bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case fatality inequalities of critically ill COVID-19 patients according to patient-, hospital- and region-related factors: a French nationwide study
Authors: Guillon Antoine , Laurent Emeline , Duclos Antoine , Godillon Lucile , Dequin Pierre-François , Agrinier Nelly , Kimmoun Antoine , Grammatico-Guillon Leslie 
Published: August 2021

Abstract
Background
The COVID-19 sanitary crisis inflicted different challenges regarding the reorganization of the human and logistic resources, particularly in intensive care unit (ICU). Interdependence between regional pandemic burden and individual outcome remains unknown. The study aimed to assess the association between ICU bed occupancy and case fatality rate of critically ill COVID-19 patients.

Methods
A cross-sectional study was performed in France, using the national hospital discharge database from March to May, 2020. All patients admitted to ICU for COVID-19 were included. Case fatality was described according to: (i) patient’s characteristics (age, sex, comorbid conditions, ICU interventions); (ii) hospital’s characteristics (baseline ICU experience assessed by the number of ICU stays in 2019, number of ICU physicians per bed), and (iii) the regional outbreak-related profiles (workload indicator based on ICU bed occupancy). The determinants of lethal outcome were identified using a logistic regression model.

Results
14,513 COVID-19 patients were admitted to ICU; 4256 died (29.3%), with important regional inequalities in case fatality (from 17.6 to 33.5%). Older age, multimorbidity and clinical severity were associated with higher mortality, as well as a lower baseline ICU experience of the health structure. Regions with more than 10 days with ≥ 75% of ICU occupancy by COVID-19 patients experienced an excess of mortality (up to adjusted OR = 2.2 [1.9–2.6] for region with the highest occupancy rate of ICU beds).

Conclusions
The regions with the highest burden of care in ICU were associated with up to 2.2-fold increase of death rate.
A five-component infection control bundle to permanently eliminate a carbapenem-resistant Acinetobacter baumannii spreading in an intensive care unit
Authors: Meschiari Marianna , Lòpez-Lozano José-María , Di Pilato Vincenzo , Gimenez-Esparza Carola , Vecchi Elena , Bacca Erica , Orlando Gabriella , Franceschini Erica , Sarti Mario , Pecorari Monica , Grottola Antonella , Venturelli Claudia , Busani Stefano , Serio Lucia , Girardis Massimo , Rossolini Gian Maria , Gyssens Inge C. , Monnet Dominique L. , Mussini Cristina 
Published: August 2021

Abstract
Background
Carbapenem-resistant Acinetobacter baumannii (CRAB) infection outbreaks are difficult to control and sometimes require cohorting of CRAB-positive patients or temporary ward closure for environmental cleaning. We aimed at controlling the deadly 2018 CRAB outbreak in a 12 bed- intensive care unit (ICU) including 9 beds in a 220 m2 open space. We implemented a new multimodal approach without ward closure, cohorting or temporarily limiting admissions.

Methods
A five-component bundle was introduced in 2018 including reinforcement of hand hygiene and sample extension of screening, application of contact precautions to all patients, enhanced environmental sampling and the one-time application of a cycling radical environmental cleaning and disinfection procedure of the entire ICU.
The ICU-CRAB incidence density (ID), ICU alcohol-based hand rub consumption and antibiotic use were calculated over a period of 6 years and intervention time series analysis was performed. Whole genome sequencing analysis (WGS) was done on clinical and environmental isolates in the study period.

Results
From January 2013, nosocomial ICU-CRAB ID decreased from 30.4 CRAB cases per 1000 patients-days to zero cases per 1000 patients-days. Our intervention showed a significant impact (-2.9 nosocomial ICU-CRAB cases per 1000 bed-days), while no influence was observed for antibiotic and alcohol-based hand rub (AHR) consumption.
WGS demonstrated that CRAB strains were clonally related to an environmental reservoir which confirms the primary role of the environment in CRAB ICU spreading.

Conclusion
A five-component bundle of continuous hand hygiene improvement, extended sampling at screening including the environment, universal contact precautions and a novel cycling radical environmental cleaning and disinfection procedure proved to be effective for permanently eliminating CRAB spreading within the ICU. Cohorting, admission restriction or ICU closure were avoided.
The metabolic footprint of Clostridia and Erysipelotrichia reveals their role in depleting sugar alcohols in the cecum
Authors: Tiffany Connor R. , Lee Jee-Yon , Rogers Andrew W. L. , Olsan Erin E. , Morales Pavel , Faber Franziska , Bäumler Andreas J. 
Published: August 2021

Abstract
Background
The catabolic activity of the microbiota contributes to health by aiding in nutrition, immune education, and niche protection against pathogens. However, the nutrients consumed by common taxa within the gut microbiota remain incompletely understood.

