bluuebunny/crossref_metadata_2025 huggingface dataset:
Guided Self-Assembly of ES-Derived Lung Progenitors into Biomimetic Tube Structures That Impact Cell Differentiation
Authors: Soleas John P. , Huang Linwen , D’Arcangelo Elisa , Nostro Maria Cristina , Waddell Thomas K. , McGuigan Alison P. , Karoubi Golnaz
Published: December 2021

Chemically directed differentiation of pluripotent stem cells (PSCs) into defined cell types is a potent strategy for creating regenerative tissue models and cell therapies. In vitro observations suggest that physical cues can augment directed differentiation. We recently demonstrated that confining human PSC-derived lung progenitor cells in a tube with a diameter that mimics those observed during lung development results in the alteration of cell differentiation towards SOX2−SOX9+ lung cells. Here we set out to assess the robustness of this geometric confinement effect with respect to different culture parameters in order to explore the corresponding changes in cell morphometry and determine the feasibility of using such an approach to enhance directed differentiation protocols. Culture of progenitor cells in polydimethylsiloxane (PDMS) tubes reliably induced self-organization into tube structures and was insensitive to a variety of extracellular matrix coatings. Cellular morphology and differentiation status were found to be sensitive to the diameter of tube cells that were cultured within but not to seeding density. These data suggest that geometric cues impose constraints on cells, homogenize cellular morphology, and influence fate status.
Immunoautophagy-Related Long Noncoding RNA (IAR-lncRNA) Signature Predicts Survival in Hepatocellular Carcinoma
Authors: Wang Yulu , Ge Fangfang , Sharma Amit , Rudan Oliver , Setiawan Maria F. , Gonzalez-Carmona Maria A. , Kornek Miroslaw T. , Strassburg Christian P. , Schmid Matthias , Schmidt-Wolf Ingo G. H.
Published: December 2021

Background: The dysregulation of autophagy and immunological processes has been linked to various pathophysiological conditions, including cancer. Most notably, their particular involvement in hepatocellular carcinoma (HCC) is becoming increasingly evident. This has led to the possibility of developing a prognostic signature based on immuno-autophagy-related (IAR) genes. Given that long non-coding RNAs (lncRNAs) also play a special role in HCC, a combined signature utilizing IAR genes and HCC-associated long noncoding RNAs (as IARlncRNA) may potentially help in the clinical scenario. Method: We used Pearson correlation analysis, Kaplan–Meier survival curves, univariate and multivariate Cox regression, and ROC curves to generate and validate a prognostic immuno-autophagy-related long non-coding RNA (IARlncRNA) signature. The Chi-squared test was utilized to investigate the correlation between the obtained signature and the clinical characteristics. CIBERSORT algorithms and the Wilcoxon rank sum test were applied to investigate the correlation between signature and infiltrating immune cells. GO and KEGG analyses were performed to derived signature-dependent pathways. Results: Herein, we build an IAR-lncRNA signature (as first in the literature) and demonstrate its prognostic ability in hepatocellular carcinoma. Primarily, we identified three IARlncRNAs (MIR210HG, AC099850.3 and CYTOR) as unfavorable prognostic determinants. The obtained signature predicted the high-risk HCC group with shorter overall survival, and was further associated with clinical characteristics such as tumor grade (t = 10.918, p = 0.001). Additionally, several infiltrating immune cells showed varied fractions between the low-risk group and the high-risk HCC groups in association with the obtained signature. In addition, pathways analysis described by the signature clearly distinguishes both risk groups in HCC. Conclusions: The immuno-autophagy-related long non-coding RNA (IARlncRNA) signature we established exhibits a prognostic ability in hepatocellular carcinoma. To our knowledge, this is the first attempt in the literature to combine three determinants (immune, autophagy and LnRNAs), thus requiring molecular validation of this obtained signature in clinical samples.
Structural and Predicted Functional Diversities of Bacterial Microbiome in Response to Sewage Sludge Amendment in Coastal Mudflat Soil
Authors: Li Yunlong , Wang Yimin , Shen Chao , Xu Lu , Yi Siqiang , Zhao Yilin , Zuo Wengang , Gu Chuanhui , Shan Yuhua , Bai Yanchao
Published: December 2021

The study investigated the influence of sewage sludge application at rates of 0 (CK), 30 (ST), 75 (MT), and 150 (HT) t ha−1 to mudflats on bacterial community diversity and predicted functions using amplicon-based sequencing. Soils under sewage sludge treatments, especially the HT treatment, exhibited lower pH, salinity and higher nutrient contents (C, N, and P). Moreover, restructured bacterial communities with significantly higher diversities and distinct core and unique microbiomes were observed in all sewage sludge-amended soils as compared to the control. Specifically, core bacterial families, such as Hyphomicrobiaceae, Cytophagaceae, Pirellulaceae Microbacteriaceae, and Phyllobacteriaceae, were significantly enriched in sewage sludge-amended soils. In addition, sewage sludge amendment significantly improved predicted functional diversities of core microbiomes, with significantly higher accumulative relative abundances of functions related to carbon and nitrogen cycling processes compared to the unamended treatment. Correlation analyses showed that modified soil physicochemical properties were conducive for the improvement of diversities of bacterial communities and predicted functionalities. These outcomes demonstrated that sewage sludge amendment not only alleviated saline–sodic and nutrient deficiency conditions, but also restructured bacterial communities with higher diversities and versatile functions, which may be particularly important for the fertility formation and development of mudflat soils.
Beta vulgaris L. (Beetroot) Methanolic Extract Prevents Hepatic Steatosis and Liver Damage in T2DM Rats by Hypoglycemic, Insulin-Sensitizing, Antioxidant Effects, and Upregulation of PPARα
Authors: Al-Harbi Laila Naif , Alshammari Ghedeir M. , Al-Dossari Alhanouf Mohammed , Subash-Babu Pandurangan , Binobead Manal Abdulaziz , Alhussain Maha H. , AlSedairy Sahar Abdulaziz , Al-Nouri Doha M. , Shamlan Ghalia
Published: December 2021

