bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decreasing Incidence and Determinants of Bacterial Pneumonia in People With HIV: The Swiss HIV Cohort Study
Authors: Balakrishna Suraj , Wolfensberger Aline , Kachalov Viacheslav , Roth Jan A , Kusejko Katharina , Scherrer Alexandra U , Furrer Hansjakob , Hauser Christoph , Calmy Alexandra , Cavassini Matthias , Schmid Patrick , Bernasconi Enos , Battegay Manuel , Günthard Huldrych F , Kouyos Roger D ,   Swiss HIV Cohort Study, Anagnostopoulos A , Battegay M , Bernasconi E , Böni J , Braun D L , Bucher H C , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux C A , Günthard H , Haerry D , Hasse B , Hirsch H H , Hoffmann M , Hösli I , Huber M , Kahlert C R , Kaiser L , Keiser O , Klimkait T , Kouyos R D , Kovari H , Ledergerber B , Martinetti G , de Tejada B Martinez , Marzolini C , Metzner K J , Müller N , Nicca D , Paioni P , Pantaleo G , Perreau M , Rauch A , Rudin C , Scherrer A U , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Vernazza P , Wandeler G , Weber R , Yerly S 
Published: November 2021

Abstract

Background
Bacterial pneumonia is a leading reason for hospitalization among people with HIV (PWH); however, evidence regarding its drivers in the era of potent antiretroviral therapy is limited.

Methods
We assessed risk factors for bacterial pneumonia in the Swiss HIV Cohort Study using marginal models. We further assessed the relationship between risk factors and changes in bacterial pneumonia incidence using mediation analysis.

Results
We included 12927 PWH with follow-ups between 2008 and 2018. These patients had 985 bacterial pneumonia events during a follow-up of 100779 person-years. Bacterial pneumonia incidence significantly decreased from 13.2 cases/1000 person-years in 2008 to 6.8 cases/1000 person-years in 2018. Older age, lower education level, intravenous drug use, smoking, lower CD4-cell count, higher HIV load, and prior pneumonia were significantly associated with higher bacterial pneumonia incidence. Notably, CD4 cell counts 350–499 cells/μL were significantly associated with an increased risk compared to CD4 ≥ 500 cells/µL (adjusted hazard ratio, 1.39; 95% confidence interval, 1.01–1.89). Decreasing incidence over the last decade can be explained by increased CD4-cell counts and viral suppression and decreased smoking frequency.

Conclusions
Improvements in cascade of care of HIV and decrease in smoking may have mediated a substantial decrease in bacterial pneumonia incidence.
COVID-19 Vaccination Rates in a Global HIV Cohort
Authors: Fulda Evelynne S , Fitch Kathleen V , Overton Edgar T , Zanni Markella V , Aberg Judith A , Currier Judith S , Lu Michael T , Malvestutto Carlos , Fichtenbaum Carl J , Martinez Esteban , Umbleja Triin , Douglas Pamela S , Ribaudo Heather J , Grinspoon Steven K 
Published: November 2021

Abstract
Little is known regarding coronavirus disease 2019 (COVID-19) vaccination rates in people with HIV (PWH), a vulnerable population with significant morbidity from COVID-19. We assessed COVID-19 vaccination rates among 6952 PWH in the Randomized Trial to Prevent Vascular Events in HIV (REPRIEVE) compared to region- and country-specific vaccination data. The global probability of COVID-19 vaccination through end of July 2021 was 55% among REPRIEVE participants with rates varying substantially by Global Burden of Disease (GBD) superregion. Among PWH, factors associated with COVID-19 vaccination included residence in high-income regions, age, white race, male sex, body mass index, and higher cardiovascular risk.
Clinical Trials Registration. NCT02344290.
Short-cycle therapy in HIV-infected adults: rilpivirine combination 4 days on/3 days off therapy
Authors: Luise Dora , Lattuada Emanuela , Rizzardo Sebastiano , Nicolè Stefano , Lambertenghi Lorenza , Coledan Ilaria , Gambino Silvia , Gottardo Rossella , Lanzafame Massimiliano , Vento Sandro 
Published: November 2021

Abstract

Background
Short-cycle therapy (SCT) is the administration of ART for 4 or 5 consecutive days a week, followed by 3 or 2 days off therapy. Its benefits include improving patient satisfaction and reducing ART toxicity and costs.