Methods
Here we combined microbiota profiling with an un-targeted metabolomics approach to determine whether depletion of small metabolites in the cecum of mice correlated with the presence of specific bacterial taxa. Causality was investigated by engrafting germ-free or antibiotic-treated mice with complex or defined microbial communities.

Results
We noted that a depletion of Clostridia and Erysipelotrichia from the gut microbiota triggered by antibiotic treatment was associated with an increase in the cecal concentration of sugar acids and sugar alcohols (polyols). Notably, when we inoculated germ-free mice with a defined microbial community of 14 Clostridia and 3 Erysipelotrichia isolates, we observed the inverse, with a marked decrease in the concentrations of sugar acids and polyols in cecal contents. The carbohydrate footprint produced by the defined microbial community was similar to that observed in gnotobiotic mice receiving a cecal microbiota transplant from conventional mice. Supplementation with sorbitol, a polyol used as artificial sweetener, increased cecal sorbitol concentrations in antibiotic-treated mice, which was abrogated after inoculation with a Clostridia isolate able to grow on sorbitol in vitro.

Conclusions
We conclude that consumption of sugar alcohols by Clostridia and Erysipelotrichia species depletes these metabolites from the intestinal lumen during homeostasis.
Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery
Authors: Hunter Mandana , Spiller Krista J. , Dominique Myrna A. , Xu Hong , Hunter Francis W. , Fang Terry C. , Canter Rebecca G. , Roberts Christopher J. , Ransohoff Richard M. , Trojanowski John Q. , Lee Virginia M.-Y. 
Published: August 2021

AbstractThe microglial reaction is a hallmark of neurodegenerative conditions, and elements thereof may exert differential effects on disease progression, either worsening or ameliorating severity. In amyotrophic lateral sclerosis (ALS), a syndrome characterized by cytoplasmic aggregation of TDP-43 protein and atrophy of motor neurons in the cortex and spinal cord, the transcriptomic signatures of microglia during disease progression are incompletely understood. Here, we performed longitudinal RNAseq analysis of cortical and spinal cord microglia from rNLS8 mice, in which doxycycline-regulatable expression of human TDP-43 (hTDP-43) in the cytoplasm of neurons recapitulates many features of ALS. Transgene suppression in rNLS8 mice leads to functional, anatomical and electrophysiological resolution that is dependent on a microglial reaction that is concurrent with recovery rather than disease onset. We identified basal differences between the gene expression profiles of microglia dependent on localization in spinal cord or cortex. Microglia subjected to chronic hTDP-43 overexpression demonstrated transcriptomic changes in both locations. We noted strong upregulation of Apoe, Axl, Cd63, Clec7a, Csf1, Cst7, Igf1, Itgax, Lgals3, Lilrb4, Lpl and Spp1 during late disease and recovery. Importantly, we identified a distinct suite of differentially expressed genes associated with each phase of disease progression and recovery. Differentially expressed genes were associated with chemotaxis, phagocytosis, inflammation, and production of neuroprotective factors. These data provide new insights into the microglial reaction in TDP-43 proteinopathy. Genes differentially expressed during progression and recovery may provide insight into a unique instance in which the microglial reaction promotes functional recovery after neuronal insult.
A novel strategy for D-psicose and lipase co-production using a co-culture system of engineered Bacillus subtilis and Escherichia coli and bioprocess analysis using metabolomics
Authors: Zhang Jun , Luo Wen , Wang Zhiyuan , Chen Xiaoyan , Lv Pengmei , Xu Jingliang 
Published: August 2021

