bluuebunny/crossref_metadata_2025_split huggingface dataset:
Odontogenic Necrotizing Fasciitis of Face and Scalp
Authors: Amponsah Emmanuel Kofi , Sodnom-Ish Buyanbileg , Nguyen Truc Thi Hoang , Kim Soung Min 
Published: February 2021

Abstract
Necrotizing fasciitis of the face and scalp is a severe bacterial infection that can result in long-term morbidity or even mortality if not properly managed. In a third-world country like Ghana, where most of the population relies on daily income for livelihood, citizens with diseases that have long-term morbidity suffer financial difficulty, particularly when the patient is the breadwinner.
This brief clinical study demonstrates the severity of necrotizing fasciitis of the face and scalp originated from oral infection, and its capability to affect any part of the body if proper treatment is not established at early onset of disease. Correct diagnosis, patient education, early antibiotic treatment, and timely surgery are crucial for controlling infection and for preventing irreparable damage. Therefore, public education is crucial in preventing such infection by discouraging use of over-the-counter medication in such situations.
Outcomes of COVID-19 in Solid Organ Transplant Recipients: A Propensity-matched Analysis of a Large Research Network
Authors: Hadi Yousaf B. , Naqvi Syeda F.Z. , Kupec Justin T. , Sofka Sarah , Sarwari Arif 
Published: February 2021

Background.
Organ transplant recipients comprise an immunocompromised and vulnerable cohort. Outcomes of coronavirus disease 2019 (COVID-19) in solid organ transplant (SOT) recipients remain understudied.

Methods.
We used a multicenter federated research network to compare clinical outcomes of COVID-19 in patients with SOT to a propensity--matched cohort of patients without SOT.

Results.
We identified 2307 SOT recipients and 231 047 nontransplant patients with COVID-19. Transplant patients were more likely to be male individuals, older, have a body mass index >30 kg/m2, and have comorbid hypertension, diabetes, nicotine dependence, heart failure, and ischemic heart disease compared with the nontransplant group (P < 0.05). One-to-one matching was performed for diabetes, hypertension, chronic lung diseases, race, nicotine dependence, heart failure, ischemic heart disease, and gender. There was no difference in the composite outcome of intubation or mechanical ventilation at 30 days (risk ratio [RR], 1.04; 95% confidence interval [CI], 0.86-1.26) or 60 days (RR, 1.03; 95% CI, 0.86-1.24) between the 2 groups. Hospitalization rate was higher in the transplant cohort (30.97% versus 25.47%; RR, 1.22; 95% CI, 1.11-1.34). There was no difference in mortality at 30 days (6.45% versus 5.29%; RR, 1.22; 95% CI, 0.88-1.68) or 60 days postdiagnosis (RR, 1.05; 95% CI, 0.83-1.32). More patients in the SOT group developed acute renal injury compared with non-SOT cohort (24.73% versus 14.29%; RR, 1.73; 95% CI, 1.53-1.96).

Conclusions.
Patients with SOT have high COVID-19-related mortality; however, propensity-matched analyses reveal that this increased risk is secondary to higher burden of comorbidities. SOT status independently increases risk of hospital admission and acute kidney injury.
SARS-CoV-2-specific Cell-mediated Immunity in Kidney Transplant Recipients Recovered From COVID-19
Authors: Fernández-Ruiz Mario , Olea Beatriz , Giménez Estela , Laguna-Goya Rocío , Trujillo Hernando , Caravaca-Fontán Fernando , Gutiérrez Eduardo , López-Medrano Francisco , Remigia María José , Almendro-Vazquez Patricia , Polanco Natalia , González Esther , Ruiz-Merlo Tamara , Parra Patricia , San Juan Rafael , Andrés Amado , Navarro David , Aguado José María 
Published: February 2021

Background.
The magnitude and kinetics of severe acute respiratory syndrome coronavirus 2–specific cell-mediated immunity (SARS-CoV-2-CMI) in kidney transplant (KT) recipients remain largely unknown.

Methods.
We enumerated SARS-CoV-2-specific interferon-γ-producing CD69+ CD4+ and CD8+ T cells at months 4 and 6 from the diagnosis of coronavirus disease 2019 (COVID-19) in 21 KT recipients by intracellular cytokine staining. Overlapping peptides encompassing the SARS-CoV-2 spike (S) glycoprotein N-terminal 1- to 643-amino acid sequence and the membrane protein were used as stimulus. SARS-CoV-2 IgG antibodies targeting the S1 protein were assessed by ELISA at month 6.

