bluuebunny/crossref_metadata_2025 huggingface dataset:
Retention of Key Characteristics of Unprocessed Chorion Tissue Resulting in a Robust Scaffold to Support Wound Healing
Authors: Harmon Katrina A. , Kammer MaryRose , Avery Justin T. , Kimmerling Kelly A. , Mowry Katie C.
Published: October 2023

Placental membranes have been widely studied and used clinically for wound care applications, but there is limited published information on the benefits of using the chorion membrane. The chorion membrane represents a promising source of placental-derived tissue to support wound healing, with its native composition of extracellular matrix (ECM) proteins and key regulatory proteins. This study examined the impact of hypothermic storage on the structure of chorion membrane, ECM content, and response to degradation in vitro. Hypothermically stored chorion membrane (HSCM) was further characterized for its proteomic content, and for its functionality as a scaffold for cell attachment and proliferation in vitro. HSCM retained the native ECM structure, composition, and integrity of native unprocessed chorion membrane and showed no differences in response to degradation in an in vitro wound model. HSCM retained key regulatory proteins previously shown to be present in placental membranes and promoted the attachment and proliferation of fibroblasts in vitro. These data support the fact that hypothermic storage does not significantly impact the structure and characteristics of the chorion membrane compared to unprocessed tissue or its functionality as a scaffold to support tissue growth.
Advanced Optical Materials: From Materials to Applications
Authors: Jun Bong-Hyun
Published: October 2023

Optical materials interact significantly with electromagnetic radiation in the visible, ultraviolet, and infrared regions of the spectrum [...]
KIM-1, IL-18, and NGAL, in the Machine Learning Prediction of Kidney Injury among Children Undergoing Hematopoietic Stem Cell Transplantation—A Pilot Study
Authors: Musiał Kinga , Stojanowski Jakub , Miśkiewicz-Bujna Justyna , Kałwak Krzysztof , Ussowicz Marek
Published: October 2023

Children undergoing allogeneic hematopoietic stem cell transplantation (HSCT) are prone to developing acute kidney injury (AKI). Markers of kidney damage: kidney injury molecule (KIM)-1, interleukin (IL)-18, and neutrophil gelatinase-associated lipocalin (NGAL) may ease early diagnosis of AKI. The aim of this study was to assess serum concentrations of KIM-1, IL-18, and NGAL in children undergoing HSCT in relation to classical markers of kidney function (creatinine, cystatin C, estimated glomerular filtration rate (eGFR)) and to analyze their usefulness as predictors of kidney damage with the use of artificial intelligence tools. Serum concentrations of KIM-1, IL-18, NGAL, and cystatin C were assessed by ELISA in 27 children undergoing HSCT before transplantation and up to 4 weeks after the procedure. The data was used to build a Random Forest Classifier (RFC) model of renal injury prediction. The RFC model established on the basis of 3 input variables, KIM-1, IL-18, and NGAL concentrations in the serum of children before HSCT, was able to effectively assess the rate of patients with hyperfiltration, a surrogate marker of kidney injury 4 weeks after the procedure. With the use of the RFC model, serum KIM-1, IL-18, and NGAL may serve as markers of incipient renal dysfunction in children after HSCT.
Combined Exogenous Activation of Bovine Oocytes: Effects on Maturation-Promoting Factor, Mitogen-Activated Protein Kinases, and Embryonic Competence
Authors: Valencia Cecilia , Pérez-García Felipe , Aguila Luis , Felmer Ricardo , Arias María Elena
Published: October 2023

Oocyte activation via dual inhibition of protein synthesis and phosphorylation has improved in vitro embryo production in different mammalian species. In this study, we evaluated the effects of the combination of cycloheximide (CHX), dimethyl amino purine (DMAP), and anisomycin (ANY) on the activation of bovine oocytes, particularly on dynamics of MPF and MAPKs, embryonic developmental potential, and quality. The results showed that the cleavage and blastocyst rates, as well as levels of CCNB1, CDK1, p-CDK1Thr161, and p-CDK1Thr14-Tyr15, were similar among groups; ANY and ANY + CHX reduced the expression of ERK1/2 compared to DMAP-combinations (p < 0.05), whereas ANY + DMAP, CHX + DMAP, and ANY + CHX + DMAP reduced p-ERK1/2 compared to ANY and ANY + CHX treatments (p < 0.05). The quality of blastocysts in terms of cell counts, their allocation, and the numbers of TUNEL-positive cells did not differ among groups. However, transcript levels of POU5F1 were higher in embryos derived from ANY + CHX + DMAP treatment compared to other groups, while expression levels of CDX2 did not show differences. In addition, the BCL2A1/BAX ratio of the ANY + CHX + DMAP treatment was significantly low compared to the ANY treatment (p < 0.05) and did not differ significantly from the other treatments. In conclusion, oocyte activation by dual inhibition of protein synthesis and phosphorylation induces MPF inactivation without degradation of CCNB1, while MAPK inactivation occurs differentially between these inhibitors. Thus, although the combined use of these inhibitors does not affect early developmental competence in vitro, it positively impacts the expression of transcripts associated with embryonic quality.
A Multimodel Study of the Role of Novel PKC Isoforms in the DNA Integrity Checkpoint
Authors: Saiz-Baggetto Sara , Dolz-Edo Laura , Méndez Ester , García-Bolufer Pau , Marí Miquel , Bañó M. Carmen , Fariñas Isabel , Morante-Redolat José Manuel , Igual J. Carlos , Quilis Inma
Published: October 2023

