bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genetics of group B Streptococcus from maternal carriage in an ethnically diverse community in London
Authors: Jamrozy Dorota , Gopal Rao Guduru , Feltwell Theresa , Lamagni Theresa , Khanna Priya , Efstratiou Androulla , Parkhill Julian , Bentley Stephen D. 
Published: May 2023

IntroductionMaternal immunization against Group B Streptococcus (GBS) has the potential to significantly reduce the burden of neonatal GBS infections. Population genetics of GBS from maternal carriage can offer key insights into vaccine target distribution.MethodsIn this study we characterized the population structure of GBS isolates from maternal carriage (n = 535) in an ethnically diverse community in London, using whole genome sequencing.ResultsThe isolates clustered into nine clonal complexes (CCs) but the majority (95%) belonged to five lineages: CC1 (26%), CC19 (26%), CC23 (20%), CC17 (13%) and CC8/10 (10%). Nine serotypes were identified, the most common were serotypes III (26%), V (21%), II (19%) and Ia (19%). Other serotypes (Ib, IV, VI, VII, IX) represented less than 10% of all isolates each. Intra-lineage serotype diversity was observed in all major CCs but was highest in CC1, which revealed nine serotypes. Nearly all isolates (99%) carried at least one of the four alpha family protein genes (alpha, alp1, alp23, and rib). All isolates were susceptible to penicillin. We found 21% and 13% of isolates to be resistant to clarithromycin and clindamycin, respectively. Prevalence of macrolide-lincosamide-streptogramin B (MLSB) resistance genes was 22% and they were most common in CC19 (37%) and CC1 (28%), and isolates with serotypes V (38%) and IV (32%). We identified some associations between maternal ethnicity and GBS population structure. Serotype Ib was significantly less common among the South Asian compared to Black women (S. Asian: 3/142, Black: 15/135, p = 0.03). There was also a significantly lower proportion of CC1 isolates among the White other (24/142) in comparison to Black (43/135) and S. Asian (44/142) women (p = 0.04). We found a significantly higher proportion of CC17 isolates among the White other compared to S. Asian women (White other: 32/142, S. Asian: 10/142, p = 0.004).ConclusionOur study showed high prevalence of GBS vaccine targets among isolates from pregnant women in London. However, the observed serotype diversity in CC1 and high prevalence of MLSB resistance genes in CC19 demonstrates presence of high risk lineages, which might act as a reservoir of non-vaccine strains and antimicrobial resistance determinants.
Arbuscular mycorrhizal fungi community analysis revealed the significant impact of arsenic in antimony- and arsenic-contaminated soil in three Guizhou regions
Authors: Mi Yidong , Xu Chao , Li Xinru , Zhou Min , Cao Ke , Dong Cuimin , Li Xuemei , Ji Ningning , Wang Fanfan , Su Hailei , Liu Xuesong , Wei Yuan 
Published: May 2023

IntroductionThe lack of systematic investigations of arbuscular mycorrhizal fungi (AMF) community composition is an obstacle to AMF biotechnological applications in antimony (Sb)- and arsenic (As)-polluted soil.MethodsMorphological and molecular identification were applied to study the AMF community composition in Sb- and As-contaminated areas, and the main influencing factors of AMF community composition in Sb- and As-contaminated areas were explored.Results(1) A total of 513,546 sequences were obtained, and the majority belonged to Glomeraceae [88.27%, 193 operational taxonomic units (OTUs)], followed by Diversisporaceae, Paraglomeraceae, Acaulosporaceae, Gigasporaceae, and Archaeosporaceae; (2) the affinity between AMF and plants was mainly related to plant species (F = 3.488, p = 0.022 &lt; 0.050), which was not significantly correlated with the total Sb (TSb) and total As (TAs) in soil; (3) the AMF spore density was mainly related to the available nitrogen, available potassium, and total organic carbon; (4) The effect of soil nutrients on AMF community composition (total explanation: 15.36%) was greater than that of soil Sb and As content (total explanation: 5.80%); (5) the effect of TAs on AMF community composition (λ = −0.96) was more drastic than that of TSb (λ = −0.21), and the effect of As on AMF community composition was exacerbated by the interaction between As and phosphorus in the soil; and (6) Diversisporaceae was positively correlated with the TSb and TAs.DiscussionThe potential impact of As on the effective application of mycorrhizal technology should be further considered when applied to the ecological restoration of Sb- and As-contaminated areas.
Bradyrhizobium diazoefficiens USDA 110 displays plasticity in the attachment phenotype when grown in different soybean root exudate compounds
Authors: Sandhu Armaan Kaur , Brown McKenzie Rae , Subramanian Senthil , Brözel Volker S. 
Published: May 2023