Methods
In this observational study we included HIV-infected adults with a three-drug ART containing rilpivirine, a history of long-term virological suppression and no evidence of resistance to previous drug regimens. Patients switched to a SCT of 4 days on/3 days off and were followed for 48 weeks with regular check-ups. The primary outcome was virological suppression; secondary outcomes were changes in CD4+ cells and rilpivirine plasma concentration, the occurrence of adverse events and resistance in the case of failure, and patient satisfaction.

Results
At week 48 no virological failure was observed, with a virological suppression rate of 30/30 (100%). Three patients switched back to continuous therapy for other reasons, with an overall success rate of SCT of 30/33 (90.9%, 95% CI = 81.24% to 100%). The CD4+ mean value increased by +64 cells/mm3 (95% CI = −59 to +187 cells/mm3; P = 0.052). No adverse events were observed and the mean total score in the satisfaction questionnaire was 57.7/60 (96.22%). Rilpivirine plasma concentration was below the efficacy threshold in 71.3% of the samples, suggesting that the patients’ characteristics, more than the drug’s pharmacokinetics, played a role in maintaining virological suppression.

Conclusions
SCT with rilpivirine-containing regimens could be an effective alternative to continuous therapy in selected HIV-infected patients with previous long-term virological suppression.
Effect of RecA inactivation and detoxification systems on the evolution of ciprofloxacin resistance in Escherichia coli
Authors: Diaz-Diaz S , Recacha E , García-Duque A , Docobo-Pérez F , Blázquez J , Pascual A , Rodríguez-Martínez J M 
Published: November 2021

Abstract

Background
Suppression of SOS response and overproduction of reactive oxygen species (ROS) through detoxification system suppression enhance the activity of fluoroquinolones.

Objectives
To evaluate the role of both systems in the evolution of resistance to ciprofloxacin in an isogenic model of Escherichia coli.

Methods
Single-gene deletion mutants of E. coli BW25113 (wild-type) (ΔrecA, ΔkatG, ΔkatE, ΔsodA, ΔsodB), double-gene (ΔrecA-ΔkatG, ΔrecA-ΔkatE, ΔrecA-ΔsodA, ΔrecA-ΔsodB, ΔkatG-ΔkatE, ΔsodB-ΔsodA) and triple-gene (ΔrecA-ΔkatG-ΔkatE) mutants were included. The response to sudden high ciprofloxacin pressure was evaluated by mutant prevention concentration (MPC). The gradual antimicrobial pressure response was evaluated through experimental evolution and antibiotic resistance assays.

Results
For E. coli BW25113 strain, ΔkatE, ΔsodB and ΔsodB/ΔsodA mutants, MPC values were 0.25 mg/L. The ΔkatG, ΔsodA, ΔkatG/katE and ΔrecA mutants showed 2-fold reductions (0.125 mg/L). The ΔkatG/ΔrecA, ΔkatE/ΔrecA, ΔsodA/ΔrecA, ΔsodB/ΔrecA and ΔkatG/ΔkatE/ΔrecA strains showed 4–8-fold reductions (0.03–0.06 mg/L) relative to the wild-type. Gradual antimicrobial pressure increased growth capacity for ΔsodA and ΔsodB and ΔsodB/ΔsodA mutants (no growth in 4 mg/L) compared with the wild-type (no growth in the range of 0.5–2 mg/L). Accordingly, increased growth was observed with the mutants ΔrecA/ΔkatG (no growth in 2 mg/L), ΔrecA/ΔkatE (no growth in 2 mg/L), ΔrecA/ΔsodA (no growth in 0.06 mg/L), ΔrecA/ΔsodB (no growth in 0.25 mg/L) and ΔrecA/ΔkatG/ΔkatE (no growth in 0.5 mg/L) compared with ΔrecA (no growth in the range of 0.002–0.015 mg/L).