The protein kinase C (PKC) family plays important regulatory roles in numerous cellular processes. Saccharomyces cerevisiae contains a single PKC, Pkc1, whereas in mammals, the PKC family comprises nine isoforms. Both Pkc1 and the novel isoform PKCδ are involved in the control of DNA integrity checkpoint activation, demonstrating that this mechanism is conserved from yeast to mammals. To explore the function of PKCδ in a non-tumor cell line, we employed CRISPR-Cas9 technology to obtain PKCδ knocked-out mouse embryonic stem cells (mESCs). This model demonstrated that the absence of PKCδ reduced the activation of the effector kinase CHK1, although it suggested that other isoform(s) might contribute to this function. Therefore, we used yeast to study the ability of each single PKC isoform to activate the DNA integrity checkpoint. Our analysis identified that PKCθ, the closest isoform to PKCδ, was also able to perform this function, although with less efficiency. Then, by generating truncated and mutant versions in key residues, we uncovered differences between the activation mechanisms of PKCδ and PKCθ and identified their essential domains. Our work strongly supports the role of PKC as a key player in the DNA integrity checkpoint pathway and highlights the advantages of combining distinct research models.
Physiologic and Transcriptomic Effects Triggered by Overexpression of Wild Type and Mutant DNA Topoisomerase I in Streptococcus pneumoniae
Authors: García-López Miriam , Hernández Pablo , Megias Diego , Ferrándiz María-José , Campa Adela G. de la
Published: October 2023

Topoisomerase I (TopoI) in Streptococcus pneumoniae, encoded by topA, is a suitable target for drug development. Seconeolitsine (SCN) is a new antibiotic that specifically blocks this enzyme. We obtained the topARA mutant, which encodes an enzyme less active than the wild type (topAWT) and more resistant to SCN inhibition. Likely due to the essentiality of TopoI, we were unable to replace the topAWT allele by the mutant topARA version. We compared the in vivo activity of TopoIRA and TopoIWT using regulated overexpression strains, whose genes were either under the control of a moderately (PZn) or a highly active promoter (PMal). Overproduction of TopoIRA impaired growth, increased SCN resistance and, in the presence of the gyrase inhibitor novobiocin (NOV), caused lower relaxation than TopoIWT. Differential transcriptomes were observed when the topAWT and topARA expression levels were increased about 5-fold. However, higher increases (10–15 times), produced a similar transcriptome, affecting about 52% of the genome, and correlating with a high DNA relaxation level with most responsive genes locating in topological domains. These results confirmed that TopoI is indeed the target of SCN in S. pneumoniae and show the important role of TopoI in global transcription, supporting its suitability as an antibiotic target.
Constitutive Interleukin-7 Cytokine Signaling Enhances the Persistence of Epstein–Barr Virus-Specific T-Cells
Authors: Sharma Sandhya , Sauer Tim , Omer Bilal A. , Shum Thomas , Rollins Lisa A. , Rooney Cliona M.
Published: October 2023

The efficacy of therapeutic T-cells is limited by a lack of positive signals and excess inhibitory signaling in tumor microenvironments. We previously showed that a constitutively active IL7 receptor (C7R) enhanced the persistence, expansion, and anti-tumor activity of T-cells expressing chimeric antigen receptors (CARs), and C7R-modified GD2.CAR T-cells are currently undergoing clinical trials. To determine if the C7R could also enhance the activity of T-cells recognizing tumors via their native T-cell receptors (TCRs), we evaluated its effects in Epstein–Barr virus (EBV)-specific T-cells (EBVSTs) that have produced clinical benefits in patients with EBV-associated malignancies. EBVSTs were generated by stimulation of peripheral blood T-cells with overlapping peptide libraries spanning the EBV lymphoma antigens, LMP1, LMP2, and EBNA 1, followed by retroviral vector transduction to express the C7R. The C7R increased STAT5 signaling in EBVSTs and enhanced their expansion over 30 days of culture in the presence or absence of exogenous cytokines. C7R-EBVSTs maintained EBV antigen specificity but were dependent on TCR stimulation for continued expansion. C7R-EBVSTs produced more rapid lymphoma control in a murine xenograft model than unmodified EBVSTs and persisted for longer. The findings have led to a clinical trial, evaluating C7R-EBVSTs for the treatment of refractory or relapsed EBV-positive lymphoma (NCT04664179).
The Physiological Function of nNOS-Associated CAPON Proteins and the Roles of CAPON in Diseases
Authors: Xie Wenshuo , Xing Nianhong , Qu Jicheng , Liu Dongwu , Pang Qiuxiang
Published: October 2023

In this review, the structure, isoform, and physiological role of the carboxy-terminal PDZ ligand of neuronal nitric oxide synthase (CAPON) are summarized. There are three isoforms of CAPON in humans, including long CAPON protein (CAPON-L), short CAPON protein (CAPON-S), and CAPON-S’ protein. CAPON-L includes three functional regions: a C-terminal PDZ-binding motif, carboxypeptidase (CPE)-binding region, and N-terminal phosphotyrosine (PTB) structural domain. Both CAPON-S and CAPON-S’ only contain the C-terminal PDZ-binding motif. The C-terminal PDZ-binding motif of CAPON can bind with neuronal nitric oxide synthase (nNOS) and participates in regulating NO production and neuronal development. An overview is given on the relationship between CAPON and heart diseases, diabetes, psychiatric disorders, and tumors. This review will clarify future research directions on the signal pathways related to CAPON, which will be helpful for studying the regulatory mechanism of CAPON. CAPON may be used as a drug target, which will provide new ideas and solutions for treating human diseases.
NLRP3 Inflammasome Activates Endothelial-to-Mesenchymal Transition via Focal Adhesion Kinase Pathway in Bleomycin-Induced Pulmonary Fibrosis
Authors: Chen Wei-Chih , Yu Wen-Kuang , Su Vincent Yi-Fong , Hsu Han-Shui , Yang Kuang-Yao
Published: October 2023

