bluuebunny/crossref_metadata_2025_split huggingface dataset:
Provider-To-Provider Communication About Care Transitions: Considering Different Health Technology Tools
Authors: Beal Eliza W. , Kurien Natasha , DePuccio Matthew J. , Tsung Allan , McAlearney Ann Scheck 
Published: February 2023

ABSTRACT
Transitions in patient care require exchanges of information between providers. This period of transition presents a range of challenges, and inadequate transitions can have serious consequences for patients. Our objective was to understand providers' perspectives about patient care transitions, especially around communication between providers and the role of health information technology in provider-to-provider communication. Semi-structured interviews were conducted. Deductive-dominant thematic analysis was used to allow categorization of data based on general themes derived from the interview guides, as well as identification of emergent themes. We characterized three main themes involving providers' perspectives about care transitions. Themes included communication challenges, communication preferences, and suggestions for improving the care transition processes. With respect to challenges around communication, providers highlighted four main concerns. These concerns included the existence of too many methods of communication, high volume of communication, challenges with involvement of multiple providers delivering longitudinal care, and difficulty communicating with providers outside the health system. Providers noted opportunities to improve transitions including improving standardization, enhancing the specialty to primary care transition process, and increasing communication back to the referring provider. Implementation and evaluation of these improvements could be considered by health systems to enhance care transitions.
Peripheral Blood Monocytosis Is Associated With Long-Term Disease Severity in Pediatric-Onset Inflammatory Bowel Disease
Authors: Zhang Xiaoyi , Ramos-Rivers Claudia , Prathapan Krishnapriya , Wang Xianling , Tang Gong , Kim Sandra , Binion David G. 
Published: February 2023

Objectives:
Peripheral blood monocytosis (PBM) is a marker of increased disease severity in adults with inflammatory bowel diseases (IBDs). We sought to determine whether PBM serves as a prognostic biomarker in patients with pediatric-onset IBD for a more aggressive long-term disease course when followed into adulthood.

Methods:
Patients with pediatric-onset inflammatory bowel disease were identified within an adult tertiary care center, within a consented, prospectively collected natural history disease registry, to compare clinical outcomes between patients with and without PBM from the years 2009 to 2019. Patients demonstrating elevation in PBM at any time defined membership and long-term clinical trajectories were compared with pediatric-onset patients without PBM.

Results:
A total of 581 patients with IBD, diagnosed by 18 years of age, were identified for inclusion, of which 440 patients were diagnosed with Crohn disease and 141 with ulcerative colitis. Monocytosis was detected by complete blood cell counts in 40.1% of patients. PBM was associated with steroid and biologic exposure, number of IBD-related surgeries, and increased health care utilization. Multivariate logistic regression analyses, accounting for elevation of inflammatory markers and other values associated with acute disease activity as well as steroid use, showed persistently increased odds of biologic exposure, emergency department visits, and hospitalizations, but not surgeries, after detection of monocytosis.

Conclusions:
Within patients with pediatric-onset IBD, the sub-cohort with PBM had associated worse clinical outcomes and other markers of increased disease severity.
Estrogen alleviates post-hemorrhagic shock mesenteric lymph-mediated lung injury through autophagy inhibition
Authors: Sun Qi , Zhang Hong , Du Hui-Bo , Zhao Zhen-Ao , Li Cai-Juan , Chen Si-Jie , Li Yi-Ming , Zhang Sen-Lu , Liu Jun-Chao , Niu Chun-Yu , Zhao Zi-Gang 
Published: February 2023

Abstract

Background
Hemorrhagic shock-induced acute lung injury (ALI) is commonly associated with the post-hemorrhagic shock mesenteric lymph (PHSML) return. Whether excessive autophagy is involved in PHSML-mediated ALI remains unclear. The relationship between estrogen treatment and PHSML or autophagy needs to verify. The current study will clarify the role of estrogen in reducing PHSML-mediated ALI through inhibition of autophagy.

Methods
Firstly, a hemorrhagic shock model in conscious rats was employed to observe the effects of 17β-estradiol (E2) on intestinal blood flow, pulmonary function, intestinal and pulmonary morphology, and expression of autophagy marker proteins. Meanwhile, the effect of PHSML and autophagy agonist during E2 treatment was also investigated. Secondly, rat primary pulmonary microvascular endothelial cells (PMVECs) were used to observe the effect of PHSML, PHSML plus E2, and E2-PHSML (PHSML obtained from rats treated by E2) on the cell viability.