IntroductionBradyrhizobium diazoefficiens, a symbiotic nitrogen fixer for soybean, forms nodules after developing a symbiotic association with the root. For this association, bacteria need to move toward and attach to the root. These steps are mediated by the surface and phenotypic cell properties of bacteria and secreted root exudate compounds. Immense work has been carried out on nodule formation and nitrogen fixation, but little is known about the phenotype of these microorganisms under the influence of different root exudate chemical compounds (RECCs) or how this phenotype impacts the root attachment ability.MethodsTo address this knowledge gap, we studied the impact of 12 different RECCs, one commonly used carbon source, and soil-extracted solubilized organic matter (SESOM) on attachment and attachment-related properties of B. diazoefficiens USDA110. We measured motility-related properties (swimming, swarming, chemotaxis, and flagellar expression), attachment-related properties (surface hydrophobicity, biofilm formation, and attachment to cellulose and soybean roots), and surface polysaccharide properties (colony morphology, exopolysaccharide quantification, lectin binding profile, and lipopolysaccharide profiling).Results and discussionWe found that USDA 110 displays a high degree of surface phenotypic plasticity when grown on the various individual RECCs. Some of the RECCs played specific roles in modulating the motility and root attachment processes. Serine increased cell surface hydrophobicity and root and cellulose attachment, with no EPS formed. Gluconate and lactate increased EPS production and biofilm formation, while decreasing hydrophobicity and root attachment, and raffinose and gentisate promoted motility and chemotaxis. The results also indicated that the biofilm formation trait on hydrophilic surfaces (polystyrene) cannot be related to the attachment ability of Bradyrhizobium to the soybean root. Among the tested phenotypic properties, bacterial cell surface hydrophobicity was the one with a significant impact on root attachment ability. We conclude that USDA 110 displays surface plasticity properties and attachment phenotype determined by individual RECCs from the soybean. Conclusions made based on its behavior in standard carbon sources, such as arabinose or mannitol, do not hold for its behavior in soil.
Phase I-II study using DeltaRex-G, a tumor-targeted retrovector encoding a cyclin G1 inhibitor for metastatic carcinoma of breast
Authors: Bruckner Howard W. , Chawla Sant P. , Omelchenko Nadezhda , Brigham Don A. , Gordon Erlinda M. 
Published: May 2023

