bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intravesical instillation of platelet-rich plasma for treatment of interstitial cystitis/bladder pain syndrome: A pilot study
Authors: El Hefnawy Ahmed S. , Hasan Mohamed Attya Ahmed , El Sawy Esam , Abdel-Razik Mohamed , El-Tabey Nasr 
Published: October 2022

Abstract

Objective
The aim of this study was to evaluate the feasibility of intravesical instillation of platelet-rich plasma (PRP) to treat interstitial cystitis/bladder pain syndrome (IC/BPS).

Materials and methods
Twenty PRP samples were tested in vitro for stability after exposure to urine samples with different pH. A pilot study involving 21 female patients with IC/BPS was conducted, and 6 weekly doses of autologous PRP (50 mL) were administered. Patients were followed up at the 2nd, 4th, 8th, and 12th weeks after terminating instillation. The primary endpoint was the visual analog scale (VAS) for pain, and the secondary endpoints included the IC symptom index, IC problem index of the O'Leary-Sant questionnaire and global response assessment, urine culture, and uroflowmetry. Success was defined as a reduction in VAS by 30% or more compared with basal level, and adverse events were recorded.

Results
The mean ± SD of VAS was significantly reduced compared with basal level (4.4 ± 2.6 vs. 8.8 ± 1.1, respectively, p = 0.001). Meanwhile, 80% of cases were considered successful, with a 50.1% reduction in the mean score compared with the basal level. The mean ± SD of IC symptom index and IC problem index significantly improved compared with the basal level. Global response assessment was markedly, moderately, and slightly improved in 2 (10%), 10 (50%), and 5 (25%) patients, respectively, and showed no change in 3 (15%). Three patients had positive urine cultures at follow-up, but 1 withdrew after 2 sessions because of a lack of efficacy.

Conclusions
Repeated intravesical instillation of PRP could be considered an effective and safe approach for treating IC/BPS.
Lung Cancer Screening Knowledge, Attitudes and Practice Patterns Among Primary and Pulmonary Care Clinicians
Authors: Carter-Bawa Lisa , Walsh Leah E. , Schofield Elizabeth , Williamson Timothy J. , Hamann Heidi A. , Ostroff Jamie S. 
Published: October 2022

Abstract

Background
Lung cancer screening has the potential to identify lung cancer at an early stage when more treatment options exist. However, discussions with and referrals of screening-eligible patients remain unacceptably low. We need to better understand clinician knowledge, attitudes, and practice patterns to identify strategies to improve lung cancer screening uptake. Prior studies have focused on understanding these factors from physicians only. Nevertheless, many patients receive primary care from nurse practitioners and physician assistants where prevention and early detection conversations are most likely to occur. Therefore, we must engage the full range of clinicians treating screening-eligible patients.

Objectives
To describe attitudes, beliefs and referral practice patterns, lung cancer screening knowledge, and concordance with lung cancer screening guidelines among nurse practitioners, physicians, and physician assistants in the U.S.

Methods
Descriptive, cross-sectional study using survey methodology with clinical vignettes to examine clinician factors and concordance with U.S. Preventive Services Task Force (USPSTF) Lung Cancer Screening Guidelines.

Results
Participants scored low on attitudes toward shared decision-making, high on the importance of shared decision-making in lung cancer screening, and low on barriers to lung cancer screening referral. In addition, midrange scores on empathy toward patients with smoking history were noted. Lung cancer screening knowledge was low regardless of clinician specialty; the most endorsed response when presented with a hypothetical patient was to refer for lung cancer screening using a chest X-ray.

Discussion
Findings demonstrate that most clinicians are nonconcordant with USPSTF guidelines, erroneously believing a chest X-ray is appropriate for lung cancer screening. Clinicians must follow evidence-based practice guidelines, highlighting the need for targeted continuing education about lung cancer screening for clinicians who treat screening-eligible patients.
Critical Incident Reports Related to Ventilator Use: Analysis of the Japan Quality Council National Database
Authors: Akiyama Naomi , Kajiwara Shihoko , Tamaki Takahiro , Shiroiwa Takeru 
Published: October 2022

Objective
This study aimed to assess the factors associated with medical device incidents.

