bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ionizing radiation and solid cancer mortality among US nuclear facility workers
Authors: Kelly-Reif Kaitlin , Bertke Steven J , Daniels Robert D , Richardson David B , Schubauer-Berigan Mary K 
Published: May 2023

Abstract

Background
The risk of solid cancers from low-level protracted ionizing radiation is not well characterized. Nuclear workers provide valuable information on the effects of ionizing radiation in contemporary exposure scenarios relevant to workers and the public.

Methods
We evaluated the association between penetrating ionizing radiation exposure and solid cancer mortality among a pooled cohort of nuclear workers in the USA, with extended follow-up to examine cancers with long latencies. This analysis includes 101 363 workers from five nuclear facilities, with 12 069 solid cancer deaths between 1944 and 2016. The association between cumulative equivalent dose measured in sieverts (Sv) and solid cancer subtypes were modelled as the excess relative rate per Sv (ERR Sv–1) using Cox regression.

Results
For the association between ionizing radiation exposure and all solid cancer mortality we observed an elevated rate (ERR Sv–1=0.19; 95% CI: –0.10, 0.52), which was higher among a contemporary sub-cohort of workers first hired in 1960 or later (ERR Sv–1= 2.23; 95% CI: 1.13, 3.49). Similarly, we observed an elevated rate for lung cancer mortality (ERR Sv–1= 0.65; 95% CI: 0.09, 1.30) that was higher among contemporary hires (ERR Sv–1= 2.90; 95% CI: 1.00, 5.26).

Conclusions
Although concerns remain about confounding, measurement error and precision, this analysis strengthens the evidence base indicating there are radiogenic risks for several solid cancer types.
High-titer convalescent plasma plus nirmatrelvir/ritonavir treatment for non-resolving COVID-19 in six immunocompromised patients
Authors: Huygens Sammy , Gharbharan Arvind , Serroukh Yasmina , Snoek Britt , Franken Bas , Oude Munnink Bas B , Van Hagen P Martin , Bogers Susanne , Geurtsvankessel Corine H , Rijnders Bart J A 
Published: May 2023

Abstract

Objectives
Immunocompromised patients have an increased risk of severe or prolonged COVID-19. Currently available drugs are registered to treat COVID-19 during the first 5 to 7 days after symptom onset. Data on the effectivity in immunocompromised patients with chronic non-resolving COVID-19 are urgently needed. Here, we report the outcome of patients treated with nirmatrelvir/ritonavir together with high-titer convalescent plasma (CP) in six immunocompromised patients with non-resolving COVID-19.

Methods
Immunocompromised patients with persisting COVID-19 (positive PCR with Ct values &lt;30 for ≥20 days) received off-label therapy with nirmatrelvir/ritonavir. It was combined with CP containing BA.5 neutralizing titers of ≥1/640 whenever available. Follow-up was done by PCR and sequencing on nasopharyngeal swabs on a weekly basis until viral genome was undetectable consecutively.

Results
Five immunocompromised patients were treated with high-titer CP and 5 days of nirmatrelvir/ritonavir. One patient received nirmatrelvir/ritonavir monotherapy. Median duration of SARS-CoV-2 PCR positivity was 70 (range 20–231) days before nirmatrelvir/ritonavir treatment. In four patients receiving combination therapy, no viral genome of SARS-CoV-2 was detected on day 7 and 14 after treatment while the patient receiving nirmatrelvir/ritonavir monotherapy, the day 7 Ct value increased to 34 and viral genome was undetectable thereafter. Treatment was unsuccessful in one patient. In this patient, sequencing after nirmatrelvir/ritonavir treatment did not show protease gene mutations.

Conclusions
In immunocompromised patients with non-resolving COVID-19, the combination of nirmatrelvir/ritonavir and CP may be an effective treatment. Larger prospective studies are needed to confirm these preliminary results and should compare different treatment durations.
Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat
Authors: Brouwer Michael S M , Zandbergen Van Essen Alieda , Kant Arie , Rapallini Michel , Harders Frank , Bossers Alex , Wullings Bart , Wit Ben , Veldman Kees T 
Published: May 2023

Abstract

Background
As WGS comes of age, changes in EU legislation implemented in 2021 allow its usage for systematic monitoring of ESBL-producing Escherichia coli from livestock and meat, replacing phenotypic testing. Presently, phenotypic testing correlates well with antimicrobial resistance predicted from WGS data. WGS has added value in the wealth of additional information that is present in the data.

