bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integron detection for prediction of trimethoprim/sulfamethoxazole susceptibility in children with Enterobacterales urinary tract infections
Authors: Elias Peter , Barraud Olivier , El Hamel Chahrazed , Chainier Delphine , Dallochio Aymeric , Grélaud Carole , Ploy Marie-Cécile , Guigonis Vincent , Garnier Fabien 
Published: November 2021

Abstract

Objectives
In some countries, third-generation cephalosporins (3GCs) serve as first-line therapy in children with urinary tract infections (UTIs). However, their use may contribute to the emergence of antibiotic resistance, notably among Gram-negative bacteria (GNB). Integrons are bacterial genetic elements involved in antibiotic resistance in GNB. Their absence is associated with &gt;97% susceptibility to trimethoprim/sulfamethoxazole in adults infected with GNB. The objective of this study was to examine the value of integron detection directly from urine samples as a predictive marker of resistance to trimethoprim/sulfamethoxazole in children with GNB-related UTIs.

Methods
Children admitted to the Limoges University Hospital’s paediatric emergency department between February 2018 and March 2019 with a suspicion of UTI were eligible for the study. Only confirmed cases presenting a positive urine culture with unique GNB were retained for further study analyses. Integrons were detected directly from urines using real-time PCR.

Results
The data of 72 patients were analysed and integrons were detected in 15 urine samples. The negative predictive value of integron detection for resistance to trimethoprim/sulfamethoxazole was 100% as all of the GNB (all were Enterobacterales) isolated from patients with no integrons detected in their urine samples were susceptible to trimethoprim/sulfamethoxazole.

Conclusions
The detection of integrons in cases of paediatric patients with suspected UTI could help limit 3GC empirical use and empower an empirical first-line strategy better tailored to the needs of each patient.
C-reactive protein-guided use of procalcitonin in COVID-19
Authors: Houghton Rebecca , Moore Nathan , Williams Rebecca , El-Bakri Fatima , Peters Jonathan , Mori Matilde , Vernet Gabrielle , Lynch Jessica , Lewis Henry , Tavener Maryanna , Durham Tom , Bowyer Jack , Saeed Kordo , Pollara Gabriele 
Published: November 2021

Abstract

Background
A low procalcitonin (PCT) concentration facilitates exclusion of bacterial co-infections in COVID-19, but high costs associated with PCT measurements preclude universal adoption. Changes in inflammatory markers, including C-reactive protein (CRP), can be concordant, and predicting low PCT concentrations may avoid costs of redundant tests and support more cost-effective deployment of this diagnostic biomarker.

Objectives
To explore whether, in COVID-19, low PCT values could be predicted by the presence of low CRP concentrations.

Methods
Unselected cohort of 224 COVID-19 patients admitted to hospital that underwent daily PCT and CRP measurements as standard care. Both 0.25 ng/mL and 0.5 ng/mL were used as cut-offs for positive PCT test results. Geometric mean was used to define high and low CRP values at each timepoint assessed.

Results
Admission PCT was &lt;0.25 ng/mL in 160/224 (71.4%), 0.25–0.5 ng/mL in 27 (12.0%) and &gt;0.5 ng/mL in 37 (16.5%). Elevated PCT was associated with increased risk of death (P = 0.0004) and was more commonly associated with microbiological evidence of bacterial co-infection (P &lt; 0.0001). For high CRP values, significant heterogeneity in PCT measurements was observed, with maximal positive predictive value of 50% even for a PCT cut-off of 0.25 ng/mL. In contrast, low CRP was strongly predictive of low PCT concentrations, particularly &lt;0.5 ng/mL, with a negative predictive value of 97.6% at time of hospital admission and 100% 48 hours into hospital stay.

