bluuebunny/crossref_metadata_2025_split huggingface dataset:
Luteirhabdus pelagi gen. nov., sp. nov., a novel member of the family Flavobacteriaceae, isolated from the West Pacific Ocean
Authors: Ren Wen-Ting , Meng Fan-Xu , Guo Li-Li , Sun Li , Xu Xue-Wei , Zhou Peng , Wu Yue-Hong 
Published: October 2021

AbstractA Gram-stain-negative, aerobic, and yellow-pigmented bacterium, designated A3-108T, was isolated from seawater of the West Pacific Ocean. Cells were non-motile and rod-shaped, with carotenoid-type pigments. Strain A3-108Tgrew at pH 6.0–8.5 (optimum 6.5) and 15–40 °C (optimum 28 °C), in the presence of 0.5–10% (w/v) NaCl (optimum 1.0%). It possessed the ability to produce H2S. Based on the 16S rRNA gene analysis, strain A3-108Texhibited highest similarity withAureisphaera salinaA6D-50T(90.6%). Phylogenetic analysis shown that strain A3-108Taffiliated with members of the familyFlavobacteriaceaeand represented an independent lineage. The principal fatty acids were iso-C15:0, iso-C17:03-OH, iso-C15:1G, and summed feature 3 (C16:1ω7cand/or C16:1ω6c). The sole isoprenoid quinone was MK-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminolipid and one unidentified lipid. The ANIb, in silico DDH and AAI values among the genomes of strain A3-108Tand three reference strains were 67.3–71.1%, 18.7–22.1%, and 58.8–71.4%, respectively. The G + C content was 41.0%. Distinctness of the phylogenetic position as well as differentiating chemotaxonomic and other phenotypic traits revealed that strain A3-108Trepresented a novel genus and species of the familyFlavobacteriaceae, for which the nameLuteirhabdus pelagigen. nov., sp. nov. is proposed (type strain, A3-108T = CGMCC 1.18821T = KCTC 82563T).
Activatable MRI probes for the specific detection of bacteria
Authors: Periyathambi Prabu , Balian Alien , Hu Zhangjun , Padro Daniel , Hernandez Luiza I. , Uvdal Kajsa , Duarte Joao , Hernandez Frank J. 
Published: October 2021

AbstractActivatable fluorescent probes have been successfully used as molecular tools for biomedical research in the last decades. Fluorescent probes allow the detection of molecular events, providing an extraordinary platform for protein and cellular research. Nevertheless, most of the fluorescent probes reported are susceptible to interferences from endogenous fluorescence (background signal) and limited tissue penetration is expected. These drawbacks prevent the use of fluorescent tracers in the clinical setting. To overcome the limitation of fluorescent probes, we and others have developed activatable magnetic resonance probes. Herein, we report for the first time, an oligonucleotide-based probe with the capability to detect bacteria using magnetic resonance imaging (MRI). The activatable MRI probe consists of a specific oligonucleotide that targets micrococcal nuclease (MN), a nuclease derived from Staphylococcus aureus. The oligonucleotide is flanked by a superparamagnetic iron oxide nanoparticle (SPION) at one end, and by a dendron functionalized with several gadolinium complexes as enhancers, at the other end. Therefore, only upon recognition of the MRI probe by the specific bacteria is the probe activated and the MRI signal can be detected. This approach may be widely applied to detect bacterial infections or other human conditions with the potential to be translated into the clinic as an activatable contrast agent.
Using Machine Learning to Establish Predictors of Mortality in Patients Undergoing Laparotomy for Emergency General Surgical Conditions
Authors: Smith Michelle T. D. , Bruce John L. , Clarke Damian L. 
Published: October 2021

