bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moving Toward a Safer Health Care Facility: Improving Patient Identification at a Public Hospital in Saudi Arabia
Authors: AlYaqoub Fatemah , AlMubarak Sama'a H. 
Published: July 2022

Background and Objectives:
Patient misidentification errors continue to represent a significant risk to patients, health care staff, and hospitals. The study's purpose was to present a successful quality improvement project implemented in a public hospital in Saudi Arabia. The project focused on increasing staff's compliance with and awareness of the hospital's patient identification policy to thus reducing the number of patient misidentification-related incidents.

Methods:
Through a quality improvement project, we employed FOCUS PDSA to address the issue of patient misidentification at outpatient departments. A total of 640 staff members participated in the educational program including physicians, nurses, receptionists, radiologists, physiotherapists, and laboratory staff. Collected data included measures of compliance and awareness levels as well as patient misidentification incidents, before and after the project. Statistical analysis was conducted to measure significant differences in the study indicators before and after the project.

Results:
Results from the post-project assessment revealed that the project was successful in achieving its objectives. The overall compliance rate and awareness level increased from 59% to 78% and from 75% to 90%, respectively. Improvement in the levels of compliance and awareness was statistically significant. The average number of patient misidentification errors also reduced after the project's implementation with an average of 3 errors per month. The mean difference of patient misidentification errors before and after the project was significant (P < .01).

Conclusion:
This project demonstrated how quality improvement projects can be used to address a critical issue such as patient misidentification. The project furthers efforts made by national and international agencies to improve patient safety. It also highlights the importance of continuous education and training to ensure compliance with patient identification policies that ultimately contributes to a safer hospital environment.
Prediction and Assessment of Potential Microbial Substrate Utilisation Among More Recently Identified Health-Associated Gut Taxa
Authors: Lordan Cathy , Thapa Dinesh , Walsh Aaron , Ross Paul , Cotter Paul 
Published: July 2022

The contribution of the gut microbiota to health and disease is becoming ever more apparent in the last number of years, due to developments in DNA sequencing technology and more well-defined cultivation techniques. This has resulted in the identification of health-promoting bacteria. Until recently, prebiotics, non-digestible food substrates which are selectively utilised by beneficial bacteria, were employed with a view to increasing the growth of well-established health promoting bacteria, namely Lactobacillus and Bifidobacterium. However, other beneficial bacteria recently revealed may also be targeted to enhance their growth as they establish themselves as the next generation of health-promoting microbes. These include anaerobes such as Akkermansia muciniphila, Faecalibacterium prausnitziiand Eubacterium rectale. Identification of growth substrates/bioactives through the analysis of genome sequence data can aid in elucidating which substrates may best enhance the growth of these microbes which are often difficult to grow.
The phenotypic microbial trait analyser, Traitar, can predict 67 phenotypes based on the genome sequence inputted. Some of these traits include substrates that could potentially be utilised by the bacteria. Another tool, CarveMe, which has been created with the aim of making metabolic modelling more user-friendly, was also used with the same genomes. A select number of substrates identified in both tools have been chosen to be evaluated in vitroin order to establish the accuracy of these predictive tools as well as giving an indication as to how these beneficial microbes can be modulated through dietary components.
Antimicrobial Susceptibility Patterns of Anaerobic Bacteria at an Irish University Hospital over the past Decade
Authors: Ali Saied , McNicholas Sinead 
Published: July 2022

Background
Various studies have demonstrated poor outcomes in infections caused by anaerobic bacteria due to inappropriate therapy, directly due to emergence of resistant strains. To date there is a paucity of available data on antimicrobial resistance trends of anaerobic bacteria among the Irish population, and our study aims to determine such patterns among isolates processed at our institution over the previous decade.

Methodology
Selected anaerobic bacteria isolated from clinical specimens processed at our laboratory from January 2010 to January 2020 inclusive were collected and studied. Bacteria were identified using MALDI-TOF, with VITEK and E-tests for antimicrobial susceptibility testing. Data was processed through WHONET.

