bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of Oat β-Glucan on the Survival and Proteolytic Activity of Lactobacillus rhamnosus GG in Milk Fermentation: Optimization by Response Surface
Authors: Chávez de la Vega María Isabel , Alatorre-Santamaría Sergio , Gómez-Ruiz Lorena , García-Garibay Mariano , Guzmán-Rodríguez Francisco , González-Olivares Luis Guillermo , Cruz-Guerrero Alma Elizabeth , Rodríguez-Serrano Gabriela Mariana
Published: September 2021

β-glucans come from cereals that have been located within compounds with prebiotic activity. They have presented several bioactivities that have determined their high functional value. The aim of this study was to identify the influence of oat β-glucan on the survival and proteolytic activity of Lactobacillus rhamnosus GG in a milk fermentation through an experimental design to optimize the process. For β-glucan extraction after dry milling of oats, two methods were applied: with and without enzymatic inactivation of the semolina. The highest extraction yield (45.25 g/L) was obtained with enzymatic inactivation. For the optimization of survival and proteolytic activity, a central design composed of axial points with two factors on three levels was used. Control factors were β-glucan and inoculum concentrations. According to response surface, the best survival growth rate of probiotic was observed with 4.38% of inoculum and 22.46 g/L of β-glucan, and the highest production of free amino groups was observed with 4.18% of inoculum and 22.71 g/L of β-glucan. Thus, β-glucan promotes the proteolytic activity of Lb. rhamnosus GG in milk fermentation.
Loss and Recovery of Carbon in Repeatedly Burned Degraded Peatlands of Kalimantan, Indonesia
Authors: Volkova Liubov , Adinugroho Wahyu Catur , Krisnawati Haruni , Imanuddin Rinaldi , Weston Christopher John
Published: September 2021

Although accurate estimates of biomass loss during peat fires, and recovery over time, are critical in understanding net peat ecosystem carbon balance, empirical data to inform carbon models are scarce. During the 2019 dry season, fires burned through 133,631 ha of degraded peatlands of Central Kalimantan. This study reports carbon loss from surface fuels and the top peat layer of 18.5 Mg C ha−1 (3.5 from surface fuels and 15.0 from root/peat layer), releasing an average of 2.5 Gg (range 1.8–3.1 Gg) carbon in these fires. Peat surface change measurements over one month, as the fires continued to smolder, indicated that about 20 cm of the surface was lost to combustion of peat and fern rhizomes, roots and recently incorporated organic residues that we sampled as the top peat layer. Time series analysis of live green vegetation (NDVI trend), combined with field observations of vegetation recovery two years after the fires, indicated that vegetation recovery equivalent to fire-released carbon is likely to occur around 3 years after fires.
Guaranteed Cost Leaderless Consensus Protocol Design for Fractional-Order Uncertain Multi-Agent Systems with State and Input Delays
Authors: Tian Yingming , Xia Qin , Chai Yi , Chen Liping , Lopes António M. , Chen YangQuan
Published: September 2021

This paper addresses the guaranteed cost leaderless consensus of delayed fractional-order (FO) multi-agent systems (FOMASs) with nonlinearities and uncertainties. A guaranteed cost function for FOMAS is proposed to simultaneously consider consensus performance and energy consumption. By employing the linear matrix inequality approach and the FO Razumikhin theorem, a delay-dependent and order-dependent consensus protocol is formulated for FOMASs with input delay. The proposed protocol not only guarantees the robust stability of the closed-loop system error but also ensures that the performance degradation caused by the system uncertainty is lesser than that obtained with other approaches. Two numerical examples are provided in order to verify the effectiveness and accuracy of the proposed protocol.
RETRACTED: Using Comorbidity Pattern Analysis to Detect Reliable Methylated Genes in Colorectal Cancer Verified by Stool DNA Test
Authors: Cheng Yi-Chiao , Wu Po-Hsien , Chen Yen-Ju , Yang Cing-Han , Huang Jhen-Li , Chou Yu-Ching , Chang Pi-Kai , Wen Chia-Cheng , Jao Shu-Wen , Huang Hsin-Hui , Tsai Yi-Hsuan , Pai Tun-Wen
Published: September 2021

Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide in 2020. Colonoscopy and the fecal immunochemical test (FIT) are commonly used as CRC screening tests, but both types of tests possess different limitations. Recently, liquid biopsy-based DNA methylation test has become a powerful tool for cancer screening, and the detection of abnormal DNA methylation in stool specimens is considered as an effective approach for CRC screening. The aim of this study was to develop a novel approach in biomarker selection based on integrating primary biomarkers from genome-wide methylation profiles and secondary biomarkers from CRC comorbidity analytics. A total of 125 differential methylated probes (DMPs) were identified as primary biomarkers from 352 genome-wide methylation profiles. Among them, 51 biomarkers, including 48 hypermethylated DMPs and 3 hypomethylated DMPs, were considered as suitable DMP candidates for CRC screening tests. After comparing with commercial kits, three genes (ADHFE1, SDC2, and PPP2R5C) were selected as candidate epigenetic biomarkers for CRC screening tests. Methylation levels of these three biomarkers were significantly higher for patients with CRC than normal subjects. The sensitivity and specificity of integrating methylated ADHFE1, SDC2, and PPP2R5C for CRC detection achieved 84.6% and 92.3%, respectively. Through an integrated approach using genome-wide DNA methylation profiles and electronic medical records, we could design a biomarker panel that allows for early and accurate noninvasive detection of CRC using stool samples.
Genetic and Genomic Pathways of Melanoma Development, Invasion and Metastasis
Authors: Motwani Jyoti , Eccles Michael R.
Published: September 2021