Methods
In this mixed-methods study, we used incident reporting data from the Japan Council for Quality Health Care. Of the 232 medical device–related reports that were downloaded, 34 (14.7%) were ventilator-associated incidents. Data related to patients, situations, and incidents were collected and coded.

Results
The frequencies of ventilator-associated accidents were 20 (58.8%) during the daytime and 14 (41.2%) during the night/early morning. Ventilator-associated accidents occurred more frequently in the hospital room (n = 22 [64.7%]) than in the intensive care unit (n = 4 [11.8%]). Problems with ventilators occurred in only 4 cases (11.8%); in most cases, medical professionals experienced difficulty with the use or management of ventilators (n = 30 [88.2%]), and 50% of them were due to misuse/misapplication of ventilators (n = 17 [50.0%]). Ventilator-associated accidents were caused by an entanglement of complex factors—hardware, software, environment, liveware, and liveware-liveware interaction. Communication and alarm-related errors were reported to be related, as were intuitiveness or complicated specifications of the device.

Conclusions
Our study revealed that ventilator-associated accidents were caused by an entanglement of complex factors and were related to inadequate communication among caregivers and families. Moreover, alarms were overlooked owing to inattentiveness. Mistakes were generally caused by a lack of experience, insufficient training, or outright negligence. To reduce the occurrence of ventilator-associated accidents, hospital administrators should develop protocols for employment of new devices. Medical devices should be developed from the perspective of human engineering, which could be one of the systems approaches.
Niabella agricola sp. nov., isolated from paddy soil
Authors: Lin Shih-Yao , Tsai Chia-Fang , Hameed Asif , Lee Tzung-Han , Young Chiu-Chung 
Published: October 2022

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative, orange-coloured bacterium (designated strain CC-SYL272T) isolated from paddy soil. Cells were observed to be strictly aerobic, non-motile and non-spore-forming rods, exhibiting positive catalase and oxidase. Strain CC-SYL272T was found to grow optimally at 20–40 °C, pH 6.0–8.0 and NaCl 0–2 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CC-SYL272T belongs to the genus

Niabella

, family

Chitinophagaceae

, and is most closely related to

Niabella pedocola

(97.8 %) followed by

Niabella drilacis

(97.2 %) and established a distinct taxonomic lineage associated with these species. The highest orthologous average nucleotide identity (OrthoANI) values were recorded for strain CC-SYL272T
versus Niabella species (69.1–83.5 %, n=8). The mean digital DNA–DNA hybridization (dDDH) value obtained for strain CC-SYL272T against

N. pedocola

was 27.3 %. The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The major polyamines were putrescine and sym-homospermidine. The dominating cellular fatty acids (>5 %) included iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3OH and C16 : 1
ω6c/C16 : 1
ω7c. The draft genome (6.25 Mb) of strain CC-SYL272T spanned three contigs having 47.1 mol% DNA G+C content, 5087 protein-encoding genes, 10 rRNA genes and 44 tRNA genes. The genome harboured genes involved in the depolymerization of both animal and plant polysaccharides. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, dDDH and the phylogenomic placement, strain CC-SYL272T is considered to represent a novel species of the genus

Niabella

, affiliated to the family

Chitinophagaceae

, for which the name Niabella agricola sp. nov. is proposed. The type strain is CC-SYL272T (=BCRC 81319T=JCM 34758T).
Evaluation of eleven commercially available PCR kits for the detection of Monkeypox virus DNA
Authors: Michel Janine , Targosz Angelina , Rinner Thomas , Bourquain Daniel , Brinkmann Annika , Sacks Jilian A. , Schaade Lars , Nitsche Andreas 
Published: October 2022

AbstractPrior to the international spread of Monkeypox in May 2022, PCR kits for the detection of Orthopoxviruses, and specifically for monkeypox virus, were rarely available. Here we describe the evaluation of eleven recently-developed commercially available PCR kits for the detection of Monkeypox virus DNA.
Chronic activation of dopaminergic neurons via bioluminescence-optogenetics provides neuroprotection in a rodent model of Parkinson’s disease
Authors: Shiu Fu Hung , Skelton Henry , Berglund Ken , Fernandez Alejandra M. , Gutekunst Claire-Anne N. , Robinson Elizabeth R. , Wang Zuhui , Gross Robert E. 
Published: October 2022