Conclusions
CRP-guided PCT testing algorithms can reduce unnecessary PCT measurement and costs, supporting antimicrobial stewardship strategies in COVID-19.
Live yeast and yeast extracts with and without pharmacological levels of zinc on nursery pig growth performance and antimicrobial susceptibilities of fecalEscherichia coli
Authors: Chance Jenna A , DeRouchey Joel M , Amachawadi Raghavendra G , Ishengoma Victor , Nagaraja Tiruvoor G , Goodband Robert D , Woodworth Jason C , Tokach Mike D , Calderón Hilda I , Kang Qing , Loughmiller Joseph A , Hotze Brian , Gebhardt Jordan T 
Published: November 2021

AbstractA total of 360 weanling barrows (Line 200 ×400, DNA, Columbus NE; initially 5.6 ± 0.03 kg) were used in a 42-d study to evaluate yeast-based pre- and probiotics (Phileo by Lesaffre, Milwaukee, WI) in diets with or without pharmacological levels of Zn on growth performance and antimicrobial resistance (AMR) patterns of fecal Escherichia coli. Pens were assigned to one of four dietary treatments with five pigs per pen and 18 pens per treatment. Dietary treatments were arranged in a 2 × 2 factorial with main effects of yeast-based pre- and probiotics (none vs. 0.10% ActiSaf Sc 47 HR+, 0.05% SafMannan, and 0.05% NucleoSaf from days 0 to 7, then concentrations were lowered by 50% from days 7 to 21) and pharmacological levels of Zn (110 vs. 3,000 mg/kg from days 0 to 7, and 2,000 mg/kg from days 7 to 21 with added Zn provided by ZnO). All pigs were fed a common diet from days 21 to 42 post-weaning. There were no yeast ×Zn interactions or effects from yeast additives observed on any response criteria. From days 0 to 21 and 0 to 42, pigs fed pharmacological levels of Zn had increased (P &lt; 0.001) ADG and ADFI. Fecal samples were collected on days 4, 21, and 42 from the same three pigs per pen for fecal dry matter (DM) and AMR patterns of E. coli. On day 4, pigs fed pharmacological levels of Zn had greater fecal DM (P = 0.043); however, no differences were observed on day 21 or 42. Escherichia coli was isolated from fecal samples and the microbroth dilution method was used to determine the minimal inhibitory concentrations (MIC) of E. coli isolates to 14 different antimicrobials. Isolates were categorized as either susceptible, intermediate, or resistant based on Clinical and Laboratory Standards Institute (CLSI) guidelines. The addition of pharmacological levels of Zn had a tendency (P = 0.051) to increase the MIC values of ciprofloxacin; however, these MIC values were still well under the CLSI classified resistant breakpoint for ciprofloxacin. There was no evidence for differences (P &gt; 0.10) for yeast additives or Zn for AMR of fecal E. coli isolates to any of the remaining antibiotics. In conclusion, pharmacological levels of Zn improved ADG, ADFI, and all isolates were classified as susceptible to ciprofloxacin although the MIC of fecal E. coli tended to be increased. Thus, the short-term use of pharmacological levels of Zn did not increase antimicrobial resistance. There was no response observed from live yeast and yeast extracts for any of the growth, fecal DM, or AMR of fecal E. coli criteria.
The (In)visible Woman at the International Monetary Fund: Engendering National Economic Rule-making
Authors: Duran Camila Villard 
Published: November 2021

ABSTRACT
For decades, the International Monetary Fund (IMF) was silent about gender inequality. In 2013, the IMF finally adopted a discourse linking macroeconomic stability and gender inequality. Engendering means the integration of gender equality into the IMF’s activities, thus, generating change. By deploying different institutional mechanisms (e.g. the Article IV reports and conditionality in exchange for financial support), the IMF is contributing to engendering economic rulemaking process at the national level. Discourses matter. Economic laws at national level are shaped by the IMF’s ideas: the meaning-making process of rules at the global level is an integral part of the economic rulemaking process at the national level. Particularly, legal ideas are key to explain the structure of the IMF’s discourse and its potential to promote gender equality. The IMF is an important case study to understand the mechanisms of engendering international organizations with important repercussions for other international institutions.
Caecal volvulus: high index of suspicion is the key to early diagnosis
Authors: Rout Alexandra , Pillai Sandhya 
Published: November 2021

Abstract
Caecal volvulus represents an uncommon acute surgical presentation of bowel obstruction. Familiarity with particular long-term symptoms and pre-disposing factors can help a clinician identify caecal volvulus as a possible diagnosis. There has been a changing vogue of radiological investigation and surgical interventions. We present a summary of these options.
Protecting the Identity of Participants in Qualitative Research
Authors: Pascale Joanne , Lineback Joanna Fane , Bates Nancy , Beatty Paul 
Published: November 2021