AbstractIntroductionPatients undergoing laparotomy for emergency general surgery (EGS) conditions, constitute a high‐risk group with poor outcomes. These patients have a high prevalence of comorbidities. This study aims to identify patient factors, physiological and time‐related factors, which place patients into a group at increased risk of mortality.MethodologyIn a retrospective analysis of all patients undergoing an emergency laparotomy at Greys Hospital from December 2012 to 2018, we used decision tree discrimination to identify high‐risk groups.ResultsOur cohort included 1461 patients undergoing a laparotomy for an EGS condition. The mortality rate was 12.4% (181). Nine hundred and ten patients (62.3%) had at least one known comorbidity on admission. There was a higher rate of comorbidities among those that died (154; 85.1%). Patient factors found to be associated with mortality were the age of 46 years or greater (p < 0.001), current tuberculosis (p < 0.001), hypertension (p = 0.014), at least one comorbidity (0.006), and malignancy (0.033). Significant physiological risk factors for mortality were base excess less than −6.8 mmol/L (p < 0.001), serum urea greater than 7.0 mmol/L (p < 0.001) and waiting time from admission to operation (p = 0.014). In patients with an enteric breach, those younger than 46 years and a Shock Index of more than 1.0 were high‐risk. Patients without an enteric breach were high‐risk if operative duration exceeded 90 min (p = 0.004) and serum urea exceeding 7 mmol/dl (p = 0.016).ConclusionIn EGS patients, patient factors as well as physiological factors place patients into a high‐risk group. Identifying a high‐risk group should prompt consideration for an adjusted approach that ameliorates outcomes.
Tipping the balance: intricate roles of the complement system in disease and therapy
Authors: Pouw Richard B. , Ricklin Daniel 
Published: October 2021

AbstractThe ability of the complement system to rapidly and broadly react to microbial intruders, apoptotic cells and other threats by inducing forceful elimination responses is indispensable for its role as host defense and surveillance system. However, the danger sensing versatility of complement may come at a steep price for patients suffering from various immune, inflammatory, age-related, or biomaterial-induced conditions. Misguided recognition of cell debris or transplants, excessive activation by microbial or damaged host cells, autoimmune events, and dysregulation of the complement response may all induce effector functions that damage rather than protect host tissue. Although complement has long been associated with disease, the prevalence, impact and complexity of complement’s involvement in pathological processes is only now becoming fully recognized. While complement rarely constitutes the sole driver of disease, it acts as initiator, contributor, and/or exacerbator in numerous disorders. Identifying the factors that tip complement’s balance from protective to damaging effects in a particular disease continues to prove challenging. Fortunately, however, molecular insight into complement functions, improved disease models, and growing clinical experience has led to a greatly improved understanding of complement’s pathological side. The identification of novel complement-mediated indications and the clinical availability of the first therapeutic complement inhibitors has also sparked a renewed interest in developing complement-targeted drugs, which meanwhile led to new approvals and promising candidates in late-stage evaluation. More than a century after its description, complement now has truly reached the clinic and the recent developments hold great promise for diagnosis and therapy alike.
Progress towards completing the mutant mouse null resource
Authors: Peterson Kevin A. , Murray Stephen A. 
Published: October 2021

AbstractThe generation of a comprehensive catalog of null alleles covering all protein-coding genes is the goal of the International Mouse Phenotyping Consortium. Over the past 20 years, significant progress has been made towards achieving this goal through the combined efforts of many large-scale programs that built an embryonic stem cell resource to generate knockout mice and more recently employed CRISPR/Cas9-based mutagenesis to delete critical regions predicted to result in frameshift mutations, thus, ablating gene function. The IMPC initiative builds on prior and ongoing work by individual research groups creating gene knockouts in the mouse. Here, we analyze the collective efforts focusing on the combined null allele resource resulting from strains developed by the research community and large-scale production programs. Based upon this pooled analysis, we examine the remaining fraction of protein-coding genes focusing on clearly defined mouse–human orthologs as the highest priority for completing the mutant mouse null resource. In summary, we find that there are less than 3400 mouse–human orthologs remaining in the genome without a targeted null allele that can be further prioritized to achieve our overall goal of the complete functional annotation of the protein-coding portion of a mammalian genome.
Nonhuman primates’ tissue banks: resources for all model organism research
Authors: Witham Claire , Wells Sara 
Published: October 2021

AbstractBiobanks containing tissue and other biological samples from many model organisms provide easy and faster access to ex vivo resources for a wide-range of research programmes. For all laboratory animals, collecting and preserving tissue at post-mortem is an effective way of maximising the benefits of individual animals and potentially reducing the numbers required for experimentation in the future. For primate tissues, biobanks represent the scarcest of these resources but quite possibly those most valuable for preclinical and translation studies.
Heat strain and mortality effects of prolonged central European heat wave—an example of June 2019 in Poland
Authors: Błażejczyk Krzysztof , Twardosz Robert , Wałach Piotr , Czarnecka Kaja , Błażejczyk Anna 
Published: October 2021