Results
A total of 2098 clinically significant anaerobic bacterial isolates were reviewed during the study period; with the majority of isolates being Bacteroides spp (32.79%, n=688) and Clostridium spp (18.68%, n=392). Bacteroides spp and Prevotella spp were unsurprisingly highly penicillin-resistant at 98.8% (n=680) and 77% (n=114) respectively. Resistance rates against metronidazole were expectedly high amongst Propionibacterium spp (100%, n=341), Actinomyces spp (98.8%, n=79), Lactobacillus spp (59.7%, n=95) and Bifidobacterium spp (53.8%, n=7); whilst remaining anaerobes were largely susceptibility. All isolates were particularly susceptible to co-amoxiclav, piperacillin-tazobactam and meropenem. Clindamycin exhibited a more variable susceptibility pattern, from 6.7% resistance in Staphylococcus saccharolyticus to 81.1% resistance in Prevotella spp.

Conclusion
Metronidazole and beta-lactams remain highly efficacious against the majority of anaerobic isolates reviewed, and remain the backbone of empiric therapy in suspected infections. However, it remains important for periodic surveillance of resistance trends.
Virulence traits and differential translocation of gut-derived Candida albicans
Authors: Devlin Edward , Munro Carol , MacCallum Donna , Gratz Silvia 
Published: July 2022

Candida albicansis an opportunistic pathogenic yeast commonly found as part of the gut microbiome, which is thought to be the major reservoir of C. albicans in humans. The ability of C. albicans to adhere to, invade and damage epithelium, along with subsequent escape from the gut lumen into the bloodstream, can lead to life-threatening disseminated fungal infections. Examining the interactions of C. albicans with the intestinal epithelial barrier is vital to understanding its ability to disseminate and cause systemic infections.
A set of seven C. albicans strains (six of gut origin: one healthy donor, one cancer patient, one Crohn’s disease patient and three unknown health status; alongside ‘non-gut’ reference strain SC5314) was profiled for virulence traits. C. albicans strains were profiled for biofilm formation (crystal violet staining), hyphal formation (microscopy) and cytotoxicity (lactate dehydrogenase release; during coculture with confluent Caco-2 gut epithelial cells). Additionally, the ability of C. albicans strains to translocate across epithelial cell layers was assessed during coculture with differentiated Caco-2 monolayers on Transwell™ permeable supports.
Common virulence traits of hyphal formation and cytotoxicity were reduced in gut C. albicanscompared to non-gut reference strain SC5314, while biofilm formation compared to SC5314 was variable. Translocation assays revealed that gut strains of C. albicans are capable of translocating across Caco-2 epithelial cell layers in greater numbers than non-gut reference strain SC5314, with the highest levels of translocation observed from a Crohn’s disease isolate. These insights suggest that gut-specific adaptations may influence luminal escape and pathogenicity of C. albicans.
Microfluidics for single-cell noise measurements in budding yeast
Authors: Reed Alan , McCarthy John 
Published: July 2022

The combination of microfluidics and time-lapse microscopy is a powerful one, with the potential for the generation of time-series data for single-cell measurements across a whole population of cells. This project aims to employ these tools for the development of technologies and strategies that facilitate the study of stochastic events at the single-cell level. A key focus of the work is the development of microfluidic and image analysis techniques.
Such developments within this project are being applied to study the specific example of noise within the expression of the yeast GCN4 transcriptional regulator. This is activated during amino acid starvation, through a novel post-transcriptional regulatory system. The majority of research into gene expression noise thus far has focused on transcriptional noise, so the impact of post-transcriptional regulation on noise is relatively poorly understood.
Biological systems show many apparently deterministic behaviours at the macroscopic level, but their underlying mechanisms are often stochastic in nature. Noise in gene expression generates heterogeneity across clonal cell populations, and is an important factor in many cellular processes (e.g. circadian rhythms). Even within the well-known “repressilator” synthetic gene circuit, noise had a significant impact on the circuit output. An appreciation of stochasticity in gene expression is therefore crucial for a complete understanding of biology, and will also be essential for the successful design of future synthetic biological systems.
CNN and transfer learning-based classification model for automated cow’s feeding behaviour recognition from accelerometer data
Authors: Bloch Victor , Frondelius Lilli , Arcidiacono Claudia , Mancino Massimo , Pastell Matti 
Published: July 2022