Conclusions
After RecA inactivation, gradual exposure to ciprofloxacin reduces the evolution of resistance. After suppression of RecA and detoxification systems, sudden high exposure to ciprofloxacin reduces the evolution of resistance in E. coli.
The role of unprotected and privately protected areas for ocelot conservation: densities in Colombia and Brazil
Authors: Boron Valeria , Bardales Rocío , Hyde Matthew , Jaimes-Rodriguez Laura , Stasiukynas Diana , Barragan Jorge , Passos Viana Diego Francis , Payán Esteban 
Published: November 2021

AbstractThe ocelot (Leopardus pardalis) is a widely distributed, medium-sized felid in the Americas with declining population size. We estimated ocelot densities and home ranges in one agricultural area in the Magdalena River valley in Colombia, a private reserve and cattle ranch in the Colombian Llanos, and a private reserve in the Serra do Amolar in the Brazilian Pantanal. We used camera trapping (39–52 stations) and spatially explicit capture-recapture (SECR) models. Density estimates (individuals/100 km2) were 11.0 ± 2.7 (SE) in the Magdalena River valley; 13.2 ± 3.2 (SE) in the Llanos, and 10.3 ± 2.9 (SE) in the Serra do Amolar. Overall, despite an impact of agriculture and human disturbance, our results highlight the importance of unprotected areas and privately protected ranching areas for ocelot conservation. As agriculture continues to expand across the tropics causing habitat loss, and negatively affecting ocelot densities, we recommend land use planning and best agricultural practices to maintain natural habitats, thereby limiting human impacts on ocelot conservation.
Lysophosphatidic acid acyltransferases: a link with intracellular protein trafficking in Arabidopsis root cells?
Authors: Wattelet-Boyer Valérie , Le Guédard Marina , Dittrich-Domergue Franziska , Maneta-Peyret Lilly , Kriechbaumer Verena , Boutté Yohann , Bessoule Jean-Jacques , Moreau Patrick 
Published: November 2021

Abstract
Phosphatidic acid (PA) and lysophosphatidic acid acyltransferases (LPAATs) might be critical for the secretory pathway. Four extra-plastidial LPAATs (LPAAT2, 3, 4, and 5) were identified in Arabidopsis thaliana. These AtLPAATs display a specific enzymatic activity converting lysophosphatidic acid to PA and are located in the endomembrane system. We investigate a putative role for AtLPAATs 3, 4, and 5 in the secretory pathway of root cells through genetical (knockout mutants), biochemical (activity inhibitor, lipid analyses), and imaging (live and immuno-confocal microscopy) approaches. Treating a lpaat4;lpaat5 double mutant with the LPAAT inhibitor CI976 produced a significant decrease in primary root growth. The trafficking of the auxin transporter PIN2 was disturbed in this lpaat4;lpaat5 double mutant treated with CI976, whereas trafficking of H+-ATPases was unaffected. The lpaat4;lpaat5 double mutant is sensitive to salt stress, and the trafficking of the aquaporin PIP2;7 to the plasma membrane in the lpaat4;lpaat5 double mutant treated with CI976 was reduced. We measured the amounts of neo-synthesized PA in roots, and found a decrease in PA only in the lpaat4;lpaat5 double mutant treated with CI976, suggesting that the protein trafficking impairment was due to a critical PA concentration threshold.
Synthetic galaxy clusters and observations based on Dark Energy Survey Year 3 Data
Authors: Varga T N , Gruen D , Seitz S , MacCrann N , Sheldon E , Hartley W G , Amon A , Choi A , Palmese A , Zhang Y , Becker M R , McCullough J , Rozo E , Rykoff E S , To C , Grandis S , Bernstein G M , Dodelson S , Eckert K , Everett S , Gruendl R A , Harrison I , Herner K , Rollins R P , Sevilla-Noarbe I , Troxel M A , Yanny B , Zuntz J , Diehl H T , Jarvis M , Aguena M , Allam S , Annis J , Bertin E , Bhargava S , Brooks D , Carnero Rosell A , Carrasco Kind M , Carretero J , Costanzi M , da Costa L N , Pereira M E S , De Vicente J , Desai S , Dietrich J P , Ferrero I , Flaugher B , García-Bellido J , Gaztanaga E , Gerdes D W , Gschwend J , Gutierrez G , Hinton S R , Honscheid K , Jeltema T , Kuehn K , Kuropatkin N , Maia M A G , March M , Melchior P , Menanteau F , Miquel R , Morgan R , Myles J , Paz-Chinchón F , Plazas A A , Romer A K , Sanchez E , Scarpine V , Schubnell M , Serrano S , Smith M , Soares-Santos M , Suchyta E , Swanson M E C , Tarle G , Thomas D , Weller J ,   (DES Collaboration)
Published: November 2021

