bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dry preserved multilayered fibroblast cell sheets are a new manageable tool for regenerative medicine to promote wound healing
Authors: Matsuno Yutaro , Yanagihara Masashi , Ueno Koji , Saito Toshiro , Kurazumi Hiroshi , Suzuki Ryo , Katsura Shunsaku , Oga Atsunori , Hamano Kimikazu 
Published: July 2022

AbstractThis study investigated the therapeutic effects of dry-preserved multi-layered fibroblast cell sheets (dry sheets) on cutaneous ulcers. Dry sheets were prepared by air-drying multi-layered fibroblast cell sheets (living sheets) to cease their life activities. Before in vivo application, we tested the release of growth factors into the medium to examine the mechanisms of dry sheets in wound healing. Vascular endothelial growth factor (VEGF) and hepatocyte growth factor (HGF) were released from both dry and living sheets, while high levels of fibroblast growth factor-2 (FGF-2) and high mobility group box 1 (HMGB1) protein were only from dry sheets. An in vitro fibroblast proliferation assay revealed that the dry sheet eluate significantly enhanced cell proliferation and VEGF and HGF production compared with living sheet eluate. FGF-2-neutralizing antibodies significantly blocked this proliferative response. In wounds created on diabetic mice, the dry sheet-treatment groups using autologous or allogeneic cells showed significantly accelerated wound closure compared with that in the no-treatment group. The storage stability of the dry sheet was better at refrigeration temperature than at room temperature and remained stable for at least 4 weeks. Our data indicated that allogeneic dry sheets represent a promising new tool for regenerative medicine that promotes wound healing.
Mortality and biochemical recurrence after surgery, brachytherapy, or external radiotherapy for localized prostate cancer: a 10-year follow-up cohort study
Authors: Suárez José Francisco , Zamora Víctor , Garin Olatz , Gutiérrez Cristina , Pont Àngels , Pardo Yolanda , Goñi Alai , Mariño Alfonso , Hervás Asunción , Herruzo Ismael , Cabrera Patricia , Sancho Gemma , Ponce de León Javier , Macías Víctor , Guedea Ferran , Vigués Francesc , Castells Manuel , Ferrer Montse ,   Multicentric Spanish Group of Clinically Localized Prostate Cancer, Ferrer Montse , Garin Olatz , Pont Àngels , Pardo Yolanda , Alonso Jordi , Zamora Víctor , Guedea Ferran , Ventura Montse , Gutiérrez Cristina , Ferrer Ferran , Boladeras Ana , Suárez José Francisco , Castells Manel , Bonet Xavier , Ávila Mónica , Pastor Sergi , Bonet Carmen , Sancho Gemma , Ponce de León Javier , Palou Joan , de Paula Belén , Goñi Alai , Fernández Pablo , Herruzo Ismael , Hervás Asunción , Ramos Alfredo , Macías Víctor , Solé Josep , Bonet Marta , Mariño Alfonso , Cabrera Patricia , Ortiz María José 
Published: July 2022

AbstractTo compare the effectiveness at ten years of follow-up of radical prostatectomy, brachytherapy and external radiotherapy, in terms of overall survival, prostate cancer-specific mortality and biochemical recurrence. Cohort of men diagnosed with localized prostate cancer (T1/T2 and low/intermediate risk) from ten Spanish hospitals, followed for 10 years. The treatment selection was decided jointly by patients and physicians. Of 704 participants, 192 were treated with open radical retropubic prostatectomy, 317 with 125I brachytherapy alone, and 195 with 3D external beam radiation. We evaluated overall survival, prostate cancer-specific mortality, and biochemical recurrence. Kaplan–Meier estimators were plotted, and Cox proportional-hazards regression models were constructed to estimate hazard ratios (HR), adjusted by propensity scores. Of the 704 participants, 542 patients were alive ten years after treatment, and a total of 13 patients have been lost during follow-up. After adjusting by propensity score and Gleason score, brachytherapy and external radiotherapy were not associated with decreased 10-year overall survival (aHR = 1.36, p = 0.292 and aHR = 1.44, p = 0.222), but presented higher biochemical recurrence (aHR = 1.93, p = 0.004 and aHR = 2.56, p < 0.001) than radical prostatectomy at ten years of follow-up. Higher prostate cancer-specific mortality was also observed in external radiotherapy (aHR = 9.37, p = 0.015). Novel long-term results are provided on the effectiveness of brachytherapy to control localized prostate cancer ten years after treatment, compared to radical prostatectomy and external radiotherapy, presenting high overall survival, similarly to radical prostatectomy, but higher risk of biochemical progression. These findings provide valuable information to facilitate shared clinical decision-making.Study identifier at ClinicalTrials.gov: NCT01492751.
An in silico approach to study the role of epitope order in the multi-epitope-based peptide (MEBP) vaccine design
Authors: Salaikumaran Muthu Raj , Kasamuthu Prasanna Sudharson , Aathmanathan Veeranarayanan Surya , Burra V. L. S. Prasad 
Published: July 2022