Background: Metastatic breast cancer is associated with a poor prognosis and therefore, innovative therapies are urgently needed. Here, we report on the results of a Phase I-II study using DeltaRex-G for chemotherapy resistant metastatic carcinoma of breast.Patients and Methods:Endpoints: Dose limiting toxicity; Antitumor activity. Eligibility: ≥18 years of age, pathologic diagnosis of breast carcinoma, adequate hematologic and organ function. Treatment: Dose escalation of DeltaRex-G 1-4 x 1011cfu intravenously thrice weekly x 4 weeks with 2-week rest period. Treatment cycles repeated if there is ≤ Grade 1 toxicity until disease progression or unacceptable toxicity. Safety: NCI CTCAE v3 for adverse events reporting, vector related testing. Efficacy: RECIST v1.0, International PET criteria and Choi criteria for response, progression free and overall survival.Results: Twenty patients received escalating doses of DeltaRex-G from 1 × 1011 cfu to 4 × 1011 cfu thrice weekly for 4 weeks with a 2-week rest period. Safety: ≥ Grade 3 treatment-related adverse event: pruritic rash (n = 1), no dose limiting toxicity, no replication-competent retrovirus, nor vector-neutralizing antibodies detected. No vector DNA integration was observed in peripheral blood lymphocytes evaluated. Efficacy: by RECIST v1.0: 13 stable disease, 4 progressive disease; tumor control rate 76%; by PET and Choi Criteria: 3 partial responses, 11 stable disease, 3 progressive disease; tumor control rate 82%. Combined median progression free survival by RECIST v1.0, 3.0 months; combined median overall survival, 20 months; 1-year overall survival rate 83% for Dose Level IV. Biopsy of residual tumor in a participant showed abundant CD8+ killer T-cells and CD45+ macrophages suggesting an innate immune response. Two patients with pure bone metastases had &gt;12-month progression free survival and overall survival and are alive 12 years from the start of DeltaRex-G therapy. These patients further received DeltaRex-G + DeltaVax for 6 months.Conclusion: Taken together, these data indicate that 1) DeltaRex-G has a distinctively high level of safety and exhibits anti-cancer activity, 2) PET/Choi provide a higher level of sensitivity in detecting early signs of tumor response to DeltaRex-G, 3) DeltaRex-G induced 12- year survival in 2 patients with pure bone metastases who subsequently received DeltaVax immunotherapy, and 4) DeltaRex-G may prove to be a biochemical and/or immune modulator when combined with other cancer therapy/immunotherapy.
Long-term effects of anti-N-methyl-d-aspartate receptor encephalitis on quality of life
Authors: Hirose Satoshi , Hara Makoto , Yokota Yuki , Nakajima Hideto 
Published: May 2023

BackgroundPatients with anti-N-methyl-d-aspartate receptor encephalitis (NMDARE) usually achieve neurologically favorable outcomes in the post-acute-phase. Even when motor function recovers, many patients experience numerous non-motor sequelae and cannot resume their pre-NMDARE lives even years later. Additionally, the needs of patients with NMDARE may impose a severe caregiver burden. Unfortunately, few studies have comprehensively examined patients recovering from NMDARE. We investigated the long-term effects of NMDARE on patients’ quality of life (QOL).MethodsData collected via structured self-reported questionnaires included clinical features, long-term outcomes, and QOL. These questionnaires were administered to adult members of the Japanese Anti-NMDARE Patients’ Association. We used the NeuroQOL battery to assess QOL in physical, mental, and social domains. Raw NeuroQOL scores were converted to T-scores for comparison with controls.ResultsTwenty-two patients completed the questionnaire. The median interval between disease onset and questionnaire response was 78  months. Forty-six percent of patients reported persistent sequelae, with only 73% able to resume prior work/school activities. Although patients’ Global QOL was similar to controls, patients with NMDARE had significantly worse social QOL. Patients with worse social QOL had more frequent sequelae than those with better social QOL. Furthermore, patients with persistent sequelae had significantly worse Global QOL than those without sequelae and controls.ConclusionPatients with NMDARE had worse social QOL than controls. Given the adverse effects of disease sequelae on QOL, treatment strategies that minimize sequelae during the acute-phase may improve patients’ QOL, even years post-disease onset.
Insights into perceived listening difficulties post COVID-19 infection: no measurable hearing difficulty on clinical tests despite increased self-reported listening effort
Authors: Alhanbali Sara , Alkharabsheh Ana'am , Alanati Wafa'a , Joudeh Khader , Munro Kevin J. 
Published: May 2023

ObjectiveThe aim was to use a battery of clinic-based auditory assessment procedures to compare participants with and without self-reported hearing difficulties following a confirmed COVID-19 infection. A further aim was to compare the groups on self-reported measures of listening effort and fatigue.MethodsThere were 25 participants in each group (age range 20–59 years, 80% females). Participants were recruited after a minimum of 4 weeks of testing positive. Hearing assessment involved tympanometry, acoustic reflex thresholds, pure-tone audiometry (PTA; 0.25–14 kHz), and distortion product otoacoustic emissions (DPOAEs; 0.5–10 kHz). Listening effort was assessed using the Arabic version of the Effort Assessment Scale (EAS-A) and fatigue was assessed using the Arabic version of the Fatigue Assessment Scale (FAS-A).ResultsThere was no difference between groups on any measure except for greater self-reported listening effort in the perceived hearing difficulty group (p = 0.01).ConclusionThe only difference between groups was self-reported listening effort. This could be due to a subclinical auditory deficit following COVID-19, increased listening effort due to the impact of COVID-19 on cognitive processes, or a psychosomatic response/health anxiety.
Establishing a pediatric acute stroke protocol: experience of a new pediatric stroke program and predictors of acute stroke
Authors: Phelps Kamal , Silos Christin , De La Torre Susan , Moreno Amee , Lapus Robert , Sanghani Nipa , Koenig Mary , Savitz Sean , Green Charles , Fraser Stuart 
Published: May 2023