ABSTRACT
We develop a novel data-driven method for generating synthetic optical observations of galaxy clusters. In cluster weak lensing, the interplay between analysis choices and systematic effects related to source galaxy selection, shape measurement, and photometric redshift estimation can be best characterized in end-to-end tests going from mock observations to recovered cluster masses. To create such test scenarios, we measure and model the photometric properties of galaxy clusters and their sky environments from the Dark Energy Survey Year 3 (DES Y3) data in two bins of cluster richness $\lambda \in [30; 45)$, $\lambda \in [45; 60)$ and three bins in cluster redshift ($z\in [0.3; 0.35)$, $z\in [0.45; 0.5)$ and $z\in [0.6; 0.65)$. Using deep-field imaging data, we extrapolate galaxy populations beyond the limiting magnitude of DES Y3 and calculate the properties of cluster member galaxies via statistical background subtraction. We construct mock galaxy clusters as random draws from a distribution function, and render mock clusters and line-of-sight catalogues into synthetic images in the same format as actual survey observations. Synthetic galaxy clusters are generated from real observational data, and thus are independent from the assumptions inherent to cosmological simulations. The recipe can be straightforwardly modified to incorporate extra information, and correct for survey incompleteness. New realizations of synthetic clusters can be created at minimal cost, which will allow future analyses to generate the large number of images needed to characterize systematic uncertainties in cluster mass measurements.
The physics of galactic winds driven by cosmic rays I: Diffusion
Authors: Quataert Eliot , Thompson Todd A , Jiang (姜燕飞) Yan-Fei 
Published: November 2021

ABSTRACT
The physics of Cosmic ray (CR) transport remains a key uncertainty in assessing whether CRs can produce galaxy-scale outflows consistent with observations. In this paper, we elucidate the physics of CR-driven galactic winds for CR transport dominated by diffusion. A companion paper considers CR streaming. We use analytic estimates validated by time-dependent spherically symmetric simulations to derive expressions for the mass-loss rate, momentum flux, and speed of CR-driven galactic winds, suitable for cosmological-scale or semi-analytic models of galaxy formation. For CR diffusion coefficients κ ≳ r0ci, where r0 is the base radius of the wind and ci is the isothermal gas sound speed, the asymptotic wind energy flux is comparable to that supplied to CRs, and the outflow rapidly accelerates to supersonic speeds. By contrast, for κ ≲ r0ci, CR-driven winds accelerate more slowly and lose most of their energy to gravity, a CR analogue of photon-tired stellar winds. Given CR diffusion coefficients estimated using Fermi gamma-ray observations of pion decay, we predict mass-loss rates in CR-driven galactic winds of the order of the star formation rate for dwarf and disc galaxies. The dwarf galaxy mass-loss rates are small compared to the mass-loadings needed to reconcile the stellar and dark matter halo mass functions. For nuclear starbursts (e.g. M82, Arp 220), CR diffusion and pion losses suppress the CR pressure in the galaxy and the strength of CR-driven winds. We discuss the implications of our results for interpreting observations of galactic winds and for the role of CRs in galaxy formation.
The physics of galactic winds driven by cosmic rays – II. Isothermal streaming solutions
Authors: Quataert Eliot , Jiang (姜燕飞) Yan-Fei , Thompson Todd A 
Published: November 2021

