bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determinants of Transmission Risk During the Late Stage of the West African Ebola Epidemic
Authors: Robert Alexis , Edmunds W John , Watson Conall H , Henao-Restrepo Ana Maria , Gsell Pierre-Stéphane , Williamson Elizabeth , Longini Ira M , Sakoba Keïta , Kucharski Adam J , Touré Alhassane , Nadlaou Sévérine Danmadji , Diallo Boubacar , Barry Mamamdou Saidou , Fofana Thierno Oumar , Camara Louceny , Kaba Ibrahima Lansana , Sylla Lansana , Diaby Mohamed Lamine , Soumah Ousmane , Diallo Abdourahime , Niare Amadou , Diallo Abdourahmane , Eggo Rosalind M 
Published: March 2019

Abstract
Understanding risk factors for Ebola transmission is key for effective prediction and design of interventions. We used data on 860 cases in 129 chains of transmission from the latter half of the 2013–2016 Ebola epidemic in Guinea. Using negative binomial regression, we determined characteristics associated with the number of secondary cases resulting from each infected individual. We found that attending an Ebola treatment unit was associated with a 38% decrease in secondary cases (incidence rate ratio (IRR) = 0.62, 95% confidence interval (CI): 0.38, 0.99) among individuals that did not survive. Unsafe burial was associated with a higher number of secondary cases (IRR = 1.82, 95% CI: 1.10, 3.02). The average number of secondary cases was higher for the first generation of a transmission chain (mean = 1.77) compared with subsequent generations (mean = 0.70). Children were least likely to transmit (IRR = 0.35, 95% CI: 0.21, 0.57) compared with adults, whereas older adults were associated with higher numbers of secondary cases. Men were less likely to transmit than women (IRR = 0.71, 95% CI: 0.55, 0.93). This detailed surveillance data set provided an invaluable insight into transmission routes and risks. Our analysis highlights the key role that age, receiving treatment, and safe burial played in the spread of EVD.
A superb solo, or a deviant duet? Overlapping songs in superb fairy-wrens
Authors: Taylor Claire J , Hall Michelle L , Cain Kristal E , Langmore Naomi E 
Published: March 2019

Abstract
Avian duets are formed when 2 birds coordinate their songs. Most research on the evolution and function of duetting has focused on species with highly coordinated duets, and less is known about the context and function of overlapping songs that are more loosely coordinated, in part due to the challenge of determining whether such vocalizations coincide by chance or through coordination between the partners. Here, we use field recordings and playback experiments to test whether breeding pairs of superb fairy-wrens, Malurus cyaneus, coordinate their territorial songs to form duets. We test 3 key characteristics of duetting; whether partners’ songs 1) overlap more than expected by chance; 2) have a stereotyped structure that occurs repeatedly and predictably in time, and 3) show evidence of a constant time lag between the contributions of the 2 participants, indicating that individuals are coordinating their songs. This is the first study to quantify the temporal precision of song between partners to investigate coordination in the Malurus genus, an important model taxon for song, sexual selection, and speciation. We found variation in the extent to which partners’ songs overlapped, with some individuals overlapping their partners’ songs more than expected by chance, no difference in structure of solo and overlapping songs, and no evidence of a consistent response interval. Thus song overlap in superb fairy-wrens meets only some criteria for duetting. We suggest that overlapping songs in this species may be due to individuals responding independently of the same stimulus and/or “call and answer” between pair members.
The second life of Plasmodium in the mosquito host: gene regulation on the move
Authors: Ruiz José L , Gómez-Díaz Elena 
Published: March 2019

AbstractMalaria parasites face dynamically changing environments and strong selective constraints within human and mosquito hosts. To survive such hostile and shifting conditions, Plasmodium switches transcriptional programs during development and has evolved mechanisms to adjust its phenotype through heterogeneous patterns of gene expression. In vitro studies on culture-adapted isolates have served to set the link between chromatin structure and functional gene expression. Yet, experimental evidence is limited to certain stages of the parasite in the vertebrate, i.e. blood, while the precise mechanisms underlying the dynamic regulatory landscapes during development and in the adaptation to within-host conditions remain poorly understood. In this review, we discuss available data on transcriptional and epigenetic regulation in Plasmodium mosquito stages in the context of sporogonic development and phenotypic variation, including both bet-hedging and environmentally triggered direct transcriptional responses. With this, we advocate the mosquito offers an in vivo biological model to investigate the regulatory networks, transcription factors and chromatin-modifying enzymes and their modes of interaction with regulatory sequences, which might be responsible for the plasticity of the Plasmodium genome that dictates stage- and cell type-specific blueprints of gene expression.
A Bayesian model integration for mutation calling through data partitioning
Authors: Moriyama Takuya , Imoto Seiya , Hayashi Shuto , Shiraishi Yuichi , Miyano Satoru , Yamaguchi Rui 
Published: March 2019

