bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation Study for PathogenDx EnviroX-F Assay for the Detection of Listeria, L. monocytogenes, and Salmonella in Environmental Surface Samples: AOAC Performance Tested MethodSM 092001
Authors: Katchman Benjamin A , Newland Cory S , Eggers Rick , Wen Fushi , O’Brien Kevin 
Published: March 2022

Abstract

Background
The PathogenDx EnviroX-F uses microarray technology to simultaneously detect Listeria species, Listeria monocytogenes, and Salmonella species from environmental samples without the need for enrichment.

Objective
The validation study included a matrix study of four matrices (stainless steel, plastic, rubber, and sealed concrete) comparing the PathogenDx EnviroX-F assay to the US Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Chapter 10, “Detection of L. monocytogenes in Foods and Environmental Samples, and Enumeration of L. monocytogenes in Foods” (revised March 2017), and FDA BAM Chapter 5,“Salmonella” (revised February 2020). Other required Performance Tested MethodSM parameters evaluated included: inclusivity and exclusivity, robustness, instrument variation, and product consistency and stability.

Methods
The PathogenDx EnviroX-F assay was evaluated with 30 unpaired replicate surface areas for each environmental surface. The candidate method was evaluated without an enrichment step.

Results
In the inclusivity and exclusivity study 50 out of 50 Listeria isolates were detected, 50 out of 50 L. monocytogenes strains were detected, 108 out of 108 Salmonella strains were detected, and 95 out of 95 exclusivity strains were correctly excluded. In the matrix study, the PathogenDx EnviroX-F assay showed no significant differences between confirmed results or between candidate and reference method results for 4” × 4” environmental surface areas for each matrix.

Conclusion
The PathogenDx EnviroX-F assay is an effective method for the qualitative detection of Listeria spp., L. monocytogenes, and Salmonella spp. from environmental surface swabs.

Highlights
The PathogenDx EnviroX-F assay will be the first PTM-approved multiplex assay for Listeria spp., L. monocytogenes, and Salmonella without the need for an environment step.
Association Between Baloxavir Marboxil Prescription for Children with Influenza B Infections and Short-Term Healthcare Consumption in Japan During the 2018–2019 Influenza Season
Authors: Shinno Kazuma , Takeuchi Masato , Kawakami Koji 
Published: March 2022

AbstractBackgroundBaloxavir marboxil is an anti-influenza medication that was newly introduced into clinical practice in 2018. Baloxavir might be more beneficial than neuraminidase inhibitors (NAIs), as suggested by a subgroup analysis of a clinical trial. Although the association between baloxavir prescription and healthcare use pertains mainly to influenza A, few studies have investigated the association in influenza B.MethodsWe evaluated the healthcare utilization of children (0–15 years old) treated with either baloxavir or NAIs between December 2018 and May 2019 using claims records in Japan. The primary endpoint was the composite of medical resource utilization, including hospitalization, antibiotic use, laboratory tests, radiological images, and fluid replacement therapy, over 1–9 days after antiviral prescription. Secondary outcomes representing each single outcome in the composite were examined. Subgroup analyses comparing baloxavir with each NAI were also performed.ResultsOf 4490 patients with influenza B who received antiviral treatment, 51.6% were male, and the median age was 8 years old. Baloxavir was prescribed for 29.4% of the population, and NAIs were prescribed for 70.6%. In the total cohort, 49.3% of patients had any comorbidity related to complicated influenza infection. Concerning the composite endpoint, baloxavir prescription was not associated with a risk of subsequent medical resource use (adjusted odds ratio 1.11; 95% confidence interval 0.90–1.38; P = 0.34). Secondary outcomes and subgroup analyses showed similar results to the primary outcome.ConclusionsIn a single-year comparative study in Japan, baloxavir prescription for influenza B was not associated with less healthcare consumption than NAIs within 9 days of treatment.
Incidence rate and management of diaphragmatic injury during laparoscopic nephrectomies: single-center experience
Authors: Baio Raffaele , Molisso Giovanni , Caruana Christian , Intilla Oliviero , Di Mauro Umberto , Pane Umberto , Campitelli Antonio , Pentimalli Francesca , Sanseverino Roberto 
Published: March 2022