The present study examined if methanolic beetroot extract (BE) could prevent dyslipidemia and hepatic steatosis and damage in a type-2 diabetes mellitus (T2DM) rat model and studied some mechanisms of action. T2DM was induced in adult male Wistar rats by a low single dose of streptozotocin (STZ) (35 mg/kg, i.p) and a high-fat diet (HFD) feeding for 5 weeks. Control or T2DM rats then continued on standard or HFDs for another 12 weeks and were treated with the vehicle or BE (250 or 500 mg/kg). BE, at both doses, significantly improved liver structure and reduced hepatic lipid accumulation in the livers of T2DM rats. They also reduced body weight gain, serum glucose, insulin levels, serum and hepatic levels of cholesterol, triglycerides, free fatty acids, and serum levels of low-density lipoproteins in T2DM rats. In concomitant, they significantly reduced serum levels of aspartate and alanine aminotransferases, hepatic levels of malondialdehyde, tumor-necrosis factor-α, interleukin-6, and mRNA of Bax, cleaved caspase-3, and SREBP1/2. However, both doses of BE significantly increased hepatic levels of total glutathione, superoxide dismutase, and mRNA levels of Bcl2 and PPARα in the livers of both the control and T2DM rats. All of these effects were dose-dependent and more profound with doses of 500 mg/kg. In conclusion, chronic feeding of BE to STZ/HFD-induced T2DM in rats prevents hepatic steatosis and liver damage by its hypoglycemic and insulin-sensitizing effects and its ability to upregulate antioxidants and PPARα.
A Blood–Bone–Tooth Model for Age Prediction in Forensic Contexts
Authors: Correia Dias Helena , Manco Licínio , Corte Real Francisco , Cunha Eugénia
Published: December 2021

The development of age prediction models (APMs) focusing on DNA methylation (DNAm) levels has revolutionized the forensic age estimation field. Meanwhile, the predictive ability of multi-tissue models with similar high accuracy needs to be explored. This study aimed to build multi-tissue APMs combining blood, bones and tooth samples, herein named blood–bone–tooth-APM (BBT-APM), using two different methodologies. A total of 185 and 168 bisulfite-converted DNA samples previously addressed by Sanger sequencing and SNaPshot methodologies, respectively, were considered for this study. The relationship between DNAm and age was assessed using simple and multiple linear regression models. Through the Sanger sequencing methodology, we built a BBT-APM with seven CpGs in genes ELOVL2, EDARADD, PDE4C, FHL2 and C1orf132, allowing us to obtain a Mean Absolute Deviation (MAD) between chronological and predicted ages of 6.06 years, explaining 87.8% of the variation in age. Using the SNaPshot assay, we developed a BBT-APM with three CpGs at ELOVL2, KLF14 and C1orf132 genes with a MAD of 6.49 years, explaining 84.7% of the variation in age. Our results showed the usefulness of DNAm age in forensic contexts and brought new insights into the development of multi-tissue APMs applied to blood, bone and teeth.
Understanding the Role of Estrogen Receptor Status in PRODH/POX-Dependent Apoptosis/Survival in Breast Cancer Cells
Authors: Lewoniewska Sylwia , Oscilowska Ilona , Forlino Antonella , Palka Jerzy
Published: December 2021

It has been suggested that activation of estrogen receptor α (ER α) stimulates cell proliferation. In contrast, estrogen receptor β (ER β) has anti-proliferative and pro-apoptotic activity. Although the role of estrogens in estrogen receptor-positive breast cancer progression has been well established, the mechanism of their effect on apoptosis is not fully understood. It has been considered that ER status of breast cancer cells and estrogen availability might determine proline dehydrogenase/proline oxidase (PRODH/POX)-dependent apoptosis. PRODH/POX is a mitochondrial enzyme that converts proline into pyrroline-5-carboxylate (P5C). During this process, ATP (adenosine triphosphate) or ROS (reactive oxygen species) are produced, facilitating cell survival or death, respectively. However, the critical factor in driving PRODH/POX-dependent functions is proline availability. The amount of this amino acid is regulated at the level of prolidase (proline releasing enzyme), collagen biosynthesis (proline utilizing process), and glutamine, glutamate, α-ketoglutarate, and ornithine metabolism. Estrogens were found to upregulate prolidase activity and collagen biosynthesis. It seems that in estrogen receptor-positive breast cancer cells, prolidase supports proline for collagen biosynthesis, limiting its availability for PRODH/POX-dependent apoptosis. Moreover, lack of free proline (known to upregulate the transcriptional activity of hypoxia-inducible factor 1, HIF-1) contributes to downregulation of HIF-1-dependent pro-survival activity. The complex regulatory mechanism also involves PRODH/POX expression and activity. It is induced transcriptionally by p53 and post-transcriptionally by AMPK (AMP-activated protein kinase), which is regulated by ERs. The review also discusses the role of interconversion of proline/glutamate/ornithine in supporting proline to PRODH/POX-dependent functions. The data suggest that PRODH/POX-induced apoptosis is dependent on ER status in breast cancer cells.
The Annexin A2/S100A10 Complex: The Mutualistic Symbiosis of Two Distinct Proteins
Authors: Bharadwaj Alamelu , Kempster Emma , Waisman David Morton
Published: December 2021

