bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance Evaluation of the IR Biotyper® System for Clinical Microbiology: Application for Detection of Staphylococcus aureus Sequence Type 8 Strains
Authors: Hong Jun Sung , Kim Dokyun , Jeong Seok Hoon
Published: July 2022

Background: Methicillin-resistant S. aureus (MRSA) clonal lineages have been classified based on sequence type (ST) and pulsotype associated with human infection. Providing rapid and accurate epidemiological insight is important to address proper infection control in both community-acquired and nosocomial hospital settings. In this regard, this study was performed to evaluate the IR Biotyper® (IRBT®) for strain typing of S. aureus clinical isolates on three media. Methods: A total of 24 S. aureus clinical isolates comprising 15 MRSA isolates (six ST5, three ST72, three ST8, and three ST188 isolates) and nine methicillin-susceptible S. aureus (MSSA) isolates (three ST5, three ST72, and three ST8 isolates) were included for evaluating the IRBT®. Molecular characterization of all S. aureus isolates was performed by conventional PCR and sequencing methods. The IRBT® was evaluated according to manufacturer instructions and a modified sample procedure on commonly used BAP, MHA, and TSA media. Subsequently, the spectra obtained by IRBT® software were compared with dendrograms of PFGE analysis. Results: In this study, the modified sample procedure for reducing the amount of bacteria and bacterial concentration improved the acquisition quality pass rate of the IRBT®. Each spectrum of S. aureus ST5, ST72, and ST188 isolates on all three media could not be clustered by IRBT®. However, the dendrogram obtained from the spectra of S. aureus ST8 isolates on TSA medium were in concordance with that obtained by PFGE analysis. In addition, the visual distribution of S. aureus ST8 isolates on TSA medium in a 2D scatter plot appeared as separated point set from those of S. aureus ST5, ST72, and ST188 isolates. Conclusions: The IRBT® system is a rapid strain typing tool using the FTIR spectroscopic method. This system demonstrated the possibility of discriminating the strain types of S. aureus clinical isolates. Indeed, S. aureus ST8 isolates on TSA medium were successfully differentiated from other strain type isolates.
Novel Formula of Antiprotozoal Mixtures
Authors: Iwiński Hubert , Łyczko Jacek , Różański Henryk , Szumny Antoni
Published: July 2022

Antimicrobial resistance (AMR) is becoming more common in both bacteria and pathogenic protozoa. Therefore, new solutions are being sought as alternatives to currently used agents. There are many new ideas and solutions, especially compounds of natural origin, including essential oils. In the present study, the antiprotozoal activity of a mixture of essential oils (eucalyptus, lavender, cedar and tea tree), organic acids (acetic acid, propionic acid and lactic acid) and metal ions (Cu, Zn, Mn) were tested. As a model, protozoans were selected: Euglena gracilis, Gregarina blattarum, Amoeba proteus, Paramecium caudatum, Pentatrichomonas hominis. The tested concentrations of mixtures were in the range of 0.001–1.5%. The analyses show unexpected, very strong protozoicidal activity of combinations, presenting the synergy of compounds via determination of LD50 and LD100 values. Obtained mixtures showed significantly higher activity against protozoans, compared to chloramphenicol and metronidazole. Most of the analyzed samples show high antiprotozoal activity at very low concentration, in the range of 0.001–0.009%. The most effective combinations for all analyzed protozoans were the cedar essential oil and tea tree essential oil with a mixture of acids and manganese or zinc ions. Innovative combinations of essential oils, organic acids and metal ions are characterized by very high antiprotozoal activity at low doses, which, after further investigation, can be applicable for control of protozoan pathogens.
Evolutionary Dynamics between Phages and Bacteria as a Possible Approach for Designing Effective Phage Therapies against Antibiotic-Resistant Bacteria
Authors: Hasan Mahadi , Ahn Juhee
Published: July 2022

With the increasing global threat of antibiotic resistance, there is an urgent need to develop new effective therapies to tackle antibiotic-resistant bacterial infections. Bacteriophage therapy is considered as a possible alternative over antibiotics to treat antibiotic-resistant bacteria. However, bacteria can evolve resistance towards bacteriophages through antiphage defense mechanisms, which is a major limitation of phage therapy. The antiphage mechanisms target the phage life cycle, including adsorption, the injection of DNA, synthesis, the assembly of phage particles, and the release of progeny virions. The non-specific bacterial defense mechanisms include adsorption inhibition, superinfection exclusion, restriction-modification, and abortive infection systems. The antiphage defense mechanism includes a clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) system. At the same time, phages can execute a counterstrategy against antiphage defense mechanisms. However, the antibiotic susceptibility and antibiotic resistance in bacteriophage-resistant bacteria still remain unclear in terms of evolutionary trade-offs and trade-ups between phages and bacteria. Since phage resistance has been a major barrier in phage therapy, the trade-offs can be a possible approach to design effective bacteriophage-mediated intervention strategies. Specifically, the trade-offs between phage resistance and antibiotic resistance can be used as therapeutic models for promoting antibiotic susceptibility and reducing virulence traits, known as bacteriophage steering or evolutionary medicine. Therefore, this review highlights the synergistic application of bacteriophages and antibiotics in association with the pleiotropic trade-offs of bacteriophage resistance.
Network Security Node-Edge Scoring System Using Attack Graph Based on Vulnerability Correlation
Authors: Shin Gun-Yoon , Hong Sung-Sam , Lee Jung-Sik , Han In-Sung , Kim Hwa-Kyung , Oh Haeng-Rok
Published: July 2022