Abstract
Pneumothorax is a rare complication in laparoscopic renal surgery. However, due to the increasing renal pathologies managed by laparoscopic technique, this infrequent complication is a potential risk. We investigated the incidence rate of this complication in our experience of laparoscopic renal surgery, taking into account the laparoscopic approach, the type of intervention, the character of the pathology (neoplastic or other), the site of the intervention, as well as the localization of the lesion (in case of malignant pathology). About 384 laparoscopic nephrectomies were reviewed at our institution, with a total of four cases (1.04%) of diaphragmatic injury. Diaphragmatic repair was always carried out by intracorporeal suturing, with no complications. Repair of diaphragmatic injuries should always be attempted with intracorporeal suture since this is a safe and effective technique. Then, although in the retroperitoneal approach pneumothorax is more likely, our experience has shown that transperitoneal access is not free from this complication.
Geotrichum spp: An overlooked and fatal etiologic agent in immunocompromised patients. A case series from a referral center in Mexico
Authors: Rajme-López Sandra , González-Lara María F , Martínez-Gamboa R Areli , Rangel-Cordero Andrea , Ponce-de-León Alfredo 
Published: March 2022

Abstract

Geotrichum spp. is an emergent pathogen. We aimed to describe Geotrichum spp. invasive fungal infections (IFI) in patients from Mexico. We reviewed cases with Geotrichum spp. isolated in clinical samples, from 2001 to 2019. Descriptive analysis was used for clinical data. Twenty patients with proven/probable Geotrichum spp. IFI were analyzed. The median age was 43; 55% were males. Hematologic malignancy was found in 60% (12/20); 75% (15/20) received systemic immunosuppressors. The most common presentation was lower respiratory tract infection. In-hospital mortality was 45% (9/20). Geotrichum spp. should be acknowledged as a pathogen causing atypical pneumonia in immunocompromised Latin American patients.

Lay Summary
Geotrichum spp. causes invasive infection in immunocompromised hosts. We describe a case series of 20 patients from Mexico City. Hematologic malignancy was the most common comorbidity. Clinical presentation was mainly lower respiratory tract infection. Mortality was high despite antifungal therapy.
Discovery of quasi-periodic oscillations in the persistent X-ray emission of accreting binary X-ray pulsar LMC X-4
Authors: Rikame Ketan , Paul Biswajit , Pradhan Pragati , Paul K T 
Published: March 2022

ABSTRACTWe report the discovery of quasi-periodic oscillations (QPOs) in the high-mass X-ray binary (HMXB) pulsar LMC X-4 in its non-flaring (persistent) state using observations with XMM–Newton. In addition to the 74 mHz coherent pulsations, the persistent emission light curve shows a QPO feature in the frequency range of 20–30 mHz. Quasi-periodic flares have been previously observed from LMC X-4 in observations made with Rossi X-ray Timing Explorer (RXTE). However, this is the first time QPOs have been observed in the persistent emission observations of LMC X-4. QPOs in X-ray binaries are generally thought to be related to the rotation of the inhomogeneous matter distribution in the inner accretion disc. In HMXBs such as LMC X-4 where the compact object is a neutron star with a high magnetic field, the radius of the inner accretion disc is determined by the mass accretion rate and the magnetic moment of the neutron star. In such systems, the QPO feature, along with the pulse period and X-ray luminosity measurement, helps us to constrain the magnetic field strength of the neutron star. We use considerations of magnetospheric accretion to have an approximate value of the magnetic field strength of the neutron star in LMC X-4.
A search for stellar structures around nine outer halo globular clusters in the Milky Way
Authors: Zhang Shumeng , Mackey Dougal , Da Costa Gary S 
Published: March 2022

ABSTRACT
We use deep imaging from the Dark Energy Camera to explore the peripheral regions of nine globular clusters in the outer halo of the Milky Way. Apart from Whiting 1 and NGC 7492, which are projected against the Sagittarius stream, we see no evidence for adjacent stellar populations to indicate any of these clusters is associated with coherent tidal debris from a destroyed host dwarf. We also find no evidence for tidal tails around any of the clusters in our sample; however, both NGC 1904 and 6981 appear to possess outer envelopes. Motivated by a slew of recent Gaia-based discoveries, we compile a sample of clusters with robust detections of extra-tidal structure, and search for correlations with orbital properties. While we observe that clusters with tidal tails are typically on moderately or very eccentric orbits that are highly inclined to the Galactic plane and often retrograde, these are neither necessary nor sufficient conditions for the formation of extra-tidal structure. That many objects with tidal tails appear to be accreted leads us to speculate that this lack of consistency may stem from the inhomogeneous dynamical history of the Milky Way globular cluster system. Finally, we note that clusters with prominent stellar envelopes detected in ground-based imaging (such as NGC 1851 and 7089) are now all known from Gaia to possess long tidal tails – experimental confirmation that the presence of an extended envelope is indicative of tidal erosion.
Can radio emission escape from the magnetosphere of υ Andromedae b – a new method to constrain the minimum mass of Hot Jupiters
Authors: Erkaev N V , Weber C , Grießmeier J-M , Lammer H , Ivanov V A , Odert P 
Published: March 2022

