bluuebunny/crossref_metadata_2025_split huggingface dataset:
Per-partnership transmission probabilities for Chlamydia trachomatis infection: evidence synthesis of population-based survey data
Authors: Lewis Joanna , White Peter J , Price Malcolm J 
Published: September 2020

Abstract

Background
Chlamydia is the most commonly diagnosed sexually transmitted infection worldwide. Mathematical models used to plan and assess control measures rely on accurate estimates of chlamydia’s natural history, including the probability of transmission within a partnership. Several methods for estimating transmission probability have been proposed, but all have limitations.

Methods
We have developed a new model for estimating per-partnership chlamydia transmission probabilities from infected to uninfected individuals, using data from population-based surveys. We used data on sexual behaviour and prevalent chlamydia infection from the second UK National Study of Sexual Attitudes and Lifestyles (Natsal-2) and the US National Health and Nutrition Examination Surveys 2009–2014 (NHANES) for Bayesian inference of average transmission probabilities, across all new heterosexual partnerships reported. Posterior distributions were estimated by Markov chain Monte Carlo sampling using the Stan software.

Results
Posterior median male-to-female transmission probabilities per partnership were 32.1% [95% credible interval (CrI) 18.4–55.9%] (Natsal-2) and 34.9% (95%CrI 22.6–54.9%) (NHANES). Female-to-male transmission probabilities were 21.4% (95%CrI 5.1–67.0%) (Natsal-2) and 4.6% (95%CrI 1.0–13.1%) (NHANES). Posterior predictive checks indicated a well-specified model, although there was some discrepancy between reported and predicted numbers of partners, especially in women.

Conclusions
The model provides statistically rigorous estimates of per-partnership transmission probability, with associated uncertainty, which is crucial for modelling and understanding chlamydia epidemiology and control. Our estimates incorporate data from several sources, including population-based surveys, and use information contained in the correlation between number of partners and the probability of chlamydia infection. The evidence synthesis approach means that it is easy to include further data as it becomes available.
Ethnic-minority groups in England and Wales—factors associated with the size and timing of elevated COVID-19 mortality: a retrospective cohort study linking census and death records
Authors: Ayoubkhani Daniel , Nafilyan Vahé , White Chris , Goldblatt Peter , Gaughan Charlotte , Blackwell Louisa , Rogers Nicky , Banerjee Amitava , Khunti Kamlesh , Glickman Myer , Humberstone Ben , Diamond Ian 
Published: September 2020

AbstractBackgroundWe estimated population-level associations between ethnicity and coronavirus disease 2019 (COVID-19) mortality using a newly linked census-based data set and investigated how ethnicity-specific mortality risk evolved during the pandemic.MethodsWe conducted a retrospective cohort study of respondents to the 2011 Census of England and Wales in private households, linked to death registrations and adjusted for emigration (n = 47 872 412). The outcome of interest was death involving COVID-19 between 2 March 2020 and 15 May 2020. We estimated hazard ratios (HRs) for ethnic-minority groups compared with the White population, controlling for individual, household and area characteristics. HRs were estimated on the full outcome period and separately for pre- and post-lockdown periods.ResultsIn age-adjusted models, people from all ethnic-minority groups were at elevated risk of COVID-19 mortality; the HRs for Black males and females were 3.13 (95% confidence interval: 2.93 to 3.34) and 2.40 (2.20 to 2.61), respectively. However, in fully adjusted models for females, the HRs were close to unity for all ethnic groups except Black [1.29 (1.18 to 1.42)]. For males, the mortality risk remained elevated for the Black [1.76 (1.63 to 1.90)], Bangladeshi/Pakistani [1.35 (1.21 to 1.49)] and Indian [1.30 (1.19 to 1.43)] groups. The HRs decreased after lockdown for all ethnic groups, particularly Black and Bangladeshi/Pakistani females.ConclusionDifferences in COVID-19 mortality between ethnic groups were largely attenuated by geographical and socio-demographic factors, though some residual differences remained. Lockdown was associated with reductions in excess mortality risk in ethnic-minority populations, which has implications for a second wave of infection.
Effective Cylindrical Cell Decompositions for Restricted Sub-Pfaffian Sets
Authors: Binyamini Gal , Vorobjov Nicolai 
Published: September 2020