Abstract

Motivation
Detection of somatic mutations from tumor and matched normal sequencing data has become among the most important analysis methods in cancer research. Some existing mutation callers have focused on additional information, e.g. heterozygous single-nucleotide polymorphisms (SNPs) nearby mutation candidates or overlapping paired-end read information. However, existing methods cannot take multiple information sources into account simultaneously. Existing Bayesian hierarchical model-based methods construct two generative models, the tumor model and error model, and limited information sources have been modeled.

Results
We proposed a Bayesian model integration framework named as partitioning-based model integration. In this framework, through introducing partitions for paired-end reads based on given information sources, we integrate existing generative models and utilize multiple information sources. Based on that, we constructed a novel Bayesian hierarchical model-based method named as OHVarfinDer. In both the tumor model and error model, we introduced partitions for a set of paired-end reads that cover a mutation candidate position, and applied a different generative model for each category of paired-end reads. We demonstrated that our method can utilize both heterozygous SNP information and overlapping paired-end read information effectively in simulation datasets and real datasets.

Availability and implementation
https://github.com/takumorizo/OHVarfinDer.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bayesian adaptive basket trial design using model averaging
Authors: Psioda Matthew A , Xu Jiawei , Jiang Qi , Ke Chunlei , Yang Zhao , Ibrahim Joseph G 
Published: March 2019

SummaryIn this article, we develop a Bayesian adaptive design methodology for oncology basket trials with binary endpoints using a Bayesian model averaging framework. Most existing methods seek to borrow information based on the degree of homogeneity of estimated response rates across all baskets. In reality, an investigational product may only demonstrate activity for a subset of baskets, and the degree of activity may vary across the subset. A key benefit of our Bayesian model averaging approach is that it explicitly accounts for the possibility that any subset of baskets may have similar activity and that some may not. Our proposed approach performs inference on the basket-specific response rates by averaging over the complete model space for the response rates, which can include thousands of models. We present results that demonstrate that this computationally feasible Bayesian approach performs favorably compared to existing state-of-the-art approaches, even when held to stringent requirements regarding false positive rates.
Very Low Hepatitis C Viral Loads in Treatment-naive Persons: Do They Compromise Hepatitis C Virus Antigen Testing?
Authors: Bertisch Barbara , Brezzi Matteo , Negro Francesco , Müllhaupt Beat , Ottiger Cornelia , Künzler-Heule Patrizia , Schmid Patrick , Giudici Fabio , Clerc Olivier , Moriggia Alberto , Roelens Maroussia , Marinucci Francesco , Zehnder Cinzia , Moradpour Darius , Keiser Olivia ,   Swiss Hepatitis C Cohort Study, Negro Francesco , Kaiser Laurent , Heim Markus , Hirsch Hans , Dufour Jean-François , Semmo Nasser , Moradpour Darius , Aubert Vincent , Siegrist Hans H , Cerny Andreas , Martinetti Lucchini Gladys , Malinverni Raffaele , Semela David , Schmid Patrick , Dollenmaier Günter , Müllhaupt Beat , Probst-Müller Elsbeth , Fabbro Thomas , Rutquist Marielle , Benkert Pascal , Sluka Constantin 
Published: March 2019

Abstract

Background
Hepatitis C virus (HCV) antigen testing is less expensive than quantitative reverse-transcription polymerase chain reaction but has lower sensitivity for very low viral load (VLVL; HCV RNA ≤3000 IU/mL). Currently the benefits of antigen testing for screening are discussed, but data on prevalence and outcomes of persons with VLVL are scarce.

