bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring temporal trends and risk factors for resistance in Escherichia coli-causing bacteraemia in England between 2013 and 2018: an ecological study
Authors: Aliabadi Shirin , Jauneikaite Elita , Müller-Pebody Berit , Hope Russell , Vihta Karina-Doris , Horner Carolyne , Costelloe Céire E 
Published: November 2021

Abstract

Background
Escherichia coli are Gram-negative bacteria associated with an increasing burden of antimicrobial resistance (AMR) in England.

Objectives
To create a comprehensive epidemiological picture of E. coli bacteraemia resistance trends and risk factors in England by linking national microbiology data sources and performing a longitudinal analysis of rates.

Methods
A retrospective observational study was conducted on all national records for antimicrobial susceptibility testing on E. coli bacteraemia in England from 1 January 2013 to 31 December 2018 from the UK Health Security Agency (UKHSA) and the BSAC Resistance Surveillance Programme (BSAC-RSP). Trends in AMR and MDR were estimated using iterative sequential regression. Logistic regression analyses were performed on UKHSA data to estimate the relationship between risk factors and AMR or MDR in E. coli bacteraemia isolates.

Results
An increase in resistance rates was observed in community- and hospital-onset bacteraemia for third-generation cephalosporins, co-amoxiclav, gentamicin and ciprofloxacin. Among community-acquired cases, and after adjustment for other factors, patients aged &gt;65 years were more likely to be infected by E. coli isolates resistant to at least one of 11 antibiotics than those aged 18–64 years (OR: 1.21, 95% CI: 1.18–1.25; P &lt; 0.05). In hospital-onset cases, E. coli isolates from those aged 1–17 years were more likely to be resistant than those aged 18–64 years (OR: 1.33, 95% CI: 1.02–1.73; P &lt; 0.05).

Conclusions
Antibiotic resistance rates in E. coli-causing bacteraemia increased between 2013 and 2018 in England for key antimicrobial agents. Findings of this study have implications for guiding future policies on a prescribing of antimicrobial agents, for specific patient populations in particular.
Next Step for Global Adolescent and Young Adult Oncology: A Core Patient-Centered Outcome Set
Authors: Husson Olga , Reeve Bryce B , Darlington Anne-Sophie , Cheung Christabel K , Sodergren Samantha , van der Graaf Winette T A , Salsman John M 
Published: November 2021

Abstract
The relatively small number of cancers in the adolescent and young adult (AYA) age group, those aged 15-39 years, does not appropriately reflect the personal and societal costs of cancer in this population, as reflected in the potential years of life lost or saved, the decreased productivity and health-related quality of life due to the impact of the disease during formative years, and long-term complications or disabilities. Improvements in care and outcomes for AYAs with cancer require collaboration among different stakeholders at different levels (patients, caregivers, health-care professionals, researchers, industry, and policymakers). Development of a Core Outcome Set (COS), an agreed minimum set of outcomes that should be measured globally in research and routine clinical practice—specifically for AYAs with cancer—with outcomes that are well defined based on the perspective of those who are affected and assessed with validated measures, is urgently required. A globally implemented COS for AYAs with cancer will facilitate better pooling of research data and the implementation of high-quality health-care registries, which by benchmarking not only nationally but also internationally, may ultimately improve the value of the care given to these underserved young cancer patients. We reflect on the need to develop a COS for AYAs with cancer, the arenas of application, and the challenges of implementing an age-specific COS in research and clinical practice.
A National Survey of Outpatient Parenteral Antibiotic Therapy Practices
Authors: Vaz Louise E , Felder Kimberly K , Newland Jason G , Hersh Adam L , Rajapakse Nipunie S , Willis Zachary I , Banerjee Ritu , Gerber Jeffrey S , Schwenk Hayden T , Wang Marie E 
Published: November 2021

Abstract
We conducted a national survey of pediatric infectious diseases (ID) clinicians on outpatient parenteral antibiotic therapy (OPAT) practices and post-discharge ID follow-up. Only 15% of sites required ID consultation for all OPAT. ID division resources for post-discharge care varied. Opportunities exist to increase ID involvement in post-discharge management of serious infections.
A comparative study between curcumin and curcumin nanoemulsion on high-fat, high-fructose diet-induced impaired spermatogenesis in rats
Authors: Nasr Maha , Abd-Allah Hend , Ahmed-Farid Omar A H , Bakeer Rofanda M , Hassan Nabila S , Ahmed Rania F 
Published: November 2021

Abstract

Objectives
Curcumin is a promising nutraceutical with reported diverse therapeutic properties, but of limited oral bioavailability. The current manuscript investigates the role of encapsulation of curcumin in nanoemulsion form in counteracting the adverse effect of chronic ingestion of a high-fat high-fructose diet (HFHF) by juvenile male rats regarding testicular abnormalities and declined spermatogenesis.

