bluuebunny/crossref_metadata_2025 huggingface dataset:
Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell
Authors: Halstead Michelle M. , Islas-Trejo Alma , Goszczynski Daniel E. , Medrano Juan F. , Zhou Huaijun , Ross Pablo J.
Published: May 2021

A comprehensive annotation of transcript isoforms in domesticated species is lacking. Especially considering that transcriptome complexity and splicing patterns are not well-conserved between species, this presents a substantial obstacle to genomic selection programs that seek to improve production, disease resistance, and reproduction. Recent advances in long-read sequencing technology have made it possible to directly extrapolate the structure of full-length transcripts without the need for transcript reconstruction. In this study, we demonstrate the power of long-read sequencing for transcriptome annotation by coupling Oxford Nanopore Technology (ONT) with large-scale multiplexing of 93 samples, comprising 32 tissues collected from adult male and female Hereford cattle. More than 30 million uniquely mapping full-length reads were obtained from a single ONT flow cell, and used to identify and characterize the expression dynamics of 99,044 transcript isoforms at 31,824 loci. Of these predicted transcripts, 21% exactly matched a reference transcript, and 61% were novel isoforms of reference genes, substantially increasing the ratio of transcript variants per gene, and suggesting that the complexity of the bovine transcriptome is comparable to that in humans. Over 7,000 transcript isoforms were extremely tissue-specific, and 61% of these were attributed to testis, which exhibited the most complex transcriptome of all interrogated tissues. Despite profiling over 30 tissues, transcription was only detected at about 60% of reference loci. Consequently, additional studies will be necessary to continue characterizing the bovine transcriptome in additional cell types, developmental stages, and physiological conditions. However, by here demonstrating the power of ONT sequencing coupled with large-scale multiplexing, the task of exhaustively annotating the bovine transcriptome – or any mammalian transcriptome – appears significantly more feasible.
Clinical and Basic Research Progress on Treg-Induced Immune Tolerance in Liver Transplantation
Authors: Ni Xuhao , Wang Qi , Gu Jian , Lu Ling
Published: May 2021

Rejection after organ transplantation is a cause of graft failure. Effectively reducing rejection and inducing tolerance is a challenge in the field of transplantation immunology. The liver, as an immunologically privileged organ, has high rates of spontaneous and operational tolerance after transplantation, allowing it to maintain its normal function for long periods. Although modern immunosuppression regimens have serious toxicity and side effects, it is very risky to discontinue immunosuppression regimens blindly. A more effective treatment to induce immune tolerance is the most sought-after goal in transplant medicine. Tregs have been shown to play a pivotal role in the regulation of immune balance, and infusion of Tregs can also effectively prevent rejection and cure autoimmune diseases without significant side effects. Given the immune characteristics of the liver, the correct use of Tregs can more effectively induce the occurrence of operational tolerance for liver transplants than for other organ transplants. This review mainly summarizes the latest research advances regarding the characteristics of the hepatic immune microenvironment, operational tolerance, Treg generation in vitro, and the application of Tregs in liver transplantation. It is hoped that this review will provide a deeper understanding of Tregs as the most effective treatment to induce and maintain operational tolerance after liver transplantation.
Climate Projections for the Southern Ocean Reveal Impacts in the Marine Microbial Communities Following Increases in Sea Surface Temperature
Authors: Tonelli Marcos , Signori Camila Negrão , Bendia Amanda , Neiva Juliana , Ferrero Bruno , Pellizari Vivian , Wainer Ilana
Published: May 2021

Anthropogenic global warming can have strong impacts on marine ecosystems, especially on climate-sensitive regions such as the Southern Ocean (SO). As key drivers of biogeochemical cycles, pelagic microbial communities are likely to respond to increases in sea surface temperature (SST). Thus, it is critical to understand how SST may change in future scenarios and how these changes will affect the composition and structure of microbial communities. By using a suite of Earth System Models participating in the Coupled Model Intercomparison Project Phase 6 (CMIP6), machine learning, and 16S rRNA sequencing data, we investigated the long-term changes as projected by CMIP6 simulations in SST throughout the twenty first century and the microbial diversity responses in the SO. Four Shared Socioeconomic Pathways (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5) were considered to assess the SO surface sensitivity to a warming climate. The SST changes across SSPs were ≈0.3, ≈0.7, ≈1.25, and ≈1.6oC between 2015 and 2100, respectively, and the high emissions scenarios projected a much sooner emergence of the human-induced temperature change throughout the SO. The impacts on Antarctic marine diversity of bacteria and archaea are expected to be significant and persistent by the late twenty first century, especially within the higher end of the range of future forcing pathways.
Conceptual Design of Extreme Sea-Level Early Warning Systems Based on Uncertainty Quantification and Engineering Optimization Methods
Authors: Denamiel Cléa , Huan Xun , Vilibić Ivica
Published: May 2021

