bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Development of Cefiderocol Resistance in Carbapenem-resistant Enterobacter cloacae During Therapy Is Associated With Heterogeneous Mutations in the Catecholate Siderophore Receptor cirA
Authors: Klein Sabrina , Boutin Sébastien , Kocer Kaan , Fiedler Mascha O , Störzinger Dominic , Weigand Markus A , Tan Benjamin , Richter Daniel , Rupp Christian , Mieth Markus , Mehrabi Arianeb , Hackert Thilo , Zimmermann Stefan , Heeg Klaus , Nurjadi Dennis 
Published: June 2021

Abstract
We report a case of resistance development toward cefiderocol in a patient with intra-abdominal and bloodstream infections caused by carbapenemase-producing Enterobacter cloacae within 21 days of cefiderocol therapy. Whole genome sequencing revealed heterogeneous mutations in the cirA gene, encoding a catecholate siderophore receptor, conferring phenotypic resistance to cefiderocol.
Epidemiology, Natural History, Diagnosis, and Treatment of Trichomonas vaginalis in Men
Authors: Van Gerwen Olivia T , Camino Andres F , Sharma Jyoti , Kissinger Patricia J , Muzny Christina A 
Published: June 2021

Abstract
Trichomonas vaginalis infections in men are traditionally considered to be benign and consequently have been overlooked. However, men with this common sexually transmitted infection can experience urethritis, prostatitis, reduced fertility, and amplified human immunodeficiency virus risk. In addition, men are often asymptomatic and can unknowingly spread the infection to their female sexual partners. With advances in T. vaginalis diagnostics, more men are being diagnosed, yet the optimal method of treatment in men remains unknown. The purpose of this review is to discuss the epidemiology, natural history, diagnosis, and treatment of T. vaginalis among men.
Reconstructing income inequality in a colonial cash crop economy: five social tables for Uganda, 1925–1965
Authors: de Haas Michiel 
Published: June 2021

AbstractThis study contributes to an expanding literature on historical African inequality, presenting five social tables and income inequality estimates for Uganda between 1925 and 1965. I find that income inequality was mostly stable and overall low compared to other African colonies. Decomposition reveals important underlying fault lines and shifts. Income gaps between the African majority and a tiny Asian and European income elite accounted for a large share of overall inequality. Over time, inequality among Africans increased. Income from self-provisioning was a major equalizer in Uganda’s economy, which was characterized by land abundance and widespread smallholder cultivation of labor-intensive export crops.
Effectiveness of home-based cardiac telerehabilitation as an alternative to Phase 2 cardiac rehabilitation of coronary heart disease: a systematic review and meta-analysis
Authors: Ramachandran Hadassah Joann , Jiang Ying , Tam Wilson Wai San , Yeo Tee Joo , Wang Wenru 
Published: June 2021

Abstract

Aims
The onset of the COVID-19 pandemic saw the suspension of centre-based cardiac rehabilitation (CBCR) and has underscored the need for home-based cardiac telerehabilitation (HBCTR) as a feasible alternative rehabilitation delivery model. Yet, the effectiveness of HBCTR as an alternative to Phase 2 CBCR is unknown. We aimed to conduct a meta-analysis to quantitatively appraise the effectiveness of HBCTR.

Methods and results
PubMed, EMBASE, CENTRAL, CINAHL, Scopus, and PsycINFO were searched from inception to January 2021. We included randomized controlled trials (RCTs) comparing HBCTR to Phase 2 CBCR or usual care in patients with coronary heart disease (CHD). Out of 1588 studies, 14 RCTs involving 2869 CHD patients were included in this review. When compared with usual care, participation in HBCTR showed significant improvement in functional capacity {6-min walking test distance [mean difference (MD) 25.58 m, 95% confidence interval (CI) 14.74–36.42]}; daily step count (MD 1.05 K, 95% CI 0.36–1.75) and exercise habits [odds ratio (OR) 2.28, 95% CI 1.30–4.00)]; depression scores (standardized MD −0.16, 95% CI −0.32 to 0.01) and quality of life [Short-Form mental component summary (MD 2.63, 95% CI 0.06–5.20) and physical component summary (MD 1.99, 95% CI 0.83–3.16)]. Effects on medication adherence were synthesized narratively. HBCTR and CBCR were comparably effective.

