bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and validation of an angiogenesis-related signature associated with preeclampsia by bioinformatic analysis
Authors: Ma Jiancai , Wu Hong , Yang Xiaofang , Zheng Lulu , Feng Haiqin , Yang Liping
Published: February 2023

Preeclampsia (PE) is a pregnancy disorder with high morbidity and mortality rates for both mothers and newborns. This study explores potential diagnostic indicators of PE.

We downloaded the messenger ribonucleic acid profiles of the GSE75010 dataset from the Gene Expression Omnibus database, and used placenta samples to carry out different analyses including differential expression, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analyses. Least absolute shrinkage and selection operator regression was constructed and the receiver operating characteristic curve was drawn to evaluate the accuracy of the model. An external validation was conducted to prove the stability of the risk model.

We found 140 angiogenesis-related genes and identified 29 angiogenesis-related genes between the 2 groups, including 12 upregulated genes and 17 downregulated genes. In addition, we established a 12-gene risk signature, which has a high accuracy in predicting PE during pregnancy (area under curve = 0.90). The immune infiltration characteristics are differentially distributed in the 2 groups, which may be the cause of hypertension during pregnancy. The external validation with the GSE25906 dataset confirmed the high accuracy of our model (area under curve = 0.87).

Our results outline the characteristics of a set of genes potentially involved in PE and its subgroups, contributing to a better understanding of the molecular mechanisms of PE.
Clinical effect and safety of thread embedding acupuncture on facial nerve palsy sequelae: A retrospective observational study
Authors: Ko Min-Jung , Goo Bonhyuk , Kim Jung-Hyun , Nam Sang-Soo
Published: February 2023

The purpose of this study was to investigate the clinical effect and safety of thread embedding acupuncture (TEA) in patients with facial nerve palsy sequelae. This was a retrospective observational study on 82 patients treated with TEA from January 2021 to May 2022. The Facial Disability Index (FDI) reported by patients and Sunnybrook Facial Grading System scores assessed by clinical practitioners were used to evaluate the intensity of facial movements, functional problems, and psychosocial status. One-way repeated measure analysis of variance showed that the Sunnybrook Facial Grading System scores improved significantly following the 2nd to 6th TEA treatments (Txs). FDI scores also showed significant increases except for the 4th Tx. Additionally, the physical scores improved significantly among the subscales of FDI, but the social/well-being scores did not. There were no reported serious adverse events or adverse events requiring medical Tx. TEA is a safe Tx that has a clinically cumulative effect, in terms of patient-oriented self-assessment of functional problems and objective facial movements, for treating facial nerve palsy sequelae.
Bioinformatics identify the role of chordin-like 1 in thyroid cancer
Authors: Yu Jia-Wei , Pang Rui , Liu Bo , Zhang Liang , Zhang Jie-Wu
Published: February 2023

The abnormal expression of chordin-like 1 (CHRDL1) is identified in many cancers, while the effect of CHRDL1 in thyroid cancer (THCA) remains unclear. The University of California Santa Cruz, Gene Expression Profiling Interactive Analysis, University of Alabama at Birmingham Cancer, and Gene Expression Omnibus database (GSE33570, GSE33630, and GSE60542) were used for determining the mRNA and methylation expression of CHRDL1 in tumor and normal tissues. Human Protein Atlas was used for exploring the protein expression level of CHRDL1. The genes correlated to CHRDL1 were assessed by cBioPortal database. The prognostic value of CHRDL1 was evaluated through Kaplan–Meier method, cox regression, and nomogram analysis. Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and gene set enrichment analysis were used for predicting potential function of CHRDL1. The relationship between CHRDL1 and immune cell infiltration was determined by Pearson method. The downregulated mRNA and protein expressions of CHRDL1 were identified in THCA through the analysis of data from The Cancer Genome Atlas, Gene Expression Omnibus, and Human Protein Atlas database. The survival analysis showed that the CHRDL1 expression significantly affected disease-free interval (DFI) and progression-free interval, and CHRDL1 was an independent predictor of DFI. Besides, we found that C-C motif chemokine ligand 21 could significantly affect DFI time when it was co-expressed with CHRDL1. Additionally, the function of CHRDL1 was enriched in cell migration, apoptosis, and immune cell receptor. The downregulated expression of CHRDL1 was observed in THCA and caused poor prognosis. CHRDL1 may be involved in signal pathway related to cancer development and immune response, which suggested it could be a potential biomarker.
Impact of the COVID-19 pandemic on lifestyle and mental state in patients with schizophrenia: A retrospective study
Authors: Cheng Xiaoling , Huang Xiaoling , Wu Xinghu , Lin Sulan
Published: February 2023