As network technology has advanced, and as larger and larger quantities of data are being collected, networks are becoming increasingly complex. Various vulnerabilities are being identified in such networks, and related attacks are continuously occurring. To solve these problems and improve the overall quality of network security, a network risk scoring technique using attack graphs and vulnerability information must be used. This technology calculates the degree of risk by collecting information and related vulnerabilities in the nodes and the edges existing in the network-based attack graph, and then determining the degree of risk in a specific network location or the degree of risk occurring when a specific route is passed within the network. However, in most previous research, the risk of the entire route has been calculated and evaluated based on node information, rather than edge information. Since these methods do not include correlations between nodes, it is relatively difficult to evaluate the risk. Therefore, in this paper, we propose a vulnerability Correlation and Attack Graph-based node-edge Scoring System (VCAG-SS) that can accurately measure the risk of a specific route. The proposed method uses the Common Vulnerability Scoring System (CVSS) along with node and edge information. Performing the previously proposed arithmetic evaluation of confidentiality, integrity, and availability (CIA) and analyzing the correlation of vulnerabilities between each node make it possible to calculate the attack priority. In the experiment, the risk scores of nodes and edges and the risk of each attack route were calculated. Moreover, the most threatening attack route was found by comparing the attack route risk. This confirmed that the proposed method calculated the risk of the network attack route and was able to effectively select the network route by providing the network route priority according to the risk score.
Data Privacy Security Mechanism of Industrial Internet of Things Based on Block Chain
Authors: Xie Yinggang , Li Yuxin , Ma Yunbin
Published: July 2022

In order to solve the problem that data of the industrial Internet of Things (IIoT) is easily tampered with and therefore, the authenticity of data may be questioned, a data-privacy security mechanism of the IIoT based on blockchain is proposed. At the same time, to solve the problem of master node selection and low efficiency in the practical Byzantine fault tolerance (PBFT) algorithm, a reward mechanism based on node behavior is introduced and an improved PBFT algorithm is proposed. The improved PBFT algorithm is more efficient, in line with the application scenarios of the IIoT. Comparative analysis results showed that the proposed blockchain-based data-privacy security mechanism of the IIoT is superior to other models in terms of consensus efficiency, throughput, and block generation speed.
An End-to-End Classifier Based on CNN for In-Air Handwritten-Chinese-Character Recognition
Authors: Hu Mianjun , Qu Xiwen , Huang Jun , Wu Xuangou
Published: July 2022

A convolutional neural network (CNN) has been successfully applied to in-air handwritten-Chinese-character recognition (IAHCCR). However, the existing models based on CNN for IAHCCR need to convert the coordinate sequence of a character into images. This conversion process increases training and classifying time, and leads to the loss of information. In order to solve this problem, we propose an end-to-end classifier based on CNN for IAHCCR in this paper, which, to knowledge, is novel for online handwritten-Chinese-character recognition (OLHCCR). Specifically, our model based on CNN directly takes the original coordinate sequence of an in-air handwritten-Chinese-character as input, and the output of the full connection layer is pooled by global average pooling to form a fixed-size feature vector, which is sent to softmax for classification. Our model can not only directly process coordinate sequences such as the models based on recurrent neural network (RNN), but can also obtain the global structure information of characters. We conducted experiments on two datasets, IAHCC-UCAS2016 and SCUT-COUCH2009. The experimental results show a comparison with existing CNN models based on image processing or RNN-based methods; our method does not require data augmentation techniques nor an ensemble of multiple trained models, and only uses a more compact structure to obtain higher recognition accuracy.
SPEEDY Quantum Circuit for Grover’s Algorithm
Authors: Song Gyeongju , Jang Kyoungbae , Kim Hyunjun , Eum Siwoo , Sim Minjoo , Kim Hyunji , Lee Waikong , Seo Hwajeong
Published: July 2022

In this paper, we propose a quantum circuit for the SPEEDY block cipher for the first time and estimate its security strength based on the post-quantum security strength presented by NIST. The strength of post-quantum security for symmetric key cryptography is estimated at the cost of the Grover key retrieval algorithm. Grover’s algorithm in quantum computers reduces the n-bit security of block ciphers to n2 bits. The implementation of a quantum circuit is required to estimate the Grover’s algorithm cost for the target cipher. We estimate the quantum resource required for Grover’s algorithm by implementing a quantum circuit for SPEEDY in an optimized way and show that SPEEDY provides either 128-bit security (i.e., NIST security level 1) or 192-bit security (i.e., NIST security level 3) depending on the number of rounds. Based on our estimated cost, increasing the number of rounds is insufficient to satisfy the security against quantum attacks on quantum computers.
Fast 3D Analytical Affine Transformation for Polygon-Based Computer-Generated Holograms
Authors: Fan Houxin , Zhang Bing , Zhang Yaping , Wang Fan , Qin Wenlong , Fu Qingyang , Poon Ting-Chung
Published: July 2022

We present a fast 3D analytical affine transformation (F3DAAT) method to obtain polygon-based computer-generated holograms (CGHs). CGHs consisting of tens of thousands of triangles from 3D objects are obtained by this method. We have attempted a revised method based on previous 3D affine transformation methods. In order to improve computational efficiency, we have derived and analyzed our proposed affine transformation matrix. We show that we have further increased the computational efficiency compared with previous affine methods. We also have added flat shading to improve the reconstructed image quality. A 3D object from a 3D camera is reconstructed holographically by numerical and optical experiments.
Computational Methods for Neuron Segmentation in Two-Photon Calcium Imaging Data: A Survey
Authors: Abbas Waseem , Masip David
Published: July 2022