Conclusion
In patients with CHD, HBCTR was associated with an increase in functional capacity, physical activity (PA) behaviour, and depression when compared with UC. When HBCTR was compared to CBCR, an equivalent effect on functional capacity, PA behaviour, QoL, medication adherence, smoking behaviour, physiological risk factors, depression, and cardiac-related hospitalization was observed.
The impacts of including information about the number of carcinogens in smoke on standardized cigarette packs in the UK
Authors: Moodie Crawford , Best Catherine , Critchlow Nathan , Hitchman Sara , Stead Martine , McNeill Ann 
Published: June 2021

Abstract

Background
Since May 2017, standardized packaging has been mandatory in the UK, with packs required to display an ‘information message’ explaining that there are more than 70 carcinogens in tobacco smoke.

Methods
Three waves of a longitudinal online survey in the UK with smokers pre-standardized packaging (Wave 1: April–May 2016) and followed up post-standardized packaging (Wave 2: September–November 2017, Wave 3: May–July 2019). Of the 6233 smokers at Wave 1, 4293 responded at Wave 2 and 3175 at Wave 3. We explored knowledge of the number of carcinogens in smoke, and whether knowing that smoke contains more than 70 carcinogens mediated change in the belief that the dangers of smoking are exaggerated (risk perception), stubbing out cigarettes, quit intentions and quitting. As the information message is larger on roll-your-own packs than on cigarette packs, as the packs are larger, we also explored whether there was any difference in knowing that smoke contains more than 70 carcinogens between exclusive cigarette smokers and exclusive roll-your-own smokers.

Results
Knowledge that there are over 70 carcinogens in smoke increased among smokers across waves, with the increase from Waves 1 to 3 greater for exclusive roll-your-own smokers than exclusive cigarette smokers (adjusted odds ratio=1.44; 95% CI 1.03–2.03). Knowledge that there are over 70 carcinogens in smoke mediated higher risk perception but not stubbing cigarettes out, quit intentions or quitting.

Conclusions
The information message improved knowledge of how many carcinogens are in smoke, particularly among exclusive roll-your-own smokers, and this was linked to higher risk perception.
Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome
Authors: McMullen John G , Bueno Eduardo , Blow Frances , Douglas Angela E 
Published: June 2021

Abstract
Annotated genome sequences provide valuable insight into the functional capabilities of members of microbial communities. Nevertheless, most studies on the microbiome in animal guts use metagenomic data, hampering the assignment of genes to specific microbial taxa. Here, we make use of the readily culturable bacterial communities in the gut of the fruit fly Drosophila melanogaster to obtain draft genome sequences for 96 isolates from wild flies. These include 81 new de novo assembled genomes, assigned to three orders (Enterobacterales, Lactobacillales, and Rhodospirillales) with 80% of strains identified to species level using average nucleotide identity and phylogenomic reconstruction. Based on annotations by the RAST pipeline, among-isolate variation in metabolic function partitioned strongly by bacterial order, particularly by amino acid metabolism (Rhodospirillales), fermentation, and nucleotide metabolism (Lactobacillales) and arginine, urea, and polyamine metabolism (Enterobacterales). Seven bacterial species, comprising 2–3 species in each order, were well-represented among the isolates and included ≥5 strains, permitting analysis of metabolic functions in the accessory genome (i.e., genes not present in every strain). Overall, the metabolic function in the accessory genome partitioned by bacterial order. Two species, Gluconobacter cerinus (Rhodospirillales) and Lactiplantibacillus plantarum (Lactobacillales) had large accessory genomes, and metabolic functions were dominated by amino acid metabolism (G. cerinus) and carbohydrate metabolism (La. plantarum). The patterns of variation in metabolic capabilities at multiple phylogenetic scales provide the basis for future studies of the ecological and evolutionary processes shaping the diversity of microorganisms associated with natural populations of Drosophila.
De novo genome assemblies of butterflies
Authors: Ellis Emily A , Storer Caroline G , Kawahara Akito Y 
Published: June 2021

Abstract

Background
The availability of thousands of genomes has enabled new advancements in biology. However, many genomes have not been investigated for their quality. Here we examine quality trends in a taxonomically diverse and well-known group, butterflies (Papilionoidea), and provide draft, de novo assemblies for all available butterfly genomes. Owing to massive genome sequencing investment and taxonomic curation, this is an excellent group to explore genome quality.

