bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ageing, cellular senescence and chronic kidney disease: experimental evidence
Authors: Tan Huishi , Xu Jie , Liu Youhua 
Published: February 2022

Purpose of review
Chronic kidney disease (CKD) is often viewed as an accelerated and premature ageing of the kidney, as they share common pathological features characterized by cellular senescence. In this review, we summarize the experimental evidence linking cellular senescence to the pathobiology of kidney ageing and CKD, and discuss the strategies for targeting senescent cells in developing therapeutics for ageing-related kidney disorders.

Recent findings
Kidney ageing and CKD are featured with increased cellular senescence, an irreversible state of cell cycle arrest and the cessation of cell division. Senescent cells secrete a diverse array of proinflammatory and profibrotic factors known as senescence-associated secretory phenotype (SASP). Secondary senescence can be induced by primary senescent cells via a mechanism involving direct contact or the SASP. Various senolytic therapies aiming to selectively remove senescent cells in vivo have been developed. Senostatic approaches to suppress senescence or inhibit SASP, as well as nutrient signalling regulators are also validated in animal models of ageing.

Summary
These recent studies provide experimental evidence supporting the notion that accumulation of senescent cells and their associated SASP is a main driver leading to structural and functional organ degeneration in CKD and other ageing-related disorder.
Memes and Poetry
Authors: Reynolds Staci S. , Sova Christopher 
Published: February 2022

Background:
Health care workers (HCWs) face high levels of burnout, which can lead to workforce turnover and poor patient outcomes. Health care leaders should identify strategies to improve staff resilience.

Purpose:
The purpose of this study was to describe HCWs' perspective on using creative arts therapy to reduce burnout and improve resiliency.

Methods:
During Infection Prevention week, staff were encouraged to submit and vote on educational memes and haikus. Staff were asked their perspectives on how this activity could be used to reduce burnout and improve resiliency using a 4-point Likert scale.

Results:
Twenty-two staff members submitted 26 memes and 27 haikus. Staff felt this activity could be an effective strategy to help reduce burnout and improve resiliency.

Conclusions:
Further research is warranted to better understand the correlation between this form of art therapy and burnout and resiliency; however, health care leaders may consider using this as a tool for staff well-being.
Diagnostic Performance of 18F-FDG PET/CT for Lymph Node Staging in Penile Cancer
Authors: Lee Sang Woo , Kim Seong-Jang 
Published: February 2022

Objective
The purpose of the current study was to evaluate the diagnostic accuracies of 18F-FDG PET/CT for detection of lymph node (LN) metastasis in penile cancer (PeCA) patients through a systematic review and meta-analysis.

Patients and Methods
The PubMed, Cochrane database, and Embase database, from the earliest available date of indexing through August 31, 2021, were searched for studies evaluating diagnostic performance of 18F-FDG PET/CT for detection of metastatic LN in PeCA patients. We determined the sensitivities and specificities across studies, calculated positive and negative likelihood ratios (LR+ and LR−, respectively), and constructed summary receiver operating characteristic curves.

Results
Across 12 studies (479 patients), the pooled sensitivity of 18F-FDG PET/CT was 0.87 (95% confidence interval [CI], 0.79–0.92) and the pooled specificity was 0.88 (95% CI, 0.79–0.93). Likelihood ratio syntheses gave an overall LR+ of 7.2 (95% CI, 3.9–13.1) and LR− of 0.15 (95% CI, 0.1–0.24). The pooled diagnostic odds ratio was 47 (95% CI, 19–116). In meta-regression analysis, no variable was the source of the study heterogeneity.

Conclusions

18F-FDG PET/CT showed a good diagnostic performances for detection of metastatic LN in PeCA patients. Also, 18F-FDG PET/CT revealed similar diagnostic accuracy for detection of inguinal and pelvic LN metastasis in PeCA patients.
Analysis of the Lamina Papyracea Dehiscence Based on Computed Tomography Findings
Authors: Xu Jing , Qin Le , Wang Daohe 
Published: February 2022

Objectives:
Aim to evaluate the incidence and characteristics of nontraumatic dehiscence of the lamina papyracea (LP) via computed tomography (CT).

Methods:
The authors retrospectively studied 893 patients' history and paranasal sinus CT from February to September 2020. The datum of incidence and the characteristics of LP dehiscence were collected and analyzed.