Methods
We assessed prevalence and predictors of VLVL by logistic regression in treatment-naive participants in the Swiss Hepatitis C Cohort Study. We analyzed if the last viral load after VLVL was low, compared cirrhosis and mortality in persons with and without VLVL, and evaluated the number of samples with VLVL that were reactive by antigen testing.

Results
We included 2533 treatment-naive persons with available quantitative HCV RNA testing results. Overall, 133 persons (5.3%) had a VLVL. Age 18–40 years, female sex, and human immunodeficiency virus coinfection were associated with VLVL. Of 72 persons with a viral load available after VLVL, 14% had a VLVL and 17% had spontaneous viral clearance. The prevalence and incidence of cirrhosis and mortality were comparable in persons with and without VLVL; all 24 persons with VLVL and cirrhosis had excessive alcohol consumption or immunosuppression. Overall, 33% of samples with VLVL were reactive by antigen testing.

Conclusions
The frequency of VLVL was low. Among the persons who would probably be missed by antigen screening, some had a favorable disease course, but some had immunosuppression and liver cirrhosis. The benefit of HCV antigen testing for screening may be limited by the risk of missing patients with severe liver disease.
Loss of Cajal bodies in motor neurons from patients with novel mutations in VRK1
Authors: El-Bazzal Lara , Rihan Khalil , Bernard-Marissal Nathalie , Castro Christel , Chouery-Khoury Eliane , Desvignes Jean-Pierre , Atkinson Alexandre , Bertaux Karine , Koussa Salam , Lévy Nicolas , Bartoli Marc , Mégarbané André , Jabbour Rosette , Delague Valérie 
Published: March 2019

Abstract
Distal hereditary motor neuropathies (dHMNs) are a heterogeneous group of diseases, resembling Charcot–Marie–Tooth syndromes, but characterized by an exclusive involvement of the motor part of the peripheral nervous system.
Here, we describe two new compound heterozygous mutations in VRK1, the vaccinia-related kinase 1 gene, in two siblings from a Lebanese family, affected with dHMN associated with upper motor neurons (MNs) signs. The mutations lead to severely reduced levels of VRK1 by impairing its stability, and to a shift of nuclear VRK1 to cytoplasm. Depletion of VRK1 from the nucleus alters the dynamics of coilin, a phosphorylation target of VRK1, by reducing its stability through increased proteasomal degradation. In human-induced pluripotent stem cell-derived MNs from patients, we demonstrate that this drop in VRK1 levels leads to Cajal bodies (CBs) disassembly and to defects in neurite outgrowth and branching. Mutations in VRK1 have been previously reported in several neurological diseases affecting lower or both upper and lower MNs. Here, we describe a new phenotype linked to VRK1 mutations, presenting as a classical slowly progressive motor neuropathy, beginning in the second decade of life, with associated upper MN signs. We provide, for the first time, evidence for a role of VRK1 in regulating CB assembly in MNs. The observed MN defects are consistent with a length dependent axonopathy affecting lower and upper MNs, and we propose that diseases due to mutations in VRK1 should be grouped under a unique entity named `VRK1-related motor neuron disease’.
Intestinal CD103+CD4+ and CD103+CD8+ T-Cell Subsets in the Gut of Inflammatory Bowel Disease Patients at Diagnosis and During Follow-up
Authors: Roosenboom Britt , Wahab Peter J , Smids Carolijn , Groenen Marcel J M , van Koolwijk Elly , van Lochem Ellen G , Horjus Talabur Horje Carmen S 
Published: March 2019

