bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021
Authors: Oh Djin Ye , Hölzer Martin , Paraskevopoulou Sofia , Trofimova Maria , Hartkopf Felix , Budt Matthias , Wedde Marianne , Richard Hugues , Haldemann Berit , Domaszewska Teresa , Reiche Janine , Keeren Kathrin , Radonić Aleksandar , Ramos Calderón Julia Patricia , Smith Maureen Rebecca , Brinkmann Annika , Trappe Kathrin , Drechsel Oliver , Klaper Kathleen , Hein Sascha , Hildt Eberhardt , Haas Walter , Calvignac-Spencer Sébastien , Semmler Torsten , Dürrwald Ralf , Thürmer Andrea , Drosten Christian , Fuchs Stephan , Kröger Stefan , von Kleist Max , Wolff Thorsten ,   for the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) Laboratory Network, Biere Barbara , Bode Konrad , Corman Victor , Erren Michael , Finzer Patrick , Grosser Roger , Haffner Manuel , Hermann Beate , Kiel Christina , Krumbholz Andi , Meinck Kristian , Nitsche Andreas , Petzold Markus , Schwanz Thomas , Szabados Florian , Tewald Friedemann , Tiemann Carsten 
Published: June 2022

Abstract

Background
Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany.

Methods
At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2–positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI.

Results
We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modeled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave.

Conclusions
SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling coronavirus disease 2019 spread as the virus evolves.
High Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Associated With Decreased Contact Tracing Effectiveness for Identifying Persons at Elevated Risk of Infection—Vermont
Authors: Borah Brian F , Pringle Julia , Flaherty Michael , Oeltmann John E , Moonan Patrick K , Kelso Patsy 
Published: June 2022

Abstract
Vermont contact tracing consistently identified people at risk for coronavirus disease 2019 (COVID-19). However, the prevalence ratio (PR) of COVID-19 among contacts compared with noncontacts when viral transmission was high (PR, 13.5 [95% confidence interval {CI}, 13.2–13.9]) was significantly less than when transmission was low (PR, 49.3 [95% CI, 43.2–56.3]).
Current state of artificial intelligence-based algorithms for hospital admission prediction in patients with heart failure: a scoping review
Authors: Croon P M , Selder J L , Allaart C P , Bleijendaal H , Chamuleau S A J , Hofstra L , Išgum I , Ziesemer K A , Winter M M 
Published: June 2022

Abstract

Aims
Patients with congestive heart failure (HF) are prone to clinical deterioration leading to hospital admissions, burdening both patients and the healthcare system. Predicting hospital admission in this patient group could enable timely intervention, with subsequent reduction of these admissions. To date, hospital admission prediction remains challenging. Increasing amounts of acquired data and development of artificial intelligence (AI) technology allow for the creation of reliable hospital prediction algorithms for HF patients. This scoping review describes the current literature on strategies and performance of AI-based algorithms for prediction of hospital admission in patients with HF.

Methods and results
PubMed, EMBASE, and the Web of Science were used to search for articles using machine learning (ML) and deep learning methods to predict hospitalization in patients with HF. After eligibility screening, 23 articles were included. Sixteen articles predicted 30-day hospital (re-)admission resulting in an area under the curve (AUC) ranging from 0.61 to 0.79. Six studies predicted hospital admission over longer time periods ranging from 6 months to 3 years, with AUC’s ranging from 0.65 to 0.78. One study prospectively evaluated performance of a disposable sensory patch at home after hospitalization which resulted in an AUC of 0.89 for unplanned hospital admission prediction.