Results:
The LP dehiscence was identified in 23 of 893 patients (2.58%). Lamina papyracea anatomical variations were categorized into Grade I, II, and III, which account 69.56%, 21.74%, and 8.70% of the entire dehiscence group. The average depth of LP ingression was 5.5 ± 0.7 mm. There was no statistical difference between bilateral incidence. The medial rectus muscle was involved in 3 lesions. In all CT reports, this anatomic variation was misdiagnosed as ethmoid sinusitis in 8 cases.

Conclusions:
Preoperative cognition of the anatomic variation of LP via CT is conducive to decrease misdiagnosis and postoperative complications.
Genomic analysis reveals high intra-species diversity of Shewanella algae
Authors: Huang Zhenzhou , Yu Keyi , Fu Songzhe , Xiao Yue , Wei Qiang , Wang Duochun 
Published: February 2022

Shewanella algae

is widely distributed in marine and freshwater habitats, and has been proved to be an emerging marine zoonotic and human pathogen. However, the genomic characteristics and pathogenicity of

Shewanella algae

are unclear. Here, the whole-genome features of 55

S

.

algae

strains isolated from different sources were described. Pan-genome analysis yielded 2863 (19.4 %) genes shared among all strains. Functional annotation of the core genome showed that the main functions are focused on basic lifestyle such as metabolism and energy production. Meanwhile, the phylogenetic tree of the single nucleotide polymorphisms (SNPs) of core genome divided the 55 strains into three clades, with the majority of strains from China falling into the first two clades. As for the accessory genome, 167 genomic islands (GIs) and 65 phage-related elements were detected. The CRISPR-Cas system with a high degree of confidence was predicted in 23 strains. The GIs carried a suite of virulence genes and mobile genetic elements, while prophages contained several transposases and integrases. Horizontal genes transfer based on homology analysis indicated that these GIs and prophages were parts of major drivers for the evolution and the environmental adaptation of

S. algae

. In addition, a rich putative virulence-associated gene pool was found. Eight classes of antibiotic-associated resistance genes were detected, and the carriage rate of β-lactam resistance genes was 100 %. In conclusion,

S. algae

exhibits a high intra-species diversity in the aspects of population structure, virulence-associated genes and potential drug resistance, which is helpful for its evolution in pathogenesis and environmental adaptability.
Phylotyping, Pathotyping and Phenotypic Characteristics of Escherichia coli Isolated from Various Street Foods in Bangladesh
Authors: Bhowmik Anindita , Goswami Sharmistha , Sirajee Ahmad Salman , Ahsan Sunjukta 
Published: February 2022

AbstractThe burden of street food contamination remains significantly higher among developing countries, making its consumers’ health compromised. This study aimed at identifying Escherichia coli in local street foods, track their sources and characterize their virulence properties, antimicrobial susceptibility patterns, and incidence of recent fecal contamination. Twelve E. coli isolates isolated from 28 types of street foods sold at different locations of Dhaka metropolitan city were confirmed by both culture-based and molecular methods. Phylogroup B1 of environment origin was the most predominant (58%, n=12) among the isolates, followed by commensal phylogroup A (16%), phylogroup C (8%), D (8%), and E (8%). Alarmingly, 8% of the isolates were confirmed to be Enteropathogenic E. coli (EPEC), harboring hlyA gene, and 41% were due to recent fecal contamination cases confirmed by the presence of the eae gene. Isolates showed the highest resistance to ampicillin, followed by chloramphenicol. However, resistance could not be correlated to the presence of class 1 integron as isolates sensitive to these antibiotics also harbored this mobile genetic element. The findings of this study demonstrated the presence of antibiotic-resistant, potentially pathogenic E. coli in street food which emphasizes the health hazard associated with consumption of such foods.
Enviromic prediction is useful to define the limits of climate adaptation: A case study of common beans in Brazil
Authors: Heinemann Alexandre Bryan , da Matta David Henriques , Fernandes Igor Kuivjogi , Fritsche-Neto Roberto , Costa-Neto Germano 
Published: February 2022