Mutualistic symbiosis refers to the symbiotic relationship between individuals of different species in which both individuals benefit from the association. S100A10, a member of the S100 family of Ca2+-binding proteins, exists as a tight dimer and binds two annexin A2 molecules. This association forms the annexin A2/S100A10 complex known as AIIt, and modifies the distinct functions of both proteins. Annexin A2 is a Ca2+-binding protein that binds F-actin, phospholipid, RNA, and specific polysaccharides such as heparin. S100A10 does not bind Ca2+, but binds tPA, plasminogen, certain plasma membrane ion channels, neurotransmitter receptors, and the structural scaffold protein, AHNAK. S100A10 relies on annexin A2 for its intracellular survival: in the absence of annexin A2, it is rapidly destroyed by ubiquitin-dependent and independent proteasomal degradation. Annexin A2 requires S100A10 to increase its affinity for Ca2+, facilitating its participation in Ca2+-dependent processes such as membrane binding. S100A10 binds tissue plasminogen activator and plasminogen, and promotes plasminogen activation to plasmin, which is a process stimulated by annexin A2. In contrast, annexin A2 acts as a plasmin reductase and facilitates the autoproteolytic destruction of plasmin. This review examines the relationship between annexin A2 and S100A10, and how their mutualistic symbiosis affects the function of both proteins.
Structural Characterization of Rat Galectin-5, an N-Tailed Monomeric Proto-Type-like Galectin
Authors: Ruiz Federico M. , Medrano Francisco J. , Ludwig Anna-Kristin , Kaltner Herbert , Shilova Nadezhda V. , Bovin Nicolai V. , Gabius Hans-Joachim , Romero Antonio
Published: December 2021

Galectins are multi-purpose effectors acting via interactions with distinct counterreceptors based on protein-glycan/protein recognition. These processes are emerging to involve several regions on the protein so that the availability of a detailed structural characterization of a full-length galectin is essential. We report here the first crystallographic information on the N-terminal extension of the carbohydrate recognition domain of rat galectin-5, which is precisely described as an N-tailed proto-type-like galectin. In the ligand-free protein, the three amino-acid stretch from Ser2 to Ser5 is revealed to form an extra β-strand (F0), and the residues from Thr6 to Asn12 are part of a loop protruding from strands S1 and F0. In the ligand-bound structure, amino acids Ser2–Tyr10 switch position and are aligned to the edge of the β-sandwich. Interestingly, the signal profile in our glycan array screening shows the sugar-binding site to preferentially accommodate the histo-blood-group B (type 2) tetrasaccharide and N-acetyllactosamine-based di- and oligomers. The crystal structures revealed the characteristically preformed structural organization around the central Trp77 of the CRD with involvement of the sequence signature’s amino acids in binding. Ligand binding was also characterized calorimetrically. The presented data shows that the N-terminal extension can adopt an ordered structure and shapes the hypothesis that a ligand-induced shift in the equilibrium between flexible and ordered conformers potentially acts as a molecular switch, enabling new contacts in this region.
Salting-Out Approach Is Worthy of Comparison with Ultracentrifugation for Extracellular Vesicle Isolation from Tumor and Healthy Models
Authors: Serratì Simona , Palazzo Antonio , Lapenna Annamaria , Mateos Helena , Mallardi Antonia , Marsano René Massimiliano , Quarta Alessandra , Del Rosso Mario , Azzariti Amalia
Published: December 2021

The role of extracellular vesicles (EVs) has been completely re-evaluated in the recent decades, and EVs are currently considered to be among the main players in intercellular communication. Beyond their functional aspects, there is strong interest in the development of faster and less expensive isolation protocols that are as reliable for post-isolation characterisations as already-established methods. Therefore, the identification of easy and accessible EV isolation techniques with a low price/performance ratio is of paramount importance. We isolated EVs from a wide spectrum of samples of biological and clinical interest by choosing two isolation techniques, based on their wide use and affordability: ultracentrifugation and salting-out. We collected EVs from human cancer and healthy cell culture media, yeast, bacteria and Drosophila culture media and human fluids (plasma, urine and saliva). The size distribution and concentration of EVs were measured by nanoparticle tracking analysis and dynamic light scattering, and protein depletion was measured by a colorimetric nanoplasmonic assay. Finally, the EVs were characterised by flow cytometry. Our results showed that the salting-out method had a good efficiency in EV separation and was more efficient in protein depletion than ultracentrifugation. Thus, salting-out may represent a good alternative to ultracentrifugation.
In Vitro Anti-SARS-CoV-2 Activity of Selected Metal Compounds and Potential Molecular Basis for Their Actions Based on Computational Study
Authors: Cirri Damiano , Marzo Tiziano , Tolbatov Iogann , Marrone Alessandro , Saladini Francesco , Vicenti Ilaria , Dragoni Filippo , Boccuto Adele , Messori Luigi
Published: December 2021

Metal-based drugs represent a rich source of chemical substances of potential interest for the treatment of COVID-19. To this end, we have developed a small but representative panel of nine metal compounds, including both synthesized and commercially available complexes, suitable for medical application and tested them in vitro against the SARS-CoV-2 virus. The screening revealed that three compounds from the panel, i.e., the organogold(III) compound Aubipyc, the ruthenium(III) complex KP1019, and antimony trichloride (SbCl3), are endowed with notable antiviral properties and an acceptable cytotoxicity profile. These initial findings prompted us to perform a computational study to unveil the likely molecular basis of their antiviral actions. Calculations evidenced that the metalation of nucleophile sites in SARS-CoV-2 proteins or nucleobase strands, induced by Aubipyc, SbCl3, and KP1019, is likely to occur. Remarkably, we found that only the deprotonated forms of Cys and Sec residues can react favorably with these metallodrugs. The mechanistic implications of these findings are discussed.
AlphaFold-Predicted Structures of KCTD Proteins Unravel Previously Undetected Relationships among the Members of the Family
Authors: Esposito Luciana , Balasco Nicole , Smaldone Giovanni , Berisio Rita , Ruggiero Alessia , Vitagliano Luigi
Published: December 2021