AbstractPrevious studies in human patients and rodent models of Parkinson’s disease (PD) have established neuroprotection of dopaminergic (DA) neurons in substantia nigra pars compacta (SNC) by physical exercise, but the precise origin of this neuroprotective effect has yet to be elucidated. In this study, we tested a hypothesis that enhanced activity of DA neurons in SNC results in neuroprotection using the unilateral 6-hydroxydopamine (6-OHDA) injection model in mice. To increase activity of DA neurons chronically and specifically, we injected an adeno-associated viral vector carrying a step-function luminopsin (SFL) – a fusion protein of light-emittingGaussialuciferase and light-sensing step-function channelrhodopsin 2 – into SNC ipsilateral to 6-OHDA using the pan-neuronal human synapsin I promoter or the Cre-lox system in transgenic mice expressing the recombinase under control of the tyrosine hydroxylase (TH) promoter. Upon application of SFL substrate, coelenterazine (CTZ), the luciferase moiety of luminopsin emits bioluminescence which in turn activate the opsin moiety. Daily injection of CTZ for 4 weeks ameliorated a stereotypical behavior, namely ipsiversive rotations, induced by unilateral 6-OHDA. In addition, postmortem immunohistochemistry against TH revealed less severe neurodegeneration of DA neurons compared to vehicle-injected control animals. Furthermore, when mice were pretreated with ANA-12, a selective antagonist for tropomyosin receptor kinase B (TrkB), the behavioral improvement and neuroprotective effect were diminished. These results suggest that increased neuronal activity of DA neurons provides neuroprotection against 6-OHDA injury and alleviates its symptoms through the brain-derived neurotrophic factor-TrkB pathway.
Infection of primary nasal epithelial cells differentiates among lethal and seasonal human coronaviruses
Authors: Otter Clayton J. , Fausto Alejandra , Tan Li Hui , Cohen Noam A. , Weiss Susan R. 
Published: October 2022

SUMMARYThe nasal epithelium is the initial entry portal and primary barrier to infection by all human coronaviruses (HCoVs). We utilize primary nasal epithelial cells grown at air-liquid interface, which recapitulate the heterogeneous cellular population as well as mucociliary clearance functions of thein vivonasal epithelium, to compare lethal (SARS-CoV-2 and MERS-CoV) and seasonal (HCoV-NL63 and HCoV-229E) HCoVs. All four HCoVs replicate productively in nasal cultures but diverge significantly in terms of cytotoxicity induced following infection, as the seasonal HCoVs as well as SARS-CoV-2 cause cellular cytotoxicity as well as epithelial barrier disruption, while MERS-CoV does not. Treatment of nasal cultures with type 2 cytokine IL-13 to mimic asthmatic airways differentially impacts HCoV replication, enhancing MERS-CoV replication but reducing that of SARS-CoV-2 and HCoV-NL63. This study highlights diversity among HCoVs during infection of the nasal epithelium, which is likely to influence downstream infection outcomes such as disease severity and transmissibility.
Deep learning-based Drug discovery of Mac domain of SARS-CoV-2 (WT) Spike inhibitors: using experimental ACE2 Inhibition TR-FRET Assay Screening and Molecular Dynamic Simulations
Authors: Iqbal Saleem , Sheng-Xiang-Lin  
Published: October 2022