Melanoma is a serious form of skin cancer that accounts for 80% of skin cancer deaths. Recent studies have suggested that melanoma invasiveness is attributed to phenotype switching, which is a reversible type of cell behaviour with similarities to epithelial to mesenchymal transition. Phenotype switching in melanoma is reported to be independent of genetic alterations, whereas changes in gene transcription, and epigenetic alterations have been associated with invasiveness in melanoma cell lines. Here, we review mutational, transcriptional, and epigenomic alterations that contribute to tumour heterogeneity in melanoma, and their potential to drive melanoma invasion and metastasis. We also discuss three models that are hypothesized to contribute towards aspects of tumour heterogeneity and tumour progression in melanoma, namely the clonal evolution model, the cancer stem cell model, and the phenotype switching model. We discuss the merits and disadvantages of each model in explaining tumour heterogeneity in melanoma, as a precursor to invasion and metastasis.
A Novel Variant in Superoxide Dismutase 1 Gene (p.V119M) in Als Patients with Pure Lower Motor Neuron Presentation
Authors: Ricci Claudia , Giannini Fabio , Riolo Giulia , Bocci Silvia , Casali Stefania , Battistini Stefania
Published: September 2021

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal disorder characterized by degeneration of motor neurons in the cerebral cortex, brain stem, and spinal cord. Most cases of ALS appear sporadically, but 5–10% of patients have a family history of disease. Mutations in the superoxide dismutase 1 gene (SOD1) have been found in 12–23% of familial cases and in 1–2% of sporadic cases. Currently, more than 180 different SOD1 gene variants have been identified in ALS patients. Here, we describe two apparently sporadic ALS patients carrying the same SOD1 c.355G>A variant, leading to the p.V119M substitution, not previously described. Both the patients showed pure lower motor neuron phenotype. The former presented with the flail leg syndrome, a rare ALS variant, characterized by progressive distal onset weakness and atrophy of lower limbs, slow progression and better survival than typical ALS. The latter exhibited rapidly progressive weakness of upper and lower limbs, neither upper motor neuron nor bulbar involvement, and shorter survival than typical ALS. We provide an accurate description of the phenotype, and a bioinformatics analysis of the p.V119M variant on protein structure. This study may increase the knowledge about genotype-phenotype correlations in ALS and improve the approach to ALS patients.
Comparative Transcriptome Analysis in Monocyte-Derived Macrophages of Asymptomatic GBA Mutation Carriers and Patients with GBA-Associated Parkinson’s Disease
Authors: Usenko Tatiana , Bezrukova Anastasia , Basharova Katerina , Panteleeva Alexandra , Nikolaev Mikhail , Kopytova Alena , Miliukhina Irina , Emelyanov Anton , Zakharova Ekaterina , Pchelina Sofya
Published: September 2021

Mutations of the GBA gene, encoding for lysosomal enzyme glucocerebrosidase (GCase), are the greatest genetic risk factor for Parkinson’s disease (PD) with frequency between 5% and 20% across the world. N370S and L444P are the two most common mutations in the GBA gene. PD carriers of severe mutation L444P in the GBA gene is characterized by the earlier age at onset compared to N370S. Not every carrier of GBA mutations develop PD during one’s lifetime. In the current study we aimed to find common gene expression signatures in PD associated with mutation in the GBA gene (GBA-PD) using RNA-seq. We compared transcriptome of monocyte-derived macrophages of 5 patients with GBA-PD (4 L444P/N, 1 N370S/N) and 4 asymptomatic GBA mutation carriers (GBA-carriers) (3 L444P/N, 1 N370S/N) and 4 controls. We also conducted comparative transcriptome analysis for L444P/N only GBA-PD patients and GBA-carriers. Revealed deregulated genes in GBA-PD independently of GBA mutations (L444P or N370S) were involved in immune response, neuronal function. We found upregulated pathway associated with zinc metabolism in L444P/N GBA-PD patients. The potential important role of DUSP1 in the pathogenesis of GBA-PD was suggested.
Enhanced Steady-State Solution of the Infinite Moving Line Source Model for the Thermal Design of Grouted Borehole Heat Exchangers with Groundwater Advection
Authors: Van de Ven Adinda , Koenigsdorff Roland , Bayer Peter
Published: September 2021

The objective of this study is to assess the suitability of the analytical infinite moving line source (MLS) model in determining the temperature of vertical grouted borehole heat exchangers (BHEs) for steady-state conditions when horizontal groundwater advection is present. Therefore, a numerical model of a grouted borehole is used as a virtual reality for further analysis. As a result of the first analysis, it has been discovered that established analytical methods to determine the borehole thermal resistance as a mean value over the borehole radius can also be applied to BHEs with groundwater advection. Furthermore, the deviation between a finite MLS and the infinite MLS is found to be only less than 5% for BHEs of a depth of 30 m or more, and Péclet numbers greater than 0.05. Finally, the accuracy of the temperature change calculated with the infinite MLS model at the radius of the borehole wall compared to the temperature change at a numerically simulated grouted borehole is addressed. A discrepancy of the g-functions resulting in a poor dimensioning of BHEs by the infinite MLS model is revealed, which is ascribed to the impermeable grouting material of the numerical model. A correction function has been developed and applied to the infinite MLS model for steady-state conditions to overcome this discrepancy and to avoid poor dimensioning of BHEs.
Molecular Insights into SARS-CoV2-Induced Alterations of the Gut/Brain Axis
Authors: Nataf Serge , Pays Laurent
Published: September 2021