Idiopathic pulmonary fibrosis has poor clinical outcomes despite antifibrotic treatment. The nucleotide-binding domain leucine-rich repeat-containing receptor, pyrin domain-containing-3 (NLRP3) inflammasome and endothelial-to-mesenchymal transition (EndoMT) were shown to be involved in the pathogenesis of pulmonary fibrosis. However, the detailed mechanism is unknown. Our study aimed to investigate the role of the NLRP3 inflammasome in the regulation of EndoMT in pulmonary fibrosis. The inhibition of the NLRP3 inflammasome via a caspase-1 inhibitor, Ac-YVAD-cmk (YVAD), was intraperitoneally administered to male C57BL/6 mice (8–12 weeks old) one hour before bleomycin intratracheal injection (1.5 U/kg). Immunohistochemical staining, Masson’s trichrome staining, enzyme-linked immunosorbent assay, immunofluorescence, and Western blotting were used to assess the activity of the NLRP3 inflammasome and EndoMT in lung samples from mice. Human pulmonary microvascular endothelial cells (HPMECs) were used as a model of EndoMT in vitro with YVAD and bleomycin stimulation. We observed the activation of the NLRP3 inflammasome and EndoMT (decreased vascular endothelial cadherin with increased alpha-smooth muscle actin and vimentin) in the lung samples after bleomycin. However, inhibition of the NLRP3 inflammasome significantly reduces EndoMT via inhibiting focal adhesion kinase (FAK). In vitro studies also confirmed these findings. In conclusion, NLRP3 inflammasome inhibition could reduce lung inflammation and fibrosis via the regulation of EndoMT by the FAK pathway.
Regulation of Cathelicidin Antimicrobial Peptide (CAMP) Gene Expression by TNFα and cfDNA in Adipocytes
Authors: Höpfinger Alexandra , Schmid Andreas , Schweitzer Leonie , Patz Marissa , Weber Anja , Schäffler Andreas , Karrasch Thomas
Published: October 2023

Understanding the complex interactions between metabolism and the immune system (“metaflammation”) is crucial for the identification of key immunomodulatory factors as potential therapeutic targets in obesity and in cardiovascular diseases. Cathelicidin antimicrobial peptide (CAMP) is an important factor of innate immunity and is expressed in adipocytes. CAMP, therefore, might play a role as an adipokine in metaflammation and adipose inflammation. TNFα, cell-free nucleic acids (cfDNA), and toll-like receptor (TLR) 9 are components of the innate immune system and are functionally active in adipose tissue. The aim of the present study was to investigate the impact of TNFα and cfDNA on CAMP expression in adipocytes. Since cfDNA acts as a physiological TLR9 agonist, we additionally investigated TLR9-mediated CAMP regulation in adipocytes and adipose tissue. CAMP gene expression in murine 3T3-L1 and human SGBS adipocytes and in murine and human adipose tissues was quantified by real-time PCR. Adipocyte inflammation was induced in vitro by TNFα and cfDNA stimulation. Serum CAMP concentrations in TLR9 knockout (KO) and in wildtype mice were quantified by ELISA. In primary adipocytes of wildtype and TLR9 KO mice, CAMP gene expression was quantified by real-time PCR. CAMP gene expression was considerably increased in 3T3-L1 and SGBS adipocytes during differentiation. TNFα significantly induced CAMP gene expression in mature adipocytes, which was effectively antagonized by inhibition of PI3K signaling. Cell-free nucleic acids (cfDNA) significantly impaired CAMP gene expression, whereas synthetic agonistic and antagonistic TLR9 ligands had no effect. CAMP and TLR9 gene expression were correlated positively in murine and human subcutaneous but not in intra-abdominal/visceral adipose tissues. Male TLR9 knockout mice exhibited lower systemic CAMP concentrations than wildtype mice. CAMP gene expression levels in primary adipocytes did not significantly differ between wildtype and TLR9 KO mice. These findings suggest a regulatory role of inflammatory mediators, such as TNFα and cfDNA, in adipocytic CAMP expression as a novel putative molecular mechanism in adipose tissue innate immunity.
mRNA and Protein Expression in Human Fetal Membrane Cells: Potential Biomarkers for Preterm Prelabor Rupture of the Fetal Membranes?
Authors: Mikkelsen Emmeli , Huppertz Berthold , Singh Ripudaman , Ravn Katarina , Hatt Lotte , Kruhøffer Mogens , Urrabaz-Garza Rheanna , Uldbjerg Niels , Menon Ramkumar , Steiniche Torben
Published: October 2023

