bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling
Authors: Schöpping Marie , Gaspar Paula , Neves Ana Rute , Franzén Carl Johan , Zeidan Ahmad A. 
Published: December 2021

AbstractAlthough bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lactis BB-12® and B. longum subsp. longum BB-46, and subjected to iterative cycles of manual curation and experimental validation. A constraint-based modeling framework was used to probe the metabolic landscape of the strains and identify their essential nutritional requirements. Both strains showed an absolute requirement for pantethine as a precursor for coenzyme A biosynthesis. Menaquinone-4 was found to be essential only for BB-46 growth, whereas nicotinic acid was only required by BB-12®. The model-generated insights were used to formulate a chemically defined medium that supports the growth of both strains to the same extent as a complex culture medium. Carbohydrate utilization profiles predicted by the models were experimentally validated. Furthermore, model predictions were quantitatively validated in the newly formulated medium in lab-scale batch fermentations. The models and the formulated medium represent valuable tools to further explore the metabolism and physiology of the two species, investigate the mechanisms underlying their health-promoting effects and guide the optimization of their industrial production processes.
Malaria transmission-blocking conjugate vaccine in ALFQ adjuvant induces durable functional immune responses in rhesus macaques
Authors: Scaria Puthupparampil V. , Anderson Charles , Muratova Olga , Alani Nada , Trinh Hung V. , Nadakal Steven T. , Zaidi Irfan , Lambert Lynn , Beck Zoltan , Barnafo Emma K. , Rausch Kelly M. , Rowe Chris , Chen Beth , Matyas Gary R. , Rao Mangala , Alving Carl R. , Narum David L. , Duffy Patrick E. 
Published: December 2021

AbstractMalaria transmission-blocking vaccines candidates based on Pfs25 and Pfs230 have advanced to clinical studies. Exoprotein A (EPA) conjugate of Pfs25 in Alhydrogel® developed functional immunity in humans, with limited durability. Pfs230 conjugated to EPA (Pfs230D1-EPA) with liposomal adjuvant AS01 is currently in clinical trials in Mali. Studies with these conjugates revealed that non-human primates are better than mice to recapitulate the human immunogenicity and functional activity. Here, we evaluated the effect of ALFQ, a liposomal adjuvant consisting of TLR4 agonist and QS21, on the immunogenicity of Pfs25-EPA and Pfs230D1-EPA in Rhesus macaques. Both conjugates generated strong antibody responses and functional activity after two vaccinations though activity declined rapidly. A third vaccination of Pfs230D1-EPA induced functional activity lasting at least 9 months. Antibody avidity increased with each vaccination and correlated strongly with functional activity. IgG subclass analysis showed induction of Th1 and Th2 subclass antibody levels that correlated with activity.
Reactive oxygen species limit intestinal mucosa-bacteria homeostasis in vitro
Authors: Luchan Joshua , Choi Christian , Carrier Rebecca L. 
Published: December 2021

AbstractInteractions between epithelial and immune cells with the gut microbiota have wide-ranging effects on many aspects of human health. Therefore, there is value in developing in vitro models capable of performing highly controlled studies of such interactions. However, several critical factors that enable long term homeostasis between bacterial and mammalian cultures have yet to be established. In this study, we explored a model consisting of epithelial and immune cells, as well as four different bacterial species (Bacteroides fragilis KLE1958, Escherichia coli MG1655, Lactobacillus rhamnosus KLE2101, or Ruminococcus gnavus KLE1940), over a 50 hour culture period. Interestingly, both obligate and facultative anaerobes grew to similar extents in aerobic culture environments during the co-culture period, likely due to measured microaerobic oxygen levels near the apical surface of the epithelia. It was demonstrated that bacteria elicited reactive oxygen species (ROS) production, and that the resulting oxidative damage heavily contributed to observed epithelial barrier damage in these static cultures. Introduction of a ROS scavenger significantly mitigated oxidative damage, improving cell monolayer integrity and reducing lipid peroxidation, although not to control (bacteria-free culture) levels. These results indicate that monitoring and mitigating ROS accumulation and oxidative damage can enable longer term bacteria-intestinal epithelial cultures, while also highlighting the significance of additional factors that impact homeostasis in mammalian cell-bacteria systems.
Circular RNA mediated gene regulation in chronic diabetic complications
Authors: Patil Nikhil S. , Feng Biao , Su Zhaoliang , Castellani Christina A. , Chakrabarti Subrata 
Published: December 2021