ABSTRACT
We investigate the atmospheric and magnetospheric conditions of the massive, close-in exoplanet υ Andromedae b (hereafter ups And b). In particular, we explore whether radio emission can be produced by the Cyclotron Maser Instability (CMI), and whether this emission can escape from its source region. For this, we compare the local cyclotron frequency to the local plasma frequency. The planetary mass has a decisive impact on both of these frequencies: the cyclotron frequency depends on the (mass-dependent) estimate of the planetary magnetic moment, and the plasma frequency is determined by the (gravity-dependent) atmospheric profile. For this reason, the planetary mass is one of the decisive parameters determining whether the CMI can operate efficiently. As the precise planetary mass is unknown in the case of ups And b, we compare the plasma conditions for a range of hypothetical masses of the planet in order to determine at which mass the atmosphere becomes ‘compact’, i.e. is not strongly extended, and thus provides favourable conditions for the CMI. In the case of detected planetary radio emission, this approach can provide a new way to constrain the mass of an exoplanet for which only a minimum mass is known.
State-to-state rate coefficients for HCS+ in rotationally inelastic collisions with H2 at low temperatures
Authors: Denis-Alpizar Otoniel , Quintas-Sánchez Ernesto , Dawes Richard 
Published: March 2022

ABSTRACTHCS+ ions have been detected in several regions of the interstellar medium (ISM), but an accurate determination of the chemical-physical conditions in the molecular clouds where this molecule is observed requires detailed knowledge of the collisional rate coefficients with the most common colliders in those environments. In this work, we study the dynamics of rotationally inelastic collisions of HCS+ + H2 at low temperature, and report, for the first time, a set of rate coefficients for this system. We used a recently developed potential energy surface for the HCS+–H2 van der Waals complex and computed state-to-state rotational rate coefficients for the lower rotational states of HCS+ in collision with both para- and ortho-H2, analysing the influence of the computed rate coefficients on the determination of critical densities. Additionally, the computed rate coefficients are compared with those obtained by scaling the ones from HCS+ in collision with He (an approximation that is sometimes used when data is lacking), and large differences are found. Furthermore, the approximation of using the rates for the HCO+ + H2 collision as a rough approximation for those of the HCS+ + H2 system is also evaluated. Finally, the complete set of de-excitation rate coefficients for the lowest 30 rotational states of HCS+ by collision with H2 is reported from 5 to 100 K.
Phylogenetic position of the deep-sea snail family Haloceratidae and new insights into caenogastropod relationships
Authors: Takano Tsuyoshi , Warén Anders , Kano Yasunori 
Published: March 2022

ABSTRACT
The phylogenetic position of Haloceratidae, a little-known family of the subclass Caenogastropoda, is contested due to its extreme rarity in bathyal waters worldwide (c. 800–3,500 m deep). Haloceratids share several morphological and ecological traits with members of Vanikoroidea, Tonnoidea, Capuloidea and Velutinoidea, and were provisionally included in Vanikoroidea based on the absence of certain apomorphic features of the latter three taxa. Here, we first investigate the phylogenetic position of the family based on molecular data from both of the recognized genera, Haloceras and Zygoceras. Reconstruction based on three nuclear and three mitochondrial gene sequences suggests that the Haloceratidae constitute a sister clade to the Capulidae and that the two families collectively form the superfamily Capuloidea. This superfamily is united in a large, robust clade with Calyptraeoidea, Velutinoidea, Tonnoidea and Neogastropoda. The superfamily Cypraeoidea, as previously conceived, was found to be polyphyletic; we propose new concepts of Cypraeoidea (including Cypraeidae and Ovulidae) and Velutinoidea (including Velutinidae, Eratoidae and Triviidae). This topology also confirms the polyphyly of taxa with the ‘echinospira’ type of larvae (Echinospirida). The morphological resemblance of these polyphyletic taxa highlights parallel acquisition of traits in response to the same selective pressures.
Drug treatment algorithm and recommendations from the 2020 update of the Japan College of Rheumatology clinical practice guidelines for the management of rheumatoid arthritis—secondary publication
Authors: Kawahito Yutaka , Morinobu Akio , Kaneko Yuko , Kohno Masataka , Hirata Shintaro , Kishimoto Mitsumasa , Seto Yohei , Sugihara Takahiko , Tanaka Eiichi , Ito Hiromu , Kojima Toshihisa , Matsushita Isao , Nishida Keiichiro , Mori Masaaki , Murashima Atsuko , Yamanaka Hisashi , Nakayama Takeo , Kojima Masayo , Harigai Masayoshi 
Published: March 2022