Objectives
In this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli.

Methods
Susceptibility testing was performed with broth microdilution of selectively isolated E. coli. Short-read WGS was performed in parallel and phenotypes predicted based on the sequence data, which was also used to determine the phylogeny of the isolates.

Results
The phenotypically determined resistance and the predicted resistance correlated 90%–100% for the different antimicrobial classes. Furthermore, clonal relationships were detected amongst ESBL-producing E. coli within livestock sectors and the meat produced by this sector.

Conclusions
Further implementation of WGS analysis of ESBL/AmpC-producing E. coli within the AMR monitoring programme of EU member states and global surveillance programmes will contribute to determining the attribution of livestock in the prevalence of ESBL/AmpC-encoding E. coli in humans.
In vitro dynamics and mechanisms of cefiderocol resistance development in wild-type, mutator and XDR Pseudomonas aeruginosa
Authors: Gomis-Font María A , Sastre-Femenia Miquel À , Taltavull Biel , Cabot Gabriel , Oliver Antonio 
Published: May 2023

Abstract

Objectives
To analyse the dynamics and mechanisms of stepwise resistance development to cefiderocol in Pseudomonas aeruginosa.

Methods
Cefiderocol resistance evolution was analysed in WT PAO1, PAOMS (mutS mutator derivate) and three XDR clinical isolates belonging to ST111, ST175 and ST235 clones. Strains were incubated in triplicate experiments for 24 h in iron-depleted CAMHB with 0.06–128 mg/L cefiderocol. Tubes from the highest antibiotic concentration showing growth were reinoculated into fresh medium containing concentrations up to 128 mg/L for 7 consecutive days. Two colonies per strain and experiment were characterized by determining the susceptibility profiles and WGS.

Results
Evolution of resistance was significantly enhanced in PAOMS, but was variable for the XDR strains, including levels similar to PAOMS (ST235), similar to PAO1 (ST175) or even below PAO1 (ST111). WGS revealed 2–5 mutations for PAO1 lineages and 35–58 for PAOMS. The number of mutations in the XDR clinical strains ranged from 2 to 4 except for one of the ST235 experiments in which a mutL lineage was selected, thus increasing the number of mutations. The most frequently mutated genes were piuC, fptA and pirR, related to iron uptake. Additionally, an L320P AmpC mutation was selected in multiple lineages and cloning confirmed its major impact on cefiderocol (but not ceftolozane/tazobactam or ceftazidime/avibactam) resistance. Mutations in CpxS and PBP3 were also documented.

Conclusions
This work deciphers the potential resistance mechanisms that may emerge upon the introduction of cefiderocol into clinical practice, and highlights that the risk of resistance development might be strain-specific even for XDR high-risk clones.
Chlorpyrifos and chlorfenapyr resistance in Spodoptera frugiperda (Lepidoptera: Noctuidae) relies on UDP-glucuronosyltransferases
Authors: Su Xiang-ning , Li Chuan-ying , Zhang Yu-ping 
Published: May 2023