AbstractThe o-minimal structure generated by the restricted Pfaffian functions, known as restricted sub-Pfaffian sets, admits a natural measure of complexity in terms of a format${{\mathcal{F}}}$, recording information like the number of variables and quantifiers involved in the definition of the set, and a degree$D$, recording the degrees of the equations involved. Khovanskii and later Gabrielov and Vorobjov have established many effective estimates for the geometric complexity of sub-Pfaffian sets in terms of these parameters. It is often important in applications that these estimates are polynomial in $D$. Despite much research done in this area, it is still not known whether cell decomposition, the foundational operation of o-minimal geometry, preserves polynomial dependence on $D$. We slightly modify the usual notions of format and degree and prove that with these revised notions, this does in fact hold. As one consequence, we also obtain the first polynomial (in $D$) upper bounds for the sum of Betti numbers of sets defined using quantified formulas in the restricted sub-Pfaffian structure.
Asymptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in a Rehabilitation Facility: Evolution of the Presence of Nasopharyngeal SARS-CoV-2 and Serological Antibody Responses
Authors: Harris Benjamin H L , Zuhair Mohamed , Di Giovannantonio Matteo , Rosadas Carolina , Khan Maryam , Short Charlotte-Eve , Thaventhiran Thilipan , Quinlan Rachael , Taylor Andrew , Calvez Ronan , Taylor Graham P , Tedder Richard S , McClure Myra O , Fertleman Michael 
Published: September 2020

Abstract
At the start of the UK coronavirus disease 2019 epidemic, this rare point prevalence study revealed that one-third of patients (15 of 45) in a London inpatient rehabilitation unit were found to be infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) but asymptomatic. We report on 8 patients in detail, including their clinical stability, the evolution of their nasopharyngeal viral reverse-transcription polymerase chain reaction (RT-PCR) burden, and their antibody levels over time, revealing the infection dynamics by RT-PCR and serology during the acute phase. Notably, a novel serological test for antibodies against the receptor binding domain of SARS-CoV-2 showed that 100% of our asymptomatic cohort remained seropositive 3—6 weeks after diagnosis.
Epitope-Specific Antibody Responses to a Plasmodium falciparum Subunit Vaccine Target in a Malaria-Endemic Population
Authors: Friedman-Klabanoff DeAnna J , Travassos Mark A , Ifeonu Olukemi O , Agrawal Sonia , Ouattara Amed , Pike Andrew , Bailey Jason A , Adams Matthew , Coulibaly Drissa , Lyke Kirsten E , Laurens Matthew B , Takala-Harrison Shannon , Kouriba Bourema , Kone Abdoulaye K , Doumbo Ogobara K , Patel Jigar J , Thera Mahamadou A , Felgner Philip L , Tan John C , Plowe Christopher V , Berry Andrea A 
Published: September 2020

Abstract
Circumsporozoite protein (CSP) coats the Plasmodium falciparum sporozoite surface and is a major malaria subunit vaccine target. We measured epitope-specific reactivity to field-derived CSP haplotypes in serum samples from Malian adults and children on a custom peptide microarray. Compared to children, adults showed greater antibody responses and responses to more variants in regions proximal to and within the central repeat region. Children acquired short-lived immunity to an epitope proximal to the central repeat region but not to the central repeat region itself. This approach has the potential to differentiate immunodominant from protective epitope-specific responses when combined with longitudinal infection data.
DOCK8 controls survival of group 3 innate lymphoid cells in the gut through Cdc42 activation
Authors: Aihara Ryosuke , Kunimura Kazufumi , Watanabe Mayuki , Uruno Takehito , Yamane Nana , Sakurai Tetsuya , Sakata Daiji , Nishimura Fusanori , Fukui Yoshinori 
Published: September 2020