AbstractSARS-CoV-2 exploits the homotrimer transmembrane Spike glycoproteins (S protein) during host cell invasion. Omicron, delta, and prototype SARS-CoV-2 receptor-binding domain show similar binding strength to hACE2 (Angiotensin-Converting Enzyme 2). Here we utilized multi-ligand virtual screening to identify small molecule inhibitors for their efficacy against SARS-CoV-2 virus using quantum Docking, pseudovirus ACE2 Inhibition TR-FRET Assay Screening, and Molecular Dynamic simulations (MDS). 350-thousand compounds were screened against the macrodomain of non-structural protein 3 of SARS-CoV-2. Using TR-FRET Assay, we filtered out two of 10 compounds that had no reported activity inin-vitroscreen against Spike S1: ACE2 binding assay. Percentage Inhibition at 30 µM was found to be 79% for “Compound F1877-0839” and 69% for “Compound F0470-0003”. This first of its kind study identified “FILLY” pocket in macrodomains. Our 200 ns MDS revealed stable binding poses of both leads. They can be used for further development of preclinical candidates.Abstract ImageIn BriefIqbal et al., described a deep learning guided drug discovery, efficacy against SARS-CoV-2 Spike inhibitors: using experimental pseudovirus ACE2 Inhibition TR-FRET Assay. Our molecular dynamic simulation results were next validated a posteriori against the corresponding experimental data of identified leads with 80 percent inhibition. Moreover, this study is first of kind to identify “FILLY” pocket in macrodomains.HighlightsExperimental pseudovirus ACE2 Inhibition TR-FRET Assay and HTS lead to identification of two potential clinical leads.Conformational Dynamics analysis reveal the structural stability of complexes throughout 200 ns molecular dynamic simulations.Unveiling of the impact surface charge on the Variant of ConcernsDetection of conformational changes within ACE2/RBD complexWe identified the FILLY pocket in the SARS viruses.
Application of a multispecies probiotic reduces gastro-intestinal discomfort and induces microbial changes after colonoscopy
Authors: Labenz J. , Borkenstein D. P. , Heil F. J. , Madisch A. , Tappe U. , Schmidt H. , Terjung B. , Klymiuk I. , Horvath A. , Gross M. , Stadlbauer V. 
Published: October 2022

AbstractEven after decades of research and pharmaceutical development, cancer is still one of the most common causes of death in the western population and the management of cancer will remain a major challenge of medical research. One of the most common types of cancer is colorectal cancer (CRC). Prevention by detection of early-stage precursors is the most reliable method to prevent CRC development. In dependence of age, familial predisposition, and other risk factors the preventative routine screening for CRC by colonoscopy should be performed at least twice in intervals of about ten years. Although colonoscopy is a life-saving clinical examination reducing both incidence and mortality of CRC significantly, it has still a bad reputation in the population as an uncomfortable procedure with unpleasant side effects lasting sometimes over days to weeks. These effects are most likely caused by the bowel preparation before colonoscopy, which is crucial for a successful colonoscopy with high quality. Beside pain, bleeding and other rare but severe complications of colonoscopy, cleaning of the intestinal mucosa alters the gut microbiome significantly and consistently. Abdominal pain, cramps, diarrhea, nausea, bloating, and constipation are common adverse events which can continue to affect patients for days or even weeks after the procedure. In this multicenter, placebo controlled, double blind clinical trial, we investigated the effect of an intervention with a multispecies probiotic formulation for 30 days on the adverse events due to bowel preparation. We show that the treatment of participants with the multispecies probiotic formulation decreases the number of days with constipation significantly, and reduced pain, bloating, diarrhea, and general discomfort. 16S based amplicon analyses reveal recovery of administered probiotic strains from stool samples and differences in alpha diversity dynamics with higher variability in the probiotic group compared to the placebo group. In conclusion, the probiotic ameliorates the side effects after colonoscopy and might be an important supplement to increase acceptance of this life-saving preventative examination. Further, we present here for the first time that probiotic intervention of only 30 days affects alpha diversity parameters in stool samples.
Isolation and characterization of a neoxanthin synthase gene functioning in fucoxanthin biosynthesis ofPhaeodactyum tricornutum
Authors: Sui J.K. , Zhang Z.Y. , Han J.C. , Yang G.P. , Liu T.Z. , Wang H. 
Published: October 2022

