ value for PSR B1937+21 and consider possible options for its origin. Significant (95 per cent C.L.) values for $\ddot{\nu }$ are also measured for PSRs J0621+1002 and J1022+1001, thus future studies should consider including it in their ephemerides. For binary pulsars with small orbital eccentricities, such as PSR J1909−3744, extended ELL1 models should be used to overcome computational issues. The impacts of our results on the detection of gravitational waves are also discussed.
Formation of hydrogen in the early universe: quasi-molecular mechanism of recombination
Authors: Kereselidze Tamaz , Noselidze Irakli , Ogilvie John F 
Published: July 2019

ABSTRACT
The recombination of an electron and a proton is assumed to occur in the presence of another proton, which participates in the process. The system of colliding particles is considered as a quasi-molecule temporarily formed during a collision. This model is employed to treat the formation of atomic hydrogen in the pre-recombination period of evolution of the early universe. According to a quasi-molecular mechanism of recombination, two processes are responsible for the formation of hydrogen in the early universe – a radiative transition of an electron to an excited repulsive state of $\mathrm{ H}_2^ + $ with a subsequent dissociation into a hydrogen atom and a proton, and a radiative transition of an electron to an excited attractive state of $\mathrm{ H}_2^ + $ with a subsequent cascade downward to a low-lying repulsive state. The participation of the nearest neighbouring proton in the process is shown to decrease the probability of recombination on an isolated proton.
Radio emission from accreting isolated black holes in our galaxy
Authors: Tsuna Daichi , Kawanaka Norita 
Published: July 2019

ABSTRACT
Apart from the few tens of stellar-mass black holes discovered in binary systems, an order of 108 isolated black holes (IBHs) are believed to be lurking in our Galaxy. Although some IBHs are able to accrete matter from the interstellar medium, the accretion flow is usually weak and thus radiatively inefficient, which results in significant material outflow. We study electron acceleration generated by the shock formed between this outflow and the surrounding material, and the subsequent radio synchrotron emission from accelerated electrons. By numerically calculating orbits of IBHs to obtain their spatial and velocity distributions, we estimate the number of IBHs detectable by surveys using SKA1-mid (SKA2) as ∼30 (∼700) for the most optimistic case. The SKA’s parallax measurements may accurately give their distances, possibly shedding light on the properties of the black holes in our Galaxy.
Are stellar-mass black-hole binaries too quiet for LISA?
Authors: Moore Christopher J , Gerosa Davide , Klein Antoine 
Published: July 2019

ABSTRACT
The progenitors of the high-mass black-hole mergers observed by LIGO and Virgo are potential LISA sources and promising candidates for multiband GW observations. In this letter, we consider the minimum signal-to-noise ratio these sources must have to be detected by LISA bearing in mind the long duration and complexity of the signals. Our revised threshold of ρthr ∼ 15 is higher than previous estimates, which significantly reduces the expected number of events. We also point out the importance of the detector performance at high frequencies and the duration of the LISA mission, which both influence the event rate substantially.
Functional interplay between DEAD-box RNA helicases Ded1 and Dbp1 in preinitiation complex attachment and scanning on structured mRNAs in vivo
Authors: Sen Neelam Dabas , Gupta Neha , K. Archer Stuart , Preiss Thomas , Lorsch Jon R , Hinnebusch Alan G 
Published: July 2019

Abstract
RNA structures that impede ribosome binding or subsequent scanning of the 5′-untranslated region (5′-UTR) for the AUG initiation codon reduce translation efficiency. Yeast DEAD-box RNA helicase Ded1 appears to promote translation by resolving 5′-UTR structures, but whether its paralog, Dbp1, performs similar functions is unknown. Furthermore, direct in vivo evidence was lacking that Ded1 or Dbp1 resolves 5′-UTR structures that impede attachment of the 43S preinitiation complex (PIC) or scanning. Here, profiling of translating 80S ribosomes reveals that the translational efficiencies of many more mRNAs are reduced in a ded1-ts dbp1Δ double mutant versus either single mutant, becoming highly dependent on Dbp1 or Ded1 only when the other helicase is impaired. Such ‘conditionally hyperdependent’ mRNAs contain unusually long 5′-UTRs with heightened propensity for secondary structure and longer transcript lengths. Consistently, overexpressing Dbp1 in ded1 cells improves the translation of many such Ded1-hyperdependent mRNAs. Importantly, Dbp1 mimics Ded1 in conferring greater acceleration of 48S PIC assembly in a purified system on mRNAs harboring structured 5′-UTRs. Profiling 40S initiation complexes in ded1 and dbp1 mutants provides direct evidence that Ded1 and Dbp1 cooperate to stimulate both PIC attachment and scanning on many Ded1/Dbp1-hyperdependent mRNAs in vivo.
Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets
Authors: Pont Frédéric , Tosolini Marie , Fournié Jean J 
Published: July 2019

Abstract
The momentum of scRNA-seq datasets prompts for simple and powerful tools exploring their meaningful signatures. Here we present Single-Cell_Signature_Explorer (https://sites.google.com/site/fredsoftwares/products/single-cell-signature-explorer), the first method for qualitative and high-throughput scoring of any gene set-based signature at the single cell level and its visualization using t-SNE or UMAP. By scanning datasets for single or combined signatures, it rapidly maps any multi-gene feature, exemplified here with signatures of cell lineages, biological hallmarks and metabolic pathways in large scRNAseq datasets of human PBMC, melanoma, lung cancer and adult testis.
Initiation of sodium polystyrene sulphonate and the risk of gastrointestinal adverse events in advanced chronic kidney disease: a nationwide study
Authors: Laureati Paola , Xu Yang , Trevisan Marco , Schalin Lovisa , Mariani Illaria , Bellocco Rino , Sood Manish M , Barany Peter , Sjölander Arvid , Evans Marie , Carrero Juan J 
Published: July 2019

AbstractBackgroundDespite long-standing clinical use of sodium polystyrene sulphonate (SPS) for hyperkalaemia management in chronic kidney disease (CKD), its safety profile remains poorly investigated.MethodsWe undertook an observational analysis of nephrology-referred adults with incident CKD Stage 4+ in Sweden during 2006–16 and with no previous SPS use. We studied patterns of use and adverse events associated to SPS initiation during follow-up. Patterns of SPS use were defined by chronicity of treatment and by prescribed dose. We estimated hazard ratios (HRs) and 95% confidence intervals (CIs) associated with SPS initiation (time-varying exposure) for the risk of severe (intestinal ischaemia, thrombosis or ulceration/perforation) and minor (de novo dispensation of laxatives or anti-diarrheal drugs) gastrointestinal (GI) events.ResultsOf 19 530 SPS-naïve patients with CKD, 3690 initiated SPS during follow-up. A total of 59% took SPS chronically, with an average of three dispensations/year. The majority (85%) were prescribed lower dosages than specified on the product label. During follow-up, 202 severe and 1149 minor GI events were recorded. SPS initiation was associated with a higher incidence of severe adverse events [adjusted HR 1.25 95% CI 1.05–1.49)], particularly in those receiving per label doses [1.54 (1.09–2.17)] and mainly attributed to ulcers and perforations. SPS initiation was also associated with higher incidence of minor GI events [adjusted HR 1.11 (95% CI 1.03–1.19)], regardless of dose, and mainly accounted for by de novo dispensation of laxatives.ConclusionsInitiation of SPS in patients with advanced CKD is associated with a higher risk of severe GI complications as well as the initiation of GI-related medications, particularly when prescribed at per label doses.