Coastal hazards linked to extreme sea-level events are projected to have a direct impact (by flooding) on 630 million of people by year 2100. Numerous operational forecasts already provide coastal hazard assessments around the world. However, they are largely based on either deterministic tools (e.g., numerical ocean and atmospheric models) or ensemble approaches which are both highly demanding in terms of high-performance computing (HPC) resources. Through a robust learning process, we propose conceptual design of an innovative architecture for extreme sea-level early warning systems based on uncertainty quantification/reduction and optimization methods. This approach might be cost-effective in terms of real-time computational needs while maintaining reliability and trustworthiness of the hazard assessments. The proposed architecture relies on three main tools aligning numerical forecasts with observations: (1) surrogate models of extreme sea-levels using polynomial chaos expansion, Gaussian processes or machine learning, (2) fast data assimilation via Bayesian inference, and (3) optimal experimental design of the observational network. A surrogate model developed for meteotsunami events – i.e., atmospherically induced long ocean waves in a tsunami frequency band – has already been proven to greatly improve the reliability of extreme sea-level hazard assessments. Such an approach might be promising for several coastal hazards known to destructively impact the world coasts, like hurricanes or typhoons and seismic tsunamis.
Projections of Directional Spectra Help to Unravel the Future Behavior of Wind Waves
Authors: Lobeto Hector , Menendez Melisa , Losada Iñigo J.
Published: May 2021

Based on a novel approach, present-day and future spectral wind-wave conditions in a high-emission scenario from a seven-member wave climate projection ensemble are compared. The spectral analysis at the selected locations aids in understanding the propagation of swell projected changes from the generation areas across the ocean basins. For example, a projected increase in the energy from Southern Ocean swells can be observed in all ocean basins and both hemispheres, which is especially relevant in the west coast of North America due to the penetration of these swells beyond 30°N. Similarly, a consistent decrease in the energy of large northern Atlantic swells is noted close to the equator. This work provides evidence that assessments based on only integrated wave parameters (e.g., significant wave height and mean wave period) can mask information about the sign, magnitude, and robustness of the actual wave climate changes due to the offset of positive and negative variations within the spectrum, leading to a significant underestimation of the change associated with certain wave systems.
An IFN-STAT Axis Augments Tissue Damage and Inflammation in a Mouse Model of Crohn's Disease
Authors: Stolzer Iris , Dressel Anja , Chiriac Mircea T. , Neurath Markus F. , Günther Claudia
Published: May 2021

Blocking interferon-function by therapeutic intervention of the JAK-STAT-axis is a novel promising treatment option for inflammatory bowel disease (IBD). Although JAK inhibitors have proven efficacy in patients with active ulcerative colitis (UC), they failed to induce clinical remission in patients with Crohn's disease (CD). This finding strongly implicates a differential contribution of JAK signaling in both entities. Here, we dissected the contribution of different STAT members downstream of JAK to inflammation and barrier dysfunction in a mouse model of Crohn's disease like ileitis and colitis (Casp8ΔIEC mice). Deletion of STAT1 in Casp8ΔIEC mice was associated with reduced cell death and a partial rescue of Paneth cell function in the small intestine. Likewise, organoids derived from the small intestine of these mice were less sensitive to cell death triggered by IBD-key cytokines such as TNFα or IFNs. Further functional in vitro and in vivo analyses revealed the impairment of MLKL-mediated necrosis as a result of deficient STAT1 function, which was in turn associated with improved cell survival. However, a decrease in inflammatory cell death was still associated with mild inflammation in the small intestine. The impact of STAT1 signaling on gastrointestinal inflammation dependent on the localization of inflammation, as STAT1 is essential for intestinal epithelial cell death regulation in the small intestine, whereas it is not the key factor for intestinal epithelial cell death in the context of colitis. Of note, additional deletion of STAT2 was not sufficient to restore Paneth cell function but strongly ameliorated ileitis. In summary, we provide here compelling molecular evidence that STAT1 and STAT2, both contribute to intestinal homeostasis, but have non-redundant functions. Our results further demonstrate that STATs individually affect the distinct pathophysiology of inflammation in the ileum and colon, respectively, which might explain the diverse outcome of JAK inhibitors on inflammatory bowel diseases.
Rituximab Therapy for Primary Membranous Nephropathy in a Chinese Cohort
Authors: Gao Shuang , Cui Zhao , Wang Xin , Zhang Yi-miao , Wang Fang , Cheng Xu-yang , Meng Li-qiang , Zhou Fu-de , Liu Gang , Zhao Ming-hui
Published: May 2021

Background: Rituximab has become one of the first-line therapies for the treatment of moderate and high-risk primary membranous nephropathy (pMN). We retrospectively reviewed 95 patients with pMN who received rituximab therapy and focused on the therapeutic effects and safety of this therapy in a Chinese cohort.

Methods: Ninety-five consecutive patients with pMN diagnosed by kidney biopsy received rituximab and were followed up for >6 months. Four weekly doses of rituximab (375 mg/m2) was adopted as the initial administration. Repeated single infusions were administrated to maintain B cell depletion levels of <5 cells/mL.

Results: A total of 91 patients completed rituximab therapy with the total dose of 2.4 (2.0, 3.0) g; 64/78 (82.1%) patients achieved anti-PLA2R antibody depletion in 6.0 (1.0, 12.0) months; 53/91 (58.2%) patients achieved clinical remission in 12.0 (6.0, 24.0) months, including complete remission in 18.7% of patients and partial remission in 39.6% of patients. Multivariate logistic regression analysis showed that severe proteinuria (OR = 1.22, P = 0.006) and the persistent positivity of anti-PLA2R antibodies (OR = 9.00, P = 0.002) were independent risk factors for no-remission. The remission rate of rituximab as an initial therapy was higher than rituximab as an alternative therapy (73.1 vs. 52.3%, P = 0.038). Lastly, 45 adverse events occurred in 37 patients, but only one patient withdrew from treatment due to severe pulmonary infection.