Methods
Curcumin nanoemulsion was administered orally to Wistar rats at a dose of 5 or 10 mg/kg and compared with curcumin powder, followed by a pharmacological and histological assessment.

Key findings
Results demonstrated that curcumin nanoemulsion was superior to curcumin powder, particularly in enhancing the percentage progressive motility of spermatozoa, normalization of essential and non-essential amino acids in semen, normalization of serum leptin and testosterone levels, as well as normalization of oxidative and nitrosative parameters. It was also proven to reduce testicular DNA fragmentation, while elevating testicular cellular energy. In addition, curcumin nanoemulsion administered at a dose of 10 mg/kg induced the highest level of spermatogenesis, delineated by histological examination of the seminiferous tubules.

Conclusions
It can be concluded that curcumin nanoemulsion administered at a dose of 10 mg/kg successfully ameliorates the adverse effects of a HFHF on spermatogenesis.
Immunity-associated volatile emissions of β-ionone and nonanal propagate defence responses in neighbouring barley plants
Authors: Brambilla Alessandro , Sommer Anna , Ghirardo Andrea , Wenig Marion , Knappe Claudia , Weber Baris , Amesmaier Melissa , Lenk Miriam , Schnitzler Jörg-Peter , Vlot A Corina 
Published: November 2021

Abstract
Plants activate biochemical responses to combat stress. (Hemi-)biotrophic pathogens are fended off by systemic acquired resistance (SAR), a primed state allowing plants to respond faster and more strongly upon subsequent infection. Here, we show that SAR-like defences in barley (Hordeum vulgare) are propagated between neighbouring plants, which respond with enhanced resistance to the volatile cues from infected senders. The emissions of the sender plants contained 15 volatile organic compounds (VOCs) associated with infection. Two of these, β-ionone and nonanal, elicited resistance upon plant exposure. Whole-genome transcriptomics analysis confirmed that interplant propagation of defence in barley is established as a form of priming. Although gene expression changes were more pronounced after challenge infection of the receiver plants with Blumeria graminis f. sp. hordei, differential gene expression in response to the volatile cues of the sender plants included an induction of HISTONE DEACETYLASE 2 (HvHDA2) and priming of TETRATRICOPEPTIDE REPEAT-LIKE superfamily protein (HvTPL). Because HvHDA2 and HvTPL transcript accumulation was also enhanced by exposure of barley to β-ionone and nonanal, our data identify both genes as possible defence/priming markers in barley. Our results suggest that VOCs and plant–plant interactions are relevant for possible crop protection strategies priming defence responses in barley.
Loop restricted existential rules and first-order rewritability for query answering
Authors: Asuncion Vernon , Zhang Yan , Zhang Heng , Bai Yun 
Published: November 2021

Abstract
In ontology-based data access (OBDA), the classical database is enhanced with an ontology in the form of logical assertions generating new intensional knowledge. A powerful form of such logical assertions is the tuple-generating dependencies (TGDs), also called existential rules, where Horn rules are extended by allowing existential quantifiers to appear in the rule heads. In this paper, we introduce a new language called loop restricted (LR) TGDs (existential rules), which are TGDs with certain restrictions on the loops embedded in the underlying rule set. We study the complexity of this new language. We show that the conjunctive query answering (CQA) under the LR TGDs is decidable. In particular, we prove that this language satisfies the so-called bounded derivation-depth property (BDDP), which implies that the CQA is first-order rewritable, and its data complexity is in Ac$^{0}$. We also prove that the combined complexity of the CQA is 2-ExpTime complete, while the language membership is Pspace complete. Then we extend the LR TGDs language to the generalized loop restricted (GLR) TGDs language and prove that this class of TGDs still remains to be first-order rewritable and properly contains most of other first-order rewritable TGDs classes discovered in the literature so far.
The survival of multiphase dusty clouds in hot winds
Authors: Farber Ryan J , Gronke Max 
Published: November 2021