Results
Hemorrhagic shock induced intestinal and pulmonary tissue damage and increased wet/dry ratio, reduced intestinal blood flow, along with pulmonary dysfunction characterized by increased functional residual capacity and lung resistance and decreased inspiratory capacity and peak expiratory flow. Hemorrhagic shock also enhanced the autophagy levels in intestinal and pulmonary tissue, which was characterized by increased expressions of LC3 II/I and Beclin-1 and decreased expression of p62. E2 treatment significantly attenuated these adverse changes following hemorrhagic shock, which was reversed by PHSML or rapamycin administration. Importantly, PHSML incubation decreased the viability of PMVECs, while E2 co-incubation or E2-treated lymph counteracted the adverse roles of PHSML.

Conclusions
The role of estrogen reducing PHSML-mediated ALI is associated with the inhibition of autophagy.
Identification of further variation at the lipooligosaccharide outer core locus inAcinetobacter baumanniigenomes and extension of the OCL reference sequence database forKaptive
Authors: Sorbello Bianca , Cahill Sarah M. , Kenyon Johanna J. 
Published: February 2023

ABSTRACTThe outer core locus (OCL) that includes genes for the synthesis of the variable outer core region of the lipooligosaccharide (LOS) is one of the key epidemiological markers used for tracing the spread ofAcinetobacter baumannii, a bacterial pathogen of global concern. In this study, we screened 12476 publicly availableA. baumanniigenome assemblies for novel OCL sequences, detecting six new OCL types that were designated OCL17-OCL22. These were compiled with previously characterised OCL to create an updated version of theA. baumanniiOCL reference database, providing a total of 22 OCL reference sequences for use with the bioinformatics tool,Kaptive. Use of this database against the 12476 downloaded assemblies found OCL1 to be the most common locus, present in 73.6% of sequenced genomes assigned byKaptivewith a match confidence score of ‘Good’ or above. OCL1 was most common amongst isolates belonging to sequence types, ST1, ST2, ST3 and ST78, all of which are over-represented clonal lineages associated with extensive antibiotic resistance. The highest level of diversity in OCL types was found in ST2, with eight different OCL identified. The updated OCL reference database is available for download from GitHub (https://github.com/katholt/Kaptive; under versionv 2.0.5), and has been integrated for use onKaptive-Web (https://kaptive-web.erc.monash.edu/) and PathogenWatch (https://pathogen.watch/), enhancing current methods forA. baumanniistrain identification, classification and surveillance.IMPACT STATEMENTIn the absence of effective treatment options for multi-drug resistantAcinetobacter baumannii, the highest-ranking critical priority bacterial pathogen of global concern, national and global surveillance is necessary to detect, track and subsequently curb the spread of isolates that resist current therapies. Several epidemiological markers are used to characteriseA. baumanniistrains by detecting genetic differences in specific regions of the genome. One of these is the chromosomal OC locus (OCL) responsible for the synthesis of the outer core (OC) component of the lipooligosaccharide (LOS). Here, we provide an update to the internationalA. baumanniiOCL reference sequence database, extending the number of known OCL types to assist with clinical surveillance of important strains or clonal lineages.Data summaryThe updatedA. baumanniiOCL reference sequence database including 22 annotated OCL sequences is available for download underKaptive v. 2.0.5athttps://github.com/katholt/Kaptive.Genome assemblies or GenBank records used as representative reference sequences are listed in Table 1 and acknowledged in each record in the database.
The pluripotency factor Tex10 finetunes Wnt signaling for PGC and male germline development
Authors: Li Dan , Yang Jihong , Ma Fanglin , Malik Vikas , Zang Ruge , Shi Xianle , Huang Xin , Zhou Hongwei , Wang Jianlong 
Published: February 2023