Conclusion: Rituximab is a safe and effective treatment option for Chinese patients with pMN, especially as an initial therapy.
Juvenile Spondyloarthritis: What More Do We Know About HLA-B27, Enthesitis, and New Bone Formation?
Authors: Tay Shi Huan , Yeo Joo Guan , Leong Jing Yao , Albani Salvatore , Arkachaisri Thaschawee
Published: May 2021

Juvenile spondyloarthritis (JSpA) refers to a diverse spectrum of immune-mediated inflammatory arthritides whose onset occurs in late childhood and adolescence. Like its adult counterpart, JSpA is typified by a strong association with human leukocyte antigen-B27 (HLA-B27) and potential axial involvement, while lacking rheumatoid factor (RF) and distinguishing autoantibodies. A characteristic manifestation of JSpA is enthesitis (inflammation of insertion sites of tendons, ligaments, joint capsules or fascia to bone), which is commonly accompanied by bone resorption and new bone formation at affected sites. In this Review, advances in the role of HLA-B27, enthesitis and its associated osteoproliferation in JSpA pathophysiology and treatment options will be discussed. A deeper appreciation of how these elements contribute to the JSpA disease mechanism will better inform diagnosis, prognosis and therapy, which in turn translates to an improved quality of life for patients.
Atherosclerosis and Bone Loss in Humans–Results From Deceased Donors and From Patients Submitted to Carotid Endarterectomy
Authors: Carmona-Fernandes Diana , Barreira Sofia C. , Leonardo Natacha , Casimiro Renata I. , Castro Alice M. , Santos Pedro Oliveira , Fernandes António N. , Cortes-Figueiredo Filipe , Gonçalves Carolina A. , Cruz Rafael , Fernandes Mariana L. , Ivo Margarida , Pedro Luis M. , Canhão Helena , Fonseca João Eurico , Santos Maria José
Published: May 2021

Background and Aims: Atherosclerosis and osteoporosis share common risk factors, as well as inflammatory mechanisms. Our aim was to understand how atherosclerotic lesions are related with disturbances in bone.

Methods: Gene expression of pro-inflammatory and bone metabolism related proteins (IL-1β, IL-6, IL-17A, TNF, RANKL, OPG, COL1, CTSK, OCL, TRAP, CBFA1, DKK1, SOST, ADIPOQ, and ADIPOR1) were analyzed in arteries and bones from 45 deceased donors and adipose tissue was used as control. Additionally, in 139 patients with advanced atherosclerosis submitted to carotid endarterectomy we compared calcium content (Alizarin red) and plaque inflammatory scores (CD3+, CD68+, and adiponectin) of patients with normal bone mineral density (BMD) with those with low BMD and explored the associations between gene expression in atherosclerotic plaques and BMD. Serum levels of pro-inflammatory and bone related proteins were measured both in donors and patients. Associations were investigated by the Pearson or Spearman correlation tests, and multivariate regression analyzes were performed when justified.

Results: Gene expression of bone remodeling and pro-inflammatory proteins correlated positively in bone and aorta, independently of age and sex of donors, but not in adipose tissue. The expression of bone formation genes was significantly higher in atheroma plaques from endarterectomized patients with normal vs. low BMD as well as inflammatory CD68+ scores, regardless of patients' age and sex, but not of body mass index. No relationship was observed between serum levels and gene expression levels of pro-inflammatory or bone remodeling proteins.

Conclusions: Our results suggest that the relationship between bones and vessels in the context of atherosclerotic disease and osteoporosis may rely on the intrinsic connection between the tissues involved, independently of disease stage. Serum measurements of pro-inflammatory and bone-remodeling proteins do not accurately translate tissue pathologic processes.
Bacterial Spectrum of Spontaneously Ruptured Otitis Media in a 7-Year, Longitudinal, Multicenter, Epidemiological Cross-Sectional Study in Germany
Authors: Imöhl Matthias , Perniciaro Stephanie , Busse Andreas , van der Linden Mark
Published: May 2021

We analyzed middle ear fluid (MEF) and nasopharyngeal swabs (NPS) from spontaneously ruptured acute otitis media (AOM) cases occurring in children under 5 years in Germany. The aim of the study was the assessment of disease burden and bacterial etiology in the era of routine pneumococcal vaccination. Furthermore, we aimed to compare isolates from MEF with isolates from NPS and to analyze the Streptococcus pneumoniae serotype distribution. We analyzed MEF and NPS samples in children 2 months to 5 years for vaccination status, frequency of bacterial strains, serotype/emm-type distribution of S. pneumoniae, Haemophilus influenzae, and Streptococcus pyogenes; and intraindividual correlation between MEF and NPS. From 2008 to 2014, MEF samples were collected from 2,138 subjects of which 2,001 (93.6%) also provided an NPS sample. In 851 of 2,138 MEF samples (39.8%), we identified organisms with confirmed pathogenic potential—S. pyogenes: 315 (14.7%), S. pneumoniae: 170 (8.0%), Staphylococcus aureus: 168 (7.9%), H. influenzae: 133 (6.2%), and Moraxella catarrhalis. Among NPS samples, 1,018 (50.9%) contained S. pneumoniae, 775 (38.7%) H. influenzae, 648 (32.4%) M. catarrhalis, and 344 (17.2%) S. pyogenes. Over the seven study years, the number of AOM patients steadily decreased, while the recruiting base remained constant. S. pneumoniae MEF isolates decreased by 86%, with serotype 3 being the most prevalent (25.7–42.9%). PCV13-non-PCV7-non-3 serotypes reduced to 0%. Among NPS, PCV7 serotypes decreased from 14.1 to 3.7%, PCV10: 17.6 to 3.7%, and PCV13: 55.3 to 25.7%. PCV13-non-PCV7-non-3 serotypes increased in the first 3 years of the study (17.1–22.9%), then decreased to 4.6% in year 7. Non-typeable H. influenzae reduced from 87.1 to 41.7% in MEF and from 91.4 to 54.2% in NPS. MEF and NPS isolates from the same subject were identical for 91.9% of S. pneumoniae, 99.0% of S. pyogenes, and 83.3% of H. influenzae. Among PCV7-vaccinated children, 5.6% had a PCV7 vaccine type in the MEF sample, and among PCV13-vaccinated children, 51.7% had a PCV13 serotype. Among non-vaccinated children, the percentages were 14.8 and 70.4. Pneumococcal conjugate vaccination has impacted the prevalence and etiology of spontaneously ruptured otitis media among children in Germany. Overall case numbers and pneumococcal vaccine type cases have strongly decreased.
Prevalence of Sarcopenia and Its Association With Diabetes: A Meta-Analysis of Community-Dwelling Asian Population
Authors: Chung Seung Min , Moon Jun Sung , Chang Min Cheol
Published: May 2021