For a yet unknown reason, a substantial share of patients suffering from COVID-19 develop long-lasting neuropsychiatric symptoms ranging from cognitive deficits to mood disorders and/or an extreme fatigue. We previously reported that in non-neural cells, angiotensin-1 converting enzyme 2 (ACE2), the gene coding for the SARS-CoV2 host receptor, harbors tight co-expression links with dopa-decarboxylase (DDC), an enzyme involved in the metabolism of dopamine. Here, we mined and integrated data from distinct human expression atlases and found that, among a wide range of tissues and cells, enterocytes of the small intestine express the highest expression levels of ACE2, DDC and several key genes supporting the metabolism of neurotransmitters. Based on these results, we performed co-expression analyses on a recently published set of RNA-seq data obtained from SARS-CoV2-infected human intestinal organoids. We observed that in SARS-CoV2-infected enterocytes, ACE2 co-regulates not only with DDC but also with a specific group of genes involved in (i) the dopamine/trace amines metabolic pathway, (ii) the absorption of microbiota-derived L-DOPA and (iii) the absorption of neutral amino acids serving as precursors to neurotransmitters. We conclude that in patients with long COVID, a chronic infection and inflammation of small intestine enterocytes might be indirectly responsible for prolonged brain alterations.
Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity of Vitis
Authors: Park Minkyu , Sarkhosh Ali , Tsolova Violeta , El-Sharkawy Islam
Published: September 2021

While horizontally transferred transposable elements (TEs) have been reported in several groups of plants, their importance for genome evolution remains poorly understood. To understand how horizontally transferred TEs contribute to plant genome evolution, we investigated the composition and activity of horizontally transferred TEs in the genomes of four Vitis species. A total of 35 horizontal transfer (HT) events were identified between the four Vitis species and 21 other plant species belonging to 14 different families. We determined the donor and recipient species for 28 of these HTs, with the Vitis species being recipients of 15 of them. As a result of HTs, 8–10 LTR retrotransposon clusters were newly formed in the genomes of the four Vitis species. The activities of the horizontally acquired LTR retrotransposons differed among Vitis species, showing that the consequences of HTs vary during the diversification of the recipient lineage. Our study provides the first evidence that the HT of TEs contributes to the diversification of plant genomes by generating additional TE subfamilies and causing their differential proliferation in host genomes.
Regulation of B Cell Responses in SLE by Three Classes of Interferons
Authors: Domeier Phillip P. , Rahman Ziaur S. M.
Published: September 2021

There are three classes of interferons (type 1, 2, and 3) that can contribute to the development and maintenance of various autoimmune diseases, including systemic lupus erythematosus (SLE). Each class of interferons promotes the generation of autoreactive B cells and SLE-associated autoantibodies by distinct signaling mechanisms. SLE patients treated with various type 1 interferon-blocking biologics have diverse outcomes, suggesting that additional environmental and genetic factors may dictate how these cytokines contribute to the development of autoreactive B cells and SLE. Understanding how each class of interferons controls B cell responses in SLE is necessary for developing optimized B cell- and interferon-targeted therapeutics. In this review, we will discuss how each class of interferons differentially promotes the loss of peripheral B cell tolerance and leads to the development of autoreactive B cells, autoantibodies, and SLE.
TNAP: A New Multitask Enzyme in Energy Metabolism
Authors: Briolay Anne , Bessueille Laurence , Magne David
Published: September 2021

Tissue-nonspecific alkaline phosphatase (TNAP) is mainly known for its necessary role in skeletal and dental mineralization, which relies on the hydrolysis of the mineralization inhibitor inorganic pyrophosphate (PPi). Mutations in the gene encoding TNAP leading to severe hypophosphatasia result in strongly reduced mineralization and perinatal death. Fortunately, the relatively recent development of a recombinant TNAP with a bone anchor has allowed to correct the bone defects and prolong the life of affected babies and children. Researches on TNAP must however not be slowed down, because accumulating evidence indicates that TNAP activation in individuals with metabolic syndrome (MetS) is associated with enhanced cardiovascular mortality, presumably in relation with cardiovascular calcification. On the other hand, TNAP appears to be necessary to prevent the development of steatohepatitis in mice, suggesting that TNAP plays protective roles. The aim of the present review is to highlight the known or suspected functions of TNAP in energy metabolism that may be associated with the development of MetS. The location of TNAP in liver and its function in bile excretion, lipopolysaccharide (LPS) detoxification and fatty acid transport will be presented. The expression and function of TNAP in adipocyte differentiation and thermogenesis will also be discussed. Given that TNAP is a tissue- and substrate-nonspecific phosphatase, we believe that it exerts several crucial pathophysiological functions that are just beginning to be discovered.
Using the Zebrafish as a Genetic Model to Study Erythropoiesis
Authors: Zhang Yuhan , Chen Mengying , Chen Caiyong
Published: September 2021