Abstract
Fall armyworm, Spodoptera frugiperda (J. E. Smith), has become an important agricultural pest worldwide. S. frugiperda is mainly controlled by the chemical insecticides, whereas the frequent application of insecticides would result in the resistance development. Insect uridine diphosphate-glucuronosyltransferases (UGTs), as phase II metabolism enzymes, play vital roles in the breakdown of endobiotic and xenobiotics. In this study, 42 UGT genes were identified by RNA-seq, including 29 UGT genes were elevated compared to the susceptible population, and the transcript levels of 3 UGTs (UGT40F20, UGT40R18, and UGT40D17) were increased by more than 2.0-fold in the field populations. Expression pattern analysis revealed that S. frugiperda UGT40F20, UGT40R18, and UGT40D17 were increased by 6.34-, 4.26-, and 8.28-fold, compared the susceptible populations, respectively. The expression of UGT40D17, UGT40F20, and UGT40R18 was affected after exposure to phenobarbital, chlorpyrifos, chlorfenapyr, sulfinpyrazone, and 5-nitrouracil. The induced expression of UGT genes may have improved UGT enzymatic activity, while the inhibition of UGTs genes expression may decreased UGT enzymatic activity. Sulfinpyrazone, and 5-nitrouracil, significantly increased the toxicity of chlorpyrifos and chlorfenapyr, as well as phenobarbital significantly reduced the toxicity of chlorpyrifos and chlorfenapyr against the susceptible populations and field populations of S. frugiperda. The suppression of UGTs (UGT40D17, UGT40F20, and UGT40R18) significantly increased the insensitivity of the field populations to chlorpyrifos and chlorfenapyr. These findings strongly supported our viewpoint that UGTs may play a critical role in insecticide detoxification. This study provides a scientific basis for the management of S. frugiperda.
Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)
Authors: Kliver Sergei , Houck Marlys L , Perelman Polina L , Totikov Azamat , Tomarovsky Andrey , Dudchenko Olga , Omer Arina D , Colaric Zane , Weisz David , Aiden Erez Lieberman , Chan Saki , Hastie Alex , Komissarov Aleksey , Ryder Oliver A , Graphodatsky Alexander , Johnson Warren E , Maldonado Jesús E , Pukazhenthi Budhan S , Marinari Paul E , Wildt David E , Koepfli Klaus-Peter 
Published: May 2023

AbstractThe black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.
Reranking cancer mortality using years of life lost
Authors: Radkiewicz Cecilia , Andersson Therese M-L , Lagergren Jesper 
Published: May 2023

Abstract
Incidence and mortality are default measures to describe cancer trends. Mortality compounds incidence and survival but not age at death. We calculated years of life lost (YLL) due to 1 of the 10 solid tumors causing most deaths (lung, colorectal, prostate, pancreatic, breast, hepatobiliary, urinary, central nervous system, gastric, melanoma) using Swedish National Cancer and Cause of Death Registers. Comparing YLL with mortality in 2019, lung (43 152 YLL) and colorectal (32 340 YLL) cancer remained at the top, pancreatic cancer was upranked fourth to third (22 592 YLL) and breast cancer fifth to fourth (21 810 YLL), while prostate cancer was downranked third to fifth (17 380 YLL). Assessing YLL over 2010-2019, women lost consistently more life years because of lung and pancreatic cancer. A downward colorectal cancer mortality trend was reflected as a YLL decline only in women. YLL is simple to calculate, is intuitive to interpret, and expands the understanding of the cancer burden on society.
Complications of surgical management of osteopetrosis. A case report of multiple surgeries performed on one patient
Authors: Lamut Anže , Kovač Simon 
Published: May 2023

Abstract
Osteopetrosis is a rare form of sclerosing bone dysplasias which in some cases requires orthopedic surgical management of its complications. It is characterized by osteosclerosis, brittle bones and obliteration of the medullary cavity. Therefore, surgery in these cases is difficult and results can be compromised by postoperative complications. We present a case of a 73-year-old patient treated at our institution in a period of 24 years. In this period, the patient had bilateral primary hip arthroplasty (THA), total knee arthroplasty, revision surgeries of both THA’s and lumbar spine surgeries. The treatment of infected THA and periprosthetic fractures ended with satisfactory results but complications of the spinal surgery resulted in a poor clinical outcome.
Drop impact dynamics on the hydrophobic leaf surface of an aquatic plant: a case study of Pistia stratiotes
Authors: Papierowska Ewa , Beczek Michał , Mazur Rafał , Szatyłowicz Jan , Szewińska Joanna , Polakowski Cezary , Ryżak Magdalena , Stańczyk Tomasz , Sochan Agata , Frankowska-Łukawska Justyna , Bieganowski Andrzej 
Published: May 2023