Calcium imaging has rapidly become a methodology of choice for real-time in vivo neuron analysis. Its application to large sets of data requires automated tools to annotate and segment cells, allowing scalable image segmentation under reproducible criteria. In this paper, we review and summarize the most recent methods for computational segmentation of calcium imaging. The contributions of the paper are three-fold: we provide an overview of the main algorithms taxonomized in three categories (signal processing, matrix factorization and machine learning-based approaches), we highlight the main advantages and disadvantages of each category and we provide a summary of the performance of the methods that have been tested on public benchmarks (with links to the public code when available).
Physical and Metaphysical Visualities: Vasily Rozanov and Historical Artefacts
Authors: Mondry Henrietta
Published: July 2022

In Russian modernism, the work of writer Vasily Rozanov (1856–1919) presents an understudied case of constructing a worldview based on the study of the parallel history of human physicality and artefacts, which he articulated within the framework of the physical and metaphysical. I argue that Rozanov widened the domain of what was viewed as “compelling visuality” at his time, in line with the subjective synthesising principles of his worldview. He looked in art for the manifestations of that which he considered to be eternal and trans-historical: the mystery of the metaphysical roots of human sexuality.
Post-Mortem Interval of Human Skeletal Remains Estimated with Handheld NIR Spectrometry
Authors: Schmidt Verena Maria , Zelger Philipp , Wöss Claudia , Huck Christian Wolfgang , Arora Rohit , Bechtel Etienne , Stahl Andreas , Brunner Andrea , Zelger Bettina , Schirmer Michael , Rabl Walter , Pallua Johannes Dominikus
Published: July 2022

Estimating the post-mortem interval (PMI) of human skeletal remains is a critical issue of forensic analysis, with important limitations such as sample preparation and practicability. In this work, NIR spectroscopy (NIRONE® Sensor X; Spectral Engines, 61449, Germany) was applied to estimate the PMI of 104 human bone samples between 1 day and 2000 years. Reflectance data were repeatedly collected from eight independent spectrometers between 1950 and 1550 nm with a spectral resolution of 14 nm and a step size of 2 nm, each from the external and internal bone. An Artificial Neural Network was used to analyze the 66,560 distinct diagnostic spectra, and clearly distinguished between forensic and archaeological bone material: the classification accuracies for PMIs of 0–2 weeks, 2 weeks–6 months, 6 months–1 year, 1 year–10 years, and >100 years were 0.90, 0.94, 0.94, 0.93, and 1.00, respectively. PMI of archaeological bones could be determined with an accuracy of 100%, demonstrating the adequate predictive performance of the model. Applying a handheld NIR spectrometer to estimate the PMI of human skeletal remains is rapid and extends the repertoire of forensic analyses as a distinct, novel approach.
Maternal Adipocyte Connexin43 Gap Junctions Affect Breastmilk Lactose Levels and Neonate Growth in Mice
Authors: Huang Mingyang , Song Anying , Chen Xi , Ishtiaq Sarah , Wang Chunmei , Hadsell Darryl L. , Wang Qiong A. , Zhu Yi
Published: July 2022

Breastfeeding offers a broad spectrum of health benefits for infants. However, overnutrition and a steady increase in maternal obesity in the U.S. have made it harder for many mothers to produce and express breastmilk, and the quality of milk from obese mothers is also frequently compromised. Adipocytes, the primary cell type in the non-lactating breast, display a drastic morphological and functional change during lactation in mice. Lipid-filled adipocytes undergo lipolysis, and lipid droplets disappear to provide fatty acids and energy for breastmilk production. Once the animal stops lactation, these lipid-depleted adipocytes return as lipid-laden cells. This dynamic remodeling of the tissue is likely the result of active intercellular communications. Connexin43 (Cx43) is the most abundant connexin in the mammary adipose tissue that makes up the gap junctions for direct intercellular communications. Its expression is increased during lactation and reduced in obese mammary adipose tissue, which is resistant to lactation-induced remodeling. However, whether Cx43 is required for adipocyte remodeling and breastmilk production to support neonates’ growth has not been established. In this study, we used doxycycline-inducible adipocyte-specific Cx43-deleted mice and demonstrated that adipocyte Cx43 played a vital role in determining the carbohydrate levels in breastmilk, which may subsequently affect neonates’ growth.
Machine Learning Algorithms Highlight tRNA Information Content and Chargaff’s Second Parity Rule Score as Important Features in Discriminating Probiotics from Non-Probiotics
Authors: Bergamini Carlo M. , Bianchi Nicoletta , Giaccone Valerio , Catellani Paolo , Alberghini Leonardo , Stella Alessandra , Biffani Stefano , Yaddehige Sachithra Kalhari , Bobbo Tania , Taccioli Cristian
Published: July 2022

Probiotic bacteria are microorganisms with beneficial effects on human health and are currently used in numerous food supplements. However, no selection process is able to effectively distinguish probiotics from non-probiotic organisms on the basis of their genomic characteristics. In the current study, four Machine Learning algorithms were employed to accurately identify probiotic bacteria based on their DNA characteristics. Although the prediction accuracies of all algorithms were excellent, the Neural Network returned the highest scores in all the evaluation metrics, managing to discriminate probiotics from non-probiotics with an accuracy greater than 90%. Interestingly, our analysis also highlighted the information content of the tRNA sequences as the most important feature in distinguishing the two groups of organisms probably because tRNAs have regulatory functions and might have allowed probiotics to evolve faster in the human gut environment. Through the methodology presented here, it was also possible to identify seven promising new probiotics that have a higher information content in their tRNA sequences compared to non-probiotics. In conclusion, we prove for the first time that Machine Learning methods can discriminate human probiotic from non-probiotic organisms underlining information within tRNA sequences as the most important genomic feature in distinguishing them.
Cell Confluence Modulates TRPV4 Channel Activity in Response to Hypoxia
Authors: Barbeau Solène , Joushomme Alexandre , Chappe Yann , Cardouat Guillaume , Baudrimont Isabelle , Freund-Michel Véronique , Guibert Christelle , Marthan Roger , Berger Patrick , Vacher Pierre , Percherancier Yann , Quignard Jean-François , Ducret Thomas
Published: July 2022