Vertebrates generate mature red blood cells (RBCs) via a highly regulated, multistep process called erythropoiesis. Erythropoiesis involves synthesis of heme and hemoglobin, clearance of the nuclei and other organelles, and remodeling of the plasma membrane, and these processes are exquisitely coordinated by specific regulatory factors including transcriptional factors and signaling molecules. Defects in erythropoiesis can lead to blood disorders such as congenital dyserythropoietic anemias, Diamond–Blackfan anemias, sideroblastic anemias, myelodysplastic syndrome, and porphyria. The molecular mechanisms of erythropoiesis are highly conserved between fish and mammals, and the zebrafish (Danio rerio) has provided a powerful genetic model for studying erythropoiesis. Studies in zebrafish have yielded important insights into RBC development and established a number of models for human blood diseases. Here, we focus on latest discoveries of the molecular processes and mechanisms regulating zebrafish erythropoiesis and summarize newly established zebrafish models of human anemias.
Phase Transitions in Two-Dimensional Systems of Janus-like Particles on a Triangular Lattice
Authors: Patrykiejew Andrzej
Published: September 2021

We studied the phase behavior of two-dimensional systems of Janus-like particles on a triangular lattice using Monte Carlo methods. The model assumes that each particle can take on one of the six orientations with respect to the lattice, and the interactions between neighboring particles were weighted depending on the degree to which their A and B halves overlap. In this work, we assumed that the AA interaction was fixed and attractive, while the AB and BB interactions varied. We demonstrated that the phase behavior of the systems considered strongly depended on the magnitude of the interaction energies between the AB and BB halves. Here, we considered systems with non-repulsive interactions only and determined phase diagrams for several systems. We demonstrated that the phase diagram topology depends on the temperature at which the close-packed systems undergo the orientational order–disorder transition.
Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes
Authors: Park Seongjun , Jun Minji , Park Sunmi , Park SeonJoo
Published: September 2021

Caprifoliaceae s.l. plastid genomes (plastomes) show that one inversion and two inverted repeat boundary shifts occurred in the common ancestor of this family, after which the plastomes are generally conserved. This study reports plastome sequences of five additional species, Fedia cornucopiae, Valeriana fauriei, and Valerianella locusta from the subfamily Valerianoideae, as well as Dipsacus japonicus and Scabiosa comosa from the subfamily Dipsacoideae. Combined with the published plastomes, these plastomes provide new insights into the structural evolution of plastomes within the family. Moreover, the three plastomes from the subfamily Valerianoideae exhibited accelerated nucleotide substitution rates, particularly at synonymous sites, across the family. The patterns of accD sequence divergence in the family are dynamic with structural changes, including interruption of the conserved domain and increases in nonsynonymous substitution rates. In particular, the Valeriana accD gene harbors a large insertion of amino acid repeat (AAR) motifs, and intraspecific polymorphism with a variable number of AARs in the Valeriana accD gene was detected. We found a correlation between intron losses and increased ratios of nonsynonymous to synonymous substitution rates in the clpP gene with intensified positive selection. In addition, two Dipsacoideae plastomes revealed the loss of the plastid-encoded rps15, and a potential functional gene transfer to the nucleus was confirmed.
Photodynamic Therapy Induced Cell Death Mechanisms in Breast Cancer
Authors: Mokoena Dimakatso R. , George Blassan P. , Abrahamse Heidi
Published: September 2021

Breast cancer is the second most common cancer globally and the pioneering cause of mortality among women. It usually begins from the ducts or lobules, referred to as ductal carcinoma in situ, or lobular carcinoma in situ. Age, mutations in Breast Cancer Gene 1 or 2 (BRCA1 or BRCA2) genes, and dense breast tissue are the highest risk factors. Current treatments are associated with various side effects, relapse, and a low quality of life. Although conventional treatments, such as surgery and chemotherapy, have been used for decades, their adverse side effects on normal cells and tissues pose a major weakness, which calls for a non-invasive treatment option. Photodynamic therapy (PDT) has proven to be a promising form of cancer therapy. It is less invasive, target-specific, and with reduced cytotoxicity to normal cells and tissues. It involves the use of a photosensitizer (PS) and light at a specific wavelength to produce reactive oxygen species. One of the reasons for the target specificity is associated with the dense vascularization of cancer tissues, which tends to increase the surface area for the PS uptake. Photosensitizers are light-sensitive molecules, which result in cancer cell destruction followed by light irradiation. Depending on the localization of the PS within the cancer cell, its destruction may be via apoptosis, necrosis, or autophagy. This review focuses on the breast cancer etiopathology and PDT-induced cell death mechanisms in breast cancer cells.
LRGCPND: Predicting Associations between ncRNA and Drug Resistance via Linear Residual Graph Convolution
Authors: Li Yizhan , Wang Runqi , Zhang Shuo , Xu Hanlin , Deng Lei
Published: September 2021