Purpose: Sarcopenia is a major disease affecting mortality and quality of life in the elderly population. We performed a meta-analysis of studies on the community-dwelling population to investigate the prevalence of sarcopenia and its association with diabetes.

Methods: Databases were searched for studies published up to February 3, 2021, reporting the prevalence of sarcopenia in patients with and without diabetes. Data extraction and quality assessment were performed according to the Newcastle-Ottawa scale.

Results: Six articles were included in the systematic review. All the patients were Asian, aged ≥60 years (women 53.4%), and the diabetic and non-diabetic population was 1,537 and 5,485, respectively. In all six studies, the Asian Working Group for Sarcopenia criteria were used to diagnose sarcopenia. The prevalence of sarcopenia was 15.9% in diabetics and 10.8% in non-diabetics. Diabetics showed a significantly higher risk of sarcopenia than non-diabetics (pooled OR = 1.518, 95% CI = 1.110 to 2.076, Z-value = 2.611, p = 0.009).

Conclusion: Among the Asian community-dwelling geriatric population, the prevalence of sarcopenia was significantly higher in diabetics than in non-diabetics. These results suggest that strategies for the management of sarcopenia are required in Asian elderly patients, especially with diabetes.
The Hyperthermophilic Restriction-Modification Systems of Thermococcus kodakarensis Protect Genome Integrity
Authors: Zatopek Kelly M. , Burkhart Brett W. , Morgan Richard D. , Gehring Alexandra M. , Scott Kristin A. , Santangelo Thomas J. , Gardner Andrew F.
Published: May 2021

Thermococcus kodakarensis (T. kodakarensis), a hyperthermophilic, genetically accessible model archaeon, encodes two putative restriction modification (R-M) defense systems, TkoI and TkoII. TkoI is encoded by TK1460 while TkoII is encoded by TK1158. Bioinformative analysis suggests both R-M enzymes are large, fused methyltransferase (MTase)-endonuclease polypeptides that contain both restriction endonuclease (REase) activity to degrade foreign invading DNA and MTase activity to methylate host genomic DNA at specific recognition sites. In this work, we demonsrate T. kodakarensis strains deleted for either or both R-M enzymes grow more slowly but display significantly increased competency compared to strains with intact R-M systems, suggesting that both TkoI and TkoII assist in maintenance of genomic integrity in vivo and likely protect against viral- or plasmid-based DNA transfers. Pacific Biosciences single molecule real-time (SMRT) sequencing of T. kodakarensis strains containing both, one or neither R-M systems permitted assignment of the recognition sites for TkoI and TkoII and demonstrated that both R-M enzymes are TypeIIL; TkoI and TkoII methylate the N6 position of adenine on one strand of the recognition sequences GTGAAG and TTCAAG, respectively. Further in vitro biochemical characterization of the REase activities reveal TkoI and TkoII cleave the DNA backbone GTGAAG(N)20/(N)18 and TTCAAG(N)10/(N)8, respectively, away from the recognition sequences, while in vitro characterization of the MTase activities reveal transfer of tritiated S-adenosyl methionine by TkoI and TkoII to their respective recognition sites. Together these results demonstrate TkoI and TkoII restriction systems are important for protecting T. kodakarensis genome integrity from invading foreign DNA.
Retrospective Analysis of the Clinical Characteristics of Candida auris Infection Worldwide From 2009 to 2020
Authors: Hu Shan , Zhu Feilong , Jiang Weiwei , Wang Yuehua , Quan Yongqiang , Zhang Guoming , Gu Feng , Yang Ying
Published: May 2021

Introduction

Candida auris is an emerging multidrug-resistant fungus that may cause infections with a high mortality rate. The first case of C. auris infection was reported in 2009 and infections have been reported in 44 countries. The fungus now represents a major global public health threat. We analyzed cases from the emergence of C. auris infections up until the end of 2020. It is hoped that the results of this analysis will raise awareness in scientists to promote protection and control research pertaining to this pathogen.

Methods

PubMed and Web of Science databases were searched for all papers related to C. auris infections up until December 31, 2020. We sorted and organized these data into the following categories: date of publication, patient age and sex, underlying diseases, risk factors for infection, patient mortality information, drug sensitivity information of C. auris isolates, and genetic classification. The χ2 test was used to screen for factors that may affect patient mortality.