AbstractDue to technological developments, wearable sensors for monitoring farm animal behaviour have become cheaper, with longer life and more accessible for small farms and researchers. In this study, an acceleration measuring tag connected by BLE for monitoring behaviour of dairy cows was used. An optimal CNN-based model for the feeding behaviour classification was trained and the training process was analysed considering training dataset and the use of transfer learning. A classifier based on a neural network was trained by acceleration data collected in a research barn. Based on a dataset including 33.7 cow*days (21 cow recorded during 1-3 days) of labelled data and an additional free access dataset with similar acceleration data, a classifier with F1=93.9% was developed. The optimal classification window size was 90s. In addition, the influence of the training dataset size on the classifier accuracy was analysed for different neural networks using the transfer learning technique. During increasing of the training dataset size, the rate of the accuracy improvement decreased, and, starting from a specific point, the use of additional training data can be impractical. Relatively high accuracy was achieved with few training data when the classifier was trained using randomly initialised model weights, and higher accuracy was achieved when transfer learning was used. These findings can be used for estimation of the necessary dataset size for training neural network classifiers intended for other environments and conditions.HighlightsCNN cow feeding behaviour classifier was optimised for neck tags.Transfer learning technique significantly improves accuracy of CNN.Relation between the training dataset size and CNN accuracy was estimated.NN trained by one dataset can be inapplicable for others.BLE tags measuring acceleration transferred data in real time.
Robust capability of renal tubule fatty acid uptake from apical and basolateral membranes in physiology and disease
Authors: Kawakami Ryo , Hanaoka Hirofumi , Kanai Ayaka , Obinata Hideru , Nakano Daisuke , Ikeuchi Hidekazu , Matsui Miki , Matsuzaki Toshiyuki , Tanaka Rina , Sunaga Hiroaki , Goto Sawako , Matsui Hiroki , Koitabashi Norimichi , Saegusa Keiko , Yokoyama Tomoyuki , Hiromura Keiju , Nishiyama Akira , Saito Akihiko , Yanagita Motoko , Ishii Hideki , Kurabayashi Masahiko , Iso Tatsuya 
Published: July 2022

AbstractExcess lipid accumulation is associated with obesity-related chronic kidney disease, but the mechanisms of fatty acid (FA) uptake have been poorly understood. To this end, we investigated how FAs are taken up by tubular epithelial cells (TECs) in mice by using in vivo FA tracing and histological methods. Immunohistochemistry showed that CD36, which is a well-known FA transporter, was abundantly expressed on the basolateral side of proximal TECs (PTECs). The uptake of 125I-BMIPP (a radiolabeled FA tracer) was significantly reduced in CD36-knockout kidneys at 1 min after injection. In vivo imaging with multiphoton microscopy revealed that BODIPY-C12 (a fluorescence-labeled FA tracer) accumulated on both the basolateral and apical sides of PTECs. Numerous lipid droplets accumulated in PTECs after accelerated lipolysis. Furthermore, PTEC-specific injury via diphtheria toxin (DT) injection in transgenic mice expressing the DT receptor resulted in a compensatory increase in lipid accumulation in downstream TECs. Importantly, urinary FAs were undetectable, even in mice and humans with remarkable albuminuria. Our data demonstrate that renal TECs take up FAs from blood (CD36-dependent) and primary urine (CD36-independent) and can store excess FAs as neutral lipids. The results further show that renal tubules have hitherto largely unappreciated mechanisms by which the excretion of FAs into the urine is avoided.
Signatures of EMT, immunosuppression and inflammation of primary and recurrent human cutaneous squamous cell carcinoma at single-cell resolution
Authors: Li Xin , Zhao Shuang , Bian Xiaohui , Zhang Lining , Lu Lixia , Pei Shiyao , Dong Liang , Shi Wensheng , Huang Lingjuan , Zhang Xiyuan , Chen Mingliang , Chen Xiang , Yin Mingzhu 
Published: July 2022