IntroductionPediatric stroke is among the top 10 causes of death in pediatrics. Rapid recognition and treatment can improve outcomes in select patients, as evidenced by recent retrospective studies in pediatric thrombectomy. We established a collaborative protocol involving the vascular neurology and pediatric neurology division in our institution to rapidly diagnose and treat pediatric suspected stroke. We also prospectively collected data to attempt to identify predictors of acute stroke in pediatric patients.MethodsIRB approval was obtained to prospectively collect clinical data on pediatric code stroke activations based on timing metrics in resident-physician note templates. The protocol emphasized magnetic resonance imaging over computed tomography imaging when possible. We analyzed performance of the system with descriptive statistics. We then performed a Bayesian statistical analysis to search for predictors of pediatric stroke.ResultsThere were 40 pediatric code strokes over the 2.5-year study period with a median age of 10.8 years old. 12 (30%) of patients had stroke, and 28 (70%) of code stroke patients were diagnosed with a stroke mimic. Median time from code stroke activation to completion of imaging confirming or ruling out stroke was 1 h. In the Bayesian analysis, altered mental status, hemiparesis, and vasculopathy history were associated with increased odds of stroke, though credible intervals were wide due to the small sample size.ConclusionA trainee developed and initiated pediatric acute stroke protocol quickly implemented a hospital wide change in management that led to rapid diagnosis and triage of pediatric stroke and suspected stroke. No additional personnel or resources were needed for this change, and we encourage other hospitals and emergency departments to implement similar systems. Additionally, hemiparesis and altered mental status were predictors of stroke for pediatric acute stroke activation in our Bayesian statistical analysis. However credible intervals were wide due to the small sample size. Further multicenter data collection could more definitively analyze predictors of stroke, as well as the help in the creation of diagnostic tools for clinicians in the emergency setting.
SSVEP detection assessment by combining visual stimuli paradigms and no-training detection methods
Authors: Chailloux Peguero Juan David , Hernández-Rojas Luis G. , Mendoza-Montoya Omar , Caraza Ricardo , Antelis Javier M. 
Published: May 2023

IntroductionBrain-Computer Interfaces (BCI) based on Steady-State Visually Evoked Potentials (SSVEP) have great potential for use in communication applications because of their relatively simple assembly and in some cases the possibility of bypassing the time-consuming training stage. However, among multiple factors, the efficient performance of this technology is highly dependent on the stimulation paradigm applied in combination with the SSVEP detection algorithm employed. This paper proposes the performance assessment of the classification of target events with respect to non-target events by applying four types of visual paradigms, rectangular modulated On-Off (OOR), sinusoidal modulated On-Off (OOS), rectangular modulated Checkerboard (CBR), and sinusoidal modulated Checkerboard (CBS), with three types of SSVEP detection methods, Canonical Correlation Analysis (CCA), Filter-Bank CCA (FBCCA), and Minimum Energy Combination (MEC).MethodsWe set up an experimental protocol in which the four types of visual stimuli were presented randomly to twenty-seven participants and after acquiring their electroencephalographic responses to five stimulation frequencies (8.57, 10.909, 15, 20, and 24 Hz), the three detection methods were applied to the collected data.ResultsThe results are conclusive, obtaining the best performance with the combination of either OOR or OOS visual stimulus and the FBCCA as a detection method, however, this finding contrasts with the opinion of almost half of the participants in terms of visual comfort, where the 51.9% of the subjects felt more comfortable and focused with CBR or CBS stimulation.DiscussionFinally, the EEG recordings correspond to the SSVEP response of 27 subjects to four visual paradigms when selecting five items on a screen, which is useful in BCI navigation applications. The dataset is available to anyone interested in studying and evaluating signal processing and machine-learning algorithms for SSVEP-BCI systems.
Cortical depth-dependent human fMRI of resting-state networks using EPIK
Authors: Pais-Roldán Patricia , Yun Seong Dae , Palomero-Gallagher Nicola , Shah N. Jon 
Published: May 2023