AbstractWith different countries facing multiple waves, with some SARS-CoV-2 variants more deadly and virulent, the COVID-19 pandemic is becoming more dangerous by the day and the world is facing an even more dreadful extended pandemic with exponential positive cases and increasing death rates. There is an urgent need for more efficient and faster methods of vaccine development against SARS-CoV-2. Compared to experimental protocols, the opportunities to innovate are very high in immunoinformatics/in silico approaches, especially with the recent adoption of structural bioinformatics in peptide vaccine design. In recent times, multi-epitope-based peptide vaccine candidates (MEBPVCs) have shown extraordinarily high humoral and cellular responses to immunization. Most of the publications claim that respective reported MEBPVC(s) assembled using a set of in silico predicted epitopes, to be the computationally validated potent vaccine candidate(s) ready for experimental validation. However, in this article, for a given set of predicted epitopes, it is shown that the published MEBPVC is one among the many possible variants and there is high likelihood of finding more potent MEBPVCs than the published candidates. To test the same, a methodology is developed where novel MEBP variants are derived by changing the epitope order of the published MEBPVC. Further, to overcome the limitations of current qualitative methods of assessment of MEBPVC, to enable quantitative comparison and ranking for the discovery of more potent MEBPVCs, novel predictors, Percent Epitope Accessibility (PEA), Receptor specific MEBP vaccine potency (RMVP), MEBP vaccine potency (MVP) are introduced. The MEBP variants indeed showed varied MVP scores indicating varied immunogenicity. Further, the MEBP variants with IDs, SPVC_446 and SPVC_537, had the highest MVP scores indicating these variants to be more potent MEBPVCs than the published MEBPVC and hence should be preferred candidates for immediate experimental testing and validation. The method enables quicker selection and high throughput experimental validation of vaccine candidates. This study also opens the opportunity to develop new software tools for designing more potent MEBPVCs in less time.
A comparison of high-throughput SARS-CoV-2 sequencing methods from nasopharyngeal samples
Authors: Gerber Zuzana , Daviaud Christian , Delafoy Damien , Sandron Florian , Alidjinou Enagnon Kazali , Mercier Jonathan , Gerber Sylvain , Meyer Vincent , Boland Anne , Bocket Laurence , Olaso Robert , Deleuze Jean-François 
Published: July 2022

AbstractThe COVID-19 pandemic caused by the new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to threaten public health and burden healthcare systems worldwide. Whole SARS-CoV-2 genome sequencing has become essential for epidemiological monitoring and identification of new variants, which could represent a risk of increased transmissibility, virulence, or resistance to vaccines or treatment. Different next-generation sequencing approaches are used in SARS-CoV-2 sequencing, although with different ability to provide whole genome coverage without gaps and to reliably detect new variants. In this study, we compared the performance of three target enrichment methods (two multiplex amplification methods and one hybridization capture) using nasopharyngeal swabs from infected individuals. We applied these target enrichment methods to the same set of nasopharyngeal samples (N = 93) in high-throughput mode. SARS-CoV-2 genome was obtained using short-read next-generation sequencing. We observed that each method has some advantages, such as high mapping rate (CleanPlex and COVIDSeq) or absence of systematic variant calling error (SureSelect) as well as their limitations such as suboptimal uniformity of coverage (CleanPlex), high cost (SureSelect) or supply shortages (COVIDSeq). Nevertheless, each of the three target enrichment kits tested in this study yielded acceptable results of whole SARS-CoV-2 genome sequencing and either of them can therefore be used in prospective programs of genomic surveillance of SARS-CoV-2. Genomic surveillance will be crucial to overcoming the ongoing pandemic of COVID-19, despite its successive waves and continually emerging variants.
The screening for anticoagulant rodenticide gene VKORC1 polymorphism in the rat Rattus norvegicus, Rattus tanezumi and Rattus losea in Hong Kong
Authors: Huang Elaine Y. Y. , Law Sean T. S. , Nong Wenyan , Yip Ho Yin , Uea-Anuwong Theethawat , Magouras Ioannis , Hui Jerome H. L. 
Published: July 2022

