bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial susceptibility testing of Staphylococcus aureus isolates from patients at a tertiary hospital in Tehran, Iran, 2018–2019
Authors: Qodrati Mohammad , SeyedAlinaghi SeyedAhmad , Dehghan Manshadi Seyed Ali , Abdollahi Alireza , Dadras Omid 
Published: August 2022

Abstract
Background
Staphylococcus aureus, a human skin and mucous membranes colonizer, could opportunistically cause a variety of infectious diseases. Frequently, it is resistant to methicillin (MRSA), and often, co-resistant to many clinically available antibiotics. MRSA is a major burden for healthcare systems and communities all over the world, especially in developing countries. We addressed the issue that more than a decade had passed since the last report about cumulative antibiogram for S. aureus from our center, whereas The Clinical and Laboratory Standards Institute (CLSI) recommends to analyze and report it on an annual basis in order to guide clinicians to select the best initial empiric antimicrobial therapy.

Methods
In a cross-sectional retrospective design, data of culture-proven S. aureus from clinical specimens of hospitalized patients at Imam Khomeini Hospital Complex, Tehran, Iran, were collected from September 2018 to September 2019. Antimicrobial susceptibility testing (AST) had been performed using either Kirby–Bauer disk diffusion or VITEK 2 automated system which is based on minimum inhibitory concentration (MIC). The Chi-squared test was used considering the critical p-value to be ≤ .05.

Results
Among 576 unique isolates, the overall prevalence of MRSA was 37.5%. Patients admitted to the infectious diseases ward and ICUs have a greater chance to have such an isolate. Methicillin resistance was predictive of resistance to most antibiotics: erythromycin (90.9%), clindamycin (85.4% including inducible resistance), gentamicin, cipro-/levo-/moxi-floxacin, trimethoprim–sulfamethoxazole (58.3%), tetracycline, and rifampin. Resistance rate of zero was observed for daptomycin, linezolid, tigecycline, and (roughly) vancomycin. The prevalence of multiple-drug resistant (MDR) isolates was 48.5%.

Conclusions
Although in this study, the prevalence of MRSA was lower than the previous ones from the same hospital, it is still far from the desired rates. Besides, resistance to clindamycin and trimethoprim–sulfamethoxazole were remarkable. So far, vancomycin is the best choice for empiric treatment of MRSA, with linezolid as the second choice. It is advised to avoid prescribing the newer antibacterial agents as long as the older ones are effective to prevent the emergence of MDR species.
Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining
Authors: Du Kang , Yang Feng , Zhang Jun-Tao , Yu Rong-Cheng , Deng Ziqing , Li Wei-Fang , Chen Yuxing , Li Qiong , Zhou Cong-Zhao 
Published: August 2022

Abstract
Background
As important producers using photosynthesis on Earth, cyanobacteria contribute to the oxygenation of atmosphere and the primary production of biosphere. However, due to the eutrophication of urban waterbodies and global warming, uncontrollable growth of cyanobacteria usually leads to the seasonal outbreak of cyanobacterial blooms. Cyanophages, a group of viruses that specifically infect and lyse cyanobacteria, are considered as potential environment-friendly agents to control the harmful blooms. Compared to the marine counterparts, only a few freshwater cyanophages have been isolated and genome sequenced to date, largely limiting their characterizations and applications.

Results
Here, we isolated five freshwater cyanophages varying in tail morphology, termed Pam1~Pam5, all of which infect the cyanobacterium Pseudanabaena mucicola Chao 1806 that was isolated from the bloom-suffering Lake Chaohu in Anhui, China. The whole-genome sequencing showed that cyanophages Pam1~Pam5 all contain a dsDNA genome, varying in size from 36 to 142 Kb. Phylogenetic analyses suggested that Pam1~Pam5 possess different DNA packaging mechanisms and are evolutionarily distinct from each other. Notably, Pam1 and Pam5 have lysogeny-associated gene clusters, whereas Pam2 possesses 9 punctuated DNA segments identical to the CRISPR spacers in the host genome. Metagenomic data-based calculation of the relative abundance of Pam1~Pam5 at the Nanfei estuary towards the Lake Chaohu revealed that the short-tailed Pam1 and Pam5 account for the majority of the five cyanophages. Moreover, comparative analyses of the reference genomes of Pam1~Pam5 and previously reported cyanophages enabled us to identify three circular and seven linear contigs of virtual freshwater cyanophages from the metagenomic data of the Lake Chaohu.