The corona virus disease 2019 pandemic’s movement restrictions have an effect on people’s lifestyles and mental health, and the most susceptible, such as persons with schizophrenia, are more subject to external influences. To analyze the lifestyle, anxiety, depression and stress status of inpatients with schizophrenia during corona virus disease 2019. A total of 205 patients with stable schizophrenia who were hospitalized during the epidemic period were selected. The general epidemiological information was recorded, and the depression screening scale (Patient Health Questionnaire-9), the Generalized Anxiety Disorder Scale-7, and the perceived stress scale were used to determine the mental status and stress level of the included patients. Restricted physical activity and perceptual bias might result in decreased food intake, higher body mass index, and increased psychotropic medicine dosages. According to Pearson correlation analysis, stress perception was positively connected with anxiety and depression scores. The anxiety score was positively associated with the depression score, indicating that stress influenced the patient’s emotional alterations. During the pandemic, the lifestyle and psychological load of people with schizophrenia may be impacted. Medical personnel should be alert to changes in anxiety, depression, and stress in patients with schizophrenia and take appropriate action.
Outcome analysis of ICSI assisted pregnancy using testicular sperm versus ejaculated sperm in man with severe oligozoospermia in the same ART cycle: A case report
Authors: Li Liang , Zhao Shi bin
Published: February 2023

Rationale:

Intracytoplasmic sperm injection (ICSI) has become the most common method for couples with male factor infertility, and source of sperm for the procedure have evolved over time. but few have examined testicular sperm extraction vs. ejaculated sperm use for severe oligozoospermia in the same assisted reproductive technology (ART) cycle.

Patient concerns:

Here, we evaluated the clinical outcomes after ICSI with testicular sperm or ejaculated in man with severe oligozoospermia in the same ART cycle. A couple who had failed the first ART cycle with ejaculated sperm, using the freshly ejaculated sperm and testicular sperm for ICSI during the second ART cycle by lack of enough sperm to fertilize in an ICSI attempt.

Diagnoses:

The patient was diagnosed with severe oligozoospermia, and routine semen analysis revealed sperm concentration is less than 2 million/mL.

Interventions:

The patient using testicular sperm versus ejaculated sperm with ICSI assisted pregnancy in the same ART cycle.

Outcomes:

We found that superior cleavage rate, number of embryos transferred and blastocyst rate with the use of testicular rather than ejaculated sperm-ICSI in the couple. The results described here suggest that use of testicular sperm may improve biologic outcomes, especially for couples with male-partner oligozoospermia who previous ICSI failures.

Lessons:

Our case report supported the efficacy of testicular sperm preference over ejaculated sperm for ICSI in men with severe male factor infertility. It is a paradigm shift concerning the use of ejaculated sperm as the preferable source of sperm for ICSI, add to the small amount of literature on testicular sperm extraction vs. ejaculated sperm use for severe oligozoospermia in the same ART cycle.
Ultrasonographic features of ulnar nerve instability around the elbow in fresh cadavers
Authors: Kim Beom Suk , Rhyu Im Joo , Kim Dong Hwee
Published: February 2023

Ultrasound (US) is commonly used to evaluate ulnar nerve instability (UNI) and snapping of the medial head of the triceps brachii muscle (ST). We aimed to determine the diagnostic accuracy of US in evaluating UNI, through cadaveric dissection, and to evaluate the US features and relationships of UNI and ST according to elbow flexion. Dynamic US was performed with elbow extension, 90° flexion, and full flexion positions on 18 elbows from 9 fresh cadavers. UNI was classified into N (normal), S (subluxation), and D (dislocation) types. On US exams, the following findings and parameters were evaluated: the presence of UNI and ST; the horizontal distance from the apex of the medial epicondyle (ME) to the margins of the UN and medial head of the triceps brachii muscle (ME_UN and ME_TB, respectively); cross-sectional area and flattening ratio (FR) of UN. After US, all cadavers were dissected to expose the UN and TB, and elbow flexion and extension were simulated to confirm UNI and ST. The gross anatomic findings of UNI and ST were consistent with the US findings. In extension and 90° flexion positions, all cases were type N. In full flexion position, types N and S occurred in 10 (56%) and 8 (44%) elbows, respectively. FR and ME_UN in 90° flexion position, FR, ME_UN, and ME_TB in full flexion position differed significantly between types S and N. Positive correlations were found between ME_UN and ME_TB in 90° flexion and full flexion positions. Dynamic US accurately assessed UNI and ST. UNI was positively correlated to medial TB movement.
The gastric double-stripe sign of chronic mesenteric ischemia: A case report
Authors: Yamamoto Hiroyuki , Hashimoto Toru
Published: February 2023

Rationale:

Atherosclerotic chronic mesenteric ischemia (CMI) is caused by stenosis or occlusion of mesenteric arteries and can progress to potentially life-threatening acute mesenteric ischemia if left untreated. However, correct diagnosis and timely treatment remain a challenge due to a lack of awareness, variable symptoms, and inconclusive diagnostic testing.

Patient concerns:

An 82-year-old man with multiple cardiovascular risk factors, including chronic kidney disease, presented with dyspnea, anorexia, and oliguria. Laboratory results revealed severe renal dysfunction (raised serum blood urea nitrogen of 83.8 mg/dL, serum creatinine levels of 8.20 mg/dL, and decreased estimated glomerular filtration rate of 5.5 mL/min/1.73 m2), hypoalbuminemia, and moderate anemia. A provisional diagnosis of acute exacerbation of chronic kidney disease was made and the patient required tentative intermittent hemodialysis, received blood transfusions, and was eventually placed on maintenance hemodialysis. However, the patient’s symptoms did not improve. Esophagogastroduodenoscopy (EGD) revealed longitudinal gastric ulcers on the anterior and posterior walls of the stomach, which were named “a gastric double-stripe sign” because the lesions corresponded to the watershed areas of the stomach. No Helicobacter pylori infection or malignancy was identified, and increasing the dose of lansoprazole had no beneficial effects. Doppler ultrasound revealed high peak systolic velocity (270 cm/s) of the celiac artery (CA), suggesting CA stenosis, which was confirmed by magnetic resonance angiography.