Abstract
Pistia stratiotes is an aquatic plant with a complex structure that allows it to stay afloat. It grows quickly, and in large numbers becomes an undesirable plant as an invasive species. Describing the dynamics of a water drop splash on P. stratiotes leaves can contribute to increasing knowledge of its behavior and finding alternative methods for eradicating it or using it for the benefit of the environment. The non-wettable surface of P. stratiotes presents a complex structure—simple uniseriate trichomes and also ridges and veins. We analyzed the drop impact on a leaf placed on the water surface and recorded it by high-speed cameras. Based on the recordings, quantitative and qualitative analyses were performed. After impacting the leaf, the water drop spread until it reached its maximum surface area accompanied by the ejection of early droplets in the initial stage. Thereafter, three scenarios of water behavior were observed: (i) drop receding and stabilization; (ii) drop receding and ejection of late droplets formed in the later stage as an effect of elastic deformation of the leaf; and (iii) drop breaking apart and ejection of late droplets. The results indicated that the increasing kinetic energy of the impacting drops expressed by the Weber number and the complex leaf surface have an effect on the course of the splash. The simple uniseriate trichomes of the P. stratiotes leaf and the high energy of the falling drops were responsible for the formation and characteristics of the early droplets. The presence of ridges and veins and the leaf’s mechanical response had an impact on the occurrence of late droplets.
The value of metagenomic next-generation sequencing for the diagnosis of pulmonary tuberculosis using bronchoalveolar lavage fluid
Authors: Gao Jiali , Zhao Lu , Chen Gongqi , Huang Chunli , Kong Weiqiang , Feng Yuchen , Zhen Guohua 
Published: June 2023

Abstract

Objective
The aim of this study was to compare metagenomic next-generation sequencing (mNGS) with other methods, including Xpert MTB/RIF, Mycobacterium tuberculosis (MTB) culture, and acid-fast bacillus (AFB) staining in the diagnosis of pulmonary tuberculosis (PTB) using bronchoalveolar lavage fluid (BALF).

Methods
The data of 186 patients with suspected PTB were retrospectively collected from January 2020 to May 2021 at Tongji Hospital. BALF samples were collected from all patients and analyzed using AFB staining, MTB culture, Xpert MTB/RIF, and mNGS.

Results
Of the 186 patients, 38 patients were ultimately diagnosed as PTB. Metagenomic next-generation sequencing exhibited a sensitivity of 78.95%, which was higher than AFB staining (27.59%) and MTB culture (44.12%) but similar to Xpert MTB/RIF (72.73%). Utilization of combined methods demonstrates improvement for PTB diagnosis. In support of this, the area under the receiver operating characteristic curve for the combination of mNGS and MTB culture (0.933, 95% CI: 0.871, 0.995) was larger than those of mNGS, Xpert MTB/RIF, MTB culture, and the combination of Xpert MTB/RIF and MTB culture.

Conclusion
The sensitivity of mNGS in the diagnosis of PTB using BALF specimen is similar to Xpert MTB/RIF. Metagenomic next-generation sequencing in combination with MTB culture may further improve the diagnosis of pulmonary tuberculosis.
Comparison of Sampson and extended Martin/Hopkins methods of low-density lipoprotein cholesterol calculations with direct measurement in pediatric patients with hypertriglyceridemia
Authors: Touhidul Islam SM , Muthukumar Alagar R , Mary Jones Patricia , Hashim Ibrahim , Cao Jing 
Published: May 2023

Abstract

Objective
The Friedewald equation is the commonly used method of low-density lipoprotein cholesterol (LDL-C) calculation, requiring reflex to direct LDL-C measurement when triglycerides (TG) ≥ 400 mg/dL. Recently formulated Sampson and extended Martin/Hopkins methods have been validated with TG up to 800 mg/dL and thus have the potential to replace direct LDL-C measurement. Given the growing prevalence of childhood dyslipidemia, the objective of this study was to compare Sampson and extended Martin/Hopkins methods of LDL-C calculation with the direct measurement in a pediatric cohort with 400 ≤ TG ≤ 799 mg/dL.