ABSTRACTObjectiveThe aim of this study was to update the Japan College of Rheumatology (JCR) clinical practice guidelines (CPG) for the management of rheumatoid arthritis (RA; JCR CPG for RA) according to recent changes in the medical environment in Japan. This article is a digest version of the guidance.MethodsWe used the Grading of Recommendations, Assessment, Development, and Evaluation method to update the 2014 JCR CPG for RA. A consensus was formed by CPG panel members.ResultsWe identified 36 important clinical questions regarding drug treatment and developed corresponding recommendations for RA. The recommendations included the following RA medications: non-steroidal anti-inflammatory drugs, corticosteroids, conventional synthetic disease-modifying antirheumatic drugs, biological disease-modifying antirheumatic drugs, anti-receptor activator for nuclear factor-κB ligand antibodies, and Janus kinase inhibitors, as well as the tapering and discontinuation of these medications. Recommendations regarding the efficacy and safety of treatments in the elderly and patients with comorbidities were also developed. Finally, we used these recommendations to create an original algorithm for drug treatment for RA based on the Treat-to-Target approach.ConclusionThe 2020 JCR CPG for RA provides a useful tool for rheumatologists, health care professionals, and patients with RA, enabling shared decision-making in a variety of clinical situations.
Blood-Based Next-Generation Sequencing in Adrenocortical Carcinoma
Authors: Nazha Bassel , Zhuang Tony Z , Dada Hiba I , Drusbosky Leylah M , Brown Jacqueline T , Ravindranathan Deepak , Carthon Bradley C , Kucuk Omer , Goldman Jamie , Master Viraj A , Bilen Mehmet Asim 
Published: March 2022

AbstractBackgroundAdrenocortical carcinoma (ACC) is a rare and heterogeneous malignancy with poor prognosis. We aimed to evaluate the feasibility of next-generation sequencing (NGS) testing of circulating cell-free tumor DNA (ctDNA) in patients with ACC, to characterize the genomic landscape of alterations, and to identify potential clinically actionable mutations.MethodsRetrospective analysis of genomic data from 120 patients with ACC who had ctDNA testing between 12/2016 and 10/2021 using Guardant360 (Guardant Health, CA) was performed. ctDNA NGS analysis interrogated single nucleotide variants, fusions, indels, and copy number amplifications of up to 83 genes. The frequency of genomic alterations, landscape of co-occurring mutations, and pathogenic/likely pathogenic alterations with potential targeted therapies was identified. The prevalence of alterations identified in ctDNA was compared to those detected in tissue using a publicly available database (cBioPortal).ResultsThe median age of this cohort was 53 years (range 21-81), and 56% of patients were female. Ninety-six patients (80%) had ≥1 somatic alteration detected. TP53 (52%), EGFR (23%), CTNNB1 (18%), MET (18%), and ATM (14%) were found to be the most frequently altered genes in ACC samples. Pathogenic and/or likely pathogenic mutations in therapeutically relevant genes were observed in 56 patients (47%) and included EGFR, BRAF, MET, CDKN2A, CDK4/6, and ATM. The most frequent co-occurring mutations were EGFR + MET (9%), MET + CDK4 (7%), EGFR + CDK4 (7%), and BRAF + MET (7%). The frequencies of mutations detected in ctDNA were similar to those detected in tissue.ConclusionsUtilizing blood-based NGS to characterize genomic alterations in advanced ACC is feasible in over 80% of patients. Almost half of the patients had actionable mutations with approved therapies in other cancers. This approach might inform the development of personalized treatment options or identify clinical trials available for this aggressive malignancy.
Contagious inequality: economic disparities and excess mortality during the COVID-19 pandemic
Authors: Zaki Bishoy Louis , Nicoli Francesco , Wayenberg Ellen , Verschuere Bram 
Published: March 2022