AbstractTo develop an economically feasible fermentation process, this study designed a novel bioprocess based on the co-culture of engineered Bacillus subtilis and Escherichia coli for the co-production of extracellular D-psicose and intracellular lipase. After optimizing the co-culture bioprocess, 11.70 g/L of D-psicose along with 16.03 U/mg of lipase was obtained; the glucose and fructose were completely utilized. Hence, the conversion rate of D-psicose reached 69.54%. Compared with mono-culture, lipase activity increased by 58.24%, and D-psicose production increased by 7.08%. In addition, the co-culture bioprocess was explored through metabolomics analysis, which included 168 carboxylic acids and derivatives, 70 organooxygen compounds, 34 diazines, 32 pyridines and derivatives, 30 benzene and substituted derivatives, and other compounds. It also could be found that the relative abundance of differential metabolites in the co-culture system was significantly higher than that in the mono-culture system. Pathway analysis revealed that, tryptophan metabolism and β-alanine metabolism had the highest correlation and played an important role in the co-culture system; among them, tryptophan metabolism regulates protein synthesis and β-alanine metabolism, which is related to the formation of metabolic by-products. These results confirm that the co-cultivation of B. subtilis and E. coli can provide a novel idea for D-psicose and lipase biorefinery, and are beneficial for the discovery of valuable secondary metabolites such as turanose and morusin.
Evaluation of Iodine-123 and Iodine-131 SPECT activity quantification: a Monte Carlo study
Authors: Morphis Michaella , van Staden Johan A. , du Raan Hanlie , Ljungberg Michael 
Published: August 2021

Abstract
Purpose
The quantitative accuracy of Nuclear Medicine images, acquired for both planar and SPECT studies, is influenced by the isotope-collimator combination as well as image corrections incorporated in the iterative reconstruction process. These factors can be investigated and optimised using Monte Carlo simulations. This study aimed to evaluate SPECT quantification accuracy for 123I with both the low-energy high resolution (LEHR) and medium-energy (ME) collimators and 131I with the high-energy (HE) collimator.

Methods
Simulated SPECT projection images were reconstructed using the OS-EM iterative algorithm, which was optimised for the number of updates, with appropriate corrections for scatter, attenuation and collimator detector response (CDR), including septal scatter and penetration compensation. An appropriate calibration factor (CF) was determined from four different source geometries (activity-filled: water-filled cylindrical phantom, sphere in water-filled (cold) cylindrical phantom, sphere in air and point-like source), investigated with different volume of interest (VOI) diameters. Recovery curves were constructed from recovery coefficients to correct for partial volume effects (PVEs). The quantitative method was evaluated for spheres in voxel-based digital cylindrical and patient phantoms.

Results
The optimal number of OS-EM updates was 60 for all isotope-collimator combinations. The CFpoint with a VOI diameter equal to the physical size plus a 3.0-cm margin was selected, for all isotope-collimator geometries. The spheres’ quantification errors in the voxel-based digital cylindrical and patient phantoms were less than 3.2% and 5.4%, respectively, for all isotope-collimator combinations.

Conclusion
The study showed that quantification errors of less than 6.0% could be attained, for all isotope-collimator combinations, if corrections for; scatter, attenuation, CDR (including septal scatter and penetration) and PVEs are performed. 123I LEHR and 123I ME quantification accuracies compared well when appropriate corrections for septal scatter and penetration were applied. This can be useful in departments that perform 123I studies and may not have access to ME collimators.
Biological control of Ralstonia solanacearum (Smith), the causal pathogen of bacterial wilt disease by using Pantoea spp
Authors: Abo-Elyousr Kamal A. M. , Hassan Sabry A. 
Published: August 2021

Abstract
Background
Bacterial wilt of tomato (BWP) caused by Ralstonia solanacearum (Smith) is a very important disease. Biological control of this disease is a very important tool to protect the plant and environment from pollution of chemical control.

Results
Twenty isolates of genus, Pantoea were isolated from healthy tomato root. Out of 20 isolates, 2 strains, PHYTPO1 and PHYTPO2, showed highly antagonistic property to control the growth of R. solanacearum in vitro conditions. They were identified as P. agglomerans by using 16S rRNA nucleotide sequence analysis. The 2 isolates were selected to study their effect (as cell suspension or culture filtrate) on the bacterial wilt under greenhouse conditions. PHYTPO1 inhibited maximum growth reduction of R. solanacearum and formed 2.5 cm2 of inhibition zone, followed by 1.2 cm2 in PHYTOPO2 under in vitro conditions. Treating with both isolates of P. agglomerans was significantly reduced disease severity of tomato wilt disease. The disease severity was reduced to 74.1 when treated as cell suspension, while when treated as culture filtrate, it reduced the disease severity up to 69.4 than infected control.