Conclusions
We propose a high-throughput strategy to systematically identify cyanophages based on the currently available metagenomic data and the very limited reference genomes of experimentally isolated cyanophages. This strategy could be applied to mine the complete or partial genomes of unculturable bacteriophages and viruses. Transformation of the synthesized whole genomes of these virtual phages/viruses to proper hosts will enable the rescue of bona fide viral particles and eventually enrich the library of microorganisms that exist on Earth.
Spatial distribution of insecticide resistant populations of Aedes aegypti and Ae. albopictus and first detection of V410L mutation in Ae. aegypti from Cameroon
Authors: Montgomery Matthew , Harwood James F. , Yougang Aurelie P. , Wilson-Bahun Theodel A. , Tedjou Armel N. , Keumeni Christophe Rostand , Kilpatrick Auston Marm , Wondji Charles S. , Kamgang Basile 
Published: August 2022

Abstract
Background
Dengue (DENV), chikungunya (CHIKV) and Zika virus (ZIKV), are mosquito-borne viruses of medical importance in most tropical and subtropical regions. Vector control, primarily through insecticides, remains the primary method to prevent their transmission. Here, we evaluated insecticide resistance profiles and identified important underlying resistance mechanisms in populations of Aedes aegypti and Ae. albopictus from six different regions in Cameroon to pesticides commonly used during military and civilian public health vector control operations.

Methods
Aedes mosquitoes were sampled as larvae or pupae between August 2020 and July 2021 in six locations across Cameroon and reared until the next generation, G1. Ae. aegypti and Ae. albopictus adults from G1 were tested following World Health Organization (WHO) recommendations and Ae. aegypti G0 adults screened with real time melting curve qPCR analyses to genotype the F1534C, V1016I and V410L Aedes kdr mutations. Piperonyl butoxide (PBO) assays and real time qPCR were carried out from some cytochrome p450 genes known to be involved in metabolic resistance. Statistical analyses were performed using Chi-square test and generalized linear models.

Results
Loss of susceptibility was observed to all insecticides tested. Mortality rates from tests with 0.25% permethrin varied from 24.27 to 85.89% in Ae. aegypti and from 17.35% to 68.08% in Ae. albopictus. Mortality rates for 0.03% deltamethrin were between 23.30% and 88.20% in Ae. aegypti and between 69.47 and 84.11% in Ae. albopictus. We found a moderate level of resistance against bendiocarb, with mortality rates ranging from 69.31% to 90.26% in Ae. aegypti and from 86.75 to 98.95% in Ae. albopictus. With PBO pre-exposure, we found partial or fully restored susceptibility to pyrethroids and bendiocarb. The genes Cyp9M6F88/87 and Cyp9J10 were overexpressed in Ae. aegypti populations from Douala sites resistant to permethrin and deltamethrin. Cyp6P12 was highly expressed in alphacypermethrin and permethrin resistant Ae. albopictus samples. F1534C and V1016I mutations were detected in A. aegypti mosquitoes and for the first time V410L was reported in Cameroon.

Conclusions
This study revealed that Ae. aegypti and Ae. albopictus are resistant to multiple insecticide classes with multiple resistance mechanisms implicated. These findings could guide insecticide use to control arbovirus vectors in Cameroon.
Sporadic Creutzfeldt-Jakob disease VM1: phenotypic and molecular characterization of a novel subtype of human prion disease
Authors: Gelpi Ellen , Baiardi Simone , Nos Carlos , Dellavalle Sofia , Aldecoa Iban , Ruiz-Garcia Raquel , Ispierto Lourdes , Escudero Domingo , Casado Virgina , Barranco Elena , Boltes Anuncia , Molina-Porcel Laura , Bargalló Nuria , Rossi Marcello , Mammana Angela , Tiple Dorina , Vaianella Luana , Stoegmann Elisabeth , Simonitsch-Klupp Ingrid , Kasprian Gregor , Klotz Sigrid , Höftberger Romana , Budka Herbert , Kovacs Gabor G. , Ferrer Isidre , Capellari Sabina , Sanchez-Valle Raquel , Parchi Piero 
Published: August 2022