SUMMARYTestis-specific transcript 10 (Tex10) is a critical factor for pluripotent stem cell maintenance and preimplantation development. Here, we dissect its late developmental roles in primordial germ cell (PGC) specification and spermatogenesis using cellular and animal models. We discover that Tex10 binds the Wnt negative regulator genes, marked by H3K4me3, at the PGC-like cell (PGCLC) stage in restraining Wnt signaling. Depletion and overexpression of Tex10 hyperactivate and attenuate the Wnt signaling, resulting in compromised and enhanced PGCLC specification efficiency, respectively. Using the Tex10 conditional knockout mouse models combined with single-cell RNA sequencing, we further uncover critical roles of Tex10 in spermatogenesis with Tex10 loss causing reduced sperm number and motility associated with compromised round spermatid formation. Notably, defective spermatogenesis in Tex10 knockout mice correlates with aberrant Wnt signaling upregulation. Therefore, our study establishes Tex10 as a previously unappreciated player in PGC specification and male germline development by fine-tuning Wnt signaling.
Pharmacometric assessment of primaquine induced haemolysis in glucose-6-phosphate dehydrogenase deficiency
Authors: Pukrittayakamee Sasithon , Jittamala Podjanee , Watson James A , Hanboonkunupakarn Borimas , Leungsinsiri Pawanrat , Poovorawan Kittiyod , Chotivanich Kesinee , Bancone Germana , Chu Cindy S , Imwong Mallika , Day Nicholas PJ , Taylor Walter RJ , White Nicholas J 
Published: February 2023

AbstractBackgroundPrimaquine is an 8-aminoquinoline antimalarial. It is the only widely available treatment to prevent relapses ofPlasmodium vivaxmalaria. The 8-aminoquinolines cause dose dependent haemolysis in glucose-6-phosphate dehydrogenase deficient (G6PDd) individuals. G6PDd is common in malaria endemic areas but testing is often not available. As a consequence primaquine is underused.MethodsWe conducted a pharmacometric study to characterise the relationship between primaquine dose and haemolysis in G6PDd. The aim was to explore shorter and safer primaquine radical cure regimens compared to the currently recommended 8-weekly regimen (0.75 mg/kg once weekly), potentially obviating the need for G6PD testing. Hemizygous G6PDd healthy adult Thai and Burmese male volunteers were admitted to the Hospital for Tropical Diseases in Bangkok. In Part 1, volunteers were given ascending dose primaquine regimens whereby daily doses were increased from 7.5 mg up to 45 mg over 15 to 20 days. In Part 2, a single primaquine 45 mg dose was given.Results24 volunteers were enrolled in Part 1, and 16 in Part 2 (13 participated in both studies). In three volunteers, the ascending dose regimen was stopped because of haemolysis (n=1) and asymptomatic increases in transaminases (n=2; one was hepatitis E positive). Otherwise the ascending regimens were well tolerated with no drug-related serious adverse events. In Part 1, the median haemoglobin concentration decline was 3.7 g/dL (range: 2.1 to 5.9; relative decline of 26% [range: 15 to 40%]). Primaquine doses up to 0.87 mg/kg/day were tolerated subsequently without clinically significant further falls in haemoglobin. In Part 2, the median haemoglobin concentration decline was 1.7 g/dL (range 0.9 to 4.1; relative fall of 12% [range: 7 to 30% decrease]). The ascending dose primaquine regimens gave 7 times more drug but resulted in only double the haemoglobin decline.Conclusions and InterpretationIn patients with Southeast Asian G6PDd variants full radical cure treatment can be given in under three weeks compared with the current 8 week regimen.
Ecogenomics reveals distinctive viral-bacterial communities in the surface microlayer of a natural surface slick
Authors: Rahlff Janina , Wietz Matthias , Giebel Helge-Ansgar , Bayfield Oliver , Nilsson Emelie , Bergström Kristofer , Kieft Kristopher , Anantharaman Karthik , Ribas-Ribas Mariana , Wurl Oliver , Hoetzinger Matthias , Antson Alfred , Holmfeldt Karin 
Published: February 2023

AbstractVisible surface films, termed slicks, can extensively cover the sea surface, particularly in coastal regions. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (slick SML) harbors a distinctive bacterial community, but little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we investigated viruses and the bacterial community from a brackish slick SML in comparison to non-slick SML as well as the seawater below (SSW). We conducted size-fractionated filtration of all samples to distinguish viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. The distinctness was underlined by specific metabolic profiles of bacterial metagenome assembled genomes and isolates, which revealed prevalence of motility genes and diversity of CAZymes in the slick SML. Despite overall lower diversity, several vOTUs were enriched in slick SML over slick SSW. Nine vOTUs were only found in slick SML and six of them were targeted by slick SML-specific CRISPR spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages forAlishewanellasp. andPseudoalteromonas tunicata, representing abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks can contribute to biogeochemical cycling in coastal ecosystems.
Combining biophysical models and machine learning to optimize implant geometry and stimulation protocol for intraneural electrodes
Authors: Romeni Simone , Losanno Elena , Koert Elisabeth , Pierantoni Luca , Delgado-Martinez Ignacio , Navarro Xavier , Micera Silvestro 
Published: February 2023