AbstractAnticoagulants are a major component of rodenticides used worldwide, which function by effectively blocking the vitamin K cycle in rodents. The rat Vitamin K epoxide Reductase Complex (VKORC) subunit 1 is the enzyme responsible for recycling vitamin K, and five substitution mutations (Tyr139Cys, Tyr139Ser, Tyr139Phe and Leu128Gln and Leu120Gln) located in the VKORC1 could result in resistance to anticoagulant rodenticides. This study carried out a VKORC1-based survey to estimate the anticoagulant rodenticide resistance in three Rattus species (R. losea, R. norvegicus, and R. tanezumi) collected in Hong Kong. A total of 202 rats captured in Hong Kong between 2017 and 2021 were analysed. Sequencing of molecular marker cytochrome c oxidase subunit 1 (COX1) was carried out to assist the species identification, and the identities of 52 lesser ricefield rats (R. losea), 81 common rats (R. norvegicus) and 69 house rats (R. tanezumi) were confirmed. Three VKORC1 exons were amplified from individuals by PCR followed by Sanger sequencing. A total of 47 R. tanezumi (68.1%) contained Tyr139Cys mutation in VKORC1 gene, and half of them were homozygous. None of the collected R. losea and R. norvegicus were detected with the five known substitutions leading to anticoagulant rodenticides resistance, and previously undescribed missense mutations were revealed in each species. Whole genome sequencing was further carried out on some individuals, and single nucleotide polymorphisms (SNPs) were also identified in the introns. This is the first study investigating the situation of anticoagulant rodenticide resistance in the rats collected in Hong Kong. Given that the efficacy of rodenticides is crucial for effective rodent management, regular genetic testing as well as population genomic analyses will be required to both monitor the situation and understand the adaption of different rat haplotypes for integrated pest management. Susceptibility tests for individual rodenticides should also be conducted regularly to assess their effectiveness on local species.
Development of microbial communities in biofilm and activated sludge in a hybrid reactor
Authors: Godzieba Martyna , Zubrowska-Sudol Monika , Walczak Justyna , Ciesielski Slawomir 
Published: July 2022

AbstractMicroorganisms play a key role in biological wastewater treatment. The form in which biomass develops determines the efficiency and mechanisms of organic compound conversion, due to different conditions in various microbial structures. However, the results of studies comparing the microbial communities in biofilm and activated sludge have often conflicted. Therefore, this study compared the composition and development of the bacterial communities in biofilm and activated sludge in a hybrid reactor, employing 16S rRNA sequencing. Statistical analysis of the sequencing data included the identification of taxa characteristic to the biofilm and activated sludge, alpha and beta diversity analysis, and network analysis. These analyses indicated that the biofilm bacterial community was richer and more diverse than the activated sludge community. The mean numbers of OTU were 1614 in the biofilm and 993 in the activated sludge, and the mean values of the Chao1 (1735 vs. 1105) and Shannon (5.3 vs. 4.3) biodiversity indices were significantly higher for the biofilm. The biofilm was a better environment for development of nitrifiers (e.g., Nitrosomonas, Nitrospira) and phosphorus accumulating organisms (Candidatus Accumulibacter). Bacteria in the biofilm co-occurrence network had more connections (based on Spearman's rank correlation coefficient) with each other, indicating that they interact more than those in the activated sludge.
The French EVAL-PLH cohort of persons with polyhandicap
Authors: Hamouda Ilyes , Rousseau Marie-Christine , Beltran Anzola Any , Aim Marie-Anastasie , de Villemeur Thierry Billette , Auquier Pascal , Baumstarck Karine ,   the EVAL-PLH group, de Villemeur Thierry Billette , Rousseau Marie-Christine , Khaldi-Cherif Sherezad , Maincent Kim , Felce Agnès , Baumstarck Karine , Auquier Pascal , Dany Lionel , Beltran Any , Hamouda Ilyes , Aim Marie-Anastasie , Boutalbi Narjess , Kemlin Isabelle , Roger Julie , Julien Patrick , Heng Ponha , Willocq Daniel , Valkov Maria , Pietra Stéphane , Lenormand Stéphane , Lind Katia 
Published: July 2022