Clinically, unique markers in fetal membrane cells may contribute to the search for biomarkers for preterm prelabor rupture of the fetal membranes (pPROM) in maternal blood. pPROM is associated with overwhelming inflammation and premature cellular senescence causing “biological microfractures” of the fetal membranes. We hypothesize that these pathological processes are associated with the shedding of fetal membrane cells into the maternal circulation. The aim of this study was to identify markers expressed exclusively in fetal membrane cells to facilitate their isolation, characterization, and determination of biomarker potential in maternal blood. We have (1), by their transcriptomic profile, identified markers that are upregulated in amnion and chorion tissue compared to maternal white blood cells, and (2), by immunohistochemistry, confirmed the localization of the differentially expressed proteins in fetal membranes, placenta, and the placental bed of the uterus. RNA sequencing revealed 31 transcripts in the amnion and 42 transcripts in the chorion that were upregulated. Among these, 22 proteins were evaluated by immunohistochemistry. All but two transcripts were expressed both on mRNA and protein level in at least one fetal membrane cell type. Among these remaining 20 proteins, 9 proteins were not significantly expressed in the villous and extravillous trophoblasts of the placenta.
Switching Rat Resident Macrophages from M1 to M2 Phenotype by Iba1 Silencing Has Analgesic Effects in SNL-Induced Neuropathic Pain
Authors: Gheorghe Roxana-Olimpia , Grosu Andreea Violeta , Magercu Melania , Ghenghea Mihail-Sebastian , Zbarcea Cristina Elena , Tanase Alexandra , Negres Simona , Filippi Alexandru , Chiritoiu Gabriela , Gherghiceanu Mihaela , Dinescu Sorina , Gaina Gisela , Sapunar Damir , Ristoiu Violeta
Published: October 2023

Resident macrophages from dorsal root ganglia are important for the development of traumatic-induced neuropathic pain. In the first 5–7 days after a traumatic sciatic nerve injury (i.e., spinal nerve ligation (SNL), spared nerve injury (SNI), sciatic nerve transection or sciatic nerve ligation and transection), Ionized binding adapter protein 1 (Iba1) (+) resident macrophages cluster around dorsal root ganglia neurons, possibly contributing to nerve injury-induced hypersensitivity. Since infiltrating macrophages gradually recruited to the lesion site peak at about 7 days, the first few days post-lesion offer a window of opportunity when the contribution of Iba1 (+) resident macrophages to neuropathic pain pathogenesis could be investigated. Iba1 is an actin cross-linking cytoskeleton protein, specifically located only in macrophages and microglia. In this study, we explored the contribution of rat Iba1 (+) macrophages in SNL-induced neuropathic pain by using intra-ganglionic injections of naked Iba1-siRNA, delivered at the time the lesion occurred. The results show that 5 days after Iba1 silencing, Iba1 (+) resident macrophages are switched from an M1 (pro-inflammatory) phenotype to an M2 (anti-inflammatory) phenotype, which was confirmed by a significant decrease of M1 markers (CD32 and CD86), a significant increase of M2 markers (CD163 and Arginase-1), a reduced secretion of pro-inflammatory cytokines (IL-6, TNF-α and IL-1β) and an increased release of pro-regenerative factors (BDNF, NGF and NT-3) which initiated the regrowth of adult DRG neurites and reduced SNL-induced neuropathic pain. Our data show for the first time, that it is possible to induce macrophages towards an anti-inflammatory phenotype by interacting with their cytoskeleton.
Increased Levels of Galectin-3 in Critical COVID-19
Authors: Nikitopoulou Ioanna , Vassiliou Alice G. , Athanasiou Nikolaos , Jahaj Edison , Akinosoglou Karolina , Dimopoulou Ioanna , Orfanos Stylianos E. , Dimakopoulou Vasiliki , Schinas Georgios , Tzouvelekis Argyrios , Aidinis Vassilis , Kotanidou Anastasia
Published: October 2023

Severe COVID-19 is related to hyperinflammation and multiple organ injury, including respiratory failure, thus requiring intensive care unit (ICU) admission. Galectin-3, a carbohydrate-binding protein exhibiting pleiotropic effects, has been previously recognized to participate in inflammation, the immune response to infections and fibrosis. The aim of this study was to evaluate the relationship between galectin-3 and the clinical severity of COVID-19, as well as assess the prognostic accuracy of galectin-3 for the probability of ICU mortality. The study included 235 COVID-19 patients with active disease, treated in two different Greek hospitals in total. Our results showed that median galectin-3 serum levels on admission were significantly increased in critical COVID-19 patients (7.2 ng/mL), as compared to the median levels of patients with less severe disease (2.9 ng/mL, p = 0.003). Galectin-3 levels of the non-survivors hospitalized in the ICU were significantly higher than those of the survivors (median 9.1 ng/mL versus 5.8 ng/mL, p = 0.001). The prognostic accuracy of galectin-3 for the probability of ICU mortality was studied with a receiver operating characteristic (ROC) curve and a multivariate analysis further demonstrated that galectin-3 concentration at hospital admission could be assumed as an independent risk factor associated with ICU mortality. Our results were validated with galectin-3 measurements in a second patient cohort from a different Greek university hospital. Our results, apart from strongly confirming and advancing previous knowledge with two patient cohorts, explore the possibility of predicting ICU mortality, which could provide useful information to clinicians. Therefore, galectin-3 seems to establish its involvement in the prognosis of hospitalized COVID-19 patients, suggesting that it could serve as a promising biomarker in critical COVID-19.
Analysis of Potential Gene Doping Preparations for Transgenic DNA in the Context of Sports Drug Testing Programs
Authors: Naumann Nana , Paßreiter Alina , Thomas Andreas , Krug Oliver , Walpurgis Katja , Thevis Mario
Published: October 2023

