bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrence of Klebsiella pneumoniae ST244 and ST11 extensively drug-resistant producing KPC, NDM, OXA-370 in wastewater, Brazil
Authors: Montenegro Kaylanne , Flores Claudia , Nascimento Ana Paula Alves , Farias Beatriz Oliveira , Brito Andressa S Gonçalves , Magaldi Mariana , Gimenez Aline , de Filippis Ivano , Clementino Maysa Mandetta , Bianco Kayo , Saggioro Enrico , Barrocas Paulo 
Published: July 2023

Abstract

Aims
To investigate the occurrence of carbapenem-resistant Klebsiella pneumoniae (CRKP) and their clonal relationships from hospital and municipal wastewater treatment plants (WWTPs).

Methods and results
Eighteen Kl. pneumoniae strains recovered from three WWTPs were identified by matrix-assisted laser desorption-ionization–time of flight (MALDI-TOF). The antimicrobial susceptibility were evaluated by disk-diffusion and the carbapenemases production by Carbapenembac®. The carbapenemases genes were investigated by real-time PCR and the clonal relationship through multilocus sequence typing (MLST). Thirty nine % (7/18) of isolates were classified as multidrug-resistant (MDR), 61.1% (11/18) extensively drug-resistant (XDR), and 83.3% (15/18) showed carbapenemase activity. Three carbapenemase-encoding genes were found, blaKPC (55%), blaNDM (27.8%) and blaOXA-370 (11.1%) as well five sequencing types ST11, ST37, ST147, ST244, and ST281. ST11 and ST244, sharing four alleles were grouped into clonal complex 11 (CC11).

Conclusions
Our results show the importance of monitoring antimicrobial resistance in WWTPs effluents to minimize the risk of spreading bacterial load and ARGs in aquatic ecosystems, using advanced treatment technologies to reduce these emerging pollutants at WWTPs.
A computable case definition for patients with SARS-CoV2 testing that occurred outside the hospital
Authors: Wang Lijing , Zipursky Amy R , Geva Alon , McMurry Andrew J , Mandl Kenneth D , Miller Timothy A 
Published: July 2023

Abstract

Objective
To identify a cohort of COVID-19 cases, including when evidence of virus positivity was only mentioned in the clinical text, not in structured laboratory data in the electronic health record (EHR).

Materials and Methods
Statistical classifiers were trained on feature representations derived from unstructured text in patient EHRs. We used a proxy dataset of patients with COVID-19 polymerase chain reaction (PCR) tests for training. We selected a model based on performance on our proxy dataset and applied it to instances without COVID-19 PCR tests. A physician reviewed a sample of these instances to validate the classifier.

Results
On the test split of the proxy dataset, our best classifier obtained 0.56 F1, 0.6 precision, and 0.52 recall scores for SARS-CoV2 positive cases. In an expert validation, the classifier correctly identified 97.6% (81/84) as COVID-19 positive and 97.8% (91/93) as not SARS-CoV2 positive. The classifier labeled an additional 960 cases as not having SARS-CoV2 lab tests in hospital, and only 177 of those cases had the ICD-10 code for COVID-19.

Discussion
Proxy dataset performance may be worse because these instances sometimes include discussion of pending lab tests. The most predictive features are meaningful and interpretable. The type of external test that was performed is rarely mentioned.

Conclusion
COVID-19 cases that had testing done outside of the hospital can be reliably detected from the text in EHRs. Training on a proxy dataset was a suitable method for developing a highly performant classifier without labor-intensive labeling efforts.
Not Just about Price: How Benefit Focus Determines Consumers’ Retailer Pricing Strategy Preference
Authors: Hydock Chris , Wathieu Luc 
Published: July 2023

Abstract
Recent research has highlighted a difference in the way consumers approach choice sets. Some consumers focus on products’ quality benefits (vertical differentiation): their selections are driven by the level of quality obtained relative to the price paid. Other consumers focus on products’ taste benefits (horizontal differentiation): their selections are driven by acquiring personal tastes at favorable prices. This article aims to investigate how consumers’ benefit focus, a continuum anchored by quality and taste, drives their preferences between retailers differing in pricing strategies. All else equal, consumers who focus on taste benefits will prefer EDLP stores (infrequent discounters), while consumers who focus on quality benefits will prefer Hi-Lo stores (frequent discounters). Findings from our experiments and an analysis of consumer panel data corroborate this relationship. This work also shows the mediating role of perceived value and the effect of several moderators: the strength of the price–quality relationship, the pattern of discounts, and cherry-picking costs.
The situational window for boundary-spanning infrastructure professions: Making sense of cyberinfrastructure emergence
Authors: Hayes Cassandra , Kulkarni Chaitra , Kee Kerk F 
Published: July 2023