Results.
Detectable (≥0.1%) SARS-CoV-2-specific CD4+ T-cell response was found in 57.1% and 47.4% of patients at months 4 and 6. Corresponding rates for CD8+ T cells were 19.0% and 42.1%, respectively. Absolute SARS-CoV-2-specific T-cell counts increased from month 4 to month 6 in CD8+ (P = 0.086) but not CD4+ subsets (P = 0.349). Four of 10 patients with any detectable response at month 4 had lost SARS-CoV-2-CMI by month 6, whereas 5 of 9 patients mounted SARS-CoV-2-CMI within this period. All but 2 patients (89.5%) tested positive for SARS-CoV-2 IgG. Patients lacking detectable SARS-CoV-2-specific CD4+ response by month 6 were more likely to be under tacrolimus (100.0% versus 66.7%; P = 0.087) and to have received tocilizumab for the previous COVID-19 episode (40.0% versus 0.0%; P = 0.087).

Conclusions.
Although still exploratory and limited by small sample size, the present study suggests that a substantial proportion of KT recipients exhibited detectable SARS-CoV-2-CMI after 6 months from COVID-19 diagnosis.
A Novel Multidrug Combination Mitigates Rat Liver Steatosis Through Activating AMPK Pathway During Normothermic Machine Perfusion
Authors: Xu Min , Zhou Fangyu , Ahmed Ola , Upadhya Gundumi A. , Jia Jianluo , Lee Choonghee , Xing Jianwei , Ye Li , Shim So Hee , Zhang Zhengyan , Byrnes Kathleen , Wong Brian , Kim Jae-Sung , Lin Yiing , Chapman William C. 
Published: February 2021

Background.
Hepatic steatosis is now the leading cause of liver discards in deceased donors. Previous studies [Yarmush formula (Y) defatting] have successfully reduced the fat content by treating rat steatotic livers on extracorporeal normothermic machine perfusion (NMP) with a multidrug combination including the GW compounds that were linked to an increased risk of carcinogenesis.

Methods.
We developed a novel multidrug combination by replacing the GW compounds with 2 polyphenols, epigallocatechin-3-gallate (E) and resveratrol (R). Sixteen rat livers were placed on NMP and assigned to control, Y defatting, Y + E + R defatting, or Y′−GW + E + R defatting groups (Y′−GW = 90% dose-reduced Y defatting, n = 4/group).

Results.
All livers in defatting groups had significant decreases in hepatic triglyceride content at the end of the experiment. However, livers treated with our novel Y′−GW + E + R combination had evidence of increased metabolism and less hepatocyte damage and carcinogenic potential. Our Y′−GW + E + R combination had increased phosphorylation of AMP-activated protein kinase (P = 0.019) and acetyl-CoA carboxylase (P = 0.023) compared with control; these were not increased in Y + E + R group and actually decreased in the Y group. Furthermore, the Y′−GW + E + R group had less evidence of carcinogenic potential with no increase in AKT phosphorylation compared with control (P = 0.089); the Y (P = 0.031) and Y + E + R (P = 0.035) groups had striking increases in AKT phosphorylation. Finally, our Y′−GW + E + R showed less evidence of hepatocyte damage with significantly lower perfusate alanine aminotransferase (P = 0.007) and aspartate aminotransferase (P = 0.014) levels.

Conclusions.
We have developed a novel multidrug combination demonstrating promising defatting efficacy via activation of the AMP-activated protein kinase pathway with an optimized safety profile and reduced hepatotoxicity during ex vivo NMP.
Rituximab Was Effective for Treatment of Anti–N-Methyl-d-Aspartate Receptor Encephalitis in Early Adolescence in Initially Suspected Dissociative Disorder
Authors: Shibata Takashi , Kawai Hiroki , Sakamoto Shinji , Tsutsui Ko , Kanbayashi Takashi , Tanaka Keiko , Takaki Manabu 
Published: February 2021

Objectives
Anti–N-methyl-d-aspartate receptor (NMDAR) encephalitis is an increasingly recognized etiology of psychiatric symptoms. Because patients with anti-NMDAR encephalitis frequently show aggression, mania, hallucination, depression, or delusion, they are initially diagnosed with schizophrenia or mood disorders. There is only 1 case report of an initially diagnosed dissociative disorder.

Methods
We obtained consent for the presentation and have not identified individuals for ethical reasons.