Accurate inference of the relationship between non-coding RNAs (ncRNAs) and drug resistance is essential for understanding the complicated mechanisms of drug actions and clinical treatment. Traditional biological experiments are time-consuming, laborious, and minor in scale. Although several databases provide relevant resources, computational method for predicting this type of association has not yet been developed. In this paper, we leverage the verified association data of ncRNA and drug resistance to construct a bipartite graph and then develop a linear residual graph convolution approach for predicting associations between non-coding RNA and drug resistance (LRGCPND) without introducing or defining additional data. LRGCPND first aggregates the potential features of neighboring nodes per graph convolutional layer. Next, we transform the information between layers through a linear function. Eventually, LRGCPND unites the embedding representations of each layer to complete the prediction. Results of comparison experiments demonstrate that LRGCPND has more reliable performance than seven other state-of-the-art approaches with an average AUC value of 0.8987. Case studies illustrate that LRGCPND is an effective tool for inferring the associations between ncRNA and drug resistance.
Fractal-Percolation Structure Architectonics in Sol-Gel Synthesis
Authors: Kononova Irina , Kononov Pavel , Moshnikov Vyacheslav , Ignat’ev Sergey
Published: September 2021

It was developed a new technique to assess micro- and mesopores with sizes below a few nanometers. The porous materials with hierarchical fractal-percolation structure were obtained with the sol-gel method. The tetraethoxysilane hydrolysis and polycondensation reactions were performed in the presence of salts as the sources of metal oxides. The porous materials were obtained under spinodal decomposition conditions during application of the polymer sol to the substrate surface and thermal treatment of the structures. The model is based on an enhanced Kepler net of the 4612 type with hexagonal cells filled with a quasi-two-dimensional projection of the Jullien fractal after the 2nd iteration. The materials obtained with the sol-gel method were studied using the atomic force microscopy, electron microscopy, thermal desorption, as well as an AutoCAD 2022 computer simulation of the percolation transition in a two-component system using the proposed multimodal model. Based on the results obtained, a new method was suggested to assess micro- and mesopores with sizes below a few nanometrs, which cannot be analyzed using the atomic force microscopy and electron microscopy.
Pear Defect Detection Method Based on ResNet and DCGAN
Authors: Zhang Yan , Wa Shiyun , Sun Pengshuo , Wang Yaojun
Published: September 2021

To address the current situation, in which pear defect detection is still based on a workforce with low efficiency, we propose the use of the CNN model to detect pear defects. Since it is challenging to obtain defect images in the implementation process, a deep convolutional adversarial generation network was used to augment the defect images. As the experimental results indicated, the detection accuracy of the proposed method on the 3000 validation set was as high as 97.35%. Variant mainstream CNNs were compared to evaluate the model’s performance thoroughly, and the top performer was selected to conduct further comparative experiments with traditional machine learning methods, such as support vector machine algorithm, random forest algorithm, and k-nearest neighbor clustering algorithm. Moreover, the other two varieties of pears that have not been trained were chosen to validate the robustness and generalization capability of the model. The validation results illustrated that the proposed method is more accurate than the commonly used algorithms for pear defect detection. It is robust enough to be generalized well to other datasets. In order to allow the method proposed in this paper to be applied in agriculture, an intelligent pear defect detection system was built based on an iOS device.
The Impact of Organizational Practices on the Information Security Management Performance
Authors: Alzahrani Latifa , Seth Kavita Panwar
Published: September 2021

Information explosion and pressures are leading organizations to invest heavily in information security to ensure that information technology decisions align with business goals and manage risks. Limited studies have been done using small- and-medium-sized enterprises (SMEs) in the manufacturing sector. Furthermore, a small number of parameters have been used in the previous studies. This research aims to examine and analyze the effect of security organizational practices on information security management performance with many parameters. A model has been developed together with hypotheses to evaluate the impact of organizational practices on information security management performance. The data is collected from 171 UK employees at manufacturing SMEs that had already implemented security policies. The structure equation model is employed via the SPSS Amos 22 tool for the evaluation of results. Our results state that security training, knowledge sharing, security education, and security visibility significantly impact information security performance. In addition, this study highlights a significant impact of both security training and knowledge sharing on trust in the organization. Business leaders and decision-makers can reference the proposed model and the corresponding study results to develop favourable tactics to achieve their goals regarding information security management.
Simple but Effective Knowledge-Based Query Reformulations for Precision Medicine Retrieval
Authors: Marchesin Stefano , Di Nunzio Giorgio Maria , Agosti Maristella
Published: September 2021

In Information Retrieval (IR), the semantic gap represents the mismatch between users’ queries and how retrieval models answer to these queries. In this paper, we explore how to use external knowledge resources to enhance bag-of-words representations and reduce the effect of the semantic gap between queries and documents. In this regard, we propose several simple but effective knowledge-based query expansion and reduction techniques, and we evaluate them for the medical domain. The query reformulations proposed are used to increase the probability of retrieving relevant documents through the addition to, or the removal from, the original query of highly specific terms. The experimental analyses on different test collections for Precision Medicine IR show the effectiveness of the developed techniques. In particular, a specific subset of query reformulations allow retrieval models to achieve top performing results in all the considered test collections.
Persistent Post-COVID-19 Syndrome in Hemodialyzed Patients—A Longitudinal Cohort Study from the North of Poland
Authors: Och Aleksander , Tylicki Piotr , Polewska Karolina , Puchalska-Reglińska Ewelina , Parczewska Aleksandra , Szabat Krzysztof , Biedunkiewicz Bogdan , Dębska-Ślizień Alicja , Tylicki Leszek
Published: September 2021

