bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overall Vertical Transmission of Hepatitis C Virus, Transmission Net of Clearance, and Timing of Transmission
Authors: Ades Anthony E , Gordon Fabiana , Scott Karen , Collins Intira J , Claire Thorne , Pembrey Lucy , Chappell Elizabeth , Mariné-Barjoan Eugènia , Butler Karina , Indolfi Giuseppe , Gibb Diana M , Judd Ali 
Published: April 2022

AbstractBackgroundIt is widely accepted that the risk of hepatitis C virus (HCV) vertical transmission (VT) is 5%–6% in monoinfected women, and that 25%–40% of HCV infection clears spontaneously within 5 years. However, there is no consensus on how VT rates should be estimated, and there is a lack of information on VT rates “net” of clearance.MethodsWe reanalyzed data on 1749 children in 3 prospective cohorts to obtain coherent estimates of overall VT rate and VT rates net of clearance at different ages. Clearance rates were used to impute the proportion of uninfected children who had been infected and then cleared before testing negative. The proportion of transmission early in utero, late in utero, and at delivery was estimated from data on the proportion of HCV RNA positive within 3 days of birth, and differences between elective cesarean and nonelective cesarean deliveries.ResultsOverall VT rates were 7.2% (95% credible interval [CrI], 5.6%–8.9%) in mothers who were human immunodeficiency virus (HIV) negative and 12.1% (95% CrI, 8.6%–16.8%) in HIV-coinfected women. The corresponding rates net of clearance at 5 years were 2.4% (95% CrI, 1.1%–4.1%), and 4.1% (95% CrI, 1.7%–7.3%). We estimated that 24.8% (95% CrI, 12.1%–40.8%) of infections occur early in utero, 66.0% (95% CrI, 42.5%–83.3%) later in utero, and 9.3% (95% CrI, 0.5%–30.6%) during delivery.ConclusionsOverall VT rates are about 24% higher than previously assumed, but the risk of infection persisting beyond age 5 years is about 38% lower. The results can inform design of trials of interventions to prevent or treat pediatric HCV infection, and strategies to manage children exposed in utero.
The Structural and Functional Correlates of Frailty in Persons With Human Immunodeficiency Virus
Authors: Strain Jeremy F , Cooley Sarah , Kilgore Collin , Nelson Brittany , Doyle John , Thompson Regina , Westerhaus Elizabeth , Petersen Kalen J , Wisch Julie , Ances Beau M 
Published: April 2022

Abstract

Background
Persons with HIV (PWH) are at increased risk of frailty, a clinically recognizable state of increased vulnerability resulting from aging-associated decline in multiple physiologic systems. Frailty is often defined by the Fried criteria, which includes subjective and objective standards concerning health resiliency. However, these frailty metrics do not incorporate cognitive performance or neuroimaging measures.

Methods
We compared structural (diffusion tensor imaging [DTI]) and functional (cerebral blood flow [CBF]) neuroimaging markers in PWH with frailty and cognitive performance. Virologically controlled PWH were dichotomized as either frail (≥3) or nonfrail (&lt;3) using the Fried criteria. Cognitive Z-scores, both domain (executive, psychomotor speed, language, and memory) and global, were derived from a battery of tests. We identified three regions of reduced CBF, based on a voxel-wise comparison of frail PWH compared with nonfrail PWH. These clusters (bilateral frontal and posterior cingulate) were subsequently used as seed regions of interest (ROIs) for DTI probabilistic white matter tractography.

Results
White matter integrity connecting the ROIs was significantly decreased in frail compared with nonfrail PWH. No differences in cognition were observed between frail and nonfrail PWH. However, reductions in white matter integrity among these ROIs was significantly associated with worse psychomotor speed and executive function across the entire cohort.