Findings
We provide de novo assemblies for all 822 available butterfly genomes and interpret their quality in terms of completeness and continuity. We identify the 50 highest quality genomes across butterflies and conclude that the ringlet, Aphantopus hyperantus, has the highest quality genome. Our post-processing of draft genome assemblies identified 118 butterfly genomes that should not be reused owing to contamination or extremely low quality. However, many draft genomes are of high utility, especially because permissibility of low-quality genomes is dependent on the objective of the study. Our assemblies will serve as a key resource for papilionid genomics, especially for researchers without computational resources.

Conclusions
Quality metrics and assemblies are typically presented with annotated genome accessions but rarely with de novo genomes. We recommend that studies presenting genome sequences provide the assembly and some metrics of quality because quality will significantly affect downstream results. Transparency in quality metrics is needed to improve the field of genome science and encourage data reuse.
Placental endocrine insufficiency programs anxiety, deficits in cognition and atypical social behaviour in offspring
Authors: Harrison David J , Creeth Hugo D J , Tyson Hannah R , Boque-Sastre Raquel , Hunter Susan , Dwyer Dominic M , Isles Anthony R , John Rosalind M 
Published: June 2021

Abstract
Abnormally elevated expression of the imprinted PHLDA2 gene has been reported in the placenta of human babies that are growth restricted in utero in several studies. We previously modelled this gene alteration in mice and found that just 2-fold increased expression of Phlda2 resulted in placental endocrine insufficiency. In addition, elevated Phlda2 was found to drive fetal growth restriction (FGR) of transgenic offspring and impaired maternal care by their wildtype mothers. Being born small and being exposed to suboptimal maternal care have both been associated with the increased risk of mental health disorders in human populations. In the current study we probed behavioural consequences of elevated Phlda2 for the offspring. We discovered increased anxiety-like behaviours, deficits in cognition and atypical social behaviours, with the greatest impact on male offspring. Subsequent analysis revealed alterations in the transcriptome of the adult offspring hippocampus, hypothalamus and amygdala, regions consistent with these behavioural observations. The inclusion of a group of fully wildtype controls raised in a normal maternal environment allowed us to attribute behavioural and molecular alterations to the adverse maternal environment induced by placental endocrine insufficiency rather than the specific gene change of elevated Phlda2. Our work demonstrates that a highly common alteration reported in human FGR is associated with negative behavioural outcomes later in life. Importantly, we also establish the experimental paradigm that placental endocrine insufficiency can program atypical behaviour in offspring highlighting the under-appreciated role of placental endocrine insufficiency in driving disorders of later life behaviour.
Targeting immunometabolism to treat COVID-19
Authors: O’Carroll Shane M , O’Neill Luke A J 
Published: June 2021

SummaryThe COVID-19 crisis has emphasised the need for antiviral therapies to combat current and future viral zoonoses. Recent studies have shown that immune cells such as macrophages are the main contributors to the inflammatory response seen in the later inflammatory phase of COVID-19. Immune cells in the context of a viral infection such as SARS-CoV-2 undergo metabolic reprogramming to elicit these pro-inflammatory effector functions. The evidence of metabolic reprogramming in COVID-19 offers opportunities for metabolites with immunomodulatory properties to be investigated as potential therapies to combat this hyper-inflammatory response. Recent research indicates that the metabolite itaconate, previously known to be broadly antibacterial, may have both antiviral and immunomodulatory potential. Furthermore, low itaconate levels have shown to correlate with COVID-19 disease severity, potentially implicating its importance in the disease. The antiviral potential of itaconate has encouraged researchers to synthesise itaconate derivatives for antiviral screening, with some encouraging results. This review summarises the antiviral and immunomodulatory potential of immunometabolic modulators including metformin, peroxisome proliferator-activated receptor agonists and TEPP-46 as well as itaconate, and its derivatives and their potential use as broad spectrum anti-viral agents.
Factors affecting performance response of pigs exposed to different challenge models: a multivariate approach
Authors: Rodrigues Lucas A , Ferreira Felipe N A , Costa Matheus O , Wellington Michael O , Columbus Daniel A 
Published: June 2021