Background: After recovery from COVID-19, patients frequently face so-called “Post-COVID-19 Syndrome” defined by clusters of persistent symptoms lasting for >12 weeks which may arise from any system in the body. The long-term health consequences of COVID-19 in maintenance hemodialyzed (HD) patients remain to be investigated. Methods: In this longitudinal cohort study we described the health consequences in HD patients requiring hospitalization due to COVID-19. They were interviewed three and six months (M3 and M6) after discharge with a series of standardized questionnaires. Results: Of 144 HD patients discharged from the 7th Naval Hospital in Gdansk, 79 participants were enrolled, 39 m (49.4%) and 40 f (50.6%) with a median age of 70.0 (64.0–76.5) and an HD vintage of 40 months (17.5–88). After discharge, 93.7% and 81% reported at least one persistent symptom at M3 and M6, respectively. The most common symptoms were fatigue or muscle weakness (60.76% and 47.04%) and palpitations (40.51% and 30.14%). Dyspnea with an mMRC scale grade of at least 1 was reported by 21.5% before infection, and by 43.03% and 34.25% at M3 and M6, respectively. A decrease in the quality of life was reported in all domains of the EQ-5D-5L questionnaire but mainly in the pain/discomfort and anxiety dimensions. Mean EQ-VAS scores were 69.05, 61.58 and 64.38, respectively. Conclusion: Our study showed that HD patients may still experience persistent symptoms six months after recovery from COVID-19, which can further reduce their already poor health-related quality of life. This study highlights the need for long-term follow-up on these patients for diagnostic and rehabilitation programs.
Circulating Hydrogen Sulfide (H2S) and Nitric Oxide (NO) Levels Are Significantly Reduced in HIV Patients Concomitant with Increased Oxidative Stress Biomarkers
Authors: Islam Rahib K. , Donnelly Erinn , Islam Kazi N.
Published: September 2021

Human immunodeficiency virus (HIV) attacks the immune system and weakens the ability to fight infections/disease. Furthermore, HIV infection confers approximately two-fold higher risk of cardiac events compared with the general population. The pathological mechanisms responsible for the increased incidence of cardiovascular disease in HIV patients are largely unknown. We hypothesized that increased oxidative stress and attenuated circulating levels of the cardioprotective gaseous signaling molecules, nitric oxide (NO), and hydrogen sulfide (H2S) were involved in the cardiovascular pathobiology observed in HIV patients. Plasma samples from both HIV patients and age–matched normal subjects were used for all assays. Oxidative stress was determined by analyzing the levels of advanced oxidation protein products (AOPP) and H2O2. Antioxidant levels were determined by measuring the levels of trolox equivalent capacity. ADMA, hs-CRP, and IL-6 were determined by using ELISA. The levels of H2S (free H2S and sulfane sulfur) and NO2 (nitrite) were determined in the plasma samples by using gas chromatography and HPLC, respectively. In the present study we observed a marked induction in the levels of oxidative stress and decreased antioxidant status in the plasma of HIV patients as compared with the controls. Circulating levels of the cardiovascular disease biomarkers: ADMA, hs-CRP (high-sensitivity C-reactive protein), and IL-6 were significantly increased in the circulatory system of HIV patients. The levels of both nitrite and H2S/sulfane sulfur were significantly reduced in the plasma of HIV patients as compared with normal subjects. Our data demonstrate significant increases in circulating biomarkers of oxidative stress and cardiovascular (CV) in conjunction with decreased bioavailability of H2S and NO in HIV patients. Diminished levels of these two cardioprotective gaseous signaling molecules may be involved in the pathogenesis of CV disease in the setting of HIV.
Changes in Alcohol Use during the COVID-19 Pandemic among Young Adults: The Prospective Effect of Anxiety and Depression
Authors: Vera Belén del Valle , Carmona-Márquez José , Lozano-Rojas Óscar Martín , Parrado-González Alberto , Vidal-Giné Claudio , Pautassi Ricardo Marcos , Fernández-Calderón Fermín
Published: September 2021

Health measures instantiated to reduce the spread of COVID-19 have imposed significant constraints for the population and impacted on drinking habits and mental health. This study longitudinally compared changes in alcohol consumption before and after the COVID-19 outbreak and the impact of sociodemographic and mental health variables on such changes among a community sample of young adults. Data were collected in the context of a larger, ongoing longitudinal study. The sample consisted of 305 young adults from Spain aged between 18 and 26 years (mean age = 21.27, (SD = 2.21), female = 53.4%; college students = 61.6%) who completed first (November-2019 and February-2020; i.e., before the outbreak of COVID-19) and second follow-up questionnaires (March 2021, a year after the COVID-19 outbreak). Alcohol use (quantity and drinking frequency), depression and anxiety symptoms were measured. Quantity and frequency of alcohol use decreased from the pre- to post-COVID-19 period. A decrease in drinking frequency was observed among college students, but not in noncollege peers. Although we found no effect of pre-COVID-19 anxiety on alcohol use changes, those with more depressive symptoms at the pre-COVID assessment were more resistant to decreasing their drinking quantity and frequency after the COVID-19 outbreak. This information will be of value when designing interventions aimed at reducing harmful alcohol use and highlights the role of mental health status when identifying high risk populations of young-adults during this, and future, public health crises.
A Comparison of Patients Undergoing On- vs. Off-Pump Coronary Artery Bypass Surgery Managed with a Fast-Track Protocol
Authors: Grützner Henrike , Flo Forner Anna , Meineri Massimiliano , Janai Aniruddha , Ender Jörg , Zakhary Waseem Zakaria Aziz
Published: September 2021