One of the most striking features of KCTD proteins is their involvement in apparently unrelated yet fundamental physio-pathological processes. Unfortunately, comprehensive structure–function relationships for this protein family have been hampered by the scarcity of the structural data available. This scenario is rapidly changing due to the release of the protein three-dimensional models predicted by AlphaFold (AF). Here, we exploited the structural information contained in the AF database to gain insights into the relationships among the members of the KCTD family with the aim of facilitating the definition of the structural and molecular basis of key roles that these proteins play in many biological processes. The most important finding that emerged from this investigation is the discovery that, in addition to the BTB domain, the vast majority of these proteins also share a structurally similar domain in the C-terminal region despite the absence of general sequence similarities detectable in this region. Using this domain as reference, we generated a novel and comprehensive structure-based pseudo-phylogenetic tree that unraveled previously undetected similarities among the protein family. In particular, we generated a new clustering of the KCTD proteins that will represent a solid ground for interpreting their many functions.
Colorectal Cancer: From Pathophysiology to Novel Therapeutic Approaches
Authors: Barresi Valeria
Published: December 2021

According to the Global Cancer Statistics 2020, colorectal cancer (CRC) represents the third most frequent malignancy worldwide, and is the second in terms of mortality [...]
Mitochondrial Respiration of Platelets: Comparison of Isolation Methods
Authors: Vernerova Andrea , Garcia-Souza Luiz Felipe , Soucek Ondrej , Kostal Milan , Rehacek Vit , Kujovska Krcmova Lenka , Gnaiger Erich , Sobotka Ondrej
Published: December 2021

Multiple non-aggregatory functions of human platelets (PLT) are widely acknowledged, yet their functional examination is limited mainly due to a lack of standardized isolation and analytic methods. Platelet apheresis (PA) is an established clinical method for PLT isolation aiming at the treatment of bleeding diathesis in severe thrombocytopenia. On the other hand, density gradient centrifugation (DC) is an isolation method applied in research for the analysis of the mitochondrial metabolic profile of oxidative phosphorylation (OXPHOS) in PLT obtained from small samples of human blood. We studied PLT obtained from 29 healthy donors by high-resolution respirometry for comparison of PA and DC isolates. ROUTINE respiration and electron transfer capacity of living PLT isolated by PA were significantly higher than in the DC group, whereas plasma membrane permeabilization resulted in a 57% decrease of succinate oxidation in PA compared to DC. These differences were eliminated after washing the PA platelets with phosphate buffer containing 10 mmol·L−1 ethylene glycol-bis (2-aminoethyl ether)-N,N,N′,N′-tetra-acetic acid, suggesting that several components, particularly Ca2+ and fuel substrates, were carried over into the respiratory assay from the serum in PA. A simple washing step was sufficient to enable functional mitochondrial analysis in subsamples obtained from PA. The combination of the standard clinical PA isolation procedure with PLT quality control and routine mitochondrial OXPHOS diagnostics meets an acute clinical demand in biomedical research of patients suffering from thrombocytopenia and metabolic diseases.
Analyzing the Therapeutic Efficacy of Bis-Choline-Tetrathiomolybdate in the Atp7b−/− Copper Overload Mouse Model
Authors: Kim Philipp , Zhang Chengcheng Christine , Thoröe-Boveleth Sven , Buhl Eva Miriam , Weiskirchen Sabine , Stremmel Wolfgang , Merle Uta , Weiskirchen Ralf
Published: December 2021

Bis-choline-tetrathiomolybdate, introduced as WTX101 (now known as ALXN1840), is a first-in-class copper-protein-binding agent for oral therapy of Wilson’s disease. In contrast to other decoppering agents such as trientine or D-penicillamine it acts by forming a tripartite complex with copper and albumin, thereby detoxifying excess liver and blood copper through biliary excretion. Preclinical animal experimentation with this drug was typically done with the alternative ammonium salt of tetrathiomolybdate, which is expected to have identical properties in terms of copper binding. Here, we comparatively analyzed the therapeutic efficacy of ALXN1840, D-penicillamine and trientine in lowering hepatic copper content in Atp7b−/− mouse. Liver specimens were subjected to laser ablation inductively conductively plasma mass spectrometry and electron microscopic analysis. We found that ALXN1840 caused a massive increase of hepatic copper and molybdenum during early stages of therapy. Prolonged treatment with ALXN1840 reduced hepatic copper to an extent that was similar to that observed after administration of D-penicillamine and trientine. Electron microscopic analysis showed a significant increase of lysosomal electron-dense particles in the liver confirming the proposed excretory pathway of ALXN1840. Ultrastructural analysis of mice treated with dosages comparable to the bis-choline-tetrathiomolybdate dosage used in an ongoing phase III trial in Wilson’s disease patients, as well as D-penicillamine and trientine, did not show relevant mitochondrial damage. In contrast, a high dose of ALXN1840 applied for four weeks triggered dramatic structural changes in mitochondria, which were notably characterized by the formation of holes with variable sizes. Although these experimental results may not be applicable to patients with Wilson’s disease, the data suggests that ALXN1840 should be administered at low concentrations to prevent mitochondrial dysfunction and overload of hepatic excretory pathways.
Rapid Androgen-Responsive Proteome Is Involved in Prostate Cancer Progression
Authors: Kim Jong-Kwang , Jung Jae-Hun , Shin Dong-Hoon , You Hye-Jin , Cha Seho , Song Bo-Seul , Joung Jae-Young , Park Weon-Seo , Kim Kwang-Pyo , Myung Jae-Kyung
Published: December 2021