AbstractThe recurrence of cutaneous squamous cell carcinoma (cSCC) after surgery remains a key factor affecting cSCC outcomes, which is related to the reprogramming of the tumour microenvironment (TME). Herein, we utilized single-cell RNA sequencing (scRNA-seq) to examine the dynamic changes in epithelial cells, T cells, myeloid cells and fibroblasts between primary and recurrent cSCC. We uncovered the immunosuppressed microenvironment in recurrent cSCC, which exhibited a T-cell- excluded and SPP1+ TAM-enriched status. In recurrent cSCC, CD8+ T cells showed high exhaustion and low inflammatory features, while SPP1+ TAMs displayed global protumour characteristics, including decreased phagocytosis and inflammation as well as increased angiogenesis. Furthermore, we found that the subgroups of SPP1+ tumour- associated macrophages (TAMs) harboured distinct functions. SPP1+ CD209high TAMs showed obvious features of phagocytosis, while SPP1+ CD209low TAMs tended to have a high angiogenic ability. A subpopulation of tumour-specific keratinocytes (TSKs) showed significant epithelial–mesenchymal transition (EMT) features in recurrent cSCC, which might be due to their active communication with IL7R+ cancer-associated fibroblasts (CAFs). In addition, we found that MDK could provoke different cell–cell interactions in cSCCs with distinctive staging. In primary cSCC, MDK was highly expressed in fibroblasts and could promote their proliferation and block the migration of tumour cells, while in recurrent cSCC, the high expression of MDK in TSKs promotes their proliferation and metastasis. Overall, our study provides insights into the critical mechanisms of cSCC progression, which might facilitate the development of a powerful system for the prevention and treatment of cSCC recurrence.
The contraction-expansion behaviour in the demosponge Tethya wilhelma is diurnal and light-controlled
Authors: Flensburg Sarah B. , Garm Anders , Funch Peter 
Published: July 2022

AbstractSponges (phylum Porifera) are metazoans without muscles and nervous system. Still, they perform coordinated behaviours, such as whole body contrations. Previous studies have indicated diurnal variability in number of contractions, and in expression of circadian clock genes. Here we show that diurnal patterns are present in the contraction-expansion behaviour of the demosponge Tethya wilhelma using infrared videography and a simulated night/day-cycle including sunset and sunrise mimic. In addition, we show that this behaviour is at least strongly influenced by the ambient light intensity and therefore implicates light-sensing capabilities in this sponge species. This is backed by our finding that T. wilhelma consistently contracts at sunrise, and that this pattern disappears both when the sponge is kept in constant darkness and when in constant light.
ppGpp and RNA-Polymerase Backtracking Guide Antibiotic-Induced Mutable Gambler Cells
Authors: Zhai Yin , Minnick P.J. , Pribis John P. , Garcia-Villada Libertad , Hastings P.J. , Herman Christophe , Rosenberg Susan M. 
Published: July 2022

SUMMARYAntibiotics can induce mutations that cause antibiotic resistance, triggered by stress responses. The identities of the stress-response activators reveal environmental cues that elicit mutagenesis, and are weak links in mutagenesis networks, inhibition of which could slow evolution of resistance during antibiotic therapies. Despite pivotal importance, few identities and fewer functions of stress responses in mutagenesis are clear. Here, we identify the stringent starvation response in fluoroquinolone-antibiotic ciprofloxacin (stress)-induced mutagenesis. We show its role in transient differentiation of a mutable “gambler” cell subpopulation. Stringent activity is induced by reactive oxygen and upregulates two small (s)RNAs that induce the general stress response, which allows mutagenic DNA-break repair. Surprisingly, RNA polymerase and response-activator nucleotide (p)ppGpp promote ciprofloxacin-induced DNA-damage signaling. We propose a model for their regulation of DNA-damage processing in transcribed regions. The data demonstrate a critical node in ciprofloxacin-induced mutagenesis, imply RNA-polymerase regulation of DNA-break repair, and identify promising targets for resistance-resisting drugs.
Eight Unexpected Selenoprotein Families in ABC transport, in Organometallic Biochemistry in Clostridium difficile and other anaerobes, and in Methylmercury Biosynthesis
Authors: Haft Daniel H. , Gwadz Marc 
Published: July 2022