The purpose of this study was to compare patients who underwent on- vs. off-pump coronary artery bypass surgery managed with a fast-track protocol. Between September 2012 and December 2018, n = 3505 coronary artery bypass surgeries were managed with a fast-track protocol in our specialized post-anesthesia care unit. Propensity score matching was applied and resulted in two equal groups of n = 926. There was no significant difference in ventilation time (on-pump 75 (55–120) min vs. off-pump 80 (55–120) min, p = 0.973). We found no statistically significant difference in primary fast-track failure in on-pump (8.2% (76)) vs. off-pump (6% (56)) groups (p = 0.702). The secondary fast-track failure rate was comparable (on-pump 12.9% (110) vs. off-pump 12.3% (107), p = 0.702). There were no significant differences between groups in regard to the post-anesthesia care unit, the intermediate care unit, and the hospital length of stay. Postoperative outcome and complications were also comparable, except for a statistically significant difference in PACU postoperative blood loss in on-pump (234 mL) vs. off-pump (323 mL, p < 0.0001) and red blood cell transfusion (11%) and (5%, p < 0.001), respectively. Our results suggest that on- and off-pump coronary artery bypass surgery in fast-track settings are comparable in terms of ventilation time, fast-track failure rate, and postoperative complications rate.
Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer
Authors: Rodríguez-Casanova Aitor , Bao-Caamano Aida , Lago-Lestón Ramón M. , Brozos-Vázquez Elena , Costa-Fraga Nicolás , Ferreirós-Vidal Isabel , Abdulkader Ihab , Vidal-Insua Yolanda , Rivera Francisca Vázquez , Candamio Folgar Sonia , López-López Rafael , Muinelo-Romay Laura , Diaz-Lagares Angel
Published: September 2021

Molecular profiling of circulating cell-free DNA (cfDNA) has shown utility for the management of colorectal cancer (CRC). TruSight Tumor 170 (TST170) is a next-generation sequencing (NGS) panel that covers 170 cancer-related genes, including KRAS, which is a key driver gene in CRC. We evaluated the capacity of TST170 to detect gene variants in cfDNA from a retrospective cohort of 20 metastatic CRC patients with known KRAS variants in tumor tissue and in cfDNA previously analyzed by pyrosequencing and BEAMing, respectively. The cfDNA of most of the patients (95%) was successfully sequenced. We frequently detected variants with clinical significance in KRAS (79%, 15/19) and PIK3CA (26%, 5/19) genes. Variants with potential clinical significance were also identified in another 27 cancer genes, such as APC. The type of KRAS variant detected in cfDNA by TST170 showed high concordance with those detected in tumor tissue (77%), and very high concordance with cfDNA analyzed by BEAMing (94%). The variant allele fractions for KRAS obtained in cfDNA by TST170 and BEAMing correlated strongly. This proof-of-principle study indicates that targeted NGS analysis of cfDNA with TST170 could be useful for non-invasive detection of gene variants in metastatic CRC patients, providing an assay that could be easily implemented for detecting somatic alterations in the clinic.
Tissue Expansion after Non-Skin-Sparing Mastectomy: A Comparative Study of Expansion Courses of Prepectoral and Subpectoral Tissue Expander Placement with Acellular Dermal Matrix
Authors: Jun Daiwon , Kim Jin Kwan , Kwon Byung Yeun , Kim Young Jin , Rhu Ji Young , Lee Kwan Ho , Lee Jung Ho
Published: September 2021

Although skin- or nipple-sparing mastectomy has been popular in the treatment of breast cancer, the radical excision of breast tissue is unavoidable in certain circumstances. However, the ability of an acellular dermal matrix (ADM) to expand remains questionable, and this situation may further hinder tissue expansion. From October 2017 to January 2020, patients who underwent immediate breast reconstruction with tissue expander placement using ADM whose initial fill volume was less than 50 mL were retrospectively reviewed. The primary outcomes were the number of visits and number of days required to complete the expansion, and the secondary outcomes were the amount of postoperative expansions, expander fill ratio and expander volume. Between the prepectoral group (n = 26) and subpectoral group (n = 39), the mean number of days (81.46 days versus 88.64 days, p = 0.365) and mean number of visits (5.08 versus 5.69, p = 0.91) required to complete expansion exhibited no significant differences. Additionally, there were no significant differences in the mean amount of postoperative expansion (314.23 mL versus 315.38 mL, p = 0.950), the mean final volume (353.08 mL versus 339.62 mL, p = 0.481) or the mean final volume ratio (0.89 versus 0.86, p = 0.35) between the two groups. Therefore, we suggest that prepectoral tissue expander placement after conventional mastectomy can be a valid option.
Prevention of Preterm Birth with Progesterone
Authors: Di Renzo Gian Carlo , Tosto Valentina , Tsibizova Valentina , Fonseca Eduardo
Published: September 2021