ABSTRACT
Much progress has been made recently in the acceleration of ∼104 K clouds to explain absorption line measurements of the circumgalactic medium and the warm, atomic phase of galactic winds. However, the origin of the cold, molecular phase in galactic winds has received relatively little theoretical attention. Studies of the survival of ∼104 K clouds suggest efficient radiative cooling may enable the survival of expelled material from galactic discs. Alternatively, gas colder than 104 K may form within the outflow, including molecules if dust survives the acceleration process. We explore the survival of dusty clouds in a hot wind with three-dimensional hydrodynamic simulations including radiative cooling and dust modelled as tracer particles. We find that cold ∼103 K gas can be destroyed, survive, or transformed entirely to ${\sim}10^4\,$ K gas. We establish analytic criteria distinguishing these three outcomes that compare characteristic cooling times to the system’s ‘cloud crushing’ time. In contrast to typically studied ∼104 K clouds, colder clouds are entrained faster than the drag time as a result of efficient mixing. We find that while dust can in principle survive embedded in the accelerated clouds, the survival fraction depends critically on the time dust spends in the hot phase and on the effective threshold temperature for destruction. We discuss our results in the context of polluting the circumgalactic medium with dust and metals, as well as understanding observations suggesting rapid acceleration of molecular galactic winds and ram-pressure-stripped tails of jellyfish galaxies.
Internally driven warps in disc galaxies
Authors: Sellwood J A , Debattista Victor P 
Published: November 2021

ABSTRACT
Any perturbation to a disc galaxy that creates a misalignment between the planes of the inner and outer disc, will excite a slowly evolving bending wave in the outer disc. The torque from the stiff inner disc drives a retrograde, leading spiral bending wave that grows in amplitude as it propagates outwards over a period of several Gyr. The part of the disc left behind by the outwardly propagating wave is brought into alignment with the inner disc. This behaviour creates warps that obey the rules established from observations, and operates no matter what the original cause of the misalignment between the inner and outer disc. Here, we confirm that mild warps in simulations of disc galaxies can be excited by shot noise in the halo, as was recently reported. We show that the quadrupole component of the noise creates disc distortions most effectively. Bending waves caused by shot noise in carefully constructed equilibrium simulations of isolated galaxies are far too mild to be observable, but perturbations from halo substructure and galaxy assembly must excite larger amplitude bending waves in real galaxies.
Removal and replacement of interference in tied-array radio pulsar observations using the spectral kurtosis estimator
Authors: Purver M , Bassa C G , Cognard I , Janssen G H , Karuppusamy R , Kramer M , Lee K J , Liu K , McKee J W , Perrodin D , Sanidas S , Smits R , Stappers B W 
Published: November 2021

ABSTRACT
We describe how to implement the spectral kurtosis method of interference removal (zapping) on a digitized signal of averaged power values. Spectral kurtosis is a hypothesis test, analogous to the t-test, with a null hypothesis that the amplitudes from which power is formed belong to a ‘good’ distribution – typically Gaussian with zero mean – where power values are zapped if the hypothesis is rejected at a specified confidence level. We derive signal-to-noise ratios (SNRs) as a function of amount of zapping for folded radio pulsar observations consisting of a sum of signals from multiple telescopes in independent radio-frequency interference environments, comparing four methods to compensate for lost data with coherent (tied-array) and incoherent summation. For coherently summed amplitudes, scaling amplitudes from non-zapped telescopes achieves a higher SNR than replacing zapped amplitudes with artificial noise. For incoherently summed power values, the highest SNR is given by scaling power from non-zapped telescopes to maintain a constant mean. We use spectral kurtosis to clean a tied-array radio pulsar observation by the Large European Array for Pulsars: the signal from one telescope is zapped with time and frequency resolutions of $6.25\, \mathrm{ms}$ and $0.16\, \mathrm{MHz}$, removing interference, along with 0.27 per cent of ‘good’ data, giving an uncertainty of $0.25\, \mathrm{\mu \mathrm{ s}}$ in pulse time of arrival (TOA) for PSR J1022+1001. We use a single-telescope observation to demonstrate recovery of the pulse profile shape, with 0.6 per cent of data zapped and a reduction from 1.22 to $0.70\, \mathrm{\mu \mathrm{ s}}$ in TOA uncertainty.
Identification and targeting of G-quadruplex structures in MALAT1 long non-coding RNA
Authors: Mou Xi , Liew Shiau Wei , Kwok Chun Kit 
Published: November 2021