AbstractObjectivePeripheral nerve interfaces have the potential to restore sensory, motor, and visceral functions. In particular, intraneural interfaces allow targeting deep neural structures with high selectivity, even if their performance strongly depends upon the implantation procedure and the subject’s anatomy. Currently, few alternatives exist for the determination of the target subject structural and functional anatomy, and statistical characterizations from cadaveric samples are limited because of their high cost. We propose an optimization workflow that can guide both the pre-surgical planning and the determination of maximally selective multisite stimulation protocols for implants consisting of several intraneural electrodes, and we characterize its performance in silico. We show that the availability of structural and functional information leads to very high performances and allows taking informed decisions on neuroprosthetic design.ApproachWe employ hybrid models (HMs) of neuromodulation in conjunction with a machine learning-based surrogate model to determine fiber activation under electrical stimulation, and two steps of optimization through particle swarm optimization (PSO) to optimize in silico implant geometry, implantation and stimulation protocols using morphological data from the human median nerve at a reduced computational cost.Main resultsOur method allows establishing the optimal geometry of multi-electrode transverse intra-fascicular multichannel electrode (TIME) implants, the optimal number of electrodes to implant, their optimal insertion, and a set of multipolar stimulation protocols that lead in silico to selective activation of all the muscles innervated by the human median nerve.SignificanceWe show how to use effectively HMs for optimizing personalized neuroprostheses for motor function restoration. We provide in-silico evidences about the potential of multipolar stimulation to increase greatly selectivity. We also show that the knowledge of structural and functional anatomies of the target subject leads to very high selectivity and motivate the development of methods for their in vivo characterization.
Inhibiting mitochondrial translation overcomes multidrug resistance in MYC-driven neuroblastoma via OMA1-mediated integrated stress response
Authors: Borankova Karolina , Krchniakova Maria , Leck Lionel YW , Neradil Jakub , Kubistova Adela , Jansson Patric J , Hogarty Michael D , Skoda Jan 
Published: February 2023

ABSTRACTHigh-risk neuroblastoma remains a clinically challenging childhood tumor with a 5-year survival of only 50%. Tumors overexpressing N-MYC or c-MYC oncoproteins define a group of MYC-driven high-risk neuroblastoma with the most dismal outcomes, mainly caused by treatment failure due to the emergence and regrowth of multidrug-resistant cancer cells. Specific mitochondrial processes have been implicated in the maintenance of aggressive stem-like phenotypes in various cancers. We have recently identified a novel mitochondria-mediated mechanism of neuroblastoma multidrug resistance. However, the potential of pharmacological targeting of mitochondria to overcome therapy resistance and stemness in neuroblastoma remains unclear. Here, we show that c-MYC/N-MYC-driven multidrug-resistant neuroblastoma cells are highly vulnerable to cell death induced by the inhibition of mitochondrial translation. In contrast with normal fibroblasts, doxycycline (DOXY)-mediated inhibition of mitochondrial ribosomes efficiently impaired the survival of neuroblastoma cells regardless of their multidrug resistance and stem-like phenotypes. Mechanistically, inhibiting mitochondrial translation induced the mitochondrial stress-activated integrated stress response (ISR) via the OMA1-eIF2α axis, which preceded neuroblastoma cell death. Strikingly, several oncoproteins associated with poor neuroblastoma prognosis, including c-MYC and N-MYC, were markedly downregulated upon ISR activation. Comparing models of various neuroectodermal tumors and normal fibroblasts, we identified high levels of phosphorylated c-MYC and N-MYC (indicating their activity and rapid turnover) as a factor that predetermines susceptibility of neuroblastoma cells to DOXY-induced cell death. Neuroblastoma cells failed to develop significant DOXY resistance over a long-term repeated (pulsed) selection pressure, further demonstrating mitochondrial protein balance as a clinically relevant vulnerability of cancer cells that rely on high MYC activity. Together, our findings provide insight into mitochondrial retrograde regulatory networks in the context of MYC dependence and demonstrate the mitochondrial translation machinery as a promising therapeutic target in multidrug-resistant MYC-driven neuroblastoma.
Neisseria leonissp. nov. isolated from rabbits, reclassification ofUruburuella suis, Uruburuella testudinis, Kingella potus, Bergeriella denitrificansandMorococcus cerebrosusintoNeisseriagenus and reclassification ofNeisseria shayeganiiintoEikenellagenus
Authors: Boutroux M. , Favre-Rochex S. , Gorgette O. , Touak G. , Muhle E. , Chesneau O. , Clermont D. , Rahi P. 
Published: February 2023