ABSTRACTFuture environmental shifts foster plant research aiming to develop climate-smart cultivars but the past and current impacts on the environment are also a key to unraveling a major part of the phenotypic adaptation of crops. These studies may determine the most relevant environmental components of yield stability and adaptability within a breeding framework. Here, as a proof-concept study, we quantified the impacts of climate drivers in adapting common bean across Brazilian regions and seasons. We developed an ‘enviromic prediction’ approach based on Generalized Additive Models (GAM), large-scale environmental covariate data (EC), and grain yield (GY) of 18 years of a common bean breeding program. Then, we predicted the optimum limits for ECs for each production scenario. We verified the ability of GAM-based models to explain the climate driver GY variation and performed accurate predictions for diverse production scenarios (four regions, three seasons, and two grain types). Our results indicates that air temperature (maximum and minimum), accumulated solar radiation, and rainfalls are mostly associated as the main drivers of GY variation in most regions. We also observed a huge variability of the climate drivers impact for the same germplasm cultivated across different seasons for each region. Furthermore, this climate influence in common beans adaptation is more evident during the vegetative for some seasons, while more impressive for reproductive stages for other seasons. Consequently, it demands higher efforts from breeding programs in developing region- or season-specific ideotype cultivars. Enviromics prediction with GAM was useful to identify the effect of climate on critical crop stages, which indirectly might help breeders in developing climate-smart varieties. We envisage its use with research field trial data (e.g., advanced yield testing) and historical farm field yield aimed at understanding breeding gaps in developing adapted cultivars for growing scenarios.HighlightsWe developed an ‘enviromic prediction’ approach based on Generalized Additive Models (GAM) for a large-scale environmental covariate data and grain yieldWe verified the ability of GAM-based models to explain the climate driver grain yield variation and performed accurate predictions for diverse production scenarios (four regions, three seasons, and two grain types)Climatic limitations for cropping commun beans were identified across seasons and regions.“Optimum” values for climate variables in different common bean regions productions were obtained .
Whole-genome sequencing of Bantu-speakers from Angola and Mozambique reveals complex dispersal patterns and interactions throughout sub-Saharan Africa
Authors: Tallman Sam , das Dores Sungo Maria , Saranga Sílvio , Beleza Sandra 
Published: February 2022

AbstractAs the continent of origin for our species, Africa harbours the highest levels of diversity anywhere on Earth. This trove of diversity provides rich opportunities to discover unknown genomic variation and explore how human populations have moved and interacted on the continent over thousands of years. However, many regions of Africa remain under-sampled. Here we present the first collection of whole-genomes from Angola and Mozambique, enabling the construction of a high-quality reference variation catalogue including three million novel SNPs. Leveraging the power and flexibility of whole-genome sequencing data, we model the development and continuity of Bantu-population structure through time, widespread admixture involving source populations from these regions across sub-Saharan Africa, and the heterogeneous population histories of Western and Eastern Bantu-speakers. In contrast to depictions of the Bantu expansion as a single, continuous macro-event, we recover evidence of admixture among distinct Bantu-speaking groups in South-Eastern Africa and bring together concordant patterns from linguistics and archaeology to paint a more complex picture of Iron Age migrations into the region. Moreover, we generate reference panels that better represents the complete diversity of African populations involved in the Atlantic slave trade, improving imputation accuracy in African Americans and Brazilians over the 1000 Genomes Project. This study fills important gaps in the current record of global genetic diversity and informs on the most significant demographic events in the recent history of Africa. We anticipate that our collection of genomes will form the foundation for future genomic healthcare initiatives involving under-represented communities in Angola and Mozambique.
Eradicating Citrus Greening By Dual Action Targeting of Liberibacter asiaticus and Diaphorina citri
Authors: Farrell Catherine , Triplett Eric W. , Theise Neil D. , Lowell Cadance A. , Arment Anthony R. 
Published: February 2022