Conclusions
We conclude that frailty in PWH can lead to structural and functional brain changes, including subtle changes that are not detectable by standard neuropsychological tests. Multimodal neuroimaging in conjunction with frailty assessment could identify pathological brain changes observed in PWH.
Baseline characteristics and evolution of Brazilian patients with atypical hemolytic uremic syndrome: first report of the Brazilian aHUS Registry
Authors: Vaisbich Maria Helena , de Andrade Luís Gustavo Modelli , de Menezes Neves Precil Diego Miranda , Palma Lílian Monteiro Pereira , de Castro Maria Cristina Ribeiro , Silva Cassiano Augusto Braga , de Holanda Barbosa Maria Izabel Neves , Penido Maria Goretti Moreira Guimarães , Neto Oreste Ângelo Ferra , Sobral Roberta Mendes Lima , Miranda Silvana Maria Carvalho , de Almeida Araújo Stanley , Pietrobom Igor Gouveia , Takase Henrique Mochida , Ribeiro Cláudia , da Silva Rafael Marques , de Carvalho César Augusto Almeida , Machado David José Barros , e Silva Ana Mateus Simões Teixeira , da Silva Andreia Ribeiro , Russo Enzo Ricardo , Barros Flávio Henrique Soares , Nasserala Jarinne Camilo Landim , de Oliveira Luciana Schmitt Cardon , de Castro Sylvestre Lucimary , Weissheimer Rafael , Nascimento Sueli Oliveira , Bianchini Gilson , de Carvalho Barreto Fellype , Veloso Valéria Soares Pigozzi , Fortes Patrícia Marques , Colares Vinicius Sardão , Gomes Jaelson Guilhem , Leite André Falcão Pedrosa , Mesquita Pablo Girardelli Mendonça , Vieira-Neto Osvaldo Merege 
Published: April 2022

ABSTRACT

Background
Atypical hemolytic uremic syndrome (aHUS) is an ultra-rare disease. Therefore, studies involving large samples are scarce, making registries powerful tools to evaluate cases. We present herein the first analysis of the Brazilian aHUS Registry (BRaHUS).

Methods
Analysis of clinical, laboratory, genetic and treatment data from patients inserted in the BRaHUS, from 2017 to 2020, as an initiative of the Rare Diseases Committee of the Brazilian Society of Nephrology.

Results
The cohort consisted of 75 patients (40 adults and 35 pediatric). There was a predominance of women (56%), median age at diagnosis of 20.7 years and a positive family history in 8% of cases. Renal involvement was observed in all cases and 37% had low C3 levels. In the &lt;2 years of age group, males were predominant. Children presented lower levels of hemoglobin (P = .01) and platelets (P = .003), and higher levels of lactate dehydrogenase (LDH) (P = .004) than adults. Genetic analysis performed in 44% of patients revealed pathogenic variants in 66.6% of them, mainly in CFH and the CFHR1-3 deletion. Plasmapheresis was performed more often in adults (P = .005) and 97.3% of patients were treated with eculizumab and its earlier administration was associated with dialysis-free after 3 months (P = .08).

Conclusions
The cohort of BRaHUS was predominantly composed of female young adults, with renal involvement in all cases. Pediatric patients had lower hemoglobin and platelet levels and higher LDH levels than adults, and the most common genetic variants were identified in CFH and the CFHR1-3 deletion with no preference of age, a peculiar pattern of Brazilian patients.
An update of the salmon louse (Lepeophtheirus salmonis) reference genome assembly
Authors: Joshi Jay , Flores Anne-Marie , Christensen Kris A , Johnson Hollie , Siah Ahmed , Koop Ben F 
Published: April 2022