Abstract
Factors associated with the severity with which different challenge models (CMs) compromise growth performance in pigs were investigated using hierarchical clustering on principal components (HCPC) analysis. One hundred seventy-eight studies reporting growth performance variables (average daily gain [ADG], average daily feed intake [ADFI], gain:feed [GF], and final body weight [FBW]) of a Control (Ct) vs. a Challenged (Ch) group of pigs using different CMs (enteric [ENT], environmental [ENV], lipopolysaccharide [LPS], respiratory [RES], or sanitary condition [SAN] challenges) were included. Studies were grouped by similarity in performance in three clusters (C1, C2, and C3) by HCPC. The effects of CM, cluster, and sex (males [M], females [F], mixed [Mi]) were investigated. Linear (LRP) and quadratic (QRP) response plateau models were fitted to assess the interrelationships between the change in ADG (∆ADG) and ADFI (∆ADFI) and the duration of challenge. All variables increased from C1 through C3, except for GF, which decreased (P &lt; 0.05). LPS was more detrimental to ADG than ENV, RES, and SAN models (P &lt; 0.05). Furthermore, LPS also lowered GF more than all the other CMs (P &lt; 0.05). The ∆ADG independent of ∆ADFI was significant in LPS and SAN (P &lt; 0.05), showed a trend toward the significance in ENT and RES (P &lt; 0.10), and was not significant in ENV (P &gt; 0.10), while the ∆ADG dependent on ∆ADFI was significant in ENT, ENV, and LPS only (P &lt; 0.05). The critical value of ∆ADFI influencing the ∆ADG was significant in pigs belonging to C1 (P &lt; 0.05) but not C2 or C3 (P &gt; 0.10). The ∆ADG independent of duration post-Ch (irreparable portion of growth) was significant in C1 and C2 pigs, whereas the ∆ADFI independent of duration post-Ch (irreparable portion of feed intake) was significant in C1 pigs only (P &lt; 0.05). Moreover, the time for recovery of ADG and ADFI after Ch was significant in pigs belonging to C1 and C2 (P &lt; 0.05). Control F showed reduced ADG compared with Ct-M, and Ch-F showed reduced ADFI compared with Ch-M (P &lt; 0.05). Moreover, the irreparable portion of ΔADG was 4.8 higher in F (−187.7; P &lt; 0.05) compared with M (−39.1; P &lt; 0.05). There are significant differences in growth performance response to CM based on cluster and sex. Furthermore, bacterial lipopolysaccharide appears to be an appropriate noninfectious model for immune stimulation and growth impairment in pigs.
Middle cerebral artery occlusion due to cardiac tissue following catheter ablation in Wolff–Parkinson–White syndrome
Authors: Phuyal Subash , Paudel Raju , Agrawal Pooja , Lamsal Ritesh 
Published: June 2021

Abstract
Catheter ablation is a commonly performed procedure in patients with Wolff–Parkinson–White syndrome. A 56-year-old man developed an acute ischemic stroke immediately after undergoing radiofrequency catheter ablation of the left-sided accessory pathway. Neuroimaging revealed complete occlusion of the proximal middle cerebral artery. Mechanical thrombectomy (MT) was performed with successful retrieval of the thrombo-embolus. Histopathological examination of the thrombo-embolus confirmed organic cardiac tissue. The patient was later discharged from the hospital with no neurologic deficit. There is no report of successful MT in patients with large-vessel occlusion because of the embolization of cardiac tissue after catheter ablation. This report highlights the need to remain vigilant for signs of stroke after any cardiac intervention.
Detection of the metabolic response to drought stress using hyperspectral reflectance
Authors: Burnett Angela C , Serbin Shawn P , Davidson Kenneth J , Ely Kim S , Rogers Alistair 
Published: June 2021

Abstract
Drought is the most important limitation on crop yield. Understanding and detecting drought stress in crops is vital for improving water use efficiency through effective breeding and management. Leaf reflectance spectroscopy offers a rapid, non-destructive alternative to traditional techniques for measuring plant traits involved in a drought response. We measured drought stress in six glasshouse-grown agronomic species using physiological, biochemical, and spectral data. In contrast to physiological traits, leaf metabolite concentrations revealed drought stress before it was visible to the naked eye. We used full-spectrum leaf reflectance data to predict metabolite concentrations using partial least-squares regression, with validation R2 values of 0.49–0.87. We show for the first time that spectroscopy may be used for the quantitative estimation of proline and abscisic acid, demonstrating the first use of hyperspectral data to detect a phytohormone. We used linear discriminant analysis and partial least squares discriminant analysis to differentiate between watered plants and those subjected to drought based on measured traits (accuracy: 71%) and raw spectral data (66%). Finally, we validated our glasshouse-developed models in an independent field trial. We demonstrate that spectroscopy can detect drought stress via underlying biochemical changes, before visual differences occur, representing a powerful advance for measuring limitations on yield.
On possible proxies of AGN light-curves cadence selection in future time domain surveys
Authors: Kovačević Andjelka B , Ilić Dragana , Popović Luka Č , Radović Viktor , Jankov Isidora , Yoon Ilsang , Caplar Neven , Čvorović-Hajdinjak Iva , Simić Saša 
Published: June 2021