AbstractBackgroundThe integrin CD103 is proposed to be a potential therapeutical target in inflammatory bowel disease (IBD), as it can form a heterodimeric integrin with β7 (Etrolizumab, anti-β7 integrin) on epithelial T cells. Therefore, we aimed to study the frequencies of different intestinal CD103+T-cell subsets, both CD4+ and CD8+, in newly diagnosed, untreated IBD patients at baseline and during follow-up, compared with healthy controls.MethodsIntestinal biopsies from inflamed segments during colonoscopy and peripheral blood samples were prospectively taken from IBD patients at diagnosis and during follow-up. Blood and single cell suspensions from biopsies were analyzed for CD103+ T-cell subpopulations by flow cytometry and expressed as median percentages of the total T-cell population.ResultsIn total, 75 Crohn’s disease (CD) patients, 49 ulcerative colitis (UC) patients, and 16 healthy controls were included. At presentation, IBD patients displayed lower percentages of CD103+T-cell subsets in inflamed biopsies: 3% (1 to 5) CD103+CD4+ in IBD vs 5% (5 to 7) in healthy controls (P = 0.007) and 9% (4 to 15) CD103+CD8+ compared with 42% (23 to 57) in healthy controls (P = 0.001). The majority of intestinal T cells was composed of CD103-CD4+ T cells (65% [52 to 74]) in IBD compared with 30% (21 to 50) in healthy controls (P = 0.001). In patients with endoscopic remission during follow-up (n = 27), frequencies of CD103+ and CD103-T-cell subsets were comparable with healthy controls.ConclusionAt diagnosis, active inflammation in IBD was associated with decreased percentages of both CD103+CD4+ and CD103+CD8+T-cell subsets in colon and ileum biopsies. In active disease during follow-up, these T-cell populations remained low but increased in remission to values comparable with healthy controls. A shift toward more CD103-T cells was observed during active inflammation.
Spectral Gaps of Random Graphs and Applications
Authors: Hoffman Christopher , Kahle Matthew , Paquette Elliot 
Published: March 2019

AbstractWe study the spectral gap of the Erdős–Rényi random graph through the connectivity threshold. In particular, we show that for any fixed $\delta&gt; 0$ if $$\begin{equation*} p \geq \frac{(1/2 + \delta) \log n}{n}, \end{equation*}$$then the normalized graph Laplacian of an Erdős–Rényi graph has all of its nonzero eigenvalues tightly concentrated around $1$. This is a strong expander property. We estimate both the decay rate of the spectral gap to $1$ and the failure probability, up to a constant factor. We also show that the $1/2$ in the above is optimal, and that if $p = \frac{c \log n}{n}$ for $c &lt; 1/2,$ then there are eigenvalues of the Laplacian restricted to the giant component that are separated from $1.$ We then describe several applications of our spectral gap results to stochastic topology and geometric group theory. These all depend on Garland’s method [24], a kind of spectral geometry for simplicial complexes. The following can all be considered to be higher-dimensional expander properties. First, we exhibit a sharp threshold for the fundamental group of the Bernoulli random $2$-complex to have Kazhdan’s property (T). We also obtain slightly more information and can describe the large-scale structure of the group just before the (T) threshold. In this regime, the random fundamental group is with high probability the free product of a (T) group with a free group, where the free group has one generator for every isolated edge. The (T) group plays a role analogous to that of a “giant component” in percolation theory. Next we give a new, short, self-contained proof of the Linial–Meshulam–Wallach theorem [35, 39], identifying the cohomology-vanishing threshold of Bernoulli random $d$-complexes. Since we use spectral techniques, it only holds for $\mathbb{Q}$ or $\mathbb{R}$ coefficients rather than finite field coefficients, as in [35] and [39]. However, it is sharp from a probabilistic point of view, providing for example, hitting time type results and limiting Poisson distributions inside the critical window. It is also a new method of proof, circumventing the combinatorial complications of cocycle counting. Similarly, results in an earlier preprint version of this article were already applied in [33] to obtain sharp cohomology-vanishing thresholds in every dimension for the random flag complex model.
Improvement on Natural Enemies of Bemisia tabaci (Hemiptera: Aleyrodidae) Using Extracts of Agrimonia pilosa
Authors: Guo Huifang , Qu Yufeng 
Published: March 2019