ABSTRACT
We use analytical calculations and time-dependent spherically symmetric simulations to study the properties of isothermal galactic winds driven by cosmic rays (CRs) streaming at the Alfvén velocity. The simulations produce time-dependent flows permeated by strong shocks; we identify a new linear instability of sound waves that sources these shocks. The shocks substantially modify the wind dynamics, invalidating previous steady state models: the CR pressure pc has a staircase-like structure with dpc/dr ≃ 0 in most of the volume, and the time-averaged CR energetics are in many cases better approximated by pc ∝ ρ1/2, rather than the canonical pc ∝ ρ2/3. Accounting for this change in CR energetics, we analytically derive new expressions for the mass-loss rate, momentum flux, wind speed, and wind kinetic power in galactic winds driven by CR streaming. We show that streaming CRs are ineffective at directly driving cold gas out of galaxies, though CR-driven winds in hotter ISM phases may entrain cool gas. For the same physical conditions, diffusive CR transport (Paper I) yields mass-loss rates that are a few-100 times larger than streaming transport, and asymptotic wind powers that are a factor of ≃4 larger. We discuss the implications of our results for galactic wind theory and observations; strong shocks driven by CR-streaming-induced instabilities produce gas with a wide range of densities and temperatures, consistent with the multiphase nature of observed winds. We also quantify the applicability of the isothermal gas approximation for modelling streaming CRs and highlight the need for calculations with more realistic thermodynamics.
Sparse data inpainting for the recovery of Galactic-binary gravitational wave signals from gapped data
Authors: Blelly Aurore , Bobin Jérôme , Moutarde Hervé 
Published: November 2021

ABSTRACT
The forthcoming space-based gravitational wave observatory LISA will open a new window for the measurement of Galactic binaries, which will deliver unprecedented information about these systems. However, the detection of Galactic binary gravitational wave signals is challenged by the presence of gaps in the data. Whether being planned or not, gapped data reduce our ability to detect faint signals and increase the risk of misdetection. Inspired by advances in signal processing, we introduce a non-parametric inpainting algorithm based on the sparse representation of the Galactic binary signal in the Fourier domain. In contrast to traditional inpainting approaches, noise statistics are known theoretically on ungapped measurements only. This calls for the joint recovery of both the ungapped noise and the Galactic binary signal. We thoroughly show that sparse inpainting yields an accurate estimation of the gravitational imprint of the Galactic binaries. Additionally, we highlight that the proposed algorithm produces a statistically consistent ungapped noise estimate. We further evaluate the performances of the proposed inpainting methods to recover the gravitational wave signal on a simple example involving verification Galactic binaries recently proposed in LISA data challenges.
Gravitational waves from spinning neutron stars as not-quite-standard sirens
Authors: Sieniawska Magdalena , Jones David Ian 
Published: November 2021