IntroductionRecent laminar-fMRI studies have substantially improved understanding of the evoked cortical responses in multiple sub-systems; in contrast, the laminar component of resting-state networks spread over the whole brain has been less studied due to technical limitations. Animal research strongly suggests that the supragranular layers of the cortex play a critical role in maintaining communication within the default mode network (DMN); however, whether this is true in this and other human cortical networks remains unclear.MethodsHere, we used EPIK, which offers unprecedented coverage at sub-millimeter resolution, to investigate cortical broad resting-state dynamics with depth specificity in healthy volunteers.ResultsOur results suggest that human DMN connectivity is primarily supported by intermediate and superficial layers of the cortex, and furthermore, the preferred cortical depth used for communication can vary from one network to another. In addition, the laminar connectivity profile of some networks showed a tendency to change upon engagement in a motor task. In line with these connectivity changes, we observed that the amplitude of the low-frequency-fluctuations (ALFF), as well as the regional homogeneity (ReHo), exhibited a different laminar slope when subjects were either performing a task or were in a resting state (less variation among laminae, i.e., lower slope, during task performance compared to rest).DiscussionThe identification of varied laminar profiles concerning network connectivity, ALFF, and ReHo, observed across two brain states (task vs. rest) has major implications for the characterization of network-related diseases and suggests the potential diagnostic value of laminar fMRI in psychiatric disorders, e.g., to differentiate the cortical dynamics associated with disease stages linked, or not linked, to behavioral changes. The evaluation of laminar-fMRI across the brain encompasses computational challenges; nonetheless, it enables the investigation of a new dimension of the human neocortex, which may be key to understanding neurological disorders from a novel perspective.
Multiple sclerosis lesion segmentation: revisiting weighting mechanisms for federated learning
Authors: Liu Dongnan , Cabezas Mariano , Wang Dongang , Tang Zihao , Bai Lei , Zhan Geng , Luo Yuling , Kyle Kain , Ly Linda , Yu James , Shieh Chun-Chien , Nguyen Aria , Kandasamy Karuppiah Ettikan , Sullivan Ryan , Calamante Fernando , Barnett Michael , Ouyang Wanli , Cai Weidong , Wang Chenyu 
Published: May 2023

Background and introductionFederated learning (FL) has been widely employed for medical image analysis to facilitate multi-client collaborative learning without sharing raw data. Despite great success, FL's applications remain suboptimal in neuroimage analysis tasks such as lesion segmentation in multiple sclerosis (MS), due to variance in lesion characteristics imparted by different scanners and acquisition parameters.MethodsIn this work, we propose the first FL MS lesion segmentation framework via two effective re-weighting mechanisms. Specifically, a learnable weight is assigned to each local node during the aggregation process, based on its segmentation performance. In addition, the segmentation loss function in each client is also re-weighted according to the lesion volume for the data during training.ResultsThe proposed method has been validated on two FL MS segmentation scenarios using public and clinical datasets. Specifically, the case-wise and voxel-wise Dice score of the proposed method under the first public dataset is 65.20 and 74.30, respectively. On the second in-house dataset, the case-wise and voxel-wise Dice score is 53.66, and 62.31, respectively.Discussions and conclusionsThe Comparison experiments on two FL MS segmentation scenarios using public and clinical datasets have demonstrated the effectiveness of the proposed method by significantly outperforming other FL methods. Furthermore, the segmentation performance of FL incorporating our proposed aggregation mechanism can achieve comparable performance to that from centralized training with all the raw data.