Diagnosis:

Final diagnosis of CMI was made based on patient’s symptoms, EGD findings, Doppler ultrasound, and magnetic resonance angiography.

Interventions:

Endovascular revascularization for CA stenosis was performed.

Outcomes:

The patient obtained symptomatic relief concomitant with the resolution of the gastric ulcers. The post-procedural course of the patient was uneventful and he remained healthy at the 1-year follow-up.

Lessons:

This is the first case of CMI with EGD finding of a gastric double-stripe sign specific for gastric ischemia. This case highlights the clinical importance of this endoscopic finding in patients with suspected atherosclerotic CMI.
Understanding the mechanism of twenty-five ingredient decoction for setting a fracture in the treatment of fractures based on network pharmacology
Authors: Tian Zenghui , Hao Yanke , Wang Mingliang , Li Yingying , Cui Kaiying , Hou Pengfei , Wang Xiaoying , Lv Dengwan , Shi Jie
Published: February 2023

To study the mechanism of 25 ingredient decoction for setting a fracture (TDSF) in fracture treatment using network pharmacology. The TCMSP, BATMAN-TCM, HERB, and Uniprot protein databases were used to identify the active ingredients and targets of TDSF. Fracture-related targets were collected from the gene cards and the online mendelian inheritance in man databases. The acquisition of common genes of active compounds of TDSF and disease fractures was carried out using the Venny software. The Cytoscape 3.7.1 software and String database were used to construct a network diagram of drug-active ingredient-target-disease and the main core targets were obtained by protein interaction analysis. The Metascape platform was used to perform gene oncology functional and Kyoto encyclopedia of genes and genomes pathway enrichment analyses for common drug-disease targets. A total of 311 active ingredients and 348 targets were associated with TDSF, with 5197 targets related to fractures and 224 common targets between the 2 keywords. Key targets included serine/threonine protein kinase 1, tumor necrosis factor, interleukin 6, tumor protein 53, and vascular endothelial growth factor. Important roles of the following pathway were identified: cancer, lipid, and atherosclerosis; AGE-RAGE signaling pathway in diabetic complications; chemical carcinogenesis – receptor activation; PI3K -Akt signaling pathway; platinum drug resistance; cAMP signaling pathway; transcriptional mis regulation in cancer; serotonergic synapse; and malaria. TDSF mainly treats fractures by acting on multiple targets, such as serine/threonine protein kinase 1, tumor necrosis factor, interleukin 6, tumor protein 53, and vascular endothelial growth factor, and regulating the PI3K/AKT and cAMP signaling pathways.
Comparison of dual-trigger and human chorionic gonadotropin-only trigger among polycystic ovary syndrome couples who underwent controlled ovarian stimulation and intrauterine insemination: A retrospective cohort study
Authors: Wang Bin , Li Zhiling
Published: February 2023

The dual-trigger regime, consisting of gonadotrophin releasing hormone agonist and human chorionic gonadotropin (HCG), has been shown to offer advantage over the HCG-only trigger regime. However, little is known about the influence of dual-trigger or HCG-only trigger regime on the reproductive outcome of polycystic ovary syndrome (PCOS) couples undergoing controlled ovarian stimulation (COS) and intrauterine insemination (IUI). A total of 404 cycles of COS and IUI treatments from couples with PCOS were enrolled, and divided, according to the regime of trigger, into dual-trigger group (n = 109, 0.1–0.2 mg gonadotrophin releasing hormone agonist plus 6000 IU HCG) and HCG-only group (n = 295, 10,000 IU HCG or 250 μg recombinant HCG). Baseline characteristics of the 2 groups were comparable (all P > .05). In dual-trigger group, live birth rate, clinical pregnancy rate and β-HCG positive rate were all higher as compared to the HCG-only group (20.18% vs 18.98%, 25.69% vs 23.39% and 28.44% vs 25.08% respectively), despite the differences failed to achieve statistical significances (all P > .05). Moreover, early miscarriage rate and multiple pregnancy rate of the dual-trigger group were lower than those of the HCG-only group (17.86% vs 18.84% and 3.57% vs 7.25% respectively), although no statistical significances were found (all P > .05). Additionally, logistic regression analysis revealed that age contributed significantly to the live birth of couples with PCOS (P = .043, OR = 0.900). Dual-trigger regime for oocyte maturation seems to associate with beneficial improvements in reproductive outcomes of PCOS couples undergoing COS and IUI. Instead of HCG-only trigger, dual-trigger regime might be an alternative option in COS and IUI cycles for couples with PCOS.
Correlation of Adenoviral Titers with Severity of Adenoviral Conjunctivitis and Time to Viral Clearance over 21 Days
Authors: Morettin Christina E. , Harthan Jennifer S. , Huecker Julia B. , Perera Chamila D. , Than Tammy , Whiteside Meredith , Johnson Spencer D. , Shorter Ellen , Migneco Mary K. , Olson Christian K. , Alferez Christopher S. , Camp Devon , Hartwick Andrew T.E. , Gordon Mae O.
Published: February 2023

Significance

This investigation reports the correlation of conjunctival viral titers in adenoviral conjunctivitis with patient-reported symptoms and clinician-graded signs over 21 days of follow-up.