AbstractChronic diabetic complications affect multiple organs causing widespread organ damage. Although there are some commonalities, the phenotype of such changes show tissue specific variation. Given this, we examined whether differences in circular RNA (circRNA) mediated gene regulatory mechanisms contribute to changes in gene expression at the basal level and in diabetes. CircRNAs are single-stranded RNA with covalently closed loop structures and act as miRNA sponges, factors of RNA splicing, scaffolding for proteins, regulators of transcription, and modulators of the expression of parental genes, among other roles. We examined heart and retinal tissue from Streptozotocin-induced diabetic mice with established diabetes related tissue damage and tissue from non-diabetic controls. A custom array analysis was performed and the data were analysed. Two major circRNA mediated processes were uniquely upregulated in diabetic heart tissue, namely, positive regulation of endothelial cell migration and regulation of mitochondria: mitochondrial electron transport. In the retina, circRNAs regulating extracellular matrix protein production and endothelial to mesenchymal transition (EndMT) were found to be upregulated. The current study identified regulatory and potential pathogenetic roles of specific circRNA in diabetic retinopathy and cardiomyopathy. Understanding such novel mechanisms, may in the future, be useful to develop RNA based treatment strategies.
Mechanism of kinetin-induced death of Vicia faba ssp. minor root cortex cells
Authors: Kaźmierczak Andrzej , Kunikowska Anita , Doniak Magdalena , Kornaś Andrzej 
Published: December 2021

AbstractCell death (CD) may be induced by endogenous or exogenous factors and contributes to all the steps of plant development. This paper presents results related to the mechanism of CD regulation induced by kinetin (Kin) in the root cortex of Vicia faba ssp. minor. To explain the process, 6-(2-hydroxy-3-methylbenzylamino)purine (PI-55), adenine (Ad), 5′-amine-5′-deoxyadenosine (Ado) and N-(2-chloro-4-piridylo)-N′-phenylurea (CPPU) were applied to (i) block cytokinin receptors (CKs) and inhibit the activities of enzymes of CK metabolism, i.e., (ii) phosphoribosyltransferase, (iii) kinases, and (iv) oxidases, respectively. Moreover, ethylene glycol-bis(β-aminoethyl ether)-N,N,N′,N′-tetraacetic acid (EGTA), lanthanum chloride (LaCl3), ruthenium red (RRed) and cyclosporine A (CS-A) were applied to (i) chelate extracellular calcium ions (Ca2+) as well as blocks of (ii) plasma-, (iii) endoplasmic reticulum- (ER) membrane Ca2+ ion channels and (iv) mitochondria- (MIT) Ca2+ ions release by permeability transition por (PTP), respectively. The measured physiological effectiveness of these factors was the number of living and dying cortex cells estimated with orange acridine (OA) and ethidium bromide (EB), the amounts of cytosolic Ca2+ ions with chlortetracycline (CTC) staining and the intensity of chromatin and Ca2+-CTC complex fluorescence, respectively. Moreover, the role of sorafenib, an inhibitor of RAF kinase, on the vitality of cortex cells and ethylene levels as well as the activities of RAF-like kinase and MEK2 with Syntide-2 and Mek2 as substrates were studied. The results clarified the previously presented suggestion that Kin is converted to appropriate ribotides (5′-monophosphate ribonucleotides), which cooperate with the ethylene and Ca2+ ion signalling pathways to transduce the signal of kinetin-programmed cell death (Kin-PCD). Based on the present and previously published results related to Kin-PCD, the crosstalk between ethylene and MAP kinase signalling, as well as inhibitors of CK receptors and enzymes of their metabolism, is proposed.
High-throughput nanofluidic real-time PCR to discriminate Pneumococcal Conjugate Vaccine (PCV)-associated serogroups 6, 18, and 22 to serotypes using modified oligonucleotides
Authors: Downs S. L. , Madhi S. A. , Van der Merwe L. , Nunes M. C. , Olwagen C. P. 
Published: December 2021