AbstractInnate lymphoid cells (ILCs) are a family of developmentally related leukocytes that rapidly secrete polarized sets of cytokines to combat infection and promote tissue repair at mucosal barriers. Among them, group 3 ILCs (ILC3s) play an important role in maintenance of the gut homeostasis by producing IL-22, and their development and function critically depend on the transcription factor RORγt. Although recent evidence indicates that RORγt+ ILC3s are reduced in the gut in the absence of the Cdc42 activator DOCK8 (dedicator of cytokinesis 8), the underlying mechanism remains unclear. We found that genetic deletion of Dock8 in RORγt+-lineage cells markedly reduced ILC3s in the lamina propria of the small intestine. By analyzing BrdU incorporation, it was revealed that DOCK8 deficiency did not affect the cell proliferation. Furthermore, when lineage marker-negative (Lin–) α4β7+ CD127+ RORγt– fetal liver cells were cultured with OP9 stromal cells in the presence of stem cell factor (SCF) and IL-7 in vitro, RORγt+ ILC3s normally developed irrespective of DOCK8 expression. However, DOCK8-deficient ILC3s exhibited a severe defect in survival of ILC3s under the condition with or without IL-7. Similar defects were observed when we analyzed Dock8VAGR mice having mutations in the catalytic center of DOCK8, thereby failing to activate Cdc42. Thus, DOCK8 acts in cell-autonomous manner to control survival of ILC3s in the gut through Cdc42 activation.
Forum on Pedagogy: The Introductory Course in International Relations: Regional Variations
Authors: Frueh Jamie , Diehl Paul F , Li Xiaoting , Gokcek Gigi , Kalpakian Jack , Vlcek William , Bower Adam , Espinoza Raúl Salgado , Carranco Santiago , de Matos-Ala Jacqui , Behera Navnita Chadha , Acharya Amitav 
Published: September 2020

AbstractThis forum explores how societal contexts affect how instructors teach introductory undergraduate courses in international relations (IR), global politics, and international studies. Contributors teach at universities in China, Ecuador, India, Morocco, South Africa, the United Kingdom–Scotland, and the United States. Because instructors vary the structure, content, and pedagogical approaches in their courses (and perhaps most in their introductory courses) to account for their students’ backgrounds, conditions, and paradigms, the discipline can learn about contemporary global patterns by putting regionally diverse pedagogical approaches in conversation with each other. A concluding essay explores emergent patterns of a global IR and sets up points for further conversation. The authors hope sharing their pedagogical strategies will inspire instructors to devote the creativity necessary to improve how they teach introductory IR courses in their own societal contexts.
Double prenylation of SNARE protein Ykt6 is required for lysosomal hydrolase trafficking
Authors: Sakata Natsumi , Shirakawa Ryutaro , Goto Kota , Trinh Duc Anh , Horiuchi Hisanori 
Published: September 2020

Abstract
Ykt6 is an evolutionarily conserved SNARE protein regulating Golgi membrane fusion and other diverse membrane trafficking pathways. Unlike most SNARE proteins, Ykt6 lacks a transmembrane domain but instead has a tandem cysteine motif at the C-terminus. Recently, we have demonstrated that Ykt6 undergoes double prenylation at the C-terminal two cysteines first by farnesyltransferase and then by a newly identified protein prenyltransferase named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of a novel α subunit prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of Rab geranylgeranyltransferase. PTAR1 knockout (KO) cells, where Ykt6 is singly prenylated with a farnesyl moiety, exhibit structural and functional abnormalities in the Golgi apparatus with delayed intra-Golgi trafficking and impaired protein glycosylation. It remains unclear whether the second prenylation of Ykt6 is required for proper trafficking of lysosomal hydrolases from Golgi to lysosomes. Here, we show that lysosomal hydrolases, cathepsin D and β-hexosaminidase, were missorted at the trans-Golgi network and secreted into the extracellular space in PTAR1 KO cells. Moreover, maturation of these hydrolases was disturbed. LC3B, an autophagy marker, was accumulated in PTAR1 KO cells, suggesting defects in cellular degradation pathways. Thus, doubly prenylated Ykt6, but not singly prenylated Ykt6, is critical for the efficient sorting and trafficking of acid hydrolases to lysosomes.
The roles of nuclear myosin in the DNA damage response
Authors: Cook Alexander W , Toseland Christopher P 
Published: September 2020