Abstract
RNA G-quadruplexes (rG4s) have functional roles in many cellular processes in diverse organisms. While a number of rG4 examples have been reported in coding messenger RNAs (mRNA), so far only limited works have studied rG4s in non-coding RNAs (ncRNAs), especially in long non-coding RNAs (lncRNAs) that are of emerging interest and significance in biology. Herein, we report that MALAT1 lncRNA contains conserved rG4 motifs, forming thermostable rG4 structures with parallel topology. We also show that rG4s in MALAT1 lncRNA can interact with NONO protein with high specificity and affinity in vitro and in nuclear cell lysate, and we provide cellular data to support that NONO protein recognizes MALAT1 lncRNA via rG4 motifs. Notably, we demonstrate that rG4s in MALAT1 lncRNA can be targeted by the rG4-specific small molecule, peptide, and L-aptamer, leading to the dissociation of MALAT1 rG4-NONO protein interaction. Altogether, this study uncovers new and important rG4s in MALAT1 lncRNAs, reveals their specific interactions with NONO protein, offers multiple strategies for targeting MALAT1 and its RNA–protein complex via its rG4 structure and illustrates the prevalence and significance of rG4s in ncRNAs.
Atherosclerosis progression in antiphospholipid syndrome is comparable to diabetes mellitus: a 3 year prospective study
Authors: Evangelatos Gerasimos , Kravvariti Evrydiki , Konstantonis George , Tentolouris Nikolaos , Sfikakis Petros P , Tektonidou Maria G 
Published: November 2021

Abstract

Background
Antiphospholipid syndrome (APS) is an autoimmune thrombophilia leading to life-threatening cardiovascular events. Cross-sectional data support that APS is associated with accelerated atherosclerosis, but this has not been confirmed in prospective studies. We aimed to compare the rate of atherosclerosis progression over a 3 year period between patients with APS, diabetes mellitus (DM) and healthy controls (HCs).

Methods
Eighty-six patients with APS [43 with primary APS (PAPS), 43 with SLE-related APS (SLE-APS)] and an equal number of age- and sex-matched patients with DM and HCs who underwent a baseline US of the carotid and femoral arteries were invited for a 3 year follow-up evaluation for atherosclerotic plaque progression. Multivariate analysis was performed for the assessment of determinants of plaque progression after adjustment for disease-related and traditional cardiovascular risk factors.

Results
Seventy-four APS patients (74.3% female, 38 with PAPS), 58 DM patients and 73 HCs were included. APS patients exhibited a 3.3-fold higher risk of new atherosclerotic plaque formation compared with HCs (P = 0.031), similar to that in DM [odds ratio (OR) 3.45, P = 0.028]. In APS patients, plaque development risk was higher in SLE-APS vs PAPS (OR 7.75, P = 0.038) and was independently associated with the presence of traditional cardiovascular risk factors as expressed by the Systematic Coronary Risk Evaluation risk (OR 2.31, P = 0.008).

Conclusion
APS is characterized by accelerated rates of subclinical atherosclerosis to a degree comparable to DM, which is more pronounced in SLE-APS patients. Traditional cardiovascular risk factors are major determinants of this risk, warranting aggressive management as in other disorders with high cardiovascular risk.
Lumbar Spinal Stenosis with Degenerative Spondylolisthesis Treated with Decompression Alone. A Cohort of 346 Patients at a Large Spine Unit. Clinical Outcome, Complications and Subsequent Surgery
Authors: Pazarlis Konstantinos , Frost Anders , Försth Peter 
Published: November 2021

Study Design.
Cohort study.

Objective.
To study the clinical outcome, complications and subsequent surgery rate of DA for lumbar spinal stenosis (LSS) with DS.

Summary of Background Data.
There is still no consensus regarding the treatment approach for LSS with DS.

Methods.
We performed a retrospectively designed cohort study on prospectively collected data from a single high productive spine surgical center. Results from the Swedish Spine Registry and a local register for complications were used for the analyses. Patients with LSS and DS (>3 mm) who underwent DA during January 2012 to August 2017 were included. Patient reported outcome measures at baseline and 2 years after surgery were analyzed. Complications within 30 days of surgery and all subsequent surgery in the lumbar spine were registered.