AbstractThe COVID-19 pandemic has emphasized the need to consider multiple and often novel perspectives on contemporary policymaking in the context of technically complex, ambiguous, and large-scale crises. In this article, we focus on exploring a territory that remains relatively unchartered on a large scale, namely the relationship between economic inequalities and excess mortality during the COVID-19 pandemic, using a dataset of 25 European countries spanning 300 regions. Our findings reveal two pathways by which economic asymmetries and inequalities can observably influence excess mortality: labor market structures (capturing concentrations of industrial jobs) and income inequalities (capturing concentrations and asymmetries in income distribution). We leverage our findings to offer recommendations for policymakers toward a more deliberate consideration of the multidimensionality of technically complex, large-scale crises with a high degree of societal embeddedness. These findings also urge future scholarship to utilize a range of parameters and indicators for better understanding the relationship between cues and outcomes in such complex settings.
A scenario for an evolutionary selection of ageing
Authors: Roget T. , MacMurray C. , Jolivet P. , Méléard S. , Rera M. 
Published: March 2022

AbstractSigns of ageing become apparent only late in life, after organismal development is finalized. Ageing, most notably, decreases an individual’s fitness. As such, it is most commonly perceived as a non-adaptive force of evolution and considered a by-product of natural selection.Building upon the evolutionarily conserved age-related Smurf phenotype, we propose a simple mathematical life-history trait model in which an organism is characterized by two core abilities: reproduction and homeostasis.Through the simulation of this model, we observe 1) the convergence of fertility’s end with the onset of senescence, 2) the relative success of ageing populations, as compared to non-ageing populations, and 3) the enhanced evolvability (i.e. the generation of genetic variability) of ageing populations. In addition, we formally demonstrate the mathematical convergence observed in 1).We thus theorize that mechanisms that link the timing of fertility and ageing have been selected and fixed over evolutionary history, which, in turn, explains why ageing populations are more evolvable and therefore more successful. Broadly speaking, our work suggests that ageing is an adaptive force of evolution.
Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability
Authors: Lü YiQing , Cho Tiffany , Mukherjee Saptaparna , Malik Ahmad , Gonzalez-Foutel Nicolas S. , Suarez Carmen Florencia , Dervovic Dzana , Oh Robin Hyunseo , Langille Ellen , Al-Zahrani Khalid N. , Lin Zhen Yuan , Tsai Ricky , Rotter Varda , Ashton-Prolla Patricia , Chemes Lucia B. , Moffat Jason , Gingras Anne-Claude , Oren Moshe , Durocher Daniel , Schramek Daniel 
Published: March 2022

AbstractTumour suppressor p53 (TP53) is the most frequently mutated gene in cancer. Several hotspot p53 mutants not only lose tumour suppressive capabilities, but also function in a dominant-negative manner, suppressing canonical wild-type p53 function. Furthermore, some hotspot p53 mutants promote oncogenesis by gain-of-function mechanisms. Levels of p53 are regulated predominantly through regulation of protein stability and while wild-type p53 is normally kept at very low levels at steady-state, p53 mutants are often stabilized in tumours, which may be vital for their oncogenic properties. Here, we systematically profiled the factors that regulate protein stability of wild-type and mutant p53 using marker-based genome-wide CRISPR screens. We found that most proteins that regulate wild-type p53 also regulate a subset of p53 mutants with the exception of p53 R337H regulators, which are largely private to this mutant. Mechanistically, we identified FBXO42 as a novel positive regulator of a subset of p53 mutants comprising R273H, R248Q and R248W. We show that FBXO42 acts together with CCDC6 to regulate USP28-mediated p53 stabilization. Our work also identifies C16orf72 as a negative regulator of the stability of wild-type p53 and of all p53 mutants tested. C16orf72 is amplified in breast cancer, and we show that C16orf72 regulates p53 levels in mammary epithelium of mice and its overexpression results in accelerated breast cancer with reduced p53 levels. Together, this work provides a network view of the processes that regulate p53 stability, which might provide clues for reinforcing wild-type p53 or targeting mutant p53 in cancer.