AbstractSalmon lice have plagued the salmon farming industry and have negatively impacted salmon populations in the wild. In response, researchers have generated high density genetic maps, genome assemblies, transcriptomes, and whole-genome resequencing data to better understand this parasite. In this study, we used long-read sequencing technology to update the previous genome assemblies of Atlantic Ocean salmon lice with a more contiguous assembly and a more comprehensive gene catalog of Pacific Ocean salmon lice. We were also able to further characterize genomic features previously identified from other studies by using published resequenced genomes of 25 Atlantic and 15 Pacific salmon lice. One example was further characterizing the ZW sex chromosomes. For both the Atlantic and Pacific Ocean salmon lice subspecies, we found that the female W-chromosome is only a small fraction of the Z-chromosome and that the vast majority of the W and Z-chromosome do not contain conserved regions (i.e. pseudoautosomal regions). However, conserved orthologous protein sequences can still be identified between the W- and Z-chromosomes.
Comparable Pregnancy Outcomes for HIV-Uninfected and HIV-Infected Women on Antiretroviral Treatment in Kenya
Authors: Mugo Cyrus , Nduati Ruth , Osoro Eric , Nyawanda Bryan O , Mirieri Harriet , Hunsperger Elizabeth , Verani Jennifer R , Jin Hafsa , Mwaengo Dufton , Maugo Brian , Machoki James , Otieno Nancy A , Ombok Cynthia , Shabibi Mufida , Okutoyi Lydia , Kinuthia John , Widdowson Marc Alain , Njenga Kariuki , Inwani Irene , Wamalwa Dalton 
Published: April 2022

Abstract

Background
The impact of human immunodeficiency virus (HIV) on pregnancy outcomes for women on antiretroviral therapy (ART) in sub-Saharan Africa remains unclear.

Methods
Pregnant women in Kenya were enrolled in the second trimester and followed up to delivery. We estimated effects of treated HIV with 3 pregnancy outcomes: loss, premature birth, and low birth weight and factors associated with HIV-positive status.

Results
Of 2113 participants, 311 (15%) were HIV infected and on ART. Ninety-one of 1762 (5%) experienced a pregnancy loss, 169/1725 (10%) a premature birth (&lt;37 weeks), and 74/1317 (6%) had a low-birth-weight newborn (&lt;2500 g). There was no evidence of associations between treated HIV infection and pregnancy loss (adjusted relative risk [aRR], 1.19; 95% confidence interval [CI], .65–2.16; P = .57), prematurity (aRR, 1.09; 95% CI, .70–1.70; P = .69), and low birth weight (aRR, 1.36; 95% CI, .77–2.40; P = .27). Factors associated with an HIV-positive status included older age, food insecurity, lower education level, higher parity, lower gestation at first antenatal clinic, anemia, and syphilis. Women who were overweight or underweight were less likely to be HIV infected compared to those with normal weight.

Conclusions
Currently treated HIV was not significantly associated with adverse pregnancy outcomes. HIV-infected women, however, had a higher prevalence of other factors associated with adverse pregnancy outcomes.
Defective Monocyte Enzymatic Function and an Inhibitory Immune Phenotype in Human Immunodeficiency Virus-Exposed Uninfected African Infants in the Era of Antiretroviral Therapy
Authors: Afran Louise , Jambo Kondwani C , Nedi Wilfred , Miles David J C , Kiran Anmol , Banda Dominic H , Kamg’ona Ralph , Tembo Dumizulu , Pachnio Annette , Nastouli Eleni , Ferne Brigit , Mwandumba Henry C , Moss Paul , Goldblatt David , Rowland-Jones Sarah , Finn Adam , Heyderman Robert S 
Published: April 2022

Abstract

Background
Human immunodeficiency virus-exposed uninfected (HEU) infants are a rapidly expanding population in sub-Saharan Africa and are highly susceptible to encapsulated bacterial disease in the first year of life. The mechanism of this increased risk is still poorly understood. We investigated whether human immunodeficiency virus (HIV)-exposure dysregulates HEU immunity, vaccine-antibody production, and human herpes virus amplify this effect.

Methods
Thirty-four HIV-infected and 44 HIV-uninfected pregnant women were recruited into the birth cohort and observed up to 6 weeks of age; and then a subsequent 43 HIV-infected and 61 HIV-uninfected mother-infant pairs were recruited into a longitudinal infant cohort at either: 5–7 to 14–15; or 14–15 to 18–23 weeks of age. We compared monocyte function, innate and adaptive immune cell phenotype, and vaccine-induced antibody responses between HEU and HIV-unexposed uninfected (HU) infants.