Purpose

Adenoviral conjunctivitis is a highly contagious viral eye infection with significant morbidity and economic impact. This study investigates whether severity of signs and symptoms and time to viral clearance are correlated with conjunctival viral titers at baseline and during 21 days of follow-up.

Methods

The Reducing Adenoviral Patient Infected Days (RAPID) study was a pilot study of the efficacy of a single in-office administration of ophthalmic 5% povidone-iodine. This manuscript outlines longitudinal analyses after the primary outcomes report. Of 212 participants screened, 28 participants with qPCR confirmed adenoviral conjunctivitis were randomized and had follow-up visits on days 1-2, 4, 7, 14 and 21. At each visit, clinician-graded signs, participant-reported symptoms, and a conjunctival swab for qPCR analysis were obtained. The correlation of viral titers with symptoms and signs was calculated: 1. cross-sectionally at each visit; and 2. longitudinally over 21 days using a repeated measures mixed effects model.

Results

Twenty-five of 28 participants had sufficient data for this report. Higher viral titers over 21 days were correlated with greater severity of symptoms (tearing, matting, and redness, r ≥ 0.70; P < .02), greater severity of clinical signs (bulbar redness and serous discharge, r ≥ 0.60; P < .01). Eyes with highest baseline viral titers required longer time to viral clearance (r = 0.59, P = .008). Signs and symptoms persisted in approximately half of the eyes even after viral clearance.

Conclusions

Higher conjunctival viral titers across 21 days were strongly correlated with more severe signs and symptoms, and longer time to viral clearance. Our results also indicate that symptoms and signs can persist after viral clearance.
Maximizing the Virtual Surgical Planning Session for Orthognathic Surgery
Authors: Ibelli Taylor J. , Janssen Pierce , Baker Stephen B. , Kumar Anand , Taub Peter J.
Published: February 2023

Virtual surgical planning (VSP) and computer-aided design/computer-aided manufacturing have become essential tools for planning orthognathic surgery. Despite widespread use, empirical gaps still exist in the literature regarding the logistics of the orthognathic planning session itself. More precisely, there is a need to explicate the VSP workflow on which specific parameters are needed for a translation into 3D software. Although each surgeon has his/her theoretical framework, none have been elucidated to properly communicate the necessary pieces of information needed to plan the correction of a variety of dentofacial deformities. The authors provide an outline for conducting a successful VSP planning session for orthognathic surgery.
Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes
Authors: Göker Markus , Oren Aharon
Published: February 2023

Observations made after introduction of the phylum category into the International Code of Nomenclature of Prokaryotes (ICNP) indicate that the addition of a category should usually be conducted before informal names at that rank become widely used. It is thus investigated whether it would be beneficial to add further categories. An extrapolation from the number of names validly published under the ICNP at the distinct principal categories was conducted. This extrapolation indicated that two principal ranks above phylum rank would also harbour validly published names if the according categories were covered by the ICNP. The appropriate categories would be kingdom and domain, regarded as separate principal ranks. The benefit from introducing these ranks is confirmed by analysing the previous taxonomic activity above phylum level and the nomenclatural problems associated with this activity. An etymological examination of the way names of taxa above genus level are formed under distinct codes of nomenclature provides hints for implementing additional categories. According emendations of the ICNP are proposed to include kingdom and domain as a means of further stabilizing prokaryotic nomenclature.
Vibrio floridensis sp. nov., a novel species closely related to the human pathogen Vibrio vulnificus isolated from a cyanobacterial bloom
Authors: Grant Trudy-Ann , Jayakumar Jane M. , López-Pérez Mario , Almagro-Moreno Salvador
Published: February 2023

A Gram-stain-negative, rod-shaped bacterial strain, designated Vibrio floridensis IRLE0018 (=NRRL B-65642=NCTC 14661), was isolated from a cyanobacterial bloom along the Indian River Lagoon (IRL), a large and highly biodiverse estuary in eastern Florida (USA). The results of phylogenetic, biochemical, and phenotypic analyses indicate that this isolate is distinct from species of the genus

Vibrio

with validly published names and is the closest relative to the emergent human pathogen,

Vibrio vulnificus

. Here, we present the complete genome sequence of V. floridensis strain IRLE0018 (4 535 135 bp). On the basis of the established average nucleotide identity (ANI) values for the determination of different species (ANI <95 %), strain IRLE0018, with an ANI of approximately 92 % compared with its closest relative,

V. vulnificus

, represents a novel species within the genus

Vibrio

. To our knowledge, this represents the first time this species has been described. The results of genomic analyses of V. floridensis IRLE0018 indicate the presence of antibiotic resistance genes and several known virulence factors, however, its pathogenicity profile (e.g. survival in serum, phagocytosis avoidance) reveals limited virulence potential of this species in contrast to