AbstractGolden-brown xanthophyll fucoxanthin in marine organisms, especially in diatoms, has attracted widespread attention because of its diverse biological activities. However, the biosynthetic pathway of fucoxanthin remains unclear in diatoms. Fucoxanthin may derive from either neoxanthin or diadinoxanthin pathway. However, the key point is whether neoxanthin and its synthesizing genes exist or not. In this study, we successfully identified a few xanthophylls in trace amounts in the concentrated fraction of carotenoids of diatomPhaeodactylum tricornutumcultured at different light intensities with the co-chromatography method, and cloned the neoxanthin synthase (NXS) gene which was not annotated in diatom genome. TheNXSknockdown and knockout experiment show a positive correlation in the accumulation of neoxanthin and zeaxanthin while a negative correlation in violaxanthin and fucoxanthin with the expression ofNXS. In vitroassay evidenced that neoxanthin is the precursor for fucoxanthin biosynthesis, indicating that other molecules intermediate the conversion between violaxanthin and fucoxanthin. Overall, we cloned a novel gene functioning in neoxanthin biosynthesis, which should aid to clarifying the fucoxanthin biosynthetic pathway in diatom.
Role of Caveolin 1 in metabolic programming of fetal brain
Authors: Islam Maliha , Behura Susanta K 
Published: October 2022

AbstractCaveolin-1 (Cav1) encodes a major protein of the lipid rafts, called caveolae, which are plasma membrane invaginations found in most cells of mammals.Cav1-null mice, at an early adult age, exhibit symptoms that are hallmarks of Alzheimer’s disease, and show brain aging similar to that of one and half year old wildtype mice. In the present study, integrative analysis of metabolomics, transcriptomics, epigenetics and single cell data was performed to test the hypothesis that metabolic deregulation of fetal brain due to lack ofCav1influenced brain aging in these mice. The results of this study show that lack ofCav1deregulated lipid and amino acid metabolism in the fetal brain. Genes associated with the deregulated metabolites were significantly altered in specific glial cells of the fetal brain, and epigenetically altered in a coordinated manner with specific genes of mouse epigenetic clock. The interaction between metabolic and epigenetic changes in the fetal brain altered gene expression of the brain at old age. Together, these results suggested that metabolic deregulation in the fetal life elicited an epigenetic memory that altered brain programming for aging inCav1-null mice.
Single Cell RNA Sequencing of the AdultDrosophilaEye Reveals Distinct Clusters and Novel Marker Genes for All Major Cell Types
Authors: Yeung Kelvin , Raja Komal Kumar Bollepogu , Shim Yoon-Kyung , Li Yumei , Chen Rui , Mardon Graeme 
Published: October 2022

AbstractThe adultDrosophilaeye is a powerful model system for phototransduction and neurodegeneration research. However, single cell resolution transcriptomic data are lacking for this tissue. We present single cell RNA-seq data on 1-day male and female, 3-day and 7-day old male adult eyes, covering early to mature adult eyes. All major cell types, including photoreceptors, cone and pigment cells in the adult eye were captured and identified. Our data sets identified novel cell type specific marker genes, some of which were validatedin vivo. R7 and R8 photoreceptors form clusters that reflect their specificRhodopsinexpression and the specificRhodopsinexpression by each R7 and R8 cluster is the major determinant to their clustering. The transcriptomic data presented in this report will facilitate a deeper mechanistic understanding of the adult fly eye as a model system.
Identifying cell culturing parameters that improve endocytic uptake of the HIV-TAT cell penetrating peptide
Authors: Diaz Joshua , Pellois Jean-Philippe 
Published: October 2022

AbstractDelivery tools, including cell-penetrating peptides (CPPs) are often inefficient due to a combination of poor endocytosis and endosomal escape. Herein, the impact of cell culturing techniques on the endocytic uptake of a typical CPP, the TAT peptide (derived from HIV1-TAT), was quantified. Parameters previously found to generally modulate endocytosis such as cell density, washing steps, and cell aging did not affect TAT endocytosis. In contrast, cell dissociation methods, media, temperature, serum starvation, and media composition all contributed to changes in uptake. The combination of these parameters in worst versus best-uptake protocols, led to changes in uptake of more than 13-fold and indicated that small variations in cell culturing techniques have a cumulative effect on CPP uptake. More specifically, modulating cell culture protocols does not result in an increased amount of peptide inside endosomes, rather the number of TMR-TAT containing endosomes increases. Taken together this study highlights how technical aspects of cell culture protocols can be used to improve experimental reproducibility, as well as parameters that can be potentially exploited to improve CPP accumulation in endosomes, and hence increase the possibility of endosomal escape and cytosolic access.