Results
We demonstrate (1) altered monocyte phagosomal function and B-cell subset homeostasis and (2) lower vaccine-induced anti-Haemophilus influenzae type b (Hib) and anti-tetanus toxoid immunoglobulin G titers in HEU compared with HU infants. Human herpes virus infection was similar between HEU and HU infants.

Conclusions
In the era of antiretroviral therapy-mediated viral suppression, HIV exposure may dysregulate monocyte and B-cell function, during the vulnerable period of immune maturation. This may contribute to the high rates of invasive bacterial disease and pneumonia in HEU infants.
Functional roles of xylanase enhancing intestinal health and growth performance of nursery pigs by reducing the digesta viscosity and modulating the mucosa-associated microbiota in the jejunum
Authors: Moita Vitor Hugo C , Duarte Marcos Elias , Kim Sung Woo 
Published: April 2022

Abstract
This study was conducted to investigate the functional roles of an endo-β-1,4-xylanase on the intestinal health and growth performance of nursery pigs. A total of 60 pigs (21 d old, 6.9 ± 0.8 kg body weight [BW]) were allotted based on a randomized complete block design with sex and initial BW as blocks. Dietary treatments had nutrients meeting the requirements with increasing levels of endo-β-1,4-xylanase (0, 220, 440, 880, 1,760 xylanase unit [XU] per kg feed) and fed to pigs in three phases (phases 1, 2, and 3 for 10, 14, and 14 d, respectively). Titanium dioxide (0.4%) was added to the phase 3 diets as an indigestible marker. On day 38, all pigs were euthanized to collect ileal digesta to measure apparent ileal digestibility (AID), jejunal digesta to measure viscosity, and jejunal mucosa to evaluate intestinal health. Data were analyzed using the MIXED procedure for polynomial contrasts and the NLMIXED procedure for broken line analysis of SAS. Increasing xylanase in the nursery diets reduced (linear, P &lt; 0.05) the digesta viscosity in the jejunum. Increasing xylanase tended to reduce the relative abundance of Cupriavidus (P = 0.073) and Megasphaera (P = 0.063); tended to increase the relative abundance of Succinivibrio (P = 0.076) and Pseudomonas (P = 0.060); and had a quadratic effect (P &lt; 0.05) on the relative abundance of Acinetobacter (maximum: 2.01% at 867 XU per kg feed). Xylanase from 0 to 1,087 XU per kg feed reduced (P &lt; 0.05) jejunal malondialdehyde. Xylanase from 0 to 1,475 XU per kg feed increased (P &lt; 0.05) the AID of neutral detergent fiber. Increasing xylanase increased (P &lt; 0.05) the AID of ether extract and tended to increase (P = 0.058) the AID of crude protein. Increasing xylanase did not affect growth performance on overall period, whereas xylanase from 0 to 736 XU per kg feed increased (P &lt; 0.05) average daily gain (ADG) during days 31 to 38. In conclusion, xylanase supplementation showed benefits on intestinal health by reducing digesta viscosity, the relative abundance of potentially harmful bacteria, and the oxidative stress in the jejunal mucosa, collectively enhancing intestinal morphology and the AID of nutrients. Xylanase supplementation at a range of 750 to 1,500 XU per kg feed provided benefits associated with reduced oxidative stress, increased nutrient digestibility, resulting in potential improvement on growth performance of nursery pigs by increasing the average daily feed intake and moderately improving the ADG throughout the last week of feeding.
Cancer Mortality Patterns by Birthplace and Generation Status of Mexican Latinos: The Multiethnic Cohort
Authors: Chen Hongjie , Wu Anna H , Wang Songren , Bookstein Arthur , Le Marchand Loïc , Wilkens Lynne R , Haiman Christopher A , Cheng Iona , Monroe Kristine R , Setiawan Veronica Wendy 
Published: April 2022

Abstract

Background
Latinos are the largest minority group in the United States. We assessed cancer mortality by birthplace and generation status of Mexican Latinos in the Multiethnic Cohort.