Conclusion
AI has the potential to enable prediction of hospital admission in HF patients. Improvement of data management, adding new data sources such as telemonitoring data and ML models and prospective and external validation of current models must be performed before clinical applicability is possible.
One-stage total arch and proximal descending aorta replacement via a single median sternotomy
Authors: Shi Enyi , Tang Rui , Jiang Xuan , Gu Tianxiang 
Published: June 2022

Abstract
For extended arch pathologies involving the proximal descending aorta, the exposure afforded by the median sternotomy is less than ideal, and radical replacement of the distal arch by conventional total arch replacement is difficult. We developed a surgical manoeuvre to replace the total arch and proximal descending aorta in 1 stage through a single median sternotomy.
Microbial community response to a bioaugmentation test to degrade trichloroethylene in a fractured rock aquifer, Trenton, N.J
Authors: Underwood Jennifer C , Akob Denise M , Lorah Michelle M , Imbrigiotta Thomas E , Harvey Ronald W , Tiedeman Claire R 
Published: June 2022

AbstractBioaugmentation is a promising strategy for enhancing trichloroethylene (TCE) degradation in fractured rock. However, slow or incomplete biodegradation can lead to stalling at degradation byproducts such as 1,2-dichloroethene (cis-DCE) and vinyl chloride (VC). Over the course of 7 years, we examined the response of groundwater microbial populations in a bioaugmentation test where an emulsified vegetable oil solution (EOS®) and a dechlorinating consortium (KB-1®), containing the established dechlorinator Dehalococcoides (DHC), were injected into a TCE-contaminated fractured rock aquifer. Indigenous microbial communities responded within 2 days to added substrate and outcompeted KB-1®, and over the years of monitoring, several other notable turnover events were observed. Concentrations of ethene, the end product in reductive dechlorination, had the strongest correlations (P&lt; .05) with members of Candidatus Colwellbacteria but their involvement in reductive dechlorination is unknown and warrants further investigation.DHC never exceeded 0.6% relative abundance of groundwater microbial communities, despite its previously presumed importance at the site. Increased concentrations of carbon dioxide, acetic acid, and methane were positively correlated with increasing ethene concentrations; however, concentrations of cis-DCE and VC remained high by the end of the monitoring period suggesting preferential enrichment of indigenous partial dechlorinators over bioaugmented complete dechlorinators. This study highlights the importance of characterizing in situ microbial populations to understand how they can potentially enhance or inhibit augmented TCE degradation.
Dark stress for improved lipid quantity and quality in bioprospected acid-tolerant green microalgae
Authors: Desjardins Sabrina M , Laamanen Corey A , Basiliko Nathan , Senhorinho Gerusa N A , Scott John A 
Published: June 2022

Abstract
The cost of microalgae cultivation is one of the largest limitations to achieving sustainable, large-scale microalgae production of commercially desirable lipids. Utilizing CO2 as a ‘free’ carbon source from waste industrial flue gas emissions can offer wide-ranging cost savings. However, these gas streams typically create acidic environments, in which most microalgae cannot survive due to the concentration of CO2 and the presence of other acidic gasses such as NO2 and SO2. To address this situation, we investigated growth of a mixed acid-tolerant green microalgal culture (91% dominated by a single Coccomyxa sp. taxon) bioprospected at pH 2.8 from an acid mine drainage impacted water body. The culture was grown at pH 2.5 and fed with a simulated flue gas containing 6% CO2 and 94% N2. On reaching the end of the exponential growth phase, the culture was exposed to either continued light-dark cycle conditions or continual dark conditions. After three days in the dark, the biomass consisted of 28% of lipids, which was 42% higher than at the end of the exponential phase and 55% higher than the maximum lipid content achieved under light/dark conditions. The stress caused by being continually in the dark also favoured the production of omega-3 and omega-6 polyunsaturated fatty acids (PUFAs; 19.47% and 21.04%, respectively, after 7 days) compared to 7-days of light-dark treatment (1.94% and 9.53%, respectively) and showed an increase in nitrogen content (C:N ratio of 6.4) compared to light-dark treatment (C:N ratio of 11.9). The results of the research indicate that use of acid tolerant microalgae overcomes issues using flue gasses that will create an acidic environment and that applying dark stress is a low-cost stressor stimulates production of desirable dietary lipids.
Plume height, duration and volume of sustained explosive eruptions inferred from eruption tremor amplitudes
Authors: Mori Azusa , Kumagai Hiroyuki , Londoño John Makario 
Published: June 2022