Gene doping has been classified as a prohibited method by the World Anti-Doping Agency (WADA) and the International Olympic Committee (IOC) for over two decades. As gene therapeutic approaches improve and, concomitantly, safety concerns regarding clinical applications decline, apprehensions about their illicit use in elite sports continue to grow. Two products available via Internet-based providers and advertised as EPO-gene- and IGF1-gene-containing materials were analyzed for the presence of potential gene doping agents using a newly developed analytical approach, allowing for the detection of transgenic DNA corresponding to seven potential targets (EPO, FST, GH1, MSTN (Propeptide), IGF1, VEGFA, and VEGFD). Panel detection was based on a 20-plex polymerase chain reaction (PCR) followed by a single base extension (SBE) reaction and subsequent SBE product analyses via matrix-assisted time-of-flight laser desorption/ionization mass spectrometry (MALDI-TOF MS). Extracts of both products were found to contain transgenic EPO-DNA, while transgenic DNA for IGF-1 was not detected. The results were confirmed using SYBR Green qPCR with primer sets directed against EPO and IGF1 cDNA, and the CMV promotor sequence. In this case study, the detection of authentic (whilst low concentrated) transgenes, potentially intended for gene doping practices in readily available products, is reported for the first time.
The Improvement of Fluorescence In Situ Hybridization Technique Based on Explorations of Symbionts in Cicadas
Authors: Huang Zhi , Wang Dandan , Zhou Jinrui , He Hong , Wei Cong
Published: October 2023

Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is widely used for the identification of microbes in complex samples, but it suffers from some limitations resulting in the weak or even absence of fluorescence signals of microbe(s), which may lead to the underestimation or misunderstanding of a microbial community. Herein, we explored symbionts in the bacteriomes and fat bodies of cicadas using modified FISH, aiming to improve this technique. We initially revealed that the probes of Candidatus Sulcia muelleri (Sulcia) and the yeast-like fungal symbiont (YLS) are suitable for detection of these symbionts in all cicadas and some other species of Auchenorrhyncha, whereas the probe of Candidatus Hodgkinia cicadicola (Hodgkinia) is only suitable for detection of Hodgkinia in a few cicada species. The fluorescence signal of Sulcia, Hodgkinia and YLS exhibited weak intensity without the addition of unlabeled oligonucleotides (helpers) and heat shock in some cicadas; however, it can be significantly improved by the addition of both helpers and heat shock. Results of this study suggest that heat shock denaturing rRNA and proteins of related microbe(s) together with helpers binding to the adjacent region of the probe’s target sites prevent the re-establishment of the native secondary structure of rRNA; therefore, suitable probe(s) can more easily access to the probe’s target sites of rRNA. Our results provide new information for the significant improvement of hybridization signal intensities of microbes in the FISH experiment, making it possible to achieve a more precise understanding of the microbial distribution, community and density in complex samples.
Glucokinase Variant Proteins Are Resistant to Fasting-Induced Uridine Diphosphate Glucose-Dependent Degradation in Maturity-Onset Diabetes of the Young Type 2 Patients
Authors: Cho Jaeyong , Horikawa Yukio , Oiwa Yuki , Hosomichi Kazuyoshi , Yabe Daisuke , Imai Takeshi
Published: October 2023

We previously reported that glucokinase undergoes ubiquitination and subsequent degradation, a process mediated by cereblon, particularly in the presence of uridine diphosphate glucose (UDP-glucose). In this context, we hereby present evidence showcasing the resilience of variant glucokinase proteins of maturity-onset diabetes of the young type 2 (MODY2) against degradation and, concomitantly, their influence on insulin secretion, both in cell lines and in the afflicted MODY2 patient. Hence, glucose-1-phodphate promotes UDP-glucose production by UDP-glucose pyrophosphorylase 2; consequently, UDP-glucose-dependent glucokinase degradation may occur during fasting. Next, we analyzed glucokinase variant proteins from MODY2 or persistent hyperinsulinemic hypoglycemia in infancy (PHHI). Among the eleven MODY2 glucokinase-mutated proteins tested, those with a lower glucose-binding affinity exhibited resistance to UDP-glucose-dependent degradation. Conversely, the glucokinaseA456V-mutated protein from PHHI had a higher glucose affinity and was sensitive to UDP-glucose-dependent degradation. Furthermore, in vitro studies involving UDP-glucose-dependent glucokinase variant proteins and insulin secretion during fasting in Japanese MODY2 patients revealed a strong correlation and a higher coefficient of determination. This suggests that UDP-glucose-dependent glucokinase degradation plays a significant role in the pathogenesis of glucose-homeostasis-related hereditary diseases, such as MODY2 and PHHI.
Phylogenetics and Population Genetics of the Petrolisthes lamarckii–P. haswelli Complex in China: Old Lineage and New Species
Authors: Fang Xuefeng , Dong Dong , Yang Mei , Li Xinzheng
Published: October 2023

Petrolisthes lamarckii (Leach, 1821) and P. haswelli Miers, 1884 are a pair of sister species of porcelain crabs, both of which are common in the intertidal zone of southern China, typically found under rocks and in the crevices of coral reefs. However, the distribution, genetic relationship and diversity of the two species in China have not been rigorously studied. Meanwhile, P. lamarckii is considered as a complex of cryptic species due to their diverse morphological features. In this study, we identified 127 specimens of the P. lamarckii–P. haswelli complex (LH complex) and recognised a new species through morphological and molecular analysis. Furthermore, we constructed a time-calibrated phylogeny of the LH complex using three mitochondrial and two nuclear genes from all three species, finding that the divergence of the LH complex can be traced back to the Miocene epoch, and that the genetic diversity increased during the Mid-Pleistocene transition period. Glacial refugia formed during the Pleistocene climatic oscillations has been regarded as one of the contributing factors to the diversification of marine organisms in the north-western Pacific. Petrolisthes haswelli demonstrates a wide distribution along the southern coast of China, while other lineages display more restricted distributions. The research on the demographic history and gene flow of P. haswelli revealed that the Chinese coastal populations experienced an expansion event approximately 12.5 thousand years ago (Kya) and the asymmetrical gene flows were observed between the two sides of the Taiwan Strait and Qiongzhou Strait, respectively, which is likely influenced by the restriction of ocean currents.
Competitive Chemical Reaction Kinetic Model of Nucleosome Assembly Using the Histone Variant H2A.Z and H2A In Vitro
Authors: Zhao Hongyu , Shao Xueqin , Guo Mingxin , Xing Yongqiang , Wang Jingyan , Luo Liaofu , Cai Lu
Published: October 2023