Abstract
In the twenty-first century, professions are complex and difficult to define due to their fluid and interdisciplinary natures. In this study, we examined the personal career stories of professionals in the field of cyberinfrastructure (CI) to identify the narrative patterns used to make sense of CI as a boundary-spanning profession. Overall, we found that professionalization of CI is a sensemaking process of communal, retrospective storytelling. The meaning-making of CI as a profession occurred through three levels of narrative patterns: individual traits of CI professionals, situational introductions to CI, and inspirational convictions about CI. The situational level, which connected innate qualities and internal motivations with external forces to join CI as a career, was especially important to the professionalization of CI. Our findings have implications for re-examining professionalization as an ongoing sensemaking process, as well as offering guidance for recruitment and retention in critical boundary-spanning professions.
Identification of taxon through classification with partial reject options
Authors: Karlsson Måns , Hössjer Ola 
Published: July 2023

AbstractIdentification of taxa can significantly be assisted by statistical classification based on trait measurements either individually or by phylogenetic (clustering) methods. In this article, we present a general Bayesian approach for classifying species individually based on measurements of a mixture of continuous and ordinal traits, and any type of covariates. The trait vector is derived from a latent variable with a multivariate Gaussian distribution. Decision rules based on supervised learning are presented that estimate model parameters through blocked Gibbs sampling. These decision regions allow for uncertainty (partial rejection), so that not necessarily one specific category (taxon) is output when new subjects are classified, but rather a set of categories including the most probable taxa. This type of discriminant analysis employs reward functions with a set-valued input argument, so that an optimal Bayes classifier can be defined. We also present a way of safeguarding against outlying new observations, using an analogue of a p-value within our Bayesian setting. We refer to our Bayesian set-valued classifier as the Karlsson–Hössjer method, and it is illustrated on an original ornithological data set of birds. We also incorporate model selection through cross-validation, exemplified on another original data set of birds.
Intraoperative push enteroscopy for treatment of occult small bowel bleed due to hemorrhagic bleed and tumor: a report of two cases
Authors: Sofia Maribona A , Dwight Philip , Zaineb Shatawi , Christopher Seaver 
Published: July 2023

Abstract
Small bowel bleeds, while uncommon, are often challenging with regard to diagnosis and therapeutic intervention. This is primarily due to their occult nature, the location offending lesions and limitations of current technology used to assess them. This review highlights two patients who presented with signs and symptoms of a small bowel bleed, where initial diagnostic workups were inconclusive, and intraoperative enteroscopy served a diagnostic and therapeutic role. We discuss the current literature on intraoperative endoscopy and propose an algorithm that introduces intraoperative enteroscopy earlier as a viable curative option, particularly in a rural setting. This case series proposes considerations for earlier introduction of intraoperative enteroscopy for diagnosis and treatment of small bowel bleeds.
Brassicaceae display variation in efficiency of photorespiratory carbon-recapturing mechanisms
Authors: Schlüter Urte , Bouvier Jacques W , Guerreiro Ricardo , Malisic Milena , Kontny Carina , Westhoff Philipp , Stich Benjamin , Weber Andreas P M 
Published: July 2023

Abstract
Carbon-concentrating mechanisms enhance the carboxylase efficiency of Rubisco by providing supra-atmospheric concentrations of CO2 in its surroundings. Beside the C4 photosynthesis pathway, carbon concentration can also be achieved by the photorespiratory glycine shuttle which requires fewer and less complex modifications. Plants displaying CO2 compensation points between 10 ppm and 40 ppm are often considered to utilize such a photorespiratory shuttle and are termed ‘C3–C4 intermediates’. In the present study, we perform a physiological, biochemical, and anatomical survey of a large number of Brassicaceae species to better understand the C3–C4 intermediate phenotype, including its basic components and its plasticity. Our phylogenetic analysis suggested that C3–C4 metabolism evolved up to five times independently in the Brassicaceae. The efficiency of the pathway showed considerable variation. Centripetal accumulation of organelles in the bundle sheath was consistently observed in all C3–C4-classified taxa, indicating a crucial role for anatomical features in CO2-concentrating pathways. Leaf metabolite patterns were strongly influenced by the individual species, but accumulation of photorespiratory shuttle metabolites glycine and serine was generally observed. Analysis of phosphoenolpyruvate carboxylase activities suggested that C4-like shuttles have not evolved in the investigated Brassicaceae. Convergent evolution of the photorespiratory shuttle indicates that it represents a distinct photosynthesis type that is beneficial in some environments.
Diagnostic and Therapeutic Challenges in a Military Recruit Training Center of the Hellenic Navy: A Retrospective Analysis of the Poros Registry Serving as a Quality Improvement Project for Medical Officers
Authors: Papazoglou Andreas S , Athanaseas Ioannis , Fousekis Konstantinos , Kasotakis Nikolaos , Kolokouris Spyridon , Zisakis Thomas , Kyriakoulis Konstantinos G 
Published: July 2023