AbstractThe occurrence of long-lasting severe heat stress, such as in July–August 2003, July 2010, or in April–May 2018 has been one of the biggest meteorological threats in Europe in recent years. The paper focuses on the biometeorological and mortality effects of the hot June that was observed in Central Europe in 2019. The basis of the study was hourly and daily Universal Thermal Climate Index (UTCI) values at meteorological stations in Poland for June 2019. The average monthly air temperature and UTCI values from 1951 to 2018 were analysed as background. Grosswetterlagen calendar of atmospheric circulation was used to assess synoptic conditions of heat wave. Several heat strain measures were applied : net heat storage (S), modelled heart rate (HR), sultriness (HSI), and UTCI index. Actual total mortality (TM) and modelled strong heat-related mortality (SHRM) were taken as indicators of biometeorological consequences of the hot June in 2019. The results indicate that prolonged persistence of unusually warm weather in June 2019 was determined by the synoptic conditions occurring over the European region and causing advection of tropical air. They led to the emergence of heat waves causing 10% increase in TM and 5 times bigger SHRM then in preceding 10 years. Such increase in SHRM was an effect of overheating and overload of circulatory system of human organism.
Palbociclib as an early-line treatment for Japanese patients with hormone receptor–positive/human epidermal growth factor receptor 2–negative advanced breast cancer: a review of clinical trial and real-world data
Authors: Masuda Norikazu , Kosaka Nobuyoshi , Iwata Hiroji , Toi Masakazu 
Published: October 2021

AbstractBreast cancer is the most common type of cancer among women worldwide and in Japan. The majority of breast cancers are hormone receptor–positive (HR+)/human epidermal growth factor receptor 2–negative (HER2‒), and endocrine therapy is an effective therapy for this type of breast cancer. However, recent substantial advances have been made in the management of HR+/HER2‒ advanced breast cancer (ABC) with the advent of targeted therapies, such as cyclin-dependent kinase 4/6 (CDK4/6) inhibitors, resulting in significant improvements in survival outcomes versus endocrine therapy alone. To evaluate the optimal use of palbociclib, a CDK4/6 inhibitor, in HR+/HER2– ABC, this review summarizes clinical trial and real-world data for palbociclib. In addition, current biomarker studies in palbociclib clinical research are reviewed. In Japanese patients, palbociclib was shown to be effective with a manageable safety profile, although differences were observed in the frequency of adverse event and dosing parameters. Current evidence supporting palbociclib as a first-line treatment strategy for patients with HR+/HER2‒ ABC in Asia, and specifically japan, is also discussed.
Effects of soil heterogeneity on susceptibility of shallow landslides
Authors: Oguz Emir Ahmet , Depina Ivan , Thakur Vikas 
Published: October 2021

AbstractUncertainties in parameters of landslide susceptibility models often hinder them from providing accurate spatial and temporal predictions of landslide occurrences. Substantial contribution to the uncertainties in landslide assessment originates from spatially variable geotechnical and hydrological parameters. These input parameters may often vary significantly through space, even within the same geological deposit, and there is a need to quantify the effects of the uncertainties in these parameters. This study addresses this issue with a new three-dimensional probabilistic landslide susceptibility model. The spatial variability of the model parameters is modeled with the random field approach and coupled with the Monte Carlo method to propagate uncertainties from the model parameters to landslide predictions (i.e., factor of safety). The resulting uncertainties in landslide predictions allow the effects of spatial variability in the input parameters to be quantified. The performance of the proposed model in capturing the effect of spatial variability and predicting landslide occurrence has been compared with a conventional physical-based landslide susceptibility model that does not account for three-dimensional effects on slope stability. The results indicate that the proposed model has better performance in landslide prediction with higher accuracy and precision than the conventional model. The novelty of this study is illustrating the effects of the soil heterogeneity on the susceptibility of shallow landslides, which was made possible by the development of a three-dimensional slope stability model that was coupled with random field model and the Monte Carlo method.
Methylation studies in Peromyscus: aging, altitude adaptation, and monogamy
Authors: Horvath Steve , Haghani Amin , Zoller Joseph A. , Naderi Asieh , Soltanmohammadi Elham , Farmaki Elena , Kaza Vimala , Chatzistamou Ioulia , Kiaris Hippokratis 
Published: October 2021