Conclusion
The strains of Pantoea can be used as an ecofriendly method to control of the most economic pathogen of tomato under greenhouse conditions. Further study is needed to find an appropriate formulation and approving application of these bacteria under field conditions.
Cannabis sativa and/or melatonin do not alter brain lipid but alter oxidative mechanisms in female rats
Authors: Abdulrahim Halimat Amin , Alagbonsi Isiaka Abdullateef , Amuda Oluwasola , Omeiza Noah Adavize , Feyitimi Abdul-Rahuf Aderemi , Olayaki Luqman Aribidesi 
Published: August 2021

Abstract
Background
Lipid profile and redox status play a role in brain (dys)functions. Cannabinoid and melatonergic systems operate in the brain and contribute to brain (patho)physiology, but their roles in the modulation of brain lipid and redox status are not well-known. We studied the effect of ethanol extract of Cannabis sativa (CS) and/or melatonin (M) on the lipid profile and anti-oxidant system of the rat brain.

Methods
We randomly divided twenty-four (24) female Wistar rats into 4 groups (n = 6 rats each). Group 1 (control) received distilled water mixed with DMSO. Groups II–IV received CS (2 mg/kg), M (4 mg/kg), and co-administration of CS and M (CS + M) respectively via oral gavage between 8:00 am and 10:00 am once daily for 14 days. Animals underwent 12-h fasting after the last day of treatment and sacrificed under ketamine anesthesia (20 mg/kg; i.m). The brain tissues were excised and homogenized for assay of the concentrations of the total cholesterol (TC), triacylglycerol (TG), high-density lipoprotein cholesterol (HDL-C), nitric oxide (NO), malondialdehyde (MDA), and the activities of glucose-6-phosphate dehydrogenase (G6PD), glutathione reductase (GR), glutathione peroxidase (GPx), catalase (CAT), superoxide dismutase (SOD), and acetylcholinesterase (AChE). One-way analysis of variance (ANOVA) was used to compare means across groups, followed by the least significant difference (LSD) post-hoc test.

Results
CS and/or M did not affect the lipid profile parameters. However, CS increased the G6PD (from 15.58 ± 1.09 to 21.02 ± 1.45 U/L; p = 0.047), GPx (from 10.47 ± 0.86 to 17.71 ± 1.04 U/L; p = 0.019), and SOD (from 0.81 ± 0.02 to 0.90 ± 0.01 μM; p = 0.007), but decreased NO (from 9.40 ± 0.51 to 6.75 ± 0.21 μM; p = 0.010) and had no effect on MDA (p = 0.905), CAT (p = 0.831), GR (p = 0.639), and AChE (p = 0.571) in comparison with the control group. M augmented the increase in G6PD (from 21.02 ± 1.45 U/L to 27.18 ± 1.81 U/L; p = 0.032) and decrease in NO (from 6.75 ± 0.21 to 4.86 ± 0.13 μM; p = 0.034) but abolished the increase in GPx (from 17.71 ± 1.04 to 8.59 ± 2.06 U/L; p = 0.006) and SOD (from 0.90 ± 0.01 to 0.70 ± 0.00 μM; p = 0.000) elicited by CS in the rat brain in comparison with the CS group.

Conclusions
CS and M do not alter brain lipid profile. Our data support the contention that CS elicits an anti-oxidative effect on the brain tissue and that CS + M elicits a pro-oxidant effect in rat brain.
The STArgardt Remofuscin Treatment Trial (STARTT): design and baseline characteristics of enrolled Stargardt patients
Authors: Dhooge Patty P.A. , Möller Philipp T. , Boon Camiel J.F. , Lotery Andrew J. , Herrmann Philipp , Battaglia Parodi Maurizio , Klein Wolfgang , Fsadni Mario G. , Wheeler-Schilling Thomas H. , Jungmann Oliver , Müller Hans , Holz Frank G. , Schmitz-Valckenberg Steffen , Peters Tobias M. , Stingl Katarina , Hoyng Carel B. ,   Soraprazan Consortium
Published: August 2021