ABSTRACT
Motivated by upcoming photometric and spectroscopic surveys [Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST), Manuakea Spectroscopic Explorer], we design the statistical proxies to measure the cadence effects on active galactic nuclei (AGNs) variability-observables [time-lags, periodicity, and structure-function (SF)]. We constructed a multiple-regression model to statistically identify the cadence-formal error pattern knowing AGN time-lags and periodicity from different surveys. We defined the simple metric for the SF’s properties, accounting for the ‘observed’ SF’s deviation relative to those obtained from the homogenously sampled light curves. We tested the regression models on different observing strategies: the optical data set of long light curves of eight AGN with peculiarities and the artificial data sets based on several idealized and LSST-like cadences. The SFs metric is assessed on synthetic data sets. The regression models (for both data types) predict similar cadences for time-lags and oscillation detection, whereas for light curves with low variability (${\sim}10{{\ \rm per\ cent}}$), cadences for oscillation detection differ. For higher variability (${\sim}20{{\ \rm per\ cent}}$), predicted cadences are larger than for $F_{var}\sim 10{{\ \rm per\ cent}}$. The predicted cadences are decreasing with redshift. SFs with dense and homogenous cadences are more likely to behave similarly. SFs with oscillatory signals are sensitive to the cadences, possibly impacting LSST-like operation strategy. The proposed proxies can help to select spectroscopic and photometric-surveys cadence strategies, and they will be tested further in larger samples of objects.
HIV-Infected Individuals on ART With Impaired Immune Recovery Have Altered Plasma Metabolite Profiles
Authors: Nyström Sofia , Govender Melissa , Yap Siew Hwei , Kamarulzaman Adeeba , Rajasuriar Reena , Larsson Marie 
Published: June 2021

Abstract

Background
Multiple host factors may influence immune reconstitution in HIV-infected people after the initiation of suppressive antiretroviral therapy (ART). Aberrant metabolic pathways have been reported in people with HIV (PWH) on ART. We hypothesized that alterations in plasma metabolites were associated with immune recovery following ART.

Methods
In this cross-sectional study, the plasma metabolomic profiles of PWH on ART were evaluated. PWH of slow and fast immune recovery were classified by increase in CD4 T cells following 2 years of ART. Targeted plasma metabolite profiling by liquid chromatography–mass spectrometry and gas chromatography–mass spectrometry to determine metabolite signatures for HIV recovery identified &gt;200 metabolites.

Results
Notably, indole-3-propionic acid was downregulated during HIV, possibly reflecting impaired gastrointestinal epithelium homeostasis. The most important metabolite discriminating between the PWH with fast and slow immune recovery was cysteine. Upregulated cysteine and cysteine pathways may contribute to redox-balance maintenance and T-cell function in PWH with fast immune recovery. Additionally, serine and glycine metabolism and bile acid biosynthesis were the most perturbed metabolic pathways in PWH.

Conclusions
These results provide a starting point for developing biomarker candidates for immune recovery in PWH on ART and provide insight into the interplay of metabolism and immune response in HIV infection.
Infected Nonunion of the Tibia Due to Paenibacillus turicensis in a Healthy Young Adult After an All-Terrain Vehicle Accident
Authors: Schade Meredith , French Cristy N 
Published: June 2021

Abstract
We present the case of a 19-year-old man with an open fracture of the tibia and fibula secondary to an accident with an all-terrain vehicle. He underwent operative excisional irrigation, debridement, and fixation on the day of injury. His course was complicated by nonunion of the tibia fracture. Infection is a common factor in fracture nonunion, even in patients who receive appropriate surgical and antimicrobial management. Paenibacillus turicensis, an organism adapted to survive in the environment via spore formation, was responsible for nonunion in our patient. A brief discussion of this unusual organism, fracture nonunion, and the role of infection in etiology of nonunion follows.