Abstract
Social science researchers rely on study participants to provide information about themselves, and pledging to protect their identities is generally standard practice. This is usually specified through professional associations or policies and laws governing research agencies and institutions. Conventional methods of protecting participants’ identities in quantitative research are undergoing a major overhaul in response to relatively new threats brought about by the sheer volume of large publicly available datasets along with powerful and affordable computing capabilities that enable data linkages and respondent re-identification. These developments have raised new questions about qualitative research products that previously may have been considered less vulnerable to re-identification. In this paper, we first summarize a range of conventional methods of protecting respondents’ identities used in both quantitative and qualitative research. We then discuss the relatively new threats to confidentiality brought about by the internet, computing, and social media age. Next, we bring the focus to qualitative research specifically and discuss the development of a novel approach to a systematic method of disclosure avoidance for at least a subset of qualitative research products: typical research aimed at pretesting and evaluation of survey questions, data collection instruments, and related materials used for household surveys in the federal statistical system. We frame the discussion in terms of risk and mitigation. That is, we aim to articulate the nature of qualitative methods and data, the risks posed by the dissemination of qualitative information products, and consider how these risks might reasonably be mitigated while maximizing utility. Finally, we pull back the lens and discuss how the method could be applied to research outside the context of the federal statistical system if certain criteria are met.
Detective Fictions: The ‘baby-farming detective’ in Britain, 1867–97
Authors: Hinks Jim 
Published: November 2021

Abstract
This article examines a series of investigations into the activities of women engaged in the provision of paid childcare and collectively labelled with the term ‘baby-farmer’. This paper looks at the practice of writers representing themselves as ‘baby-farming detectives’. Along with exploring the use of the detective investigation as a stylistic device, it will contend that the strictures it imposed informed the relationship these writers have with paid child-carers. The article also explores how the notion of ‘detectives’ and ‘suspects’ spoke of an assumed right to subject working-class women to inspection. It concludes that these detective fantasies were ultimately unsuccessful as they were unable to solve either the cases they encountered, or the symbolic problem of baby-farming, leaving these narratives curiously unresolved and their writers impotent. This article not only seeks to explain how and why the link between pecuniary childcare and infant murder was forged and maintained but asserts that this narrative technique has wider implications for scholars of nineteenth-century culture.
The impact of the Internet on migration aspirations and intentions
Authors: Grubanov-Boskovic Sara , Kalantaryan Sona , Migali Silvia , Scipioni Marco 
Published: November 2021

Abstract
This study investigates the relationship between Internet access and migration aspirations and intentions in Africa. While empirical evidence on the role of telecommunications in shaping migration flows is increasing, the relationship between aspirations (desire to migrate) and intentions (migration preparation) has been paid little attention. The analysis is based on the nationally representative 2014 and 2015 surveys of Gallup World Poll in 29 African countries. We modelled migration desire and migration preparation through Probit and Heckman Probit models. The results indicate that having Internet access is positively associated with the desire to move abroad and preparations to migrate once controlling for the socio-demographic characteristics of the respondents. The association is higher in the case of migration preparation than in the case of migration desire. Slightly diverse effects are documented in low- and lower-middle-income countries, where the effect of Internet access on migration desire is somewhat higher than in the sample as a whole.
Deuterated ammonia in Galactic massive star-forming regions
Authors: Li Yuqiang , Wang Junzhi , Li Juan , Liu Shu , Luo Qiuyi 
Published: November 2021

