bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic features of predominant non-PCV13 serotypes responsible for adult invasive pneumococcal disease in Spain
Authors: González-Díaz Aida , Berbel Dàmaris , Ercibengoa María , Cercenado Emilia , Larrosa Nieves , Quesada Mª Dolores , Casabella Antonio , Cubero Meritxell , Marimón José María , Domínguez M Ángeles , Carrera-Salinas Anna , Càmara Jordi , Martín-Galiano Antonio J , Yuste José , Martí Sara , Ardanuy Carmen 
Published: July 2022

Abstract

Background
Although pneumococcal conjugate vaccines (PCVs) effectively prevent invasive pneumococcal disease (IPD), serotype replacement has occurred.

Objectives
We studied the pangenome, antibiotic resistance mechanisms and presence of mobile elements in predominant non-PCV13 serotypes causing adult IPD after PCV13 vaccine introduction in Spain.

Methods
We conducted a multicentre study comparing three periods in six Spanish hospitals and analysed through whole genome sequencing representative strains collected in the pre-PCV13, early-PCV13 and late-PCV13 periods.

Results
Among 2197 cases of adult IPD identified, 110 pneumococci expressing non-PCV13 capsules were sequenced. Seven predominant serotypes accounted for 42.6% of IPD episodes in the late-PCV13 period: serotypes 8 (14.4%), 12F (7.5%), 9N (5.2%), 11A (4.1%), 22F (3.9%), 24F (3.9%) and 16F (3.6%). All predominant non-PCV13 serotypes were highly clonal, comprising one or two clonal complexes (CC). In general, CC538, CC4048, CC3016F, CC43322F and CC669N, related to predominant non-PCV13 serotypes, were antibiotic susceptible. CC15611A was associated with resistance to co-trimoxazole, penicillin and amoxicillin. CC23024F was non-susceptible to penicillin and resistant to erythromycin, clindamycin, and tetracycline. Six composite transposon structures of the Tn5252-family were found in CC23024F, CC98912F and CC3016F carrying different combinations of erm(B), tet(M), and cat. Pangenome analysis revealed differences in accessory genomes among the different CC, with most variety in CC3016F (23.9%) and more conservation in CC15611A (8.5%).

Conclusions
We identified highly clonal predominant serotypes responsible for IPD in adults. The detection of not only conjugative elements carrying resistance determinants but also clones previously associated with vaccine serotypes (CC15611A and CC23024F) highlights the importance of the accessory genome.
Evolution of β-lactamase-mediated cefiderocol resistance
Authors: Fröhlich Christopher , Sørum Vidar , Tokuriki Nobuhiko , Johnsen Pål Jarle , Samuelsen Ørjan 
Published: July 2022

Abstract

Background
Cefiderocol is a novel siderophore β-lactam with improved hydrolytic stability toward β-lactamases, including carbapenemases, achieved by combining structural moieties of two clinically efficient cephalosporins, ceftazidime and cefepime. Consequently, cefiderocol represents a treatment alternative for infections caused by MDR Gram-negatives.

Objectives
To study the role of cefiderocol on resistance development and on the evolution of β-lactamases from all Ambler classes, including KPC-2, CTX-M-15, NDM-1, CMY-2 and OXA-48.

Methods
Directed evolution, using error-prone PCR followed by selective plating, was utilized to investigate how the production and the evolution of different β-lactamases cause changes in cefiderocol susceptibility determined using microbroth dilution assays (MIC and IC50).

Results
We found that the expression of blaOXA-48 did not affect cefiderocol susceptibility. On the contrary, the expression of blaKPC-2, blaCMY-2, blaCTX-M-15 and blaNDM-1 substantially reduced cefiderocol susceptibility by 4-, 16-, 8- and 32-fold, respectively. Further, directed evolution on these enzymes showed that, with the acquisition of only 1–2 non-synonymous mutations, all β-lactamases were evolvable to further cefiderocol resistance by 2- (NDM-1, CTX-M-15), 4- (CMY-2), 8- (OXA-48) and 16-fold (KPC-2). Cefiderocol resistance development was often associated with collateral susceptibility changes including increased resistance to ceftazidime and ceftazidime/avibactam as well as functional trade-offs against different β-lactam drugs.