Nucleosomes not only serve as the basic building blocks for eukaryotic chromatin but also regulate many biological processes, such as DNA replication, repair, and recombination. To modulate gene expression in vivo, the histone variant H2A.Z can be dynamically incorporated into the nucleosome. However, the assembly dynamics of H2A.Z-containing nucleosomes remain elusive. Here, we demonstrate that our previous chemical kinetic model for nucleosome assembly can be extended to H2A.Z-containing nucleosome assembly processes. The efficiency of H2A.Z-containing nucleosome assembly, like that of canonical nucleosome assembly, was also positively correlated with the total histone octamer concentration, reaction rate constant, and reaction time. We expanded the kinetic model to represent the competitive dynamics of H2A and H2A.Z in nucleosome assembly, thus providing a novel method through which to assess the competitive ability of histones to assemble nucleosomes. Based on this model, we confirmed that histone H2A has a higher competitive ability to assemble nucleosomes in vitro than histone H2A.Z. Our competitive kinetic model and experimental results also confirmed that in vitro H2A.Z-containing nucleosome assembly is governed by chemical kinetic principles.
The β Isoform of Human ATP-Binding Cassette B5 Transporter, ABCB5β, Localizes to the Endoplasmic Reticulum
Authors: Díaz-Anaya Adriana María , Gerard Louise , Albert Martine , Gaussin Jean-François , Boonen Marielle , Gillet Jean-Pierre
Published: October 2023

ABCB5β is a member of the ABC transporter superfamily cloned from melanocytes. It has been reported as a marker of skin progenitor cells and melanoma stem cells. ABCB5β has also been shown to exert an oncogenic activity and promote cancer metastasis. However, this protein remains poorly characterized. To elucidate its subcellular localization, we tested several anti-ABCB5 antibodies and prepared several tagged ABCB5β cDNA constructs. We then used a combination of immunofluorescence and biochemical analyses to investigate the presence of ABCB5β in different subcellular compartments of HeLa and MelJuSo cell lines. Treatment of the cells with the proteasome inhibitor MG132 showed that part of the population of newly synthesized ABCB5β is degraded by the proteasome system. Interestingly, treatment with SAHA, a molecule that promotes chaperone-assisted folding, largely increased the expression of ABCB5β. Nevertheless, the overall protein distribution in the cells remained similar to that of control conditions; the protein extensively colocalized with the endoplasmic reticulum marker calnexin. Taken together with cell surface biotinylation studies demonstrating that the protein does not reach the plasma membrane (even after SAHA treatment), the data indicate that ABCB5β is a microsomal protein predominantly localized to the ER.
Federated Secure Computing
Authors: Ballhausen Hendrik , Hinske Ludwig Christian
Published: October 2023

Privacy-preserving computation (PPC) enables encrypted computation of private data. While advantageous in theory, the complex technology has steep barriers to entry in practice. Here, we derive design goals and principles for a middleware that encapsulates the demanding cryptography server side and provides a simple-to-use interface to client-side application developers. The resulting architecture, “Federated Secure Computing”, offloads computing-intensive tasks to the server and separates concerns of cryptography and business logic. It provides microservices through an Open API 3.0 definition and hosts multiple protocols through self-discovered plugins. It requires only minimal DevSecOps capabilities and is straightforward and secure. Finally, it is small enough to work in the internet of things (IoT) and in propaedeutic settings on consumer hardware. We provide benchmarks for calculations with a secure multiparty computation (SMPC) protocol, both for vertically and horizontally partitioned data. Runtimes are in the range of seconds on both dedicated workstations and IoT devices such as Raspberry Pi or smartphones. A reference implementation is available as free and open source software under the MIT license.
Functional Response and Intraspecific Competition of Three Ladybird Species Feeding on Aphids on Goji Berry Plants in Laboratory and Semi-Field Conditions
Authors: Wu Pengxiang , He Jia , Dong Huan , Zhang Runzhi
Published: October 2023

The aphid, Aphis gossypii Glover, is identified as a significant pest that causes severe damage to goji berries in China. To analyze the ladybird consumption of aphids, the functional responses of three ladybird species, Harmonia axyridis, Coccinella septempunctata, and Hippodamia variegata, and intraspecific competition among ladybird individuals were evaluated under laboratory conditions. Moreover, the practical impact of ladybirds on aphid population reduction was investigated in semi-field conditions. We found that all adult ladybirds of the three species exhibited a type II functional response toward aphids. According to Holling’s disc equation, H. axyridis exhibited the highest searching efficiency (a = 0.79), while C. septempunctata had the shortest handling time (Th = 5.07 min) among the three ladybird species studied. Additionally, intraspecific competition had a greater impact on H. variegata (m = 0.41) compared to the other two ladybird species. The semi-field study demonstrated that H. axyridis (83.9% reduction) and C. septempunctata (78.7% reduction) exhibited higher efficacy in reducing aphid populations compared to H. variegata (27.3% reduction). This study suggests that H. axyridis and C. septempunctata exhibit potential as effective biological control agents against aphids on goji berry plants and highlights the importance of considering intraspecific competition. However, the results obtained from laboratory and semi-field studies cannot be directly extrapolated to field conditions due to the simplification of these experimental systems. Future field studies are crucial in ensuring the effective implementation of a biological control program.
Photocatalytic Reduction of Cr(VI) and Pb(II) with Biogenically Synthesized Copper Oxide Nanoparticles Using an Extract of the Myriophyllum spicatum Plant
Authors: Oyewo Opeyemi A. , Makgato Seshibe S.
Published: October 2023