Results
We first report an adolescent female patient with anti-NMDAR encephalitis who was initially suspected of having dissociative disorder but was responsive to immunotherapies including rituximab. In this case, her symptoms and electroencephalogram findings were proportional to the antibody titer in the cerebrospinal fluid.

Conclusions
It is important to consider the possibility of autoimmune encephalitis and immunotherapy including rituximab in cases of not only acute psychosis but also dissociation.
Grimontia sedimenti sp. nov., isolated from benthic sediments near coral reefs south of Kuwait
Authors: Mahmoud Huda , Jose Liny , Eapen Susan 
Published: February 2021

A Gram-stain-negative, rod and rod-curved shaped motile bacterium designated strain S25T was obtained from benthic sediment collected near the Kubbar Island coral reefs south of Kuwait. Phenotypic analysis revealed that strain S25T was slightly halophilic, mesophilic and facultative anaerobic, fermenting d-glucose, d-ribose, d-mannose, d-mannitol, maltose, fructose, gentiobiose, cellobiose, melibiose, trehalose and sucrose. It was positive for oxidase and indole production and negative for arginine dihydrolase and lysine and ornithine decarboxylases. It contained C16 : 1
ω7c/C16 : 1
ω6c (summed feature 3), C18 : 1 ω7c (summed feature 8) and C16 : 0 as the major fatty acids. Strain S25T grew optimally at 30 °C and pH 8 in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA sequences revealed that strain S25T is related to species of the genus

Grimontia

, having 99.15 % similarity to ‘Grimontia indica’ AK16T, 99.08 % to

Grimontia celer

96-237T and 98.66 % to

Grimontia marina

IMCC 5001T. The DNA G+C content was 48.8 mol% and the full genome analysis for the strain S25T showed that the bacterium has a genome size of 5 158 621 bp and contains 4730 predicted protein-encoding genes. The average nucleotide identity values between the S25T genome and the genomes of its nearest matches ranged between 81.39 and 94.16 %. The strain was distinguishable from the phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strain S25T represents a novel species in the genus

Grimontia

, for which the name Grimontia sedimenti sp. nov. is proposed. The type strain of Grimontia sedimenti is S25T (=DSM 28878T=LMG 28315T).
Miltefosine enhances infectivity of miltefosine-resistantLeishmania infantumby attenuating innate immune recognition
Authors: Bulté Dimitri , Bockstal Lieselotte Van , Dirkx Laura , Van den Kerkhof Magali , Trez Carl De , Timmermans Jean-Pierre , Hendrickx Sarah , Maes Louis , Caljon Guy 
Published: February 2021

AbstractMiltefosine (MIL) is currently the only oral drug available to treat visceral leishmaniasis but its use as first-line monotherapy has been compromised by an increasing treatment failure. Despite the scarce number of resistant clinical isolates, MIL-resistance by mutations in a single aminophospholipid transporter gene can easily be selected in a laboratory environment. These mutations result in a reduced survival in the mammalian host, which can partially be restored by exposure to MIL, suggesting a kind of drug-dependency. To enable a combined study of the infection dynamics and underlying immunological events for differentialin vivosurvival, firefly luciferase (PpyRE9) / red fluorescent protein (DsRed) double-reporter strains were generated of MIL-resistant (MIL-R) and syngeneic MIL-sensitive (MIL-S)Leishmania infantum. Results in C57Bl/6 and BALB/c mice show that MIL-R parasites induce an increased innate immune response that is characterized by enhanced influx and infection of neutrophils, monocytes and dendritic cells in the liver and elevated serum IFN-γ levels, finally resulting in a less efficient establishment in liver macrophages. The elevated IFN-γ levels were shown to originate from an increased response of hepatic NK and NKT cells to the MIL-R parasites. In addition, we demonstrated that MIL could increase thein vivofitness of MIL-R parasites by lowering NK and NKT cell activation, leading to a reduced IFN-γ production. These data provide an immunological basis for the MIL-R-associated attenuated phenotype and for the peculiar drug-dependency that may constitute one of the mechanisms of treatment failure.ImportanceRecently, our laboratory demonstrated anin vivofitness loss of experimentally selected MIL-R parasites in both the sand fly vector and vertebrate host. These findings could explain the scarce number of MIL-R clinical isolates. Surprisingly, MIL-R parasites developed a MIL-dependency which could partially rescue their fitness loss and which may constitute a mechanism of treatment failure. This research aimed to better understand the immunological basis of the attenuated phenotype and the effect of MIL on infectivity traits. Together, this study provides new insights into the complex interplay between the parasite, drug and host and discloses an immune-related mechanism of treatment failure.
A comparison of denoising methods in dynamic MRS using pseudo-synthetic data
Authors: Rowland Benjamin C. , Sreepada Lasya , Lin Alexander P. 
Published: February 2021