SUMMARY
Seismic source amplitudes determined by using the amplitudes of high-frequency (5−10 Hz) tremor signals generated by sustained explosive eruptions have been shown to be related to eruption plume height by power-law and exponential relations and to eruption volume flux by a proportional relation. We further examined these relations and extended this source quantification approach to investigate eruption duration by using the envelope width, defined by the ratio of the cumulative source amplitude to the source amplitude. We first confirmed that the relationship between source amplitude and plume height proposed by a previous study holds for small eruptions at Nevado del Ruiz (Colombia), although slight modifications were required. We then showed that the relations of envelope width with source amplitude and with cumulative source amplitude of eruption tremor associated with sub-Plinian eruptions at Kirishima (Japan) and Tungurahua (Ecuador) could be described by a power law. The source amplitude functions of these tremors were characterized by three periods and could be approximated by a trapezoidal shape. A power-law function fitted to the relation between eruption volume and eruption duration obtained from these relations was similar to that estimated by fitting a power-law function to previously reported eruption volume and duration data of well-documented silicic and andesitic eruptions. Our results suggest that eruption duration may systematically vary with eruption volume when the conduit is stably open during the second period of the trapezoidal source amplitude function. This study demonstrated that source amplitudes can be used for real-time predictions of both plume height and eruption duration, which in turn may be used to estimate ashfall distributions and tephra transport for local residents and aviation operations.
Obesity and adipose tissue impact on T-cell response and cancer immune checkpoint blockade therapy
Authors: Pasquarelli-do-Nascimento Gabriel , Machado Sabrina Azevedo , de Carvalho Juliana Maria Andrade , Magalhães Kelly Grace 
Published: June 2022

SummaryMany different types of cancer are now well known to have increased occurrence or severity in individuals with obesity. The influence of obesity on cancer and the immune cells in the tumor microenvironment has been thought to be a pleiotropic effect. As key endocrine and immune organs, the highly plastic adipose tissues play crucial roles in obesity pathophysiology, as they show alterations according to environmental cues. Adipose tissues of lean subjects present mostly anti-inflammatory cells that are crucial in tissue remodeling, favoring uncoupling protein 1 expression and non-shivering thermogenesis. Oppositely, obese adipose tissues display massive proinflammatory immune cell infiltration, dying adipocytes, and enhanced crown-like structure formation. In this review, we discuss how obesity can lead to derangements and dysfunctions in antitumor CD8+ T lymphocytes dysfunction. Moreover, we explain how obesity can affect the efficiency of cancer immunotherapy, depicting the mechanisms involved in this process. Cancer immunotherapy management includes monoclonal antibodies targeting the immune checkpoint blockade. Exhausted CD8+ T lymphocytes show elevated programmed cell death-1 (PD-1) expression and highly glycolytic tumors tend to show a good response to anti-PD-1/PD-L1 immunotherapy. Although obesity is a risk factor for the development of several neoplasms and is linked with increased tumor growth and aggressiveness, obesity is also related to improved response to cancer immunotherapy, a phenomenon called the obesity paradox. However, patients affected by obesity present higher incidences of adverse events related to this therapy. These limitations highlight the necessity of a deeper investigation of factors that influence the obesity paradox to improve the application of these therapies.
On the Crossing Estimates for Simple Conformal Loop Ensembles
Authors: Bai Tianyi , Wan Yijun 
Published: June 2022

Abstract
We prove a super-exponential decay of probabilities that there exist $n$ crossings of a given quad for a simple $\textrm {CLE}_\kappa (\Omega )$, $\frac {8}{3}&lt;\kappa \le 4$, as $n$ goes to infinity. Besides, being of independent interest, this also provides the missing ingredient in [2] for proving the convergence of probabilities of cylindrical events for the double-dimer loop ensembles to those for the nested $\textrm {CLE}_4(\Omega )$.
Nitazoxanide potentiates linezolid against linezolid-resistant Staphylococcus aureus in vitro and in vivo
Authors: Kaul Grace , Akhir Abdul , Shukla Manjulika , Rawat Kundan S , Sharma Chandra P , Sangu Komal G , Rode Haridas B , Goel Atul , Chopra Sidharth 
Published: June 2022

Abstract

Background
Antimicrobial resistance is a growing menace, claiming millions of lives all over the world. In this context, drug repurposing is one approach gaining interest as a suitable alternative to conventional drug discovery and development.