ABSTRACT

Introduction
Basic military training (BMT) has been associated with increased morbidity burden. Nevertheless, the exact epidemiology of the encountered cases in the BMT of Greek recruits has never been assessed. The aim of this quality improvement project was to investigate for the first time the clinical patterns, rates, and severity of symptoms leading recruits to visit the infirmary of a recruit training center and use this knowledge to provide a practical guidance for the physicians in charge.

Materials and Methods
All medical cases which were consecutively examined for the time range from November 2021 to September 2022 at the infirmary of the Hellenic Naval recruit training center in Poros, Greece, were retrospectively analyzed. Logistic regression analyses were performed to identify independent predictors of “severe clinical status” (i.e., overnight sick bay confinement and/or transfer to a tertiary hospital within 24 h) and absence from BMT for at least 1 day.

Results
A total of 2,623 medical cases were examined during four recruit seasons from November 2021 to September 2022. Upper respiratory tract infections (URTIs) and musculoskeletal injuries were the most frequent reasons for a recruit’s visit to the infirmary (33.9% and 30.2%, respectively). 6.7% of the total cases were identified as having “severe clinical status.” Specifically, in psychiatric, urological, and cardiovascular cases, febrile events were all independently associated with increased risk of “severe clinical status.” There was a positive association between training week and absence from BMT, while febrile events and spring recruit season were also independently linked with increased probability of absence from BMT for at least 1 day.

Conclusions
URTIs and musculoskeletal complaints were the primary reasons for recruits’ presentation at the infirmary of a Greek recruit training center, leading to severe rates of attrition. Further registries and quality improvement projects are warranted to reach specific conclusions and reduce BMT-related morbidity and its subsequent implications.
Hydrodynamic simulations of the disc of gas around supermassive black holes (HDGAS) – I. Molecular gas dynamics
Authors: Raouf Mojtaba , Viti Serena , García-Burillo S , Richings Alexander J , Schaye Joop , Bemis Ashley , Nobels Folkert S J , Guainazzi Matteo , Huang Ko-Yun , Schaller Matthieu , Impellizzeri Violette , Holdship Jon 
Published: July 2023

ABSTRACT
We present hydrodynamic simulations of the interstellar medium (ISM) within the circumnuclear disc (CND) of a typical active galactic nucleus (AGN)-dominated galaxy influenced by mechanical feedback from an AGN. The simulations are coupled with the CHIMES non-equilibrium chemistry network to treat the radiative-cooling and AGN-heating. A focus is placed on the central 100 pc scale where AGN outflows are coupled to the ISM and constrained by observational Seyfert-2 galaxies. AGN-feedback models are implemented with different wind-velocity and mass-loading factors. We post-process the simulation snapshots with a radiative-transfer code to obtain the molecular emission lines. We find that the inclusion of an AGN promotes the formation of CO in clumpy and dense regions surrounding supermassive black holes (SMBHs). The CO(1-0) intensity maps (&lt;6 Myr) in the CND seem to match well with observations of NGC 1068 with a best match for a model with 5000 km s−1 wind-velocity and a high mass-loading factor. We attempt to discern between competing explanations for the apparent counter-rotating gas disc in the NGC 1068 through an analysis of kinematic maps of the CO line emission. We suggest that mechanical AGN-feedback could explain the alignment-stability of position-angle across the different CND radii around the SMBH through momentum and energy loading of the wind. It is the wind-velocity that drives the disc out of alignment on a 100 pc scale for a long period of time. The position–velocity diagrams are in broad agreement with the predicted Keplerian rotation-curve in the model without AGN, but the AGN models exhibit a larger degree of scatter, in better agreement with NGC 1068 observations.
An enigmatic 380 kpc long linear collimated galactic tail
Authors: Zaritsky Dennis , Crossett Jacob P , Jaffé Yara L , Donnerstein Richard , Karunakaran Ananthan , Khim Donghyeon J , Lourenço Ana C C , Spekkens Kristine , Sun Ming , Vulcani Benedetta 
Published: July 2023