AbstractDNA methylation-based biomarkers of aging have been developed for humans and many other mammals and could be used to assess how stress factors impact aging. Deer mice (Peromyscus) are long-living rodents that have emerged as an informative model to study aging, adaptation to extreme environments, and monogamous behavior. In the present study, we have undertaken an exhaustive, genome-wide analysis of DNA methylation inPeromyscus, spanning different species, stocks, sexes, tissues, and age cohorts. We describe DNA methylation-based estimators of age for different species of deer mice based on novel DNA methylation data generated on highly conserved mammalian CpGs measured with a custom array. The multi-tissue epigenetic clock for deer mice was trained on 3 tissues (tail, liver, and brain). Two human-Peromyscusclocks accurately measure age and relative age, respectively. We present CpGs and enriched pathways that relate to different conditions such as chronological age, high altitude, and monogamous behavior. Overall, this study provides a first step towards studying the epigenetic correlates of monogamous behavior and adaptation to high altitude inPeromyscus. The human-Peromyscusepigenetic clocks are expected to provide a significant boost to the attractiveness ofPeromyscusas a biological model.
Quantification of pulmonary involvement in COVID-19 pneumonia by means of a cascade of two U-nets: training and assessment on multiple datasets using different annotation criteria
Authors: Lizzi Francesca , Agosti Abramo , Brero Francesca , Cabini Raffaella Fiamma , Fantacci Maria Evelina , Figini Silvia , Lascialfari Alessandro , Laruina Francesco , Oliva Piernicola , Piffer Stefano , Postuma Ian , Rinaldi Lisa , Talamonti Cinzia , Retico Alessandra 
Published: October 2021

Abstract
Purpose
This study aims at exploiting artificial intelligence (AI) for the identification, segmentation and quantification of COVID-19 pulmonary lesions. The limited data availability and the annotation quality are relevant factors in training AI-methods. We investigated the effects of using multiple datasets, heterogeneously populated and annotated according to different criteria.

Methods
We developed an automated analysis pipeline, the LungQuant system, based on a cascade of two U-nets. The first one (U-net$$_1$$

1

) is devoted to the identification of the lung parenchyma; the second one (U-net$$_2$$

2

) acts on a bounding box enclosing the segmented lungs to identify the areas affected by COVID-19 lesions. Different public datasets were used to train the U-nets and to evaluate their segmentation performances, which have been quantified in terms of the Dice Similarity Coefficients. The accuracy in predicting the CT-Severity Score (CT-SS) of the LungQuant system has been also evaluated.

Results
Both the volumetric DSC (vDSC) and the accuracy showed a dependency on the annotation quality of the released data samples. On an independent dataset (COVID-19-CT-Seg), both the vDSC and the surface DSC (sDSC) were measured between the masks predicted by LungQuant system and the reference ones. The vDSC (sDSC) values of 0.95±0.01 and 0.66±0.13 (0.95±0.02 and 0.76±0.18, with 5 mm tolerance) were obtained for the segmentation of lungs and COVID-19 lesions, respectively. The system achieved an accuracy of 90% in CT-SS identification on this benchmark dataset.

Conclusion
We analysed the impact of using data samples with different annotation criteria in training an AI-based quantification system for pulmonary involvement in COVID-19 pneumonia. In terms of vDSC measures, the U-net segmentation strongly depends on the quality of the lesion annotations. Nevertheless, the CT-SS can be accurately predicted on independent test sets, demonstrating the satisfactory generalization ability of the LungQuant.
An image processing tool for the detection of anthracycline-induced cardiotoxicity by evaluating the myocardial metabolic activity in [18F]FDG PET/CT
Authors: Seiffert Alexander P. , Gómez-Grande Adolfo , Castro-Leal Gonzalo , Rodríguez Antonia , Palomino-Fernández David , Gómez Enrique J. , Sánchez-González Patricia , Bueno Héctor 
Published: October 2021

Abstract
Purpose
Chemotherapy-induced cardiotoxicity is one of the main complications during and after cancer treatment. While echocardiography is the most used technique in clinical practice to evaluate left ventricular (LV) dysfunction, a multimodal approach is preferred for the early detection of anthracycline-induced cardiotoxicity. In this paper, an image processing tool allowing the qualitative and quantitative analysis of myocardial metabolic activity by [18F]fluorodeoxyglucose (FDG) positron emission tomography computed tomography (PET/CT) images, acquired routinely during and after cancer treatment, is presented.