Conclusions
The expression of contemporary β-lactamase genes can potentially contribute to cefiderocol resistance development and the acquisition of mutations in these genes results in enzymes adapting to increasing cefiderocol concentrations. Resistance development caused clinically important cross-resistance, especially against ceftazidime and ceftazidime/avibactam.
Impact of feminizing hormone therapy on tenofovir and emtricitabine plasma pharmacokinetics: a nested drug–drug interaction study in a cohort of Brazilian transgender women using HIV pre-exposure prophylaxis
Authors: Cattani Vitória Berg , Jalil Emilia Moreira , Eksterman Leonardo , Torres Thiago , Cardoso Sandra Wagner , Castro Cristiane R V , Monteiro Laylla , Wilson Erin , Bushman Lane , Anderson Peter , Veloso Valdilea Gonçalves , Grinsztejn Beatriz , Estrela Rita ,   PrEParadas study team, Moura Isabele , Waite Daniel M McMahon , Vieira Desirée , Granjeiro José Roberto , Freitas Josias , Santos Toni , Fernandes Nilo , Nazer Sandro , Marins Luana M S , Ribeiro Valéria R T , Silva Robson P N , Costa Giovanna G , Vieira Ana Carolina , Bastos Renata A , Alves Aline , Krstic Tania , Ferreira Ana Cristina G , Derrico Monica , Kamel Luciana , Jalil Cristina M , Netto Eduardo Carvalheira , de Sousa Marcos Davi G , Leite Pedro , Mattos Kim Geraldo , Felix Jessica Bezerra , Baião Tamires Vilela , Hottz Gisele , Maia Natália Gomes , da Silva Tamiris Paixão , Ramos Michelle , Tiago Porto 
Published: July 2022

Abstract

Objectives
Potential interactions between feminizing hormone therapy (FHT) and pre-exposure prophylaxis (PrEP) may be a barrier to PrEP use among transgender women (TGW). We aimed to assess the impact of FHT on PrEP plasma pharmacokinetics (PK) among TGW.

Methods
This was a PK substudy of the effects of FHT on tenofovir disoproxil fumarate/emtricitabine nested to a trans-specific PrEP demonstration study (NCT03220152). Participants were assigned to receive PrEP only (noFHT) or standardized FHT (sFHT; oestradiol valerate 2–6 mg plus spironolactone 100–300 mg) plus PrEP for 12 weeks, after which they could start any FHT (aFHT). Short- and long-term PK assessment occurred at Weeks 12 and 30–48, respectively (plasma samples prior and 0.5, 1, 2, 4, 6, 8 and 24 h after dose). Non-compartmental PK parameters of tenofovir and emtricitabine were compared as geometric mean ratios (GMRs) between noFHT and PrEP and FHT (sFHT at short-term PK; aFHT at long-term PK) participants.

Results
No differences in tenofovir and emtricitabine plasma PK parameters were observed between the short-term PK of noFHT (n = 12) and sFHT participants (n = 18), except for emtricitabine Cmax [GMR: 1.15 (95% CI: 1.01–1.32)], or between noFHT short-term PK and aFHT long-term PK (n = 13). Most participants were on oestradiol valerate 2 mg at the short-term PK (56%) and 4 mg at the long-term PK (54%). Median (IQR) oestradiol levels were 56.8 (43.2–65.4) pg/mL at short-term PK (sFHT) and 44.8 (24.70–57.30) pg/mL at long-term PK (aFHT). No participants in this analysis seroconverted during the study.

Conclusions
Our results indicate no interaction of FHT on tenofovir levels, further supporting PrEP use among TGW using FHT.
Assessment of antibiotic appropriateness at discharge: experience from a quaternary care hospital setting
Authors: Saleh Joanna , El Nekidy Wasim S , El Lababidi Rania 
Published: July 2022

Abstract

Background
There is a gap in antimicrobial stewardship in transitions of care.

Objectives
To assess the appropriateness of antibiotics utilized and prescribing habits at hospital discharge.

Methods
A retrospective, observational study was conducted at our quaternary care hospital between January 2021 and March 2021. During the study period, all patients discharged on antibiotics for pneumonia (PNA), skin and soft tissue infections (SSTI), urinary tract infections (UTI) and intra-abdominal infections (IAI) were included. The overall appropriateness of therapy was assessed based on the following combined criteria: agent, dose, frequency, duration of therapy, and ability to meet diagnostic criteria.

Results
One hundred and forty-five subjects met the inclusion criteria. Of these, 44 (30.3%) were determined to have received overall appropriate antibiotic therapy. The most common infections were UTI, followed by IAI, PNA, and SSTI, respectively. Further, from the group deemed to have received overall inappropriate therapy, 26 of the 101 (25.7%) patients received an inappropriate antibiotic choice, 6 (5.9%) an inappropriate dose, and 84 (83.2%) an inappropriate duration of therapy.