ABSTRACT
We present a serendipitously detected system consisting of an S0/a galaxy, which we refer to as the ‘Kite,’ and a highly collimated tail of gas and stars that extends over 380 kpc and contains pockets of star formation. In its length, narrowness, and linearity the Kite’s tail is an extreme example relative to known tails. The Kite (PGC 1000273) has a companion galaxy, Mrk 0926 (PGC 070409), which together comprise a binary galaxy system in which both galaxies host active galactic nuclei. Despite this systems being previously searched for signs of tidal interactions, the tail had not been discovered prior to our identification as part of the validation process of the SMUDGes survey for low surface brightness galaxies. We confirm the kinematic association between various H α knots along the tail, a small galaxy, and the Kite galaxy using optical spectroscopy obtained with the Magellan telescope and measure a velocity gradient along the tail. The Kite shares characteristics common to those formed via ram pressure stripping (‘jellyfish’ galaxies) and formed via tidal interactions. However, both scenarios face significant challenges that we discuss, leaving open the question of how such an extreme tail formed. We propose that the tail resulted from a three-body interaction from which the lowest mass galaxy was ejected at high velocity.
An ever-present Gaia snail shell triggered by a dark matter wake
Authors: Grand Robert J J , Pakmor Rüdiger , Fragkoudi Francesca , Gómez Facundo A , Trick Wilma , Simpson Christine M , van de Voort Freeke , Bieri Rebekka 
Published: July 2023

ABSTRACT
We utilize a novel numerical technique to model star formation in cosmological simulations of galaxy formation – called superstars – to simulate a Milky Way-like galaxy with ≳108 star particles to study the formation and evolution of out-of-equilibrium stellar disc structures in a full cosmological setting. In the plane defined by the coordinate and velocity perpendicular to the mid-plane [vertical phase space, (Z, VZ)], stars in solar-like volumes at late times exhibit clear spirals qualitatively similar in shape and amplitude to the Gaia ‘snail shell’ phase spiral. We show that the phase spiral forms at a lookback time of ∼6 Gyr during the pericentric passage of an ∼1010$\rm {\rm M}_{\odot }$ satellite on a polar orbit. This satellite stimulates the formation of a resonant wake in the dark matter halo while losing mass at a rate of ∼0.5–1 dex per orbit loop. The peak magnitude of the wake-induced gravitational torque at the solar radius is ∼8 times that from the satellite, and triggers the formation of a disc warp that wraps up into a vertical phase spiral over time. As the wake decays, the phase spiral propagates several gigayears to present day and can be described as ‘ever-present’ once stable disc evolution is established. These results suggest an alternative scenario to explain the Gaia phase spiral, which does not rely on a perturbation from bar buckling or a recent direct hit from a satellite.
Intensive blood pressure control and the progression of IgA nephropathy: a cohort study using marginal structural models
Authors: Tang Chen , Chen Pei , Si Feng-Lei , Yao Yu-Xuan , Lv Ji-Cheng , Shi Su-Fang , Zhou Xu-Jie , Liu Li-Jun , Zhang Hong 
Published: July 2023

ABSTRACT

Background
In chronic kidney disease, current guidelines recommend systolic blood pressure (SBP) below 120 mmHg. However, the renoprotective effect of intensive blood-pressure (BP) lowering on immunoglobulin A nephropathy (IgAN) remains undetermined. We aimed to determine the effect of intensive BP control on the progression of IgAN.

Methods
At Peking University First Hospital, 1530 patients with IgAN were enrolled. An examination of the relationship between baseline and time-updated BP and composite kidney outcomes, defined as development of end-stage kidney disease (ESKD) or a 30% decline in estimated glomerular filtration rate (eGFR), was conducted. Baseline and time-updated BPs were modeled using multivariate causal hazards models and marginal structural models (MSMs).