Androgen exerts its functions by binding with an androgen receptor (AR). It can activate many signaling pathways that are important to the progression of castration-resistant prostate cancer (CRPC). Here, we characterized the rapid proteomic changes seen at 5, 15, 30, and 60 min after the androgen treatment of VCaP cells via the tandem mass tag (TMT) labeling strategy. A total of 5529 proteins were successfully identified and quantified. Dynamic time profiling of protein expression patterns allowed us to identify five protein clusters involved in various stages of androgen-initiated signal transmission and processing. More details of protein functions and localization patterns, and our elucidation of an AR-interacting protein network, were obtained. Finally, we validated the expression level of AR-regulated proteins known to be significantly regulated in CRPC patients using the mouse xenograft model and patient samples. Our work offers a systematic analysis of the rapid proteomic changes induced by androgen and provides a global view of the molecular mechanisms underlying CRPC progression.
Construction of a Fibroblast-Associated Tumor Spheroid Model Based on a Collagen Drop Array Chip
Authors: Roh Hyewon , Kim Hwisoo , Park Je-Kyun
Published: December 2021

Spheroid, a 3D aggregate of tumor cells in a spherical shape, has overcome the limitations of conventional 3D cell models to accurately mimic the in-vivo environment of a human body. The spheroids are cultured with other primary cells and embedded in collagen drops using hang drop plates and low-attachment well plates to construct a spheroid–hydrogel model that better mimics the cell–cell and cell–extracellular matrix (ECM) interactions. However, the conventional methods of culturing and embedding spheroids into ECM have several shortcomings. The procedure of transferring a single spheroid at a time by manual pipetting results in well-to-well variation and even loss or damage of the spheroid. Based on the previously introduced droplet contact-based spheroid transfer technique, we present a poly(dimethylsiloxane) and resin-based drop array chip and a pillar array chip with alignment stoppers, which enhances the alignment between the chips for uniform placement of spheroids. This method allows the facile and stable transfer of the spheroid array and even eliminates the need for a stereomicroscope while handling the cell models. The novel platform demonstrates a homogeneous and time-efficient construction and diverse analysis of an array of fibroblast-associated glioblastoma multiforme spheroids that are embedded in collagen.
Rare among Rare: Phenotypes of Uncommon CMT Genotypes
Authors: Gentile Luca , Russo Massimo , Taioli Federica , Ferrarini Moreno , Aguennouz M’Hammed , Rodolico Carmelo , Toscano Antonio , Fabrizi Gian Maria , Mazzeo Anna
Published: December 2021

(1) Background: Charcot–Marie–Tooth disease (CMT) is the most frequent form of inherited chronic motor and sensory polyneuropathy. Over 100 CMT causative genes have been identified. Previous reports found PMP22, GJB1, MPZ, and MFN2 as the most frequently involved genes. Other genes, such as BSCL2, MORC2, HINT1, LITAF, GARS, and autosomal dominant GDAP1 are responsible for only a minority of CMT cases. (2) Methods: we present here our records of CMT patients harboring a mutation in one of these rare genes (BSCL2, MORC2, HINT1, LITAF, GARS, autosomal dominant GDAP1). We studied 17 patients from 8 unrelated families. All subjects underwent neurologic evaluation and genetic testing by next-generation sequencing on an Ion Torrent PGM (Thermo Fischer) with a 44-gene custom panel. (3) Results: the following variants were found: BSCL2 c.263A > G p.Asn88Ser (eight subjects), MORC2 c.1503A > T p.Gln501His (one subject), HINT1 c.110G > C p.Arg37Pro (one subject), LITAF c.404C > G p.Pro135Arg (two subjects), GARS c.1660G > A p.Asp554Asn (three subjects), GDAP1 c.374G > A p.Arg125Gln (two subjects). (4) Expanding the spectrum of CMT phenotypes is of high relevance, especially for less common variants that have a higher risk of remaining undiagnosed. The necessity of reaching a genetic definition for most patients is great, potentially making them eligible for future experimentations.
A Mechanism-Based Approach to Anti-Aggression Psychotherapy in Borderline Personality Disorder: Group Treatment Affects Amygdala Activation and Connectivity
Authors: Neukel Corinne , Bertsch Katja , Wenigmann Marc , Spieß Karen , Krauch Marlene , Steinmann Sylvia , Herpertz Sabine C.
Published: December 2021

Aggression is highly prevalent in borderline personality disorder (BPD). Previous studies have identified specific biobehavioral mechanisms underlying aggression in BPD, threat sensitivity being among them. We composited the mechanism-based anti-aggression psychotherapy (MAAP) in order to target these specific mechanisms, and MAAP was found to be superior to non-specific supportive psychotherapy (NSSP) in reducing aggressive behavior. In the present study, we investigated whether underlying brain mechanisms expected to be involved were affected by MAAP. To this end, n = 33 patients with BPD and overt aggressive behavior (n = 20 in MAAP, n = 13 in NSSP) and n = 25 healthy participants took part in a functional magnetic resonance imaging emotional face-matching task before and after treatment, or at a similar time interval for controls. Overt aggressive behavior was assessed using the overt aggression scale, modified. Results showed a decrease in amygdala activation in response to facial stimuli after MAAP, whereas an increase in amygdala activation was found after NSSP. Furthermore, in the MAAP group, connectivity between amygdala and dorsomedial prefrontal cortex increased from pre- to post-treatment compared to the NSSP group. Hence, the results suggest an impact of MAAP on brain mechanisms underlying the salience circuit in response to threat cues.
Factors Influencing Green Building Development in Kazakhstan
Authors: Assylbekov Daniyar , Nadeem Abid , Hossain Md Aslam , Akhanova Gulzhanat , Khalfan Malik
Published: December 2021