Conclusions
Inappropriate duration of therapy represented the most challenging problem with antibiotic regimens at discharge. Larger studies are needed to identify potential interventions that are effective, and can be implemented in all settings, including resource-limited ones.
Tying One’s Hand: The Effect of Fiscal Rules on the Political Business Cycle in Africa
Authors: Strong Christine Olivia 
Published: July 2022

Abstract
In this paper, we test whether fiscal rules can act as a constraint on the ability of incumbent politicians to generate political business cycles using fiscal and monetary expansions, to improve their re-election prospects. Using data on fiscal rules for a sample of thirty-two African countries, fourteen of which have a budget balanced rule, our results show that stringent fiscal rules can indeed dampen political cycles. In particular, we find that prior to a presidential election, there is a statistically significant increase in money growth, but that increase is on average 50% less in countries with fiscal rules compared with countries with no rule. Our results hold even when we control for institutional quality, developmental assistance or electoral competitiveness. Moreover, we find evidence of political cycles in African dictatorships, which we argue potentially reflect African dictators’ strong desire to reduce the occurrence of civil unrest during elections.
A new species ofTanymastigitesBrtek, 1972 (Anostraca: Tanymastigidae) from Libya, with a revised key to the genus and new crustacean records (Branchiopoda, Copepoda, Ostracoda) from Algeria
Authors: Thiéry Alain , Rogers D Christopher 
Published: July 2022

AbstractThe fairy shrimp Tanymastigites ajjeri n. sp. is described from a temporary water body, or guelta, in the Sahara Desert near the Tadrart mountains, east of Tassili n’Ajjer National Park, Libya. Males are readily separated from congeners by the morphology of the frontal appendages, which have an undivided lateral ramus and ≥ 0.4× the length of the medial ramus, and by the second antennae, in which the medial lamellar process bears a spatulate distal lobe. The new species is most similar to congeners T. perrieri (Daday, 1910) and T. mzabica (Gauthier, 1928), and it represents the sixth described species in this genus. We provide an updated key to the genus and comments on its diagnosis and definition, particularly concerning the descriptive terminology of the second antennae. In addition, we provide a list of new records of species of Branchiopoda, Copepoda, and Ostracoda from Tassili n’Ajjer National Park.
Experimental and numerical investigations on undulatory motion of a soft-fin-based underwater robot
Authors: Lin Yu-Chih , Zhang Dai-Nong 
Published: July 2022

ABSTRACT
An undulatory fin bionic underwater robot that is able to mimic the undulation motions of the median and/or the paired fin of fish is designed and analyzed. A simplified rays-membrane structure system has been developed in order to save computational cost in finite element analysis. The undulatory motion of the soft fins in the water is experimentally measured by using two cameras and the DLTdv system. The dynamic characteristics of the fin structure and the hydrodynamics of the fluid are analyzed by a fluid-structure interaction model developed by the commercial software ANSYS, and the results are compared to those of the experiment for validation. The fin motion of different fin amplitudes (ray swing angles), membrane dimensions and phase difference of adjacent rays are compared to realize the influence of robot design on the motion. It is found in the results that the displacements of the points on the fin membrane obtained by the finite element analysis have the same trend as those by the experiment; hence, the finite element model is verified. It is indicated by the finite element analysis results that the stress of the points on the fin membrane increases with the amplitude. The maximum velocity in one section plane is largest for the 40 mm width fin. The average stress on the fin with 45° phase difference is larger than that of 90° phase difference. Because of the complexity of the soft fin's material behavior and fluid-structure interaction analysis, the finite element analysis model developed in this study has a significant contribution for the soft-fin-based underwater robot design.
Dust coagulation and fragmentation in a collapsing cloud core and their influence on non-ideal magnetohydrodynamic effects
Authors: Kawasaki Yoshihiro , Koga Shunta , Machida Masahiro N 
Published: July 2022