V. vulnificus

.
Aminithiophilus ramosus gen. nov., sp. nov., a sulphur-reducing bacterium isolated from a pyrite-forming enrichment culture, and taxonomic revision of the family Synergistaceae
Authors: Pradel Nathalie , Fardeau Marie-Laure , Bunk Boyke , Spröer Cathrin , Boedeker Christian , Wolf Jacqueline , Neumann-Schaal Meina , Pester Michael , Spring Stefan
Published: February 2023

A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2T could be affiliated with the phylum

Synergistota

. Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with

Aminiphilus circumscriptus

ILE-2T (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a

Methanospirillum

species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2T (=DSM 107166T=NBRC 114655T) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the

Synergistaceae

into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.
Pseudomonas nunensis sp. nov. isolated from a suppressive potato field in Greenland
Authors: Ntana Fani , Hennessy Rosanna C. , Zervas Athanasios , Stougaard Peter
Published: February 2023

The bacterial strain In5T was previously isolated from a suppressive potato field in southern Greenland and has been characterized and described as

Pseudomonas fluorescens

. However, the results of new polyphasic analyses coupled with those of phenotypic, phylogenetic and genomic analyses reported here demonstrate that the affiliation to the species

P. fluorescens

was incorrect. The strain is Gram-stain-negative, rod-shaped, aerobic and displays growth at 4–28 °C (optimum temperature 20–25 °C) and at pH 5–9 (optimum pH 6–7). Major fatty acids were C16 : 0 (38.2 %), a summed feature consisting of C16 : 1ω6c and/or C16 : 1ω7c) (20.7 %), C17 : 0cyclo ω7c (14.3 %) and a summed feature consisting of C18 : 1ω6c and/or C18 : 1ω7c (11.7 %). The respiratory quinones were determined to be Q9 (95.5 %) and Q8 (4.5 %) and major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was determined to be 59.4 mol%. The results of phylogenetic analysis based on the 16S rRNA gene and multi-locus sequence analysis (MLSA; concatenated 16S rRNA, gyrB, rpoB and rpoD sequences) indicated that In5T was affiliated with the

Pseudomonas mandelii

subgroup within the genus

Pseudomonas

. Comparison of the genome sequence of In5T and those of related type strains of species of the genus

Pseudomonas

revealed an average nucleotide identity (ANI) of 87.7 % or less and digital DNA–DNA hybridization (dDDH) of less than 34.5 % relatedness, respectively. Two more strains, In614 and In655, isolated from the same suppressive soil were included in the genome analysis. The ANI and dDDH of In614 and In655 compared with In5T were ANI: 99.9 and 97.6 and dDDH (GGDC) 99.9 and 79.4, respectively, indicating that In5T, In614 and In655 are representatives of the same species. The results of the phenotypic, phylogenetic and genomic analyses support the hypothesis that strain In5T represents a novel species of the genus

Pseudomonas

, for which the name Pseudomonas nunensis sp. nov. is proposed. The type strain is In5T(=LMG 32653T=NCIMB 15428T).
Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma
Authors: Chen Jiung-Wen , Shih Chao-Jen , Wu Li-Wha , Wu Yen-Chi , Chiang Wei-Fan , Chen Yuh-Ling , Wu Jer-Horng
Published: February 2023

A Gram-stain-negative or -positive, strictly anaerobic, non-spore-forming and pleomorphic bacterium (designated 14-104T) was isolated from the saliva sample of a patient with oral squamous cell carcinoma. It was an acid-tolerant neutralophilic mesophile, growing at between 20 and 40 °C (with optimum growth at 30 °C) and pH between pH 3.0 and 7.0 (with optimum growth at pH 6.0–7.0). It contained anteiso-C15 : 0 and C15 : 0 as the major fatty acids. The genome size of strain 14-104T was 2.98 Mbp, and the G+C content was 39.6 mol%. It shared <87 % 16S rRNA sequence similarity, <71 % orthologous average nucleotide identity, <76 % average amino acid identity and <68 %% of conserved proteins with its closest relative,

Phocaeicola abscessus

CCUG 55929T. Reconstruction of phylogenetic and phylogenomic trees revealed that strain 14-104T and

P. abscessus

CCUG 55929T were clustered as a distinct clade without any other terminal node. The phylogenetic and phylogenomic analyses along with physiological and chemotaxonomic data indicated that strain 14-104T represents a novel species in the genus

Phocaeicola

, for which the name Phocaeicola oris sp. nov. is proposed. The type strain is 14-104T (=BCRC 81305T= NBRC 115041T).
Heterologous inactivated virus/mRNA vaccination response to BF.7, BQ.1.1, and XBB.1
Authors: Zuo Fanglei , Sun Rui , Abolhassani Hassan , Du Likun , Wang Yating , Vlachiotis Stelios , Bertoglio Federico , Schubert Maren , Rezaei Nima , Chavoshzadeh Zahra , Guerra Concetta , Cavalli Andrea , Andréll Juni , Kumagai-Braesch Makiko , Xue Yintong , Cao Yunlong , Hust Michael , Robbiani Davide F. , Xie Xiaoliang Sunney , Hammarström Lennart , Marcotte Harold , Pan-Hammarström Qiang
Published: February 2023