Results.
We identified and included 346 patients with completed 2-year follow-up registration. At 2-year follow-up there was a significant improvement in all outcome measures. The global assessment success rate for back and leg pain was 68.3% and 67.6% respectively. Forty-one patients had at least 1 intra- or postoperative complication (11.9%). Nine patients (2.6%), underwent subsequent surgery within 2 years of the primary surgery whereof 2 underwent fusion. During the whole period of data collection, that is, as of June 2020, 28 patients had undergone subsequent surgery (8.1%) whereas 8 of them had had 2 surgeries. Fifteen patients underwent fusion.

Conclusion.
DA provides good clinical outcome at 2-year follow-up in patients with LSS and DS with low rate of intra- and postoperative complications and subsequent surgery. Our data supports the evidence that DA is effective and safe for LSS with DS.

Level of Evidence: 3
Factors Affecting Inpatient Mortality and Length of Stay in Nonmetastatic Colorectal Cancer
Authors: Ulanja Mark B. , Beutler Bryce D. , Antwi-Amoabeng Daniel , Moody Alastair E. , Chang Phoebe T. , Rahman Ganiyu A. , Apanga Paschal A. , Alese Olatunji B. 
Published: November 2021

Objective:
The objective of this study was to assess the effect of opioid use and other factors on inpatient length of stay (LOS) and mortality among patients hospitalized with nonmetastatic colorectal cancer (NMCRC).

Materials and Methods:
We analyzed discharge encounters collected from the 2016 to 2017 National Inpatient Sample (NIS) to evaluate the effect of long-term opioid use (90 d or longer) and cancer-related complications on LOS and mortality among hospitalized patients with NMCRC.

Results:
A total of 94,535 patients with NMCRC were included in the analysis. Long-term opioid users had a shorter average LOS and reduced inpatient mortality as compared with nonopioid users (5.97±5.75 vs. 6.66±6.92 d, P<0.01; and adjusted odds ratio=0.72, 95% confidence interval: 0.56-0.93, respectively). Factors that significantly increased both LOS and mortality included infection, venous thromboembolism, and chemotherapy-induced neutropenia; the average LOS was 2.7, 2.6, and 0.7 days longer, and the adjusted odds ratio for risk of inpatient mortality was 3.7, 1.2, and 1.2, respectively (P<0.05), for patients admitted with these cancer-related complications.

Conclusions:
Long-term opioid use is associated with decreased LOS and inpatient mortality among patients with NMCRC. Individuals admitted for cancer-related complications face a longer LOS and increased mortality as compared with those admitted without these morbidities.
Health Service Utilization Among Children and Adolescents with Posttraumatic Stress Disorder: A Case-Control Study
Authors: Goger Pauline , Zerr Argero A. , Weersing V. Robin , Dickerson John F. , Crawford Phillip M. , Sterling Stacy A. , Waitzfelder Beth , Daida Yihe G. , Ahmedani Brian K. , Penfold Robert B. , Lynch Frances L. 
Published: November 2021

ABSTRACT:

Objective:
Trauma exposure is widely prevalent, with more than 60% of adolescents having experienced at least 1 traumatic event and a third of those at high risk to develop posttraumatic stress disorder (PTSD). Data are scarce and out of date on the services children and adolescents with PTSD receive, impeding efforts to improve care and outcomes. This study examines health service use for a large and diverse sample of children and adolescents with and without a diagnosis of PTSD.

Method:
Using a matched case-control study, we gathered information from 4 large health care systems participating in the Mental Health Research Network. Data from each site's electronic medical records on diagnoses, health care encounters, and demographics were analyzed. Nine hundred fifty-five 4- to 18-year-olds with a diagnosis of PTSD were identified and matched on a 1:5 ratio to 4770 controls. We compared cases with controls on frequency of service use in outpatient primary care, medical specialty care, acute care, and mental health care. We also assessed psychotropic medication use.

Results:
Children and adolescents diagnosed with PTSD used nearly all physical and mental health service categories at a higher rate than controls. However, one-third of children and adolescents did not receive even 1 outpatient mental health visit (36.86%) during the year-long sampling window.

Conclusion:
Our findings suggest that children and adolescents diagnosed with PTSD may have unmet mental health needs. They are high utilizers of health services overall, but lower utilizers of the sectors that may be most helpful in resolving their symptoms.