Methods
Whole-cell assays were used to screen FDA-approved drugs to identify novel antimicrobial agents active against bacterial pathogens. Following identification of nitazoxanide, its various characteristics, such as antimicrobial activity against MDR isolates, time–kill kinetics, ability to synergize with approved drugs, antibiofilm activity and ability to generate resistance in Staphylococcus aureus, were determined, followed by determination of its in vivo potential against MDR S. aureus.

Results
Nitazoxanide demonstrated a potent in vitro antistaphylococcal profile, including equipotent activity against clinical drug-resistant S. aureus and Enterococcus spp. Nitazoxanide exhibited concentration-dependent killing, significantly eradicated preformed S. aureus biofilm and S. aureus did not generate resistance to it. Nitazoxanide strongly synergized with linezolid both in vitro and in vivo against linezolid-susceptible and -resistant S. aureus, displaying superior activity to untreated control and drug-alone treatment groups.

Conclusions
Nitazoxanide can be utilized in combination with linezolid against infections caused by linezolid-resistant S. aureus as it exhibits strong synergism in vitro and in vivo.
Subgroup analysis of Japanese patients in a phase III randomized, controlled study of neoadjuvant atezolizumab or placebo, combined with nab-paclitaxel and anthracycline-based chemotherapy in early triple-negative breast cancer (IMpassion031)
Authors: Saji Shigehira , Ohsumi Shozo , Ito Mitsuya , Hayashi Naoki , Kobayashi Kokoro , Masuda Norikazu , Niikura Naoki , Yamashita Toshinari , Kiyama Keiichiro , Hasegawa Ayumi , Nakagawa Shizuka , Hattori Masaya 
Published: June 2022

Abstract

Background
In the global phase III IMpassion031 study, neoadjuvant atezolizumab plus nab-paclitaxel/anthracycline-based chemotherapy improved pathological complete response in patients with early stage triple-negative breast cancer. Here, we report primary analysis results from a subgroup of Japanese patients.

Methods
Patients with histologically documented, previously untreated, stage cT2–cT4, cN0–cN3, cM0 triple-negative breast cancer were randomized 1:1 to receive intravenous atezolizumab 840 mg or placebo every 2 weeks in combination with chemotherapy consisting of nab-paclitaxel intravenous 125 mg/m2 once a week, followed by doxorubicin intravenous 60 mg/m2 and cyclophosphamide intravenous 600 mg/m2 every 2 weeks. Patients then underwent surgery. Pathological complete response (ypT0/is ypN0) in the intention-to-treat and PD-L1-positive (≥1% PD-L1-expressing tumor-infiltrating immune cells) populations were co-primary endpoints.

Results
This subanalysis (data cutoff: 3 April 2020) included 36 patients from Japan (intention-to-treat; atezolizumab arm, n = 17; placebo arm, n = 19). Pathological complete response occurred in 41% (n = 7; 95% confidence interval, 18–67) of patients in the atezolizumab arm and 37% (n = 7; 95% confidence interval, 16–62) in the placebo arm. In the PD-L1-positive population, pathological complete response occurred in 50% (n = 5; 95% confidence interval, 19–81) of patients in the atezolizumab arm and 45% (n = 5; 95% confidence interval, 17–77) in the placebo arm. Treatment-related grade 3–4 adverse events occurred in 71% and 68% of patients in the respective arms.