The emergence of highly immune-escape Omicron variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as BQ and XBB, has led to concerns about the efficacy of vaccines. Using lentivirus-based pseudovirus neutralizing assay, we showed that heterologous vaccination involving parental mRNA vaccine as a booster or second booster in individuals that received two or three doses of inactivated vaccines strongly augments the neutralizing activity against emerging Omicron subvariants, including BF.7, BQ.1.1, and XBB.1, by 4.3-to 219-folds. Therefore, a heterologous boosting strategy with mRNA-based vaccines should be considered in populations where inactivated vaccines were primarily used.
Associations of COVID-19 Symptoms with Omicron Subvariants BA.2 and BA.5, Host Status, and Clinical Outcomes: A Registry-Based Observational Study in Sapporo, Japan
Authors: Nakakubo Sho , Kishida Naoki , Okuda Kenichi , Kamada Keisuke , Iwama Masami , Suzuki Masaru , Yokota Isao , Ito Yoichi M. , Nasuhara Yasuyuki , Boucher Richard C. , Konno Satoshi
Published: February 2023

Background

Previous SARS-CoV-2 infection and vaccination, coupled to rapid evolution of SARS-CoV-2 variants, have modified COVID-19 clinical manifestations. We characterized clinical symptoms of COVID-19 individuals in omicron BA.2 and BA.5 Japanese pandemic periods to identify omicron and subvariant associations between symptoms, immune status, and clinical outcomes.

Methods

Individuals registered in Sapporo’s web-based COVID-19 information system entered 12 pre-selected symptoms, days since symptom onset, vaccination history, SARS-CoV-2 infection history, and background. Symptom frequencies, variables associated with symptoms, and symptoms associated with progression to severe disease were analysed.

Results

For all omicron-infected individuals, cough was the most common symptom (62.7%), followed by sore throat (60.7%), nasal discharge (44.3%), and fever (38.8%). Omicron BA.5 infection was associated with a higher symptom burden than BA.2 in vaccinated and unvaccinated individuals. Omicron breakthrough-infected individuals with ≥ 3 vaccinations or previous infection were less likely to exhibit systemic symptoms, but more likely to exhibit upper respiratory symptoms. Infected elderly individuals had lower odds for all symptoms, but, when symptoms were manifest, systemic symptoms were associated with an increased risk, whereas upper respiratory symptoms with a decreased risk, of severe disease.

Conclusion

Host immunological status, omicron subvariant, and age were associated with a spectrum of COVID-19 symptoms and outcomes. BA.5 produced a greater symptom burden than BA.2. Vaccination and prior infection mitigated systemic symptoms and improved outcomes, but increased upper respiratory tract symptom burden. Systemic, but not upper respiratory, symptoms in the elderly heralded severe disease.
The Business of Quality: Evaluating the Impact of Healthcare Quality Improvements on Staff Numbers and Patient Utilization in Sub-Saharan Africa
Authors: Gómez-Pérez Gloria P. , Brals Daniëlla , de Graaff Aafke E. , Dada Ibironke , Agyei Bonifacia Benefo , Risha Peter , Bonareri Elizabeth , Dekker John T. , Rinke de Wit Tobias F. , Spieker Nicole , Janssens Wendy
Published: February 2023

Every year an estimated 5 to 8 million people die in low- and middle-income countries (LMICs) due to poor-quality care. Although quality improvements in healthcare facilities in LMICs are well-possible with tailored implementation plans, costs are often mentioned as a prohibiting factor. However, if quality improvements increase trust among patients, this might translate into increased visits and higher revenues for providers and enable them to further invest in quality. This paper assesses the potential business case of quality improvements in Sub-Saharan Africa (SSA). It focuses on both the public and private sector since the latter provides at least half of all health services in SSA. The analysis is based on a dataset including multiple assessments of quality and business performance indicators for almost 500 health facilities in Tanzania, Kenya, Ghana, Nigeria, and other SSA-countries. We studied the association between changes in quality assessment scores and subsequent changes in numbers of patient visits and staff as proxies for business growth. We found that quality improvements significantly improved business performance indicators, but only for those facilities that had already reached a certain level of quality to begin with. These findings suggest an S-shaped relationship between quality and business performance, leading to the existence of a ‘low-quality trap’. Substantial financial investments might be needed initially to support facilities at the bottom of the distribution in reaching a basic level of quality, after which further quality investments may start translating into increased revenues, enhancing business performance.

Key messages

Millions of people die every year in low- and middle-income countries (LMICs) due to low quality of care

To reach Universal Health Coverage, drastic quality improvements are essential

Achieving quality of care in LMICs is possible but challenging because it requires substantial financial investments, specialized skills and sufficient human resources

We found there is a business case for quality investments in SSA, as quality improvements are associated with a significant increase in the number of patient visits and staff over time, indicative of greater revenue streams and financial capacity

Targeted financing programmes together with technical assistance to healthcare facilities are critical to drive quality investments, especially for facilities at the beginning of their quality improvement journeys
Is vestibular function related to human hippocampal volume?
Authors: Bosmans Joyce , Gommeren Hanne , Eulenburg Peter zu , Gilles Annick , Mertens Griet , Ombergen Angelique Van , Cras Patrick , Engelborghs Sebastiaan , Rompaey Vincent Van
Published: February 2023

OBJECTIVES

Recent studies implicate the effect of vestibular loss on cognitive decline, including hippocampal volume loss. As hippocampal atrophy is an important biomarker of Alzheimer’s disease, exploring vestibular dysfunction as a risk factor for dementia and its role in hippocampal atrophy is of interest. The main objective is to replicate previous literature on whole-brain and hippocampal volumes in a group with bilateral vestibulopathy (BV).