AbstractPolyhandicap is characterized by a combination of profound intellectual disability and serious motor deficit, resulting in the extreme restriction of autonomy and communication. The aim of the EVAL-PLH (EVALuation PoLyHandicap) study is to identify the impact of socioeconomic, environmental, and epidemiological determinants on the health status of the persons with polyhandicap and the daily lives of their caregivers. EVAL-PLH is a prospective cohort study. The study involved persons with severe polyhandicap (who were cared for at reeducation centers, residential facilities, and one specialized pediatric/neurological department of a university hospital), their familial caregivers and the institutional caregivers. Data collection included sociodemographics, heath status, and psychocomportemental information. Data have been collected at 2 points (2015-2016 and 2020-2021). The French EVAL-PLH cohort is the first cohort study focusing on persons with polyhandicap, their families, and the health care workers caring for them. The sustainability of the device is essential to assist patients, families, clinicians, and health decision-making authorities in the optimization of care management.
Fractional quantum oscillator and disorder in the vibrational spectra
Authors: Stephanovich V. A. , Kirichenko E. V. , Dugaev V. K. , Sauco Jackie Harjani , Brito Belén López 
Published: July 2022

AbstractWe study the role of disorder in the vibration spectra of molecules and atoms in solids. This disorder may be described phenomenologically by a fractional generalization of ordinary quantum-mechanical oscillator problem. To be specific, this is accomplished by the introduction of a so-called fractional Laplacian (Riesz fractional derivative) to the Scrödinger equation with three-dimensional (3D) quadratic potential. To solve the obtained 3D spectral problem, we pass to the momentum space, where the problem simplifies greatly as fractional Laplacian becomes simply$$k^\mu $$kμ,kis a modulus of the momentum vector and$$\mu $$μis Lévy index, characterizing the degree of disorder. In this case,$$\mu \rightarrow 0$$μ→0corresponds to the strongest disorder, while$$\mu \rightarrow 2$$μ→2to the weakest so that the case$$\mu =2$$μ=2corresponds to “ordinary” (i.e. that without fractional derivatives) 3D quantum harmonic oscillator. Combining analytical (variational) and numerical methods, we have shown that in the fractional (disordered) 3D oscillator problem, the famous orbital momentum degeneracy is lifted so that its energy starts to depend on orbital quantum numberl. These features can have a strong impact on the physical properties of many solids, ranging from multiferroics to oxide heterostructures, which, in turn, are usable in modern microelectronic devices.
Maternal stress induced endoplasmic reticulum stress and impaired pancreatic islets’ insulin secretion via glucocorticoid receptor upregulation in adult male rat offspring
Authors: Salimi Mina , Eskandari Farzaneh , Binayi Fateme , Eliassi Afsaneh , Ghanbarian Hossein , Hedayati Mehdi , Fahanik-babaei Javad , Eftekhary Mohamad , Keyhanmanesh ‬Rana , Zardooz Homeira 
Published: July 2022

AbstractExposure to perinatal (prenatal and/or postnatal) stress is considered as a risk factor for metabolic disorders in later life. Accordingly, this study aimed to investigate the perinatal stress effects on the pancreatic endoplasmic reticulum (ER) stress induction, insulin secretion impairment and WFS1 (wolframin ER transmembrane Glycoprotein, which is involved in ER homeostasis and insulin secretion) expression changes, in rat offspring. According to the dams’ period of exposure to variable stress, their male offspring were divided into, control (CTRL); pre-pregnancy, pregnancy, lactation stress (PPPLS); pre-pregnancy stress (PPS); pregnancy stress (PS); lactation stress (LS); pre-pregnancy, pregnancy stress (PPPS); pregnancy, lactation stress (PLS); pre-pregnancy, lactation stress (PPLS) groups. Offspring pancreases were removed for ER extraction and the assessment of ER stress biomarkers, WFS1 gene DNA methylation, and isolated islets’ insulin secretion. Glucose tolerance was also tested. In the stressed groups, maternal stress significantly increased plasma corticosterone levels. In PPS, PS, and PPPS groups, maternal stress increased Bip (Hsp70; heat shock protein family A member 4), Chop (Ddit3; DNA- damage inducible transcript3), and WFS1 protein levels in pancreatic extracted ER. Moreover, the islets’ insulin secretion and content along with glucose tolerance were impaired in these groups. In PPS, PS, LS and PPPS groups, the pancreatic glucocorticoid receptor (GR) expression increased. Maternal stress did not affect pancreatic WFS1 DNA methylation. Thus, maternal stress, during prenatal period, impaired the islets’ insulin secretion and glucose homeostasis in adult male offspring, possibly through the induction of ER stress and GR expression in the pancreas, in this regard the role of WFS1 protein alteration in pancreatic ER should also be considered.
Face mediated human–robot interaction for remote medical examination
Authors: Lalitharatne Thilina D. , Costi Leone , Hashem Ryman , Nisky Ilana , Jack Rachael E. , Nanayakkara Thrishantha , Iida Fumiya 
Published: July 2022