Transient receptor potential vanilloid 4 (TRPV4) is a polymodal Ca2+-permeable channel involved in various hypoxia-sensitive pathophysiological phenomena. Different tools are available to study channel activity, requiring cells to be cultured at specific optimal densities. In the present study, we examined if cell density may influence the effect of hypoxia on TRPV4 activity. Transiently TRPV4-transfected HEK293T cells were seeded at low or high densities corresponding to non-confluent or confluent cells, respectively, on the day of experiments, and cultured under in vitro normoxia or hypoxia. TRPV4-mediated cytosolic Ca2+ responses, single-channel currents, and Ca2+ influx through the channel were measured using Ca2+ imaging/microspectrofluorimetric assay, patch-clamp, and Bioluminescence Resonance Energy Transfer (BRET), respectively. TRPV4 plasma membrane translocation was studied using confocal microscopy, biotinylation of cell surface proteins, and BRET. Our results show that hypoxia exposure has a differential effect on TRPV4 activation depending on cell confluence. At low confluence levels, TRPV4 response is increased in hypoxia, whereas at high confluence levels, TRPV4 response is strongly inhibited, due to channel internalization. Thus, cell density appears to be a crucial parameter for TRPV4 channel activity.
A Systematic Review of Sleep–Wake Disorder Diagnostic Criteria Reliability Studies
Authors: Gauld Christophe , Lopez Régis , Philip Pierre , Taillard Jacques , Morin Charles M. , Geoffroy Pierre Alexis , Micoulaud-Franchi Jean-Arthur
Published: July 2022

The aim of this article is to provide a systematic review of reliability studies of the sleep–wake disorder diagnostic criteria of the international classifications used in sleep medicine. Electronic databases (ubMed (1946–2021) and Web of Science (—2021)) were searched up to December 2021 for studies computing the Cohen’s kappa coefficient of diagnostic criteria for the main sleep–wake disorder categories described in the principal classifications. Cohen’s kappa coefficients were extracted for each main sleep–wake disorder category, for each classification subtype, and for the different types of methods used to test the degree of agreement about a diagnosis. The database search identified 383 studies. Fifteen studies were analyzed in this systematic review. Insomnia disorder (10/15) and parasomnia disorder (7/15) diagnostic criteria were the most studied. The reliability of all sleep–wake disorders presented a Cohen’s kappa with substantial agreement (Cohen’s kappa mean = 0.66). The two main reliability methods identified were “test–retest reliability” (11/15), principally used for International Classification of Sleep Disorders (ICSD), and “joint interrater reliability” (4/15), principally used for Diagnostic and Statistical Manual of Mental Disorders (DSM) subtype diagnostic criteria, in particularl, the DSM-5. The implications in terms of the design of the methods used to test the degree of agreement about a diagnosis in sleep medicine are discussed.
Association between Cholesterol Level and the Risk of Hematologic Malignancy According to Menopausal Status: A Korean Nationwide Cohort Study
Authors: Jung Wonyoung , Jeon Keun Hye , Kang Jihun , Choi Taewoong , Han Kyungdo , Jin Sang-Man , Jeong Su-Min , Shin Dong Wook
Published: July 2022

Recent studies have revealed the possible association between serum cholesterol levels and hematologic malignancy (HM). However, limited information is available about how reproductive factors interact with this association. Therefore, we investigated the roles of serum cholesterol in the risk of HM according to the menopausal status. We finally identified 1,189,806 premenopausal and 1,621,604 postmenopausal women who underwent a national health screening program in 2009 using data from the Korean National Health Insurance Service database. Overall, 5449 (0.19%) developed HM. Among postmenopausal women, the inverse associations were observed between total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) levels, and the risk of overall HM. In premenopausal women, the highest quartile of HDL-C was associated with a reduced risk of HM compared with the lowest quartile of HDL-C consistent with results in postmenopausal women (adjusted hazard ratio [aHR] 0.80, 95% confidence interval [CI] [0.68–0.95]), whereas the highest quartile of triglyceride (TG) showed an increased risk of HM compared to the lowest quartile of TG, (aHR 1.22, 95% CI [1.02,1.44]) only in premenopausal women. Our finding suggests that lipid profiles are differently associated with HM risk by menopausal status.
Kinetin Ameliorates Cisplatin-Induced Hepatotoxicity and Lymphotoxicity via Attenuating Oxidative Damage, Cell Apoptosis and Inflammation in Rats
Authors: Fathy Moustafa , Darwish Mostafa A. , Abdelhamid Al-Shaimaa M. , Alrashedy Gehad M. , Othman Othman Ali , Naseem Muhammad , Dandekar Thomas , Othman Eman M.
Published: July 2022