ABSTRACT
We present sensitive observations of NH2D $1_{11}^\mathrm{ a}\!-\!1_{01}^\mathrm{ s}$ at 110.153 599 GHz toward 50 Galactic massive star-forming regions with the Institut de Radioastronomie Millimétrique (IRAM) 30-m telescope. The NH2D $1_{11}^\mathrm{ a}\!-\!1_{01}^\mathrm{ s}$ transition is detected toward 36 objects, yielding a detection rate of 72 per cent. Column densities of NH2D, HC3N, and C18O for each source are derived by assuming local thermal equilibrium conditions with a fixed excitation temperature. The deuterium ratio of NH3, defined as the abundance ratio of NH2D to NH3, for 19 sources is also obtained with the NH3 information from the literature. The range of deuterium fractionation bends to be large in the late-stage star-forming regions in this work, with the value from 0.043 to 0.0006. The highest deuterium ratio of NH3 is 0.043 in G081.75+00.78 (DR21). We also find that the deuterium ratio of NH3 increases with Galactocentric distance and decreases with line width.
Multiple components in the molecular outflow of the red supergiant NML Cyg
Authors: Andrews H , De Beck E , Hirvonen P 
Published: November 2021

ABSTRACT
Despite their large impact on stellar and galactic evolution, the properties of outflows from red supergiants are not well characterized. We used the Onsala 20m telescope to perform a spectral survey at 3 and 4 mm (68–116  GHz) of the red supergiant NML Cyg, alongside the yellow hypergiant IRC + 10420. Our observations of NML Cyg were combined with complementary archival data to enable a search for signatures of morphological complexity in the circumstellar environment, using emission lines from 15 molecular species. The recovered parameters imply the presence of three distinct, coherent, and persistent components, comprised of blue-shifted and red-shifted components, in addition to an underlying outflow centred at the stellar systemic velocity. Furthermore, to reproduce 12CO emission with 3D radiative transfer models required a spherical outflow with three superposed conical outflows, one towards and one away from the observer, and one in the plane of the sky. These components are higher in density than the spherical outflow by up to an order of magnitude. We hence propose that NML Cyg’s circumstellar environment consists of a small number of high-density large-scale coherent outflows embedded in a spherical wind. This would make the mass-loss history similar to that of VY CMa, and distinct from μ Cep, where the outflow contains many randomly distributed smaller clumps. A possible correlation between stellar properties, outflow structures, and content is critical in understanding the evolution of massive stars and their environmental impact.
Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent,Treponema pallidum
Authors: Pla-Díaz Marta , Sánchez-Busó Leonor , Giacani Lorenzo , Šmajs David , Bosshard Philipp P , Bagheri Homayoun C , Schuenemann Verena J , Nieselt Kay , Arora Natasha , González-Candelas Fernando 
Published: November 2021

AbstractThe incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.
Beneficial effects of apremilast on genital ulcers, skin lesions, and arthritis in patients with Behçet’s disease: A systematic review and meta-analysis
Authors: Iizuka Yuki , Takase-Minegishi Kaoru , Hirahara Lisa , Kirino Yohei , Soejima Yutaro , Namkoong H o , Horita Nobuyuki , Yoshimi Ryusuke , Takeuchi Masaki , Takeno Mitsuhiro , Mizuki Nobuhisa , Nakajima Hideaki 
Published: November 2021

ABSTRACTObjectivesThis study aimed to determine the clinical efficacy of apremilast for oral ulcers (OUs), extra-oral manifestations, and overall disease activity in patients with Behçet’s disease (BD).MethodsA systematic literature search was performed in PubMed, Embase, Cochrane Library, and Web of Science Core Collection. Studies assessing the treatment effects of apremilast in BD were included. The odds ratios (ORs) of being symptom-free for individual manifestations and mean difference (MD) of Behçet’s Disease Current Activity Form (BDCAF) scores were calculated with 95% confidence intervals (CIs) at 12 and 24 weeks using a random-model meta-analysis.ResultsOf 259 screened articles, eight were included. After 12 weeks of apremilast treatment the OR of symptom-free was as followings: OUs, 45.76 (95% CI, 13.23–158.31); genital ulcers, 4.56 (95% CI, 2.47–8.44); erythema nodosum, 3.59 (95% CI, 1.11–11.61); pseudofolliculitis, 2.81 (95% CI, 1.29–6.15); and arthritis, 3.55 (95% CI, 1.71–7.40). Furthermore, BDCAF scores at 12 weeks were significantly reduced (MD=−1.38; −1.78 to −0.99). However, the proportion of oral-ulcer-free patients increased at 24 weeks (OR = 14.88; 4.81 to 46.07).ConclusionsThe currently accumulated data indicate an improvement in mucocutaneous and articular symptoms by short-term apremilast treatment in patients with BD.
Rhea, the reaction knowledgebase in 2022
Authors: Bansal Parit , Morgat Anne , Axelsen Kristian B , Muthukrishnan Venkatesh , Coudert Elisabeth , Aimo Lucila , Hyka-Nouspikel Nevila , Gasteiger Elisabeth , Kerhornou Arnaud , Neto Teresa Batista , Pozzato Monica , Blatter Marie-Claude , Ignatchenko Alex , Redaschi Nicole , Bridge Alan 
Published: November 2021