AbstractHuanglongbing (citrus greening) is caused by the unculturable, gram negative bacterium Liberibacter asiaticus and transmitted by the Asian Citrus Psyllid (Diaphorina citri). Prior research demonstrated that the rifampicin-derivative TPR-1 as well as Palisades Therapeutic (PT) compounds PT159 and PT160 were effective at inhibiting growth of the L. cresens, the only culturable model for Las, showing 100% inhibition at 0.5 μg mL−1, and 80% inhibition at 0.05 μg mL−1.Research with the PT glucocorticoid antagonist compounds demonstrated an inhibition of bacterial growth in L crescens as well, possibly a synergistic addition to TPR-1. A search of the L. asiaticus genome revealed the presence of 3 putative glucocorticoid response elements (GRE). Putative GRE are present in all organisms and may be involved in organism signaling as well as host-pathogen crosstalk.In Drosophila, the estrogen-related receptor (ERR) transcription factor is a master regulator of larval and pupal maturation. ERR binds to GRE promoter elements in the genome to regulate the transcription of pathways involved in glucose metabolism. Null mutations of ERR fail to leave pupation and demonstrate elevated glucose levels when compared to wild-type. Treatment of Drosophila larvae with PT compounds demonstrated developmental delay disruptions in pupation, including premature pupation and increased lethality. Pupae that had been fed PT compounds as larvae showed elevated glucose levels when compared to controls. Sequences identified in Drosophila ERR showed high homology to 2 proteins in D. citri (ERR-like 1 and ERR-like 2), leading us to hypothesize that a glucocorticoid antagonist may disrupt psyllid development. Because these genes and signaling pathways are highly conserved between these taxa, we propose that Drosophila serves as a good model for screening potential compounds for the control of psyllid populations.Collectively, we hypothesize that the dual action of these compounds offers a solution to HLB that can salvage the dying citrus industry in Florida and provide the first effective treatment. By simultaneous targeting of both Las and D. citri, it may be possible to both cure infected trees and block psyllid development in adults feeding on those same trees. Disruption of the psyllid’s ability to carry Las or cure Las from the psyllid gut are also both substantial possibilities.
Neurobeachin controls the asymmetric subcellular distribution of electrical synapse proteins
Authors: Martin E. Anne , Michel Jennifer Carlisle , Kissinger Jane S. , Echeverry Fabio A. , Lin Ya-Ping , O’Brien John , Pereda Alberto E. , Miller Adam C. 
Published: February 2022

AbstractThe subcellular positioning of synapses and their specialized molecular compositions form the fundamental basis of neural circuits. Like chemical synapses, electrical synapses are constructed from an assortment of adhesion, scaffolding, and regulatory molecules, yet little is known about how these molecules localize at specified subcellular neuronal compartments. Here we investigated the relationship between the autism- and epilepsy-associated gene Neurobeachin, neuronal gap junction channelforming Connexins, and the scaffold ZO1. Using the zebrafish Mauthner circuit we found Neurobeachin localizes to the electrical synapse independent of ZO1 and Connexins. By contrast, we show Neurobeachin is required postsynaptically for the robust localization of ZO1 and Connexins. We demonstrate Neurobeachin binds ZO1 but not Connexins. Finally, we find Neurobeachin is required to restrict postsynaptic electrical synapse proteins to dendrites. These findings reveal a mechanism for the asymmetric synaptic localization of electrical synapse components providing a basis for the subcellular specialization of neuronal gap junctions.
Carbapenem-resistant Klebsiella pneumoniae in university-affiliated hospitals: risk factors for isolation among hospitalized patients and molecular subtyping
Authors: Kobaidze Ketevan , Jacob Jesse , Leong Traci , Flanders W. Dana 
Published: February 2022

AbstractBackgroundCarbapenem-resistant Klebsiella pneumoniae (CRKP) is an important healthcare-associated pathogen. This study aimed to identify factors associated with CRKP isolation among hospitalized patients, describe molecular epidemiology, and mortality associated with CRKP isolation.MethodsWe performed a retrospective case-control study at the two university-affiliated teaching hospitals. 150 patients were included (30 cases and 120 controls) in this study.Each patient with CRKP, a case-patient, was matched with four controls by admission facility, age, and sex. Controls, patients without CRKP were randomly selected from a computerized list of inpatients whose admission date was the same as that of the case, within 48 hours of the date of the initial positive culture. We calculated the risk of in-hospital death as the number of deaths divided by the number of cases and evaluated the risk of mortality associated with the site of positive culture. Molecular epidemiology investigation using comparison of restricted DNA patterns of CRKP by pulsed-field gel electrophoresis (PFGE) was conducted.ResultsA greater proportion of cases than controls had undergone an invasive procedure, including use of a central vein catheter (p=0.007, OR, 3.4, 95% CI, 1.4-8.7), and mechanical ventilation (p=0.002, OR, 3.6, 95% CI, 1.6-8.1), nutrition by tube feeding (p=0.001, OR, 4.2, 95% CI, 1.8 −10).Pre-admission treatment within two months with the following antibiotic classes was associated with CRKP isolation: carbapenems (p=0.001, OR, 24.4, 95% CI, 2.73-217.96), fluoroquinolones (p<0.0001, OR, 6.17, 95% CI, 2.4 – 15.83), anti-pseudomonal penicillin (p = 0.02; OR, 6.03; 95% CI, 1.98 −18.32), and cephalosporins (p=0.001, OR, 5.36, 95% CI, 2.07 −13.87).The molecular analysis detected that over 90% of isolates shared similar PFGE patterns.CRKP isolation was associated with significantly higher In-hospital mortality (36.7% vs 3.3%) in comparison to controls (p<.0001).Positive cultures from sites other than urine were associated with substantially higher mortality than was a positive urine culture (RR= 4.0).
Model-based estimates of deaths averted and cost per life saved by scaling-up mRNA COVID-19 vaccination in low and lower-middle income countries in the COVID-19 Omicron variant era
Authors: Savinkina Alexandra , Bilinski Alyssa , Fitzpatrick Meagan C. , Paltiel A. David , Rizvi Zain , Salomon Joshua A. , Thornhill Tommy , Gonsalves Gregg 
Published: February 2022