AbstractMyosin within the nucleus has often been overlooked due to their importance in cytoplasmic processes and a lack of investigation. However, more recently, it has been shown that their nuclear roles are just as fundamental to cell function and survival with roles in transcription, DNA damage and viral replication. Myosins can act as molecular transporters and anchors that rely on their actin binding and ATPase capabilities. Their roles within the DNA damage response can varies from a transcriptional response, moving chromatin and stabilizing chromosome contacts. This review aims to highlight their key roles in the DNA damage response and how they impact nuclear organization and transcription.
Quadruplex Negatio Invertit? The On-Line Processing of Depth Charge Sentences
Authors: Paape Dario , Vasishth Shravan , von der Malsburg Titus 
Published: September 2020

AbstractSo-called “depth charge” sentences (No head injury is too trivial to be ignored) are interpreted by the vast majority of speakers to mean the opposite of what their compositional semantics would dictate. The semantic inversion that is observed for sentences of this type is the strongest and most persistent linguistic illusion known to the field ( Wason & Reich, 1979). However, it has recently been argued that the preferred interpretation arises not because of a prevailing failure of the processing system, but rather because the non-compositional meaning is grammaticalized in the form of a stored construction ( Cook & Stevenson, 2010; Fortuin, 2014). In a series of five experiments, we investigate whether the depth charge effect is better explained by processing failure due to memory overload (the overloading hypothesis) or by the existence of an underlying grammaticalized construction with two available meanings (the ambiguity hypothesis). To our knowledge, our experiments are the first to explore the on-line processing profile of depth charge sentences. Overall, the data are consistent with specific variants of the ambiguity and overloading hypotheses while providing evidence against other variants. As an extension of the overloading hypothesis, we suggest two heuristic processes that may ultimately yield the incorrect reading when compositional processing is suspended for strategic reasons.
Multiwavelength power-spectrum analysis of NGC 5548
Authors: Panagiotou C , Papadakis I E , Kammoun E S , Dovčiak M 
Published: September 2020

ABSTRACT
NGC 5548 was recently monitored intensively from NIR to X-rays as part of the STORM campaign. Its disc emission was found to lag behind the observed X-rays, while the measured time lag was increasing with wavelength. These results are consistent with the assumption that short-term variability in AGN emission is driven by the X-ray illumination of the accretion disc. In this work, we studied the power spectrum of UV/optical and X-ray emission of NGC 5548, using the data of the STORM campaign as well as previous Swift data, in order to investigate the relation between the UV/optical and X-ray variability and to examine its consistency with the above picture. We demonstrate that even the power spectrum results are compatible with a standard disc being illuminated by X-rays, with low accretion rates, but the details are not entirely consistent with the results from the modelling of the ‘τ versus λ’ relation. The differences indicate that the inner disc might be covered by a ‘warm corona’ which does not allow the detection of UV/optical emission from the inner disc. Finally, we found strong evidence that the UV emission of NGC 5548 is not stationary.
The MOSDEF-LRIS Survey: The connection between massive stars and ionized gas in individual galaxies at z ∼ 2
Authors: Topping Michael W , Shapley Alice E , Reddy Naveen A , Sanders Ryan L , Coil Alison L , Kriek Mariska , Mobasher Bahram , Siana Brian 
Published: September 2020

ABSTRACT
We present constraints on the massive star and ionized gas properties for a sample of 62 star-forming galaxies at z ∼ 2.3. Using BPASS stellar population models, we fit the rest-UV spectra of galaxies in our sample to estimate age and stellar metallicity which, in turn, determine the ionizing spectrum. In addition to the median properties of well-defined subsets of our sample, we derive the ages and stellar metallicities for 30 high-SNR individual galaxies – the largest sample of individual galaxies at high redshift with such measurements. Most galaxies in this high-SNR subsample have stellar metallicities of 0.001 &lt; Z* &lt; 0.004. We then use Cloudy + BPASS photoionization models to match observed rest-optical line ratios and infer nebular properties. Our high-SNR subsample is characterized by a median ionization parameter and oxygen abundance, respectively, of log (U)med = −2.98 ± 0.25 and 12 + log (O/H)med = 8.48 ± 0.11. Accordingly, we find that all galaxies in our sample show evidence for α-enhancement. In addition, based on inferred log (U) and 12 + log (O/H) values, we find that the local relationship between ionization parameter and metallicity applies at z ∼ 2. Finally, we find that the high-redshift galaxies most offset from the local excitation sequence in the BPT diagram are the most α-enhanced. This trend suggests that α-enhancement resulting in a harder ionizing spectrum at fixed oxygen abundance is a significant driver of the high-redshift galaxy offset on the BPT diagram relative to local systems. The ubiquity of α-enhancement among z ∼ 2.3 star-forming galaxies indicates important differences between high-redshift and local galaxies that must be accounted for in order to derive physical properties at high redshift.
Probing the origin of low-frequency radio emission in PG quasars with the uGMRT – I
Authors: S Silpa , Kharb P , Ho L C , Ishwara-Chandra C H , Jarvis M E , Harrison C 
Published: September 2020