Results

A total of 912 patients were included in the analysis. There’s a higher proportion of men and a high proportion of patients were premature babies and elderly people. The proportions of patients with underlying diseases such as diabetes, kidney disease, trauma, and ear disease were also high. More than half of patients had a history of central venous catheter use and a history of broad-spectrum antibiotic use. The χ2 test revealed that only kidney disease (P < 0.05) was an important risk factor for mortality in C. auris-infected patients.

Conclusions

A comprehensive understanding of C. auris was achieved following this retrospective analysis, including the characteristics of C. auris-infected patients. In recent years, increasing numbers of multidrug-resistant C. auris isolates have been identified, and the high mortality rates associated with infection merit greater attention from the medical world.
A Novel Antimicrobial Peptides From Pine Needles of Pinus densiflora Sieb. et Zucc. Against Foodborne Bacteria
Authors: Lee Junho , Kang Hee Kyoung , Cheong Hyeonsook , Park Yoonkyung
Published: May 2021

Pine needles are used in several East Asian countries as food or traditional medicine. It contains functional components that exhibit a wide spectrum of pharmacological effects such as antioxidant, antimicrobial, anti-diabetic, and anti-inflammatory activities. We determined and characterized the novel antimicrobial peptides (AMPs) isolated from Pinus densiflora Sieb. et Zucc. The four active pine-needle (PN) peptides showed antimicrobial activity against foodborne bacteria with minimum inhibitory concentration (MIC) values within the range of 8–128 μg/ml. PN peptides showed no detectable hemolytic activity or cytotoxicity at the antimicrobial concentrations. The N-terminal amino acid sequence of the PN5 was identified using Edman degradation and Antimicrobial Peptide Database (APD) homology analysis showed that it was not identical to any other plant peptide. This suggests that PN5 can serve as an alternative therapeutic agent to be used in the food industry.
An Economical and Flexible Dual Barcoding, Two-Step PCR Approach for Highly Multiplexed Amplicon Sequencing
Authors: Pjevac Petra , Hausmann Bela , Schwarz Jasmin , Kohl Gudrun , Herbold Craig W. , Loy Alexander , Berry David
Published: May 2021

In microbiome research, phylogenetic and functional marker gene amplicon sequencing is the most commonly-used community profiling approach. Consequently, a plethora of protocols for the preparation and multiplexing of samples for amplicon sequencing have been developed. Here, we present two economical high-throughput gene amplification and sequencing workflows that are implemented as standard operating procedures at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna. These workflows are based on a previously-published two-step PCR approach, but have been updated to either increase the accuracy of results, or alternatively to achieve orders of magnitude higher numbers of samples to be multiplexed in a single sequencing run. The high-accuracy workflow relies on unique dual sample barcoding. It allows the same level of sample multiplexing as the previously-published two-step PCR approach, but effectively eliminates residual read missasignments between samples (crosstalk) which are inherent to single barcoding approaches. The high-multiplexing workflow is based on combinatorial dual sample barcoding, which theoretically allows for multiplexing up to 299,756 amplicon libraries of the same target gene in a single massively-parallelized amplicon sequencing run. Both workflows presented here are highly economical, easy to implement, and can, without significant modifications or cost, be applied to any target gene of interest.
The Transcription-Repair Coupling Factor Mfd Prevents and Promotes Mutagenesis in a Context-Dependent Manner
Authors: Lindsey-Boltz Laura A. , Sancar Aziz
Published: May 2021

The mfd (mutation frequency decline) gene was identified by screening an auxotrophic Escherichia coli strain exposed to UV and held in a minimal medium before plating onto rich or minimal agar plates. It was found that, under these conditions, holding cells in minimal (nongrowth) conditions resulted in mutations that enabled cells to grow on minimal media. Using this observation as a starting point, a mutant was isolated that failed to mutate to auxotrophy under the prescribed conditions, and the gene responsible for this phenomenon (mutation frequency decline) was named mfd. Later work revealed that mfd encoded a translocase that recognizes a stalled RNA polymerase (RNAP) at damage sites and binds to the stalled RNAP, recruits the nucleotide excision repair damage recognition complex UvrA2UvrB to the site, and facilitates damage recognition and repair while dissociating the stalled RNAP from the DNA along with the truncated RNA. Recent single-molecule and genome-wide repair studies have revealed time-resolved features and structural aspects of this transcription-coupled repair (TCR) phenomenon. Interestingly, recent work has shown that in certain bacterial species, mfd also plays roles in recombination, bacterial virulence, and the development of drug resistance.
Autophagy-Related Gene Pairs Signature for the Prognosis of Hepatocellular Carcinoma
Authors: Luo Yiming , Liu Furong , Han Shenqi , Qi Yongqiang , Hu Xinsheng , Zhou Chenyang , Liang Huifang , Zhang Zhiwei
Published: May 2021