PurposeMR spectroscopy of dynamic systems is limited by low signal to noise. Denoising along a series of acquired spectra exploits their temporal correlation to improve the quality of individual spectra, and reduce errors in fitting metabolite peaks. In this study we compare the performance of several denoising methods.MethodsSix different denoising methods were considered: SIFT (Spectral Improvement by Fourier Thresholding), HSVD (Hankel Singular Value Decomposition), spline, wavelet, sliding window and sliding Gaussian. Pseudo-synthetic data was constructed to mimic 31Phosphorus spectra from exercising muscle. For each method the optimal tuning parameters were determined for SNRs of 2, 5, 10 and 20 using a Monte Carlo approach. Denoised data from each method was then fitted using the AMARES algorithm and the results compared to the pseudo-synthetic ground truth.ResultsAll six methods produced improvements in both fitting accuracy and agreement with the ground truth, compared to unprocessed noisy data. The least effective methods, SIFT and HSVD, achieved around 10-20% reduction in RMS error, while the most effective, Spline, reduced RMS error by 70%. The improvement from denoising was typically greater for lower SNR data.ConclusionsIndirect time domain denoising of dynamic MR spectroscopy data can substantially improve subsequent metabolite fitting. Spline-based denoising was found to be the most flexible and effective technique.
The nonstructural protein 5 of coronaviruses antagonizes GSDMD-mediated pyroptosis by cleaving and inactivating its pore-forming p30 fragment
Authors: Shi Fushan , Lv Qian , Wang Tingjun , Xu Jidong , Xu Wei , Shi Yuhua , Fu Xinyu , Yang Tianming , Yang Yang , Zhuang Lenan , Fang Weihuan , Gu Jinyan , Li Xiaoliang 
Published: February 2021

AbstractCoronaviruses (CoV) are a family of RNA viruses that typically cause respiratory, enteric and hepatic diseases in animals and humans. Here, we used porcine epidemic diarrhea virus (PEDV) as a model of coronaviruses (CoVs) to illustrate the reciprocal regulation between CoVs infection and pyroptosis. For the first time, we clarified the molecular mechanism of porcine Gasdermin D (pGSDMD)-mediated pyroptosis and demonstrated that amino acids T239 and F240 within pGSDMD-p30 are critical for pyroptosis. Furthermore, 3C-like protease Nsp5 from SARS-CoV-2, MERS-CoV, PDCoV and PEDV can cleave human/porcine GSDMD at the Q193-G194 junction upstream of the caspase-1 cleavage site to produce two fragments which fail to trigger pyroptosis or inhibit viral replication. Thus, we provide clear evidence that coronoviruses may utilize viral Nsp5-GSDMD pathway to help their host cells escaping from pyroptosis, protecting the replication of the virus during the initial period, which suggest an important strategy for coronoviruses infection and sustain.
Quasi-species evolution maximizes genotypic reproductive value (not fitness or flatness)
Authors: Smerlak Matteo 
Published: February 2021

AbstractGrowing efforts to measure fitness landscapes in molecular and microbial systems are motivated by a longstanding goal to predict future evolutionary trajectories. Sometimes under-appreciated, however, is that the fitness landscape and its topography do not by themselves determine the direction of evolution: under sufficiently high mutation rates, populations can climb the closest fitness peak (survival of the fittest), settle in lower regions with higher mutational robustness (survival of the flattest), or even fail to adapt altogether (error catastrophes). I show that another measure of reproductive success, Fisher’sreproductive value, resolves the trade-off between fitness and robustness in the quasi-species regime of evolution: to forecast the motion of a population in genotype space, one should look for peaks in the (mutation-rate dependent) landscape of genotypic reproductive values—whether or not these peaks correspond to local fitness maxima or flat fitness plateaus. This new landscape picture turns quasi-species dynamics into an instance of non-equilibrium dynamics, in the physical sense of Markovian processes, potential landscapes, entropy production, etc.
Genetic variation in haemoglobin alters breathing in high-altitude deer mice
Authors: Ivy Catherine M. , Wearing Oliver H. , Natarajan Chandrasekhar , Schweizer Rena M. , Gutiérrez-Pinto Natalia , Velotta Jonathan P. , Campbell-Staton Shane C. , Petersen Elin E. , Fago Angela , Cheviron Zachary A. , Storz Jay F. , Scott Graham R. 
Published: February 2021