AbstractCurrent real-time high-throughput Polymerase Chain Reaction (qPCR) methods do not distinguish serotypes 6A from 6B, 18C from 18A/B and 22F from 22A. We established a nanofluidic real-time PCR (Fluidigm) for serotyping that included Dual-Priming-Oligonucleotides (DPO), a Locked-Nucleic-Acid (LNA) probe and TaqMan assay-sets for high-throughput serotyping. The designed assay-sets target capsular gene wciP in serogroup 6, wciX and wxcM in serogroup 18, and wcwA in serogroup 22. An algorithm combining results from published assay-sets (6A/B/C/D; 6C/D; 18A/B/C; 22A/F) and designed assay-sets for 6A/C; 18B/C/F; 18C/F, 18F and 22F was validated through blind analysis of 1973 archived clinical samples collected from South African children ≤ 5-years-old (2009–2011), previously serotyped with the culture-based Quellung method. All assay-sets were efficient (92–101%), had low variation between replicates (R2 > 0.98), and were able to detect targets at a limit of detection (LOD) of < 100 Colony-Forming-Units (CFU)/mL of sample. There was high concordance (Kappa = 0.73–0.92); sensitivity (85–100%) and specificity (96–100%) for Fluidigm compared with Quellung for serotyping 6A; 6B; 6C; 18C and 22F. Fluidigm distinguishes vaccine-serotypes 6A, 6B, 18C, next-generation PCV-serotype 22F and non-vaccine-serotypes 6C, 6D, 18A, 18B, 18F and 22A. Discriminating single serotypes is important for assessing serotype replacement and the impact of PCVs on vaccine- and non-vaccine serotypes.
Respiratory function modulated during execution, observation, and imagination of walking via SII
Authors: Pellicano Antonello , Mingoia Gianluca , Ritter Christoph , Buccino Giovanni , Binkofski Ferdinand 
Published: December 2021

AbstractThe Mirror Neurons System (MNS) consists of brain areas active during actions execution, as well as observation-imagination of the same actions. MNS represents a potential mechanism by which we understand other's action goals. We investigated MNS activation for legs actions, and its interaction with the autonomic nervous system. We performed a physiological and fMRI investigation on the common neural structures recruited during the execution, observation, and imagination of walking, and their effects on respiratory activity. Bilateral SMA were activated by all three tasks, suggesting that these areas are responsible for the core of the MNS effect for walking. Moreover, we observed in bilateral parietal opercula (OP1, secondary somatosensory cortex-SII) evidence of an MNS subtending walking execution-observation-imagination that also modulated the respiratory function. We suggest that SII, in modulating the vegetative response during motor activity but also during observation-imagination, consists of a re-enacting function which facilitates the understanding of motor actions.
Kinetics of DNA looping by Anabaena sensory rhodopsin transducer (ASRT) by using DNA cyclization assay
Authors: Lee Jae Jin , Kim Sung Hyun , Lee Keon Ah , Chuon Kimleng , Jung Kwang-Hwan , Kim Doseok 
Published: December 2021

AbstractDNA cyclization assay together with single-molecule FRET was employed to monitor protein-mediated bending of a short dsDNA (~ 100 bp). This method provides a simple and easy way to monitor the structural change of DNA in real-time without necessitating prior knowledge of the molecular structures for the optimal dye-labeling. This assay was applied to study how Anabaena sensory rhodopsin transducer (ASRT) facilitates loop formation of DNA as a possible mechanism for gene regulation. The ASRT-induced DNA looping was maximized at 50 mM of Na+, while Mg2+ also played an essential role in the loop formation.
iTRAQ based protein profile analysis revealed key proteins involved in regulation of drought-tolerance during seed germination in Adzuki bean
Authors: Han Xuesong , Yang Fangwen , Zhao Yongguo , Chen Hongwei , Wan Zhenghuang , Li Li , Sun Longqing , Liu Liangjun , Jiao Chunhai , Liu Changyan , Sha Aihua 
Published: December 2021