Abstract
Compared with the numerous natural enemies against insect pests that have been identified, the commercialization of natural biological control resources remains very limited. To increase the use of natural enemies for biological control, determining how to improve the low efficacy, slow speed, and high cost of natural enemies is very important. Mediterranean species of The whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodoidea), increasingly threatens many crops in China, and control primarily depends on chemical insecticides. Here, the effect of ethanol extracts from two plants, Agrimonia pilosa (Ledeb) (Rosales: Rosaceae) and Melia azedarach (Linn) (Meliaceae: Melia), on predominant natural enemies of B. tabaci was investigated using a leaf dipping or spraying method. The results showed that the ethanol extract of A. pilosa significantly improved the infectivity of the fungus Isaria javanica (Friedrichs & Bally) (Ascomycota: Hypocreales), and the mortality of whiteflies caused by the combination of fungus (105 spores/mL) with the extract of A. pilosa (2 mg/mL dried powder of A. pilosa containing 0.0942 mg/mL total polyphenols) was 81.6%, which was significantly higher than that caused by the fungus only. However, the ethanol extract of M. azedarach had no effect on fungus infectivity. Additionally, insecticide tolerance of the predator Pardosa pseudoannulata was also significantly improved by the extract of A. pilosa. The longevity of the parasitoid Encarsia formosa was not affected by the extracts. These findings indicate that the extract of A. pilosa played a dual role that included improving pathogenic fungi infectivity and insecticidal tolerance of a predator and thus could be a synergist in the biological control of B. tabaci.
ExoMol line lists – XXXII. The rovibronic spectrum of MgO
Authors: Li Heng Ying , Tennyson Jonathan , Yurchenko Sergei N 
Published: March 2019

AbstractLine lists for magnesium oxide are computed and extensive comparisons are made with existing experimental spectra. The LiTY line lists cover all rovibration transitions within the five lowest lying electronic states ($X\, {}^1\Sigma ^+$, $a\, {}^3\Pi$, $A\, {}^1\Pi$, $B\, {}^1\Sigma ^+$ and $b\, {}^3\Sigma ^{+}$) and five isotopologues: 24Mg16O, 25Mg16O, 26Mg16O, 24Mg17O and 24Mg18O. The calculations use potential energy cures, spin-orbit and electronic angular momentum coupling curves determined by fitting to empirical energy levels; these levels are reproduced to within 0.01 cm−1 in most cases. Computed nuclear-motion wavefunctions are combined with ab initio dipole moment curves to give transition intensities and excited state radiative lifetimes, which are compared with laboratory measurements. The 24Mg16O line list comprises 186 842 (J ≤ 320) rovibronic states and 72 833 173 transitions with angular momenta, J, up to 300 and covering wavenumbers up to 33 000 cm−1 (λ &gt; 0.3 μm). The line lists are suitable for temperatures up to about 5000 K. They are relevant to astrophysical studies of exoplanet atmospheres, cool stars and brown dwarfs, and are made available in electronic form in the CDS and ExoMol databases.
Ninety-Day Bundled Payment Reimbursement for Patients Undergoing Anterior and Posterior Procedures for Degenerative Cervical Radiculopathy
Authors: Alhourani Ahmad , Sharma Mayur , Ugiliweneza Beatrice , Wang Dengzhi , Nuño Miriam , Drazin Doniel , Boakye Maxwell 
Published: March 2019

Abstract

BACKGROUND
Anterior cervical discectomy with fusion (ACDF) or posterior cervical foraminotomy (PCF) are the mainstay surgical treatment options for patients with degenerative cervical radiculopathy (DCR).

OBJECTIVE
To compare 90-d bundled payments between ACDF and PCF for DCR in a cohort study.

METHODS
Data were extracted from MarketScan database (2000-2016) using ICD-9, ICD-10, and CPT-4 codes. The bundle payments were calculated as the payments accumulated from the index hospitalization admission to 90 d postsurgery. We also analyzed the index hospitalization (physician, hospital, and total) and the postdischarge payments (hospital readmission, outpatient services, medications, and total). Surgical groups were matched based on baseline characteristics (age, sex, insurance type, and Elixhauser score).

RESULTS
A total of 100 041 patients met the inclusion criteria. 94.9% of patients (n = 95 031). Patients underwent ACDF with 5.1% (n = 5 010) treated via PCF. Overall, median 90-d costs were significantly higher for ACDF than for PCF ($31567 vs $18412; P < .0001). The median total index hospitalization ($27841 vs $15043), physician ($4572 vs $1920), and hospital payments ($14540 vs $7404) were higher for ACDF compared to PCF for both single- and multiple-level cohorts (P < .0001). There was no difference in overall 90-d postdischarge payments. Factors associated with higher 90-d payments for both cohorts included age and comorbidity scores.

CONCLUSION
ACDF is associated with greater bundle payments in patients diagnosed with DCR. No difference was noted for the total postdischarge payments. PCF may be a cost-effective surgical option in appropriately selected patients with unilateral, paracentral, and foraminal soft herniated discs.