Though several previous studies reported the in vitro and in vivo antioxidant effect of kinetin (Kn), details on its action in cisplatin-induced toxicity are still scarce. In this study we evaluated, for the first time, the effects of kinetin in cisplatin (cp)- induced liver and lymphocyte toxicity in rats. Wistar male albino rats were divided into nine groups: (i) the control (C), (ii) groups 2,3 and 4, which received 0.25, 0.5 and 1 mg/kg kinetin for 10 days; (iii) the cisplatin (cp) group, which received a single intraperitoneal injection of CP (7.0 mg/kg); and (iv) groups 6, 7, 8 and 9, which received, for 10 days, 0.25, 0.5 and 1 mg/kg kinetin or 200 mg/kg vitamin C, respectively, and Cp on the fourth day. CP-injected rats showed a significant impairment in biochemical, oxidative stress and inflammatory parameters in hepatic tissue and lymphocytes. PCR showed a profound increase in caspase-3, and a significant decline in AKT gene expression. Intriguingly, Kn treatment restored the biochemical, redox status and inflammatory parameters. Hepatic AKT and caspase-3 expression as well as CD95 levels in lymphocytes were also restored. In conclusion, Kn mitigated oxidative imbalance, inflammation and apoptosis in CP-induced liver and lymphocyte toxicity; therefore, it can be considered as a promising therapy.
Prediction of Conserved HLA Class I and Class II Epitopes from SARS-CoV-2 Licensed Vaccines Supports T-Cell Cross-Protection against SARS-CoV-1
Authors: López Daniel
Published: July 2022

Heterologous immunity-inducing vaccines against different pathogens are necessary to deal with new pandemics. In this study, the possible impact of COVID-19 licensed formulations in the cytotoxic and the helper cellular immune responses against SARS-CoV-1 is analyzed for the 567 and 41 most abundant HLA class I and II alleles, respectively. Computational prediction showed that most of these 608 alleles, which cover >90% of the human population, contain enough conserved T-cell epitopes among SARS-CoV-1 and SARS-CoV-2 spike proteins. In addition, the vast majority of these predicted peptides were defined as epitopes recognized by CD4+ or CD8+ T lymphocytes, showing a very high correlation between the bioinformatics prediction and the experimental assays. These data suggest that both cytotoxic and helper cellular immune protection elicited by the currently licensed COVID-19 vaccines should be effective against SARS-CoV-1 infection. Lastly, this study has potential implications for public health against current and future pandemics, given that the SARS-CoV-1 vaccines in pipeline since the early 20th century could generate similarly cross-protection against COVID-19.
The Upregulation of Caffeic Acid Phenethyl Ester on Growth Differentiation Factor 15 Inhibits Transforming Growth Factor β/Smad Signaling in Bladder Carcinoma Cells
Authors: Hou Chen-Pang , Tsui Ke-Hung , Chen Syue-Ting , Chang Kang-Shuo , Sung Hsin-Ching , Hsu Shu-Yuan , Lin Yu-Hsiang , Feng Tsui-Hsia , Juang Horng-Heng
Published: July 2022

Growth differentiation factor 15 (GDF15) is known as a TGFβ-like cytokine acting on the TGFβ receptor to modulate target genes. GDF15 is regarded as a tumor suppressor gene in the human bladder and the caffeic acid phenethyl ester (CAPE) induces GDF15 expression to inhibit the tumor growth in vitro and in vivo. However, the interactions among GDF15, CAPE, and TGFβ/Smads signaling in the human bladder carcinoma cells remain unexplored. Results revealed that TGFβ downregulated the expression of GDF15 via the activation of Smad 2/3 and Smad 1/5. Induction of GDF15 on its downstream genes, NDRG1 and maspin, is dependent on the TGFβ/Smad pathways. Moreover, TGFβ blocked the CAPE-inducing expressions of GDF15, maspin, and NDRG1. Pretreatment of TGF receptor kinase inhibitor not only blocked the activation of TGFβ but also attenuated the activation of GDF15 on the expressions of maspin and NDRG1. The CAPE treatment attenuated the activation of TGFβ on cell proliferation and invasion. Our findings indicate that TGFβ downregulated the expressions of GDF15, maspin, and NDRG1 via TGFβ/Smad signaling. Whereas, CAPE acts as an antagonist on TGFβ/Smad signaling to block the effect of TGFβ on the GDF15 expression and cell proliferation and invasion in bladder carcinoma cells.
Solubility-Aware Protein Binding Peptide Design Using AlphaFold
Authors: Kosugi Takatsugu , Ohue Masahito
Published: July 2022

New protein–protein interactions (PPIs) are identified, but PPIs have different physicochemical properties compared with conventional targets, making it difficult to use small molecules. Peptides offer a new modality to target PPIs, but designing appropriate peptide sequences by computation is challenging. Recently, AlphaFold and RoseTTAFold have made it possible to predict protein structures from amino acid sequences with ultra-high accuracy, enabling de novo protein design. We designed peptides likely to have PPI as the target protein using the “binder hallucination” protocol of AfDesign, a de novo protein design method using AlphaFold. However, the solubility of the peptides tended to be low. Therefore, we designed a solubility loss function using solubility indices for amino acids and developed a solubility-aware AfDesign binder hallucination protocol. The peptide solubility in sequences designed using the new protocol increased with the weight of the solubility loss function; moreover, they captured the characteristics of the solubility indices. Moreover, the new protocol sequences tended to have higher affinity than random or single residue substitution sequences when evaluated by docking binding affinity. Our approach shows that it is possible to design peptide sequences that can bind to the interface of PPI while controlling solubility.
Lipotoxicity in a Vicious Cycle of Pancreatic Beta Cell Exhaustion
Authors: Grubelnik Vladimir , Zmazek Jan , Završnik Matej , Marhl Marko
Published: July 2022