AbstractThe methionine (M)—valine (V) polymorphic codon 129 of the prion protein gene (PRNP) plays a central role in both susceptibility and phenotypic expression of sporadic Creutzfeldt-Jakob diseases (sCJD). Experimental transmissions of sCJD in humanized transgenic mice led to the isolation of five prion strains, named M1, M2C, M2T, V2, and V1, based on two major conformations of the pathological prion protein (PrPSc, type 1 and type 2), and the codon 129 genotype determining susceptibility and propagation efficiency. While the most frequent sCJD strains have been described in codon 129 homozygosis (MM1, MM2C, VV2) and heterozygosis (MV1, MV2K, and MV2C), the V1 strain has only been found in patients carrying VV. We identified six sCJD cases, 4 in Catalonia and 2 in Italy, carrying MV at PRNP codon 129 in combination with PrPSc type 1 and a new clinical and neuropathological profile reminiscent of the VV1 sCJD subtype rather than typical MM1/MV1. All patients had a relatively long duration (mean of 20.5 vs. 3.5 months of MM1/MV1 patients) and lacked electroencephalographic periodic sharp-wave complexes at diagnosis. Distinctive histopathological features included the spongiform change with vacuoles of larger size than those seen in sCJD MM1/MV1, the lesion profile with prominent cortical and striatal involvement, and the pattern of PrPSc deposition characterized by a dissociation between florid spongiform change and mild synaptic deposits associated with coarse, patch-like deposits in the cerebellar molecular layer. Western blot analysis of brain homogenates revealed a PrPSc type 1 profile with physicochemical properties reminiscent of the type 1 protein linked to the VV1 sCJD subtype. In summary, we have identified a new subtype of sCJD with distinctive clinicopathological features significantly overlapping with those of the VV1 subtype, possibly representing the missing evidence of V1 sCJD strain propagation in the 129MV host genotype.
C5aR1 antagonism alters microglial polarization and mitigates disease progression in a mouse model of Alzheimer’s disease
Authors: Gomez-Arboledas Angela , Carvalho Klebea , Balderrama-Gutierrez Gabriela , Chu Shu-Hui , Liang Heidi Yahan , Schartz Nicole D. , Selvan Purnika , Petrisko Tiffany J. , Pan Miranda A. , Mortazavi Ali , Tenner Andrea J. 
Published: August 2022

AbstractMultiple studies have recognized the involvement of the complement cascade during Alzheimer’s disease pathogenesis. However, the specific role of C5a-C5aR1 signaling in the progression of this neurodegenerative disease is still not clear. Furthermore, its potential as a therapeutic target to treat AD still remains to be elucidated. Canonically, generation of the anaphylatoxin C5a as the result of complement activation and interaction with its receptor C5aR1 triggers a potent inflammatory response. Previously, genetic ablation of C5aR1 in a mouse model of Alzheimer’s disease exerted a protective effect by preventing cognitive deficits. Here, using PMX205, a potent, specific C5aR1 antagonist, in the Tg2576 mouse model of Alzheimer’s disease we show a striking reduction in dystrophic neurites in parallel with the reduced amyloid load, rescue of the excessive pre-synaptic loss associated with AD cognitive impairment and the polarization of microglial gene expression towards a DAM-like phenotype that are consistent with the neuroprotective effects seen. These data support the beneficial effect of a pharmacological inhibition of C5aR1 as a promising therapeutic approach to treat Alzheimer’s disease. Supportive of the safety of this treatment is the recent FDA-approval of another other C5a receptor 1 antagonist, Avacopan, as a treatment for autoimmune inflammatory diseases.
An analysis of COVID-19 information sources
Authors: Umeta Belachew , Mulugeta Temesgen , Mamo Girma , Alemu Sintayehu , Berhanu Nimona , Milkessa Gudina , Mengistu Birhanu , Melaku Tsegaye 
Published: August 2022

﻿Abstract
Background
The COVID-19 pandemic has brought new situations that require the effective delivery of health information across the world and it’s important to offer clear, consistent, and credible information on the pandemic to mitigate and control the outbreak.

Aim
To assess COVID-19 information source, need and trust among the rural community of southwest Ethiopia.

Methods
A community-based cross-sectional study design was conducted among 634 rural communities of southwest Ethiopia. The data were collected by interviewing individuals from selected households and analyzed by SPSS version 26. A multivariable logistic regression model was used to assess factors affecting information needs.