Methods
We included 26 751 Latinos of Mexican origin and 6093 non-Latino Whites aged 45-74 years at cohort entry (1993-1996) from the California Multiethnic Cohort component. The Mexican Latinos comprised 42% first-generation Mexico-born immigrants, 42% second-generation (28% US-born with both parents Mexico-born and 14% US-born with 1 parent US-born and 1 parent Mexico-born), and 16% third-generation or more who were US-born with both parents US-born. Multivariable Cox models were used to calculate covariate adjusted hazard ratios and 95% confidence intervals for overall and site-specific cancer mortality by birthplace and generation status. All statistical tests were 2-sided.

Results
Cancer death rate was highest among the US-born with 1 parent US-born and 1 parent Mexico-born (age-adjusted rate = 471.0 per 100 000 person-years) and US-born with both parents US-born (age-adjusted rate = 469.0 per 100 000 person-years) groups. The US-born with both parents Mexico-born group had a 30% (hazard ratio = 1.30, 95% confidence interval = 1.18 to 1.44) higher risk of cancer death than the first-generation Mexico-born immigrants group, showing US birthplace was associated with an elevated cancer mortality. For cancer-specific mortality, US birthplace was positively associated with colorectal, liver and lung, and ovarian cancer (P values ranged from .04 to .005). Among US-born Mexican Latinos, generation status was not statistically significantly associated with overall cancer or site-specific cancer mortality.

Conclusions
Our findings suggest that US birthplace is a risk factor for cancer death in Mexican Americans. Identification of the contributing factors is important to curtail patterns of increasing cancer mortality in US-born Mexican Latinos.
A policy-aware epistemic framework for social networks
Authors: Moezkarimi Zahra , Ghassemi Fatemeh , Mousavi Mohammad Reza 
Published: April 2022

Abstract
We provide a semantic framework to specify information propagation in social networks; our semantic framework features both the operational description of information propagation and the epistemic aspects in social networks. In our framework, based on annotated labelled transition systems, actions are decorated with function views to specify different types of announcements. Our function views enforce various common types of local privacy policies, i.e. those policies concerning a single action. Furthermore, we specify global privacy policies, those concerning multiple actions, using a combination of modal $\mu $-calculus and epistemic logic. To illustrate the applicability of our framework, we apply it to the specification of a real-world case study. As a fundamental property for the epistemic aspect of our semantic model, we prove that its indistinguishability relations are equivalence relations, namely they are reflexive, symmetric and transitive. We also study the complexity bounds for the model-checking problem concerning a subset of our logic and show that model checking is PSPACE-complete for the studied subset.
Core formation via filament fragmentation and the impact of ambient pressure on it
Authors: Anathpindika S V , Francesco J Di 
Published: April 2022

ABSTRACT
Prestellar cores are generally spheroidal, some of which appear oblate while others appear prolate. Very few of them appear circular in projection. Little, however, is understood about the processes or the physical conditions under which prolate/oblate cores form. We find that an initially subcritical filament experiencing relatively low pressure (≲104 K cm−3) forms prolate cores (i.e. those with axial ratios in excess of unity) via gradual accumulation of gas in density crests. Meanwhile, a filament that is initially transcritical and experiences pressure similar to that in the Solar neighbourhood (between few × 104 and few × 105 K cm−3) forms oblate cores (i.e. those with axial ratios less than unity) via Jeans-like fragmentation. At higher pressure, however, fragments within the filament do not tend to survive as they rebound soon after formation. We also argue that quasi-oscillatory features of velocity gradient observed along the filament axis, and in the direction orthogonal to the axis, are integral to the filament evolution process and arise due to the growth of corrugations on its surface. The axial component of the velocity gradient, in particular, traces the gas flow along the filament length. We therefore posit that it could be used to constrain the filament-formation mechanism. The magnitude of the respective components of velocity gradients increases with increasing external pressure.
Dust spectral energy distributions in Milky Way-like galaxies in the IllustrisTNG simulations based on the evolution of grain size distribution
Authors: Chang Chiung-Yin , Huang Yu-Hsiu , Hirashita Hiroyuki , Cooper Andrew P 
Published: April 2022