ABSTRACTPhysiological systems often have emergent properties but the effects of genetic variation on physiology are often unknown, which presents a major challenge to understanding the mechanisms of phenotypic evolution. We investigated thein vivoeffects on respiratory physiology of genetic variants in haemoglobin (Hb) that contribute to hypoxia adaptation in high-altitude deer mice (Peromyscus maniculatus). We created F2inter-population hybrids of highland and lowland deer mice to test the phenotypic effects of α- and β-globin variants on a mixed genetic background. High-altitude genotypes were associated with breathing phenotypes that enhance O2uptake in hypoxia, including a deeper more effective breathing pattern and an augmented hypoxic ventilatory response. These effects could not be explained by erythrocyte Hb-O2affinity or globin gene expression in the brainstem. Therefore, adaptive variation in haemoglobin can have unexpected effects on physiology that are distinct from the canonical function of this protein in circulatory O2transport.
Low rank approximation of difference between correlation matrices by using inner product
Authors: Tanioka Kensuke , Hiwa Satoru 
Published: February 2021

ABSTRACTIntroductionIn the domain of functional magnetic resonance imaging (fMRI) data analysis, given two correlation matrices between regions of interest (ROIs) for the same subject, it is important to reveal relatively large differences to ensure accurate interpretations. However, clustering results based only on difference tend to be unsatisfactory, and interpreting features is difficult because the difference suffers from noise. Therefore, to overcome these problems, we propose a new approach for dimensional reduction clustering.MethodsOur proposed dimensional reduction clustering approach consists of low rank approximation and a clustering algorithm. The low rank matrix, which reflects the difference, is estimated from the inner product of the difference matrix, not only the difference. In addition, the low rank matrix is calculated based on the majorize-minimization (MM) algorithm such that the difference is bounded from 1 to 1. For the clustering process, ordinalk-means is applied to the estimated low rank matrix, which emphasizes the clustering structure.ResultsNumerical simulations show that, compared with other approaches that are based only on difference, the proposed method provides superior performance in recovering the true clustering structure. Moreover, as demonstrated through a real data example of brain activity while performing a working memory task measured by fMRI, the proposed method can visually provide interpretable community structures consisted of well-known brain functional networks which can be associated with human working memory system.ConclusionsThe proposed dimensional reduction clustering approach is a very useful tool for revealing and interpreting the differences between correlation matrices, even if the true difference tends to be relatively small.
Spontaneous Facet Joint Osteoarthritis in NFAT1-Mutant Mice
Authors: Wang Jinxi , Lu Qinghua , Mackay Matthew J. , Liu Xiangliang , Feng Yi , Burton Douglas C. , Asher Marc A. 
Published: February 2021

ABSTRACTObjectivesAlthough rodent models of traumatically or chemically induced intervertebral facet joint osteoarthritis (FJOA) were previously described, the characteristics of spontaneous FJOA animal models have not been documented. This study aimed to identify the characteristics of a murine model of spontaneous FJOA and its underlying mechanisms.MethodsThe lumbar facet joints of mutant mice carrying a disrupted NFAT1 (nuclear factor of activated T cells 1) allele and of wild-type control mice were examined by histochemistry, quantitative gene expression analysis, immunohistochemistry, and histomorphometry using a novel FJOA scoring system at 2, 6, 12, and 18 months of age. The reproducibility of the FJOA scoring system was analyzed by inter-observer and intra-observer variability tests. Tissue-specific histomorphometric and gene expression changes were statistically analyzed.ResultsNFAT1-mutant facet joints displayed dysfunction of articular chondrocytes and synovial cells with aberrant gene and protein expression in cartilage and synovium as early as 2 months, followed by osteoarthritic structural changes such as articular surface fissuring and chondro-osteophyte formation at 6 months. Deeper cartilage lesions, synovitis, separation of cartilage from thickened subchondral bone, and tissue-specific molecular and cellular alterations in NFAT1-mutant facet joints became evident at 12 and 18 months. Osteoarthritic structural changes were not detected in wild-type facet joints at any ages, though age-related cartilage degeneration was observed at 18 months.ConclusionsUsing NFAT1-mutant mice, this study has identified for the first time an animal model of spontaneous FJOA with age-dependent osteoarthritic characteristics, developed the first FJOA scoring system, and elucidated the molecular mechanisms of NFAT1 mutation-mediated FJOA.