Hepatocellular carcinoma (HCC) has been recognized as the third leading cause of cancer-related deaths worldwide. There is increasing evidence that the abnormal expression of autophagy-related genes plays an important role in the occurrence and development of HCC. Therefore, the study of autophagy-related genes can further elucidate the genetic drivers of cancer and provide valuable therapeutic targets for clinical treatment. In this study, we used 232 autophagy-related genes extracted from the Human Autophagy Database (HADb) and Molecular Signatures Database (MSigDB) to construct 1884 autophagy-related gene pairs. On this basis, we developed a prognostic model based on autophagy-related gene pairs using least absolute shrinkage and selection operator (LASSO) Cox regression to evaluate the prognosis of patients after liver cancer resection. We then used 845 liver cancer samples from three different databases to test the reliability of the risk signature through survival analysis, receiver operating characteristic (ROC) curve analysis, univariate and multivariate analysis. To further explore the underlying biological mechanisms, we conducted an enrichment analysis of autophagy-related genes. Finally, we combined the signature with independent prognostic factors to construct a nomogram. Based on the autophagy-related gene pair (ARGP) signature, we can divide patients into high- or low-risk groups. Survival analysis and ROC curve analysis verified the validity of the signature (AUC: 0.786—0.828). Multivariate Cox regression showed that the risk score can be used as an independent predictor of the clinical outcomes of liver cancer patients. Notably, this model has a more accurate predictive effect than most prognostic models for hepatocellular carcinoma. Moreover, our model is a powerful supplement to the HCC staging indicator, and a nomogram comprising both indicators can provide a better prognostic effect. Based on pairs of multiple autophagy-related genes, we proposed a prognostic model for predicting the overall survival rate of HCC patients after surgery, which is a promising prognostic indicator. This study confirms the importance of autophagy in the occurrence and development of HCC, and also provides potential biomarkers for targeted treatments.
Modulating Enzyme Function via Dynamic Allostery within Biliverdin Reductase B
Authors: Redzic Jasmina S. , Duff Michael R. , Blue Ashley , Pitts Todd M. , Agarwal Pratul , Eisenmesser Elan Zohar
Published: May 2021

The biliverdin reductase B (BLVRB) class of enzymes catalyze the NADPH-dependent reduction of multiple flavin substrates and are emerging as critical players in cellular redox regulation. However, the role of dynamics and allostery have not been addressed, prompting studies here that have revealed a position 15 Å away from the active site within human BLVRB (T164) that is inherently dynamic and can be mutated to control global micro-millisecond motions and function. By comparing the inherent dynamics through nuclear magnetic resonance (NMR) relaxation approaches of evolutionarily distinct BLVRB homologues and by applying our previously developed Relaxation And Single Site Multiple Mutations (RASSMM) approach that monitors both the functional and dynamic effects of multiple mutations to the single T164 site, we have discovered that the most dramatic mutagenic effects coincide with evolutionary changes and these modulate coenzyme binding. Thus, evolutionarily changing sites distal to the active site serve as dynamic “dials” to globally modulate motions and function. Despite the distal dynamic and functional coupling modulated by this site, micro-millisecond motions span an order of magnitude in their apparent kinetic rates of motions. Thus, global dynamics within BLVRB are a collection of partially coupled motions tied to catalytic function.
Ion Channels and Electrophysiological Properties of Astrocytes: Implications for Emergent Stimulation Technologies
Authors: McNeill Jessica , Rudyk Christopher , Hildebrand Michael E. , Salmaso Natalina
Published: May 2021

Astrocytes comprise a heterogeneous cell population characterized by distinct morphologies, protein expression and function. Unlike neurons, astrocytes do not generate action potentials, however, they are electrically dynamic cells with extensive electrophysiological heterogeneity and diversity. Astrocytes are hyperpolarized cells with low membrane resistance. They are heavily involved in the modulation of K+ and express an array of different voltage-dependent and voltage-independent channels to help with this ion regulation. In addition to these K+ channels, astrocytes also express several different types of Na+ channels; intracellular Na+ signaling in astrocytes has been linked to some of their functional properties. The physiological hallmark of astrocytes is their extensive intracellular Ca2+ signaling cascades, which vary at the regional, subregional, and cellular levels. In this review article, we highlight the physiological properties of astrocytes and the implications for their function and influence of network and synaptic activity. Furthermore, we discuss the implications of these differences in the context of optogenetic and DREADD experiments and consider whether these tools represent physiologically relevant techniques for the interrogation of astrocyte function.
High Chloride Burden and Clinical Outcomes in Critically Ill Patients With Large Hemispheric Infarction
Authors: Gwak Dong-Seok , Chung Inyoung , Kim Baik-Kyun , Lee Sukyoon , Jeong Han-Gil , Kim Yong Soo , Chae Heeyun , Park Chan-Young , Han Moon-Ku
Published: May 2021

Background: In general, disease severity has been found to be associated with abnormal chloride levels in critically ill patients, but hyperchloremia is associated with mixed results regarding patient-centered clinical outcomes. We aimed to investigate the impact of maximum serum chloride concentration on the clinical outcomes of critically ill patients with large hemispheric infarction (LHI).

Methods: We conducted a retrospective observational cohort study using prospective institutional neurocritical care registry data from 2013 to 2018. Patients with LHIs involving over two-thirds of middle cerebral artery territory, with or without infarction of other vascular territories, and a baseline National Institutes of Health Stroke Scale score of ≥13 were assessed. Those with a baseline creatinine clearance of <15 mL/min and required neurocritical care for <72 h were excluded. Primary outcome was in-hospital mortality. Secondary outcomes included 3-month mortality and acute kidney injury (AKI) occurrence. Outcomes were compared to different maximum serum chloride levels (5 mmol/L increases) during the entire hospitalization period using multivariable logistic regression analyses.