AbstractBackgroundWhile almost 60% of the world has received at least one dose of COVID-19 vaccine, the global distribution of vaccination has not been equitable. Only 4% of the population of low-income countries has received a full primary vaccine series, compared to over 70% of the population of high-income nations.MethodsWe used economic and epidemiologic models, parameterized with public data on global vaccination and COVID-19 deaths, to estimate the potential benefits of scaling up vaccination programs in low and lower-middle income countries (LIC/LMIC) in 2022 in the context of global spread of the Omicron variant of SARS-CoV2. Outcomes were expressed as number of avertable deaths through vaccination, costs of scale-up, and cost per death averted. We conducted sensitivity analyses over a wide range of parameter estimates to account for uncertainty around key inputs.FindingsGlobal scale up of vaccination to provide two doses of mRNA vaccine to everyone in LIC/LMIC would cost $35.5 billion and avert 1.3 million deaths from COVID-19, at a cost of $26,900 per death averted. Scaling up vaccination to provide three doses of mRNA vaccine to everyone in LIC/LMIC would cost $61.2 billion and avert 1.5 million deaths from COVID-19 at a cost of $40,800 per death averted. Lower estimated infection fatality ratios, higher cost-per-dose, and lower vaccine effectiveness or uptake lead to higher cost-per-death averted estimates in the analysis.InterpretationScaling up COVID-19 global vaccination would avert millions of COVID-19 deaths and represents a reasonable investment in the context of the value of a statistical life (VSL). Given the magnitude of expected mortality facing LIC/LMIC without vaccination, this effort should be an urgent priority.
Signatures of immune senescence predict outcomes and define checkpoint blockade-unresponsive microenvironments in acute myeloid leukemia
Authors: Rutella Sergio , Vadakekolathu Jayakumar , Mazziotta Francesco , Reeder Stephen , Yau Tung-On , Mukhopadhyay Rupkatha , Dickins Benjamin , Altmann Heidi , Kramer Michael , Knaus Hanna , Blazar Bruce R. , Radojcic Vedran , Zeidner Joshua F. , Arruda Andrea , Minden Mark D. , Tasian Sarah K. , Bornhäuser Martin , Gojo Ivana , Luznik Leo 
Published: February 2022

SummaryThe function of senescent-like T cells, transcriptomic features of immune effector senescence (IES) and their influence on therapeutic response were investigated in independent AML clinical cohorts comprising 1,864 patients treated with chemotherapy and/or immune checkpoint blockade (ICB). We show that senescent-like bone marrow CD8+T cells are impaired in killing autologous AML blasts, and that their proportion negatively correlates with overall survival (OS). We define new IES signatures using two gene expression platforms and report that IES scores correlate with adverse-risk molecular lesions, stemness, and poor outcomes as a potentially more powerful predictor of OS than 2017-ELN risk or LSC17 stemness score. IES expression signatures also identify an ICB- unresponsive tumor microenvironment and predict significantly worse OS in AML as well as in solid tumors. The newly described IES scores provide improved AML risk stratification and could facilitate the delivery of personalized immunotherapies to patients who are most likely to benefit.