The biogenic synthesis of copper oxide nanoparticles was explored using the Myriophyllum spicatum plant through a process involving co-precipitation and was utilized as an effective photocatalyst for the reduction of Cr(VI) and Pb(II) ions in an aqueous solution. The plant-mediated CuO nanoparticles were characterized using microscopic techniques (TEM and SEM), FT-IR, and XRD analyses. The amount of the reduced metal ions was determined by UV–visible and Atomic Absorption (AA) spectrophotometers. The analyses of the functional group present in the leaf extract revealed the type of bioactive molecules that were involved in the formation of copper oxide nanoparticles. The nanoparticles were used in the photo-enhanced reduction of hexavalent Cr and divalent Pb ions, and the impact of solution pH, initial metal concentrations, and photocatalyst dosage was investigated to establish the optimal performance of the CuO nanoparticles. Results revealed a direct association between the reduction of metal ions and catalyst dosage in both cases. A maximum percentage reduction of 89.2% and 79.1% was achieved for Cr(VI) and Pb(II), respectively, using 3 g of the CuO nanoparticles. This confirms that the CuO nanoparticles exhibited higher efficiency for Cr(VI) reduction as compared to Pb(II) reduction and indicates that CuO nanoparticles are a promising photocatalyst that is capable of reducing these metal ions into less toxic products.
Improving ISOMAP Efficiency with RKS: A Comparative Study with t-Distributed Stochastic Neighbor Embedding on Protein Sequences
Authors: Ali Sarwan , Patterson Murray
Published: October 2023

Data visualization plays a crucial role in gaining insights from high-dimensional datasets. ISOMAP is a popular algorithm that maps high-dimensional data into a lower-dimensional space while preserving the underlying geometric structure. However, ISOMAP can be computationally expensive, especially for large datasets, due to the computation of the pairwise distances between data points. The motivation behind this study is to improve efficiency by leveraging an approximate method, which is based on random kitchen sinks (RKS). This approach provides a faster way to compute the kernel matrix. Using RKS significantly reduces the computational complexity of ISOMAP while still obtaining a meaningful low-dimensional representation of the data. We compare the performance of the approximate ISOMAP approach using RKS with the traditional t-SNE algorithm. The comparison involves computing the distance matrix using the original high-dimensional data and the low-dimensional data computed from both t-SNE and ISOMAP. The quality of the low-dimensional embeddings is measured using several metrics, including mean squared error (MSE), mean absolute error (MAE), and explained variance score (EVS). Additionally, the runtime of each algorithm is recorded to assess its computational efficiency. The comparison is conducted on a set of protein sequences, used in many bioinformatics tasks. We use three different embedding methods based on k-mers, minimizers, and position weight matrix (PWM) to capture various aspects of the underlying structure and the relationships between the protein sequences. By comparing different embeddings and by evaluating the effectiveness of the approximate ISOMAP approach using RKS and comparing it against t-SNE, we provide insights on the efficacy of our proposed approach. Our goal is to retain the quality of the low-dimensional embeddings while improving the computational performance.
The Neutrophil to Lymphocyte Ratio in Children with Bronchial Asthma
Authors: Wawryk-Gawda Ewelina , Żybowska Monika , Ostrowicz Klaudia
Published: October 2023

The discovery of an effective airway inflammation marker which correctly identifies the condition and phenotype of asthma still constitutes a significant challenge. The determination of NLR, that is, the ratio of neutrophils to lymphocytes, would overcome this challenge. The role of the neutrophil–lymphocytic index in the diagnosis of specific types of asthma is investigated in the present study. The results of laboratory tests of 482 pediatric patients were used for the analysis. The results of 107 children without allergic disease symptoms were selected for the control group. The mean NLR in patients with asthma was 3.42 ± 4.05, and in the control group it was 1.94 ± 1.91. The difference between the NLR in allergic and non-allergic asthma was statistically significant in the allergic asthma and control groups. There was no statistically significant difference between NLR and body temperature, BMI, and gender. The value of NLR was significantly higher in the blood of patients suffering from asthma compared to the control group. The NLR was the highest among patients with allergic asthma. The use of this blood test in daily practice may facilitate the diagnosis of asthma and differentiation between asthma types, especially when the results of other tests are inconclusive.
Lower Urinary Tract Symptoms (LUTS) as a New Clinical Presentation of Histamine Intolerance: A Prevalence Study of Genetic Diamine Oxidase Deficiency
Authors: Ponce Díaz-Reixa Jose , Aller Rodríguez Marcos , Martínez Breijo Sara , Suanzes Hernández Jorge , Ruiz Casares Eva , Perucho Alcalde Teresa , Bohorquez Cruz Manuel , Mosquera Seoane Teresa , Sánchez Merino Jose M. , Freire Calvo Jacobo , Fernández Suárez Paula , Chantada Abal Venancio
Published: October 2023