Methods
This study retrieved standard lipid panels and corresponding direct LDL-C measurements of 131 patients with 400 ≤ TG ≤ 799 mg/dL from a pediatric population. Following the application of Sampson and extended Martin/Hopkins calculations, calculated values were compared with direct LDL-C measurements using ordinary least squares linear regression analysis and bias plotting.

Results
Both Sampson and extended Martin/Hopkins LDL-C calculations exhibited a strong correlation with the direct measurements (Pearson r = 0.89) in patients with 400 ≤ TG ≤ 800 mg/dL. Average percentages of bias of 45% and 21% were found between the direct LDL-C measurements and Sampson or extended Martin/Hopkins calculations, respectively.

Conclusion
Both Sampson and extended Martin/Hopkins calculations are applicable as clinical alternatives of direct LDL-C measurement in pediatric patients given 400 ≤ TG ≤ 799 mg/dL.
Nitrogen enhancements 440 Myr after the big bang: supersolar N/O, a tidal disruption event, or a dense stellar cluster in GN-z11?
Authors: Cameron Alex J , Katz Harley , Rey Martin P , Saxena Aayush 
Published: May 2023

ABSTRACT
Recent observations of GN-z11 with JWST/NIRSpec revealed numerous oxygen, carbon, nitrogen, and helium emission lines at z = 10.6. Using the measured line fluxes, we derive abundance ratios of individual elements within the interstellar medium (ISM) of this superluminous galaxy. Driven by the unusually-bright N iii] λ1750 and N iv] λ1486 emission lines (and by comparison, faint O iii] λλ1660, 1666 lines), our fiducial model prefers log (N/O) &gt; −0.25, greater than four times solar and in stark contrast to lower-redshift star-forming galaxies. The derived log (C/O) &gt; −0.78, (≈30 per cent solar) is also elevated with respect to galaxies of similar metallicity (12 + log (O/H) ≈ 7.82), although less at odds with lower-redshift measurements. We explore the feasibility of achieving these abundance ratios via several enrichment mechanisms using metal yields available in the literature. Given the long time-scale typically expected to enrich nitrogen with stellar winds, traditional scenarios require a very fine-tuned formation history to reproduce such an elevated N/O. We find no compelling evidence that nitrogen enhancement in GN-z11 can be explained by enrichment from metal-free Population III stars. Interestingly, yields from runaway stellar collisions in a dense stellar cluster or a tidal disruption event provide promising solutions to give rise to these unusual emission lines at z = 10.6, and explain the resemblance between GN-z11 and a nitrogen-loud quasar. These recent observations showcase the new frontier opened by JWST to constrain galactic enrichment and stellar evolution within 440 Myr of the big bang.
Studying the link between radio galaxies and AGN fuelling with relativistic hydrodynamic simulations of flickering jets
Authors: Whitehead Henry W , Matthews James H 
Published: May 2023

ABSTRACT
We present two- and three-dimensional hydrodynamic simulations of ∼kpc-scale AGN jets with mean jet powers in the range 1–7 × 1045 erg s−1, in which the jet power varies (through variation of the Lorentz factor) according to a flicker or pink noise power spectrum. We find the morphology and dynamics of the jet–cocoon system depends on the amplitude of the variability with a clear correspondence between the shape of the cocoon and the historical activity. The jet advances quickly during high-power states, whereas quiescent periods instead produce passive periods of inflation resembling Sedov–Taylor blast waves. Periods of high activity preferentially produce hotspots and create stronger backflow as they maximize the pressure gradient between the jet head and cocoon. The variability can also lead to propagating internal shock structures along the jet. Our work suggests that variability and flickering in the jet power has important implications, which we discuss, for observations of radio galaxies, ultrahigh energy cosmic ray acceleration and jet power to luminosity correlations. We explore the link between morphology and fuelling, and suggest that chaotic cold accretion should introduce a relatively small scatter in radio luminosity (∼0.2 dex) and modest imprints on morphology; sources such as Hercules A and Fornax A, which show evidence for more dramatic variability, may therefore require redder power spectra, or be triggered by mergers or other discrete events. We suggest ways to search for jet flickering observationally and propose that radio galaxies may be an important diagnostic of Myr time-scale AGN fuelling, due to their ‘long-term memory’.