Hyperlipidemia is a common metabolic disorder in modern society and may precede hyperglycemia and diabetes by several years. Exactly how disorders of lipid and glucose metabolism are related is still a mystery in many respects. We analyze the effects of hyperlipidemia, particularly free fatty acids, on pancreatic beta cells and insulin secretion. We have developed a computational model to quantitatively estimate the effects of specific metabolic pathways on insulin secretion and to assess the effects of short- and long-term exposure of beta cells to elevated concentrations of free fatty acids. We show that the major trigger for insulin secretion is the anaplerotic pathway via the phosphoenolpyruvate cycle, which is affected by free fatty acids via uncoupling protein 2 and proton leak and is particularly destructive in long-term chronic exposure to free fatty acids, leading to increased insulin secretion at low blood glucose and inadequate insulin secretion at high blood glucose. This results in beta cells remaining highly active in the “resting” state at low glucose and being unable to respond to anaplerotic signals at high pyruvate levels, as is the case with high blood glucose. The observed fatty-acid-induced disruption of anaplerotic pathways makes sense in the context of the physiological role of insulin as one of the major anabolic hormones.
Distinct Subtyping of Successful Weaning from Acute Kidney Injury Requiring Renal Replacement Therapy by Consensus Clustering in Critically Ill Patients
Authors: Pan Heng-Chih , Sun Chiao-Yin , Huang Thomas Tao-Min , Huang Chun-Te , Tsao Chun-Hao , Lai Chien-Heng , Chen Yung-Ming , Wu Vin-Cent
Published: July 2022

Background: Clinical decisions regarding the appropriate timing of weaning off renal replacement therapy (RRT) in critically ill patients are complex and multifactorial. The aim of the current study was to identify which critical patients with acute kidney injury (AKI) may be more likely to be successfully weaned off RRT using consensus cluster analysis. Methods: In this study, critically ill patients who received RRT at three multicenter referral hospitals at several timepoints from August 2016 to July 2018 were enrolled. An unsupervised consensus clustering algorithm was used to identify distinct phenotypes. The outcomes of interest were the ability to wean off RTT and 90-day mortality. Results: A total of 124 patients with AKI requiring RRT (AKI-RRT) were enrolled. The 90-day mortality rate was 30.7% (38/124), and 49.2% (61/124) of the patients were successfully weaned off RRT for over 90 days. The consensus clustering algorithm identified three clusters from a total of 45 features. The three clusters had distinct features and could be separated according to the combination of urinary neutrophil gelatinase-associated lipocalin to creatinine ratio (uNGAL/Cr), Sequential Organ Failure Assessment (SOFA) score, and estimated glomerular filtration rate at the time of weaning off RRT. uNGAL/Cr (hazard ratio [HR] 2.43, 95% confidence interval [CI]: 1.36–4.33) and clustering phenotype (cluster 1 vs. 3, HR 2.7, 95% CI: 1.11–6.57; cluster 2 vs. 3, HR 44.5, 95% CI: 11.92–166.39) could predict 90-day mortality or re-dialysis. Conclusions: Almost half of the critical patients with AKI-RRT could wean off dialysis for over 90 days. Urinary NGAL/Cr and distinct clustering phenotypes could predict 90-day mortality or re-dialysis.
Diagnostic Cerebrospinal Fluid Biomarker in Early and Late Onset Multiple Sclerosis
Authors: Konen Franz Felix , Hannich Malte Johannes , Schwenkenbecher Philipp , Grothe Matthias , Gag Konrad , Jendretzky Konstantin Fritz , Gingele Stefan , Sühs Kurt-Wolfram , Witte Torsten , Skripuletz Thomas , Süße Marie
Published: July 2022

Background: The intrathecal humoral response is the characteristic diagnostic finding in the cerebrospinal fluid (CSF) analysis of patients with multiple sclerosis (MS). Although the average age of MS patients increases, little is known about the sensitivity of diagnostic markers in elderly MS patients. Methods: In this retrospective two-center study, intrathecal free light chains kappa fraction (FLCk IF) and oligoclonal bands (OCB) were studied in a large cohort of patients with early and late onset relapsing (RMS) and progressive (PMS) MS. Furthermore, the humoral immune profile in CSF was analyzed, including the polyspecific intrathecal immune response measured as the MRZ reaction. Results: While the frequency of CSF-specific OCB did not differ between early and late onset RMS and PMS, the sensitivity of positive FLCk IF and absolute FLCk IF values were lower in PMS. The positivity of the MRZ reaction was equally frequent in early and late onset RMS and PMS. PMS patients had higher local IgA concentrations than RMS patients (p = 0.0123). Conclusions: OCB are slightly superior to FLCk IF in progressive MS in terms of sensitivity for detecting intrathecal immunoglobulin synthesis. The MRZ reaction, as the most specific parameter for MS, is also applicable in patients with late onset and progressive MS.
Effects of Extracorporeal Shockwave Therapy on Functional Recovery and Circulating miR-375 and miR-382-5p after Subacute and Chronic Spinal Cord Contusion Injury in Rats
Authors: Ashmwe Mohamed , Posa Katja , Rührnößl Alexander , Heinzel Johannes Christoph , Heimel Patrick , Mock Michael , Schädl Barbara , Keibl Claudia , Couillard-Despres Sebastien , Redl Heinz , Mittermayr Rainer , Hercher David
Published: July 2022