Green buildings have been actively spreading as a solution for sustainability issues of the construction industry in at least the last two decades. As green building practices unfold in developing countries, the need of identifying factors that both hinder and drive its spread rises. Multiple studies reveal a general inconsistency among results in different parts of the world, caused by each country’s environmental, economic, and social conditions. Taking into account the experience of developing international green buildings and the current state of green building development in Kazakhstan, this study aims to spread the understanding of the factors that hinder and have the potential to drive the development of green buildings in Kazakhstan. A questionnaire survey was carried out among 38 industry experts in Kazakhstan to accomplish study objectives. Multiple data analysis methods were used to identify correlations among groups of experts and rank the factors. The results revealed a lack of skill/experience, a lack of government support, and the high cost of sustainable materials and products as the most crucial barriers. Water and energy efficiency, improved health of occupants, comfort, and satisfaction were identified as the most influential drivers. By expanding knowledge on factors affecting the implementation of green buildings, the study uncovered common trends in the responses of professionals, providing valuable information for field professionals and suggesting future research recommendations.
Rehabilitation after Allogeneic Haematopoietic Stem Cell Transplantation: A Special Challenge
Authors: Bertz Hartmut
Published: December 2021

The general population is getting older and suffer more haematological malignancies despite being physically fit. These malignancies are mainly only curable via an alloHCT, and they are now carried out more frequently. Patients benefit from intensive rehabilitation earlier and may need it repeatedly in cases of severe side effects (e.g., graft-versus-host disease). They can suffer many problems that other cancer patients do not experience, such as severe infections, continued immunosuppression, nutritional restrictions, acute or chronic GvHD, or organ impairments (e.g., lung, eyes). They may also encounter various associated psychological problems, e.g., feeling like a chimera. Rehabilitation centres willing to care for patients after alloHCT should have an experienced multidisciplinary team and should work in close co-operation with the primary transplant centre.
Targeting Cross-Presentation as a Route to Improve the Efficiency of Peptide-Based Cancer Vaccines
Authors: Wylie Ben , Ong Ferrer , Belhoul-Fakir Hanane , Priebatsch Kristin , Bogdawa Heique , Stirnweiss Anja , Watt Paul , Cunningham Paula , Stone Shane R. , Waithman Jason
Published: December 2021

Cross-presenting dendritic cells (DC) offer an attractive target for vaccination due to their unique ability to process exogenous antigens for presentation on MHC class I molecules. Recent reports have established that these DC express unique surface receptors and play a critical role in the initiation of anti-tumor immunity, opening the way for the development of vaccination strategies specifically targeting these cells. This study investigated whether targeting cross-presenting DC by two complementary mechanisms could improve vaccine effectiveness, in both a viral setting and in a murine melanoma model. Our novel vaccine construct contained the XCL1 ligand, to target uptake to XCR1+ cross-presenting DC, and a cell penetrating peptide (CPP) with endosomal escape properties, to enhance antigen delivery into the cross-presentation pathway. Using a prime-boost regimen, we demonstrated robust expansion of antigen-specific T cells following vaccination with our CPP-linked peptide vaccine and protective immunity against HSV-1 skin infection, where vaccine epitopes were natively expressed by the virus. Additionally, our novel vaccination strategy slowed tumor outgrowth in a B16 murine melanoma model, compared to adjuvant only controls, suggesting antigen-specific anti-tumor immunity was generated following vaccination. These findings suggest that novel strategies to target the antigen cross-presentation pathway in DC may be beneficial for the generation of anti-tumor immunity.
Long-Term Outcomes of Lymph Node Transfer in Secondary Lymphedema and Its Correlation with Flap Characteristics
Authors: Dionyssiou Dimitrios , Sarafis Alexandros , Tsimponis Antonios , Kalaitzoglou Asterios , Arsos Georgios , Demiri Efterpi
Published: December 2021

Background: This retrospective study aimed to assess the impact of certain flap characteristics on long-term outcomes following microsurgical treatment in Breast Cancer-Related Lymphedema (BCRL) patients. Methods: Sixty-four out of 65 BCRL patients, guided by the “Selected Lymph Node” (“SeLyN”) technique, underwent Vascularized Lymph Node Transfer (VLNT) between 2012 and 2018. According to their surface size, flaps were divided into small (<25 cm2, n = 32) and large (>25 cm2, n = 32). Twelve large and six small flaps were combined with free abdominally based breast reconstruction procedures. Lymphedema stage, flap size, vascular pedicle and number of lymph nodes (LNs) were analyzed in correlation with long-term Volume Differential Reduction (VDR). Results: At 36-month follow-up, no major complication was recorded in 64 cases; one flap failure was excluded from the study. Mean flap size was 27.4 cm2, mean LNs/flap 3.3 and mean VDR 55.7%. Small and large flaps had 2.8 vs. 3.8 LNs/flap (p = 0.001), resulting in 49.6% vs. 61.8% VDR (p = 0.032), respectively. Lymphedema stage and vascular pedicle (SIEA or SCIA/SCIP) had no significant impact on VDR. Conclusion: In our series, larger flaps included a higher number of functional LNs, directly associated with better outcomes as quantified by improved VDR.
Heavy Ion Minibeam Therapy: Side Effects in Normal Brain
Authors: Eley John G. , Haga Catherine W. , Keller Asaf , Lazenby Ellis M. , Raver Charles , Rusek Adam , Dilmanian Farrokh Avraham , Krishnan Sunil , Waddell Jaylyn
Published: December 2021