AbstractGenome sequence-based identification of two strains (3986Tand 51.81) isolated from rabbits in France in 1972 and 1981 and deposited in the Collection of Institut Pasteur (CIP) has led to the description of a novel species in the genusNeisseria. The cells of both strains were non-motile, Gram-stain-negative and diplococcobacilli. Optimal growth on trypticase soy agar was recorded at 37°C and pH 8.5 in aerobic conditions. Phylogeny based on 16S rRNA gene placed the strains close toNeisseria bacilliformisATCC BAA-1200T(96.38%) nesting with the members of Neisseriaceae family. Furthermore, the phylogenetic analysis based onbac120gene set from the Genome Taxonomy Database (GTDB) placed both strains within the monophyleticNeisseriaclade, which also included type strains ofMorococcus cerebrosus, Bergeriella denitrificans,Kingella potus, Uruburuella suisandUruburuella testudinis. However,Neisseria shayeganiistrain 871Twas placed outsideNeisseriaclade and close to the members ofEikenellagenus. Strains 3986Tand 51.81 were placed in a branch distinct from all species of the genusNeisseriaand exhibited the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values below the species demarcation values. In contrast, ANI value within the two strains was 96.9% confirming that they represent same species. The genomic DNA G+C content of strain 3986Twas 56.92%. Based on the phylogenetic and phenotypic data, the strains 3986Tand 51.81 represent a novel species of the genusNeisseria, for which the nameNeisseria leonissp. nov. is proposed (type strain 3986T= CIP 109994T= LMG 32907T). Additionally, based on phylogenetic analysis, DUS dialect and average amino acid identity (AAI) values, we also proposed the reclassification ofMorococcus cerebrosus,Bergeriella denitrificans,Kingella potus, Uruburuella suisandUruburuella testudinisintoNeisseriagenus andNeisseria shayeganiiintoEikenellagenus.Author NotesThe GenBank accession numbers for the 16S rRNA gene sequence of strains 3986Tand 51.81 are respectively OQ121838.1 and OQ428162.1. The draft genome sequences have been deposited in GenBank under the accession numbers JAPQFK000000000 (strain 3986T) and JAPQFL000000000 (strain 51.81).Further explanations mentioned in the article as well as 7 supplementary tables and 7 supplementary figures are available with the online version of this article.
IFN-λ is protective against lethal oralToxoplasma gondiiinfection
Authors: Murillo-León Mateo , Bastidas-Quintero Aura M. , Endres Niklas S. , Schnepf Daniel , Delgado-Betancourt Estefanía , Ohnemus Annette , Taylor Gregory A. , Schwemmle Martin , Staeheli Peter , Steinfeldt Tobias 
Published: February 2023

AbstractInterferons are essential for innate and adaptive immune responses against a wide variety of pathogens. Interferon lambda (IFN-λ) protects mucosal barriers during pathogen exposure. The intestinal epithelium is the first contact site forToxoplasma gondii(T. gondii) with its hosts and the first defense line that limits parasite infection. Knowledge of very earlyT. gondiiinfection events in the gut tissue is limited and a possible contribution of IFN-λ has not been investigated so far. Here, we demonstrate with systemic interferon lambda receptor (IFNLR1) and conditional (Villin-Cre) knockout mouse models and bone marrow chimeras of oralT. gondiiinfection and mouse intestinal organoids a significant impact of IFN-λ signaling in intestinal epithelial cells and neutrophils toT. gondiicontrol in the gastrointestinal tract. Our results expand the repertoire of interferons that contribute to the control ofT. gondiiand may lead to novel therapeutic approaches against this world-wide zoonotic pathogen.