Extracorporeal shockwave therapy (ESWT) can stimulate processes to promote regeneration, including cell proliferation and modulation of inflammation. Specific miRNA expression panels have been established to define correlations with regulatory targets within these pathways. This study aims to investigate the influence of low-energy ESWT—applied within the subacute and chronic phase of SCI (spinal cord injury) on recovery in a rat spinal cord contusion model. Outcomes were evaluated by gait analysis, µCT and histological analysis of spinal cords. A panel of serum-derived miRNAs after SCI and after ESWT was investigated to identify injury-, regeneration- and treatment-associated expression patterns. Rats receiving ESWT showed significant improvement in motor function in both a subacute and a chronic experimental setting. This effect was not reflected in changes in morphology, µCT-parameters or histological markers after ESWT. Expression analysis of various miRNAs, however, revealed changes after SCI and ESWT, with increased miR-375, indicating a neuroprotective effect, and decreased miR-382-5p potentially improving neuroplasticity via its regulatory involvement with BDNF. We were able to demonstrate a functional improvement of ESWT-treated animals after SCI in a subacute and chronic setting. Furthermore, the identification of miR-375 and miR-382-5p could potentially provide new targets for therapeutic intervention in future studies.
Hypoxia Preconditioned Serum (HPS) Promotes Osteoblast Proliferation, Migration and Matrix Deposition
Authors: Jiang Jun , Röper Lynn , Alageel Sarah , Dornseifer Ulf , Schilling Arndt F. , Hadjipanayi Ektoras , Machens Hans-Günther , Moog Philipp
Published: July 2022

Interest in discovering new methods of employing natural growth factor preparations to promote bone fracture healing is becoming increasingly popular in the field of regenerative medicine. In this study, we were able to demonstrate the osteogenic potential of hypoxia preconditioned serum (HPS) on human osteoblasts in vitro. Human osteoblasts were stimulated with two HPS concentrations (10% and 40%) and subsequently analyzed at time points of days 2 and 4. In comparison to controls, a time- and dose-dependent (up to 14.2× higher) proliferation of osteoblasts was observed after 4 days of HPS-40% stimulation with lower lactate dehydrogenase (LDH)-levels detected than controls, indicating the absence of cytotoxic/stress effects of HPS on human osteoblasts. With regards to cell migration, it was found to be significantly faster with HPS-10% application after 72 h in comparison to controls. Further osteogenic response to HPS treatment was evaluated by employing culture supernatant analysis, which exhibited significant upregulation of OPG (Osteoprotegerin) with higher dosage (HPS-10% vs. HPS-40%) and longer duration (2 d vs. 4 d) of HPS stimulation. There was no detection of anti-osteogenic sRANKL (soluble Receptor Activator of NF-κB Ligand) after 4 days of HPS stimulation. In addition, ALP (alkaline phosphatase)-enzyme activity, was found to be upregulated, dose-dependently, after 4 days of HPS-40% application. When assessing ossification through Alizarin-Red staining, HPS dose-dependently achieved greater (up to 2.8× higher) extracellular deposition of calcium-phosphate with HPS-40% in comparison to controls. These findings indicate that HPS holds the potential to accelerate bone regeneration by osteogenic promotion of human osteoblasts.
IL-17 Cytokines and Chronic Lung Diseases
Authors: Ritzmann Felix , Lunding Lars Peter , Bals Robert , Wegmann Michael , Beisswenger Christoph
Published: July 2022

IL-17 cytokines are expressed by numerous cells (e.g., gamma delta (γδ) T, innate lymphoid (ILC), Th17, epithelial cells). They contribute to the elimination of bacteria through the induction of cytokines and chemokines which mediate the recruitment of inflammatory cells to the site of infection. However, IL-17-driven inflammation also likely promotes the progression of chronic lung diseases, such as chronic obstructive pulmonary disease (COPD), lung cancer, cystic fibrosis, and asthma. In this review, we highlight the role of IL-17 cytokines in chronic lung diseases.
Targeting of p21-Activated Kinase 4 Radiosensitizes Glioblastoma Cells via Impaired DNA Repair
Authors: Blankenstein Leon J. , Cordes Nils , Kunz-Schughart Leoni A. , Vehlow Anne
Published: July 2022

Glioblastoma is a devastating malignant disease with poor patient overall survival. Strong invasiveness and resistance to radiochemotherapy have challenged the identification of molecular targets that can finally improve treatment outcomes. This study evaluates the influence of all six known p21-activated kinase (PAK) protein family members on the invasion capacity and radio-response of glioblastoma cells by employing a siRNA-based screen. In a panel of human glioblastoma cell models, we identified PAK4 as the main PAK isoform regulating invasion and clonogenic survival upon irradiation and demonstrated the radiosensitizing potential of PAK4 inhibition. Mechanistically, we show that PAK4 depletion and pharmacological inhibition enhanced the number of irradiation-induced DNA double-strand breaks and reduced the expression levels of various DNA repair proteins. In conclusion, our data suggest PAK4 as a putative target for radiosensitization and impairing DNA repair in glioblastoma, deserving further scrutiny in extended combinatorial treatment testing.
Progress and Setbacks in Translating a Decade of Ferroptosis Research into Clinical Practice
Authors: von Samson-Himmelstjerna Friedrich Alexander , Kolbrink Benedikt , Riebeling Theresa , Kunzendorf Ulrich , Krautwald Stefan
Published: July 2022