Results
Radio 484 (76.3%) was mostly used as a source of information for COVID-19, and government 404 (63.7%) and health professionals 345 (57.7%) were trusted. However, only 10 (1.6%) of the participants acquired information from health professionals. Around 395 (62.3%) of the participants needed additional information on COVID-19. Around 230 (58.2%) and 186 (47.1%) of the participants required additional information on cause and sign and symptoms, respectively. Age of < 45 years old (AOR: 2.11, 95% CI: 1.43, 3.12, P < 0.001), and absence of formal education (AOR: 2.00, 95% CI: 1.35, 2.95, P: 0.001) were factors positively affecting the information needs of the participants on COVID-19. Church goers (AOR: 3.24; 95% CI: 2.03, 5.19; P < 0.001), television (AOR: 2.39; 95% CI: 1.63, 3.49; P < 0.001) and social media users (AOR: 4.52; 95% CI: 2.26, 9.04; P < 0.001) as source of information required additional information on COVID-19, and the participants that trusted social media (AOR: 2.52; 95% CI: 1.64, 3.87; P < 0.001) and friends/relatives (AOR: 2.95: 95% CI: 1.51, 5.76; P < 0.001) were also required additional information on COVID-19.

Conclusions
The popular sources of COVID-19-related information were radio and television. The participants trusted the government and health professionals on COVID-19. However, less than 2% of the participants had information from health professionals. The majority of the participants wanted to learn more about COVID-19. The areas the participants required additional information include cause and signs and symptoms. Age, educational status, trust in social media, trust in friends, using the church, television and social media as a source were factors associated with information needs.
Rehabilitation and return to sports after isolated meniscal repairs: a new evidence-based protocol
Authors: Calanna Filippo , Duthon Victoria , Menetrey Jacques 
Published: August 2022

Abstract
Purpose
Despite many protocols that have been proposed, there’s no consensus in the literature regarding the optimal rehabilitation program and return to sports (RTS) protocol following isolated meniscal repair. The aim of this current concept review is to look at the evidence of rehabilitation and RTS program after isolated meniscal repair, focusing on general and specific protocols per type of injury trying to give some guidelines based on the current state of knowledge.

Methods
A narrative literature review was performed searching PubMed database to identify relevant articles from January 1985 to October 2021 on rehabilitation and RTS after isolated meniscal repair. Randomized controlled trials (RCTs), prospective and retrospective cohort studies, case series, systematic reviews, meta-analyses, cadaveric studies and basic science studies were included.

Results
When the hoop tensile stress effect is preserved, an accelerated rehabilitation program may be suggested. Hence, partial weight bearing (20 kg) in association with ROM limited to 90° is allowed for the first four weeks, followed by weight bearing as tolerated.
In contrast, when circumferential hoop fibers are disrupted, a restricted rehabilitation protocol may be recommended. In this scenario no weight bearing is allowed for the first six weeks after the surgery and range of motion (ROM) is limited to 90°.

Conclusion
Biomechanical evidence suggests that tailoring an individualized protocol based upon the type of lesion and meniscus stability is reasonable.

Level of evidence
Level V.
Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome
Authors: Mon Maria Laura , Marrero Díaz de Villegas Rubén , Campos Eleonora , Soria Marcelo A. , Talia Paola M. 
Published: August 2022

AbstractThe aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase (Xyl10B) identified in a termite gut microbiome by a shotgun metagenomic approach. This endoxylanase candidate was amplified, cloned, heterologously expressed in Escherichia coli and purified. The recombinant enzyme was active at a broad range of temperatures (37–60 ºC) and pH values (4–10), with optimal activity at 50 ºC and pH 9. Moreover, its activity remained at more than 80% of its maximum at 50 °C for 8 h. In addition, Xyl10B was found to be stable in the presence of salt and several ions and chemical reagents frequently used in the industry. These characteristics make this enzyme an interesting candidate for pulp and paper bleaching industries, since this process requires enzymes without cellulase activity and resistant to high temperatures and alkaline pH (thermo-alkaliphilic enzymes). The products of xylan hydrolysis by Xyl10B (short xylooligosaccharides, xylose and xylobiose) could be suitable for application as prebiotics and in the production of bioethanol.
Graphical Abstract
Impact of the dead-time correction method on quantitative 177Lu-SPECT (QSPECT) and dosimetry during radiopharmaceutical therapy
Authors: Desy Alessandro , Bouvet Guillaume F. , Lafrenière Nancy , Zamanian Atefeh , Després Philippe , Beauregard Jean-Mathieu 
Published: August 2022

Abstract
Background
Dead-time correction is required for accurate quantitative SPECT-based dosimetry in the context of personalised 177Lu radiopharmaceutical therapy. We aimed to evaluate the impact of applying dead-time correction on the reconstructed SPECT image versus on the acquisition projections before reconstruction.