DESIGN

Hippocampal and whole-brain MRI volumes were compared in adults aged between 55 and 83 years: (1) to substantiate previous literature, participants with BV (n=16) were compared to healthy controls (n=19), (2) to correct for a potential confounding effect of concomitant hearing loss, participants with BV were compared to healthy controls matched on age, sex, and hearing status (n=16), (3) to additionally evaluate the isolated effect of hearing loss on brain structure, participants with sensorineural hearing loss (SNHL; n=15) were compared to healthy controls. Furthermore, (4) to delineate otolith influence on hippocampal volume in a population with preserved vestibular function (healthy controls and SNHL combined; n=34), the role of saccular function was investigated.

RESULTS

Whole-brain and targeted hippocampal approaches using volumetric and surface-based measures yielded no significant differences in either of three comparisons: (1) BV versus controls, (2) BV versus matched controls, and (3) SNHL versus controls. Binary support vector machines were unable to classify inner ear health status above chance level. (4) Otolith parameters were not associated with hippocampal volume in a population with preserved vestibular function.

CONCLUSIONS

No significant differences in whole-brain or hippocampal volume were found when comparing BV participants with healthy controls, nor did concomitant SNHL confound this relationship. Saccular parameters in subjects with preserved vestibular function were not associated with hippocampal volume changes.

Key points

Recent research suggests an association between vestibular function and cognition.

Hippocampal atrophy is an important biomarker of Alzheimer’s disease.

Bilateral vestibular loss did not modulate hippocampal or whole-brain volume.
Development of a Novel Score to Predict Urgent Mechanical Circulatory Support in Chronic Total Occlusion Percutaneous Coronary Intervention
Authors: Karacsonyi Judit , Stanberry Larissa , Simsek Bahadir , Kostantinis Spyridon , Allana Salman S. , Rempakos Athanasios , Okeson Brynn , Alaswad Khaldoon , Basir Mir B. , Jaffer Farouc , Poommipanit Paul , Khatri Jaikirshan , Patel Mitul , Mahmud Ehtisham , Sheikh Abdul , Wollmuth Jason R. , Yeh Robert W , Chandwaney Raj H. , ElGuindy Ahmed M , AbiRafeh Nidal , Schimmel Daniel R. , Benzuly Keith , Burke M. Nicholas , Rangan Bavana V. , Mastrodemos Olga C. , Sandoval Yader , Ungi Imre , Brilakis Emmanouil S.
Published: February 2023

Background

Estimating the likelihood of urgent mechanical circulatory support (MCS) can facilitate procedural planning and clinical decision making in chronic total occlusion (CTO) percutaneous coronary intervention (PCI).

Methods

We analyzed 2,784 CTO PCIs performed between 2012 and 2021 at 12 centers. The variable importance was estimated by a bootstrap applying a random forest algorithm to a propensity-matched sample (a ratio of 1:5 matching cases with controls on center). The identified variables were used to predict the risk of urgent MCS. The performance of the risk model was assessed in-sample as well as on 2411 out-of-sample procedures who did not require urgent MCS.

Results

Urgent MCS was used in 62 (2.2%) of cases. Patients who required urgent MCS were older (70 [63, 77] vs. 66 [58, 73] years, p=0.003) compared with those who did not require urgent MCS. Technical (68% vs. 87%, p<0.001) and procedural successes (40% vs. 85%, p<0.001) were lower in the urgent MCS group compared with no urgent MCS cases. The risk model for urgent MCS use included retrograde crossing strategy, left ventricular ejection fraction, and lesion length. The resulting model demonstrated good calibration and discriminatory capacity with AUC (95%CI) of 0.79 (0.73, 0.86) and specificity and sensitivity of 86% and 52%, respectively. On the out-of-sample set, the specificity of the model was 87%.

Conclusion

The PROGRESS CTO MCS score can help estimate the risk of urgent MCS use during CTO PCI.

What Is Known?

Estimating the likelihood of urgent mechanical circulatory support (MCS) can facilitate procedural planning and clinical decision making in chronic total occlusion (CTO) percutaneous coronary intervention (PCI).

What the Study Adds?

We developed a risk model for urgent MCS use during CTO PCI using retrograde crossing strategy, left ventricular ejection fraction, and lesion length.