The purpose of this work was to investigate whether minibeam therapy with heavy ions might offer improvements of the therapeutic ratio for the treatment of human brain cancers. To assess neurotoxicity, we irradiated normal juvenile rats using 120 MeV lithium-7 ions at an absorbed integral dose of 20 Gy. Beams were configured either as a solid parallel circular beam or as an array of planar parallel minibeams having 300-micron width and 1-mm center-to-center spacing within a circular array. We followed animals for 6 months after treatment and utilized behavioral testing and immunohistochemical studies to investigate the resulting cognitive impairment and chronic pathologic changes. We found both solid-beam therapy and minibeam therapy to result in cognitive impairment compared with sham controls, with no apparent reduction in neurotoxicity using heavy ion minibeams instead of solid beams under the conditions of this study.
Kaposi’s Sarcoma-Associated Herpesvirus, the Etiological Agent of All Epidemiological Forms of Kaposi’s Sarcoma
Authors: Jary Aude , Veyri Marianne , Gothland Adélie , Leducq Valentin , Calvez Vincent , Marcelin Anne-Geneviève
Published: December 2021

Kaposi’s sarcoma-associated herpesvirus (KSHV), also called human herpesvirus 8 (HHV-8), is an oncogenic virus belonging to the Herpesviridae family. The viral particle is composed of a double-stranded DNA harboring 90 open reading frames, incorporated in an icosahedral capsid and enveloped. The viral cycle is divided in the following two states: a short lytic phase, and a latency phase that leads to a persistent infection in target cells and the expression of a small number of genes, including LANA-1, v-FLIP and v-cyclin. The seroprevalence and risk factors of infection differ around the world, and saliva seems to play a major role in viral transmission. KSHV is found in all epidemiological forms of Kaposi’s sarcoma including classic, endemic, iatrogenic, epidemic and non-epidemic forms. In a Kaposi’s sarcoma lesion, KSHV is mainly in a latent state; however, a small proportion of viral particles (<5%) are in a replicative state and are reported to be potentially involved in the proliferation of neighboring cells, suggesting they have crucial roles in the process of tumorigenesis. KSHV encodes oncogenic proteins (LANA-1, v-FLIP, v-cyclin, v-GPCR, v-IL6, v-CCL, v-MIP, v-IRF, etc.) that can modulate cellular pathways in order to induce the characteristics found in all cancer, including the inhibition of apoptosis, cells’ proliferation stimulation, angiogenesis, inflammation and immune escape, and, therefore, are involved in the development of Kaposi’s sarcoma.
Machine Learning for Prediction of Immunotherapy Efficacy in Non-Small Cell Lung Cancer from Simple Clinical and Biological Data
Authors: Benzekry Sébastien , Grangeon Mathieu , Karlsen Mélanie , Alexa Maria , Bicalho-Frazeto Isabella , Chaleat Solène , Tomasini Pascale , Barbolosi Dominique , Barlesi Fabrice , Greillier Laurent
Published: December 2021

Background: Immune checkpoint inhibitors (ICIs) are now a therapeutic standard in advanced non-small cell lung cancer (NSCLC), but strong predictive markers for ICIs efficacy are still lacking. We evaluated machine learning models built on simple clinical and biological data to individually predict response to ICIs. Methods: Patients with metastatic NSCLC who received ICI in second line or later were included. We collected clinical and hematological data and studied the association of this data with disease control rate (DCR), progression free survival (PFS) and overall survival (OS). Multiple machine learning (ML) algorithms were assessed for their ability to predict response. Results: Overall, 298 patients were enrolled. The overall response rate and DCR were 15.3% and 53%, respectively. Median PFS and OS were 3.3 and 11.4 months, respectively. In multivariable analysis, DCR was significantly associated with performance status (PS) and hemoglobin level (OR 0.58, p < 0.0001; OR 1.8, p < 0.001). These variables were also associated with PFS and OS and ranked top in random forest-based feature importance. Neutrophil-to-lymphocyte ratio was also associated with DCR, PFS and OS. The best ML algorithm was a random forest. It could predict DCR with satisfactory efficacy based on these three variables. Ten-fold cross-validated performances were: accuracy 0.68 ± 0.04, sensitivity 0.58 ± 0.08; specificity 0.78 ± 0.06; positive predictive value 0.70 ± 0.08; negative predictive value 0.68 ± 0.06; AUC 0.74 ± 0.03. Conclusion: Combination of simple clinical and biological data could accurately predict disease control rate at the individual level.
Interplay between Genome, Metabolome and Microbiome in Colorectal Cancer
Authors: Garcia-Etxebarria Koldo , Clos-Garcia Marc , Telleria Oiana , Nafría Beatriz , Alonso Cristina , Iruarrizaga-Lejarreta Marta , Franke Andre , Crespo Anais , Iglesias Agueda , Cubiella Joaquín , Bujanda Luis , Falcón-Pérez Juan
Published: December 2021