AbstractRealtime visual feedback from consequences of actions is useful for future safety-critical human–robot interaction applications such as remote physical examination of patients. Given multiple formats to present visual feedback, using face as feedback for mediating human–robot interaction in remote examination remains understudied. Here we describe a face mediated human–robot interaction approach for remote palpation. It builds upon a robodoctor–robopatient platform where user can palpate on the robopatient to remotely control the robodoctor to diagnose a patient. A tactile sensor array mounted on the end effector of the robodoctor measures the haptic response of the patient under diagnosis and transfers it to the robopatient to render pain facial expressions in response to palpation forces. We compare this approach against a direct presentation of tactile sensor data in a visual tactile map. As feedback, the former has the advantage of recruiting advanced human capabilities to decode expressions on a human face whereas the later has the advantage of being able to present details such as intensity and spatial information of palpation. In a user study, we compare these two approaches in a teleoperated palpation task to find the hard nodule embedded in the remote abdominal phantom. We show that the face mediated human–robot interaction approach leads to statistically significant improvements in localizing the hard nodule without compromising the nodule position estimation time. We highlight the inherent power of facial expressions as communicative signals to enhance the utility and effectiveness of human–robot interaction in remote medical examinations.
Quantum coherence of a circularly accelerated atom in a spacetime with a reflecting boundary
Authors: Zhang Wanhe , Liu Xiaobao , Yang Tingli 
Published: July 2022

AbstractWe investigate, in the paradigm of open quantum systems, the dynamics of quantum coherence of a circularly accelerated atom coupled to a bath of vacuum fluctuating massless scalar field in a spacetime with a reflecting boundary. The master equation that governs the system evolution is derived. Our results show that in the case without a boundary, the vacuum fluctuations and centripetal acceleration will always cause the quantum coherence to decrease. However, with the presence of a boundary, the quantum fluctuations of the scalar field are modified, which makes that quantum coherence could be enhanced as compared to that in the case without a boundary. Particularly, when the atom is very close to the boundary, although the atom still interacts with the environment, it behaves as if it were a closed system and quantum coherence can be shielded from the effect of the vacuum fluctuating scalar field.
Glycometabolism change during Burkholderia pseudomallei infection in RAW264.7 cells by proteomic analysis
Authors: Li Xuexia , Zeng Yingfei , Guo Shengnan , Chen Chen , Liu Lin , Xia Qianfeng 
Published: July 2022

AbstractBurkholderia pseudomallei is a Gram-negative intracellular bacterium that causes melioidosis, a life-threatening disease. The interaction of B. pseudomallei with its host is complicated, and cellular response to B. pseudomallei infection is still largely unknown. In this study, we aimed to determine host-cell responses to B. pseudomallei at the proteomics level. We performed proteomic profiling of B. pseudomallei HNBP001-infected mouse macrophage RAW264.7 cells to characterize the cellular response dynamics during infection. Western blot analysis was utilized for the validation of changes in protein expression. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted using the clusterProfiler R package. Compared with the negative control (NC) group, 811 common proteins varied over time, with a cut-off level of two fold change and an adjusted P-value less than 0.05. The bioinformatics analysis revealed that the proteins significantly changed in the B. pseudomallei HNBP001 infection group (Bp group) were enriched in glycometabolism pathways, including glycolysis, fructose and mannose metabolism, pentose phosphate pathway, galactose metabolism, and carbon metabolism. Western blot analysis verified three selected proteins involved in glycometabolism pathways, namely PGM1, PKM, and PGK1 were increase over time post the infection. Furthermore, in vitro functional analysis revealed an increased glucose uptake and decreased ATP production and O-GlcNAcylation in the Bp group compared with control group, suggesting that B. pseudomallei HNBP001 infection induces changes in glycometabolism in RAW264.7 cells. These results indicate that glycometabolism pathways change in RAW264.7 cells post B. pseudomallei HNBP001 infection, providing important insights into the intimate interaction between B. pseudomallei and macrophages.