AbstractRhea (https://www.rhea-db.org) is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI (Chemical Entities of Biological Interest) (https://www.ebi.ac.uk/chebi). In this paper, we describe a number of key developments in Rhea since our last report in the database issue of Nucleic Acids Research in 2019. These include improved reaction coverage in Rhea, the adoption of Rhea as the reference vocabulary for enzyme annotation in the UniProt knowledgebase UniProtKB (https://www.uniprot.org), the development of a new Rhea website, and the designation of Rhea as an ELIXIR Core Data Resource. We hope that these and other developments will enhance the utility of Rhea as a reference resource to study and engineer enzymes and the metabolic systems in which they function.
Regulation of PDGFR-β gene expression by targeting the G-vacancy bearing G-quadruplex in promoter
Authors: Chen Juan-nan , He Yi-de , Liang Hui-ting , Cai Ting-ting , Chen Qi , Zheng Ke-wei 
Published: November 2021

Abstract
G-quadruplex is an essential element in gene transcription that serves as a promising drug target. Guanine-vacancy-bearing G-quadruplex (GVBQ) is a newly identified G-quadruplex that has distinct structural features from the canonical G-quadruplex. Potential GVBQ-forming motifs are widely distributed in gene promoter regions. However, whether GVBQ can form in genomic DNA and be an effective target for manipulating gene expression is unknown. Using photo-crosslinking, dimethyl sulfate footprinting, exonuclease digestion and in vitro transcription, we demonstrated the formation of a GVBQ in the G-rich nuclease hypersensitivity element within the human PDGFR-β gene promoter region in both single-stranded and double-stranded DNA. The formation of GVBQ in dsDNA could be induced by negative supercoiling created by downstream transcription. We also found that the PDGFR-β GVBQ was specifically recognized and stabilized by a new synthetic porphyrin guanine conjugate (mPG). Targeting the PDGFR-β GVBQ in human cancer cells using the mPG could specifically alter PDGFR-β gene expression. Our work illustrates that targeting GVBQ with mPG in human cells can regulate the expression level of a specific gene, thus indicating a novel strategy for drug development.
Chromosome segregation in Archaea: SegA– and SegB–DNA complex structures provide insights into segrosome assembly
Authors: Yen Cheng-Yi , Lin Min-Guan , Chen Bo-Wei , Ng Irene W , Read Nicholas , Kabli Azhar F , Wu Che-Ting , Shen Yo-You , Chen Chen-Hao , Barillà Daniela , Sun Yuh-Ju , Hsiao Chwan-Deng 
Published: November 2021

Abstract
Genome segregation is a vital process in all organisms. Chromosome partitioning remains obscure in Archaea, the third domain of life. Here, we investigated the SegAB system from Sulfolobus solfataricus. SegA is a ParA Walker-type ATPase and SegB is a site-specific DNA-binding protein. We determined the structures of both proteins and those of SegA–DNA and SegB–DNA complexes. The SegA structure revealed an atypical, novel non-sandwich dimer that binds DNA either in the presence or in the absence of ATP. The SegB structure disclosed a ribbon–helix–helix motif through which the protein binds DNA site specifically. The association of multiple interacting SegB dimers with the DNA results in a higher order chromatin-like structure. The unstructured SegB N-terminus plays an essential catalytic role in stimulating SegA ATPase activity and an architectural regulatory role in segrosome (SegA–SegB–DNA) formation. Electron microscopy results also provide a compact ring-like segrosome structure related to chromosome organization. These findings contribute a novel mechanistic perspective on archaeal chromosome segregation.