Results: Of 90 patients, 20 (22.2%) died in-hospital. Patients who died in-hospital had significantly higher maximum serum chloride levels than did those who survived up to hospital discharge (139.7 ± 8.1 vs. 119.1 ± 10.4 mmol/L; p < 0.001). After adjusting for age, sex, and Glasgow coma scale score, each 5-mmol/L increase in maximum serum chloride concentration was independently associated with an increased risk of in-hospital mortality (adjusted odds ratio (aOR), 4.34; 95% confidence interval [CI], 1.98–9.50; p < 0.001). Maximum serum chloride level was also an independent risk factor for 3-month mortality (aOR, 1.99 [per 5 mmol/L increase]; 95% CI, 1.42–2.79; p < 0.001) and AKI occurrence (aOR, 1.57 [per 5 mmol/L increase]; 95% CI, 1.18–2.08; p = 0.002).

Conclusions: High maximum serum chloride concentrations were associated with poor clinical outcomes in critically ill patients with LHI. This study highlights the importance of monitoring serum chloride levels and avoiding hyperchloremia in this patient population.
Physical Activity as a Predictor of Cognitive Decline in an Elderly Essential Tremor Cohort: A Prospective, Longitudinal Study
Authors: Radler Keith H. , Chapman Silvia , Zdrodowska Maria Anna , Dowd Hollie N. , Liu Xinhua , Huey Edward D. , Cosentino Stephanie , Louis Elan D.
Published: May 2021

Background:Essential tremor (ET), one of the most common neurological diseases, is associated with cognitive impairment. Surprisingly, predictors of cognitive decline in ET remain largely unidentified, as longitudinal studies are rare. In the general population, however, lower physical activity has been linked to cognitive decline.

Objectives:To determine whether baseline physical activity level is a predictor of cognitive decline in ET.

Methods:One hundred and twenty-seven ET cases (78.1 ± 9.5 years, range = 55–95), enrolled in a prospective, longitudinal study of cognition. At baseline, each completed the Physical Activity Scale for the Elderly (PASE), a validated, self-rated assessment of physical activity. Cases underwent an extensive battery of motor-free neuropsychological testing at baseline, 1.5 years, and 3 years, which incorporated assessments of cognitive subdomains. Generalized estimating equations (GEEs) were used to assess the predictive utility of baseline physical activity for cognitive change.

Results:Mean follow-up was 2.9 ± 0.4 years (range = 1.3–3.5). In cross-sectional analyses using baseline data, lower physical activity was associated with lower overall cognitive function as well as lower cognitive scores in numerous cognitive domains (memory, language, executive function, visuospatial function and attention, allp< 0.05). In adjusted GEE models, lower baseline physical activity level significantly predicted overall cognitive decline over time (p=0.047), and declines in the subdomains of memory (p= 0.001) and executive function (p= 0.03).

Conclusions:We identified reduced physical activity as a predictor of greater cognitive decline in ET. The identification of risk factors often assists clinicians in determining which patients are at higher risk of cognitive decline over time. Interventional studies, to determine whether increasing physical activity could modify the risk of developing cognitive decline in ET, may be warranted.
Satisfaction of Telehealth in Patients With Established Neuromuscular Disorders
Authors: Hooshmand Sara , Cho Junsang , Singh Shivangi , Govindarajan Raghav
Published: May 2021

Introduction/aims: Determine established neuromuscular disease patients' satisfaction with telehealth during the COVID-19 pandemic.

Methods: We received 50 completed Utah telehealth satisfaction surveys from a cohort of 90 from April 2020 to June 2020. Returning neuromuscular disease patients rated seven aspects from 1 (strongly disagree) to 5 (strongly agree): Communication, timeliness of physician, picture quality, sound quality, protection of privacy, the comfort of the physical exam, the ease of healthcare, and whether patients would prefer “in-person” visits despite safety precaution. A favorable response was defined as a response of “Agree” or “Strongly Agree” to the survey questions. An independent t-test, Fisher's or chi-square test were used to compare demographic factors on outcomes for each survey question.

Results: The average age was 47.54 ± 20.63, 54% were female, 70% from rural areas, 60% had family present “webside,” and 14% had family present remotely. The majority of patients reported “Agree” or “Strongly Agree” to each survey question assessing their telehealth satisfaction, except for whether patients preferred in-person appointments. Demographic factors, including location and clinical diagnosis, did not influence survey responses.

Discussion: The vast majority of established neuromuscular disease patients responded favorably to their telehealth experience during the COVID-19 pandemic.
Results From an Italian Expanded Access Program on Cannabidiol Treatment in Highly Refractory Dravet Syndrome and Lennox–Gastaut Syndrome
Authors: Iannone Luigi Francesco , Arena Gabriele , Battaglia Domenica , Bisulli Francesca , Bonanni Paolo , Boni Antonella , Canevini Maria Paola , Cantalupo Gaetano , Cesaroni Elisabetta , Contin Manuela , Coppola Antonietta , Cordelli Duccio Maria , Cricchiuti Giovanni , De Giorgis Valentina , De Leva Maria Fulvia , De Rinaldis Marta , d'Orsi Giuseppe , Elia Maurizio , Galimberti Carlo Andrea , Morano Alessandra , Granata Tiziana , Guerrini Renzo , Lodi Monica A. M. , La Neve Angela , Marchese Francesca , Masnada Silvia , Michelucci Roberto , Nosadini Margherita , Pilolli Nicola , Pruna Dario , Ragona Francesca , Rosati Anna , Santucci Margherita , Spalice Alberto , Pietrafusa Nicola , Striano Pasquale , Tartara Elena , Tassi Laura , Papa Amanda , Zucca Claudio , Russo Emilio , Mecarelli Oriano ,   The CBD LICE Italy Study Group
Published: May 2021

Background: Purified cannabidiol (CBD) was administered to highly refractory patients with Dravet (DS) or Lennox–Gastaut (LGS) syndromes in an ongoing expanded access program (EAP). Herein, we report interim results on CBD safety and seizure outcomes in patients treated for a 12-month period.