AbstractA novel protein family related to mercury resistance protein MerB, which cleaves Hg-C bonds of organomercurial compounds, is a newly recognized selenoprotein, typically seen truncated in sequence databases at CU (cysteine-selenocysteine) dipeptide sites fifty residues before the true C-terminus. Inspection shows this protein occurs in a nine-gene neighborhood conserved in more than fifty bacterial species, taxonomically diverse but exclusively anaerobic, including spirochetes, deltaproteobacteria, and Gram-positive spore-formers Clostridium difficile and C. botulinum. Three included families are novel selenoproteins in most instances, including two ABC transporter subunits, one a substrate-binding protein with another CU motif, the other a permease subunit with selenocysteine at the substrate-gating position. Phylogenetic profiling shows a strong pattern of co-occurrence with Stickland metabolism selenoproteins, but an even closer link to a group of 8Fe-9S cofactor-type double-cubane proteins. These 8Fe-9S enzymes vary in count and in genome location but frequently sit next to the nine-gene locus. We have named the locus SAO, because of the Selenocysteine-Assisted Organometallic (SAO) biochemistry implied by an uptake ABC transporter with apparent metal-binding selenocysteines, complementary metal efflux pump SaoE, the MerB-like cytosolic enzyme now called SaoL, and comparative genomics signatures suggesting energy metabolism rather than metal resistance. Hypothesizing cycles of formation and dismutation of organometallic compounds involved in fermentative metabolism, we examined methylmercury formation proteins, and discovered most HgcA proteins are selenoproteins as well, with a CU motif N-terminal to the previously predicted start. Seeking additional rare and overlooked selenoproteins, tricky because of their rarity, could help reveal more candidate cryptic biochemical processes.
Bioorthogonal in-cell Labeling and Profiling of N6-isopentenyladenosine (i6A) Modified RNA
Authors: Wang Sheng , Li Yuanyuan , Zhou Hongling , Wang Li , Gan Youfang , Zhang Shusheng , Zheng Ya Ying , Sheng Jia , Wang Rui 
Published: July 2022

AbstractChemical modifications in RNAs play critical roles in structural diversification and functional regulation of many vital biochemical processes. Several hydrophobic prenyl-modifications have been discovered in a variety of RNA species since the 1990s. Prenyl groups are the feedstocks of terpene and many other biological molecules and the processes of prenylation in different macromolecules have been widely studied. We present here a new chemical biology technique to identify and label i6A, a prenyl-modified RNA residue, based on the unique reactivity of the prenyl group. We also found that iodine-mediated cycloaddition reactions of the prenyl group occurs in a superfast manner, and converts i6A from a hydrogen-bond acceptor into a donor. Based on this reactivity, we developed an iodine-mediated oxidation and reverse transcription (IMORT) method to profile cellular i6A residues with a single-base resolution, allowing for the transcriptome-wide detection and analysis of various i6A-containing RNA species.
Myoscaffolds reveal laminin scarring is detrimental for stem cell function while sarcospan induces compensatory fibrosis
Authors: Stearns-Reider Kristen M. , Hicks Michael R. , Hammond Katherine G. , Reynolds Joseph C. , Maity Alok , Kurmangaliyev Yerbol Z. , Chin Jesse , Stieg Adam , Geisse Nicholas A. , Hohlbauch Sophia , Kaemmer Stefan , Schmitt Lauren R. , Pham Thanh T. , Yamauchi Ken , Novitch Bennett G. , Wollman Roy , Hansen Kirk C. , Pyle April D. , Crosbie Rachelle H. 
Published: July 2022

ABSTRACTWe developed an on-slide decellularization approach to generate acellular extracellular matrix (ECM) scaffolds that can be repopulated with various cell types to interrogate cell-ECM interactions. Using this platform, we investigated whether fibrotic ECM scarring affected human skeletal muscle progenitor cell (SMPC) functions that are essential for myoregeneration. SMPCs exhibited robust adhesion, motility, and differentiation on healthy muscle-derived myoscaffolds. All SPMC interactions with fibrotic myoscaffolds from dystrophic muscle were severely blunted including reduced motility rate and migration. Furthermore, SMPCs were unable to remodel laminin dense fibrotic scars within diseased myoscaffolds. Proteomics and structural analysis revealed that excessive collagen deposition alone is not pathological, and can be compensatory, as revealed by overexpression of sarcospan and its associated ECM receptors in dystrophic muscle. Our in vivo data also supported that ECM remodeling is important for SMPC engraftment and that fibrotic scars may represent one barrier to efficient cell therapy.