Use of the PROGRESS CTO urgent MCS score may facilitate patient selection for prophylactic hemodynamic support optimizing the risk benefit ratio of the procedure.
Heuristics for the De Bruijn Graph Sequence Mapping Problem
Authors: Rocha Lucas B. , Adi Said Sadique , Araujo Eloi
Published: February 2023

In computational biology, mapping a sequencesonto a sequence graphGis a significant challenge. One possible approach to addressing this problem is to identify a walkpinGthat spells a sequence which is most similar tos. This problem is known as the Graph Sequence Mapping Problem (GSMP). In this paper, we study an alternative problem formulation, namely the De Bruijn Graph Sequence Mapping Problem (BSMP), which can be stated as follows: given a sequencesand a De Bruijn graphGk(wherek≥ 2), find a walkpinGkthat spells a sequence which is most similar tosaccording to a distance metric. We present both exact algorithms and approximate distance heuristics for solving this problem, using edit distance as a criterion for measuring similarity.
A high-resolution aerial camera survey of Uganda’s Queen Elizabeth Protected Area improves detection of wildlife and delivers a surprisingly high estimate of the elephant population
Authors: Lamprey Richard H , Keigwin Michael , Tumwesigye Charles
Published: February 2023

The Queen Elizabeth Protected Area (QEPA) hosts some 60% of Uganda’s elephants and large populations of buffalo, hippopotamus and Uganda kob. However, the area is subjected to continued poaching, livestock incursions, animal disease and invasive plant species. Population estimates derived from aerial observers have shown great variability, and therefore trends are hard to discern. The Uganda Wildlife Authority (UWA) reguires precise wildlife population estimates to guide conservation actions. The aim of this study is to provide accurate and precise baseline estimates for wildlife populations of QEPA using aerial imagery and high sampling intensity, and to improve survey methods for determining future trends. High-resolution cameras, orientated at 45°, captured images along sample strips to left and right of the aircraft. Transects at 1 km separation gave a high sampling intensity of 28% to improve precision. We captured 43000 images for visual enumeration of 13 wildlife species. Population estimates (Ŷ), standard errors (SE) and relative margins of error (RME =95% c.l/Ŷ) were determined using ‘Jolly II’, Marriott and bootstrapping methods. With improved detection using imagery the QEPA elephant population is estimated at 4 711 ± 1106 (95% c. I), which is 62% higher than the previous observer-based estimate of 2900 in 2014, and the highest since counts began in the 1960s. The survey achieved an RME for elephants of 23%, making this one of the most precise counts for any similar-sized elephant area in Africa. The buffalo, Uganda kob and hippopotamus populations have stabilized at ‘safe’ levels but remain well below the high point of the mid-1990s; the high density of bone patches indicate high mortality, attributable to disease and to the continued invasion of the unpalatable grass speciesImperata cylindrica, which now covers 50% of the grassland area. Our methods indicate that methods and sample parameters prescribed by international elephant counting standards can be revised and improved using aerial cameras, especially for smaller survey areas.

Short Summary Text

Uganda’s Queen Elizabeth Protected Area (QEPA) continues its recovery since the decimation of wildlife by militias in the 1970s, but it is challenging to track wildlife trends due to the variability in population estimates. To improve accuracy and precision, we conducted the first aerial count of QEPA using high-resolution imaging. This approach has indicated that the elephant population is at its highest levels since surveys began in the 1960s. Meanwhile, buffalo, topi and Uganda kob are stagnating below previous 1990s levels. We suggest the use of camera systems in future surveys to improve the accuracy and precision of counts, in order to guide effective management.
UPF3A is a ubiquitously expressed NMD factor among mouse tissues
Authors: Ma Xin , Li Yan , Chen Chengyan , Li Tangliang
Published: February 2023

Nonsense-mediated mRNA decay (NMD), an important post-transcriptional regulatory mechanism in gene expression, is actively involved in a series of cellular and physiological processes, thus controlling cell fate and tissue homeostasis. Defects in NMD cause human diseases such as neurodevelopmental disorders, tumorigenesis and autoimmunity. UPF3 (Up- frameshift protein 3), first identified in the baker’s yeast, is a core NMD factor. UPF3A and UPF3B, the two UPF3 paralogs emerging in vertebrates, have either activating or suppressing roles in NMD. Previous studies found that UPF3B protein is ubiquitously expressed in almost all mammalian organs, while UPF3A protein is hardly detectable in most of mammalian tissues, except in the testis. One hypothesis explaining this phenomena is the functional antognism between UPF3A and UPF3B in NMD. Thus, UPF3B competitively binds to UPF2 with higher affinity than UPF3A, which finally destabilizes UPF3A protein. In the present study, we quantitatively evaluated the expression of UPF3A and UPF3B in nine major tissues and reproductive organs of wild type male and female mice. Our study confirmed that UPF3A has the highest expression in male germlines. To our surprise, we found in most tissues, including brain and thymus, the protein level of UPF3A is comparable with that of UPF3B. In spleen and lung, UPF3A is higher than UPF3B. These findings are further supported by publicly available gene expression data. Thus, our study demonstrated that UPF3A protein is ubiquitously expressed in mouse tissues, and may play important roles in the homeostasis of multiple mammalian tissues.
Microxanox: an R package for simulating an aquaticMICRobial ecosystem that can occupyOXic orANOXic states
Authors: Krug Rainer M , Petchey Owen L.
Published: February 2023

Microxanoxis an R package to simulate a three functional group ecosystem (cyanobacteria, phototrophic sulfur bacteria, and sulfate-reducing bacteria) with four chemical substrates (phosphorus, oxygen, reduced sulfur, and oxidized sulfur) using a set of ordinary differential equations. Simulations can be run individually or over a parameter range, to find stable states. The model can be implemented with different numbers of species per functional group. The package is constructed in such a way that the results contain the input parameter used, so that a saved results can be loaded again and the simulation be repeated. Furthermore, the package framework and code should serve as a useful starting point for making simulation models of other types of ecosystem.