Gestational age at birth is a critical factor for perinatal and adulthood outcomes, and even for transgenerational conditions’ effects. Preterm birth (PTB) (prematurity) is still the main determinant for infant mortality and morbidity leading cause of infant morbidity and mortality. Unfortunately, preterm birth (PTB) is a relevant public health issue worldwide and the global PTB rate is around 11%. The premature activation of labor is underlined by complex mechanisms, with a multifactorial origin influenced by numerous known and probably unknown triggers. The possible mechanisms involved in a too early labor activation have been partially explained, and involve chemokines, receptors, and imbalanced inflammatory paths. Strategies for the early detection and prevention of this obstetric condition were proposed in clinical settings with interesting results. Progesterone has been demonstrated to have a key role in PTB prevention, showing several positive effects, such as lower prostaglandin synthesis, the inhibition of cervical stromal degradation, modulating the inflammatory response, reducing gap junction formation, and decreasing myometrial activation. The available scientific knowledge, data and recommendations address multiple current areas of debate regarding the use of progesterone in multifetal gestation, including different formulations, doses and routes of administration and its safety profile in pregnancy.
Influence of Component Ratio on Thermal and Mechanical Properties of Terpenoid-Sulfur Composites
Authors: Maladeniya Charini P. , Smith Rhett C.
Published: September 2021

Terpenoids are potentially sustainable replacements for petrochemical olefins. Sulfur is a waste product produced in large quantities from fossil fuel refining. Several composites with attractive properties have recently been made from terpenoids and sulfur. This report details the extent to which the ratio of sulfur to terpenoid and the terpenoid olefin content influences the thermal and mechanical properties of such terpenoid-sulfur composites. The terpenoids selected were diunsaturated geraniol and triunsaturated farnesol that, upon their inverse vulcanization with elemental sulfur, yield composites GerSx and FarSx, respectively (x = wt % sulfur). The wt % sulfur in the monomer feed was varied from 30–95 for this study, providing twelve materials. Mechanical analysis of these materials was undertaken by compressive and tensile strength techniques. Differential scanning calorimetric analysis revealed both polymeric and orthorhombic sulfur present in the materials with glass transition temperatures (Tg) of −37 °C to −13 °C and melt temperatures (Tm) of 119 to 104 °C. The crystallinity of composites decreases as the weight fraction of sulfur decreases and composites having the highest olefin content exhibit no detectable crystalline microstructures. The compressive strength of the materials showed increasing strength for higher olefin-content materials for both GerSx (with compressive strength of up to 32 MPa) and FarSx (with compressive strength of up to 43 MPa). The improved strength with increasing olefin content levels off at around 80–85% of terpenoid, after which point both tensile and compressive strength diminish.
Detection of Manipulated Face Videos over Social Networks: A Large-Scale Study
Authors: Marcon Federico , Pasquini Cecilia , Boato Giulia
Published: September 2021

The detection of manipulated videos represents a highly relevant problem in multimedia forensics, which has been widely investigated in the last years. However, a common trait of published studies is the fact that the forensic analysis is typically applied on data prior to their potential dissemination over the web. This work addresses the challenging scenario where manipulated videos are first shared through social media platforms and then are subject to the forensic analysis. In this context, a large scale performance evaluation has been carried out involving general purpose deep networks and state-of-the-art manipulated data, and studying different effects. Results confirm that a performance drop is observed in every case when unseen shared data are tested by networks trained on non-shared data; however, fine-tuning operations can mitigate this problem. Also, we show that the output of differently trained networks can carry useful forensic information for the identification of the specific technique used for visual manipulation, both for shared and non-shared data.
Roadmap on Recent Progress in FINCH Technology
Authors: Rosen Joseph , Alford Simon , Anand Vijayakumar , Art Jonathan , Bouchal Petr , Bouchal Zdeněk , Erdenebat Munkh-Uchral , Huang Lingling , Ishii Ayumi , Juodkazis Saulius , Kim Nam , Kner Peter , Koujin Takako , Kozawa Yuichi , Liang Dong , Liu Jun , Mann Christopher , Marar Abhijit , Matsuda Atsushi , Nobukawa Teruyoshi , Nomura Takanori , Oi Ryutaro , Potcoava Mariana , Tahara Tatsuki , Thanh Bang Le , Zhou Hongqiang
Published: September 2021

Fresnel incoherent correlation holography (FINCH) was a milestone in incoherent holography. In this roadmap, two pathways, namely the development of FINCH and applications of FINCH explored by many prominent research groups, are discussed. The current state-of-the-art FINCH technology, challenges, and future perspectives of FINCH technology as recognized by a diverse group of researchers contributing to different facets of research in FINCH have been presented.
An Optimized and Efficient CRISPR/Cas9 System for the Endophytic Fungus Pestalotiopsis fici
Authors: Xu Xinran , Huang Runye , Yin Wen-Bing
Published: September 2021

Endophytic fungi are emerging as attractive producers of natural products with diverse bioactivities and novel structures. However, difficulties in the genetic manipulation of endophytic fungi limit the search of novel secondary metabolites. In this study, we improved the polyethylene glycol (PEG)-mediated protoplast transformation method by introducing the CRISPR/Cas9 system into endophytic fungus Pestalotiopsis fici. Using this approach, we performed genome editing such as site-specific gene insertion, dual-locus mutations, and long DNA fragment deletions in P. fici efficiently. The average efficiency for site-specific gene insertion and two-site gene editing was up to 48.0% and 44.4%, respectively. In addition, the genetic manipulation time with long DNA fragment (5–10 kb) deletion was greatly shortened to one week in comparison with traditional methods such as Agrobacterium tumefaciens-mediated transformation (ATMT). Taken together, the development of the CRISPR/Cas9 system in the endophytic fungus will accelerate the discovery of novel natural products and further biological study.