AbstractAdzuki bean is an important legume crop due to its high-quality protein, fiber, vitamins, minerals as well as rich bioactive substances. However, it is vulnerable to drought at the germination stage. However, little information is available about the genetic control of drought tolerance during seed germination in adzuki bean. In this study, some differential expression proteins (DEPs) were identified during seed germination between the drought-tolerant variety 17235 and drought-sensitive variety 17033 in adzuki bean using iTRAQ method. A total of 2834 proteins were identified in the germinating seeds of these two adzuki beans. Compared with the variety 17033, 87 and 80 DEPs were increased and decreased accumulation in variety 17235 under drought, respectively. Meanwhile, in the control group, a few DEPs, including 9 up-regulated and 21 down-regulated proteins, were detected in variety 17235, respectively. GO, KEGG, and PPI analysis revealed that the DEPs related to carbohydrate metabolism and energy production were significantly increased in response to drought stresses. To validate the proteomic function, the ectopic overexpression of V-ATPase in tobacco was performed and the result showed that V-ATPase upregulation could enhance the drought tolerance of tobacco. The results provide valuable insights into genetic response to drought stress in adzuki bean, and the DEPs could be applied to develop biomarkers related to drought tolerant in adzuki bean breeding projects.
C-reactive protein independently predicts survival in pancreatic neuroendocrine neoplasms
Authors: Nießen Anna , Schimmack Simon , Sandini Marta , Fliegner Dominik , Hinz Ulf , Lewosinska Magdalena , Hackert Thilo , Büchler Markus W. , Strobel Oliver 
Published: December 2021

AbstractPancreatic neuroendocrine neoplasms (pNEN) are highly variable in their postresection survival. Determination of preoperative risk factors is essential for treatment strategies. C-reactive protein (CRP) has been implicated in the pathogenesis of pNEN and shown to be associated with survival in different tumour entities. Patients undergoing surgery for pNEN were retrospectively analysed. Patients were divided into three subgroups according to preoperative CRP serum levels. Clinicopathological features, overall and disease-free survival were assessed. Uni- and multivariable survival analyses were performed. 517 surgically resected pNEN patients were analysed. CRP levels were significantly associated with relevant clinicopathological parameters and prognosis and were able to stratify subgroups with significant and clinically relevant differences in overall and disease-free survival. In univariable sensitivity analyses CRP was confirmed as a prognostic factor for overall survival in subgroups with G2 differentiation, T1/T2 and T3/T4 tumour stages, patients with node positive disease and with and without distant metastases. By multivariable analysis, preoperative CRP was confirmed as an independent predictor of postresection survival together with patient age and the established postoperative pathological predictors grading, T-stage and metastases. Preoperative serum CRP is a strong predictive biomarker for both overall and disease free survival of surgically resected pNEN. CRP is associated with prognosis independently of grading and tumour stage and may be of additional use for treatment decisions.
Stimulation efficiency of an actuator driven piston at the biological interface to the inner ear
Authors: Busch Susan , Ghoncheh Mohammad , Lenarz Thomas , Maier Hannes 
Published: December 2021

AbstractDirect acoustic cochlear stimulation uses piston motion to substitute for stapes footplate (SFP) motion. The ratio of piston to stapes footplate motion amplitude, to generate the same loudness percept, is an indicator of stimulation efficiency. We determined the relationship between piston displacement to perceived loudness, the achieved maximum power output and investigated stapes fixation and obliteration as confounding factors. The electro-mechanical transfer function of the actuator was determined preoperatively on the bench and intraoperatively by laser Doppler vibrometry. Clinically, perceived loudness as a function of actuator input voltage was calculated from bone conduction thresholds and direct thresholds via the implant. The displacement of a 0.4 mm diameter piston required for a perception equivalent to 94 dB SPL at the tympanic membrane compared to normal SFP piston displacement was 27.6–35.9 dB larger, consistent with the hypothesis that the ratio between areas is responsible for stimulation efficiency. Actuator output was 110 ± 10 eq dB SPLFF @1Vrms ≤ 3 kHz and decreased to 100 eq dB SPLFF at 10 kHz. Output was significantly higher for mobile SFPs but independent from obliteration. Our findings from clinical data strongly support the assumption of a geometrical dependency on piston diameter at the biological interface to the cochlea.
Pharmacogenetics of induction therapy-related toxicities in childhood acute lymphoblastic leukemia patients treated with UKALL 2003 protocol
Authors: Aslam Sara , Ameer Sonia , Shabana N. A. , Ahmed Mehboob 
Published: December 2021