ABSTRACT
We present the results from 685 MHz observations with the upgraded Giant Metrewave Radio Telescope (uGMRT) of 22 quasars belonging to the Palomar-Green (PG) quasar sample. Only four sources reveal extended radio structures on ∼10–30 kpc scales, while the rest are largely a combination of a radio core unresolved at the uGMRT resolution of ∼3–5 arcsec, surrounded by diffuse emission on few kpc to ∼10 kpc scales. A few sources reveal signatures of barely resolved jets and lobes in their spectral index images that are created using the 685 MHz uGMRT data and similar resolution GHz-frequency data from the Very Large Array. On the basis of their position on the radio–IR correlation as well as the spectral index images, we find that the radio emission in the two radio-loud (RL) quasars and nearly one-third of the radio-quiet (RQ) quasars is active galactic nucleus (AGN) dominated whereas the remaining sources appear to have significant contributions from stellar-related processes along with the AGN. While the two RL sources exhibit inverted spectral index in their cores, the RQ sources exhibit a range of spectral indices varying from flat to steep (−0.1 $\gtrsim $ αR $\gtrsim $ −1.1) indicating the presence of unresolved jets/lobes or winds. Except for a significant correlation between the 685 MHz radio luminosity and the Eddington ratio, we do not find strong correlations between other 685 MHz radio properties and black hole (BH) properties in the RQ PG sources. This lack of correlations could be explained by the contribution of stellar-related emission, or radio emission from previous AGN activity episodes that may not be related to the current BH activity state.
Biased Mutation and Selection in RNA Viruses
Authors: Kustin Talia , Stern Adi 
Published: September 2020

AbstractRNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and COVID-19. One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates. We set out to search for shared evolutionary characteristics that may aid in gaining a broader understanding of RNA virus evolution, and constructed a phylogeny-based data set spanning thousands of sequences from diverse single-stranded RNA viruses of animals. Strikingly, we found that the vast majority of these viruses have a skewed nucleotide composition, manifested as adenine rich (A-rich) coding sequences. In order to test whether A-richness is driven by selection or by biased mutation processes, we harnessed the effects of incomplete purifying selection at the tips of virus phylogenies. Our results revealed consistent mutational biases toward U rather than A in genomes of all viruses. In +ssRNA viruses, we found that this bias is compensated by selection against U and selection for A, which leads to A-rich genomes. In −ssRNA viruses, the genomic mutational bias toward U on the negative strand manifests as A-rich coding sequences, on the positive strand. We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses.
Ionotropic Receptors as a Driving Force behind Human Synapse Establishment
Authors: Viscardi Lucas Henriques , Imparato Danilo Oliveira , Bortolini Maria Cátira , Dalmolin Rodrigo Juliani Siqueira 
Published: September 2020

Abstract
The origin of nervous systems is a main theme in biology and its mechanisms are largely underlied by synaptic neurotransmission. One problem to explain synapse establishment is that synaptic orthologs are present in multiple aneural organisms. We questioned how the interactions among these elements evolved and to what extent it relates to our understanding of the nervous systems complexity. We identified the human neurotransmission gene network based on genes present in GABAergic, glutamatergic, serotonergic, dopaminergic, and cholinergic systems. The network comprises 321 human genes, 83 of which act exclusively in the nervous system. We reconstructed the evolutionary scenario of synapse emergence by looking for synaptic orthologs in 476 eukaryotes. The Human–Cnidaria common ancestor displayed a massive emergence of neuroexclusive genes, mainly ionotropic receptors, which might have been crucial to the evolution of synapses. Very few synaptic genes had their origin after the Human–Cnidaria common ancestor. We also identified a higher abundance of synaptic proteins in vertebrates, which suggests an increase in the synaptic network complexity of those organisms.