ABSTRACT
We determine the time-evolution of the dust particle size distribution during the collapse of a cloud core, accounting for both dust coagulation and dust fragmentation, to investigate the influence of dust growth on non-ideal magnetohydrodynamic (MHD) effects. The density evolution of the collapsing core is given by a one-zone model. We assume two types of dust model: dust composed only of silicate (silicate dust) and dust with a surface covered by H2O ice (H2O ice dust). When only considering collisional coagulation, the non-ideal MHD effects are not effective in the high-density region for both the silicate and H2O ice dust cases. This is because dust coagulation reduces the abundance of small dust particles, resulting in less efficient adsorption of charged particles on the dust surface. For the silicate dust case, when collisional fragmentation is included, the non-ideal MHD effects do apply at a high density of nH &gt; 1012 cm−3 because of the abundant production of small dust particles. On the other hand, for the H2O ice dust case, the production of small dust particles due to fragmentation is not efficient. Therefore, for the H2O ice dust case, non-ideal magnetohydrodynamic effects apply only in the range nH ≳ 1014 cm−3, even when collisional fragmentation is considered. Our results suggest that it is necessary to consider both dust collisional coagulation and fragmentation to activate non-ideal magnetohydrodynamic effects, which should play a significant role in the star and disc formation processes.
Variational Phylodynamic Inference Using Pandemic-scale Data
Authors: Ki Caleb , Terhorst Jonathan 
Published: July 2022

Abstract
The ongoing global pandemic has sharply increased the amount of data available to researchers in epidemiology and public health. Unfortunately, few existing analysis tools are capable of exploiting all of the information contained in a pandemic-scale data set, resulting in missed opportunities for improved surveillance and contact tracing. In this paper, we develop the variational Bayesian skyline (VBSKY), a method for fitting Bayesian phylodynamic models to very large pathogen genetic data sets. By combining recent advances in phylodynamic modeling, scalable Bayesian inference and differentiable programming, along with a few tailored heuristics, VBSKY is capable of analyzing thousands of genomes in a few minutes, providing accurate estimates of epidemiologically relevant quantities such as the effective reproduction number and overall sampling effort through time. We illustrate the utility of our method by performing a rapid analysis of a large number of SARS-CoV-2 genomes, and demonstrate that the resulting estimates closely track those derived from alternative sources of public health data.
Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea
Authors: Villain Paul , Catchpole Ryan , Forterre Patrick , Oberto Jacques , da Cunha Violette , Basta Tamara 
Published: July 2022

Abstract
DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, DNA gyrase has an essential role in the homeostatic regulation of supercoiling. While ubiquitous in bacteria, DNA gyrase was previously reported to have a patchy distribution in Archaea but its emergent function and evolutionary history in this domain of life remains elusive. In this study, we used phylogenomic approaches and an up-to date sequence dataset to establish global and archaea-specific phylogenies of DNA gyrases. The most parsimonious evolutionary scenario infers that DNA gyrase was introduced into the lineage leading to Euryarchaeal group II via a single horizontal gene transfer from a bacterial donor which we identified as an ancestor of Gracilicutes and/or Terrabacteria. The archaea-focused trees indicate that DNA gyrase spread from Euryarchaeal group II to some DPANN and Asgard lineages via rare horizontal gene transfers. The analysis of successful recent transfers suggests a requirement for syntropic or symbiotic/parasitic relationship between donor and recipient organisms. We further show that the ubiquitous archaeal Topoisomerase VI may have co-evolved with DNA gyrase to allow the division of labor in the management of topological constraints. Collectively, our study reveals the evolutionary history of DNA gyrase in Archaea and provides testable hypotheses to understand the prerequisites for successful establishment of DNA gyrase in a naive archaeon and the associated adaptations in the management of topological constraints.
Expanding the strategic and clinical leadership role of accredited specialists
Authors: Parsons V , Pattani S , Gilbey A , Madan I , Harling C , Muiry R , de Bono A 
Published: July 2022

Abstract

Background
We sought to explore the value and benefits of accredited specialists employed in the National Health Service (NHS), and proposed strategies for expanding their role.

Aims
To explore the core characteristics of accredited specialists and to examine how their skills could be further utilized to enhance occupational health (OH) services.

Methods
Mixed methods comprising a survey and qualitative work.

Results
OH survey was completed by 65 of 128 (51%) respondents. Nine accredited specialists and 16 stakeholders contributed qualitative data. Most OH departments were located in acute NHS trusts and additionally provided externally contracted services. We found a large variation in OH staffing and OH services delivered. The COVID pandemic created unprecedented challenges and required expansion in services to meet demand. The majority of respondents described greater recognition and appreciation by others of accredited specialists and OH teams for their specialist contribution during the pandemic. From the qualitative data, we identified two overarching themes. ‘Professional credibility has currency’ (Theme 1) and ‘A visionary future’ (Theme 2). A series of sub-themes are described.