Ten years after its initial description, ferroptosis has emerged as the most intensely studied entity among the non-apoptotic forms of regulated cell death. The molecular features of ferroptotic cell death and its functional role have been characterized in vitro and in an ever-growing number of animal studies, demonstrating that it exerts either highly detrimental or, depending on the context, occasionally beneficial effects on the organism. Consequently, two contrary therapeutic approaches are being explored to exploit our detailed understanding of this cell death pathway: the inhibition of ferroptosis to limit organ damage in disorders such as drug-induced toxicity or ischemia-reperfusion injury, and the induction of ferroptosis in cancer cells to ameliorate anti-tumor strategies. However, the path from basic science to clinical utility is rocky. Emphasizing ferroptosis inhibition, we review the success and failures thus far in the translational process from basic research in the laboratory to the treatment of patients.
Activation of the Ventrolateral Preoptic Neurons Projecting to the Perifornical-Hypothalamic Area Promotes Sleep: DREADD Activation in Wild-Type Rats
Authors: Kostin Andrey , Alam Md. Aftab , Saevskiy Anton , McGinty Dennis , Alam Md. Noor
Published: July 2022

The ventrolateral preoptic area (VLPO) predominantly contains sleep-active neurons and is involved in sleep regulation. The perifornical-hypothalamic area (PF-HA) is a wake-regulatory region and predominantly contains wake-active neurons. VLPO GABAergic/galaninergic neurons project to the PF-HA. Previously, the specific contribution of VLPO neurons projecting to the PF-HA (VLPO > PF-HAPRJ) in sleep regulation in rats could not be investigated due to the lack of tools that could selectively target these neurons. We determined the contribution of VLPO > PF-HAPRJ neurons in sleep regulation by selectively activating them using designer receptors exclusively activated by designer drugs (DREADDs) in wild-type Fischer-344 rats. We used a combination of two viral vectors to retrogradely deliver the Cre-recombinase gene, specifically, in VLPO > PF-HA neurons, and further express hM3Dq in those neurons to selectively activate them for delineating their specific contributions to sleep–wake functions. Compared to the control, in DREADD rats, clozapine-N-oxide (CNO) significantly increased fos-expression, a marker of neuronal activation, in VLPO > PF-HAPRJ neurons (2% vs. 20%, p < 0.01) during the dark phase. CNO treatment also increased nonREM sleep (27% vs. 40%, p < 0.01) during the first 3 h of the dark phase, when rats are typically awake, and after exposure to the novel environment (55% vs. 65%; p < 0.01), which induces acute arousal during the light phase. These results support a hypothesis that VLPO > PF-HAPRJ neurons constitute a critical component of the hypothalamic sleep–wake regulatory circuitry and promote sleep by suppressing wake-active PF-HA neurons.
Investigation of Targeted Process Control for Adjusting the Macrostructure of Freeze Foams Using In Situ Computed Tomography
Authors: Maier Johanna , Geske Vinzenz , Werner David , Behnisch Thomas , Ahlhelm Matthias , Moritz Tassilo , Michaelis Alexander , Gude Maik
Published: July 2022

Freeze foams are novel and innovative cellular structures that are based on a direct foaming process and that can be manufactured using any material that can be processed by powder technology. The foam formation process is characterized by the highly complex interaction of various process and material parameters that were chosen empirically and that have so far been difficult to reproduce. To allow properties to be specifically tailored towards certain applications, it is necessary to examine the phenomena observed during foam formation as well as the impact of the process and material parameters on the structural constitution to deduce guidelines for manufacturing and quality assessment (e.g., mechanical strength, cell and pore sizes, pore size distribution). The variety of possible applications are a result of the wide spectrum of initial suspensions and especially the foam structure properties derived from process parameters such as the cell geometry, pore size distribution, fraction of open and closed porosity, and the textures of the cell struts. Due to earlier findings, the focus of this paper focuses on adjusting and tailoring the macrostructure (homogenization of the pore sizes and their distribution inside foam cells) to create load- and application-adapted ceramic foams. To this end, an experiment was designed using previously identified pore and characteristic influencers (air and water content, temperature of the suspension, pressure reduction rate) as influencing parameters. Their interconnected impacts on selected target values were examined during the freeze foaming process using an in situ freeze foaming device inside an X-ray.
Outcome Prognostic Factors in MRI during Spica Cast Therapy Treating Developmental Hip Dysplasia with Midterm Follow-Up
Authors: Gather Katharina Susanne , Mavrev Ivan , Gantz Simone , Dreher Thomas , Hagmann Sébastien , Beckmann Nicholas Andreas
Published: July 2022

Closed reduction followed by spica casting is a conservative treatment for developmental dysplasia of the hip (DDH). Magnetic resonance imaging (MRI) can verify proper closed reduction of the dysplastic hip. Our aim was to find prognostic factors in the first MRI to predict the possible outcome of the initial treatment success by means of ultrasound monitoring according to Graf and the further development of the hip dysplasia or risk of recurrence in the radiological follow-up examinations. A total of 48 patients (96 hips) with DDH on at least one side, and who were treated with closed reduction and spica cast were included in this retrospective cohort study. Treatment began at a mean age of 9.9 weeks. The children were followed for 47.4 months on average. We performed closed reduction and spica casting under general balanced anaesthesia. This was directly followed by MRI to control the position/reduction of the femoral head without anaesthesia. The following parameters were measured in the MRI: hip abduction angle, coronal, anterior and posterior bony axial acetabular angles and pelvic width. A Graf alpha angle of at least 60° was considered successful. In the radiological follow-up controls, we evaluated for residual dysplasia or recurrence. In our cohort, we only found the abduction angle to be an influencing factor for improvement of the DDH. No other prognostic factors in MRI measurements, such as gender, age at time of the first spica cast, or treatment involving overhead extension were found to be predictive of mid-term outcomes. This may, however, be due to the relatively small number of treatment failures.