Results
In a median follow-up of 43.5 (interquartile range 27.2, 72.7) months, 367 (24.0%) patients experienced the composite kidney outcomes. No significant associations were found between baseline BP and the composite outcomes. Using MSMs with time-updated SBP for analysis, a U-shaped association was found. In reference to SBP 110–119 mmHg, hazard ratios (95% confidence intervals) for the SBP categories &lt;110, 120–129, 130–139 and ≥140 mmHg were 1.48 (1.02–2.17), 1.13 (0.80–1.60), 2.21 (1.54–3.16) and 2.91 (1.94–4.35), respectively. The trend was more prominent in patients with proteinuria ≥1 g/day and eGFR ≥60 mL/min/1.73 m2. After analyzing time-updated diastolic BP, no similar trend was observed.

Conclusions
In patients with IgAN, intensive BP control during the treatment period may retard the kidney disease progression, but the potential risk of hypotension still needs to be considered.
Distribution, Trends, and Antimicrobial Susceptibility ofBacteroides,Clostridium,Fusobacterium, andPrevotellaSpecies Causing Bacteremia in Japan During 2011–2020: A Retrospective Observational Study Based on National Surveillance Data
Authors: Kajihara Toshiki , Yahara Koji , Kitamura Norikazu , Hirabayashi Aki , Hosaka Yumiko , Sugai Motoyuki 
Published: July 2023

AbstractBackgroundThe increasing prevalence of anaerobic bacteremia is a major concern worldwide and requires longitudinal monitoring.MethodsWe present one of the largest and longest longitudinal studies on the prevalence and antimicrobial resistance of Bacteroides, Clostridium, Fusobacterium, and Prevotella spp. isolated from blood culture samples using national comprehensive surveillance data in Japan during 2011–2020 as part of the Japan Nosocomial Infections Surveillance.ResultsData for 41 949 Bacteroides spp., 40 603 Clostridium spp., 7013 Fusobacterium spp., and 5428 Prevotella spp. isolates were obtained. The incidences of bacteremia caused by Bacteroides fragilis, Clostridium perfringens, and Fusobacterium nucleatum significantly increased during the period (P &lt; .0001). Among the 20 species analyzed, 18 showed no significant changes in susceptibility over time, including B. fragilis, C perfringens, and F. nucleatum. However, resistance to clindamycin increased in B. thetaiotaomicron (P = .0312), and resistance to ampicillin increased in B. ovatus (P = .0008).ConclusionsOur comprehensive national surveillance data analysis demonstrated a continuous increase in the incidence of anaerobic bacteremia, particularly in B. fragilis, C. perfringens, and F. nucleatum. This may be linked to the increasing number of colorectal cancer cases or advancing methods for species identification and susceptibility testing, requiring cautious interpretation. The discovery of an upsurge in anaerobic bacteremia and potential alterations in susceptibility highlights the necessity for more extensive studies in this field.
Evaluation of Male Breast Cancer and the Application of Sentinel Lymph Node Biopsy: A Multicenter Retrospective Study
Authors: Shang Qingyao , Feng Kexin , Wei Ya , Wang Kaipeng , Yang Chenxuan , Zhao Shuangtao , Liu Jiaxiang , Meng Xiangzhi , Li Yalun , Du Chuang , Wang Jing , Qiao Guangdong , Li Jingruo , Wang Xin , Wang Xiang 
Published: July 2023

Abstract
Sentinel lymph node biopsy (SLNB) is currently used as a routine treatment for patients with breast cancer. However, it may not be applicable for patients with male breast cancer (MBC), because they have notably different clinicopathological features from those occurring in females. There is a lack of evidence of SLNB application and safe exemption from axillary lymph node dissection (ALND) in patients with MBC. This study aimed to evaluate the application of SLNB to provide information for the standardized treatment of patients with MBC. The MBC patient records from 4 institutions ranging from January 2001 to November 2020 were retrospectively reviewed. There were 220 patients with MBC with a median age of 60 (range 24-88) years and an average tumor size of 2.3 cm (range 0.5 cm-6.5 cm). Sixty-six percent of patients underwent SLNB, and 39% of them showed positive results. A total of 157 patients underwent ALND, while only half of them had positive nodes, causing unnecessary complications. For patients in the clinical early stage, we found that the SLNB showed a noninferiority to the ALND treatment in DFS (P = .18) and OS (P = .055). In conclusion, there are certain obstacles to the broad application of SLNB due to the lower proportion of patients with clinically negative lymph nodes. However, it is undeniable that SLNB can safely and effectively exempt patients with MBC at early stage with clinically negative nodes from ALND to reduce subsequent complications. It is still an ideal criterion for the axillary staging of patients with MBC.