Methods
The methodology is based on cardiac single photon emission computed tomography image processing protocols used in clinical practice. LV polar maps are created, and quantitative regional values are calculated. The tool was validated in a study group of 24 patients with Hodgkin or non-Hodgkin lymphoma (HL and NHL, respectively) treated with anthracyclines. Staging, interim and end-of-treatment [18F]FDG PET/CT images were acquired and the presented tool was used to extract the quantitative metrics of LV metabolic activity.

Results
Results show an overall increase of metabolic activity in the interim PET image acquired while on treatment compared to staging PET, which then decreased in the end-of-treatment scan. Positive correlation coefficients between staging and interim scans, and negative correlation coefficients between interim and end-of-treatment scans also support this finding. Metabolic changes occur predominantly in the septal region.

Conclusion
The proposed methodology and presented software solution provides the capability to assess quantitatively myocardial metabolism acquired by routine [18F]FDG PET/CT scanning during cancer treatment for evaluating anthracycline-induced cardiotoxicity. The [18F]FDG PET/CT septal-lateral uptake ratio is proposed as a new quantitative measure of myocardial metabolism.
Effect of Temperature and Acoustic Pressure During Ultrasound Liquid-Phase Processing of Graphite in Water
Authors: Morton Justin A. , Eskin Dmitry G. , Grobert Nicole , Mi Jiawei , Porfyrakis Kyriakos , Prentice Paul , Tzanakis Iakovos 
Published: October 2021

AbstractUltrasound-assisted liquid-phase exfoliation is a promising method for manufacturing two-dimensional materials. Understanding the effect of ultrasonication parameters such as the temperature and input power on the developed pressure field is pivotal for optimization of the process. Limited research has been carried out to determine the optimal temperature for exfoliation, with some data generating disputed results. Simply maximizing the sonication power does not necessarily produce a higher yield because of shielding. In this study, a high-temperature calibrated cavitometer was used to measure the acoustic pressure generated in different graphite solutions in deionized water at various temperatures (from 10°C to 70°C) and input power conditions (from 20% to 100%). In addition, high-speed optical imaging provided insight on the shock wave generation from transient bubble collapses under different sonication conditions. The optimal sono-exfoliation parameters were determined to be 20% input power at 10°C for graphite flake solution, and 100% input power at 40°C to 50°C for graphite powder solution.
Impact of propofol sedation on the diagnostic accuracy of hepatic venous pressure gradient measurements in patients with cirrhosis
Authors: Ebrahimi Fahim , Semela David , Heim Markus 
Published: October 2021

Abstract
Background
Measurement of the hepatic venous pressure gradient (HVPG) is the gold standard to evaluate the presence and severity of portal hypertension. The procedure is generally safe and well tolerated, but nevertheless, some patients demand for sedation. However, it is unknown whether propofol sedation would impair the accuracy of portal pressure measurements.

Methods
This is a prospective observational cohort study including cirrhotic patients with suspected portal hypertension undergoing invasive measurement of HVPG. Measurements of HVPG were performed in awake condition as well as under sedation with propofol infusion.

Results
In total, 37 patients were included. Mean HVPG in awake condition was 15.9 mmHg (IQR 13–19) and during sedation 14.1 mmHg (IQR 12–17). While measures of free hepatic vein pressure (FHVP) were not altered after propofol sedation (p = 0.34), wedged hepatic vein pressure values (WHVP) decreased in an average by 2.05 mmHg (95% CI − 2.46 to − 1.16; p < 0.001) which was proportional to the magnitude of HVPG. In 31 out of 37 patients (83.8%), portal hypertension with HVPG ≥ 12 mmHg was found. Under sedation with propofol, two patients (5.4%) with borderline values would have been incorrectly classified as < 12 mmHg. After adjustment for the average difference of − 10%, all patients were correctly classified. Intraclass correlation coefficient between HVPG measurement in awake condition and under propofol sedation was 0.927 (95% CI 0.594–0.975).

Conclusions
Propofol sedation during HVPG measurements is generally safe, however it may lead to relevant alterations of HVPG readings.