ABSTRACT
To understand how the evolution of grain size distribution in galaxies affects observed dust properties, we apply a post-processing dust evolution model to galaxy merger trees from the IllustrisTNG cosmological hydrodynamical simulation. Our dust model includes stellar dust production, sputtering in hot gas, dust growth by accretion and coagulation in the dense interstellar medium (ISM), and shattering in the diffuse ISM. We decompose the grain size distribution into different dust species depending on the elemental abundances and the dense ISM fraction given by the simulation. In our previous work, we focused on Milky Way (MW) analogues and reproduced the observed MW extinction curve. In this study, we compute dust spectral energy distributions (SEDs) for the MW analogues. Our simulated SEDs broadly reproduce the observed MW SED within their dispersion and so does the observational data of nearby galaxies, although they tend to underpredict the MW SED at short wavelengths where emission is dominated by polycyclic aromatic hydrocarbons. We find that metallicity and dense gas fraction are the most critical factors for the SED shape, through their influence on coagulation and shattering. The overall success of our models in reproducing the MW SED further justifies the dust evolution processes included in the model and predicts the dispersion in the SEDs caused by the variety in the assembly history. We also show that the most significant increase in the dust SED occurs between redshifts z ∼ 3 and 2 in the progenitors of the simulated MW-like galaxies.
MIGHTEE – H i. The relation between the H i gas in galaxies and the cosmic web
Authors: Tudorache Madalina N , Jarvis M J , Heywood I , Ponomareva A A , Maddox N , Frank B S , Adams N J , Bowler R A A , Whittam I H , Baes M , Pan H , Rajohnson S H A , Sinigaglia F , Spekkens K 
Published: April 2022

ABSTRACT
We study the 3D axis of rotation (3D spin) of 77 H i galaxies from the MIGHTEE-H i Early Science observations, and its relation to the filaments of the cosmic web. For this H i-selected sample, the alignment between the spin axis and the closest filament (|cos ψ|) is higher for galaxies closer to the filaments, with 〈|cos ψ|〉 = 0.66 ± 0.04 for galaxies &lt;5 Mpc from their closest filament compared to 〈|cos ψ|〉 = 0.37 ± 0.08 for galaxies at 5 &lt; d &lt; 10 Mpc. We find that galaxies with a low H i-to-stellar mass ratio (log10(MH i/M⋆) &lt; 0.11) are more aligned with their closest filaments, with 〈|cos ψ|〉 = 0.58 ± 0.04; whilst galaxies with (log10(MH i/M⋆) &gt; 0.11) tend to be mis-aligned, with 〈|cos ψ|〉 = 0.44 ± 0.04. We find tentative evidence that the spin axis of H i-selected galaxies tend to be aligned with associated filaments (d &lt; 10 Mpc), but this depends on the gas fractions. Galaxies that have accumulated more stellar mass compared to their gas mass tend towards stronger alignment. Our results suggest that those galaxies that have accrued high gas fraction with respect to their stellar mass may have had their spin axis alignment with the filament disrupted by a recent gas-rich merger, whereas the spin vector for those galaxies in which the neutral gas has not been strongly replenished through a recent merger tend to orientate towards alignment with the filament. We also investigate the spin transition between galaxies with a high H i content and a low H i content at a threshold of $M_{\rm{H\,{\small {I}}}}\approx 10^{9.5} \mathrm{ M}_{\odot }$ found in simulations; however, we find no evidence for such a transition with the current data.