Methods
Data from 16 SPECT/CT acquisitions of a decaying 177Lu-filled phantom (up to 20.75 GBq) and dual-timepoint SPECT/CT in 14 patients treated with personalised 177Lu peptide receptor radionuclide therapy were analysed. Dead time was determined based on the acquisition wide-spectrum count rate for each projection and averaged for the entire acquisition. Three dead-time correction methods (DTCMs) were used: the per-projection correction, where each projection was individually corrected before reconstruction (DTCM1, the standard of reference), and two per-volume methods using the average dead-time correction factor of the acquisition applied to all projections before reconstruction (DTCM2) or to the SPECT image after reconstruction (DTCM3). Relative differences in quantification were assessed for various volumes of interest (VOIs) on the phantom and patient SPECT images. In patients, the resulting dosimetry estimates for tissues of interest were also compared between DTCMs.

Results
Both per-volume DTCMs (DTCM2 and DTCM3) were found to be equivalent, with VOI count differences not exceeding 0.8%. When comparing the per-volume post-reconstruction DTCM3 versus the per-projection pre-reconstruction DTCM1, differences in VOI counts and absorbed dose estimates did not exceed 2%, with very few exceptions. The largest absorbed dose deviation was observed for a kidney at 3.5%.

Conclusion
While per-projection dead-time correction appears ideal for QSPECT, post-reconstruction correction is an acceptable alternative that is more practical to implement in the clinics, and that results in minimal deviations in quantitative accuracy and dosimetry estimates, as compared to the per-projection correction.
A deep learning-based whole-body solution for PET/MRI attenuation correction
Authors: Ahangari Sahar , Beck Olin Anders , Kinggård Federspiel Marianne , Jakoby Bjoern , Andersen Thomas Lund , Hansen Adam Espe , Fischer Barbara Malene , Littrup Andersen Flemming 
Published: August 2022

AbstractBackgroundDeep convolutional neural networks have demonstrated robust and reliable PET attenuation correction (AC) as an alternative to conventional AC methods in integrated PET/MRI systems. However, its whole-body implementation is still challenging due to anatomical variations and the limited MRI field of view. The aim of this study is to investigate a deep learning (DL) method to generate voxel-based synthetic CT (sCT) from Dixon MRI and use it as a whole-body solution for PET AC in a PET/MRI system.Materials and methodsFifteen patients underwent PET/CT followed by PET/MRI with whole-body coverage from skull to feet. We performed MRI truncation correction and employed co-registered MRI and CT images for training and leave-one-out cross-validation. The network was pretrained with region-specific images. The accuracy of the AC maps and reconstructed PET images were assessed by performing a voxel-wise analysis and calculating the quantification error in SUV obtained using DL-based sCT (PETsCT) and a vendor-provided atlas-based method (PETAtlas), with the CT-based reconstruction (PETCT) serving as the reference. In addition, region-specific analysis was performed to compare the performances of the methods in brain, lung, liver, spine, pelvic bone, and aorta.ResultsOur DL-based method resulted in better estimates of AC maps with a mean absolute error of 62 HU, compared to 109 HU for the atlas-based method. We found an excellent voxel-by-voxel correlation between PETCTand PETsCT(R2 = 0.98). The absolute percentage difference in PET quantification for the entire image was 6.1% for PETsCTand 11.2% for PETAtlas. The regional analysis showed that the average errors and the variability for PETsCTwere lower than PETAtlasin all regions. The largest errors were observed in the lung, while the smallest biases were observed in the brain and liver.ConclusionsExperimental results demonstrated that a DL approach for whole-body PET AC in PET/MRI is feasible and allows for more accurate results compared with conventional methods. Further evaluation using a larger training cohort is required for more accurate and robust performance.