AbstractChemotherapy related toxicities have been the major factor limiting the success of acute lymphoblastic leukemia (ALL) induction therapy. Several factors, including the pharmacogenetics of asparaginase and anthracyclines, could contribute to difference in treatment outcome in ALL. We investigated the significance of variations in genes involved in hepatic and cardiac toxicity in acute lymphoblastic leukemia (ALL). Genotyping of SOD2 (rs4880), PNPL3 (rs738409) and ABCC1 (rs4148350), CBR1 (rs9024) and ABCG2 (rs2231142) was performed by Tetra-ARMS PCR-based technique to evaluate the genotype–phenotype correlation. Our results showed only minor allele G of SOD2 rs4880 increase the risk of hepatic toxicity [OR 2.63 (1.42–4.84), P =  < 0.05] while minor alleles of other SNPs showed protective impact. However, the genetic contrast analysis showed a recessive form of SOD2 rs4880 [OR 7.82 (3.86–15.85), P =  < 0.05] and PNPLA3 I148M [OR 5.82 (3.43–9.87), P =  < 0.05] variants whereas dominant genotype of ABCC1 rs4148350 [OR 2.52 (1.55–4.10), P =  < 0.05] significantly predisposes hepatotoxicity. Furthermore, heterozygous form of ABCG2 rs2231142 [OR 5.25 (1.84–14.95), P =  < 0.05] and recessive genotype of 3′UTR variant CBR1 rs9024 [OR 2.31 (1.31–4.07), P =  < 0.05] were strongly associated with cardiotoxicity. The information obtained from these genetic variations could offer biomarkers for individualization of therapeutic intervention in ALL.
Deep learning for anatomical interpretation of video bronchoscopy images
Authors: Yoo Ji Young , Kang Se Yoon , Park Jong Sun , Cho Young-Jae , Park Sung Yong , Yoon Ho Il , Park Sang Jun , Jeong Han-Gil , Kim Tackeun 
Published: December 2021

AbstractAnesthesiologists commonly use video bronchoscopy to facilitate intubation or confirm the location of the endotracheal tube; however, depth and orientation in the bronchial tree can often be confused because anesthesiologists cannot trace the airway from the oropharynx when it is performed using an endotracheal tube. Moreover, the decubitus position is often used in certain surgeries. Although it occurs rarely, the misinterpretation of tube location can cause accidental extubation or endobronchial intubation, which can lead to hyperinflation. Thus, video bronchoscopy with a decision supporting system using artificial intelligence would be useful in the anesthesiologic process. In this study, we aimed to develop an artificial intelligence model robust to rotation and covering using video bronchoscopy images. We collected video bronchoscopic images from an institutional database. Collected images were automatically labeled by an optical character recognition engine as the carina and left/right main bronchus. Except 180 images for the evaluation dataset, 80% were randomly allocated to the training dataset. The remaining images were assigned to the validation and test datasets in a 7:3 ratio. Random image rotation and circular cropping were applied. Ten kinds of pretrained models with < 25 million parameters were trained on the training and validation datasets. The model showing the best prediction accuracy for the test dataset was selected as the final model. Six human experts reviewed the evaluation dataset for the inference of anatomical locations to compare its performance with that of the final model. In the experiments, 8688 images were prepared and assigned to the evaluation (180), training (6806), validation (1191), and test (511) datasets. The EfficientNetB1 model showed the highest accuracy (0.86) and was selected as the final model. For the evaluation dataset, the final model showed better performance (accuracy, 0.84) than almost all human experts (0.38, 0.44, 0.51, 0.68, and 0.63), and only the most-experienced pulmonologist showed performance comparable (0.82) with that of the final model. The performance of human experts was generally proportional to their experiences. The performance difference between anesthesiologists and pulmonologists was marked in discrimination of the right main bronchus. Using bronchoscopic images, our model could distinguish anatomical locations among the carina and both main bronchi under random rotation and covering. The performance was comparable with that of the most-experienced human expert. This model can be a basis for designing a clinical decision support system with video bronchoscopy.