Material and Methods: Thirty centers were enrolled from December 2018 to December 2019 within the open-label prospective EAP up to a maximum of 25 mg/kg per day. Adverse effects and liver function tests were assessed after 2 weeks; 1, 3, and 6 months of treatment; and periodically thereafter. Seizure endpoints were the percentage of patients with ≥50 and 100% reduction in seizures compared to baseline.

Results: A total of 93 patients were enrolled and included in the safety analysis. Eighty-two patients [27 (32.9%) DS, 55 (67.1%) LGS] with at least 3 months of treatment have been included in the effectiveness analysis; median previously failed antiseizure medications was eight. Pediatric and adult patients were uniformly represented in the cohort. At 3-month follow-up, compared to the 28-day baseline period, the percentage of patients with at least a 50% reduction in seizure frequency was 40.2% (plus 1.2% seizure-free). Retention rate was similar according to diagnosis, while we found an increased number of patients remaining under treatment in the adult group. CBD was mostly coadministered with valproic acid (62.2%) and clobazam (41.5%). In the safety dataset, 29 (31.2%) dropped out: reasons were lack of efficacy [16 (17.2%)] and adverse events (AEs) [12 (12.9%)], and one met withdrawal criteria (1.1%). Most reported AEs were somnolence (22.6%) and diarrhea (11.9%), followed by transaminase elevation and loss of appetite.

Conclusions: CBD is associated with improved seizure control also in a considerable proportion of highly refractory patients with DS and LGS independently from clobazam use. Overall, CBD safety and effectiveness are not dose-related in this cohort.
Scaphium affine Ethanol Extract Induces Anoikis by Regulating the EGFR/Akt Pathway in HCT116 Colorectal Cancer Cells
Authors: Kawk Hye Won , Nam Gun-He , Kim Myeong Jin , Kim Sang-Yong , Kim Young-Min
Published: May 2021

Scaphium affine ethanol extracts (SAE) is a species that has been shown to contain various physiological effects; however, its anticancer effects have yet to be revealed. We qualitatively evaluated β-sitosterol in SAE through high-performance liquid chromatography (HPLC). The cytotoxicity in HCT116 and HT29 colorectal cancer cells and CCD841 normal colon cells was confirmed through WST-1 assays. Selective cytotoxicity was observed in colorectal cancer cells, with greater cytotoxicity demonstrated in the HCT116 cell line. As such, the HCT116 colorectal cell line was selected for subsequent experiments. After HCT116 cells were treated with SAE, it was confirmed that the apoptosis rate was increased in a SAE dose-dependent manner through Annexin V assay. SAE further showed dose-dependent suppression of invasion through invasion assays. Anoikis induction through the EGFR/Akt pathway in HCT116 colorectal cancer cells was confirmed by Western blotting. The tumor suppressive effects of SAE was assessed in vivo using a xenograft model of human HCT116 colorectal cancer cells. As a result, we confirmed that SAE decreased tumor size in a dose-dependent manner and that p-EGFR and cleaved-caspase 3 in tumors were also regulated in a dose-dependent manner. This study showed that SAE, by containing β-sitosterol with proven anticancer effects, induces anoikis through the EGFR/Akt pathway in HCT116 colorectal cancer cells both in vitro and in vivo.
Durable Response to Immunotherapy With Antiangiogenic Drug in Large-Cell Lung Carcinoma With Multiple Fulminant Postoperative Metastases: A Case Report
Authors: Luo Zhilin , Zhang Hong , Xiao Yajie , Wang Rui , Zhang Liping , Huang Chenglu , Cao Yu , Sun Chao , Zhao Yongtian , Lin Hanqing , Wu Dongfang , Wang Tianhu
Published: May 2021

Immunotherapy alone or chemo-immunotherapy has recently been recommended for treating advanced lung carcinoma in patients without driver mutations. However, the efficacy of immunotherapy and molecular mechanism in large-cell lung cancer (LCLC) remains unclear. Here, we reported a rare case of multiple fulminant postoperative body and mouth metastases in LCLC treating with combination immunotherapy. Initially, the patient was diagnosed as early stage LCLC and underwent a radical resection of the right lower lobe. Just one month later, multiple fulminant body and mouth lesions appeared in the right upper arm, right elbow, right waist, and tongue root. Meanwhile, serum neuron specific enolase (NSE) concentration dramatically increased from 12.12 to 30.14 ng/ml. Immumohistochemistry findings demonstrated moderate PD-L1 expressions with tumor proportion score (TPS), while next-generation sequencing indicated moderate tumor mutational burden (TMB) levels and gene mutations in PBRM1 L1230P and TP53 L194R of both foci. Besides, loss of heterozygosity (LOH) at human leukocyte antigen (HLA) class I (HLA-A*02:03, HLA-B*55:02 and HLA-C*12:03) were detected in the right upper arm metastasis, which may facilitate malignant postoperative metastases in this case. Notably, this patient received combination therapy with anti-PD-1 antibody sintilimab plus anlotinib, and achieved a partial response for at least 12 months. Using an integrated computational method, the mutant peptide TEIPENDIPL derived from PBRM1 L1230P was predicted to be a specific neoantigen and could still be presented by HLA-B*40:01. This case suggests that immunotherapy plus antiangiogenic drug may provide an alternative therapeutic option for advanced LCLC patients without common gene mutations.