Conclusion
Atezolizumab added to neoadjuvant chemotherapy numerically improved pathological complete response versus placebo in this small exploratory analysis of Japanese patients with early stage triple-negative breast cancer, a trend directionally consistent with the global study results. No new safety signals were identified.
MAX2-dependent competence for callus formation and shoot regeneration from Arabidopsis thaliana root explants
Authors: Temmerman Arne , Marquez-Garcia Belen , Depuydt Stephen , Bruznican Silvia , De Cuyper Carolien , De Keyser Annick , Boyer François-Didier , Vereecke Danny , Struk Sylwia , Goormachtig Sofie 
Published: June 2022

Abstract
Although the division of the pericycle cells initiates both lateral root development and root-derived callus formation, these developmental processes are affected differently in the strigolactone and karrikin/KARRIKIN INSENSITIVE 2 (KAI2) ligand signalling mutant more axillary growth 2 (max2). Whereas max2 produces more lateral roots than the wild type, it is defective in the regeneration of shoots from root explants. We suggest that the decreased shoot regeneration of max2 originates from delayed formation of callus primordium, yielding less callus material to regenerate shoots. Indeed, when incubated on callus-inducing medium, the pericycle cell division was reduced in max2 and the early gene expression varied when compared with the wild type, as determined by a transcriptomics analysis. Furthermore, the expression of the LATERAL ORGAN BOUNDARIES DOMAIN genes and of callus-induction genes was modified in correlation with the max2 phenotype, suggesting a role for MAX2 in the regulation of the interplay between cytokinin, auxin, and light signalling in callus initiation. Additionally, we found that the in vitro shoot regeneration phenotype of max2 might be caused by a defect in KAI2, rather than in DWARF14, signalling. Nevertheless, the shoot regeneration assays revealed that the strigolactone biosynthesis mutants max3 and max4 also play a minor role.
Clinical and microbiological analysis of fungal keratitis in Toronto, Canada: A 20-year study
Authors: Trinh Tanya , Emami Seema , Gould Jonah , Mimouni Michael , Cohen Eyal , Rootman David S , Slomovic Allan R , Chan Clara C 
Published: June 2022

Abstract

Fungal keratitis is a devastating and difficult-to-treat ocular infection with high morbidity. Understanding geographic microbiological and clinical trends helps to guide rapid and effective treatment. We therefore report the characteristics and outcomes of fungal keratitis in Toronto,ON Canada, over a 20-year period. An electronic search of microbiology records at University Health Network, Toronto, ON, Canada identified all patients with positive corneal fungal culture over a 20-year period seen at our tertiary referral cornea practice. Review of corresponding patient charts identified demographic and microbiological details, clinical course, treatment regimen, and final outcomes associated with each episode of culture-positive fungal keratitis. A total of 46 patients with 51 discrete fungal keratitis episodes were included. Five patients experienced recurrent fungal keratitis. Candida species accounted for 60.8% of positive fungal cultures, followed by Filamentous species at 35.3%. Preferred initial anti-fungal treatment was topical amphotericin at 36.7% followed by topical voriconazole at 32.6%. Surgical intervention was required in 48.9% with therapeutic penetrating keratoplasty being the most common procedure (22.4%). Final visual acuity (VA) of &lt;20/200 was attributed to 58% of patients in this study. Risk factors for poor outcomes included poor VA, topical steroid use at presentation, Candida involvement, history of ocular surface disease, organic ocular trauma, or prior corneal transplantation. Candida is the most frequent keratomycotic pathogen in Toronto. Risk factors for poor visual outcome include prior corneal transplantation, ocular surface disease/trauma, or pre-existing topical steroid use. Early suspicion, diagnosis and treatment are paramount for best clinical outcomes.

Lay Summary
Fungal keratitis can cause severe vision loss without effective treatment. In Toronto, Candida had been the most common species over a 20-year period. Poor clinical outcome was associated with low presenting visual acuity, previous corneal transplant, topical steroid use, trauma, and Candida involvement.