ABSTRACT
As is well known, gravitational wave detections of coalescing binaries are standard sirens, allowing a measurement of source distance by gravitational wave means alone. In this paper we explore the analogue of this capability for continuous gravitational wave emission from individual spinning neutron stars, whose spin-down is driven purely by gravitational wave emission. We show that in this case, the distance measurement is always degenerate with one other parameter, which can be taken to be the moment of inertia of the star. We quantify the accuracy to which such degenerate measurements can be made. We also discuss the practical application of this method to scenarios where one or other of distance or moment of inertia is constrained, breaking this degeneracy and allowing a measurement of the remaining parameter. We consider a broad range of possible unknown parameters, as well as we present results for the aLIGO and Einstein Telescope sensitivities. Our results will be of use following the eventual detection of a neutron star spinning down through such gravitational wave emission.
Controlled RISC loading efficiency of miR168 defined by miRNA duplex structure adjusts ARGONAUTE1 homeostasis
Authors: Dalmadi Ágnes , Miloro Fabio , Bálint Jeannette , Várallyay Éva , Havelda Zoltán 
Published: November 2021

AbstractMicro RNAs (miRNAs) are processed from precursor RNA molecules with precisely defined secondary stem-loop structures. ARGONAUTE1 (AGO1) is the main executor component of miRNA pathway and its expression is controlled via the auto-regulatory feedback loop activity of miR168 in plants. Previously we have shown that AGO1 loading of miR168 is strongly restricted leading to abundant cytoplasmic accumulation of AGO-unbound miR168. Here, we report, that intrinsic RNA secondary structure of MIR168a precursor not only defines the processing of miR168, but also precisely adjusts AGO1 loading efficiency determining the biologically active subset of miR168 pool. Our results show, that modification of miRNA duplex structure of MIR168a precursor fragment or expression from artificial precursors can alter the finely adjusted loading efficiency of miR168. In dcl1-9 mutant where, except for miR168, production of most miRNAs is severely reduced this mechanism ensures the elimination of unloaded AGO1 proteins via enhanced AGO1 loading of miR168. Based on this data, we propose a new competitive loading mechanism model for miR168 action: the miR168 surplus functions as a molecular buffer for controlled AGO1 loading continuously adjusting the amount of AGO1 protein in accordance with the changing size of the cellular miRNA pool.
Functional adaptation after kidney tissue removal in patients is associated with increased plasma atrial natriuretic peptide concentration
Authors: Azawi Nessn , Jensen Mia , Jensen Boye L , Gϕtze Jens P , Bistrup Claus , Lund Lars 
Published: November 2021

ABSTRACT

Background
Following nephrectomy, the remaining kidney tissue adapts by an increase in glomerular filtration rate (GFR). In rats, hyperfiltration can be transferred by plasma. We examined whether natriuretic peptides, atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) increase in plasma proportionally with kidney mass reduction and, if so, whether the increase relates to an increase in GFR.

Methods
Patients (n = 54) undergoing partial or total unilateral nephrectomy at two Danish centres were followed for 1 year in an observational study. Glomerular filtration rate was measured before, and 3 and 12 months after surgery. Natriuretic propeptides (proANP and proBNP) and aldosterone were measured in plasma before and at 24 h, 5 days, 21 days, 3 months and 12 months. Cyclic guanosine monophosphate (cGMP) was determined in urine.

Results
There was no baseline difference in GFR between total and partial nephrectomy (90.1 mL/min/1.73 m2 ± 14.6 versus 82.9 ± 18; P = 0.16). Single-kidney GFR increased after 3 and 12 months (12.0 and 11.9 mL/min/1.73 m2, +23.3%). There was no change in measured GFR 3 and 12 months after partial nephrectomy. ProANP and proBNP increased 3-fold 24 h after surgery and returned to baseline after 5 days. The magnitude of acute proANP and proBNP increases did not relate to kidney mass removed. ProANP, not proBNP, increased 12 months after nephrectomy. Plasma aldosterone and urine cGMP did not change. Urine albumin/creatinine ratio increased transiently after partial nephrectomy. Blood pressure was similar between the groups.

Conclusion
ANP and BNP increase acutely in plasma with no relation to degree of kidney tissue ablation. After 1 year, only unilateral nephrectomy patients displayed increased plasma ANP, which could support adaptation.