Conclusions
Accredited specialists employed in the NHS possess a core set of attributes and capabilities, and are skilful at delivering strong, influential and impactful clinical and strategic leadership across the NHS hierarchy and landscape. The COVID pandemic provided valuable opportunities for them to showcase their specialist clinical and leadership skills. The current wider reorientation of NHS clinical services offers bold new ways to expand their role beyond traditional clinical boundaries.
Nested calcium dynamics support daily cell unity and diversity in the suprachiasmatic nuclei of free-behaving mice
Authors: El Cheikh Hussein Lama , Fontanaud Pierre , Mollard Patrice , Bonnefont Xavier 
Published: July 2022

Abstract
The suprachiasmatic nuclei (SCN) of the anterior hypothalamus host the circadian pacemaker that synchronizes mammalian rhythms with the day–night cycle. SCN neurons are intrinsically rhythmic, thanks to a conserved cell-autonomous clock mechanism. In addition, circuit-level emergent properties confer a unique degree of precision and robustness to SCN neuronal rhythmicity. However, the multicellular functional organization of the SCN is not yet fully understood. Indeed, although SCN neurons are well-coordinated, experimental evidences indicate that some neurons oscillate out of phase in SCN explants, and possibly to a larger extent in vivo. Here, to tackle this issue we used microendoscopic Ca2+i imaging and investigated SCN rhythmicity at a single cell resolution in free-behaving mice. We found that SCN neurons in vivo exhibited fast Ca2+i spikes superimposed upon slow changes in baseline Ca2+i levels. Both spikes and baseline followed a time-of-day modulation in many neurons, but independently from each other. Daily rhythms in basal Ca2+i were highly coordinated, while spike activity from the same neurons peaked at multiple times of the light cycle, and unveiled clock-independent coactivity in neuron subsets. Hence, fast Ca2+i spikes and slow changes in baseline Ca2+i levels highlighted how multiple individual activity patterns could articulate within the temporal unity of the SCN cell network in vivo, and provided support for a multiplex neuronal code in the circadian pacemaker.
Evidence-based management of patients with nonalcoholic fatty liver disease
Authors: Patel Minal 
Published: July 2022

ABSTRACT
Over the past decade, fatty liver disease has become a forefront health issue. The clinical implication of this silent disease extends well beyond just the liver and is linked to a variety of health concerns, including cardiovascular disease, diabetes, and cancer. The prevalence of fatty liver disease in the United States is estimated to be 25% and increasing. This article reviews the pathophysiology of fatty liver disease, how clinicians can recognize contributing factors, and appropriate interventions based on the American Association for the Study of Liver Disease's guidelines.
Open Reduction Internal Fixation Versus Distal Femoral Replacement (DFR) for Treatment of OTA/AO 33C Fractures in the Elderly: A Review of Functional Outcomes and Cost Analysis
Authors: Caines Andrew , Adamczyk Andrew , Mahaffey Ryan , Pickell Michael 
Published: July 2022

Objectives:
To determine the economic cost associated with the treatment of OTA/AO 33C fractures in patients older than 65 years of age using open reduction internal fixation (ORIF) or DFR and to assess the perioperative outcomes of elderly patients treated surgically following OTA/AO 33C fractures.

Design:
Retrospective cohort over a 10-year period.

Setting:
A single level-1 trauma center.

Participants and Intervention:
Thirty-nine patients 65 or older with OTA/AO 33C fractures who underwent treatment with ORIF (n = 27) or DFR (n = 12) were included.

Main Outcome Measurements:
Direct cost associated with surgical treatment along with LOS, functional outcomes, patient-reported outcomes, and all-cause reoperation.

Results:
Index procedure costs were as follows: DFR: $ 61,259 vs. ORIF: $44,490 (P = 0.056). Five (20%) ORIF patients required revision versus one (8%) in the DFR group. Total cost when including reoperation resulted in DFR being $14,805 more costly, which was not significant. Hospital LOS was similar between groups; however, convalescent LOS was longer in ORIF patients (43.2 vs. 23.1 days, P = 0.02).

Conclusion:
This study demonstrates that there is no significant difference in overall cost between ORIF and DFR when all costs are considered. A larger portion of DFR patients were able to mobilize postoperatively, with subacute length of stay being longer in ORIF patients. A multicenter trial is warranted to determine optimal treatment for this complex problem.

Level of Evidence:
Economic Level IV. See Instructions for Authors for a complete description of levels of evidence.