Background: Colorectal cancer (CRC), a major health concern, is developed depending on environmental, genetic and microbial factors. The microbiome and metabolome have been analyzed to study their role in CRC. However, the interplay of host genetics with those layers in CRC remains unclear. Methods: 120 individuals were sequenced and association analyses were carried out for adenoma and CRC risk, and for selected components of the microbiome and metabolome. The epistasis between genes located in cholesterol pathways was analyzed; modifiable risk factors were studied using Mendelian randomization; and the three omic layers were used to integrate their data and to build risk prediction models. Results: We detected genetic variants that were associated to components of metabolome or microbiome and adenoma or CRC risk (e.g., in LINC01605, PROKR2 and CCSER1 genes). In addition, we found interactions between genes of cholesterol metabolism, and HDL cholesterol levels affected adenoma (p = 0.0448) and CRC (p = 0.0148) risk. The combination of the three omic layers to build risk prediction models reached high AUC values (>0.91). Conclusions: The use of the three omic layers allowed for the finding of biological mechanisms related to the development of adenoma and CRC, and each layer provided complementary information to build risk prediction models.
A Review of the Use of Semiconductors as Catalysts in the Photocatalytic Inactivation of Microorganisms
Authors: Elgohary Elzahraa A. , Mohamed Yasser Mahmoud A. , El Nazer Hossam A. , Baaloudj Oussama , Alyami Mohammed S. S. , El Jery Atef , Assadi Aymen Amine , Amrane Abdeltif
Published: December 2021

Obtaining clean and high-quality water free of pathogenic microorganisms is a worldwide challenge. Various techniques have been investigated for achieving an effective removal or inactivation of these pathogenic microorganisms. One of those promising techniques is photocatalysis. In recent years, photocatalytic processes used semiconductors as photocatalysts. They were widely studied as a green and safe technology for water disinfection due to their high efficiency, being non-toxic and inexpensive, and their ability to disinfect a wide range of microorganisms under UV or visible light. In this review, we summarized the inactivation mechanisms of different waterborne pathogenic microorganisms by semiconductor photocatalysts. However, the photocatalytic efficiency of semiconductors photocatalysts, especially titanium dioxide, under visible light is limited and hence needs further improvements. Several strategies have been studied to improve their efficiencies which are briefly discussed in this review. With the developing of nanotechnology, doping with nanomaterials can increase and promote the semiconductor’s photocatalytic efficiency, which can enhance the deactivation or damage of a large number of waterborne pathogenic microorganisms. Here, we present an overview of antimicrobial effects for a wide range of nano-photocatalysts, including titanium dioxide-based, other metal-containing, and metal-free photocatalysts. Promising future directions and challenges for materials research in photocatalytic water disinfection are also concluded in this review.
Green Synthesis of Ag Nanoparticles for Plasmon-Assisted Photocatalytic Degradation of Methylene Blue
Authors: Ma Ying , Tao Liyiming , Bai Shi , Hu Anming
Published: December 2021

Green synthesis of metal nanoparticles has been gaining great interest due to the increasing need for eco-friendly manufacturing and application of nanomaterials. Metal nanoparticles, especially silver nanoparticles, are widely used in water treatments and as environmental remedy. Here we present a method to synthesize silver nanoparticles at room temperature using green tea extract under visible light irradiation, along with an application for enhanced photocatalytic degradation on methylene blue (MB) dye. Ag nanoparticles were synthesized under different photoreduction times and then further characterized. The photocatalytic rate of synthesized nanoparticles was also investigated and compared with TiO2 nanowires under UV and visible light irradiations. The results showed that Ag nanoparticles can directly degrade MB dye through plasmonic excitation and electron transferring under visible light, and Ag nanoparticles can further enhance TiO2 photonic degradation by enhanced e-h separation with UV and/or a wide band light, including UV light. Ag nanoparticles under visible light photoreduction for 0.5 h presented better behavior for two kinds of plasmonic enhanced photodegradation; the average size of the nanoparticles is about 30 nm. Therefore, the green synthesized Ag nanoparticles exhibit promising prospects in chemical and biological pollutant treatment.
Synthesis and Characterization of Zinc Oxide Nanoparticles Using Acacia caesia Bark Extract and Its Photocatalytic and Antimicrobial Activities
Authors: Ashwini Jayachandran , Aswathy Thankamani Ravikumar , Rahul Anil Babu , Thara Gautham M. , Nair Achuthsankar S.
Published: December 2021

This paper presents the green synthesis and characterization of ZnO nanoparticles and their microbial and photocatalytic application. The green synthesis of ZnO nanoparticles was carried out using Zinc nitrate hexahydrate and the bark extract of Acacia caesia (L.) Willd. The nanoparticles were synthesized at an optimum temperature of 65 °C followed by calcination at 400 °C. The samples were characterized using UV-visible spectroscopy, SEM, XRD, FTIR and EDX analysis. UV-visible spectroscopy showed a characteristic peak at 338 nm and the bandgap energy was found to be 3 eV which is specific for ZnO. SEM confirmed the presence of ZnO on its nanoscale. EDX gave the elemental details of Zinc constituting to 37.77% and Oxygen comprising 20.77% of its atomic weight. XRD analysis gave the diffractogram indexed at various angles corresponding to ZnO nanoparticles. It also revealed the average crystalline size to be 32.32 nm and the shape was found to be hexagonal. The functional group present in the nanoparticles was characterized using FTIR, which gave a characteristic peak at 485 cm−1. The synthesized nanoparticles exhibited significant photocatalytic (methyl blue under UV irradiation). The presence of nanoparticles induces changes in its kinetics, whose rate constants and correlation coefficients were analyzed during the photocatalytic degradation of the model pollutant Methyl Blue. Studies on antibacterial (Escherichia coli, Staphylococcus aureus), antifungal (Aspergillus niger, Candida albicans) and anti-inflammatory (COX assay) properties were also carried out. The nanoparticles were synthesized in an eco-friendly and cost-effective method. The study opens new horizons in the field of water treatment, biosensors and nanotechnology.