Lower urinary tract symptoms (LUTS) are highly prevalent, and their treatment is mainly focused on the control of symptoms. Histamine intolerance (HIT) has been related to a variety of systemic symptoms. DAO deficiency has been identified as a significant factor contributing to histamine intolerance (HIT). Preclinical evidence indicates the involvement of histamine in the lower urinary tract. This study aimed to assess the prevalence of diamine oxidase deficiency (DAO) in a prospective cohort of 100 patients with at least moderate LUTS. A genetic study of four single nucleotide polymorphisms (SNPs) (c.-691G>T, c.47C>T, c.995C>T, and c.1990C>G) was performed. HIT was found in 85.9% of patients. The prevalence of at least one minor allele in the SNPs analyzed was 88%, without gender differences. Storage symptoms were more intense in the presence of HIT as well as asthenia and neurological and musculoskeletal symptoms. The presence of minor alleles of the AOC1 gene was associated with a higher intensity of symptoms. Minor alleles from c.-691G>T and c.47C>T SNPs were also associated with a greater severity of obstructive symptoms. Thirty-one percent of patients presented the four SNPS with at least one associated minor allele. The relationship between HIT and LUTS in a mixed population of men and women found in this study supports further investigations to define the pathophysiology of histamine in LUTS.
One Anastomosis Gastric Bypass in 6722 Patients: Early Outcomes from a Private Hospital Registry
Authors: Sakran Nasser , Sherf-Dagan Shiri , Hod Keren , Kaplan Uri , Azaria Bella , Raziel Asnat ,   Assuta Bariatric Surgeons Collaborative
Published: October 2023

Background: One-anastomosis gastric bypass (OAGB) is an emerging metabolic bariatric surgery (MBS) type used in both primary OAGB (pOAGB) and revisional OAGB (rOAGB). We studied ≤30-day outcomes of pOAGB and rOAGB and identified predictors of early complications. Methods: Electronic medical records of all OAGBs performed between January 2017 and December 2021 at a high-volume bariatric clinic in Israel comprising four hospital centers were scanned retrospectively using specialized data software (MDClone software, version 6.1). Data gathered were patients’ characteristics, surgical procedure, and ≤30-day complications with Clavien–Dindo Classification (CDC). Multivariate logistic regression analyses were used to identify factors related to early complications of pOAGB and rOAGB. Results: A total of 6722 patients underwent a pOAGB (n = 5088, 75.7%) or rOAGB (n = 1634, 24.3%) procedure at our institution. Preoperative mean age and body mass index (BMI) were 40.6 ± 11.5 years and 41.2 ± 4.6 kg/m2, respectively. Early complications occurred in 258 (3.8%) patients (176 pOAGB and 82 rOAGB) and included mainly bleeding (n = 133, 2.0%), leaks (n = 31, 0.5%), and obstruction/strictures (n = 19, 0.3%). CDC complications for grades 1–2 and grades 3a-–5 were 1.5% and 1.6%, respectively. The overall mortality rate was 0.03% (n = 2). Age, operative time ≥3 h, and any additional concomitant procedure were independent predictors of early complications following pOAGB, while a diagnosis of diabetes mellitus and operative time ≥3 h were independent predictors of early complications following rOAGB. Conclusions: OAGB was found to be a safe primary and revisional MBS procedure in the ≤30-postoperative day term. The most common complications were gastrointestinal bleeding, leaks, and obstruction/stricture.
Sensory Information Modulates Voluntary Movement in an Individual with a Clinically Motor- and Sensory-Complete Spinal Cord Injury: A Case Report
Authors: Angeli Claudia , Wagers Sarah , Harkema Susan , Rejc Enrico
Published: October 2023

Motor recovery following a complete spinal cord injury is not likely. This is partially due to insurance limitations. Rehabilitation strategies for individuals with this type of severe injury focus on the compensation for the activities of daily living in the home and community and not on the restoration of function. With limited time in therapies, the initial goals must focus on getting the patient home safely without the expectation of recovery of voluntary movement below the level of injury. In this study, we report a case of an individual with a chronic, cervical (C3)-level clinically motor- and sensory-complete injury who was able to perform voluntary movements with both upper and lower extremities when positioned in a sensory-rich environment conducive to the specific motor task. We show how he is able to intentionally perform push-ups, trunk extensions and leg presses only when appropriate sensory information is available to the spinal circuitry. These data show that the human spinal circuitry, even in the absence of clinically detectable supraspinal input, can generate motor patterns effective for the execution of various upper and lower extremity tasks, only when appropriate sensory information is present. Neurorehabilitation in the right sensory–motor environment that can promote partial recovery of voluntary movements below the level of injury, even in individuals diagnosed with a clinically motor-complete spinal cord injury.
Demographics and Comorbidities of United States Service Members with Combat-Related Lower Extremity Limb Salvage
Authors: Goldman Stephen M. , Eskridge Susan L. , Franco Sarah R. , Dearth Christopher L.
Published: October 2023

Introduction: This retrospective study describes the demographics and injury characteristics of a recently identified cohort of US Service members with combat-related lower extremity limb salvage (LS). Methods: US Service members with combat trauma were identified from the Expeditionary Medical Encounter Database and Military Health System Data Repository and stratified into primary amputation (PA), LS, and non-threatened limb trauma (NTLT) cohorts based on ICD-9 codes. Disparities in demographic factors and injury characteristics were investigated across cohorts and within the LS cohort based on limb retention outcome. Results: Cohort demographics varied by age but not by sex, branch, or rank. The mechanism of injury and injury characteristics were found to be different between the cohorts, with the LS cohort exhibiting more blast injuries and greater injury burden than their peers with NTLT. A sub-analysis of the LS population revealed more blast injuries and fewer gunshot wounds in those that underwent secondary amputation. Neither demographic factors nor total injury burden varied with limb retention outcome, despite slight disparities in AIS distribution within the LS cohort. Conclusions: In accordance with historic dogma, the LS population presents high injury severity. Demographics and injury characteristics are largely invariant with respect to limb retention outcomes, despite secondary amputation being moderately more prevalent in LS patients with blast-induced injuries. Further study of this population is necessary to better understand the factors that impact the outcomes of LS in the Military Health System.