Background: This report describes the study design and baseline characteristics of patients with Stargardt disease (STGD1) enrolled in the STArgardt Remofuscin Treatment Trial (STARTT). Methods: In total, 87 patients with genetically confirmed STGD1 were randomized in a double-masked, placebo-controlled proof of concept trial to evaluate the safety and efficacy of 20 milligram oral remofuscin for 24 months. The primary outcome measure is change in mean quantitative autofluorescence value of an 8-segment ring centred on the fovea (qAF8). Secondary efficacy variables are best corrected visual acuity (BCVA), low-luminance visual acuity (LLVA), mesopic microperimetry (mMP), spectral domain optical coherence tomography (SD-OCT), reading speed on Radner reading charts, and patient-reported visual function as assessed by the National Eye Institute Visual Functioning Questionnaire 25 (NEI VFQ-25) and Functional Reading Independence (FRI) Index. Results: Mean age of participants was 35±11 years with 49 (56%) female. Median qAF8 value was 438 Units (range 210-729). Median BCVA and LLVA in decimal units were 0.50 (range 0.13-0.80) and 0.20 (range 0.06-0.63), respectively. The median of the mean retinal sensitivity with mMP was 20.4 dB (range 0.0-28.8). SD-OCT showed median central subfield retinal thickness of 142 µm (range 72-265) and median macular volume of 1.65 mm3 (range 1.13-2.19). Compared to persons without vision impairment, both reading performance and patient-reported visual function were significantly lower (p<0.001, one sample t-test). Mean reading speed was 108±39 words/minute with logRAD-score of 0.45±0.28. Mean VFQ-25 composite score was 72±13. Mean FRI Index score 2.8±0.6. Conclusions: This trial design may serve as reference for future clinical trials as it explores the utility of qAF8 as primary outcome measure. The baseline data represent the largest, multi-national, STGD1 cohort to date that underwent standardized qAF imaging, reading speed assessment and vision-related quality of life measures which all contribute to the characterization of STGD1. EudraCT registration: 2018-001496-20 (09/05/2019)
Ten-mega-pixel snapshot compressive imaging with a hybrid coded aperture
Authors: Zhang Zhihong , Deng Chao , Liu Yang , Yuan Xin , Suo Jinli , Dai Qionghai 
Published: August 2021

High-resolution images are widely used in our everyday life; however, high-speed video capture is more challenging due to the low frame rate of cameras working at the high-resolution mode. The main bottleneck lies in the low throughput of existing imaging systems. Toward this end, snapshot compressive imaging (SCI) was proposed as a promising solution to improve the throughput of imaging systems by compressive sampling and computational reconstruction. During acquisition, multiple high-speed images are encoded and collapsed to a single measurement. Then, algorithms are employed to retrieve the video frames from the coded snapshot. Recently developed plug-and-play algorithms made the SCI reconstruction possible in large-scale problems. However, the lack of high-resolution encoding systems still precludes SCI’s wide application. Thus, in this paper, we build, to the best of our knowledge, a novel hybrid coded aperture snapshot compressive imaging (HCA-SCI) system by incorporating a dynamic liquid crystal on silicon and a high-resolution lithography mask. We further implement a PnP reconstruction algorithm with cascaded denoisers for high-quality reconstruction. Based on the proposed HCA-SCI system and algorithm, we obtain a 10-mega-pixel SCI system to capture high-speed scenes, leading to a high throughput of 4.6 × 109 voxels per second. Both simulation and real-data experiments verify the feasibility and performance of our proposed HCA-SCI scheme.
Research on the reproductive biological characteristics of Amomum villosum Lour. and Amomum longiligulare T. L. Wu
Authors: Yang Ruipei , Wang Jie , Gao Wei , Jiang Ye , Su Jing , Sun Dongmei , He Guozhen 
Published: August 2021

Objective
To explore the influence of biological characteristics on the yield of Amomum villosum Lour. and Amomum longiligulare T. L. Wu, to find an effective pollen viability evaluation method and storage method to solve the problem of the low yield of Amomum plants.

Methods
Five germplasm of Amomum plants were used to investigate the effects of the phenological phase, pollen viability, and stigma receptivity on natural and artificial fruit set.

Results
Amomum longiligulare T. L. Wu showed late flowering, and its natural pollination rate is higher than that of Amomum villosum Lour. In all germplasm, the artificial pollination rate and fruit setting rate are more than 3 times higher than that under natural conditions. Fruits begin to drop seven days after successful pollination, and the fruit drop is basically stable after one month. The hybridization verification showed that TTC method was simpler and more accurate than in vitro germination method. Optimal storage conditions for pollen are 4°C and high humidity. After 36 h of storage, pollen can still be used for artificial cross-pollination or as hybrid parents.

Conclusion
The special biological characteristics are the fundamental reason for the low natural pollination rate of Amomum plants. The accurate measurement method of Amomum plants pollen is the TTC method, and storage at 4°C and high humidity can increase the yield, which was six times that of the natural yield.